National

Synchrotron

Light 

Source

Activity Report 2005

 BNL 75555 National Synchrotron Light Source Activity Report 2005
BNL-75555-2005

UC400

(General Energy Research)

Disclaimer

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1. from Science Highlight: “The Structure of Ba@C74,” page 2-38

2. from Science Highlight: “Mediator-Template Assembly of Nanoparticles,” page 2-76

3. from Science Highlight: “Physical Properties and 20 K Synchrotron X-ray Charge Density of a Magnetic Metal 

Organic Framework Structure, Mn3(C8O4H4)3(C5H11ON)2,” page 2-30

4. from Feature Highlight: “Nanotubes in a New Light,” page 2-12

5. from Science Highlight: “Zinc Oxide Nanowires Grown by Vapor-Phase Transport Using Selected Metal Catalysts: 

A Comparative Study,” page 2-22

6. from Feature Highlight: “Hunting the RNA Slicer,” page 2-8

Cover Images

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4

5 6
National Synchrotron Light Source

2005 Activity Report

Lisa M. Miller

managing editor

Laura Y. Mgrdichian

science editor

Nancye A. Wright & Stephen A. Giordano

design & layout

managed for the U.S. Department of Ene gy 

by Brookhaven Science Associates, a coy m

founded by Stony Brook University and Ba

The National Synchrotron Light Source Department is supported by the

Office of Basic Energy Sciences, United States Department of Energy, Washington, D.C.

Brookhaven National Laboratory, Brookhaven Science Associates, Inc., Upton, New York 11973

Under contract no. DE-AC02-98CH10886
Introduction

 Introduction by the Chairman ...................................................................................................1-3

 Users’ Executive Committee Report ........................................................................................1-5

 

Science Highlights 

 Introduction...............................................................................................................................2-3

 Table of Contents .....................................................................................................................2-4

 Feature Highlights ....................................................................................................................2-8

 Chemical Science...................................................................................................................2-22

 Condensed Matter Physics ....................................................................................................2-36

 Geology and Environmental Science .....................................................................................2-46

 Life Science............................................................................................................................2-56

 Materials Science...................................................................................................................2-70

 Soft Condensed Matter and Biophysics .................................................................................2-82

 

Year in Review

 Short Course Participants Learn the Value of Synchrotron Light for Powder Diffraction .........3-3

 NSLS Engineer John Skaritka Wins BNL's Engineering Award ...............................................3-3

 Unique Global Light Source Website Launched.......................................................................3-4

 X6A Workbench Provides Hands-On Training in Synchrotron Crystallography .......................3-4

 BNLers Help Promote Community Interest in Science.............................................................3-5

 Scientists Create, Study Methane Hydrates in "Ocean Floor" Lab ..........................................3-5

 Ceria Nanoparticle Experiments at NSLS Promise Cleaner Fuel Future.................................3-6

 What Do You Do At Work? Tom Seda: Bringing Bright Ideas to the Light Source ...................3-7

 Brookhaven Town Honors Two BNL Scientists ........................................................................3-8

 EnviroSuite: Environmental Science at the NSLS....................................................................3-8

 Crystallographers Bloom at RapiData 2005.............................................................................3-9

 CFN Site Dedication Draws Special Guests at the NSLS .....................................................3-10

 Strain-Mapping Workshop Marked by Enthusiasm and Idea-Sharing ...................................3-11

 Four BNLers Win Environmental Stewardship Awards ..........................................................3-12

 NSLS Daughters and Sons are Forensic Scientists for a Day ...............................................3-12.

 Women in Science Career Day at BNL..................................................................................3-13

 BNL Workshop on Intense Coherent THz Pulses ..................................................................3-13

 A Passion for Synchrotron Science and its Future: News from the NSLS Users' Meeting ....3-14

 Nanomagnetism: Materials and Probe Workshop..................................................................3-17

 Synchrotron Imaging of Biominerals Workshop ....................................................................3-18

 Cryogenic Specimen Automounters and the Future of Macromolecular Crystallography......3-20

 Spectroscopic Studies of Nanoscaled Systems Workshop ...................................................3-21

 
 Application of SAXS to Biological Structures Workshop .......................................................3-22

 In-Situ Kinetic Analyses in Environmental and Chemical Systems Workshop.......................3-23

 Tony Lenhard Receives the 2005 UEC Community Service Award.......................................3-24

 NSLS Physicist, Zhong Zhong, Awarded Tenure ...................................................................3-25

 Crystallization Workshop Gets Top Marks from Participants .................................................3-25

 BioCD-2005 ...........................................................................................................................3-26

 Changes to NSLS User Access Policy...................................................................................3-27

 NSLS Scientists Recognized by the American Physical Society............................................3-27

 Protein Rush at the NSLS......................................................................................................3-28

 Highlights from the 2005 NSLS Summer Sunday ..................................................................3-28

 Meet the NSLS Summer Students of 2005 ............................................................................3-30

 NSLS-II Gets CD-0! ...............................................................................................................3-31

 Synchrotron Environmental Science III (SES) Meeting..........................................................3-31

 The 2005 NSLS Barbeque Wraps up the Year.......................................................................3-33

 SBU Student Wins First Dr. Mow Shiah Lin Scholarship........................................................3-34

 New Grant for Catalysis Research at the NSLS.....................................................................3-35

 EXAFS Course: Theory, Experiments and Advanced Applications ........................................3-35

 Brookhaven Lab Breaks Ground for New Nanocenter...........................................................3-36

 NSLS Users Recognized........................................................................................................3-37

 COMPRES Sponsored Workshop on High Pressure Synchrotron IR Spectroscopy .............3-38

 The NSLS Remembers Bill Oosterhuis..................................................................................3-39

 BNL Establishes NSLS-II Project in Light Sources Directorate..............................................3-40

 NSLS Visitors and Tours in 2005............................................................................................3-41

 NSLS Workshops in 2005 ......................................................................................................3-43

 

NSLS Organization

 Organization Chart .................................................................................................................. 4-3

 Advisory Committees .............................................................................................................. 4-4

 

Facility Report 

 Accelerator Division Report..................................................................................................... 5-3

 Operations and Engineering Division Report .......................................................................... 5-5

 User Science Division Report.................................................................................................. 5-9

 User Administration Report ................................................................................................... 5-14

 Safety Report ........................................................................................................................ 5-16

 Building Administration Report .............................................................................................. 5-18
Facts and Figures

 Beamline Guide....................................................................................................................... 6-3

 Linac and Booster Parameters.............................................................................................. 6-10

 VUV Storage Ring Parameters ..............................................................................................6-11

 X-Ray Storage Ring Parameters........................................................................................... 6-12

 2005 Ring Performance and Usage...................................................................................... 6-13

Publications

 NSLS Users............................................................................................................................. 7-4

 NSLS Staff............................................................................................................................. 7-29

 

 
Introduction
Introduction 1-3

Chairman’s Introduction

Steven Dierker

Chairman, National Synchrotron Light Source

In 2005, the NSLS proved itself, once again, to be a center of scientific excellence. This remarkable facility, commissioned in the early 1980s, is still attracting some of the world’s best researchers in almost every scientific field, who 

produce more than seven hundred scientific papers every year using the NSLS.

The “Science Highlights” and “Feature Highlights” sections of this report are just a small sampling of the many, many 

impressive research projects conducted at the NSLS in 2005. For example, a user group synthesized and studied 

zinc-oxide nanowires, which have applications in many optical and electrical devices. Another user group studied how 

strontium and uranium are removed from high-level radioactive waste. And in another interesting study, users deciphered the basis for antibiotic resistance.

However, as always, the success of these projects depends on the performance of the facility. Again this year, the 

rings were in top form — reliability was 96 percent for the x-ray ring and 99 percent for the VUV-IR ring. Additionally, 

to keep the NSLS as productive as possible and to continue to attract users, many beamline upgrade projects were 

completed this year. One of the highlights of these upgrades is the new mini-gap undulator installed at beamline X25. 

This insertion device is providing a much brighter x-ray source for the program at X25.

In the always important area of safety, several noteworthy activities took place this year. In particular, NSLS staff 

made a major commitment to labeling and inspecting electrical equipment. And perhaps the best news is what didn’t 

happen — there were no reportable occurrences related to environmental, safety, or health issues in 2005, and no 

injuries that resulted in restricted or lost time. We all owe thanks to the dedicated NSLS staff and users who have 

ensured that the NSLS remains a reliable, safe, up-to-date research facility.

As 2005 came to an end, I stepped down as NSLS Chairman in order to focus my primary efforts on NSLS-II, the 

world-leading third-generation synchrotron planned for construction at BNL. NSLS-II passed a critical milestone in 

2005 with the approval by the Department of Energy of CD-0. BNL has established the NSLS-II Project Organization 

within the Light Sources Directorate to put in place the management systems and infrastructure necessary to execute 

this complex undertaking. I will serve as NSLS-II Project Director and also retain my position as Associate Laboratory 

Director for Light Sources, with the NSLS reporting to me.

Another exciting development is the planned establishment of the Joint 

Photon Sciences Institute (JPSI). JPSI will be devoted to cultivating and 

fostering collaborative, interdisciplinary R&D in areas of the physical 

sciences, engineering, and the life sciences that are united in employing 

synchrotron-based methods. JPSI will also develop new methods and 

applications that exploit the unique capabilities of NSLS-II and will serve 

as a gateway for NSLS-II users.

JPSI will be a partnership between the Department of Energy and New 

York State, and I am delighted that New York State Governor George 

Pataki has pledged $30 million for the construction of the JPSI building. 
1-4 NSLS Activity Report 

The building will be located adjacent to NSLS-II and will contain offices, meeting rooms, and specialized laboratories. 

The operating expenses of JPSI and funding for its research programs will be provided by the federal government.

Until a permanent NSLS Director is selected, NSLS User Science Division Associate Chair Chi-Chang Kao will serve 

as the Interim NSLS Director. I couldn’t be leaving the facility in more capable hands. Chi-Chang will lead NSLS staff 

and users this year in the development of a five-year strategic plan for the NSLS, scheduled for completion by the end 

of summer 2006. The plan will outline the course for the future operation and development of the NSLS, and will help 

ensure that the future of the NSLS remains as bright as its past.
Introduction 1-5

Users' Executive Committee Report

Peter Stephens

Stony Brook University

The NSLS is an environment of vital and exciting research, even as it continues in its third decade of operations. It is 

a strong testament to the staff of the NSLS that it operates so well. As users, we must not take their experience and 

ingenuity for granted. Keeping the NSLS at the top of its form in scientific productivity is a significant challenge. 

In its previous (2001) review of the facility, the Office of Basic Energy Sciences (BES) of the DOE recommended 

that the NSLS staff should operate more beamlines for the benefit of general users, a policy that has been continuously implemented as resources permit. Early in 2005, the Science Advisory Committee was charged with the task 

of reviewing each beamline and advising the NSLS of which were being operated safely and effectively, and which 

required improvement or a significant change of management. It is gratifying to see that nearly all of the beamlines 

operating at that time were indeed found to be fulfilling their mission to serve the community of users. 

This year, the DOE also released the preliminary results of an assessment of beamlines in all four BES synchrotron 

radiation facilities. I strongly recommend that everybody involved in research with synchrotron radiation take a look. 

It counts 179 beamlines throughout the system, 77 of which are at the NSLS. However, of 45 beamlines rated on various technical grounds as “best in class,” only four are at the NSLS. This is partly a consequence of the small number 

of insertion device ports available on the NSLS storage rings, and partly a result of the fact that most NSLS beamlines 

are relatively old. That is not to say, however, that the NSLS and its user community are letting the cutting edge pass 

us by. Highlights include the new X29 undulator line for macromolecular crystallography and recently constructed instruments at the X21 wiggler for small-angle scattering and studies of in-situ materials preparation. A new undulator is 

being put in place for X25, and an undulator beamline dedicated to small-angle scattering, to be operated in conjunction with the Center for Functional Nanomaterials, is planned for the near future. Perhaps less immediately visible to 

users, but no less important, is the steady upgrade of storage-ring components, such as RF cavities, the meticulous 

analysis of faults by the Operations & Engineering Group, and actions such as the formation of an orbit task force to 

assess users’ needs and meet them.

In the years from 1984 to 1993, the number of users coming to the NSLS rose essentially linearly, to somewhat more 

than 2000. Since 1993, that number has held essentially constant, while the number of users at all four DOE-operated synchrotron radiation sources has risen to nearly 8000. At the same time, we have seen the NSLS increasingly 

become a regional facility, with 62% of its users coming from the northeastern part of the country, compared, say, with 

15% of Advanced Photon Source users coming from the northeast.

The above notwithstanding, the NSLS will continue to fill a critical need 

and play an indispensable role in American science for many years into 

the future. We continue to hold our own as a leading source of research 

productivity in many fields. But it is equally clear that the opportunity is 

upon us to push the envelope of science and technology beyond the capabilities of any existing synchrotron radiation source. This is the case 

for NSLS-II, a new machine with brightness beyond any synchrotron 

source in existence or planned, essentially to the theoretical limits of 

storage ring performance. Along with research that can be performed at 
1-6 NSLS Activity Report

other facilities, NSLS-II will indeed be a national facility, as the original NSLS once was, with capabilities unequalled 

elsewhere in the world.

Defining the scientific needs and opportunities of what will be the world’s brightest storage ring for synchrotron radiation is an enormous job. For this, we gratefully acknowledge years of effort by many people: countless current synchrotron radiation users and members of the NSLS user science division, who organized and participated in workshops in 2003; the NSLS Accelerator and Operations & Engineering divisions, who have been pushing (so far, theoretically) the limits of storage ring brightness; and especially NSLS-II Project Director Steve Dierker and BES Associate 

Director Pat Dehmer, who have advanced and refined the case within DOE. Earlier this year, these efforts bore fruit 

with the signing of Critical Decision Zero (CD-0) for NSLS-II by the DOE. This signifies that the DOE acknowledges 

the need for the facility, and is receptive to a proposal for a specific plan and design. As I write these words, the 

President’s budget for fiscal year 2007 has just been announced, with substantial resources committed to the NSLS-II 

project. This promises to be an exciting time for all of us associated with the NSLS.

It has been a stimulating year for the NSLS, and for the Users’ Executive Committee. I am grateful for the hard work 

and thoughtful suggestions of the other members of the UEC and its special interest groups, and to all of you who 

have communicated your needs and interests to our representatives in the federal government. But I especially salute 

your most important achievement, safely doing excellent science at the NSLS!
Science Highlights
2-3 NSLS Activity Report

Science at the NSLS

Laura Mgrdichian

NSLS Science Writer

Another year has passed, and the NSLS is still a thriving, rich, and productive scientific facility. Who would have 

thought 23 years ago, when the VUV ring produced its first beams of light, that the year 2005 would see the NSLS so 

vibrant? It really is remarkable.

As the NSLS science writer, I’ve had a great view of this continuing success. In order to choose which research 

projects I’ll write about, in the form of “feature highlight” stories, or which ones will become scientist-written “science 

highlights,” I am exposed to nearly 800 published papers throughout the year — all the result of NSLS experiments.

Sifting through these papers, typically about 40 at a time, is always humbling. It really drives home the amount of 

science that goes on here. Perhaps more importantly, it makes me appreciate the hard work and dedication of the 

scientists that come to the NSLS. This is why choosing which research papers will receive special attention is such a 

difficult task.

So what are these scientists studying, analyzing, probing? Almost every type of 

material you can think of. As you look through this year’s feature and science 

highlight stories, that diversity becomes apparent. For example, if you haven’t 

heard of a “tryptophan zipper” or a “fluoropolymer,” here’s where you can read 

about them. Interested in environmental cleanup or nanomaterials? Several 

studies took place this year that you might just want to take a look at.

In short, the following pages make it clear that the NSLS, for lack of a better 

phrase, goes on. However, I cannot say the same thing for myself. This will be 

my last Activity Report letter, as I will soon be leaving the NSLS. Since I have 

this platform, I want to say that’s it’s been a privilege to do this job. My sincere thanks and best wishes to all the NSLS users and staff members that I’ve 

worked with — I will miss you!
2-4 NSLS Activity Report

Science Highlights

 Feature Highlights

 Hunting the RNA “Slicer”.................................................................................................................................................2-8

 Floating Films on Liquid Mercury................................................................................................................................... .2-9

 A Catalyst Uncovered....................................................................................................................................................2-10

 Nematodes: Nature’s Tiny Lead Filters? ....................................................................................................................... 2-11

 Nanotubes in a New Light ............................................................................................................................................2-12

 The Role of Titanium in Hydrogen Storage...................................................................................................................2-14

 Yale Scientists “See” Basis of Antibiotic Resistance .....................................................................................................2-15

 NSLS Vortex-Tube Study is a Win for Safety................................................................................................................2-16

 Studying the Effects of Acid Mine Drainage ..................................................................................................................2-17

 A New Structural View of Organic Electronic Devices ..................................................................................................2-18

 Scientists Describe New Way to Peer Inside Bacteria..................................................................................................2-19

 Removing Uranium From Contaminated Steel Surfaces ..............................................................................................2-20

 Filling "Nanocontainers" with Liquid ..............................................................................................................................2-21

 

 Chemical Science

 Zinc Oxide Nanowires Grown by Vapor-Phase Transport Using Selected Metal Catalysts: 

 A Comparative Study ...........................................................................................................................2-22

 Z. Zhu, T.-L. Chen, Y. Gu, J. Warren, and R.M. Osgood, Jr.

 Chain Length Dependence of the Conformational Order in Self-Assembled Dialkylammonium 

Monolayers on Mica Studied with Soft X-ray Absorption...................................................................................2-24

G. Hähner, M. Zwahlen, and W. Caseri

 A Step Closer to Understanding Immobilized Organo- and Bio-Molecular Complexes on Solid Surfaces ...................2-26

S.-J. Xiao, S. Brunner, and M. Wieland

 Preparation and Comparison of Supported Gold Nanocatalysts on Anatase, Brookite, Rutile, and 

P25 Polymorphs of TiO2

 for Catalytic Oxidation of CO......................................................................................2-28

W. Yan, B. Chen, S.M. Mahurin, V. Schwartz, D.R. Mullins, A.R. Lupini, 

S.J. Pennycook, S. Dai, and S.H. Overbury

 Physical Properties and 20 K Synchrotron X-ray Charge Density of a Magnetic Metal Organic 

 Framework Structure, Mn3

(C8O4H4)3(C5H11ON)2 ......................................................................................2-30

 R.D. Poulsen, A. Bentien, M. Chevalier, and B.B. Iversen

 Structure Sensitivity in Methanol Oxidation over Model Rhenium Oxide Catalysts ......................................................2-32

A.S.Y. Chan, W. Chen, H. Wang, J.E. Rowe, and T.E. Madey

 Activation Energies for Oxygen Reduction on Platinum Alloys: Theory and Experiment..............................................2-34

A.B. Anderson, J. Roques, S. Mukerjee, V.S. Murthi, N.M. Markovic, and V. Stamenkovic
2-5 NSLS Activity Report

 Condensed Matter Physics

 Robust TaNx Diffusion Barrier for Cu Interconnect Technology with Sub-Nanometer Thickness 

 by Metal Organic Plasma-Enhanced Atomic Layer Deposition..........................................................................2-36

 H. Kim, C. Detavenier, O. van der Straten, S.M. Rossnagel, A.J. Kellock, and D.-G. Park

 The Structure of Ba@C74 ..............................................................................................................................................2-38

 A. Reich, M. Panthöfer, H. Modrow, U. Wedig, and M. Jansen 

 The Electron-Boson Spectral Function α2F(ω) of High-Tc Superconductors .................................................................2-40

S.V. Dordevic, C.C. Homes, J.J. Tu, T. Valla, M. Strongin, P.D. Johnson, G.D. Gu, and D.N. Basov 

 Microscopic Origin of Polarity in Quasi-Amorphous BaTiO3 ................................................................................2-42

A.I. Frenkel, Y. Feldman, V. Lyahovitskaya, E. Wachtel, and I. Lubomirsky

 High Pressure Study of Structural Phase Transitions and Superconductivity in La1.48Nd0.4Sr0.12CuO4 .......................2-44

M.K. Crawford, R.L. Harlow, S. Deemyad, V. Tissen, J.S. Schilling, E.M. McCarron, S.W. Tozer, D.E. Cox, 

N. Ichikawa, S. Uchida, and Q. Huang

 

 Geology and Environmental Science

 Arsenic Leachability in Water-Treatment Adsorbents .........................................................................................2-46

C. Jing, S. Liu, M. Patel, and X. Meng

 Mechanisms of Strontium and Uranium Removal from Radioactive Waste Simulant 

 Solutions by the Sorbent Monosodium Titanate ................................................................................................2-48

 M.C. Duff, D.B. Hunter, D.T. Hobbs, S.D. Fink, Z. Dai, and J.P. Bradley

 Immobilization Processes in Soils Contaminated with Several Heavy Metals........................................................2-50

 A. Voegelin and R. Kretzschmar

 NaMgF3 Perovskite Under Pressure: Octahedral Tilting Evolution and Phase Transition.............................................2-52

H. Liu, J. Chen, J. Hu, C.D. Martin, D.J. Weidner, D. Häusermann, H.-k. Mao

 Methylmercury Binding Sites in Humic Substances: An X-ray Absorption Study..........................................................2-54

S.-j. Yoon, L.M. Diener, P.R. Bloom, E.A. Nater, and W.F. Bleam

 

 Life Science

 Disulfide Trapped Structure of a Repair Enzyme Interrogating Undamaged DNA Sheds Light

on Damaged DNA Recognition..........................................................................................................................2-56

A. Banerjee, W. Yang, M. Karplus, and G.L. Verdine

 Structural and Biochemical Studies Identify SABP2 as a Methylsalicylate Esterase and Further Implicate it 

in Plant Innate Immunity ....................................................................................................................................2-58

F. Forouhar, Y. Yang , D. Kumar, Y. Chen, E. Fridman , S.W. Park, Y. Chiang, T.B. Acton, 

G.T. Montelione, E. Pichersky, D.F. Klessig, and L. Tong

 
2-6 NSLS Activity Report

 Evolution of Xylem Lignification and Hydrogel Transport Regulation.................................................................... 2-60

 C.K. Boyce, M.A. Zwieniecki, G.D. Cody, C. Jacobsen, S. Wirick, A.H. Knoll, and N.M. Holbrook

 A Hairpin Turn in a HIV-Gag–Derived Peptide Bound to HLA-DR1 Orients Peptide Residues 

Outside the Binding Groove for T Cell Recognition........................................................................................... 2-62

Z. Zavala-Ruiz, I. Strug, B.D. Walter, P.J. Norris, and L.J. Stern

 A New Addition to the Folding Repertory: An Engineered Five-Stranded Tryptophan Zipper....................................... 2-64

J. Liu and M. Lu

 Crystal Structures of Nitroalkane Oxidase: High Resolution Data Collection Strategy for 

 Crystals with a Very Long Unit Cell Edge ............................................................................................... 2-66

 A. Nagpal, M.P. Valley, P.F. Fitzpatrick, and A.M. Orville 

 Shape Selective RNA Recognition by Cysteinyl-tRNA Synthetase............................................................................... 2-68

S.I. Hauenstein, C.-M. Zhang, Y.-M. Hou, and J.J. Perona

 

Materials Science

 Effect of Interfacial Bonds on Morphological Instability of Slightly Lattice Mismatched 

 Epitaxial Thin Films ...........................................................................................................................................2-70

 J.H. Li, D.W. Stokes, O. Caha, S.L. Ammu, J. Bai, K.E. Bassler, and S.C. Moss

 Perovskite Thin Films Under Strain...............................................................................................................................2-72

 F. He, B.O. Wells, and S.M. Shapiro

 Epitaxial Tilting of GaN Grown on Vicinal Surfaces of Sapphire ...................................................................................2-74

X.R. Huang, J. Bai, M. Dudley, R.D. Dupuis, and U. Chowdhury

 Mediator-Template Assembly of Nanoparticles.................................................................................................. 2-76

 M.M. Maye, I-I.S. Lim, J. Luo, Z. Rab, D. Rabinovich, T. Liu, and C.-J. Zhong

 Time-Resolved Morphology Development of Tri-axial Reinforced Epoxy Montmorillonites 

 Nanocomposites in Uni-Axial Magnetic Fields ..................................................................................................2-78

 H. Koerner, E. Hampton, D. Dean, Z. Turgut, L. Drummy, P. Mirau, and R.Vaia

Resonant X-ray Scattering from a Magnetic Multilayer Reflection Grating...................................................................2-80

 L.-A. Michez, C.H. Marrows, P. Steadman, B.J. Hickey, D.A. Arena, J. Dvorak, H.-L. Zhang, 

 D.G. Bucknall, and S. Langridge

Soft Condensed Matter and Biophysics

 Crystallization and Melting Behavior of Poly(ε-caprolactone) Under Physical Confinement.........................................2-82

 R.-M. Ho, Y.-W. Chiang, C.-C. Lin, and B.-H. Huang

 Jamming and Crystallization of Polymeric Micelles ......................................................................................................2-84

 T. Nicolai, F. Laflèche, and A. Gibaud
2-7 NSLS Activity Report

 Characterization of Ionomer Compatibilized Blend Morphology Using Synchrotron Small-Angle 

X-ray Scattering ................................................................................................................................................2-86.

G.C. Gemeinhardt and R.B. Moore

 Control of Surface Properties Using Fluorinated Polymer Brushes Produced by Surface-Initiated 

 Controlled Radical Polymerization......................................................................................................... 2-88

 L. Andruzzi, A. Hexemer, X. Li, C.K. Ober, E.J. Kramer, G. Galli, E. Chiellini, and D. Fischer 
2-8 NSLS Activity Report

Hunting the RNA “Slicer”

NSLS users may have found a key player in RNA interference

As the result of work done at the NSLS, scientists from Cold Spring Harbor Laboratory have very likely determined the identity of a sought-after protein that is vital to RNA interference (RNAi). RNAi is fundamental cellular process intimately involved 

in the development and virus-fighting ability of all organisms, as well as gene expression — how genes produce certain cell 

features. The researchers’ result, the crystal structure of the protein, will significantly impact the field of biology by helping to 

illuminate the details of these mechanisms.

Before the protein was identified, biologists only knew that there should be a protein, dubbed the “Slicer,” that performed 

a critical role in RNAi. It received this nickname for the function the scientists suspected it carried out: slicing, or cleaving, 

strands of messenger RNA into pieces, much like a pair of molecular “scissors.” Messenger RNA is the type of RNA that 

decodes the information contained in DNA (i.e. genes) and carries it out of the cell nucleus, where it is used to synthesize 

proteins. The Slicer is one component of a large multi-protein structure, called the RNA-induced silencing complex (RISC), 

that “interferes” with messenger RNA’s mission.

This research team is the first to discover very convincing evidence that a certain protein is, in fact, the Slicer. The protein 

is known as Argonaute. It is discussed in the group’s research paper on the work, which appears in the September 4, 2004 

edition of Science.

“The crystal structure of Argonaute 

contained a clue that led us to identify 

it as the Slicer,” said Leemor JoshuaTor, a structural biologist and the 

study’s lead researcher. “We observed 

that an important structural feature 

on Argonaute was very similar to that 

of another enzyme already known to 

cleave RNA.”

The group found that Argonaute is 

composed of a large crescent-shaped base and a smaller globular region that sits over it, tethered by a thin stalk-like region. 

The crescent has its own sub-structure, made up of three distinct parts, or “domains” — a center domain and two outer ones.

Based on these features, Joshua-Tor and her colleagues postulated how Argonaute might act as the Slicer. In their scenario, 

a strand of “small interfering” RNA (siRNA), which is a short type of RNA created earlier in the interference process, binds 

to Argonaute and guides it to a complementary strand of messenger RNA. The siRNA positions the messenger RNA in the 

groove created by Argonaute’s crescent and globular segments. Once in place, the crescent’s “PIWI” domain cleaves the 

messenger RNA, leaving the siRNA intact.

“This is an important result, but many questions still remain,” said Joshua-Tor. “For example, we still do not know how Argonaute proteins participate in developmental processes.”

Gene silencing during RNAi (the act of blocking gene expression) may sound destructive, 

but the process can prevent messenger RNA from carrying out the orders of potentially 

malicious genes — genes for defects, for example. RNAi also appears to play an important role in normal organ function. Currently, biologists are experimenting with ways to 

silence specific genes for medical purposes.

Joshua-Tor and her colleagues, including student researcher Ji-Joon Song, collected 

data at NSLS beamline X25 and later used the data to determine Argonaute’s structure. 

Using protein crystallography, they directed a beam of x-rays at a crystal of Argonaute 

protein and used a detector to collect the x-rays as they scattered away from the atoms 

in the crystal. The researchers then analyzed this pattern, which is unique to Argonaute, 

to create a three-dimensional model of the protein.

This research was funded by Cold Spring Harbor Laboratory. Ji-Joon Song is a BristolMyers Squibb fellow.

For more information, see: J.J. Song, S.K. Smith, G.J. Hannon, and L. Joshua-Tor, 

"Crystal Structure of Argonaute and its Implications for RISC Slicer Activity," Science, 305, 

1434-1437 (2004).

— Laura Mgrdichian

Authors (from left) Leemor Joshua-Tor, Gregory J. Hannon, Ji-Joon Song, and Stephanie K. Smith

A schematic depiction of the model 

for siRNA-guided messenger RNA 

cleavage. The siRNA (yellow) binds 

with its 3’ end in the cleft in the globular 

domain (red). The 5’ end is predicted to 

bind near the other end of the cleft. The 

messenger RNA strand (brown) comes 

in between the crescent’s N-terminal 

(blue) and globular domains and out 

between the globular domain and the 

crescent’s middle domain (purple).
Floating Films on Liquid Mercury

New results may lead to advances in nanotechnology, molecular electronics

Scientists from Brookhaven National Laboratory, Bar-Ilan University, and Harvard University have grown ultrathin films of organic chain molecules on the surface of liquid mercury and discovered that the molecules form ordered structures. Similar to 

sixty years ago when fundamental studies of silicon paved the way to the semiconductor-electronics age, these results help 

to build a foundation for the development of tiny circuits built using organic molecules — called molecular electronics — a 

field believed to be the future of many electronic applications.

The scientists are participating in an ongoing program at Brookhaven to grow ultrathin organic films on solid and liquid 

surfaces. They are most interested in films that have controllable properties at a thickness of just a few nanometers, or billionths of a meter, so that they can engineer technologies based on these properties. In addition to being useful for molecular electronics development, ultrathin organic films are becoming increasingly important for many other emerging technologies, such as flexible electronic displays and advanced biotechnological materials that can, for example, mimic the function 

of cell membranes.

“We decided to use liquid mercury as a surface, instead of a solid,” said Brookhaven 

physicist Benjamin Ocko, the lead author of the study, reported in the January 14, 2005 

edition of Physical Review Letters. “Liquid surfaces are disordered, hence they do not 

impose a structure of their own on the film. This makes them important testing grounds 

for organic thin film growth.” 

The researchers filled a small tray with a layer of liquid mercury and deposited a controlled amount of the organic molecules, called alkyl-thiol, onto its surface. “We chose 

alkyl-thiol because one end of each molecule is terminated by a sulfur atom that bonds 

strongly to metal surfaces,” explained Henning Kraack, a physicist from Bar-Ilan who 

participated in the study. “Thiol molecules have been studied extensively on gold surfaces, but the exact nature of the sulfur-gold bond has remained controversial. One of 

our main goals was to determine the nature of the bond between a similar pair: sulfur and 

mercury.”

At NSLS beamline X22, the scientists measured how x-rays scattered off the film from 

different angles using a unique instrument they developed that tilts the x-rays downward 

onto the liquid mercury surface. The scientists repeated this procedure several times, 

adding more alkyl-thiol each time to follow how the structure of the film evolved as the 

density of molecules increased.

The scientists discovered that three distinct scattering patterns emerged as the alky-thiol density was increased on the mercury surface, with each pattern corresponding to a different degree of molecular order. At the lowest density, the molecules 

lay flat on the mercury’s surface. At an intermediate density, the molecules tilt so that the sulfur end is in contact with the 

mercury. Finally, at the highest density, the molecules stand up straight.

The x-ray analysis of the lying-down phase showed that the alkyl-thiol molecules are disordered, pointing in all different 

directions. However, the standing-up and tilted phases are very ordered, with the molecules arranged in crystalline patterns, 

despite the disordered liquid nature of the underlying mercury. Additionally, the tilted phase contains an unusual structural 

feature: The alkyl-thiol chain portions and sulfur atoms line up differently so that the chains form one pattern while the sulfur 

atoms form another.

“The x-ray analysis indicates that the sulfur atoms from two neighboring chains chemically bond to one underyling mercury 

atom,” explained Ocko. “In the tilted phase, the sulfur-mercury bonds exhibit crystalline order. These bonds also form in the 

standing-up phase, but, surprisingly, they appear disordered.” 

“These specific structural and chemical details are necessary for understanding the electronic properties of the film, which is 

necessary for determining how to use them in new technologies,” he said.

In upcoming research, Ocko and his colleagues plan to study the structure of molecular layers sandwiched between two conducting surfaces, a configuration directly relevant to molecular electronics. This work was funded by the Office of Basic Energy Sciences within the U.S. Department of Energy’s Office of Science and the U.S.-Israel Binational Science Foundation.

For more information, see: B. Ocko, H. Kraack, P. Pershan, E. Sloutskin, L. Tamam, and M. Deutsch, “Crystalline Phases of 

Alkyl-Thiol Monolayers on Liquid Mercury,” Phys. Rev. Lett., 94, 017802 (2005).

— Laura Mgrdichian

Benjamin Ocko

Feature Highlights 2-9
2-10 NSLS Activity Report

A Catalyst Uncovered

To many, the phrase “synthetic organic chemistry” probably sounds a bit dull. But this scientific field — the making, or “synthesizing,” of carbon-based (i.e. organic) chemical compounds — has produced many, many products that we use every day. 

Examples include medicines, fuel, pesticides, paper, and even fabric for clothing. These breakthroughs are the results of 

many specific, intricate studies into how molecular reactions work.

One such study was recently completed at the National Synchrotron Light Source. Led by chemist Simon Bare, a user 

scientist from the corporation UOP LLC, the group used x-rays to investigate a new, safe catalyst for an important type of 

reaction called Baeyer-Villiger (B-V) oxidation. Their results, reported in the September 21, 2005 edition of the Journal of the 

American Chemical Society, add a link to the long chain of discovery that leads, eventually, to better consumer and industrial 

products.

“Baeyer-Villiger oxidation is an important reaction in 

synthetic organic chemistry,” said Bare. “Our aim is to 

make the reaction more stable and efficient by producing 

a better catalyst.”

The B-V reaction involves transforming “ketones” – a 

class of organic solvents – into “esters,” a type of 

compound formed by reacting an alcohol with an acid. 

Typically, this transformation is catalyzed by a group of 

acids called peracids, but these compounds are inherently unstable and require caution when used in large 

amounts. In contrast, the catalyst Bare’s group is studying is a silicon-based mineral compound known as Snβ-zeolite. In previous work, they showed Sn-β-zeolite to 

be an efficient, safe catalyst for B-V oxidation. Now, they 

have evidence that helps to explain, at the molecular 

level, why the catalyst is so successful.

Their results show that the effectiveness of Sn-β-zeolite 

as a catalyst depends on the “Sn” portion of the mineral — that is, the tin (Sn) atoms that are dispersed within the mineral’s 

crystal structure. By shining x-rays at a Sn-β-zeolite crystal sample, they discovered that the tin atoms are not randomly 

placed within the crystal, but instead are found at regular, specific locations.

“We believe that the uniform distribution of tin atoms produces sites in the mineral with uniform catalytic activity, which, in total, leads to the excellent overall 

behavior of the catalyst,” said Bare. “However, we are still not sure why the Sn 

atoms are positioned so evenly in the crystal.”

In future work, Bare’s group will try to resolve this issue. In the meantime, they 

hope that this study illustrates that it is possible to synthesize catalysts with uniformly spaced reactivity sites. As long as those sites are easily accessible to the 

compounds taking part in the reaction, this approach has the potential to produce 

many effective, efficient catalysts.

This study was supported by the U.S. Department of Energy, the Frederick Seitz 

Materials Research Laboratory at the University of Illinois at Urbana-Champaign, 

the National Institute of Standards and Technology, and UOP LLC.

For more information, see: S.R. Bare, S.D. Kelly, W. Sinkler, J.J. Low, F.S. 

Modica, S. Valencia, A. Corma, and L.T. Nemeth, "Uniform Catalytic Site in Snβ-Zeolite Determined Using X-ray Absorption Fine Structure," J. Am. Chem. Soc., 

127(37), 12924-12932 (2005).

— Laura Mgrdichian

A representation of the Sn-β-zeolite structure 

as derived from the x-ray data Bare and his 

group collected. The red areas mark one 

possible Sn-atom pair.

Authors (from left) Wharton Sinkler, Frank Modica, Laszlo Nemeth, Simon 

Bare, John Low. (Not pictured) Shelly Kelly, Susanna Valencia, and Avelino 

Corma
Nematodes: Nature’s Tiny Lead Filters?

A study performed at the National Synchrotron Light Source has revealed evidence that members of a family of tiny soildwelling roundworms, called nematodes, may naturally help lower soluble-lead levels in metal-contaminated soils. 

Researchers from the University of Georgia and the University of Chicago exposed the worms to lead in solution and used 

x-rays to “see” how the metal distributed within their bodies. They found that the lead concentrated in the nematodes’ pharynx regions, or throats, in the form of a solid crystalline material — pyromorphite, a lead-containing mineral. The results are 

described in the August 1, 2005 edition of Environmental Science & Technology.

“The nematodes seem to ‘trap’ the lead, somehow converting it into crystalline pyromorphite. We 

think this is the first report of this occurring,” said the study’s lead researcher, Brian Jackson, an 

environmental scientist now at the Center for Environmental Health Sciences at Dartmouth College, formerly with the University of Georgia’s Savannah River Ecology Laboratory.

The results also suggest that the nematodes took in the lead via ingestion using the same mechanism they use to feed. This may explain the high concentration of lead in the pharynx.

A nematode is typically less than one millimeter in length with a pharynx of only 10 – 20 micrometers, or millionths of a meter, in diameter. To characterize the distribution of lead within the 

organism Jackson and his group used a synchrotron x-ray “microprobe,” a tool that can produce 

very narrow, intense beams of x-rays. The group then used a technique called x-ray fluorescence 

(XRF) to create an image of the distribution of lead within the worm (areas of high lead concentration in the nematodes are bright and low concentrations are darker).

In XRF, a beam of high-energy x-rays is aimed at a sample, which absorbs the rays and almost 

instantly re-emits them. The emitted x-rays have varying energies depending on the types of atoms in the sample. Lead 

atoms, for example, emit x-rays with a different energy than any other element. Scientists use a device called a spectrometer 

to analyze the emitted rays and determine which elements, and approximately how much of each, are present in the sample 

or in parts of the sample.

Once the team identified areas of high lead content in the nematodes, they then 

used another research method, called x-ray diffraction, to identify the lead-rich 

areas of the worm as pyromorphite. In this technique, x-rays passing through the 

mineral emerge in a pattern as a result of diffracting through the closely spaced 

lattice of atoms in the crystal. Each crystalline solid has a characteristic x-ray 

diffraction pattern, much like a unique “fingerprint.”

The researchers also tested the nematodes’ response to copper and found that, 

unlike the lead, the copper did not localize in a specific area. Instead, it dispersed evenly within the worms.

“Given the high numbers of nematodes in soil, their ability to convert lead in 

pyromorphite may help detoxify lead in contaminated soils and mediate lead in 

non-contaminated soils,” said Jackson. 

He continued, “In the future, we will look to see if lead in these invertebrates 

becomes absorbed by predators or, because pyromorphite is so insoluble, if the 

lead could pass through the digestive system of a predator unchanged.”

This study was supported by the Office of Biological and Environmental Research within the U.S. Department of Energy’s Office of Science via a Financial 

Assistance Award to the University of Georgia Research Foundation.

For more information, see: B.P. Jackson, P.L. Williams, A. Lanzirotti, and P.M. 

Bertsch, "Evidence for Biogenic Pyromorphite Formation by the Nematode Caenorhabditis elegans," Environ. Sci. Technol., 39(15), 5620-5625 (2005).

— Laura Mgrdichian

Optical (A) and XRF (B and C) images of a 

nematode exposed to both copper (B) and 

lead (C).

Y (mm) Y (mm)

X (mm)

X (mm)

Brian Jackson

Feature Highlights 2-11
2-12 NSLS Activity Report

Nanotubes in a New Light

Using x-rays to investigate order and function in nanotube systems

Nanotubes are cylindrical molecules just a few nanometers (billionths of a meter) in diameter. However, their potential for 

new technologies is vast. They are extraordinarily strong, conduct electricity well, and can even emit light, properties suitable 

for many applications, from flat-panel television displays to building materials. But nanotubes must be extensively studied 

before they can be used in industrial applications.

A collaboration of scientists has pioneered a novel way of using x-rays to study arrays of nanotubes. In ongoing research, 

they have determined the degree of order contained in certain nanotube systems — that is, to what extent they form organized patterns — and have investigated the structural and chemical properties of others.

The team includes Mahalingam Balasubramanian, Brookhaven National Laboratory (BNL); Sarbajit Banerjee, Stony Brook 

University (SBU); Tirandai Hemraj-Benny, SBU; Daniel Fischer, National Institute of Standards and Technology (NIST); Weiqiang Han, BNL; James Misewich, BNL; Sharadha Sambasivan, NIST; and Stanislaus Wong, BNL and SBU.

The group is investigating two types of carbon nanotubes: single-walled nanotubes (SWNTs), consisting of a single cylinder, 

and multi-walled nanotubes (MWNTs), which resemble cylinders concentrically nested together. They have also completed a 

study of boron nitride nanotubes, which are equally intriguing.

A New Approach

Nanotubes are being studied across the globe, and the technique used in this case has been used for years to study various 

materials. Now, the technique has been applied to nanotubes, with excellent results.

The technique is called “near-edge x-ray absorption fine structure,” or NEXAFS. In NEXAFS analysis, a nanotube sample is 

bombarded by a beam of low-energy x-ray “photons,” or particles of light. The photons are absorbed by each carbon atom’s 

“core” electrons — those closest to the nucleus - giving them an energy boost. As a result, they jump to an orbit further away 

from the nucleus. When this occurs across many, many atoms, scientists can record the sample’s absorption “spectrum,” 

which measures its absorption behavior.

At beamline U7A (owned by NIST and The Dow Chemical Company), the researchers aimed the x-rays at each sample from 

several angles, producing several spectra for each array. By analyzing the spectra, they uncovered information about the 

nanotubes’ electronic and physical structures.

“The beauty of using NEXAFS to study nanotubes is that it is able to provide us with detailed information that is truly complementary to what can be obtained using other techniques,” said Fischer.

Your Order, Please

In the May 5, 2005 issue of the Journal of Physical Chemistry, the group describes how they used NEXAFS to determine the 

degree of order in very thin films of single-walled nanotubes, known as “buckypaper,” and a MWNT film grown on a surface 

of platinum. They compared their results to two “control” groups: 

graphite, a highly ordered form of carbon, and SWNT and MWNT 

powders, which have essentially no order.

The group found that the buckypaper spectra are similar to graphite’s. For both, the spectra change when the x-rays graze the sample 

rather than strike head-on. This property — the tendency of a material to react differently to outside fields depending on the direction 

the field is applied — is called “anisotropy.” It is very useful to study, 

since high anisotropy often implies a high degree of order. Conversely, a material shows “isotropy” when its reaction to an outside field is 

the always the same. Nanotube powders, containing nanotubes in all 

possible orientations, display isotropy.

The buckypaper displayed anisotropy, but not as extensively as 

graphite — approximately 87 percent of the nanotubes were on their 

sides. The MWNT film was also quite anisotropic, behaving as if most 

of the nanotubes were standing upright.

“These results are encouraging because they indicate that two com- Authors (from left) Tirandai Hemraj-Benny, Dan Fischer, Jim 

Misewich, Stanislaus Wong, and Sharadha Sambasivan
mon nanotube systems already contain a fair degree of order,” said Wong. “We plan 

to continue studying MWNT and SWNT films. Our hope is to find a way to produce a 

nanotube array with order comparable to graphite.”

A Matter of Function

“Functionalizing” a set of nanotubes is a process that allows scientists to manipulate 

the tubes into ordered arrays with specific properties. One way to do this is “ozonolysis” — reacting the nanotubes with ozone, a form of oxygen gas. This produces tiny 

holes into the nanotubes’ walls and creates various oxygenated compounds along 

their surfaces, which serve as tethering points for a variety of other compounds.

Ozonolysis can also cleanse the nanotubes or produce reactions that “unhinge” the 

nanotubes’ half-sphere end caps, leaving the tubes open to a variety of interesting 

“stuffings.” Filling the tubes with metal atoms, for example, could boost their ability 

to conduct electricity.

But studying the specific electronic structure of the nanotubes, as well as the chemical make-up and ordering of the oxygen-carbon compounds, which are called functional groups, has been difficult. Most techniques are unable to simultaneously yield 

both types of information. The team showed that NEXAFS is an important complement to these other methods.

For example, their article in the September 20, 2004 issue of ChemPhysChem, focuses on MWNTs exposed to ozone. 

NEXAFS showed that the ozone treatment cleared the nanotubes of “amorphous” carbon — carbon atoms not incorporated 

into the ordered structure of the nanotubes themselves — opened the end caps, and produced functional groups along the 

nanotubes.

A Nanotube by Another Name

The word “nanotube” is very often preceded by the word “carbon,” but nanotubes made of other materials can be equally — or

even more — interesting. One such material is boron nitride.

Boron nitride nanotubes are also tremendously strong. But they 

possess some superior properties, such as flexibility without 

compromising strength and the ability to withstand very high temperatures. Like carbon nanotubes, they are being investigated 

for a wide array of potential applications.

In the March 21, 2005 issue of the journal Physical Chemistry 

Chemical Physics, the team describes how they used NEXAFS 

to gain valuable structural information about a sample of boron nitride nanotubes. Their results show that the nanotubes in 

their sample have atomic structures that mimic a type of carbon

nanotube with hexagonally bonded carbon atoms (like a rolledup sheet of chicken-wire fence). NEXAFS also revealed that the 

boron nitride nanotubes have few defects and are highly crystalline, perhaps even more so than carbon nanotubes.

For more information, see:

S. Banerjee, T. Hemraj-Benny, S. Sambasivan, D.A. Fischer, J.A. Misewich, and S.S. Wong, "Near-Edge X-ray Absorption 

Fine Structure Investigations of Order in Carbon Nanotube-Based Systems," J. Phys. Chem. B, 109(17), 8489-8495 (2005).

S. Banerjee, T. Hemraj-Benny, M. Balasubramanian, D.A. Fischer, J.A. Misewich, and S.S. Wong, "Surface Chemistry and 

Structure of Purified, Ozonized, Multiwalled Carbon Nanotubes Probed by NEXAFS and Vibrational Spectroscopies," ChemPhysChem., 5(9), 1416-1422, (2004).

T. Hemraj-Benny, S. Banerjee, S. Sambasivan, D.A. Fischer, W. Han, J.A. Misewich, and S.S. Wong, "Investigating the 

Structure of Boron Nitride Nanotubes by Near-Edge X-ray Absorption Fine Structure (NEXAFS) Spectroscopy," Phys. Chem. 

Chem. Phys., 7(6), 1103-1106 (2005).

— Laura Mgrdichian

A rendering of carbon nanotubes being 

studied using NEXAFS. Light comes in (left) 

and electrons are emitted (right).

Scanning electron microscope images of (a) MWNT powder, (b) 

SWNT powder, (c) SWNT buckypaper, and (d) aligned MWNTs.

Feature Highlights 2-13
2-14 NSLS Activity Report

The Role of Titanium in Hydrogen Storage

As part of ongoing research to make hydrogen a mainstream source of clean, renewable energy, scientists from the U.S. 

Department of Energy’s Brookhaven National Laboratory have determined how titanium atoms help hydrogen atoms attach 

to an aluminum surface. Their study isolates the role of titanium, which is used as a catalyst in the crucial first step to trap 

hydrogen within a particular class of hydrogen-storage materials. The work may also help identify and develop similar hydrogen-storage systems. 

Brookhaven chemist Santanu Chaudhuri presented this research at the 

230th National Meeting of the American Chemical Society in Washington, 

D.C. on August 28, 2005.

To be a mainstream source of fuel, hydrogen must be stored safely and efficiently. Conventional high-pressure storage tanks can be dangerous and are 

too big and heavy for certain applications, such as hydrogen-based fuel cells 

in automobiles. Hydrogen-storage materials, however, incorporate hydrogen 

safely and compactly, and temporarily hold large quantities of it that can be 

recovered easily under safe, controlled conditions. 

“A hydrogen-storage material must be able to store hydrogen quickly under 

‘normal’ conditions — that is, without very high temperatures and pressures,” 

said Chaudhuri. “In tiny amounts, an appropriate catalyst, such as titanium, can speed up the reaction and make the hydrogen-storage process suitable for practical applications. Our study has helped us better understand the role of these catalysts.” 

Through this research, Chaudhuri and his collaborator, Brookhaven chemist James Muckerman, hope to improve the performance of sodium alanate, a hydrogen-storage material composed of sodium and aluminum hydride. Sodium alanate, known 

as a “complex metal hydride,” expels hydrogen gas (the fuel) and aluminum when heated, leaving a mixture of sodium hydride and metallic aluminum. But because neither aluminum nor sodium hydride absorb hydrogen well, putting the hydrogen 

back in — to reform sodium alanate and allow reuse of the material — becomes difficult. 

“We found that aluminum absorbs significantly more hydrogen — and does 

so more quickly and at lower temperatures — when a small number of titanium atoms are incorporated into its surface,” Chaudhuri said. 

Chaudhuri and Muckerman created a computer model that provides a plausible mechanism of the reaction. Their model agrees with an experimental 

x-ray absorption study of sodium alanate, performed at the National Synchrotron Light Source.

Chaudhuri and Muckerman’s collaborators at Brookhaven used x-rays to 

“see” and thus calculate how the titanium atoms subtly changed the atomiclevel structure of the aluminum, resulting in a more hydrogen-absorbent 

surface. Results from these two studies agree on the role of titanium atoms 

on an aluminum surface and mechanisms of subsequent steps in hydrogen 

capture. 

In the future, Chaudhuri and Muckerman’s group plans to study the subsequent steps in the sodium alanate hydrogen-storage process, in which aluminum and hydrogen react with sodium hydride to reform the starting material. 

This research was funded by the Office of Basic Energy Sciences within the 

U.S. Department of Energy’s Office of Science.

— Laura Mgrdichian

James Muckerman Santanu Chaudhuri

Molecular orbital rearrangements (left) during 

the dissociation and subsequent absorption of a 

hydrogen molecule (H2

) onto an aluminum surface. 

This process is facilitated by a tiny amount of titanium 

that is present in the aluminum phase of depleted 

sodium alanate (the hydrogen-storage material under 

study). Then, small, mobile molecular clusters of 

aluminum hydride (AlHx

) transport the hydrogen and 

aluminum to sodium hydride (right), where the sodium 

alanate is reformed.
Yale Scientists “See” Basis of Antibiotic Resistance

Using x-ray crystallography, researchers at Yale have “seen” the structural basis for antibiotic resistance to common pathogenic bacteria, facilitating design of a new class of antibiotic drugs, according to an article in the April, 2005 issue of Cell.

In recent years, common disease–causing bacteria have increasingly become resistant to antibiotics, such as erythromycin 

and azithromycin. Although the macrolide antibiotics in this group are structurally different, all work by inhibiting the protein 

synthesis of bacteria, but not of humans. They bind 

tightly to an RNA site on the bacterial ribosomes, the 

cellular machinery that makes protein, but not to the 

human ribosomes. Bacteria can become resistant to 

antibiotics in several different ways. When bacteria 

mutate to become resistant to one of these antibiotics, 

they usually are resistant to all antibiotics in the group.

Studies led by Sterling Professors Thomas A. Steitz 

and Peter B. Moore in the Departments of Molecular 

Biophysics and Biochemistry, and Chemistry at Yale 

University illuminate one of the ways that bacteria can 

become resistant to macrolide antibiotics.

“A major health concern of antibiotic resistance is that two million people every year get infections in hospital facilities and 

90,000 per year die from them,” said Steitz. “Macrolide-resistant Staphylococcus aureus is the most common of these infections.”

Some of the clinically important bacteria are resistant because of mutation of a single nucleotide base, from an A to a G, in 

the site where macrolide antibiotics bind to the ribosome. The Yale group was able to “see” structural alterations when antibiotics were bound to ribosomes with different sensitivity to the drugs because of mutation. They can now explain why that mutation has the effect that it does. “The mutant G has an amino group that pokes into the center of the macrolide ring, causing 

it to back off the ribosome by an Angstrom or so,” said Steitz. The change of that one base in the ribosomal RNA reduced the 

ability of the antibiotic to bind by a factor of 10,000.

Mutation of this type happens naturally, but rarely — only one in 100,000 to one in 10,000,000 bacterial mutations will cause 

this kind of resistance. However, each bacterium can divide as often as every 20 minutes, allowing one with a resistant mutation to rapidly cause a dangerous infection.

Daqi Tu, a student, and Gregor Blaha, a postdoctoral fellow in molecular 

biophysics and biochemistry and associate of the Howard Hughes Medical Institute, are co-authors on the study. Funding for this research was 

obtained from the National Institutes of Health and the Agouron Institute.

For more information, see: D. Tu, G. Blaha, P.B. Moore, and T.A. Steitz, 

"Structures of MLSBK Antibiotics Bound to Mutated Large Ribosomal 

Subunits Provide a Structural Explanation for Resistance," Cell, 121(2), 

257-270 (2005).

— Janet Rettig Emanuel, Yale University

Interactions of macrolides with G2099A large ribosomal subunits. (A) A (Fo(mutant + 

drug) – Fo(wild type – drug)) difference map calculated using wild-type phases shows 

positive 4 σ density (black) for erythromycin, and a negative 4 σ peak (red) at N2 of 

G2099. (B) No convincing difference density is observed when erythromycin is soaked 

into wild type H. marismortui 50S crystal with ~ 3 mM concentration (left), but when it 

is soaked into 50S crystals containing 33% G2099A mutants, clear density is observed 

when the drug concentration is 3 μM (right). (C) Erythromycin binds in the hydrophobic 

pocket formed by residue A2100 (A2059), A2099 (A2058) and G2646 (C2611), with 

its desosamine nitrogen hydrogen bonded to A2099N1. (D) Telithromycin binds in the 

hydrophobic pocket formed by residue A2100, A2099 and G2646 the way erythromycin 

does, with its alkyl-aryl extension making an additional stacking interaction with the 

base of C2644 (U2609), and a hydrogen bond to the 2’OH of C2644 (U2609). (E) The 

lactone rings of erythromycin and telithromycin bound to Hma ribosomes are perfectly 

superimposable. (F) Comparison of azithromycin bound to G2099 (blue) and G2099A

(yellow) ribosomes. The N2 of a G was modeled onto residue A2099. The two structures 

were aligned by least squares superimposition of ribosomal RNA phosphorus atoms.

Authors (from left) Daqi Tu, Peter B. Moore,Thomas A. Steitz, and Gregor Blaha

Feature Highlights 2-15
2-16 NSLS Activity Report

NSLS Vortex-Tube Study is a Win for Safety

During machining at the NSLS, a vortex-tube device that directs chilled air to cool the cutting tool is often utilized because

it reduces the amount of fluid coolant that needs to be used. This makes it more environmentally friendly than other cooling 

methods — always a good thing. But the safety of vortex tubes — whether they make a machine operator more or less safe 

— has been in debate.

Recently, however, the debate was put to rest by NSLS engineer Ed Haas, technical supervisor Bob Scheuerer, and machinist Ed Losee, who designed and completed a series of tests to determine if vortex tubes enhance or diminish safety during 

machining. Their work is summarized in an article, which they co-wrote, 

that published in September 2005 trade journal Modern Machine Shop.

Said Haas, “At Brookhaven, uncertainty when it comes to safety is 

considered not acceptable. We wanted to settle this safety issue using 

objective tests.”

The issue of vortex-tube safety lies in the fact that the chilled air flow 

produced by the vortex tube may increase the amount of high-speed 

metal chips that are directed toward the machine tool operator. Therefore, one way to gauge the safety or lack of safety of a vortex tube is 

to measure (by weight) the quantity of those chips. To help make this 

measurement, Haas, Scheuerer, and Losee designed a “chip catcher” 

— cloth clamped to a metal frame — which they placed on a milling 

machine.

Under identical conditions, using nine identical chip catchers, the men 

ran nine trials using a one-inch-thick piece of aluminum: three trials with no coolant whatsoever, three with a vortex tube, 

and three using coolant spray. After each run, Haas, Scheurer, and Losee weighed the chips caught by the chip catcher (the 

chips from the last three runs were rinsed and dried to remove the liquid coolant, before they were weighed).

The results? Compared to the no-coolant and spray-coolant runs, which produced nearly the same volume of chips compared 

to each other, the vortex-tube runs resulted in more than 60 percent fewer chips directed toward the machine operator.

“We concluded that using a vortex tube does in fact enhance the safety of the operator compared to cases in which no coolant or spray coolant is used,” said Haas. “This is particularly true if guarding or shielding is used behind the machine tool so 

that chips cannot travel toward any other personnel in the area. Clean-up would then be easier since dry chips would then 

accumulate against the shield.”

In the future, Haas, Scheurer, and Losee may consider performing additional vortex-tube safety tests using other conditions, 

such as denser materials and higher cutter speeds.

For more information, see: E. Haas, R. Scheuerer, and E. Losee, "Vortex Tube Machining Improves Safety While Reducing 

Environmental Waste," Mod. Mach. Shop., 78, 54 (2005).

— Laura Mgrdichian

Vortex tube and chip catcher test set-up Chips collected by chip-catcher using vortex 

tube during machining

Chips collected by chip-catcher during dry 

machining

Authors (from left) Ed Haas, Ed Losee, and Bob Scheuerer
Studying the Effects of Acid Mine Drainage

New information from a study performed at the NSLS may one day help to mitigate the contamination caused by acid mine 

drainage, in which the breakdown of minerals in mines causes harmful materials to leach into waters and soils.

NSLS user scientists from Princeton University used infrared light and x-rays to study the interactions between two main 

components of acid mine drainage: two different positively charged iron ions, known as iron(II) and iron(III), and a negative 

sulfate ion (a sulfur-oxygen molecule). These substances are typically produced by the weathering of pyrite, a common mine 

ore.

“Acid mine drainage contaminates surface waters, groundwater, and soils 

in many locations around the world,” said geoscientist Juraj Majzlan, the 

paper’s lead author, now a faculty member at Albert-Ludwig-University of 

Freiburg (this work was performed when he was at Princeton).

“We studied how iron and sulfate interact in solution, such as how they 

combine to form various iron-sulfate compounds,” he explained. “This 

is important, since the presence of iron-sulfate compounds affects the 

solubility of other harmful substances in water contaminated by acid mine 

drainage, such as trace metals and other ions, which contribute to its 

toxicity.”

The work is published in the January 1, 2005 edition of Environmental 

Science & Technology.

Majzlan and Princeton geoscientist Satish C.B. Myneni, the paper’s co-author, prepared two types of solutions, the first type 

containing sulfate and iron(II) and the second containing sulfate and iron(III). These solutions simulate the concentrations 

found in contaminated water. For each type, they prepared samples with varying concentrations of iron(II) and iron(III). They 

studied the solutions using infrared and x-ray “spectroscopy,” a technique that 

measures how the light is absorbed by the solution. The absorption behavior of 

the solution provides scientists with structural and compositional information, 

such as the types of atomic clusters, known as complexes, that form within it.

Majzlan and Myneni focused on the sulfate ion, using it as an indicator. That is, 

they studied how the sulfate was altered in the presence of iron(II) or iron(III) 

and, based on any changes, inferred how it had interacted with the iron.

The researchers found that sulfate and iron(II) either interacted very weakly 

or did not form any complexes at all. However, they measured a significant 

distortion of the sulfate ion in the presence of iron(III). Upon further study, 

they determined that sulfate and iron(III) formed molecular complexes strongly 

bound together by hydrogen atoms.

This system serves as a model for acid-polluted waters. The sulfate-iron(III) 

complexes are small-scale versions of the mineral precipitates — solid materials that crystallize out of a liquid — that appear in acid-mine drainage. Based 

on the particular complexes that form in the sulfate-iron(III) solutions, the 

scientists can predict which precipitates are most likely to occur in acid mine 

drainage. One day, this information may assist in devising clean-up strategies 

for water contaminated by acid mine drainage.

This study was supported by the National Science Foundation and a Hess Fellowship from the Princeton University Geosciences Department.

For more information, see: J. Majzlan and S.C.B. Myneni, "Speciation of Iron 

and Sulfate in Acid Waters: Aqueous Clusters to Mineral Precipitates," Environ. 

Sci. Technol., 39(1), 188-194 (2005).

— Laura Mgrdichian

Examples of water contaminated by acid mine 

drainage.

Juraj Majzlan Satish Myneni

Feature Highlights 2-17
2-18 NSLS Activity Report

A New Structural View of Organic Electronic Devices

Although still in the qualifying rounds, U.S. researchers are helping manufacturers win the race to develop low-cost ways to 

commercialize a multitude of products based on inexpensive organic electronic materials — from large solar-power arrays to 

electronic newspapers that can be bent and folded.

In the October 4, 2005 issue of Advanced Materials, researchers from the National Institute of 

Standards and Technology (NIST) and the University of California at Berkeley report success in 

using a non-destructive measurement method to detail three structural properties crucial to making reliable electronic devices with thin films of the carbon-rich (organic) semiconductors. The 

new capability could help industry clear hurdles responsible for high manufacturing development 

costs that stand in the way of widespread commercial application of the materials.

With the technique called near-edge x-ray absorption fine-structure spectroscopy, or NEXAFS, 

the team tracked chemical reactions, molecular reordering and defect formation over a range of 

processing temperatures.

They then evaluated how process-induced changes in thin-film composition and structure affected 

the movement of charge carriers (either electrons or electron “holes”) in organic field effect transistors, devices basic to electronic circuits. With NEXAFS measurements taken over the range 

from room temperature to 300 degrees Celsius, the team monitored the conversion of a precursor 

chemical to an oligothiophene, an organic semiconductor. The molecular organization and composition achieved at 250 degrees Celsius yielded the highest levels of charge carrier movement 

and, consequently, maximum electric-current flow.

 As chemical conversion progressed, the researchers calculated how the molecules arranged themselves on top of an electrical insulator. Top transistor performance corresponded to a vertical alignment of molecules. In addition, they used NEXAFS 

to determine the angles of chemical bonds and to assess the thickness and uniformity of film coverage, also critical to performance.

NEXAFS has the potential to be the “ideal measurement platform for systematic 

investigation” of organic electronic materials, says lead investigator Dean DeLongchamp, a NIST materials scientist. “A straightforward means of correlating 

chemical and physical structure to the electronic performance of organic semiconductor films is a much-needed tool.”

The research was conducted at beamline U7A, the NIST/Dow Chemical materials characterization facility at the National Synchrotron Light Source. Funding 

providers included the U.S. Department of Energy, Defense Advanced Research 

Projects Agency, and the Microelectronics Advanced Research Corporation.

Article originally published at http://www.msel.nist.gov/OE_Highlight.htm.

For more information, see: D.M. DeLongchamp, S. Sambasivan, D.A. Fischer, 

E.K. Lin, P. Chang, A.R. Murphy, J.M.J. Frechet, and V. Subramanian, "Direct 

Correlation of Organic Semiconductor Film Structure to Field-Effect Mobility," 

Adv. Mater., 17(19), 2340-2344 (2005).

— Mark Bello, NIST Media Contact

NIST researchers (clockwise from top) Dean 

DeLongchamp, Daniel Fischer, and Sharadha 

Sambasivan.

The group’s research is 

showcased on the cover of 

the October 4, 2005, edition 

of Advanced Materials.
Scientists Describe New Way to Peer Inside Bacteria

X-rays yield pictures and chemical clues that may help trace contaminants, thwart terrorists

As part of the search for better ways to track and clean up soil contaminants, scientists at the U.S. Department of Energy’s 

Brookhaven National Laboratory and Stony Brook University have developed a new way to “image” the internal chemistry of 

bacteria. The technique will allow scientists to “see” at the molecular level how 

soil-dwelling microbes interact with various pollutants. The method might also 

help scientists better understand and prevent bacterial diseases, or find ways 

to detect or disable bacteria used in a terror attack. 

“The more we learn about soil microbe chemistry, the better we’ll be able to 

predict the movement of contaminants in the environment,” said Brookhaven 

microbiologist Jeffrey Gillow. “What we learn might also suggest new ways to 

harness microorganisms to immobilize things like heavy metals and radioactive contaminants,” he said. Gillow gave a talk on the new method at the 230th 

National Meeting of the American Chemical Society in Washington, D.C. on 

August 28, 2005.

Called x-ray spectromicroscopy, the method uses the extremely bright x-rays 

available at Brookhaven’s National Synchrotron Light Source (NSLS) -- but not 

just to take pictures. At the NSLS, the scientists can actually “tune” the energy 

level of the beam to measure subtle differences in the energy absorbed by 

different forms of carbon. This carbon absorption spectrum, or “fingerprint,” 

reveals detailed biochemical information about what is inside and around the 

bacterial cells — and can even detect the formation of bacterial spores at an 

early stage invisible to other methods. 

“We are starting to learn a lot more about the molecular chemistry of these 

bacteria,” said Gillow. “The goal is to understand better how they interact with 

metals and radionuclides.” 

The technique may also reveal details about the process of bacterial spore formation. This could be important to environmental cleanup because spore-forming microbes often live in contaminated environments. It might also offer new targets for the 

detection of weaponized bacteria (by finding spores at an early stage), or help thwart disease or a terrorist attack by finding 

ways to prevent the spores from germinating into active, infective bacterial cells. 

With this technique, Gillow added, samples can be studied wet or dry, without staining, 

sectioning, or any other intervention such as those used in electron and fluorescence 

microscopy. 

This work is a collaborative effort of the Center for Environmental Molecular Science, 

which consists of scientists from Stony Brook University and Brookhaven Lab, and the 

University of Guelph in Canada. The work was funded by the U.S. National Science 

Foundation and the Office of Biological and Environmental Research within the U.S. 

Department of Energy’s Office of Science.

— Karen McNulty Walsh

Researchers (from left, top) Sue Wirick, Bjorg 

Larson, and Jeffrey Gillow

A single cell of Clostridium sp. (a strictlyanaerobic, soil-dwelling bacterium) as 

imaged by scanning trasmission x-ray 

spectromicroscopy (left). By analyzing the 

x-ray absorption spectrum, scientists can 

pick up subtle biochemical differences 

between the bulk of the cell body (yellow) 

and a tiny spore (green) forming inside. 

This early stage of spore formation would 

be invisible to other imaging techniques.

Feature Highlights 2-19
2-20 NSLS Activity Report

Removing Uranium From Contaminated Steel Surfaces

2000 DOE student intern who assisted in research is among authors of published paper

Scientists from BNL’s Environmental Sciences Department and Stony Brook University (SBU) Environmental & Molecular 

Sciences, have developed a simple, safe method of removing uranium from contaminated metallic surfaces using citric acid 

formulations so that the materials can be recycled or disposed of as low-level radioactive or nonradioactive waste. This 

research, published in the July 1, 2005 issue of Environmental Science and Technology, is funded by the Environmental 

Management Science Program of the Environmental Remediation Sciences Division, Office of Biological & Environmental 

Research of DOE’s Office of Science.

Decontamination of radionuclides from metallic and other surfaces contaminated by radiological incidents is a major environmental challenge. A.J. Francis, assisted by Cleveland Dodge, BNL, and by SBU’s Gary Halada, developed an innovative and 

improved process for decontaminating metal surfaces and other materials. Another team member named among the authors 

was BNL 2000 summer intern Jason McDonald, currently pursuing his Ph.D. at Louisiana State University. Material Science 

Department, both affiliated with the Center for The research team developed an environmentally friendly green-chemistry 

process that uses all naturally occurring materials — citric acid, common soil bacteria, and sunlight.

Present methods of removing uranium from contaminated metal 

surfaces include sand blasting, chemical extraction, and electrochemical dissolution. These methods generate secondary waste 

streams, creating additional disposal problems. “In the event of a 

radiological incident, such as a ‘dirty bomb,’ this technology can 

be used to clean up contaminated materials,” Francis said. “It 

will also treat the secondary waste generated from the treatment 

process, resulting in waste minimization. It is a comprehensive

process.”

For more information, see: A.J. Francis, C.J. Dodge, J.A. McDonald, and G.P. Halada, "Decontamination of Uranium-Contaminated 

Steel Surfaces by Hydroxycarboxylic Acid with Uranium Recovery," 

Environ. Sci. Technol., 39, 5015-5021 (2005).

— Kay Cordtz

Discussing their uranium decontamination research conducted 

at BNLs National Synchrotron Light Source are scientists: (from

left) A.J. Francis, BNL; Gary Halada, Stony Brook University; 

and Cleveland Dodge, BNL. Also participating in this research 

was Jason McDonald (not shown). McDonald worked with the 

research team at BNL in summer 2000 through a DOE summer 

internship program administered by BNL’s Office of Educational 

Programs and is currently working on his Ph.D. in agronomy and 

environmental management at Louisiana State University, Baton 

Rouge.
2-22 Chemical Science

Zinc Oxide Nanowires Grown by Vapor-Phase Transport Using Selected Metal Catalysts: A Comparative 

Study

Z. Zhu1, T.-L. Chen2, Y. Gu1, J. Warren3, and R.M. Osgood, Jr.1,2,3

1

Department of Applied Physics and Applied Mathematics and 2Department of Electrical Engineering, Columbia 

University; 3

Center for Functional Nanomaterials, Brookhaven National Laboratory

The search for new methods of synthesizing nanomaterials is a key goal of the 

national nanoscience initiative. Our research involves a comparative study of 

metal-surface-catalyzed growth of ZnO nanowires using four different metal 

catalysts and using substrates of differing materials and differing crystal orientations. We have employed multiple materials diagnostic techniques to compare the material, structural, and optical properties of nanowires grown using 

these different surface systems. In particular, we have found that the growth 

modes of nanowires are dependent on the choice of surface catalysts, e.g. for 

the Fe thin-film catalysts, the growth of ZnO nanowires may occur via a vaporsolid process, while, for the case of Au, Ag, and Ni catalysts, the vapor-liquidsolid process usually dominates the wire growth.

Nanowire growth has been investigated as a route to low-dimensional crystal 

structures. These nanostructures have potential applications in a variety of 

optical- and electronic-devices, such as lasers or light-emitting diodes. While 

the growth of these wires has been achieved under a wide variety of conditions, including liquid and vapor growth, one of the most reliable and well-studied approaches uses vapor-phase transport of the constituents coupled with 

surface catalysis of the nucleation and growth steps. Prof. Peidong Yang and 

his collaborators at Lawrence Berkeley National Laboratory have described an 

excellent example of this approach for the growth of ZnO nanowires. In this 

method, small surface-bound droplets of Au are formed on a solid substrate 

surface, such as Si(100), by heating a thin Au film and depositing it on the Si 

surface. These droplets served as alloying sites for the condensation of Zn vapor from a nearby solid-ZnO source. Single-crystal ZnO nanowires then grew 

from the supersaturated AuZn alloy, in the presence of constant trace amounts 

of oxygen (Figure 1). The orientation of the wires was thought to be governed 

by registration on the substrate crystalline lattice.

The success of this method in growing nanoobjects caused us to ask a series 

of questions: Can other catalysts be used? How general is the technique? 

What exactly controls the properties of the nanowires? Answering such questions is difficult because both the catalyst and substrate play important roles in 

determining the properties and the structure of the nanowires. In addition, the 

attainment of good nanowire material properties, such as good crystallinity and 

low impurity concentration, plays an important role in the practicality of various 

nanowire applications in electronics and optics.

Thus, we have employed multiple materials diagnostics, including x-ray diffraction, to compare the material, structural, and optical properties of the 

nanowires grown using these different surface systems. In particular, our research shows that the growth modes of nanowires depends on the exact metal 

surface catalysts used. Thus, for Fe or Ni thin-film catalysts, the growth of ZnO 

nanowires apparently proceeds via a vapor-solid process, while, for the case 

of Au, Ag, and sometimes Ni catalysts, the vapor-liquid-solid process appears 

BEAMLINE X18A

Funding

National Science Foundation; Instrumentation (Columbia and Brookhaven National 

Laboratory) by the U.S. Department of 

Energy

Publication

Z.M. Zhu, T. Chen, Y. Gu, J. Warren, and 

R.M. Osgood, Jr., “Zinc-Oxide Nanowires 

Grown by Vapor-Phase Transport Using 

Selected Metal Catalysts: A Comparative 

Study,” Chem. Mater., 17, 4227 (2005).

For More Information

Richard Osgood, Applied Physics 

Department, Columbia University 

Email: osgood@columbia.edu

Authors (from left) Zuoming Zhu, 

Richard M. Osgood, Jr., and TsungLiang Chen
to dominate the wire growth. These differences are apparent in the high-resolution SEMs taken at the BNL Center for Functional Nanomaterials (CFN); see 

Figure 2. Further, as shown in Figure 3, our study shows that the degree of 

nanowire alignment on the substrates is a function of both the substrate lattice 

matching with the lattice of the nanowires, as well as the growth mode and its 

role in affecting the substrate-interfacial properties. 

From a more general point of view, our investigation shows that the use of 

different catalysts provides versatility in the growth of one-dimensional ZnO 

nanostructures with different ranges of parameters such as diameters, areal 

densities, and aspect ratios. In particular, our studies suggest that, compared to 

noble-metal catalysts, the rate of growth using transition-metal catalysts is relatively faster and therefore typically yields thicker wires with a higher aspect ratio. However, this high growth rate is achieved at the expense of inducing more 

oxygen vacancies. These differences in growth properties would be expected to 

affect other properties of the wires, such as their electrical transport and surface 

chemistry. Exploring these aspects is of interest for practical applications of ZnO 

and other metal-oxide nanowires in nanodevices and chemical sensors.

Figure 3. A series of XRD 

spectra for ZnO nanowires 

synthesized using several 

different metal catalysts. The 

spectra were recorded at 

angles covering three major 

characteristic XRD diffraction 

peaks of the wurtzite ZnO.

ZnO wires grown

by Ag catalysts

Figure 1. Illustration of the vaporphase-transport process for ZnO 

nanowire growth.

Figure 2. A FE-SEM image of ZnO 

nanowires grown on (a) a Si(111) 

substrate with Au as the catalyst; 

the predominant growth direction 

is 30o

 to the surface; (b) an a-plane 

(110) sapphire substrate with Fe as 

the catalyst; the predominant growth 

direction is at the surface normal. 

(Pictures taken at the BNL/CFN).

2 Theta (deg)

XRD Intensity (arb. units)

(a)

(b)

Science Highlights 2-23
2-24 Chemical Science

Chain Length Dependence of the Conformational Order in Self-Assembled Dialkylammonium Monolayers 

on Mica Studied with Soft X-ray Absorption

G. Hähner1, M. Zwahlen1,2, and W. Caseri2

1

EaStCHEM School of Chemistry, University of St Andrews, UK; 2Department of Materials, ETH-Hönggerberg, 

Switzerland

Self-assembled alkyl chain-based monolayers on mica are important for industrial and technological processes because they can be used to organically 

modify inorganic substrates. The conformational structure and orientational 

order of the films determine how the modified substrate interacts with the environment and also determines the chemical character and stability of its surface. Using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy, 

we have systematically studied the conformational order in ion-exchanged 

dialkylammonium monolayers adsorbed on mica and how that order depends 

on the length of the alkyl chains. We found that the absolute number of gauche 

defects in the films increases with decreasing chain length. 

Organic monolayer coatings can be employed to modify the surface properties 

of inorganic materials. The molecular order and orientation of the films are 

important parameters, since they determine the homogeneity, stability, and 

chemical properties of the modified surface. Films on mica have attracted 

less attention than the more widely studied thiol-gold system, despite their 

importance to industrial and technological processes. For alkane thiols on 

gold, it is known that the number of “gauche” conformations in the film — that 

is, conformational defects — depends on the temperature. But for alkyl chains 

with more than 11 carbon atoms, that number is rather independent of the 

chain length. Results from the thiol-gold system, however, cannot simply be 

transferred to films on mica, since the bonding mechanism and molecular 

arrangements are different. In the case of ion-exchanged films on mica, the 

packing density in the resulting film is determined by the surface cation density 

of the layered silicate surface.

We prepared films of dialkylammonium cations (2Cn) with n=8-18 carbon 

atoms per chain on mica substrates and characterized them with NEXAFS. 

Figure 1 shows spectra recorded at the carbon 1s edge at grazing and normal 

photon incidence (left). On the right hand side, we show the corresponding 

difference spectra between grazing and normal incidence. 

The high anisotropy of the C-H (labeled 3) and C-C related signals (labeled 4) 

indicates a high degree of conformational order of the alkyl chains. 

The observed anisotropy can be converted into an (average) number of 

gauche defects per molecule. Note that each molecule contains two alkyl 

chains. Table 1 summarizes these numbers for the molecular ions investigated.

Interestingly, the absolute number of defects in these films increases with 

decreasing chain length. This is in contrast to the thiol-gold system. Figure 2

illustrates this result schematically. 

Dialkylammonium species films with 12 or more methylene units per chain 

BEAMLINE U1A

Funding

Swiss National Science Foundation; 

Deutsche Forschungsgemeinschaft; U.S. 

Department of Energy 

Publication

G. Hähner, M. Zwahlen, and W. Caseri, 

"Chain Length Dependence of the 

Conformational Order in Self-Assembled 

Dialkylammonium Monolayers on Mica 

Studied with Soft X-ray Absorption," 

Langmuir, 21, 1424-1427 (2005).

For More Information

Georg Hähner, EaStCHEM School of 

Chemistry, University of St Andrews

Email: gh23@st-and.ac.uk

Georg Hähner
show a significantly high degree of molecular orientation. The higher number 

of gauche defects found for shorter chains can be attributed to a decreasing 

van der Waals interaction between neighboring molecules in connection with an 

overall coverage of about 80%. 

The employment of long alkyl chains for well ordered monolayers appears to 

be more important for films on mica prepared by ion-exchange compared to 

alkanethiols on gold. This is due to the lower overall coverage and packing 

density of the films on mica, which leaves more molecules exposed to 

uncovered regions and leads to weaker intermolecular interactions, resulting 

in a strong increase in the number of gauche defects for shorter alkyl chains. 

In order to prepare densely packed and highly ordered monomolecular films on 

mica, quaternary dialkyldimethylammonium ions with 16 or more carbon atoms 

should be employed.

Figure 2. Schematic of the 

average molecular order for 

dialkylammonium ions of different 

chain length adsorbed onto mica.

Figure 1. NEXAFS C 1s spectra of 

dialkyldimethylammonium films with 

various chain lengths adsorbed on 

mica recorded at normal (dashed 

line) and grazing (solid line) photon 

incidence. On the right hand side 

the corresponding difference spectra 

are shown.

Table 1. Number of gauche defects 

per molecule. The numbers in 

brackets denote the error limits.

Photon Energy (eV) Photon Energy (eV)

Electron Yield [a.u]

C-H C-C

2C18 5.4(3.2) 8.3(2.5)

2C16 7.4(2.2) 11.2(1.6)

2C14 13.2(2.8) 15.4(1.4)

2C12 13.2(1.2) 15.4(1.2)

2C8 - 15.4(0.8)

Science Highlights 2-25
2-26 Chemical Science

A Step Closer to Understanding Immobilized Organoand Bio-Molecular Complexes on Solid Surfaces

S.-J. Xiao1, S. Brunner2, and M. Wieland1

1

Laboratory for Surface Science and Technology, Swiss Federal Institute of Technology, Switzerland; 2EMPA 

(Swiss Federal Laboratories for Materials Testing and Research), Materials Science and Technology, Switzerland

Organic reactions on plane metal surfaces are of much interest for applications 

in biosensors, biomaterials, and biochips. However, the details of the reactions 

are not easy to characterize because surface-sensitive technologies cannot 

fully determine molecular structures, and collecting enough grafted materials 

for sufficient bulk analyses is tremendously difficult. In this study, a well-known 

amine-reactive cross-linking reaction for biomolecular conjugation occurs on 

an amine-pendant self-assembled monolayer on gold. The infrared reflection 

absorption spectroscopy (IRRAS) of that reaction and other analogous reactions produces significantly different spectra. With the help of x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure spectroscopy (NEXAFS), we deduced that a so-called side reaction, accompanying 

the main reaction, occurred in this case. Furthermore, a peptide bearing both a 

free amino and a free thiol group was immobilized as two configurations on the 

surface, either one-end or two-end fixed.

Self-assembled monolayers (SAMs) on metal surfaces such as gold, silicon, 

and titanium have been the subject of intense investigations over the past 20 

years. The driving force for these endeavors is the goal of combining microand nano-electronics with biotechnology. Unlike in a bulk reaction, however, 

where the pure product from organic reactions can be separated and definitely 

identified by well-established analysis methods such as nuclear magnetic 

resonance (NMR), elemental analysis, and x-ray single crystal diffraction, the 

molecular structure of a surface product on a plane metal surface can only be 

deduced from surface-sensitive analysis techniques, such as IRRAS, XPS, 

NEXAFS, and time-of-flight secondary ion mass spectroscopy (TOF-SIMS). But 

each of these methods provides partial information only. Therefore, an integrated analysis and logical interpretation of the results from these surface-sensitive techniques is necessary. 

We investigated a well known cross-linking reaction on gold surfaces as a 

method for biomolecular immobilization, i.e. fixing biological molecules onto 

a substrate (Scheme I). The reaction includes three steps: 1) the activation 

of the inert gold surface via the self-assembly an amino-terminated species, 

cystamine, which contains both a disulfide and two end-amines; 2) the subsequent surface reaction of the primary amines with hetero-bifunctional crosslinkers bearing both an amine-reactive species, succinimidyl ester (NHS), and 

a thiol-reactive species, maleimide; and finally 3) the covalent attachment of 

biomolecules onto the surface. 

In step 2, we found that a surface derived from N-succinimidyl-6-maleimidylhexanoate (SMH) presented a specific IRRAS spectrum, where four bands 

were observed in the carbonyl stretching region (1700-1900 cm-1), while only 

one band around 1710 cm-1 was observed for its analogous surfaces (Figure 

1). It is widely believed that the reaction occurs between amine and NHS, 

eliminating NHS as the leaving group and producing a maleimide-terminated 

surface. In this case, due to the asymmetric stretching mode of maleimide, 

Beamline U1A

Funding

Swiss Priority Program on Materials (PPM)

Publication

S.-J. Xiao, S. Brunner, and M. 

Wieland, "Reactions of Surface 

Amines with Heterobifunctional CrossLinkers Bearing Both Succinimidyl 

Ester and Maleimide for Grafting 

Biomolecules," J. Phys. Chem. B, 108, 

16508-16517 (2004).

For More Information

Shou-Jun Xiao, State Key Laboratory of 

Coordination Chemistry, Nanjing University, P.R. China

Email: sjxiao@nju.edu.cn

Authors (from left) Shou-Jun Xiao, 

Samuel Brunner, and Marco Wieland
the infrared spectra should exhibit one strong band around 1710 cm-1. What 

caused the other three bands? We first thought that either a side reaction or 

an orientation of maleimide might account for them. Since NEXAFS studies for 

the orientation of functional groups are well understood by our colleagues, G. 

Hähner and D. Brovelli from the Laboratory of Surface Science and Technology 

at the Swiss Federal Institute of Technology in Switzerland, they collected the 

NEXAFS data at beamline U1A on our behalf. The results (Figure 2) confirmed 

the existence of the double bond (C=C) of maleimide and the random orientation 

of C=C and C=O. This measurement helped us to identify the real culprit, a side 

reaction of amine with maleimide, and thus the resulted terminal NHS groups, 

for the anomalous IRRAS spectrum. Further, we cross-proved our deduction 

with another experiment: the synthesis of the expected surface product, N,N'-bis

(maleimidylhexanoyl)cystamine (BMHC), in which BMHC self-assembles on gold 

surfaces. The IRRAS spectrum of BMHC only presents one strong band around 

1710 cm-1, corresponding to the maleimide-terminated surfaces, but is different 

than the spectrum for the SMH-derived surface that contains NHS. 

Finally, a cell-adhesive peptide bearing both a free amino and a free thiol group 

was grafted to two functionalized surfaces, a singular maleimidyl-pendant 

(BMHC-derived) surface and a two-linker (SMH-derived maleimide and NHS) 

modified surface, respectively. The first reaction produced an amino-terminated 

peptide structure via a thioether linkage; the latter produced a bridging peptide 

structure via both amide and thioether linkages. The above conclusions are 

carefully deduced from IRRAS measurements, and additionally supported by 

XPS, NEXAFS, and TOF-SIMS.

The different configurations of biomolecules on solid surfaces will have a significant impact on the development of applications in biomaterials, biosensors, 

and biochips. The geometry and topology of the attached biomolecules affect 

surface charges, hydrophobic and hydrophilic properties, molecular orientations, 

and native conformations. In turn, these surface properties determine the 

molecules' biological activity and function.

Figure 2. NEXAFS spectra of 

surface 2 in Scheme 1 at the C 1s 

edge recorded for two angles of 

incidence. The overlapping of two 

lines between grazing (20°

) and 

normal (90°

) angles indicates the 

random orientation of maleimidyl 

groups.

Scheme 1. Sketch of the 

subsequent surface reactions. 1) 

cystamine SAMs, 2) a side-reactionresulted two-linker (maleimide and 

NHS)-terminated surface from 

SMH, 3) a one-end fixed peptide, 

and 4) a two-end fixed peptide. The 

linkage atoms S and N (marked a)

are highlighted from amino acids 

Cys and Gly, respectively, but the 

peptide sequence H-Gly-Arg-GlyAsp-Ser-Pro-Cys-OH (GRGDSPC) 

is still kept. SMH is N-succinimidyl6-maleimidylhexanoate.

Figure 1. IRRAS spectra of a series 

of linker-functionalized surfaces, 

where the side-reaction-resulted 

curve 2f (surface 2 in Scheme 1) on 

the top is significantly different from 

its analogs (2a-g, 2h).

Wavenumber (1/cm)

Absorbance

Photon energy (eV)

Intensity (arb. units)

Science Highlights 2-27
2-28 Chemical Science

BEAMLINE X18B

Funding

U.S. Department of Energy, Office of 

Basic Energy Sciences

Publication

W.F. Yan, B. Chen, S.M. Mahurin, V. 

Schwartz, D.R. Mullins, A.R. Lupini, S.J. 

Pennycook, S. Dai, and S.H. Overbury, 

“Preparation and Comparison of Supported Gold Nanocatalysts on Anatase, 

Brookite, Rutile, and P25 Polymorphs 

of TiO2

 for Catalytic Oxidation of CO,” J. 

Phys. Chem. B, 109, 10676-10685 (2005).

For More Information

Sheng Dai, Surface Sciences Divsion, 

Oak Ridge National Laboratory

Email: dais@ornl.gov

Sheng Dai (photo courtesy of ORNL)

Preparation and Comparison of Supported Gold 

Nanocatalysts on Anatase, Brookite, Rutile, and P25 

Polymorphs of TiO2

 for Catalytic Oxidation of CO

W. Yan1, B. Chen1, S.M. Mahurin1, V. Schwartz1, D.R. Mullins1, A.R. Lupini2, S.J. Pennycook2, 

S. Dai1, and S.H. Overbury1

1

Chemical Sciences Division and 2Condensed Matter Physics Division, Oak Ridge National Laboratory

Scientists working at the Oak Ridge National Laboratory have prepared and 

characterized gold nanocatalysts supported on anatase, rutile, and brookite, 

which are polymorphs of titanium dioxide (TiO2). The objective of this investigation was to probe the effect of different catalyst supports on the gold’s catalytic activities. All catalysts in the study were exposed to an identical sequence 

of treatment and measurement. The as-synthesized catalysts exhibited high 

activity rates with concomitant Au reduction upon exposure to the CO-containing reactant stream. The reduction of cationic gold species was verified by 

x-ray absorption near-edge spectroscopy (XANES), suggesting what the dominant contribution of the reduced gold species to the observed catalytic activity 

could be. The deactivation of the catalysts was observed following a treatment 

sequence at temperatures up to 573 K. The brookite-supported gold catalyst 

sustains the highest catalytic activity after all treatments. Both x-ray diffraction 

(XRD) and transmission electron microscope (TEM) results indicate that, following the reaction and pretreatment sequences, the gold particles supported 

by the brookite are smaller than those on the other supports.

In the late 1980s and the early 1990s, Haruta and coworkers (J. Catal. 1989, 

115, 301) discovered that gold particles deposited on titanium dioxide exhibited a surprisingly high catalytic activity for low-temperature CO oxidation. 

This discovery has prompted worldwide research into the applications of gold 

catalysts in a number of industrially important reactions. The unique catalytic 

properties of gold nanoparticles have been correlated to many factors and 

structural parameters. Among them, the type of oxide support used plays a key 

role in controlling the catalytic activities of gold nanoparticles. The titanium-oxide support used originally by Haruta and coworkers consists of a polymorphic 

mixture (P25) of anatase and rutile. To more deeply understand the reaction 

mechanism associated with gold nanoparticles, it is useful to study the support 

effect induced by allotropic forms. Titanium dioxide is a good candidate because it exists in three different allotropic forms: anatase, brookite, and rutile.

The main objective of our study was to prepare and test Au catalysts supported on three polymorphs of TiO2, as well as on P25. EXAFS and XANES were 

employed along with other spectroscopic techniques for probing structural 

properties associated with the above systems. Our results indicated that when 

other experimental factors are kept constant, the catalytic activity is not much 

affected by the variation of the TiO2 phases. However, the stability of the Au 

nanoparticles varies with the specific support structure. We demonstrated that 

the brookite-supported Au catalyst is the most stable catalytic system.

Scanning transmission electron microscopy (STEM) analyses on the most 

active samples show predominantly 0.5 – 2 nm-sized gold particles on the 

TiO2 surface. On rutile and anatase these ultra-small gold nanoparticles are 

susceptible to aggregation under reaction conditions. Both the XRD and STEM 

techniques can be used to follow the size variation of gold nanoparticles. In 
Figure 2. Au XANES spectra of the 

14 wt% Au-rutile sample recorded 

in the as-synthesized state, b) after 

exposing to the reaction mixture 

of 1% CO/air for 50 minutes, c) 

after heating to 473 K in Ar for 30 

minutes, and d) after reducing for 

30 minutes in 4% H2/He. Spectra 

were collected using a fluorescence 

detector.

Figure 1. The HRTEM micrograph 

of Au on brookite gold catalysts 

recorded in (a) the as-synthesized 

state), (b) following mild reduction at 

423K, and (c) following calcination 

at 573 K. Micrographs in (a) and (b) 

are obtained at 2 x 107

 magnification 

and (c) is obtained at 5 x107

magnification.

Photon Energy (eV)

Edge Jump (au)

contrast to the gold catalysts supported on anatase and rutile, the brookite-supported gold catalyst is much more stable. No gold XRD peaks were observed 

even after extended exposure to catalytic reaction conditions, suggesting that 

Au nanoparticles are stable on the brookite support under reaction conditions. 

The Z-contrast microscopy results were obtained on the brookite-supported 

samples at three different stages: 1) as-synthesized, 2) after reduction at 423 K, 

and 3) after calcination at 573 K. The micrographs in each of these stages are 

shown in Figure 1. The Au nanoparticles are visible in the as-synthesized state 

as very small, apparently thin rafts with sizes of 0.5 to 2 nm (Figure 1a). Little 

is changed following a mild treatment at 423 K (Figure 1b). The lattice fringes 

of the needle-like TiO2 crystallite are readily visible in both micrographs. After 

calcination at 573 K, these small rafts were not observed and Au particles were 

few or absent in several micrographs obtained by using the highest magnification. The micrograph in Figure 1c shows a single Au particle that is 2 – 3 nm in 

size and exhibits fringes, suggesting that it is a faceted 3-D particle. At a lower 

magnification, many particles in the range of 1 – 10 nm are visible, and still 

lower magnification reveals many particles in the range of 30 – 70 nm.

XANES was used to extract information about the oxidation state of the Au 

species during the pre-treatment steps used in each of the sequences. Typical 

XANES spectra are shown for the Au-rutile surface in Figure 2. The pre-edge 

of the Au LIII absorption edges exhibits a sharp peak for the as-synthesized 

state, indicating that it is highly oxidized, probably mostly in the Au3+ state. This 

peak is slowly diminished by exposure to the reaction mixture of 1% CO/air at 

room temperature (Figure 2). This result demonstrates that reaction conditions 

at room temperature bring about the partial reduction of the Au, even though 

excess oxygen is present. Heating in Ar causes an additional decrease of the 

peak, indicating that some auto reduction is possible due to heating. Finally, 

reduction at 423 K causes a complete loss of the peak and leaves a spectrum 

that, except for slightly less pronounced oscillations, closely matches that of an 

Au foil. Additional treatments in hydrogen and in oxygen were performed up to 

573 K and subsequent spectra were run in the CO/air mixture. These treatments 

did not further alter the general shape of the spectrum or bring about any growth 

of the peak at the Au edge. Therefore, no re-oxidation occurs as a result of 

these treatments or exposure to reaction conditions.

Science Highlights 2-29
2-30 Chemical Science

BEAMLINE X3A1

Funding

The Danish Research Councils (Dansync)

Publication

R.D. Poulsen, A. Bentien, M. Chevalier, 

and B.B. Iversen, "Synthesis, Physical 

Properties, Multitemperature Crystal Structure, and 20 K Synchrotron 

X-ray Charge Density of a Magnetic 

Metal Organic Framework Structure, 

Mn3

(C8O4H4)3(C5H11ON)2," J. Am. Chem. 

Soc., 127(25), 9156-9166 (2005).

For More Information

Bo Brummerstedt Iversen, Department of 

Chemistry, University of Aarhus, Denmark

Email: bo@chem.au.dk

Physical Properties and 20 K Synchrotron X-ray 

Charge Density of a Magnetic Metal Organic 

Framework Structure, Mn3

(C8O4H4)

3

(C5H11ON)2

R.D. Poulsen, A. Bentien, M. Chevalier, and B.B. Iversen

Department of Chemistry, University of Aarhus, Denmark

Interest in metal organic frameworks (MOFs) has exploded recently due to 

the potential gas-storage applications of these nanoporous materials. Here 

we present an investigation of a new magnetic MOF, Mn3(C8O4H4)3(C5H11ON)2, 

performed using a combination of physical properties measurements and 

x-ray charge density modeling. We found that the structure has an antiferromagnetic ordering at ~4 K. The electron density, determined from 

multipole modelling of 20 K single-crystal synchrotron x-ray diffraction data,

provides a microscopic understanding of the macroscopic magnetic properties. 

Furthermore, it allows for a detailed analysis of the chemical bonding as well 

as the calculation of derived properties, such as the electrostatic potential.

Experimental determination of electron densities (EDs) demands x-ray 

diffraction data of high quality. In order to reduce systematic errors in the data, 

such as extinction and absorption, x-ray diffraction experiments are preferably carried out on very small crystal samples. Extinction and absorption 

effects are also reduced if high-energy radiation is used. Thus, synchrotron 

radiation is highly advantageous in accurate x-ray charge density studies. 

Proper description of thermal motion requires high-resolution data, and this 

necessitates the use of helium cryostats. Very low temperature experiments 

have the added benefit of drastically reducing thermal diffuse scattering 

(TDS) effects. If accurate data have been measured, the ED can be modeled 

using the multipole method. A Bader topological analysis of the ED provides a 

characterisation of the chemical bonding.

The structure of Mn3(C8O4H4)3(C5H11ON)2, 1, consists of 1D chains of 

carboxylate-bridged manganese atoms, which are interconnected by 

the organic benzene-1,4-dicarboxylate linker (C8H4O4, BDC), forming 

rhombic cavities. A multitemperature structural characterization reveals a 

possible phase transition between 100 K and 20 K due to ordering of the 

diethylformamide molecules, (C5H11ON, DEF), bonded directly to the 1D 

chain and located in the rhombic cavities (Figure 1). The synthesis, physical 

property characterisation, and synchrotron x-ray charge density of a similar 1D 

manganese chain metal organic framework structure, Mn2(C8O4H4)2(C3H7ON)2, 

2, have been reported previously1. As for the structure of 1, this framework 

also consists of rhombic cavities spanned by the BDC linker, which

interconnect the 1D manganese chains. However, contrary to 1, the magnetic 

susceptibility and heat-capacity measurements revealed no magnetic ordering 

down to 2 K. 

The topological analysis of the EDs of 1 and 2 reveal that no direct Mn-Mn 

bonds are present. The magnetic ordering in 1 is due to super-exchange via 

oxygen bridges between the Mn atoms within the 1D chain, whereas the lack 

of ordering in 2 is the result of one bridge being an entire carboxylate group 

(Figure 1). The 3D ordering in 1 is due to the alignment of the BDC π-systems 

at low temperature. The analysis of the magnetic susceptibility and heatAuthors (from left) Rasmus D. 

Poulsen, Bo B. Iversen, Anders 

Bentien, and Marie Chevalier
capacity data suggest Mn2+ ions for both 1 and 2. However, the ED analyses 

reveal very different Mn centers in 1 and 2. Orbital populations and a topological 

analysis show that both Mn atoms of 1 are almost neutral with a substantial 

anisotropy of the d-orbitals, whereas the Mn atoms of 2 are spherical, high-spin 

Mn2+ ions. The oxygen ligands have similar atomic properties in 1 and 2, and the 

difference between the Mn charges is due to a reversed polarity of the carbon 

atoms (slightly positive in 1, slightly negative in 2).

It is somewhat surprising that two structurally similar MOFs have quite different 

chemical-bonding and atomic properties. The differences can be directly observed in the electrostatic potentials (Figure 2) calculated from the experimental 

EDs. For 1 the potential is fairly uniform, whereas the potential for 2 shows both 

negative and positive regions. Whether these observations can be correlated 

with the gas-absorption properties is not yet known, but future ED studies of 

similar MOFs will be of considerable interest. 

1R.D. Poulsen, A. Bentien, T. Graber, and B.B. Iversen, Acta Crystallogr. Sect. A,

60, 382-389 (2004).

Figure 2. The electrostatic 

potentials of 1 and 2, calculated 

from the experimental electron 

density and plotted on density 

isosurfaces of 0.01 e/Å3

. The 

potentials are drawn with the same 

color coding, which ranges from -0.3 

e/Å (blue) to 0.3 e/Å (red).

Figure 1. (A) A view of the crystal 

structure along the a-axis. In one 

of the nanopores an electron 

microscope image of a single crystal 

specimen is overlaid. Approximate 

pore dimensions are given in Å. (B) 

The 1D manganese chain of 1. (C) 

The Mn-chain in 2. The Mn-chain 

runs approximately along the a-axis. 

Thermal ellipsoids are drawn at 50% 

level, and in all figures the axes 

directions are shown with arrows.

(A)

(B)

(C)

Science Highlights 2-31
2-32 Chemical Science

Structure Sensitivity in Methanol Oxidation over 

Model Rhenium Oxide Catalysts

A.S.Y. Chan1, W. Chen1, H. Wang1, J.E. Rowe2, and T.E. Madey1

1

Rutgers, The State University of New Jersey; 2University of North Carolina, Chapel Hill

The catalytic oxidation of methanol into products that serve as primary reagents for organic synthesis, such as formaldehyde, is a leading process in 

the chemical industry. Metal oxide catalysts are conventionally used in methanol oxidation, but understanding the active phases in these catalysts is challenging since they usually have a wide range of geometric structures and oxide 

compositions. Using soft x-rays produced at the National Synchrotron Light 

Source, scientists at Rutgers University and the University of North Carolina 

have shown a direct correlation between the presence of rhenium oxides in 

low oxidation states and catalyst deactivation. Disordered oxygen phases are 

revealed to enhance catalytic activity and the formation of these phases is affected by catalyst structure.

How active a catalyst is depends strongly on its morphology and surface structure. Most industrial catalysts contain an active component, typically nanometer-scale particles of transition metals and oxides, which are dispersed on a 

high-area support made of a relatively inert oxide. In these composite materials, catalyst particles of varying sizes expose a number of different structural 

planes, each with its own contribution to the overall catalytic activity. Because 

the complex structures of a real catalyst often hinder the development of 

rational connections to its performance, studies on model catalysts with welldefined structures allow scientists to establish more precise structure−activity 

relationships in catalysis.

We prepared model rhenium (Re) oxide catalysts with different morphologies, 

atomic-scale structures, and oxidation states, since Re oxides are demonstrated to be selective catalysts for methanol oxidation reactions. Using soft 

x-ray photoelectron spectroscopy (SXPS) at NSLS beamline U4A, we characterized the chemical states of Re atoms and cations on the surfaces of the 

model catalysts. The energy range of soft x-rays at beamline U4A matches 

the binding energies of Re states well, which allows us to probe the surface 

region of the model catalysts — where chemical reactions take place — with 

ultrahigh sensitivity and resolution. We also tested the chemical reactivity of 

these model catalysts towards methanol by applying temperature programmed 

reaction spectroscopy.

We chose the atomically rough Re (1231) surface, shown in Figure 1, because it easily converts to different structures when treated with oxygen. When 

covered with oxygen at room temperature, this surface retains its planar form. 

When heated in small quantities of oxygen, however, Re (1231) undergoes 

massive structural rearrangements to build nanosized ‘hill-and-valley’ facets 

that cover the entire surface. These tiny facets have (1121) and (0110) surface 

structures, each of which is much smoother on the atomic scale than the planar (1231) surface. SXPS data show that both planar and faceted Re remain 

covered with an oxygen layer, such that Re atoms at the surface are bonded to 

1-, 2-, and 3-oxygen neighbors. But the planar surface has a broader distribution of these Re−O bonds, indicating more disorder in this oxygen overlayer 

compared to the faceted surface. On both surfaces, a small amount of oxygen 

Beamline U4A

Funding

U.S. Department of Energy, Office of Basic Energy Sciences; U. S. Army Research 

Office

Publication

A.S.Y. Chan, W. Chen, H. Wang, J.E. 

Rowe, and T.E. Madey, “Methanol Reactions over Oxygen-Modified Re Surfaces: 

Influence of Surface Structure and Oxidation,” J. Phys. Chem. B 108, 14643-14651 

(2004).

For More Information

Theodore E. Madey, Department of Physics and Astronomy, Rutgers University

Email: madey@physics.rutgers.edu

Authors (clockwise from top left) Hao 

Wang, Ally Chan, Theodore Madey, 

and Wenhua Chen
also reacts with the metal to form an oxide, ReO.

To increase oxide formation, Re (1231) is exposed to a high overpressure of 

oxygen at an elevated temperature. This produces a thin oxide film on the facets 

composed of Re cations in low oxidation states, mainly ReO and Re2O3 (Figure 

1). So, we can prepare oxygen-covered rhenium surfaces with different planar 

and faceted structures, as well as rhenium oxide films, in order to investigate 

how surface structure and oxide composition affect the activity of methanol oxidation catalysis. 

Methanol reacts on the planar and faceted surfaces to yield the oxidation products, formaldehyde and carbon monoxide, as shown in Figure 2. A competing 

reaction to methanol oxidation is non-selective decomposition of methanol to 

its constituent atoms. Notably, the faceted surface is much less active towards 

methanol conversion, and a portion of methanol leaves the surface unreacted. 

In contrast, the thin oxide film exhibits virtually no activity for methanol reaction.

Our studies indicate that rhenium oxides in low oxidation states are completely 

inert towards methanol, and that surface structure plays a key role in enhancing 

the activity of oxide catalysts towards oxidation reactions. These findings were 

made possible by using soft x-ray photoelectron spectroscopy to characterize 

the catalytically active states on the model catalysts.

Figure 2. Methanol conversion 

activity and product selectivity from 

the model Re oxide catalysts.

Figure 1. (Top) Surface structure 

of atomically rough Re (1231). 

(Bottom) High resolution soft x-ray 

photoelectron spectra (SXPS) of 

the planar and faceted oxygencovered Re surfaces, and of the thin 

Re oxide film, formed by different 

oxygen treatments to the Re (1231) 

surface.

Science Highlights 2-33
2-34 Chemical Science

Activation Energies for Oxygen Reduction on 

Platinum Alloys: Theory and Experiment

A.B. Anderson1, J. Roques1, S. Mukerjee2, V.S. Murthi2, N.M. Markovic3, and V. Stamenkovic3

1

Chemistry Department, Case Western Reserve University; 2Chemistry Department, Northeastern University; 3

Materials Science Division, Lawrence Berkeley National Laboratory, University of California

We present a quantum chemical and experimental analysis of the electrodepotential dependencies of activation energies for the first step in oxygen 

reduction over platinum and platinum-alloy catalysts in both polycrystalline 

and carbon-supported form. Tafel data for several of the catalysts are used to 

predict potential-dependent activation energies for oxygen reduction over the 

0.6-0.9 V range in acid. Comparisons with the theoretical curve show good 

agreement above 0.8 V, suggesting a fairly constant pre-exponential factor. 

Arrhenius determinations of activation energies over the 0.7-0.9 V range for 

strong acid trend with the potential, as predicted by theory. These combined 

results provide strong support that, during the four-electron reduction of O2 

to H2O on fuel-cell platinum cathodes, the first electron-transfer step has the 

highest activation energy.

Determining the compositions and structures of electrocatalyst surfaces and 

the mechanisms and kinetic parameters of reactions occurring on them are 

goals at the frontier of the field of electrochemistry. In this study, we found that 

measured kinetic results for oxygen reduction on unsupported polycrystalline 

platinum and platinum alloy (Pt3M) electrodes and on carbon-supported nanoclusters are quite similar. The similarity is justified theoretically with a simple 

local reaction center model for the first reduction step, which involves just two 

Pt atoms. 

For the unsupported electrodes studied by the Lawrence Berkeley National 

Laboratory (LBL) group, surface compositions were determined using low-energy ion-scattering (LEIS) spectroscopy. The group found that the annealed 

electrodes were covered with a Pt skin. Supported nanoclusters studied by 

the Northeastern University group were characterized using x-ray diffraction (XDS), x-ray absorption near edge fine structure (XANES), and extended 

x-ray absorption fine structure (EXAFS) spectroscopies at beamline X11A. 

That group determined, respectively, nanocatalyst particle sizes, atomic ratio, 

and atom-coordination and nearest-neighbor distances. They found that the 

particles have average sizes of 2.5 nm for Pt/C, 3.6 nm for PtCo/C, and 3.9 

nm for PtFe/C. The XANES and EXAFS results were consistent with Pt3M alloy 

composition and the presence of a Pt skin on their surfaces.

Rotating disc electrodes were used to ensure accurate current density measurements at the chosen electrode potentials, and the temperature dependencies yielded Arrhenius activation energies. For all the unsupported polycrystalline electrodes (Pt, sputtered Pt3Ni and Pt3Co, and annealed Pt3Co), activation 

energies centered on 0.24 eV ± 0.025 eV and did not demonstrate a dependence on potential, the results being the same as earlier studies of supported 

nanoparticles at LBL. In its measurements of supported nanoclusters, the 

Northeastern group was able to reduce the uncertainties in activation energies 

to about 0.02 eV for Pt/C and 0.005 eV for PtCo/C. For PtFe/C the uncertainties were the same as in the LBL measurements. The Northeastern activation 

energies for Pt/C and PtCo/C displayed the same trend as the theoretically Alfred Anderson

BEAMLINE X11A

Funding

U.S. Department of Energy; UTC Fuel 

Cells; Army Research Office

Publication

A.B. Anderson, J. Roques, S. Mukerjee, 

V.S. Murthi, N.M. Markovic, and V. Stamenkovic, “Activation Energy for Oxygen 

Reduction on Platinum Alloys: Theory and 

Experiment,” J. Phys Chem. B, 109, 1198 

(2005).

For More Information

Alfred B. Anderson, Chemistry Department, Case Western Reserve University

Email: aba@po.cwru.edu
predicted electrode potential values, as shown in Figure 1. The theoretical 

values determined using the local reaction center model electron transfer theory 

developed at Case Western Reserve University (Case) are systematically about 

0.1 eV smaller than the Arrhenius values, for unknown reasons. 

We then took the Arrhenius/Tafel expression

log[i(U)] = log(A) – Ea(U)/(2.3026RT)

where i is the kinetic current density, A is the preexponential factor, U is the 

potential, and Ea is the activation energy, and determined the A values by fitting 

one of the experimental Ea values. With the A values, we used the above equation to calculate activation energies, as shown in Figure 2. The trends in Ea vs.

U over the 0.8 V – 0.95 V range are in good agreement with the trend predicted 

at Case. 

The overall agreement between the theoretical predictions and the measured 

current densities suggest that (i) the first electroreduction step, forming 

adsorbed OOH, is the rate-limiting step; and (ii) the active catalyst sites for 

the various catalyst systems are similar, and the presence of alloying atoms 

adjacent to the active site does not dramatically affect the activation energy. 

The ability to calculate qualitative apparent activation energies as functions of 

electrode potential from the Tafel plot data suggests that the surface density of 

active sites may remain fairly constant over the 0.8 to 0.95 V range on each of 

the catalysts.

Figure 1. Experimental activation 

energies at different electrode 

potentials (SHE) for carbonsupported Pt, Pt3

Co, and Pt3Fe in 

1M CF3

SO3H.

Figure 2. Calculated activation 

energies at different electrode 

potentials (SHE) determined from 

Tafel plots data. Open circles are 

for unsupported electrodes at LBL 

and filled circles are for supported 

nanoparticles at Northeastern.

Potential (V)

Activation Energy (eV) Activation Energy (eV)

Potential (V)

Science Highlights 2-35
2-36 Condensed Matter Physics

Robust TaNx Diffusion Barrier for Cu Interconnect 

Technology with Sub-Nanometer Thickness by Metal 

Organic Plasma-Enhanced Atomic Layer Deposition

H. Kim1, C. Detavenier2, O. van der Straten2, S.M. Rossnagel2, A.J. Kellock3, and D.-G. Park4

1

Department of Materials Science and Technology, Pohang University of Science and Technology, South Korea; 

2

IBM T.J. Watson Research Center; 3IBM Almaden Research Center; 4IBM Microelectronics Division

TaNx diffusion barriers with good barrier properties at sub-nanometer thickness 

were deposited by plasma-enhanced atomic layer deposition (PE-ALD) from 

pentakis(dimethylamino)Ta. A hydrogen and/or nitrogen plasma was used as 

the reactant, producing TaNx

 thin films with different nitrogen content. The film 

properties, including the carbon and oxygen impurity content, were affected 

by the nitrogen flow during this process. The film, deposited using the hydrogen-only plasma, forms nanocrystalline grains while an amorphous structure 

was obtained by using the nitrogen plasma. The diffusion-barrier properties of 

deposited TaN films, as for Cu interconnects, have been studied using thermal 

stress tests based upon synchrotron x-ray diffraction. The results indicate that 

the PE-ALD TaN films are good diffusion barriers even at thicknesses as small 

as 0.6 nm. Better diffusion barrier properties were obtained for films with higher nitrogen content. Based on a diffusion kinetics analysis, the nanocrystalline 

microstructure of the films was responsible for the better diffusion barrier properties compared to polycrystalline PE-ALD TaN films deposited from TaCl5.

Among the key materials used for today’s semiconductor processing, thin films 

of inert, refractory materials are expected to be used continuously in Cu interconnect applications, such as diffusion barriers and seed and adhesion layers, 

as well as for potential front-end applications, such as contacts or gate metallization. With the scaling down of these devices, atomic layer deposition (ALD) 

has been spotlighted due to its ability to produce highly conformal films. The 

use of a metal organic (MO) precursor for diffusion-barrier ALD has the benefit 

of producing a chlorine-free diffusion barrier. However, the diffusion-barrier 

properties of MO-based ALD TaN layers for Cu interconnects were not studied 

systematically.

In this study, we have developed a metal organic PE-ALD method for depositing TaN thin films from pentakis(dimethylamino)Ta (PDMAT) using nitrogen and 

hydrogen plasmas as the reactants. A solid PDMAT (powder) source contained 

in a glass tube was used as a metal precursor. Atomic hydrogen and activated 

N2 were generated by a quartz tube connected to the sample chamber via a 

gate valve, and hydrogen and nitrogen gases were supplied via a leak valve. 

For Cu diffusion-barrier measurements, a 200 nm Cu layer (created via physical vapor deposition (PVD)) was deposited on top of the PE-ALD TaN layer, 

without breaking the vacuum, using a UHV (ultra high vacuum) sputtering 

system with a power level of 1 kW (dc). A SiO2 buffer layer placed between the 

poly-Si layer and Si (100) substrate was used on the other samples to electrically isolate the Si(100) substrate during the sheet-resistance analysis.

Copper diffusion-barrier failure was studied using three different in situ techniques, including synchrotron x-ray diffraction (XRD), optical scattering, and 

sheet resistance measurements, conducted simultaneously, while the samples 

were annealed at a temperature ramp rate of 3 °C/s from 100 to 1000 °C in a 

He environment. The analysis was completed at National Synchrotron Light 

Source beamline X20C.

Hyungjun Kim

BEAMLINE X20C

Funding

IBM Research; U.S. Department of Energy

Publication

H. Kim, C. Detavenier, O. van der Straten, 

S.M. Rossnagel, A.J. Kellock, and D.-G. 

Park, “Robust TaNx Diffusion Barrier for 

Cu Interconnect Technology with SubNanometer Thickness by Metal Organic 

Plasma-Enhanced Atomic Layer Deposition,” J. Appl. Phys., 98, 14308 (2005).

For More Information

Hyungjun Kim, Dept. of Materials Science 

and Engineering, Pohang University of 

Science and Technology, Rep. of Korea

Email: hyungjun@postech.ac.kr
Figure 1 shows the synchrotron XRD contour map for MO PE-ALD TaN films of 

three different thicknesses — 3 nm, 0.6 nm, and 0.3 nm — that were all grown 

with hydrogen plasma. For the 3 nm thick film, the Cu 111 peak begins to disappear at about 750 °C, indicating the good diffusion-barrier property of the MO 

PE-ALD TaN film. Even after decreasing the thickness to 0.6 nm, the Cu 111 

peak begins to disappear at temperatures higher than 700 °C. Thus, the thermal 

diffusion-barrier properties of MO PE-ALD TaN films are excellent even at subnanometer thicknesses. Only for film thicknesses smaller than 0.3 nm, where 

the film is only a couple of monolayers thick, does the Cu silicide formation 

occur at a temperature below 500 °C. Even for this ultra-thin film, however, most 

of the Cu layer stays intact, judging from the observation that the Cu 111 peak 

intensity remains high up to 720 °C. Thus, we can conclude that the formation 

of silicide occurs locally (where the TaN film is not formed evenly). The barrierfailure temperatures for MO PE-ALD TaN layers, obtained from Figure 1, are 

represented in Figure 2. The barrier-failure temperatures increase with increasing thickness. For comparison, the previously reported barrier-failure temperatures for PE-ALD TaN films from TaCl5 and a hydrogen and nitrogen mixture 

with stoichiometric composition, which were analyzed using exactly the same 

conditions, are also shown. From the microstructure analysis, done via XRD 

and transmission electron microscopy (TEM), the good diffusion barrier property 

of MO PE-ALD TaN is due to the amorphous microstructure of the film. In this 

sense, PE-ALD films with engineered microstructures and compositions are very 

promising barriers in the near-future integration of Cu interconnect technology.

Figure 1. Synchrotron x-ray 

diffraction analysis as a function of 

annealing temperature for a 200 nm 

PVD Cu/ MO PE-ALD TaN/poly-Si 

test structure with TaN thicknesses 

of (a) 3 nm, (b) 0.6 nm, and (c) 0.3 

nm. The samples were annealed 

at 3 °C/s from 100 to 1000 °C in 

forming gas.

Figure 2. Barrier-failure 

temperatures determined using 

synchrotron x-ray diffraction analysis 

for MO PE-ALD TaN (black squares) 

and chloride PE-ALD Ta (open 

circles). Also shown are the failure 

temperatures of 0.5 nm MO PE-ALD 

TaNx

 deposited at different nitrogen 

plasma conditions (open squares).

Temperature (°C)

2θ (deg)

Thickness (nm)

Failure Temperature (°C)

Science Highlights 2-37
2-38 Condensed Matter Physics

The Structure of Ba@C74

A. Reich1, M. Panthöfer1, H. Modrow2, U. Wedig1, and M. Jansen1

1

Max Planck Institute for Solid State Research, Germany; 2 Institute of Physics of the University of Bonn, Germany

For the first time, the structure of a monometallofullerene has been analyzed using single-crystal synchrotron diffraction on microcrystals of 

Ba@C74⋅Co(OEP)⋅2C6H6 (where Co(OEP) is cobalt(II)-octaethylporphyrin) at 

100 K. This monometallofullerene exhibits a high degree of localization of its 

endohedral metal ion, with just two split positions for barium and two orientations for the C74 cage. The crystal structure consists of complex units (Ba@C

74)[Co(OEP)]2(Ba@C74) arranged in a distorted, primitive hexagonal packing. 

Despite the disorder still present, we have derived a consistent and conclusive 

structure model for the title compound by employing a combination of x-ray 

diffraction, x-ray absorption near-edge structure (XANES) spectroscopy, and 

quantum chemical calculations.

Since the discovery of fullerenes, information about the molecular and electronic structure of this new family of carbon allotropes, which include “endohedral” metallofullerenes (those with metal atoms inside the fullerene cage) and 

fullerene compounds, has been essential for understanding their physical and 

chemical properties. To acquire such information, the availability of precise 

crystal structure data is a crucial prerequisite.

In ongoing research efforts, we have developed a method that allows a highyield synthesis of small and mid-sized endohedral fullerenes consisting of 

divalent metals that follow M@Cm (where m = 60, 70, 72, 74, 76; M = Ca, Sr, 

Ba, Eu). In this method, we inductively heat graphite and the corresponding 

metal inside a radiofrequency field to temperatures of up to 3000 K (Figure 1), 

and then isolate individual species from the raw soot extracts using multi-step 

high-performance liquid chromatography (HPLC).

By employing micro-crystal synchrotron diffraction techniques, computational chemistry, and XANES spectroscopy in a synergetic manner, we were 

able to determine the structure of Ba@C74 as a co-crystallizate with Co-octaethylporphyrin (Co(OEP)) and C6H6 (benzene). The crystal structure of 

Ba@C74⋅Co(OEP)⋅2C6H6 consists of complex units (Ba@C74)[Co(OEP)]2(Ba

@C74) exhibiting a back-to-back orientation of two Co(OEP) molecules, each 

coordinating one Ba@C74 molecule (Figure 2). The overall structure may be 

regarded as a distorted, primitive hexagonal packing of these complex units. 

Yet, the fullerene substructure is disordered, with two orientations for the C74

cage and two positions for the barium atom. Thus, four different barium-to-C74

coordination schemes have to be discussed. Out of those, two are similar to 

those found from the results of the quantum-chemical investigations. Yet, the 

shortest Ba-C distances do not correspond to the central 6:6 bond of a pyracylene unit located at one of the three pockets of the cloverleaf-shaped C74

molecule, but to its vicinity.

As stated above, computational investigations on Ba@C74 show that the local 

minimum structure of Ba@C74 corresponds to a three-fold degenerate arrangement with barium located in one of the three pockets of C74, coordinating to 

the central 6:6 pyracylene bond. Remarkably, the molecular structure of the 

neutral C74 cage in Ba@C74 differs only slightly from the molecular structure 

(Authors left to right) (top) Martin 

Jansen, Andreas Reich, (middle) 

Hartwig Modrow, Martin Panthöfer, 

and (bottom) Ulrich Wedig

BEAMLINE X3A1

Funding

Max Planck Society (Germany)

Publication

A. Reich, M. Panthöfer, H. Modrow, U. 

Wedig, and M. Jansen, “The Structure of 

Ba@C74,” J. Am. Chem. Soc., 126 (44), 

14428-14434 (2004).

For More Information

Martin Jansen, Max Planck Institute for 

Solid State Research, Germany

Email: M.Jansen@fkf.mpg.de
of a C74

2- dianion (both determined using the density-functional theory in localdensity approximation). Those differences are highly localized in the central 6:6 

bond of the pyracylene units.

This discrepancy between the results of the experimental and the computational 

investigations is clearly due to the intermolecular interactions present in the 

co-crystallizate. On one hand, those Co(OEP)-Ba@C74 configurations that result 

in a large contact surface between the two molecules allow attractive π-π and 

dispersion interactions. On the other hand, configurations where the pyracylene 

unit at the pocket of Ba@C74 is pointed towards the Co-atom of the Co(OEP) 

molecule allow stabilization via multipole-multipole interactions. The competition 

between these two different intermolecular interactions triggers the orientational 

disorder of the C74 cage. Furthermore, molecular dynamics simulations reveal a 

nearly flat potential hypersurface around the local minima positions within the 

pocket of the cloverleaf-shaped molecule. This suggests an easy displacement 

of the Ba atom near a minimum that is produced by a direct interaction between 

the Ba2+ cation and the Co(OEP) molecule. Thus, the positional disorder of the 

barium atom is a consequence of the orientational disorder of the C74 cage, 

which is due to the competition of π-π and electrostatic interactions.

Figure 2. A (Ba@C74)[Co

(OEP)]2

(Ba@C74) unit in 

Ba@C74⋅Co(OEP)⋅2C6H6 (for clarity, 

only one fullerene orientation is 

given). 

Figure 1. The radio-frequency 

furnace for endohedral fullerene 

synthesis in action.

Science Highlights 2-39
2-40 Condensed Matter Physics

The Electron-Boson Spectral Function α2F(ω) of 

High-Tc

 Superconductors

S.V. Dordevic1, C.C. Homes1, J.J. Tu1, T. Valla1, M. Strongin1, P.D. Johnson1, G.D. Gu1, and D.N. 

Basov2

1

Department of Physics, Brookhaven National Laboratory; 2Department of Physics, University of California, San 

Diego

We have developed and implemented a new numerical procedure for extracting electron-boson spectral functions from infrared (IR) and angle-resolved 

photoemission spectroscopy (ARPES) data. The new method is based on inverse theory and has numerous advantages over previously employed procedures. Using this new method we have calculated the electron-boson spectral 

functions of high-critical-temperature (high-Tc) cuprates, from both IR and 

ARPES data obtained at the NSLS. The spectral functions have a characteristic shape, dominated by a pronounced peak at low energies and a significant 

contribution at higher energies.

The nature of the collective boson mode responsible for superconductivity in 

the cuprate family of high-critical-temperature (high-Tc

) superconductors is 

currently the center of great controversy in the field. Two opposing views have 

been battling for supremacy. The older scenario, dating back to the early 90s, 

argues for spin-fluctuations as the pairing glue for high-Tc

 superconductivity. More recently, phonons have been put forward as possible mediators for 

superconductivity in the cuprates.

The physical quantity that characterizes coupling between charge carriers and 

collective bosonic modes is a so-called Eliashberg electron-boson spectral 

function α2F(ω). It is one of the most important characteristics of a boson-exchange superconductor. This function can be obtained from tunneling, photoemission (ARPES), or infrared (IR) spectroscopy. However, the process of 

obtaining α2F(ω) is nontrivial because α2F(ω) is convoluted in the experimental 

data. For example, in the IR case the celebrated Allen result relates α2F(ω) to 

the experimentally accessible quasiparticle scattering rate 1/τ(ω) through an 

integral relation:

 

 

We have recently developed a new numerical procedure for extracting α2F(ω) 

based on a mathematical procedure called inverse theory. The method uses a 

so-called singular value decomposition (SVD) of matrices and has numerous 

advantages over previously employed procedures. For example, the inversion 

can be performed not only at T= 0 K but also at higher temperatures, the effect 

of the superconducting energy gap can be taken into account, and the numerical error can be controlled. Using this new procedure we have re-analyzed our 

IR and ARPES data on several families of cuprate data, part of which were 

obtained on NSLS beamlines U10A and U13UB.

Figure 1 displays inversion calculations on IR data at 10 K for underdoped 

YBa2Cu3O6.6 (YBCO) with Tc

= 59 K. The right panels show scattering-rate 

data (green lines) and the left panels present the calculated spectral function 

α2F(ω) (blue lines). The right panels also show the scattering rate 1/τcal(ω) (red 

lines) calculated from the corresponding spectral function on the left. Different panels display inversion results with different levels of smoothing, i.e. 

Sasa Dordevic

∫

∞

0

1 2π

τ(ω) ω = (ω − Ω)α2

F(Ω)dΩ. (Equation 1)

BEAMLINES U10A, U13UB

Funding

U.S. Department of Energy

Publication

S.V. Dordevic et al., “Extracting the Electron-Boson Spectral Function α2

F(ω) from 

Infrared and Photoemission Data using 

Inverse Theory”, Phys. Rev. B, 71, 104529 

(2005).

For More Information

Sasa V. Dordevic, Department of Physics, 

The University of Akron

Email: sasha@physics.uakron.edu
different levels of error. The spectral function has a characteristic shape, with a 

pronounced peak in the far-IR followed by a strong dip and a significant contribution at higher frequencies. The peak is believed to originate from the coupling 

of charge carriers to the so-called (π, π)-resonance observed in neutron-scattering experiments. More recently, phonons have been advocated as an alternative 

explanation.

Similar numerical procedures can also be applied to ARPES. Figure 2 displays 

inversion calculations of ARPES data of optimally doped Bi2Sr2CaCu2O8+δ (BSCCO) with Tc

= 92 K obtained at beamline U13UB. The top panels display data in 

the normal state (above Tc

), whereas the bottom panels display the data in the 

superconducting state. The right panels are measured quasiparticle dispersions 

(red dots) and the left panels are calculated α2F(ω) values. The right panels also 

show calculated spectral functions (green lines).

The importance of this new numerical procedure goes beyond high-Tc

 superconductors, IR, and ARPES. Similar numerical procedures can be applied to 

conventional superconductors, as well as to other experimental methods whose 

data can be described by an integral equation similar to Equation 1.

Figure 2. The spectral function 

α2

F(ω) of optimally doped BSCCO 

with Tc

=92 K, extracted from ARPES 

data. The left panels show α2

F(ω) 

spectra and the right panels show 

the ARPES quasiparticle dispersion 

Ek

 (green circles) and calculated 

dispersion Ek,cal (blue lines).

Figure 1. Spectral function α2F(ω) 

for underdoped YBa2

Cu3O6.6 with 

Tc

= 59 K. The left panels show 

α2

F(ω) and the right panels show 

the experimental 1/τ((ω)) along 

with 1/τcal(ω) calculated from the 

corresponding spectral function 

on the left. The level of smoothing 

is easily controlled by the new 

inversion procedure.

Frequency [cm-1]

α2F(ω)

1/τ[103 cm-1]

k-k1 Frequency [cm-1]

α2F(ω)

Εκ[meV]

Science Highlights 2-41
2-42 Condensed Matter Physics

Microscopic Origin of Polarity in Quasi-Amorphous 

BaTiO3

A.I. Frenkel1, Y. Feldman2, V. Lyahovitskaya2, E. Wachtel2, and I. Lubomirsky2

1

Yeshiva University; 2Weizmann Institute of Science

The recent demonstration of pyroelectricity in quasi-amorphous thin films of 

BaTiO3 introduced a new type of material: non-crystalline polar ionic solids. To 

elucidate the origin of polarity in this system we investigated its local bonding 

environment using the x-ray absorption near-edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) techniques. We found that the 

local bonding unit of TiO6 octahedra is identical in amorphous (as-deposited, 

non-polar), quasi-amorphous (non-crystalline, polar), and crystalline (highly 

polar) BaTiO3. The TiO6 octahedra are distorted due to the off-center displacement of the Ti ion; therefore, these octahedra have a local dipole moment. 

This implies that the macroscopic dipole moment in the quasi-amorphous films 

is the result of the partial alignment (<5%) of the TiO6 octahedra.

A group from the Weizmann Institute of Science, led by Igor Lubomirsky, 

recently synthesized a new type of amorphous ionic solid that is polar but 

lacks long-range order. Radio frequency magnetron-sputtered BaTiO3 thin 

films (100-180 nm) on Si (100) are pulled through a temperature gradient with 

a peak temperature of 600 °C. The resulting non-crystalline but pyroelectric 

and, therefore, polar phase was named “quasi-amorphous,” in contrast to the 

as-deposited amorphous phase that is neither pyroelectric nor piezoelectric 

and, therefore, non-polar. A collaboration between Yeshiva University’s Anatoly 

Frenkel and Lubomirsky’s group investigated the origin of polarity in this new 

type of material. Another objective of their investigation was to find out whether the local dipoles responsible for the polarity of the quasi-amorphous BaTiO3

had already existed in the as-deposited films, or if they were formed during the 

temperature-gradient step.

Ti K-edge XANES and EXAFS were the techniques of choice due to their 

sensitivities to the short-range ordering around Ti atoms. In addition to the asdeposited and quasi-amorphous films, we also studied the partially crystallized 

films prepared by isothermally annealing the as-deposited films. The XANES 

data features the peak A located at 4967 eV, the region corresponding to the 

1s-3d transition, which is dipole-forbidden in the atom by the ΔL = 1 selection 

rule (Figure 1). In order to contribute significantly to XANES data in this range 

of energies, the final state of the photoelectron must have some p-like character in the solid, via a hybridization of the Ti 3d and O 2p orbitals and the concomitant displacement of the Ti atom away from the TiO6 octahedra’s center of 

inversion symmetry. Both the height and position of the pre-edge feature, A, 

are directly related to the degree of p-d mixing and, therefore, to the coordination geometry and oxidation state of Ti. The majority of Ti atoms were found 

to be in an octahedral environment in all samples (Figure 2). This result was 

independently confirmed by the EXAFS data (the first shell signals in all the 

data were identical), which implies that the local environment of the Ti4+ ion did 

not undergo detectable changes during the transformation of the amorphous 

(non-polar) phase into the quasi-amorphous (polar) phase (Figure 3) and that 

it was octahedral in both cases.

As shown by Krayzman et al, the area under the peak A is a measure of the 

displacement (d) of the Ti ion from the center of the TiO6 octahedron: A ~ d2. 

Anatoly Frenkel

BEAMLINE X16C

Funding

U.S. Department of Energy; Israel Science 

Foundation; U.S.-Israel Binational Science 

Foundation

Publication

A.I. Frenkel, et al., "Microscopic Origin 

of Polarity in Quasi-Amorphous BaTiO3

," 

Phys. Rev. B, 71, 024116 (2005).

For More Information

Anatoly I. Frenkel, Physics Department, 

Yeshiva University

Email: Anatoly.Frenkel@yu.edu
The strength of the local dipole moment is proportional to d and can therefore 

be measured in the XANES experiment. We obtained the values of d in all samples and found that they exceeded that of bulk BaTiO3 (0.23 Å), the amorphous 

and quasi-amorphous samples being the most distorted (0.45 Å). 

Preservation of the local bonding unit in amorphous BaTiO3 implies that the 

formation of the macroscopic dipole moment (polarity) in the quasi-amorphous 

material occurs via the partial alignment of the TiO6 octahedra in the temperature gradient. The degree of alignment, estimated from the magnitude of the 

pyroelectric effect, is below 5%, which indicates that even a relatively small 

deviation from the random orientation of local dipoles may lead to macroscopic 

dipole moments, comparable to those observed in pyroelectric crystals. This 

was confirmed experimentally by polarized XANES measurements in quasiamorphous films oriented at different angles with respect to the incident x-ray 

beam. The anisotropy of Ti-atom displacements in the in- and out-of-film plane 

directions was found to be less than 5%. 

The origin of polarity in quasi-amorphous BaTiO3 is caused by 1) the existence 

of large off-center displacements of the Ti atoms within relatively stable TiO6 local bonding units; 2) their weak orientational order, generated by the gradient of 

mechanical strain produced in the temperature gradient; and 3) the electric field 

resulting from the concomitant flexoelectric effect. Therefore, the quasi-amorphous films can be viewed as being analogous to a poorly aligned nematic liquid 

crystal. These results imply that, under similar conditions, it may be possible 

to align and/or manipulate polar local bonding units (for instance, in TiO4, TiO6, 

NbO4, NbO6, or VO6) to create other quasi-amorphous materials, which will 

similarly possess an unusual combination of properties, such as polarity in the 

absence of crystallinity.

Figure 1. XANES spectra of 

as-deposited amorphous, quasiamorphous, and crystalline films. 

The data for bulk BaTiO3

 and 

a sample of EuTiO3

 are given 

for comparison. The feature A

(insert) is affected by the size of Ti 

displacements that range from small 

and dynamic (as in cubic EuTiO3

) to 

large and static (as in BaTiO3

). 

Figure 2. Intensities and positions of 

XANES feature A in four-, five-, and 

six-fold coordinated Ti in different 

reference compounds (hollow 

squares) and in our BaTiO3

 films 

(color symbols).

Figure 3. EXAFS data in r-space of 

the amorphous, quasi-amorphous, 

crystalline, and bulk BaTiO3

samples. 

X-ray energy, eV

r, Å

Normalized abs. coefficient Normalized abs. coefficient

Energy, eV

FT Magnitude, Å-3

Science Highlights 2-43
2-44 Condensed Matter Physics

High Pressure Study of Structural Phase Transitions 

and Superconductivity in La1.48Nd0.4Sr0.12CuO4

M.K. Crawford1, R.L. Harlow1, S. Deemyad2, V. Tissen2, J.S. Schilling2, E.M. McCarron1, S.W. 

Tozer3, D.E. Cox4, N. Ichikawa5, S. Uchida5, and Q. Huang6

1

DuPont Co.; 2Washington University; 3National High Magnetic Field Laboratory; 4Brookhaven National Laboratory; 5

University of Tokyo, Japan; 6National Institute of Standards & Technology Center for Neutron Research

We have determined the crystal structures and superconducting transition 

temperatures of La1.48Nd0.4Sr0.12CuO4 under nearly hydrostatic pressures in 

diamond anvil cells to 5.0 GPa and 19.0 GPa, respectively. Synchrotron x-ray 

powder diffraction measurements were used to establish the material’s pressure-temperature structural phase diagram. Under pressure the superconducting transition temperature (Tc

) increases rapidly from Tc ≈ 3 K to a maximum 

value of 22 K at 5 GPa, a pressure slightly greater than required to stabilize 

the undistorted I4/mmm structure in the superconducting state.

Superconductivity is among the most remarkable physical phenomena discovered during the 20th century. Although the famous Bardeen-Cooper-Schrieffer 

theory of superconductivity can explain most experimental observations for 

conventional superconductors, the high-temperature superconducting cuprates 

have yet to be completely understood in a similar way.

Perhaps the simplest superconducting cuprates are based upon the parent 

compound lanthanum cuprate (La2CuO4), whose structure is shown in Figure 1. 

This material, when doped with increasing amounts of alkaline-earth ions such 

as Sr2+ (i.e. La2-xSrx

CuO4), transforms from a Mott insulator to a metal, and then 

superconducts with a critical temperature (Tc

) as high as 38 K when x = 0.15. 

Lanthanum cuprates for which some of the La3+ is replaced with both Sr2+ and

Nd3+ (i.e. La2-x-yNdy

SrxCuO4) exhibit structural phase transitions involving tilts of 

the CuO6 octahedra (Figure 1) that strongly suppress Tc

. The suppression of 

Tc

 is most pronounced when the Sr2+ doping, x, is 1/8. These structural phase 

transitions are sensitive to external parameters such as pressure and temperature, and thus it is interesting to observe the effect of applied pressure at various temperatures upon the structure (and superconductivity) of these materials. 

Here we describe a set of x-ray powder diffraction experiments conducted for 

that purpose at beamline X7A.

The x-ray powder sample of composition La1.48Nd0.4Sr0.12CuO4 was immersed in a 

4:1 ethanol:methanol mixture within a Merrill-Bassett diamond anvil cell that was 

then mounted in a displex closed-cycle refrigerator. A position-sensitive detector was used to detect the scattered x-rays of wavelength near 0.7 Å (energy of 

about 17 keV). Pressures were measured using laser-excited fluorescence from 

small ruby chips placed inside the diamond anvil cells, as well as by measurements of the lattice parameters of small quantities of NaCl or CaF2 also included 

in the cells.

In Figure 2 we show two typical x-ray diffraction patterns, obtained at pressures of 2.2 and 4.2 GPa, for a sample of composition La1.48Nd0.4Sr0.12CuO4. In 

Figure 3 we show the structural phase diagram for this material (based upon 

the x-ray data), compared with the superconducting transition temperature, as a 

function of pressure. At ambient pressure this material has a low superconducting Tc ≈ 3 K associated with the low-temperature tetragonal (LTT) structure and 

the special Sr2+ concentration of x = 1/8. Under pressure the LTT phase is first 

Authors (from left) Richard Harlow 

and Michael Crawford

BEAMLINE X7A

Funding

National Science Foundation; U.S. Department of Energy Division of Materials Sciences & Division of Chemical Sciences

Publication

M.K. Crawford, R.L. Harlow, S. Deemyad, 

V. Tissen, J.S. Schilling, E.M. McCarron, 

S.W. Tozer, D.E. Cox, N. Ichikawa, S. 

Uchida, and Q. Huang, "High-Pressure 

Study of Structural Phase Transitions and 

Superconductivity in La1.48Nd0.4Sr0.12CuO4

," 

Phys. Rev. B, 71, 104513 (2005).

For More Information

Michael K. Crawford, Central Research 

and Development, DuPont Company

Email: michael.k.crawford@usa.dupont.com
replaced by the low-temperature orthorhombic LTO2 phase, then at pressures 

above 4.0 GPa the high-temperature tetragonal (HTT) structure remains stable to 

T = 10 K. The superconducting transition temperature increases dramatically under pressure and reaches a maximum value of Tc

 = 22 K near 5.0 GPa, coincident 

with the appearance of the undistorted HTT phase.

The results we describe here have implications for the presence of charge ordering in cuprates. The LTT structure of La1.48Nd0.4Sr0.12CuO4 was the first cuprate 

shown to exhibit static one-dimensional charge and spin stripes (in experiments 

performed at the High Flux Beam Reactor at Brookhaven National Laboratory 

by Tranquada, Axe, and coworkers). This observation provided an explanation 

for the previously known suppression of superconductivity in this material at 1/8 

doping: commensurate one-dimensional static charge and spin stripes compete 

with superconductivity. Pressure is a convenient way to change the structure at 

constant chemical composition, and it is clear from our results that superconductivity is strongly enhanced by suppressing the structural phase transitions in 

La1.48Nd0.4Sr0.12CuO4. This observation suggests that the static charge and spin 

order is also eliminated by pressure. However, recent scanning tunneling microscope studies of other tetragonal cuprates in which the copper-oxygen planes are 

flat, as they are in the HTT structure of La1.48Nd0.4Sr0.12CuO4, have shown the presence of two-dimensional charge order. One way to reconcile these observations 

is to assume that the charge and spin order are one-dimensional in the LTT and 

LTO2 structures, but become two-dimensional in the HTT and LTO1 structures, 

with the latter situation more favorable toward superconductivity. This scenario 

would be consistent with the accumulating evidence for both one-dimensional and 

two-dimensional charge and spin order in the cuprates. Our results explicitly illustrate the impact of subtle changes of crystal structure upon superconductivity, and 

by implication upon charge and spin order, in these fascinating materials.

Figure 3. (Top) Pressure-temperature 

phase diagram for La1.48Nd0.4Sr0.12CuO4

determined by high-pressure xray powder diffraction. (Bottom) 

Superconducting transition temperature 

(Tc

) versus pressure (P) for 

La1.48Nd0.4Sr0.12CuO4

. In both frames the 

LTT phase region is shown in red, the 

LTO2 region in green, the LTO1 region 

in dark blue, and the HTT region in light 

blue.

Figure 1. (Top) The crystal structure 

of La2

CuO4, showing the twodimensional layers of corner-sharing 

CuO6

 octahedra (blue), the oxygen 

atoms (light red), and the La atoms 

(dark red). (Bottom) A schematic 

view of a single CuO6

 octahedron 

illustrating the relative orientations 

of the (110) and (1-10) axes of 

the HTT structure, for which Q1



= Q2 = 0. The LTO1 structure is 

obtained by a single rotation of 

magnitude Q1

 or Q2 about either 

of these axes (yielding one of the 

two orthorhombic twin structures). 

The LTO2 structure is obtained by 

rotations of magnitude Q1

 and Q2

about both axes (where Q1

 ≠ Q2). 

The LTT structure has rotations of 

equal magnitude about both axes, 

Q1

 = Q2 ≠ 0.

Figure 2. The x-ray powder diffraction patterns 

and results of General Structure Analysis 

Structure refinements for La1.48Nd0.4Sr0.12CuO4

at pressures of 4.2 GPa (top frame) or 2.2 GPa 

(bottom frame), at a temperature of 10 K. In the 

upper trace for each frame the crosses are the 

data, and the solid line is the calculated pattern; 

the lowest trace is the residual. The vertical tick 

marks are located at the positions of (top) NaCl 

included in the diamond anvil cell as an internal 

manometer, (middle) Fe due to the diamond anvil 

cell gasket, and (bottom) La1.48Nd0.4Sr0.12CuO4

.

400

300

100

 0

200

400

300

100

 0

200

 10 15 20 25 30

T(K)

P(GPa)

Tc(K)

500

400

200

 100

300

 25

 20

 15

 10

 5

 0

 0 5 10 15 20

P = 4.2 GPa

HTT

P = 2.2 GPa

LTO2

Science Highlights 2-45
2-46 Geology and Environmental Science 

BEAMLINE X19A

Funding

New Jersey Department of Environmental 

Protection 

Publication

C. Jing, S. Liu, M. Patel, and X. Meng, 

"Arsenic Leachability in Water Treatment 

Adsorbents," Environ. Sci. and Tech., 39, 

5481-5487 (2005).

For More Information

Chuanyong Jing, Center for Environmental 

Systems, Stevens Institute of Technology

Email: cjing@stevens.edu

Authors (from top) Chuanyong Jing 

and Suqin Liu

Arsenic Leachability in Water-Treatment Adsorbents

C. Jing1, S. Liu1, M. Patel1,2, and X. Meng1

1

Center for Environmental Systems, Stevens Institute of Technology; 2New Jersey Department of Environmental 

Protection

At NSLS beamline X19A, we used extended x-ray absorption fine structure 

(EXAFS) spectroscopy and leaching tests to investigate arsenic (As) leachability in spent water-treatment adsorbents. The EXAFS results indicate that 

arsenic forms inner-sphere bidentate binuclear surface complexes on the 

adsorbents, which include granular ferric hydroxide, granular ferric oxide, 

titanium dioxide, activated alumina, and modified activated alumina. This study 

improved the understanding of arsenic bonding structures on adsorptive media 

surfaces and As leaching behavior for different adsorbents.

The U.S. Environmental Protection Agency (EPA) has adopted an arsenic 

maximum contaminant level (MCL) of 10 μg/L, which will be enforceable as of 

January 23, 2006. This more stringent arsenic drinking water standard requires the installation of new water-treatment systems and the upgrading of 

existing ones. Filtering arsenic in water using adsorbents is especially suitable 

for small community systems and individual homes because the filters do not 

require much effort to operate. Recently, more effective adsorbent media have 

been developed and used for arsenic removal. As a result of the enhanced 

removal efficiency, large amounts of spent media with elevated arsenic content 

will be generated. Accurately determining the leachability of arsenic in this 

waste is crucial for both economic concerns and the evaluation of environmental impacts.

In this study, EXAFS spectroscopy at NSLS beamline X19A was employed 

to determine the arsenic local coordination environment of spent adsorbent 

media. Spent adsorbents were collected from five pilot-scale filters that were 

tested for their ability to remove arsenic from groundwater in New Jersey. The 

spent media included granular ferric hydroxide (GFH), granular ferric oxide 

(GFO), titanium dioxide (TiO2), activated alumina (AA), and modified activated 

alumina (MAA).

The As leachability, determined with the Toxicity Characteristic Leaching 

Procedure (TCLP), was below 180 μg/L for all spent media. The leachate As 

concentration in the California Waste Extraction Test (WET) was more than 

10 times higher than that in the TCLP, and reached as high as 6650 μg/L in 

the spent GFH sample. The EXAFS analysis shows that the first and strongest peak in the Fourier transform (FT) curve was contributed by four oxygen atoms at an average As-O distance of 1.69 Å for all five media samples 

(Figure 1). The constant As-O interatomic distance was independent of the 

media to which the As(V) was adsorbed. The second shell atom (distance) 

was Fe (3.32 Å), Fe (3.28 Å), Ti (3.27 Å), Al (3.14 Å), and Al (3.13 Å) for GFO, 

GFH, TiO2, AA, and MAA, respectively. The EXAFS results show that arsenic 

formed bidentate binuclear inner-sphere complexes on the surfaces of these 

five spent adsorbents. This stable structure can be used to explain the high 

affinity of arsenic for the adsorbent surfaces. The difference in the leachate As 

concentrations determined with WET and TCLP could be attributed to different acids used in the leaching solutions. An aggressive chelating agent, such 

as the citric acid used in the WET process, could form soluble complexes with 
Science Highlights 2-47

Figure 1. The observed (dotted line) 

and model calculated (solid line) As 

K-edge FT EXAFS spectra resulting 

in a radial distance structure for the 

spent media. The peak positions are 

uncorrected for phase shift. Arsenic 

formed binuclear bidentate surface 

complexes on the media surface.

R (Å)

FT Magnitude

the adsorbent and release the arsenic. This is especially important for the GFH, 

which failed in the WET. A moderate organic acid, such as the acetic acid used 

in the TCLP, could only extract arsenic at a low concentration, less than 180 μg 

L-1. However, this kind of organic acid is a relatively stable degradation product 

of organic matter and is widely available in landfill leachate. Thus, the co-disposal of arsenic containing wastes with municipal solid waste (MSW) may have 

a potential risk of arsenic re-contamination.

The correlation of the percentage of As leached with the percentage of the 

adsorbent dissolved for the media is shown in Figure 2. The amount of As released was positively related to the amount of adsorbent dissolved in the leachate, which suggests that adsorbent dissolution may be the main mechanism of 

enhanced As release in the WET.

Figure 2. Correlation of percentage 

As leached and adsorbent 

dissolution in GFH (♦, ◊), GFO (●, 

○), AA (■, □), and MAA (▲, ∆) for 

the WET (close) and TCLP (open), 

respectively. The solid line is the 

regression and the dashed lines are 

99% confidence limits.

Adsorbent dissolved, %

As leached, %
2-48 Geology and Environmental Science 

BEAMLINES X23A2, X26A

Funding

U.S. Department of Energy

Publication

M.C. Duff, D.B. Hunter, D. T. Hobbs, S.D, 

Fink, Z. Dai, and J.P. Bradley, "Mechanisms of Strontium and Uranium Removal 

from High-Level Radioactive Waste Simulant Solutions by the Sorbent Monosodium 

Titanate," Environ. Sci. Technol., 38, 

5201-5207 (2004).

For More Information

Martine C. Duff, Savannah River National 

Laboratory

Email: Martine.Duff@srs.gov

Mechanisms of Strontium and Uranium Removal from 

Radioactive Waste Simulant Solutions by the Sorbent 

Monosodium Titanate

M.C. Duff1, D.B. Hunter1, D.T. Hobbs1, S.D. Fink1, Z. Dai2, and J.P. Bradley2

1

Savannah River National Laboratory; 2Lawrence Livermore National Laboratory

High-Level Radioactive Waste (HLW) is the priority problem for the U.S. 

Department of Energy’s Environmental Management Program. Current HLW 

treatment processes at the Savannah River Site (Aiken, SC) include the use of 

monosodium titanate (MST, similar to NaTi2O5

.

xH2O) to concentrate radioactive 

strontium (Sr) and actinides. Mechanistic information about radionuclide uptake will provide us with insight into the reliability of MST treatments. We characterized the morphology of MST and the chemistry of sorbed Sr2+ and uranium [U(VI)] on MST with x-ray based spectroscopic and electron microscopic 

techniques. Sorbed Sr2+ exhibited specific adsorption as partially-hydrated 

species, whereas sorbed U exhibited site-specific adsorption as monomeric 

and dimeric U(VI)-carbonate complexes. These differences in site specificity 

and mechanism may account for the difficulties associated with predicting MST 

loading and removal kinetics.

High-Level Waste (HLW) is the radioactive waste associated with the dissolution of spent nuclear fuel rods for the recovery of weapons-grade material. At 

the Savannah River Site (SRS) nearly 130 million liters of HLW await disposal. 

This waste is highly alkaline and rich in Na+, NO3

-

, and NO2

-

. Waste treatment 

involves concentrating the radionuclides (which consists of mainly 90Sr and the 

actinides, such as uranium, plutonium, and neptunium) from the waste, and 

then vitrifying the waste concentrate. Titanate solids, such as monosodium titanate (MST), are chemically stable in high pH solutions, making MST an ideal 

candidate material for waste treatment. 

Our x-ray diffraction studies with MST indicate it is highly amorphous, and 

scanning electron microscopy reveals that it contains spherical (snowball-like) 

particles with a typical size range of 5 to 12 μm. Our high-resolution transmission electron microscopy analyses indicate that MST has two prominent morphological populations of titanate material, the first being a very fine fibrous 

nanocrystalline surficial material, and the second being an amorphous glasslike material (data not shown).

We conducted synchrotron-based x-ray absorption fine structure (XAFS) 

analyses with Sr- and U-loaded MST that was made by exposing a MST suspension to dissolved Sr and U(VI) (individually) in a HLW simulant solution. 

Our findings indicate that the sorbed Sr2+ and UO2

2+ (the uranyl ion) exhibit 

inner sphere (specific adsorption) sorption behavior with the MST, as opposed 

to other mechanistic behaviors, such as precipitation, outer sphere adsorption, 

or structural incorporation with the amorphous MST material (see generalized 

mechanisms delineated in Figure 1A-D). 

Our chi XAFS data for the Sr- and U-loaded MST are shown in Figures 2A 

and 2B. The XAFS analyses indicate that the local environment of Sr2+ on 

the MST is partially hydrated (for example, see the spectral comparison with 

dissolved SrCl2(s) in Figure 2A). However, the XAFS data for the outer shells 

of the added Sr2+ indicate that titanium (Ti) atoms are present at two radial disAuthors (from top) Douglas B. Hunter 

and Martine C. Duff
Science Highlights 2-49

tances. We conclude that the Sr2+ is sorbed as a partially hydrated species that 

is specifically adsorbed on the MST surface — indicating that specific adsorption 

is the likely Sr uptake mechanism (as described in Figure 1C).

Model fits of the U XAFS data indicate that the sorbed U(VI) has an outer shell 

environment that is consistent with specifically adsorbed U(VI) carbonato species. The data also indicate that at low U(VI) surface loadings, there is specific 

adsorption of monomeric U(VI) carbonato species at the MST surface (as shown 

in Figure 3A). At high U(VI) surface loadings, however, there is dimerization of 

sorbed U(VI) carbonato species at the MST surface (as shown in Figure 3B). 

These studies that characterized the uptake of U and Sr on MST show that there 

is a strong interaction between MST and the target solution species. This study 

improves our understanding of this highly amorphous MST material.

Figure 1. Mechanisms by which 

metals can interact with a solids 

shown relative to the type of 

information that can be obtained 

with XAFS (such as local structural 

atom identification, radial distances, 

and coordination number). (A) 

Structural incorporation with MST, 

where the addition of the metal 

to the MST-containing solution 

facilitates precipitation and uptake 

of metals. In this example, the 

structural environment appears 

much like the bulk material 

that is crystallizing. (B) Outer 

sphere sorption, where the local 

environment of the sorbed species 

resembles that of a truly hydrated 

metal species. (C) Inner sphere 

sorption of the added metal by MST, 

where a large amount of Ti would 

be visible in the XAFS data. This is 

in contrast to outer sphere sorption, 

where no Ti would exist in the outer 

shell of the Sr or U XAFS data. 

(D) Precipitation/polymerization of 

added metal at or away from the 

MST surface, where little Ti (from 

the MST) is observed relative to the 

outer shell metals that was present 

in the XAFS data.

Figure 2. Chi data for (A) Sr (K edge) 

in the Sr-loaded MST samples and 

(B) for U (L3

 edge) in the U(VI)-loaded 

MST samples.

Figure 3. Atom scale pictorial representations of sorbed U(VI) 

carbonato species on MST at (A) low and (B) high U loadings.

Structural Incorporation

Outer Sphere Sorption/

Ion Exchange/

Electrostatic Sorption

Inner Sphere Sorption/Specific

Absorption/Chemisorption

Surface Precipitation/Polymerization

Blue circles denote 

coordination shells. 

Surface shown not 

representative of MST.

Legend

(A)

(B)

(C)

(D)

(B)

(A)

κ(Å-1)

κ (Å-1)

χ(κ)*κ3 χ(κ)*κ3

(A)

(B)

At low U loadings, inner sphere 

sorption with bidentate, monomeric 

U(VI)-hydroxo and carbonato species

--on two types of distorted TiO6

octahedra

At higher loadings, dimerization of U occurs 

inner sphere sorption as U(VI)-hydroxo and 

U(VI)-carbonato species distorted TiO6

octahedra
2-50 Geology and Environmental Science 

BEAMLINE X11A

Funding

Swiss Federal Institute of Technology 

Research Grant

Publication

A. Voegelin and R. Kretzschmar, "Formation and Dissolution of Single and Mixed 

Zn and Ni Precipitates in Soil: Evidence 

from Column Experiments and Extended 

X-ray Absorption Fine Structure Spectroscopy," Environ. Sci. and Tech., 39, 

5311-5318 (2005).

For More Information

Andreas Voegelin, Soil Chemistry Group, 

Department of Environmental Sciences, 

Swiss Federal Insitute of Technology 

(ETH) Zurich, Switzerland

Email: voegelin@env.ethz.ch

Ruben Kretzschmar, Professor of Soil 

Chemistry, Department of Environmental 

Sciences, Swiss Federal Insitute of Technology (ETH) Zurich, Switzerland

Email: kretzschmar@env.ethz.ch

Immobilization Processes in Soils Contaminated with 

Several Heavy Metals

A. Voegelin and R. Kretzschmar

Department of Environmental Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland

Contaminated soils are often polluted with a mixture of heavy metals. Little is 

currently known about the effects of these cocktails on the immobilizing role 

of heavy-metal precipitates in contaminated soils. For the case of Zn-Ni, we 

found that more Zn than Ni was retained in a soil leached with heavy-metal 

containing solutions and that the amounts did not vary whether the metals 

were present alone or together. Synchrotron spectroscopy showed that Zn and 

Ni formed individual precipitates when present alone and a single mixed precipitate when present together. This mixed precipitate dissolves much faster 

than the pure Ni precipitate, indicating a mobilizing effect of Zn on Ni in the 

case of a combined contamination. Our results demonstrate that the interactions of different metals need to be considered when assessing the relevance 

of heavy-metal precipitation reactions in contaminated soils.

Contamination of soils with heavy metals can cause a reduction in crop yield 

or a contamination of underlying groundwater. The formation of heavy-metal 

bearing minerals in soils may attenuate those adverse effects and has been 

therefore extensively studied in recent years. However, soils are often contaminated by several heavy metals and little is still known about the effects 

to be expected in such cases. We therefore systematically investigated the 

formation and dissolution of nickel (Ni) and zinc (Zn) precipitates in soil in the 

presence of only one or both of these metals. Heavy-metal precipitates in soils 

are weakly crystalline and occur at low concentrations. Synchrotron-based xray absorption spectroscopy is a unique method for obtaining direct molecularscale information on the binding of metals in those systems. Taking advantage 

of these possibilities, we employed a combined approach of controlled laboratory column studies and extended x-ray absorption fine structure (EXAFS) 

spectroscopy to investigate the interaction of Ni with Zn in a natural soil.

A neutral soil was packed into a chromatographic column and leached over a 

long period of time with solutions containing low concentrations of Zn and/or 

Ni that are realistic for actual environmental systems. We found that about 

twice as much Zn than Ni was retained in the soil when reacted with either Zn 

or Ni. Interestingly, the same amounts of Zn and Ni were retained in the soil 

when present together in solution. While this finding might suggest that Zn and 

Ni acted independently, a different picture was obtained from EXAFS spectroscopy.

Figure 1 shows (A) EXAFS spectra of the reacted soil samples, (B) their Fourier transforms, and (C) the structure of a layered double hydroxide (LDH) type 

phase (see also caption). Following a fingerprinting approach, i.e. comparing 

the experimental spectra (A) to those of known reference minerals, we concluded that Ni and Zn were incorporated into LDH-type minerals in all studied 

cases. Considering the mixed-metal experiment, the question to be answered 

by EXAFS spectroscopy was whether Zn and Ni would precipitate into a mixed 

ZnNi-LDH or form individual precipitates as in the single-metal experiments. 

We therefore analyzed the Fourier transforms of the EXAFS spectra (see 

panel B), in which peaks at an increasing distance from the central atom of 

Authors (from left) Ruben 

Kretzschmar and Andreas Voegelin
Science Highlights 2-51

interest (Ni or Zn) correspond to different shells of neighboring atoms. While the 

first peak results from the six oxygens of the hydroxyl groups surrounding Zn 

or Ni in the octahedra, the second peak results from the next nearest Zn or Ni 

neighbors in the octahedral sheet (see panel C). For the experiments with either 

Zn or Ni, we find that the distance between neighboring Zn atoms is significantly 

larger than between neighboring Ni atoms, due to the larger ionic radius of Zn2+

than Ni2+. In the mixed-metal experiment, we would find the same distance if 

the metals had precipitated into individual phases. However, the analysis of the 

Fourier transforms of the mixed-metal sample clearly shows that the distances 

for Zn and Ni converge. Zn and Ni therefore seem to have precipitated into a 

single mixed ZnNi-LDH.

Formation of such a mixed NiZn-LDH has a significant impact on the immobilization of Ni or Zn in soil. Leaching the metal-enriched soils with acidified water at 

pH 3.0, we found that the Zn-LDH dissolved much more rapidly (within minutes) 

than the Ni-LDH (within days). The mixed NiZn-LDH in the mixed-metal system 

dissolved almost as fast as the pure Zn-LDH, and considerably faster than the 

pure Ni-LDH. Thus, the presence of Ni only had a minimal immobilizing effect on 

Zn, while the presence of Zn in turn led to the incorporation of Ni in a substantially less acid-resistant phase.

Our results show that heavy metals present in mixtures may behave significantly 

different than if present alone. Further research on this issue is warranted to 

improve our understanding of heavy metals in contaminated environmental 

systems. While sorption and extraction studies provide macroscopic information 

on the interactions of different types of heavy metals in soils, synchrotron-based 

spectroscopy is required to obtain complementary molecular-scale information 

on the effective reaction mechanisms.

Figure 1. (A) EXAFS spectra of a) 

Ni in soil reacted with Ni, b) Zn in 

soil reacted with Zn, c) Ni and d) 

Zn in soil reacted with Ni and Zn. 

(B) Fourier transforms of EXAFS 

spectra shown in the left panel, 

indicating the position of different 

atomic shells around the central 

atom. (C) Structure of layered 

double hydroxide (LDH), which is 

composed of divalent (Zn or Ni) and 

trivalent (Al) cations (double) that 

are coordinated by six OH groups 

(hydroxide), forming octahedral 

sheets in a layered arrangement.

(A)

(B)

(C)

 k [Å-1]

EXAFS Signal [χκ3

] Fourier Transform

Distance from Central Atom [Å]

Ni or Zn atom surrounded by 6 OH groups

Al atom surrounded by 6 OH groups

Interlayer Anions
2-52 Geology and Environmental Science 

NaMgF3 Perovskite Under Pressure: Octahedral Tilting Evolution and Phase Transition

H. Liu1, J. Chen2, J. Hu1, C.D. Martin2, D.J. Weidner2, D. Häusermann1, H.-k. Mao1

1

High Pressure Collaborative Access Team, Carnegie Institution of Washington, Advanced Photon Source, 

Argonne National Laboratory; 2

Mineral Physics Institute, Stony Brook University

A high-pressure test of an analog for a common deep-Earth mineral may allow 

researchers to estimate the physical properties of materials in the planet's 

lower mantle. We induced pressures greater than 16 gigapascals (GPa), more 

than 160,000 times the normal atmospheric pressure on the Earth's surface, 

on a perovskite material with a similar makeup as the ubiquitous deep-mantle 

perovskite MgSiO3 and analyzed the change in its physical makeup under the 

stress. We observed slight changes to its chemical bonds beginning at 6 GPa 

and a compression that destroyed the perovskite crystal structure at pressures 

approaching 20 GPa. 

Geophysical interest in the perovskite family of materials dates from the 

1960s when geologist A.E. Ringwood proposed that the Earth’s lower mantle 

is dominated by iron-bearing MgSiO3 perovskite. A fundamental understanding 

of the behavior of selected representatives of the perovskite family of structures to high-pressure/high-temperature conditions is valuable for establishing 

possible behaviors of this family in general. We have chosen to study NaMgF3

perovskite (neighborite) as it has gained significant attention as an analogue 

material of MgSiO3 perovskite since O'Keeffe et al pointed out their structural similarity in 1970s. Neighborite is isoelectronic with MgSiO3, and they 

are isostructural, possessing the same type of distortion from the ideal cubic 

perovskite structure to crystallize in space group Pbnm.

We used a diamond anvil cell high-pressure device and synchrotron x-ray 

micro-diffraction to in situ study the crystalline change of the sample under 

high-pressure conditions. A series of experiments were carried out using various pressure-transmitting media, the focusing beam size and grain size of the 

sample (at NSLS beamline X17C and the High Pressure Collaborative Access 

Team facility at the Advanced Photon Source) to optimize the quality of our diffraction data. The structural evolution of NaMgF3 under high pressure, therefore, could be analyzed from the Rietveld refinement of the high-quality x-ray 

diffraction patterns. The atomic positions could be obtained under high pressure; for example, Figure 1 demonstrates the crystalline structure of neighborite under 10.1 GPa when helium was used as the pressure medium.

The centrosymmetrically distorted orthorhombic perovskite with space group 

Pbnm is distorted by two independent octahedral tilting angles θ and φ, where 

θ is an anti-phase tilt and φ is an in-phase tilt. It can also be conceived as the 

tilting Φ about the threefold <111>pc axes of the regular octahedra (see Figure 

2 insert). The octahedral tilting of the NaMgF3 perovskite could be quantitatively derived from the cell parameters (macro-approach) as well as from the 

positional parameters of atoms (micro-approach), as shown in Figure 2. The 

overall trends of the octahedral tilting angles, i.e. increasing with increasing 

pressure, are similar for both the macro and micro approaches. The volumetric 

compression was dominated by the shortening of the octahedral Mg-F bond at 

the beginning of compression below 6 GPa. In the 6-12 GPa pressure range, 

the contribution from the octahedral tilting matches that of the bond length 

BEAMLINE X17C

Funding

National Science Foundation; U.S. 

Department of Energy; U.S. Department 

of Defense 

Publication

H.-Z. Liu, J. Chen, J. Hu, C.D. Martin, 

D.J. Weidner, D. Häusermann, and H.-K. 

Mao, "Octahedral Tilting Evolution and 

Phase Transition in Orthorhombic 

NaMgF3

 Perovskite Under Pressure," 

Geophys. Res. Lett., 32, L04304 

(2005).

For More Information

Dr. Haozhe Liu, HPCAT, Advanced Photon 

Source, Argonne National Laboratory

Email: hliu@hpcat.aps.anl.gov

Authors (from top) Jingzhu Hu, 

Haozhe Liu, and Jiuhua Chen
Science Highlights 2-53

Figure 2. Pressure evolution of the 

octahedral tilting angles of NaMgF3

perovskite as derived from lattice 

parameters (macro-approach), and 

atomic positions (micro-approach) 

plotted as solid and open symbols, 

respectively. Insertion shows the 

octahedral tilting angles referred to 

an ideal cubic Pmm perovskite.

Figure 1. The crystalline structure 

of NaMgF3

 under pressure of 

10.1GPa, was featured on the cover 

of Geophysical Research Letters.

Pressure (GPa)

Octahedral tilting angles (degrees)

Neighborite under pressure

Helium medium

Solid symbol: Macro-approach

Open symbol: Micro-approach

compression. This is followed by an increasing contribution from the octahedral 

tilting above 12 GPa.

The octahedral tilting, increasing with pressure, finally destroys the perovskite 

structure. An experiment was carried out using silicone oil as the pressure medium, which could generate more shear stress to accelerate the phase transition. 

We observed a phase transition at about 19.4 GPa, and the patterns above this 

pressure can no longer be indexed by the Pbnm perovskite structure, but can 

be indexed with the layering-type post-perovskite structural model with space 

group Cmcm. This distinct material created under these extremely high-pressure 

conditions should be further studied to establish its properties. Such research 

could help scientists better understand the mechanisms of perovskite, including 

the temperatures and pressures required for it to stabilize near the Earth's core.
2-54 Geology and Environmental Science 

Methylmercury Binding Sites in Humic Substances: 

An X-ray Absorption Study

S.-j. Yoon1, L.M. Diener1, P.R. Bloom2, E.A. Nater2, and W.F. Bleam1

1

Department of Soil Science, University of Wisconsin; 2Department of Soil, Water, and Climate, University of 

Minnesota

Methylmercury, a highly toxic and bioaccumulative form of mercury, is known 

to have a strong affinity for binding to organic matter in soil, sedimentary, and 

aquatic environments. The objective of our study was to determine the dominant ligands that bind to the methylmercury cation (CH3Hg+) in humic acids 

(complex organic compound mixtures) by evaluating several CH3Hg+-ligand 

complexation models. Mercury LIII-edge extended x-ray absorption fine structure (EXAFS) results show that CH3Hg+ preferentially binds to thiol ligands 

(-SH), also known as sulfhydryl. After saturating reactive thiol ligands, the 

remaining CH3Hg+ binds to carboxyl ligands rather than to amine or reducedsulfur ligands other than thiol.

In organisms, such as fish, the dominant form of accumulated mercury is the 

organometallic methylmercury cation CH3Hg+, rather than the inorganic cation 

Hg2+. Scientists have reported that the biotic and abiotic methylation of inorganic mercury is affected by natural organic matter. Humic substances, for 

example, either stimulate mercury methylation, acting as methyl donors for 

Hg2+, or suppress it by forming complexes with Hg2+. Examining the nature of 

organic and inorganic mercury complexes with natural organic matter is important for understanding the biogeochemical cycle of mercury as well as the fate 

of mercury in the environment.

Both Hg2+ and CH3Hg+ have strong affinities for organic matter in terrestrial 

and aquatic environments, with CH3Hg+ having a lower affinity than Hg2+. The 

principle of hard and soft acids and bases (the HSAB principle) predicts the 

strong affinity of reduced-sulfur ligands for Hg2+ and CH3Hg+. Previous mercury 

LIII-edge extended x-ray absorption fine structure (EXAFS) studies show that 

humic sulfur ligands bind both Hg2+ and CH3Hg+. Scientists, however, have reported that only a small fraction of reduced sulfur in humic substances binds to 

CH3Hg+, with oxygen or nitrogen binding to the remaining CH3Hg+. They speculated that CH3Hg+-binding sulfur ligands were, most likely, thiol and possibly 

sulfide, disulfide, and hydrogen disulfide groups. In this study, we determined 

the major CH3Hg+-binding humic ligands using mercury LIII-edge EXAFS. Our 

spectra were obtained at NSLS beamlines X11A and X10C.

We examined several CH3Hg+-ligand models as potential CH3Hg+-binding 

structures in humic acids: thiol (-SH), sulfide (-S-), disulfide (-SS-), hydrogen 

polysulfide (-SSH or -SSSH), carboxyl (-COOH), and amine (-NH2). We examined carboxyl and amine ligands, although they are hard Lewis ligands, because CH3Hg+-amine complexes exhibit relatively high complexation constants, 

and carboxyl is the most abundant ligand in humic acids.

We equilibrated two different humic-acid solutions (soil and aquatic) at 

CH3Hg+-to-reduced-sulfur ratios ranging from 0.3 to 1.5, quantifying the reduced-sulfur (e.g., thiol, sulfide, and hydrogen polysulfide) content using sulfur 

K-edge x-ray absorption near edge structure (XANES) spectroscopy at beamline X19A.

BEAMLINES X10C, X11A, X19A

Funding

U.S. Department of Agriculture; U.S. 

Department of Energy 

Publication

S. Yoon, L.M. Diener, P.R. Bloom, E.D. 

Nater, and W.F. Bleam, "X-ray Absorption 

Studies of CH3

Hg+-Binding Sites in Humic 

Substances," Geochim. et Cosmochim. 

Acta, 69, 1111-1121 (2005).

For More Information

Soh-joung Yoon, Department of Crop 

and Soil Sciences, Pennsylvania State 

University

Email: syoon@psu.edu

Authors (from top) Soh-joung Yoon, 

Paul Bloom, and William Bleam
Science Highlights 2-55

Figure 2. Experimental (solid 

lines) and least-squares fitted 

(dotted lines) Hg LIII-edge EXAFS 

of CH3

Hg+-humic carboxyl complex 

(soil humic acid; CH3

Hg+ to reduced 

sulfur ratio, 1.3, pH 4): (a) radial 

structure function and (b) EXAFS 

scattering curves (full scattering 

curve and Fourier-filtered scattering 

curves of peak A2

 and scattering 

region B2

).

Figure 1. Experimental (solid 

lines) and least-squares fitted 

(dotted lines) Hg LIII-edge EXAFS 

of CH3

Hg+-humic thiol complex 

(aquatic humic acid; CH3

Hg+ to 

reduced sulfur ratio, 0.3, pH 5): 

(a) radial structure function and 

(b) EXAFS scattering curves (full 

scattering curve and Fourier-filtered 

scattering curves of peak A1

 and 

peak B1

). 

Intensity

R + Φ (Å)

R + Φ (Å)

Intensity

Our results show that thiol is the dominant CH3Hg+ complexing ligand among 

the reduced sulfur ligands (Figure 1). We did not observe EXAFS evidence of 

CH3Hg+ complexation to sulfide, disulfide, or hydrogen disulfide ligands in any 

of our samples. CH3Hg+ complexation by carboxyl ligands (Figure 2) becomes 

significant after CH3Hg+ saturates the available thiol ligands. Carboxyl ligands, 

rather than amine, eclipse thiol ligands as the CH3Hg+-to-reduced-sulfur ratio 

approaches and then exceeds 1. We also found evidence for proximately coordinated heavy atoms in a sample where the CH3Hg+-to-reduced-sulfur ratio slightly 

exceeded 1. The heavy-atom backscattering behavior agrees the best with that 

of mercury or, possibly, other atoms with similar atomic numbers.
2-56 Life Science 

Disulfide Trapped Structure of a Repair Enzyme Interrogating Undamaged DNA Sheds Light on Damaged 

DNA Recognition

A. Banerjee1, W. Yang1, M. Karplus1,3, and G.L. Verdine1,2

1

Departments of Chemistry and Chemical Biology and 2Molecular and Cellular Biology, Harvard University; 3

L’Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université Louis Pasteur, France

The integrity of the genome is constantly threatened in living cells by spontaneous alterations in the chemical structure of DNA that are caused by endogenous and exogenous agents. DNA repair pathways counteract these modifications and restore DNA to its undamaged state. Enzymes known as DNA glycosylases initiate the process, called base excision repair (BER), by locating a 

damaged nucleobase in the genome and then excising it from double-stranded 

(duplex) DNA. But how DNA glycosylases discriminate between very few damage sites amongst a huge amount of normal DNA is not well understood. We 

have used an efficient trapping strategy to capture a human repair protein, 

called 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA for damage. By combining the structures of the protein-DNA 

complexes with free-energy calculations, we have gained novel insights into 

the mechanism by which hOGG1 is able to discriminate between normal and 

damaged DNA, and is able to prevent aberrant cleavage of normal DNA.

In humans, the DNA glycosylase hOGG1 is responsible for recognizing and removing 8-oxoguanine (oxoG), which is an oxidized form of the DNA base guanine 

(G) (Figure 1c). In general, DNA glycosylases bind at the site of the damaged 

base (lesion base), bend the duplex DNA considerably, and flip the lesion out in 

an active site pocket so that excision may occur (Figure 2, left). To understand 

how hOGG1 discriminates between the substrate oxoG and its normal counterpart G, which differ by only two atoms, it is imperative to obtain a three-dimensional structure of hOGG1 bound to undamaged DNA and compare it with existing 

oxoG-bound structures. The challenge lies in obtaining a homogeneous complex 

of hOGG1 with undamaged DNA in solution in the absence of a damaged base in 

the DNA to fix the “binding register.” This problem was solved using the “disulfide 

crosslinking” technique (Figure 3a) that we have developed, which stabilizes protein-DNA complexes that would otherwise be transient. We use existing structural 

and/or biochemical data to decipher sites in which the protein and the DNA are in 

close proximity. The residue on the protein is then mutated to the amino acid cysteine and a disulfide-bearing tether is introduced on the DNA.

In the case of hOGG1, we reasoned that if the normal base G is extruded from 

the DNA helix — even transiently — we should be able to implant a disulfide bond 

between a tether emanating from G’s partner base, cytosine (also called estranged 

C), and Asn149 (the amino acid asparagine, which is mutated to cysteine). Asn149 

is one of the residues involved in recognizing the estranged C when the duplex 

DNA is invaded by hOGG1 in the complex with oxoG-containing DNA (Figure 

3b,c).

The structure of the crosslinked complex of hOGG1 with undamaged DNA containing a G (G-complex) (Figure 2, right) resembled the structure of hOGG1 with 

oxoG-containing DNA (oxoG-complex) (Figure 2, left) that was solved earlier in 

our lab. However, the G residue, in spite of being extruded from duplex DNA, is 

rejected from entering the active site and lies at an alternative extrahelical site 

(exo-site). This explains how hOGG1 is able to scan long lengths of DNA without 

BEAMLINE X4A

Funding

National Institutes of Health

Publication

A. Banerjee, W. Yang, M. Karplus, and 

G.L. Verdine, “Structure of a Repair 

Enzyme Interrogating Undamaged DNA 

Elucidates Recognition of Damaged DNA,” 

Nature, 434, 612-618 (2005).

For More Information

Gregory L. Verdine, Department of Chemistry, Harvard University

Email: verdine@chemistry.harvard.edu

Authors (from left) Martin Karplus, Wei 

Yang, Anirban Banerjee, and Gregory 

L. Verdine
Science Highlights 2-57

accidentally excising normal bases. A superposition of the DNA molecules in the two 

structures reveals that large rotations about three backbone bonds in the DNA are 

enough to shift the G from the exo-site into the active site, leading us to propose 

that the G-complex is probably analogous to a late-stage intermediate in the baseextrusion pathway of oxoG. Contacts between the phosphate backbone of the DNA 

and the protein are almost identical on the 3’ side of the oxoG/G. On the 5’ side, 

however, the sole DNA contact (mediated by histidine, His270) is dislodged in the Gcomplex, leading to an over-twisted and considerably different conformation of the 

DNA on that side (Figure 1a).

Free-energy calculations using the G-complex and the oxoG-complex of hOGG1 

help reveal how hOGG1 discriminates between oxoG and G. Computational work indicates that Lys249 (lysine), which participates in the excision reaction, forms a salt 

bridge with a conserved cysteine residue at the active site. Further analysis shows, 

quite unexpectedly, that the favorable electrostatic interaction of the salt-bridge dipole with oxoG and the unfavorable interaction with G (Figure 1b) is a major factor 

contributing to hOGG1’s discrimination between G and oxoG. Although G is denied 

entry into the active site, computational data suggested that analogs of G (with a 

C-H replacing a nitrogen atom, N7) should be stabilized in the active site. We solved 

the structures of hOGG1 crosslinked to DNA containing analogs of guanine (Figure 

1c). Indeed, the analogs were inserted into the active site at exactly the same place 

as oxoG.

Figure 1. (a) Superposition of the 

oxoG-complex with the G-complex 

in the region around the protein/

DNA interface. The overlay uses 

the protein backbone only (gray) 

for superposition, with the DNA 

backbone of the oxoG-complex 

in green and the G-complex in 

gold. Spheres are Ca2+ ions. The 

residues that interact with DNA 

through the backbone amid nitrogen 

atoms are denoted in magenta, 

and those that interact through 

side-chains are shown in black. 

Dotted lines are hydrogen bonds. 

(b) The electrostatic potential 

difference (from computational data) 

between oxoG and G. Regions 

of positive charge are in blue 

and negative regions are in red. 

Dipoles are in cyan, with Mülliken 

charges indicated. (c) A structural 

representation of the expected 

interactions between the main-chain 

carbonyl Gly42 and nucleobases 

examined in this study. Whereas 

oxoG is known to hydrogenbond with Gly42, the lone pair of 

electrons on G produces a repulsive 

interaction with the lone pairs on 

Gly42. 7-deazaG and 7-deaza-8-

aza-G are analogs of G.

Figure 2. A comparison of the 

overall structures of the trapped 

complexes obtained with oxoGcontaining (top) or G-containing 

(bottom) DNA. Both protein 

and DNA are represented as 

backbone ribbon traces, with the 

protein in cyan and the DNA in 

gold. The estranged C (magenta) 

and oxoG or G (red) are rendered 

in ball-and-stick representations. 

Note that oxoG is bound in the 

lesion-recognition pocket, while 

the G is bound at the alternative 

extrahelical site.

Figure 3. An overview of the strategy for obtaining 

a complex with G-containing DNA. (a) Based on the 

structure of the recognition complex, crosslinking sites 

are chosen first. The crosslinking strategy is validated 

by inspecting the structure of the crosslinked complex 

with oxoG-containing DNA and ensuring the absence 

of crosslinking-induced structural perturbations. 

Finally, oxoG in the DNA is replaced by G to obtain 

a crosslinked complex. (b) Details of the crosslinking 

strategy used in this case. The Asn149 contact with the 

estranged C was replaced with a disulfide crosslink by 

introducing a Cys149 point mutation and synthetically 

modifying DNA by introducing a tether with a disulfide 

linkage on the exocyclic amine. Note that introducing 

the tether does not perturb the Watson-Crick edge of 

the C as evident from existing structural information 

on similarly tethered DNA duplex. (c) The sequence 

of the DNA duplex. The crosslinking site is on the 

complementary strand of the oxoG/G-containing strand.

(A)

(B)

(C)

C C G

oxoG-complex G-complex

oxoG

Figure 2

C G

-complex G-complex

oxoG
2-58 Life Science 

Structural and Biochemical Studies Identify SABP2 as 

a Methylsalicylate Esterase and Further Implicate it in 

Plant Innate Immunity

F. Forouhar 1, Y. Yang 2, D. Kumar 3, Y. Chen 1, E. Fridman 2, S.W. Park 3, Y. Chiang 4, T.B. Acton 4, 

G.T. Montelione 4, E. Pichersky 2, D.F. Klessig 3, and L. Tong 1

1

Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University; 2Department of Molecular, Cellular, and Developmental Biology, University of Michigan; 3

Boyce Thompson Institute 

for Plant Research; 4

Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and 

Biochemistry, Northeast Structural Genomics Consortium, Rutgers University, and Department of Biochemistry, 

Robert Wood Johnson Medical School 

Salicylic acid (SA) is a critical signaling compound for the activation of plant 

defense responses against pathogen infections. SA binding protein 2 (SABP2) 

displays a high binding affinity for SA and plays a crucial role in the activation of systemic acquired resistance (SAR) — the triggering of defenses in 

uninfected parts of the plant — to pathogens. As a project of the Northeast 

Structural Genomics Consortium, we have determined the crystal structures 

of SABP2, alone and in complex with SA. SA is bound in the active site and 

is completely shielded from the solvent. Our biochemical studies reveal, for 

the first time, that SABP2 has strong esterase activity with methylsalicylate 

(MeSA) as the substrate, and that SA is a potent product-inhibitor of this catalysis. Our results suggest that SABP2 may be required to convert MeSA to 

SA as part of the signal transduction pathways that activate SAR.

Salicylic acid (SA) is a critical signaling compound for the activation of plant 

defense responses both at the site of infection and, systemically, in distal tissues such as leaves. For example, plants that are SA deficient fail to develop 

systemic acquired resistance (SAR) (the activation of defenses in uninfected 

parts of the plant), do not express pathogenesis-related (PR) genes in the 

uninoculated leaves, and display an enhanced susceptibility to pathogens. We 

recently identified and characterized a high-affinity SA-binding protein (SABP), 

termed SABP2, from tobacco. Silencing SABP2 expression via RNA interference suppresses the plant’s local resistance to Tobacco Mosaic Virus and SAinduced PR-1 gene expression, and blocks the development of SAR.

To understand the biochemical and biological functions of SABP2, we have 

determined its structure in the absence and presence of SA at up to 2.1 Å 

resolution. The active site of SABP2 is located at the interface between the 

“core” and the “cap” domains of the enzyme, with the “catalytic triad” of amino 

acids — Ser81, His238, and Asp210 (Figure 1A). SA is bound in the active 

site, where it is completely shielded from the solvent and shows intimate polar 

and van der Waals contacts with the enzyme (Figure 1B). This provides a molecular explanation for the high affinity of SABP2 for SA.

We next demonstrated that SABP2 has esterase activity with methylsalicylate (MeSA), a methyl ester of SA, as the substrate (Figure 2A) and that SA 

is a potent product-inhibitor of this activity (Figure 2B). While SABP2 displays esterase activity with MeSA and the methylated derivatives of two plant 

hormones — methyl jasmonate (MeJA) and methyl indole acetic acid (MeIAA) 

— when they are present at high concentrations, it is highly specific for MeSA 

(among the substrates tested) at more physiologically relevant concentrations 

(Figure 2A).

To understand how SABP2 can catalyze the hydrolysis of MeSA, we modeled 

BEAMLINE X4A

Funding

National Institutes of Health; National Science Foundation

Publication

F. Forouhar, Y. Yang, D. Kumar, Y. Chen, 

E. Fridman, S.W. Park, Y. Chiang, T.B. 

Acton, G.T. Montelione, E. Pichersky, 

D.F. Klessig, and L. Tong, "Structural and 

Biochemical Studies Identify Tobacco 

SABP2 as a Methylsalicylate Esterase 

and Implicate it in Plant Innate Immunity," 

Proc. Natl. Acad. Sci. USA, 102, 1773-

1778 (2005).

For More Information

Liang Tong, Department of Biological 

Sciences, Northeast Structural Genomics 

Consortium, Columbia University

Email: tong@como.bio.columbia.edu

Authors (from top left) Yang Chen, 

and Farhad Forouhar; Dhirendra 

Kumar and Daniel Klessig; Yue Yang 

and Eyad Fridman
Science Highlights 2-59

this substrate into the SABP2 active site based on the structure of the complex 

obtained with SA (Figure 1C), which is the product of the reaction. By assuming 

a different torsion angle, the side chain of Ser81 can become hydrogen-bonded 

to the side chain of His238, completing the catalytic triad (Figure 1C). In addition, the side-chain hydroxyl is placed directly over the carboxyl carbon of 

MeSA, in a perfect position for initiating the nucleophilic attack. The model also 

shows that the active site is only large enough to accommodate the phenyl ring 

of MeSA, therefore explaining the poor activity of SABP2 with the MeIAA and 

MeJA substrates (Figure 2A). 

These results, together with the genetic and physiological experiments previously reported for SABP2, suggest that MeSA may have an important role in SAR 

that is distinct from the role of SA. Since MeSA is more hydrophobic than SA and 

can thereby cross membranes more readily, it is possible that both short- and 

long-distance transmission of SA synthesized at the site of infection requires 

converting it first to MeSA. Our studies suggest that the role of SABP2 in plant 

host defense may be the hydrolysis of biologically inactive MeSA into active SA 

in the target cells. The potent inhibition of SABP2 by the product of the reaction, 

SA, may further help fine-tune intracellular SA levels. The presence of homologous proteins with MeSA esterase activity in other plant species suggests that 

MeSA may be a component of the plant innate immune response in general.

Figure 2. Comparisons of methyl esterase activities and binding affinities of SABP2. (A). 

Relative methyl esterase activity of SABP2 with MeSA, MeIAA, and MeJA substrates at 

three different concentrations (10 μM, 100 μM, and 1 mM). The activity with MeSA at each 

of the substrate concentrations was set at 100%. (B). SABP2 binds MeSA but not MeJA. 

MeSA (blue) competes with [3

H]SA for binding to SABP2 with the same potency as SA 

(green), whereas MeJA (red) does not compete for binding. 

Figure 1. Structure of SABP2 in 

complex with SA. (A) Stereoview 

of the SABP2 monomer in complex 

with SA. SA (in green for carbon 

atoms) is located in the active 

site. (B) Active site of SABP2 in 

complex with SA, showing that 

the SA molecule (in green for 

carbon atoms) is shielded from 

the solvent in the active site. (C) 

Model of the binding mode of the 

MeSA substrate (green) to SABP2. 

The side chain of the catalytic 

Ser81 residue assumes a different 

conformation for catalysis (cyan and 

gold in complex with SA and MeSA, 

respectively). The hydrogen bonds 

are indicated in dashed lines in red, 

and the distance between Ser81 

and the MeSA carboxylate carbon is 

indicated in black.

(A)

(B)

(C)

(A)Relative Esterase Activity

Substrate

10 μM 100 μM 1 mM (B)% [3H] SA binding (dpm)

0μM 0.01μM 0.1μM 1μM 10μM 100μM
2-60 Life Science 

Evolution of Xylem Lignification and Hydrogel Transport Regulation

C.K. Boyce1, M.A. Zwieniecki2, G.D. Cody3, C. Jacobsen4, S. Wirick4, A.H. Knoll5, and 

N.M. Holbrook5

1

Department of Geophysical Sciences, University of Chicago; 2Arnold Arboretum of Harvard University; 3

Geophysical Laboratory, Carnegie Institution of Washington; 4Department of Physics, Stony Brook University; 5

Department of Organismic & Evolutionary Biology, Harvard University

We have mapped the micron-scale distribution of cell-wall compounds in 

water-conducting cells with x-ray microscopy and shown that it varies across 

vascular plants. We have also shown that the extent to which water-transport 

properties can be modified by changes in the ionic content of transported 

water correlates with wall chemistry, which is consistent with the proposed 

wall-chemistry-based mechanism for this hydraulic response. Thus, the distribution of two key cell-wall compounds — hydrophilic polysaccharides and 

hydrophobic lignin — can likely affect the hydraulic and mechanical properties 

of cell walls. The evolutionary diversification of vascular cell types may reflect 

biochemical innovations evolved to fulfill opposing transport and structural 

support functions. 

All land plants have primary cell walls that are largely made of polysaccharides, such as cellulose and pectin. The water-conducting cells of vascular 

plants also have complexly sculpted secondary wall thickenings that reinforce 

the primary walls and are impregnated with the polyphenolic polymer lignin. 

These vascular cells, comprising the xylem tissue, are typically responsible 

both for water transport and structural support in the plant — wood is an example.

Vascular cells are dead at maturity and can only physiologically interact with 

the rest of the organism through their cell walls. The distribution of hydrophilic 

polysaccharides and hydrophobic lignin within individual cell-wall layers may 

greatly influence the cells’ structural and transport properties. For example, 

lignin would be optimally placed in the primary wall and middle lamella layer 

between adjacent cells in order to maximize the cell adhesion necessary for 

structural support, but such placement may interfere with aspects of hydraulic 

function as discussed below. Despite the functional importance of cell walls, 

details of their composition are difficult to observe due to the submicron scale 

of cell-wall layering. X-ray microscopy at the NSLS has allowed us to document the detailed distribution of wall polymers and demonstrate that sites of 

lignin deposition within cell walls vary substantially across vascular plants 

(Figure 1).

It was previously discovered that the resistance properties of xylem can be 

reversibly modified by altering the ionic concentration of the water being transported. The mechanism proposed for this was that the pectin in the middle 

lamella layer acts as a hydrogel and reversibly contracts and expands due to 

the binding and release of ions from solution, thereby altering the size of the 

pores through which water travels from one xylem cell to the next. We hypothesized that the lignification of the middle lamella, which provides structural 

support, would disrupt this capacity to modify the xylem’s transport-resistance 

properties. We then demonstrated that, in fact, patterns of lignin deposition 

and resistance properties are strongly correlated (Figures 1 and 2).

BEAMLINE X1A

Funding

NASA Astrobiology Institute; National 

Science Foundation; Andrew W. Mellon 

Foundation; U.S. Department of Agriculture; U.S. Department of Energy

Publication

C.K. Boyce, M.A. Zwieniecki, G.D. Cody, 

C. Jacobsen, S. Wirick, A.H. Knoll, and 

N.M. Holbrook, "Evolution of Xylem 

Lignification and Hydrogel Transport 

Regulation," Proc. Natl. Acad. Sci. USA, 

101,17555-17558 (2004).

For More Information

Kevin Boyce, Department of Geophysical 

Sciences, University of Chicago

Email: ckboyce@uchicago.edu

Authors (from left) Kevin Boyce, Missy 

Holbrook, Maciej Zwieniecki, and 

George Cody
Science Highlights 2-61

Figure 2. Percent increase of 

stem hydraulic conductance (mean 

± standard deviation) measured 

with 20 mMol KCl solution over 

conductance determined with 

deionized water. Numbers in 

parentheses reflect the number 

of different species used in the 

analysis.

Figure 1. X-ray microscopy images 

of xylem cells, with darker shades 

indicating greater x-ray absorbance 

and lignin abundance. Images were 

taken at 285.2-286 eV absorption 

peak for aromatic carbon, which 

is most prevalent in lignin. All of 

the images depict cross-sections 

of xylem cells: water conducting 

tracheids and vessels, or nonconducting fibers specialized for 

support. Selaginella and Psilotum 

are basal vascular plants with a 

fern-grade organization. Maple is 

a flowering plant. Primary walls (1) 

and secondary walls (2) are labeled 

in each image. Nearly black or 

white areas found in cell lumens are 

epoxy or holes in the section. Scale 

bars are 6 microns.

This work suggests that a number of important evolutionary trends in vascular 

cells that have been traditionally framed in terms of changes in cell shape and 

wall anatomy must also be considered in terms of the evolution of wall chemistry, including the diversification of vascular cell types. For example, the primitive 

condition in vascular plants is to have a single cell type (tracheids) responsible 

for both support and transport, but flowering plants have evolved morphologically distinct cell types specialized either for transport (vessels) or for support 

(fibers). This appears also to involve a divergence in patterns of lignin deposition. Vessels have a lignification pattern that might compromise structural support, but fibers that maintain an alternative lignification pattern are available to 

provide that support (Figure 1). It is likely that a number of such shifts in wall 

biochemistry may be documented through further studies of living and fossil 

plants.
2-62 Life Science 

BEAMLINE X12B

Funding

National Institutes of Health; Doris Duke 

Charitable Foundation

Publication

Z. Zavala-Ruiz, I. Strug, I., B.D. Walker, 

P.J. Norris, and L.J. Stern, "A Hairpin Turn 

in a Class II MHC-Bound Peptide Orients 

Residues Outside the Binding Groove for 

T Cell Recognition," Proc. Natl. Acad. Sci. 

USA, 101(36),13279-84 (2004).

For More Information

Lawrence J. Stern, Ph.D., Department of 

Pathology, University of Massachusetts 

Medical School

Email: Lawrence.Stern@umassmed.edu

Authors (from left) Zarixia Zavala-Ruiz 

and Lawrence J. Stern

A Hairpin Turn in a HIV-Gag–Derived Peptide Bound 

to HLA-DR1 Orients Peptide Residues Outside the 

Binding Groove for T Cell Recognition

Z. Zavala-Ruiz1, I. Strug2, B.D. Walter3, P.J. Norris3,4, and L.J. Stern2

1

Department of Chemistry, Massachusetts Institute of Technology; 2Department of Pathology, University of 

Massachusetts Medical School; 3

Partners AIDS Research Center and Infectious Disease Unit, Massachusetts 

General Hospital and Harvard Medical School; 4

Blood Systems Research Institute

T-cell receptors (TCRs) recognize peptide antigens bound to class II Major Histocompatibility Complex (MHC) proteins — molecules that transport and present the antigens to the T-cells, thus activating the immune system response. 

The receptors contact the antigen residues within or immediately flanking the 

seven-to-nine-residue sequence accommodated by the MHC-peptide binding 

groove. We identified a HIV-Gag-specific T-cell clone that requires an unusually long peptide for activation. The crystal structure of the HIV-gag peptide 

bound to an MHC protein known as HLA-DR1 shows that the peptide binds in 

an unexpected conformation, with its C-terminal region making a hairpin turn 

that bends back over the groove. The residues at the C-terminus are critical 

for T-cell recognition, and disrupting the hairpin cancels the immune response. 

The results suggest a new mode of MHC-peptide-TCR interaction.

Major Histocompatibility Complex (MHC) proteins are heterodimeric cell surface proteins that present antigens to T-cells, triggering the cell-mediated immune system. Peptides isolated from class II MHCs found in antigen-presenting cells are usually 15-20 residues long. Approximately one-third of the total 

peptide surface (the central region of the peptide) is accessible to solvent, 

which is necessary for recognition by the T-cell receptors (TCRs). Typically, 

TCRs specifically recognize a stretch of approximately nine residues. 

We investigated the binding of peptides to class II MHC molecules using x-ray 

crystallography. The structures show that peptides bind in a polyproline type-II 

conformation with several conserved binding pockets within the overall MHC 

peptide-binding groove. Generally, the pockets accommodate the side chains 

of peptide residues at the P1, P4, P6, and P9 positions, with smaller pockets 

or shelves for the P3 and P7 residues. In the canonical conformation, the side 

chains of residues at the P-1, P2, P5, and P8 locations are solvent-accessible 

and point toward the TCRs. Mutagenesis studies of many MHC-TCR pairs, in 

addition to the two available MHC-peptide-TCR crystal structures, show that 

the TCRs contact the MHC-bound peptide in the region circumscribed by MHCpeptide contacts at the P-1, P2, P3, P5, and P8 positions. 

A T-cell clone isolated from an individual acutely infected with HIV-1 recognizes a peptide antigen derived from the HIV-Gag protein bound to the human 

class II MHC protein HLA-DR1. This clone requires an unusually long version 

of the peptide for activation. 

The crystal structure of HLA-DR1 in complex with the unusually long Gag-derived peptide, Gag[PP16], shows that the peptide binds in an unexpected bent 

conformation, forming a hairpin turn that orients the C-terminal region above 

the remainder of the peptide. An alignment of HLA-DR1-Gag[PP16] with other 

crystal structures of HLA-DR complexes for which clear electron density can 

be seen beyond the P10 peptide residue is shown in Figure 1. On each of the 
Science Highlights 2-63

other HLA-DR complex structures, the peptide extends straight out of the binding site. 

To determine the importance of the C-terminal region in T-cell activation and 

to confirm the physiological relevance of the hairpin observed in the crystal 

structure, we performed alanine scanning mutagenesis. Each Gag[PP16] peptide residue was changed independently to alanine and standard MHC-peptide 

binding assays and T-cell activation experiments were conducted. In the MHCpeptide binding assay, we saw some significant reductions in binding affinity 

upon alanine substitution of Val(P1) and Met(P4) and Ser(P9). These effects 

are consistent with the binding frame observed in the crystal structure. In the 

T-cell activation assay, alanine substitutions of Glu(P-1), Ile(P2), Phe(P5) and 

Thr(P13) completely abolished T-cell activation. The side chains located at positions P-1, P2, and P5 are solvent-exposed and therefore accessible for recognition by the TCRs (Figure 2). Substitution of Gly(P11) to proline, which cannot be 

accommodated in the hairpin, also abolished T-cell activation. 

In conclusion, our study shows that peptides can bind to MHC II in previously 

unobserved conformations in which residues outside the binding groove can 

bend back and become accessible for TCR recognition. This provides evidence 

for a new mode for MHC-peptide-TCR interaction.

Figure 2. The Gag[PP16] hairpin 

turns orients important C-terminal 

residues in position to interact 

with the TCR. Side view of surface 

of HLA-DR1 with the Gag[PP16] 

peptide shown as a stick model. 

Peptide side chains essential for 

T-cell activation are red and those 

important for peptide binding to 

HLA-DR1 are blue. Met(P4) is in 

orange; it affects both MHC peptide 

binding and T-cell activation. 

Figure 1. Alignment of HLA-DR 

crystal structure exhibiting ordered 

peptide density beyond the P10 

residue. Complexes were aligned 

by least-squares fitting of α1 and 

β1 domains of the MHC protein. 

Peptides are shown as Cα traces. 

DR1/TPI is red (PDB ID code 

1KLU), DR2a/MBP is blue (PDB ID 

code 1FV1), DR3/CLIP is magenta 

(PDB ID code 1A6A), DR1/Ha is 

cyan (PDB ID code 1DLH), DR2a/

EBV is gray (PDB ID code 1H15), 

and DR4/collagen is orange (PDB 

ID code 2SEB).
2-64 Life Science 

A New Addition to the Folding Repertory: An 

Engineered Five-Stranded Tryptophan Zipper

J. Liu and M. Lu

Cornell University

Coiled-coil motifs are ubiquitous mediators of specific protein-protein interactions through the formation of interlocking hydrophobic seams between α-helical chains. We engineered a “Trp-zipper” protein with tryptophan (Trp) residues 

at 14 first and fourth heptad positions. The protein forms a discrete, stable, 

α-helical pentamer in water at physiological pH. Its 1.45 Å crystal structure 

reveals a parallel, five-stranded coiled coil, a new type of “knobs-into-holes” 

packing interaction, and an unusual ~8 Å diameter axial channel lined with 

indole rings. The engineered Trp-zipper pentamer expands current views of 

coiled-coil assembly, molecular recognition, and protein engineering, and may 

serve as a soluble model for membrane ion channels.

Coiled coils are one of the most common motifs in protein-protein interactions 

and have been used as the basis for the design of helical bundles and many 

related structures. They consist of entwined alpha helices that form a hydrophobic seam based on nonpolar side chains located at the first (a) and fourth 

(d) positions in a characteristic seven-amino-acid sequence repeat, called a 

heptad. Despite their simple sequence pattern, coiled coils exhibit great diversity in the number and orientation of the chains involved. Proteins composed 

of two to twelve “strands” are known, and general principles for assembling 

dimers as well as higher-order structures, including hexamers and dodecamers, have been deduced. 

About five years ago, we became interested in the E. coli lipoprotein (a 

protein-lipid molecule, denoted Lpp) that contains a three-stranded coiledcoil domain (Lpp-56) embedded between the outer cell membrane and the 

periplasmic peptidoglycan. Surprisingly, the crystal structure of this trimeric 

domain shows that the superhelical structure is not a uniform cylinder, but has 

a pinched-in region where three adjacent alanines (small hydrophobic amino 

acids) occupy the normally bulky nonpolar side chains at the a and d heptad 

positions. This unusual flexibility in the local helix geometry has not been seen 

in GCN4 leucine-zipper models, and led us to undertake a systematic analysis 

of the effect that the number and size of the side chains at the a and d positions might have on the structure and stability of the protein. Replacing all of 

the a and d residues with alanine, for example, completely unfolds the protein 

in solution, although the trimer is stable in crystals. This effect had not been 

reported before, to our knowledge: Intermolecular interactions in the crystal were sufficient to stabilize a coiled-coil trimer that could not fold in solution. Even when we cross-linked the chains covalently, the protein in solution 

remained monomeric. The monomer provided a useful model for defining the 

folding pathway in this system because we could identify a nascent helical sequence near the carboxyl terminus that unfolded as the temperature increased. 

To explore the effects of helix geometry on coiled-coil formation, we engineered a Lpp-56 variant that contains exclusively Trp residues at the a and d

positions (Figure 1). This Trp-zipper protein (denoted Trp-14) forms a stable 

pentameric coiled coil in solution. Its 1.45 Å crystal structure reveals a neverBEAMLINE X4A

Funding

National Institutes of Health and the Irma 

T. Hirschl Trust

Publication

J. Liu et al., “Atomic Structure of A Tryptophan-Zipper Pentamer,” Proc. Natl. Acad. 

Sci. USA, 101, 16156 (2004).

For More Information

Min Lu, Cornell University

Email: lu@mail.med.cornell.edu

Authors (from left) Min Lu and Jie Liu
Science Highlights 2-65

Figure 1. Crystal structure of Trp14. The top panel shows a side 

view of the pentamer. The bottom 

panel shows the cross-section of the 

pentamer in the W18 (a, left) and 

W21 (d, right) layers. The view is 

from the amino terminus of the Trp14 pentamer.

seen-before interface between five parallel helices formed by interacting Trp 

residues. Only the residues at the a positions obey classical “knobs-into-holes” 

packing, while the d positions exhibit a more perpendicular stacking arrangement of the indole rings. This result suggests that the a and d layers in larger 

diameter helical barrels may unequally contribute to the stability of the structure. The Trp-14 structure also contains an irregular hydrophobic cavity (with a 

diameter of 8 Å) running along the long axis. This engineered Trp-zipper structure shows that we have not achieved a complete understanding of the principles of coiled-coil assembly. We are exploring additional variants of Lpp-56 that 

will help us to do so. Meanwhile, we note that the channel in Trp-14 may serve 

as a soluble model for membrane ion channels, and may help determine the 

thermodynamic effect of binding various ligands in such a channel.
2-66 Life Science 

BEAMLINE X26C

Funding

American Chemical Society Petroleum 

Research Fund; National Institutes of 

Health

Publication

A. Nagpal, M.P. Valley, P.F. Fitzpatrick, 

and A.M. Orville, "Crystallization and 

Preliminary Analysis of Active Nitroalkane 

Oxidase in Three Crystal Forms," Acta 

Cryst., D60, 1456-1460 (2004).

For More Information

Allen M. Orville, School of Chemistry 

and Biochemistry, Georgia Institute of 

Technology

Email: allen.orville@chemistry.gatech.edu

Crystal Structures of Nitroalkane Oxidase: High Resolution Data Collection Strategy for Crystals with a 

Very Long Unit Cell Edge

A. Nagpal1, M.P. Valley2, P.F. Fitzpatrick2, and A.M. Orville1

1 School of Chemistry & Biochemistry, Georgia Institute of Technology; 2 Department of Biochemistry & Biophysics, Texas A&M University

Nitroalkane oxidase (NAO) catalyzes the oxidation of neutral nitroalkanes 

to the corresponding aldehydes or ketones with the production of H2O2 and 

nitrite. Oxidized NAO readily crystallizes in a trigonal space group, diffracts 

to beyond 1.6 Å, but with a c unit-cell edge of 488 Å. These characteristics 

push data collection facilities to the limit. Using a combination of 2θ detector 

offsets, kappa geometry, and multiple data sets, a complete data set to 1.6 Å 

resolution has been achieved. To determine the structure we used crystals of 

a Se-Met enriched form of NAO, but trapped in a stable reaction intermediate 

complex (Ered-S*). Although the orthorhombic unit cell of Ered-S* was smaller, it 

nevertheless required analysis of 52 Se sites with MAD phasing methods. The 

2.2 Å structure of Ered-S* was then used to solve the structure of NAO in the 

large unit-cell crystal form.

One of the research interests of the Orville lab is the structure/function analysis of enzymes that catalyze nitrite elimination from natural and “xenobiotic” nitrochemicals. Nitroaliphatic compounds are often produced by plants to inhibit 

the central metabolic enzymes of the TCA cycle in potential pathogens. Nitroalkane oxidase (NAO) is an FAD-dependent enzyme in fungus, which is induced 

by nitroalkanes and enables the microbe to obtain all its nitrogen from these 

types of compounds. Oxidized NAO crystallizes easily, which encouraged us to 

vigorously pursue the structure. However, the diffraction pattern observed with 

our in-house Cu Kα x-rays was very streaky, even at the maximum crystal-tofilm distance (Figure 1). In contrast, our first diffraction images obtained at 

X26C clearly indicated a different story. The NAO crystals diffracted to beyond 

1.6 Å resolution in space group P3221, but with unit cell dimensions of a = b

=104 Å, c = 488 Å. 

As of January 2005 only 158 x-ray structures (out of 29,040) deposited in the 

PDB contain a c axis unit cell edge greater than 450 Å. Moreover, only 16 of 

these structures were to at least 2.5 Å resolution. Thus, NAO would set the 

highest resolution record for a large unit cell, provided that high-resolution diffraction data could be collected, the phases could be solved, and the structure refined. We visited several beamlines at NSLS and APS to achieve these 

goals.

The observed x-ray diffraction pattern has a reciprocal relationship with the 

unit cell dimensions of the crystal in real space. Therefore, the resulting x-ray 

reflections for NAO crystals are very close together and appear as streaks with 

Cu Kα x-rays. In order to resolve closely spaced reflections, the crystal-todetector distance must be sufficiently large to allow the reflections to diverge 

from each other before they reach the detector. However, this also significantly 

decreases the maximum Bragg angle of reflection, so consequently the highresolution data are not observed. 

To collect the high-resolution data of NAO, several data sets were merged. 

Authors (from top) Akanksha Nagpal 

and Allen M. Orville
Science Highlights 2-67

They were obtained with different detector vertical offsets (approximately 

equivalent to 2θ) and optimized kappa geometry to align the long cell axis approximately parallel to the crystal rotation axis. This strategy was first utilized 

at X26C to collect three data sets. The first two data sets used a vertical offset 

of 75 mm and a kappa of either 0° or 40°. The third data set was standard, 

employing no vertical or kappa offset. Merging these data sets yielded a 90% 

complete dataset to 2.5 Å resolution with I/σ(I) of 8.3 in the highest resolution 

shell. We subsequently collected data at APS beamline 14-BMC (operated by 

BioCARS) using the strategy established at X26C and a 150 mm maximum vertical offset. The merged data is 93.5% complete to 2.07 Å resolution, including 

80% completeness in the 2.07 Å resolution shell, but still only 60% complete to 

1.6 Å resolution. Further high-resolution studies are ongoing at several synchrotron beamlines.

To solve the structure, we took advantage of the fact that during NAO turnover 

of nitroethane a N5-(2-nitrobutyl)-1,5-dihydro-FAD adduct (Figure 2) can be 

trapped at low temperature (Ered-S*). This form of the enzyme crystallizes in a 

smaller, orthorhombic space group and contains one holoenzyme (α4) per asymmetric unit. A Se-Met enriched form of Ered-S* was used for MAD data analysis 

(52 selenium sites) and solved to 2.2 Å resolution. 

The larger unit cell for oxidized NAO contains 11⁄2 holoenzymes (six subunits) 

per asymmetric unit. The structure was solved by molecular replacement using 

Ered-S* as a search model. The structure of oxidized NAO has been refined to 

2.07 Å resolution. We are currently analyzing our structures to characterize a 

subtle rearrangement of subunits associated with the conversion of oxidized 

NAO to Ered-S*. The approximately 26° rotation for the subunits is unique to 

NAO, since analogous conformational changes are not observed in the acyl-CoA 

dehydrogenases, which are structural but not functional homologs of NAO.

Figure 2. The structures of NAO 

and Ered-S* are homotetramers 

(top). The 2.2 Å resolution electron 

density for the N5-FAD adduct within 

the Ered-S* trapped intermediate 

(bottom) clearly indicates the 

presence of the 2-nitrobutyl moiety.

Figure 1. The x-ray diffraction 

patterns obtained from crystals 

of oxidized NAO. The diffraction 

pattern on the left was obtained with 

Cu Kα x-rays (1.54 Å), whereas the 

pattern on the right was collected 

with 1 Å synchrotron radiation. 

Synchrotron facilities provide a 

more intense, smaller, and focused 

x-ray beam. This enables longer 

crystal-to-film distances and the 

ability to resolve very closely spaced 

reflections from large unit cells.
2-68 Life Science 

Shape Selective RNA Recognition by Cysteinyl-tRNA 

Synthetase

S.I. Hauenstein1, C.-M. Zhang2, Y.-M. Hou2, and J.J. Perona1

1

Department of Chemistry and Biochemistry, University of California at Santa Barbara; 2Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University

Cysteinyl-tRNA synthetase (CysRS) is the enzyme responsible for attaching 

cysteine (Cys) to the 3’-end of cysteine-specific transfer RNA (tRNACys ). The 

synthesis of Cys-tRNACys is a crucial preliminary step required to incorporate 

cysteine into new proteins. We determined the three-dimensional structure of 

the complex formed between CysRS and tRNACys at high resolution, revealing 

that the complex has an extensive enzyme-RNA recognition interface. An intricate network of hydrogen-bonding, steric, and electrostatic interactions was 

found at the inner-corner of the tRNA L-shape, near an unusual tertiary basepair previously implicated in tRNA aminoacylation. Our combined mutational 

analysis of enzyme and tRNA groups showed that tRNA recognition by CysRS 

is shape-selective.

Aminoacyl-tRNA synthetases are the class of enzymes responsible for the 

covalent attachment of amino acids to the 3’-ends of cognate transfer RNA 

molecules (tRNAs) — the process known as aminoacylation. Cysteinyl-tRNA 

synthetase (CysRS) is the smallest monomeric tRNA synthetase in E. coli, 

and is an excellent model for exploring how the enzymes discriminate among 

a large number of structurally similar L-shaped tRNAs. Biochemical data has 

previously suggested that CysRS may rely on the distinctive globular shape 

of the tRNACys core to recognize critical molecular elements, via a general 

mechanism known as “indirect readout.” A striking feature of the tRNACys core 

is the presence of a rare G15:G48 noncanonical tertiary base-pair. To provide 

the essential framework for interpreting this type of functional data, we crystallized E. coli CysRS bound to tRNACys and determined the crystal structure to 

2.3 Å resolution. 

Our previously determined structure of the unbound CysRS revealed that it has 

an elongated shape. It features a Rossman fold catalytic domain, an inserted 

domain adjacent to the tRNA-acceptor end, a bridging stem-contact fold, and 

an α-helical bundle domain conserved among a subclass of other tRNA synthetases. While the relative orientations of these four domains are identical in 

CysRS bound to tRNA, a fifth domain — consisting of approximately 60 amino 

acids forming a mixed α/β fold — appears at the C-terminus of the helical 

domain, adjacent to the anticodon loop (Figure 1). This is a unique feature not 

previously observed in tRNA synthetases.

A significant fraction of the binding surface between CysRS and tRNACys

consists of interactions between the CysRS α-helical bundle domain and the 

tRNA’s D and anticodon domains (which together form the vertical arm of 

the L-shape). The structure of the arm shows that there are no base-specific 

contacts at the key G15-G48 base-pair (where G is the nucleotide guanine). 

Instead, hydrogen bonds are made at a non-bridging phosphate oxygen atom 

located on the G15 and at the 2’OH on A14 (the nucleotide adenine) by the 

side-chains of Asn351 and Glu354 (the amino acids asparagine and glutamic 

acid, respectively) (Figure 2). In addition, a water-mediated hydrogen bond 

links G15 with the side chains of Asp348 (aspartic acid) and Lys12 (lysine), 

which form an adjacent salt-bridge.

BEAMLINE X8C

Funding

National Institutes of Health

Publication

S. Hauenstein, C.M. Zhang, Y.-M. Hou, 

and J.J. Perona, "Shape Selective RNA 

Recognition by Cysteinyl-tRNA Synthetase," Nat. Struct. Mol. Biol., 11(11), 

1134-1141 (2004).

For More Information

John Perona, Department of Chemistry 

and Biochemistry, University of California 

at Santa Barbara

Email: perona@chem.ucsb.edu

Authors (from left) Scott Hauenstein 

and John Perona
Science Highlights 2-69

To test how cysteinylation relies on these sugar-phosphate backbone contacts at 

G15, we carried out a combined mutational analysis of the CysRS enzyme and 

tRNA in this region. The data revealed that variant enzymes mutated at Asn351 

were no longer able to distinguish between tRNAs possessing the unusual G15-

G48 pair and a canonical G15-C48 pair found in most tRNAs. Asn351 mutants 

are just six times more likely to prefer G15:G48 tRNACys, compared with a 125-

fold preference that native CysRS has for the wild-type tRNA. Together with the 

highly complementary sugar-phosphate backbone interactions observed in the 

structure, these data indicate that the Asn351-G15 phosphate contact mediates 

tRNA recognition by indirect readout.

Because the 3’-terminus of the tRNA is disordered in the crystals, we do not yet 

know how interactions with the sugar-phosphate backbone are transmitted to 

the enzyme active site. The extent to which tRNA selectivity may be coupled to 

a unique zinc ion-mediated mechanism for amino acid selection is also unresolved. We are currently performing crystallographic and enzymological experiments to address these questions.

Figure 2. Indirect readout of the 

tertiary core. Asn351 makes a 

hydrogen bond with the phosphate 

of G15 in the G15-G48 Levitt pair 

(red). Glu354 makes secondary 

contact with the 2’OH group of A14 

from the U8-A14-A46 pair (blue) 

stacked directly beneath the G15:

G48 pair. A red sphere represents 

the water molecule involved in 

hydrogen bonding between the 

phosphate of G15 and Asp348/

Lys12.

Figure 1. Ribbon representation of 

the E. coli CysRS-tRNACys structure. 

The CP domain (1), Rossman fold 

(2), SC fold (3), helical bundle 

domain (4), and AB domain (5) are 

colored tan, red, green, blue, and 

light purple, respectively. The tRNA 

molecule is shown as a gold tube 

and the active-site zinc ion as a blue 

sphere.
2-70 Materials Science 

BEAMLINE X14A

Funding

National Science Foundation, Texas Center for Superconductivity and Advanced 

Materials at the University of Houston, 

Alfred P. Sloan Foundation

Publication

"Morphological Instability in InAs/GaSb 

Superlattices Due to Interfacial Bonds," 

Phys. Rev. Lett., 95, 96104-7 (2005).

For More Information

Donna Stokes and Jianhua Li, Department 

of Physics, University of Houston

Email: dwstokes@uh.edu; jli3@uh.edu

Effect of Interfacial Bonds on Morphological 

Instability of Slightly Lattice Mismatched Epitaxial 

Thin Films

J.H. Li1,2, D.W. Stokes1, O. Caha1, S.L. Ammu1,2, J. Bai3, K.E. Bassler1, and S.C. Moss1,2

1

Department of Physics, University of Houston; 2Texas Center for Superconductivity and Advanced Materials, 

University of Houston; 3

Oak Ridge National Laboratory

Using x-ray diffraction, we have investigated the strain and composition of 

InAs/GaSb superlattices grown on GaSb or InAs (001) substrates with InSb or 

GaAs interfacial bonds. An ordered InAs nanowire array is formed in the superlattice on GaSb (001) with InSb interfacial bonds, while the superlattice on 

InAs (001) with GaAs interfacial bonds remains planar. We have determined 

the composition and strain in both superlattices and found that the InAs layers 

are under compressive strain, rather than under the expected tensile strain or 

strain-free as we expected. We suggest that the strain state of the interfacial 

bonds is crucial for the morphological instability. This may provide a new channel in which to manipulate the self-assembling of nanowire structures.

The formation of self-organized semiconductor nanoscale structures, based 

on the morphological instability of strained films grown using molecular beam 

epitaxy, has been observed in many III-V systems. Instability occurs at some 

critical layer thickness, which is large for many III-V systems with a misfit of 

less than 1% (>150 Å), when the misfit strain energy is reduced more than the 

surface energy is increased. However, unusual instability phenomena have 

been observed in some non-common anion strained III-V single layers and 

heterostructures. For example, In0.45Ga0.55As/InP (001) with a misfit of 0.5% 

demonstrates instability at an early stage of the growth. Similarly, InAs/GaSb 

(001) heterostructures have a misfit of 0.62%, but instability is observed at a 

thickness of a few monolayers. 

In this work, two (InAs)13/(GaSb)13 superlattices, one with In-Sb interfacial 

bonds and one with Ga-As interfacial bonds, have been analyzed. Cross-sectional scanning tunneling microscope images showed that the sample with 

In-Sb interfacial bonds formed an array of nanowires, as shown in Figure 1. 

However, the sample with Ga-As interfacial bonds remained planar. Figure 

2(a) shows the reciprocal space map around the GaSb (-224) substrate reciprocal lattice point for the nanowire sample. Figures 2(b) and (c) show line 

scans along the Qx

||[-110] and Qz||[001] directions (indicated by the dashed 

lines in the map). The appearance of high-order two-dimensional satellites 

in these scans indicates the long-range ordering of the nanowire array. X-ray 

results from the planar superlattice sample (not shown) show one-dimensional 

satellites as expected. 

Theoretical simulations of the x-ray results for the nanowire sample based 

on a structural model derived from Figure 1 were performed considering the 

shape function of the nanowires — including the spacers, the scattering amplitude of a single nanowire, and the strain distribution in the nanowire array 

— through a direct solution of the equations of linear continuum elasticity. The 

simulations, also shown in Figure 2, yield that (1) the “InAs” nanowires were 

actually an InAs0.88Sb0.12 alloy due to Sb contamination and/or segregation, 

with a positive mismatch of +0.21%, and (2) the In-Sb interfacial bonds have a 

large positive mismatch of +6.28% with respect to the substrate. 

Authors (from left) Donna Stokes, 

Kevin Bassler, and Jianhua Li
Science Highlights 2-71

For the planar sample, the x-ray rocking curve revealed that the “InAs” layers 

were also InAs0.88Sb0.12 alloy layers with a mismatch of +0.83%, which is much 

larger than that of the layers grown on the GaSb substrate. This sample is different because it contains Ga-As interfacial bonds, which experience a large 

negative mismatch of -6.69% with respect to the InAs substrate.

For the nanowire sample, the InAs0.88Sb0.12 and the InSb interfacial have a positive misfit. Thus, it is favorable for them to relax together. The strain energy is 

proportional to the layer thickness; therefore, the high misfit strain in the InSb 

interfacial reduces the critical layer thickness of InAs0.88Sb0.12, making it possible for instability to occur in just a few monolayers. For the planar sample, the 

InAs0.88Sb0.12 and the GaAs interfacial have opposite misfits. Relaxation of these 

two materials involves atomic displacements in opposite directions; therefore, it 

is unfavorable for them to relax together to form a planar sample. This suggests 

that it may be possible to manipulate the self-assembling of nanowire structures through the control of the strain relationship with respect to the substrate 

between the superlattice layers and interfacial bonds.

Figure 1. A reconstructed 3D 

structure of the nanowire array in the 

nanowire sample based on XSTM 

measurements. The dark areas 

are "InAs" and the bright areas are 

"GaSb." Enclosed in the solid lines 

is a nanowire model used in our 

simulation. The bright circles mark a 

super face-centered-rectangle unit 

cell that the nanowires form.

Figure 2. Experimental and 

simulated (a) x-ray reciprocal space 

map around (-224) reciprocal 

lattice point (b) Qx

||[-110] scan 

(dots) corresponding to the dashed 

horizontal line in the map and (c) 

Qz

||[001] scan (dots) corresponding 

to the dashed vertical line in the 

map. (m,n) indicates the lateral and 

vertical orders of the satellites.

Experiment Simulation

Qx

 (r.i.u.)

Qz (r.i.u.)

Qx (r.i.u.)

(a)

(b) (c)

Qx

 (r.i.u.) Qx

 (r.i.u.)

Intensity (arb. unit)
2-72 Materials Science 

BEAMLINES X22A, X22C

Funding

National Science Foundation; Cottrell 

Scholar Program of the Research Corporation; Division of Material Sciences, U.S. 

Department of Energy

Publication

F. He, B.O. Wells, and S.M. Shapiro, 

"Strain Phase Diagram and Domain Orientation in SrTiO3

 Thin Films," Phys. Rev. 

Letts., 94, 176101 (2005).

For More Information

Feizhou He, Canadian Light Source, 

University of Saskatchewan

Email: feizhou.he@lightsource.ca

Perovskite Thin Films Under Strain

F. He1, B.O. Wells1, and S.M. Shapiro2

1

Department of Physics, University of Connecticut; 2Department of Physics, Brookhaven National 

Laboratory

Strontium titanate (SrTiO3) nanoscale films were studied as a model oxide film 

system. Highly strained films were grown on different substrates, resulting in 

either compressive or tensile strain. The measured strain-temperature phase 

diagram is qualitatively consistent with theory; however, the change in transition temperature is much larger than predicted. Further, the film is constrained 

because it is epitaxially clamped to the substrate, which causes the SrTiO3

to be tetragonal at all temperatures. Therefore, the phase transition involves 

only a lowering of symmetry. This leads to the unique situation in which the 

low temperature phase under tensile strain has an orthorhombic Cmcm space 

group but a tetragonal lattice, a situation not possible for bulk materials.

In epitaxial films only several nanometers thick, the film atoms tend to align 

with the underlying substrate atoms. If the lattice parameters of the film and 

substrate material are different, the film will be strained from its natural bulk 

atomic spacing. An important area of research in recent years has focused on 

understanding exactly why the properties of strained films differ from related 

bulk materials. An ultimate goal is to learn how to use these differences to 

enhance the performance of devices, or as a tool to probe the fundamental 

physics of materials with strong electron interactions. 

The many fascinating properties of perovskite-related materials, such as ferroelectricity and high-temperature superconductivity, are particularly sensitive 

to strain. Our experiments used synchrotron x-ray scattering to investigate the 

structural phase transitions in very highly strained films of various perovskitebased film materials. Our main model system has been SrTiO3, which has a 

well-known structural phase transition involving rotations of the internal TiO6

octahedral, as shown in Figure 1(a). In this case, the transition is from a high 

symmetry cubic phase at a high temperature to a lower symmetry tetragonal 

phase below the transition temperature. The structural phase transition in 

SrTiO3 is monitored through the superlattice diffraction peaks associated with 

the low-temperature phase.

We produced SrTiO3 films with different amounts and types (compressive or 

tensile) of strain by carefully growing them on different underlying crystals. 

Under compressive strain, the phase transitions in SrTiO3 films go from a 

high-symmetry tetragonal structure to a low-symmetry tetragonal phase. Under 

tensile strain, the transition is from high-symmetry tetragonal to orthorhombic. 

The structural phase transition temperature Ts

 is enhanced under both compressive strain and tensile strain. The main difference between the two cases 

is that the orientation of the rotation axis is different for compressive strain 

and tensile strain, as illustrated in Figure 1(b). A very similar effect happens to 

the spontaneous polarization in related ferroelectric films. 

An interesting phenomenon in epitaxial films is that, although internally there 

are structural changes corresponding to the phase transitions, externally the 

dimensions of the unit cells do not change because of the strong bonding, 

or clamping, from the substrates. Therefore, the tetragonality of the unit cell, 

Authors (from left) Barry Wells and

Feizhou He
Science Highlights 2-73

which is the secondary order parameter for bulk SrTiO3, is no longer a good order parameter for phase transitions in films. The internal transitions without the 

external changes in the shapes of the unit cells create unique morphologies that 

are not possible in bulk materials. For example, the low-temperature phase in 

SrTiO3 films under tensile strain has an orthorhombic space group (Cmcm) but a 

tetragonal lattice as a consequence of strain and substrate clamping.

The strain phase diagram based on our experimental data is compared with 

the theoretical calculations by Pertsev et al, shown in Figure 2. Many aspects 

of the strain-temperature phase diagram, such as the domain structures and 

the general trend of the phase boundary, are well described by current theory, 

though improvements are necessary to describe the magnitude of the increase 

in transition temperature.

Figure 2. Strain-phase diagram for 

SrTiO3

 thin films. High-symmetry 

tetragonal, low-symmetry tetragonal, 

and orthorhombic phases are 

labeled HT, LT, and LO, respectively. 

For tensile strain, Ts

 increases 

rapidly over the small strain regime, 

then stabilizes at about 160–170 

K for larger strain. Compressive 

strain induces a more dramatic 

effect. Only 0.5% compressive strain 

results in an increase in Ts of over 

200 K versus the bulk value, nearing 

room temperature.

Figure 1. (a) Unit cell of SrTiO3. 

The phase transition involves 

the rotation of internal TiO6

octahedral. (b) The rotation axis 

of internal TiO6

 octahedral (red 

arrow) in SrTiO3

 oriented differently 

under compressive strain and 

tensile strain. The spontaneous 

polarizations in ferroelectric 

materials behave similarly.

Misfit Strain (%)

Temperature (K)
2-74 Materials Science 

Epitaxial Tilting of GaN Grown on Vicinal Surfaces of 

Sapphire

X.R. Huang1, J. Bai1, M. Dudley1, R.D. Dupuis2, and U. Chowdhury2

1

Department of Materials Science and Engineering, Stony Brook University; 2School of Electrical and Computer 

Engineering, Georgia Institute of Technology

Using the synchrotron Laue method and high-resolution x-ray diffraction, we 

have revealed the epitaxial tilting effect of gallium nitrite (GaN) films grown on 

vicinal (0001) surfaces of sapphire and their relationship to the offcut angles 

and the substrate surface steps. This effect is a consequence of the large outof-plane lattice mismatch between GaN and sapphire, and can be explained 

by an extended Nagai theory. The large lattice tilts and their formation mechanism indicate that the substrate surface morphology is an important factor that 

affects the epitaxy process and the crystalline quality of GaN films grown via 

vicinal-surface epitaxy.

Although the growth of III-nitrides on sapphire (Al2O3) has been extensively investigated, little attention has been paid on the large c lattice mismatch (∆c/c ≈

20% for GaN/sapphire), particularly the case of vicinal surface epitaxy (VSE). 

We have recently demonstrated that GaN grown on a vicinal sapphire surface 

is generally tilted from the substrate (known as a Nagai tilt). For 1-bilayer 

steps of sapphire, shown in Figure 1a, the tilt α is related to the offcut angle 

φ by the relationship tanα = −(∆c/c)tanφ ≈ 0.2tanφ (<0). For step bunches, 

however, this principle may change. In Figure 1c, due to 3c ≈ 2.5ce, the GaN 

lattices can be tilted in two directions with equal probabilities, tanα ≈ ±0.2

tanφ, leading to α ≈ 0 on average. For 4-bilayer steps, the GaN lattice is tilted 

toward the offcut direction by tanα = [(4c−3ce)/(4c)]tanφ ≈ 0.1 tanφ (>0). Similarly, the tilt for 5-bilayer steps is tanα = [(5c−4ce)/(5c)]tanφ ≈ 0.04 tanφ (>0).

The above principles have been explicitly verified by synchrotron Laue patterns and high-resolution x-ray diffraction performed on vicinal GaN/sapphire. 

GaN films 4 μm thick were grown using low-pressure metal organic chemical 

vapor deposition (MOCVD) in a temperature range of 1020-1080°C. Figure 2

shows the back-reflection Laue patterns of three samples, where the displacement of the 0001 spot from O (white arrows) is caused by the offcut, and the 

displacement of the GaN 0001 spot from that of sapphire reflects the epilayer 

tilt, which is always parallel to the offcut direction nc

. In Figure 2a, the measured tilt (negative) is in perfect agreement with the tilting model in Figures 1a

and 1b, indicating that on the small-offcut substrate the steps are dominantly 

1- or 2-bilayer steps. For the 6.29°-off sample, the tilt shows that steps of various types coexist on the substrate surface, with 1- or 2-bilayer steps contributing to negative tilts and the other types reducing this tendency. The positive 

tilt of the 10.6°-off sample shows that 4- or 5-bilayer steps outweigh the other 

steps.

The tilting effect reveals a series of important mechanisms of GaN epitaxy 

that have been widely ignored in the past, including: 1) the sapphire surface 

morphology can greatly affect the epitaxy process and the crystalline quality of GaN films; 2) drastic step bunching and faceting of sapphire can occur 

during nitridation; 3) mismatch strains are dominantly relaxed by pure basal 

plane dislocations without out-of-plane Burgers vector components; and 4) 

the epilayer tilt-related shear stresses are believed to significantly affect the 

BEAMLINE X19C

Funding

Office of Naval Research; U.S. Department of Energy, Office of Basic Energy 

Sciences

Publication

X.R. Huang, J. Bai, M. Dudley, R.D. 

Dupuis, and U. Chowdhury, "Epitaxial 

Tilting of GaN Grown on Vicinal Surfaces 

of Sapphire," Appl. Phys. Lett., 86, 211916 

(2005). 

For More Information

Michael Dudley, Department of Materials 

Science and Engineering, Stony Brook 

University

Email: mdudley@notes.cc.sunysb.edu

Authors (from left) Xian-Rong Huang, 

Michael Dudley, and Jie Bai
Science Highlights 2-75

Figure 2. Laser-guided backreflection synchrotron Laue patterns 

of vicinal GaN/Al2

O3 samples 

showing the epitaxial tilts. The filmto-sample distance is 30 cm. Inset: a 

side view of the diffraction geometry.

Figure 1. Epilayer tilts induced by 

steps of various heights in VSE of 

GaN on sapphire. ns

 – substrate 

surface normal, nc

 – offcut direction.

growth kinetics and strain relaxation. In our latest work, we also found the tilting 

effect and the related mechanisms in GaN/SiC systems [X.R. Huang et al., PRL 

95, 086101 (2005)] where, compared to flat-surface epitaxy, VSE shows explicit 

advantages for relaxing strains and improving epilayer quality.
2-76 Materials Science 

BEAMLINE X10A

Funding

National Science Foundation

Publication

M.M. Maye, I-I.S. Lim, J. Luo, Z. Rab, 

D. Rabinovich, T. Liu, and C.-J. Zhong, 

“Mediator-Template Assembly of Nanoparticles,” J. Am. Chem. Soc., 127, 1519-

1529 (2005).

For More Information

C.J. Zhong, Department of Chemistry, 

State University of New York at Binghamton

Email: cjzhong@binghamton.edu

Mediator-Template Assembly of Nanoparticles

M.M. Maye1, I-I.S. Lim1, J. Luo1, Z. Rab1, D. Rabinovich2, T. Liu3, and C.-J. Zhong1

1

Department of Chemistry, State University of New York at Binghamton; 2Department of Chemistry, The University of North Carolina at Charlotte; 3

Department of Chemistry, Lehigh University

The ability to construct size- and shape-controllable architectures using 

nanoparticles as building blocks is essential for exploring the properties of 

nanostructures. Our mediator-template strategy explores multidentate ligands 

as molecular mediators and surfactant-capped nanoparticles as templates in 

order to build size-controllable and monodispersed particle assemblies. Such 

assemblies display both soft and hard properties, depending on how they interact with their substrates. This duality could form the basis of a new strategy for 

manipulating nanoscale linkages, soldering nanoelectronics, and constructing 

nanosensor devices. The assemblies also allow for controlled disassembly and 

size regulation by a third molecular component, which could lead to developments in nanotechnological applications in controlled drug delivery. 

Many areas of nanotechnology involve the use of nanoparticle-based materials in applications such as sensors, catalysis, and information storage. These 

applications require the ability to assemble nanoparticles into a structure 

with controllable size, shape, and interparticle spatial properties, resulting in 

unique nanoscale properties that can be effectively exploited. While a variety 

of assembly methods have been demonstrated, the ability to precisely control size, shape, and interparticle spatial properties is rarely reported due to 

the lack of molecular-level understanding of the interparticle interactions and 

reactivities. 

The key element of our assembly approach is a mediator-template strategy. 

The understanding of molecular driving forces exerted by molecular linkers 

or multidentate thioethers as mediators, as well as monolayer or surfactant 

capping molecules as templating agents, could lead to a general assembly 

strategy that would maximize our ability to control the structure’s size, shape, 

and spatial properties. Consider, for example, a system in which multidentate 

thioethers, Me4-nSi(CH2SMe)n (2), are used as mediators and tetraalkylammonium bromides, [CH3(CH2)m]

4N+Br-

 (1), are used as templating agents. Scheme 

1 illustrates the general concept of the 2-mediated assembly of 1-capped gold 

nanoparticles (1/Au). This mediator-template combination is simple and effective. The mediation force exploits the coordination reactivity between 2 and 

Au, which can be manipulated by the number of thioether groups on 2. Simultaneously, the templating force resulting from the surfactant reactivity of 1

determines the geometry of the assembly, depending on the chain length and 

structure of 1.

The average diameters of the spherical assembly (the TEM image in Scheme 

1) are dependent on the relative ratios of mediators vs. templates. One important finding is from a small-angle x-ray scattering measurement that (Figure 

1A) revealed a subtle decrease of the edge-to-edge distance with increasing 

mediator-to-template ratio, falling between the expected molecular lengths of 1

and 2. Another important finding is from a spectrophotometric measurement of 

the surface plasmon resonance band (Figure 1B), which led to two important 

findings: that the mediator-template assembly of nanoparticles is an enthalpydriven process, and that the enthalpy change (-1.3 kcal/mole) is close to the 

magnitude of the van der Waals interaction energy for alkyl chains. These 

Authors (from left) Lisa Cousineau, Li 

Han, Mathew Maye, Lingyan Wang, 

Qiang Rendeng, Nancy Kariuki, Mark 

Schadt, Yan Lin, Jin Luo, Stephanie 

Lim, Kaylie Young, Chuan-Jian 

Zhong (Group leader), Elizabeth 

Crew, Derrick Mott, Peter Njoki, and 

Xiangting Dong
Science Highlights 2-77

findings establish the important role played by the templating molecules in the 

mediate-template assembly.

The spherical assembly on mica does not wet the surface, and thus retains its 

shape. In contrast, the spherical assembly wets highly ordered pyrolytic graphite 

(HOPG), and thus the particles tend to spread over the surface. The interaction 

between the spherical assembly and HOPG must be relatively strong in view of 

the hydrophobic character of the HOPG surface and the hydrophobic character 

of 1-capped Au nanoparticles and their assemblies.

The soft-hard nature of the nanoparticle assemblies and their interactions with 

contacting substrates could form the basis of a new strategy for manipulating 

nanoscale linkages, soldering nanoelectronics, and constructing nanosensor 

devices. Interestingly, the nanoparticle assemblies display interesting optical 

properties that are highly responsive to changes in assembly size, chemical 

environment, and molecular structures. The chemically responsive optical properties could find applications in devices such as sensors and biosensors. Such 

assemblies also allow for controlled disassembly and size regulation by a third 

molecular component, which could form the basis of nanotechnological applications in controlled drug delivery.

Figure 1. (A) SAXS data for 

the 2-mediated assembly of 

1/Au in solutions at three different 

concentration ratios (r = 2.5 (a), 10 

(b), and 400 (c)). Curve d is for 1/Au 

solution. Inset: a magnified view of 

the peak region. (B) UV-Vis spectral 

evolution for the assembly of Aunm

upon addition of 2 (T = 5  ̊C). The 

spectral evolutions were recorded 

within the time frame of one hour.

Scheme 1. A schematic illustration 

of the mediation-template strategy 

for 2-mediated assembly of 1-

capped gold nanoparticles. The 

bottom image shows an example of 

the assembly.

Intensity

q (nm-1)

Absorbance

Wavelength (nm)

(A) (B)
2-78 Materials Science 

BEAMLINE X27C

Funding

Air Force Office of Scientific Research; 

Air Force Research Laboratory and the 

Materials and Manufacturing Directorate

Publication

H. Koerner, E. Hampton, D. Dean, Z. 

Turgut, L. Drummy, P. Mirau, and R. Vaia, 

“Generating Tri-axial Reinforced Epoxy 

Montmorillonite Nanocomposites With UniAxial Magnetic Fields,” Chem. Mater., 18, 

1990-1996 (2005).

For More Information

Richard A. Vaia, Air Force Research 

Laboratory

Email: richard.vaia@wpafb.af.mil

Time-Resolved Morphology Development of Tri-axial 

Reinforced Epoxy Montmorillonite Nanocomposites 

in Uni-Axial Magnetic Fields

H. Koerner1, E. Hampton2, D. Dean2, Z. Turgut3, L. Drummy4, P. Mirau4, and R.Vaia4

1

University of Dayton Research Institute; 2Tuskegee University; 3Zafer Turgut, UES Inc.; 4Air Force Research 

Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base

Numerous papers and patents have been published on polymeric nanocomposites. However, extensive research has not yielded nanocomposites with 

vastly improved properties, as was envisioned, but has instead mimicked the 

results of conventionally filled systems. This is mostly due to a poor nanoparticle-matrix interface and the lack of control over dispersion and orientation of 

nanofillers to an extent comparable to what has been accomplished in continuousfiber reinforced composites. Utilizing the orthogonal magnetic susceptibility 

of Montmorillonite nanocomposites (MMTs) from different deposits with comparable Fe content (3.4%), we have generated a three-dimensional morphology composed of orthogonally aligned aluminosilicate layers from a mixture 

of Montmorillonites subjected to a uniaxial external magnetic field. Depending 

on the source, MMTs exhibit remnant magnetization arising from antiferro- and 

ferromagnetic impurities, and align with their layers parallel or perpendicular 

to the field. In-situ X-ray measurements show that within a few minutes an 

applied static magnetic field (1.2 or 11.7 Tesla) induces the stable alignment 

of an organically-modified MMT within an epoxy resin at room temperature. 

Structural relaxation is orders of magnitude slower. Overall, these studies 

demonstrate that a critical component of the chemistry in these nanofillers 

has been overlooked in the past. Remarkably minor compositional differences 

may allow researchers to explore many more possible techniques to address 

nanocomposite issues.

Real-time x-ray experiments were carried out at beamline X27C at the NSLS 

using a marCCD detector at a sample-to-detector distance of 82.5 cm. Two 

types of layered silicates, Southern Clay MMT modified with octadecylamine 

(SC18) and Nanocor I30.E (NC18), were dispersed in epoxy (an Epon 862 

monomer) via sonication and high-shear mixing. After additional short mixing 

with a curing agent and subsequent degassing, the suspensions were deposited into x-ray capillaries for use in a 1.2-Tesla rare-earth permanent magnet.

The morphology response to the application of the magnetic field at room 

temperature (~ 27oC) was monitored in-situ by positioning the magnet such 

that the x-ray beam passed between the poles of the magnet and through the 

capillary. The capillaries were dropped into the magnetic field remotely via 

a solenoid switch and a paper clip attached to the top of the capillary. After 

alignment, the capillary was removed from the magnet and repositioned within 

the beam to examine the degree of randomization, or was fixed by a two-stage 

curing reaction (120 oC for 2 hours; 175 oC for two hours).

Figure 1 reveals that alignment of the 3 wt% SC18/NC18 mixture is 90% 

complete after 10 minutes in the 1.2-Tesla magnetic field at room temperature. 

Figure 1a shows a series of x-ray patterns at three-minute time intervals during the alignment process of that mixture. The final pattern was taken after a 

complete cure cycle and shows the partial exfoliation of the system, with the 

d-spacings of the galleries increasing from 3.7 nm to 12.5 nm. For this mixture, a two-dimensional contour plot of azimuthal scans at the d001 reflections 

Authors (from left) Richard Vaia, Peter 

Mirau, Hilmar Koerner, and Larry 

Drummy
Science Highlights 2-79

↓curing

is shown in Figure 1b. This plot emphasizes the rapid formation of the four-point 

pattern, which reflects triaxial reinforcement by the OMM layers. A plot of the intensity of the d001-layer diffraction at an azimuthal angle of 0 degrees (meridian) 

(Figure 1c) shows that steady-state alignment of the SC18/NC18 mixture (3wt% 

total) within the 1.2-Tesla magnetic is achieved after 15 minutes. This time scale 

is very similar to other OMMs and no indication of faster or slower orientation 

has been observed. 

These experiments also show that once alignment has been achieved the 

sample does not quickly relax back to its random alignment, which is in agreement with rheology studies on similar systems. Alignment is possible in several 

solvents (Toluene, water) and epoxy monomers (Epon 862, Epon 828). The slow 

relaxation behavior is to be expected, considering the matrix viscosity and the 

Brownian motion of particles at room temperature. Rotational diffusion is hindered by particle-particle interaction and the high viscosity of the epoxy resin 

formulation. 

The magnetic field alignment does not affect the curing chemistry, which agrees 

with electric field experiments on the same system. 

Measurements on the coefficient of thermal expansion (CTE) confirm that morphology control leads to significant differences depending on the alignment of 

the layered silicates, decreasing CTE the most in the direction of maximum MMT 

alignment. Understanding the detailed mechanism that leads to a change of the 

magnetic easy axis within layered silicates opens up opportunities to design 

novel synthetic layered silicates with unusual magnetic properties.

Figure 1. a) A series of x-ray 

patterns of a 3 wt% SC18/NC18 

suspension in Epon 862 at room 

temperature. Orthogonal alignment 

of the two different clays starts at 

about five minutes. Beginning to 

end (left to right) is 30 minutes. The 

last image shows the fully cured 

nanocomposite with a false color 

HRTEM to the left; b) 2D contour 

plot with azimuthally averaged line 

scans through the gallery diffraction 

peak at 3.7 nm showing the four 

point pattern development with 

time; c) normalized intensity at 90 

degrees of azimuthal scan versus 

time for 3 wt% SC18, NC18 and 

SC18/NC18 in Epon 862.

azimuthal angle, degrees

Time, min

Normalized intensity, a.u.

(a)

(b)

(c)

Time, sec
2-80 Materials Science 

Resonant X-ray Scattering from a Magnetic Multilayer 

Reflection Grating

L.-A. Michez1, C.H. Marrows1, P. Steadman1,2, B.J. Hickey1, D.A. Arena3, J. Dvorak4, H.-L. Zhang5, 

D.G. Bucknall5, and S. Langridge6

1

School of Physics and Astronomy, E. C. Stoner Laboratory, University of Leeds, United Kingdom; 2Diamond 

Light Source, Rutherford Appleton Laboratory, United Kingdom; 3

National Synchrotron Light Source, Brookhaven 

National Laboratory; 4

Department of Physics, Montana State University; 5Department of Materials, University of 

Oxford, United Kingdom; 6

ISIS Facility, Rutherford Appleton, United Kingdom

Magnetic multilayers exhibit a very diverse range of fundamental phenomena that 

underpin much of the data-storage technology we now rely upon, and are of great 

interest in the emergent technology of spin-electronics. Recently, techniques have 

allowed the patterning of such systems so that all three spatial dimensions are 

accessible and controllable at the nanoscale, but it is important to determine how 

the magnetic microstructure responds to the physical structures imposed upon it. 

Using soft x-ray magnetic resonant scattering we have studied this behaviour in a 

system in which the physical structure was deliberately patterned to observe the 

response of the magnetism to such a perturbation. We found that the magnetisation 

only tracks the highest Fourier components of the physical structure effectively.

It is well known that the competition between the interaction energies in 

a ferromagnetic material may lead to the formation of magnetic domains 

— regions in which there is microscopic ordering of the electron spin to 

minimise the free energy. If we then impose a physical in-plane pattern on this 

system, we will have additional competition introduced through the physical 

shape of the magnetic element. Such a situation has led to the proposal to use 

patterned arrays to provide ultra-high magnetic storage densities and move 

beyond the super-paramagnetic limit, in which the magnetic structure becomes 

thermally unstable (>100Gb/in2). 

To more fully understand this interaction we have prepared 

antiferromagnetically coupled multilayers of cobalt/ruthenium (Co/Ru) with a 

nominal structure [Co(4nm)/Ru(3.4nm)]x10 on top of a polystyrene (PS) line 

array. The array was produced by micro-contact printing, in which a mold is 

pressed into the PS at a pressure of 10 kPa to produce a line array with a 400 

nm period and a 1:1 mark/space ratio. The advantage of such a technique 

is that large-area patterning is readily achievable. A scanning electron 

micrograph of the completed sample is shown in Figure 1. 

Numerous techniques exist to study the structural morphology of multilayers. 

However, studying the magnetic structure of the buried layers of this patterned 

Co/Ru multilayer requires a scattering technique such as soft x-ray resonant 

magnetic scattering (XRMS). By tuning the incident photon energy to the LIII

absorption edge of the Co (778eV) we can observe both structural morphology 

and the cross-correlation of the magnetic structure with the physical structure. 

The diffraction pattern from such a grating structure is shown in Figure 2a. 

In the XRMS measurement we can either change the helicity of the circularly 

polarized photons or reverse the magnetization of the sample (curves I+, I-

 in 

Figure 2a). The sum of these two data (Figure 2b) is related to the selfcorrelation of the physical structure whilst the difference is sensitive to the 

cross-correlation of the physical and magnetic structures. A very sensitive 

measure is then to plot the asymmetry ratio (I+-I-

)/(I++I-) (Figure 2c). Only the 

first harmonic is present in Figure 2c, clearly showing that the magnetic inplane wave form is significantly different from that of the structural one. The 

Chris Marrows

BEAMLINE U4B

Funding

Engineering and Physical Sciences 

Research Council

Publication

L.-A. Michez, C.H. Marrows, P. Steadman, 

B.J. Hickey, D.A. Arena, J. Dvorak, H.-L. 

Zhang, D.G. Bucknall and S. Langridge," 

Appl. Phys. Letts., 86, 112502 (2005).

For More Information

C.H. Marrows, School of Physics and 

Astronomy, E. C. Stoner Laboratory, University of Leeds, United Kingdom

Email: c.h.marrows@leeds.ac.uk
Science Highlights 2-81

Figure 1. A scanning electron 

micrograph of the multilayer-coated 

PS line array. The inset shows the 

magnetization loop, measured by 

MOKE, parallel and perpendicular 

to the line direction. Parallel 

to the lines is a slightly easier 

magnetization axis.

Figure 2. (a) The diffraction pattern 

from the PS line array. QX is the 

in-plane momentum wave-vector 

transfer (parallel to the sample 

surface). The two curves represent 

the magnetization of the sample. (b) 

The average and difference of the 

data presented in panel (a). (c) The 

asymmetry ratio as defined in the 

text showing the strong suppression 

of the higher-order Fourier 

harmonics. Normalized intensity Normalized intensity

Qx(Å-1)

(1+-1-)/1++1)

results suggest that the magnetic structure only tracks the gross features of the 

physical structure, i.e. the fundamental period of the physical grating. However, 

it does not track the finer details that are present in the structural data as higher 

order harmonics (Figure 2b), but are very weak in the asymmetry ratio (Figure 

2c).

We are complementing these measurements by using polarized neutron 

scattering, magnetic microscopy, and micromagnetic simulations. This apparent 

smoothing of the magnetic structure must be accounted for in any patterned 

recording media based on this type of technology.
2-82 Soft Condensed Matter and Biophysics 

BEAMLINE X27C

Funding

The National Science Council of Taiwan

Publication

R.-M. Ho, Y.-W. Chiang, C.-C. Lin, and 

B.-H. Huang, “Crystallization and Melting 

Behavior of Poly(ε-caprolactone) under 

Physical Confinement,” Macromolecules, 

38, 4769-4779 (2005).

For More Information

Rong-Ming Ho, Department of Chemical 

Engineering, National Tsing Hua University, Taiwan

Email: rmho@mx.nthu.edu.tw

Crystallization and Melting Behavior of Poly

(ε-caprolactone) Under Physical Confinement

R.-M. Ho1, Y.-W. Chiang1, C.-C. Lin2, and B.-H. Huang2

1

Department of Chemical Engineering, National Tsing Hua University, Taiwan; 2Department of Chemistry, National Chung Hsing University, Taiwan

We studied the crystallization behavior of poly(ε-caprolactone) (PCL) in a physically confined system, the self-assembly of poly(ε-caprolactone)/polystyreneb-poly(ethylenepropylene) (PCL/PS-PEP) blends, using simultaneous smallangle x-ray scattering (SAXS) and wide-angle x-ray diffraction (WAXD). The 

glassy PS-rich phases effectively confined the PCL crystallization due to the 

localization behavior of PCL. Contrary to a typical microphase-separated morphology of semi-crystalline copolymers (i.e. a chemically confined system), the 

physically confined system for the crystallization of PCL provides a representative system for understanding crystallization behavior under spatial confinement. With effective confinement, the crystalline chains of PCL appeared in a 

random orientation at low crystallization temperatures but in a parallel orientation at high crystallization temperatures. 

Crystallization behavior under nanoscale confinement has drawn attention due 

to the necessity of having a basic understanding of crystallization in order to 

develop nanotechnology applications. In particular, the crystallization behavior 

of semi-crystalline block copolymers, in which at least one of the constituted 

blocks is crystallizable, has been thoroughly studied as illustrated in Figure 

1a (namely, a chemical confinement). By contrast, the unique morphology with 

a crystallizable PCL component localized between the lamellar microdomains 

of PS-PEP gives rise to a specific crystallization environment in which the 

crystallization is carried out in a nanometer-scale confined environment without 

the restraint of a chemical connection (Figure 1b, a physical confinement). 

This unique morphology, a crystallizable PCL component localized favorably 

within PS-rich constituted lamellar in a PS-PEP block copolymer, has been 

obtained via melt-mixing in a MiniMax mixer. Shear (velocity), vorticity, and 

velocity gradient directions are labeled x, y, and z, respectively. Two-dimensional SAXS patterns along the x, y, and z directions indicate that microphaseseparated microdomains can be oriented after melt-mixing, as illustrated in 

Figure 2 for PCL11/PS-PEP blends (the Mw of PCL11 is 11000g/mol). Up to 

four orders of lamellar scattering peaks (q/q* = 1 : 2 : 3: 4) can be identified 

when the incident x-ray beams are along x and y, as shown in Figures 2a and 

2b. By contrast, we found no significant scattering peak along the z direction in 

the two-dimensional SAXS pattern (Figure 2c). These two-dimensional SAXS 

results indicate that microphase-separated lamellae of PCL11/PS-PEP are 

aligned parallel to the x-y plane (i.e. the shear plane). Moreover, the oriented 

microphase-separated lamellar microstructure was preserved after PCL crystallization so that the PCL is completely confined in the PS-PEP lamellar layer.

For PCL crystallization at low crystallization temperatures (for instance, at Tc

= 

-20oC), the two-dimensional WAXD patterns exhibit a typical ring pattern in all 

directions, suggesting that PCL crystals appear randomly oriented under confinement. However, a specific orientation of the PCL crystals can be identified 

when the shear-aligned samples are crystallized at high crystallization temperatures (for instance, 40oC). Two-dimensional WAXD patterns along the x and 

y directions are practically identical, and exhibit oriented features (Figures 2d 

Authors (from left) Yeo-Wan Chiang 

and Rong-Ming Ho
Science Highlights 2-83

and 2e). Only an isotropic ring pattern along the z direction was observed (Figure 2f). On the basis of the orthorhombic lattice structure of PCL crystals with a 

unit cell of a=0.749 nm, b=0.498 nm, c=1.703 nm, and α = β = γ = 90o, the corresponding reflections were identified as {110} and {200}. The azimuthal profiles 

(Figure 3a) were obtained from the two-dimensional WAXD pattern (Figure 

2d). The intense {110} diffraction peaks are separated into four diffraction arcs 

and appear at Φ=56o, 124o, 236o, and 304o, and two {200} reflections appear 

at Φ=0o, 180o, respectively. According to the azimuthal results, the diffraction 

pattern is illustrated in Figure 3b. The fiber-pattern-like diffractions suggest a 

parallel-type orientation with PCL crystalline chains parallel to the microphaseseparated lamellae (i.e. the x and y directions). Figure 3c shows the molecular 

disposition of crystalline PCL chains, and indicates their parallel orientation 

at high crystallization temperatures in a physically confined environment. The 

crystalline orientation is strongly dependent upon the crystallization temperature 

under physical confinement. As a result, the orientation of the PCL crystalline 

chain localized between the PS-PEP layers can be thoroughly understood by 

two-dimensional SAXS and WAXD techniques at a synchrotron light source.

Figure 3. (a) Azimuthal scanning 

profiles of the {110} and {200} 

reflections of the WAXD patterns in 

Figure 2d for the PCL11/PS-PEP 

blends isothermally crystallized at 

40 °C. (b) Schematic diagram of 

the WAXD pattern with indexed 

reflections. (c) Schematic 

diagram of the microstructure of 

oriented PCL11/PS-PEP samples 

isothermally crystallized at 40o

C 

from ordered melt at 100o

C. The 

crystallization of PCL is confined 

between the preformed lamellar 

PS layers, and the a and c axes of 

the PCL crystals are preferentially 

parallel and perpendicular to the 

axes of the PS lamellar normal, 

respectively.

Figure 1. Schematic pictures of 

(a) chemical confinement and (b) 

physical confinement.

Figure 2. Simultaneous SAXS 

and WAXD patterns of orientated 

PCL11/PS-PEP samples 

isothermally crystallized at 40o

C 

from ordered melt at 100o

C. 2D 

SAXS (top row) and 2D WAXD 

(bottom row) obtained (a,d) along 

the x-direction, (b,c) along the 

y-direction, and (c,f) along the 

z-direction.

(a) Chemical Confinement

(b) Physical Confinement

Nanometer range

Chemical linkage

Crystalline segment

Amorphous segment

Crystallization

Nanometer range

Amorphous segment

Crystalline segment

Crystallization

(c)

(a) (b)
2-84 Soft Condensed Matter and Biophysics 

BEAMLINE X21

Funding

Marie Curie Program of the European 

Union

Publication

Taco Nicolai, Fabrice Lafleche, and Alain 

Gibaud, "Jamming and Crystallization of 

Polymeric Micelles," Macromolecules, 37, 

8066-8071 (2004).

For More Information

Taco Nicolai, Polymères, Colloïdes, 

Interfaces, UMR CNRS, Université du 

Maine

Email: Taco.Nicolai@univ-lemans.fr

Jamming and Crystallization of Polymeric Micelles

T. Nicolai1, F. Laflèche1, and A. Gibaud2

1

Polymères, Colloïdes, Interfaces, UMR CNRS, Université du Maine, France; 2Laboratoire de Physique de l’Etat 

Condensé, UMR CNRS, Université du Maine, France 

Polymeric micelles formed by hydrophobically end-capped poly(ethylene 

oxide) (PEO) copolymers in water show a discontinuous liquid-solid transition, which occurs above a critical concentration that increases with increasing 

temperature. The solid state contains a body-centered cubic phase in equilibrium with a disordered phase. The fraction of crystalline phase increases with 

increasing concentration and decreasing temperature. A comparison of the 

structure and the rheology during cooling shows that the micelles jam before 

the ordered phase is formed. The discontinuous liquid-solid transition and 

the distinct bcc phase over a wide range of concentrations are not observed 

for true star polymers. The difference is perhaps due to the adjustment of the 

number of arms in the case of close packed polymeric micelles.

Polymeric micelles are formed by the association of block copolymers with a 

relatively small insoluble block. They show an abrupt transition from a freeflowing liquid to solid-like behaviour above a critical concentration or below a 

critical temperature. Generally, liquid crystalline order is observed in the solid 

state. The coincidence between the liquid-solid transition and the appearance 

of liquid crystalline order has induced some authors to conclude that the solidification is a result of micelle ordering. The objective of our work was to investigate in more detail the correspondence between the liquid-solid transition and 

the formation of the ordered phase. 

We studied poly(ethylene oxide) (PEO) with a molar mass of 4500 g/mol that 

was end-capped with octadecyl. In water, this polymer forms micelles containing 24 chains. With increasing polymer concentration, the viscosity increases 

similarly to that observed for equivalent star polymers. However, above a critical concentration that increases with increasing temperature, a discontinuous 

transition is observed and PEO goes from a viscous liquid to a solid that does 

not flow when the sample is tilted. The transition, which can also be observed 

by cooling the sample at a fixed concentration, is fast at temperatures far 

below the critical value, but can take more than 10 hours just below the critical 

temperature. 

Small-angle x-ray scattering (SAXS) shows narrow Bragg peaks in the solid 

state, indicating a body-centred cubic phase. However, the amplitude of the 

peaks is very small when the sample is close to the transition and becomes 

progressively larger with increasing concentration or decreasing temperature. 

The underlying amorphous structure can still be clearly distinguished, showing 

that the solid contains both a crystalline and a disordered phase in equilibrium. 

The position of the Bragg peaks is independent of the temperature, but shifts 

to lower scattering wave vectors with increasing concentration. The concentration dependence of the peak position shows that the aggregation number of 

the micelles in the solid state increases with increasing concentration. 

Figure 1 shows, for the same concentration (300 g/L), a comparison of the 

variation of the shear modulus and the structure factor during a cooling ramp. 

It is clear that the liquid-solid transition occurs at a higher temperature than 

the formation of the bcc phase, even though the cooling rate was much faster 

Authors (from left) Alain Gibaud and 

Taco Nicolai
Science Highlights 2-85

for the shear measurement. This implies that the crystalline phase is formed 

only after the micelles have jammed and, thus, that the formation of the ordered 

structure is not the origin of the liquid-solid transition. 

Polymeric micelles resemble multi-arm star polymers and their behavior is 

similar at low-volume fractions. The viscosity of true star polymer solutions increases steeply above the overlap concentration, but the increase is continuous. 

In addition, liquid crystalline order is rarely, and only with difficulty, observed 

for concentrated star polymers. The essential difference between star polymers 

and polymeric micelles is that in the latter case the number of arms is variable, 

which gives the system an extra degree of freedom to minimize the free energy. 

This is probably the origin of the observed differences.

Figure 1. Comparison of the 

evolution of the shear moduli (top) 

and the SAXS spectra (bottom) 

during cooling for suspensions 

of polymeric micelles at 300g/L. 

The cooling rate for the rheology 

experiment was faster (5 degrees/

min) than for the SAXS experiment 

(less than 1 degree/min).

T(C°)

G',G" (Pa)

q(nm-1)

log (I) (arbitrary units)
2-86 Soft Condensed Matter and Biophysics 

BEAMLINE X3A2

Funding

Eastman Chemical Company

Publication

G.C. Gemeinhardt and R.B. Moore, 

“Characterization of Ionomer Compatibilized Blend Morphology Using Synchrotron 

Small Angle X-ray Scattering,” Macromolecules, 38, 2813-2819 (2005).

For More Information

Robert B. Moore, Department of Polymer Science, The University of Southern 

Mississippi

Email: rbmoore@usm.edu

Characterization of Ionomer Compatibilized Blend 

Morphology Using Synchrotron Small-Angle X-ray 

Scattering

G.C. Gemeinhardt and R.B. Moore

Department of Polymer Science, The University of Southern Mississippi

Synchrotron small-angle x-ray scattering (SAXS) was used to characterize 

the morphology of a non-crystalline polyester/polyamide blend. The blend’s 

components were made compatible via the addition of a sulfonated, polyester 

copolymer (that is also an ionomer). We used a two-component correlation 

function to provide detailed information on the size and structure of the phaseseparated domains. With increasing ionic functionality, achieved by varying either the ion content or the ionomer loading, the sizes of the dispersed domains 

in the blends decreased. In addition, SAXS analysis of the 50/50 blend series 

indicated that the ionic incorporation led to a shift in the morphology to a more 

elongated, co-continuous structure.

While small-angle laser light scattering (SALS) has often been used to investigate the micro-scale phase separation of polymer blends, small-angle neutron 

scattering (SANS) and small-angle x-ray scattering (SAXS) are particularly 

useful in the study of these complex heterogeneous systems due to their ability to probe much smaller size scales. Although SANS has been used to probe 

information such as the radius of gyration, correlation lengths, and Flory-Huggins interaction parameters of blend components, recent reports have outlined 

the advantages of using synchrotron SAXS to measure these important blend 

parameters. The advantages of using SAXS over SANS include: the elimination of isotopic labeling, the high intensity/resolution that allows for fast data 

collection, and the ability to dynamically examine the phase-separation process in real time.

In the area of blend compatibilization, research efforts using SAXS have been 

primarily limited to studying the effect of block copolymers on blend morphology and interfacial properties. Here, we describe our efforts to apply synchrotron SAXS to an amorphous polyester (PETG)/polyamide (T40) blend system. 

This system is compatibilized through the incorporation of an ionomer (known 

as SPETG) that bears charged groups capable of forming strong, specific 

intermolecular interactions with the uncharged, polar blend components. In 

these blends, the specific interactions (Figure 1) act at the interface to lower 

the interfacial tension and thereby lower the domain size of the dispersed 

phase.

With SAXS, we investigated the morphological features of the blends using 

the Debye-Bueche scattering theory, employing a two-parameter correlation 

function. The resulting scattering curves of the binary blends are shown in Figure 2. The solid lines represent the nonlinear regression fits (using the inset 

equation) to the scattering data and show the excellent agreement between 

the theoretical and experimental curves. As shown in the inset graph, the twoparameter correlation function divides the scattering into contributions from 

short-range (a1) and long-range (a2) fluctuations present in the system. The 

relative contribution of each is described by the fractional contribution term, f. 

In comparison to the blend with pure PETG, the scattering curves for the 

Authors (from left) Robert Moore and 

Greg Gemeinhardt
Science Highlights 2-87

SPETG/T40 samples show a prominent increase in intensity at small values 

of q. This scattering behavior indicates a decrease in the dimensions of the 

dispersed phase with the incorporation of functional groups capable of forming 

intermolecular interactions. From the fits for the SPETG/T40 blend series, the 

short-range correlation length decreases by 17.6% with increasing ion content, 

which indicates that the size of the minor phase domain becomes smaller with 

increasing ion content. In contrast, the long-range correlation length remains 

relatively constant, while the interfacial surface area of the minor phase (calculated from the volume fractions and values of a1) increases dramatically with 

increasing ion content. These trends suggest that the minor phase adopts a 

more elongated structure and indicate the onset of dual-phase continuity with 

increasing ion content. A SAXS analysis of the ternary blends containing less 

than 10% ionomer indicates that these blends behave like the binary blends with 

varying ion content, as both methods of blending vary only the concentration of 

ionic functional groups in the blend.

Figure 2. SAXS profiles for the 

50/50 polyamide/polyester binary 

blends: T40/PETG (•), T40/

1.9SPETG (▼), T40/3.0SPETG 

(■) and T40/5.5SPETG (♦). Lines 

represent the fits to the data from 

the nonlinear regression analysis 

using the inset equation. The 

inset graph shows the relative 

contribution of the short-range and 

long-range correlation terms in the 

nonlinear regression analysis of the 

measured intensity profiles.

Figure 1. Role of the ionomer 

(SPETG) in the compatibilization 

of 50/50 blends of polyamide(T40) 

and polyester(PETG) binary system. 

Optical micrographs (left) show 

that the ionomer yields a profound 

decrease in dispersed phase size 

(i.e., below the resolution limit of 

visible light microscopy/scattering 

methods).

Ionomer Compatibilization

Through Specific Interactions

Interface/Interphase

With 3 mol% Ionomer

q(nm-1)

Iq(cm-1)

q(nm-1)

Iq(cm-1)

0.05 0.10 0.15 0.20 0.25

1200

1000

800

600

400

200

0
2-88 Soft Condensed Matter and Biophysics 

BEAMLINE U7A

Funding

National Science Foundation, Office of 

Naval Research

Publication

L. Andruzzi, A. Hexemer, X. Li, C. Ober, 

E. Kramer, G. Galli, E. Chiellini, and D. 

Fischer, "Control of Surface Properties 

Using Fluorinated Polymer Brushes 

Produced by Surface-Initiated Controlled 

Radical Polymerization," Langmuir, 20, 

10498-10506 (2004).

For More Information

Christopher Ober, Francis Norwood Bard 

Professor of Materials Engineering, Cornell University

Email: cober@ccmr.cornell.edu

Control of Surface Properties Using Fluorinated 

Polymer Brushes Produced by Surface-Initiated 

Controlled Radical Polymerization

L. Andruzzi1, A. Hexemer2, X. Li1, C.K. Ober1, E.J. Kramer2, G. Galli3, E. Chiellini3, and D. Fischer4

1

Cornell University; 2University of California; 3Università di Pisa; 4National Institute of Standards and Technology

Fluorinated polymers possess the important technological property of having 

very low surface energy. One familiar fluoropolymer is Teflon. When a surface 

prepared using a polymer that contains a fluorinated component is thermally 

annealed above its glass transition temperature, the low-energy fluorinated 

component will migrate to the air-coating interface. We are interested in fluorinated block copolymers for the creation of environmentally friendly, foulingresistant coatings for marine applications. Anyone who owns a boat will know 

that it can quickly foul, that is, its hull can become coated with a biofilm created by marine flora and fauna. Fluoropolymers may permit the easy removal 

of foulants without the need for the toxic materials presently used in marine 

coatings. In a prime candidate for such a coating, surface segregation of a 

fluorinated block in a block copolymer can be effectively studied by near-edge 

x-ray absorption fine structure (NEXAFS) and detected by the presence of a 

sharp peak at 292.0 eV due to the C 1s → σ*C−F transition in the spectrum of 

Auger electron yield versus energy of the incident x-ray photon. In collaboration with researchers from the National Institute of Standards and Technology 

(NIST), NEXAFS studies are proving vital in understanding the surface properties of fluoropolymers.

Grafting a fluoropolymer to a surface seems like an ideal way to coat a substrate with a low-energy polymer. When a block copolymer containing a 

polystyrene block and a fluorinated block has the free end of the polystyrene 

block tethered to a substrate, and is then annealed under vacuum, there are 

surprising results. The mobility of the fluorinated block is so restricted due to 

chemical bonding with the surface that the air-polymer interface is populated 

with the higher surface-energy polystyrene block. These were some of the 

important findings in the paper by Andruzzi et al. [L. Andruzzi, A. Hexemer, 

X. Li, C. K. Ober, E. J. Kramer, G. Galli, E. Chiellini, D. A. Fisher, Langmuir,

20, 10498-10506 (2004)]. Andruzzi and coworkers prepared fluorinated block 

copolymer brushes using surface-initiated controlled free radical polymerization. The polymerization reactions were set into motion by initiator molecules 

covalently bound to a silicon substrate. The thicknesses of the brushes were 

found to be greater than the radius of gyration of the block copolymer molecules. This indicated that the tethered polymer chains were densely packed on 

the surface and were in a stretched configuration. The dense packing was also 

evident when a surface with a tethered polystyrene block and a free fluorinated 

block had a NEXAFS spectrum almost identical to a fluorinated homopolymer 

surface. In other words, the polystyrene block in this case was hidden below at 

least the top 3 nm of the surface, the depth probed by NEXAFS. This was also 

confirmed by x-ray photoelectron spectroscopy measurements. 

The fluorinated block copolymers we studied are unique because of their 

liquid crystalline properties. The fluoroalkyl side-chains of the block copolymer formed a liquid crystalline phase at the surface, with the -(CF2)- helices 

oriented at an angle to the surface. This orientation was quantified from the 

observed variation in the intensities of the peak at 292.0 eV with the angle of 

Authors (from left) Alex Hexemer and 

Daniel Fischer
Science Highlights 2-89

incidence of the x-ray beam on the surface. We found that a longer fluorinated 

block resulted in a higher-order parameter of the -(CF2)- helix. The well-packed 

fluorinated brushes showed a remarkable stability against reconstruction of the 

non-polar surface when immersed in a polar environment such as water. There 

was only a small decrease in the water contact angle when the surfaces were 

immersed in water for a week.

We propose that, in addition to their fouling-resistant properties, surfaces bearing tethered fluorinated polymer brushes could be used to fabricate analytical 

devices for microbiology studies, and to create devices for the separation or 

microfiltration of proteins.

Figure 2. Carbon K-edge NEXAFS 

spectra of (a) fluorinated brush, 

(b) block copolymer brush with 

polystyrene block tethered to 

surface, (c) block copolymer brush 

with fluorinated block tethered to 

surface, and (d) polystyrene brush.

Figure 1. Synthesis of surfacegrown fluorinated block copolymer 

brushes.

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PEY (a.u.) PEY (a.u.) PEY (a.u.) PEY (a.u.)

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(b)

(c)

(d)
Year in Review
NSLS Engineer John Skaritka Wins BNL’s 

Engineering Award

January 26, 2005

At the BNL Employee Recognition 

Award Ceremony held on January 

26, 2005, NSLS engineer, John 

Skaritka was presented with a 2005 

Engineering Award by BNL’s Deputy 

Director for Operations, Michael 

Bebon. The award, consisting of 

a plaque and $5,000, was also 

presented to BNL employees Ove 

Dyling, Joseph Harder, and Alan 

Raphael.

The award recognizes distinguished 

contributions to BNL’s engineering and computing objectives 

over one or more years. Contributions may be in any engineering or computing discipline. Nominees are evaluated on the 

exceptional nature and level of difficulty of the contributions as 

well as their benefit to the Lab. 

John Skaritka was cited for a body of work that contains semiShort Course Participants Learn the Value of 

Synchrotron Light for Powder Diffraction

January 25-27, 2005

Fifteen participants recently attended the High Resolution 

Powder Diffraction Data Collection and Analysis Short Course, 

which was held at the NSLS from January 25-27, 2005. The 

3-day course consisted of lectures, guest talks, hands-on data 

collection, and data analysis, and was co-organized by Peter 

Stephens (Stony Brook), Christie Nelson (NSLS), and ChiChang Kao (NSLS), with administrative support provided by 

Corinne Messana (NSLS).

The 15 participants included graduate students, post-docs, and 

scientists from national labs and universities. While most of the 

students were familiar with lab-based powder diffraction techniques, very few had synchrotron experience. The participants 

were all quite eager to learn about the impact that synchrotronbased powder diffraction could have on their own research.

The lectures were presented by Peter Stephens, Pat Woodward (Ohio State), and John Parise (Stony Brook), and covered 

the basic physics of powder diffraction, experimental aspects 

of data collection, Rietveld refinement, and indexing. In addition, specialized talks on cutting edge research on high-pressure, high-temperature, and time-resolved powder diffraction 

were given by guest speakers Yongjae Lee (BNL-CMP), Cam 

Hubbard (ORNL), and Jonathon Hanson (BNL-Chemistry), 

respectively.

The hands-on data collection component of the course was 

carried out on NSLS 

beamlines X3B1, 

X7A, and X14A, with 

beamline instructors 

Peter Stephens, 

Yongjae Lee, and Jianming Bai (ORNL), 

respectively. The 

participants first 

learned about beamline operation and 

sample preparation, 

and then collected 

data from a corundum standard. 

Next, the participants collected 

high-resolution data 

from samples of 

interest in their own 

research projects.

In addition to the 

lectures and data 

collection, the participants also spent time learning about data 

analysis techniques. “Homework” assignments included refining the corundum standard data as well as additional data sets,

and then students tackled the data obtained from their own 

samples. The participants were greatly aided in the completion 

of these tasks by their three lecturers.

At the end of the intensive three-day course, the participants 

left with a foundation of knowledge about applying high-resolution powder diffraction to their own research projects. Many 

expressed interest in becoming NSLS general users, and we 

look forward to seeing them back here soon.

The organizers would like to thank the lecturers, guest speakers, beamline instructors, Elaine Dimasi (NSLS), Jae-Hyuk Her 

(Stony Brook), Corinne Messana, and the NSLS User Administration Office and safety staff for all of their help in making the 

short course such a success.

— Christie Nelson

Participants of the 2005 High Resolution Powder Diffraction Data Collection and 

Analysis Short Course

Data collection at beamline X3B1

Setting up at beamline X7A

John Skaritka

Year in Review 3-3
3-4 NSLS Activity Report

Unique Global Light Source Website 

Launched 

February 17, 2005 

On February 17, 2005, the international light source community 

launched the first website dedicated to providing the media, 

general public, and scientific community with the latest news 

and information on the world’s accelerator-driven light sources 

(synchrotrons and free-electron lasers) and the science they 

produce. 

The web site — 

www.lightsources.org

— was developed and is 

jointly maintained by the 

Light Source Communicators Group, whose members represent the world's 

light source facilities in 

Europe, North America and Asia. Funding for the project is 

provided by science funding agencies of many nations.

Accelerator-driven light sources can be large, roughly circular

machines or linear machines (usually about the size of a football field to much larger) that accelerate electrons to almost the 

speed of light. They act like gigantic microscopes that generate 

intense beams of brilliant light to view the microstructure of 

materials.

Light sources around the world are advancing research and 

development in fields as diverse as medicine, drug design, 

nal as well as sustained contributions. His many achievements 

speak collectively to outstanding breadth, creativity, drive, and 

dedication in support of BNL missions.

Skaritka was the sole mechanical engineer for BNL’s Accelerator Test Facility (ATF) for many years, making key contributions 

to the design of elements of the accelerator and experiments 

that were essential to the success of those projects. He contributed to the design of ATF Gun III and Gun IV, regarded now 

as standard in the world and running at many other facilities.

He was also the mechanical engineer in charge of coordinating 

all mechanical design, fabrication, and installation activities at 

the Source Development Laboratory, resulting in a state-of-the 

art facility that produced both a self-amplified spontaneous 

emission free electron laser and a high gain harmonic generation free electron laser.

Skaritka is also known for his considerable talent in supporting 

the NSLS User Science programs, recently, for example, in 

the construction of a unique instrument pivotal in research on 

three-dimensional strain mapping to study crack propagation 

and fatigue failure in alloys.

— Liz Seubert

environmental science, agriculture, minerals explorations, 

advanced materials, forensics, engineering, and materials 

fabrication.

Visit www.lightsources.org for the latest news releases on 

cutting-edge areas of advanced light source applications for 

science and technology from facilities around the world.

Anyone can subscribe free of charge to “News Flash,” which 

will email subscribers when news releases and other light 

source information are posted to the website. Also available on 

the website are an image bank of light source-related photos 

and graphics, clippings of news stories, links to light source 

facility websites, and relevant articles and presentations. 

Educators will find links to websites relating to light sources 

and the science conducted at these facilities. Researchers 

can find specific information regarding each light source facility, including job opportunities and events related to science 

outreach activities.

Sponsors of this collaborative project include:

• Advanced Light Source (ALS)

• Advanced Photon Source (APS)

• Canadian Light Source (CLS) 

• ELETTRA (Sincrotrone Trieste)

• European Synchrotron Radiation Facility (ESRF)

• Hamburger Synchrotronstrahlungs Labor (HASYLAB)

• National Synchrotron Radiation Research Center 

 (NSRRC)

• National Synchrotron Light Source (NSLS)

• Photon Factory (KEK Laboratory)

• Pohang Light Source (PLS)

• Stanford Synchrotron Radiation Laboratory (SSRL)

• SPring-8 

• Synchrotron Radiation Center (SRC)

• Synchrotron Ultraviolet Radiation Facility (SURF III)

• Swiss Light Source (SLS)

• The Free-Electron Laser at the Thomas Jefferson National 

 Accelerator Facility (JLab)

X6A Workbench Provides Hands-On Training in Synchrotron Crystallography

March 1-4, 2005

Beamline X6A, the National Institute of General Medical Sciences facility at the National Synchrotron Light Source, offers 

comprehensive hands-on training in synchrotron data collection and analysis for biophysicists, biochemists, and molecular

biologists.
The first “The X6A 

Workbench: Advanced 

Structural Biology Tools” 

workshop took place this 

year from March 1-4. 

Participants practiced 

cryogenic protection of 

their samples and learned 

how to load sample 

cassettes for the X6A automounter. The program 

followed with hands-on 

crystallography data 

collection and analysis. 

Molecular replacement 

and multiwavelength 

anomalous diffraction 

(MAD) software suites were discussed. Participants screened 

their own samples and applied the new data-analysis concepts 

introduced during the workshop. 

The X6A workbench is regularly offered throughout the year. 

The other three workshops were held on April 26-29, July 12-

15, and October 25-28. For more details and registration information, go to: http://protein.nsls.bnl.gov/news/workbench.php.

— Vivian Stojanoff

X6A Workbench: Advanced Structural 

Biology Tools workshop participants

BNLers Help Promote Community Interest 

in Science

March 4, 2005

Two BNL “Peters” — Peter Wanderer of the Superconducting 

Magnet Division and Peter Takacs of the Instrumentation Division — are not only passionate about doing their own science 

but also about spreading the fascination of science to others in 

the community. That’s how they came to join a group of people 

who formed a board and set up the Long Island ScienCenter, a 

new science museum in Riverhead.

“It’s been a busy time,” says Wanderer. “We are still working on 

the museum and getting more exhibits.” Through the BNL Science Museum, some key current exhibits have been lent to the 

ScienCenter by the Lab, for example, the Videosphere.

“The BNL Science Museum staff and directors, first Janet Tempel, then Dolores O’Connor, and now, Gail Donoghue, have 

been very helpful,” Wanderer says.

Another BNLer, retiree Marty Woodle, now a National Synchrotron Light Source Department guest scientist, is a keen 

ScienCenter supporter. Woodle most recently volunteered his 

help with a bridge-building program held in late February.

“This March, the ScienCenter is presenting an adult lecture 

series open to the public, with three interesting talks,” says 

Takacs. “I believe people at BNL would enjoy them.”

Three LI ScienCenter Lectures, March 4, 11, and 18 were:

• March 4: “Wine: Science or Magic,” Louisa Thomas Hargrave, 

founder of the first winery on Long Island.

• March 11: “The History and Destiny of Fisheries near Long 

Island and in the World,” Carl Safina, President, Blue Ocean 

Institute, Cold Spring Harbor.

• March 18: “The Adventure of Wildlife Photography,” George 

Loweth, professional photographer.

— Liz Seubert

Three BNLers who volunteer time with the Long Island ScienCenter are (from 

left) Peter Takacs, Marty Woodle, and Peter Wanderer, who are examining model 

bridges used for demonstration during a recent bridge-building program at the 

ScienCenter. The bridges are loaned by BNL’s Office of Educational Programs 

(OEP), examples of previous years’ bridges made for BNL’s annual high-school 

model bridge-building contest. Woodle, a founder technical advisor in the 

organization of the contest, helped OEP in this past year’s event that was held 

on March 12.

Scientists Create, Study Methane Hydrates in 

“Ocean Floor” Lab

Data may help develop strategies for mining natural gas 

locked up in seafloor sediments

March 13, 2005

Scientists at BNL have recreated the high-pressure, low-temperature conditions of the seafloor in a tabletop apparatus 

for the study of methane-hydrates, an abundant but currently 

out-of-reach source of natural gas trapped within sediments 

below the ocean floor. Michael Eaton, a Stony Brook University 

graduate student working for Brookhaven chemist Devinder 

Mahajan, presented a talk outlining the use of the apparatus 

for the creation and study of methane hydrates during a special

two-day symposium co-organized by Mahajan at the 229th National Meeting of the American Chemical Society in San Diego, 

California. The talk took place on Sunday, March 13, at 3:05 

p.m. in room Madeleine C-D of the Hyatt Regency. 

“The amount of natural gas that is tied up in methane hydrates 

beneath the seafloor and in permafrost on Earth is several 

orders of magnitude higher than all other known conventional 

Year in Review 3-5
3-6 NSLS Activity Report

Devinder Mahajan (left) and Michael Eaton

sources of natural gas — enough to meet our energy needs for 

several decades,” Mahajan says. But extracting this resource 

poses several challenges. 

For one thing, methane hydrates — which are ice-like cages 

made of water molecules surrounding individual methane 

molecules — are only stable at the very low temperatures and 

high pressures present at the ocean floor. “If you try to bring it 

up, these things fizzle and decompose, releasing the trapped 

methane,” Mahajan says. 

So a multi-agency team led by the Department of Energy — as 

part of its mission to secure America’s future energy needs 

— is trying to learn about the conditions necessary for keeping

hydrates locked up so they can be extracted safely and tapped 

for fuel. 

Mahajan’s group has 

built a vessel that 

mimics the seafloor 

temperature and pressure conditions, where 

they can study the 

kinetics of methane 

hydrate formation and 

decomposition. Unlike 

other high-pressure 

research vessels, the 

Brookhaven apparatus 

allows scientists to 

interchange vessels 

of different volumes, 

study even fine sediments, and visualize 

and record the entire 

hydrate-forming event 

through a 12-inch window along the vessel. In addition, massbalance instrumentation allows the Brookhaven group to collect 

reproducible data in the bench-top unit. Even better, Mahajan 

says, they can study the kinetics in actual samples of sediment

that once contained hydrates — as close to the natural conditions as you can get in a lab. 

“You fill the vessel with water and sediment, put in methane 

gas, and cool it down under high pressure. After a few hours, 

the hydrates form. You can actually see it. They look like ice, 

but they are not. They are stable at 4 degrees Celsius,” he 

explains. 

One further advantage of doing this work at Brookhaven Lab 

is that the scientists can use the NSLS — a source of intense 

x-rays, ultraviolet, and infrared light — to measure physical 

characteristics of the sediments under study. Using x-ray computed microtomography, the scientists gain information about 

the porosity and other physical characteristics that may affect 

the availability of nucleation sites where hydrates can form. 

Such data about hydrate formation in natural host sediment 

samples are scarce. By studying different samples and learnCeria Nanoparticle Experiments at NSLS 

Promise Cleaner Fuel Future

March 15, 2005

Experiments on ceria (cerium oxide) nanoparticles carried 

out at BNL may lead to catalytic converters that are better at 

cleaning up auto exhaust, and/or to more-efficient ways of 

generating hydrogen — a promising zero-emission fuel for the 

future. Jose Rodriguez of the Chemistry Department presented 

results from two studies exploring the composition, structure, 

and reactivity of these versatile nanoparticles during the 229th 

National Meeting of the American Chemical Society on March 

15 in San Diego, California. This research was funded by the 

Office of Basic Energy Sciences within DOE’s Office of Science.

After using a novel technique to synthesize the ceria nanoparticles, Rodriguez and coworkers Xianqin Wang and Jonathan 

Hanson, also both of Chemistry, used beams of x-rays at the 

NSLS to study how their composition, structure, and reactivity 

changed in response to doping with zirconium in one case, and 

impregnation with gold in another.

“In a catalytic converter, ceria acts as a buffer, absorbing or 

releasing oxygen depending on the conditions of the engine 

to maintain the catalyst in its optimum operating condition for

converting harmful emissions such as carbon monoxide and 

nitrogen oxide to carbon dioxide and nitrogen gas,” Rodriguez 

said. Others have found that adding zirconium improves ceria’s 

ability to store and release oxygen.

The studies at the NSLS explain why zirconium changes 

ing what combinations of pressure and temperature keep the 

methane locked up, the scientists hope to identify ways to compensate for the changes the hydrates experience as they are 

brought to the ocean’s surface so they can be extracted with a 

minimum loss. The comparisons of different sediment samples 

might also help pinpoint the most abundant sources of lockedup methane. 

“It may be at least a decade before we can even think about 

mining these deposits, but answering these fundamental questions is certainly the place to start,” says Mahajan, who holds 

a joint appointment as a Stony Brook University professor. 

“This is a very important issue tied to our future national energy 

security.” 

This research was initially funded by Brookhaven’s Laboratory Directed Research and Development program and is now 

funded by the Department of Energy’s Office of Fossil Energy. 

The symposium on Gas Hydrates and Clathrates was co-sponsored by the Petroleum and Fuel Divisions of the American 

Chemical Society.

— Karen McNulty Walsh
Jose Rodriguez

Jonathan Hanson

Xianqin Wang

What Do You Do At Work? 

Tom Seda: Bringing Bright Ideas to the Light Source

March 18, 2005 

This story was the first in a series entitled “What Do You Do at 

Work?” featuring BNL employees and their jobs at the Lab. 

When I first came to BNL in 1992, I was told that I’d be working 

on everything from plumbing to programming,” said Tom Seda, 

then a principal technician for the Power Systems Group at 

NSLS, specializing in the Linac, the linear accelerator that 

supplies the initial high energy electrons for the NSLS. 

While Seda has not yet worked on plumbing on the job, he 

has constructed and programmed a single-chip programmable 

logic device (PLD) to handle the timing that controls the Linac’s 

electron gun. The PLD replaces three logic chassis that control 

the release of electrons from the electron gun, the origin of 

electron bunches for x-rays, infrared light and ultraviolet light 

for experiments at the NSLS. 

Seda is now a senior technical specialist assigned to the 

Operations Group at the NSLS and his primary task is to 

work on a new design for the extraction magnets of the NSLS 

Booster Ring. The current magnets — which kick electron 

bunches at an energy of 800 MeV into the NSLS storage rings, 

where the energy is ramped up to 2.8 billion eV — are encased 

in a vacuum chamber. 

“The problem with the 

current design is the 

short power pulse has 

to be fed through long 

conductors to get into 

the vacuum-encased 

pulse magnet, known 

as a kicker. That’s 

not an efficient way 

to bump the beam,” 

Seda said. “I’m going 

to try to redesign the 

system with the pulse 

magnet outside the 

vacuum chamber. 

That would make 

storing the beam 

much less troublesome.” 

The kicker magnets date back to 1983, when the Booster was 

built, and they are constructed with the standard ferrites that

were available at the time. Seda is now investigating newer 

ferrites for these magnets — specific ferrite alloys currently 

manufactured for the next generation high-energy accelerators. 

“We may be able to reconfigure our current bunch patterns with 

the faster kicker magnets,” he said.

“I’m researching the current papers on kicker designs as well 

as speaking with the scientist and design engineers at other 

national laboratories,” said Seda. “They have been very helpful

in identifying vendors who may have the materials and manufacturing skills needed for the new design.”

In the past, Seda had constructed and tested a new modulator 

for the Deep Ultraviolet Free Electron Laser energy upgrade, 

and he worked on two klystron units in the accelerator Test 

Facility, which supply RF power to a linear accelerator for 

advanced laser experiments. Among his suggestions was to 

replace the PCB-contaminated oil in the klystrons with biodegradable oil.

Tom Seda

the ceria’s structure to increase 

the number of oxygen “vacancies” 

— or places for oxygen uptake and 

release.

Furthermore, Rodriguez said, “The 

ceria nanoparticles we studied have 

much better performance, higher 

chemical reactivity, than the bulk 

form of ceria currently used in catalytic converters.”

Thus, this research holds promise 

for more efficient catalytic converters 

— and cleaner air.

In the second study, Wang, Hanson, 

and Rodriguez deposited gold on the 

surface of ceria nanoparticles and 

used x-rays at the NSLS to determine the catalyst’s “active phase” 

— the conformation responsible for 

the catalytic activity — in the conversion of water and carbon monoxide 

to hydrogen gas and carbon dioxide.

This “water-gas shift” reaction is 

important for generating hydrogen, 

which can be used for chemical 

transformations and as a fuel in a 

hydrogen-based economy. Hydrogen 

is one of the leading energy sources 

being investigated by scientists 

sponsored by DOE as part of its 

mission to ensure the nation’s future 

energy needs.

“In both cases, we are learning about 

the fundamental conditions necessary for optimal operation of the catalysts,” Rodriguez said. 

“This kind of knowledge eventually will lead to a rational design 

of even more effective catalysts.” 

— Karen McNulty Walsh

Year in Review 3-7
3-8 NSLS Activity Report

Seda also helped to test the Marx generator section of the 

Sandia Pulser Terra Watt Laser, which BNL tested for DOE’s 

Sandia National Laboratory. For his exceptional job performance on this project coupled with helping recover the NSLS 

after only one week of downtime due to an equipment fire, he 

is a two-time winner of the BNL Spotlight Award.

“Working as a technician at the NSLS brings opportunities to 

be involved in all aspects of electronics, with the added benefit 

of being involved in interesting and ever-changing projects,” 

Seda commented. “I love working firsthand with these amazing 

machines along with dedicated, talented employees who often 

go beyond what is expected of them on the job.”

Born in the Philippines, Seda, who is of Puerto Rican and 

Filipino descent, immigrated to the Bronx, NY, with his family 

when he was an infant. The first in his family to earn a college 

degree, he received a B.S. in electronic engineering technology from the DeVry Institute of Technology, Chicago, Illinois, in 

1988. He then worked as a technician at Magnetico of Holtsville, NY, where his responsibilities included designing custom 

military-grade transformers and inductors, before he joined 

BNL in February, 1992.

Seda is married to Anna Seda, an administrative assistant in 

the Energy Sciences & Technology Department. The couple 

has an 8-year-old son and a 2-year-old daughter. Tom Seda is 

the president of the BERA Camping Club, and both Anna and 

Tom Seda are participants in the BERA kickboxing class offered on site. In addition, he and his wife enjoy traveling abroad 

and going on cruises.

— Diane Greenberg

Brookhaven Town Honors Two BNL 

Scientists

March 22, 2005

Two BNL scientists — Rita Goldstein and Lisa Miller — were 

among 11 women honored for their accomplishments at the 

Brookhaven Town-sponsored Women’s Recognition Night at 

Brookhaven Town Hall on March 22. Goldstein and Miller were 

recognized for their contributions to science in the Town ceremony, which celebrates National Women’s History Month.

Lisa Miller, a biophysicist at the NSLS, uses infrared light and 

x-rays at the NSLS to study the chemical composition of bone 

tissue in diseases such as osteoarthritis and osteoporosis. She

also investigates protein-folding diseases, such as Alzheimer’s 

disease and scrapie, the sheep form of mad cow disease, in 

which specific proteins in the brain fold into incorrect shapes 

and cause damage to brain cells.

Miller also plays an important role in science education and the 

public understanding of science. She often mentors students 

from high school to the postgraduate level. In addition, Miller

is responsible for outreach activities on behalf of the NSLS, 

including publications, the website and tours. For example, she

organizes an annual open house at the NSLS for BNL’s Summer Sundays, when the Lab’s facilities are open to the public.

“I am very pleased to receive this honor from Brookhaven 

Town,” Miller said. “I’m glad that my research is recognized, 

and I am happy that many of 

the students I’ve mentored 

have chosen to pursue scientific careers.”

Miller earned a B.S. in 

chemistry from John Carroll 

University in 1989, an M.S. in 

chemistry from Georgetown 

University in 1992, and a 

Ph.D. in biophysics from the 

Albert Einstein College of 

Medicine in 1995. After serving as a postdoctoral fellow at 

Lawrence Berkeley National 

Laboratory and BNL, she 

joined BNL in 1999 as an assistant biophysicist, and she was 

promoted to biophysicist in 2003. Since 2002, she also has 

been an adjunct assistant professor in Stony Brook University’s 

Department of Biomedical Engineering.

This year, Miller was invited to serve on the scientific advisory 

committee of the Canadian Light Source, a role served only 

by world-class scientists. For her work with students, Miller 

received DOE’s Outstanding Mentor Award in 2002.

— Diane Greenberg

Lisa Miller

EnviroSuite: Environmental Science at the 

NSLS

March 30, 2005

Created in response to rapidly growing interest in environmental synchrotron science, the EnviroSuite Strategic Initiative 

is designed to support and develop a suite of state-of-the-art 

resources at the NSLS for molecular environmental science 

research. Its mission is to optimize and expand synchrotronbased techniques for exploring environmental questions, to 

establish substantial involvement in several beamlines to bring

a multifaceted approach to complex environmental processes, 

and to introduce new users to these capabilities at the NSLS. 

EnviroSuite now provides a unified voice for the diverse community of environmental science users. 

EnviroSuite is coordinated by the Environmental Research and 

Technology Division of BNL's Environmental Sciences Department, and is funded by the DOE Office of Biological & Environmental Research, Environmental Remediation Sciences 

Division (BER:ERSD). Similar programs have been initiated 
Crystallographers Bloom at RapiData 2005

April 5-11, 2005

Once again in the spring, nearly 50 budding crystallographers 

from around the world gathered at Brookhaven National 

Laboratory for RapiData 2005, a week-long course designed to 

introduce students to the best people, newest equipment, and 

latest techniques in the field of macromolecular x-ray crystallography.

The course is offered annually by Brookhaven’s Biology and 

NSLS departments, and is always a successful event for participants and instructors alike. In 2005, it ran from April 5 to 11.

The course began with two days of lectures and tutorials 

taught by scientists from Brookhaven, industry, academia, and 

other national labs. Then, the instructors and other participants 

guided the students through a marathon, 60-hour data-collection session on eight NSLS beamlines. Half of the 48 students 

came with their own specimens to analyze, while the other half 

learned as observers. Six students left with solved structures 

that may be publishable in scientific journals.

The course was organized primarily by Bob Sweet and Denise 

Robertson of Biology. However, they emphasize that its success absolutely depended on enthusiastic help from most of 

the 24 members of the PXRR (the Biology and NSLS Macromolecular Crystallography Research Resource), NSLS staff 

members, and several outside teachers.

The majority of the funding for the course comes from the 

National Institutes of Health’s National Center for Research 

Resources and the Office of Biological & Environmental 

at all four DOE synchrotron facilities. Its BNL core consists 

of a number of environmental scientists, who work closely 

with the NSLS and with CEMS, the NSF/DOE-funded Center 

for Environmental Molecular Science based at Stony Brook 

(www.cems.stonybrook.edu). 

EnviroSuite is taking an active role in both PRT and NSLS 

facility beamlines, in order to direct the course of beamline 

development and harness the resources to conduct leading 

research. As a result, both capital funding and scientific staff 

have been brought to the NSLS. Some of these are described 

in more detail below. In addition, a key goal of the EnviroSuite 

program is to establish the framework for multi-beamline studies, such as combining bulk EXAFS with microspectroscopy 

and imaging of elemental and species distributions. 

NSLS facility beamline X27A, a new hard X-ray microprobe 

beamline, was highlighted in the December 2004 NSLS Newsletter. It has a 5x15 μm spot size at 3.5 - 32 keV, a 13-element solid state detector, and control software modeled after 

the beamline X26A system. EnviroSuite collaborated with the 

NSLS, X26A, and CEMS for the design and commissioning of 

X27A, and provided the detector. This beamline will greatly 

increase available microbeam resources at the NSLS. Environmental applications include X-ray fluorescence microanalysis of trace elements, mapping of their distribution, and 

microspectroscopy. 

Beamline X11 is one of 

the most scientifically 

productive and historically important beamlines at the NSLS, being 

used primarily for bulk 

EXAFS experiments. It 

has an unfocused beam 

(0.5x10 mm), and operates in the energy range 

from 4.5 - 35 keV. It is 

versatile, and can accommodate a variety of 

sample types as well as 

in-situ studies. EnviroSuite is adding a new 

13-element Ge detector 

to X11A, to enhance its 

capabilities for low-concentration and otherwise 

challenging environmental samples. Detector 

capability at X11B will 

also be upgraded. 

Beamline X15B is 

designed for low- to medium-energy bulk and surface XAS 

(optimized for 1.7 - 5 keV). It has a 1 mm focused spot size, 

and can address samples in ultra-high vacuum or air/He 

atmosphere. Current research includes phosphorus, sulfur, 

and silicon K-edge, cadmium L-edge, and uranium and lead 

M-edge spectroscopy. 

Beamline X1A is a soft X-ray beamline used for scanning transmission x-ray spectromicroscopy. Its primary emphasis is on 

organic materials at the carbon and oxygen absorption edges. 

With a resolution of ~30 nm, X1A is well-suited for imaging 

molecular chemical features on a sub-cellular scale, such as 

for research exploring mechanisms of biotransformation of radioactive and toxic species. Recent upgrades include a BER:

ERSD-funded laser interferometer. 

EnviroSuite provides guidance for new and experienced 

general users with environmental science research at these 

and other beamlines. BNL Environmental Science Department 

resources include laboratory facilities for handling radioactive 

and hazardous materials and wastes, and for sample preparation. Experimental protocols are being developed to facilitate

safe handling and analysis of samples containing radionuclides. For further information, see the EnviroSuite web page 

(www.bnl.gov/envirosuite) or contact Jeff Fitts (fitts@bnl.gov). 

— Paul Northrup

Environmental scientists (from left) Jeff Fitts 

(EnviroSuite Coordinator), Mark Fuhrmann 

(X11 Spokesperson), and Paul Northrup 

(X15B Spokesperson) at the X15B end 

station.

Year in Review 3-9
3-10 NSLS Activity Report

Participants in the RapiData 2005 Macromolecular Crystallography course

CFN Site Dedication Draws Special Guests 

to the NSLS

April 15, 2005

Several distinguished guests visited the NSLS on April 15 as 

part of activities for the Center for Functional Nanomaterials 

(CFN) site dedication ceremony. The guests included Congressman David Hobson, Chairman of the Energy and Water 

Development Appropriations Subcommittee in the House of 

Representatives; Congressman Tim Bishop; DOE Office of Science Director Raymond Orbach; and Patricia Dehmer, Associate Director of the Office of Basic Energy Sciences within the 

Office of Science.

After a welcome by NSLS Chairman Steve Dierker, the group 

gathered in front of the lobby viewing window, which gives 

an impressive view of the VUV experimental floor. Dierker 

then gave an overview of the NSLS and its research. He also 

discussed the bright, new light source proposed at Brookhaven 

Lab, NSLS-II, and how the new synchrotron would act as a 

sister facility to the CFN, complementing and enhancing the 

nanoscience research to be done there.

On this key theme, Hobson mentioned the cutting-edge, thirdgeneration synchrotrons that exist or are under construction is 

several other countries. “Nanoscience is a whole new era,” he 

said, that requires advanced machinery. In response, Dierker 

discussed how NSLS-II would take the U.S. to the forefront of 

synchrotron science and nanoscience. For example, NSLS-II 

would use CFN instrumentation to focus its beams down to 

very small sizes, enabling studies of nanowires, which are the 

basis for a new class of electronic circuits.

“NSLS x-rays can’t get down to the nanoscale,” said Dierker. 

“We need a powerful new photon microscope, a new technology for a whole new industry.”

He continued, “It is the remarkable behavior of materials at the 

nanoscale that is thought to hold the key to the future of United 

States energy problems. NSLS-II will give us the tools we need 

to regain world leadership in this area.”

Later, at the site dedication ceremony, the CFN site sign was 

unveiled by several of the invited dignitaries and BNL leaders. 

A crowd of BNL employees came out to participate in the event 

and, after a welcome by Lab Director Praveen Chaudhari, 

heard remarks by Hobson, Bishop, and Orbach.

In his talk, Orbach touched on NSLS-II and its planned relationship to the CFN. “Think of the two as a team,” he said. “Without 

both, we will be robbed of opportunities that they uniquely can

bring. NSLS-II will give us a leg up on every other laboratory in 

the world.”

He also had an important message: “We need to convey to the 

public what science can and will do, to convey to everyone the 

nature of scientific enterprise and scientific discovery,” he said. 

“What we’re doing here today is conveying that message in a 

whole new era of opportunity. No one knows the dimensions of 

discoveries that are present.”

“Research into nanomaterials is one of the most exciting things 

since the microchip,” said Hobson. “Right here at Brookhaven, 

you’re getting to be in the middle of that.”

Hobson also praised BNL for its status as a basic-energy 

research lab, stressing that basic research is an essential, 

but waning, component of U.S. science. “The [DOE] labs are 

the last areas of basic research in our country,” he said. “You 

should all be very proud of what you’re doing.”

From left, NSLS Chairman Steve Dierker, Congressman Tim Bishop, 

Congressman David Hobson, DOE Office of Science Director Raymond Orbach, 

and BNL Director Praveen Chaudhari.

Research within the U.S. Department of Energy’s Office of Science. Additional support is provided by the NSLS and several 

equipment vendors and drug companies. For more information, 

go to: www.px.nsls.bnl.gov/RapiData2005/

— Laura Mgrdichian
Strain-Mapping Workshop Marked by 

Enthusiasm and Idea-Sharing

April 18-19, 2005

Useful, lively discussions characterized the recent workshop 

on Strain Mapping in Engineering Materials with High-Energy 

Synchrotron X-Rays, held at the NSLS from April 18-19. The 

workshop brought together researchers in the field of strain 

mapping to discuss their work and talk about how to advance 

NSLS strain-mapping capabilities. Some of the talks are summarized below.

Asuri Vasudevan, from the U.S. Navy’s Office of Naval Research, discussed how he works to extend and predict the life 

of aircraft and helicopters by studying “residual stresses” — the 

stresses within a material left over after a single or repeated

use, which are caused by temperature or the material’s chemical environment. Residual stresses can cause cracks on surfaces that may be stable or unstable. Vasudevan is interested 

in studying these cracks, but said that the tools available to him 

limit the size of the crack he can study as well as the sample’s 

thickness and particular composition.

Mel Roquemore and Ruth Sikorski from the Air Force Research 

Laboratory addressed the potential applications of strain mapping to evaluate jet engine components. Their aims include 

using the determined stresses that occur within the engine 

components to predict and model how complicated engine 

systems will respond to duty-cycle loading. This information 

will help them determine how to increase the life of engine 

components.

Another key speaker was Roger Klaffky, who runs the X-Ray 

Participants in the Strain-Mapping workshop

Bishop was equally supportive. “We have on this site some of 

the world’s best minds. The CFN will bring more of the best 

minds here, and Long Island will benefit from that.”

Among other distinguished guests invited to the Lab were 

Dennis Kovar, Associate Director for Nuclear Physics, who is 

also DOE landlord of the BNL site; Michael Holland, Manager 

of DOE’s Brookhaven Site Office; Vice Admiral Dennis McGinn, 

who is Vice President for Strategic Planning for Battelle; and 

Robert McGrath, SBU Provost and Executive Vice President 

for Academic Affairs, who also serves as SBU Vice President 

for Brookhaven Affairs.

Earlier in the day, the special guests also toured BNL’s Relativistic Heavy Ion Collider and the Positron Emission Tomography 

facility to learn about the research performed at each. The keynote speaker at the luncheon preceding the event was Shirley 

Strum Kenny, Stony Brook University (SBU) President and also 

Vice President of Brookhaven Science Associates, an institution formed of SBU and Battelle, which manages BNL for DOE.

— Laura Mgrdichian

and Neutron Scattering Facilities program within the U.S. 

Department of Energy’s Office of Science. He spoke about the 

DOE’s mission to advance nanoscience research for energy 

needs, and the advantages of x-ray diffraction in this respect. 

He also gave examples of current stress/strain research now 

being done at DOE national labs, such as studying why fractures occur over time in stents and how that process may be 

stunted.

Additionally, an overview of the NSLS beamlines and user 

community was presented by NSLS scientist Chi-Chang Kao. 

He laid out the NSLS three-to-five year plan, which aims to 

continue the growth of life and geo/environmental science user 

groups, and attempt to reverse the decline in materials and 

chemical science users. Other initiatives are to advance the 

biomedical imaging program here and develop a new nanoscience user base. But in the area of strain mapping using highenergy x-rays, Kao said the NSLS needs to win funding for a 

new end station dedicated solely to that field.

The scheduled discussion period at the end of the workshop, 

and the several smaller discussions in between, produced 

many ideas and ways to bolster the strain-mapping program at 

the NSLS. The participants compiled a “wishlist” of capabilities 

they would like to see at X17B1, which is where strain-mapping 

research is now performed, and described current limitations to

their research. For example, they discussed how to decrease 

the time it takes to make a strain map, which is one limitation

may now prevent industrial users from coming to the NSLS.

The group also talked about potential future beamline X17A, 

which could free up X17B1 to become a strain-mapping-only 

beamline. Currently, high-energy x-ray scattering and medical 

researchers share the limited beamtime at X17B1 with scientists in the strain-mapping program.

— Laura Mgrdichian

Year in Review 3-11
3-12 NSLS Activity Report

NSLS Daughters and Sons are Forensic 

Scientists for a Day

April 28, 2005

On April 28, approximately 30 daughters and sons of NSLS 

staff and scientists questioned suspects, analyzed crime-scene 

evidence, and caught a thief — all in one morning. The activities were part of the national Take our Daughters and Sons to 

Work Day. This year at the NSLS, the day had a theme: forensic 

science.

First, the children gathered in the NSLS seminar room to 

hear a brief safety talk by Nick Gmur, and then learned about Participants in the NSLS Sons and Daughters Day

NSLS scientist Randy Smith demonstrates the 

process of “blood”-typing.

Four BNLers Win Environmental Stewardship Awards

April 22, 2005 

At the annual Earth Day Awards Ceremony held on April 22 

by George Goode, Manager of the Environmental and Waste 

Management Division, Goode and Peter Bond, Interim Deputy 

Director for Science & Technology, presented four BNL employees with Environmental Stewardship Awards for demonstrating 

an outstanding effort in pollution prevention, waste minimization, or conservation. The four were: Mary Ann Corwin, National Synchrotron Light Source Department (NSLS); Michael 

Kindya, Plant Engineering Division (PE); Michael Paquette, PE; 

and Joel Scott, Collider-Accelerator Department (C-AD).

Mary Anne Corwin, who heads the User Administration Office 

at the National Synchrotron Light Source (NSLS), was awarded 

for leading the effort to create a virtually “paperless office.” 

By using the Lab’s web-based Guest Information System and 

the NSLS Proposal, Access, Safety and Scheduling (PASS) 

System, considerable resources were saved by reducing the 

use of paper copies, improving records retention methods, and 

recovering office space.

— Liz Seubert

George Goode (left) and Peter Bond (right) present the awards to (from left) Joel 

Scott, Mary Ann Corwin, Michael Paquette, and Michael Kindya.

light in its different 

forms from NSLS 

scientist Lisa Miller, 

in her talk, “What 

Kind of Light?” The 

kids guessed which 

type of light is used 

in many common 

objects, such as 

remote controls and 

microwave ovens.

After the talk, the 

main event began. 

Lisa introduced the 

crime — The Case of the Missing iPod — and then presented 

the “evidence” that had been found at the scene: a white powdery substance, a black powdery substance, a strand of hair, 

and a piece of notebook paper. In a nearby trash basket, there 

was also a soda can with a drop of “blood” on it.

The “victim,” NSLS student researcher Meghan Ruppel, then 

told her story. She said she was studying for a test in the 

library, got up to talk to some friends, and returned to find her 

iPod missing. Her story revealed several possible suspects: 

Adele Wang, Meghan’s friend; Michael Appel, the library’s 

custodian; Laura Mgrdichian, the librarian; and Steve Giordano, a library patron. The suspects filed in, told their own 

stories of what happened, and were questioned by several of 

the children.

After seeing the evidence, hearing the victim’s and suspects’ 

stories, and interrogating everyone involved, the daughters 

and sons split into groups to analyze the evidence. They tested 

the “blood” on the soda can to determine the blood type, and 

dusted the can and the victim’s notebook paper for fingerprints. 

They compared their results with the suspects’ blood types and 

fingerprints.

Next, the children went down to the NSLS experimental floor. 

There, NSLS scientists Tony Lanzirotti and Bill Rao helped 

them analyze hair samples from the suspects using x-rays, 
which measure the levels of various trace elements (such as 

zinc, copper, or calcium) that are present in the hair. The analysis yielded a unique “signature” for each sample, which was 

compared to the signature of the strand of hair found at the 

crime scene. The group also analyzed the powders found at 

the crime scene with a synchrotron infrared microscope. They 

determined that the white powder was powdered sugar and the 

black powder was ground coffee.

With all the evidence properly analyzed, the daughters and 

sons returned to the seminar room, knowing who had taken the 

iPod.

And who was the culprit? Laura the librarian! She took the iPod

“because iPods are not allowed in the library.” In her introductory story, she only 

revealed that she 

made coffee and 

ate a powdered 

doughnut that 

morning. Caught, 

however, she further explained that 

she noticed a soda 

can on Meghan’s 

desk and, because 

food and drinks are 

not allowed in the 

library, went over 

to throw it way. 

She cut her finger 

on the top, leaving a blood drop. Then she noticed the iPod, 

another forbidden item. She took it, but left behind coffee and 

sugar powders, a strand of hair, and many fingerprints. The 

NSLS daughters and sons successfully analyzed these clues 

to catch the true “thief.”

— Laura Mgrdichian

NSLS scientist Lisa Miller uses a synchrotron 

infrared microscope to identify the unknown white 

and black powders.

Women in Science Career Day at BNL

May 9, 2005

Ten female students from the Henry Viscardi School, an 

Albertson, Long Island-based school for children with physical 

disabilities and health impairments, learned about scientific 

careers first-hand from female researchers at BNL. The career 

day was coordinated by Brookhaven Women in Science and 

funded by Brookhaven Science Associates. During the day, 

Jeanne Petschauer (standing, left) from the Community Relations Office gave an overview of BNL’s breadth of scientific 

interests, and Lisa Miller (right) of the NSLS discussed her path 

to becoming a chemist and her research on such diseases as 

osteoarthritis, osteoporosis, and Alzheimer’s disease. Linda 

Bowerman of the Atmospheric Sciences Division explained 

some of BNL’s environmental research, and physicist Angelika 

Drees described 

her work with 

other scientists 

to discover more 

about the earliest 

moments of the 

universe now being 

studied at the Relativistic Heavy Ion 

Collider. Among the 

students present 

were (front, from 

left) Adeline Joshua 

and Stephanie 

Avramenko.

— Diane Greenberg

BNL Workshop on Intense Coherent THz 

Pulses 

May 10, 2005

The first workshop on intense coherent THz pulses at 

Brookhaven National Laboratory (BNL) was held during the 

spring of 2005. Participants included scientists from regional 

universities and institutions as well as members of the BNL 

scientific community. 

The workshop focused on the science enabled by linac sources of intense coherent terahertz (THz) radiation. The NSLS 

Source Development Lab (SDL) linac is one such source, 

producing 100-microjoule, single-cycle coherent pulses with 

spectral content reaching to a few THz. The full-day workshop 

began with a presentation by Xijie Wang (NSLS) that described 

how the SDL linac produces ultra-short, high-charge electron 

bunches that generate coherent THz pulses or deep ultraviolet free-electron laser light. Larry Carr (NSLS) followed with a 

description of the SDL’s THz pulses, including measurements 

of the pulse energy, spectral content, and electro-optic detection instrumentation. He emphasized applications where the 

Participants in the Intense Coherent THz Pulses workshop

Year in Review 3-13
3-14 NSLS Activity Report

A Passion for Synchrotron Science and its 

Future: News from the 2005 NSLS Annual 

Users’ Meeting

May 23-25, 2005

The speakers at the main session of the 2005 National 

Synchrotron Light Source (NSLS) Annual Users’ Meeting, 

held on Tuesday, May 24, at Brookhaven National Laboratory 

(BNL), spoke on many different topics. But they all conveyed 

fierce enthusiasm for the science performed at the NSLS and 

expressed hope that its proposed successor, the world-leading 

NSLS-II, would become a reality.

NSLS Users’ Executive Committee Vice-Chair Peter Stephens 

welcomed the audience to the main meeting, setting a positive 

and enthusiastic tone for the day’s events. He then opened the 

stage to BNL Director Praveen Chaudhari.

Chaudhari commended many attendees for their work to 

advance NSLS-II. “You’ve helped tell us what is needed in this 

new light source, including the workshop last fall that defined 

NSLS-II,” he said. “The struggle to get NSLS-II is just beginning — we need to design it and then get funding. But once the 

machine is built, you’ll have the best machine in the world, and 

we need your help to make that happen.”

Pat Dehmer (third from right), head of the Office of Basic Energy Sciences within 

the Department of Energy’s Office of Science, was a special guest at the 2005 

NSLS Annual Users’ Meeting. She stands with (from left) NSLS Associate Chair 

for User Science Chi-Chang Kao, incoming Users’ Executive Committee (UEC) 

Chair Peter Stephens, NSLS Chairman and Associate Lab Director for Light 

Sources Steve Dierker, BNL Director Praveen Chaudhari, and outgoing UEC 

Chair Larry Shapiro.

Chaudhari then introduced Patricia Dehmer, head of the Office of Basic Energy Sciences within the U.S. Department of 

Energy’s Office of Science, who plays an important role in 

efforts to move NSLS-II forward. Dehmer elaborated further on 

the status of the proposed new facility and made several key 

points, many concerning the tough budget years ahead.

The Office of Science, she said, led by Raymond Orbach, has 

set a philosophy in place for fiscal year 2006: making the U.S. 

the leader in every major field of research, regardless of the 

declining budgets to come. “These are very scary times, and 

being bold and aggressive is probably the only way to face 

this,” she said.

However, her talk was full of encouraging messages. NSLS-II, 

she said, falls into one of the “mission challenges” of the Office 

of Basic Energy Sciences — that is, enabling the construction 

of major scientific facilities.

“NSLS-II will undoubtedly be the world’s finest synchrotron; 

it will be a stunning facility,” she said. Soon, she added, she 

and Orbach will present the Laboratory’s NSLS-II proposal to 

Deputy Secretary of Energy Clay Sell for his approval.

She spoke emphatically to NSLS-II supporters. “I think we have 

a very high probability for success with NSLS-II. But we need 

your help, too. You have to understand the realities of the budget and be sophisticated when you talk to folks in Washington. 

You can’t rely on Congress to launch something like NSLS-II 

— you have to talk to the administration.”

In her closing remarks, Dehmer left off on a very positive note. 

“This laboratory has a wonderful history of constructing and 

operating major user facilities,” she said. “The run of the NSLS 

has been nothing short of remarkable, and NSLS-II will take 

that tradition and move it into the future.” She also praised 

THz pulses serve as an excitation source rather than simply a 

probe of a material’s response. Tony Heinz (Columbia University) gave an overview of THz methods, current scientific efforts, 

and the frontiers opened by a source of high intensity THz 

pulses. Ivan Bozovic (BNL Materials Science) described ultrafast THz studies of correlated electron systems and complex 

oxides — material systems of great interest at Brookhaven. 

Toni Taylor (Los Alamos National Laboratory) presented other 

THz studies of complex materials in a seminar the following day. The National Institute of Standards and Technology 

(NIST) uses THz methods to study complex biomolecules. Ted 

Heilweil (NIST) discussed that activity as well as applications of 

THz in homeland security and imaging. It has been noted that 

the magnetic field portion of a THz wave could be sufficient to 

change the magnetization state of some magnetic alloys, a topic Dario Arena (NSLS) summarized in his talk. The connection 

between THz and magnetization dynamics was also described 

in Toni Taylor’s presentation. 

Attendees were given a tour of the SDL facility and the location 

for future THz studies. This was followed by a discussion session that helped to define experimental directions and provide 

recommendations on the facility and instrumentation requirements.

For more details, see http://www.nsls.bnl.gov/newsroom/

events/workshops/THz/. This workshop was sponsored by the 

NSLS.

— Larry Carr
The 2005 NSLS Annual Users’ Meeting Planning Committee: (from left) Mary 

Anne Corwin, Liz Flynn, Melissa Abramowitz, Ron Pindak, Lisa Miller, Dan 

Fischer, Gretchen Cisco, and Peter Stephens.

NSLS Chairman Steve Dierker. “Steve has been a superb 

leader for NSLS-II, and there’s no way we could have made 

our case to Ray Orbach without him. NSLS-II has moved up in 

the DOE 20-year plan largely because of Steve’s efforts.”

Dierker, who spoke next, showed the audience that the NSLS 

continues to thrive, even as third-generation synchrotrons draw

more and more users. “We’ve held our own and then some,” 

he said. “The number of users served by the NSLS has been 

stable at about 2,300 per year.”

He described the NSLS as “very cost effective, highly productive, and highly reliable.” Since 2001, the facility has met many 

key goals, such as maintaining and strengthening its user 

program, expanding its user base, and developing a compelling proposal for NSLS-II.

In addition, there has been a “dramatic” evolution of NSLS 

beamlines, including better support to several beamlines to 

make them more useful and modern, and many major beamline upgrades.

Looking into the future, Dierker said he looks forward to continuing user input on NSLS-II. “The community has responded 

very enthusiastically and vigorously,” he said. “I think we have 

put forward a compelling design that is critically needed in order to probe materials at high-energy resolution, and at spatial 

resolutions on the order of one nanometer, which would be 

unprecedented.”

“There is a host of important and exciting scientific opportunities that will be enabled by NSLS-II,” he concluded. “This is 

something the U.S. absolutely needs to regain leadership in 

synchrotron radiation science.”

Next, in the first scientific talk of the day, Henk Schenk of the 

University of Amsterdam discussed “The Structure of Cocoa Butter and the Quality of Chocolate.” In this interesting 

presentation, Schenk described his group’s work using x-ray 

diffraction to study the structure of cocoa butter. Cocoa butter 

is an essential component of chocolate that determines the 

Speakers at the main meeting included (from left) Bob Casey (BNL-NSLS), John 

Rehr (University of Washington), Benjamin Chu (Stony Brook University), and 

Henk Schenk (University of Amsterdam).

chocolate’s characteristic properties, such as its sheen and 

meltability. By studying the various phases of cocoa butter 

via melting-cooling processes, he and his group patented a 

method to produce chocolate that stays fresh longer than other 

chocolates, and even devised a chocolate-making machine.

Schenk was followed by a talk on safety delivered by Peter 

Stephens and Bob Casey, the NSLS Associate Chair for Environment, Safety, Health, and Quality. In a back-and-forth style, 

Casey and Stephens discussed safety from the point of view of 

NSLS users and administration, particularly in the wake of the 

electrical incident last year at the Stanford Linear Accelerator 

(SLAC). The issues raised during their talk were presented in 

further detail, and subject to more extensive discussion, at a 

special “Electrical Safety in the Research Community” workshop the following day.

The workshop covered several topics. NSLS Safety Officer 

Andrew Ackerman discussed National Fire Protection Association electrical standards implemented at the NSLS. He also 

elaborated on a new NSLS rule that all electrical devices in the 

NSLS be certified by a nationally recognized testing laboratory 

within five years, including equipment brought in by users. He 

showed several photos of unsafe and/or “homemade” electrical 

equipment and configurations found on the NSLS floor, which 

illustrated the need for such rules.

Bob Chmiel, the NSLS Environmental, Safety, and Health 

engineer, expanded on this. He displayed actual examples 

of unsafe electrical configurations found during routine NSLS 

inspections, and encouraged users to routinely check their 

equipment. Finally, Casey gave a more detailed account of the 

SLAC incident, the many violations of procedure and practice 

that led to it, and lessons learned. He also went over some 

recent NSLS electrical incidents, and the lessons learned from 

them.

The second scientific talk at the main meeting was delivered 

by John Rehr of the University of Washington. Rehr spoke 

Year in Review 3-15
3-16 NSLS Activity Report

This year’s poster session winners were (from left) Tejas Telivala (Stony Brook 

University), Ashtosh Ganjoo (Lehigh University), Angelo Dragone (BNLInstrumentation Division), Holger Fleckenstein (SBU), Meghan Ruppel (SBU), 

and Brandon Chapman (BNL-NSLS).

Steve Almo

Peter Abbamonte

NSLS historian Bob Crease took the banquet attendees back in time during his 

presentation on the history of the NSLS.

about the theory involved in interpreting x-ray data obtained 

from many synchrotron analysis techniques, such as extended 

x-ray absorption fine structure (EXAFS) and nuclear resonant 

inelastic x-ray scattering.

In the afternoon, Benjamin Chu from Stony Brook University 

talked about the polymer experiments he performs with his 

group at beamline X27C, using wide-angle x-ray diffraction 

(WAXD) and small-angle x-ray 

scattering (SAXS). Their end station 

contains several specialized instruments, such as spinning, stretching, 

and high-pressure devices, which 

allow them to investigate various 

properties of the polymers.

Next, Steve Almo from the Albert 

Einstein College of Medicine discussed “Structural Genomics in the 

3rd Millenium.” Almo said that scientists are solving protein structures 

at amazing rates, but that the future 

of structural biology is determining the structures of protein 

complexes — many proteins interacting at once. He described 

a new technique to study proteins, called synchrotron x-ray 

footprinting, which may help structural biologists look beneath

cell membranes to study many cell 

components at once.

Finally, NSLS scientist Peter Abbamonte presented his work on 

antiferromagnetism, a state of 

magnetism in certain materials in 

which ions orient themselves into 

regions of opposite alignment, called 

“stripes.” Antiferromagnetic materials 

can become superconductors, and 

Abbamonte and his group are trying 

to determine if stripes play a role 

— do they assist or compete with superconductivity?

At the end of Tuesday’s main meeting, the outgoing NSLS 

Users’ Executive Committee Chair, Larry Shapiro, announced 

the three newest members of the UEC: Chris Jacobsen of 

Stony Brook University (SBU), Steve Almo, and Chris Cahill 

of George Washington University. NSLS scientist Lisa Miller, 

the poster session organizer, announced the poster sessions 

winners: Brandon Chapman (BNL-NSLS), Angelo Dragone 

(BNL-Instrumentation), Holger Fleckenstein (SBU), Ashtosh 

Ganjoo (Lehigh University), Meghan Ruppel (SBU), and Tejas 

Telivala (SBU).

Later that day, meeting participants attended the evening banquet in Berkner Hall for good food, drinks, and conversation. 

During dinner, photos of the NSLS and NSLS staff cycled on a 

large screen at the front of the room, sparking conversations. 

Stephens also presented the UEC Community Service Award 

to Tony Lenhard.

After dinner, NSLS historian Robert Crease treated everyone 

to a bit of history during a special presentation. In a narrative 

accompanied by old photos, he recounted the days before the 

NSLS was built, the roadblocks encountered before and during 

its construction, and the ultimate success of the facility. 

During the two days surrounding the main meeting, Monday 

the 23rd and Wednesday the 25th, several additional workshops were held at locations across the Laboratory. They were 

“Nanomagnetism: Materials and Probes,” “Imaging Nanoscale 

Structure in Biominerals: New Results and Challenges,” “The 

Impact of Cryogenic Specimen Automounters on the Future 

of Macromolecular Crystallography,” “Spectroscopic Studies 

of Nanoscaled Systems,” “Application of Small-Angle X-Ray 

Scattering to Biological Structures,” and “In-situ Analyses in 

Environmental and Chemical Systems.”

— Laura Mgrdichian
Nanomagnetism: Materials and Probes 

Workshop

May 23, 2005

The connection between magnetism and nanoscience is clear: 

The nanometer is the natural length scale of magnetism, as 

it characterizes the domain wall. Unanticipated phenomena 

occur when the materials’ structural scale coincides with the 

magnetic length scale. To support research into nanomagnetism, recent advances in materials synthesis and nanofabrication technology have made it possible to create a wide range 

of nanomagnetic systems with unprecedented precision. These 

novel magnetic systems are used as model systems for testing 

longstanding theories in magnetism, as well as for exploring 

new device concepts and applications. In parallel, synchrotron 

radiation, with its unique polarization properties, tunability, and 

time structure, has become an indispensable tool for the study 

of magnetism and magnetic materials. 

The 2005 NSLS Users’ Meeting Workshop “Nanomagnetism: 

Materials and Probes” provided an overview of the latest synchrotron characterization techniques as well as introduced new 

materials concepts for magnetic materials. The workshop was 

jointly sponsored by the Brookhaven National Laboratory Center for Functional Nanomaterials, a new U.S. Department of 

Energy nanoscience user facility. Presentations were delivered 

by seven experts in the application of synchrotron radiation 

to magnetic materials, and in the synthesis and application of 

magnetic nanomaterials, with the goal of presenting an up-todate snapshot of the forefront issues in nanomagnetism. 

Daniel Haskel of the Advanced Photon Source at Argonne National Laboratory inaugurated the workshop with a presentation 

on recent synchrotron characterization advances that elucidate 

the role surfaces and interfaces at play in the overall magnetic 

response, especially in thin-film layered systems. 

Professor J.M.D. Coey of Trinity College in Dublin, Ireland, followed with surprising but well-documented results that systems 

with nominally no d-electrons, such as HfO2

 and RhO2, exhibit 

ferromagnetism under certain conditions. The results are currently attributed to the defect state of the material. 

Continuing the focus on novel magnetic materials, Distinguished Professor Myriam P. Sarachik of City College–CUNY 

presented new results on molecular magnets or single-molecule magnets. These systems, which bridge the classical and 

the quantum worlds, hold potential as quantum computation 

materials (qubits) and exhibit clear quantum-mechanical tunneling signals under the influence of magnetic fields. 

Professor Sara A. Majetich of Carnegie Mellon University 

discussed recent results obtained from highly uniform monodisperse arrays of ferromagnetic Fe, Co, and FePt nanoparticles 

(Figure 1). The competition between dipolar and anisotropy 

energies in these systems creates spin-glass-like mictomagnetic behavior, as revealed by small-angle x-ray scattering and 

small-angle neutron scattering. 

Glenn A. Held of the IBM T. J. Watson Research Center in 

Yorktown Heights, New York, presented an overview of magnetic ferrite nanoparticles encapsulated by biologically active

molecules to create bio-functionalized entities for monitoring 

and influencing cellular processes. 

The workshop concluded with two presentations on advanced 

synchrotron techniques for magnetism characterization. Dario 

Arena of the NSLS discussed new techniques that probe the 

dynamics of magnetization precession in the time domain, 

with element specificity. In this work, time-resolved magnetic 

circular dichroism in a pump-probe architecture was employed 

to examine the moment response in permalloy-based systems. 

Andreas Scholl of Lawrence Berkeley National Laboratory 

described the application of ultrafast x-ray pulses (picosecond

to femtosecond) to image magnetic dynamics with high spatial 

resolution. As an example of the technique, real-time movies with associated analyses of the precessional dynamics of 

magnetic vortices were presented.

— Laura H. Lewis and Chi-Chang Kao

Figure 1. Large view (1.5 mm x 1.5 mm) of uniform ε-Co ferromagnetic 

nanoparticles with a high degree of order induced by lateral com-pression to form 

a compressed Langmuir film. The inset shows the presence of dislocations but 

no grain boundaries in the film. (D. Farrell, Y. Cheng, R.W. McCallum, M. Sachan, 

and S.A. Majetich, J. Phys. Chem. B, 109(28), 13409-13419 (2005).

Nanomagnetism: Materials and Probes workshop attendees

Year in Review 3-17
3-18 NSLS Activity Report

Annual NSLS Users’ Meeting. Our six invited speakers were 

followed by four short talks from BNL and Stony Brook University scientists, including student presentations. This workshop 

was also videotaped and is posted on the web at 

http://www.solids.bnl.gov/~dimasi/nsls05ws2/.

Matthias Epple of University Duisburg-Essen, Germany, emphasized the 

importance of studying well-characterized biological samples in collaboration 

with biologists, who can help interpret 

the information. Epple then went on to 

show how high-resolution powder diffraction, EXAFS, and tomography were used 

in tandem to obtain structural information from a variety of small animal shells 

and structural organs. High-resolution 

measurements are necessary to distinguish between calcite, magnesian calcite, and small amounts 

of metastable polytypes only observable with synchrotron 

radiation. In more unusual animals, extremely unlikely minerals, such as calcium sulfate hemihydrate statoliths in deep-sea

medusae, were discovered. Finally, selected amorphous calcite 

carbonate mineral formers were surveyed. Effective measurement of the metastable amorphous biominerals is particularly 

valuable since biomineralization is thought to often proceed by 

means of amorphous precursors.

Emil Zolotoyabko, from the TechnionIsrael Institute of Technology, focused 

on his newly developed technique for 

depth-resolved measurements using 

energy-variable x-ray diffraction. The 

motivation is that biominerals have 

complex, multilayered structures. While 

many synchrotrons have developed 

micron beam spots to resolve diffraction 

patterns laterally (across the sample 

surface), it is necessary to match this 

spatial resolution in the third direction for a complete picture. 

Zolotoyabko’s technique is based on theoretical analysis of the 

shapes of diffraction profiles taken under slight misalignment 

of the diffraction instrument. The interplay between the probability of the x-ray registration in the detecting system and the 

depth-dependent attenuation of the primary x-ray beam defines 

at each energy a specific depth from which the maximum diffraction signal is collected. By measuring diffraction profiles at 

different energies, the depth-dependent effects in the preferred 

orientation, grain size, microstrain fluctuations, and residual 

strains could be observed. Zolotoyabko highlighted information 

obtained from mollusk shells in which microstructural parameters in the successive layers of a material can tell the story of 

a biomineral growth.

Stuart R. Stock of Northwestern University presented the history and latest advances in x-ray absorption computed microtomography and phase radiography. These non-invasive threeMatthias Epple

Synchrotron Imaging of Biominerals 

Workshop

May 23, 2005

Biominerals, the mineralized tissues of animals, plants, and 

microorganisms, have inspired humanity since prehistory. 

Bones and shells have been used for tools, currency, symbolic 

objects, and art in every culture. Both the fascination and the

importance that biominerals present for science are made clear 

in Darwin’s 19th century writings, and in D’Arcy Wentworth 

Thompson’s 1917 On Growth and Form, with its memorable 

cover illustration of the multi-chambered calcium carbonate 

nautilus shell.

Now, biomineralization is a field of study in its own right. 

Biologists, paleontologists, materials chemists, physicists, 

engineers, and medical professionals all contribute to our 

understanding of how biominerals grow; how they achieve their 

submicron hierarchical architectures and their precise control 

over crystal orientation and habit; how they are able to stabilize non-thermodynamically-favored mineral polytypes; and 

most importantly, how the biomineralization process might be 

harnessed or mimicked to produce new nanostructured, multicomponent materials for medicine and technology. 

Recent advances in synchrotron science, as applied to these 

materials, have uncovered a wealth of new information in the 

past ten years. Synchrotrons now enable diffraction-enhanced 

imaging, x-ray microbeam analysis, computed tomography, 

and phase radiography to probe the microstructures of biominerals. Chemical information is obtained from soft x-ray photoemission and infrared spectromicroscopy techniques, with 

submicron spatial resolution. High-resolution diffraction, smallangle scattering, and x-ray absorption methods all contribute 

to the picture of the crystalline and amorphous phases formed. 

Finally, many of these experiments are sensitive to crucial organic components: the matrix of proteins and polysaccharides 

that help give biominerals their special properties.

Such new results and challenges were highlighted in a 

workshop, “Synchrotron Imaging of Biominerals,” at the 2005 

Synchrotron Imaging of Biominerals workshop attendees

Emil Zolotoyabko
dimensional imaging techniques can be applied to both medical and materials studies. Stock first gave a detailed discussion 

of the technique’s mathematical basis and practical limitations. 

He next described how spatial and temporal variations in microstructure could be observed for mouse skull tissue response 

to bone resorption-inducing agents, for 

the mineralized collagen of regenerated 

newt limbs, and to study a rabbit model 

for vascular mineralization, probing 

treatments to ameliorate the effects of 

cholesterol. Finally, interesting questions 

about some similar proteins implicated in 

skeletal evolution were brought up, contrasting the calcium carbonate skeletons 

of echinoderms with the calcium phosphate bones of vertebrates: How does 

the spatial distribution of protein relate 

to the microarchitecture and mineral density? Sea-urchin teeth 

exhibit a remarkable array of materials engineering “tricks” in

the design of their composite microstructures, as a functional

analysis of the images demonstrates.

Gelsomina “pupa” De Stasio, University of Wisconsin 

- Madison, and Synchrotron Radiation Center. A lively talk 

from De Stasio showcased SPHINX, an x-ray PEEM spectromicroscope. With monochromatic soft x-rays incident onto 

the sample surface, photoelectron emission imaging with a 

field of view of 2 to 200 microns can be 

accomplished. By scanning the energy, 

XANES or EXAFS spectra are obtained, 

with sensitivity to all elements present 

in biological and mineral systems. This 

makes chemical and spectroscopic 

information available with 10 nm spatial 

resolution. De Stasio discussed wideranging examples of biomineralization 

not previously covered, including the 

formation of bacterial biofilms and the 

“reverse-biomineralization” activity of 

antifreeze proteins — emphasizing, in all cases, the organicinorganic interface. She also presented another mystery in 

mollusk nacre: a polarization dependence, suggesting that the 

carbonate groups in aragonite do not align along the tablet axis 

as is currently thought.

Helga Lichtenegger, from the Vienna 

University of Technology, presented 

research on another unusual family 

of biominerals: marine worms whose 

mandibles are reinforced with the copper-based mineral atacamite. Lichtenegger has explored the distribution of 

copper, zinc and iron in Glycera and 

Nereis worm jaws, and the experimental 

achievement is an elegant combination 

of microbeam x-ray absorption spectroscopy, diffraction, and small-angle scattering. Each of these 

techniques had a necessary role in determining which metals 

form crystals within the jaws, and which instead are present 

in trace quantities and may play some role in the tissue other 

than structural support; and in the case of SAXS, what morphology the mineralized parts exhibit and how that relates to 

the structure of the whole jaw.

Teresa Nicolson joined us from the 

Oregon Hearing Research Center and 

Vollum Institute, Oregon Health and Science University. Nicolson studies the molecular basis of mechanotransduction in 

sensory hair cells. This research uncovered a puzzle in biomineralization when 

genes required for hearing and balance 

in zebrafish were explored. Nicolson 

demonstrated that a previously unknown 

gene, starmaker, was required for the proper development of 

the calcium carbonate otoliths or stone-like particles, which 

serve as balance sensing organs in the ear. The starmaker activity was experimentally disrupted in zebrafish embryos. With 

mild disruption the aragonite mineral otoliths were changed 

from round to chunky morphologies, and in more excessive 

cases another calcium carbonate mineral, calcite, was formed. 

Synchrotron microbeam diffraction was necessary to detect 

these changes. 

Selected local efforts were showcased in short talks following the invited program. Zhong Zhong (NSLS) presented the 

superior contrast achieved from Diffraction Enhanced Imaging 

using x-rays. Meghan Ruppel (NSLS) used infrared spectromicroscopy to compare the chemical makeup of microdamaged 

versus undamaged bone. Karthikeyan Subburaman (Stony 

Brook University) described the biomimetic mineralization of 

synthetic protein films, and Seo-Young Kwak (NSLS) measured the orientation and Mg-incorporation of calcite grown on 

functionalized self-assembled monolayers.

Interdisciplinary symposia can be a challenge as well as a 

pleasure for the participants. Aside from the compliments, other 

Stuart R. Stock

Gelsomina "pupa" De Stasio

Helga Lichtenegger

Teresa Nicolson

Biomineral Imaging at the NSLS

Year in Review 3-19
3-20 NSLS Activity Report

The Impact of Cryogenic Specimen Automounters on the Future of Macromolecular 

Crystallography Workshop

May 23, 2005

Cryogenic “automounters” are becoming common at synchrotron x-ray sources and in a few commercial laboratories, 

employed especially in macromolecular crystallography (PX). 

There are several commercially available models, and several home-built ones, used in a range of synchrotron radiation 

sources around the world. This workshop gave the PX community an opportunity to hear the major builders of these instruments describe important features of the operation of their 

instruments, and the ways the scientific community is using 

them. 

Thomas Earnest’s group at Lawrence Berkeley National 

Laboratory’s Advanced Light Source (LBL-ALS) designed one 

of the most imitated automounter systems, based on pneumatic actuators. He summarized their experience at the ALS 

with the design, now exported to several locations (the NSLS, 

the Advanced Photon Source (APS), and the Macromolecular 

Diffraction Facility at the Cornell High-Energy Synchrotron 

Source (CHESS)). He emphasizes an “open source” view of 

the design to encourage information sharing and described 

many small improvements since the original design. They’re 

working on a Cartesian robot to replace the current system, 

which would not require the crystal-supply dewar to move, and 

would have a larger capacity. Dieter Schneider, BNL Biology 

Department, described his group’s refinement of the LBL-ALS 

system. They devised a three-jaw gripper that is being adopted 

at several places, developed innovations that minimize frosting

of the lid, and are beginning to develop EPICS-based control. 

Gerd Rosenbaum, of the Southeast Regional Collaborative 

Access Team at the APS, described his group’s adaptation of 

this design. This instrument is just now coming into operation. 

Quan Hao, CHESS, gave the same sort of report, one innovation being a miniature liquid nitrogen pump for filling the sample 

dewar, and described his use of a Java-based camera system 

for sample viewing. 

comments (that the organizer, perhaps, was not intended to 

hear) included: “That was way too technical for me”; “The biology was over my head”; and “Definitely not the way I’m used to 

thinking about problems.” It’s our hope that such symposia can 

continue to increase awareness of the problems and methods 

encountered in a research area like biomineralization, which 

presents so many faces. For this reason, we are especially 

appreciative of the support and participation that this workshop 

received. We would like to thank the NSLS, the NSLS Users’ 

Executive Committee, the Center for Functional Nanomaterials, 

and BNL videographer Alex Reben.

— Elaine DiMasi

The Impact of Cryogenic Specimen Automounters on the Future of Macromolecular Crystallography Workshop attendees

Aina Cohen represented the Stanford Synchrotron Radiation 

Laboratory (SSRL) robot effort, one of the earliest in the PX 

community, whose device depends on an industrial robot for 

flexibility. They have very much experience and have made 

many refinements to the original system to provide reliability. 

The SSRL group has developed a web site for sharing ideas 

about automounters: http://smb.slac.stanford.edu/robosync/.

Franck Felisaz, of the Joint Structural Biology Group at the European Synchrotron Radiation Facility’s (ESRF) European Molecular Biology Laboratory (EMBL), Medical Research Council 

Grenoble, described a robot named SC3 that was developed 

at the EMBL. Eight of these have been built for ESRF, commercialized through Maatel and marketed through Accel. An 

especially attractive feature is the software, which can be used 

with a pocket PC to read bar code labels on crystal-growth 

trays in order to transfer that information to the data-collection 

software. Bernard Lavault, also from EMBL, described imagerecognition software (“C3D”) for locating and centering crystals 

on the goniometer. It has an impressive record of finding the 

real crystal in globs of vitrified liquid. He emphasized the importance of lighting and the ability to vary lighting direction and intensity. Deming Shu, a member of the instrument-development 

group at the APS, described their design of a custom robotic 

system based on a commercial six-axis robot. There are many 

refinements, in particular a force-sensing gripper. 

Several commercially available robotic systems were described 

as well. Ross Doyle of Mar USA described the MAR Cryogenic 

Sample Changer, which can be provided as part of MAR dtb 

(desk-top beamline). This system is used at several places in 

Europe and at the Structural GenomiX beam line at the APS. 

Anne Mulichak, a member of the Industrial Macromolecular Crystallography Association Collaborative Access Team 

(IMCA-CAT) at the APS, described their experience using 

ACTOR, the six-axis robot produced by Molecular Structure 

Corporation of The Woodlands, Texas. This instrument is an 

engineered adaptation of the first such robot ever produced 

(by Abbott Pharmaceuticals for their internal use). After a few 

years’ experience at IMCA-CAT the machine is in fairly routine 

use now. Ehmke Pohl of the Swiss Light Source reported that 

they purchased one two-Dewar ACTOR system. They put 

special effort into accurately intersecting the x-ray beam with 

the crystal, employing x-ray beam position monitors to provide 
Spectroscopic Studies of Nanoscaled Systems 

Workshop

May 25, 2005

A workshop titled “Spectroscopic Studies of Nanoscaled 

Systems” was held on May 25, 2005, as part of the National 

Synchrotron Light Source 2005 Annual Users’ Meeting. This 

workshop was intended to be a forum on the connection between nanoscience and the physics of interacting electron systems, particularly the occurrence of electronic ordering at the

nanoscale in oxides, both in extended crystals and in artificial 

heterostructures. Our hope was that this session might feed 

the discussion concerning the correlated electron thrust area at 

Brookhaven Lab’s planned Center for Functional Nanomaterials.

The day opened with a presentation on quantum confinement 

effects in thin films by Tai Chiang from the University of Illinois. 

Chiang’s group carried out angle-resolved photoemission 

measurements on thin films of lead and determined a direct 

correlation between the thermal stability of layers of different thickness and the binding energy of the highest occupied 

orbital. This stability arises from the confinement of the electron 

in the direction perpendicular to the film and turns out to be 

periodic in the layer thickness. This periodicity can be thought 

of as a one-dimensional analogue of the periodic table.

The next speaker was Seamus Davis from Cornell University, 

who presented scanning tunneling spectroscopy (STS) measurements of the copper-oxide superconductor 

Ca2-xNax

CuO2Cl2. In an earlier study this material was reputed 

to contain an electronic (i.e. Wigner) crystal, and the current

presentation contained additional measurements showing 

spectral weight modulations at a large binding energy (~ 200 

meV). These measurements spurred a continuation of the 

debate over the definition of the term “Wigner crystal” and what 

Spectroscopic Studies of Nanoscaled Systems Workshop attendees

feedback for 10-micrometer positional stability. They’re looking 

into using ultraviolet sensing together with visible light to locate 

the sample. Finally, Bob He, from the Bruker-Nonius company 

of Madison, Wisconsin, described yet another quite successful 

commercial robot based on a six-axis system. This system has 

found acceptance in the home-lab small-molecule community, 

and it works just fine in PX. 

An hour and a half were reserved at the end of the workshop 

for open discussion. Both builders and users seriously discussed the standardization of the fixtures the experimenters 

use to handle their specimens: crystal “caps” and pins, and the

cassettes used to carry the caps to the automount robot. The 

discussion yielded important, detailed ideas that have been 

passed on to the American Crystallographic Association Data, 

Standards, and Computing Committee.

— Robert Sweet

aspect of STS measurements may be thought of as charge 

order.

After Davis, Ali Yazdani from Princeton University presented 

similar measurements on underdoped Bi2

Sr2CaCu2O8+δ with 

trace quantities of zinc. These STS measurements were 

carried out in the pseudogap state, i.e. Tc

 < T < T*. Yazdani 

observed a “checkerboard” pattern that appears to be electronic in origin, disappears when the sample is cooled into the

superconducting state, and was speculated to arise from some 

competing order responsible for the pseudogap. What relation 

these measurements have to Davis’ Wigner crystal, or to the 

stripe phases seen with neutron scattering, is still a mystery. 

After a lunch break, Girsh Blumberg of Bell Laboratories presented Raman measurements of very lightly doped La2

CuO4+y

(LCO), as well as the spin ladder material Sr14Cu24O41, to 

characterize the nature of the inhomogeneity in these systems. 

From his measurements he concludes that the inhomogeneity 

in LCO is actually two dimensional (“giraffe disorder”), rather 

than one-dimensional (“zebra disorder”).

The discussion turned from intrinsic-occurring order to artificial 

order with a presentation on quantum wires of underdoped 

YBa2

Cu3O6+y by Dale Van Harlingen of the University of Illinois. 

The Van Harlingen group carried out four-probe transport measurements on such wires and observed quasi-random “telegraph” noise in the IV characteristics. This noise was seen only 

at temperatures around the pseudogap temperature T*, and 

was speculated to arise from stripe domains that exist above 

Tc

 and thermally switch at random times. Such switching is not 

seen in optimally doped wires.

A major topic of discussion at the workshop was whether the 

physics of oxides differs substantially if patterned into nanostructures. Insight into this subject was provided by Antonio 

Castro-Neto of Boston University, who gave a theoretical perspective on the edge states that might arise at the surface of 

a (1,0,0) terminated doped Mott insulator. In a study based on 

density matrix renormalization group techniques, carried out in

collaboration with Stephen White of the University of California 

at Irvine, Castro-Neto concluded that static stripes form near a 

terminated surface and, with increasing U, spread out from the 

bulk and move to the surface. These effects may be important 

for the properties of transition metal oxide devices.

Year in Review 3-21
3-22 NSLS Activity Report

Application of SAXS to Biological Structures 

Workshop

May 25, 2005

The development new synchrotron sources has enabled challenging small-angle x-ray scattering (SAXS) experiments that 

require extremely small, yet intense x-ray beams. An example 

is time-resolved scattering from proteins undergoing folding 

at millisecond or better time resolution. However, the emergence of these new sources does not make SAXS instruments 

that are based on older second-generation sources, such as 

the NSLS, obsolete. Instead, these instruments continue to 

contribute to biology and biomaterials research. This workshop 

was intended to show the user community how SAXS can be 

used to facilitate structural studies of biological systems with 

examples of studies achievable at second-generation synchrotron sources.

The morning session of this workshop focused on solution 

scattering from proteins and protein complexes. Dmitri Svergun 

(European Molecular Biology Laboratory) described applications of the low-resolution structural modeling programs developed in his group. These data analysis methods are based 

on static measurements that do not require very high source 

brightness. He gave examples for a broad range of sizes, from 

individual macromolecules to multi-domain proteins and large 

macromolecular assemblies. Structural modelling of molecular 

complexes is particularly effective when combined with highresolution structures of the constituting subunits.

The scattering at higher angles corresponds to structures 

at smaller length scales. Lee Makowski (Argonne National 

Laboratory) showed that scattering within this region contains 

information on the secondary structures and folding motif of the 

protein. Wide-angle x-ray scattering (WAXS) data can therefore 

be utilized to quantify the structural difference between protein 

structures as a distance in the WAXS space. Proteins known 

to have similar structural motifs have the shortest distances. 

This method, therefore, may be a sensitive, global method for 

detecting structural changes in proteins, narrowly categorizing

proteins based on their scattering homology to known folds 

Application of SAXS to Biological Structures Workshop attendees

The session closed with a presentation by Satoshi Okamoto of 

Columbia University on the subject of electronic reconstruction

in oxides with reduced dimensions, such as at surfaces and 

interfaces in artificial structures. Okamoto carried out a computational study of the interface between LaTiO3

 (a Mott insulator) and SrTiO3

 (a band insulator), and found that the interface 

between the two is, in fact, highly metallic and exhibits orbital 

ordering. The precise form of the orbital ordering depends on 

the thickness of the interface and the geometry of the structure. 

Such effects may have already been seen by groups at Bell 

Labs and in Korea.

— Peter Abbamonte and Peter Johnson

and elucidating the differences between crystal structures and 

aqueous conformations. 

Scattering from protein solutions is not only capable of 

charactering the structure of proteins, but also the interaction 

potential between them. This capability is employed by Annette 

Tardieu (Centre Nationale de la Recherche Scientifique) to 

study the conditions that are optimal to obtain protein crystals. 

The major result from her research is that attraction between 

protein molecules may be tuned with salt and/or with PEG. The 

optimal condition depends upon the macromolecular size: With 

small compact proteins the Hofmeister effect may be sufficient 

to induce an attractive regime and crystallization, whereas 

the presence of PEG is required with higher molecular weight 

complexes. 

The last speaker of the morning session was Jack Johnson 

(The Scripps Research Institute), who studied the maturation of 

HK97 bacteriophage capsid. This dynamical process proceeds 

at a moderate speed (on the order of seconds) and was monitored with time-resolved SAXS. This study is a great example 

of how protein crystallography, electron microscopy, smallangle scattering, and fluorescence complement each other to 

provide a more complete picture of the biological process that 

may not be elucidated by any of these techniques alone.

The afternoon session moved on to the application of SAXS to 

more complex structures in biological tissues. Due to the presence of various periodic structures, scattering data from tissues 

often contain diffraction peaks and there is no uniform method 

of analyzing the data. Ben Hsiao (Stony Brook University) modeled the shape and position of small-angle diffraction peaks 

from fish bones. His data analysis quantified the diameter of 

collagen fibrils, the orientation distribution of fibrils, the coherence length, as well as the mineral (calcium phosphate) dimensions and orientation in the bones. Myosins and actin fibers 

in muscle also produce diffraction peaks. Leepo Yu (National 

Institutes of Health) studied the structural change in muscles 

as the chemical-to-mechanical energy conversion that drives 

muscle movement takes place. In search for materials for 

replacing defective heart valves, Jun Liao (University of Pittsburgh) studied candidate tissues under biaxial stretch either 

with constant force or constant displacement. The response of 

the tissue gives a good indication of its mechanical integrity. 
In-Situ Kinetic Analyses in Environmental 

and Chemical Systems Workshop

May 25, 2005

Natural environmental systems, such as soils, sediments, and 

subsurface aquifers, are always in a state of disequilibrium. 

Changes in porewater chemistry, biological activity, and chemical properties, such as particle-water interfacial composition,

redox potential, and pH, occur over time scales ranging from 

microseconds to years. Research on the kinetics of chemical 

and physical processes at different time scales is essential for 

understanding the fate and transport of environmental contaminants. A workshop organized by Dean Hesterberg and Jeff Fitts 

for the NSLS Annual Users’ Meeting on May 25, 2005, brought 

together a multidisciplinary group of scientists who discussed 

in-situ approaches for studying time-dependent chemical 

processes.

The workshop was dedicated to the memory of the late Dale E. 

Sayers. Ed Stern (University of Washington) provided a historical perspective on Sayers, discussing how, as a Ph.D. student 

in 1971, Sayers pioneered (along with Stern and Farrell Lytle) 

the first correct physical model explaining the extended x-ray 

absorption fine structure (EXAFS). This breakthrough led to development of XAFS spectroscopy as an analytical tool for determining the local molecular structure of condensed phases. 

Stern discussed the unique advantages of XAFS spectroscopy 

in determining short-range structure, valence, local symmetry, and angular deviation of atoms from collinearity. He also 

described nanosecond-scale time-dependent studies involving 

laser excitations of atoms in tandem with photon pulses inherent in synchrotron radiation.

Donald L. Sparks (University of Delaware) gave an overview of 

the importance of understanding the kinetics of reactions and 

processes in soils and sediments. Given the extreme complexity of such matrices, it is challenging to measure chemical

kinetics separate from diffusion. Soil chemical reactions involving inorganic and organic contaminants often show an initially 

rapid rate followed by a slow approach to steady state, with 

hysteresis upon reversal. Very short, real-time, molecular-scale 

analyses are needed to determine chemical kinetics in isolation

from transport, and elucidate reaction mechanisms that determine the fate of environmental contaminants.

One promising method for measuring short-term kinetics is 

Quick-EXAFS. Wolfgang Caliebe (NSLS) compared various 

Quick-EXAFS systems and showed Quick-EXAFS spectra 

collected at the NSLS on time scales of seconds. The ratelimiting component for Quick-EXAFS is typically the detector. The application of time-resolved in-situ EXAFS analysis 

was illustrated for battery materials by Mali Balasubramanian 

(Advanced Photon Source). These examples showed how 

quasi-equilibrium states of chemical reactions could be probed 

on times scales of three to 30 minutes. For example, XAFS 

spectra revealed how chromium ions migrate between octahedral and tetrahedral positions in Mn-oxide systems.

The precipitation, growth, and crystallization of naturally occurring iron oxides under various redox and pH conditions 

regulate the mobility of chemicals in the environment by, for 

example, adsorption and encapsulation. Sam Shaw (Oxford 

University) described in-situ, synchrotron-based time-resolved 

small-angle x-ray scattering (SAXS) and time-resolved x-ray 

diffraction (TRXRD) studies that followed the growth of poorly 

ordered iron oxyhydroxide (ferrihydrite) and its transformation

into goethite and hematite, which are more stable crystalline 

endproducts. Rapid (seconds to minutes) precipitation and 

crystal growth of ferrihydrite was followed with SAXS using a 

stopped-flow reaction cell. Adsorption of chemical species such 

as phosphate on freshly precipitated mineral phases slows the 

overall crystal growth and retards growth on specific crystal 

faces. Based on activation energies calculated from TRXRD, 

ferrihydrite apparently transforms to goethite by dissolution and 

precipitation and to hematite by solid-state transformations.

John Parise (Stony Brook University) and James D. Martin 

(North Carolina State University) gave additional examples of 

using TRXRD to follow chemical kinetics. Parise showed how 

this technique could be used to optimize the synthesis of a 

titanium silicate material to maximize its selectivity for cesium, 

an important radioactive contaminant in nuclear waste. Highly 

selective binding of this element by ion exchange was attributed to structural distortions in the material. By following total 

scattering from nanocrystalline materials over time, evolution 

of the pair-distribution functions for FeS minerals were also 

determined. Martin used TRXRD coupled with differential scanning calorimetry to study the nucleation and growth of ZnCl2

from melts. The rate of crystal growth was inversely related to 

the initial temperature of the melt. For sodalite, templating was 

In-Situ Kinetic Analyses in Environmental and Chemical Systems Workshop 

attendees

The workshop also included a brief tour of SAXS beamlines 

X27C and the newly renovated wiggler-based X21 beamline, 

and ended with a discussion session during which a number of 

NSLS SAXS users presented their results.

— Lin Yang

Year in Review 3-23
3-24 NSLS Activity Report

Tony Lenhard Receives the 2005 UEC Community Service Award

May 24, 2005

This year, the NSLS Users’ Executive Committee (UEC) presented the UEC Community Service Award to Tony Lenhard, 

Senior Technical Supervisor, NSLS User Science Division. The 

award is given for service, innovation, and dedication to NSLS 

users, and Tony is well deserving 

of that honor.

As a tribute to nearly 25 years 

of dedicated support for NSLS 

experimenters and beamlines, 

members of the NSLS user community nominated Tony Lenhard 

for this year’s award. Tony has 

demonstrated an uncommon 

dedication to improving the 

experimental setups at the NSLS. 

Here are quotes and paraphrased 

comments from some of the users 

who nominated Tony:

• Tony has supervised the Beamline Development and Support group that has been central to the construction, upgrade, 

and maintenance of all of the User Science Division beamlines: 

x-ray, ultraviolet, and infrared, including the insertion devices.

• As supervisor of that group, his superior traits have set the 

standard and inspired all of the NSLS User Science Division 

technical staff to excellence. 

• “Tony is always ready to advise on the mechanical design of 

users’ experimental apparatus, even under acute time pressure.”

• “Tony is a treasure house of technical knowledge and skill 

in setting up beamlines and experiments. He has had a huge 

impact on the user community, based on his supervision of the 

technical work on every one of the NSLS-operated beamlines. 

Since many of the PRT beamlines look to the NSLS-constructTony Lenhard

found to be critical to crystal growth, with isothermal crystallization only occurring if the melt reached a critical temperature 

below the melting temperature, which allowed proper ordering 

of the templating cations.

In summary, in-situ synchrotron-based x-ray absorption, scattering, and diffraction are successfully used to follow the kinetics and mechanisms of chemical processes in a variety of systems. Further developments and applications of these methods 

to probe reactions at increasingly shorter time scales in highly 

heterogeneous natural systems will advance our understanding of the short- and long-term fate of chemical contaminants in 

the environment.

— Dean Hesterberg and Jeff Fitts

NSLS UEC Vice Chair Peter Stephens presents the 2005 UEC Community 

Service Award to Tony Lenhard at the Users’ Meeting banquet.

ed beamlines for technical guidance, Tony’s mark is probably 

on every single beamline at the NSLS.”

• Many of the people who wrote in support of his nomination 

made particular mention of his special talent for coming up with 

a simple solution to a mechanical problem, often quite different 

from what the experimenter initially visualized.

• “I don’t believe the community properly appreciates his contributions to the many experiments that otherwise would have 

been delayed.”

• Tony is patient and unflappable to a remarkable degree, 

especially considering the excited state that experimenters 

are often in when facing technical difficulties at the start of an 

experiment.

• “Tony may be one of the most underappreciated treasures 

in the NSLS. He is often on the spot when users arrive and he 

has to make some quick modifications to equipment to allow 

them to complete an experiment.”

• “Tony plays a crucial role in assisting NSLS users while they 

are performing experiments. Every user facility needs a person 

like Tony: someone who knows how to build or modify any mechanical part in a short amount of time, and someone who is 

kind enough to help guide experimenters in the right direction.”

• Tony has served the NSLS User Community in the ways 

described above for essentially the entire life of the NSLS. 

Ironically, many of the users whose experiments run well have 

never even met him. It is time for him to be recognized for this 

service via this Community Service Award.

Peter Stephens vice chair of the UEC, presented the award to 

Tony at the NSLS Users’ Meeting banquet on the evening of 

Tuesday, May 24th. Tony received a $250 gift certificate and 

his name was engraved on the plaque on display in the NSLS 

lobby. Congratulations Tony, and thanks for a job well done!

— Peter Stephens
Crystallization Workshop Gets Top Marks 

From Participants

June 6-8, 2005

The “Crystallization: Focus on Optimization Techniques, 

Soluble and Membrane Proteins” course organized by Naomi 

Chayen (Imperial College of London) and Vivian Stojanoff 

(NSLS) took place at the NSLS from June 6 through June 8. 

During those three days, 55 researchers from the U.S. and 

abroad discussed and experienced hands-on the complexity of 

the protein-crystal growth process. 

Several lectures to introduce the subject and eight parallel 

practical sessions were held by experts in the field during three 

days. Neer Asherie (Yeshiva University) discussed “Understanding of the Protein Phase Behavior,” Pat Loll (Drexel 

University) discussed the “Effects of Detergents,” Marie Claude 

Marchand (Nextal) discussed the “Vapor Diffusion Method and 

Optimization Techniques,” Gwen Nneji (Imperial College of 

London) discussed “Non-standard Crystallization Techniques,” 

Petra Fromme (Arizona State University) discussed “Phase 

Diagrams: A Way for the Rational Design of Membrane Protein 

Crystallization,” and Peter Nollert (deCODE Genetics) discussed “Micro Crystallization Using the Lipidic Cubic Phase 

Methodology.”

The practical sessions also included talks on “Purification TechCrystallization Workshop attendees

NSLS Physicist, Zhong Zhong, Awarded 

Tenure

June 1, 2005

BSA granted tenure on June 1 to five Brookhaven scientists. 

They were: Ivan Bozovic, Materials Science Department; Sergei Lymar, Chemistry Department; James Misewich, Materials 

Science; Werner Vogelsang, Physics Department; and Zhong 

Zhong, National Synchrotron Light Source Department.

Tenure appointments are granted by action of the BSA Board 

after a rigorous selection procedure overseen by the BSA Science & Technology Steering Committee. 

In making tenure decisions, the BSA Board is advised by 

members of the Brookhaven Council, an elected body that 

advises the Director 

on matters affecting 

the scientific staff.

At the NSLS, physicist Zhong Zhong 

received tenure for his 

contributions to instrumentation, leadership, 

and for his innovative 

and creative original 

research. “Zhong is 

widely recognized for 

his major and creative 

contributions to the 

design and implementation of novel 

x-ray optics and as 

the co-inventor of a 

new medical imaging 

technique that has great potential as a powerful and unique 

diagnostic tool,” said Steven Dierker, Brookhaven’s Associate 

Laboratory Director for Light Sources.

Conducting theoretical and experimental studies, Zhong 

devised a novel method for focusing high-energy x-rays and 

also a powerful new tool for fluorescence detection — offering 

scientists new ways to study previously inaccessible materials.

Zhong is also coinventor of diffraction-enhanced imaging, or 

DEI, a technique that makes use of variations in how tissues 

refract and/or scatter x-rays, rather than absorption, which can 

be used to visualize soft tissues as well as bone at considerably lower x-ray doses than traditional radiography. DEI shows 

promise in diagnosing breast cancer and other soft-tissue 

diseases. In addition, Zhong serves as spokesperson for two 

NSLS beam lines, and is expected to help establish a Biomedical Imaging Research Resource at the facility.

According to Dierker, “Zhong’s talent and expertise in finding 

creative solutions to the most challenging optics and instrumentation problems will be especially crucial at NSLS-II, which

will present new and difficult instrumentation challenges to take 

Zhong Zhong

advantage of its world-leading brightness.”

Zhong received a B.S. in physics from Beijing University in 

1990, an M.S. in applied physics from Michigan Technological 

University in 1992, and a Ph.D. in physics from Stony Brook 

University in 1996. He joined the NSLS as a postdoctoral 

research associate in 1997, and has since been promoted to 

assistant scientist (1998), x-ray ring manager (1999), associate physicist (2000), and physicist (2002). He has also been an

adjunct assistant professor in Biomedical Engineering at Stony 

Brook University since 2001. 

— Karen McNulty Walsh

Year in Review 3-25
3-26 NSLS Activity Report

BioCD-2005

June 20-24, 2005

An intensive weeklong course on circular dichroism (CD) was 

presented at the NSLS at Brookhaven National Laboratory, 

from June 20-24.

CD is the difference in absorption of left and right circularly polarized light. It is observed in the spectral regions of absorption 

of molecules that are chiral, i.e. lacking a center of symmetry. 

While most CD spectra are small — only a tiny fraction of the 

total absorption — biopolymers with helical structures, such as 

proteins, DNA, RNA and polysaccharides, exhibit informative 

CD spectra.

The objective of BioCD-2005 was to acquaint the participants 

with the theory of ultraviolet CD spectroscopy, techniques, 

and instrumentation for acquiring CD data with laboratory and 

synchrotron-source instruments, as well as computational tools 

for analysing CD spectra, with special emphasis on determinations of the net secondary structure of proteins.

The motivation for a new course on CD spectroscopy is due, 

in part, to recent advances in CD spectrometers and accessory equipment, plus the development of new software for data 

analysis. The initial synchrotron beamlines for CD spectrosBioCD-2005 participants

copy were built at Tantalus and SURF II, moving to Aladdin and 

the NSLS, respectively, when these facilities opened. Within 

recent years, there has been a significant increase in interest 

in synchrotron radiation CD (SRCD). NSLS beamline U11 is 

being commissioned as a dedicated facility for UV CD spectroscopy and the Synchrotron Radiation Source at Daresbury 

(United Kingdom) recently brought beamline 12.1 online in 

the same role. SRCD instruments are also operating at the 

Institute for Storage Ring Facilities in at the University of Århus 

in Denmark, BESSY II in Berlin, HiSOR in Hiroshima, and the 

Beijing Synchrotron Radiation Facility. Additionally, there are 

plans for new CD beamlines at the Diamond Light Source in 

the UK and at SOLEIL in France.

Students attending BioCD-2005 were from the United States, 

the UK, Sweden, Ireland, Portugal, and Mexico, and included 

graduate students, postdoctoral researchers, and established 

investigators from industrial and governmental laboratories. 

Lectures were presented by Bonnie Wallace and Lee Whitmore 

(Birkbeck College, University of London), Robert Janes (Queen 

Mary College, University of London), John Sutherland and Lisa 

Miller (BNL), and Eugene Stevens (State University of New 

York at Binghamton). Sutherland, Wallace, Janes, and Miller 

organized the course. John Trunk, Denise Monteleone. and 

Michael Appel provided technical support. The hands-on laboratories included data collection on beamlines U9B and U11 

plus a conventional (lab-based, commercial) CD spectrometer. 

On-line data analysis of protein structures used the DichroWeb 

web site, based at Birkbeck College in London.

Topics covered by the workshop included: "Principles of CD 

Spectroscopy," "CD of Proteins, Analyses of Protein Secondary 

Structures and Practical Considerations in Measurements of 

CD Spectra," "Instrumentation for CD and SRCD," "CD Bioinformatics," "Demonstrations of Software for CD Spectroscopy," 

"Time Resolved Spectroscopy," "CD of Membrane Proteins," 

"Data Bases for Analysis of CD Spectra," "CD of Nucleic Acids 

and Polysaccharides (ES)," "Vibrational Spectroscopy," and 

"Linear Dichroism and Applications of SRCD to Structural and 

Functional Genomics". The workshop ended with an open disniques” by Janmeet Anand and Debbie Cohen (GE Healthcare), “The Light Scattering as a Diagnosis of Protein Purity” 

by Trevor Harvard (Precision Detectors), and “High-Throughput 

Screening of Crystallization Conditions” by Chris Gawronski 

(Fluidigm). 

The 40 participants were divided into eight groups and rotated 

through the two-hour practical sessions. The course was 

designed to allow participants to experience different crystallization techniques and discuss the available optimization tools. 

The importance of protein purity and knowledge of phase diagrams were stressed in several lectures and practical sessions. 

Participants had the opportunity to try the different methods 

on standard or known proteins, such as lysozyme, thaumatin 

proteinase K, photosystem I, and bacteriordopsin. 

Several participants brought their own proteins and tried the 

different methods and screening techniques to screen or optimize crystallization conditions. They used plates from Nextal, 

Hampton Research, Douglas Instruments, Molecular Dimensions, and Jena Biosciences. Several participants characterized their proteins by light scattering using the system provided 

by Precision Detectors, first finding possible improvements in 

the crystallization conditions they were using.

Overall, all the participants recommended organizing similar 

workshops in the future, as this is the only course in the U.S.

that offers real experience in protein crystallization. 

— Laura Mgrdichian
Changes to NSLS User Access Policy

June 30, 2005

Important changes to operations at the NSLS were incorporated into the NSLS User Access Policy. This policy will support 

the NSLS in its mission to perform outstanding science in 

a safe and environmentally friendly manner. The document 

outlines the general policies for user access to the NSLS and 

is designed to ensure open and fair access to the NSLS by the 

scientific community at large, to sustain the highest standards 

of scientific and technical excellence, and to be responsive 

and adaptable to varying user needs and funding realities. The 

policy changes were made after consulting with the NSLS User 

Executive Committee and were approved by the NSLS Science 

Advisory Committee.

Facility Beamlines

One major change in the new policy is the creation of “facility” 

beamlines, which are controlled and managed by the NSLS. At 

least 75% of the available beam time on each facility beamline 

will be allocated to general users and one or more contributing

users, with at least 50% of the available beam time going to 

general users.

Contributing Users

Another major change is the establishment of a new mode 

of user access, known as contributing users (CUs). CUs are 

individuals or groups who carry out research at facility beamlines as well as enhance the capabilities of those beamlines 

or contribute to their operation. CUs typically develop instrumentation in some manner, bringing external financial and/or 

intellectual capital into the development of the beamlines or 

making an external contribution to the operation of the beamlines. To encourage involvement, and in exchange for supporting the general user program, CUs may be recognized for their 

investments by receiving a specified percentage of beam time 

on one or more beamlines for a period of up to three years, 

with the possibility of renewal. The first group of CUs will be 

selected on September 1, 2005.

The new NSLS User Access Policy can be found at: 

http://www.nsls.bnl.gov/newsroom/publications/manuals/ppm/.

— Chi-Chang Kao

cussion on the future of CD and SRCD in structural molecular 

biology.

BioCD-2005 was supported by the Office of Biological and Environmental Research within the U.S. Department of Energy’s 

Office of Science, and BNL’s Biology and NSLS departments.

— John Sutherland

NSLS Scientists Recognized 

by the American Physical 

Society

June 30, 2005

Three NSLS user researchers —Jan 

Genzer, Thomas Russell, and Gabriel 

Aeppli — were honored with prestigious American Physical Society (APS) 

awards. Additionally, two other NSLS scientists — user Robert Bartynski and the 

NSLS’ own Li-Hua Yu — were elected as 

fellows of the APS. 

“For his highly creative manipulation of 

surface properties via monolayer and 

macromolecular films,” Genzer, a materials scientist at North Carolina State University, was awarded the Dillon Medal.

The Polymer Physics Prize went to Russell, a polymer scientist with the University of Massachusetts. He was cited “for 

his pioneering research and fundamental 

elucidation of the surface and interfacial 

behavior of polymers.”

Aeppli, a condensed matter physicist 

with University College London, received 

the Oliver Buckley Prize “for fundamental 

contributions to experimental studies of 

quantum spin dynamics and spin coherence in condensed matter systems.”

Bartynski, a condensed matter physicist 

at Rutgers University, was elected “for 

pioneering experiments to determine the 

electronic properties of surfaces, especially for leadership in developing Auger 

Photoelectron Coincidence Spectroscopy (APECS) with synchrotron radiation 

as a tool for local electronic structure.”

Yu, a beam physicist at the Deep Ultraviolet Free-Electron Laser at the NSLS, 

was elected “for creative contributions to 

the theory of self-amplified spontaneous 

emissions and high-gain harmonic-generation, and the experimental demonstration of the high-gain harmonic-generation free-electron laser.”

More information on the awards is available at 

http://www.aps.org.praw/05winners.cfm.

— Laura Mgrdichian

Jan Genzer

Thomas Russell

Robert Bartynski

Gabriel Aeppli

Li-Hua Yu

Year in Review 3-27
3-28 NSLS Activity Report

Protein Rush at the NSLS

July 1, 2005

In the spring of 2005, the Protein Structure Initiative (PSI) 

launched the second phase of its national effort to find the 

three-dimensional shapes of a wide range of proteins. This is 

good news for the NSLS, since many of those structures will be 

determined here. But more importantly, the structural information will help reveal the roles that proteins play in health and 

disease and will help point the way to designing new medicines.

The highlight of the PSI second phase was the announcement 

of 10 new research centers, which marks the second half of the 

decade-long initiative. The centers are slated to receive about 

$300 million in grants over the next five years.

When the PSI established its pilot centers in 2000, its goal was 

twofold: to develop innovative approaches and tools, such as 

robotic instruments, that streamline and speed many steps of 

generating protein structures, and to incorporate those new 

methods into pipelines that turn DNA sequence information into 

protein structures. 

Now, the focus shifts to production. The new centers will 

use methods developed during the pilot period to rapidly 

determine thousands of protein structures found in organisms ranging from bacteria 

to humans. These efforts will 

facilitate structure determination on a much larger number 

of proteins through computer 

modeling.

The PSI production phase 

includes two types of centers. 

Four large-scale centers, 

established during the pilot 

phase, hope to generate 

between 3,000 and 4,000 

structures. Six smaller, specialized centers will develop 

novel methods for quickly 

determining the structures 

of proteins that traditionally 

have been difficult to study. 

These include small protein 

complexes, proteins that 

attach to a cell’s outer “skin,” 

or membrane, and many proteins from higher organisms, 

including humans.

As before, the PSI centers 

will submit their structures 

and related findings to the Protein Data Bank, an NSF- and 

NIH-supported public repository of three-dimensional biological

structure data.

The Protein Structure Initiative is funded largely by the National 

Institute of General Medical Sciences (NIGMS) and also receives funding from the National Center for Research Resources. Both centers are part of the National Institutes of Health.

More on how BNL and NSLS are involved

In 2000, an organization called the New York Structural GenomiX Research Consortium was formed as part of the PSI 

pilot program. During the pilot period, members of this consortium developed many innovative methods and determined approximately 200 new protein structures. The majority of these 

structures were deciphered at the NSLS, with about 50 of them 

being determined by Brookhaven scientists. In fact, two of the 

consortium’s principal investigators are Brookhaven Lab biologists Subramanyam Swaminathan and William Studier.

In the second PSI phase, the Brookhaven group will continue 

to solve structures at the NSLS and work to improve their 

methods. Over the five years, the consortium will receive approximately $48 million, with about $9.5 million of that supporting research at Brookhaven Lab.

The consortium’s other member institutions are Albert Einstein 

College of Medicine, Mount Sinai School of Medicine, The 

Rockefeller University, and Weill Medical College of Cornell 

University.

— Laura Mgrdichian

Three protein structures determined 

at the NSLS as part of the Protein 

Structure Initiative (Images courtesy 

www.nysgrc.org.)

Highlights from the 2005 NSLS Summer 

Sunday

August 7, 2005

An enthusiastic crowd of 700-plus visitors came to the National

Synchrotron Light Source on August 7 as part of Brookhaven 

Lab’s Summer Sundays program, crowding the lobby, seminar 

room, and front patio 

to see what the NSLS 

had in store for them. 

The program welcomes 

the public to the Lab 

on several consecutive 

Sundays in the summer, 

highlighting a different 

facility each week.

Guests arrived at 

Berkner Hall, where an 

NSLS scientist first gave 

a brief NSLS overview 

talk and discussed how 

Out on the patio there were several fun, 

interesting exhibits
A steady stream of visitors filled the NSLS lobby

“MC” Gerry Van Derlaske with a happy raffle 

winner

Summer Sunday volunteers help young guests build 

“crystals” out of toothpicks and gumdrops

Volunteer Ted Feldman shows visitors how the 

“Electron Catapult” display works

they use the NSLS 

to perform their 

own research. 

From there, visitors 

boarded a bus to 

the NSLS.

There were many 

things to do and 

see at the facility. 

Fifteen hands-on 

displays were set 

up in the lobby, 

seminar room, 

and patio to show visitors how the NSLS works and teach 

them about the science performed there. For example, the 

new “Electron Catapult” display showed visitors how different 

amounts of energy are required to propel an electron from an 

atom’s “ground state” level to higher levels. This concept is key 

to many NSLS experiments.

At the “Crystals: Unlocking the Secrets of Life” 

display, many kids had a 

great time building “crystals” from toothpicks and 

gumdrops — some left 

with gigantic creations!

Another, always popular 

display was “Sounds of 

Silence,” where guests 

watched how a vacuum 

pump caused Marshmallow Peeps to expand 

and then, when turned 

off, to shrivel down to a smaller size than when the experiment 

began. Guests learned that the shrunken candies were still edible (perhaps even tastier that way).

And at “See the Light,” visitors could see actual synchrotron 

light, guided to the lobby from the experimental floor by a fiberoptic cable.

Upon entering the building, each guest received a quiz with 

several questions 

that could be answered by visiting 

each display. Every 

finished quiz was 

handed in and 

redeemed for an 

NSLS keychain 

flashlight and, every half-hour, one 

quiz was selected 

raffle-style to receive another prize 

— an NSLS baseball cap or BNL polo shirt.

Always a powerful sight for guests are the lobby and secondfloor viewing windows that look down over the NSLS experimental floor. Looking down across the expanse of hardware, 

aluminum foil, and wiring is always fascinating for first-time 

visitors. At both windows, NSLS scientists were available to 

answer questions. Large neon numbers placed on the floor 

clearly labeled various components.

Outside the building, on the patio, NSLS scientists demonstrated how solar cars and water rockets worked, among other 

fun and interesting toys.

The day’s success was 

made possible by many 

volunteers: Marc Allaire, 

Michael Appel, Steve 

Bennett, Mike Buckley, Wolfgang Caliebe, 

Shailendra Chouhan, 

John Dabrowski, Elaine 

Di Masi, Matt Engel, Larry Fareria, Ted Feldman, 

Ed Haas, Sarah Heins, 

Steve Hulbert, Anubav 

Jain, Ariane Kretlow, 

Kathryn Krycka, Tony 

Kuczewski, Tony Lanzirotti, Alan Levine, Andreana Leskovjan, 

William Little, Ebrahim Mahajna, Corinne Messana, Laura Mgrdichian, Laura Miller, Lisa Miller, Eileen Morello, Wendy Morrin, 

Susila Ramamoorthy, Perumal Ramasamy, Lydia Rogers, Ray 

Raynis, Meghan Ruppel, Sami Khouri Salameh, Sharadha 

Sambasivan, Cecilia Sanchez-Hanke, Anne Schirmer, Randy 

Smith, Peter Stephens, Raji Sundaramoorthy, Tejas Telivala, 

Heather Turbush, Gerry Van Derlaske, Adele Wang, Gary 

Weiner, Marty Woodle, Nancye Wright, Lin Yang, and Zhong 

Zhong.

— Laura Mgrdichian

Three successful crystal-builders

Year in Review 3-29
3-30 NSLS Activity Report

Meet the NSLS Summer Students of 2005

August 31, 2005

Each summer, a number of high school and college students 

perform research projects at the NSLS. Most of the students 

work at the NSLS as part of Laboratory-sponsored research 

internship programs. 

The students work with scientists and engineers from the department in a wide range of research fields: medical sciences, 

geology and environmental sciences, chemistry, materials 

science, physics, and electrical and mechanical engineering. 

The students also attend scientific lectures, tour BNL research 

facilities, and participate in numerous social activities.

Interested students apply to 

these programs in the spring 

and the programs range from six 

to 10 weeks long. More information and application procedures 

can be found on the BNL Science Education website at http:

//www.bnl.gov/scied/.

Jeff Borack, now a senior at 

SUNY Binghamton, spent his 

summer trying to determine 

how to differentiate between two forms of chronic lymphocytic 

leukemia (CLL). In his project, developed by Dr. Nick Chiorazzi 

from the North Shore Long Island Jewish Hospital and NSLS 

scientist Lisa Miller, he analyzed 

B-cells (a type of white blood 

cell) using an infrared microscope. This research may lead 

to the development of a new diagnostic tool capable of helping 

doctors and patients determine 

which treatment options are best 

for CLL.

For the past two summers, 

Michael DiBiccari, a senior at 

Hauppauge High School, has 

worked with Elaine DiMasi, studying the growth process of 

biological minerals. They examined the diffraction patterns of 

x-rays that reflected off the mineral crystals, which helped them 

understand how the crystals 

formed. This research will be 

helpful in understanding the 

process of biomineralization.

Anubhav Jain is now a senior 

at Cornell University. Both this 

summer and last, he worked 

with NSLS scientist Vivian 

Stojanoff, developing software 

to help automate the process of 

determining the molecular structure of proteins. This research 

will help structural biologists get 

three-dimensional structures of 

proteins more quickly, allowing 

scientists to develop treatments 

Jean Christian Brutus is a 

sophomore at Stony Brook University. This summer, he worked 

with engineer John Skaritka 

in the NSLS design room. His 

project involved designing a superconducting undulator (a device used in synchrotron rings), 

manufacturing it, and finding a way to wind and cool down 

the system. This undulator will 

be used as an insertion device 

for the electron accelerator in 

NSLS-II, the planned NSLS 

successor.

Gabriel Sanchez, a senior at 

Stony Brook University, worked 

with mentor Cheo Teng, the 

NSLS systems administrator. 

His project involved systems/

network administration. The 

NSLS uses Hewlett-Packard 

UniX machines to monitor the daily operations and data collection of the particle accelerators. These machines are configured on a network; Sanchez’ 

objective was to successfully 

add another machine to this 

existing network. This involved 

the setup of a Network Information Service, the Domain Name 

System, and a Network File 

System.

Theodore Feldman, now a 

junior at Stony Brook University, 

worked with Lisa Miller studying 

compositional changes in developing mouse bone. They used 

infrared microspectroscopy to study changes in the chemical 

makeup of bone as it mineralizes by analyzing the infrared 

spectrum of bone’s organic and inorganic components. This 

work may help elucidate the role 

chemistry plays in determining 

bone strength and quality, which 

may be used to better treat and 

diagnose osteoporosis and 

similar bone diseases.

Matthew Engel worked with 

NSLS scientist Marc Allaire 

on a protein crystallography 

project. The particular protein he 

isolated and worked with is from 

Michael DiBiccari

Jeff Borack

Anubhav Jain

Jean Christian Brutus

Gabriel Sanchez

Theodore Feldman

Matthew Engel
the capsid (protein 

coating) of a human 

virus that surrounds 

its DNA and controls 

infectivity. Solving the 

protein’s structure 

will allow researchers 

to engineer capsids 

with less ability to 

produce an immunesystem response or 

even target specific 

membrane receptors.

Ebrahim Mahajna, Mahmoud Simri, and Sami Khouri Salameh 

are seniors at Ben Gurion University in Israel. They performed 

research at the NSLS as part of a U.S. Department of Energy 

Cooperative Research Program. Simri, working with Vivian 

Stojanoff, crystallized a protein and determined its structure 

using x-ray crystallography. Salameh, with Lisa Miller, studied 

a potential therapy for skin melanoma by imaging skin cancer 

cells using infrared light. Mahajna worked with Zhong Zhong 

and Avraham Dilmanian, studying whether diffraction-enhanced 

imaging could detect early stages of Alzheimer’s disease.

— Laura Mgrdichian

Ebrahim Mahajna, Mahmoud Simri, and Sami 

Khouri Salameh

NSLS-II Gets CD-0!

September 9, 2005

The Laboratory received fantastic news in September 2005: 

The Department of Energy granted “Critical Decision Zero” 

(CD-0) status to National Synchrotron Light Source-II, the 

planned world-leading NSLS successor. This is the key 

first step in the long process to make NSLS-II a reality at 

Brookhaven.

Accompanied by Lab Director Praveen Chaudhari 

and Steve Dierker, Associate Laboratory Director 

for Light Sources, DOE 

Brookhaven Site Office 

Manager Michael Holland 

announced the news at an 

NSLS All-Hands meeting 

on Friday, September 9.

“This is a tremendous step 

forward for science,” said 

Holland. “The effort that 

went into this by Steve 

Dierker and others on the project was tremendous. I thank 

everyone for their hard work and accomplishments.”

Holland noted that as part of the process that leads to CD-1, 

the next critical decision for the project, the physical site for 

ALD for Light Sources Steve Dierker

DOE Brookhaven Site Office Manager 

Michael Holland

Lab Director Praveen Chaudhari

the facility will be chosen, determining whether 

NSLS-II will be located at 

BNL. “There will certainly 

be a strong case made for 

NSLS-II at Brookhaven. 

There is an awful lot of 

work ahead of us in the 

next eight to 12 months,” 

he said.

In his comments, Chaudhari congratulated the 

NSLS staff and many 

others for their efforts in 

maintaining the NSLS 

while working to make the case for NSLS-II. “You ought to take 

a moment and clap for yourself,” he said. “It’s been difficult to 

keep the NSLS running and design a new machine. You are 

going to have to continue to work very hard, but I expect that 

you can do it.”

Dierker called the announcement a “wonderful occasion.” He 

then presented an overview of the history of the NSLS-II project, from the initial idea to the proposal to the major reviews by 

DOE, as well as the large and successful NSLS-II workshop in 

March 2004 — all the results of hard, hard work and cooperation. He thanked everyone for helping to achieve this critical 

milestone and emphasized the continuing teamwork necessary 

to continue the process and 

secure the site.

“There is a strong research 

community in the Northeast 

and a tremendous density 

of academic and research 

institutions,” he said. “Moreover, U.S. synchrotrons 

are far oversubscribed. We 

need NSLS-II more than 

ever, or the science and 

benefits from that science 

will move overseas.”

— Laura Mgrdichian

Synchrotron Environmental Science III 

(SES) Meeting

September 19-21, 2005

On September 19-21, the Synchrotron Environmental Sciences III (SES III) conference was held at Brookhaven National 

Laboratory (BNL). Continuing the tradition established by previous SES conferences held at Argonne National Lab, SES-III 

brought together the diverse community of scientists who apply 

Year in Review 3-31
3-32 NSLS Activity Report

Synchrotron Environmental Science III (SES-III) Meeting attendees

synchrotron-based radiation techniques to study the biological 

and geochemical aspects of both local and global environmental issues. The conference included two days of topical sessions that addressed the application of innovative synchrotron 

methods in environmental science along with applications in 

bioavailability and remediation science. The third day included 

a workshop on microbeam methods. Attendees reported on 

environmental science activities conducted at synchrotron 

facilities worldwide.

The SES meetings are an outgrowth of EnviroSync, a grass 

roots organization with almost 400 members established in 

early 1998 to represent the growing multidisciplinary community of synchrotron radiation users who focus on molecular environmental science problems (http://www.cems.stonybrook.edu/

envirosync/history.html). Stephen Sutton (GSECARS, University of Chicago) has been Chair of EnviroSync since 2002. 

An EnviroSync open meeting was also held as part of the 

SES-III conference, during which Richard Reeder (Stony Brook 

University) was elected as the new EnviroSync Chair and John 

Bargar (Stanford Synchrotron Radiation Lab) its Secretary for 

2005-2007.

BNL Director Praveen Chaudhari opened the SES-III conference with very supportive comments emphasizing the 

increasingly important role environmental science research 

plays at BNL and how well suited light sources are to answer the questions asked by environmental scientists. There 

were also welcoming remarks from Martin Schoonen, Stony 

Brook University’s Associate Vice President for Research, 

and Creighton Wirick, Chair of BNL’s Environmental Sciences 

Department. Steve Dierker, BNL’s Associate Lab Director for 

Light Sources, then gave an update on the National Synchrotron Light Source (NSLS) and in particular the progress that the 

NSLS has made in bringing additional beamlines into operation 

that support environmental science users. He emphasized that 

this is need driven by the rapidly increasing number of environmental science users at the NSLS and the over-subscription of 

beamlines that cater to the community. Steve also updated the 

attendees on the status of NSLS-II, which was recently granted 

“Critical Decision Zero” (CD-0) status by the Department of 

Energy (DOE). NSLS-II is a proposed new state-of-the-art 

medium energy storage ring designed to deliver world leading 

brightness and flux with top-off operation for constant output. 

DOE program managers Nicolas Woodward (Basic Energy 

Sciences – Geosciences Research Program) and Roland 

Hirsch (Biological & Environmental Research – Environmental 

Remediation Sciences Division) also gave updates on DOE 

support for environmental research and how these programs 

have stressed availability of synchrotrons to earth and environmental scientists. Todd Anderson from the Office of Biological 

& Environmental Research was also in attendance.

Gordon Brown (Stanford University) opened the scientific 

presentations of the first day with an overview of recent environmental science activities that have been made possible 

by using synchrotron-based approaches, as well as future 

possibilities. The first day’s sessions also included talks by Ken 

Kemner (Argonne National Lab), Neil Sturchio (Univ. Illinois), 

Sanjit Kumar Ghose (GSECARS, Univ. Chicago), David Shuh 

(Lawrence Berkeley Lab), and Lynda Soderholm (Argonne 

National Lab). Talks on the first day focused on the use of 

innovative synchrotron based techniques in biogeosciences 

and how studies of mineral surfaces can employ x-ray standing 

wave imaging, resonant anomalous x-ray reflectivity, and crystal truncation rod scattering. There were also discussions about 

the application of soft x-ray emission spectroscopy, resonant 

inelastic x-ray scattering, and extended x-ray absorption fine 

structure investigations in the study of actinides. The first day 

concluded with a poster session.

Sessions on the second day included a number of talks on the 

application of synchrotron techniques to biological-environmental systems. Topics included metal ions in living systems, the 

structural chemistry of bacteriogenic manganese oxides, the 

reduction of U(VI) by Fe(II) at cell surfaces, and the application 

of synchrotron infrared microspectroscopy to environmental 

studies. There were also discussions of the use of multiple 

synchrotron x-ray techniques in the study of plant-metalsoil interactions, the effect of microbial siderophores on Pb 

speciation and adsorption, and the application of synchrotron 

micro-diffraction in prediction of environmental risks associated with arsenic-bearing mine wastes. Attendees also heard 

about the benefits of combining x-ray and neutron scattering techniques for obtaining fundamental information about 

processes of importance to environmental sciences. Speakers included Graham George (Univ. of Saskatchewan), John 

Bargar (Stanford Synchrotron Radiation Lab), Maxim Boyanov 

(Argonne National Lab), Stefan Vogt (Argonne National Lab), 

Lisa Miller (Brookhaven National Lab), Ryan Tapperro (Univ. 

of Delaware), Bhoopesh Mishra (Univ. of Notre Dame), John 

Parise (Stony Brook Univ.), Heather Jamieson (Queen’s Univ., 

Canada), and Matthew Ginder-Vogel (Stanford Univ.). The 

day’s sessions concluded with a classic Long Island clambake, 

where attendees gorged themselves on fresh lobsters, clams, 

and mussels well into the evening.

The meeting concluded with a workshop on the application 
The 2005 NSLS Barbeque Wraps Up the 

Year

September 23, 2005

The unusually warm, sunny weather of September 23 did not 

hint at the cool autumn days to come, but did make for an enjoyable 2005 NSLS Barbeque. However, it was the NSLS staff 

members in attendance, particularly the service and spotlightaward winners, that made the event memorable.

Service Awards

Nick Gmur and Dennis Carlson 

were honored for 30 years of 

service at Brookhaven Lab, 

and 25-year awards went to 

Shu Cheung, John Klug, Gloria 

Ramirez, and Peter Zuhoski. 

In the 20-year category were 

Erik Johnson, Eileen Morello, 

Mihai (Mike) Radulescu, Lydia 

Rogers, David (Peter) Siddons, 

and Yong-Nian Tang. Mary 

Anne Corwin and Zhijian Yin 

celebrated 10 years.

Not available to receive their 

awards at the barbeque were Wayne Rasmussen, for a very 

impressive 40-year award; John Bohenek for 25 years of service; Sorin Pop, Leonard Pharr, and Madeline Hughes for 20 

years; and Syed Khalid and Elio Vescovo for 10 years.

Spotlight Awards

The Spotlight awards are tributes to NSLS staff members who 

NSLS Chairman Steve Dierker

of microbeam methods to environmental sciences. Workshop 

speakers included Steve Sutton, Daniel Grolimund (Swiss 

Light Source), Matthew Marcus (Lawrence Berkeley Lab), 

Mary Gilles (Lawrence Berkeley Lab), and Chris Jacobsen 

(Stony Brook Univ.). The speakers described beamlines at the 

Advanced Photon Source, Advanced Light Source, National 

Synchrotron Light Source, and the Swiss Light Source and 

applications of hard x-ray microbeam fluorescence, absorption, 

diffraction, and tomography techniques and soft x-ray spectromicroscopy techniques for characterization of environmental 

materials. 

Overall, the meeting proved to be a rousing success, and 

everyone looks forward to SES-IV in the near future. This 

workshop was co-sponsored by EnviroSync, the National Synchrotron Light Source, the Center for Environmental Molecular 

Science (Stony Brook Univ.), Brookhaven National Laboratory, 

Stony Brook University, the National Science Foundation, and 

the Department of Energy.

— Antonio Lanzirotti

have shown exceptional dedication to their jobs during the 

year. This year, the winners were: John Aloi, nominated by Bob 

Casey; Angela Bowden, nominated by Laura Miller; Michael 

Caruso, nominated by Gary Nintzel; Bob Kiss, nominated by 

Gerry Van Derlaske; Patrick Moylan, nominated by Ed Haas; 

Dennis Poshka, nominated by Anthony Kuczewski; John 

Vaughn, nominated by Gloria Ramirez; and Zhijian Yin, nominated by Peter Siddons.

John Aloi: John installed and commissioned a complex request-tracking system for the User Science Division that keeps 

a more accurate record of requests. The system, a significant 

programming effort one would expect to take several months, 

took John just a month and a half. This effort involved many 

late hours, during which John experimented with and tested 

the system. Now, jobs are easier to monitor and requests are 

handled much more efficiently.

Angela Bowden: For five weeks in April and into May, Angela 

worked under the pressure of a tight deadline to bring the 

NSLS into compliance with a Department of Energy “Corrective Action” item. She volunteered to learn two new computer 

programs, and then used them to create more than 3,000 

safety warning labels for hazardous equipment on the NSLS 

experimental floor. All the labels were accurate and completed 

before the deadline.

Michael Caruso: Caruso is recognized for providing invaluable 

assistance to the NSLS Vacuum Group over the past several 

years. Notably, he helped develop a coating process that 

greatly reduces the time necessary to coat a ceramic chamber, and then used the method to titanium-coat three ceramic 

chambers. He demonstrated excellent knowledge and skills in 

vacuum processes, and all three chamber coatings proved to 

have excellent mechanical and electrical properties.

Bob Kiss: In response to a Brookhaven Lab directive, Bob 

crafted and implemented new and improved procedures for the 

NSLS Hoisting and Lifting program. He created new check-out 

sheets tailored for equipment at each beamline, came up with 

an NSLS-specific rigging-training program, took control of 49 

NSLS overhead cranes by preventing unauthorized people 

Steve Dierker presents a 30-year service award to Nick Gmur

Year in Review 3-33
3-34 NSLS Activity Report

A group of NSLS staff members watch the awards ceremony

SBU Student Wins First Dr. Mow Shiah Lin 

Scholarship

September 27, 2005

Yuanzhi Tang, a graduate student in the Department of Geosciences at Stony Brook University (SBU), won the first annual 

Dr. Mow Shiah Lin Scholarship. The Asian Pacific American 

Association (APAA) at the Lab initiated the scholarship, which 

consists of $1,000 and a plaque, to honor the late distinguished 

Brookhaven Lab scientist for which it is named.

Mow Shiah Lin began his career at BNL in 1975 as a postdoctoral fellow and advanced to co-lead a research team working 

with an environmental remediation company to use selected 

bacteria to convert toxic oil wastes, such as used motor oils, 

into useful products. In 2001, Lin shared the R&D 100 Award, 

given by R&D Magazine to the top 100 technological achievements of the year, for a technology to recover silica from geothermal brine. Lin died suddenly due to a brain aneurysm at the 

height of his career in 2003, and his fellow employees, friends, 

and family contributed funds to establish the scholarship.

In honor of Lin’s research, achievements, and inventions, the 

scholarship will be granted annually to an Asian immigrant with 

a student visa who is matriculating toward a graduate degree 

at an accredited institution of higher education in environmental 

science, biology, or chemistry, in remembrance of the manner 

in which Lin began his career.

Tang’s research at SBU involves the use of various analytic 

techniques — including x-ray imaging at the NSLS — to study 

the mechanisms of the reaction of contaminants in natural 

environments, especially reactions at the interfaces of minerals 

and water.

— Diane Greenberg

With Mow Lin Scholarship winner Yuznhi Tang (fifth from left) in the photo are: 

(from left) Susan Eng Wong, co-coordinator, APAA; Thomas Butcher, BNL 

scientist and head of the scholarship selection committee; Satoshi Ozaki, BNL 

scientist/administrator and APAA advisor; Beth Y. Lin, APAA co-coordinator and 

widow of Mow Shiah Lin; Lucinda Lin, daughter of Beth and Mow Shiah Lin; 

Richard J. Reeder, Director, SBU Center for Environmental Molecular Sciences 

and thesis advisor for Tang; Samantha Lin Alvarado, daughter of Beth and Mow 

Shiah Lin; Marie Van Buren, member of the APAA scholarship committee, and 

(front, center) Josephine Alvarado, granddaughter of Beth and Mow Shiah Lin.

from operating them, and assigned to each beamline a person 

responsible for hoisting and lifting activities at that beamline. 

These actions helped make the NSLS experimental floor a 

safer place.

Patrick Moylan: Pat demonstrated exceptional initiative and 

written skills by putting together Worker Qualification and Training forms for the Mechanical Tech Group, which falls outside of 

his own training and work area. On top of that, he put together

a training program designed to enhance on-the-job safety in 

the x-ray ring tunnel for workers who need unescorted access 

to the tunnel. He then presented that training to all NSLS staff, 

to inform them of potential hazards in the tunnel.

Dennis Poshka: By starting up a verification and maintenance routine for the facility beamline user interlock systems,

a project he undertook on his own accord, Dennis uncovered 

many beamlines in which legacy interlocks were disconnected 

or inadequately instrumented. Identifying these interlocks prevented a potentially huge loss of equipment and greatly added 

to the measure of safety at the NSLS.

John Vaughn: After a period of repeated beam dumps on the 

x-ray ring in 2004, caused by random trips of a faulty power 

supply, John assisted in several studies to trace the origin of 

the trips in the power supply. When nothing surfaced, he set up 

diagnostics, and logged and charted events to establish a correlation between the trip frequency and the x-ray ring maintenance periods. These efforts led him to a solution after months 

of efforts by other staff members did not.

Zhijian Yin: Zhijian installed and commissioned a complex 

request-tracking system for the User Science Division over a 

very short time period. He discovered an open-source software package that fit the needs of the division and successfully incorporated it into the existing email, web, and database 

servers. This complex task involved many extended hours of 

experimenting and testing to make sure the software worked 

properly. Since then, more than 100 requests have been 

tracked without problems and the system has proved to be 

easy to use and efficient.

— Laura Mgrdichian
New Grant for Catalysis Research at the 

NSLS

September 28, 2005

A group of scientists was awarded a $900,000 grant by the 

Department of Energy to create dedicated facilities for catalysis 

research at NSLS beamlines X18B and X19A. The two facilities will be operated by the Synchrotron Catalysis Consortium, 

charged with improving and expanding catalysis research by 

taking advantage of the unique investigation tools available at

the NSLS.

Catalysis is a major area of research in the United States 

because it is very important to U.S. industry, particularly 

the chemical and petroleum industries. It is estimated to be 

involved in 90% of all chemical processes and the creation 

of 60% of the chemical products available on the market. In 

addition, catalysis is becoming more important to several other

fields, including environmental protection, pharmaceuticals and 

bioengineering, and the development of fuel cells.

The consortium’s main investigation tool will be x-ray absorption fine-structure (XAFS) spectroscopy, which measures how 

a material absorbs x-rays to learn about its molecular structure 

and electronic behavior.

“XAFS is well suited to studying catalysis, and can often yield

more in-depth information on a material’s structural, electronic, 

and catalytic properties than more widely used techniques,” 

said Anatoly Frenkel of Yeshiva University, one of the consortium’s principal investigators. “We hope to help make more 

scientists aware of the advantages of using synchrotron radiation in general, and XAFS in particular, and provide support for 

scientists who wish to start catalysis experiments at the NSLS.”

The two other principal investigators are Jingguang Chen 

of the University of Delaware and Radoslav Adzic of 

Brookhaven’s Chemistry Department. Chen said, “Synchrotron 

techniques are currently underutilized or unexplored by the 

catalysis community due to various perceived and real barriers. The primary purpose of the consortium is to promote the 

utilization of synchrotron techniques to perform cutting-edge 

catalytic research under in-situ conditions.”

Said Adzic, “This consortium is expected to have a particularly 

strong impact on the research and development of fuel cell 

electrocatalysts. Capabilities for in situ characterization of electrocatalysts in fuel cell environment under various conditions 

will be provided by adequate cell designs.”

The consortium’s co-principal investigators are Chi-Chang Kao 

and Steve Hulbert (NSLS), Jan Hrbek, Jose Rodriguez and 

Jonathan Hanson (BNL-Chemistry), David Mullins and Steve 

Overbury (Oak Ridge National Laboratory), and Simon Bare 

(UOP, LLC).

The grant will fund new hardware additions and changes at 

X18B and X19A, allowing scientists to study chemical transformations in catalytic materials over a wide range of energies 

in real time and at realistic operation conditions. Examples of

new devices that will benefit the catalysis-research community 

are state-of-the-art reactor cells, gas-handling equipment, and

detectors. The upgrades will also include the latest advances 

in beamline instrumentation. All these changes will provide new 

experimental opportunities for scientists interested in catalysis.

In addition, the grant includes funds to hire a beamline staff to 

run the new facility and provide support for visiting research 

groups. The budget also includes funds for travel, which will 

help new user scientists start synchrotron research programs 

as well as attend catalysis workshops and training courses.

Most components at X18B and X19A will be in place by April 

2006. Catalysis users are now being contacted with invitations 

to start their research program at the NSLS, and the first users 

will start experiments in February 2006. The grant covers a 

time span of three years.

— Laura Mgrdichian

Some of the key members of the Synchrotron Catalysis Consortium. In the front 

row, from left, are principal investigators Jingguang Chen and Anatoly Frenkel. In 

the back, from left, is NSLS scientist Syed Khalid, who runs beamline X18B, and 

co-principal investigators Radoslav Adzic, Steve Hulbert, and Jonathan Hanson.

EXAFS Course: Theory, Experiment, and 

Advanced Applications

September 28-30, 2005

X-ray absorption fine structure (XAFS) data collection and 

analysis courses have been held at the NSLS annually since 

2001. While previous courses were aimed at beginners and 

thus broad in scope, this three-day (September 28-30) course 

was devoted to one technique: extended XAFS (EXAFS). 

Year in Review 3-35
3-36 NSLS Activity Report

Partcipants in the EXAFS course

Brookhaven Lab Breaks Ground for New 

Nanocenter

October 3, 2005

The U.S. Department of Energy’s (DOE) Brookhaven National 

Laboratory held a groundbreaking ceremony on October 3 for 

the Center for Functional Nanomaterials (CFN). The CFN will 

provide researchers with advanced probes and the ability to 

use new fabrication techniques to study materials at nanoscale 

dimensions — typically, billionths of a meter, or 1,000 times 

smaller than a human hair. These materials have different 

chemical and physical properties than bulk materials and could 

form the basis of new technologies.

The CFN — one of five Nanoscale Science Research Centers 

to be built at DOE national laboratories — was designed by 

HDR Architecture, Inc., of Alexandria, Virginia, and is being 

constructed by E. W. Howell Co., Inc., of Woodbury, New York. 

The 94,500-square-foot state-of-the-art laboratory/office facility 

is expected to attract an estimated 300 researchers from the 

Northeast annually. 

Brookhaven employees and distinguished guests, including local Congressman Tim Bishop and Dr. Patricia Dehmer, 

Associate Director for the U.S. Department of Energy’s Office 

of Basic Energy Sciences, attended the ceremony against a 

backdrop of heavy equipment at the CFN location in the center 

of Brookhaven’s 5,300-acre site. 

“The Center for Functional Nanomaterials will be at the forefront of research that is expected to lead to new technologies,

such as faster computers, new communications devices, improved solar energy and new energy alternatives,” Congressman Bishop said. “Long Island is fortunate to have this center 

here. Everyone reaps benefits when the best minds and the 

best technology merge to explore the frontiers of science.” 

DOE’s Office of Basic Energy Sciences is funding the $81-

(L to R) Laboratory Director Praveen Chaudhari, DOE Brookhaven Site Office 

Manager Michael Holland, Battelle Memorial Institute Senior Vice President and 

Chief Operating Officer Donald McConnell, Associate Director for the DOE Office 

of Basic Energy Sciences Patricia Dehmer, Congressman Timothy Bishop, CFN 

Director Robert Hwang, and Associate Lab Director for Basic Energy Sciences 

Doon Gibbs.

Participants in this course (32 scientists from U.S. and Canada, 

representing universities, national laboratories, and industrial 

companies) had prior familiarity with the basics of the technique and were interested in learning how to correctly design, 

perform, and analyze EXAFS experiments in application to 

their research. The course was self-contained, starting with the 

fundamentals and proceeding to the more advanced topics, 

including recent theoretical developments, data analysis techniques, and specific applications of EXAFS. 

The course consisted of three lecture sessions in the mornings, 

two hands-on experimental sessions in the afternoons, and 

one data analysis session during the last day of the course. 

The organizers identified four areas of interest: nanocatalysis, 

environmental/bio/geo chemistry, disordered alloys/thin films, 

and transition metal oxides, and designed several research experiments in each of these areas. Experiments were conducted 

at eight beamlines. 

Lectures were taught by invited speakers: Edward Stern and 

Josh Kas (University of Washington), Grant Bunker (Illinois 

Institute of Technology), Anatoly Frenkel (Yeshiva University), 

Trevor Tyson (New Jersey Institute of Technology), Joseph 

Woicik (National Institute of Standards and Technology), Douglas Hunter (Savannah River National Laboratory), Scott Calvin 

(Sarah Lawrence College), and Douglas Pease (University 

of Connecticut). Among the highlights of the course were two 

talks, “History of EXAFS” and the “Pitfalls of the Experiment 

and Data Analysis,” which was taught by Edward Stern, one of 

the founders of the technique.

Beamline instructors were F. Alamgir (City University of 

New York), T. Tyson, A. Frenkel, J. Woicik, A. Ignatov (Case 

Western Reserve University), K. Pandya (Brookhaven National Laboratory), P. Northrup (Brookhaven National Laboratory), W. Caliebe (Brookhaven National Laboratory), S. Khalid 

(Brookhaven National Laboratory). Data analysis session were 

led by S. Calvin, A. Frenkel, F. Alamgir, T. Tyson, J. Woicik, S. 

Khalid and P. Northrup. 

The course administrator was Corinne Messana (BNL). The 

course was possible due to generous sponsorship by the 

National Synchrotron Light Source, Yeshiva University, and the 

DOE Synchrotron Catalysis Consortium.

— Anatoly Frenkel
NSLS Users Recognized

October 21, 2005

Each year, a number of NSLS users win prestigious awards in 

their field of scientific research. The following represent a collection of some of the awards from 2005.

Russell Hemley and David Mao Win the Balzan Prize

This year, the International Balzan 

Foundation Prize for Mineral Physics was awarded to Russell Hemley 

and Ho-Kwang (David) Mao, both 

scientists with the Geophysical 

Laboratory at the Carnegie Institute 

of Washington.

Hemley and Mao received the 

award “for the impressive impact of 

their joint work leading to fundamental breakthroughs, theoretical 

and experimental, in the field of 

minerals submitted to extreme 

physical conditions.” Much of their work — particularly their 

early, pioneering studies — has been, and is currently, performed at the NSLS.

They began working at the NSLS in 1986, using beamline 

Russell Hemley

David Mao

million CFN project. The contemporary building, which has a 

metal and glass exterior, will cost $38 million to build, while 

specialized equipment, such as electron microscopy facilities 

and lithography-based fabrication facilities, and engineering 

and project management will account for the balance of the 

budget. The facility, which will occupy nine square acres and 

will accommodate 150 people, will be considered “green,” or 

energy efficient and environmentally friendly, based on the 

U.S. Green Building Council’s rating system. Construction is 

expected to be completed by March 2007, and experiments are 

due to begin shortly after that date. 

The overarching research goal of the CFN is to help solve 

energy problems in the U.S. by exploring materials that use 

energy more efficiently and by researching practical alternatives to fossil fuels, such as hydrogen-based energy sources 

and improved, economical solar energy systems. 

Under the energy banner, CFN studies will focus on three key 

areas: nanocatalysis, the acceleration of chemical reactions 

using nanostructures; biological and soft nanomaterials, such 

as polymers and liquid crystals, in which specialized design is 

expected to lead to new functions; and electronic nanomaterials that exhibit unprecedented control of electrons, which are 

expected to lead to new communication and energy-control 

devices. 

— Diane Greenberg

X13A (later renamed X7A) to 

perform x-ray diffraction studies of 

materials subjected to extremely 

high pressures. Later, they helped 

build X17C — the world’s first 

dedicated high-pressure beamline 

— and also conducted high-pressure infrared spectroscopy studies 

at U4IR, U2B, and U2A (the world’s 

only dedicated beamline for that 

type of research).

“They have operated as a highly 

effective team,” remarked the award committee, “characterized 

by twenty years of research contributions at the highest level.

They have developed techniques which allow them to study 

the behavior of a wide range of minerals, such as hydrogen, 

the most abundant ‘mineral’ in the universe. Their results have 

deep implications for our understanding of nature.”

The prize will be given out on November 11 in Berne, Switzerland at the Swiss Federal Parliament Buildings. Each prize 

consists of one million Swiss francs (about $773,000), half of 

which must be used to fund research projects by students and 

young scientists at the winners’ home institution.

Philip Coppens Receives the 

Ewald Prize

Longtime NSLS user scientist Philip 

Coppens, a Distinguished Professor 

and Henry M. Woodburn Chair of 

Chemistry at the State University of 

New York at Buffalo, was awarded 

the prestigious Ewald Prize by the 

International Union of Crystallography (IUCr).

The prize honors Coppens’ contributions to developing the fields of electron density determination and the crystallography of molecular

excited states. He was also recognized for his commitment to 

the education of future crystallographers through many courses 

and workshops.

A significant part of the work for which he received the award 

is the result of studies at former NSLS beamline X3, which was 

operated by a collaboration of several SUNY campuses and for 

which Coppens was principal investigator for many years.

At X3, Coppens developed many of the methods he now uses 

in his research. Early on, he and his group performed several 

studies to determine the charge densities in various materials 

using x-ray diffraction. These experiments provided valuable insight into the properties of crystalline materials and the 

nature of chemical bonds within molecules and interactions 

between molecules. In later research, the group performed 

their first time-resolved studies at X3, using x-rays to determine 

the nature of molecular excited states that exist for very short 

Philip Coppens

Year in Review 3-37
3-38 NSLS Activity Report

Barbara Illman Noel Clark

Highlights from the COMPRES Sponsored 

Workshop on Synchrotron Infrared Spectroscopy for High Pressure Geoscience and 

Planetary Science

November 3-5, 2005

In recent years, infrared (IR) microscopy and spectroscopy 

have greatly benefited from new synchrotron techniques. New 

infrared synchrotron radiation sources provide a tremendous 

improvement in flux on a sample, with well-collimated beams 

from far- to near-IR that give high spatial resolution with 

unmatched signal-to-noise. This has opened up new scientific 

directions in a range of fields, including physics, biology, chemistry, materials science, high-technology, and forensics. One of 

the most exciting areas, however, is high-pressure geoscience 

and planetary science. High-pressure synchrotron IR spectromicroscopy is an ideal coupling of the diamond anvil cell device 

and synchrotron IR radiation. In addition, the technique serves 

as a useful, if not unique, tool to study minerals quenched from 

high pressures and temperatures, and natural samples (including natural high-pressure assemblages) at ambient conditions.

Sponsored by COMPRES (the Consortium for Materials Properties Research in Earth Sciences) and the NSLS, the workperiods but are highly reactive. The first results of this research 

were published in 2002.

Coppens formally received the Prize during the IUCr’s Florence Congress Opening Ceremony on August 23. The Prize, 

presented just once every three years at the triennial International Congresses of Crystallography, consists of a medal, 

certificate, and $30,000.

2005 Chief’s Honor Award for Distinguished Science Goes 

to Barbara Illman

Research plant pathologist and 

NSLS user Barbara L. Illman, 

who is Director of the Institute for 

Microbial and Biochemical Technology at the Forest Products Lab 

in Madison, Wisconsin, received 

the USDA Forest Service’s 2005 

Chief’s Honor Award for Distinguished Science for her studies in 

four major areas of research.

The award recognizes Illman for 

her efforts in “applying solid-state 

physics techniques to forestry problems, invasive species 

mitigation research, bioremediation research, and contributions 

to long-term ecological research programs.”

At the NSLS, Illman developed techniques for using x-rays to 

study wood decay, recycling of wood biomass material, and 

bioremediation of toxic chemicals in the environment. This 

work led to discoveries about the biochemical mechanisms of 

brown-rot fungi, the most destructive wood-decay organisms. 

Nearly 10 percent of the 300 million tons of trees harvested annually in the United States are used to replace wood products 

damaged by the decay fungi. The discoveries could lead to 

improved methods for protecting wood from fungi. 

Illman’s many other achievements include measures to control 

the spread of highly destructive non-native insects, especially 

in shipping materials. Roughly half of all international trade 

goods move in wood crates or on wood pallets or spools, or 

involve other wood material, creating a major pathway for the 

spread of invasive insects.

The award was presented to Illman in a Washington, D.C. ceremony by Dale Bosworth, chief of the Forest Service.

Noel Clark: Co-Winner of the APS Oliver E. Buckley Prize

The 2006 American Physical Society Oliver E. Buckley Prize, 

recognizing “outstanding theoretical or experimental contributions to condensed matter physics,” was awarded to Noel 

Clark, physicist at the University of Colorado and a user at 

beamline X10. He shares the prize with Robert Meyer of 

Brandeis University.

The two scientists received the award “for groundbreaking 

experimental and theoretical contributions to the fundamental 

science and applications of liquid crystals, particularly their ferroelectric and chiral properties.”

Clark and Meyer have made very significant contributions to 

developing the concepts that underlie the fields of liquid-crystal 

science and technology. Beyond that, they have designed novel, highly creative experiments that verify these concepts. Their 

efforts also extend to studies of other complex fluid systems, 

such as liquid-crystal polymers, colloids, and protein solutions.

Individually, Clark has performed a great deal of significant 

research. One example is his groundbreaking studies of ferroelectric liquid-crystal display cells 

that made it possible for displaycell manufacturers to use them in 

commercial devices. And recently, 

using freeze-fracture electron 

microscopy and x-ray diffraction, 

he studied the liquid crystal phases 

exhibited by banana-shaped 

molecules and determined their 

complex structure, which had perplexed the liquid-crystal research 

community.

The Buckley prize was formally 

awarded to Clark and Meyer on March 16 during the March 

2006 APS meeting in Baltimore, Maryland. It consists of 

$10,000 and a certificate.

— Laura Mgrdichian
Synchrotron Infrared Spectroscopy for High Pressure Geoscience and Planetary 

Science workshop participants

shop on Synchrotron Infrared Spectroscopy for High Pressure 

Geoscience and Planetary Science was held at the NSLS in 

November. The conveners were Zhenxian Liu and Russell J. 

Hemley (Geophysical Laboratory, Carnegie Institution of Washington). Thanks to the members of the COMPRES Executive 

Committee and the NSLS staff for suggesting, promoting, and 

supporting this IR workshop. It was a great success in terms 

of the excellence of the lectures, its broad attendance that included many new potential users and student participation, its 

extensive program, and plenty of hands-on experience for new 

users. More than 50 attendees took part (this was the maximum allowed by the budget and the size of the lecture room). 

The workshop consisted of five sessions designed to accommodate the broad spectrum of attendees, ranging from 

experts to new users. The Friday morning session was directed 

toward attendees who were new to the modern IR spectroscopy techniques used in this field, but, for experienced users, 

it was also a very useful review of the fundamentals and new 

developments. Q. Williams (University of California at Santa 

Cruz) gave a thorough overview on IR spectroscopy (and FT 

techniques in general) and its applications in the Earth sciences. G. Rossman (California Institute of Technology) gave a 

talk on hydrous components in nominally anhydrous minerals, 

which was crucially important for users who are interested in 

the calibration of the water content in minerals. A. Hofmeister 

(Washington University in St. Louis) discussed the high-pressure far-IR spectroscopy of mantle candidate minerals that are 

worth pursuing with the synchrotron technique. Finally, J. Tse 

(University of Saskatchewan, Canada) described theoretical 

methods for vibrational spectroscopy and many other applications. 

The Friday afternoon session was started by L. Carr (NSLS). 

He gave a very comprehensive talk on Fourier transform 

spectroscopy techniques using the synchrotron infrared source 

as well as an overview of the IR programs at the NSLS. There 

were seven additional speakers (A. Goncharov, V. Struzhkin, 

and S. Jacobsen, Geophysical Laboratory; D. Klug, Canadian 

Research Council; H. Scott, Indiana University at South Bend; 

G. Lager, University of Louisville; and Y. Lee, Brookhaven 

National Laboratory) who discussed different topics related to 

the work they have done at NSLS beamline U2A. These talks 

not only addressed a broad range of problems in the Earth and 

planetary sciences but also reflected new techniques developed at U2A in past years. 

The third session, held Saturday morning, focused on imaging techniques combined with synchrotron sources. L. Miller 

(NSLS) gave an extensive overview of chemical imaging at 

high spatial resolution using a synchrotron infrared microscope. 

Other speakers (L. Wang, Stony Brook University; L. Dobrzhinetskaya, University of California at Riverside; M. Koch-Müller, 

GeoForschungsZentrum Potsdam, Germany; and S. Clark, 

Advanced Light Source) gave talks featuring the applications 

of imaging techniques as well as high-pressure IR studies at 

other synchrotron sources. The facility tour and hands-on session on Saturday afternoon attracted more than 30 people. At 

the IR beamline, new users received detailed information on 

the beamline facility and its capabilities, as well as first-hand 

experience on how to perform high-pressure IR experiments 

from beginning to end.

The last session, for student/post-doc experiments at U2A, 

started right after the workshop. Two students and one postdoc submitted their research proposals and one day of beamtime was allocated per proposal. This new session offered not 

only a great opportunity to learn how to use the synchrotron 

IR facility but also a chance to collect valuable data for their 

research projects. The experiments went very well and the IR 

data they obtained were very interesting and publishable in 

scientific journals.

— Zhenxian Liu

The NSLS Remembers Bill Oosterhuis

November 16, 2005

Bill Oosterhuis, Team Leader for Condensed Matter Physics 

and Materials Chemistry in the U.S. Department of Energy’s 

Office of Basic Energy Sciences, passed away on November 

16.

Bill was a true friend of synchrotron radiation science. While at 

DOE, a position he had held since 1991, he made significant 

contributions to the field, spearheading several major changes 

to the Condensed Matter Physics 

and Materials Chemistry team. 

These include the creation of the 

X-ray and Neutron Scattering program, the Theoretical and Computational Materials Physics program, 

and the Experimental Program to 

Stimulate Competitive Research.

Before joining the DOE, Oosterhuis he worked for 17 years at 

the National Science Foundation, 

where he was a section head for its Bill Oosterhuis

Year in Review 3-39
3-40 NSLS Activity Report

BNL Establishes NSLS-II Project In Light 

Sources Directorate

December 9, 2005

In the fall of 2005, Laboratory 

Director Praveen Chaudhari 

named Steve Dierker, Associate Laboratory Director (ALD) 

for Light Sources, as Project 

Director of the newly established National Synchrotron 

Light Source II (NSLS-II) Project. The move was triggered 

by the Lab’s recent success 

in getting DOE approval for 

“Critical Decision Zero” (CD-0, 

Approval of Mission Need) for 

NSLS-II, the planned worldleading successor to BNL’s 

NSLS. NSLS-II will meet 

critical scientific challenges of the future, provide state-of-theart technology for research — complementing BNL’s Center for 

Functional Nanomaterials — and play a pivotal role in fostering

economic growth in the northeastern United States.

CD-0 is the first of five Critical Decisions that the project will 

need to achieve in order to progress through the successively 

more detailed stages of conceptual design, preliminary design, 

and final design, followed by construction, and then operations. 

While the site for NSLS-II is not formally selected until the next 

Critical Decision (CD-1, Approved Alternative Selection and 

Cost Range), BNL believes that there are strong reasons for 

citing NSLS-II at BNL.

“At Brookhaven, we have long experience and deep technical 

knowledge in the synchrotron light source field, along with an 

excellent infrastructure, demonstrated support from potential 

facility users of national and international standing, and an extraordinarily skilled and experienced workforce,” states Dierker. 

“For these and other reasons, we believe NSLS-II should be 

located here at BNL.”

NSLS-II will be a major project, with an estimated cost of 

$800M, and will employ up to 200 people during the peak of 

construction. The NSLS-II Project organization is being created 

in the Light Sources Directorate to put in place the management systems and infrastructure required to execute this complex undertaking. Building upon the groundwork laid by NSLS 

staff, the first task of the new organization will be to develop 

the documents required for CD-1, including a Conceptual Design Report and more refined cost and schedule estimates.

As NSLS-II Project Director, Dierker will retain his position as 

ALD for Light Sources and step down as Chair of the NSLS 

Department. Chi-Chang Kao, the current NSLS Department 

Deputy Chair, was named Interim NSLS Chair and assumed 

his new responsibilities in mid-January, 2006.

The NSLS-II Project Office is housed in Building 817. The 

organization plan is well under way, and includes an Administration & Finance Office, headed by an Associate Director for 

Administration & Finance; and three technical Divisions — Accelerator Systems, Experimental Facilities, and Conventional 

Facilities — each headed by a Division Director. Several advisory committees are being formed to provide broad perspective 

and expert advice, including an NSLS-II Advisory Board and 

advisory committees for each of the three Divisions.

Each Division will be responsible for design and construction 

activities within its specialty area, and will be staffed with a 

range of specialty groups. Many of these positions are expected to be filled by existing Lab personnel. With an estimated 

annual operating cost of $90M, the staff required to operate 

NSLS-II will be about twice as large as that required to operate the present NSLS, adding about 200 new positions to the 

Laboratory.

— Liz Seubert

Steve Dierker

Division of Materials Research. During this time, he became a 

driving force for progress during the U.S. transition from firstgeneration to second-generation synchrotrons.

Similarly, while at DOE, he provided support and guidance 

as third-generation synchrotrons were developed. As a result 

of his presence during these years, he is widely credited for 

playing a major role in the growth of synchrotron radiation 

research. Upon his death, he leaves behind this important 

legacy.

Bill is remembered for his overall passion for science, and materials research in particular, his finely honed sense of progress 

and forward-thinking, and, more personally, his pervasive optimism and ability to earn the trust of others. He will be missed 

by many.

— Laura Mgrdichian
2005 NSLS Tours

 1/11/2005 Infotonics Technology Center and Javelin Assoc., Rochester Federal Subcontracting Initiative

 1/24/2005 City College of New York

 1/28/2005 Islip School District Science Faculty

 2/17/2005 Rochester Institute of Technology

 2/24/2005 United States Department of the Navy

 2/25/2005 Hofstra University, Society of Physics Students

 3/18/2005 BNL Employee Tour

 3/28/2005 City College of New York

 4/4/2005 Stony Brook University Undergraduates

 4/6/2005 League of Women Voters - Suffolk County Brookhaven Chapter

 4/7/2005 University of Connecticut

 4/14/2005 Charterhouse School

 4/15/2005 Congressman David Hobson

 4/21/2005 Queens College

 4/28/2005 DOE Facility Managers Conference 

 4/29/2005 Suffolk Community College

 4/29/2005 Nassau Community College - Physics & Engineering

 5/5/2005 The Roundtable at Stony Brook University 

 5/6/2005 City College of New York - IEEE Chapter

 5/10/2005 Suffolk Community College

 5/10/2005 Suffolk County Commissioner of Public Health Services

 5/12/2005 Senator Schumer's Staff

 5/12/2005 Invision 

 5/13/2005 Literacy Volunteers of America

 5/17/2005 NASA Users' Workshop

 5/26/2005 SUNY at Farmingdale - Institute of Retirement and Learning

 6/6/2005 Stony Brook University Research Experience for Undergraduate (REU) Students 

 6/7/2005 OEP Summer Program Students

 6/20/2005 DOE - Materials Science Review for BES

 6/20/2005 Nuclear Chemistry Summer Students

 6/24/2005 DOE Contractor Attorneys Conference

 6/28/2005 Stony Brook University - BioPrep Program

 7/6/2005 Columbia University REU Students 

 7/11/2005 Stony Brook University - Garcia Center for Material Science

 7/12/2005 SUNY - REU Physics & Chemistry Program

Year in Review 3-41
3-42 NSLS Activity Report

7/13/2005 Korean Ministry of Government Legislation (MOLEG)

7/14/2005 Stony Brook University - Masters in Business Administration

7/21/2005 New York State Community College Summer Program

7/21/2005 Columbia University (Summer Chemistry Program)

7/27/2005 BNL QUARK.NET Summer Program

8/8/2005 Mt. Sinai Rotary Club

8/9/2005 Dr. Rohatgi - DOE Review

8/9/2005 Senior Advisor for Science and Engineering Workforce, NSF

8/12/2005 U.S. Army Recruits

8/15/2005 Senator Clinton's Washington Staffers

8/16/2005 Industrial Center Workshop

8/23/2005 Richard Gelfond

8/25/2005 IBM Group

9/14/2005 New York State Assemblyman Philip Ramos

9/16/2005 DOE - Materials Science Review for BES

9/28/2005 Merchant Marine Academy - Nuclear Engineering and Physics

9/28/2005 SUNY at Stony Brook - Biomedical Engineering Program

9/30/2005 Atomic Energy Regulatory Board 

10/7/2005 Small Business Administration

10/19/2005 Green Mens Club

10/25/2005 SUNY at Stony Brook - Cytotechnology Group

11/4/2005 Suffolk Community College

11/7/2005 Green Mens Club 

11/9/2005 United Federation of Teachers (retired)

11/10/2005 U.S. States Department Tour - Kazakhstan Visitors

11/14/2005 Chinese Academy of Sciences, Shanghai Institute of Applied Physics

11/15/2005 Dr. Alan Friedman, Director & CEO, New York Hall of Science 

11/16/2005 Quark.Net Physics Teachers

11/22/2005 SUNY at Stony Brook - Physics Department

12/2/2005 Green Mens Club

12/6/2005 Columbia University

12/12/2005 Southern Methodist University

12/12/2005 Office of Science and Technology Policy (OSTP) 

12/15/2005 Rensselaer Polytechnic Institute

2005 NSLS Tours
2005 NSLS Workshops

 1/25/2005 Synchrotron Light for Powder Diffraction

 3/1/2005 X6A Workbench: Hands-On Training in Synchrotron Crystallography

 4/5/2005 RapiData 2005

 4/18/2005 Strain-Mapping Workshop

 4/26/2005 X6A Workbench: Hands-On Training in Synchrotron Crystallography

 5/10/2005 Workshop on Intense Coherent THz Pulses

 5/23/2005 Nanomagnetism: Materials and Probes

 5/23/2005 Synchrotron Imaging of Biominerals

 5/23/2005 The Impact of Cryogenic Specimen Automounters on the Future of Macromolecular 

 Crystallography

 5/25/2005 Spectroscopic Studies of Nanoscaled Systems

 5/25/2005 Application of SAXS to Biological Structures

 5/25/2005 In-Situ Kinetic Analyses in Environmental and Chemical Systems

 6/6/2005 Crystallization Workshop

 6/20/2005 BioCD-2005

 7/12/2005 X6A Workbench: Hands-On Training in Synchrotron Crystallography

 9/19/2005 Synchrotron Environmental Science III (SES) Meeting 

 9/28/2005 EXAFS Course: Theory, Experiment, and Advanced Applications

 10/25/2005 X6A Workbench: Hands-On Training in Synchrotron Crystallography

 11/3/2005 COMPRES Sponsored Workshop on Synchrotron Infrared Spectroscopy for High

 Pressure Geoscience and Planetary Science

Year in Review 3-43
Organization
Organization 4-3

National Synchrotron Light Source Organization

 Steve Dierker 

 July 21, 2005 

NSLS Organization Chart 

NSLS Chair

S. Dierker 

Deputy Chair

C. Kao

ESH Division

Associate Chair 

for ESH/Q 

R. Casey

User Science

Division

Associate Chair 

for User Science

C. Kao

Operations and 

Engineering Division

Associate Chair 

for Operations 

E. Johnson

Accelerator

Division

Associate Chair 

for Accelerators

J. Murphy

Users Executive Committee (UEC)

P. Stephens 

Proposal Study Panels (PSPs)

Allocation Panels

General Users Oversight Comm. (GUOC)

Associate Laboratory Director 

for Light Sources

S. Dierker

Science Advisory Committee (SAC)

ESH/Q

R. Casey

Mechanical Engineering

E. Haas

Electrical Systems

R. Biscardi

Operations

R. Heese

User Administration

M. Corwin

Science Program Support

R. Pindak

Beamline Support

S. Hulbert

Controls & Detectors

P. Siddons

Information and Outreach

L. Miller

ESH Coord. N. Gmur 

QA Rep. M. Buckley 

Assistant to Chair 

for Administration

F. Terrano

Administrative

Services

F. Terrano 

Linac

X. Wang

Storage Ring 

and Insertion Device

B. Podobedov

J. Penner-Hahn 
4-4 NSLS Activity Report 

NSLS Advisory Committees

SCIENCE ADVISORY

COMMITTEE

The Science Advisory committee (SAC) 

evaluates science programs at the 

NSLS and makes recommendations to 

the Chairman.

Mario Amzel, Johns Hopkins School 

Joel Brock, Cornell Univ.

Thomas Ellenberger, Harvard School 

Eric D. Isaacs, ANL

Edward Kramer, Univ. of California 

Simon Mochrie, Yale Univ.

James Penner-Hahn, Univ. of Michigan

Peter Stephens, Stony Brook Univ.,

Ex-Officio, UEC Chair

William Thomlinson, CLS

USERS’ EXECUTIVE COMMITTEE

The Users Executive Committee (UEC) 

provides for organized discussions 

among the user community, NSLS administration, and laboratory directorate. 

It aims to communicate current and future needs, concerns, and trends within 

the user community to NSLS staff and 

management, and to disseminate to the 

users information about the NSLS and 

BNL plans.

CHAIR

Peter Stephens, Stony Brook Univ.

VICE CHAIR

Chris Jacobsen, Stony Brook Univ.

PAST CHAIR

Larry Shapiro, Columbia Univ.

SECRETARY/SPIG REP

Jeff Keister, SFA, Inc.

MEMBER

Steve Almo, AECOM

MEMBER

Chris Cahill, George Washington Univ.

MEMBER

Trevor Tyson, NJIT

MEMBER

Hao Wu, Cornell Univ.

SPECIAL INTEREST GROUP

REPRESENTATIVES

Special Interest Groups in areas of 

common concern communicate with 

NSLS management through the UEC.

BIO. SCATTERING AND DIFFRACTION

Ann Stock, Univ. of Medicine and 

Dentistry of NJ

INDUSTRIAL USERS

Paul Stevens, Exxon Mobil Research & 

Engineering Company

IMAGING

Sue Wirick, Stony Brook Univ. 

INFRARED USERS

Randy Smith, BNL-NSLS

UEC and SpIG Members (standing, from left): Chi-Chang Kao, Gretchen Cisco, Larry 

Shapiro, Steve Almo, Trevor Tyson, Sue Wirick, Paul Stevens, Hao Wu, Jeff Keister, 

Meghan Ruppel, John Sutherland, Mary Anne Corwin, Chris Cahill, Paul Northrup, and 

Ben Ocko. (Sitting, from left) Peter Stephens and Chris Jacobsen.

EX-OFFICIO

Chi-Chang Kao, NSLS User Science 

Division

EX-OFFICIO

Mary Anne Corwin, User 

Administration Office

EX-OFFICIO

Lisa Miller, NSLS Information and 

Outreach Office

NUCLEAR PHYSICS

Mahbub Khandaker, TJNL 

STUDENTS AND POST DOCS

Meghan Ruppel, Stony Brook Univ.

XAFS 

Paul Northrup, BNL-Environ. Sci.

X-RAY SCATTERING AND

CRYSTALLOGRAPHY

Ben Ocko, BNL-Physics

TIME RESOLVED SPECTROSCOPY

John Sutherland, BNL-Biology 

TOPOGRAPHY

Michael Dudley, Stony Brook Univ.

UV PHOTOEMISSION AND SURFACE

SCIENCE

Jeff Keister, SFA, Inc.
Organization 4-5

NSLS Advisory Committees

SAC Committee members (from left): Eric Isaacs, Peter Stephens, Joel Brock, Tom Ellenberger, Bill Thomlinson, Jim Penner-Hahn, and Simon Mochrie. (Missing from photo): 

Ed Kramer and Mario Amzel.

GENERAL USER PROPOSAL

REVIEW PANEL

The Proposal Review Panel (PRP) 

reviews and rates General User 

Proposals. Members are drawn from 

the scientific community and generally 

serve a two-year term.

IMAGING AND MICROPROBES: 

BIOLOGICAL AND MEDICAL

Leroy Chapman, Univ. of Sask.

Max Diem, City Univ. of New York

Paul Dumas, Soleil

Kathleen Gough, Univ. of Manitoba

Lindsay Keller, NASA

Barry Lai, ANL

Irit Sagi, Weizmann Institute of Sci.

IMAGING AND MICROPROBES: CHEMICAL

AND MATERIALS SCIENCES

Harald Ade, N.C. State Univ.

David Black, NIST

Gene Ice, ORNL

Nobumichi Tamara, LBNL

IMAGING AND MICROPROBES: 

ENVIRONMENTAL AND GEOSCIENCES

Don Baker, McGill Univ.

David Black, NIST

Jeffrey Fitts, BNL-Environ. Sci.

George Flynn, SUNY @ Plattsburgh

Lindsay Keller, NASA

Kenneth Kemner, ANL

David Wetzel, Kansas State Univ.

IR/UV/SOFT X-RAY SPECTROSCOPY: 

CHEMICAL SCIENCES/SOFT MATTER/

BIOPHYSICS

Jingguang Chen, Univ. of Delaware

Daniel Fischer, NIST

Jan Genzer, N.C. State Univ.

David Mullins, ORNL

Michael White, BNL-Chemistry

IR/UV/SOFT X-RAY SPECTROSCOPY: 

MAGNETISM/STRONGLY CORRELATED

ELECTRONS/SURFACES

Robert Bartynski, Rutgers Univ.

Di-Jing Huang, SRRC

Hong Ding, Boston College

Boris Sinkovic, Univ. of Connecticut

Jiufeng Tu, CUNY

Tonica Valla, BNL-Physics

Barrett Wells, Univ. of Connecticut

METHODS AND INSTRUMENTATION

Leroy Chapman, Univ. of Sask.

Kenneth Finkelstein, Cornell Univ.

Albert Macrander, ANL 

Ralf-Hendrik Menk, Sincrotrone Trieste

Peter Takacs, BNL-Instrumentation

MACROMOLECULAR CRYSTALLOGRAPHY

Alex Bohm, Tufts Univ.

Daniel Leahy, John Hopkins Univ.

Brenda Schulman, St. Jude Hospital 

Da Neng Wang, New York Univ.

Joshua Warren, Duke Univ.

POWDER/SINGLE CRYSTAL CRYSTALLOGRAPHY

Simon Billinge, Michigan State Univ.

Thomas Duffy, Princeton Univ.

Stefan Kycia, Univ. of Guelph

Peter Lee, ANL

Peter Stephens, Stony Brook Univ.

X-RAY SCATTERING: MAGNETISM/

STRONGLY CORRELATED ELECTRONS/

SURFACE

Sean Brennan, Stanford Univ.

Kenneth Finkelstein, Cornell Univ.

Valery Kiryukhin, Rutgers Univ.

Karl Ludwig, Boston Univ.

George Srajer, ANL

Trevor Tyson, NJIT

X-RAY SCATTERING: SOFT MATTER AND

BIOPHYSICS

Paul Heiney, Univ. of Pennsylvania

Ben Hsiao, Stony Brook Univ.

Huey Huang, Rice Univ.

Robert Leheny, Johns Hopkins Univ.

H. Miriam Rafailovich, Stony Brook U.

Detlef Smilgies, Cornell Univ.

Helmut Strey, Stony Brook Univ.

X-RAY SPECTROSCOPY: BIOLOGICAL, 

ENVIRONMENTAL, AND GEOSCIENCES

Martine Duff, Westinghouse Savannah 

Dean Hesterberg, N.C. State Univ.
4-6 NSLS Activity Report

ALLOCATION PANEL

The Allocation Panel allocates general 

user beam time to both new proposals and beam time requests based on 

ratings provided by the Proposal Study 

Panels. Members are drawn from the 

scientific community and generally 

serve a two-year term.

BIOLOGY-PX

Marc Allaire, BNL-NSLS

Annie Heroux, BNL-Biology

EXAFS

Jeffrey Fitts, BNL-Environ. Sci.

Syed Khalid, BNL-NSLS

IMAGING AND MICROPROBES

James Ablett, BNL-NSLS

Kenneth Evans-Lutterodt, BNL-NSLS

Antonio Lanzirotti, Univ. of Chicago

Lisa Miller, BNL-NSLS

IR/UV/SOFT X-RAY

Larry Carr, BNL-NSLS

VUV ALLOCATIONS

Elio Vescovo, BNL-NSLS

POWDER/SINGLE CRYSTAL/HIPRESS/

OPTICS

Zhong Zhong, BNL-NSLS

SCATTERING

Elaine DiMasi, BNL-NSLS

Cecilia Sanchez-Hanke, BNL-NSLS

Jean Jordan-Sweet, IBM

Christie Nelson, BNL-NSLS

Lin Yang, BNL-NSLS

NSLS Advisory Committees

GENERAL USER PROPOSAL

REVIEW PANEL (CONT.)

X-RAY SPECTROSCOPY: BIOLOGICAL, 

ENVIRONMENTAL, AND GEOSCIENCES

Douglas Hunter, Univ. of Georgia

Kenneth Kemner, ANL

Satish Myneni, Princeton Univ.

X-RAY SPECTROSCOPY: CHEMICAL AND

MATERIAL SCIENCES

Uwe Bergmann, SLAC

Simon Bare, UOP

Anatoly Frenkel, Yeshiva Univ.

Steven Heald, ANL

Jean-Pascal Rueff, Jussieu

Tsun Sham, Univ. of Western Ontario

Trevor Tyson, NJIT
Facility Report
Facility Report 5-3

BEAMLINE X12B

Funding

National Institutes of Health Grants; Doris 

Duke Charitable Foundation

Publication

Z. Zavala-Ruiz, I. Strug, I., B.D. Walker, 

P.J. Norris, and L.J. Stern, "A Hairpin Turn 

in a Class II MHC-Bound Peptide Orients 

Residues Outside the Binding Groove for 

T Cell Recognition," Proc. Natl. Acad. Sci. 

USA, 101(36),13279-84 (2004).

For More Information

Lawrence J. Stern, Ph.D., Department of 

Pathology, University of Massachusetts 

Medical School

Email: Lawrence.Stern@umassmed.edu

Zarixia Zavala-Ruiz, Department of 

Pathology, University of Massachusetts 

Medical School

Email: Zarixia.Zavala-Ruiz@umassmed.edu

Accelerator Division Report

James B. Murphy

Associate Chair for Accelerators

Organization and Mission

The NSLS Accelerator Division (AD), headed by James B. Murphy, is organized into two sections: the Linear Accelerator (Linac) section, headed by Xijie Wang, and the Storage Ring & Insertion Device section (SR & ID), headed 

by Boris Podobedov. The AD staff consists of ten accelerator physicists, two engineers, three technicians, and four 

postdocs.

The NSLS Accelerator Division has a four-part mission: 

• To ensure the quality of the electron beam in the existing NSLS booster and linear accelerator, and the x-ray & 

vacuum ultraviolet (VUV) storage rings

• To participate in the NSLS-II project, in particular the design of the storage ring and injection system

• To operate the Magnet Measurement Lab (MML) and the Source Development Laboratory

• To perform fundamental research and development in accelerator and free-electron laser physics

2005 Activities

Storage Ring & Injection System Improvements

Both storage rings have seen a steady rate of improvements in 2005. Several new or upgraded diagnostics, including electron beam profile imaging hardware and a turn-by-turn beam position monitor for injection studies, have been 

made operational in the x-ray ring. Machine studies took place to better understand and improve the injection process 

into the rings. Additional work has been done to better calibrate the x-ring lattice model, specifically to improve the 

control of the horizontal-vertical coupling and vertical dispersion. Machine studies were also performed to prepare for 

the installation of the new X25 undulator in January 2006. 

One activity that brought an immediate improvement to the VUV ring users was the fine-tuning of the lattice, which 

resulted in a beam lifetime increase. Using the “Middle Layer” software tools incorporated into the NSLS control system last year, the VUV ring symmetry was restored by correcting the quadrupole settings and adjusting the revolution 

frequency. With the restored periodicity, the lattice has a 15-20% higher lifetime, depending on the ring current. 

A task force on “Storage Ring Closed Orbit Measurement, Reproducibility, Stability & Feedback” was formed to develop a plan to provide improvements on orbit stability. The task force drew upon the experimental and theoretical 

expertise of the Accelerator, Operations & Engineering and User Science divisions. Its objective was to determine the 

factors that influence beam stability and reproducibility in the x-ray and VUV storage rings, determine the present performance of related systems, and make recommendations for improvements to these systems, up to the state-of-theart. In the course of their work, the task force systematically examined the requirements of the users, the status of key 

subsystems, such as beam position monitors, orbit feedbacks, orbit 

correction algorithms, and the noise sources that degrade beam 

stability. A report of the task force’s findings and recommendations 

is being prepared and those recommendations will be followed up

on in the coming year.

Tremendous progress was made in FY05 to improve the NSLS 

injection system. Working in collaboration with the Operation & 

Engineering Division (OED), the beam profile monitors, wall current monitors, and synchrotron light monitor for the NSLS linac and 

booster were successfully upgraded. Those newly upgraded diagnostic tools are now being used to improve the injection efficiency 

and reduce beam loss. An RF klystron was successfully re-built by 

Communications Power Industries (CPI) to ensure that the NSLS 

linac has sufficient spare klystrons for future operations. 
5-4 NSLS Activity Report 

Magnet Measurement Laboratory

During the December 2005 shutdown, the existing 15-year-old X25 hybrid wiggler was replaced by a new, state-ofthe-art, cryo-ready, in-vacuum “mini-gap undulator” (MGU), optimized for a dedicated macromolecular crystallography 

program. The X25 MGU is expected to provide X25 with between 2 and 30 times brighter x-ray beams over its entire 

tuning range, compared with the old X25 wiggler. It will also be substantially brighter, with better spectral coverage than the previous MGUs at X13 and X29. The mechanical and vacuum system was designed and fabricated by 

Advanced Design Consultants, Inc. of Lansing, NY; the magnet arrays were assembled at NSLS. The new MGU’s onemeter-long hybrid permanent magnet structure has a period of 18 mm, a minimum operating gap of 5.6 mm, and a 

peak on-axis design field of 0.91 T. The device will provide continuously tunable spectral coverage from 1.9 to 20 keV, 

using the fundamental, 2nd, 3rd, 5th, and 7th harmonics. We used a new high-remanence, high-temperature grade of 

NdFeB developed for hybrid car motors (NEOMAX 42AH) with Br = 1.3T and Hcj = 24 kOe at room temperature. The 

high intrinsic coercivity (Hcj) allows the undulator to be baked to 100 oC without a loss of magnetization for ultra-high 

vacuum (UHV) compatibility. Baking under vacuum in the lab for half a day at 90 oC showed only a 0.4% decrease in 

the peak field, and an additional five-day 85 oC bake showed negligible additional demagnetization. The final pressure 

after cool-down was less than 5x10-10 torr, well within x-ray ring requirements. 

The new MGU design incorporates several novel features, the most important being a provision for cryo-cooling the 

magnet arrays to 150 K. This will increase the remanence (Br) of the NdFeB magnets to about 1.45 T and raise the 

peak field to 1.0 T, thereby increasing the tuning range of all harmonics by 11%, as well as increasing the source 

brightness at some key photon energies.

To minimize stress and deformation of the magnet support 

beams during welding of the cooling channels, a low-temperature “friction stir welding” technique was used for the 

first time in a UHV device. The cooling channels proved 

to be vacuum-tight under repeated cryogenic cycling and 

baking. A provision for stress-free thermal expansion and 

contraction of the magnet support structure was also demonstrated during the thermal cycling.

A novel gap-measurement system using a commercial, 

high-precision, LED-based optical micrometer was incorporated to back up the linear encoders and to correct for gap 

changes due to differential contraction during cryogenic 

operation. The system optically monitors the magnet gap 

through viewports at either end of the MGU, ensuring a 

gap accuracy of ±2 micrometers. 

Magnetic measurements were performed using both pulsed 

wire and Hall probe mapping. A pair of full-length, rectangular Helmholtz coils was added to the exterior of the vacuum chamber to compensate for Earth’s field and to cancel 

a small systematic dipole error in the magnet array. These coils will be powered by one of the existing end-pole supplies from the old X25 wiggler. Despite very little time for trajectory, multipole, and phase error shimming, we achieved 

an RMS phase error of 2.5 degrees (sufficiently low to assure good spectral quality up to the 7th harmonic) and met 

the x-ray ring’s multipole tolerances. 

The new X25 MGU was completed, tested, measured, and shimmed on schedule, thanks to the outstanding efforts of 

NSLS staff members from all divisions, who worked many nights and weekends to make it happen. Most of them can 

be seen in the photo above.

NSLS-II Machine Design

The NSLS-II storage ring is the future of the NSLS, and it will provide unprecedented high-brightness photons to the 

user community. The AD staff worked in collaboration with the OED staff to produce the pre-conceptual machine design, which served as the technical basis for achieving “Critical Decision Zero” status for the NSLS-II project in August 

2005.

Proud X25 team surrounding the new mini gap X25 undulator
Facility Report 5-5

Source Development Laboratory (SDL)

The Source Development Laboratory is a platform for the development and applications of new radiation sources, 

such as free electron lasers and coherent terahertz (THz) radiation. Funding was obtained from the Office of Navy 

Research to pursue the development of laser-seeded free electron amplifiers in the 0.8 - 1.0 micron range. The SDL 

has also measured a record 100 microjoules per pulse of THz radiation, which will be used for materials science applications by BNL and external users.
5-6 NSLS Activity Report 

Operations and Engineering Division

Erik D. Johnson

Associate Chair for Operations and Engineering

Organization and Mission

The Operations and Engineering Division (OED) has three sections: Operations, which is led by Richard Heese; Electrical Systems, led by Richard Biscardi; and Mechanical Engineering, led by Ed Haas. To serve the NSLS user community, our mission falls into three main areas:

• Operating on of the NSLS 24 hours a day, seven days a week, an average of 44 weeks a year 

• Designing, fabricating, and maintaining of the NSLS accelerators, infrastructure, and instruments, including 

upgrades, modifications, and proposal development 

• Providing engineering and technical support for other NSLS divisions and the NSLS user community 

The OED staff includes one scientist, 19 engineers, and 55 technicians, making it the largest of the NSLS divisions. In 

addition to its own staff, the division coordinates the activities of five full-time skilled tradesmen from the laboratory, 

as well as shops and trades assigned for specific jobs. The breadth of our mission is such that we need to draw on 

the capabilities of the other NSLS divisions for support, and in turn provide specialized support for their activities. 

2005 Activities

Thankfully, this year was not punctuated by some of the major equipment failures that we have experienced in recent 

years. An overview of machine performance summarized for calendar year 2005 is provided in Section 6, “Facility 

Facts and Figures.” For Fiscal Year 2005, which is the DOE reporting period, overall reliability was 96% for the x-ray 

ring and 99% for the VUV ring. For a facility now into its third decade of operations, high reliability depends critically 

on an aggressive maintenance program as well as the skill of the staff operating the machine. Faults and operations 

disruptions are carefully monitored to extract trends and help us focus our efforts on the most fragile systems. A comparatively small number of disruptions over four hours in duration accounts for much of the down time. For FY 2005, 

roughly one-third of the downtime came from only six events on the x-ray ring and three on the VUV ring. This distribution is an indication of a mature operation with an effective preventive maintenance program.

Along with our maintenance program, a number of initiatives were undertaken this year aimed at improving the safety, 

performance, and reliability of the facility. After an extensive evaluation of hazards at the NSLS, our staff members 

located, identified, and labeled potential sources of stored energy that could cause injury to staff or visitors. Placing informational signs sounds like a mundane activity, but it was actually an important milestone in our program to 

enhance worker safety around the facility. During the spring shutdown, in addition to our equipment upgrade and 

preventative maintenance activities, NSLS staff members placed more than two thousand warning signs on equipment 

around the facility, much of it in use since the start of NSLS operations. This 

activity required a bottom-up assessment of the stewardship and hazards for 

all of the NSLS equipment, capturing the information in a systematic manner 

and providing suitable warning signs with information pointing to the correct 

procedures for servicing the equipment. This monumental investment of effort 

is worthwhile, since we anticipate continuing use and development of the facility for some years ahead. 

Significant effort was also directed toward becoming compliant with various 

code requirements. Major investments were made to facilitate compliance with 

the National Fire Protection Association code on electrical safety (NFPA 70E) 

in a way that minimizes impact on operations. This included providing specialized personnel protective equipment (PPE) required by the code, providing 

training on its use, and, where possible, installing systems to verify that equipment that does not require the use of PPE is de-energized. 

An Electrical Equipment Inspection (EEI) program has also been developed to 

assure that electrical equipment is free from reasonably foreseeable risk due 

to electrical hazards. This goal can be met when equipment is certified by a 
Facility Report 5-7

Group

Area/System Total X- DT U- DT X-ray UV

Total Charges to Down Time

Controls and Diagnostics 121 37 11 29.8 8.4

Power Systems 195 41 45 60.7 57.3

Utilities 95 47 26 54.3 10.7

Miscellaneous 136 86 8 36.1 1.6

547 211 90 180.9 77.9

Significant Disruptions

Ground Faults on XQB 22.5

VUV RF System Intermittant Short 20.3

X-ray Sextupole overheating (XSD1) 13.1

Trim system failures 8.1

LIPA Switchover Power Dip 4.1

3.6

VUV RF 100 W amplifier failure

XRF2 Contactor Replacement

VUV Dipole PS Water Leak

4.3

3.7

51.4 28.3

Balance to 'Routine' Faults

129.5 49.7

Number of Faults Downtime [hr]

Nationally Recognized Testing Laboratory (NRTL) or FY05 Summary Fault Analysis

through further inspection through the EEI program. 

In either case, the equipment must be inspected and 

inventoried. Equipment that does not carry NRTL 

certification will be subject to further examination 

to ensure that it will be safe for its intended use. 

This work will be performed by a cadre of inspectors comprised of longtime members of the NSLS 

community with extensive experience as electrical 

technicians or engineers. This effort will be an ongoing program, and full inspection of all equipment is 

expected by DOE by 2009.

The spring shutdown also saw a complete rebuild 

and upgrade of the UV RF1 temperature control system, substantially improving its thermal response. 

This is important because the old system could not 

adjust quickly enough to keep up with the change in 

load from injection at maximum rate, and hence extended the minimum fill time for the VUV ring. After 

the shutdown, with the new system in place, one fill 

was completed from 0 to 1000 mA in less than two 

minutes. Of course, this also depended on the ability of the injector to rapidly supply charge to the machine. 

Working with the Accelerator Division staff, this year the injection system was fitted with enhanced diagnostics to allow tracking of its performance. Wall current monitors were installed on existing ceramic breaks to follow current loss 

from the linac through the transport lines. Improved flags installed in key areas provide better imaging of the electron 

beam to help with machine tune-up. These upgrades are part of an ongoing effort to reduce lost charge and the radiation it produces around the facility. They also have the benefit of providing more user beam through reduced injection 

times.

Several other major activities underway in 2005, aimed at improving the capabilities of the facility, achieved significant 

milestones during the winter 2005 shutdown. The new undulator constructed for X25 was installed, providing a much 

brighter source for the X25 program. The construction, measurement, and testing of this novel device was a monumental and sustained undertaking for the whole department. The X25 mini-gap undulator (MGU) is described in detail 

by the Accelerator Division on page 5-4. This is only fitting, since their 

Magnetic Measurement Lab became a center of activity as the device 

came together for final assembly and testing starting in October. 

Another major program effort revolves around the creation of an insertion device based on a small angle x-ray scattering (SAXS) beamline 

to support research for the Center for Functional Nanomaterials. As it 

happens, the only available insertion device location in the x-ray ring is 

the RF straight, which feeds the X9 beamline, a slot already occupied 

by two very active beamlines that need to be relocated to make way for 

the new program. A suitable new home for the current Case Western 

X9 beamlines is the space at X3, although it was occupied by the Stony 

Brook University powder diffraction program. This program was relocated 

to X16C, which was refurbished for powder diffraction work. This cascade 

of moves is well underway, with the User Science Division coordinating 

and supporting the relocation of SBU program to X16C and dismantling 

the old beamline at X3 during 2005. This seemingly Byzantine series 

of moves was planned after careful consideration of many alternative 

sequences that would address the need to make a significant program 

change in a facility that is fully built out. Of the options considered it was 

easily the most cost effective way to free the space at X9 with minimal 

The X25 MGU in the tunnel (not surrounded by the legion 

who built it; see Accelerator Division article for more information). 

New X25 insertion device
5-8 NSLS Activity Report 

disruption for most of the user community.

To provide sufficient space within the x-ray ring for the insertion device 

that is to be located in the RF straight, the last of the new RF cavities 

was installed during the winter shutdown. Beyond making space for a new 

insertion device, as was done in the X29 RF straight, this last new cavity 

for the x-ray ring completes a long upgrade campaign. The new cavity 

design has improved thermal performance and eliminates weld joints that 

separated vacuum from water.

Further work is planned for the winter 2006 shutdown to install an insertion-device-capable exit chamber on the ring and to complete preparations of the RF straight such that it can receive an insertion device. The 

critical front-end components for the current X9 beamline will be relocated during the May 2006 shutdown, with relocation of the beamline to 

occur during the summer of 2006.

With the award of CD0 for NSLS-II in 2005, the whole NSLS community looks forward to bringing the exciting capabilities the proposal envisions into reality. In the meantime, the OED will continue to work with the other NSLS divisions 

to keep our user community on the existing facility — one of the most productive synchrotrons in the world. 

XRF 1 and XRF 2
Facility Report 5-9

User Science Division Report

Chi-Chang Kao

Associate Chair for User Science

Organization and Mission

The User Science Division coordinates major facility activities related to users so that we can be more effective in 

communicating with the user community, strengthening existing scientific programs, fostering the growth of new scientific programs, and raising the visibility of the exciting science produced by our users both inside and outside the 

scientific community. The division consists of five sections: User Administration (Mary Anne Corwin), Information and 

Outreach (Lisa Miller), Beamline Development and Support (Steve Hulbert), Scientific Program Support (Ron Pindak), 

and Detectors and Controls (Peter Siddons). The major initiatives and accomplishments of the User Science Division 

and the NSLS user community for 2005 are summarized below.

2005 Activities

Beamline Reviews

With the cooperation of participating research teams (PRTs) and assistance from a large number of NSLS staff, all 

operational beamlines at the NSLS were reviewed in January-February 2005 by the NSLS Scientific Advisory Committee (SAC). In this round of review, beamlines were divided into seven groups: macromolecular crystallography, x-ray 

scattering/soft condensed matter, x-ray scattering/hard condensed matter, powder/single crystal diffraction and high 

pressure, imaging and microprobe, x-ray spectroscopy, and IR/UV/soft x-ray spectroscopy. Each group was reviewed 

by an ad hoc beamline review committee led by one or two members of the SAC. The goal of the review was to ensure 

the highest scientific productivity and safe operation of these beamlines. Specifically, the following areas were evaluated by the review committee for each beamline: (1) importance of the scientific program; (2) quality and quantity of 

scientific productivity; (3) quality of beamline instrumentation, including beamline optics/controls, endstations, detectors, and software; (4) funding for the beamline operation and beamline/endstation upgrades; (5) effectiveness in 

beamline usage; (6) level of beamline staffing; and (7) safety-related issues, including beamline operation procedures 

and user training. The evaluation and recommendations from the beamline review were accepted by NSLS management and communicated to the PRTs soon after the review. Most of the PRTs have been renewed for another three 

years. We are working closely with the remaining PRTs to resolve the issues raised by the review.

User Access Policy

Another major undertaking in 2005 was the establishment of facility beamlines (FBs) under the new NSLS User Access Policy. A set of approximately 15 beamlines were selected as FBs in the first phase, based on coverage of the 

primary research directions of the user community, available resources, and considerations of complementary capabilities provided by the PRTs. The goal of these beamlines is to allow general users to have access to all wavelengths 

and major synchrotron techniques. In addition, general users will also have better coordinated support from the facility’s scientific and technical staff. Users will also benefit from enhanced instrumentation at these beamlines as a result 

of the beamline/endstation upgrade projects carried out over the last few years. These FBs were put into operation 

starting from the fall cycle of 2005. We are looking forward to working with and receiving feedback from users at these beamlines. 

Finally, we initiated a contributing user (CU) program on the FBs, 

with the first CU proposals submitted in September 2005. The CUs 

enhance the endstation capabilities on the FBs. In some cases, 

this enhancement involves specialized instrumentation to meet the 

needs of specific research communities, such as catalysis or environmental sciences. In other cases, the enhancement involves the 

implementation of a specific x-ray technique, such as x-ray standing wave or strain-mapping. The CUs also provide supplemental 

user support to strengthen the scientific impact of the FBs.

Education and Outreach

We continue to take steps to enhance user education, training, and 

outreach at the NSLS. In the area of user training, we organized a 

“High Resolution Powder Diffraction Data Collection and Analysis" 
5-10 NSLS Activity Report 

short course, with the help of Peter Stephens (Stony Brook University) and Christie Nelson (NSLS). It was an intensive three-day course that included lectures on the basic physics of powder diffraction, indexing, and Rietveld refinement, as well as cutting-edge research using powder diffraction. The course also involved hands-on data collection 

carried out on NSLS beamlines X3B1, X7A, and X14A. Feedback on the short course was very positive, and we are 

considering running it annually. We also continued our annual EXAFS short course in 2005, which was entitled "EXAFS Course: Theory, Experiment, and Advanced Applications." We worked closely with users to organize additional 

focused scientific workshops, including "RapidData 2005," a workshop on "Strain Mapping in Engineering Materials 

with High-Energy Synchrotron X-Rays," a "BNL Workshop on Intense Coherent THz Pulses," a "Crystallization Workshop," "Bio-CD 2005," the "Synchrotron Environmental Sciences III (SES-III)" conference, a workshop on "Synchrotron Infrared Spectroscopy for High-Pressure Geoscience and Planetary Science," and three tutorials entitled the 

"X6A Workbench: Hands-On Training in Synchrotron Crystallography," These workshops were very effective in introducing the use of synchrotron techniques to a particular area of science to non-synchrotron users. Many new research 

opportunities and fruitful collaborations have resulted from them. Finally, a concerted effort has been made this year 

to coordinate closely with the Center for Functional Nanomaterials, in order to reach out to nanoscience researchers 

through joint seminars, workshops, and visits to interested universities and institutions.

Beamline Upgrades

There were a number of significant beamline upgrade projects completed this year by the NSLS and PRTs, including 

an upgrade of the X18B monochromator, the construction of a micro-beam diffraction endstation at X13B, an upgrade 

of the U13 photoemission spectrometer, the design and testing of Quick-EXAFS, 

the development of a double-focusing high-energy monochromator for X17, and the 

implementation of high field magnets at several beamlines around the ring. These 

highlights are described in detail below.

New High-Resolution Electron-Energy Analyzer Installed on Beamline U13UB

The 1990s renaissance in the field of angle-resolved photoemission spectroscopy 

(ARPES) resulted from the combination of new parallel-detection (in energy and 

angle) photoelectron spectrometers with high-brightness VUV synchrotron beamlines. At the NSLS, such a beamline/endstation combination was constructed and 

commissioned at beamline U13UB in the late 1990s.

In 2004, the original Scienta photoelectron spectrometer that had been used since 

1998 was replaced by a higher-resolution instrument from the same company. Shown 

in Figure 1, the new instrument has a measured energy resolution of 0.7 meV, which 

is a significant improvement over the ~5 meV resolution of the previous model. A 

photoelectron spectrum recorded at low temperature from an evaporated gold film 

in the vicinity of the Fermi edge is shown in Figure 2. The energy width of the Fermi 

edge in this spectrum is limited by the temperature of the sample.

This new instrument has been used by U13UB PRT members and general users 

since late 2004. The U13UB PRT members (Brookhaven Lab’s Physics Department, 

Boston University, Boston College, and Columbia University) are using the enhanced 

energy resolution of this new instrument to study detailed information on the electronic structure and dynamics of complex electronic systems. In particular, a recent 

study of the quasiparticle scattering rates around the Fermi surface of Sr2RuO4 was 

reported in Physical Review Letters by the Brookhaven group (PRL 94, 107003 

(2005)). This study provided a microscopic picture of the origin of the crossover from 

non-Fermi liquid to Fermi liquid behavior observed in macroscopic transport measurements.

Figure 1. Photograph of the U13UB experimental endstation, the heart of which 

is a very high resolution Scienta SES200 

photoelectron spectrometer.

E (meV)

Intensity

Τ≈5 Κ

Ε≈0.6 meV ∇

Figure 2. A photoelectron spectrum recorded at low temperature (~5 K) from an 

evaporated gold film in the vicinity of the 

Fermi edge, demonstrating the superior 

(sub meV) electron energy resolution of 

the new Scienta photoelectron spectrometer at beamline U13UB.
Facility Report 5-11

An X-ray Micro-Diffraction Instrument for Materials Research 

A new x-ray micro-diffraction instrument was developed at X13B to take advantage of the small source size of the invacuum mini-gap undulator in the X13 straight section of the NSLS x-ray ring. This instrument combines sub-micron 

spatial resolution, exceptional reciprocal space access, a choice of focusing optics, and a modular design to accommodate different experimental needs.

A New High-Energy X-ray Side Station for High-Pressure Research 

A new side-diffracting double-focusing high-energy x-ray monochromator was developed to provide 30-100 keV monochromatic x-rays to a new endstation in beamline X17B2, which includes a new high-pressure press and a MAR345 

image-plate detector. It will enable high-resolution angle-resolved diffraction and pair-distribution function measurements to allow structure refinement for materials under high pressure.

A Fast Scanning Monochromator for X-ray Absorption Spectroscopy 

A new monochromator drive and data-collection scheme has been developed to allow fast measurement of x-ray 

absorption spectra. This new method reduces the collection time of a typical extended x-ray absorption fine structure 

(EXAFS) spectrum to less than one second. It will be particularly important for the study of kinetics in catalytic reactions.

X18B: A New Monochromator for X-Ray Absorption Spectroscopy Between 4.9 and 40keV

A new monochromator has been installed at beamline X18B to lower its lower energy limit from 5.6 keV down to 4.9 

keV. This change might sound small, but it opens significant opportunities for research — especially in solid-state 

physics, materials science, and catalysis research — since the K-edges of two important 3d-transition metals, titanium 

and vanadium, have their energies at 4.966 and 5.465 keV, respectively.

Beamline X18B is optimized for hard x-ray absorption spectroscopy. The original monochromator covered an energy 

range between 5.7 and 40 keV (Cr – Ce K-edges, Ce – U L-edges). An overlapping lower energy range (2-7 keV) 

is covered by beamline X19A, which is optimized for x-ray absorption spectroscopy below 4 keV. However, several 

research groups, especially in the field of catalysis research, do experiments at the K-edges of several 3d-transition 

metals. The typical duration for one of their experiments is two to three days, including a few hours of research at 

photon energies below 5.7 keV (i.e. the V and Ti K-edges). 

Rather than attempt to schedule and setup experiments at both X18B 

and X19A, we decided to extend the lower energy range of X18B down 

to 4.9 keV via a simple modification of its monochromator. The monochromator at X18B is a standard channel-cut monochromator with a 

3mm gap between the two crystals. The original length of the first crystal 

was 34 mm, which limited the maximum usable angle of operation of the 

monochromator, and in turn limited the low end of the photon energy 

range to 5.7 keV. The 34 mm length of the first crystal was chosen in order to intercept the entire beam vertically at higher energies, where the 

Bragg angle, and thus the vertical acceptance of the crystal, is smaller. 

However, as it turns out, the vertical opening angle worsens the energy resolution at higher energies, so it is better 

to limit the vertical beam size at high energies, thereby shortening the required length of the first crystal and increasing the usable angular and photon energy ranges of the monochromator. By optimizing both the energy resolution and 

intensity, the footprint of the white beam on the monochromator remains almost constant over the energy range of 

this monochromator. This allowed us to shrink the length of the first crystal to 16 mm, which is still enough to prevent 

heat-load problems like the thermal bump. 

The monochromator was first mounted in the beamline in the end of April, and tested and commissioned in April and 

May. 

New X18B monochromator with smaller first crystal.
5-12 NSLS Activity Report 

Beam Stability Tests at X18B

One important parameter in the success of experiments at the NSLS is the stability of the x-ray beam on the sample. 

Properties such as intensity, beam position, energy stability, and in a few cases degree of polarization play crucial 

rules in this success, and some can be neglected based on the experiment. Ideally, these properties, when normalized by their dependence on ring current, do not change over the course of an experiment. Change from the ideal 

performance can be caused by motions of the electron beam in the storage ring or by motions of the beamline optics. 

The latter are often thermally driven, their effect is not proportional to beam current, and they can cause any combination of beam position changes, intensity changes, or energy changes. Ideally, these motions are eliminated by stable 

supports (beamlines and storage ring), feedback systems (electron beam and, in some cases, beamline optics), and 

efficient cooling schemes. In practice, however, both the electron beam and the beamline optics move slightly over 

time, requiring regular realignment. 

During a beam studies period, we measured the effect of beam 

motion on the intensity and energy of beamline X18B, which is 

equipped with a channel-cut Si(111) monochromator located at a 

distance of 18 meters from the source. X18B accepts a vertical 

(horizontal) divergence of 50μrad (0.5-1 mrad). Since X18B is optimized for x-ray absorption spectroscopy, we do not care too much 

about position stability. In contrast, we care a lot about source angular stability, since this directly affects the photon energy selected 

by our monochromator.

Based on the geometry of the X18B beamline (slit sizes and positions), we calculate that vertical offsets of the source (electron 

beam) by 60μm or angular changes by 5μrad cannot be observed in

a typical experiment. In order to test these calculations, we aligned 

the beamline slits such that the beamline becomes sensitive to 

beam motions in one direction (angle or position), but not the other. We then moved the beam (angle and position) 

around the nominal values and measured the intensity and energy stability. We did not study the effects of orbit motion (position or angle) in the horizontal plane, since X18B is not sensitive to motion in this plane. 

The results of the orbit studies described above on the intensity and energy of beamline X18B are shown in Figures 1

and 2. It is apparent that vertical angular changes have only a small effect on the energy calibration, independent of 

the slit position, but have a relatively large effect on intensity. Theoretically, the energy should remain constant as a 

function of vertical source angle, which demonstrates that the X18B 

beamline saw a positional shift in addition to an angular change 

during these studies. The photon energy shifts significantly more for 

changes in the vertical source position, about 0.1 eV for 100 μm, as 

expected. The intensity profile in Figure 2 is an asymmetric function of vertical source position relative to the standard orbit value. 

The reason for this is that we aligned our three beamline slits/

apertures (5 mm vertical Be-window, 1mm vertical white beam slit, 

0.5 mm vertical hutch slit) such that the lower edges of their upper 

jaws were aligned, as viewed from the source point. In this situation, if the electron beam moves up, one of the slits intercepts the 

beam and the intensity is reduced immediately. Beam motions in 

the other direction, however, move the beam more towards the center of the three slits, so the intensity is much less strongly reduced, 

as can be observed in the data.

In summary, we confirmed our calculations for the sensitivity of the X18B beamline to electron beam motions and 

demonstrated that the intensity can vary significantly if the beamline is not aligned appropriately. For normal operations, we align the slits symmetrically about the nominal beam axis in order to maximize intensity and to maximize the 

intensity stability. During normal operations, the intensity varies less than 0.4%, and the energy is stable within 

0.05 eV.

Figure 1. Intensity and energy shift for changes of the vertical 

angle. The stability of the beam is better than 5 μrad.

Vertical Angle [μrad]

T

o [arb.units]

→ Energy

Energy Shift [eV]

← Intensity

Vertical Angle [μrad]

T

o [arb.units]

Energy Shift [eV]

→ Energy

← Intensity

Figure 2. Intensity and energy shift for changes of the vertical 

position. The stability of the beam is better than 50 μm.
Facility Report 5-13

High Resolution Terahertz Spectroscopy in Magnetic Field

Over the past few years a new magneto-optical facility has been developed at the U12IR beamline at the NSLS. The 

main components are an Oxford Instrument superconducting magnet, and a Bruker IFS 125HR high-resolution spectrometer. -The principal reason for using the synchrotron source in far-IR spectroscopy is the brightness advantage 

over a conventional light source -- depending on the frequency range 

and on the sample geometry, the synchrotron results in a factor of 50 

- 200 gain in the intensity, making a vast array of new measurements 

possible. 

The Bruker spectrometer is essentially an interferometer where spectral resolution is proportional to the available path difference (between the two interferometer “arms”). This particular spectrometer 

has an extremely long path difference, yielding a 0.001 cm-1 (0.125 

μeV) resolution. The available spectral range is from 5 cm-1 (0.63 

meV) to over 7000 cm-1. The magnet can produce fields up to 16 

Tesla and its 20 liter He reservoir has a hold time of nearly 1 week. 

A set of three wedged single crystal quartz windows at the bottom 

provide optical access to the sample from below, along the vertical 

axis of the magnet (see figure). The sample temperature can be 

varied between 1.8 K and room temperature.

The facility was tested extensively and the first results have been published on LaMnO3, a well-known antiferromagnet 

and the parent compound of the so-called colossal magnetoresistance materials. Other projects currently in progress 

include: the study of the single molecular magnet Mn12-acetate (in collaboration with Myriam Sarachik, City College 

of New York), spin resonance on NaNiO2 (with Sophie De Brion, Grenoble HMFL), the investigation of correlated magnetic systems, including LiCu2O2 and others (with Laszlo Forro, EPFL, Lausanne), and magneto-optical studies on 

superconductors, including carbon-doped MgB2. 

The Oxford Instruments magnet, installed next to the Bruker IFS

125HR spectometer. The stainless steel tubes contain the optical 

coupling to the VUV-IR ring and between the spectrometer and 

the magnet.

A 10T Superconducting Magnet for Magneto-Structural and Magneto-Electronic Research and Education

A horizontal-field, split-coil superconducting magnet has become available for magneto-structural and magneto-electronic research at the NSLS. The magnet can operate over the temperature range from 1.6 to 300 K and over the field 

range 0 to 10 T. The horizontal field enables x-ray absorption measurements with linearly polarized x-rays with the 

electric field of the beam parallel to or normal to the magnetic field. Care was taken in the design to ensure that the 

samples can be measured in transmission mode for energies down to 5 keV (and in small steel hutches). 

In general, this magnet is being used to study the lattice-spin coupling in complex materials. It was designed to be used on beamlines X11A, X19A, X21A and 

X23B for structural measurements (XAFS and powder XRD) in magnetic fields. 

With the use of a quarter wave plate, hard x-ray circular dichroism measurements on these beamlines will be feasible. With a differential pumping configuration, a future upgrade will make possible x-ray magnetic x-ray magnetic circular 

dichroism (XMCD) measurements on beamlines X13A and U4B. This will enable 

the study of magnetism in hard magnets as well as the induced moments on 

oxygen sites in metal oxide systems. Optical access is possible by replacing the 

kapton windows with quartz windows and/or replacing the variable temperature 

insert windows and external windows with all-quartz windows. The magnet was 

funded by a NSF IMR Grant and is now operational. 

The magnet set up at X19A. It is mounted on a 

xyz table, which can be motor-controlled for ease 

of alignment. Samples are loaded from the top 

on a vertical rod into the samples space and are 

cooled by helium vapor or liquid from the magnet 

reservoir.
5-14 NSLS Activity Report 

User Administration Report

Mary Anne Corwin

User Administrator

User Statistics

In FY05, there were 2,256 users from academia, government, industry, and other institutions (see Figure) who performed experiments at the NSLS.

Consistent with past years, more than a third were first-time users. The majority of our users come from the materials 

and life sciences arenas. Slight increases were noticed in medical applications and in the biological and life sciences. 

The numbers of users in the fields of chemistry and engineering decreased slightly. Other areas remained fairly 

stable.

Education and employment levels vary. Scientists, faculty members, 

or other professionals make up the largest user population at 43%. 

Graduate students account for 39% and post-docs make up 14%. 

Users that are between 30 and 39 years of age and are male are the 

most numerous. In FY05, 410 unique academic, government, nongovernment laboratory, and industrial institutions sent users to the 

NSLS. Nearly 260 were academic institutions.

Contributing Users

A new mode of access to beam time became available in FY05. Proposals by contributing users (CUs), who are individuals or groups who carry out research at facility beamlines and also contribute to their operation, were approved.

PASS System

The NSLS Proposal Allocation Safety and Scheduling (PASS) System, a web-based resource for proposal submissions, feasibility and peer review, allocation and scheduling of beam time, safety review, and maintenance of beamline information received several enhancements in FY05. Managers of 

crystallography data were provided with automated feeds to manage 

information more efficiently. Proprietary proposals and an automated 

billing system for proprietary charges were incorporated. User interface changes were made to provide more information to PASS users 

and to simplify the tasks of copying existing proposal and safety approval forms. The development of a component for requesting rapid 

access to beam time has been started. Plans for FY06 include completing of rapid access proposals, including contributing user access, 

and expanding the beam time scheduling component.

Safety Compliance

Due to two measures implemented in the prior fiscal year, non-compliances related to safety and security by users accessing the experimental floor were nearly eliminated in FY05. The measures involved 

encoding badges for timed access and the inclusion of various user 

expiration dates (e.g., training, badge, etc.) on the safety approval 

form.

Final Comments

As many of you know, I recently accepted the position of NSLS Training Coordinator in the ESH&Q Division, following Eva Rothman’s 

footsteps again! So, this will be my last report. I’ve learned so much 

through all the interactions that become part of the regular routine of 

a user administrator. The roles are complex, and often challenging 

The User Administration Group (top, from left) Mary Anne 

Corwin and Gretchen Cisco, (bottom, from left) Liz Flynn and 

Mercy Baez.
Facility Report 5-15

and demanding. I’m grateful for having had the opportunity to work in 

all these areas. My experience will have many benefits in carrying out 

my new responsibilities and has provided me with a strong foundation 

for my new position. As I leave this position, one thing is evident: NSLS 

User Administration staff have always been very productive, handling 

hefty workloads and challenges in a prompt, expert, and courteous 

manner. Please welcome our new User Administrator, Kathleen Nasta 

(formerly the BNL Science Museum Program Coordinator), as your 

liasion between the NSLS and the user community. Your support will 

promote a smooth transition for the NSLS and our users. 25%

40%

6%

6%

4%

8% 11%

Chemical Sciences Materials Sciences

Life Sciences Geosciences and Ecology

Applied Science and Engineering Optical/Nuclear/General Physics

None Specified

NSLS Users by Field of Research

FY 2005

NSLS Users by Affiliation

FY 2005

OTHER

7%

INDUSTRY

7%

FEDERAL

(non-DOE)

2%

DOE

(non-BNL)

2%

BNL

8%

ACADEMIC

74%
5-16 NSLS Activity Report 

Safety Report

Bob Casey

Associate Chair For ESH

Organization and Mission

The NSLS Environment, Safety, Health and Quality Division, headed by Bob Casey, consists of seven professionals 

servicing ESH, Training, and Quality Assurance, and one administrative assistant.

ESH performance within the NSLS and at Brookhaven National Laboratory in general remains an important issue 

for NSLS staff, PRT members, and users. There is great emphasis at BNL on reducing the frequency of injuries and 

incidents, and this emphasis produces heightened visibility for all matters relating to safety. The NSLS Activity Report 

provides an excellent opportunity to comment on ESH performance at the NSLS and to discuss issues that will be of 

importance in the year ahead. 

2005 Activities

Safety performance was high in 2005 in all areas.

1. We had no injuries that met recording criteria or resulted in lost or restricted time during 2005. In fact, at the time 

of this writing, we have worked more than 1.5 million person hours without a lost-time injury at the NSLS. This 

parameter is given a major weighting by BNL and Department of Energy management in judging safety performance. In the figure, on the next page, the significant reduction in DART rate since FY 1997 is clear. We can all 

take pride in that accomplishment.

2. We had no reportable occurrences related to ESH issues in 2005.

3. Radiation exposure remains very low — the total recorded dose to NSLS staff and users for 2005 was less than 

50 mRem. 

4. There were no spills or releases of hazardous materials to the environment.

5. The generation of hazardous and industrial waste continues near all-time lows. Inspections of work sites indicate 

a high degree of compliance with hazardous waste and environmental requirements.

6. Our responsiveness to inspection and audit findings and training requirements was prompt and complete in 

general. 

7. Our compliance with safety requirements, as indicated through numerous audits, is viewed as high.

These performance measures are a good indicator that NSLS staff and users are seriously addressing safety. Because of the effort of many people, the NSLS is a safe place to work. More than 1,200 experiments were conducted 

safely and approximately 2,300 users conducted research in our facility without significant incident or injury. I want to 

acknowledge the ongoing commitment and dedication of the NSLS management and staff, and that of our user community. A pat on the back is due to everyone involved.

ESH Initiatives of Importance in 2006

Two issues of importance to the user community will receive particular emphasis during 2006.

Electrical Safety 

Much has been done in the past year to identify equipment that 

has the potential to create electrical shock hazards if improperly 

handled. Labeling, increased training, and inspections have been 

a major commitment. A similar emphasis will continue this year to 

re-enforce the previous efforts. Inspections will begin on beamline 

equipment that does not have a label or sticker from a nationally 

recognized test laboratory (e.g. U.L). In addition, all equipment 

brought in by visiting users must be labeled or inspected by designated staff before it can be used on the experimental floor. 
Facility Report 5-17

Integrated Safety Management

The NSLS Safety Program is based on the principles described by the Department of Energy as Integrated Safety 

Management (ISM). It is the intent of the ISM program to ensure that all work is effectively performed by trained and 

qualified personnel and that hazards associated with the work have been fully identified and properly controlled. 

These concepts are embodied in the safety program requirements established for all users and staff. We will seek to 

ensure a good understanding and implementation of these practices and requirements throughout this year.

Conclusion

We must maintain a sharp focus on working safely, and we must continue efforts to ensure that 

our research programs capture the requirements 

of the NSLS Safety Program and the essence of 

ISM. World-class research and a rigorous safety 

program are compatible. Most importantly, a 

successful safety program is built on an ongoing 

awareness, involvement, and commitment from 

everyone. We all know that one problem can 

quickly override and out-shine many successes. 

Whether you are at your home institution or at 

the NSLS, keep an eye on the workplace. Make 

sure that all requirements are respected and that 

work is conducted safely. We all have a stake in 

safety performance.

NSLS DART Rates since FY 1997

Cases/200,000 

hours

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5-18 NSLS Activity Report 

Building Administration Report

Gerry Van Derlaske

NSLS Building Manager

Nearly 25 years since first commissioning the VUV ring, the NSLS remains one of the most widely visited research 

facilities in the DOE complex. Previous large-scale construction projects have been replaced with building upgrades, 

which have been taking place during monthly maintenance sessions and scheduled shutdown periods. As always, the 

experimental halls remain a hotbed of activity, as many trades groups, technicians, scientists, staff members, and visitors work side by side conducting cutting-edge research in a safe and efficient manner. Staff and users are asked to 

report concerns that may arise regarding safety or security issues to any NSLS staff member. We do appreciate having others act as our eyes and ears. Contacts may be reached via phone, e-mail, or in person. Our aim is to provide a 

safe and secure environment for carrying out quality scientific research programs. 

Work Planning and Controls for Maintenance and Operations

Overseeing the work-planning and work-permit process for safety and controls for a majority of the work being accomplished within the facility now resides with Al Boerner, Operations Division, who assumed the position of NSLS 

work control manager in January 2005. In keeping with the effort to have all work planned and properly reviewed prior 

to the commencement of tasks, several programs and training modules have been implemented to assure a safe and 

consistence application of the work-planning process. The work control manager, assisted by many work control coordinators, ensures that proper work planning policy is followed by both in-house staff and NSLS users. 

Material Handling and Overhead Hoists

Due to serious events across the DOE sites, material handling devices, overhead cranes, and below the hook lifting 

devices were given a high priority for assessment regarding compliance, inventory tracking, and inspections. At the 

NSLS, the point of contact for all material handling/ hoisting and lifting devices is Robert Kiss. During this assessment period, new training requirements were developed, responsible individuals were named for each of the overhead 

cranes, and administrative locks were placed on overhead cranes to prevent use by unauthorized individuals. These 

programs were established to create a safe and consistent policy for our staff and users of material-handling and 

lifting devices. All below-the-hook devices, such as slings, shackles, and lifting fixtures, are required to be inspected 

on an annual basis and inventoried into our database, along with being assigned to a responsible individual. This 

program also applies to the purchase of any lifting device for use at BNL. Prior to submitting an order to purchase any 

lifting device, the device should be reviewed by BNL Quality Assurance to check its compliance with the applicable 

American National Standards Institute (ANSI) requirements. 

Changes in the Experimental Halls

The changing landscape of the x-ray experimental hall is most dramatically noticed as one proceeds past the control 

room towards the LEGS facility. Over the course of the year, various 

groups have worked together to “green field” the X3 beamline area, preparing for relocation of the PRT from the Case Center for Synchrotron 

Biosciences from beamline X9.

During 2005, Stony Brook University beamline components and staff 

were moved from the existing X3 beamline to new quarters at X16. 

Green fielding of the X3 area began after X16 was commissioned and 

user operations were initiated. Major reconstruction of the X3 area will 

take place in 2006, in preparation for the Case PRTs' move. 

Fall Arrest Protection Equipment

NSLS compliance with OSHA regulations prompted various groups to 

assess their needs and enhance worker safety when performing tasks 

at elevated heights. In an effort to mitigate falls from heights, the NSLS 

safety group, coupled with the NSLS assigned carpenter, installed various fall-protection devices throughout the facility. Areas such as the 

roofs of experimental end station enclosures (EESEs), the exterior build-
Facility Report 5-19

ing AC cooling towers, and x-ray saw tooth areas above grade level were the areas of focused attention. Additional areas of concern will be evaluated as they are reviewed during the work-planning sessions, or during Tier 1 inspections. 

New AEDs Installed

Two additional automated external defibrillators (AEDs) have been installed in building 725. Along with the existing 

AEDs in the main lobby and in the control room area of building 729 (the DUV-FEL facility), there is an AED in the 

RF power supply area in the center of the x-ray ring, along with the AED adjacent to the north elevator on the second 

floor. Familiarity with these units and their exact locations could save a co-worker’s life. The life saved could be yours! 

HSSD System Installed to Protect the Power Supply Area Electrical Components

Due to funding secured via requests submitted to the general laboratory upgrade process, during the winter 2006 

shutdown highly sensitive smoke detectors (HSSDs) were installed in the NSLS power supply area, near the center 

roll-up doors. These detectors perform numerous air samplings over a short time interval, and can detect very minute signs of possible electrical fires, 

thereby giving operations coordinators a chance to investigate and shut 

down equipment prior to an event 

that would trigger less sensitive 

smoke-detection equipment. Testing 

of the system, in order to fine-tune 

the lowest possible thresholds prior 

to tripping the sensors that signal the 

control room, will be conducted as 

the winter shutdown ends, thereby 

establishing a real-time, true-test 

scenario.

ADA Compliant Doors Installed at 

Facility Entrances

Again, through funding supplied by 

General Plant Projects, Americans 

with Disabilities Act (ADA) compliant 

doors were installed at the main entrances to building 725. The groundlevel south and north lobby entrance 

doors have remote operational “push 

buttons” identified with the familiar international wheelchair symbol, allowing hands-free passage through the vestibule area. The push-button door 

switches are keyed into the NSLS card-swipe system for access during evening, holiday, and weekend periods. An 

additional plus is the ability to have the doors remotely open when one’s hands are full.

NSLS Trailer Park Closes

Without much ado, the fabled NSLS trailer park, located east of Railroad Avenue on the north side of Brookhaven Avenue, is now a memory. Once host to many of the original NSLS user groups who utilized these trailers as both office 

and technical shop space, the trailers' useful lifetimes have come to an end. Many of the original groups still conducting research at the NSLS have since moved to more pleasant accommodations in building 535. The trailers have been 

severed from BNL utilities and are no longer considered as space occupied or serviced by the NSLS. 

RF Penthouse Repairs and Upgraded AC Installed

Once again, with the assistance of Plant Engineering Building & Maintenance trades, a major restoration project was 

accomplished transparently to most NSLS staff and the user community. During several Tier 1 inspections, and from 

information passed along to the building management team by RF supervisors and technical staff, deficiencies with 

the structural integrity of the RF penthouse were noted and corrected. During the summer months, when weather permitted, the exterior siding and the sub-flooring of the RF penthouse was replaced without interrupting services to the 

research program. Original windows were saved for reinstallation, and the sub-floor replaced where water had seeped 

behind the exterior walls and allowed dry rot to occur. Plant Engineering carpenters worked under tarps to keep the 

Work Control Coordinators (standing from left, back row) Gary Nintzel, Ron Beauman, Mike Buckley, Steve 

Kramer, Wayne Rambo, Bob Kiss, Nick Gmur, Frank Zafonte, Emil Zitvogel, and Bob Chimel. (Standing from 

left, middle row) Bob Scheuerer, Payman Mortazavi, Toshiya Tanabe, John Gallagher, John Aloi, Dave Harder, 

Walter DeBoer, and Tony Kuczewski. (Sitting from left, front row) Randy Church, Al Boerner (Work Control 

Manager), and Andrew Ackerman (Experiment Review Coordinator). (Missing from photo) Gerry Van Derlaske 

(Work Control Manager), Mike Schwarz, Mike Fulkerson, Pete Zuhoski, Scott Buda, Gloria Ramirez, Wayne 

Rasmussen, Conrad Foerster, Anthony Lenhard, Jim Rose, and Peter Siddons.
5-20 NSLS Activity Report

interior temperatures of the penthouse at a level appropriate to keep the power supplies fully functional. Once the 

sub-floors were replaced, wet insulation in the walls was replaced and new T-111 exterior siding installed over the failing Dri-vet exterior walls. Painting of the siding to match the remaining Dri-vet siding is planned during the spring of 

2006. 

NSLS utilities and operations support group staff, in conjunction with varied Plant Engineering groups, continue the 

process of installing additional cooling capacity within the RF penthouse. This additional supply of cooled, conditioned 

air will allow a level of redundancy that did not previously exist, which is necessary to prevent “fault conditions,” such 

as those that occur in times of heavy heat loading during peak summer months and during interruptions in service 

of the chilled-water supply. In the spring of 2006, final connections of the ductwork will take place and the additional 

cooling is expected to be fully operational.

Conclusion

 As in past years, we encourage the NSLS staff and user community to keep the building management team abreast 

of any concerns with the physical plant utilities, the condition of the facilities, and daily quality-of-life issues. We will 

work to correct these issues as quickly as possible. 
Facts and Figures
Facility Facts & Figures

The National Synchrotron Light Source (NSLS) is a national user research facility funded by the U.S. Department of 

Energy’s Office of Basic Energy Science. The NSLS operates two electron storage rings: an x-ray ring (2.8 GeV, 280 

mA) and a vacuum ultraviolet (VUV) ring (800 meV, 1.0 A), which provide intense light spanning the electromagnet 

spectrum from the infrared through x-rays. The properties of this light, and the specially designed experimental stations, called beamlines, allow scientists in many fields of research to perform experiments not otherwise possible at 

their own laboratories.

Over 2,200 scientists representing more than 400 institutions, more than 60 of them corporations, come to 

Brookhaven National Laboratory annually to conduct research at the NSLS. The facility operates seven days a week, 

24 hours a day throughout the year, except during periods of maintenance and studies.

As a national user facility, the NSLS does not charge for its beamtime, providing that the research results are published in the open literature. Proprietary research is conducted on a full cost recovery basis. The primary way to 

obtain beamtime at the NSLS is through the General User program. General Users are independent investigators 

interested in using the NSLS for their research. Access is gained through a peer-reviewed proposal system. 

The NSLS currently has 53 x-ray and 13 VUV-IR operational beamlines available to users for performing a wide range 

of experiments. There are two types of beamlines at the NSLS: Facility Beamlines (FBs) and Participating Research 

Team (PRT) beamlines. In 2005, the NSLS had 19 FBs and 47 PRT beamlines. FBs are operated by the NSLS and 

reserve at least 50% of their beamtime for General Users. Some FBs host contributing users (CUs), who enhance 

the endstation capabilities and provide specialized user support on FBs. PRT beamlines are operated by user groups 

with related interests from one or more institutions. PRT beamlines reserve 25% of their beamtime for General Users. 

Membership in a PRT or CU program is open to all members of the scientific community who can contribute significantly to the program of the beamline, (i.e., funding, contribution of equipment, scientific program, design and engineering, operations manpower, etc). 

The following pages list the operational beamlines at the NSLS and their unique characteristics.

Facts & Figures 6-3

Beamline Guide Abbreviations

TECHNIQUE DESCRIPTION TECHNIQUE DESCRIPTION TECHNIQUE DESCRIPTION

ARPES

UV PHOTOELECTRON SPECTROSCOPY, 

ANGLE-RESOLVED

DAFS

X-RAY DIFFRACTION ANOMALOUS FINE

STRUCTURE

DEI 

DIFFRACTION-ENHANCED IMAGING

EXAFS

X-RAY ABSORPTION SPECTROSCOPY, 

EXTENDED FINE STRUCTURE

GISAXS

GRAZING INCIDENCE SMALL ANGLE

X-RAY SCATTERING

IRMS

INFRARED MICROSPECTROSCOPY

MAD

MULTI-WAVELENGTH ANOMOLOUS

DISPERSION

MCD

MAGNETIC CIRCULAR DICHROISM

NEXAFS

NEAR EDGE X-RAY ABSORPTION

SPECTROSCOPY

PEEM

PHOTO EMISSION ELECTRON MICROSCOPY

SAXS

SMALL ANGLE X-RAY SCATTERING

SPARPES

UV PHOTOELECTRON SPECTROSCOPY, 

SPIN- AND ANGLE-RESOLVED

STXM

SCANNING TRANSMISSION X-RAY

MICROSCOPY

UPS

UV PHOTOELECTRON SPECTROSCOPY

UV-CD

ULTRAVIOLET CIRCULAR DICHROISM

WAXD

WIDE-ANGLE X-RAY DIFFRACTION

WAXS

WIDE-ANGLE X-RAY SCATTERING

XAFS

X-RAY ABSORPTION SPECTROSCOPY, 

FINE STRUCTURE

XANES

X-RAY ABSORPTION SPECTROSCOPY, 

NEAR EDGE STRUCTURE

XAS

X-RAY ABSORPTION SPECTROSCOPY

XPS

X-RAY PHOTOELECTRON

SPECTROSCOPY

XRD

X-RAY DIFFRACTION

XSW

X-RAY STANDING WAVES
6-4 NSLS Activity Report 

U2A Bend IRMS

High pressure research

IR spectroscopy

30-8000 cm-1 FB BNL-NSLS

Carnegie Institution of Washington

COMPRES

U3C Bend Metrology 50-1000 eV PRT Bechtel Nevada

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

Sandia National Laboratory

U4B Bend X-ray scattering, resonant

MCD

UPS

X-ray fluorescence spectroscopy

XPS

20-1200 eV PRT Montana State University

Northeastern University

U7A Bend NEXAFS

XANES

XPS

180-1200 eV PRT BNL-Chemistry

Dow Chemical Company

NIST

University of Michigan

U10A Bend IRMS 100-4000 cm-1 FB BNL-NSLS

U10B Bend IRMS 500-4000 cm-1 FB BNL-NSLS

U11 Bend UV-CD 3-10 eV PRT BNL-Biology

Beamline Source Technique Energy Range Type Organization

U1A Bend XAS

XAFS

NEXAFS

XANES

270-900 eV PRT ExxonMobil Research and Engineering Co.

U2B Bend IRMS

IR spectroscopy

50-4000 cm-1 PRT Case Western Reserve University

U4A Bend UPS 10-250 eV PRT Army Research Laboratory

North Carolina State University

Rutgers University

University of North Carolina

U5UA Insertion 

Device

ARPES

UPS, spin-resolved

PEEM

15-150 eV FB BNL-NSLS

BNL-CFN

U9B Bend UV-CD

UV florescence spectroscopy

0.8 - 8.0 eV PRT BNL-Biology

VUV-IR Beamlines
Facts & Figures 6-5

Beamline Source Technique Energy Range Type Organization

U12IR Bend IR spectroscopy

THz / mm wave spectroscopy

Time-resolved spectroscopy

6-600 cm-1 FB BNL-NSLS

X1A1 Insertion 

Device

STXM 0.25-0.50 keV PRT BNL-Environmental Science

ExxonMobil Research and Engineering Co.

SUNY @ Plattsburgh

Stony Brook University

University of Texas @ Houston

X1A2 Insertion 

Device

STXM 0.25-1 keV PRT Stony Brook University

X1B Insertion 

Device

X-ray scattering, coherent

XAS

X-ray fluorescence spectroscopy

XPS

0.2-1.6 keV PRT Boston University

TJNL

University of Illinois

X2B Bend X-ray microtomography 8-35 keV PRT ExxonMobil Research and Engineering Co.

X4A Bend MAD

Macromolecular crystallography

3.5-20 keV PRT Albert Einstein College of Medicine

City University of New York (CUNY)

Columbia University

Cornell University

Mount Sinai School of Medicine

New York Structural Biology Center

New York University

SUNY @ Buffalo

Sloan-Kettering Institute

Wadsworth Center

X-ray Beamlines

U9B Bend UV-CD

UV florescence spectroscopy

0.8 - 8.0 eV PRT BNL-Biology

U10A Bend IRMS 100-4000 cm-1 FB BNL-NSLS

U11 Bend UV-CD 3-10 eV PRT BNL-Biology

U12A Bend XAS

XPS

100-800 eV PRT Oak Ridge National Laboratory

U12IR Bend IR spectroscopy

THz / mm wave spectroscopy

Time-resolved spectroscopy

6-600 cm-1 FB BNL-NSLS

U13UB Insertion 

Device

UPS

ARPES

3-30 eV PRT Boston College

Boston University

BNL-Physics

Columbia University

X1A2 Insertion 

Device

STXM 0.25-1 keV PRT Stony Brook University

X2B Bend X-ray microtomography 8-35 keV PRT ExxonMobil Research and Engineering Co.

U10B Bend IRMS 500-4000 cm-1 FB BNL-NSLS

U12A Bend XAS

XPS

100-800 eV PRT Oak Ridge National Laboratory

U13UB Insertion 

Device

UPS

ARPES

3-30 eV PRT Boston College

Boston University

BNL-Physics

Columbia University

X1A1 Insertion 

Device

STXM 0.25-0.50 keV PRT BNL-Environmental Science

ExxonMobil Research and Engineering Co.

SUNY @ Plattsburgh

Stony Brook University

University of Texas @ Houston

X1B Insertion 

Device

X-ray scattering, coherent

XAS

X-ray fluorescence spectroscopy

XPS

0.2-1.6 keV PRT Boston University

TJNL

University of Illinois

X4A Bend MAD

Macromolecular crystallography

3.5-20 keV PRT Albert Einstein College of Medicine

City University of New York (CUNY)

Columbia University

Cornell University

Mount Sinai School of Medicine

New York Structural Biology Center

New York University

SUNY @ Buffalo

Sloan-Kettering Institute

Wadsworth Center
6-6 NSLS Activity Report 

Beamline Source Technique Energy Range Type Organization

X5A Bend Laser backscattering 150-420 MeV PRT BNL-Physics

Forschungszentrum Juelich (KFA)

James Madison University

Norfolk State University

Ohio University

University of Rome II

University of South Carolina

University of Virginia

Virginia Polytechnic Institute

X6B Bend XRD, surface

WAXD

X-ray reflectivity

SAXS

GISAXS

7-19 keV FB BNL-NSLS

X8A Bend Metrology 1.0-5.9 keV PRT Bechtel Nevada

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

Sandia National Laboratory

X9A Bend MAD

Macromolecular crystallography

5-15 keV PRT Albert Einstein College of Medicine

Case Western Reserve University

Rockefeller University

Sloan-Kettering Institute

X4C Bend MAD

Macromolecular crystallography

7-20 keV PRT Albert Einstein College of Medicine

City University of New York (CUNY)

Columbia University

Cornell University

Mount Sinai School of Medicine

New York Structural Biology Center

New York University

Rockefeller University

SUNY @ Buffalo

Sloan-Kettering Institute

Wadsworth Center

X6A Bend MAD

Macromolecular crystallography

6.0-23 keV FB BNL-NSLS

National Institutes of Health

X7B Bend XRD, single crystal

XRD, time resolved

WAXD

WAXS

5-21 keV PRT BNL-Chemistry

General Electric

X8C Bend MAD

Macromolecular crystallography

5-19 keV PRT Biogen Incorporated

BNL-Biology

Hoffmann-La Roche

National Research Council of Canada
Facts & Figures 6-7

Beamline Source Technique Energy Range Type Organization

X10A Bend XRD, powder

XRD, time resolved

WAXD

X-ray reflectivity

SAXS

WAXS

6-15.2 keV PRT ExxonMobil Research and Engineering Co.

X10C Bend XAS

EXAFS

XAFS

NEXAFS

XANES

4-24 keV PRT ExxonMobil Research and Engineering Co.

X11B Bend DAFS

XAS

EXAFS

XAFS

NEXAFS

XANES

5.0-23 keV PRT BNL-Environmental Science

BNL-Material Sciences

Canadian Light Source

ETH Labs - Zuerich

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

Sarah Lawrence College

Stony Brook University

X9B Bend XAS

EXAFS

XAFS

NEXAFS

XANES

5-15 keV PRT Case Western Reserve University

X10B Bend XRD, powder

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

14 keV PRT ExxonMobil Research and Engineering Co.

X11A Bend DAFS

XAS

EXAFS

XAFS

NEXAFS

XANES

4.5-35 keV PRT BNL-Environmental Science

BNL-Material Sciences

Canadian Light Source

ETH Labs - Zuerich

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

Sarah Lawrence College

Stony Brook University

X12B Bend MAD

Macromolecular crystallography

5-20 keV PRT BNL-Biology
6-8 NSLS Activity Report 

Beamline Source Technique Energy Range Type Organization

X13A Insertion 

Device

X-ray scattering, resonant

MCD

0.2-1.6 keV FB BNL-NSLS

X14A Bend MAD

XRD, powder

XRD, single crystal

XRD, time resolved

WAXD

X-ray reflectivity

5-26 keV PRT Oak Ridge National Laboratory

Tennessee Technological University

University of Tennessee

X15B Bend XAS

EXAFS

XAFS

NEXAFS

XANES

0.8-15 keV PRT BNL-Environmental Sciences

Lucent Technologies, Inc.

Stony Brook University

Temple University

University of Texas @ Austin

X17B1 Insertion 

Device

XRD, powder 55-80 keV mono 

20-150 keV white

FB BNL-NSLS

Rutgers University

X17B3 Insertion 

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV FB BNL-NSLS

COMPRES

University of Chicago

X12C Bend MAD

Macromolecular crystallography

5.5-20.0 keV PRT BNL-Biology

X13B Insertion 

Device

Microdiffraction Imaging 4-16 KeV FB BNL-NSLS

X15A Bend XSW

DEI

3-25 keV XSW

10-60 keV DEI

FB BNL-NSLS

Northwestern University

X16C Bend XRD, powder 6-30 keV PRT Stony Brook University

X17B2 Insertion 

Device

XRD, powder

XRD, time resolved

High pressure research

20-130 keV FB BNL-NSLS

COMPRES

Stony Brook University

X17C Insertion 

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV FB BNL-NSLS

University of Chicago
Facts & Figures 6-9

Beamline Source Technique Energy Range Type Organization

X18B Bend XAS

EXAFS

XAFS

NEXAFS

XANES

4.8-40 keV FB BNL-NSLS

BNL-Chemistry

BNL-Electrochemistry

ORNL

UOP LLC

University of Delaware

Yeshiva University

X19C Bend XRD, surface

X-ray topography

X-ray reflectivity

X-ray scattering, liquid

X-ray scattering, surface

6-17 keV PRT Arizona State University

Fairfield Crystal Technology, LLC

Kansas State University

Kyushu University

SUNY @ Albany

Stony Brook University

University of Illinois @ Chicago

X20C Bend XRD, single crystal

XRD, surface

XRD, time resolved

X-ray reflectivity

X-ray scattering, surface

4-11 keV PRT IBM Research Division

X18A Bend XRD, powder

XRD, single crystal

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

4-19 keV PRT BNL-Chemistry

Indiana University @ Indianapolis

Pennsylvania State University

Purdue University

Stony Brook University

University of Missouri @ Columbia

X19A Bend X-ray scattering, resonant

XAS

EXAFS

XAFS

NEXAFS

XANES

2.1-17 keV FB BNL-NSLS

University of Delaware

Yeshiva University

X20A Bend XRD, single crystal

Microdiffraction Imaging

X-ray reflectivity

X-ray scattering, surface

4.5-13 keV PRT IBM Research Division

X21 Insertion 

Device

XRD, single crystal

X-ray scattering, magnetic

X-ray scattering, resonant

SAXS

5-20 keV FB BNL-NSLS

Boston University

University of Vermont
6-10 NSLS Activity Report 

Beamline Source Technique Energy Range Type Organization

X22B Bend X-ray scattering, liquid

X-ray scattering, surface

6.5-10 keV PRT Bar-Ilan University

BNL-X-Ray Scattering Group

BNL-CFN

Harvard University

X23A2 Bend XRD, powder

DAFS

XAS

EXAFS

XAFS

NEXAFS

XANES

4.7-30 keV PRT NIST

X24A Bend XSW

Auger spectroscopy

EXAFS

X-ray fluorescence spectroscopy

XPS

1.8-5 keV PRT NIST

X25 Insertion 

Device

MAD

Macromolecular crystallography

3-28 keV FB BNL-NSLS

BNL-Biology

X22A Bend XRD, single crystal

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

10.7 keV

32keV

PRT BNL-X-Ray Scattering Group

BNL-Chemistry

X22C Bend XRD, single crystal

XRD, surface

X-ray reflectivity

X-ray scattering, magnetic

X-ray scattering, surface

3-12 keV PRT BNL-X-Ray Scattering Group

Massachusetts Institute of Technology

Rutgers University

X23B Bend XRD, powder

XAS

EXAFS

XAFS

NEXAFS

XANES

4-10.5 keV PRT Hunter College

Montana State University

Naval Research Laboratory (NRL)

New Jersey Institute of Technology

Sarah Lawrence College

X24C Bend X-ray reflectivity

UV photoabsorption spectroscopy

UPS

XAS

0.006-1.8 keV PRT Naval Research Laboratory (NRL)
Facts & Figures 6-11

Beamline Source Technique Energy Range Type Organization

X26C Bend MAD

Macromolecular crystallography

5-20 keV PRT BNL-Biology

Cold Spring Harbor Laboratory

Stony Brook University

X27C Bend XRD, time resolved

WAXD

SAXS

WAXS

9 keV PRT Air Force Research Laboratory

National Institutes of Health

Naval Surface Warfare Center

Stony Brook University

X29A Insertion 

Device

MAD

Macromolecular crystallography

6-15keV PRT Case Western Reserve University

BNL-Biology

X26A Bend Microdiffraction Imaging

X-ray microprobe

3-30 keV PRT BNL-Environmental Science

University of Chicago

University of Georgia

X27A Bend X-ray microprobe 4.5-20 keV FB BNL-NSLS

BNL-Environmental Science

Stony Brook University

X28C Bend X-ray footprinting White Beam PRT Case Western Reserve University
6-12 NSLS Activity Report

NSLS Linac Parameters as of December 2005

 Electron Gun Injection Energy 100 keV

 Linac Final Energy 120 MeV

 Number of Accelerating Sections 3

 Number of Klystrons 3

 Linac Frequency 2856 MHz

 Horizontal Emittance into Booster (εx

) 7.6 x 10-1 m-rad

 

NSLS BOOSTER PARAMETERS

 Booster Injection Energy 120 MeV

 Booster Extraction Energy 750 MeV

 Circumference 28.35 m

 Number of Superperiods (Ns

) 4

 Dipole Bend Radius (ρ) 1.91 m

 Nominal Tunes (νx,νy) 2.42, 1.37

 Betatron Function (βx,βy) 8.63 to 1.01, 5.26 to 1.73 m

 Dispersion Function (ηx,η′x) 1.21 to 0.41 m

 Momentum Compaction (α) 0.106

 RF Frequency (frf) 52.88 MHz

 RF Peak Voltage (Vrf) 25 keV

 Horizontal Acceptance 1.66 x 10-4 m-rad

 Vertical Acceptance 6.11 x 10-5 m-rad

 Momentum Acceptance ±0.0025

 Horizontal Emittance at Extraction (εx

) 7.6 x 10-7 to 1.0 x 10-7 m-rad

 Energy Spread at Extraction (σE/E) 1.4 x 10-4

 Bunch Length at Extraction 110 mm

BOOSTER MAGNETIC ELEMENTS (FIELDS AT 750 MEV)

 Name Type Quantity B (kG) B’ (kG/m) B” (kG/m) Effective Length (m)

 BB Dipole 8 13.099 -7.97 -125 1.5

 Q1 Quadrupole 4 68.82 0.3

 Q2 Quadrupole 4 93.60 0.3

 SF Sextupole 4 1223.7 0.2
VUV Storage Ring Parameters as of December 2005

 Stored Electron Beam Energy 0.808 GeV

 Injected Current 1.0 amp

 Lifetime @ 200 mA unstretched (stretched) ~6 (9.8) hr

 Circumference 51.0 meters

PHOTON CRITICAL WAVELENGTH (ENERGY)

 Dipole Source 1.41 T λc(Ec) 19.9 Å (622 eV)

LATTICE STRUCTURE (CHASMAN-GREEN) SEPARATED FUNCTION, QUAD DOUBLETS

 Number of Superperiods (Ns) 4

 8 Bending Magnets (1.5 meters long each)

 Magnet Complement 24 Quadrupole (0.3 meters long each)

 12 Sextupole in two families (0.20 meters long each) 

 

STORAGE RING CHARACTERISTICS

 Number of Dipole Ports 18

 Number of Insertion Device Straight Sections 2

 Maximum Length of Insertion Devices 2.25 meters

 Dipole Bend Radius 1.91 meters

 Radiated Bending Magnet Power (I= 1A) 20.4 kW

 Power per Horizontal Milliradian (I= 1A) 3.2 W

 RF Frequency (frf) 52.887 MHz

 Electron Orbital Period 170.2 nanoseconds

Number of RF Buckets 9

 Typical Bunch Mode (filled buckets) 7

 Damping Times τx=τy= 13 msec; τε = 7 msec

 Nominal Tunes (νx

,νy) 3.14, 1.26

 Momentum Compaction 0.0235

 RF Peak Voltage with 52 MHz (with 211 MHz) (Vrf) 80 keV (20 keV)

 Design RF Power with 52 MHz (with 211 MHz) 50 kW (6 KW)

 Synchrotron Tune (νs) 0.0018

 Natural Energy Spread [Ib< 20 mA] (σE/E) 5.0 x 10-4

 Natural Bunch Length[Ib< 20 mA]52 MHZ(211 MHZ)(2σ) 9.7 mm (360 mm)

 Horizontal Damped Emittance (εx

) 1.6 x 10-7 m-rad

 Vertical Damped Emittance (εy

) 3.5 x 10-10 m-rad (4 x 10-9 in normal ops.)*

{

INSERTION DEVICE PARAMETERS

 Betatron Function (βx,βy) 11.1 m, 5.84 m

 Source Size (σx

,σy) 1240 μm, >45 μm (220 μm in normal ops.)*

 Source Divergence (σ′

x

, σ′

y

) 112 μrad, >7.7 μrad (22 μrad in normal ops.)*

 Betatron Function (βx

,βy) 1.18 to 2.25 m, 10.26 to 14.21 m

 Dispersion Function (ηx

,η′

x

) 0.500 to 0.062 m, 0.743 to 0.093 m

 αx,y = -β’ x,y/2 -0.046 to 1.087, 3.18 to -0.96

 γx,y =(1 +α2

x,y)/βx,y 0.738 to 0.970 m-1, 1.083 to 0.135 m-1

 Source Size (σx,σy) 536 to 568 μm, >60 to >70 μm (170-200 μm in normal ops.)*

 Source Divergence (σ′

x

,σ′

y

) 686 to 373 μrad, 19.5 to 6.9 μrad (55-20 μrad in normal ops.)*

ARC SOURCE PARAMETERS

Facts & Figures 6-13
6-14 NSLS Activity Report

X-Ray Storage Ring Parameters as of December 2005

 Stored Electron Beam Energy 2.800 GeV

 Injected Current 0.3 A

 Lifetime ~20 hours

 Circumference 170.1 meters

PHOTON CRITICAL WAVELENGTH (ENERGY)

 Dipole Source 1.36 T λc

(Ec) 1.75 Å (7.1 keV)

 Wiggler Source 5.0 T λc

(Ec) 0.48 Å (26.1 keV)

LATTICE STRUCTURE (CHASMAN-GREEN SEPARATED FUNCTION, QUAD DOUBLETS

 Number of Superperiods (Ns) 8

 16 Bending (2.7 meters long each)

 Magnet Complement 40 Quadrupole A,C and D type (0.45 meters each)

 16 Quadrupole B type (0.8 meters long each)

 32 Sextupole in two families (0.20 meters long each)

STORAGE RING CHARACTERISTICS

 Number of Dipole Ports 30

 Number of Insertion Device Straight Sections 6

 Maximum Length of Insertion Devices 4.50 meters

 Dipole Bend Radius 6.875 meters

 Radiated Bending Magnet Power (1=0.25A) 198 kW

 Power per Horizontal Milliradian (1=0.25A) 32 W

 RF Frequency (frf) 52.88 MHz

 Electron Orbital Period 567.2 nanoseconds

Number of RF Buckets 30

 Typical Bunch Mode (filled buckets) 25

 Damping Times τx

=τy= 4 msec; τε = 2 msec

 Nominal Tunes (νx

,νy) 9.8, 5.7

 Momentum Compaction 4.1 x 10-3

 RF Peak Voltage (Vrf) 1120 keV

 Design RF Power 450 kW 

 Synchrotron Tune (νs

) 0.0023

 Natural Energy Spread (σE/E) 9.2 x 10-4

 Natural Bunch Length (2σ) 87 mm 

 Horizontal Damped Emittance (εx

) 7.5 x 10-8 m-rad

 Vertical Damped Emittance (εy) 1.5 x 10-10 m-rad 

{

INSERTION DEVICE PARAMETERS

 Betatron Function (βx, βy) 1.60 m, 0.35 m

 Source Size (σx

,σy) 300 μm, 6 μm

 Source Divergence (σx

′, σy′) 260 μrad, 35 μrad

ARC SOURCE PARAMETERS

 Betatron Function (βx,βy) 1.0 to 3.8 m, 7.9 to 26.5 m

 Dispersion Function (ηx

,η′

x

) 0.47 to -0.11, -0.39 to 0.22

 αx,y = -β’ x,y/2 -0.49 to 1.62, -3.4 to 4.5

 γx,y =(1 +α2

x,y)/βx,y 0.952 to 0.962 m-1, 0.81 to 0.52 m-1

 Source Size (σx,σy) 371 to 612 μm, 27 to 53 μm

 Source Divergence (σx

′,σy′) 476 to 324 μrad, 9 to 7 μrad
CALENDAR YEAR 2005

Note: Delivered hours are only those accumulated during scheduled operations. 

Unscheduled operations do not contribute 

to this total.

 

January 468 98.3% 125.2% 334 93.7% 126.1%

February 551 98.4% 117.4% 557 98.8% 104.7%

March 623 99.9% 108.6% 516 91.7% 111.4%

April 592 99.0% 111.6% 534 95.7% 112.2%

May 216 99.7% 144.6% 175 96.8% 110.1%

June 623 99.6% 110.1% 578 95.3% 107.5%

July 463 98.2% 108.5% 429 96.8% 109.5%

August 571 94.6% 103.0% 521 98.7% 128.4%

September 591 99.5% 109.2% 545 98.8% 119.2%

October 591 97.2% 108.7% 552 96.8% 114.3%

November 488 99.6% 111.5% 365 98.5% 110.8%

December 0 - - 0 - -

 5777 5106

Calendar 2005

Delivered 5690 98.5% 112.4% 4929 96.5% 113.9%

PLANNED

MONTH HOURS

PLANNED

HOURS

VUV ACTUAL CY 05

RELIABILITY1 AVAILABILITY2

X-RAY ACTUAL CY 05

RELIABILITY1 AVAILABILITY2

Calendar Year 2005 NSLS Machine Activities

1

 Operations during scheduled time

2

 Operations compared to total scheduled 

 time

Other Activities UV/IR X-ray

Studies 2.3% 4.2%

Comm/Cond. 2.8% 4.1%

Holiday 1.9% 1.9%

Injection 0.9% 1.7%

Unscheduled Downtime 1.0% 2.0%

Interlock 0.0% 0.7%

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Facts & Figures 6-15
Publications
The following pages list all papers published in the 2005 calendar year as reported to the NSLS by February 28, 2006. Citations 

are listed in order of beamline number and then alphabetically by the last name of the first author. This list contains reported citations for journal articles, published conference proceedings, books, chapters in books, formal reports, informal reports, technical 

reports, theses, dissertations, and patents. For citation submissions where research was performed on more than one beamline, 

the citation is listed under each beamline. However, each citation was only counted once.

The first column in the table (right) lists the 

number of publications reported to the NSLS 

during the 2005 fiscal year (Oct. 1, 2004 – Sept. 

30, 2005) and published between 2002 and 

2005. Although some of these publications were 

published earlier than FY 2005, they were not 

reported to the NSLS until this fiscal year. Thus, 

they have not been counted in prior years’ activity reports.

The second column in the table lists the number 

of publications published in the 2005 calendar 

year and reported to the NSLS as of Feb. 28, 

2006. These numbers are slightly lower than 

the fiscal year values because they contain only 

publications from 2005 and it often takes many 

months or years to account for user and staff 

publications.

Several types of journal articles are reported 

in this list, including premier journals, peer-reviewed journals, and a few that are not peerreviewed. A publication is considered premier if 

the journal has an impact factor of 6 or greater 

(from Journal Citation Report 2003, Thomson 

Institute for Scientific Information). These journals represent approximately the top 3% of all 

journals.

For calendar years 2002-2005, the NSLS users and staff published in 40 premier journals. These premier journals are: Accounts of 

Chemical Research, Advanced Materials, Angewandte Chemie, Annual Review of Biophysics and Biomolecular Structure, Annual 

Review of Genomics and Human Genetics, Applied Physics Letters, Cancer Cell, Cell, Chemical Reviews, Chemistry and Biology, Current Biology, Current Opinion in Chemical Biology, Current Opinion in Structural Biology, EMBO Journal, Faseb Journal, 

Genes and Development, Genome Research, Human Molecular Genetics, Immunity, Journal of Biological Chemistry, Journal of 

Experimental Medicine, Journal of Immunology, Journal of Neuroscience, Journal of the American Chemical Society, Molecular and 

Cellular Biology, Molecular and Cellular Proteomics, Molecular Cell, Nano Letters, Nature, Nature Immunology, Nature Materials, 

Nature Structural & Molecular Biology, Neuron, Nucleic Acids Research, Physical Review Letters, PNAS, Reports on Progress in 

Physics, Science, Structure, Trends in Biochemical Sciences, and Trends in Neurosciences. Two additional journals are included 

in the premier list, Applied Physics Letters (impact factor 4.0) and Environmental Sciences and Technology (impact factor 3.6), 

because these journals represent the “best in class” for the NSLS industrial and environmental science users, even though their 

impact factors are less than 6. 

In FY 2005, NSLS users and staff had 849 publications – a record for high for the facility. Moreover, 239 papers were published in 

premier journals, representing 28% of the total publications from the facility, and demonstrating the high impact of NSLS science.

Reported in 

Fiscal Year 

2005*

Published in 

Calendar Year 

2005**

Journals, peer-reviewed, premier 239 189

Journals, other peer-reviewed 503 438

Journals, non peer-reviewed 23 23

Total Journals and Magazines 765 650

Books/Chapters in Books 7 5

Published Conference Proceedings 49 43

Reports: Technical, Formal, Informal 3 3

Theses/Dissertations 24 17

Patents 1 4

Total Misc. Publications 84 72

Total Publications 849 722

NSLS VUV User Publications 68 77

NSLS X-Ray User Publications 718 586

NSLS Staff Publications 63 59

849 722

* Publications reported to the NSLS from Oct 1, 2004 – Sept. 30, 2005 and published 

between 2002 – 2005.

** Publications published in 2005 as reported to the NSLS by Feb. 28, 2006.

Publications

Publications 7-3
7-4 NSLS Activity Report

NSLS Users

Beamline U1A

S Bocharov, Z Zhang, T Beebe, Jr., A Teplyakov. Structure of a 

Thin Barrier Film Deposited from Tetrakis-(dimethylamino)-

Titanium onto a Si(100)-2x1 Substrate. Thin Solid Films. 471

(1-2), 159-165 (2005). 

G Hahner, M Zwahlen, W Caseri. Solvent Dependence of 

the Molecular Order in Ion-Exchanged Self-Assembled 

dialkylammonium Monolayers on Mica Studied with Soft X-ray 

Absorption. J. Colloid Interface Sci.. 291 (1), 45-52 (2005). 

G Hahner, M Zwahlen, W Caseri. Chain-Length Dependence of 

the Conformational Order in Self-Assembled Dialkylammonium 

Monolayers on Mica Studied with Soft X-ray Absorption. 

Langmuir. 21, 1424-1427 (2005). 

J Horn, Z Song, D Potapenko, J Hrbek, M White. Characterization 

of Molydbenum Carbide Nanoparticles Formed on Au(111) 

Using Reactive-Layer Assisted Deposition. J. Phys. Chem. B. 

109, 44-47 (2005). 

H Hwu, M Zellner, J Chen. The Chemical and Electronic Properties 

of Oxygen-Modifed C/Mo(110): A Model System for Molybdenum 

Oxycarbides. J. Catal.. 229, 30-44 (2005). 

G Liu, S Natarajan, S Kim. Photochemical Production of 

Oligothiophene and Polythiophene Micropatterns from 2,5-

diiodothiophene on Au in UHV. Surf. Sci.. 592 (1-3), L305-L309 

(2005). 

K Rao, D Kumaran, T Binz, S Swaminathan. Structural Analysis 

of the Catalytic Domain of Tetanus Neurotoxin. Toxicon. 45 (7), 

929-939 (2005). 

M Sahiner, D Downey, S Novak, J Woicik, D Arena. The Local 

Structural Characterization of the Inactive Clusters in B, Bf2 and 

B23 Implanted Si Wafers uing X-ray Techniques. Microelectr. J.. 

36, 522-526 (2005). 

Beamline U2A

R Hemley, H Mao, V Struzhkin. Synchrotron Radiation and High 

Pressure: New Light on Materials Under Extreme Conditions`. 

J. Synch. Rad.. 12, 135-154 (2005). 

M Koch-Mu ̈ ller, P Dera, Y Fei, H Hellwig, Z Liu, J Van Orman, R 

Wirth. Polymorphic Phase Transition in Superhydrous Phase B. 

Phys. Chem. Miner.. 32 (5-6), 349-361 (2005). 

G Lager, W Marshall, Z Liu, R Downs. Re-Examination of the 

Hydrogarnet Structure at High Pressure using Neutron Powder 

Diffraction and Infrared Spectroscopy. Am. Mineral.. 90, 639 

(2005). 

H Liu, J Tse, J Hu, Z Liu, L Wang, J Chen, D Weidner, Y Meng, 

D Hausermann, H Mao. Structural Refinement of the HighPressure Phase of Aluminum Trihydroxide: In-Situ HighPressure Angle Dispersive Synchrotron X-ray Diffraction and 

Theoretical Studies. J. Phys. Chem. B. 109, 8857 (2005). 

J Lu, G Rozgonyi, A Schonecker, A Gutjahr, Z Liu. Impact of 

Oxygen on Carbon Precipitation in Polycrystalline Ribbon 

Silicon. J. Appl. Phys.. 97, 033509 (2005). 

Y Song, Z Liu, R Hemley, H Mao, D Herschbach. High-Pressure 

Vibrational Spectroscopy of Sulfur Dioxide. J. Chem. Phys.. 

122, 174511 (2005). 

Y Song, R Hemley, H Mao, D Herschbach. Nitrogen-Containing 

Molecular Systems at High Pressures and Temperatures. 

Chemistry under Extreme Conditions, p. 189-222, Elsevier 

Science, St. Louis. (2005). 

Beamline U2B

K Dokken, L Davis, N Marinkovic. Synchrotron Radiation Fourier 

Infrared Microspectroscopy (SR-IMS) as a Tool to study the Fate 

and Transport of Organic contaminants in Plants. Spectroscopy. 

20 (9), 14-20 (2005). 

K Dokken, L Davis, N Marinkovic. Use of Fourier Transform 

Infrared Microspectroscopy in Plant Growth and Development. 

Appl. Spectrosc. Rev.. 40, 1-26 (2005). 

K Dokken, L Davis, L Erickson, S Castro-Diaz, N Marinkovic. 

Synchrotron Fourier Transform Infrared Microspectroscopy: A 

New Tool to Monitor the Fate of Organic Contaminants in Plants. 

Microchem. J.. 81 (1), 86-91 (2005). 

V Joshi, D Ramamurty, R Powell, F Furuya, J Hainfeld. High Z 

Metal Carbonyls for Imaging and Microspectroscopy. Microsc. 

Microanal.. 11 (S2), 974 (2005). 

J Joshi, D Ramamurthy, R Powell, F Furuya, J 

Hainfeld. High Z Metal Carbonyls for Imgaing and 

Microscopy. Microsc. Microanal.. 10, 912 (2005). 

N Marinkovic, M Chance, K Dokken, L Davis, D Linkous, J Flinn. 

Synchrotron Infrared Spectroscopy at NSLS Beamline U2B. Am. 

Biotechnol. Lab.. 23, 12 (2005). 

N Marinkovic, S Gupta, C Zhan, M Chance. Synchrotron Radiation 

in Biosciences. Nucl. Instrum. Meth. B. 241 (1-4), 242-246 

(2005). 

L Pietrzak, S Miller. Microchemical Structure of Soybean Seeds 

Revealed in Situ by Ultraspatially Resolved Synchrotron Fourier 

Transformed Infrared Microspectroscopy. J. Agr. Food Chem.. 

53 (24), 9304-9311 (2005). 

M Shao, J Warren, N Marinkovic, P Faguy, R Adzic. In-Situ ATRSEIRAS Study of Electrooxidation of Dimethyl Ether on a Pt 

Electrode in Acid Solutions. Electrochem. Commun.. 7, 459 

(2005). 

D Wetzel, G Post, R Lodder. Synchrotron Infrared 

Microspectroscopic Analysis of Collagens I, III, and Elastin 

on the Shoulders of Human Thin-Cap Fibroatheromas. Vib. 

Spectrosc.. 38 (1-2), 53-59 (2005). 

P Yu. Molecular Chemistry Imaging to Reveal Structural Features 

of Various Plant Feed Tissues. J. Struct. Biol.. 150 (1), 81-89 

(2005). 

P Yu. Application of Cluster Analysis (CLA) in Feed Chemical 

Imaging to Accurately Reveal Structural-Chemical Features of 

Feeds within Cellular Dimension. J. Agr. Food Chem.. 53 (8), 

2872-2880 (2005). 

P Yu. Applications of Cluster Analysis (CLA) and Principal 

Component Analysis (PCA) in Feed Structure and Feed 

Molecular Chemistry Research, Using Synchrotron-Based FTIR 

Microspectroscopy.. J. Agr. Food Chem.. 53, 7115-7127 (2005). 

P Yu, C Christensen, J McKinnon, D Christensen. UltrastructuralChemical Makeup of Yellow- (Brassica Rapa) and BrownSeeded (Brassica Napus) Canola within Cellular Dimensions, 

Explored with Synchrotron Reflection FTIR Microspectroscopy. 

Can. J. Plant. Sci.. 85, 85: 533-541 (2005). 

Beamline U4A

A Chan, G Wertheim, H Wang, M Ulrich, J Rowe, T Madey. 

Surface Atom Core-Level Shifts of Clean and Oxygen-Covered 

Re(1231). Phys. Rev. B. 72, 035442 (2005). 

L Webb, E Nemanick, J Biteen, D Knapp, D Michalak, M Traub, 

A chan, B Brunschwig, N Lewis. High-Resolution X-ray 

Photelectron Spectroscopic Studies of Alkylated Silicon(111) 

Surfaces. J. Phys. Chem. B. 109, 3930-3937 (2005). 

A Yang, Z Chen, X Zuo, D Arena, J Kirkland, C Vittoria, V Harris. 
Cation-Disorder-Enhanced Magnetization in Pulsed-LaserDeposited CuFe2O4 Films. Appl. Phys. Lett.. 86, 252510 

(2005).

Beamline U4B

J Dvorak, Y Idzerda, D Arena, Y Zhao, S Ogale, T Wu, T 

Venkatesan, R Godfrey, R Ramesh. Are Strain-Induced Effects 

Truly Strain Induced? A Comprehensive Study of Strained 

LCMO Thin Films. J. Appl. Phys.. 97, 10C102 (2005). 

T Funk, A Deb, S George, H Wang, S Cramer. X-ray Magnetic 

Circular Dichroism-A High Energy Probe of Magnetic Properties. 

Coordin. Chem. Rev.. 249, 3-30 (2005). 

Y Guan, Z Dios, D Arena, L Cheng, W Bailey. Transmission-Mode 

X-ray Magnetic Circular Dichroism Characterization of Moment 

Alignment in Tb-Doped Ni81Fe19. J. Appl. Phys.. 97, 10A719 

(2005). 

A Lussier, J Dvorak, Y Idzerda, S Shinde, S Ogale, T Venkatesan. 

XAS Characterization of Growth Parameter Effects for Pulsed 

Laser Deposited CoxTi1-xO2-? Films. Phys. Scr.. T115, 623-

625 (2005). 

C Marrows, P Steadman, A Hampson, L Michez, B Hickey, N 

Telling, D Arena, J Dvorak, S Langridge. Probing Magnetic 

Ordering in Multilayers using Soft X-ray Resonant Magnetic 

Scattering. Phys. Rev. B: Condens. Matter. 72, 024421 (2005). 

L Michez, C Marrows, P Steadman, B Hickey, D Arena, J Dvorak, 

H Zhang, D Bucknall, S Langridge. Resonant X-ray Scattering 

from a Magnetic Multilayer Reflection Grating. Appl. Phys. Lett.. 

86, 112502 (2005). 

E Negusse, Y Idzerda. Extraction of Roughness Parameters from 

Specular X-ray Resonant Scattering. J. Appl. Phys.. 97, 10C901 

(2005). 

S Stadler, D Minott, D Harley, J Craig, M Khan, I Dubenko, N Ali, K 

Story, J Dvorak, et al.. Element-Specific Magnetic Properties of 

Co2MnSi Thin Films. J. Appl. Phys.. 97, 10C302 (2005).

Beamline U4IR

X Hu, C Hirschmugl. Long-Range Metal-Mediated Interactions 

Between S and CO on Cu(100). Phys. Rev. B. 72, 205439 

(2005). 

O Mercier, R Buckley, H Trodahl, C Bernhard, G Balakrishnan. 

Low-Energy Excitations in La1.2Sr1.8Mn2O7 Investigated by 

Ellipsometry. Phys. Rev. B. 72, 214437 (2005).

Beamline U5UA

E Vescovo, H Kim, J Ablett, S Chambers. Spin-polarized 

Conduction in Localized Ferromagnetic Materials: The Case of 

Fe3O4 on MgO(100). J. Appl. Phys.. 98, 084507 (2005). 

Beamline U7A

L Andruzzi, W Senaratne, A Hexemer, E Sheets, B Ilic, E Kramer, 

B Baird, C Ober. Oligo(ethylene glycol) Containing Polymer 

Brushes as Bioselective Surfaces. Langmuir. 21, 2495-2504 

(2005). 

S Banerjee, T Hemraj-Benny, S Sambasivan, D Fischer, J 

Misewich, S Wong. Near-Edge X-ray Absorption Fine Structure 

Investigations of Order in Carbon Nanotube-Based Systems. J. 

Phys. Chem. B. 109 (17), 8489-8495 (2005). 

R Bhat, J Genzer. Using Spectroscopic Ellipsometry for Quick 

Prediction of Number Density of Nanoparticles Bound to Nontransparent Solid Surfaces. Surf. Sci.. 596, 187 (2005). 

R Bubeck, L Thomas, S Rendon, W Burghardt, A Hexemer, D 

Fischer. Characterization of the Skin Orientation of Thermotropic 

Liquid-Crystalline Copolyester Moldings with Near-Edge X-ray 

Absorption Fine Structure . J. Appl. Polym. Sci.. 98, 2473-2480 

(2005). 

R Bubeck, P Dvornic, J Hu, A Hexemer, X Li, S Keinath, D Fischer. 

Near Edge X-ray Absorption Fine Structure (NEXAFS) Studies 

of Copper Ion-Containing PAMAMOS Dendrimer Networks. 

Macromol. Chem. Physic. 206, 1146 - 1153 (2005). 

D Burnett, A Gabelnick, D Fischer, A Marsh, J Gland. Mechanism 

of Acetylene Oxidation on the Pt(111) Surface using in situ 

Fluorescence Yield Near-Edge Spectroscopy. J. Catal.. 230, 

282-290 (2005). 

D Burnett, A Gabelnick, D Fischer, A Marsh, J Gland. In Situ 

Soft X-ray Studies of Ethylene Oxidation Mechanisms and 

Intermediates on the Pt(111) Surface. J. Phys. Chem. B. 109, 

5659-5666 (2005). 

C Cox, D Fischer, W Schwartz, Y Song. Improvements in the Low 

Energy Collection Efficiency of Si(Li) X-ray Detectors. Nucl. 

Instrum. Meth. B. 241 (1-4), 436-440 (2005). 

D Delongchamp, S Sambasivan, D Fischer, E Lin, P Chang, 

A Murphy, J Frechet, V Subramanian. Direct Correlation of 

Organic Semiconductor Film Structure to Field-Effect Mobility. 

Advanced Materials. 17, 2334-2338 (2005). 

D DeLongchamp, E Lin, D Fischer. Organic Semiconductor 

Structure and Chemistry from Near-Edge X-ray Absorption Fine 

Structure (NEXAFS) Spectroscopy. SPIE Organic Thin Film 

Transistors IV, Vol 5940, p. 54-64, sponsored by SPIE - The 

International Society for Optical Engineering. (2005). 

D DeLongchamp, B Vogel, Y Jung, M Gurau, C Richter, O 

Kirillov, J Obrzut, D Fischer, S Sambasivan, et al.. Variations in 

Semiconducting Polymer Microstructure and Hole Mobility with 

Spin-Coating Speed. Chem. Mater.. 17 (23), 5610-5612 (2005). 

K Efimenko, J Crowe, E Manias, D Schwark, D Fischer, J Genzer. 

Rapid Formation of Soft Hydrophilic Silicone Elastomer 

Surfaces. Polymer. 46, 9329–9341 (2005). 

L Gamble, C Lee, G Harbers, P Gong, D Grainger, D Castner. 

Characterization of Surface order and Structure of Thiolated 

Single Stranded and Hybridized DNA. Society for Biomaterials 

30th Annual Meeting, Vol , p. 121, sponsored by Society for 

Biomaterials. (2005). 

J Genzer. Templating Surfaces with Gradient Assemblies. J. 

Adhes. Sci. Technol.. 81, 417 (2005). 

T Hemraj-Benny, S Banerjee, S Sambasivan, D Fischer, W Han, J 

Misewich, S Wong. Investigating the Structure of Boron Nitride 

Nanotubes by Near-edge X-ray Absorption Fine Structure 

(NEXAFS) Spectroscopy. Phys. Chem. Chem. Phys.. 6, 1103-

1106 (2005). 

D Krapchetov, H Ma, A Jen, D Fischer, Y Loo. Solvent-Dependent 

Assembly of Terphenyl- and Quaterphenyldithiol on Gold and 

Gallium Arsenide. Langmuir. 21, 5887-5893 (2005). 

J Lenhart, D Fischer, S Sambasivan, E Lin, R Jones, C Soles, W 

Wu, D Goldfarb, M Angelopoulos. X-ray Absorption Spectroscopy 

to Probe Surface Composition and Surface Deprotection in 

Photoresist Films. Langmuir. 21, 4007-4015 (2005). 

H Lewis, D Burnett, A Gabelnick, D Fischer, J Gland. Enhanced 

Low-Temperature CO Oxidation on a Stepped Platinum Surface 

for Oxygen Pressures Above 10-5 Torr. J. Phys. Chem. B. 109, 

21847-21857 (2005). 

A Murphy, P Chang, P VanDyke, J Liu, J Frechet, V Subramanian, 

D Delongchamp, S Sambasivan, D Fischer, E Lin. SelfAssembly, Molecular Ordering, and Charge Mobility in SolutionProcessed Ultrathin Oligothiophene Films. Chem. Mater.. 17, 

6033-6041 (2005). 

L Pattison, A Hexemer, E Kramer, P Petroff, D Fischer. Temperature 

Dependence of the Ordering of Semiconducting FluoreneThiophene Copolymers on Rubbed Polyimide Alignment Layers. 

Publications 7-5
7-6 NSLS Activity Report

Proc. SPIE Int. Soc. Opt. Eng., Vol , p. 5398, sponsored by Soc. 

Opt. Eng.. (2005). 

N Samuel. Structural Characterization of Adsorbed Helical and 

Beta-Sheet Peptides. Ph.D. Thesis. University of Washington, 

Seattle. (2005). 

J Sayan, N Nguyen, J Ehrstein, D Yoder, I Levin, D Fischer, M 

Paunescu, O Celik, E Garfunkel. Effect of Nitrogen on Band 

Alignment in HfSiON Gate Dielectrics. Appl. Phys. Lett.. 87, 

212905-3 (2005). 

W Yoon, M Balasubramanian, K Chung, X Yang, J McBreen, C 

Grey, D Fischer. Investigation of the Charge Compensation 

Mechanism on the Electrochemically Li-Ion Deintercalated Li1-

xCo1/3Ni1/3Mn1/3O2 Electrode System by Combination of Soft 

and Hard X-ray Absorption Spectroscopy. J. Am. Chem. Soc.. 

127 (49), 17479-17487 (2005). 

X Zhao, P Liu, J Hrbek, J Rodriguez, M Perez. The Chemisorption 

of SO2 on the Cu/Au (1 1 1) Surface: Interplay Between 

Ensemble and Electronic Effects. Surf. Sci.. 592 (1-3), 25-36 

(2005). 

X Zhao, J Hrbek, J Rodriguez. The Decomposition and Chemistry 

of Ru3(CO)12 on TiO2(110) Studied with X-ray Photoelectron 

Spectroscoy and Temperature Programmed Desorption. Surf. 

Sci.. 575, 115-124 (2005).

Beamline U9B

S Badre, C Goncalves, K Norinaga, G Gustavson, O Mullins. 

Molecular Size and Weight of Asphaltene and Asphaltene 

Solubility Fractions from Coals, Crude Oils and Bitumen. Fuel. 

85 (1), 1-11 (2005). 

Y Nie, S Vigues, J Hobbs, G Conn, S Munger. Distinct Contributions 

of T1R2 and T1R3 Taste Receptor Subunits to the Detection of 

Sweet Stimuli. Curr. Biol.. 15 (21), 1948-1952 (2005). 

B Wallace. Shining New Light on Protein Structure and Function 

thru Synchrotron Radiation Circular Dichroism (SRCD) 

Spectroscopy. Aust. Biochem.. 35, 47-50 (2005). 

F Wien, A Miles, J Lees, S Vronning Hoffmann, B Wallace. 

VUV Irradiation Effects on Proteins in High-Flux Synchrotron 

Radiation Circular Dichroism Spectroscopy. J. Synch. Rad.. 12, 

517-523 (2005). 

F Wien, A Miles, J Lees, A Cuff, R Janes, B Wallace. A 

New Circular Dichroism Reference Dataset Covering 

Fold Space. Biophyscal Journal, Vol 88, p. 554a, (2005).

Beamline U10A

S Dordevic, C Homes, J Tu, T Valla, M Strongin, P Johnson, G 

Gu, D Basov. Extracting the Electron-Boson Spectral Function 

alpha2F(w) from Infrared and Photoemission Data using Inverse 

Theory. Phys. Rev. B: Condens. Matter. 71, 104529 (2005). 

C Homes. Scaling Laws in High-Temperature Superconductors as 

Revealed through Infrared Spectroscopy. Synch. Rad. News. 18

(3), 9-14 (2005). 

I Kezsmarki, G Mihaly, R Gaal, N Barisic, H Berger, L Forro, C 

Homes, L Mihaly. Pressure-induced Suppression of the SpinGapped Insulator Phase in BaVS{3}: An Infrared Optical Study. 

Phys. Rev. B. 71, 193103 (2005). 

J Kim, S Oh, Y Lee, E Choi, C Homes, J Rhyee, B Cho. Optical 

Spectroscopy Study on the electronic Structure of Eu{1-

x}Ca{x}B{6}. Phys. Rev. B. 71, 075105 (2005). 

R Lobo, J LaVeigne, D Reitze, D Tanner, Z Barber, E Jacques, 

P Bosland, M Burns, G Carr. Photoinduced Time-Resolved 

Electrodynamics of Superconducting Metals and Alloys. Phys. 

Rev. B. 72, 024510 (2005). 

S Miller, L Pietrzak. Preparation of Soybean Seed Samples for FTIR Microspectroscopy. Biotech. Histochem.. 80 (3-4), 117-121 

(2005). 

A Zimmers, J Tomczak, R Lobo, N Bontemps, C Hill, M Barr, Y 

Dagan, R Greene, A Millis, C Homes. Infrared Propeties of 

Electron-Doped Cuprates: Tracking Normal-State Gaps and 

Quantum Critical Behavior in Pr{2-x}Ce{x}CuO{4}. Europhys. 

Lett.. 70 (2), 225-231 (2005).

Beamline U10B

S Chakraborty, B Sahoo, I Teraoka, L Miller, R Gross. EnzymeCatalyzed Regioselective Modification of Starch Nanoparticles. 

Macromolecules. 38 (1), 61-68 (2005). 

V Joshi, D Ramamurty, R Powell, F Furuya, J Hainfeld. High Z 

Metal Carbonyls for Imaging and Microspectroscopy. Microsc. 

Microanal.. 11 (S2), 974 (2005). 

J Lehmann, B Liang, D Solomon, M Lerotic, F Luizao, J Kinyangi, 

T Schäfer, S Wirick, C Jacobsen. Near-Edge X-ray Absorption 

Fine Structure (NEXAFS) Spectroscopy for Mapping NanoScale Distribution of Organic Carbon Forms in Soil: Application 

to Black Carbon Particles. Global Biogeochem. Cy.. 19, GB1013 

(2005). 

L Miller, R Smith. Synchrotrons Versus Globars, Point-Detectors 

Versus Focal Plane Arrays: Selecting the Best Source and 

Detector for Specific Infrared Microspectroscopy and Imaging 

Applications. Vib. Spectrosc.. 38 (1-2), 237-240 (2005). 

S Miller, L Pietrzak. Preparation of Soybean Seed Samples for FTIR Microspectroscopy. Biotech. Histochem.. 80 (3-4), 117-121 

(2005). 

M Petra, J Anastassopoulou, T Theologis, T Theophanides. 

Synchrtron Micro-FT-IR Spectroscopic Evaluation of Normal 

Paediatric Human Bone. J. Mol. Struct.. 733, 101-110 (2005).

L Pietrzak, S Miller. Microchemical Structure of Soybean Seeds 

Revealed in Situ by Ultraspatially Resolved Synchrotron Fourier 

Transformed Infrared Microspectroscopy. J. Agr. Food Chem.. 

53 (24), 9304-9311 (2005). 

D Solomon, J Lehmann, J Kinyangi, B Liang, T Schäfer. Carbon 

K-Edge NEXAFS and FTIR-ATR Spectroscopic Investigations 

of Organic Carbon Speciation in Soils. Soil Sci. Soc. Am. J.. 69, 

107-119 (2005). 

T Telivala, L Miller. Effect of Metal Ions on the Secondary Structure 

of Amyloid beta (Ab) in Alzheimer’s disease. Masters Thesis. 

SUNY at Stony Brook, Stony Brook. (2005). 

Q Wang, A Kretlow, M Beekes, D Naumann, L Miller. In Situ 

Characterization of Prion Protein Structure and Metal 

Accumulation in Scrapie-Infected Cells by Synchrotron Infrared 

and X-ray Imaging. Vib. Spectrosc.. 38, 61-69 (2005). 

Q Wang, W Sanad, L Miller, A Voigt, K Klingel, R Kandolf, K Stangl, 

G Baumann. Infrared Imaging of Compositional Changes in 

Inflammatory Cardiomyopathy. Vib. Spectrosc.. 38, 217-222 

(2005). 

B Wood, K Bambery, L Miller, M Quinn, L Chiriboga, M Diem, 

D McNaughton. Infrared Imaging of Normal and Diseased 

Cervical Tissue Sections. Biomedical Applications of Micro- and 

Nanoengineering II, Vol 5651, p. 78-84, sponsored by SPIE--

The International Society for Optical Engineering. (2005). 

P Yu, R Wang, Y Bai. Reveal Protein Molecular StructuralChemical Differrences Between Two Types of Winterfat (Forage) 

Seeds with Physiological Differences in Low Temperature 

Tolerance Using Synchrotron-Based Fourier Transform Infrared 

Microspectroscopy. J. Agr. Food Chem.. 53, 9297-9303 (2005). 

P Yu. Application of Cluster Analysis (CLA) in Feed Chemical 

Imaging to Accurately Reveal Structural-Chemical Features of 

Feeds within Cellular Dimension. J. Agr. Food Chem.. 53 (8), 

2872-2880 (2005). 
P Yu. Molecular Chemistry Imaging to Reveal Structural Features 

of Various Plant Feed Tissues. J. Struct. Biol.. 150 (1), 81-89 

(2005). 

P Yu. Applications of Cluster Analysis (CLA) and Principal 

Component Analysis (PCA) in Feed Structure and Feed 

Molecular Chemistry Research, Using Synchrotron-Based 

FTIR Microspectroscopy.. J. Agr. Food Chem.. 53, 7115-7127 

(2005). 

P Yu, C Christensen, J McKinnon, D Christensen. UltrastructuralChemical Makeup of Yellow- (Brassica Rapa) and BrownSeeded (Brassica Napus) Canola within Cellular Dimensions, 

Explored with Synchrotron Reflection FTIR Microspectroscopy. 

Can. J. Plant. Sci.. 85, 85: 533-541 (2005).

Beamline U11

A Miles, F Wien, J Lees, B Wallace. Calibration and Standardisation 

of Synchrotron Radiation and Conventional Circular Dichroism 

Spectrometers. Part 2: Factors Affecting Magnitude and 

Wavelength. Spectroscopy. 19, 43-51 (2005). 

Y Nie, S Vigues, J Hobbs, G Conn, S Munger. Distinct Contributions 

of T1R2 and T1R3 Taste Receptor Subunits to the Detection of 

Sweet Stimuli. Curr. Biol.. 15 (21), 1948-1952 (2005). 

B Wallace. Shining New Light on Protein Structure and Function 

thru Synchrotron Radiation Circular Dichroism (SRCD) 

Spectroscopy. Aust. Biochem. 35, 47-50 (2005). 

F Wien, A Miles, J Lees, A Cuff, R Janes, B Wallace. A New 

Circular Dichroism Reference Dataset Covering Fold Space. . 

Biophyscal Journal, Vol 88, p. 554a, (2005).

Beamline U12A

S Senanayake, G Waterhouse, H Idriss, T Madey. Coupling of 

Carbon Monoxide Molecules over Oxygen Defected UO2 (111) 

Single Crystal and Thin Film Surfaces. Langmuir. 21, 11141-

11145 (2005). 

Beamline U12IR

R Lobo, J LaVeigne, D Reitze, D Tanner, Z Barber, E Jacques, 

P Bosland, M Burns, G Carr. Photoinduced Time-Resolved 

Electrodynamics of Superconducting Metals and Alloys. Phys. 

Rev. B. 72, 024510 (2005).

Beamline U13UB

S Dordevic, C Homes, J Tu, T Valla, M Strongin, P Johnson, G 

Gu, D Basov. Extracting the Electron-Boson Spectral Function 

alpha2F(w) from Infrared and Photoemission Data using Inverse 

Theory. Phys. Rev. B: Condens. Matter. 71, 104529 (2005). 

P Glans, T Learmonth, K Smith, T Valla, P Johnson, S Hulbert, 

W McCarroll, M Greenblatt. Charge-Density-Wave Gap in the 

Quasi-Two-Dimensional Conductor Na0.9Mo6O17 Measured 

by Angle-Resolved Photoemission Spectroscopy. Phys. Rev. B. 

72, 035115 (2005). 

T Kidd, T Valla, A Fedorov, P Johnson, R Cava, M Haas. Orbital 

Dependence of the Fermi Liquid State in Sr{2}RuO{4}. Phys. 

Rev. Lett.. 94, 107003 (2005). 

M Kralj. Hybridization Schemes for Ag Films on V(1 0 0). Surf. Sci.. 

599 (1-3), 150-159 (2005). 

T Valla. Electronic Interactions in Strongly Correlated Systems: 

What is the Glue for High Temperature Superconductivity?. 

Proceedings of the SPIE, Strongly Correlated Electron 

Materials: Physics and Nanoengineering, Vol 5932, p. 5932-

03, sponsored by SPIE-The International Society for Optical 

Engineering. (2005). 

Beamline X1A1

A Bauer, T Rabung, F Claret, T Schäfer, G Buckau, T Fanghänel. 

Influence of Temperature on Sorption of Europium onto 

Smectite: The Role of Organic Contaminants. Appl. Clay Sci.. 

30 (1), 1-10 (2005). 

A Braun, N Shah, F Huggins, K Kelly, A Sarofim, C Jacobsen, 

S Wirick, H Francis, J Havsky, et al.. X-ray Scattering and 

Spectroscopy Studies on Diesel Soot from Oxygenated Fuel 

Under Various Engine Load Conditions. Carbon. 43 (12), 2588-

2599 (2005). 

A Braun, F Huggins, N Shah, Y Chen, S Wirick, S Mun, C 

Jacobsen, G Huffman. Advantages of soft X-ray Absorption over 

TEM-EELS for Solid Carbon Studies - a Comparative Study 

on Diesel Soot with EELS and NEXAFS. Carbon. 43, 117-124 

(2005). 

F Claret, T Schäfer, T Rabung, M Wolf, A Bauer, G Buckau. 

Differences in Properties and Cm(III) Complexation Behavior of 

Isolated Humic and Fulvic Acid Derived from Opalinus Clay and 

Callovo-Oxfordian Argillite. Appl. Geochem.. 20 (6), 1158-1168 

(2005). 

M Haming. Spectroscopy on Poly-L-Lysine and Spectromicroscopy 

Study on Biomineralized Proteins in Jaws of Glycera 

Dibranchiata. M.A. Thesis. SUNY at StonyBrook, StonyBrook. 

(2005). 

R Kretzschmar, T Schäfer. Metal Retention and Transport on 

Colloidal Particles in the Environment. Elements. 1 (4), 205-210 

(2005). 

J Lehmann, B Liang, D Solomon, M Lerotic, F Luizao, J Kinyangi, 

T Schäfer, S Wirick, C Jacobsen. Near-Edge X-ray Absorption 

Fine Structure (NEXAFS) Spectroscopy for Mapping NanoScale Distribution of Organic Carbon Forms in Soil: Application 

to Black Carbon Particles. Global Biogeochem. Cy.. 19, GB1013 

(2005). 

M Lerotic, C Jacobsen, J Gillow, A Francis, S Wirick, S Vogt, 

J Maser. Cluster Analysis in Soft X-ray Spectromicroscopy: 

Finding the Patterns in Complex Specimens. J. Electron. 

Spectrosc. Relat. Phenom.. 144-147, 1137-1143 (2005). 

M Lerotic. Finding Patterns in Complex Specimens by Improving 

the Aquisition and Analysis of X-ray Spectromicroscopy Data. 

PH.D. Thesis. SUNY at StonyBrook, StonyBrook. (2005). 

D Mancosky, L Lucia, H Nanko, S Wirick, A Rudie, R Braun. Novel 

Visualization Studies of Lignocellulosic Oxidation Chemistry by 

Application of C-near Edge X-ray Absorption Fine Structure 

Spectroscopy. Cellulose. 12, 35-41 (2005). 

M Plaschke, J Rothe, M Altmaier, M Denecke, T Fanghaenel. 

Near Edge X-ray Absorption Fine Structure (NEXAFS) of model 

compounds for the humic acid / actinide ion interaction. J. 

Electron. Spectrosc. Relat. Phenom.. 148, 151-157 (2005). 

T Schäfer, G Buckau, R Artinger, J Kim, S Geyer, M Wolf, W Bleam, 

S Wirick, C Jacobsen. Origin and Mobility of Fulvic Acids in the 

Gorleben Aquifer: Implications from Isotopic Data and Carbon/

Sulfur XANES. Org. Geoch.. 36, 567-582 (2005). 

T Schäfer, F Claret, M Lerotic, G Buckau, T Rabung, A Bauer, C 

Jacobsen. Source Identification and Characterization of Humic 

and Fulvic Acids Isolated from Oxfordian Argillite and Opalinus 

Clay. Humic Substances: Molecular Details and Applications in 

Land and Water Conservation, p. 43-62, Tayloe and Francis, 

Inc., New York. (2005). 

M Schumacher. Microheterogeneity of Soil Organic Matter 

investigated by C-1s NEXAFS Spectroscopy and X-ray 

Microscopy. Ph.D. Thesis. Swiss Federal Institute of Technology 

Zurich, Zurich. (2005). 

M Schumacher, I Christl, A Scheinost, C Jacobsen, R Kretzschmar. 

Chemical Heterogeneity of Organic Soil Colloids Investigated by 

Publications 7-7
7-8 NSLS Activity Report

Scanning Transmission X-ray Microscopy and C-1s NEXAFS 

Microspectroscopy. Environ. Sci. Tech.. 39 (23), 9094-9100 

(2005). 

D Solomon, J Lehmann, J Kinyangi, B Liang, T Schäfer. Carbon 

K-Edge NEXAFS and FTIR-ATR Spectroscopic Investigations 

of Organic Carbon Speciation in Soils. Soil Sci. Soc. Am. J.. 69, 

107-119 (2005). 

Beamline X1A2

M Haming. Spectroscopy on Poly-L-Lysine and Spectromicroscopy 

Study on Biomineralized Proteins in Jaws of Glycera 

Dibranchiata. M.A. Thesis. SUNY at StonyBrook, StonyBrook. 

(2005). 

M Lerotic. Finding Patterns in Complex Specimens by Improving 

the Aquisition and Analysis of X-ray Spectromicroscopy Data. 

PH.D. Thesis. SUNY at StonyBrook, StonyBrook. (2005). 

T Schäfer, F Claret, M Lerotic, G Buckau, T Rabung, A Bauer, C 

Jacobsen. Source Identification and Characterization of Humic 

and Fulvic Acids Isolated from Oxfordian Argillite and Opalinus 

Clay. Humic Substances: Molecular Details and Applications in 

Land and Water Conservation, p. 43-62, Tayloe and Francis, 

Inc., New York. (2005). 

D Shapiro, P Thibault, T Beetz, V Elser, M Howells, C Jacobsen, 

J Kirz, E Lima, H Miao, et al.. Biological Imaging by Soft X-ray 

Diffraction Microscopy. Proc Natl Acad Sci USA. 102 (43), 

15343-15346 (2005). 

Beamline X1B

C McGuinness, J Downes, P Sheridan, P Glans, K Smith, W Si, P 

Johnson. X-ray Spectroscopic Study of the Electronic Structure 

of the High-Dielectric-Constant Material CaCu3Ti4O12. Phys. 

Rev. B. 71, 195111 (2005). 

A Rüdel, U Hergenhahn, K Maier, E Rennie, O Kugeler, J Viefhaus, 

P Lin, R Lucchese, A Bradshaw. Exchange Interaction Effects in 

NO Core Level Photoionization Cross Sections. New J. Phys.. 

7, 189 (2005). 

C Schubler-Langeheine, J Schlappa, A Tanaka, Z Hu, C Chang, E 

Schierle, M Benomar, H Ott, E Weschke, et al.. Spectroscopy 

of Stripe Order in La1.8Sr0.2NiO4 Using Resonant Soft X-Ray 

Diffraction. Phys. Rev. Lett.. 95, 156402 (2005). 

Y Zhang, S Wang, T Learmonth, L Plucinski, A Matsuura, S 

Bernardis, C O’Donnell, J Downes, K Smith. Electronic 

Excitations in Vanadium Oxide Phthalocyanine Studied via 

Resonant Soft X-ray Emission and Resonant Inelastic X-ray 

Scattering. Chem. Phys. Lett.. 413 (1-3), 95-99 (2005). 

Beamline X2B

J Borah, E Ritman, T Dufresne, S Jorgensen, S Liu, J Sacha, 

R Phipps, R Turner. The Effect of Risdronate on Bone 

Mineralization as Measured by Micro-Computed Tomography 

with Synchrotron Radiation: Correlation to Histomorphometric 

Indices of Turnover. Bone. 37 (1), 1-9 (2005). 

Beamline X3A1

P Coppens, I Vorontsov, T Graber, M Gembicky, A Kovalevsky. The 

Structure of Short-Lived Excited States of Molecular Complexes 

by Time-Resolved X-ray Diffraction. Acta Cryst. A. 61, 162-172 

(2005).

R Poulsen, A Bentien, M Chevalier, B Iverson. Synthesis, Physical 

Properties, Multitemperature Crystal Structure, and 20 K 

Synchrotron X-ray Charge Density of a Magnetic Metal Organic 

Framework Structure, Mn3(C8O4H4)3(C5H11ON)2. J. Am. 

Chem. Soc.. 127, 9156-9166 (2005). 

Beamline X3A2

D Dikovsky, G Marom, C Avila-Orta, R Somani, B Hsiao. ShearInduced Crystallization in Isotactic Polypropylene Containing 

Ultra-High Molecular Weight Polyethylene Oriented Precursor 

Domains. Polymer. 46 (9), 3096-3104 (2005). 

K Fukukawa, L Zhu, P Gopalan, M Ueda, S Yang. Synthesis 

and Characterization of Silicon-Containing Block Copolymers 

from Nitroxide-Mediated Living Free Radical Polymerizatin. 

Macromolecules. 38, 263-270 (2005). 

G Gemeinhardt, R Moore. Characterization of IonomerCompatibilized Blend Morphology Using Synchrotron SmallAngle X-ray Scattering. Macromolecules. 38, 2813-2819 

(2005). 

D Kawakami, B Hsiao, C Burger, S Ran, C Avila-Orta, I Sics, T 

Kikutani, K Jacob, B Chu. Deformation-Induced Phase Transition 

and Superstructure Formation in Poly(ethylene terephthalate). 

Macromolecules. 38, 91-103 (2005). 

J Keum, R Somani, F Zuo, C Burger, I Sics, B Hsiao, H Chen, 

R Kolb, C Lue. Probing Flow-Induced Precursor Structures 

in Blown Polyethylene Films by Synchrotron X-rays During 

Constrained Melting. Macromolecules. 38, 5128-5136 (2005). 

J Miao, G Xu, L Zhu, L Tian, K Uhrich, C Avila-Orta, B Hsiao, M 

Utz. Chain-folding and Overall Molecular Conformation in a 

Novel Amphiphilic Starlike Macromolecule. Macromolecules. 

38, 7074-7082 (2005). 

S Poompradub, M Tosaka, S Kohjiya, Y Ideda, S Toki, I Sics, B 

Hsiao. Mechanism of Strain-Induced Crystallization in Filled and 

Unfilled Natural Rubber Vulcanizates. J. Appl. Phys.. 97, 103529 

(2005). 

R Somani, L Yang, B Hsiao, T Sun, N Pogodina, A Lustiger. ShearInduced Molecular Orientation and Crystallization in Isotactic 

Polypropylene: Effects fo the Deformation Rate and Strain. 

Macromolecules. 38, 1244-1255 (2005). 

Beamline X3B1

C Blome, T Tschentscher, J Davaasambuu, P Durand, S Techert. 

Femtosecond Time-Resolved Powder Diffraction Experiments 

using Hard X-ray Free-Electron Lasers. J. Synch. Rad.. 12, 

812-819 (2005). 

L Chi, I Swainson, L Cranswick, J Her, P Stephens, O Knop. 

The Ordered Phase of Methylammonium Lead Chloride 

CH3ND3PbC13. J. Solid State Chem.. 178 (5), 1376-1385 

(2005). 

O Chmaissem, B Dabrowski, S Kolesnik, J Mais, J Jorgenson, S 

Short, C Botez, P Stephens. Effects of A-Site Ordering on the 

Structures and Properties of La1-xBaxMnO3(X~0.5). Phys. Rev. 

B. 72, 104426 (2005). 

L Hildebrandt, R Dinnebier, M Jansen. Crystal Structure and Ionic 

Conductivity of Cesium Trifluoromethyl Sulfonate, CsSO3CF3. 

Z. Anorg. Allg. Chem.. 631, 1660-1666 (2005). 

A Huq, P Stephens. Transition Temperatures and Vacancies in 

Superconducting Rb[sub 3]C[sub 60]. Phys. Rev. B: Condens. 

Matter. 72, 092511 (2005). 

C Kenney, Y Maham, A Nelson. Characterization of Monofunctional 

ZrO2-M0O3 Catalysts for Methylcyclopentane Conversion. 

Thermochim. Acta. 434 (1-2), 55-61 (2005). 

J Majzlan, C Botez, P Stephens. The Crystal Structure of Synthetic 

Fe2(So4)3(H2O)5 and the type specimen of lausenite. Am. 

Mineral.. 90, 411-416 (2005). 

M Navarro, E Pannunzio-Miner, S Pagola, M Gomex, R Carbonio. 
Structural Refinement of Nd[Fe(CN)6] 4H2O and Study of 

NdFeO3 Obtained by its Oxidative Thermal Decomposition at 

Very Low Temperatures. J. Solid State Chem.. 178 (3), 847-854 

(2005). 

I Schottenfeld, A Benesi, P Stephens, G Chen, P Eklund, T Mallouk. 

Structural Analysis and Characterization of Layer Perovskite 

Oxynitrides made from Dion-Jacobson oxide precursors. J. 

Solid State Chem.. 178, 2313-2321 (2005). 

A van der Lee, P Richez, C Tapiero. Crystal Structure of Nitarsone 

Determined from Synchrotron X-ray Powder Diffraction Data. J. 

Mol. Struct.. 743, 223-228 (2005). 

R Von Dreele. Binding of N-acetylgluocsamine Oligosaccharides 

to Hen Egg-White Lysozyme: A Powder Diffraction Study. Acta 

Cryst. D. 61, 22-32 (2005). 

P Whitfield, I Davidson, L Cranswick, I Swainson, P Stephens. 

Investigation of Possible Superstructure and Cation Disorder 

in the Lithium Battery Cathode Material Li Mn(1/3)Ni(1/

3)Co(1/3)O(2) Using Neutron and Anomalous Dispersion 

Powder Diffraction. Solid State Ionics. 176, 463-471 (2005). 

Beamline X4A

J Avalos, K Bever, C Wolberger. Mechanism of Sirtuin Inhibition 

by Nicotinamide: Altering the NAD+ Cosubstrate Specificity of a 

Sir2 Enzyme. Mol. Cell. 17 (6), 855-868 (2005). 

P Bachhawat. Regulation In The OmpR/PhoB Family of Response 

Regulators. PhD Thesis. Graduate School of Biomedical 

Sciences, University of Medicine and Dentistry, NJ and Rutgers 

University, NJ , Piscataway. (2005). 

P Bachhawat, G Swapna, G Montelione, A Stock. Mechanism of 

activation for transcription factor PhoB suggested by different 

modes of dimerization in the inactive and active states. 

Structure. 13 (9), 1353-1363 (2005). 

A Banerjee, W Yang, M Karplus, G Verdine. Structure of a Repair 

Enzyme Interrogating Undamaged DNA Elucidates Recognition 

of Damaged DNA. Nature. 434, 612-618 (2005). 

S Bouyain, P Longo, S Li, K Ferguson, D Leahy. The Extracellular 

Region of ErbB4 Adopts a Tethered Conformation in the 

Absence of Ligand. Proc Natl Acad Sci USA. 102, 15024-15029 

(2005). 

R Depetris, J Hu, I Gimpelevich, L Holt, R Daly, S Hubbard. 

Structural Basis for Inhibition of the Insulin Receptor by the 

Adaptor Protein Grb14. Mol. Cell. 20 (2), 325-333 (2005). 

D Eckert, D Chan, V Malashkevich, P Carr, P Kim. Inhibitors of HIV 

Membrane Fusion. US Patent No. 6,841,657. (2005). 

Q Fan, W Hendrickson. Structure of Human Follicle-Stimulating 

Hormone in Complex with its Receptor. Nature. 433, 269 

(2005). 

F Forouhar, Y Yang, D Kumar, Y Chen, E Fridman, S Park, 

Y Chiang, T Acton, G Montelione, et al.. Structural and 

Biochemical Studies Identify Tobacco SABP2 as a Methyl 

Salicylate Esterase and Implicate it in Plant Innate Immunity. 

Proc Natl Acad Sci USA. 102, 1773-1778 (2005). 

F Forouhar, I Lee, J Vujcic, S Vujcic, J Shen, S Vorobiev, R Xiao, T 

Acton, G Montelione, et al.. Structural and Functional Evidence 

for Bacillus subtilis PaiA as a Novel N1-spermidine/spermine 

acetyltransferase (SSAT). J. Biol. Chem.. 280, 40328-40336 

(2005). 

H Furukawa, S Singh, R Mancusso, E Gouaux. Subunit 

Arrangement and Function in NMDA Receptors. Nature. 438, 

185-192 (2005). 

B Geisbrecht, B Hamakoa, B Perman, Z Zemla, D Leahy. The 

Crystal Structure of EAP Domains from Staphylococcus Aureus 

Reveal an Unepxected Hology to Bacterial Superantigens. J. 

Biol. Chem.. 280, 17243 (2005). 

J Gorman, L Shapiro. Crystal Structures of the Tryptophan 

Repressor binding Protein WrbA and complexes with Flavin 

Mononucleotide. Protein Sci.. 14, 3004-3012 (2005). 

S Hausmann, S Zheng, C Fabrega, S Schneller, C Lima, S 

Shuman. Encephalitozoon Cuniculi MRNA Cap ( Guanine N-7) 

Methyltransferase: Methyl Acceptor Specificity, Inhibition by SAdnenosylmethionine Analogs, and Structure-Guided Mutational 

Analysis. J. Biol. Chem.. 280, 20404 (2005). 

W Hendrickson, X Jiang, K Langley, R Syed, Y Hsu. Conjugated 

Ligands for the Stimulation of blood Cell Proliferation by 

Effecting Dimerization of the Receptor for Stem Cell Factor. US 

Patent No. 6,904,369. (2005). 

J Hu, S Hubbard. Structural Characterization of a Novel Cbl 

Phosphotyrosine Recognition Motif in the APS Family of Adapter 

Proteins. J. Biol. Chem.. 280 (19), 18943 (2005). 

O Ibrahimi, B Yeh, A Eliseenkova, F Zhang, S Olsen, M Igarashi, 

S Aaronson, R Linhardt, M Mohammadi. Analysis of Mutations 

in Fibroblast Growth Factor (FGF) and a Pathogenic Mutation 

in FGF Receptor (FGFR) Provides Direct Evidence for the 

Symmetric Two-End Model for FGFR Dimerization. Mol. Cell. 

Bio.. 25, 671-684 (2005). 

A Inanobe, H Furukawa, E Gouaux. Mechanism of Partial Agonist 

Action at the NR1 Subunit of NMDA Receptors. Neuron. 47, 71-

84 (2005). 

R Jin, S Clark, A Weeks, J Dudman, E Gouaux, K Partin. 

Mechanism of Positive Allosteric Modulators Acting on AMPA 

Receptors. J. Neurosci.. 25, 9027-9036 (2005). 

G Jogl, Y Hsiao, L Tong. Crystal Structure of Mouse Carnitine 

Octanoyltransferase and Molecular Determinants of Substrate 

Selectivity. J. Biol. Chem.. 280, 738 (2005). 

J Khan, B Dunn, L Tong. Crystal Structure of Human Taspase1, a 

Crucial Protease Regulating the Function of MLL. Structure. 13

(10), 1443-1452 (2005). 

L Lois, C Lima. Structures of the Small Ubiquitin-like Modifier E1 

Activating Enzyme Provide Insights into SUMO Activation and 

the Mechanism for E2 Recruitment to E1. EMBO J.. 24, 439-451 

(2005). 

A Malay, K Allen, D Tolan. Structure of the Thermolabile Mutant 

Aldolase B, A149P: Molecular Basis of Hereditary Fructose 

Intolerance. J. Mol. Biol.. 347 (1), 135-144 (2005). 

A Marina, C Waldburger, W Hendrickson. Structure of the Entire 

Cytoplasmic Portion of a Sensor Histidine-kinase Protein. 

EMBO J.. 24, 1-13 (2005). 

E Michelotti, K Moffett, D Nguyen, M Kelly, R Shetty, X Chai, 

K Northrop, V Namboodiri, B Campbell, M Karpusas. Two 

Classes of p38ƒÑƒnMAP Kinase Inhibitors Having a Common 

Diphenylether Core but Exhibiting Divergent Binding Modes. 

BioOrg. Med. Chem.. 15 (23), 5274-5279 (2005). 

R Olson, E Gouaux. Crystal Structure of the Vibrio cholerae 

Cytolysin (VCC) Pro-toxin and its Assembly into a Heptameric 

Transmembrane Pore. J. Mol. Biol.. 350, 997-1016 (2005). 

D Reverter, K Wu, T Gan-Erdene, Z Pan, K Wilkinson, C Lima. 

Structure of the Complex Between the Ulp/Senp Protease 

Family Member Den1 and Nedd8. J. Mol. Biol.. 345, 141-151 

(2005). 

S Rubin, A Gall, N Zheng, N Pavletich. Structure of the Rb 

C-Terminal Domain Bound to E2F1-DP1: A Mechanism for 

Phosphorylation-Induced E2F Release. Cell. 123 (6), 1093-

1106 (2005). 

M Rudolph, G Amodeo, Y Bai, L Tong. Crystal Structure of the 

Protein Kinase Domain of Yeast AMP-Activated Protein Kinase 

Snf1. Biochem. Biophys. Res. Commun.. 337, 1224-1228 

(2005). 

A Ruthenburg, D Graybosch, J Huetsch, G Verdine. A Superhelical 

Spiral in the Escherichia coli DNA Gyrase A C-terminal Domain 

Publications 7-9
7-10 NSLS Activity Report

Imparts Unidirectional Supercoiling Bias. J. Biol. Chem.. 280, 

26177-26184 (2005). 

C Steegborn, T Litvin, K Hess, A Capper, R Taussig, J Buck, L 

Levin, H Wu. A Novel Mechanism for Adenylyl Cyclase Inhibition 

from the Crystal Structure of its Complex with Catechol 

Estrogen. J. Biol. Chem.. 280, 31754 (2005). 

C Steegborn, T Litvin, L Levin, J Buck, H Wu. Biocarbonate Activation 

of Adenylyl Cyclase via Promotion of Catalytic Active Site Closure 

and Metal Recruitment. Nat. Struct. Mol. Biol.. 12, 32 (2005). 

X Tao. Structural and Functional Studies on Human DJ-1 

(PARK7), a Protein Associated with Early-Onset Parkinson’s 

Disease. PhD Thesis. Columbia University, New York. (2005). 

A Toro-Roman, T Mack, A Stock. Structural Analysis and Solution 

Studies of the Activated Regulatory Domain of the Response 

Rugulator ArcA: A Symmetric Dimer Mediated by the alpha4-

beta5-alpha5 Face. J. Mol. Biol.. 349 (1), 11-26 (2005). 

A Toro-Roman, T Wu, A Stock. A Common Dimerization Interface 

in Bacterial Response Regulators KdpE and TorR. Protein Sci.. 

14 (12), 3077-3088 (2005). 

A Toro-Roman. A Model for the Mechanism of Activation of 

Response Regulators from the OmpR/PhoB Subfamily of 

Transcription Factors. Ph.D. Thesis. Rutgers, The State 

University of New Jersey, New Brunswick. (2005). 

L Vedula, M Rynkiewicz, H Pyun, R Coates, D Cane, D 

Christianson. Molecular Recognition of the Substrate 

Diphosphate Group Governs Product Diversity in Trichodiene 

Synthase Mutants. Biochemistry. 44, 6153 (2005). 

J Williams, C Sue, G Banting, H Yang, D Glerum, W Hendrickson, 

E Schon. Crystal Structure of Human SCO1: Implications for 

Redox Signaling by a Mitochondrial Cytochrome C Oxidase 

„Assembly“ Protein. J. Biol. Chem.. 280, 15202 (2005). 

J Williams, H Xie, W Hendrickson. Crystal Structure of Dynein 

Light Chain TCTEX-1. J. Biol. Chem.. 280, 21981 (2005). 

P Worley, J Tu, B Xiao, D Leahy, J Beneken, A Lanahan, P 

Brakeman. Nucleic Acid Molecule Encoding Homer 2a Protein. 

US Patent No. 6,864,083. (2005). 

Q Xu, R Roberts, H Guo. Two Crystal Forms of the Restriction 

Enzyme MspI–DNA Complex Show the Same Novel Structure. 

Protein Sci.. 14, 2590-2600 (2005). 

A Yamashita, S Singh, T Kawate, Y Jin, E Gouaux. Crystal 

Structure of a Bacterial Homologue of Na+/Cl- -Dependent 

Neurotransmitter Transporters. Nature. 437, 215 (2005). 

J Yang, L Wang, L Zheng, F Wan, M Ahmed, M Lenardo, H Wu. 

Crystal Structure of MC159 Reveals Molecular Mechanism of 

DISC Assembly and FLIP Inhibition. Mol. Cell. 20, 939 (2005). 

M Zweifel, D Leahy, D Barrick. Structure and Notch Receptor 

Binding of the Tandem WWE Domain of Deltex. Structure. 13, 

1599-1611 (2005)

Beamline X6A

M Adams, Z Jia. Structural and Biochemical Evidence for 

an Enzymatic Quinone Redox Cycle in Escherichia Coli: 

Identification of a Novel Quinol Momooxygenase. J. Biol. 

Chem.. 280, 8358 (2005). 

R DeSilva, G Kovacikova, W Lin, R Taylor, K Skorupski, F Kull. 

Crystal Structure of the Virulence Gene Activator Apha from 

Vibrio Cholerae Reveals it is a Novel Member of the Winged 

Helix Transcription Factor Superfamily. J. Biol. Chem.. 280, 

13779 (2005). 

J Helliwell. Protein Crystal Perfection and its Application. Acta 

Cryst. D. 61, 793-798 (2005). 

T Kajander, A Cortajarena, E Main, S Mochrie, L Regan. A New 

Folding Paradigm for Repeat Proteins. J. Am. Chem. Soc.. 127, 

10188-10190 (2005). 

T Kuzuyama, J Noel, S Richard. Structural Basis for the 

Promiscuous Biosynthetic Prenylation of Aromatic Natural 

Products. Nature. 435 (7044), 983-7 (2005). 

A Mildvan, Z Xia, H Azurmendi, V saraswat, P Legler, M Massiah, 

S Gabelli, M Bianchet, L Kang, L Amzel. Structures and 

Mechanisms of Nudix Hydrolases. Arch. Biochem. Biophys.. 

433 (1), 129-43 (2005). 

M Nadella, M Bianchet, S Gabelli, J Barrila, L Amzel. Structure and 

Activity of the Axon Guidance Protein MICAL. Proc Natl Acad 

Sci USA. 102 (46), 16830-16835 (2005). 

D Nair, R Johnson, L Prakash, S Prakash, A Aggarwal. Rev1 

Employs a Novel Mechanism of DNA Synthesis using a Protein 

Template. Science. 309, 2219 (2005). 

M Nicholson, M Hahn, K Wucherpfennig. Unusual features of 

Self-Peptide/MHC Binding by Autoimmune T Cell Receptors. 

Immunity. 23 (4), 351-360 (2005). 

K Pant, B Crane . Structure of a Loose Dimer: an Intermediate in 

Nitric Oxide Synthase Assembly. J. Mol. Biol.. 352 (4), 932-940 

(2005). 

E Pozharski, A Moulin, A Hewagama, A Shanafelt, G Petsko, D 

Ringe. Diversity of Hapten Recognition: Structural Study of an 

Anti-Cocaine Antibody M82G2. J. Mol. Biol.. 349 (3), 570-582 

(2005). 

A Vahedi-Faridi, V Stojanoff, J Yeh. The Effects of Flash-Annealing 

on Glycerol Kinase Crystals. Acta Cryst. D. 61 (7), 982-989 

(2005). 

Z Xia, H Azurmendi, L lairson, S Withers, S Gabelli, M Bianchet, L 

Amzel, A Mildvan. Mutational, Structural, and Kinetic Evidence 

for a Dissociative Mechanism in the GDP-mannose Mannosyl 

Hydrolase Reaction. Biochemistry. 44 (25), 8989-97 (2005). 

Beamline X6B

S Kwak, E DiMasi, Y Han, J Aizenberg, I Kuzmenko. Orientation 

and Mg Incorporation of Calcite Grown on Functionalized SelfAssembled Monolayers: A Synchrotron X-ray Study. Cryst. 

Growth Des.. 5 (6), 2139-2145 (2005). 

Beamline X7A

D Cox, B Noheda, G Shirane. Low-Temperature Phases in 

PbZr0.52Ti0.48O3: A Neutron Powder Diffraction Study. Phys. 

Rev. B: Condens. Matter. 71, 134110-10 (2005). 

M Crawford, R Harlow, S Ceemyad, V Tissen, J Schilling, E 

McCarron, S Tozer, D Cox, N Ichikawa, et al.. High-Pressure 

Study of Structural Phase Transitions and Superconductivity in 

La1.48Nd0.4Sr0.12CuO4. Phys. Rev. B. 71, 104513 (2005). 

F Drymiotis, Y Lee, G Lawes, J Lashley, T Kimura, S Shapiro, 

A Migliori, V Correa, R Fisher. Tunable Thermal Expansion 

Behavior in the Intermetallic YbGaGe. Phys. Rev. B. 71, 174304 

(2005). 

M Gateshki, V Petkov, S Pradhan, T Vogt. Structure of 

Nanocrystalline MgFe2O4 from X-ray Diffraction, Rietveld and 

Atomic Pair Distribution Function Analysis. J. Appl. Cryst.. 38, 

772-779 (2005). 

J Graetz, Y Lee, J Reilly, S Park, T Vogt. Structures and 

Thermodynamics of the Mixed Alkali Alanates. Phys. Rev. B. 71, 

184115 (2005). 

J Lai, K Shafi, A Ullman, K Loos, R Popovitz-Biro, Y Lee, T Vogt, 

C Estournes. One-Step Synthesis of Core(Cr)/Shell(gammaFe2O3) Nanoparticles. J. Am. Chem. Soc.. 127, 5730-5731 

(2005). 

Y Lee, J Hriljac, T Vogt. Pressure-Induced Migration of Zeolitic 

Water in Laumontite. Phys. Chem. Miner.. 31, 421-428 (2005). 

Y Lee, J Hriljac, T Vogt. Variable-Temperature Structural Studies of 
Tetranatrolite from Mt. Saint-Hilaire: Synchrotron X-ray Powder 

Diffraction and Rietveld Analysis. Am. Mineral.. 90, 247-251 

(2005). 

Y Lee, J Hriljac, J Parise, T Vogt. Pressure-Induced Stabilization 

of Ordered Paranatrolite: A new Insight into the Paranatrolite 

controversy. Am. Mineral.. 90, 252-257 (2005). 

R Macquart, S Kim, W Gemmill, J Stalick, Y Lee, T Vogt, H 

zur Loye. Synthesis, Structure, and Magnetic Properties of 

Sr2NiOsO6 and Ca2NiOsO6: Two New Osmium-Containing 

Double Perovskites. Inorg. Chem.. 44, 9676-9683 (2005). 

Y Mudryk, Y Lee, T Vogt, K Gschneidner, Jr., V Pecharsky. 

Polymorphism of Gd5Si2Ge2: The Equivalence of Temperature, 

Magnetic Field, and Chemical and Hydrostatic Pressures. Phys. 

Rev. B. 71, 174104 (2005). 

S Park, K Kang, W Si, W Yoon, Y Lee, A Moodenbaugh, L Lewis, 

T Vogt. Synthesis and Characterization of Na0.3RhO2.0.6H2)-A 

Seminconductor with a Weak Ferromagnetic Component. Solid 

State Commun.. 135 (1-2), 51-56 (2005). 

S Park, Y Lee, W Si, T Vogt. Synthesis and Structure of the 

Monolayer Hydrate K0.3C0O2.4H2O. Solid State Commun.. 

134 (9), 607-611 (2005). 

V Petkov, V Parvanov, D Tomalia, D Swanson, D Bergstrom, 

T Vogt. 3D Structure of Dendritic and Hyper-Branched 

Macromolecules by X-ray Diffraction. Solid State Commun.. 134

(10), 671-675 (2005). 

V Petkov, V Parvanov, P Trikalitis, C Malliakas, T Vogt, M 

Kanatzidis. Three-Dimensional Structure of Nanocomposites 

from Atomic Pair Distribution Function Analysis: Study of 

Polyaniline and (Polyaniline)0.5V2O5.1.0H2O. J. Am. Chem. 

Soc.. 127, 8805-8812 (2005). 

C Petrovic, Y Lee, T Vogt, N Lazarov, S Bud’ko, P Canfield. Kondo 

Insulator Description of Spin State Transition in FeSb2. Phys. 

Rev. B: Condens. Matter. 72, 045103 (2005). 

K Wallwork, B Kennedy, Q Zhou, Y Lee, T Vogt. Pressure and 

Temperature-Dependent Structural Studies of Ba2BiTaO6. J. 

Solid State Chem.. 178 (1), 201-211 (2005). 

X Yang, B Toby, M Camblor, Y Lee, D Olson. Propene Adsorption 

Sites in Zeolite ITQ-12: a Combined Synchrotron X-ray Neutron 

Diffraction Study. J. Phys. Chem. B. 109 (16), 7894-7899 

(2005). 

Q Zhou, B Kennedy, K Wallwork, M Elcombe, Y Lee, T Vogt. 

Temperature and Pressure Dependent Structural Studies of the 

Ordered Double Perovskites Sr2TbRu1-xIrxO6. J. Solid State 

Chem.. 178 (7), 2282-2291 (2005). 

H zur Loye, M Smith, Y Lee, T Vogt. High-Pressure Investigation of 

Sr3PbNiO6. J. Alloys Compd.. 390 (1-2), 35-40 (2005). 

Beamline X7B

A Celestian, D Medvedev, A Tripathi, J Parise, A Clearfield. 

Optimizing Synthesis of Na2Ti2SiO7 · 2H2O (Na-CST) and Ion 

Exchange Pathways for Cs0.4H1.6Ti2SiO7 · H2O (Cs-CST) 

Determined from in situ Synchrotron X-ray Powder Diffraction. 

Nucl. Instrum. Meth. B. 238, 61-69 (2005). 

R Dinnebier, S Vensky, M Jensen, J Hanson. Crystal Structure 

and Topological Aspects of the High-Temperature Phases of the 

Alkali-metal Oxalates M-2 C2O4(M= K,Rb, Cs). Chem. Eur. J.. 

11 (4), 1119-1129 (2005). 

M Fernandez-Garcia, X Wang, C Belver, A Iglesias-Juez, J 

Hanson, J Rodriguez. Ca Doping of Nanosize Ce-Zr and Ce-Tb 

Solid Solutions: Structural and Electronic Effects. Chem. Mater.. 

17, 4181-4193 (2005). 

X Guo, B Ravi, P Devi, J Hanson, J Margolies, R Gambino, J 

Parise, S Sampath. Synthesis of Yttrium Iron garnet (YIG) by 

Citrate-Nitrate Gel Combustion and Precursor Plasma Spray 

Processes. J. Magn. Magn. Mater.. 295 (2), 145-154 (2005). 

M Helliwell, R Jones, V Kaucic, N Logar. The use of Softer X-rays 

in the Structure Elucidatin of Microporous Materials. J. Synch. 

Rad.. 12 (4), 420-430 (2005). 

L Hildebrandt, R Dinnebier, M Jansen. Crystal Structure and Ionic 

Conductivity of Cesium Trifluoromethyl Sulfonate, CsSO3CF3. 

Z. Anorg. Allg. Chem.. 631, 1660-1666 (2005). 

T Jensen, A Christensen, J Hanson. Hydrothermal Transformation 

of the Calcium Aluminum Oxide Hydrates CaAl2O4 . 10H2O 

and Ca2Al2O. 8H2O to Ca3Al2(OH)12 Investigated by In Situ 

Synchrotron X-ray Powder Diffraction. Cem. Concr. Res.. 35, 

2300-2309 (2005). 

H Jeong, Z Lai, M Tsapatsis, J Hanson. Strain of MFI Crystals in 

Membranes: An in situ Synchrotron X-ray Study. Microporous 

Mesoporous Mater.. 84 (1-3), 332-337 (2005). 

Y Meng, G Ceder, C Grey, W Yoon, M Jiang, J Breger, Y ShaoHorn. Cation Ordering in Layered O3 Li[NixLi1/3-2/3Mn2/3-x/

3]O2. Chem. Mater.. 17, 2386-2394 (2005). 

J Rodriguez, X Wang, G Liu, J Hanson, J Hrbek, C Peden, A 

Iglesias-Juez, M Fernandez-Garcia. Physical and Chemical 

Properties of Ce1-xZrxO2 Nanoparticles and Ce1-xZrxO2(1 1 1) 

Surfaces: Synchrotron-Based Studies. J. Mol. Catal. A: Chem.. 

228, 11-19 (2005). 

L Solovyov, O Belousov, R Dinnebier, A Shmakov, S Kirik. X-ray 

Diffraction Structure Analysis of MCM-48 Mesoporous Silica. J. 

Phys. Chem. B. 109, 3233-3237 (2005). 

J Szanyi, J Kwak, J Hanson, C Wang, T Szailer, C Peden. 

Changing Morphology of BaO/Al2O3 During NO2 Uptake and 

Release. J. Phys. Chem. B. 109, 7339-7344 (2005). 

S van Smallen, R Dinnebier, J Hanson, J Gollwitzer, F Bullesfeld, 

A Prokofiev, W Assmus. High-Temperature Behavior of Vanadyl 

Pyrophosphate (VO)2P2O7. J. Solid State Chem.. 178 (7), 

2225-2230 (2005). 

X Wang, J Rodriguez, J Hanson, D Gamarra, A Martinez-Arias, M 

Fernandez-Garcia. Unusual Physical and Chemical Properties 

of Cu in Ce1-xCuxO2 Oxides. J. Phys. Chem. B. 109, 19595-

19603 (2005). 

X Wang, J Hanson, J Rodriguez, C Belver, M Fernandez-Garcia. 

The Structural and Electronic Prorperties of Nanostructured 

Ce(1-x-y)Zr(x)Tb(y)O(2) Ternary Oxides: Unusual Concentration 

of Tb(3+) and Metal-Oxygen-Metal Interactions. J. Chem. Phys.. 

122 (15), 154711 (2005). 

X Wang, J Rodriguez, J Hanson, M Perez, J Evans. In Situ TimeResolved Characterization of Au-CeO2 Catalysts During Water 

Gas Shift Reactions: presence of Au and O Vacancies in the 

Active Phase. J. Chem. Phys.. 123, 221101 (2005). 

W Wen, B Kumarasamy, S Mukerjee, M Auinat, Y Ein-Eli. Origin 

of 5 V Electrochemical Activity Observed in Non-Redox 

Reactive Divalent Cation Doped LiM0.5-xMn1.5+xO4 (0<XJ. 

Electrochem. Soc.. 152 (9), A1902 (2005). 

W Yoon, M Balasubramanian, X Yang, J McBreen, J Hanson. Time 

Resolved XRD Study on the Thermal Decomposition of Li1-

xNi0.8Co0.15Al0.05O2 Cathode Materials for Li-ion Batteries. 

Electrochem. Solid-State Lett.. 8, A83 (2005). 

J Zhang, F Lima, M Shao, K Sasaki, J Wang, J Hanson, R Adzic. 

Platinum Monolayer on Nonnoble Metal-Nobel Metal Core-Shell 

Nanoparticle Electrocatalysts for O2 Reduction. J. Phys. Chem. 

B. 109, 22701-22704 (2005). 

Beamline X8C

J Adams, G Pal, K Yam, H Spencer, Z Jia, S Smith. Purification 

and Crystallizatin of a Trimodular Complex Comprising the 

Type II Cohesin-Dockerin Interaction from the Cellulosome of 

Clostridium thermocellum. Acta Cryst. F. 61, 46-48 (2005). 

Publications 7-11
7-12 NSLS Activity Report

A Athanasiadis, D Placido, S Maas, B Brown, II, K Lowenhaupt, 

A Rich. The Crystal Structure of the ZB Domanin of the RNAEditing Enzyme ADAR1 Reveals Distinct Conserved Surfaces 

Among Z-Domains. J. Mol. Biol.. 351 (33), 496-507 (2005). 

R Crowther, M Georgiadis. The Crystal Structure of 5-Keto-4-

Deoxyuronate Isomerase from Escherichia Coli. Proteins: Struc. 

Func. Genet.. 61, 680 (2005). 

C Goulding, M Apostol, M Sawaya, M Phillips, A Parseghian, 

D Eisenberg. Regulation by Oligomerization a Mycobacterial 

Folate Biosynthetic Enzyme. J. Mol. Biol.. 349, 61-72 (2005). 

M Huang, A Mazar, G Parry, A Higazi, A Kuo, D Cines. 

Crystallization of Soluble Urokinase Receptor (suPAR) in 

Complex with Urokinase Amino-Terminal Fragment (1-143). 

Acta Cryst. D. 61, 697-700 (2005). 

J Johnston, V Arcus, E Baker. Structure of Naphthoate Synthase 

(MenB) From Mycobacterium Tuberculosis in Both Native 

and Product-Bound Forms. Acta Cryst. D. 61 (9), 1199-1206 

(2005). 

A Kim, T Dobransky, R Rylett, B Shilton. Surface-Entropy Reduction 

used in the Crystallization of Human Choline Acetyltransferase. 

Acta Cryst. D. 61 (9), 1306-1310 (2005). 

T Kuzuyama, J Noel, S Richard. Structural Basis for the 

Promiscuous Biosynthetic Prenylation of Aromatic Natural 

Products. Nature. 435 (7044), 983-7 (2005). 

P Lario, R Pfuetzner, E Frey, L Creagh, C Haynes, A Maurelli, N 

Strynadka. Structure and Biochemical Analysis of a Secretin 

Pilot Protein. EMBO J.. 24, 1111-1121 (2005). 

R Liu, P Loll, R Eckenhoff. Structural Basis for High Affinity Volatile 

Anesthetic Binding in a Natural 4-helix Bundle Protein. Faseb J.. 

19, 567-576 (2005). 

J Meng, D Vardar, Y Wang, H Guo, J Head, C McKnight. HighResolution Crystal Structures of Villin Headpiece nad Mutants 

with Reduced F-Actin Binding Activity. Biochemistry. 44, 11963-

11973 (2005). 

A Mezzetti, J Schrag, C Cheong, R Kazlauskas. Mirror-Image 

Packing in Enantiomer Discrimination Molecular Basis for the 

Enantioselectivity of B. Cepaci Lipase Toward 2-Methyl-3-

Phenyl-1-Propanol. Chem. Bio.. 12, 427 (2005). 

I Mirza, I Nazi, M Korczynska, G Wright, A Berghuis. Crystal 

Structure of Homoserine Transacetylase from Haemophilus 

Influenzae Reveals a New Family of alpha/beta-Hydrolases. 

Biochemistry. 44, 15768-15773 (2005). 

J Pedelacq, G Waldo, S Cabantous, E Liong, T Terwilliger. 

Structural and Functional Features of a nNDP Kinase from the 

Hyperthermophile Crenarchaeon Pyrobaculum Aerophilum. 

Protein Sci.. 14, 2562 (2005). 

E Rangarajan, Y Li, P Iannuzzi, M Cygler, A Matte. Crystal 

Structure of Escherichia coli Crotonobetianyl-CoA: Carnitine 

CoA-Transferase (CaiB) and Its Complexes with CoA and 

Carnitinyl-CoA. Biochemistry. 44, 5728-5738 (2005). 

S Raymond, A Tocilj, E Ajamian, Y Li, M Hung, A Matte, M Cygler. 

Crystal Structure of Ureidoglycolate Hydrolase (AllA) from 

Escherichia coli O157:H7. Proteins: Struc. Func. Genet.. 61 (2), 

454-459 (2005). 

J Schuermann, S Prewitt, C Davies, S Deutscher, J 

Tanner. Evidence for Structural Plasticity of Heavy Chain 

Complementarity-determining Region 3 in Antibody-ssDNA 

Recognition. J. Mol. Biol.. 347, 965 - 978 (2005). 

J Sivaraman, R Myers, L Boju, T Sulea, M Cygler, V 

Davisson, J Schrag. Crystal Structure of Methanobacterium 

thermaoautotrophicum Phosphoribosyl-AmP. Biochemistry. 44, 

10071-10080 (2005). 

D Snyder, Y Chen, N Denissova, T Acton, J Aramini, M Ciano, R 

Karlin, J Liu, P Manor, et al.. Comparisons of NMR Spectral 

Quality and Success in Crystallization Demonstrate that NMR 

and X-ray Crystallography are Complementary Methods for 

Small Protein Structure Determination. J. Am. Chem. Soc.. 127, 

16505-16511 (2005). 

M St-Jean, J Lafrance-Vanasse, B Liotard, J Sygusch. High 

Resolution Reaction Intermediates of rabbit Muscle Fructose1,6-bisphosphate Aldolase: Substrate Cleavage and Induced 

Fit. J. Biol. Chem.. 280 (29), 27262-70 (2005). 

P Telmer, B Shilton. Structural Studies of an Engineered Zinc 

Biosensor Reveal an Unanticipated Mode of Zinc Binding. J. 

Mol. Biol.. 354 (4), 829-840 (2005). 

A Tocilj, J Schrag, Y Li, B Schneider, L Reitzer, A Matte, M Cygler. 

Crystal Structure of N-succinylarginine Dihydrolase AstB, 

Bound to Substrate and Product, an Enzyme from the Arginine 

Catabolic Pathway of Escherichia Coli. J. Biol. Chem.. 280 (16), 

15800-15808 (2005). 

Z Yang, J Horton, R Maunus, G Wilson, R Roberts, X 

Cheng. Structure of HinP1I Endonuclease Reveals a 

Striking Similarity to the Monomeric Restriction Enzyme 

MspI. Nucleic Acids Res.. 33 (6), 1892-1901 (2005). 

Beamline X9A

T Ball, W Edstrom, L Mauch, J Schmitt, B Leistler, H Fiebig, W 

Sperr, A Hauswirth, P Valent, et al.. Gain of Structure and IgE 

Epitopes by Eukaryotic Expression of the Major Timothy Grass 

Pollen Allergen, Phl p. 1. FEBS Lett. 272, 217 (2005). 

W Barton, D Tzvekova, D Nikolov. Structure of the Angiopoietin2 Receptor Binding Domain and Identification of Surfaces 

Involved in Tie2 Recognition. Structure. 13 (5), 825-832 (2005). 

I Berke. Nuts and Bolts of the NPC: The Structure of Nup133. 

Ph.D. Thesis. Rockefeller University, New York. (2005). 

M Chlenov, Y Masuda, K Murakami, V Nikiforov, S Darst, A 

Mustaev. Structure and Function of Lineage-Specific Sequence 

Insertions in the Bacterial RNA Polymerase beta’ Subunit. J. 

Mol. Biol.. 353, 138-154 (2005). 

B Hao, N Zheng, B Schulman, G Wu, J Miller, M Pagano, N 

Pavletich. Structural Basis of the Cks1-Dependent Recognition 

of P27Kip1 by the SCF skp2 Ubiquitin Ligase. Mol. Cell. 20 (1), 

9-19 (2005). 

S Hegde, M Vetting, S Roderick, L Mitchenall, A Maxell, H Takiff, 

J Blanchard. A Fluoroquinolone Resistance Protein from 

Mycobacterium tuberculosis That Mimics DNA. Science. 308, 

1480 (2005). 

R Janjusevic, R Abramovitch, G Martin, C Stebbins. A Bacterial 

Inhibitor of Host Programmed Cell Death Defenses is an E3 

Ubiquitin Ligase. Science. 311, 222-226 (2005). 

D Jian, y Kim, K Maxwell, S Beasley, R Zhang, g Gussin, A 

Edwards, S Darst. Crystal Structure of Bacteriophage lamda cII 

and its DNA Complex. Mol. Cell. 19, 259-269 (2005). 

S Li, K Schmitz, P Jeffrey, J Wiltzius, P Kussie, K Ferguson. 

Structural Basis for Inhibition of the Epidermal Growth Factor 

Receptor by Cetuximab. Cancer Cell. 7 (4), 301-311 (2005). 

B Manjasetty, F Niesen, C Scheich, Y Roske, F Goetz, J Behlke, 

V Sievert, U Heinemann, K Buessow. X-ray Structure of 

Engineered Human Aortic Preferentially Expressed Protein-1 

(APEG-1). BMC Struct. Bio.. 5, 21 (2005). 

N Marinkovic, S Gupta, C Zhan, M Chance. Synchrotron Radiation 

in Biosciences. Nucl. Instrum. Meth. B. 241 (1-4), 242-246 

(2005). 

D Nikolov, C Li, W Barton, J Himanen. Crystal Structure of the 

Ephrin-B1 Ectodomain: Implications for Receptor Recognitin 

and Signaling. Biochemistry. 44, 10947-10953 (2005). 

L Patskovska, Y Patskovsky, S Almo, R Hirsch. COHbC and 

COHbS Crystallize in the R2 Quaternary State at Neutral pH in 

the Presence of PEG 4000 . Acta Cryst. D. 61, 566 (2005). 
U Ramagopal, Z Dauter, R Thirumuruhan, E Fedorov, S 

Almo. Radiation-Induced Site-Specific Damage of Mercury 

Derivatives: Phasing and Implications. Acta Cryst. D. 61 (9), 

1289-1298 (2005). 

E Sickmier, D Brekasis, S Paranawithana, J Bonanno, M Paget, S 

Burley, C Kielkopf. X-ray Structure of a Rex-Family Repressor/

NADH Complex Insights into the Mechanism of Redox Sensing. 

Structure. 13, 43-54 (2005). 

J Sun, W Wang, H Yang, S Liu, F Liang, A Fedorov, S Almo, 

Z Zhang. Structure and Biochemical Properties of PRL-1, a 

Phosphatase Implicated in Cell Growth, Differentiation, and 

Tumor Invasion. Biochemistry. 44, 12009-12021 (2005). 

T Tellinghuisen, J Marcotrigiano, C Rice. Structure of the ZincBinding Domain of an Essential Component of the Hepatitis C 

Virus Replicase. Nature. 435, 374 (2005). 

N Thoma, B Czyzewski, A Alexeev, A Mazin, N Pavletich. 

Structure of the SW12/SNF2 Chromatin-Remodeling Domain of 

Eukaryotic Rad54. Nat. Struct. Mol. Biol.. 12, 350-356 (2005). 

H Yang, Q Li, J Fan, W Hollomon, N Pavletich. The BRCA2 

Homologue Brh2 Nucleates RAD51 Filament Formation at a 

dsDNA-ssDNA Junction. Nature. 433, 653-657 (2005). 

Beamline X9B

R Breece, A Costello, B Bennett, T Sigdel, M Matthews, D Tierney, 

M Crowder. A Five-Coordinate Metal Center in Co(II)-Substituted 

VanX. J. Biol. Chem.. 280, 11074-11081 (2005). 

M Chlenov, Y Masuda, K Murakami, V Nikiforov, S Darst, A 

Mustaev. Structure and Function of Lineage-Specific Sequence 

Insertions in the Bacterial RNA Polymerase beta’ Subunit. J. 

Mol. Biol.. 353, 138-154 (2005). 

A Fokine, p Leiman, M Shneider, B Ahvazi, K Boeshans, A Steven, 

L Black, V Mesyanzhinov, M Rossman. Structural and Functional 

Similarities Between the Capsid Proteins of Bacteriophages T4 

and HK97 Point to a Common Ancestry. Proc Natl Acad Sci 

USA. 102, 7163-7168 (2005). 

A Guarne, T Brendler, Q Zhao, R Ghirlando, S Austin, W Yang. 

Crystal Structure of a SeqA-N Filament: Implications for DNA 

Replication and Chromosome Organization. EMBO J.. 24, 

1502-1511 (2005). 

K Gunter, M Aschner, L Miller, R Eliseev, J Salter, K Anderson, 

S Hammond, T Gunter. Determining the Oxidation States of 

Manganese in PC12 and Nerve Growth Factor-Induced PC12 

Cells. N/A. 39 (2), 164-181 (2005). 

A Gustchina, M Li, S Wunschmann, M Chapman, A Pomes, A 

Wlodawer. Crystal Structure of Cockroach Allergen Bla g2, an 

Unusual Zinc Binding Aspartic Protease with a Novel Mode of 

Self-Inhibition. J. Mol. Biol.. 348 (2), 433-444 (2005). 

A Hansen, Y Gu, M Li, M Andrykovitch, D Waugh, D Jin, X Ji. 

Structural Basis for the Function of Stringent Starvation Protein 

A as a Transcription Factor. J. Biol. Chem.. 280, 17380-17391 

(2005). 

M Jensen, M Costas, R Ho, J Kaizer, A Payeras, E Umnck, L Que, 

Jr., J Rohde, A Stubna. High-Valent Nonheme Iron. Two Distinct 

Iron(IV) Species Derived from a Common Iron(II) Precursor. J. 

Am. Chem. Soc.. 127, 10512-10525 (2005). 

J Kim, S Sitaraman, A Hierro, B Beach, G Odorizzi, J Hurley. 

Structural Basis For Endosomal Targeting by The Bro1 Domain. 

N/A. 8, 937~947 (2005). 

D Lansky, B Mandimutsira, B Ramdhanie, M Clausen, J 

Penner-Hahn, S Zvyagin, J Telser, J Krzystek, R Zhan, Z Ou. 

Synthesis, Characterization, and Physicochemical Properties 

of Manganese(III) and Manganese(V)-Oxo Corrolazines. Inorg. 

Chem.. 44, 4485-4498 (2005). 

Y Li, J Blaszczyk, Y Wu, G Shi, X Ji, H Yan. Is the Critical Role of 

Loop 3 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin 

Pyrophosphokinase in Catalysis Due to Loop-3 Residues 

Arginine-84 and Tryptophan-89? Site-Directed Muagenesis, 

Biochemical, and Crystallographic Studies. Biochemistry. 44, 

8590-8599 (2005). 

A Longo, C Leonard, G Bassi, D Berndt, J Krahn, T Tanaka Hall, 

K Weeks. Evolution from DNA to RNA Recognition by the bI3 

LAGLIDADG Maturase. Nat. Struct. Mol. Biol.. 12 (9), 779 

(2005). 

M Mayer. Crystal Structures of the GluR5 and GluR6 Ligand 

Binding Cores: Molecular Mechanisms Underlying Kainate 

Receptor Selectivity. Neuron. 45, 539-552 (2005). 

O Pasternak, J Biesiadka, F Dolot, L Hanschuh, G Bujacz, M 

Sikorski, M Jaskolski. Structure of a Yellow Lupin PathogensisRelated PR-10 Protein Belonging to a Novel Subclass. Acta 

Cryst. D. 61, 99-107 (2005). 

J Penner-Hahn. Characterization of “Spectroscopically Quiet” 

Metals in Biology. Coordin. Chem. Rev.. 249, 161-177 (2005). 

B Ramakrishnan, E Boeggeman, P Qasba. Mutation of Arginine 

228 to Lysine Enhances the Glucosyltransferase Activity of 

Bovine beta-1,4-Galactosyltransferase I. Biochemistry. 44, 

3202-3210 (2005). 

K Saikrishnan, G Manjunath, P Singh, J Jeyakanthan, Z Dauter, 

K Sekar, K Muniyappa, M Vijayan. Structure of Mycobacterium 

smegmatis Single-Stranded DNA-Binding Protein and a 

Comparative Study Involving Homologus SSBs: Biological 

Implications of Structural Plasticity and Variability in Quaternary 

Association. Acta Cryst. D. 61 (8), 1140-1148 (2005). 

F Schubot, S Cherry, B Austin, J Tropea, D Waugh. Crystal 

Structure of the Protease-Resistant Core Domain of Yersinia 

Pestis Virulence Factor Yopr. Protein Sci.. 14, 1679 (2005). 

K Sekar, V Rajakannan, D Gayathri, D Velmurugan, M Poi, M 

Dauter, Z Dauter, M Tsai. Atomic Resolution (0.97 Angstrom) 

Structure of the Triple Mutant (K53,56,121M) of Bovine 

Pancreatic Phopholipase A2. Acta Cryst. F. 61, 3-7 (2005). 

W Shi, C Zhan, A Lgnatov, B Manjasetty, N Marinkovic, M Sullivan, 

R Huang, M Chance, H Li, et al.. Metalloproteomics: HighThroughput Structural and Functional Annotation of Proteins in 

Structural Genomics. Structure. 13 (10), 1473-1486 (2005). 

B Strokopytov, A Fedorov, N Mahoney, M Kessels, D Drubin, 

S Slmo. Phased Translation Function Revisited: Structure 

Solution of the Cofilin-Homology Domain from Yeast ActinBinding Protein 1 Using six-Dimensinal Searches. Acta Cryst. 

D. 61, 285-293 (2005). 

P Thomas, E Stone, A Costello, D Tierney, W Fast. The 

Quorum-Quenching Lactonase from Bacillus thuringiensis is a 

Metalloprotein. Biochemistry. 44, 7559-7569 (2005). 

W Wen, B Kumarasamy, S Mukerjee, M Auinat, Y Ein-Eli. Origin 

of 5 V Electrochemical Activity Observed in Non-Redox 

Reactive Divalent Cation Doped LiM0.5-xMn1.5+xO4 (0<XJ. 

Electrochem. Soc.. 152 (9), A1902 (2005). 

Beamline X10A

H Cui, V Krikorian, J Thompson, A Nowak, T Deming, D Pochan. 

Preparation and Characterization of Synthetic Polypeptide 

Single Crystals with Controlled Thickness. Macromolecules. 38, 

7371-7377 (2005). 

S Guthrie, G Mazzanti, S Idziak. X-ray phase Identification of 

Chocolate is Possible. Eur. J Lipid Sci. Tech.. 107, 656–659 

(2005). 

M Lamm, K Rajagopal, J Schneider, D Pochan. Laminated 

Morphology of Nontwisting beta-Sheet Fibrilis Constructed via 

Peptide Self-Assembly. J. Am. Chem. Soc.. 127, 16692-16700 

(2005). 

Publications 7-13
7-14 NSLS Activity Report

M May, I Lim, J Luo, Z Rab, D Rabinovich, T Liu, C Zhong. 

Mediator-Template Assembly of Nanoparticles. J. Am. Chem. 

Soc.. 127, 1519-1529 (2005). 

G Mazzanti, A Marangoni, S Idziak. Modeling Phase Transitions 

During the Crystallization of a Multicomponent Fat Under Shear. 

Phys. Rev. E. 71, 041607 (2005). 

Beamline X10B

S Guthrie, G Mazzanti, S Idziak. X-ray phase Identification of 

Chocolate is Possible. Eur. J Lipid Sci. Tech.. 107, 656–659 

(2005). 

S Harton, T Koga, F Stevie, T Araki, H Ade. Investigation of Blend 

Miscibility of a Ternary PS/PCHMA/PMMA System Using SIMS 

and Mean-Field Theory. Macromolecules. 38, 10511-10515 

(2005). 

S Harton, F Stevie, R Spontak, T Koga, M Rafailovich, J Sokolov, H 

Ade. Low-Temperature Reactive Coupling at Polymer-Polymer 

Interfaces Facilitated by Supercritical Carbon Dioxide. Polymer. 

46, 10173-10179 (2005). 

T Koga, J Jerome, M Rafailovich, J Sokolov, C Gordon. Metalizable 

Polymer Thin Films in Supercritical Carbon Dioxide. J. Adhes.. 

81, 751-764 (2005). 

T Koga, C Li, Y Sun, M Rafailovich, J Sokolov, J Douglas, D 

Mahajan. Surface Mofification of Polymeric Nanocomposite 

Thin Films using Supercritical Carbon Dioxide. Top. Catal.. 32, 

257-262 (2005). 

Y Seo, T Koga, J Sokolov, M Rafailovich, M Tolan, S Sinha. 

Deviations from Liquidlike Behaviorinmolten Polymer Films at 

Interfaces. Phys. Rev. Lett.. 94, 157802 (2005). 

Beamline X10C

J Calla, R Davis. X-ray Absorption Spectroscopy and CO Oxidation 

Activity of Au/Alumina Treated with NaCN. Catal. Lett.. 99 (1-2), 

21-26 (2005). 

J Calla, R Davis. Investigation of Alumina-Supported Au Catalyst 

for CO Oxidation by Isotopic Transient Analysis and X-ray 

Absorption Spectroscopy. J. Phys. Chem. B. 109 (6), 2307-

2314 (2005). 

J Calla, R Davis. Influence of Dihydrogen and Water Vapor on 

the Kinetics of CO Oxidation over Au/Alumina. Ind. Eng. Chem. 

Res.. 44, 5403 (2005). 

P Haider, Y Chen, S Lim, G Haller, L Pfefferle, D Ciuparu. 

Application of the Generalized 2D Correlation Analysis to 

Dynamic Near-Edge X-ray Absorption Spectroscopy Data. J. 

Am. Chem. Soc.. 127, 1906-1912 (2005). 

H Isaacs, K Sasaki, C Jeffcoate, V Laget, R Buchheit. Formation 

of Chromate Conversion Coatings on Aluminum and Its Alloys . 

J. Electrochem. Soc.. 152, B460 (2005). 

V Murthi. Electrochemistry at Interfaces with Low Water Content: 

Applications to Proton Exchange Membrane Fuel Cells and 

Growth of Anodic Oxide Films. Ph.D Thesis. Northeastern 

University, Boston. (2005). 

Y Yang, S Lim, G Du, Y Chen, D Ciuparu, G Haller. Synthesis and 

Characterization of Highly Ordered Ni-MCM-41 Mesoporous 

Molecular Sieves. J. Phys. Chem. B. 109, 13237-13246 (2005). 

Beamline X11A

O Alexeev, F Li, M Amiridis, B Gates. Effects of Adsorbates on 

Supported Platinum and Iridium Clusters: Characterization 

in Reactive Atmospheres and During Alkene Hydrogenation 

Catalysis by X-ray Absorption Spectroscopy. J. Phys. Chem. B. 

109 (6), 2338-2349 (2005). 

Y Arai, D Sparks, J Davis. Arsenate Adsorption Mechanisms at the 

Allophane-Water Interface. Environ. Sci. Tech.. 39, 2537-2544 

(2005). 

T Boonfueng, L Axe, Y Xu. Properties and Structure of Maganese 

Oxide-Coated Clay. J. Colloid Interface Sci.. 281 (1-2), 80-92 

(2005). 

S Calvin, S Luo, C Caragianis-Broadbridge, J McGuinness, 

E Anderson, A Lehman, K Wee, S Morrison, L Kurihara. 

Comparison of Extended X-ray Absorption Fine Structure 

and Scherrer Analysis of X-ray Diffraction as Methods for 

Determining Mean Sizes of Polydisperse Nanoparticles. Appl. 

Phys. Lett.. 87 (23), 233102 (2005). 

S Calvin, C Riedel, E Carpenter, S Morrison, R Stroud, V Harris. 

Estimating Crystallite Size in Polydispersed Samples using 

EXAFS. Phys. Scr.. T115, 744-748 (2005). 

I Drake, K Fujdala, A Bell, T Tilley. Dimethyl Carbonate Production 

Via the Oxidative Carbonylation of Methanol Over Cu/SiO2 

Catalysts Prepared Via Molecular Precursor Grafting and 

Chemical Vapor Deposition Approaches. J. Catal.. 230 (1), 14-

27 (2005). 

M Grafe, D Sparks. Kinetics of Zinc and Arsenate Co-sorption at 

the Geothite-water Interface. Geochim. Cosmochim. Acta. 69

(19), 4573-4595 (2005). 

A Holland, G Li, A Shahin, G Long, A Bell, T Tilley. New Fe/

SiO2 Materials Prepared using Diiron Molecular Precursors: 

Synthesis, Characterization and Catalysis. J. Catal.. 235 (1), 

150-163 (2005). 

A Keimowitz, Y Zheng, S Chillrud, B Mailloux, H Bok Jung, M 

Stute, H Simpson. Arsenic Redistribution Between Sediments 

and Water Near a Highly Contaminated Source. Environ. Sci. 

Tech.. 39, 8606-8613 (2005). 

Y Lee, E Elzinga, R Reeder. Cu(II) Adsorption at the Calcite- Water 

Interface in the Presence of Natural Organic Matter: Kinetic 

Studies and Molecular-Scale Characterization. Geochim. 

Cosmochim. Acta. 69, 49-61 (2005). 

Y Lee, E Elzinga, R Reeder. Sorption Mechanisms of Zinc on 

Hydroxyapatite: Systematic Uptake Studies and EXAFS 

Spectroscopy Analysis. Environ. Sci. Tech.. 39, 4042-4048 

(2005). 

S Maeng, L Axe, T Tyson, A Jiang. An Investigation on Structure 

of Thermal and Anodic Tantalum Oxide Films. J. Electrochem. 

Soc.. 152 (2), B60-B64 (2005). 

A Mansour, L Croguennec, C Delmas. A Unique Structure of 

Ni(III) in LiNi_0.30Co_0.30O_2 Without Jahn-Teller Distortion. 

Electrochem. Solid-State Lett.. 8 (10), A544-A548 (2005). 

A Mansour, P Smith, M Balasubramanian, J McBreen. In Situ XRay Absorption Study of Cycled Ambigel V_2O_5.nH_2O (n ~ 

0.5) Composite Cathodes. N/A. 152 (7), A1312-A1319 (2005). 

S Morrison, C Cahill, E Carpenter, S Calvin, V Harris. Atomic 

Engineering of Mixed Ferrite and Core–Shell Nanoparticles. J. 

Nanosci. Nanotechnol.. 5 (9), 1323-1344 (2005). 

V Murthi. Electrochemistry at Interfaces with Low Water Content: 

Applications to Proton Exchange Membrane Fuel Cells and 

Growth of Anodic Oxide Films. Ph.D Thesis. Northeastern 

University, Boston. (2005). 

M Nachtegaal, M Marcus, J Sonke, J Vangronsveld, K Livi, D 

van Der Lelie, D Sparks. Effects of in situ Remediation on the 

Speciation and Bioavailability of Zinc in a Smelter Contaminated 

Soil. Geochim. Cosmochim. Acta. 69 (19), 4649-4664 (2005). 

J Roques, A Anderson, V Murthi, S Mukerjee. Potential Shift for 

OH(ads) Formation on the Pt Skin on Pt3Co(111) Electrodes in 

Acid . J. Electrochem. Soc.. 152, E193 (2005). 

M Teliska, V Murthi, S Mukerjee, D Ramaker. Correlation of Water 

Activation, Surface Properties, and Oxygen Reduction Reactivity 

of Supported Pt–M/C Bimetallic Electrocatalysts Using XAS. J. 

Electrochem. Soc.. 152, A2159 (2005). 
M Teliska, W O’Grady, D Ramaker. Determination of O and 

OH Adsorption Sites in situ from Pt L23 X-ray Absorption 

Spectroscopy. J. Phys. Chem. B. 109 (16), 8076-8084 (2005). 

M Teliska, V Murthi, S Mukerjee, D Ramaker. In Situ Determination 

of O(H) Adsorption Sites on Pt Based Alloy Electrodes using 

X-ray Absorption Spectroscopy. Fundamental Understanding of 

Electrode Processes in Memory of Professor Ernest B. Yeager, 

Vol , p. 212-215, sponsored by The Electrochemical Society. 

(2005). 

A Voegelin, R Kretzschmar. Formation and Dissolution of Single 

and Mixed Zn and Ni Precipitates in Soil: Evidence From Column 

Experiments and Extended X-ray Absorption Fine Structure 

Spectroscopy. Environ. Sci. Tech.. 39, 5311-5318 (2005). 

A Voegelin, S Pfister, A Scheinost, M Marcus, R Kretzschmar. 

Changes in Zinc Speciatin in Field Soil After Contamination with 

Zinc Oxide. Environ. Sci. Tech.. 39, 6616-6623 (2005). 

X Wang, J Spivey, H Lamb. NO Decomposition Over a Pd/MgO 

Catalyst Prepared from [Pd(acac)2]. Appl. Catal. B. 56 (4), 261-

268 (2005). 

Beamline X11B

D Ciuparu, P Haider, M Fernandez-Garcia, Y Chen, S Lim, G 

Haller, L Pfefferle. X-ray Absorption Spectroscopic Investigatin 

of Partially Reduced Cobalt Species in Co-MCM-41 Catalysts 

During Synthesis of Single-Wall Carbon Nanotubes. J. Phys. 

Chem. B. 109, 16332-16339 (2005). 

M Teliska, W O’Grady, D Ramaker. Determination of O and 

OH Adsorption Sites in situ from Pt L23 X-ray Absorption 

Spectroscopy. J. Phys. Chem. B. 109 (16), 8076-8084 (2005). 

Beamline X12A

G Carini, A Bolotnikov, G Camarda, G Wright, G De Geronimo, 

D Siddons, R James. Synchrotron Radiation Response 

Characterization of Coplanar Grid CZT Detectors. Nuclear 

Science Symposium - Room Temperature Semiconductor 

Detector, p. R2-5, sponsored by IEEE. (2005). 

G Carini, G Camarda, Z Zhong, D Siddons, A Bolotnikov, G Wright, 

B Barber, C Arnone, R James. High-Energy X-ray Diffraction 

and Topography Investigation of CdZnTe. J. Electron. Mater.. 34

(6), 804-810 (2005). 

G Carini, G Camarda, Z Zhong, D Siddons, A Bolotnikov, G 

Wright, B Barber, C Arnone. High-Energy X-ray Diffraction and 

Topography Investigation of CdZnTe. 2004 U.S. Workshop on 

the Physics and Chemistry of II-VI Materials, Vol , p. 804-810, 

sponsored by TMS, Air Force Res. Lab., Off. of Naval Res., 

U.S. Navy E-O Center Penn State Uni., U.S. Army SDMC. U.S. 

Army Res. Lab. U.S. Army RDECOM CERDEC Night Vision & 

Electronic Sensors Directorate. (2005). 

G Carini, A Bolotnikov, G Camarda, G De Geronimo, D Siddons, 

G Wright, R James. New Results from Testing of Coplanargrid CdZnTe Detectors. Hard X-ray and Gamma-Ray Detector 

Physics VII, Vol , p. 59220M-1/6, sponsored by SPIE. (2005). 

Beamline X12B

R Agarwal, T Binz, S Swaminathan. Analysis of Active Site 

Residues of Botulinum Neurotoxin E by Mutational, Functional, 

and Structural Studies: Glu335Gln is an Apoenzyme. 

Biochemistry. 44, 8291-8302 (2005). 

M Becker, J Bunikis, B Lade, J Dunn, A Barbour, C Lawson. 

Structural Investigation of Borrelia burgdorferi OspB, a 

Bactericidal Fab Target. J. Biol. Chem.. 280 (17), 17363-17370 

(2005). 

D Colleluori, R Reczkowski, F Emig, E Cama, J Cox, L Scolnick, 

K Compher, K Jude, S Han, et al. Probing the Role of the 

Hyper-Reactive Histidine Residue of Arginase. Arch. Biochem. 

Biophys.. 444 (1), 15-26 (2005). 

L Di Costanzo, G Sabio, A Mora, P Rodriguez, A Ochoa, F 

Centeno, D Christianson. Crystal Structure of Human Arginase l 

at 1.29-Angstrom Resolution and Exploration of Inhibition in the 

Immune Response. Proc Natl Acad Sci USA. 102 (37), 13058-

13063 (2005). 

G Georgiev, P Cebe, M Capel. Effects of Nematic Polymer Liquid 

Crystal on Crystallization and Structure of Pet/Vectra Blends. J. 

Mater. Sci.. 40 (5), 1141-1152 (2005). 

B Grasberger, T Lu, C Schubert, D Parks, T Carver, H Koblish, M 

Cummings, L Lafrance, K Milkiewicz. Discovery and Cocrystal 

Structure of Benzodiazepinedione HDM2 Antagonists that 

Activate. J. Med. Chem.. 48, 909 (2005). 

G Hsu, X Huang, N Luneva, N Geacintov, L Beese. Structure of 

a High Fidelity DNA Polymerase Bound to a Benzo[A]Pyrene 

Adduct that Blocks Replication. J. Biol. Chem.. 280, 3764 

(2005). 

D Huang, A Paydar, M Zhuang, M Waddell, J Holton, B Schulman. 

Structural Basis for Recruitment of Ubc12 by an E2 Binding 

Domain in NEDD8’s E1. Mol. Cell. 17 (3), 341-350 (2005). 

W Li, S Kamtekar, Y Xiong, G Sarkis, N Grindley, T Steitz. Structure 

of a Synaptic gamma delta Resolvase Tetramer Covalently 

Linked to Two Cleaved DNAs. Science. 309, 1210 (2005). 

F Perrino, S Harvey, S McMillin, T Hollis. The Human TREX2 3’-

5’ Exonuclease Structure Suggests a Mechanism for Efficient 

Nonprocessive DNA Catalysis. J. Biol. Chem.. 280 (15), 15212-

15218 (2005). 

D Shi, X Yu, L Roth, M Hiroki, Y Hathout, N Allewell, M Tuchman. 

Expression, Purification, Crystallization and Preliminary X-ray 

Crystallographic Studies of a Novel Acetylcitrulline deacetylase 

from Xanthomonas Campestris. Acta Cryst. F. 61, 676-679 

(2005). 

C Simmons, Q Hao, M Stipanuk. Preparation, Crystallization and 

X-ray Diffraction Analysis to 1.5 Å Resolution of Rat Cysteine 

Dioxygenase, a Mononuclear Iron Enzyme Responsible for 

Cysteine Thiol Oxidation. Acta Cryst. F. F61, 1013-1016 

(2005). 

A Soares, Y Vehter. Experimental methods for measuring accurate 

high-amplitude phases and their importance in isomorphous 

replacement experiments. Acta Cryst. D. D61, 1521-1527 

(2005). 

J Truglio, B Rhau, D Croteau, L Wang, M Skorvaga, E Karakas, 

M DellVecchia, H Wang, B Van Houten, C Kisker. Structural 

Insights Into the First Incision Reaction During Nucleotide 

Excision Repair. EMBO J.. 24, 885-894 (2005). 

A Varma, R Brown, G Birrane, J Ladias. Structural Basis for 

Cell Cycle Checkpoint Control by the BRCA1-CtIP Complex. 

Biochemistry. 44, 10941-10946 (2005). 

L Vedula, D Cane, D Christianson. Role of Arginine-304 in the 

Diphosphate-Triggered Active Site Closure Mechanism of 

Trichodiene Synthase. Biochemistry. 44, 12719 (2005). 

J Wang, K Stieglitz, E Kantrowitz. Metal Specificity is Correlated 

with Two Crucial Active Site Residues in Escherichia coli 

Alkaline Phosphatase. Biochemistry. 44, 8378-8386 (2005). 

A Yamashita, S Singh, T Kawate, Y Jin, E Gouaux. Crystal 

Structure of a Bacterial Homologue of Na+/Cl- -Dependent 

Neurotransmitter Transporters. Nature. 437, 215 (2005). 

Q Ye, I Imriskova-Sosova, B Hill, Z Jia. Identification of Disulfide 

Switch in BsSco, a Member of the Sco Family of Cytochrome 

c Oxidase Assembly Proteins. Biochemistry. 44, 2934-2942 

(2005). 

Publications 7-15
7-16 NSLS Activity Report

Beamline X12C

M Becker, J Bunikis, B Lade, J Dunn, A Barbour, C Lawson. 

Structural Investigation of Borrelia burgdorferi OspB, a 

Bactericidal Fab Target. J. Biol. Chem.. 280 (17), 17363-17370 

(2005). 

J Benach, W Edstrom, I Lee, K Das, B Copper, R Xiao, J Liu, B 

Rost, T Acton, et al.. The 2.35 Angstrom Structure of the TenA 

Homolog from Pyrococcus furiosus Supports an Enzymatic 

Function in Thiamine Metabolism. Acta Cryst. D. 61, 589-598 

(2005). 

J D’Aquino, J Tetenbaum-Novatt, A White, F Berkovitch, D Ringe. 

Mechanism of Metal Ion Activation of the Diphtheria Toxin 

Repressor DtxR. Proc Natl Acad Sci USA. 102 (51), 18408-

18413 (2005). 

L Feng, S Zhou, L Gu, D Gell, J MacKay, M Weiss, A Gow, Y 

Shi. Structure of Oxidized Alpha-Haemoglobin Bound to AHSP 

Reveals a Protective Mechanism for HAEM. Nature. 435, 697 

(2005). 

Q Han, Y Gao, H Robinson, H Ding, S Wilson, J Li. Crystal 

Structures of Aedes Aegypti Kynurenine Aminotransferase. 

FEBS Lett. 272, 2198 (2005). 

M Hu, P Li, L Song, P Jeffrey, T Chernova, K Wilkinson, R 

Cohen, Y Shi. Structure and Mechanisms of the Proteasomeassociated Deubiquitinating Enzyme USP14. EMBO J.. 24 (21), 

3747 (2005). 

Q Huai, H Wang, Y Liu, H Kim, D Toft, H Ke. Structures of 

the N-Terminal and Middle Domains of E. Coli Hsp90 and 

Conformation Changes Upon ADP Binding. Structure. 13, 579-

590 (2005). 

M Huang, A Mazar, G Parry, A Higazi, A Kuo, D Cines. 

Crystallization of Soluble Urokinase Receptor (suPAR) in 

Complex with Urokinase Amino-Terminal Fragment (1-143). 

Acta Cryst. D. 61, 697-700 (2005). 

L Jin, P Pandey, R Babine, J Gorga, K Seidl, E Gelfand, D 

weaver, S Abdel-Meguid, J Strickler. Crystal Structures of the 

FXIA Catalytic Domain in Complex with Ecotin Mutants Reveal 

Substrate-Like Interactions. J. Biol. Chem.. 280, 4704 (2005). 

L Jin, P Pandey, R Babine, D Weaver, S Abdel-Meguid, J Stricker. 

Mutation of Surface Residues to Promote Crystallization 

of Activated Factor XI as a Complex with Benzamidine: an 

Essential Step for the Iterative Structure-Based Design of 

Factor XI Inhibitors. Acta Cryst. D. 61, 1418-1425 (2005). 

T Jonsson, M Murray, L Johnson, L Poole, W Lowther. Structural 

basis for the retroreduction of inactivated peroxiredoxins by 

human sulfiredoxin. Biochemistry. 44, 8634-8642 (2005). 

C Kielkopf, S Luecke, M Green. U2AF-Homology-Motifs: Protein 

Recognition in the RRM World. Genes Dev.. 18, 1513-1526 

(2005). 

D Kumaran, S Eswaramoorthy, F Studier, S Swaminathan. 

Structure and Mechanism of ADP-Ribose-1’ ‘-Monophosphatase 

(Appr-1’ ‘-Pase), A Ubiquitous Cellular Processing Enzyme. 

Protein Sci.. 14, 719 (2005). 

A Moreno, M Rivera. Conceptions and First Results on the 

Electrocrystallization Behaviour of Ferritin. Acta Cryst. D. 61, 

1678-1681 (2005). 

H Nam, F Poy, H Saito, C Frederick. Structural Basis for the 

Function and Regulation of the Receptor Protein Tryosine 

Phosphatase CD45. J. Exp. Med.. 201, 441 (2005). 

F Perrino, S Harvey, S McMillin, T Hollis. The Human TREX2 3’-

5’ Exonuclease Structure Suggests a Mechanism for Efficient 

Nonprocessive DNA Catalysis. J. Biol. Chem.. 280 (15), 15212-

15218 (2005). 

M Safo, Q Zhao, T Ko, F Musayev, H Robinson, N Scarsdale, A 

Wang, G Archer. Crystal Structures of the BLAI Repressor from 

Staphylococcus aureus and its Complex with DNA: Insights into 

Transcriptional Regulation of the BLA and MEC Operons. J. 

Bacteriol.. 187, 1833 (2005). 

J Schuermann, S Prewitt, C Davies, S Deutscher, J 

Tanner. Evidence for Structural Plasticity of Heavy Chain 

Complementarity-determining Region 3 in Antibody-ssDNA 

Recognition. J. Mol. Biol.. 347, 965 - 978 (2005). 

N Silvaggi, H Josephine, A Kuzin, R Nagarajan, R Pratt, J Kelly. 

Crystal Structures of Complexes Between the R61 DDPeptidase and Peptidoglycan-Mimetic Beta-Lactams: A NonCovalent Complex with a “Perfect Penicillin”. J. Mol. Biol.. 345, 

521-533 (2005). 

D Snyder, Y Chen, N Denissova, T Acton, J Aramini, M Ciano, R 

Karlin, J Liu, P Manor, et al.. Comparisons of NMR Spectral 

Quality and Success in Crystallization Demonstrate that NMR 

and X-ray Crystallography are Complementary Methods for 

Small Protein Structure Determination. J. Am. Chem. Soc.. 127, 

16505-16511 (2005). 

A Stein, G Fuchs, C Fu, S Wolin, K Reinisch. Structural Insights 

into RNA Quality Control: The Ro Autoantigen Binds Misfolded 

RNAs Via its Central Cavity. Cell. 121 (4), 529-539 (2005). 

S Townson, J Samuelson, S Xu, A Aggarwal. Implications for 

Switching Restriction Enzyme Specificities from the Structure of 

BstYI Bound to a BglII DNA Sequence. Structure. 13 (5), 791-

801 (2005). 

A Weichsel, E Maes, J Anderson, J Valenzuela, T Shokhireva, F 

Walker, W Montfort. Heme-Assisted S-Nitrosation of a Proximal 

Thiolate in a Nitric Oxide Transport Protein. Proc Natl Acad Sci 

USA. 102, 594-599 (2005). 

C Wilson, T Kajander, L Regan. The Crystal Structure of NLPI. 

A Prokaryotic Tetratricopeptide Repeat Protein with a Globular 

Fold. FEBS Lett. 272, 166 (2005). 

S Wright, V Rath, P Genereux, D Hageman, C Levy, L McClure, 

S McCoid, R McPherson, T Schelhorn, et al.. 5-Chloroindoloyl 

Glycine Amide Inhibitors of Glycogen Phosphorylase: Synthesis, 

In Vitro, In Vivo, and X-ray Crystallographic Characterization. 

BioOrg. Med. Chem.. 15, 459 (2005). 

Z Yang, J Horton, R Maunus, G Wilson, R Roberts, X Cheng. 

Structure of HinP1I Endonuclease Reveals a Striking Similarity 

to the Monomeric Restriction Enzyme MspI. Nucleic Acids Res.. 

33 (6), 1892-1901 (2005). 

Y Zuo, Y Wang, A Malhotra. Crystal Structure of Escherichia coli 

RNase D, an Exoribonuclease Involved in Structured RNA 

Processing. Structure. 13 (7), 973-984 (2005). 

Beamline X14A

E Akdgan, C Rawn, W Porter, E Payzant, A Safari. Size Effects 

in PbTiO3 nanocrystals: Effect of Particle Size on Spontaneous 

Polarization and Strains. J. Appl. Phys.. 97, 084305 (2005). 

K Kewalramani, G Evmenenko, C YU, K Kim, J Kmetko, P Dutta. 

Evidence of Surface Reconstruction During ‘Bioinspired’ 

Inorganic Nucleation at an Organic Template. Surf. Sci. Lett.. 

591, L286-L291 (2005). 

J Li, S Moss, Y Zhang, A Mascarenhas, J BAi. Xray Characterization of Atomic-Layer Superlattices. 

J. Phys. D: Appl. Phys.. 38, A147-A153 (2005). 

J Li, D Stokes, O Caha, S Ammu, J Bai, K Bassler, S Moss. 

Morphological Instability in InAs/GaSb Superlattices Due to 

Interfacial Bonds. Phys. Rev. Lett.. 95, 096104 (2005). 

E Ma. Alloys Created Between Immiscible 

Elements. Prog. Mater. Sci.. 50, 413-509 (2005). 

N Roberts, S Jaradat, L Hirst, Y Wang, S Wang, Z Liu, C 

Huang, J Bai, R Pinidak, H Gleeson. Biaxiality and Temperature 

Dependence of 3- and 4-layer Intermediate Smectic Phase 
Structures as Revealed by resonant X-ray Scattering. Europhys. 

Lett.. 72 (6), 976-982 (2005). 

T Varga. Synthesis and Characterization of Some Low and 

Negative Thermal Expansion Materials. Ph.D. Thesis. Georgia 

Institute of Technology, Atlanta. (2005). 

P Williams, J Biernacki, C Rawn, L Walker, J Bai. Microanalytical 

and Computational Analysis of Class F Fly Ash. ACI Mater. J.. 

102, 330-337 (2005). 

K Ye, D Patel. RNA Silencing Suppressor p21 of Beet Yellows Virus 

Forms an RNA binding Octameric Ring Structure. Structure. 13

(9), 1375-1384 (2005). 

Beamline X15A

D Connor, D Sayers, D Sumner, Z Zhong. Identification of Fatigue 

Damage in Cortical Bone by Diffraction Enhanced Imaging. 

Nucl. Instrum. Meth. A. 548 (1-2), 234-239 (2005). 

M Hasnah, C Parham, E Pisano, Z Zhong, O Oltulu, D Chapman. 

Mass Density Images from the Diffraction Enhanced Imaging 

Technique. Phys. Med. Biol.. 32, 549-552 (2005). 

X Lai, K Roberts, M Bedzyk, P Lyman, L Cardoso, J Sasaki. 

Structure of Habit-Modifying trivalent Transition Metal Cations 

(Mn3+, Cr3+) in Nearly Perfect Single Crystals of Potassium 

Dihydrogen Phosphate as Examined by X-ray Standing Waves, 

X-ray Absorption Spectroscopy, and Molecular Modeling. Chem. 

Mater.. 17, 4053-4061 (2005). 

J Li, J Williams, Z Zhong, K Kuettner, M Aurich, J Mollenhauer, 

C Muehleman. Reliability of Diffraction Enhanced Imaging 

for Assessment of Cartilage Lesions, Ex Vivo. Osteoarthr. 

Cartilage. 13, 187-197 (2005). 

J Libera. In situ X-ray Structural Analysis of Polynucleotide Surface 

Adsorption and Metal-Phosphonate Self-Assembled Multilayers. 

Ph.D. Thesis. Northwestern University, Evanston. (2005). 

C Muehleman, J Li, K Kuettner, Z Zhong. Diffraction Enhanced Xray Imaging of Musculoskeletal Lesions. Osteoarthr. Cartilage. 

12, s117-s117 (2005). 

M Teng. Use of Diffraction Enhanced Imaging to Determine the Xray Refractive Indices of Various Tissues at Biologically-Relevant 

Energies. The J. of Young Investigators. 13, 340 (2005). 

M Teng, Z Zhong. Use of Diffraction Enhanced Imaging to 

Determine the X-ray Refractive Indices of Various Tissues at 

Biologically-Relevant Energies. The J. of Young Investigators. 

12, online (2005). 

W Thomlinson, P Suortti, D Chapman. Recent Advances in 

Synchrotron Radiation Medical Research. Nucl. Instrum. Meth. 

A. 543 (1), 288-296 (2005). 

A Wagner, M Aurich, N Sieber, M Stoessel, W Wetzel, K Schmuck, 

M Lohmann, B Reime, J Metge, et al.. Options and Limitations 

of Joint cartilage Imaging: DEI in Comparison to MRI and 

Sonography. Nucl. Instrum. Meth. A. 548, 47-53 (2005). 

M Wernick, L Chapman, O Oltulu, Z Zhong. Imaging Method Based 

on Attenuation, Refraction and Ultra-small-angle-scattering of 

X-rays. US Patent No. US 6,947,521 B2. (2005). 

M Wernick, J Brankov, D Chapman, Y Yang, E Pisano, C Parham, 

C Muehleman, Z Zhong, M Anastasio. Physical Model of Image 

formation in Multiple-Image Radiography. SPIE: Developments 

in X-ray Tomography IV, Vol 5535, p. 369-379, sponsored by 

SPIE . (2005). 

T Yuasa, H Sugiyama, Z Zhong, A Maksimenko, F Dilmanian, 

T Akatsuka, M Ando. High-Pass-Filtered Diffraction 

Microtomography by Coherent Hard X rays for Cell Imaging: 

Theoretical and Numerical Studies of the Imaging and 

Reconstruction Principles. J. Opt. Soc. Am. A. 22 (12), 2622-

2634 (2005).

Beamline X15B

F Alamgir, H Jain, D Williams, R Schwarz. Sub-Nanoscale 

Structural Origin of the Stability of the Pd-Ni-P Model Bullk 

Metallic Glass. The Science of Complex Alloy Phases, p. 163-

182, TMS, Warrendale. (2005). 

Beamline X16A

S Ghose, I Robinson, P Bennett, F Himpsel. Structure of Double 

Row Quantum Wires in Au/Si(5 5 3). Surf. Sci.. 581 (2-3), 199-

206 (2005). 

S Ghose, P Bennett, I Robinson. Clustering of Au on the Faulted 

Half of the Si(111)- 7 x 7 Unit Cell. Phys. Rev. B. 71, 073407 

(2005). 

Beamline X16B

L Yang, M Fukuto. Modulated Phase of Phospholipids with a 

Two-Dimensional Square Lattice. Phys. Rev. E. 72, 010901(R) 

(2005). 

Beamline X16C

A Frenkel, Y Feldman, V Lyahovitskaya, E Wachtel, I Lubomirsky. 

Microsoopic Origin of Polarity in Quasiamorphous BaTiO3. 

Phys. Rev. B. 71, 1-1 (2005). 

A Frenkel, S Nemzer, I Pister, L Soussan, T Harris, Y Sun, M 

Rafailovich. Size-Controlled Synthesis and Characterization of 

Thiol-Stabilized Gold Nanoparticles. J. Chem. Phys.. 123, 1 

(2005). 

M Pfeifer, O Robach, B Ocko, I Robinson. Thickness-Related 

Instability of Cu Thin Films on Ag(100). Physica B. 357, 152-158 

(2005). 

Beamline X17B1

K Bertagnolli, M Vail, J Qian, Y Zhao. High-Energy Synchrotron 

X-Ray Investigation of Residual Stress/Strain and Metal 

Distribution in Polycrystalline Diamond Compacts. The First 

International Industrial Diamond Conference, Vol , p. 5, 

sponsored by Element Six, UK, US Synthetic, USA. (2005). 

G Carini, G Camarda, Z Zhong, D Siddons, A Bolotnikov, G 

Wright, B Barber, C Arnone. High-Energy X-ray Diffraction and 

Topography Investigation of CdZnTe. 2004 U.S. Workshop on 

the Physics and Chemistry of II-VI Materials, Vol , p. 804-810, 

sponsored by TMS, Air Force Res. Lab., Off. of Naval Res., 

U.S. Navy E-O Center Penn State Uni., U.S. Army SDMC. U.S. 

Army Res. Lab. U.S. Army RDECOM CERDEC Night Vision & 

Electronic Sensors Directorate. (2005). 

G Carini, G Camarda, Z Zhong, D Siddons, A Bolotnikov, G Wright, 

B Barber, C Arnone, R James. High-Energy X-ray Diffraction 

and Topography Investigation of CdZnTe. J. Electron. Mater.. 34

(6), 804-810 (2005). 

M Croft, Z Zhong, N Jisrawi, I Zakharchenko, R Holtz, Y Gulak, J 

Skaritka, T Fast, K Sadananda, T Tsakalakos. Strain Profiling of 

Fatigue Crack Overload Effects Using Energy Dispersive X-Ray 

Diffraction. Int. J. Fatigue. 27, 1408-1419 (2005). 

F Dilmanian, Y Qu, S Liu, C Cool, J Gilbert, J Hainfeld, C Kruse, 

J Laterra, D Lenihan, et al.. X-ray Microbeams: Tumor Therapy 

and Central Nervous System Research. Nucl. Instrum. Meth. A. 

548 (1-2), 30-37 (2005). 

M Fernandez-Garcia, X Wang, C Belver, A Iglesias-Juez, J 

Hanson, J Rodriguez. Ca Doping of Nanosize Ce-Zr and Ce-Tb 

Publications 7-17
7-18 NSLS Activity Report

Solid Solutions: Structural and Electronic Effects. Chem. Mater.. 

17, 4181-4193 (2005). 

M Hasnah, C Parham, E Pisano, Z Zhong, O Oltulu, D Chapman. 

Mass Density Images from the Diffraction Enhanced Imaging 

Technique. Phys. Med. Biol.. 32, 549-552 (2005). 

G Shirane, G Xu, P Gehring. Dynamics and Structure of PMN and 

PZN. Ferroelectr.. 321, 7-19 (2005). 

B Unks, R Bruni, H Eguchi, P Gorenstein, S Romaine. Longterm Stability and High Energy Reflectivity Measurements of 

Depth Graded Multilayer Coatings for X-ray Optics. American 

Astronomical Society, Washington. Prepared for American 

Astronomical Society Meeting 205. (2005). 

X Wang, J Rodriguez, J Hanson, D Gamarra, A Martinez-Arias, M 

Fernandez-Garcia. Unusual Physical and Chemical Properties 

of Cu in Ce1-xCuxO2 Oxides. J. Phys. Chem. B. 109, 19595-

19603 (2005). 

Beamline X17B2

B Li, J Zhang. Pressure and Temperature Dependence of Elastic 

Wave Velocity of MgSiO3 Perovskite and the Composition of the 

Lower Mantle. Phys. Earth Planet. Interiors. 151 (1-2), 143-154 

(2005). 

B Li, J Kung, T Uchida, Y Wang. Pressure Calibration to 20 GPa by 

use of Simultaneous Ultrasonic and X-ray Techniques. J. Appl. 

Phys.. 98, 13521 (2005). 

W Liu, J Kung, B Li. Elasticity of San Carlos olivine to 8 GPa and 

1073 K. Geophys. Res. Lett.. 32 (16), L16301 (2005). 

G Voronin, C Pantea, T Zerda, L Wang, Y Zhao. Thermal Equationof-State of Osmium: A Synchrotron X-ray Diffraction Study. J. 

Phys. Chem. Solids. 66 (5), 705-710 (2005). 

J Zhang, Y Zhao, H Xu, M Zelinskas, L Wang, Y Wang, T Uchida. 

Pressure-Induced Amorphization and Phase Transformations in 

beta-LiAlSiO4. Chem. Mater.. 17, 2817-2824 (2005). 

J Zhang, Y Zhao, C Pantea, J Qian, L Daemen, P Rigg, R Hixson, 

C Greeff, G Gray III, et al.. Experimental Constraints on the 

Phase Diagram of Elemental Zirconium. J. Phys. Chem. Solids. 

66 (7), 1213-1219 (2005). 

Y Zhao, J Zhang, C Pantea, J Qian, L Daemen, P Rigg, R Hixson, 

G Gray, III, Y Yang, et al.. Thermal Equations of State of the 

alpha, beta, and omega Phases of Zirconium. Phys. Rev. B. 71, 

184119 (2005). 

Beamline X17B3

V Levitas, Y Ma, J Hashemi. Transformation-Induced Plasticity 

and Cascading Structural changes in Hexagonal Boron Nitride 

under High Pressure and Shear. Appl. Phys. Lett.. 86, 071912 

(2005). 

Y Ma, M Somayazulu, G Shen, H Mao, J Shu, R Hemley. Xray Diffraction Studies of Iron to Earth’s Core Conditions. 

New Developments in High-Pressure Minerals Physics and 

Applications to the Earth’s Interior, p. 455, Elsevier, Amsterdam. 

(2005).

Beamline X17C

T Duffy. Synchrotron Facilities and the Study of Deep Planetary 

Interiors. Rep. Prog. Phys.. 68, 1811 (2005). 

Y Feng, M Somayazulu, R Jaramillo, T Rosenbaum, E Isaacs, 

J Hu, H Mao. Energy Dispersive X-ray Diffraction of Charge 

Density Waves Via Chemical Filtering. Rev. Sci. Instrum.. 76

(6), 063913 (2005). 

R Hemley, H Mao, V Struzhkin. Synchrotron Radiation and High 

Pressure: New Light on Materials Under Extreme Conditions`. 

J. Synch. Rad.. 12, 135-154 (2005). 

B Kiefer, S Shieh, T Duffy, T Sekine. Strength, Elasticity, and 

Equation of State of Nanocrystalline Cubic Silicon Nitride (cSi3N4) to 68 Gpa. Phys. Rev. B. 72, 014102 (2005). 

V Levitas, Y Ma, J Hashemi. Transformation-Induced Plasticity and 

Cascading Structural changes in Hexagonal Boron Nitride under 

High Pressure and Shear. Appl. Phys. Lett.. 86, 071912 (2005). 

H Liu, J Tse, J Hu, Z Liu, L Wang, J Chen, D Weidner, Y Meng, 

D Hausermann, H Mao. Structural Refinement of the HighPressure Phase of Aluminum Trihydroxide: In-Situ HighPressure Angle Dispersive Synchrotron X-ray Diffraction and 

Theoretical Studies. J. Phys. Chem. B. 109, 8857 (2005). 

H Liu, J Chen, J Hu, C Martin, D Weidner, D Hausermann, H 

Mao. Octahedral Tilting Evolution and Phase Transition in 

Orthorhombic NaMgF3 Perovskite Under Pressure. Geophys. 

Res. Lett.. 32 (4), L04304 (2005). 

Y Ma, M Somayazulu, G Shen, H Mao, J Shu, R Hemley. Xray Diffraction Studies of Iron to Earth’s Core Conditions. 

New Developments in High-Pressure Minerals Physics and 

Applications to the Earth’s Interior, p. 455, Elsevier, Amsterdam. 

(2005). 

J Yang, W Bai, H Rong, Z Zhang, Z Xu, Q Fang, B Yan, T Li, Y Ren, 

S Chen. Na- and Zn- bearing (Mg,Fe)Al2O4 spinel exsolution 

from ilmenite and magnetite of eclogite in the main hole, CCSD. 

2004 AGU meeting, Vol , p. 85(4), sponsored by American 

Geologic Union. (2005). 

Beamline X18A

A Anderson, J Roques, S Mukerjee, V Murthi, N Markovic, V 

Stamenkovic. Activation Energies for Oxygen Reduction on 

Platinum Alloys: Theory and Experiment. J. Phys. Chem. B. 

109, 1198-1203 (2005). 

K Chung, W Yoon, H Lee, X Yang, J McBreen, B Deng, X Wang, M 

Yoshio, R Wang, et al.. Comparative Studies Between Oxygen 

Deficient LiMn2O4 and Al-doped LiMn2O4. J. Power Sources. 

146, 226 (2005). 

Y Ein-Eli, R Urian, W Wen, S Mukerjee. Low Temperature 

Performance of Copper/Nickel Modified LiMn2O4 Spinels. 

Electrochim. Acta. 50 (9), 1931-1937 (2005). 

C Jing, S Liu, X Meng. Arsenic Leachability and Speciation in 

Cement Immobilized Water Treatment Sludge. Chemosphere. 

59 (9), 1241-1247 (2005). 

J Jones, E Slamovich, K Bowman. Product and Component Grain 

and Domain Textures in Ferroelectric Ceramics. Mater. Sci. 

Forum. 495-497 (2), 1401-1406 (2005). 

T Key, J Jones, W Shelley, B Iverson, H Li, E Slamovish, A King, K 

Bowman. Texture and Symmetry Relationships in Piezoelectric 

Materials. Mater. Sci. Forum. 495-497 , 13-22 (2005). 

T Key, J Jones, W Shelley, K Bowman. Quantifying Domain 

Textures in Lead Zirconate Titanate using 022 : 202 and 220 

Diffraction Peaks. Solid State Phenomena. 105, 379-384 

(2005). 

Y Lee, E Elzinga, R Reeder. Cu(II) Adsorption at the Calcite- Water 

Interface in the Presence of Natural Organic Matter: Kinetic 

Studies and Molecular-Scale Characterization. Geochim. 

Cosmochim. Acta. 69, 49-61 (2005). 

Z Zhu, T Andelman, M Yin, T Chen, S Ehrlich, S O‘Brien, R 

Osgood, Jr.. Synchrotron X-ray Scattering of ZnO Nanorods: 

Periodic Ordering and Lattice Size. J. Mater. Res.. 20 (4), 1033 

(2005). 

Z Zhu, T Chen, Y Gu, J Warren, R Osgood, Jr.. Zinc Oxide 

Nanowires Grown by Vapor-Phase Transport using Selected 

Metal Catalysts: A Comparative Study. Chem. Mater.. 17, 4227-

4234 (2005). 
Beamline X18B

A Abakumov, M Rozova, E Antipov, J Hadermann, G Van 

Tendeloo, M Lobanov, M Greenblatt, M Croft, E Tsiper, et al.. 

Synthesis, Cation Ordering, and Magnetic Properties of the 

(Sb1-xPbx)2(Mn1-ySby)O4 Solid Solutions with the Sb2MnO4-

Type Structure. Chem. Mater.. 17, 1123-1134 (2005). 

O Alexeev, S Chin, M Engelhard, L Ortiz-Soto, M Amiridis. Effects 

of Reduction Temperature and Metal-Support Interactions on 

the Catalytic Activity of Pt/g-Al2O3 and Pt/TiO2 for the Oxidation 

of CO in the Presence and Absence of H2. . J. Phys. Chem. B. 

109 (49), 23430-23443 (2005). 

O Alexeev, F Li, M Amiridis, B Gates. Effects of Adsorbates on 

Supported Platinum and Iridium Clusters: Characterization 

in Reactive Atmospheres and During Alkene Hydrogenation 

Catalysis by X-ray Absorption Spectroscopy. J. Phys. Chem. B. 

109 (6), 2338-2349 (2005). 

S Bare, S Kelly, W Sinkler, J Low, F Modica, S Valencia, A Corma, 

L Nemeth. Uniform Catalytic Site in Sn-beta Zeolite Determined 

using X-ray Absorption Fine Structure. J. Am. Chem. Soc.. 127, 

12924-12932 (2005). 

V Bhirud, H Iddir, N Browning , B Gates. Intact and Fragmented 

Triosmium Clusters on MgO: Characterization by X-ray 

Absorption Spectroscopy and High-Resolution Transmission 

Electron Microscopy. J. Phys. Chem. B. 109, 12738-12741 

(2005). 

R Bindu, S Pandey, A Kumar, S Khalid, A Pimpale. Local Distortion 

of Mno6 Octahedron in La1-Xsrxmno3+Delta (X=0.1-0.9): An 

Exafs Study. J. Phys.: Condens. Matter. 17 (41), 6393-6404 

(2005). 

S Bluskov, J Arocena, O Omotoso, J Young. Uptake, Distribution 

and Speciation of Chromium. Int. J. Phytoremediation. 7, 153-

165 (2005). 

T Chen, J Dutrizac, S Beauchemin. Characterization of Gold in the 

Anodes and Anode Slimes from a European Copper Refinery. 

European Metaluurgical Conference, Vol 1, p. 165-182, 

sponsored by GDMB Gesellschaft für. (2005). 

E Chenu, G Jacobs, A Crawford, R Keogh, P Patterson, D Sparks, 

B Davis. Water-gas Shift: an Examination of Unpromoted and Pt 

Promoted MgO and Tetragonal and Monoclinic ZrO2 by In-Situ 

DRIFTS. Appl. Catal. B. 59, 45-56 (2005). 

J Dutrizac, T Chen, S Beauchemin. The Behavior of Thallium(III) 

During Jarosite Precipitation. Hydrometallurgy. 79, 138-153 

(2005). 

O Font, X Querol, F Huggins, J Chimenos, A Fernández, S Burgos, 

F Peña. Speciation of Major and Selected Trace Elements in 

IGCC Fly Ash. Fuel. 84, 1364-1371 (2005). 

K Galbreath, R Schulz, D Toman, C Nyberg, F Huggins, G 

Huffman, E Zillioux. Nickel and Sulfur Speciation of Residual Oil 

Fly Ashes from Two Electric Utility Steam-Generating Units. J. 

Air Waste Manage. Assoc.. 55, 309-318 (2005). 

A Ganjoo, H Jain, S Khalid, C Pantano. Structural Modification of 

Ge–Se Amorphous Films with the Addition of Sb. Philos. Mag. 

Lett.. 85 (10), 503-512 (2005). 

F Goodarzi, F Huggins. Speciation of Arsenic in Canadian 

Subbituminous and Bituminous Feed Coals and their Ash 

Byproducts. Energ. Fuel. 19, 905-915 (2005). 

J Guzman, B Anderson, C Vinod, K Ramesh, J Niemantsverdriet, 

B Gates. Synthesis and Reactivity of Dimethyl Gold Complexes 

Supported on MgO: Characterized by Infrared and X-ray 

Absorption Spectroscopies. Langmuir. 21, 3675-3683 (2005). 

J Guzman, S Carrettin, J Fierro-Gonzalez, Y Hao, B Gates, A 

Corma. CO oxidation Catalyzed by Supported Gold: Cooperation 

Between Gold and Nanocrystalline Rare-Earth Supports forms 

Reactive Surface Superoxide and Peroxide Species. Angew. 

Chem. Int. Ed.. 44 (30), 4778-4781 (2005). 

G Jacobs, P Patterson, U Graham, A Crawford, A Dozier, B Davis. 

Catalytic Links Among the Water-Gas shift, Water-Assisted 

Formic Acid Decomposition, and Methanol Steam Reforming 

Reactions over Pt PromotedTthoria. J. Catal.. 235, 79-91 

(2005). 

G Jacobs, U Graham, E Chenu, P Patterson, A Dozier, B Davis. 

Low Temperature Water Gas Shift: Impact of Pt Promoter 

Loading on the Partial Reduction of Ceria and consequences for 

Catalyst Design. J. Catal.. 229, 499-512 (2005). 

G Jacobs, S Ricote, P Patterson, U Graham, A Dozier, S Khalid, E 

Rhodus, B Davis. Low Temperature Water-Gas Shift: Examining 

the Efficiency of Au as a Promoter for Ceria-Based Catalysts 

Prepared by CVD of a Au Precursor. Appl. Catal. A. 292, 229-

243 (2005). 

C Jing, X Meng, S Liu, S Baidas, R Patraju, C Christodoulatos, 

G Korfiatis. Surface Complexation of Organic Arsenic on 

Nanocrystalline Titanium Oxide. J. Colloid Interface Sci.. 290

(1), 14-21 (2005). 

Y Lee, E Elzinga, R Reeder. Sorption Mechanisms of Zinc on 

Hydroxyapatite: Systematic Uptake Studies and EXAFS 

Spectroscopy Analysis. Environ. Sci. Tech.. 39, 4042-4048 

(2005). 

A Liang, V Bhirud, J Ehresmann, P Kletnieks, J Haw, B Gates. 

A Site-Isolated Rhodium-Diethylene Complex Supported on 

Highly Dealuminated Y Zeolite: Synthesis and Characterization. 

J. Phys. Chem. B. 109, 24236-24243 (2005). 

J Roques, A Anderson, V Murthi, S Mukerjee. Potential Shift for 

OH(ads) Formation on the Pt Skin on Pt3Co(111) Electrodes in 

Acid . J. Electrochem. Soc.. 152, E193 (2005). 

A Rouff, E Elzinga, R Reeder, N Fisher. The Influence of pH on the 

Kinetics, Reversibility and Mechanism of Pb(II) Sorption at the 

Calcite-Water Interface. Geochim. Cosmochim. Acta. 69 (22), 

5173-5186 (2005). 

S Sen, B Aitken, S Khalid. Short-Range Structure and Chemical 

Order in in-Ge Sulfide and Selenide Glasses by X-ray Abosrption 

Fine Structure Spectroscopy. J. Non-Cryst. Solids. 351 (19-20), 

1710-1715 (2005). 

Y Shu, S Oyama. Synthesis, Characterization, and Hydrotreating 

Activity of Carbon-Supported Transition Metal Phosphides. 

Carbon. 43, 7 (2005). 

M Teliska, V Murthi, S Mukerjee, D Ramaker. Correlation of Water 

Activation, Surface Properties, and Oxygen Reduction Reactivity 

of Supported Pt–M/C Bimetallic Electrocatalysts Using XAS. J. 

Electrochem. Soc.. 152, A2159 (2005). 

X Wang, J Rodriguez, J Hanson, M Perez, J Evans. In Situ TimeResolved Characterization of Au-CeO2 Catalysts During Water 

Gas Shift Reactions: presence of Au and O Vacancies in the 

Active Phase. J. Chem. Phys.. 123, 221101 (2005). 

S Wasson, W Linak, B Gullett, C King, A Touati, F Huggins, Y 

Chen, N Shah, G Huffman. Emissions of Chromium, Copper, 

Arsenic, and PCDDs/Fs from Open Burning of CCA-Treated 

Wood. Environ. Sci. Tech.. 39 (22), 8865-8876 (2005). 

Y Xi, C Reed, Y Lee, S Oyama. Acetone Oxidation using Ozone 

on Manganese Oxide Catalysts. J. Phys. Chem. B. 109, 17537-

17596 (2005). 

W Yan, B Chen, S Mahurin, V Schwartz, D Mullins, A Lupini, S 

Pennycook, S Dai, S Overbury. Preparation and Comparison of 

Supported Gold Nanocatalysts on Anatase, Brookite, Rutile, and 

P25 Polymorphs of TiO2 for Catalytic Oxidation of CO. J. Phys. 

Chem. B. 109, 10676-10685 (2005). 

W Yoon, M Balasubramanian, K Chung, X Yang, J McBreen, C 

Grey, D Fischer. Investigation of the Charge Compensation 

Mechanism on the Electrochemically Li-Ion Deintercalated Li1-

xCo1/3Ni1/3Mn1/3O2 Electrode System by Combination of Soft 

and Hard X-ray Absorption Spectroscopy. J. Am. Chem. Soc.. 

127 (49), 17479-17487 (2005). 

Publications 7-19
7-20 NSLS Activity Report

Beamline X19A

A Abakumov, M Rozova, E Antipov, J Hadermann, G Van 

Tendeloo, M Lobanov, M Greenblatt, M Croft, E Tsiper, et al.. 

Synthesis, Cation Ordering, and Magnetic Properties of the 

(Sb1-xPbx)2(Mn1-ySby)O4 Solid Solutions with the Sb2MnO4-

Type Structure. Chem. Mater.. 17, 1123-1134 (2005). 

B Bostick, K Theissen, R Dunbar, M Vairavamurthy. Record of 

Redox Status in Laminated Sediments from Lake Titicaca: A 

Sulfur K-Edge X-ray Absorption Near Edge Structure (XANES) 

Study. Chem. Geol.. 219, 163-174 (2005). 

O Font, X Querol, F Huggins, J Chimenos, A Fernández, S Burgos, 

F Peña. Speciation of Major and Selected Trace Elements in 

IGCC Fly Ash. Fuel. 84, 1364-1371 (2005). 

F Goodarzi, F Huggins. Speciation of Chromium in Feed Coals 

and Ash Byproducts from Canadian Power Plants Burning 

Subbituminous and Bituminous Coals. Energ. Fuel. 19, 2500-

2508 (2005). 

C Jing, S Liu, M Patel, X Meng. Arsenic Leachability in Water 

Treatment Adsorbents. Environ. Sci. Tech.. 39, 5481-5487 

(2005). 

C Jing, S Liu, X Meng. Arsenic Leachability and Speciation in 

Cement Immobilized Water Treatment Sludge. Chemosphere. 

59 (9), 1241-1247 (2005). 

N Khare, D Hesterberg, J Martin. XANES Investigatin of Phosphate 

Sorption in Single and Binary Systems of Iron and Aluminum 

Oxide Minerals. Environ. Sci. Tech.. 39, 2152-2160 (2005). 

Q Lin, M Greenblatt, M Croft. Evolution of Structure and Magnetic 

Properties in Electron-Doped Double Perovskites, Sr2-

xLaxMnWO6 (0<XJ. Solid State Chem.. 178 (5), 1356-1366 

(2005). 

J Majzlan, S Myneni. Speciation of Iron and Sulfate in Acid Waters: 

Aqueous Clusters to Mineral Precipitates. Environ. Sci. Tech.. 

39, 188-194 (2005). 

S Pattanaik. X-ray Diffraction, XAFS and Scanning Electron 

Microscopy Study of Otolith of a Crevalle Jack Fish (caranx 

hippos). Nucl. Instrum. Meth. B. 229 (3-4), 367-374 (2005). 

S Sato, D Solomon, C Hyland, Q Ketterings, J Lehmann. 

Phosphorus Speciation in Manure and Manure-Amended Soils 

Using XANES Spectroscopy . Environ. Sci. Tech.. 39 (19), 7485 

-7491 (2005). 

S Sayan, M Croft, N Nguyen, T Emge, E Gusev, H Kim, J Ehrstein, 

P McIntyre, E Garfunkel. Amorphous to Tetragonal Transition in 

Ultrathin Zirconia Films: Effect on the Electronic and Dielectric 

Properties. Appl. Phys. Lett.. 86 (15), 152902 (2005). 

D Solomon, J Lehmann, I Lobe, C Martinez, S Tveitnes, C Du 

Preez, W Amelung. Sulphur Speciation and Biogeochemical 

Cycling in Long-Term Arable Cropping of Subtropical Soils: 

Evidence From Wet-Chemical Reduction and S K-Edge XANES 

Spectroscopy. Eur. J. Soil Sci.,1-14 (2005). 

G Veith, M Greenblatt, M Croft, K Ramanujachary, J HattrickSimpers, S Lofland, I Nowik. Synthesis and Characterization 

of Sr3FeMoO6.88: An Oxygen-Deficient 2D Analogue of the 

Double Perovskite Sr2FeMoO6. Chem. Mater.. 17, 2562-2567 

(2005). 

X Wang, J Hanson, J Rodriguez, C Belver, M Fernandez-Garcia. 

The Structural and Electronic Prorperties of Nanostructured 

Ce(1-x-y)Zr(x)Tb(y)O(2) Ternary Oxides: Unusual Concentration 

of Tb(3+) and Metal-Oxygen-Metal Interactions. J. Chem. Phys.. 

122 (15), 154711 (2005). 

R Wiltfong, S Mitra-Kirtley, O Mullins, B Andrews, G Fujisawa, J 

Larsen. Sulfur Speciation of Different Kerogens using XANES 

Spectroscopy. Energ. Fuel. 19 (5), 1971-76 (2005). 

S Yoon, L Diener, P Bloom, E Nater, W Bleam. X-ray Absorption 

Studies of Ch3Hg+-Binding Sites in Humic Substances. 

Geochim. Cosmochim. Acta. 69, 1111-1121 (2005). 

F Zhao, J Lehmann, D Solomon , M Fox , S McGrath. 

Sulphur Speciation and Turnover in Soils: Evidence 

from Sulphur K-Edge XANES Spectroscopy and Isotope 

Dilution Studies. Soil Biol. Biochem.. 38, 1-8 (2005).

Beamline X19C

J Bai, X Huang, M Dudley, B Wagner, R Davis, L Wu, Y Zhu. 

Intersecting Basal Plane and Prismatic Stacking Fault Structures 

and their Formation Mechanisms in GaN. J. Appl. Phys.. 98, 

063510-1 - 063510-9 (2005). 

J Bai, M Dudley, L Chen, B Skromme, B Wagner, R Davis, U 

Chowdhury, R Dupuis. Structural Defects and Luminescence 

Features in Heteroepitaxial GaN Grown on On-Axis and 

Misoriented Substrates. J. Appl. Phys.. 97, 116101 (2005). 

J Bai, M Dudley, L Chen, B Skromme, P Hartlieb, E Michaels, J 

Kolis, B Wagner, R Davis, et al.. Relationship of Basal Plane 

and Prismatic Stacking Faults in GaN to Low Temperature 

Photoluminescence Peaks at ~3.4eV and ~3.2eV. 2004 

Materials Research Society Fall Meeting Proceedings, Vol 81, 

p. E11.37, sponsored by Materials Research Society. (2005). 

G Dhanaraj, B Raghothamachar, J Bai, H Chung, M Dudley. 

Synchrotron X-ray Topographic Characterization of Defects in 

InP Bulk Crystals. 17th Indium Phosphide and Related Materials 

Conference, Vol 8th, p. cd rom, (2005). 

M Hollingsworth, M Peterson, J Rush, M Brown, M Abel, A Black, 

M Dudley, B Raghothamachar, U Werner-Zwanziger, et al.. 

Memory and Perfection in Ferroelastic Inclusion Compounds. 

Cryst. Growth Des.. 5, 2100-2116 (2005). 

X Huang, J Bai, M Dudley, B Wagner, R Davis, Y Zhu. StepControlled Strain Relaxation in Vicinal Surface Epitaxy of 

Nitrides. Phys. Rev. Lett.. 95, 086101-1 - 086101-4 (2005). 

X Huang, J Bai, M Dudley, R Dupuis, U Chowdhury. Expitaxial 

Tilting of GaN Grown on Vicinal Surfaces of Sapphire. Appl. 

Phys. Lett.. 86, 211916 (2005). 

B Liu, J Edgar, B Raghothamachar, M Dudley, A Sarua, M Kuball, 

H Meyer, J Lin, H Jiang, et al.. Free Nucleation of Aluminum 

Nitride Single Crystals in HPBN Crucible by Sublimation. Mater. 

Sci. Eng. B. 117, 99-104 (2005). 

S Malkova, F Long, R Stahelin, S Pingali, D Murray, W Cho, M 

Schlossman. X-ray Reflectivity Studies of cPLA?-C2 Domains 

Adsorbed onto Langmuir Monolayers of SOPC. Biophys. J.. 89, 

1861 (2005). 

V Noveski, R Schlesser, B Raghothamachar, M Dudley, S Mahajan, 

S Beaudion, Z Sitar. Seeded Growth of Bulk AIN Crystals and 

Grain Evolution in Polycrystalline AIN Boules. J. Cryst. Growth. 

279, 13-19 (2005). 

S Pingali, T Takiue, G Luo, A Tikhonov, N Ideda, M Aratono, M 

Schlossman. X-ray Reflectivity and Interfacial Tension Study 

of the Structure and Phase Behavior of the Interface Between 

Water anbd Mixed Surfactant Solutions of CH3(CH2)19OH and 

CF3(CF2)7(CH2)2OH in Hexane. J. Phys. Chem. B. 109, 1210-

1225 (2005). 

M Schlossman. X-ray Scattering from Liquid-Liquid Interfaces. 

Physica B. 357 (1-2), 98-105 (2005). 

W Vetter, H Tsuchida, I Kamata, M Dudley. Simulation of Threading 

Dislocation Images in X-ray Topographs of Silicon Carbide 

Homo-Epilayers. J. Appl. Cryst.. 38, 442-447 (2005). 

Y Wang, G Ali, M Mikhov, V Vaidyanathan, B Skromme, B 

Raghothamachar, M Dudley. Correlation Between Morphological 

Defects, Electron Beam Induced Current Imaging, and the 

Electrical Properties of 4H-SiC Schottky Diodes. J. Appl. Phys.. 

97, 013540-1 (2005). 
Beamline X20A

H Chen, Y Yao, J Kysar, I Noyan, Y Wang. Fourier Analysis of X-ray 

Micro-Diffraction Profiles to Characterize Laser Shock Peened 

Metals. Int. J. Solids Struct.. 42 (11-12), 3471-3485 (2005). 

F Espinosa-Faller, R Howell, A Garcia-Adeva, S Conradson, A 

Ignatov, T Tyson, R Farrow, M Toney. Local Atomic Structure 

of Partially Ordered NiMn in NiMn/NiFe Exchange Coupled 

Layers: 1. XAFS Measurements and Structural Refinement. J. 

Phys. Chem. B. 109, 10406-10418 (2005). 

S Kaldor, I Noyan. Flexural Loading of Rectangular Si Beams and 

Plates. Mater. Sci. Eng. A. 399 (1-2), 64-71 (2005). 

Beamline X20B

J Jordan-Sweet, C Detavernier, C Lavoie, P Mooney, M Toney. 

Applications of Synchrotron X-rays in Microelectronics Industry 

Research. Nucl. Instrum. Meth. B. 241 (1-4), 247-252 (2005). 

Beamline X20C

H Kim, C Detavenier, O van der Staten, S Rossnagel, A Kellock, 

D Park. Robust TaNx Diffusion Barrier for Cu-Interconnnect 

Technology with Subnanometer Thickness by Metal-Organic 

Plasma-Enhanced Atomic Layer Deposition. J. Appl. Phys.. 98, 

014308 (2005). 

S Raoux, C Rettner, J Jordan-Sweet, M Salinga, M Toney. 

Crystallization Behavior of Phase Change Nanostructures. 

European Symposium on Phase Change and Ovonic Science, 

Vol , p. 14, sponsored by Plasmon. (2005). 

T Thomson, S Lee, M Toney, C Dewhurst, Y Ogrin, C Oates, S Sun. 

Agglomeration and Sintering in Annealed FePt Nanoparticle 

Assemblies Studied by Small Angle Neutron Scattering and Xray Diffraction. Phys. Rev. B. 72, 064441 (2005). 

Beamline X21

K Cavicchi, K Berthiaume, T Russell. Solvent Annealing Thin Films 

of Poly(isoprene-b-lactide). Polymer. 46 (25), 11635-11639 

(2005). 

J Liao, L Yang, J Grashow, M Sacks. Molecular Orientation of 

Collagen in Intact Planar Connective Tissues Under Biaxial 

Stretch. Acta Biomat.. 1 (1), 45-54 (2005). 

G Lynn, W Heller, A Mayusundari, K Minor, C Peterson. A Model for 

the Three-Dimensional Structure of Human Plasma Vitronectin 

from Small-angle Scattering Measurements. Biochemistry. 44

(2), 565-574 (2005). 

G Ozaydin, A Ozcan, Y Wang, K Ludwig, H Zhou, R Headrick, 

D Siddons. Real-Time X-ray Studies of Mo-Seeded SelfOrganized Si Nanodot Formation During Low Energy Ar+ Ion 

Bombardment. Appl. Phys. Lett.. 87, 163104 (2005). 

Q Qian, T Tyson, W Caliebe, C Kao. High-Efficiency High-energyResolution Spectrometer for Inelastic X-ray Scattering. J. Phys. 

Chem. Solids. 66 (12), 2295 (2005). 

A Sehgal, Y Lalatonne, J Berret, M Morvan. PrecipitationRedispersion of Cerium Oxide Nanoparticles with Poly(acrylic 

acid): Toward Stable Dispersions. Langmuir. 21, 9359-9364 

(2005). 

H Yang, M Ling, T Shin, C Ryu, Z Bao. Universal Effects of 

Solubility and Thermal Annealing for Structure Formation 

in Regioregular Poly(3-alkyl thiophene) Sereis. American 

Chemical Society National Meeting, Vol 92, p. 295, sponsored 

by American Chemical Society . (2005). 

H Yang, T Shin, Z Bao, K Cho, C Ryu. Volatile Solvent Solubility 

and Thermal Annealing Effects on Regio-regular P3HT Thin 

Film Structure and Its Correlation with TFT Charge Mobility. 

American Chemical Society National Meeting, Vol 92, p. 604, 

sponsored by American Chemical Society . (2005). 

H Yang, T Shin, M Ling, K Cho, C Ryu, Z Bao. Conducting AFM 

and 2D GIXD Studies on Pentacene Thin Films. J. Am. Chem. 

Soc.. 127, 11542-11543 (2005). 

L Yang, M Fukuto. Modulated Phase of Phospholipids with a 

Two-Dimensional Square Lattice. Phys. Rev. E. 72, 010901(R) 

(2005). 

H Yang, T Shin, L Yang, K Cho, C Ryu, Z Bao. Effect of Mesoscale 

Crystalline Structure on the Field-Effeft Mobility of Regioregular 

Poly(3-hexyl thiophene) in Thin-Film Transistors. Adv. Func. 

Mater.. 15 (4), 671-676 (2005). 

Beamline X22A

J Fossum, E Gudding, M Fonseca, Y Meheust, E DiMasi, T Gog, 

C Venkataraman. Observations of Orientational Ordering in 

Aqueous Suspensions of a Nano-Layered Silicate. Energy. 30

(6), 873-883 (2005). 

O Gang, K Alvine, M Fukuto, P Pershan, C Black, B Ocko. Liquids 

on Topologically Nano-Patterned Surfaces. Phys. Rev. Lett.. 95, 

217801 (2005). 

F He, B Wells, S Shapiro. Strain Phase Diagram 

and Domain Orientation in SrTiO3 Thin Films. 

Phys. Rev. Lett.. 94 (17), 176101 (2005). 

F He. Phase Transitions and Properties of

Epitaxial Perovskite Films. Ph.D. Thesis. University of Connecticut, 

Storrs. (2005). 

S Kwak, E DiMasi, Y Han, J Aizenberg, I Kuzmenko. Orientation 

and Mg Incorporation of Calcite Grown on Functionalized SelfAssembled Monolayers: A Synchrotron X-ray Study. Cryst. 

Growth Des.. 5 (6), 2139-2145 (2005). 

M Nelson, N Cain, B Ocko, D Gin, S Hammond, D Schwartz. 

Periodic Arrays of Interfacial Cylindrical reverse Micelles. 

Langmuir. 21, 9799-9802 (2005). 

G Shirane, G Xu, P Gehring. Dynamics and Structure of PMN and 

PZN. Ferroelectr.. 321, 7-19 (2005). 

B Smarsly, A Gibaud, W Ruland, D Sturmayr, C Brinker. 

Quantitative SAXS Analysis of Oriented 2D Hexagonal 

Cylindrical Silica Mesostructures in Thin Films Obtained from 

Nonionic Surfactants. Langmuir. 21, 3858-3866 (2005). 

R Turgeman, O Gershevitz, M Deutsch, B Ocko, A Gedanken, C 

Sukenik. Crystallization of Highly Oriented ZnO Microrods on 

Carboxylic Acid-Terminated SAMs. Chem. Mater.. 17, 5048-

5056 (2005). 

J Wang, I Robinson, B Ocko, R Adzic. Adsorbate-Geometry 

Specific Subsurface Relaxation in the CO/Pt(111) System. J. 

Phys. Chem. B. 109 (1), 24 (2005). 

G Xu, H Hiraka, G Shirane, J Li, J Wang, D Viehland. Low 

Symmetry Phase in (001) BiFeO3 Epitaxial Constrained Thin 

Films. Appl. Phys. Lett.. 86, 182905 (2005). 

T Xu, M Misner, S Kim, J Sievert, O Gang, B Ocko, T Russell. 

Selective Solvent Induced Reversible Surface Reconstruction 

of Diblock Copolymer Thin Films. New Polymeric Materials, p. 

158-170, Oxford University Press, New York. (2005). 

Beamline X22B

K Cavicchi, K Berthiaume, T Russell. Solvent Annealing Thin Films 

of Poly(isoprene-b-lactide). Polymer. 46 (25), 11635-11639 

(2005). 

B Discher, D Noy, J Strzalka, S Ye, C Moser, J Lear, K Blasie, L 

Dutton. Design of Amphiphilic Protein Maquettes: Controlling 

Publications 7-21
7-22 NSLS Activity Report

Assembly, Membrane Insertion, and Cofactor Interactions. 

Biochemistry. 44 (37), 12329-12343 (2005). 

S Dourdain, J Bardeau, M Colas, B Smarsly, A Mehdi, B Ocko, 

A Gibaud. Determination by X-ray Reflectivity and Small Angle 

X-ray Scattering of the Porous Properties of Mesoporous Silica 

Thin Films. Appl. Phys. Lett.. 86, 113108 (2005). 

S Dourdain, A Rezaire, A Mehdi, B Ocko, A Gibaud. Real time 

GISAXS study of Micelle hydration in CTAB templated silica thin 

films. Physica B. 357 (1-2), 180-184 (2005). 

A Grigoriev, O Shpyrko, C Steimer, P Pershan, B Ocko, M Deutsch, 

B Lin, M Meron, T Graber, J Gebhardt. Surface Oxidation of 

Liquid Sn. Surf. Sci.. 575 (3), 223-232 (2005). 

M Henderson, A Gibaud, J Bardeau, A Rennie, J White. A 

Zirconium Oxide Film Self-Assembled at the Air-Water Interface. 

Physica B. 357 (1-2), 27-33 (2005). 

B Ocko, H Kraack, P Pershan, E Sloutskin, L Tamam, M Deutsch. 

Crystalline Phases of Alkyl-Thiol Monolayers on Liquid Mercury. 

Phys. Rev. Lett.. 94, 017802 (2005). 

E Sloutskin, C Bain, B Ocko, M Deutsch. Surface Freezing of 

Chain Molecules at the Liquid-Liquid and Liquid-Air Interfaces. 

Faraday Discuss. 129, 339-352 (2005). 

E Sloutskin, B Ocko, L Taman, I Kuzmenko, T Gog, M Deutsch. 

Surface Layering in Ionic Liquids: An X-ray Reflectivity Study. J. 

Am. Chem. Soc.. 127, 7796-7804 (2005). 

L Tamam, H Kraack, E Sloutskin, B Ocko, P Pershan, A Ulman, 

M Deutsch. Structure of Mercaptobiphenyl Monolayers on 

Mercury. J. Phys. Chem.. 109, 12534-12543 (2005). 

T Xu, M Misner, S Kim, J Sievert, O Gang, B Ocko, T Russell. 

Selective Solvent Induced Reversible Surface Reconstruction 

of Diblock Copolymer Thin Films. New Polymeric Materials, p. 

158-170, Oxford University Press, New York. (2005). 

S Ye, B Discher, J Strzalka, T Xu, S Wu, D Noy, I Kuzmenko, T 

Gog, K Blasie, et al.. Amphiphilic Four-Helix Bundle Peptides 

Designed for Light-Induced Electron Transfer Across a Soft 

Interface. Nano Lett.. 5 (9), 1658-1667 (2005). 

Beamline X22C

M Castro-Colin, W Donner, S Moss, Z Islam, S Sinha, R Nemanich, 

H Metzger, P Bosecke, T Shulli. Synchrotron X-ray Studies of 

Vitreous SiO2 Over Si(001). I. Anisotropic Glass Contribution. 

Phys. Rev. B. 71, 045310 (2005). 

F He. Phase Transitions and Properties of Epitaxial Perovskite 

Films. Ph.D. Thesis. University of Connecticut, Storrs. (2005). 

M Hucker, Y Kim, G Gu, J Tranquada, B Gaulin, J Lynn. 

Neutron Scattering Study on La1.9Ca1.1Cu2O6+delta and 

La1.85Sr0.15Ca Cu2O6+delta. Phys. Rev. B. 71, 094510 

(2005). 

P Lyman, V Shneerson, R Fung, R Harder, E Lu, S Parihar, D 

Saldin. Atomic-Scale Visualization of Surfaces with X rays. 

Phys. Rev. B: Condens. Matter. 71 (8), 081402-1-4 (2005).

Beamline X23A2

J Ablett, J Woicik, C Kao. New Correction Procedure For X-ray 

Spectroscopic Fluorescence Data: Simulations and Experiment. 

Adv. X-Ray Anal.. 48, 266-273 (2005). 

F Alamgir, H Jain, D Williams, R Schwarz. Sub-Nanoscale 

Structural Origin of the Stability of the Pd-Ni-P Model Bullk 

Metallic Glass. The Science of Complex Alloy Phases, p. 163-

182, TMS, Warrendale. (2005). 

P Amama, S Lim, D Ciuparu, Y Yang, L Pfefferle, G Haller. 

Synthesis, Characterization, and Stability of Fe-MCM-41 for 

Production of Carbon Nanotubes by Acetylene Pyrolysis. J. 

Phys. Chem. B. 109, 2645-2656 (2005). 

D Ciuparu, P Haider, M Fernandez-Garcia, Y Chen, S Lim, G 

Haller, L Pfefferle. X-ray Absorption Spectroscopic Investigatin 

of Partially Reduced Cobalt Species in Co-MCM-41 Catalysts 

During Synthesis of Single-Wall Carbon Nanotubes. J. Phys. 

Chem. B. 109, 16332-16339 (2005). 

P Haider, Y Chen, S Lim, G Haller, L Pfefferle, D Ciuparu. 

Application of the Generalized 2D Correlation Analysis to 

Dynamic Near-Edge X-ray Absorption Spectroscopy Data. J. 

Am. Chem. Soc.. 127, 1906-1912 (2005). 

S Lim, D Ciuparu, Y Chen, Y Yang, L Pfefferle, G Haller. Pore 

Curvature Effect on the Stability of Co-MCM-41 and the 

Formation of Size-Controllable Subnanometer Co Clusters. J. 

Phys. Chem. B. 109, 2285-2294 (2005). 

E Ma. Alloys Created Between Immiscible Elements. Prog. Mater. 

Sci.. 50, 413-509 (2005). 

D McKeown, H Gan, I Pegg. Silver Valence and Local 

Environments in Borosilicate and Calcium Aluminoborate Waste 

Glasses as determined from X-ray Absorption Spectroscopy. J. 

Non-Cryst. Solids. 351, 3826-3833 (2005). 

A Rouff, E Elzinga, R Reeder, N Fisher. The Influence of pH on the 

Kinetics, Reversibility and Mechanism of Pb(II) Sorption at the 

Calcite-Water Interface. Geochim. Cosmochim. Acta. 69 (22), 

5173-5186 (2005). 

M Sahiner, D Downey, S Novak, J Woicik, D Arena. 

The Local Structural Characterization of the Inactive 

Clusters in B, Bf2 and B23 Implanted Si Wafers uing 

X-ray Techniques. Microelectr. J.. 36, 522-526 (2005). 

Beamline X23B

S Calvin, E Carpenter, V Cestone, L Kurihara, V Harris, E Brown. 

Automated System for X-Ray Absorption Spectroscopy of 

Nanoparticle Nucleation and Growth. Rev. Sci. Instrum.. 76 (1), 

016103-1 - 016103-3 (2005). 

Q Huang, G Evmenenko, P Dutta, p Lee, N Armstrong , T Marks. 

Covalently Bound Hole-Injecting Nanostructures. Systematics 

of Molecular Architecture, Thickness, Saturation, and ElectronBlocking Characteristics on Organic Light-Emitting Diode 

Luminance, Turn-on Voltage, and Quantum Efficiency. J. Am. 

Chem. Soc.. 127, 10227-10242 (2005). 

S Morrison, C Cahill, E Carpenter, S Calvin, V Harris. Atomic 

Engineering of Mixed Ferrite and Core–Shell Nanoparticles. J. 

Nanosci. Nanotechnol.. 5 (9), 1323-1344 (2005). 

Q Qian, T Tyson, W Caliebe, C Kao. High-Efficiency High-energyResolution Spectrometer for Inelastic X-ray Scattering. J. Phys. 

Chem. Solids. 66 (12), 2295 (2005). 

M Teliska, V Murthi, S Mukerjee, D Ramaker. In Situ Determination 

of O(H) Adsorption Sites on Pt Based Alloy Electrodes using 

X-ray Absorption Spectroscopy. Fundamental Understanding of 

Electrode Processes in Memory of Professor Ernest B. Yeager, 

Vol , p. 212-215, sponsored by The Electrochemical Society. 

(2005). 

H Yan, P Lee, N Armstrong, A Graham, G Evmenenko, P Dutta, 

T Marks. High-Performance Hole-Transport Layers for Polymer 

Light-Emitting Diodes. Implementation of Organosiloxane CrossLinging Chemistry in Polymeric Electroluminescent Devices. J. 

Am. Chem. Soc.. 127, 3172-3183 (2005). 

A Yang, Z Chen, X Zuo, D Arena, J Kirkland, C Vittoria, V Harris. 

Cation-Disorder-Enhanced Magnetization in Pulsed-LaserDeposited CuFe2O4 Films. Appl. Phys. Lett.. 86, 252510 

(2005). 

A Yang, X Zuo, I Chen, Z Chen, C Vittoria, V Harris. Magnetic 

and Structural Properties of Pulsed Laser Deposited CuFe2O4 

Films. J. Appl. Phys.. 97, 10G107 (2005). 

T Zubkov, A Lucassen, D Freeman, Y Feldman, S Cohen, 
G Evmenenko, P Dutta, M van der Boom. Photoinduced 

Deprotection and ZnO Patterning of Hydroxyl-Terminated 

Siloxane-Based Monolayers. J. Phys. Chem. B. 109, 14144-

14153 (2005). 

X Zuo, A Yang, S Yoon, J Christodoulides, V G. Harris, C Vittoria. 

Large Induced Magnetic Anisotropy in Manganese Spinel 

Ferrite Films. Appl. Phys. Lett.. 87, 152505 (2005). 

X Zuo, A Yang, S Yoon, I Christodoulides, V Harris, C Vittoria. 

Magnetic Properties of Manganese Ferrite Films Grown at 

Atomic Scale. J. Appl. Phys.. 97, 10G103 (2005). 

Beamline X24A

J Woicik. Site-Specific X-ray Photoelecton Spectroscopy using Xray Standing Waves. Nucl. Instrum. Meth. A. 547 (1), 227-234 

(2005). 

Beamline X24C

J Seely, B Kjornrattanawanich, G Holland, R Korde. Response of a 

SiC Photodiode to Extreme Ultraviolet through Visible Radiation. 

Opt. Lett.. 30 (23), 3120 (2005). 

J Seely, U Feldman, G Holland, J Weaver, A Mostovych, S 

Obenschain, A Schmitt, R Lehmberg, B Kjornarattanawanich, C 

Back. Absolutely Calibrated Vacuum Ultraviolet Spectra in the 

150-250-Nm Range from Plasmas Generated by the Nike Krf 

Laser. Phys. Plasmas. 12 (6), 062701 (2005). 

J Weaver, M Busquet, D Colombant, A Mostovych, U Feldman, 

M Klapisch, J Seely, C Brown, G Holland. Experimental 

Benchmark for an Improved Simulation of Absolute Soft-X-ray 

Emission from Polystyrene Targets Irradiated with the Nike 

Laser. Phys. Rev. Lett.. 94, 045002 (2005). 

D Windt, J Seely, B Kjornrattanawich, Y Uspenskii. TerbiumBased Extreme Ultraviolet Multilayers. Opt. Lett.. 30 (23), 3186 

(2005). 

Beamline X25

R Agarwal, T Binz, S Swaminathan. Analysis of Active Site 

Residues of Botulinum Neurotoxin E by Mutational, Functional, 

and Structural Studies: Glu335Gln is an Apoenzyme. 

Biochemistry. 44, 8291-8302 (2005). 

J Avalos, K Bever, C Wolberger. Mechanism of Sirtuin Inhibition 

by Nicotinamide: Altering the NAD+ Cosubstrate Specificity of a 

Sir2 Enzyme. Mol. Cell. 17 (6), 855-868 (2005). 

T Bai, M Becker, A Gupta, P Strike, V Murphy, R Anders, A 

Batchelor. Structure of AMA1 from Plamodium falciparum 

Reveals A Clustering of Polymorphisms that Surround a 

Conserved Hydrophobic Pocket. Proc Natl Acad Sci USA. 102

(36), 12736-12741 (2005). 

T Biswas, H Aihara, M Radman-Livaja, D Filman, A Landy, T 

Ellenberger. A Structural Basis for Allosteric Control of DNA 

Recombination by lamda Integrase. Nature. 435, 1059 (2005). 

S Bouyain, P Longo, S Li, K Ferguson, D Leahy. The Extracellular 

Region of ErbB4 Adopts a Tethered Conformation in the 

Absence of Ligand. Proc Natl Acad Sci USA. 102, 15024-15029 

(2005). 

E Campbell, O Pavlova, N Zenkin, F Leon, H Irschik, R Jansen, K 

Severinov, S Darst. Structural, Functional, and Genetic Analysis 

of Sorangicin Inhibition of Bacterial RNA Polymerase. EMBO J.. 

24, 674 (2005). 

S Cho, C Swaminathan, J Yang, M Kerzic, R Guan, M Kieke, D 

Kranz, R Mariuzza, E Sundberg. Structural Basis of Affinity 

Maturation and Intramolecular Cooperativity in a Protein-Protein 

Interaction. Structure. 13 (12), 1775-1787 (2005). 

D Colleluori, R Reczkowski, F Emig, E Cama, J Cox, L Scolnick, 

K Compher, K Jude, S Han, et al. Probing the Role of the 

Hyper-Reactive Histidine Residue of Arginase. Arch. Biochem. 

Biophys.. 444 (1), 15-26 (2005). 

G Dong, A Hutagalung, C Fu, P Novick, K Reinisch. The Structures 

of Exocyst Subunit Exo70p and the Exo84p C-terminal Domains 

Reveal a Common Motif. Nat. Struct. Mol. Biol.. 12 (12), 1094 

(2005). 

D Duda, H Walden, J Sfondouris, B Schulman. Structural Analysis 

of Escherichia Coli ThiF. J. Mol. Biol.. 349 (4), 774-786 (2005). 

S Eathiraj, X Pan, C Ritacco, D Lambright. Structural Basis of 

Family-Wide Rab GTPase Recognition by Rabenosyn-5. 

Nature. 436, 415 (2005). 

L Feng, D Gell, S Zhou, L Gu, Y Kong, J Li, M Hu, N Yan, C Lee, 

et al.. Molecular Mechanism of AHSP-Mediated Stabilization of 

Alpha-Hemoglobin. Cell. 119, 629 (2005). 

L Feng, S Zhou, L Gu, D Gell, J MacKay, M Weiss, A Gow, Y 

Shi. Structure of Oxidized Alpha-Haemoglobin Bound to AHSP 

Reveals a Protective Mechanism for HAEM. Nature. 435, 697 

(2005). 

G Golan, D Zharkov, H Feinberg, A Fernandes, E Zaika, J Kycia, A 

Grollman, G Shoham, et al.. Structure of the Uncomplexed DNA 

Repair Enzyme Interdomain Flexibility. Nucleic Acids Res.. 33, 

5006 (2005). 

A Gupta, T Bai, V Murphy, P Strike, R Anders, A Batchelor. 

Refolding, Purificatino, and Crystallization of Apical Membrane 

Antigen 1 from Plasmodium. Protein Expr. Purif.. 41 (1), 186-

198 (2005). 

L Higgins, F Yan, P Liu, H Liu, C Drennan. Structural Insight into 

Antibiotic Fosfomycin Biosynthesis by a Mononuclear Iron 

Enzyme. Nature. 437, 838–844 (2005). 

c Hobartner, R Rieder, C Kreutz, B Puffer, K Lang, A Polonskaia, 

A Serganov, R Micura. Synthesis of RNAs with up to 100 

Nucleotides Containing Site-Specific 2‘-methylseleno Labels 

for use in X-ray Crystallography. J. Am. Chem. Soc.. 127 (34), 

12035-12045 (2005). 

M Hu, P Li, L Song, P Jeffrey, T Chernova, K Wilkinson, R Cohen, 

Y Shi. Structure and Mechanisms of the Proteasome-associated 

Deubiquitinating Enzyme USP14. EMBO J.. 24 (21), 3747 

(2005). 

Q Huai, H Wang, Y Liu, H Kim, D Toft, H Ke. Structures of the NTerminal and Middle Domains of E. Coli Hsp90 and Conformation 

Changes Upon ADP Binding. Structure. 13, 579-590 (2005). 

D Huang, A Paydar, M Zhuang, M Waddell, J Holton, B Schulman. 

Structural Basis for Recruitment of Ubc12 by an E2 Binding 

Domain in NEDD8’s E1. Mol. Cell. 17 (3), 341-350 (2005). 

A Iffland, D Kohls, S Low, J Luan, Y Zhang, M Kothe, Q Cao, A 

Kamath, Y Ding, T Ellenberger. Structural Determinants for 

Inhibitor Specificity and Selectivity in PDE2A using the Wheat 

Germ in Vitro Translation System. Biochemistry. 44, 8312-8325 

(2005). 

Y Im, S Raychaudhuri, W Prinz, J Hurley. Structural Mechanism 

for Sterol Sensing and Transport by OSBP-Related Proteins. 

Nature. 437, 154-158 (2005). 

S Jayaraman, S Eswaramoorthy, S Ahmed, L Smith, S 

Swaminathan. N-Terminal Helix Reorients in Recominant CFragment of Clostridium Botulinum Type B. Biochem. Biophys. 

Res. Commun.. 330 (1), 29 (2005). 

S Kamtekar, A Berman, J Wang, J Lazaro, M de Vega, L Blanco, 

M Salas, T Steitz. Insights into Strand Displacement and 

Processivity from the Crystal Structure of the Protein-primed 

DNA Polymerase of Bacteriophage phi29.. Mol. Cell. 16, 609-

618 (2005). 

S Kang, B Crane. Effects of Interface Mutations on Association 

Modes and Electron-Transfer Rates Between Proteins. Proc 

Natl Acad Sci USA. 102 (43), 15465-15470 (2005). 

Publications 7-23
7-24 NSLS Activity Report

C Kielkopf, S Luecke, M Green. U2AF-Homology-Motifs: Protein 

Recognition in the RRM World. Genes Dev.. 18, 1513-1526 

(2005). 

S Lahr, D Engel, S Stayrook, O Maglio, B North, S Geremia, A 

Lombardi, W DeGrado. Analysis and Design of Turns in alphaHelical Hairpins. J. Mol. Biol.. 346 (5), 1441-1454 (2005). 

S Lee, A Lee, J Chen, R MacKinnon, W Chin. Structure of the 

KvAP voltage-dependent K+ channel and its dependence on 

the lipid membrane. Proc Natl Acad Sci USA. 102 (43), 15441-

15446 (2005). 

B Lepore, F Ruzicka, P Frey, D Ringe. The X-ray Crystal Structure 

of lysine-2,3-aminomutase from Clostridium Subterminale. Proc 

Natl Acad Sci USA. 102 (39), 13819-13824 (2005). 

K Li, K Zhao, B Ossareh-Nazari, G Da, C Dargemont, R 

Marmorstein. Structural Basis for Interaction Between the UBP3 

Deubiquitinating Enzyme and Its BRE5 Cofactor. J. Biol. Chem.. 

280, 29176 (2005). 

W Li, S Kamtekar, Y Xiong, G Sarkis, N Grindley, T Steitz. Structure 

of a Synaptic gamma delta Resolvase Tetramer Covalently 

Linked to Two Cleaved DNAs. Science. 309, 1210 (2005). 

S Li, R Depetris, D Barford, J Chernoff, S Hubbard. Crystal 

Structure of a Complex Between Protein Tyrosine Phosphatase 

1B and the Insulin Receptor Tyrosine Kinase. Structure. 13 (11), 

1643-1651 (2005). 

H Li, S van Vranken, Y Zhao, Z Li, Y Guo, L Eisele, Y Li. Crystal 

Structures of T Cell Receptor (Beta) Chains Related to 

Rheumatoid Arthritis. Protein Sci.. 14, 3025 (2005). 

A Liinas, N Ahmed, M Cordaro, A Laws, J Frere, M Delmarcelle, N 

Silvaggi, J Kelly, M Page. Inactivation of Bacterial DD-Peptidase 

by Beta-Sultams. Biochemistry. 44, 7738-7746 (2005). 

S Long, E Campbell, R MacKinnon. Voltage Sensor of Kv1.2: 

Structural Basis of Electromechanical Coupling. Science. 309, 

903 (2005). 

S Long, E Campbell, R MacKinnon. Crystal Structure of a 

Mammalian Voltage-Dependent Shaker Family K+ Channel. 

Science. 309, 897 (2005). 

G Miller, M Wilson, P Majerus, J Hurley. Specificity Determinants 

in Inositol Polyphosphate Synthesis: Crystal Structure of Inositol 

1,3,4-Trisphosphate 5/6-Kinase . Mol. Cell. 18 (2), 201-212 

(2005). 

M Neiditch, M Federle, S Miller, B Bassler, F Hughson. Regulation 

of LuxPQ Receptor Activity by the Quorum-Sensing Signal 

Autoinducer-2. Mol. Cell. 18 (5), 507-518 (2005). 

K Pant, B Crane . Structure of a Loose Dimer: an Intermediate in 

Nitric Oxide Synthase Assembly. J. Mol. Biol.. 352 (4), 932-940 

(2005). 

E Rangarajan, Y Li, P Iannuzzi, M Cygler, A Matte. Crystal 

Structure of Escherichia coli Crotonobetianyl-CoA: Carnitine 

CoA-Transferase (CaiB) and Its Complexes with CoA and 

Carnitinyl-CoA. Biochemistry. 44, 5728-5738 (2005). 

S Riedl, W Li, Y Chao, R Schwarzenbacher, Y Shi. Structure of the 

Apoptotic Protease-Activating Factor 1 Bound to ADP. Nature. 

434, 926 (2005). 

T Schmeing, K Huang, S Strobel, T Steitz. An Induced-fit 

Mechanism to Promote Peptidyl Bond Formation and Exclude 

Hydrolysis of Peptidyl-tRNA. Nature. 438, 520-524 (2005). 

T Schmeing, K Huang, D Kitchen, S Strobel, T Steitz. Structural 

Insights into the Mechanism of the Peptidyl Transferase 

Reaction Suggest Oxyanion Transition State Stabilization by 

Water and a Substrate Proton Shuttle. Mol. Cell. 20, 437-448 

(2005). 

A Serganov, S Keiper, L Malinina, V Tereshko, E Skripkin, C 

Hobartnet, A Polonskaia, Z Dauter, A Jaschke, D Patel. Structural 

basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond 

formation. Nat. Struct. Mol. Biol.. 12 (3), 218-224 (2005). 

K Shi, C Brown, Z Gu, B Kozlowicz, G Dunny, D Ohlendorf, 

C Earhart. Structure of Peptide Sex Pheromone Receptor 

PrgX and PrgX/Pheromone Complexes and Regulation of 

Conjugation in Enterococcus faecalis. Proc Natl Acad Sci USA. 

102 (51), 18596-18601 (2005). 

E Sickmier, D Brekasis, S Paranawithana, J Bonanno, M Paget, S 

Burley, C Kielkopf. X-ray Structure of a Rex-Family Repressor/

NADH Complex Insights into the Mechanism of Redox Sensing. 

Structure. 13, 43-54 (2005). 

X Siebert, B Eipper, R Mains, S Prigge, N Blackburn, L Amzel. 

The Catalytic Copper of Peptidylglycine alpha-Hydroxylating 

Monooxygenase also Plays a Critical Structural Role. Biophys. 

J.. 89 (5), 3312-3319 (2005). 

X Siebert. Structural Probes into the Mechanism of PAM, a 

Peptide-Amidating Enzyme. Ph. D. Thesis. Johns Hopkins 

School of Medicine, Baltimore. (2005). 

M Stahley, S Strobel. Structural Evidence for a Two-Metal-ion 

Mechanism of Group I Intron Splicing. Science. 309, 1587 

(2005). 

B Staker, M Feese, M Cushman, Y Pommier, D Zembower, L 

Stewart, A Burgin. Structures of Three Classes of Anticancer 

Agents Bound to the Human Topoisomerase I-DNA Covalent 

Complex. J. Med. Chem.. 48 (7), 2336-2345 (2005). 

A Stein, G Fuchs, C Fu, S Wolin, K Reinisch. Structural Insights 

into RNA Quality Control: The Ro Autoantigen Binds Misfolded 

RNAs Via its Central Cavity. Cell. 121 (4), 529-539 (2005). 

A Tocilj, J Schrag, Y Li, B Schneider, L Reitzer, A Matte, M Cygler. 

Crystal Structure of N-succinylarginine Dihydrolase AstB, 

Bound to Substrate and Product, an Enzyme from the Arginine 

Catabolic Pathway of Escherichia Coli. J. Biol. Chem.. 280 (16), 

15800-15808 (2005). 

N Tolia, E Enemark, B Sim, L Joshua-Tor. Structural Basis for the 

EBA-175 Erythrocyte Invasion Pathway of the Malaria Parasite 

Plasmodium Falciparum. Cell. 122, 183-193 (2005). 

D Tu, G Blaha, P Moore, T Steitz. Structures of MLSBK Antibiotics 

Bound to Mutated Large Ribosomal Subunits Provide a 

Structural Explanation for Resistance. Cell. 121 (2), 257-270 

(2005). 

S Tuske, S Sarafianos, X Wang, B Hudson, E Sineva, J 

Mukhopadhyay, J Birktof, O Leroy, S Ismail, et al.. Inhibition of 

Bacterial RNA Polymerase by Streptolydigin: Stabilizaiton of a 

Straight-Bridge-Helix Active-Center Conformation. Cell. 122 (4), 

541-552 (2005). 

H Wei, A Ruthenburg, S Bechis, G Verdine. Nucleotide-dependent 

Domain Movement in the ATPase Domain of a Human Type IIA 

DNA Topoisomerase. J. Biol. Chem.. 280 (44), 37041-37047 

(2005). 

N Yan, J Chai, E Lee, L Gu, Q Liu, J He, J Wu, D Kokel, 

H Li, et al.. Structure of the CED-4-CED-9 Complex 

Provides Insights into Programmed Cell Death in 

Caenorhabditis elegans. Nature. 437, 831 (2005). 

Beamline X26A

C Andrade, T Preharaj, H Jamieson, D Fortin. The potential for 

geochemical and microbial remobilization of arsenic from 

sediments in Yellowknife Bay, Great Slave Lake: Progress. 

Geological Sciences, Queen’s University , Kingston. Prepared 

for Indian and Northern Affairs Canada. (2005). 

T Biswas, H Aihara, M Radman-Livaja, D Filman, A Landy, T 

Ellenberger. A Structural Basis for Allosteric Control of DNA 

Recombination by lamda Integrase. Nature. 435, 1059 (2005). 

L Brieba, R Kokoska, K Bebenek, T Kunkel, T Ellenberger. 

A Lysine Residue in the Fingers Subdomain of T7 DNA 

Polymerase Modulates the Miscoding Potential of 8-Oxo-7,8-
Dihydroguanosine. Structure. 13 (11), 1653-1659 (2005). 

M Cheng, M Levy, D Schulze, D Huber. Mn Transition States 

During Infection and Early Pathogenesis in Rice Blast Relative 

to Resistance and Susceptibility. J. Phytopathology. 95, S19 

(2005). 

J Flinn, D Hunter, D Linkous, A Lanzirotti, L Smith, J Brightwell, B 

Jones. Enhanced Zinc Consumption Causes Memory Deficits 

and Increased Brain Levels of Zinc. Physiol. Behav.. 83, 793-

803 (2005). 

V Fthenakis, M Fuhrmann, J Heiser, A Lanzirotti, J Fitts, W Wang. 

Emissions and Encapsulation of Cadmium in CdTe PV Modules 

During Fires. Prog. Photovolt.. 13 (8), 713-723 (2005). 

M Fuhrmann, A Lanzirotti. 241Am, 137Cs, Sr and Pb Uptake by 

Tobacco as Influenced by Application of Fe Chelators to Soil. J. 

Environ. Radioact.. 82 (1), 33-50 (2005). 

M Ginder-Vogel, T Borch, M Mayes, P Jardine, S Fendorf. 

Chromate Reduction and Retention Processes within Arid 

Subsurface Environments. Environ. Sci. Tech.. 39 (20), 7833-

7839 (2005). 

B Jackson, P Williams, A Lanzirotti, P Bertsch. Evidence 

for Biogenic Pyromorphite Formation by the Nematode 

Caenorhabditis Elegans. Environ. Sci. Tech.. 39 (15), 5620-

5625 (2005). 

K Jones, H Feng, A Lanzirotti, D Mahajan. Mapping Metal 

Catalysts using Synchrotron Computed Microtomography 

(CMT) and Micro-X-ray Fluorescence (μXRF). Top. Catal.. 32

(3-4), 263-272 (2005). 

K Jones, H Feng, A Lanzirotti, D Mahajan. Synchrotron Xray Microprobe and Computed Microtomography for 

Characterization of Nanocatalysts. Nucl. Instrum. Meth. B. 241, 

331-334 (2005). 

G Miller, M Wilson, P Majerus, J Hurley. Specificity Determinants 

in Inositol Polyphosphate Synthesis: Crystal Structure of Inositol 

1,3,4-Trisphosphate 5/6-Kinase . Mol. Cell. 18 (2), 201-212 

(2005). 

L Miller, M Ruppel, C Ott, R Smith, A Lanzirotti. Development and 

Applications of an Epifluorescence Module for Synchrotron -ray 

Fluorescence Imaging. Rev. Sci. Instrum.. 76, 066107 (2005). 

C Negra, D Ross, A Lanzirotti. Oxidizing Behavior of Soil 

Manganese: Interactions among Abundance, Oxidation State, 

and pH . Soil Sci. Soc. Am. J.. 69 (1), 87-95 (2005). 

C Negra, D Ross, A Lanzirotti. Soil Manganese Oxides and Trace 

Metals: Competitive Sorption and Microfocused Synchrotron 

X-ray Fluorescence Mapping. Soil Sci. Soc. Am. J.. 69 (2), 353-

361 (2005). 

T Punshon, B Jackson, A Lanzirotti, W Hopkins, P Bertsch, 

J Burger. Application of Synchrotron X-ray Microbeam 

Spectroscopy to the Determination of Metal Distribution and 

Speciation in Biological Tissues. Spectrosc. Lett.. 38, 343-363 

(2005). 

T Punshon, A Lanzirotti, S Harper, P Bertsch, J Burger. Distribution 

and Speciation of Metals in Annual Rings of Black Willow. J. 

Environ. Qual.. 34 (4), 1165-1173 (2005). 

M Ruppel. Development and Applications of an Epifluorescence 

Module for Synchrotron X-ray Fluorescence Imaging. Masters 

Thesis. Stony Brook University, Stony Brook. (2005). 

T Schuler, D Ederer, S Itza-Ortiz, G Woods, T Callcott, J Woicik. 

Character of the Insulating State in NiO: a Mixture of ChargeTransfer and Mott-Hubbard Character. Phys. Rev. B. 71, 115113 

(2005). 

B Staker, M Feese, M Cushman, Y Pommier, D Zembower, L 

Stewart, A Burgin. Structures of Three Classes of Anticancer 

Agents Bound to the Human Topoisomerase I-DNA Covalent 

Complex. J. Med. Chem.. 48 (7), 2336-2345 (2005). 

T Telivala, L Miller. Effect of Metal Ions on the Secondary Structure 

of Amyloid beta (Ab) in Alzheimer’s disease. Masters Thesis. 

SUNY at Stony Brook, Stony Brook. (2005). 

I Thompson, D Huber, C Guest, D Schulze. Fungal Manganese 

Oxidation in a Reduced Soil. Environ. Microbiol.. 7 (9), 1480-

1487 (2005). 

T Tokunaga, J Wan, J Pena, E Brodie, M Firestone, T Hazen, 

S Sutton, A Lanzirotti, M Newville. Uranium Reduction in 

Sediments under Diffusion-Limited Transport of Organic Carbon. 

Environ. Sci. Tech.. 39 (18), 7077-7083 (2005). 

D Vantelon, A Lanzirotti, A Scheinost, R Kretzschmar. Spatial 

Distribution and Speciation of Lead around Corroding Bullets 

in a Shooting Range Soil Studied by Micro-X-ray Fluorescence 

and Absorption Spectroscopy. Environ. Sci. Tech.. 39 (13), 

4808-4815 (2005). 

S Walker, H Jamieson, A Lanzirotti, C Andrade, G Hall. The 

Speciation of Arsenic in Iron Oxides in Mine Wastes from the 

Giant Gold Mine, N.W.T.: Application of Synchrotron Micro-XRD 

and Micro-XANES at the Grain Scale. Can. Mineral. 43 (4), 

1205-1224 (2005). 

Q Wang, A Kretlow, M Beekes, D Naumann, L Miller. In Situ 

Characterization of Prion Protein Structure and Metal 

Accumulation in Scrapie-Infected Cells by Synchrotron Infrared 

and X-ray Imaging. Vib. Spectrosc.. 38, 61-69 (2005). 

Beamline X26C

J Amor, J Swails, X Zhu, C Roy, H Nagai, A Ingmundson, X 

Cheng, R Kahn. The Structure of RalF, an ADP-Ribosylation 

Factor Guanine Nucleotide Exchange Factor from Legionella 

pneumophila, Reveals the Presence of a Cap over the Active 

Site. J. Biol. Chem.. 280 (2), 1392-1400 (2005). 

P Cherepanov, A Ambrosio, S Rahman, T Ellenberger, A Engelman. 

Structural Basis for the Recognition Between HIV-1 Integrase 

and Transcriptional Coactivator p75. Proc Natl Acad Sci USA. 

102 (48), 17308-17313 (2005). 

P Davison, H Schubert, J Reid, C Iorg, A Heroux, C Hill, C 

Hunter. Structural and Biochemical Characterization of Gun4 

Suggests a Mechanism for Its Role in Chlorophyll Biosynthesis. 

Biochemistry. 44 (21), 7603-7612 (2005). 

B Ford, K Skowronek, S Boykevisch, D Bar-Sagi, N Nassar. 

Structure of the G60A mutant of Ras: Implications for the 

Dominant Negative Effect.. J. Biol. Chem.. 280 (27), 25697-

25705 (2005). 

B Gao, A Bertrand, W Boles, H Ellis, T Mallett. Crystallization 

and Preliminary X-ray Crystallographic Studies of the 

Alkanesulfonate FMN Reductase from Escherichia coli. Acta 

Cryst. F. 61, 837-840 (2005). 

J Horton, K Sawada, M Nishibori, X Cheng. Structural Basis for 

Inhibition of Histamine N-Methyltransferase by Diverse Drugs. 

J. Mol. Biol.. 353 (2), 334-344 (2005). 

H Hsu, B Stillman, R Xu. Structural Basis for Origin Recognition 

Complex 1 Protein-Silence Information Regulator 1 Protein 

Interaction in Epigenetic Silencing. Proc Natl Acad Sci USA. 

102, 8519-8524 (2005). 

E Karakas, H Wilson, T Graf, S Xiang, S Jaramillo-Busquets, K 

Rajagopalan, C Kisker. Structural Insights into Sulfite Oxidase 

Deficiency. J. Biol. Chem.. 280 (39), 33506-15 (2005). 

I Loftin, S Franke, S Roberts, A Weichsel, A Heroux, W Montfort, 

C Rensing, M McEvoy. A Novel Copper-Binding Fold for the 

Periplasmic Copper Resistance Protein CusF. Biochemistry. 44, 

10533-10540 (2005). 

J Ma, Y Yuan, G Meister, Y Pei, T Tuschi, D Patel. Structural Basis 

for 5’ -end-specific Recognition of Guide RNA by the A. fulgidu 

Piwi Protein. Nature. 434, 666 (2005). 

P Paaventhan, C Kong, J Joseph, M Chung, P Kolatkar. Structure 

Publications 7-25
7-26 NSLS Activity Report

of Rhodocetin Reveals Noncovalently Bound Heterodimer 

Interface. Protein Sci.. 14, 169 (2005). 

F Rivas, N Tolia, J Song, J Aragon, J Liu, G Hannon, L Joshua-Tor. 

Purified Argonaute2 and an siRNA form Recombinant Human 

RISC. Nat. Struct. Mol. Biol.. 12 (4), 340-349 (2005). 

D Shi, X Yu, L Roth, M Hiroki, Y Hathout, N Allewell, M Tuchman. 

Expression, Purification, Crystallization and Preliminary X-ray 

Crystallographic Studies of a Novel Acetylcitrulline deacetylase 

from Xanthomonas Campestris. Acta Cryst. F. 61, 676-679 

(2005). 

X Siebert, B Eipper, R Mains, S Prigge, N Blackburn, L Amzel. 

The Catalytic Copper of Peptidylglycine alpha-Hydroxylating 

Monooxygenase also Plays a Critical Structural Role. Biophys. 

J.. 89 (5), 3312-3319 (2005). 

X Siebert. Structural Probes into the Mechanism of PAM, a 

Peptide-Amidating Enzyme. Ph. D. Thesis. Johns Hopkins 

School of Medicine, Baltimore. (2005). 

A Soares, Y Vehter. Experimental methods for measuring accurate 

high-amplitude phases and their importance in isomorphous 

replacement experiments. Acta Cryst. D. D61, 1521-1527 

(2005). 

J Suryadi, E Tran, E Maxwell, B Brown, II. The Crystal Structure of 

the Methanocaldococcus jannaschii Multifunctional L7Ae RNABinding Protein Reveals an Induced-Fit Interaction with the Box 

C/D RNAs. Biochemistry. 44, 9657-9672 (2005). 

Y Tie, P Boross, Y Wang, L Gaddis, f Liu, X Chen, J Tozser, R 

Harrison, I Weber. Molecular Basis for Substrate Recognition 

and Drug Resistance from 1.1 to 1.6 Angstrom Resolution 

Crystal Structures of HIV-1 Protease Mutants with Substrate 

Analogs. FEBS J.. 272 (20), 5265 (2005). 

N Tolia, E Enemark, B Sim, L Joshua-Tor. Structural Basis for the 

EBA-175 Erythrocyte Invasion Pathway of the Malaria Parasite 

Plasmodium Falciparum. Cell. 122, 183-193 (2005). 

J Truglio, B Rhau, D Croteau, L Wang, M Skorvaga, E Karakas, 

M DellVecchia, H Wang, B Van Houten, C Kisker. Structural 

Insights Into the First Incision Reaction During Nucleotide 

Excision Repair. EMBO J.. 24, 885-894 (2005). 

J Wang, K Stieglitz, E Kantrowitz. Metal Specificity is Correlated 

with Two Crucial Active Site Residues in Escherichia coli 

Alkaline Phosphatase. Biochemistry. 44, 8378-8386 (2005). 

Beamline X27A

J Ablett. High-Brightness Hard X-ray Scanning Nano-Probes at 

NSLS II. Nucl. Instrum. Meth. B. 241, 238-241 (2005). 

K Jones, H Feng, A Lanzirotti, D Mahajan. Mapping Metal 

Catalysts using Synchrotron Computed Microtomography 

(CMT) and Micro-X-ray Fluorescence (μXRF). Top. Catal.. 32

(3-4), 263-272 (2005). 

Beamline X27B

E Kossel. NMR-Untersuchungen zum mikroskopischen Fluss in 

Perkolationsmodellobjekten. Ph.D. Thesis. Universtaet Ulm, 

Ulm. (2005). 

Beamline X27C

C Avila-Orta, C Burger, R Somani, L Yang, G Marom, F MedellinRodriguez, B Hsiao. Shear Induced Crystallization in Isotactic 

Polypropylene within the Oriented Scaffold of Non-crystalline 

Ultra High Molecular Weight Polyethylene. Polymer. 46, 8859-

8871 (2005). 

J Celli, B Gregor, B Turner, N Afdhal, R Bansil, S Erramilli. 

Viscoelastic Properties and Dynamics of Porcine Gastric Mucin. 

Biomacromolecules. 6, 1329 (2005). 

X Chen, C Burger, X Wang, W He, K Yoon, R Somani, D Fang, 

I Sics, L Rong, et al.. In-Situ X-Ray Scattering Studies of 

Fluorinated Multi-Wall Carbon Nanotube (FMWNT)/Fluorinated 

Ethylene Propylene (FEP) Composite Fiber during Stretching. 

ACS, PMSE Preprints, Vol 93, p. 751-752, sponsored by ACS. 

(2005). 

J Chen, C Burger, C Krishnan, B Chu. Morphogenesis of Highly 

Ordered Mixed-Valent Mesoporous Molybdenum Oxides. J. Am. 

Chem. Soc.. 127, 14140-14141 (2005). 

X Chen, K Yoon, C Burger, I Sics, D Fang, B Hsiao, B Chu. In-Situ 

X-ray Scattering Studies of a Unique Toughening Mechanism in 

Surface-Modified Carbon Nanofiber/UHMWPE Nanocomposite 

Films. Macromolecules. 38, 3883-3893 (2005). 

L Cui, J Miao, L Zhu, I Sics, B Hsiao. Confined Discotic Liquid 

Crystalline Self-assembly in a Novel Coil-coil-disk Triblock 

Oligomer. ACS, PMSE Preprints, Vol 93, p. 286-287, sponsored 

by ACS. (2005). 

L Cui, S Dahmane, X Tong, L Zhu, Y Zhao. Using Self-Assembly 

to Prepare Multifunctional Diblock Copolymers Containing 

Azopyridine Moiety. Macromolecules. 38, 2076-2084 (2005). 

L Cui, J Miao, L Zhu, I Sics, B Hsiao. Confined Discotic Liquid 

Crystalline Self-Assembly in a Novel Coil-Coil-Disk Triblock 

Oligomer. Macromolecules. 38, 3386-3394 (2005). 

D Dikovsky, G Marom, C Avila-orta, R Somani, B Hsiao. ShearInduced Crystallization in Isotactic Polypropylene Containing 

Ultra-High Molecular Weight Polyethylene Oriented Precursor 

Domains. Polymer. 45, 3096-3104 (2005). 

D Dikovsky, G Marom, C Avila-Orta, R Somani, B Hsiao. ShearInduced Crystallization in Isotactic Polypropylene Containing 

Ultra-High Molecular Weight Polyethylene Oriented Precursor 

Domains. Polymer. 46 (9), 3096-3104 (2005). 

L Drummy, D Phillips, M Stone, B Farmer, R Naik. Thermally 

Induced Alpha-Helix to Beta-Sheet Transition in Regenerated 

Silk Fibers and Films. Biomacromolecules. 6 (6), 3328-3333 

(2005). 

Z Espinosa, F Medellin-Rodriguez, N Stribeck, A AlmendarezCamarillo, B Hsiao, S Vega-diaz. Complex Isothermal 

Crystallization and Melting Behavior of Nylon 6 NanoclayHybrids. Macromolecules. 38 (10), 4246-4253 (2005). 

H Fong, S Dickins, G Flaim. Evaluation of Dental Restorative 

Composites Containing Polyhedral Oligomeric Silsesquioxane 

Methacrylate. Dent. Mater.. 21 (6), 520-529 (2005). 

K Fukukawa, L Zhu, P Gopalan, M Ueda, S Yang. Synthesis 

and Characterization of Silicon-containing Block Copolymers 

from Nitroxide-mediated Living Free Radical Polymerization. 

Macromolecules. 28 (2), 263-270 (2005). 

M Gelfer, C Burger, B Chu, B Hsiao, A Drozdov, M Si, M Rafailovich, 

B Sauer, J Gilman. Relationships Between Structure and 

Rheology in Model Nanocomposites of Ethylene-Vinyl-Based 

Copolymers and Organoclays. Macromolecules. 38, 3765-3775 

(2005). 

M Gelfer, C Burger, G Panek, G Jeschke, A Fadeev, M Si, 

M Rafailovich, P Nawani, J Gilman, et al.. Investigation of 

Thermally Induced Phase Transitions and Degradation of 

Organoclays Based on Synthetic Somasif Clays using in-situ 

X-ray Scattering. ACS, PMSE Preprints, , Vol 92, p. 441-442, 

sponsored by ACS. (2005). 

G Georgiev. Effects of Nematic Polymer Liquid Crystal on 

Crystallization and Structure of PET/Vectra Blends. J. Mater. 

Sci.. 40, 1140 (2005). 

G Georgiev, P Cebe, M Capel. Effects of Nematic Polymer Liquid 

Crystal on Crystallization and Structure of Pet/Vectra Blends. J. 

Mater. Sci.. 40 (5), 1141-1152 (2005). 

H Heinz, H Koerner, K Anderson, R Vaia, B Farmer. Force Field 
for Mica-Type Silicates and Dynamics of Octadecylammonium 

Chains Grafted to Montmorillonite. Chem. Mater.. 17, 5658 

(2005). 

R Ho, T Chung, J Tsai, J Kuo, B Hsiao, I Sics. Crystallization of 

Poly(styrene)-b-syndiotactic Poly(propylene) Block Copolymers 

from Confinement to Breakout. Macromol. Rapid Commun.. 26, 

107-111 (2005). 

R Ho, T Lin, M Jhong, T Chung, B Ko, y Chen. Phase Transformation 

in Self-Assembly of th Gold(Poly(4-vinylpyridine)-b-poly(ecaprolactone) Hybrid System. Macromolecules. 38 (21), 8607 

(2005). 

R Ho, Y Chiang, C Lin, B Huang. Crystallizatiion and Melting 

Behavior of Poly(E-caprolactone) Under Physical Confinement. 

Macromolecules. 38, 4769-4779 (2005). 

B Hsiao, M Gelfer. Synchrotron X-ray Techniques for the Study 

of Clay-Based Polymer Nanocomposites. American Chemical 

Society Rubber Division Preprint, Vol , p. 66, sponsored by 

American Chemical Society Rubber Division . (2005). 

B Hsiao, L Yang, R Somani, C Avila-Orta, L Zhu. Unexpected 

Shish-Kebab Structure in a Sheared Polyethylene Melt. Phys. 

Rev. Lett.. 94, 117802 (2005). 

P Huang, S Chen, R Van Horn, Y Guo, R Quirk, B Lotz, E Thomas, 

B Hsiao, C Avila-Orta, I Sics. PEO Crystal Orientation Changes 

within an Inversed Cylindrical Morphology Constructed by a 

PEO-b-PS Block Copolymer. ACS, PMSE Preprints, Vol 93, p. 

284-285, sponsored by ACS. (2005). 

A Kelarakis, K Yoon, I Sics, R Somani, B Hsiao, B Chu. Uniaxial 

Deformation of an Elastomer Nanocomposite Containing 

Modified Carbon Nanofibers by in situ Synchrotron X-ray 

Diffraction. Polymer. 46 (14), 5103-5117 (2005). 

J Keum, C Burger, F Zuo, I Sics, B Hsiao, T Sun, A Lustiger. 

Synchrotron X-ray Diffraction/Scattering Studies on the 

Nucleation and Growth Habits of Flow-induced shish-kebab 

structure in Linear Polyethylene (HDPE) Melts. ACS, PMSE 

Preprints, Vol 93, p. 759-760, sponsored by ACS. (2005). 

J Keum, C Burger, B Hsiao, R Somani, L Yang, R Kolb, H Chen, 

C Lue. Synchrotron X-ray Scattering Studies of the Nature of 

Shear-Induced Shish-kebab Structure in Polyethylene Melt. 

Prog. Coll. Pol. Sci. S.. 130, 114-126 (2005). 

J Keum, R Somani, F Zuo, C Burger, I Sics, B Hsiao, H Chen, 

R Kolb, C Lue. Probing Flow-Induced Precursor Structures 

in Blown Polyethylene Films by Synchrotron X-rays During 

Constrained Melting. Macromolecules. 38, 5128-5136 (2005). 

H Koerner, W Liu, M Alexander, P Mirau, H Dowty, R Vaia. 

Deformation-Morphology Correlations in Electrically 

Conductive Carbon Nanotube-Thermoplastic Polyurethane 

Nanocomposites. Polymer. 46 (12), 4405-4420 (2005). 

H Koerner, E Hampton, D Dean, Z Turgut, L Drummy, P Mirau, 

R Vaia. Generating Triaxial Reinforced Epoxy/Montmorillonite 

Nanocomposites with Uniaxial Magnetic Fields. Chem. Mater.. 

17, 1990-1996 (2005). 

H Koerner, G Price, N Pearce, M Alexander, R Vaia. Remotely 

Actuated Polymer Nanocomposites-Stress-Recovery of 

Carbon-Nanotube-Filled Thermoplastic Elastomers. Nat. Mater.. 

3, 115-120 (2005). 

S Kohjiya, M Tosaka, S Poompradub, A Kato, J Shimanuki, Y 

Ikeda, S Toki, B Hsiao. Nano-structural Elucidation in Carbon 

Black Loaded NR Vulcanizate by 3D-TEM and in situ WAXD 

Measurements. American Chemical Society Rubber Division 

Preprint, Vol , p. 33, sponsored by American Chemical Society 

Rubber Division . (2005). 

B Larin, G Marom, C Avila-Orta, R Somani, B Hsiao. Orientated 

Crystallization in Discontinuous Aramid Fiber/isotactic 

Polypropylene Composites under Shear Flow Conditions. J. 

Appl. Polym. Sci.. 98, 1113 (2005). 

H Lee, L Zhu, R Weiss. Formation of Nanoparticles during 

Melt mixing a Thermotropic Liquid Crystalline Polyester and 

Sulfonated Polystyrene Ionomers: Morphology and Origin of 

Formation. Polymer. 46, 10841 (2005). 

Y Loo, K Eakabayashi, Y Huang, R Register, B Hsiao. Thin 

Crystal Melting Produces the Low-Temperature Endotherm in 

Ethylene/Methacrylic Acid Ionomers. Polymer. 46 (14), 5118-

5124 (2005). 

J Miao, G Xu, L Zhu, L Tian, K Uhrich, C Avila-Orta, B Hsiao, M 

Utz. Chain-folding and Overall Molecular Conformation in a 

Novel Amphiphilic Starlike Macromolecule. Macromolecules. 

38, 7074-7082 (2005). 

C Mitchell, R Krishnamoorti. Non-isothermal Crystallization of in 

situ Polymerized Poly(E-caprolactone) Functionalized-SWNT 

Nanocomposites. Polymer. 46 (20), 8796-8804 (2005). 

P Nawani, M Gelfer, B Hsiao. Investigations of Morphology and 

Thermal Behavior of Transition Metal Ions Modified Clays using 

in-situ X-ray Scattering. ACS, PMSE Preprints, Vol 93, p. 757-

758, sponsored by ACS. (2005). 

K Page, K Cable, R Moore. Molecular Origins of the Thermal 

Transitions and Dynamic Mechanical Relaxations in 

Perfluorosulfonate Ionomers. Macromolecules. 38, 6472-6484 

(2005). 

B Pate, E Thomas, R Pytel. Processing the Right Actuator: The 

Relationship Between Nanostructure and Materials Properties 

of Higher-Order Pyrroles. 229th ACS National Meeting, Vol , p. 

ORGN-238, sponsored by American Chemical Society. (2005). 

B Pate, T Baker, K Lai, E Thomas. Synthesis and Dispersion of 

tin(IV) Sulfide Nano- and Microparticulate Fillers. 230th ACS 

National Meeting, Vol , p. INOR-399, sponsored by American 

Chemical Society. (2005). 

H Shin, W Lindquist, D Sahagian, S Song. Analysis of the Vesicular 

Structure of Basalts. Comput. Geosci.. 31 (4), 473-487 (2005). 

I Sics, L Rong, B Hsiao, B Chu. Advanced Polymers Beamline 

(X27C) at National Synchrotron Light Source, BNL. ACS, PMSE 

Preprints, Vol 93, p. 120, sponsored by ACS. (2005). 

R Somani, L Yang, L Zhu, B Hsiao. Flow-Induced Shish Kebab 

Precursor Structures in Entangled Polymer Melts. Polymer. 46, 

8587-8623 (2005). 

L Sun, E Ertel, L Zhu, B Hsiao, C Avila-Orta, I Sics. Reversible 

De-Intercalation and Intercalation Induced by Polymer 

Crystallization and Melting in a Poly(ethylene oxide)/Organoclay 

Nanocomposite. Langmuir. 21, 5672-5676 (2005). 

K Tenneti, X Chen, C Li, X Wan, Q Zhou, I Sics, B Hsiao. Asymmetric 

Liquid Crystalline Rod Coil Block Copolymer System. American 

Chemcial Society, Vol , p. TECH-100, sponsored by American 

Chemical Society. (2005). 

K Tenneti, X Chen, C Li, X Wan, Q Zhou, I Sics, B Hsiao. 

Asymmetric Liquid Crystalline Rod-Coil Block Copolymer 

System. ACS, PMSE Preprints, Vol 93, p. 364-365, sponsored 

by ACS. (2005). 

K Tenneti, C Li, Y Tu, X Wan, Q Zhou, C Avila-Orta, B Hsiao. On 

the Influence of Temperature and Volume Fraction on Liquid 

Crystalline Block Copolymer Nanoscale Architectures. APS 

National Meeting, Vol , p. LACC 505, sponsored by APS. 

(2005). 

K Tenneti, X Chen, C Li, Y Tu, X Wan, Q Zhou, I Sics, B Hsiao. 

Perforated Layer Structures in Liquid Crystalline Rod-coil 

Block Copolymers. J. Am. Chem. Soc.. 127 (44), 15481-15490 

(2005). 

S Toki, B Hsiao, S Kohjiya, M Tosaka, A Tsou, S Datta. Synchrotron 

X-Ray Studies of Vulcanized Rubbers and Thermoplastic 

Elastomers. American Chemical Society Rubber Division 

Preprint, Vol , p. 32, sponsored by American Chemical Society 

Rubber Division . (2005). 

Publications 7-27
7-28 NSLS Activity Report

S Toki, I Sics, B Hsiao, M Tosaka, S Poompradub, Y Ikeda, S 

Kohjiya. Probing the Nature of Stain-Induced Crystallization in 

Polyisoprene Rubber by Combined Thermomechanical and In 

Situ X-ray Diffraction Techniques. Macromolecules. 38, 7064-

7073 (2005). 

R Vaia, H Koerner, B Hsiao, I Sics. Morphology -- Deformation 

Correlations in Nanocomposite Elastomers. American Chemical 

Society Rubber Division Preprint, Vol , p. 63, sponsored by 

American Chemical Society Rubber Division . (2005). 

Z Wang, H Wang, K Shimizu, J Dong, B Hsiao, C Han. Structural 

and Morphological Development in Poly(ethylene-co-hexene) 

and Poly(ethylene-co-butylene) Blends Due to the Competition 

Between Liquid-Liquid Phase Separation and Crystallization. 

Polymer. 46 (8), 2675-2684 (2005). 

J Xu, B Guo, J Zhou, L Li, J Wu, M Kowalczuk. Observation of 

Banded Spherulites in Pure poly(L-lactide) and its Miscible 

Blends with Amorphous Polymers. Polymer. 46, 9176 (2005). 

H Xu. Transitions from Solid to Liquid in Isotactic Polystyrene 

Studied by Thermal Analysis and X-ray Scattering. Polymer. 46, 

8734 (2005). 

J Zhang, J Wu. Crystallinity and orientation development in 

poly(L-lactic acid) fibers during annealing and drawing. Annual 

Technical Conference - Society of Plastics Engineers , Vol , p. 

1747, sponsored by Annual Technical Conference - Society of 

Plastics Engineers . (2005). 

H Zhou, C Burger, J Chen, B Hsiao, B Chu, L Graham, M Glimcher. 

Interpretation of 2D Small-Angle X-Ray Diffraction Patterns 

from Mineralized Collagen Fibrils in Fish Bone. ACS, PMSE 

Preprints, Vol 93, p. 755-756, sponsored by ACS. (2005). 

L Zhu, L Sun, J Miao, L Cui, Q Ge, R Quirk, C Xue, S Cheng, B 

Hsiao, C Avila-Orta. Epitaxial Phase Transformation between 

Cylindrical and Double Gyroid Mesophases. Materials Research 

Society Meeting, Vol 856E, p. BB2.3.1-BB2.3.6, sponsored by 

MRS. (2005). 

F Zou, H Chen, J Li, R Wevers, G Meyers, J Keum, X Chen, B 

Hsiao. In-situ Synchrotron SAXS/WAXD Studies on Stretching 

of Isotactic Polypropylene. ACS, PMSE Preprints, , Vol 93, p. 

761-762, sponsored by ACS. (2005). 

Beamline X28C

T Adilakshmi, P Ramaswamy, S Woodson. Protein-Independent 

Folding Pathway of the 16 S rRNA 5’ Domain. J. Mol. Biol.. 351

(3), 508-519 (2005). 

M Brenowitz, D Erie, M Chance. Catching RNA Polymerase in 

the act of Binding: Intermediates in Transcription Illuminated by 

Synchrotron Footprinting. Proc Natl Acad Sci USA. 102, 4659-

4660 (2005). 

J Guan, K Takamoto, S Almo, E Reisler, M Chance. Structure and 

Dynamics of the Actin Filament. Biochemistry. 44, 3166-3175 

(2005). 

S Gupta, W Mangel, M Sullivan, K Takamoto, M Chance. 

Synchrotron Footprinting Provides Insight into Adenovirus 

Protease-DNA Interactions. Synch. Rad. News. 18, 25-33 

(2005). 

P Rangan. Folding of the Azoarcus Intron. Ph.D. 

Thesis. John Hopkins University, Baltimore. (2005). 

K Takamoto, M Chance. A New Approach for Nucleic Acid 

Footprinting Data Analysis. BioTech. J.. 5, 194-197 (2005). 

S Woodson. Metal Ions and RNA Folding: A Highly Charged 

Topic with a Dynamic Future. Curr Opin Chem Biol. 9, 104-109 

(2005). 

G Xu, J Kiselar, Q He, M Chance. Secondary Reactions and 

Strategies to Improve Quantitative Protein Footprinting. Anal. 

Chem.. 77, 3029-3037 (2005). 

G Xu, M Chance. Radiolytic Modification of Sulfur Containing 

Acidic Amino Residues in Model Peptides: Fundamental Studies 

for Protein Footprinting. Anal. Chem.. 77, 2437-2449 (2005). 

Beamline X29A

R Agarwal, T Binz, S Swaminathan. Structural Analysis of 

Botulinum Neurotoxin Serotype F Light Chain: Implications 

on Substrate Binding and Inhibitor Design. Biochemistry. 44, 

11758-11765 (2005). 

E Bitto, C Bingman, H Robinson, S Allard, G Wesenberg, G 

Phillips, Jr.. The Crystal Structure at 2.5 Angstrom Resolution of 

Human Basophilic Leukemia-Expressed Protein BLES03. Acta 

Cryst. F. 61, 812 (2005). 

J Brown, Z Zhou, L Reshetnikova, H Robinson, R Yammani, L 

Tobacman, C Cohen. Structure of the Mid-Region Tropomyosin: 

Bending and Binding Sites for Actin. Proc Natl Acad Sci USA. 

102 (52), 18878-18883 (2005). 

L Deng, C Velikovsky, C Swaminathan , S Cho, R Mariuzza. 

Structural Basis for Recognition of the T Cell Adaptor Protein 

SLP-76 by the SH3 Domain of Phospholipase CGAMMA1. J. 

Mol. Biol.. 352, 1 (2005). 

M DiMattia, L Govindasamy, H Levy, B Whitaker-Gurda, E 

Kohlbrenner, J Chiorini, R McKenna, N Muzyczka, S Zolotukhin, 

M Agbandje-McKenna. Production, Purification, Crystallization 

and Preliminary X-ray Structural Studies of Adeno-Associated 

Virus Serotype 5. Acta Cryst. F. F61, 917-921 (2005). 

G Dong, A Hutagalung, C Fu, P Novick, K Reinisch. The Structures 

of Exocyst Subunit Exo70p and the Exo84p C-terminal Domains 

Reveal a Common Motif. Nat. Struct. Mol. Biol.. 12 (12), 1094 

(2005). 

A Forster, E Masters, F Whitby, H Robinson, C Hill. The 1.9 

Angstrom Structure of a Proteasome-11S Activator Complex 

and Implications for the Proteasome-Pan/PA700 Interactions. 

Mol. Cell. Bio.. 18, 589 (2005). 

J Gorman, L Shapiro. Crystal Structures of the Tryptophan 

Repressor binding Protein WrbA and complexes with Flavin 

Mononucleotide. Protein Sci.. 14, 3004-3012 (2005). 

M Hahn, M Nicholson, J Pyrdol, K Wucherpfennig. Unconventional 

Topology of Self Peptide-Major Histocompatibility Complex 

Binding by a Human Autoimmune T Cell Receptor. Nat. 

Immunol.. 6, 490-496 (2005). 

Y Im, S Raychaudhuri, W Prinz, J Hurley. Structural Mechanism 

for Sterol Sensing and Transport by OSBP-Related Proteins. 

Nature. 437, 154-158 (2005). 

S Long, E Campbell, R MacKinnon. Crystal Structure of a 

Mammalian Voltage-Dependent Shaker Family K+ Channel. 

Science. 309, 897 (2005). 

S Long, E Campbell, R MacKinnon. Voltage Sensor of Kv1.2: 

Structural Basis of Electromechanical Coupling. Science. 309, 

903 (2005). 

I Mirza, I Nazi, M Korczynska, G Wright, A Berghuis. Crystal 

Structure of Homoserine Transacetylase from Haemophilus 

Influenzae Reveals a New Family of alpha/beta-Hydrolases. 

Biochemistry. 44, 15768-15773 (2005). 

M Nicholson, M Hahn, K Wucherpfennig. Unusual features of 

Self-Peptide/MHC Binding by Autoimmune T Cell Receptors. 

Immunity. 23 (4), 351-360 (2005). 

J Wang, K Stieglitz, J Cardia, E Kantrowitz. Structural Basis for 

Ordered Substrate Binding and Cooperativity in Aspartate 

Transcarbamoylase. Proc Natl Acad Sci USA. 102, 8881-8886 

(2005). 

H Wang, Y Liu, Y Chen, H Robinson, H Ke. Multiple Elements 

Jointly Determine Inhibitor Selectivity of Cyclic Nucleotide 

Phosphodiesterases 4 and 7. J. Biol. Chem.. 280, 30949 

(2005). 
C Zhan, E Fedorov, W Shi, U Ramagopal, R Thirumuruhan, B 

Manjasetty, S Almo, A Fiser, M Chance, A Fedorov. The ybeY 

Protein from Escherichia coli is a Metalloprotein. Acta Cryst. F. 

61 (11), 959-963 (2005).

NSLS Staff

J Ablett. High-Brightness Hard X-ray Scanning Nano-Probes at 

NSLS II. Nucl. Instrum. Meth. B. 241, 238-241 (2005). 

T Beetz, M Howells, C Kao, J Kirz, E Lima, T Mentes, H Miao, 

C Sanchez-Hanke, D Sayre, D Shapiro. Apparatus for X-ray 

Diffraction Microscopy and Tomography of Cryo Specimens. 

Nucl. Instrum. Meth. A. 545 (1-2), 459-468 (2005). 

J Bengtsson. Control of Dynamic Aperture for Synchrotron 

Light Sources. Proceedings of the 2005 Particle Accelerator 

Conference, Knoxville Tennessee, Vol , p. 1670-1672, 

sponsored by IEEE. (2005). 

R Bindu, S Pandey, A Kumar, S Khalid, A Pimpale. Local Distortion 

of Mno6 Octahedron in La1-Xsrxmno3+Delta (X=0.1-0.9): An 

Exafs Study. J. Phys.: Condens. Matter. 17 (41), 6393-6404 

(2005). 

A Blednykh, S Krinsky, B Podobedov, J Rose, N Towne. Harmonic 

Cavity Performance for NSLS-ll. Particle Accelerator 2005, p. 

2544-2546, (2005). 

Y Cai, H Mao, P Chow, J Tse, Y Ma, S Patchkovskii, J Shu, V 

Struzhkin, R Hemley, et al.. Ordering of Hydrogen Bonds in 

High-Pressure Low-Temperature H2O. Phys. Rev. Lett.. 94, 

025502 (2005). 

A Cavalieri, D Fritz, S Lee, P Bucksbaum, D Reis, J Rudati, D Mills, 

P Fuoss, G Stephenson, et al.. Clocking Femtosecond X-rays. 

Phys. Rev. Lett.. 94, 114801 (2005). 

S Chakraborty, B Sahoo, I Teraoka, L Miller, R Gross. EnzymeCatalyzed Regioselective Modification of Starch Nanoparticles. 

Macromolecules. 38 (1), 61-68 (2005). 

K Chalut, V Litvinenko, I Pinayev, S Khalid, A Pimpale. Method of 

Phase-Space Tomography of Rapidly Evolving E Beams. Phys. 

Rev. ST AB. 8 (10), 102802 (2005). 

O Chmaissem, B Dabrowski, S Kolesnik, J Mais, J Jorgenson, S 

Short, C Botez, P Stephens. Effects of A-Site Ordering on the 

Structures and Properties of La1-xBaxMnO3(X~0.5). Phys. Rev. 

B. 72, 104426 (2005). 

M Croft, Z Zhong, N Jisrawi, I Zakharchenko, R Holtz, Y Gulak, J 

Skaritka, T Fast, K Sadananda, T Tsakalakos. Strain Profiling of 

Fatigue Crack Overload Effects Using Energy Dispersive X-Ray 

Diffraction. Int. J. Fatigue. 27, 1408-1419 (2005). 

C Foerster, J Hu, E Haas. Results of Vacuum Pump Oil Testing 

to Minimize Oil Waste at the NSLS. American Vacuum Society 

Symposium, Vol , p. 1, sponsored by NSLS. (2005). 

D Fong, C Cionca, Y Yacoby, G Stephenson, J Eastman, P Fuoss, 

S Streiffer, C Thompson, R Clarke, et al.. Direct Structural 

Determination in Ultrathin Ferroelectric Films by Analysis of 

Synchrotorn X-ray Scattering Measurements . Phys. Rev. B. 71, 

144112 (2005). 

K Gaffney, A Lindenberg, J Larsson, K Sokolowski-Tinten, C 

Blome, O Synnergren, J Sheppard, C Caleman, A MacPhee, 

et al.. Observation of Structural Anisotropy and the Onset of 

Liquidlike Motion During the Nonothermal Melting of InSb. Phys. 

Rev. Lett.. 95, 125701 (2005). 

A Ganjoo, H Jain, S Khalid, C Pantano. Structural Modification of 

Ge–Se Amorphous Films with the Addition of Sb. Philos. Mag. 

Lett.. 85 (10), 503-512 (2005). 

P Glans, T Learmonth, K Smith, T Valla, P Johnson, S Hulbert, 

W McCarroll, M Greenblatt. Charge-Density-Wave Gap in the 

Quasi-Two-Dimensional Conductor Na0.9Mo6O17 Measured 

by Angle-Resolved Photoemission Spectroscopy. Phys. Rev. B. 

72, 035115 (2005). 

Y Guan, Z Dios, D Arena, L Cheng, W Bailey. Transmission-Mode 

X-ray Magnetic Circular Dichroism Characterization of Moment 

Alignment in Tb-Doped Ni81Fe19. J. Appl. Phys.. 97, 10A719 

(2005). 

E Haas, R Scheuerer, E Losee. Vortex Tube Machining Improves 

Safety While Reducing Environmental Waste. Mod. Mach. 

Shop. 78 (4), 54 (2005). 

M Hasnah, C Parham, E Pisano, Z Zhong, O Oltulu, D Chapman. 

Mass Density Images from the Diffraction Enhanced Imaging 

Technique. Med. Phys.. 32, 549 (2005). 

M Hasnah, C Parham, E Pisano, Z Zhong, O Oltulu, D Chapman. 

Mass Density Images from the Diffraction Enhanced Imaging 

Technique. Phys. Med. Biol.. 32, 549-552 (2005). 

G Jacobs, S Ricote, P Patterson, U Graham, A Dozier, S Khalid, E 

Rhodus, B Davis. Low Temperature Water-Gas Shift: Examining 

the Efficiency of Au as a Promoter for Ceria-Based Catalysts 

Prepared by CVD of a Au Precursor. Appl. Catal. A. 292, 229-

243 (2005). 

T Kajander, A Cortajarena, E Main, S Mochrie, L Regan. A New 

Folding Paradigm for Repeat Proteins. J. Am. Chem. Soc.. 127, 

10188-10190 (2005). 

H Kim, C Detavenier, O van der Staten, S Rossnagel, A Kellock, 

D Park. Robust TaNx Diffusion Barrier for Cu-Interconnnect 

Technology with Subnanometer Thickness by Metal-Organic 

Plasma-Enhanced Atomic Layer Deposition. J. Appl. Phys.. 98, 

014308 (2005). 

S Kramer, J Bengtsson. Dynamic Aperture Optimization for Low 

Emittance Light Sources. Proceedings of the 2005 Particle 

Accelerator Conference, Knoxville Tennessee, Vol , p. 3378-

3380, sponsored by IEEE. (2005). 

S Krinsky. Transverse Impedance of a Smooth Flat Taper. Phys. 

Rev. ST AB. 8, 124403 (2005). 

S Kwak, E DiMasi, Y Han, J Aizenberg, I Kuzmenko. Orientation 

and Mg Incorporation of Calcite Grown on Functionalized SelfAssembled Monolayers: A Synchrotron X-ray Study. Cryst. 

Growth Des.. 5 (6), 2139-2145 (2005). 

J Li, J Williams, Z Zhong, K Kuettner, M Aurich, J Mollenhauer, 

C Muehleman. Reliability of Diffraction Enhanced Imaging 

for Assessment of Cartilage Lesions, Ex Vivo. Osteoarthr. 

Cartilage. 13, 187-197 (2005). 

A Lindenberg, J Larsson, K Sokolowski-Tinten, K Gaffney, G 

MacPhee, D Weinstein, D Lowney, T Allison, T Matthews, et al.. 

Atomic-Scale Visualization of Inertial Dynamics. Science. 308, 

392 (2005). 

R Lobo, J LaVeigne, D Reitze, D Tanner, Z Barber, E Jacques, 

P Bosland, M Burns, G Carr. Photoinduced Time-Resolved 

Electrodynamics of Superconducting Metals and Alloys. Phys. 

Rev. B. 72, 024510 (2005). 

J Lu, G Rozgonyi, A Schonecker, A Gutjahr, Z Liu. Impact of 

Oxygen on Carbon Precipitation in Polycrystalline Ribbon 

Silicon. J. Appl. Phys.. 97, 033509 (2005). 

C Marrows, P Steadman, A Hampson, L Michez, B Hickey, N 

Telling, D Arena, J Dvorak, S Langridge. Probing Magnetic 

Ordering in Multilayers using Soft X-ray Resonant Magnetic 

Scattering. Phys. Rev. B: Condens. Matter. 72, 024421 (2005). 

L Michez, C Marrows, P Steadman, B Hickey, D Arena, J Dvorak, 

H Zhang, D Bucknall, S Langridge. Resonant X-ray Scattering 

from a Magnetic Multilayer Reflection Grating. Appl. Phys. Lett.. 

86, 112502 (2005). 

L Miller, R Smith. Synchrotrons Versus Globars, Point-Detectors 

Versus Focal Plane Arrays: Selecting the Best Source and 

Detector for Specific Infrared Microspectroscopy and Imaging 

Publications 7-29
7-30 NSLS Activity Report

Applications. Vib. Spectrosc.. 38 (1-2), 237-240 (2005). 

L Miller, M Ruppel, C Ott, R Smith, A Lanzirotti. Development and 

Applications of an Epifluorescence Module for Synchrotron -ray 

Fluorescence Imaging. Rev. Sci. Instrum.. 76, 066107 (2005). 

L Miller. National Synchrotron Light Source Activity Report 2004. 

Government Printing Office, Washington. Prepared for BNLNSLS. (2005). 

C Muehleman, J Li, K Kuettner, Z Zhong. Diffraction Enhanced Xray Imaging of Musculoskeletal Lesions. Osteoarthr. Cartilage. 

12, s117-s117 (2005). 

G Ozaydin, A Ozcan, Y Wang, K Ludwig, H Zhou, R Headrick, 

D Siddons. Real-Time X-ray Studies of Mo-Seeded SelfOrganized Si Nanodot Formation During Low Energy Ar+ Ion 

Bombardment. Appl. Phys. Lett.. 87, 163104 (2005). 

N Roberts, S Jaradat, L Hirst, Y Wang, S Wang, Z Liu, C Huang, 

J Bai, R Pinidak, H Gleeson. Biaxiality and Temperature 

Dependence of 3- and 4-layer Intermediate Smectic Phase 

Structures as Revealed by resonant X-ray Scattering. Europhys. 

Lett.. 72 (6), 976-982 (2005). 

F Sakamoto, H Iijima, K Dobashi, T Imai, T Ueda, T Watanabe, M 

Uesaka. Emittance and Energy Measurements of Low-Energy 

Electron Beam Using Optical Transition Radiation Techniques. 

Jpn. J. Appl. Phys., Part 1. 44 (3), 1485-1491 (2005). 

A Serganov, S Keiper, L Malinina, V Tereshko, E Skripkin, C 

Hobartnet, A Polonskaia, Z Dauter, A Jaschke, D Patel. Structural 

basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond 

formation. Nat. Struct. Mol. Biol.. 12 (3), 218-224 (2005). 

T Shin, M Ree. In Situ Infrared Spectroscopy Study on Imidization 

Reaction and Imidization-Induced Refractive Index and 

Thickness Variations in Microscale Thin Films of a Poly(amic 

ester). Langmuir. 21, 6081-6085 (2005). 

P Smith, I Koch, R Gordon, D Mandoli, B Chapman, K Reimer. Xray Absorption Near-Edge Structure Analysis of Arsenic Species 

for Application to Biological Environmental Samples. Environ. 

Sci. Tech.. 39, 248-254 (2005). 

S Stadler, D Minott, D Harley, J Craig, M Khan, I Dubenko, N Ali, K 

Story, J Dvorak, et al.. Element-Specific Magnetic Properties of 

Co2MnSi Thin Films. J. Appl. Phys.. 97, 10C302 (2005). 

M Teng, Z Zhong. Use of Diffraction Enhanced Imaging to 

Determine the X-ray Refractive Indices of Various Tissues at 

Biologically-Relevant Energies. The J. of Young Investigators. 

12, online (2005). 

A Vahedi-Faridi, V Stojanoff, J Yeh. The Effects of Flash-Annealing 

on Glycerol Kinase Crystals. Acta Cryst. D. 61 (7), 982-989 

(2005). 

E Vescovo, H Kim, J Ablett, S Chambers. Spin-polarized 

Conduction in Localized Ferromagnetic Materials: The Case of 

Fe3O4 on MgO(100). J. Appl. Phys.. 98, 084507 (2005). 

A Wagner, M Aurich, N Sieber, M Stoessel, W Wetzel, K Schmuck, 

M Lohmann, B Reime, J Metge, et al.. Options and Limitations 

of Joint cartilage Imaging: DEI in Comparison to MRI and 

Sonography. Nucl. Instrum. Meth. A. 548, 47-53 (2005). 

Q Wang, A Kretlow, M Beekes, D Naumann, L Miller. In Situ 

Characterization of Prion Protein Structure and Metal 

Accumulation in Scrapie-Infected Cells by Synchrotron Infrared 

and X-ray Imaging. Vib. Spectrosc.. 38, 61-69 (2005). 

Q Wang, W Sanad, L Miller, A Voigt, K Klingel, R Kandolf, K Stangl, 

G Baumann. Infrared Imaging of Compositional Changes in 

Inflammatory Cardiomyopathy. Vib. Spectrosc.. 38, 217-222 

(2005). 

M Wernick, L Chapman, O Oltulu, Z Zhong. Imaging Method Based 

on Attenuation, Refraction and Ultra-small-angle-scattering of 

X-rays. US Patent No. US 6,947,521 B2. (2005). 

M Wernick, J Brankov, D Chapman, Y Yang, E Pisano, C Parham, 

C Muehleman, Z Zhong, M Anastasio. Physical Model of Image 

formation in Multiple-Image Radiography. SPIE: Developments 

in X-ray Tomography IV, Vol 5535, p. 369-379, sponsored by 

SPIE . (2005). 

B Wood, K Bambery, L Miller, M Quinn, L Chiriboga, M Diem, 

D McNaughton. Infrared Imaging of Normal and Diseased 

Cervical Tissue Sections. Biomedical Applications of Micro- and 

Nanoengineering II, Vol 5651, p. 78-84, sponsored by SPIE--

The International Society for Optical Engineering. (2005). 

H Yang, T Shin, L Yang, K Cho, C Ryu, Z Bao. Effect of Mesoscale 

Crystalline Structure on the Field-Effeft Mobility of Regioregular 

Poly(3-hexyl thiophene) in Thin-Film Transistors. Adv. Func. 

Mater.. 15 (4), 671-676 (2005). 

L Yang, M Fukuto. Modulated Phase of Phospholipids with a 

Two-Dimensional Square Lattice. Phys. Rev. E. 72, 010901(R) 

(2005). 

H Yang, T Shin, M Ling, K Cho, C Ryu, Z Bao. Conducting AFM 

and 2D GIXD Studies on Pentacene Thin Films. J. Am. Chem. 

Soc.. 127, 11542-11543 (2005). 

A Yang, Z Chen, X Zuo, D Arena, J Kirkland, C Vittoria, V Harris. 

Cation-Disorder-Enhanced Magnetization in Pulsed-LaserDeposited CuFe2O4 Films. Appl. Phys. Lett.. 86, 252510 

(2005). 

T Yuasa, H Sugiyama, Z Zhong, A Maksimenko, F Dilmanian, 

T Akatsuka, M Ando. High-Pass-Filtered Diffraction 

Microtomography by Coherent Hard X rays for Cell Imaging: 

Theoretical and Numerical Studies of the Imaging and 

Reconstruction Principles. J. Opt. Soc. Am. A. 22 (12), 2622-

2634 (2005). 

I Zegkinoglouo, J Stempfer, C Nelson, P Hill, J Chakhalian, 

C Bernhard, J Lang, G Srajer, H Fukazawa, et al.. Orbitial 

Ordering Transition in Ca2RU)4 Observed with Resonant X-ray 

Diffraction. Phys. Rev. Lett.. 95, 136401 (2005). 

Z Zhu, T Andelman, M Yin, T Chen, S Ehrlich, S O‘Brien, R 

Osgood, Jr.. Synchrotron X-ray Scattering of ZnO Nanorods: 

Periodic Ordering and Lattice Size. J. Mater. Res.. 20 (4), 1033 

(2005).