NATIONAL SYNCHROTRON LIGHT SOURCE

ACTIVITY REPORT 2006
BNL-77450-2006

UC400

(General Energy Research)

Disclaimer

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from Feature Highlight: “Modeling Mineral Formation with X-rays,” page 2-8

Cover Images

from Feature Highlight: “Liquid Alloy Shows Solid-Like Crystal Structure at Surface,” 

page 2-24

from Science Highlight: “Characterizing the Surfaces of Carbon Nanotube Fuel Cell 

Catalysts,” page 2-30

from Feature Highlight: “Plant Studies Reveal How, Where Seeds Store Iron,” 

page 2-10

from Science Highlight: “Structural Insight into Antibiotic Fosfomycin Biosynthesis by a 

Mononuclear Iron Enzyme,” page 2-68

from Science Highlight: “Effect of Te Precipitates on the Performance of CdZnTe (CZT) 

Detectors” page 2-94

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NATIONAL SYNCHROTRON LIGHT SOURCE

2006 ACTIVITY REPORT

Lisa M. Miller

managing editor

Kendra J. Snyder

science editor

Nancye A. Wright & Stephen A. Giordano

design & layout

managed for the .S.Depar U tment of Ener gy

byBrookhaven Science Associates, a compy a

founded by Stony Brook University and Batt

The National Synchrotron Light Source Department is supported by the

Offi ce 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 ................................................................................................................................2-30

 Condensed Matter Physics ..................................................................................................................2-38

 Geology and Environmental Science...................................................................................................2-52

 Life Science .........................................................................................................................................2-62

 Materials Science.................................................................................................................................2-88

 Soft Condensed Matter and Biophysics...............................................................................................2-98

YEAR IN REVIEW 

 411th Brookhaven Lecture: 'Shining Light on the Cause of Alzheimer's Disease'...................................3-3

 NSLS One of 10 BNL Organizations to Achieve OHSAS 18001 Registration .......................................3-3

 Joint Photon Sciences Institute Established ..........................................................................................3-4

 NSLS Examines Pieces of Star Dust .....................................................................................................3-4

 Two NSLS Staff Members Awarded for Jobs Well Done........................................................................3-5

 NSLS Researchers Produce a Praiseworthy Poster..............................................................................3-7

 General Barry McCaffrey Tours the NSLS .............................................................................................3-7

 NSLS Student-Researcher Talks at The March APS Meeting ...............................................................3-8

 New Wrinkle in the Mystery of High-Tc Superconductors.......................................................................3-9

 Cerium Oxide Nanotubes Get Noticed.................................................................................................3-10

 Future Crystallographers Attend RapiData 2006 at NSLS...................................................................3-10

 Students Experience the NSLS Via Webcast ...................................................................................... 3-11

 NSLS' Youngest Scientists Learn from Light on 'Take our Daughters and Sons to Work' Day ..........3-12

 NSLS Biophysict Lisa Miller Awarded Tenure ......................................................................................3-13

 Quite a Remarkable Spring: Notes From the 2006 NSLS-CFN Joint Users' Meeting .........................3-14

 Bob Sweet, The 2006 UEC Community Service Award Recipient.......................................................3-17

 Energy Secretary, Under Secretary for Energy Tour NSLS .................................................................3-18

 Crystal Growth Workshop Has Crystallizing Results ...........................................................................3-19

 Future 'Poets,' Students Learn About Nanoscience at BNL.................................................................3-20

 In Memoriam: David Murray Zehner ....................................................................................................3-21

 In Memoriam: Julian David Baumert....................................................................................................3-22

 In Memoriam: Elizabeth A. Hicks .........................................................................................................3-23

 Jean Jakoncic Wins Esteemed Student Lecturer Award......................................................................3-24
TABLE OF CONTENTS

 NSLS Summer Sunday Draws 650 Visitors to Facility......................................................................... 3-24

 1,000 Injury-Free Days...and Counting ................................................................................................ 3-26

 Hats Off to the 2006 NSLS Summer Students..................................................................................... 3-26

 NSLS, NSLS-II Staff Celebrate at Picnic and Service Awards............................................................. 3-28

 Chi-Chang Kao Named Chair of the NSLS.......................................................................................... 3-30

 Update on the X27A Micro-Spectroscopy Facility Beamline................................................................ 3-30

 Richard Biscardi Wins Sitewide Safety Steward Award....................................................................... 3-31

 418th Brookhaven Lecture 'Bright Photon Beams: Developing New Light Sources'............................. 3-32

 BNL Wins R&D 100 Award for X-ray Focusing Device ........................................................................ 3-33

 Short Course: XAFS Studies of Nanocatalysis and Chemical Transformations .................................. 3-33

 NSLS Users Recognized ..................................................................................................................... 3-34

 Nanoscience Safety Highlighted .......................................................................................................... 3-36

 Chi-Chang Kao Among Five Named APS Fellows............................................................................... 3-36

 2006 NSLS Tours ................................................................................................................................. 3-37

 2006 NSLS Seminars .......................................................................................................................... 3-39

 2006 NSLS Workshops........................................................................................................................ 3-43

 

FACILITY REPORT

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

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

 Accelerator Division Report.................................................................................................................... 4-7

 Operations and Engineering Division Report....................................................................................... 4-10

 User Science Division Report .............................................................................................................. 4-12

 NSLS-II Report..................................................................................................................................... 4-16

 User Administration Report .................................................................................................................. 4-18

 Safety Report ....................................................................................................................................... 4-21

 Building Administration Report............................................................................................................. 4-23

 

FACTS AND FIGURES 

 Beamline Guide .....................................................................................................................................5-3

 Linac and Booster Parameters ............................................................................................................ 5-11

 VUV Storage Ring Parameters ............................................................................................................5-12

 X-Ray Storage Ring Parameters .........................................................................................................5-13

 2006 Ring Performance and Usage.....................................................................................................5-14

 

PUBLICATIONS 

 NSLS Users ...........................................................................................................................................6-4

 NSLS Staff .........................................................................................................................................6-34
INTRODUCTION
IN TRODUC TION

As the NSLS continued its legacy of scientific 

excellence in 2006, I was honored to be named 

Chairman of the department after former Chair, 

Steve Dierker, stepped down to lead the development of NSLS-II. The NSLS is a very special place 

with a long and exemplary tradition of innovation 

in accelerator con cepts and technology, as well 

as in the development of experimental techniques 

and applications of synchrotron radiation. Moreover, during the last quarter century, the NSLS has 

been one of the most widely used and productive 

scientific facilities in the world. The year 2006 was 

no exception, with a record-high 921 publications 

reported by our users and staff.

An impressive array of highlights is included in 

this Activity Report to illustrate this extraordinary 

productivity and its impact to science, technology, 

and society. For example, one user group investigated new materials for use in lithium-ion batteries, the most common type of battery found in 

portable electronics and the most promising type 

for hybrid cars. Another user group determined the 

atomic crystal structure and functional mechanism 

of an enzyme essential for eliminating unwanted, 

non-nutritional compounds such as drugs, industrial chemicals, and toxic compounds from the 

body. And in yet another interesting study, NSLS 

staff and users made improvements to microbeam 

radiation therapy, an experimental form of radiation therapy that has been under investigation for 

many years.

As always, the success of these research projects 

depends on the performance of the facility. Thanks 

to the dedication and hard work of our staff, both 

storage rings were in top form again this year 

— reliability was 94.3 percent for the x-ray ring 

and 97 percent for the VUV-IR ring. In addition, 

we have made significant progress this year in 

improving machine performance and reliability, 

including klystron replacement, improving diagnostics in the injection system, conducting an orbit 

stability study, and commissioning the new X25 

in-vacuum mini-gap undulator. Finally, to ensure 

the long-term reliability of the NSLS accelerator 

complex, Accelerator and Operation and Engineering Division staff were charged to assess the 

reliability risks and risk mitigation plans in preparation for an external review.

In the area of safety, I am very pleased that there 

were no reportable occurrences related to environmental, safety, or health issues in 2006. In addition, NSLS users and staff have worked more than 

1,000 days without a lost-time injury, and counting. This is a remarkable record and we should 

all be proud of this accomplishment. But, we have 

to continue to be vigilant and make sure safety 

is integrated into everything that we do. A major 

safety initiative lunched this year was the implementation of an Electri cal Equipment Inspection 

program at the NSLS. The goal of the program is 

to review and inspect all electrical equip ment and 

installations to ensure they are free from electrical 

shock or fire.

Additionally, many beamline upgrade projects 

were initiated or completed this year. The most 

significant ones were the X25 beamline upgrade 

and the construction of the X9 small-angle x-ray 

scattering (SAXS) beamline. The X25 upgrade 

was critically important for the NSLS to meet 

the growing demand from the macromolecular 

crystallography user community for high-brightness beamlines, which are essential for tackling 

the most challenging scientific problems. X9 will 

be a new undulator-based beamline optimized 

to provide SAXS and grazing incidence SAXS 

capabilities for nano- and bioscience studies that 

require high flux and/or small beam. The beamline 

is a collaboration between the NSLS and Center 

for Functional Nanomaterials (CFN). In 2006, with 

the collaboration of the Case Center for Synchrotron Biosciences, the existing X9 beamlines were 

relocated to X3 to make room for the construction 

of the new X9 beamline. Chi-Chang Kao

CHAIRMAN'S INTRODUCTION

Chi-Chang Kao

Chairman, National Synchrotron Light Source

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In mid-May, the first joint NSLS-CFN Users’ Meeting was carried out successfully, making way for 

close collaboration between the two facilities when 

the CFN opens next year. Progress on the NSLS-II 

also continues to press forward and we have begun to plan for the eventual transition to the new 

facility, which will provide x-rays more than 10,000 

times brighter than those produced at the NSLS. 

Finally, with extensive input from the user community, NSLS staff, and Brookhaven research departments, we have developed a five-year strategic 

plan for the NSLS. The plan identifies a number 

of exciting scientific opportunities, improvements 

needed for better accelerator performance, and 

upgrades for beamlines, detectors, and infrastructure at the NSLS. We believe that this plan 

will keep scientific productivity up and grow new 

scientific communities at the NSLS, as well as 

allow us to smoothly transition the user scientific 

programs to the NSLS-II.

1-4
IN TRODUC TION

This past year has seen both challenges and 

fantastic new opportunities for the user community 

at the NSLS.

The fantastic new opportunities are clear and 

abundant. We now have a five-year strategic plan 

for new development and continued operation of 

the NSLS. The NSLS continues to be an extremely 

productive facility, and the UEC is delighted at 

how NSLS Chair Chi-Chang Kao has consulted 

widely within the user community to develop a 

five-year plan for strategic upgrades and continued operation of the facility. The NSLS-II project, 

led by Associate Lab Director Steve Dierker, has 

done very well in its Department of Energy (DOE) 

reviews and will hopefully soon receive Critical 

Decision-1 (CD-1) approval, which in DOE lingo 

gives a go-ahead to launch the detailed design of 

the facility. 

We also held the first joint user meeting between 

the NSLS and Brookhaven’s Center for Functional 

Nanomaterials (CFN), for which the building is 

near completion. The joint user meeting is an 

important step toward the close collaboration of 

the two facilities. The CFN, led by Emilio Mendez, 

promises to provide capabilities and research foci 

that are complementary to those at the NSLS. 

Together, all of these developments give a clear 

path to an exciting future of synchrotron radiation 

research at Brookhaven!

Chris Jacobsen

USERS' EXECUTIVE COMMITTEE REPORT

Chris Jacobsen

Stony Brook University

However, with opportunities come challenges! 

One of the largest of these faced in the past 

year involved congressional support for scientific 

research in general, and DOE user facilities in 

particular. As you likely know, Congress did not 

complete its usual budget process in 2006, with 

the exceptions of the departments of Defense and 

Homeland Security. This left science funding at 

the budget levels enacted in late 2005 for FY2006, 

and unfortunately, FY2006 was not a particularly memorable vintage for science support. The 

good news is that you, the user community, have 

spoken up with unprecedented vigor about this, 

and Congress appears to be listening. As we look 

at the FY2007 budget and the years to follow, we 

need to continue to educate our elected representatives about the benefits that are provided to our 

society and our economy by scientific investigation 

including research done at DOE user facilities like 

the NSLS.

We face another interesting challenge as the 

NSLS-II project progresses: the formation of scientific research teams associated with particular 

beamlines at the new facility. In early 2007, the 

final draft of the conceptual design report will be 

available, which will describe the projected capabilities of NSLS-II, and we can expect a workshop 

in mid-2007 to launch the process leading to 

letters of intent for beamlines. This process will 

include lots of discussion about access modes, as 

we seek ways to allow scientific and technical innovators from the user community to play significant roles at NSLS-II.

Let us rise to the challenges to fully realize the 

opportunities!

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SCIENCE HIGHLIGHTS
2-3

SCIENCE HIGHLIGHTS

SCIENCE AT THE NSLS

Kendra Snyder

NSLS Science Writer

As the new science writer at the NSLS, I’m excited 

to introduce this year’s Science Highlights and 

Feature Highlights sections.

Journalists are lifetime students; by 5 p.m. each 

day, they’ve become a sort of mini-expert in a 

topic that might have been completely foreign to 

them that morning. Being the NSLS science 

writer is no exception. Out of more than 800 

articles published by NSLS users each year in 

peer-reviewed journals, about 50 are selected to 

appear on the NSLS homepage. I’m exposed to 

a number of those papers every month, and as a 

result, my knowledge of everything from nanoscience to condensed matter physics has greatly 

increased in the short time I’ve been here: I never 

thought I’d be writing about things like anisotropy, 

ferromagnetism, and biomineralization, let alone 

have those terms in my vocabulary. 

Yet, there’s so much more out there. The most 

amazing part of this job is knowing that the highlights that appear on the following pages represent 

just a small fraction of the science performed at 

the NSLS in the chemical, material, environmental, 

physical, and life sciences. Keep that in mind as 

you read this year’s Science Highlights – scientistwritten summarized versions of published papers 

– and Feature Highlights, which are written by 

Brookhaven Lab science writers and targeted at a 

general audience. 

Because I joined the NSLS in June 2006, I cannot take credit for all of the editing and writing 

involved in creating these sections. I would like to 

acknowledge Laura Mgrdichian, Lisa Miller, Karen 

McNulty Walsh, and Kay Cordtz for their work. And 

of course, thank you to all of the wonderful NSLS 

scientists and users who have welcomed me to 

this unique facility and helped me understand the 

even more unique work they accomplish. 

I look forward to another great year of working 

Kendra Snyder with all of you. 
2-4

SCIENCE HIGHLIGHTS

FEATURE HIGHLIGHTS

 Modeling Mineral Formation with X-rays ....................................................................................................................... 2-8

 Plant Studies Reveal How, Where Seeds Store Iron .................................................................................................. 2-10

 A 'Ferroelectric' Material Reveals Unexpected, Intriguing Behavior............................................................................ 2-12

 Structure of an E. Coli Membrane Protein................................................................................................................... 2-13

 Measuring Synthesis Intermediates for Better Materials............................................................................................. 2-14

 New X-ray Delivery Method Could Improve Radiation Therapy.................................................................................. 2-16

 The Unusual Insulating Properties of a Superconductor............................................................................................. 2-18

 At the NSLS, Scientists Working Toward Better Batteries........................................................................................... 2-19

 Structure of a Molecular-Scale Circuit Component ..................................................................................................... 2-20

 Nanoparticle Assembly Enters the Fast Lane ............................................................................................................. 2-21

 Visualizing the Immune System’s Missing Link........................................................................................................... 2-22

 Liquid Alloy Shows Solid-Like Crystal Structure at Surface ........................................................................................ 2-24

 Breaking the Bounds of Plasticity................................................................................................................................ 2-26

 X-ray Analysis Method Cracks the 'Lipid Phase Problem'.......................................................................... 2-27

 Scientists Take 'Snapshots' of Enzyme Action............................................................................................................ 2-28

CHEMICAL SCIENCE

 Characterizing the Surfaces of Carbon Nanotube Fuel Cell Catalysts........................................................................ 2-30

 R.V. Hull, L. Li, Y. Xing, and C.C. Chusuei

 Platinum Monolayer on Non-Noble Metal-Noble Metal Core-Shell Nanoparticles 

 Electrocatalysts for O2 Reduction................................................................................................................................ 2-32

 J. Zhang, F.H.B. Lima, M.H. Shao, K. Sasaki, J.X. Wang, J. Hanson, and R.R. Adzic

 Reductive Coupling of Carbon Monoxide Molecules Over Oxygen Defected UO2 (111) Single 

 Crystal and Thin Film Surfaces ................................................................................................................................... 2-34

 S.D. Senanayake, G.I.N. Waterhouse, H. Idriss, and T.E. Madey

 Sulfur K-Edge XANES and TR-XRD Studies of Pt-Bao/Al2O3 Lean Nox Trap Catalysts: 

 Effects of Barium Loading on Desulfation ................................................................................................................... 2-36

 D.H. Kim, J. Szanyi, J.H. Kwak, T. Szailer, J.C. Hanson, C. Wang, and C.H.F. Peden

CONDENSED MATTER PHYSICS

 Charge Order and Superconductivity in a High-Temperature Superconductor........................................................... 2-38

 C.C. Homes, S.V. Dordevic, G. Gu, Q. Li, T. Valla, and J.M. Tranquada

 Observation of Nitrogen Polarization in Fe-N Using Soft X-ray Magnetic Circular Dichroism..................................... 2-40

 C. Sánchez-Hanke, R. Gonzalez-Arrabal, and R.A Lukaszew
2-5

SCIENCE HIGHLIGHTS

 Spin-Lattice Interaction in the Quasi-One-Dimensional Helimagnet LiCu2O2.............................................................. 2-42

 L. Mihály, B. Dóra, A. Ványolos, H. Berger, and L. Forró

 Large Induced Magnetic Anisotropy in Pulsed Laser Deposited Manganese Spinel Ferrite Films ............................. 2-44

 X. Zuo, A. Yang, S.-D. Yoon, J.A. Christodoulides, J. Kirkland, V.G. Harris, and C. Vittoria

 Observation of Surface Layering in a Nonmetallic Liquid ......................................................................................... 2-46

 H. Mo, G. Evmenenko, S. Kewalramani,K. Kim, S.N. Ehrlich, and P. Dutta

 Coherent THz Synchrotron Radiation from a Storage Ring with High Frequency RF System.................................... 2-48

 F. Wang, D. Cheever, M. Farkhondeh, W. Franklin, E. Ihloff, J. van der Laan, B. McAllister, R. Milner, 

 C. Tschalaer, D. Wang, D.F. Wang, A. Zolfaghari, T. Zwart, G.L. Carr, B. Podobedov, and F. Sannibale

 Disturbing Superconductivity with Light....................................................................................................................... 2-50

 R.P.S.M. Lobo, D.B. Tanner, and G.L. Carr

GEOLOGY AND ENVIRONMENTAL SCIENCE

 Strontium Speciation During Reaction of Kaolinite with Simulated Tank-Waste Leachate: 

 Bulk and Microfocused EXAFS Analysis ..................................................................................................................... 2-52

 S. Choi, P.A. O’Day, N.A. Rivera, K.T. Mueller, M.A. Vairavamurthy, S. Seraphin, and J. Chorover

 Metal(loid) Diagenesis in Mine-Impacted Sediments of Lake Coeur d’alene, Idaho .................................................. 2-54

 G.R. Toevs, M.J. Morra, M.L. Polizzotto, D.G. Strawn, B.C. Bostick, and S. Fendorf

 Phosphorus Speciation in Manure and Manure-Amended Soils Using XANES Spectroscopy................................... 2-56

 S. Sato, D. Solomon, C. Hyland, Q.M. Ketterings, and J. Lehmann

 Spatial and Temporal Variability of Arsenic Solid-State Speciation in Historically Lead 

 Arsenate Contaminated Soils ...................................................................................................................................... 2-58

 Y. Arai, A. Lanzirotti, S.R. Sutton, M. Newville, J. Dyer, and D.L. Sparks

 Quantitative Determination of Absolute Organohalogen Concentrations in Environmental 

 Samples by X-ray Absorption Spectroscopy .............................................................................................................. 2-60

 A.C. Leri, M.B. Hay, A. Lanzirotti, W. Rao, and S.C.B. Myneni

LIFE SCIENCE

 Structure of TonB in Complex with FhuA, E. Coli Outer Membrane Receptor ............................................................ 2-62

 P.D. Pawelek, N. Croteau, C. Ng-Thow-Hing, C.M. Khursigara, N. Moiseeva, M. Allaire, and J.W. Coulton

 A New Folding Paradigm for Repeat Proteins ............................................................................................................ 2-64

 T. Kajander, A.L. Cortajarena, E.R.G. Main, S.G.J. Mochrie, and L. Regan

 Structural Basis for Gene Regulation by a Thiamine Pyrophosphate-Sensing Riboswitch......................................... 2-66

 A. Serganov, A. Polonskaia, A. Tuân Phan, R.R. Breaker, and D.J. Patel

 Structural Insight into Antibiotic Fosfomycin Biosynthesis by a Mononuclear Iron Enzyme........................................ 2-68

 L.J. Higgins, F. Yan, P. Liu, H.-W. Liu, and C.L. Drennan

 Co-Localization of β-Amyloid Deposits and Metal Accumulation in Alzheimer’s Disease........................................... 2-70

 Q. Wang, T.P. Telivala, R.J. Smith, A. Lanzirotti, J. Miklossy, and L.M. Miller
2-6

 Structural Basis for the EBA-175 Erythrocyte Invasion Pathway of the Malaria 

 Parasite Plasmodium falciparum ................................................................................................................................ 2-72

 N.H. Tolia, E.J. Enemark, B. Kim Lee Sim, and L. Joshua-Tor

 Disulfi de Trapped Structure of a Repair Enzyme Interrogating Undamaged DNA Sheds 

 Light on Damaged DNA Recognition........................................................................................................................... 2-74

 A. Banerjee, W. Santos, and G.L. Verdine

 A Redox Reaction in Axon Guidance: Structure and Enzymatic Activity of MICAL ..................................................... 2-76

 M. Nadella, M.A. Bianchet, S.B. Gabelli, and L.M. Amzel

 Crystal Structures of Catalytic Complexes of the Oxidative DNA/RNA Repair Enzyme AlkB..................................... 2-78

 B. Yu, W.C. Edstrom, J. Benach, Y. Hamuro, P.C. Weber, B.R. Gibney, and J.F. Hunt

 Crystal Structure of Human Arginase I at 1.29 Å Resolution and Exploration of 

 Inhibition in the Immune Response............................................................................................................................. 2-80

 L. Di Costanzo, G. Sabio, A. Mora, P.C. Rodriguez, A.C. Ochoa, F. Centeno, and D.W. Christianson

 Mechanism of Activation for Transcription Factor PhoB Suggested by Different Modes of 

 Dimerization in the Inactive and Active States ............................................................................................................ 2-82

 P. Bachawat, G.V.T. Swapna, G.T. Montelione, and A.M. Stock

 RNA Silencing Suppressor p21 Adopts an Unusual siRNA-Binding Octameric Ring Architecture.............................. 2-84

 K. Ye and D.J. Patel

 Mechanism of DNA Translocation in a Replicative Hexameric Helicase..................................................................... 2-86

 E.J. Enemark and L. Joshua-Tor

MATERIALS SCIENCE

 Phase Stability in Ceria-Zirconia Binary Oxide Nanoparticles..................................................................................... 2-88

 F. Zhang, C.-H. Chen, J.M. Raitano, R.D. Robinson, I.P. Herman, J.C. Hanson, W.A. Caliebe, S. Khalid, and S.-W. Chan

 Size-Controlled Synthesis and Characterization of Thiol-Stabilized Gold Nanoparticles............................................ 2-90

 A.I. Frenkel, S. Nemzer, I. Pister, L. Soussan,T. Harris,Y. Sun, and M.H. Rafailovich

 Structure of Hydrated Zn2+ at the Rutile TiO2 (110) – Aqueous Solution Interface: Comparison of X-ray 

 Standing Wave, X-ray Absorption Spectroscopy and Density Functional Theory Results .......................................... 2-92

 Z. Zhang, P. Fenter, S.D. Kelly, J.G. Catalano, A.V. Bandura, J.D. Kubicki, J.O. Sofo, D.J. Wesolowski, 

 M.L. Machesky, N.C. Sturchio, and M.J. Bedzyk

 Effect of Te Precipitates on the Performance of CdZnTe (CZT) Detectors................................................................. 2-94

 G.A. Carini, A.E. Bolotnikov, G.S. Camarda, G.W. Wright, L. Li, and R.B. James

 Metallotropic Liquid Crystals: Surfactant Induced Order in Molten Metal Halides....................................................... 2-96

 J.D. Martin, C.L. Keary, T.A. Thornton, M.P. Novotnak, J.W. Knutson, and J.C.W. Folmer
2-7

SCIENCE HIGHLIGHTS

SOFT CONDENSED MATTER AND BIOPHYSICS

 Anti-Biofouling Properties of Comblike Block Copolymers with Amphiphilic Side Chains ........................................... 2-98

 S. Krishnan, R. Ayothi, A. Hexemer, J.A. Finlay, K.E. Sohn, R. Perry, C. K. Ober, E.J. Kramer, M.E. Callow, 

 J.A. Callow, and D.A. Fischer

 Miscibility in a Ternary Polymer System .................................................................................................................... 2-100

 S.E. Harton, T. Koga, F.A. Stevie, T. Araki, and H. Ade

 Study of the Microstructure of Polymorphic Interphases in Fiber Reinforced Polypropylene 

 Composites by Synchrotron IR Microspectroscopy and X-ray Microdiffraction......................................................... 2-102

 G. Ellis, M.A. Gómez, C. Marco, J. Torre, M. Cortázar, C. Riekel, and P. Dumas

 Nanoparticle-Polymer Complexation: Electrostatic Self-Assembly as a Route to Stable Dispersions 

 of Hybrid Nanocolloids .............................................................................................................................................. 2-104

 A. Sehgal, Y. Lalatonne, J.-F. Berret, and M. Morvan
2-8

MODELING MINERAL FORMATION WITH X-RAYS

Some of the hardest and sturdiest materials aren’t 

made in the factory; they’re made inside the bodies 

of animals. Biominerals are commonly used for 

support and protection, forming in teeth, bones, 

and shells in animals ranging from humans to mollusks. The cells in an animal’s body have special 

ways of controlling the sizes and shapes of these 

mineral compounds and incorporating organic 

materials into the mix, making many materials that 

are stronger, harder and more wear-resistant than 

rocks. The trick for scientists is to mimic these 

properties to repair bones and teeth and to find 

environmentally clean and strong materials for industrial uses. At the NSLS, a group of researchers 

from Brookhaven and the University of Florida are 

working toward that goal by studying the process 

of biomineralization.

“We’re trying to understand how those minerals 

come to form,” said NSLS physicist Elaine DiMasi. 

“They’re literally as common as seashells on the 

beach, and the elements they’re made from are 

very abundant, but synthetically, people have 

trouble making the particles small enough and getting control over the structure.” 

The researchers studied the biomineralization of 

calcium carbonate by creating a model system with 

an organic layer to mimic a cell boundary and a 

liquid designed to precipitate the mineral. Using 

this model, which was set up in a water trough, the 

team focused on three factors that control calcium 

carbonate growth: the presence of magnesium, the 

presence of polyacrylic acid (PAA), and the escape 

rate of carbon dioxide. 

These three factors were studied at beamline X22B 

using a special spectrometer that sends x-rays in 

at an angle and reflects them from different layers 

in the model system. This allowed the researchers 

to measure the thickness of the minerals as a function of time while alternating which controls are 

kept constant. 

“We tried to clarify whether these things are all 

generically the same kind of calcium carbonate 

inhibitor, or whether they act differently from one 

another,” DiMasi said. “What we discovered was 

each has a unique effect that we could differentiate 

quite clearly.”

For example, the researchers found that PAA, 

which mimics the presence of proteins, stabilizes 

the calcium carbonate in the amorphous stage, a 

disordered phase that is incorporated with water. 

The amount of time before this calcium carbonate 

film thins out and dissolves is longest with large 

amounts of PAA and shortest when there’s a small 

amount of the polymer in the system.

Another controlling factor, the carbon dioxide escape rate, was studied by altering the depth of the 

tray containing the model system. Carbon dioxide 

will diffuse from the system much more quickly 

with a shallow tray than a deeper one. The team 

found that this diffusion rate was the variable that 

controls mineral growth rate.

The final factor, the presence of magnesium, 

wasn’t found to change the rate of growth as some 

expected. Instead, its presence causes a delay, in 

when the calcium carbonate film starts to grow.

Using what they discovered about these three 

factors, the researchers put together a model of 

the early formation of calcium carbonate. It goes 

something like this: PAA has many negative charges associated with it, which pull in positive calcium ions required for the amorphous film to form. 

Because the calcium is already collected and being 

held by PAA, the rate of growth depends on the 

amount of available carbonate, which is produced 

by the diffusion of carbon dioxide. The more shallow the tray, the quicker carbonate is available and 

the faster the calcium carbonate amorphous film 

This image depicts the calcium carbonate biomineralization 

model studied by the research team. The black lines at the 

top represent the membrane, the network below it is the 

amorphous, hydrated mineral fi lm and the squiggly black 

line in the circle is the PAA molecule with its collection of 

calcium cations (red balls), which get released by the fi lm. 

The three-atom carbonates (black and blue balls) diffuse 

from the bottom right. Together, the calcium and carbonate 

form the mineral fi lm.
2-9

FEATURE HIGHLIGHTS

grows. The magnesium also is attracted to PAA 

because of its positive charge, and the ion fights 

against calcium for spots on the polymer. Calcium 

ultimately binds more strongly to PAA; however, 

the presence of magnesium in the system delays 

formation of the film as the two ions compete. 

“Previously people thought that magnesium and 

PAA were both inhibitors, that they both stop 

calcite from crystallizing from the amporphous precursor phase,” DiMasi said. “Our results show that 

they do different things and this model shows why. 

PAA is not just defeating calcite crystal formation; 

it’s actually stabilizing the amorphous phase by 

adding cations. And the magnesium is not interfering with crystal formation; it’s interfering with this 

polymer-prepping action that happens.”

The time-resolved measurements, and small size 

of the biomineralization system itself, make this a 

unique study, DiMasi said. 

“A lot of people in the field grow crystals and 

study them in great detail, but we’re looking at the 

stages before that,” DiMasi said. “Our film might 

be only 20 nanometers thick while we’re measuring it, and dissolve within 10 hours. If you gave our 

recipe to someone who needed to grow crystals 

big enough to look in a microscope, they would 

probably declare it a failure and rinse it down the 

sink.”

The group’s results were published in the July 27, 

2006 edition of Physical Review Letters.

The research was funded by the U.S. Department 

of Energy, the National Science Foundation, and 

the National Institutes of Health.

For more information, see: E. DiMasi, S. Kwak, F. 

Amos, M. Olszta, D. Lush, and L. Gower, "Complementary Control by Additivies of the Kinetics of 

Amorphous CaCO

3 Mineralization at an Organic 

Interface: In-Situ Synchrotron X-ray Observations," 

Phys. Rev. Lett., 97, 045503 (2006). 

— Kendra Snyder 
2-10

largely unexplored target for increasing the iron 

content of seeds. Such nutrient-rich seeds would 

benefit both human health and agricultural productivity.”

The researchers combined traditional mutant 

analysis (turning on and off the VIT1 protein) with 

a powerful x-ray imaging technique to create a map 

of where iron is localized in the seed. Guerinot 

was surprised by the finding because most studies 

on iron storage focus on the protein ferritin. This 

paper reveals how important it is to look beyond 

ferritin to understand how iron is stored by plants. 

The researchers say their study suggests that the 

stored iron in the vacuole is an important source 

of iron for developing seedlings. Seedlings that do 

not express the VIT1 protein grow poorly when iron 

is limited.

“We have demonstrated the usefulness of synchrotron x-ray fluorescence microtomography to 

look inside a seed,” says Guerinot. “This technique 

is noninvasive and requires no sample preparation. We think our work will open the way for many 

more biologists to use this technique to examine the spatial distribution of metals in samples 

of interest.” The imaging was carried out at the 

Department of Energy’s National Synchrotron Light 

Source at Brookhaven National Laboratory. 

Other authors on the paper include Sun A. Kim 

and Tracy Punshon, both postdoctoral fellows at 

Dartmouth, Antonio Lanzirotti of the University of 

Dartmouth College issued the following press 

release detailing the storage of iron in plant seeds. 

These findings, which could lead to ways to prevent iron deficiency and malnutrition, were discovered at the National Synchrotron Light Source. At 

beamline X26A, researchers used fluorescence 

tomography, an x-ray imaging technique that allows scientists to “see” the distribution of elements 

inside the seeds without destroying them. 

Dartmouth biologists are leading a research team 

that has learned where and how some plant seeds 

store iron, a valuable discovery for scientists 

working to improve the iron content of plants. This 

research helps address the worldwide issue of iron 

deficiency and malnutrition. Their findings were 

published in the November 24, 2006 edition of the 

journal Science.

The team found that iron is stored in the developing vascular system of the seed of Arabidopsis, a 

model plant used in research; in particular, iron is 

stored in the vacuole, a plant cell’s central storage site. The researchers also learned that this 

localization is dependent on a protein called VIT1, 

shown to transport iron into the vacuole.

Dartmouth Professor of Biological Sciences Mary 

Lou Guerinot, the principal investigator on the 

study, says, “Iron deficiency is the most common 

human nutritional disorder in the world today, afflicting more than three billion people worldwide. 

Most of these people rely on plants for their dietary 

iron. However, plants are not high in iron, and the 

limited availability of iron in the soil can limit plant 

growth. Our study certainly suggests that iron storage in the vacuole is a promising and, before now, 

PLANT STUDIES REVEAL HOW, WHERE SEEDS STORE IRON

Dartmouth researchers Sun A. Kim, Mary Lou 

Guerinot, and Tracy Punshon (photo credit, Joseph 

Mehling, Dartmouth College).

Rendered three-dimensional tomographic reconstruction 

of the iron (Fe) fl uorescence from a wild type Arabidopsis 

thaliana seed (approx. 100 μm wide seed). In this seed, 

the tomographic reconstruction demonstrates that Fe is 

localized around the embryonic provasculature of the radicle 

and cotyledons. Using fl uorescence microtomography, the 

research team demonstrated the vital role the gene vacuolar 

iron transporter 1 serves in controlling Fe homeostasis in 

plants.
2-11

FEATURE HIGHLIGHTS

Chicago, Liangtao Li and Jerry Kaplan from the 

University of Utah School of Medicine, José Alonso 

with North Carolina State University, and Joseph 

Ecker with the Salk Institute for Biological Studies. 

This research was supported by grants from the 

National Science Foundation and the National 

Institutes of Health. Tracy Punshon was supported 

by a training fellowship provided by the National 

Institute of Environmental Health Sciences Superfund Basic Research Program Project through 

Dartmouth’s Center for Environmental Health Sciences.

For more information, see: S.A. Kim, T. Punshon, 

A. Lanzirotti, L. Li, J.M. Alonso, J.R. Ecker, J. 

Kaplan, and M.L. Guerinot, "Localization of Iron in 

Arabidopsis Seed Requires the Vacuolar Membrane Transporter VIT1," Science, 314, 1295-1298 

(2006). 

— Sue Knapp, Dartmouth University
2-12

In electronics-based technologies, metal-oxide 

compounds known as “relaxor ferroelectrics” 

often make up key circuit components due to their 

unique electrical behavior. They are good insulators and can sustain large electric fields, making them excellent at 

storing electric charge. 

They can also turn a 

mechanical force, like 

squeezing, into electrical energy. 

Scientists at the 

Brookhaven National 

Laboratory investigated 

the poorly understood 

origin of these abilities 

— with surprising results. Their work, which 

may lead to new ways 

to use relaxor ferroelectric materials in electronic devices, was published 

in the February 2006 edition of Nature Materials.

The group studied a characteristic feature of relaxor ferroelectrics — billionth-of-a-meter-sized subregions that each carry a tiny electric field. These 

A 'FERROELECTRIC' MATERIAL REVEALS UNEXPECTED, INTRIGUING

BEHAVIOR

“polar nanoregions” (PNRs), embedded within the 

material’s crystal lattice, are thought to produce 

the materials’ intriguing electrical traits, but little is 

known about them. The Brookhaven researchers 

studied PNRs by subjecting a relaxor ferroelectric 

sample to a strong external electric field.

“We noticed that the weak PNR fields rotated 

spatially but resisted lining up with the powerful 

outside field,” said the study’s lead researcher, 

Brookhaven Lab physicist Guangyong Xu. “This is 

very surprising and extremely interesting, as we 

know of no other material in which this has been 

observed. This finding could lead to new uses 

for these materials, such as extremely sensitive 

transducer devices that convert mechanical or light 

energy into electrical energy.”

The group used NSLS beamline X17B1 to subject 

their sample to high-energy x-rays. They then analyzed the scattering patterns made as the x-rays 

passed through the sample, both before and after 

applying the electric field.

In the “before” case, the x-rays scattered about 

in many different directions, indicating that the 

PNR fields were oriented in many different ways. 

After applying the external field, the researchers 

expected a significant change in the x-ray patterns, 

showing that the PNR fields — somewhat like magnetic metal filings in a magnetic field — had neatly 

aligned with it. But the patterns changed in a different way than predicted. They indicated, instead, 

that the PNR fields preferred to line up perpendicular to the external field, even as the surrounding to the external field, even as the surrounding

atomic lattice lined up along it.

“The reasons behind this behavior are not yet 

clear, but we plan to conduct further research that 

may help shed light on this interesting and rare 

situation,” said Xu. “For example, it is possible that 

an even stronger external field could suppress the 

PNRs, or that a different relaxor ferroelectric material could display different behavior.”

This work was funded by the Office of Basic 

Energy Sciences within the U.S. Department of Energy’s Office of Science, the U.S. Office of Naval 

Research, and the Natural Science and Research 

Council of Canada.

For more information, see: G. Xu, Z. Zhong, Y. 

Bing, Z. Ye, and G. Shirane, "Electric-Field-Induced Redistribution of Polar Nano-Regions in 

a Relaxor Ferroelectric," Nat. Mater., 5, 134-140 

(2006).

— Laura Mgrdichian

This sketch shows the distribution of three-dimensional 

x-ray scattering intensity patterns (green) in a relaxor 

ferroelectric material. This scattering pattern is due to the 

material’s polar nanoregions. The scattering was measured 

with an applied electric fi eld (E) of (a) E = 0 and (b) E = 

20 kV/cm, which is applied along the [111] direction. This 

external electric fi eld causes the scattering pattern to 

redistribute, which is due to the redistribution of the polar 

nanoregions.

Guangyong Xu
2-13

FEATURE HIGHLIGHTS

At the NSLS, a team of scientists from the University of Massachusetts Medical School and the 

University of Virginia have determined the molecular structure of a protein found in the outer membrane of the E. coli bacteria. Their work helps to 

explain how this protein 

is involved in the overall 

function of E. coli and 

may one day help in 

the creation of vaccines 

against pathogenic E. 

coli strains. The paper 

was featured as the 

cover article in the 

March 17, 2006 edition 

of the Journal of Biological Chemistry.

The protein they studied, known as “OmpW,” 

is a member of a family 

of small proteins that 

are situated within the 

cell membranes of certain bacteria. Membrane proteins have many functions. For example, they are 

involved in the cell’s metabolic processes, provide 

structural stability, aid in cell-to-cell adhesion, or 

can protect the cell from outside stresses. Many 

are also channel-like transport proteins, allowing molecules and ions to enter and exit the cell. 

However, the lack of good structural data on the 

OmpW proteins has left scientists uncertain of their 

particular role.

STRUCTURE OF AN E. COLI MEMBRANE PROTEIN

“Previous crystal structures of proteins related to 

OmpW suggest that they have channels that are 

too narrow for them to function as transporters. 

However, our structure, along with other data, suggests that it can,” said Bert van den Berg, a University of Massachusetts Medical School biologist 

involved in the study. “This helps us understand 

the role of OmpW with respect to the entire cell.”

To obtain the structure, van den Berg and his colleagues worked at NSLS beamlines X25 and X6A. 

There, they aimed powerful x-ray beams at OmpW 

protein crystals and observed, using detectors and 

computers, how the x-rays were diffracted from the 

atoms in the samples. They then analyzed these 

diffraction patterns using computer software, which 

yielded a three-dimensional “snapshot” of the 

protein’s molecular structure.

The structure shows that OmpW is a barrel-shaped 

protein formed by eight aligned molecular strands. 

The inside of the barrel forms a long and narrow 

channel, which is closed on one end. Interestingly, 

the channel is “hydrophobic,” or water-repellent, 

suggesting that OmpW could form a channel for 

greasy, hydrophobic molecules.

To learn more about the protein’s function, the 

scientists performed a series of “conductance 

experiments” on the protein. These tests, which 

are designed to determine if a membrane protein 

can form a channel for ions, revealed that OmpW 

does indeed form a channel. However, which types 

of ions and molecules are transported by OmpW in 

the bacterial cell is still unclear.

In future work, van den Berg and his colleagues 

plan to investigate which greasy molecules, referred to as substrates, are transported by OmpW 

proteins, and they hope to gain a better understanding as to how the transport process occurs.

For more information, see: H. Hong, D. Patel, L. 

Tamm, and B. van den Berg, "The Outer Membrane 

Protein OmpW Forms an Eight-Stranded β-Barrel -Barrel

with a Hydrophobic Channel," J. Biol. Chem., 281, 

7568-7577 (2006).

— Laura Mgrdichian

Cover of the March 17, 2006 

edition of the Journal of 

Biological Chemistry

A side view and top view (from the outside of the cell) of the 

molecular backbone of OmpW, with the eight strands of the 

barrel shown in green and the loops (L1 to L4) connecting 

the strands in grey. The position of the membrane is 

indicated with horizontal lines.
2-14

Involved in about 90 percent of all chemical 

processes and the creation of about 60 percent 

of the chemical products available on the market, 

catalysis is vital to American industries. Catalysis, 

the acceleration of a chemical reaction by means 

of a separate substance (the catalyst), benefits 

fields such as chemistry, petroleum production, 

environmental protection, pharmaceuticals, bioengineering, and the development of fuel cells. New 

information about catalysis can lead to better and 

more efficient materials and processes such as oil 

refining and reducing harmful emissions in motor 

vehicles. But while catalysis might sound like it’s 

all about the end product, Brookhaven National 

Laboratory and University of Connecticut researchers are focused on what happens in between. 

The properties and activity of materials can vary 

significantly with different synthesis methods or at 

different conditions, such as temperature and time. 

Using x-rays at beamline X7B of the National Synchrotron Light Source, BNL and UConn researchers measured the changes catalyst materials go 

through during synthesis, showing that kinetic 

and mechanistic information about certain materials could allow for better synthesis control. “By 

understanding the intermediate, we can define the 

conditions whereby you get the product you want,” 

said BNL chemist Jon Hanson, part of the group 

that performed the research. 

The traditional way of making these observations is done outside of the reaction environment, 

termed ex-situ. During this method, target materials are separated from the reaction systems after 

different reaction times and then washed and dried 

before structural analysis. However, this process 

can alter materials from their original state in the 

reaction systems. 

“You’re probably going to change the material 

when you measure it,” Hanson said. “You can’t 

observe the characteristics under processed conditions.”

Thanks to high-flux x-rays, scientists can avoid that 

alteration with a method called in-situ synchrotron 

x-ray diffraction. This process provides a real-time 

look at the phase transformations involved in the 

synthesis or catalysis without removing them from 

the reaction environment. At the NSLS, Hanson, 

along with Xiong-Fei Shen from Steven Suib’s 

research group at the University of Connecticut 

used this mode to study structural changes during 

the synthesis of manganese oxide octahedral molecular sieves, a group of materials that have uses 

ranging from catalysts to gas sensors.

To find out details about manganese oxide synthesis, a different type of in-situ procedure was used. 

The majority of in-situ studies use the targeted 

material in a solid or gel form. BNL and UConn 

researchers, however, used hydrothermal synthesis, in which the material is in a heterogeneous 

liquid-solid form. Researchers heated a slurry of 

dried birnessite, a layered-structure manganese 

oxide, with HNO3 solution. They then “watched” 

the effects of different temperatures on the mixture 

through x-ray diffraction and determined the conditions needed to obtain different structures of the 

compound. For example, after heating the mixture 

MEASURING SYNTHESIS INTERMEDIATES FOR BETTER MATERIALS

Schematic diagram of the tube reactor.

Back-pressure

gas

Sapphire

Capillary

Reaction

mixtures Al2O3

Heated air flow

X-ray Goniometer

(horizontal)

(underneath the tube) underneath the tube)

(A) In-Situ synchrotron XRD patterns for synthesis of a 

β-MnO2 (1×1 tunnel structure) by hydrothermal treatment of 

a layered structure manganese oxide with 1 M HNO3. The 

system was heated from 25 to 180 °C at 6.2 °C /min, and 

held at 180 °C. XRD patterns were collected continuously 

with 5 min/pattern. (B) Schematic to show transformation 

from layered structures to the fi nal 1×1 tunnel structure.

(A)

(B)

Layer compressed & closed up Layer compressed & closed up ayer compressed & closed up
2-15

FEATURE HIGHLIGHTS

for 15 minutes at 180 °C, a 1 x 2 tunnel structure 

of manganese oxide starts to form. Similar observations were performed with KOMS2, for which 

scientists determined the conditions needed to produce desired surface areas. Knowing basic characteristics, such as structure and surface area, 

as materials are synthesized can provide better 

control or “tuning” to get the catalytic properties 

scientists and industries want, Hanson said. 

The results of their work were published in the 

April 12, 2006 edition of the Journal of the American Chemical Society. Other scientists involved in 

this research include Yun-Shuang Ding, and Mark 

Aindow (University of Connecticut). Funding was 

provided by the Office of Basic Energy Sciences 

within the U.S. Department of Energy’s Office of 

Science.

For more information, see: X. Shen, Y. Ding, J. 

Hanson, M. Aindow, and S. Suib, "In Situ Synthesis 

of Mixed-Valent Manganese Oxide Nanocrystals: 

An In Situ Synchrotron X-ray Diffraction Study," J. 

Am. Chem. Soc., 128, 4570 (2006).

— Kendra Snyder
2-16

Researchers at Brookhaven National Laboratory 

and colleagues at Stony Brook University, the 

IRCCS NEUROMED Medical Center in Italy, and 

Georgetown University say improvements they 

have made to an experimental form of radiation 

therapy that has been under investigation for many 

years could make the technique more effective 

and eventually allow its use in hospitals. Results 

on the improved method, which was tested in rats, 

were published in the June 20, 2006 edition of the 

Proceedings of the National Academy of Sciences.

The technique, microbeam radiation therapy 

(MRT), previously used a high-intensity synchrotron x-ray source such as a superconducting wiggler at the NSLS to produce parallel arrays of very 

thin (25 to 90 micrometers) planar x-ray beams 

(picture the parallel panels of window blinds in the 

open position) instead of the unsegmented (solid), 

broad beams used in conventional radiation treatment. Previous studies conducted at Brookhaven 

and at the European Synchrotron Radiation Facility 

(ESRF) in Grenoble, France, demonstrated MRT’s 

ability to control malignant tumors in animals with 

high radiation doses while subjecting adjacent 

normal tissue to little collateral damage. 

But the technique has limitations. For one thing, 

only certain synchrotrons can generate its very 

thin beams at adequate intensity, and such facilities are available at only a few research centers 

around the world. 

“The new development seeks a way out of this 

situation,” explained Brookhaven scientist Avraham 

Dilmanian, lead author of the new study. In this paper, the scientists report results that demonstrate 

the potential efficacy of significantly thicker microNEW X-RAY DELIVERY METHOD COULD IMPROVE RADIATION THERAPY

beams, as well as a way to “interlace” the beams 

within a well-defined “target” inside the subject to 

increase their killing potential there, while retaining 

the technique’s hallmark feature of sparing healthy 

tissue outside that target. 

First, using NSLS beamline X17B1, researchers 

exposed the spinal cords and brains of healthy rats 

to thicker (0.27 to 0.68 millimeter) microbeams at 

high doses of radiation and monitored the animals 

for signs of tissue damage. After seven months, 

animals exposed to beams as thick as 0.68 millimeter showed no or little damage to the nervous 

system. 

“This demonstrates that the healthy-tissue-sparing nature of the technique stays strong at a beam 

thickness that is within a range that could be 

produced by specialized x-ray tubes of extremely 

high voltage and current,” Dilmanian said. Such 

x-ray sources may become available sometime in 

the future and may allow the implementation of the 

method in hospitals. 

Next, the scientists demonstrated the ability to 

“interlace” two parallel arrays of the thicker microbeams at a 90-degree angle to form a solid beam 

at a small target volume in the rats’ brains, and 

measured the effects of varying doses of radiation 

on the targeted tissue volume and the surrounding 

tissue using magnetic resonance imaging (MRI) 

scans. 

For interlacing, the gaps between the beams in 

each array were chosen to be the same as the 

thickness of each beam, so the beams from one 

array would fill the gaps in the other to produce the 

equivalent of an unsegmented beam in the target 

volume only. 

“In this way we are effectively delivering an unsegmented broad beam type of dose to just the target 

region — which could be a tumor, or a non-tumerous target we want to ablate — while exposing the 

surrounding tissue to segmented radiation from 

which it can recover,” Dilmanian said.

The MRI scans showed that at a particular dose 

of radiation, the new configuration could produce 

major damage to the target volume but virtually 

no damage beyond the target range. “The dose of 

radiation delivered to the target volume would have 

been enough to ablate a malignant tumor,” Dilmanian said. 

“These results show that thick microbeams generated by special x-ray tubes in hospitals could eventually be used to destroy selective targets while 

sparing healthy tissue,” Dilmanian said. 

Authors (sitting) Zhong Zhong; (standing, from left) 

Ruiliang Wang, David Anschel, Jeremy Welwart, and 

Avraham Dilmanian 
2-17

FEATURE HIGHLIGHTS

Said collaborator Eliot Rosen, a radiation oncologist at Lombardi Comprehensive Cancer Center, 

Georgetown University, “This form of microbeam 

radiation therapy could improve the treatment of 

many forms of cancer now treated with radiation, 

because it can deliver a more lethal dose to the 

tumor while minimizing damage to surrounding 

healthy tissue. It may also extend the use of radiation to cases where it is now used only judiciously, 

such as brain cancer in patients under three years 

of age, because of the high sensitivity of young 

brain tissue to radiation.” 

And according to collaborators David Anschel, 

a neurologist at Stony Brook University and 

Brookhaven Lab, and Pantaleo Romanelli, a neurosurgeon from NEUROMED Medical Center, the 

technique may also have applications in treating a 

wide range of benign and malignant brain tumors 

and other functional brain disorders such as epilepsy and Parkinson’s disease. 

Background on MRT

MRT research was initiated by retired Brookhaven 

scientist Daniel Slatkin, the late Per Spanne, also 

from Brookhaven, Dilmanian, and others in the 

early 1990s at Brookhaven’s NSLS. Since the 

mid-1990s, the method has been under ongoing 

investigation also at ESRF. 

It is not clear why high dose MRT is effective at 

killing tumor tissue while sparing healthy tissue. 

The researchers hypothesize that the normal tissue 

repairs itself, in part, as a result of the survival 

between the microbeams of the microvasculature’s 

angiogenic cells. This effect seems to occur more 

successfully in the normal tissue than in tumors, 

although other factors also seem to be involved. 

Neither the original nor the improved MRT technique has been tested in humans. 

The MRT research program at Brookhaven was 

funded in the past by Brookhaven’s Laboratory 

Directed Research and Development program, the 

Children’s Brain Tumor Foundation, the Office of 

Biological and Environmental Research within the 

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

by the National Institutes of Health. The studies 

were carried out at the NSLS, which is supported 

by the Office of Basic Energy Sciences within 

DOE’s Office of Science. 

For more information, see: F. Dilimanian, Z. Zhong, 

T. Bacarian, H. Benveniste, P. Romanelli, R. Wang, 

J. Welwart, T. Yuasa, E. Rosen, and D. Anschel, 

"Interlaced X-ray Microplanar Beams: A Radiosurgery Approach with Clinical Potential," Proc. Natl. 

Acad. Sci. USA, 103, 9709-9714 (2006).

— Karen McNulty Walsh
2-18

Since their discovery, high-temperature superconductors, a class of remarkable materials that 

conduct electricity with almost zero resistance, 

have perplexed scientists. Despite many, many 

studies, how these materials do what they do is 

still not well understood. At the NSLS, scientists 

have discovered a perhaps odd, yet important clue 

to the puzzle — that a common high-temperature 

superconductor actually has distinct insulating

properties.

The superconductor is known as “LBCO,” named 

for the elements it contains: lanthanum, barium, 

copper, and oxygen. LBCO is widely studied and, 

despite all there is yet to learn, researchers have 

learned some important things about it. For example, the barium atoms act as the material’s sole 

electric carriers by introducing positively charged 

vacancies, called “holes,” that electrons can jump 

to. Changing the amount of barium in LBCO thus 

changes its superconducting behavior. At a certain 

critical amount of barium — oddly enough — the 

superconductivity of LBCO disappears.

This disappearance of the superconductivity coincides with the formation of ribbon-like magnetic 

regions in the material, known as “stripes.” Stripes 

were discovered by Brookhaven Lab physicist John 

Tranquada in 1995.

“What we were able to show is that the holes in 

LBCO are sandwiched between these magnetic 

THE UNUSUAL INSULATING PROPERTIES OF A SUPERCONDUCTOR

stripes, forming ribbons of electric charge,” said 

Abbamonte. “Significantly, we also found that 

the magnetic regions have insulating properties. 

Therefore, the material as a whole is neither a 

metal nor an insulator, since it retains characteristics of both.”

These findings are the result of work performed at 

NSLS beamline X1B, where the scientists studied 

LBCO using an x-ray technique called “resonant 

soft x-ray scattering.” They aimed a beam of x-rays 

at an LBCO sample and used a detector to measure how the x-rays reflected away from the material. They then analyzed these reflections to reveal 

information about LBCO’s electronic structure.

The results of this study are important because 

they support the theory that stripes are in some 

way related to superconductivity in high-temperature superconductors.

“Our results seem to support the stripe description 

of high-temperature superconductors. This is exciting, since it could mean that the scientific community may be very close to truly understanding how 

these materials perform,” said Abbamonte.

The research was published in the December 2005 

edition of Nature Physics. The paper’s co-authors are Andrivo Rusydi (University of Hamburg), 

Serban Smadici (BNL/University of Illinois), Genda 

Gu (BNL), George Sawatzky (University of British 

Columbia and University of Groningen), and D.L. 

Feng (Fudan University). The work was supported 

by the U.S. Department of Energy, the Dutch Science Foundation, and the Netherlands Organization for Fundamental Research on Matter.

For more information, see: P. Abbamonte, A. Rusydi, S. Smadici, G. Gu, G. Sawatzky, and D. Feng, 

"Spatially Modulated ‘Mottness’ in La2-xBaxCuO4," 

Nat. Phys., 1, 155-158 (2005).

— Laura Mgrdichian

A “reciprocal space map” representation of the stripes in 

the copper-oxide layers of LBCO. “H” and “L” are measures 

of how often the ribbon-like stripes “wave.” H corresponds 

to the a direction, and L corresponds to the c direction. 

Their reciprocals, 1/H and 1/L, are a measure of the stripes’ 

wavelength. The red and pink vertical streak at H = 0.25 

indicates that the stripes have a wavelength of four lattice 

parameters and are stacked along the c direction.

H (r. l. u.)

L (r. l. u.)
2-19

FEATURE HIGHLIGHTS

As more and more people rely on cell phones, 

laptop computers, personal organizers, and even 

hybrid electric-gas vehicles, scientists are working to develop rechargeable batteries that are ever 

smaller, cheaper, lighter, safer, and longer-lasting. At the NSLS, a collaboration of scientists is 

deeply involved in this effort. They are investigating a group of promising new materials for use 

in lithium-ion batteries, the most common type of 

battery found in portable electronics and the most 

promising type for hybrid cars. 

Lithium-ion batteries work by shuttling positively 

charged lithium ions between the “cathode” (the 

battery’s positive terminal) and “anode” (the negative terminal). As the battery is charged, lithium 

ions are forced out of the cathode and moved into 

to the anode through the “electrolyte,” the solution 

inside the battery. When the battery is in use, the 

process reverses. The scientists are studying a 

group of new cathode compounds consisting of the 

elements lithium, cobalt, nickel, manganese, and 

oxygen. 

“Despite the wide use of lithium-ion batteries, 

there have been very few studies on exactly 

how the cathode material behaves in the charging process,” said the study’s lead researcher, 

Brookhaven chemist Won-Sub Yoon. “How are the 

oxygen atoms involved? What is the relationship 

between the oxygen atoms and the other metal atoms in the compound? To design a better cathode 

material, and thus a better battery, these questions 

must be answered. An in-depth understanding of 

these problems will provide a road map for the 

development of these new materials.” 

Using various x-ray techniques, Yoon and his colleagues have done just that. They discovered that 

as lithium ions leave the cathode material during 

the charging process, changes occur on the manganese and cobalt atoms that are quite different 

from those that occur on the nickel atoms. Specifically, the manganese and cobalt atoms do not lose 

electrons as the lithium ions are removed, while 

the nickel atoms, in contrast, do lose electrons. 

The group also learned more about how the cathode material compensates for the positive charge it 

loses as the lithium ions move to the anode. They 

found that empty regions with positive charge, 

called “holes,” are created in the cathode. In addition, their x-ray data show just where these holes 

are located: within the electron orbitals of oxygen 

atoms that are bound to cobalt atoms. 

Gathering these details on the cathode’s electronic 

behavior is an important step in lithium-ion battery research. This new knowledge will help the 

material become a common component of a new 

series of better lithium-ion batteries. More detailed 

information on this research can be found in the 

group’s scientific paper, which was published in the 

December 14, 2005 edition of the Journal of the 

American Chemical Society. 

The other scientists involved in this research are 

Kyung Yoon Chung, Xiao-Qing Yang, and James 

McBreen (BNL Chemistry Department); Mahalingam Balasubramanian (Argonne National Laboratory); Clare Grey (Stony Brook University); and 

Daniel Fischer (National Institute of Standards and 

Technology).

For more information, see: W. Yoon, M. Balasubramanian, K. Chung, X. Yang, J. McBreen, C. Grey, 

and 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, 

17479-17487 (2005).

— Laura Mgrdichian

AT THE NSLS, SCIENTISTS WORKING TOWARD BETTER BATTERIES

Authors (from left) Daniel Fischer, Won-Sub Yoon, James 

McBreen, and Xiao-Qing Yang
2-20

Brookhaven National Laboratory researchers 

have determined the structure of an experimental, 

organic compound-based circuit component, called 

a “molecular electronic junction,” that is only a few 

nanometers in dimension. This study may help scientists understand how the structure of molecular 

junctions relates to their performance and function 

and, in the longer term, may help incorporate these 

and other molecular-scale devices into a new 

generation of remarkably small electronics-based 

technologies. 

The research is discussed in the February 21, 

2006 edition of the Proceedings of the National 

Academy of Sciences. 

“Molecular electronics is a very exciting developing 

field, since these extremely small circuits, based 

on organic molecules rather than metal, have a 

potentially greater circuit density than conventional silicon-based technology. This means that 

more circuits could fit on one circuit board, leading 

to electronic devices that are much smaller than 

those currently produced,” said one of the study’s 

lead scientists, Brookhaven physicist Julian Baumert. “We’re interested in the structure of the junction — how the molecules are oriented and packed 

together — because it is linked to the function and 

performance of the circuit.” 

In conventional circuits, junctions are commonly 

made of two different types of silicon that, when 

layered together, allow electric current to flow in 

one direction only. Here, the junction under study 

consists of two very thin layers of two different organic compounds — “alkyl-thiol” and “alkyl-silane.” 

They are sandwiched on one side by a layer of 

solid silicon and on the other side by a layer of liquid mercury, which serve as electrodes. Alkyl-thiol 

and alkyl-silane molecules have simple structures 

and the potential to be good insulating materials. 

The scientists created the junctions by filling a 

small container with a drop of liquid mercury and 

depositing a very small amount of alkyl-thiol onto 

the mercury surface. They then topped the alkylthiol layer with an alkyl-silane-coated silicon wafer. 

This method yielded a junction with just a fivenanometer-thick gap between the two electrodes. 

“This technique is not limited to simple alkane molecules,” said Columbia University graduate student 

Michael Lefenfeld, the study’s second lead scientist. “Many other types of organic molecules could 

be used, such as semi-conducting and conducting 

molecules. These materials also have a structure 

and packing density that plays a large role in their 

electrical performance.” 

The research group studied the junction by aiming high-energy x-rays — energetic enough to 

penetrate the silicon wafer — at the junction from 

several incident angles and measured how the rays 

scattered off the organic molecules. Next, they attached electric contacts to the silicon and mercury 

electrodes and, for several different applied voltages, measured both the reflected x-ray signal and 

the electric current through the junction. 

By analyzing the x-ray scattering data, the researchers discovered that the organic molecules 

are densely packed together, with most of the 

molecules positioned vertically. Further, the combination of the electric-current and x-ray measurements revealed that the current does not deform 

that structure, even when the applied voltage was 

very high. This implies that the molecular structure 

is quite stable. 

“These are important details to know in order to 

fully understand the electronic properties of molecular-scale junctions,” said Brookhaven physicist 

Benjamin Ocko, one of the paper’s senior authors. 

“These investigation methods should be able to 

provide us with a better understanding of many 

other molecular junctions.” 

This research was supported by the Office of Basic 

Energy Sciences within the U.S. Department of 

Energy’s Office of Science, the National Science 

Foundation, the New York State Office of Science, 

Technology, and Academic Research, and the German-Israeli Foundation. 

For more information, see: M. Lefenfeld, J. Baumert, E. Sloutskin, I. Kuzmenko, P. Pershan, M. 

Deutsch, C. Nuckolls, and B. Ocko, "Direct Structural Observation of a Molecular Junction by HighEnergy X-ray Reflectometry," Proc. Natl. Acad. Sci. 

USA, 103, 2541-2545 (2006).

— Laura Mgrdichian

STRUCTURE OF A MOLECULAR-SCALE CIRCUIT COMPONENT

Authors (from left) Julian Baumert and Michael Lefenfeld
2-21

FEATURE HIGHLIGHTS

The speed of nanoparticle assembly can be accelerated with the assistance of the molecule that 

carries life’s genetic instructions, DNA, a team 

of researchers at Brookhaven National Laboratory recently found. Nanoparticles, particles with 

dimensions on the order of billionths of a meter, 

could potentially be used for more efficient energy 

generation and data storage, as well as improved 

methods for diagnosing and treating disease. 

Learning how to control and tailor the assembly of 

these miniscule particles into larger functional systems remains a major challenge for scientists. The 

Brookhaven results, published in the November 1, 

2006 edition of the Journal of the American Chemical Society, are a step in that direction.

“Understanding how to self-assemble these types 

of nanomaterials has applications in all areas 

of nanotechnology, from optics to electronics to 

magnetic materials,” said the study’s lead author 

Mathew Maye, a Brookhaven chemist. Maye is 

part of a team of interdisciplinary scientists from 

Brookhaven’s new Center for Functional Nanomaterials (CFN) and the biology department. The 

researchers found a way to control the assembly 

of gold nanoparticles using rigid, double-stranded 

DNA. Their technique takes advantage of this 

molecule’s natural tendency to pair up components 

called bases, known by the code letters A, T, G 

and C. 

“In biology, DNA is mainly an informational material, while in nanoscience, DNA is an excellent 

structural material due to its natural ability to 

self-assemble according to well-specified programmable rules,” said Oleg Gang, the Brookhaven 

physicist who leads the research team. “Using biological materials such as DNA, we are developing 

approaches to control the assembly of inorganic 

nano-objects. However, in order to really turn this 

attractive approach into nanotechnology, we have 

to understand the complexity of interaction in such 

hybrid systems.”

NANOPARTICLE ASSEMBLY ENTERS THE FAST LANE

The synthetic DNA used in the laboratory is capped 

onto individual gold nanoparticles and customized to recognize and bind to complementary DNA 

located on other particles. This process forms 

clusters, or aggregates, of gold particles. 

“It’s really by design,” Maye said. “We can sit down 

with a piece of paper, write out a DNA sequence, 

and control how these nanoparticles will assemble.” 

One limitation to the assembly process is the use 

of single-stranded DNA, which can bend backward 

and attach to the particle’s gold surface instead of 

binding with surrounding nanoparticles. This flexibility, along with the existence of multiple forms of 

single-stranded DNA, can greatly slow the assembly process. In the Brookhaven study, researchers 

introduced partially rigid, double-stranded DNA, 

which forces interacting linker segments of DNA 

to extend away from the gold surface, allowing for 

more efficient assembly. 

“By using properties of DNA, we can increase 

assembly kinetics, or speed, by relatively simple 

means without a lot of synthetic steps,” Maye said.

The research team probed the synthesized and 

assembled nanosystems with multiple imaging 

techniques, using beams of light and electrons 

as well as high-intensity x-rays at Brookhaven’s 

National Synchrotron Light Source. The scientists 

look to further improve the controllability of the 

system, focusing next on the size of the nanoparticle clusters.

This research was funded by the Office of Basic 

Energy Sciences within the U.S. Department 

of Energy’s Office of Science. The CFN at 

Brookhaven Lab is one of five Nanoscale Science 

Research Centers being constructed at national 

laboratories by the DOE’s Office of Science to 

provide the nation with resources unmatched anywhere else in the world for synthesis, processing, 

fabrication, and analysis at the nanoscale.

For more information, see: M. Maye, D. Nykypanchuk, D. van der Lelie, and O. Gang, "A Simple 

Method for Kinetic Control of DNA-Induced 

Nanoparticle Assembly," J. Am. Chem. Soc., 128, 

14020-14021 (2006).

— Kendra Snyder

Authors standing (from left) Oleg Gang and Daniel van 

der Lelie sitting, (from left) Mathew Maye and Dmytro 

Nykypanchuk
2-22

Protecting us from diseases and infections, the 

immune system is traditionally divided into two 

parts: innate immunity, a nonspecific response to 

pathogens that cause disease; and adaptive immunity, which can specifically recognize a pathogen and to mount stronger attacks each time it is 

encountered. Some invertebrates only have innate 

immunity, which, at about one billion years old, is 

the more primitive of the two subsystems. It wasn’t 

until many years later that adaptive immunity appeared along with innate immunity in jawed vertebrates. While much is known about the evolution of 

the immune system to the current two-part system 

found in lizards, humans, cats, and countless other 

VISUALIZING THE IMMUNE SYSTEM’S MISSING LINK

organisms, details of its origin remain unknown. 

At the NSLS, a team of researchers looked for this 

missing link and unveiled valuable information that 

could be used in the medical community.

“In order to find something that represents the 

transition between the innate and adaptive immune 

systems, we needed to study an organism that was 

just below the level of jawed vertebrates on the 

evolutionary scale,” said researcher David Ostrov, 

from the University of Florida College of Medicine. 

The organism chosen was amphioxus, a small, 

jawless, invertebrate marine animal. The researchers focused on specific amphioxus V-type immunoglobulin domains, which are proteins used by the 

immune system to identify and neutralize foreign 

objects. Also used in antibodies, these V-type 

domains were studied on the structural level using 

x-ray crystallography at beamline X6A. 

“We tried to answer the question, ‘Does this protein resemble the types of proteins we use in our 

immune systems?’ Ostrov said. “And the answer 

is clearly ‘yes.’ Even though the primitive immune 

response protein and the one seen in humans have 

very different sequences, at the structural level 

they’re almost identical.”

During their research, which was published in the 

August 2006 edition of Nature Immunology, the 

scientists ended up with something much more 

revealing than a simple answer. Using the multiwavelength anomalous dispersion method (MAD), 

the researchers solved the structure of the immunoglobulin protein down to atomic resolution – the 

first V-type immunoglobulin structure ever solved 

to that level. “We could see structural details at 

the core of the domain that no one has ever seen,” 

Ostrov said.

Learning the intricate details of this protein could 

allow scientists to generate more stable immune 

response proteins that might improve the treatment 

of cancers and immune diseases. “The problems 

with using antibodies as they exist is that they are 

susceptible to degradation,” Ostrov said. “If we 

could learn how to stabilize antibodies, they could 

last longer in the bloodstream and be more useful 

clinically.”

Other researchers involved in the study include 

José Hernández Prada, University of Florida College of Medicine; Robert Haire, University of South 

Florida College of Medicine; Marc Allaire, Jean Jakoncic, and Vivian Stojanoff, NSLS; John Cannon, 

University of South Florida College of Medicine 

and H. Lee Moffitt Cancer Center and Research 

Institute; and Gary Litman, University of Florida 

Authors (from left) José Hernández Prada and David Ostrov 

Non-canonical interactions in the core of VCBP3 V1 solved 

by MAD and refi ned to 1.15 Å. The side chain of Trp46 and 

the intrachain disulfi de bond (Cys27-Cys110) are shown in 

the core of VCBP3 V1 (yellow for carbon, orange for sulfur, 

blue for nitrogen). Non-canonical interactions mediated by 

p electrons and H atoms apparent in the Fo-Fc electron 

density are shown at the 3s level (red), 2s level (white) and 

superimposed onto the fi nal model (yellow for carbon, green 

for sulfur, blue for nitrogen, red for oxygen atoms). 2FoFc electron density calculated from phases to 1.15 Å was 

contoured at the 2s level (colored in blue/green).
2-23

FEATURE HIGHLIGHTS

College of Medicine, University of South Florida 

College of Medicine and All Children’s Hospital. 

This research was funded by the National Institutes of Health, the Cure Autism Now Foundation, 

and the U.S. Department of Energy.

For more information, see: J. Prada, R. Haire, M. 

Allaire, J. Jakoncic, V. Stojanoff, J. Cannon, G. Litman, and D. Ostrov, "Ancient Evolutionary Origin 

of Diversified Variable Regions Demonstrated by 

Crystal Structures of an Immune-Type Receptor in 

Amphioxus," Nat. Immunol., 7, 875-882 (2006).

— Kendra Snyder

Crystal structure of VCBP3 V1V2 solved by SAD and 

refi ned to 1.85 Å. (a,b) Secondary structure is shown 

(Gold; ß-strands, gray; loop regions, red; helices). The G 

strand and FG loop encoded by a joining gene segment-like 

element is shown in cyan. The loops corresponding to CDR 

regions in T-cell receptor and Ig: BC loop, CDR1; C’C”, 

CDR2; FG, CDR3.
2-24

Argonne National Laboratory issued the following 

press release describing research on the surface 

structure of a silicon and gold molten alloy. This 

research was conducted in part at beamline X22B 

of the National Synchrotron Light Source at DOE’s 

Brookhaven National Laboratory by physicist 

Benjamin Ocko. Atoms are arranged randomly 

within the bulk of a liquid metal, but they form into 

discreet layers at the surface. This phenomenon, 

known as surface layering, was first discovered 

for mercury and gallium at Brookhaven in 1995. 

Continued research on the structure of liquid alloys 

is important for the metals industry and could lead 

to emerging nanotechnologies. The gold-silicon 

interconnect junction, for example, is one of the 

most common connections used in cell phones, 

computers and other devices. 

A substance used in nanotechnology contains unusual structures at its surface, a team of researchers led by Oleg Shpyrko, Distinguished Postdoctoral Fellow at the U.S. Department of Energy’s 

Argonne National Laboratory have learned. The 

research results, developed at the Center for 

Nanoscale Materials at Argonne, were published in 

the July 7, 2006 issue of Science. 

The substance in question is a gold-silicon eutectic 

alloy, 82 percent gold and 18 percent silicon. The 

term eutectic means that the combination melts 

at a temperature lower than that of the melting 

temperature of either of its components. For most 

eutectic alloys, the difference between the melting 

point of the alloy and those of its pure components 

is about 100 °C; the gold-silicon eutectic alloy 

melts about 1,000 °C lower than either of its 

components, at 360 °C (680 °F).

LIQUID ALLOY SHOWS SOLID-LIKE CRYSTAL STRUCTURE AT SURFACE

But that’s not the only unusual thing about the 

gold-silicon eutectic alloy. In a crystalline solid, 

atoms are arranged in an orderly, periodic fashion, 

and in a liquid, arrangements of atoms are disordered. It’s been known for about 10 years that 

many metallic liquids show two or three distinct 

atomic layers near the surface, and usually there 

is no crystalline-like order within these layers. 

However, Shpyrko and his colleagues found that 

the gold-silicon eutectic alloy has seven or eight 

layers near its surface. In trying to understand this 

unexpected development, they found also that the 

top-most surface layer includes a crystal-like structure, similar to that normally found only in solid 

substances. 

Understanding characteristics of novel surface 

phases like this surface-frozen monolayer is important for the growing realm of nanotechnology, in 

which the basic unit of measurement is a billionth 

of a meter.

“By the time you reduce the size of an object or device down to one nanometer, practically everything 

is surfaces and interfaces,” Shpyrko said. “We 

need to understand what the new laws of physics 

and chemistry that govern the surface structures 

are.” Gold and silicon are especially important to 

understand because they are used in computer 

technology. Gold is an oxide-resistant “noble” 

metal that is easily shaped into tiny computer chip 

interconnects, and silicon is the principal component of most semiconductor devices.

“If you think about it, you have gold and silicon in 

contact with each other in about every electronic 

device,” Shpyrko said.

Shpyrko began the research as a doctoral student 

at Harvard University and finished it at Argonne. 

He used Argonne’s Advanced Photon Source, 

which provides the most brilliant x-ray beams available in the Western Hemisphere, to perform several tests on the material: x-ray specular reflectivity, 

which provides information about atomic structure 

normal to the surface; x-ray grazing incidence diffraction, which provides information about in-plane 

structure; x-ray diffuse scattering, which provides 

information about waves and other dynamics at 

the surface; and x-ray crystal truncation rod, which 

measures thickness and structure of the crystalline 

surface layer.

Co-authors on the Science article were Reinhard 

Streitel, Venkatachalapathy S.K. Balagurusamy, 

Alexei Y. Grigoriev, and Peter S. Pershan of 

Harvard University; Moshe Deutsch of Bar-Ilan University in Israel; Benjamin M. Ocko of Brookhaven 

This image represents periodically ordered gold (yellow) 

and silicon (blue) atoms within the surface-frozen 

monolayer of liquid gold-silicon eutectic alloy. Research on 

this surface was conducted at both Brookhaven National 

Laboratory and Argonne National Laboratory.
2-25

FEATURE HIGHLIGHTS

National Laboratory; and Mati Meron and Binhua 

Lin of the University of Chicago. 

This work was supported by the Department of 

Energy, through the Office of Science's Office of 

Basic Energy Sciences, and by the U.S.-Israel Binational Science Foundation, Jerusalem. Measurements at Brookhaven were also supported by the 

Office of Basic Energy Sciences. 

For more information, see: O.G. Shpyrko, R. 

Streitel, V.S.K. Balagurusamy, A.Y. Grigoriev, M. 

Deutsch, B.M. Ocko, M. Meron, B. Lin, and P.S. 

Pershan, "Surface Crystallization in a Liquid AuSi 

Alloy," Science, 313, 77-80 (2006).

— Eva Sylwester, Argonne National Laboratory
2-26

In order to understand the planet we live on, 

it’s crucial to understand the properties of the 

liquid- and plastic-like minerals flowing beneath 

the Earth’s crust. The study of the deformation 

and flow of these minerals, along with many other 

natural and manmade materials, is known as rheology. Many of Earth’s surface features, such as 

mountain belts, subduction zones, hot spots and 

seismic zones, are significantly affected by mantle 

rheology. To study these minerals, scientists mimic 

mantle conditions with high-pressure, laboratorybased experiments and modeling theories. But 

at the NSLS, a team from Stony Brook University 

found that a commonly used model in previous 

studies might be inaccurate. 

The conventional method of modeling stress and 

strain propagation in materials uses two extreme 

bounds, called Reuss and Voigt bounds. The 

Reuss bound describes a condition where all the 

grains in a sample experience identical stress 

when forces are applied to the material. The Voigt 

bound describes a condition where all the grains 

experience the same strain when the sample is 

deformed under stress. Intermediate conditions 

are described by combining the bounds to achieve 

a weight parameter between 0 and 1, with 0 representing the Voigt bound and 1 representing the 

Reuss bound. 

Using a new technology at beamline X17B2, the 

Stony Brook team found that this parameter can 

actually exceed 1, the Reuss bound. This event 

occurs when a sample is pushed beyond its normal 

elastic state. Typically, when a force is applied and 

removed from a sample, the material will bounce 

back to its initial form. But if the force is greatly 

BREAKING THE BOUNDS OF PLASTICITY

increased, the material will undergo an unrecoverable change, a characteristic known as plastic 

deformation. It’s in this situation that the classic 

Reuss and Voigt model fails. “For the first time, 

we can quantitatively recognize that this parameter under plastic deformation can go beyond the 

boundary,” said researcher Jiuhua Chen. “That 

means that this classic elastic model can no longer 

be applied in this situation.”

The finding wouldn’t have been possible without 

the development of a new type of x-ray diffraction 

experiment, Chen said. Traditionally, scientists 

have used one detector at a fixed angle to study 

materials under high pressure. But with the help of 

NSLS scientists Zhong Zhong and Chi-Chang Kao, 

the team developed a simultaneous multi-diffraction detection system that can detect x-ray diffraction along and normal to the applied principal 

stress. 

 “These techniques have offered means to reveal 

the information of material properties that was not 

obtainable before and have also enabled many 

reformations of traditional experiments,” Chen 

said. “This technical development will really enable 

us to study the rheological properties of Earth’s 

materials at a much higher pressure than before. 

And now we can explore the mantle at even deeper 

levels.”

Other scientists involved in this study, which was 

published in the June 28, 2006 edition of the 

Journal of Physics: Condensed Matter, include Li 

Li, Tony Yu, Hongbo Long, Donald Weidner, Liping 

Wang, and Michael Vaughan, all from Stony Brook 

University. Funding was provided by the Consortium for Materials Properties Research in Earth 

Sciences and the National Science Foundation.

For more information, see: J. Chen, L. Li, T. Yu, 

H. Long, D. Weidner, L. Wang, and M. Vaughan, 

"Do Reuss and Voigt Bounds Really Bound in 

High-Pressure Rheology Experiments?" J. Phys. 

Condens. Mat., 18, S1049-1059 (2006).

— Kendra Snyder 

The research group experimentally determined that the 

stress propagation parameter went beyond the classic 

Reuss (isostress) bound at larger strains. 

Plasticity

Strain

Elasticity
2-27

FEATURE HIGHLIGHTS

Water-repellent lipids, such as fats and waxes, 

are a major class of molecules that form cell 

membranes and store energy, among other key 

functions. However, although these long chain 

molecules tend to form ordered crystal structures 

suitable for a common structural analysis method 

— x-ray diffraction — determining exactly how they 

pack together is difficult. This is due to a glitch in 

the diffraction method: the “phase problem.”

The phase problem exists because the diffraction pattern produced by the x-rays can only take 

into account the intensity of the x-rays used, not 

their phase (the particular position in time of the 

x-ray light waves). This limits the quality of the 

structural data that can be obtained. But recently 

at the NSLS, a research group learned how to use 

a common crystallographic method, called multiwavelength anomalous dispersion (MAD), to determine the phases of diffraction from lipid structures. 

This important work may help elucidate many 

biological processes that involve lipids, particularly 

cell-to-cell fusion.

“Knowing just how lipid chains pack together is 

of considerable importance in biology,” said the 

study’s lead scientist, biophysicist Huey Huang 

of Rice University. “But the details of small-scale 

shape changes in these lipid structures are not 

well understood. We think that our work can help 

remedy this problem.”

Normally, how a molecular structure diffracts 

x-rays does not depend on the x-ray wavelength 

or energy. But this is not true when the structure 

contains atoms that have an absorption edge — a 

particular energy for which the x-rays are strongly 

absorbed — near the energy of the incident x-rays. 

These are called “anomalous” atoms. The MAD 

method makes use of this energy dependence to 

single out the contribution of the anomalous atoms 

in the overall diffraction behavior. This greatly 

simplifies the original phase problem. And once 

the phase problem is solved, the structure of the 

crystal can then be determined. MAD is routinely 

used to study protein structures, but, according to 

Huang and his group, this is the first time it has 

been used to solve a lipid crystal structure.

One difference between lipids and proteins is that 

lipid samples take the form of thin films deposited 

on a substrate, such as a silicon wafer. These 

thin-film samples often do not have a uniform 

thicknesses, a technical problem that makes the 

standard method of MAD analysis difficult. Huang 

and his group developed a new way to analyze the 

thin film samples.

The lipid molecules they investigated are members 

of a lipid sub-class called phospholipids, which 

are a major component of cell membranes. The 

particular phospholipids used here were “labeled” 

with a bromine atom. Together, the molecules pack 

together such that they form cylinders arranged in 

a hexagonal array. 

The Huang group’s analysis shows that the lipid 

chains pack together uniformly with each chain 

occupying the same volume, rather than one or two 

chains taking up more or less space than the others. Lipid chain volume has been assumed to be 

constant under configuration changes, but this is 

the first direct experimental proof.

The group is hoping, in particular, to shed light 

on “membrane fusion,” one step in the process by 

which two cells join to become a single cell. The 

membranes meet at one location and create a connection between the cells, allowing the exchange 

of molecules (this, for example, is how fertilization and viral infection can occur). Eventually, the 

membranes merge to create one larger membrane 

enveloping the contents of both cells. During all 

of this, the lipid layers in each membrane undergo 

a series of structural changes. Now, thanks to the 

work of Huang and his colleagues, scientists may 

be able to identify those changes to better understand membrane fusion.

This research was published in the March 22, 2006 

edition of the Journal of the American Chemical 

Society. It was funded by the National Institutes of 

Health and the Robert A. Welch Foundation.

For more information, see: D. Pan, W. Wang, W. 

Liu, L. Yang, and H. Huang, "Chain Packing in the 

Inverted Hexagonal Phase of Phospholipids: A 

Study by X-ray Anomalous Diffraction on BromineLabeled Chains," J. Am. Chem. Soc., 128, 3800-

3807 (2006).

— Laura Mgrdichian

X-RAY ANALYSIS METHOD CRACKS THE 'LIPID PHASE PROBLEM'

A three-dimensional view of the electron density distribution 

of bromine atoms in the hexagonal array of lipid cylinders.
2-28

Scientists at Brookhaven National Laboratory, 

the New York Structural Biology Center, and SGX 

Pharmaceuticals, Inc., have determined the atomic 

crystal structure and functional mechanism of an 

enzyme essential for eliminating unwanted, nonnutritional compounds such as drugs, industrial 

chemicals, and toxic compounds from the body. 

The detailed mechanism of action will help scientists understand how these compounds are eliminated and what goes wrong in cases where normal 

metabolism fails. The research was published in 

the June 27, 2006 edition of the Proceedings of the 

National Academy of Sciences.

According to Brookhaven 

biologists Eswaramoorthy Subramaniam, the 

lead author, and Subramanyam Swaminathan, 

who led the research, 

most non-nutritional, 

foreign substances such 

as drugs and industrial 

chemicals are insoluble 

in water. The body uses 

two main groups of 

enzymes — flavin-containing monooxygenases 

(FMOs) and cytochrome P450s — to convert these 

compounds to soluble forms that can be easily 

excreted. 

“For FMOs, the end result — that an oxygen atom 

gets added to make these compounds soluble — is 

simple,” Swaminathan says, “but the reactions 

SCIENTISTS TAKE 'SNAPSHOTS' OF ENZYME ACTION

require additional participants, or cofactors.” In 

order to understand the molecular mechanism, the 

scientists used high-intensity x-ray beams at the 

NSLS to identify the positions of individual atoms 

and produce crystal structures of the enzyme, the 

enzyme plus its cofactor, and the enzyme plus the 

cofactor plus the compound to be oxidized (the 

substrate). 

“These crystal structures give step-by-step snapshots of different stages of the catalytic action,” 

Swaminathan says, “and reveal a mechanism that 

is different from what had been known about this 

process.” 

Previously, it had been believed that all the 

“players” — the enzyme, cofactor and substrate 

— came together at a particular time to perform the 

function of transferring an oxygen atom from the 

enzyme to the substrate. “Our finding shows that 

the substrate and cofactor are binding to the enzyme alternately, not together,” Swaminathan says. 

First, the cofactor (known as NADPH) binds to a 

molecule known as FAD, which is a coenzyme attached to the FMO, and transfers a hydride ion to 

it. That makes the FAD group capable of accepting molecular oxygen. Then, when the substrate 

arrives, the cofactor leaves so that the substrate 

can bind to the same site on the FAD group. At this 

moment an oxygen atom from molecular oxygen 

is attached to the substrate, and the hydride ion 

obtained from the cofactor combines with the other 

oxygen atom to form a water molecule, which is released. Once the substrate is oxygenated, it leaves 

Snapshots of catalytic mechanism of FMO: The three stages in the mechanism of action of FMO are depicted here. The 

ribbon diagram represents the protein consisting of two domains with a long loop in the interface. The big and small domains 

are shown in red and purple with the interface in golden color. Figure 1 represents the fi rst stage with the coenzyme FAD 

(shown as a ball and stick model in green) bound to the enzyme. In the second stage (Figure 2), the cofactor NADPH (shown 

as a ball and stick model in cyan) approaches the enzyme and interacts with the coenzyme. In the third stage (Figure 3), the 

substrate (shown as a ball and stick model in cyan) displaces the cofactor and binds in the same place to get oxygenated. The 

molecular oxygen (shown as a dumbbell in red) is required for oxygenation of the substrate. 

S. Swaminathan

Figure 1 Figure 2 Figure 3
2-29

FEATURE HIGHLIGHTS

the enzyme and the cofactor binds again.

“With this back-and-forth, alternating binding, the 

process repeats over and over for continuous turnover of the product,” Swaminathan says. 

The details of this process may help scientists 

understand what happens in cases where compounds are not properly metabolized, and possibly 

develop corrective measures. One example is a 

condition called trimethylaminuria, also known as 

“fish odor syndrome,” which results from defective 

FMOs. Affected individuals are unable to oxygenate trimethylamine, a byproduct of protein digestion released by bacteria living in the gut. People 

with the disorder release trimethylamine through 

breath, sweat, and urine, producing a fish-like odor 

that can be embarrassing and result in psychological effects such as withdrawal and depression. 

People with defective FMOs might also suffer additional side effects from drugs, industrial compounds, or other chemicals. 

This research was funded by the National Institutes of Health and was conducted at the National 

Synchrotron Light Source, supported by the Office 

of Basic Energy Sciences within the U.S. Department of Energy’s Office of Science. 

For more information, see: S. Eswaramoorthy, J. 

Bonanno, S. Burley, and S. Swaminathan, "Mechanism of Action of a Flavin-Containing Monooxygenase," Proc. Natl. Acad. Sci. USA, 103, 9832-9837 

(2006).

— Karen McNulty Walsh
2-30

Fuel cells are devices capable of generating electrical energy directly without involving a thermal 

cycle that typically releases greenhouse gases, 

such as CO and NOx, into the atmosphere. Today, 

burning coal is still the primary and most efficient 

(with regard to power density) means of electrical energy production in the United States. New 

information obtained from a study performed at 

the NSLS may help catalyst researchers design 

improved fuel cell devices that can compete with 

current fossil fuel technology. 

The active material on the carbon-nanotube supports consists of tiny platinum particles on the 

order of a few nanometers in diameter, which are 

deposited on the carbon surface. The deposition 

of these particles on the nanotubes has been 

found to enhance the electrocatalytic activity for 

direct methanol fuel cells (DMFCs) by as much 

as 48% relative to carbon black, but the underlying reasons for this observation have yet to be 

fully described. The exact relationship between 

the interfacial structure of these carbon-supported 

metal nanoparticles and their subsequent chemical 

activity has long mystified catalyst scientists. 

Researchers from the University of Missouri-Rolla 

(UMR) used x-rays at NSLS beamline X18B to 

characterize the interfacial structure of platinum 

particles tethered to carbon-nanotube (CNT) catalyst surfaces. Graduate students Robert V. Hull 

and Liang Li and professors Charles C. Chusuei 

and Yangchuan Xing in the departments of Chemistry and Chemical and Biological Engineering at 

UMR collaborated on the study. The results of the 

work appear in the April 4, 2006 issue of Chemistry of Materials. The paper describes how the 

researchers used the extended x-ray absorption 

fine structure (EXAFS) technique in conjunction 

with x-ray photoelectron spectroscopy (XPS) 

(performed at UMR) to probe the surface and 

subsurface structures of the nanoparticles. They 

aimed to show evidence for the coordination of the 

platinum to oxygen atoms attached to the surface 

of the nanotubes (Pt-CNTs), which were functionalized with ketone, ester, and hydroxyl groups.

 

XPS is sensitive to probing approximately 50–100 

Å deep while EXAFS is sensitive only to the first 

few atomic layers of the metal particles being 

probed. Comparisons of the two sets of spectra 

show that both metallic and oxidized platinum 

were present. It was discovered that the outermost structure of the particles consisted of an 

oxide, PtOx, while the bulk of the nanoparticles 

was fully metallic. The XPS of the Pt 4f orbital 

showed a binding energy of 71.4 eV, indicative of 

the bulk metallic structure of the platinum nanoparCHARACTERIZING THE SURFACES OF CARBON NANO- TUBE FUEL CELL CATALYSTS

R.V. Hull1, L. Li2, Y. Xing2, and C.C. Chusuei1

1

Department of Chemistry and 2Department of Chemical and Biological Engineering, University 

of Missouri-Rolla 

Characterizing the surface structure of catalyst materials is important 

for the improvement of current fuel cell technology, which promises to 

deliver an environmentally benign means of energy production. Using 

x-rays produced at the National Synchrotron Light Source (NSLS), 

researchers at the University of Missouri-Rolla (UMR) were able to 

detect the presence of PtOx at the outer-most perimeters of a potential 

catalyst: platinum nanoparticles tethered to carbon nanotubes. At the 

same time, they determined that its bulk composition was predominantly metallic.

BEAMLINE 

X18B

PUBLICATION

R.V. Hull, L. Li, Y. Xing and C.C. 

Chusuei, “Pt Nanoparticle 

Binding on Multiwalled Carbon 

Nanotubes,” Chem. Mater., 18,

1780–1788 (2006). 

FUNDING

American Chemical Society 

Petroleum Research Fund; 

Foundation for Chemical 

Research, Inc.; Missouri Research 

Board; UMR Intelligent Systems 

Center

FOR MORE INFORMATION

Charles C. Chusuei

Chemistry Department

University of Missouri-Rolla

chusuei@umr.edu

Charles Chusuei
2-31

CHEMICAL SCIENCE

ticles (Figure 1). The nearest-neighbor distances 

for the metal nanoparticle tethered to the nanotubes were observed at distances of ~1.78 Å 

— much too short for the expected ~2.77 Å distance between metallic platinum atoms (Figure 2), 

which signified Pt–O at the outermost perimeter 

of the clusters. This structure accompanied the inFigure 2. Pt L3

 edge EXAFS Fourier Transformations of (A) 

Pt-CNTs in an aqueous colloidal suspension; (B) Pt-CNTs 

in dry powder-like form (solid gray line; Pt foil scan shown 

as a dotted, orange spectral line); and (C) a PtO2 standard.

Figure 1. Pt 4f core level XPS spectrum (right panel) of 

nanoparticles tethered onto multiwalled carbon nanotubes; 

arrow denotes evidence for Pt(II/IV) oxidation state albeit 

small in amount. Left panel shows a transmission electron 

micrograph of Pt nanoparticles ~3.5 nm in diameter; the 

scale bar shown corresponds to 100 nm.

creased DMFC activity observed. In addition to the 

dried powder catalyst materials, experiments were 

performed on the Pt-CNTs under aqueous solution 

environments to simulate the working conditions 

of the fuel cell, which exhibited the same surface 

structure as the dry powdered form.

Binding Energy, eV

Relative Intensity

R,Å

χ(R),Å-3
2-32

BEAMLINE 

X7B

PUBLICATION

J. Zhang, F. Lima, M. Shao, K. 

Sasaki, J. Wang, J. Hanson, and 

R. Adzic, "Platinum Monolayer 

on Nonnoble Metal-Nobel Metal 

Core-Shell Nanoparticle Electrocatalysts for O2

 Reduction," J. 

Phys. Chem. B., 109, 22701-22704 

(2005).

FUNDING

U.S. Department of Energy; Stony 

Brook University; CAPES (Brazil)

FOR MORE INFORMATION

Radoslav Adzic

Department of Chemistry

Brookhaven National Laboratory

adzic@bnl.gov

As the interest in a “hydrogen-based economy” 

grows, research on its major elements — hydrogen production and storage, and energy conversion in fuel cells — is expanding. While fuel cells 

are expected to become a major source of clean 

energy, existing fuel-cell technology still has two 

drawbacks: energy conversion that is lower than 

the theoretical efficiency, and electrocatalysts with 

a high Pt content. Both problems are connected to 

the rather slow electrocatalytic O2 reduction reaction (ORR). 

Several approaches explored in the past to ameliorate this disadvantage have had limited success. We, however, have demonstrated a promising way to solve these problems. Our method 

involves electrocatalysts consisting of a Pt monolayer supported on suitable metal nanoparticles. 

These electrocatalysts have a very high activity 

and an ultra-low Pt content that promises to 

alleviate the above problems. Platinum is deposited in a monolayer amount on the surfaces of 

carbon-supported non-noble metal/noble metal 

core-shell nanoparticles (Figure 1). Using nonnoble metals for the cores facilitates a further 

reduction of the content of the noble metal in the 

ORR electrocatalysts. In addition, by properly 

selecting the noble-metal shell, the activity of the 

Pt monolayer can be heightened through electronic and/or geometric effects. The choice of the 

metals constituting the shell and core is based 

on the segregation properties of the two metals, 

as well as their electronic and strain-inducing 

effects on the Pt monolayer. The nanoparticles 

were synthesized by segregating the atoms of the 

noble metal to the nanoparticle surface at elevated 

temperatures. A Pt monolayer was then deposited 

on the nanoparticles via the galvanic displacement 

by Pt of an adsorbed Cu monolayer. 

 

The noble-metal shell in the core-shell nanoparticle has two roles. First, it protects the non-noble 

core from contacting the acid electrolyte, i.e., it 

precludes its dissolution. Second, the proper shell 

can improve the catalytic properties of a Pt monolayer by affecting its electronic properties and/or 

by inducing strain in the monolayer, which increases its activity. A strong surface segregation of the 

noble metal component is the key feature of these 

systems. The surface segregation of Au, Pd, and 

Pt and their protection of the Ni or Co core from 

dissolution was verified by linear sweep voltammetry, underpotential deposition (UPD) of Cu, and 

x-ray diffraction techniques. The activity of these 

electrocatalysts, calculated as the current at 0.85 

V divided by the mass of Pt, is about 20 times 

above that of commercial Pt/C electrocatalysts. If 

the total noble-metal mass is counted, the activity 

PLATINUM MONOLAYER ON NON-NOBLE METAL - 

NOBLE METAL CORE-SHELL NANOPARTICLES ELECTRO- CATALYSTS FOR O2 REDUCTION

J. Zhang1, F.H.B. Lima2, M.H. Shao1, K. Sasaki1, J.X. Wang1, J. Hanson1, and R.R. 

Adzic1

1

Department of Chemistry, Brookhaven National Laboratory; 2On leave from the University of 

São Paulo, Brazil

We synthesized a new class of O2 electrocatalysts for fuel cell cathodes. They consist of a Pt monolayer deposited on carbon-supported 

nanoparticles that have non-noble-metal cores and noble-metal shells. 

These nanoparticles were formed from a mixture of noble and nonnoble metals. At elevated temperatures, the noble metal moves to the 

surface, while the non-noble metal remains in the core. The Pt monolayer was deposited onto the nanoparticles by galvanically displacing 

an adsorbed Cu monolayer. The mass activity of these electrocatalysts 

is more than an order of magnitude higher than that of commercial Pt/C 

electrocatalysts. Strain in the Pt monolayer and the reduced coverage 

of the reaction inhibitor (PtOH), revealed by x-ray absorption spectroscopy data, are the origin of the enhanced catalytic activity. 

Authors (from left): Radoslav Adzic, Junliang Zhang, 

Minhua Shao, and Kotaro Sasaki
2-33

CHEMICAL SCIENCE

is about four times larger. The very high activities appear to be a consequence of a strain that 

appears due to a mismatch in the lattice constants 

between the monolayers and these substrates, the 

changes in the d-band properties of the Pt monolayer itself (caused by its interaction with them), 

and the decreased PtOH coverage. These effects 

were observed by in situ synchrotron radiation 

techniques. 

In conclusion, we demonstrated the synthesis of 

a new class of electrocatalysts consisting of a Pt 

monolayer deposited on non-noble metal/noble 

metal core-shell nanoparticles. We showed that it 

is possible to devise ORR electrocatalysts, with 

activity surpassing that of state-of-the-art carbonsupported Pt electrocatalysts, that contain only a 

fractional amount of Pt and a very small amount 

of another noble metal. Consequently, the cost of 

fuel cells could be lowered considerably. Further 

work on these systems will address the question 

of their long-term stability.

Figure 1. Model for the synthesis of Pt monolayer catalysts on non-noble metal-noble 

metal core-shell nanoparticles.
2-34

The surface reaction of the oxide of actinides, 

such as uranium oxides, is one of the least studied, yet one of the most fascinating. Our interest 

in this surface reaction started a decade ago. The 

reaction represents one of the most challenging 

systems among all chemical reactions of solids. 

The f-orbitals of the actinide elements, because -orbitals of the actinide elements, because

they differ in symmetry from the d-orbitals, can 

adsorb a reactant in a unique configuration and 

thus may orient to different chemical pathways not 

seen on the surfaces of early transition metals. In 

addition, relativistic effects, due to the large size 

of the nucleus, result in a wide range of oxidation states of metal cations, 

making them very active but 

also unstable. The observation of this reaction on a 

solid surface has allowed the 

use of x-ray photoelectron 

spectroscopy (XPS) (Figure 

1). However, conventional 

XPS was not adequate to 

carry out accurate qualitative 

and quantitative investigations because of inevitable 

oxidations, over time, of 

the surface U atoms during 

data collection. By using the 

high-intensity, high-resolution (HR), and fast acquisition time available on NSLS 

beamline U12A, it was possible to study the mechanism 

of this reaction and outline 

quantitatively the changes 

in surface oxidation states 

before and after the reaction. 

Figure 2 shows the HRXPS spectra of the U4f 

and O1s lines of the clean oxygen-defected UO2

thin-film surface, as well as the same surface upon 

exposure to carbon monoxide. The main lines at 

380 and 391 eV are due to U4f7/2,5/2 of U4+ while the 

shoulder at the low binding energy side of the 

U4f7/2 is exclusively due to U cations in lower 

oxidation states than +4 (a detailed study of this 

region has been conducted in a separate work). 

Upon adsorption of carbon monoxide (b) the 

intensity of this shoulder decreases and becomes 

negligible at surface saturation (c and d). This is 

because CO has donated its oxygen atom to surface defects. A similar observation is seen in the 

O1s region. Detailed analysis of the C1s region 

has shown that the dissociation is not total. Parallel work has shown the formation of acetylene and 

ethylene as the end product at 550 K and above. 

The above three observations — oxidation upon 

adsorption, partial dissociation at room temperature, and desorption of C2 compounds at high 

temperature — can be explained in Scheme 1.

In Scheme 1, the η2-η2-bis-formyl species is proposed to be formed on a U surface; this could only 

be accommodated because of the particular symmetry of the fxy2 orbitals. The bis-formyl species 

react at room temperature to give the pinacolates; 

this in turn gives C2H2/C2H4 at high temperatures. 

Although the above reaction is not catalytic, its 

observation may open the routes for the design of 

new catalytic materials using uranium oxides or 

oxides of similar properties.

REDUCTIVE COUPLING OF CARBON MONOXIDE

MOLECULES OVER OXYGEN DEFECTED UO2 (111)

SINGLE CRYSTAL AND THIN FILM SURFACES

S.D. Senanayake1,3, G.I.N. Waterhouse1, H. Idriss1, and T.E. Madey2

1

Department of Chemistry, The University of Auckland, New Zealand; 2Department of Physics 

and Astronomy, and Laboratory for Surface Modifi cation, Rutgers, The State University of New 

Jersey; 3Present address: Chemical Sciences Division, Oak Ridge National Labororatory

Coupling reactions of chemical compounds have a unique place in 

chemistry because they represent a key step in building complex molecules from simple ones. Solid catalysts are often used to accelerate 

the reaction rate by stabilizing the reaction intermediate, and can thus 

enhance or initiate a reaction that often could not be conducted in their 

absence. Among the most challenging coupling reactions is the selective coupling of two carbon monoxide molecules to C2 compounds. 

This rare reaction, which has been previously observed in organometallic chemistry (solution chemistry), was successfully conducted on 

oxygen-defected uranium dioxide single crystal and thin-film surfaces. 

The oxidation/reduction reactions over the O-defected surfaces were 

studied using high-resolution x-ray photoelectron spectroscopy. This 

method revealed the reaction pathway.

BEAMLINE 

U12A

PUBLICATION

S.D. Senanayake, G.I.N. Waterhouse, H. Idriss, and T.E. Madey, 

"Coupling of Carbon Monoxide Molecules over Oxygen 

Defected UO2 (111) Single Crystal 

and Thin Film Surfaces," Langmuir, 

21, 11141-11145 (2005).

FUNDING

Foundation for Research Science 

and Technology; U.S. Department of Energy

FOR MORE INFORMATION

H. Idriss

Department of Chemistry

The University of Auckland

h.idriss@auckland.ac.nz

Authors (top) Hicham 

Idriss and Sanjaya 

Senanayake
2-35

CHEMICAL SCIENCE

Figure 2. HRXPS U4f and O1s lines of Ar-ion sputtered 

UO2 thin fi lm before (a) and after (b, c, and d) reacting with 

CO at the indicated exposures in Langmuir (L = 10-6 torr s).

Figure 1. Ball model of the UO2(111) surface showing 

the hexagonal arrangement of U and O atoms and lattice 

parameters. Red balls are U atoms and yellow balls are O 

atoms (A: top view, B: side view). C: Low Energy Electron 

Diffraction (LEED) of the UO2(111) surface showing the 

extended order (131 eV). The surface is entirely composed 

of oxygen atoms. Their partial removal makes the U 

atoms (initially in the second layer) highly reactive for both 

reduction and coupling reactions.

Binding Energy (eV) Binding Energy (eV)

Intensity (Arbitrary Units) Intensity (Arbitrary Units)

Intensity (Arbitrary Units)

η2 - η2 -bis formyl Pinacolate

Scheme 1
2-36

Internal combustion engines operating under leanburn conditions, such as diesel engines, exhibit 

high fuel efficiency. Removal of harmful NOx emissions from the exhaust in the presence of excess 

oxygen, however, presents a great challenge to 

the catalysis community because traditional threeway catalysts are ineffective under these conditions. Among the approaches being considered, 

urea and hydrocarbon selective catalytic reduction (SCR), and lean-NOx

 traps (LNTs, aka NOx

storage/reduction (NSR) catalysts or NOx adsorbers) are promising technologies. In LNT technology, an active oxide (alkali and/or alkaline earth) 

material takes up NOx under lean engine operation 

conditions and stores them as nitrates. In a brief 

rich cycle, these nitrates are released from the 

active oxide catalyst component, and reduced to 

N2 on the precious metal component of the catalyst.

Because even low concentrations of SO2 in the 

emission gradually reduces the ability of the active 

phase to store NOx, the resistance of the material 

to SO2 poisoning remains a critical issue. Meanwhile, since we have shown that NOx

 adsorption/

desorption chemistry is strongly dependent on the 

loading of barium, an important question concerns 

the variation of the desulfation chemistry as a 

function of barium content in the LNT formulation. 

As such, we performed a multi-spectroscopy study 

to understand desulfation processes on Pt-BaO/

Al2O3 LNT materials with varying barium loadings. 

In particular, we investigated the desulfation behavior of pre-sulfated Pt-BaO(8 or 20 wt%)/Al2O3

catalysts using H2 temperature programmed reaction (TPRx). These two BaO loadings were chosen 

because we have previously shown that the 

Ba-phase morphologies are significantly different; 

notably, BaO consists of a monolayer “coating” 

on the alumina surface in Pt-BaO(8)/Al2O3, while 

this monolayer phase coexists with a “particulate” 

or bulk-like BaO phase in the Pt-BaO(20)/Al2O3

sample. Thus, we also followed the changes in 

catalyst morphology and sulfur oxidation states 

during desulfation processes using synchrotron 

time-resolved x-ray diffraction (TR-XRD) and sulfur 

K-edge x-ray absorption near-edge spectroscopy 

(XANES), which were performed on the NSLS 

beamlines X7B and X19A, respectively.

Figure 1 shows the H2 TPRx spectra of sulfated 

Pt-BaO(8)/Al2O3 and Pt-BaO(20)/Al2O3 samples, 

obtained by ramping the temperature of these 

samples in a H2/He flow while continually monitoring the product gases with a mass spectrometer. 

H2S is the primary product of the reaction between H2 and sulfur species on the sample. H2S 

is formed at higher temperature for the sample 

with higher barium loading, implying that the type 

SULFUR K-EDGE XANES AND TR-XRD STUDIES OF

Pt-BaO/al2O3 LEAN NOX TRAP CATALYSTS: EFFECTS

OF BARIUM LOADING ON DESULFATION

D.H. Kim1, J. Szanyi1, J.H. Kwak1, T. Szailer1, J.C. Hanson2, C. Wang1, and C.H.F. 

Peden1

1

Institute for Interfacial Catalysis, Pacifi c Northwest National Laboratory; 2Chemistry Department, Brookhaven National Laboratory

Sulfur K-edge x-ray absorption near-edge spectroscopy (XANES) and 

in situ time-resolved x-ray diffraction (TR-XRD) are used to show that 

the removal of sulfur (in the form of BaSO4) from Pt-BaO(x)/Al ) from Pt-BaO(x)/Al 4 2O3 (x = 

wt% BaO) catalysts is strongly dependant on barium loading. Sulfated 

Pt-BaO(8)/Al2O3, consisting predominantly of monolayer BaO/BaCO3

species, displays more facile desulfation by H2 at lower temperatures 

than sulfated Pt-BaO(20)/Al2O3, a material containing primarily particulate BaO/BaCO3 species. This suggests that the initial morphology 

differences between the two samples play a crucial role in determining the extent of desulfation and the temperature at which it occurs, a 

result that may be important in developing more sulfur-resistant LNT 

catalyst systems.

BEAMLINES 

X7B, X19A

PUBLICATION

D.H. Kim, J. Szanyi, J.H. Kwak, T. 

Szailer, J.C. Hanson, C. Wang, 

C.H.F. Peden, “Effect of Barium 

Loading on the Desulfation of 

Pt-BaO/Al2O3 Studied by H2 TPRx, 

TEM, Sulfur K-edge XANES and Insitu TR-XRD,” J. Phys. Chem., 110, 

10441-10448 (2006).

FUNDING

U.S. Department of Energy

FOR MORE INFORMATION

Do Heui Kim

Institute for Interfacial Catalysis

Pacifi c Northwest National Lab

do.kim@pnl.gov

Authors (from left) Ja Hun Kwak, Janos Szanyi, Do 

Heui Kim, and Chuck Peden
2-37

CHEMICAL SCIENCE

of barium sulfate species formed upon uptake 

of SO2 is different depending on the loading of 

barium species – surface or ‘monolayer’ sulfates 

for Pt-BaO(8)/Al2O3, and ‘bulk’ BaSO4 for the PtBaO(20)/Al2O3 sample. In addition, the amount of 

H2S produced over Pt-BaO(8)/Al2O3 is two times 

larger than that of the sample with higher barium 

loadings, which suggests a more facile desulfation 

of ‘monolayer’ BaSO4.

Sulfur K-edge XANES experiments were carried 

out to investigate changes in the oxidation states 

of sulfur as a function of H2 reduction temperature. We collected samples after H2 TPRx up to 

553 K, 743 K and 1073 K (see arrows in Figure 

1). After H2 TPRx up to 553 K for the sulfated PtBaO(8)/Al2O3 sample, the spectrum in Figure 2(A)

contains a small peak at 2472 eV, which can be 

assigned to a sulfide-like (S2-) species, while the 

main sulfate (SO4

2-) peak is unchanged. After H2

TPRx up to 1073 K, the sulfate peak nearly disappears, while there is an increase in features from 

lower oxidation state sulfur species (sulfide-like 

and sulfite-like (SO3

2-)). The sulfated Pt-BaO(20)/

Al2O3 sample shows qualitatively similar behavior 

as shown in Figure 2(B). However, compared with 

the sample with lower barium loading, Pt-BaO(20)/

Al2O3 contains a significantly larger amount of 

residual sulfur species of all types after H2 TPRx 

up to 1073 K, which is consistent with the H2 TPRx 

results.

Figure 3 shows a series of XRD patterns obtained 

during H2 TPRx for the sulfated Pt-BaO(20)/Al2O3

sample. The room temperature XRD contains 

peaks assigned to BaSO4. Up to about 773 K, the 

BaSO4 phase is unchanged. However, above 773 

K, diffraction peaks associated with BaS 

appear and continue to grow with increasing 

temperature, along with a corresponding drop in 

the intensities of the BaSO4 peaks. Compared with 

the Pt-BaO(20)/Al2O3 sample, Pt-BaO(8)/Al2O3

contains much smaller amounts of BaS, confirming 

that residual sulfur species were present at much 

lower concentrations for the lower barium loading 

sample.

Figure 2. Sulfur K-edge XANES spectra of (A) sulfated PtBaO(8)/Al2

O3, and (B) sulfated Pt-BaO(20)/Al2O3 samples.

Normalized fluorescence yield (arb units)

Energy (keV)

2.465 2.470 2.475 2.480 2.485 2.490

Energy (keV)

Normalized fluorescence yield (arb units)

sulfation ulfation

H2 TPRX up to 553 K TPRX up to 553 K

H2 TPRX up to 1073 K TPRX up to 1073 K

2.465 2.470 2.475 2.480 2.485 2.490

(A)

(B)

Figure 3. TR-XRD patterns collected during H2 TPRx from 

a sulfated Pt-BaO(20)/Al2O3 sample. 

Figure 1. H2 TPRx spectra for sulfated Pt-BaO(8)/Al2O3 and 

Pt-BaO(20)/Al2O3 samples.

Temperature (K)

MS signal: H2S (m/e = 34) (A. U.)

2.465 2.470 2.475 2.480 2.485 2.490

sulfation

H2 TPRX up to 553 K

H2 TPRX up to 753 K

H2 TPRX up to 1073 K TPRX up to 1073 K

2.465 2.470 2.475 2.480 2.485 2.490

SO4

2-

SO3

2-

S2-

↑

↑

SO4

2-

S2-
2-38

In most cases, superconductivity develops from a 

metallic state, and is characterized by the formation of a superconducting energy gap at the Fermi 

surface. In metals and alloys, this gap is isotropic. 

However, a unique feature of the copper-oxide superconductors is that the gap is highly anisotropic, 

actually going to zero at some points on the Fermi 

surface (this is referred to as a d-wave gap). Optical studies allow the nature of both the metallic 

and superconducting states to be probed.

Single crystals of LBCO have been cleaved in air, 

revealing large, optically flat surfaces oriented 

parallel to the copper-oxygen planes where the 

superconductivity is thought to originate in these 

materials (Figure 1). The temperature dependence of the reflectance has been measured at 

a near-normal angle of incidence over a wide 

frequency range (about 2 meV to over 4 eV). The 

reflectance is in fact a complex quantity, consisting of an amplitude and a phase; in this case, only 

the amplitude is measured. However, if the reflectance is measured over a wide enough range (as 

is the case here), then the Kramers-Kronig relations may be used to determine the phase – once 

these two quantities are known, other quantities 

such as the optical conductivity may be calculated. 

The optical conductivity of LBCO at the 1/8 doping 

is shown in Figure 2. The conductivity of metals 

is often described by the simple Drude model, 

which may be described by a plasma frequency 

(a measure of the concentration of free carriers), 

and a scattering rate; the frequency response is a 

Lorentzian centered at the origin, and the width at 

half maximum is the scattering rate. This simple 

picture describes the optical conductivity of LBCO 

quite well, at least until about 60 K. However, 

for this particular doping, LBCO undergoes an 

orthorhombic to tetragonal transition at about 60 

K, leading to formation of static charge stripes. 

Long-range charge order in a material often leads 

to the formation of a charge gap that destroys the 

conductivity in the material. However, as Figure 2

clearly shows, while the response associated with 

the Drude component is shrinking, the conductivity remains metallic down to the lowest measured 

temperature. We interpret this response to indicate that the charge order is responsible for a partial gapping of the Fermi surface. Angle-resolved 

photoemission studies on this material do indeed 

detect a gap in this material below 60 K, but the 

gap is highly anisotropic and has a d-wave character; the metallic excitations are associated with the 

ungapped or nodal regions. This behavior is also 

CHARGE ORDER AND SUPERCONDUCTIVITY IN A

HIGH-TEMPERATURE SUPERCONDUCTOR

C.C. Homes1, S.V. Dordevic1,2, G. Gu1, Q. Li1, T. Valla1, and J.M. Tranquada1

1

Condensed Matter Physics & Materials Science Department, Brookhaven National Laboratory; 

2

Department of Physics, The University of Akron

Superconductivity at elevated temperature was originally discovered in 

the lanthanum barium copper oxide materials (La2-xBaxCuO4, or LBCO). 

However, because these materials were difficult to grow as single 

crystals, work quickly shifted to the analogous La2-xSrxCuO4 (LSCO) 

materials. Recently, large single crystals of LBCO have been grown 

that are suitable for optical studies. All high-temperature superconductors share the trait that the parent compounds are insulating, and that 

superconductivity is induced by chemical doping to produce a superconducting “dome;” LBCO is superconducting for Ba-dopings of about 

0.05 to 0.23. Curiously, at the 1/8 doping, charge-order develops and 

superconductivity is destroyed, leading to an unusual electronic state.

BEAMLINES 

U10A, U13UB

PUBLICATION

C.C. Homes, S.V. Dordevic, G. 

Gu, Q. Li, T. Valla and J.M. Tranquada, “Charge Order, Metallic 

Behavior, and Superconductivity 

in La2-xBaxCuO4 with x =1/8,” Phys. 

Rev. Letts., 96, 257002 (2006).

FUNDING

U.S. Department of Energy

FOR MORE INFORMATION

Christopher Homes

Condensed Matter Physics & 

Materials Science Dept.

Brookhaven National Laboratory

homes@bnl.gov

Authors (from left): Christopher Homes, John Tranquada, 

and Genda Gu.
2-39

CONDENSED MATTER PHYSICS

observed in the normal-state of the underdoped 

copper-oxide materials, which are referred to as 

“nodal metals.” It is tempting to associate this 

gap with a competing instability, such as a charge 

density wave. However, the fact that the superconFigure 2. The ab-plane optical conductivity of LBCO for the 

1/8 doping in the infrared region between 60 and about 5 K, 

showing a steady decrease and narrowing of the Drude-like 

component. 

ductivity recovers quickly on either side of the 1/8 

anomaly suggests that the gap we observe in the 

1/8 material is in fact the superconducting gap, but 

with a near total absence of phase coherence.

Figure 1. The unit cell of (La,Ba)2CuO4 [La, (Ba) – green, 

Cu – blue, O – red (sheet), orange (apical)] illustrating the 

copper-oxygen (ab) planes and bond coordination; the long 

axis is the c axis.

Frequency (cm-1)

Conductivity (

Ω-1 cm-1)

(meV)
2-40

OBSERVATION OF NITROGEN POLARIZATION IN Fe-N

USING SOFT X-RAY MAGNETIC CIRCULAR DICHROISM

C. Sánchez-Hanke1, R. Gonzalez-Arrabal2, and R.A Lukaszew3

1

National Synchrotron Light Source, Brookhaven National Laboratory; 2Centro de Microanálisis 

de Materiales, University Autónoma of Madrid, Spain; 3Physics and Astronomy Department, 

University of Toledo

Fe-nitrides together with transition metal oxides are part of a new 

generation of interesting magnetic materials extensively investigated 

because of their potential use in future magnetic devices. Fe-N is a 

complex system, with a rather complicated phase diagram containing multiple phases like γ’-Fe4N, ε’-Fe3N, ξ-Fe2N and α”Fe16N2. The α” 

Fe16N2 phase is the most interesting phase, with a reported magnetic 

moment up to 4 times that of the Fe one. The fabrication of singlephase samples of Fe-N is currently a complicated task, especially for 

thin films of the α” phase. Our interest to study Fe-N thin films is driven 

by the search for a better understanding of nitrogen’s role in the magnetic properties of this system. Previous structural reports place the 

N atoms in an interstitial position inside the Fe structure, suggesting 

rather weak interactions between Fe and N.

BEAMLINE 

X13A

PUBLICATION

C. Sánchez-Hanke, R. Gonzalez-Arrabal, J. E. Prieto, E. 

Andrzejewska, N. Gordillo, D.O. 

Boerma, R. Loloee, J. Skuza, and 

R.A Lukaszew, “Observation of 

Nitrogen Polarization in Fe-N using Soft X-ray Magnetic Circular 

Dichroism,” J. Appl. Phys., 99, 

08B709 (2006).

FUNDING

U.S. Department of Energy; The 

“Ramon y Cajal” program of the 

Spanish Ministry of Education and 

Science 

FOR MORE INFORMATION

Cecilia Sánchez-Hanke

NSLS-BNL

hanke@bnl.gov

Authors (from top) Cecilia 

Sanchez-Hanke and Rosa 

Alejandra Lukaszew

Using x-ray Magnetic Circular Dichroism (MCD), 

we studied a series of Fe-N thin films in a thickness range between 15 and 100 nm with predominantly γ’-Fe4N phase. Prior to the MCD measurements, the samples were structurally characterized with x-ray diffraction (XRD) and magnetically 

characterized with a Superconducting Quantum 

Interference Device (SQUID), making use of the 

Polar Magneto-Kerr effect (MOKE) (Figure 1). The 

P-MOKE data show an expected 4-fold symmetry 

as the Fe-N thin films 

were grown on a 

(001) FCC MgO substrate shown by the 

XRD measurements.

MCD measurements 

were collected at the 

National Synchrotron Light Source 

beamline X13A. This 

beamline delivers modulated soft 

x-rays in an energy 

range between 200 

and 1600 eV, switching between left and 

right polarization with 

frequencies close to 

22 Hz. MCD, or the 

difference in the absorption signal of the 

sample collected with 

left and right elliptically polarized x-rays, 

provides a unique element-specific tool to 

study magnetic properties in magnetic materials. 

With the difference signal, the sum signal, and the 

help of the Sum Rules, it is possible to determine 

the spin and orbital magnetic moment associated 

with each of the elements present in the sample. 

Modulated x-rays switching at high frequencies 

allow the simultaneous collection of the absorption and MCD signal in a single energy scan. The 

modulation also increases the sensitivity in the 

detection of small magnetic signals as well as the 

collection of the MCD signals in highly diluted ferromagnetic materials. These characteristics made 

X13A an adequate choice to conduct the experiment in order to show the contribution of nitrogen 

to the Fe-N magnetic moment.

XMCD measurements were performed on Fe-N 

thin films at different incident angles, simultaneously collecting the reflectivity and the MCD 

spectra over the Fe LII and LIII and the N K absorption edges (Figure 2). The left panel of Figure 

2 shows the N polarization in the thin film with a 

small MCD signal, indicating that the experiment 

was successful. The detected MCD signal, in 

the range of 10-5, is close to the beamline detection limit. On the right panel, the Fe reflectivity 

and MCD signal were collected at two different 

incident angles. The reflectivity spectra at the Fe 

edges show two different components at the LIII

absorption edge. These signals can be enhanced 

independently depending on the angle of incidence. Comparing these spectra with a spectrum 

recorded on pure Fe relates the presence of the 

additional features in the spectra to different Fe 

sites in structure depending on the phase. The 

signal to noise ratio in the nitrogen MCD data was 

not good enough to try to apply the Sum Rules 
2-41

CONDENSED MATTER PHYSICS

Figure 3. Hysteresis loops recorded at photon energies 

where the MCD signal presents a maximum. The N and Fe 

loops present the same coercive fi eld. 

Figure 1. Azimuthal plot, Polar MOKE for a typical FeN 

sample. We noticed four-fold symmetry characteristic 

of (001) fcc structure. The vertical axis corresponds to 

coercive fi eld (Oe).

Figure 2. Fe and N refl ectivity and XMCD spectra recorded 

at different angles. Fe spectra were obtained at 8 (dashed/

dots) and 11 (continuous/squares) incident angle of the xrays on the sample. Pure Fe signal (dashed/triangles) was 

also collected at 8 degrees.

Magnetic field (Oe)

Difference (arb. units)

Sum Intensity (arb.units)

Difference Intensity (arb.units)

Energy (eV) Energy (eV)

and calculate the contribution to the magnetic 

moment of the sample. But the signal was sufficient to perform element specific hysteresis loops 

together with the Fe (Figure 3). Hysteresis loops 

were recorded for nitrogen and for each of the Fe 

components. The loops present the same shape 

as well as the same coercive field that shows the 

intimate relation between the N and the Fe signal. 

We demonstrated that the nitrogen has some contribution to the magnetic moment of the sample, 

although small but detectable in the case we refer 

to here. Our data demonstrate an intricate Fe-N 

structure with the coexistence in the samples of 

multiple phases. We speculate that each feature 

or peak in the Fe spectra corresponds to Fe atoms 

occupying different sites inside the structure of 

the nitride. The complexity of the studied thin films 

does not allow us associate the Fe features to any 

specific phase, although we expect that an MCD 

study on single-phase samples, especially on the 

α” one, will help in the understanding of the contribution of the nitrogen, if any, to the total magnetic 

moment.
2-42

Ferromagnets are all around us – in the seal on 

the door of the refrigerator, in the headset of the 

iPod, and in the computer’s hard disk, to name a 

few examples. In ferromagnets, the interaction between the electrons makes the electron spins (and 

the associated magnetic moments) line up parallel 

to each other. What happens if the interaction is 

different, favoring spins in opposite directions? 

These materials, the so-called antiferromagnets, 

do not have widespread applications, but they are 

much less understood and the subject of intensive 

current research. 

In this study we looked at the quasi one-dimensional antiferromagnet, LiCu2O2. The copper in 

this compound has two different ionization states. 

The Cu3+ ions are magnetically neutral, but the 

Cu2+ ions carry magnetic moments with spin 1⁄2. 

These ions form quasi one-dimensional chains 

with a zig-zag “ladders” along the b direction in the 

crystal (Figure 1). 

In addition to its quasi one-dimensional structure, 

this material has two other interesting characteristics: The interaction between the moments goes 

beyond the first neighbors, and the structure has 

a triangular motif. In antiferromagnets both of 

these properties lead to frustration: it is impossible to find an arrangement of spins so that all 

interactions lead to a minimum of the energy. (For 

example, three spins on a triangle cannot all point 

opposite to each other.) Because of the absence 

of a simple classical ground state, quantum effects 

and fluctuations are expected to be important in 

this material. However, experiments, primarily 

NMR and neutron scattering, led to a somewhat 

disappointing conclusion. Instead of a fancy quantum state, the spins exhibit a helical order along 

the chains, with a wavevector Q incommensurate 

to the lattice. In zero external field all spins were 

found to be parallel to the a-b plane. (Figure 2) 

The intricate spin order was interpreted in terms of 

a classical interacting spin model, with no (or very 

little) quantum fluctuations. Why does this system 

of spin 1⁄2 electrons behave as if quantum mechanics did not exist? This was the principal question 

in our study. 

We searched for the answer by trying to measure 

the energy gap in the excitation (magnon) spectrum, since the absence of low-energy excitations 

stabilizes the classical ground state. The main 

experimental results of the study are shown in 

the upper panel of Figure 3. There is a weak, 

but visible resonance at finite frequencies in zero 

external field. This is a direct measurement of the 

SPIN-LATTICE INTERACTION IN THE QUASI-ONE- DIMENSIONAL HELIMAGNET LiCu2

O2

L. Mihály1,2, B. Dóra2, A. Ványolos2, H. Berger3, and L. Forró3

1

Department of Physics and Astronomy, Stony Brook University; 2Department of Physics, Budapest University of Technology and Economics, Hungary; 3

EPFL, Switzerland 

We studied electron spin resonance (ESR) in LiCu2O2, using the farinfrared/high magnetic field instrumentation at U12IR. The electron 

spins in this quasi one-dimensional material develop a helical order at 

low temperature. The excitation of this spin chain results in a fieldand frequency-dependent absorption feature in the IR spectrum. We 

compared the results to a theoretical analysis of the excitation, and 

we deduced the characteristic anisotropy energy of the spin system. In 

particular, we determined the interactions that keep the spins confined 

to a particular plane relative to the crystal. 

BEAMLINE 

U12IR

PUBLICATION

L. Mihály, B. Dóra, A. Ványolos, 

H. Berger, and L. Forró, “SpinLattice Interaction in the QuasiOne-Dimensional Helimagnet 

LiCu2O2,” Phys. Rev. Lett., 97, 

067206 (2006).

FUNDING

Hungarian Research Funds OTKA; 

Swiss National Science Foundation; U.S. Department of Energy

FOR MORE INFORMATION

László Mihály

Dept. of Physics and Astronomy

Stony Brook University

laszlo.mihaly@sunysb.edu

Authors (from left): Bálint Náfrádi, László Forró and László 

Mihály
2-43

CONDENSED MATTER PHYSICS

energy gap, responsible for suppressing quantum 

fluctuations. 

What is the source of the energy gap? And here is 

a related question: What makes the spins prefer 

the a-b plane instead of making a helical structure 

in some different planes? The anisotropy in interaction between the spins is needed to answer both 

of these questions. In this case the anisotropy is 

of the “easy plane” type: The interaction energies 

are larger for spins in the a-b plane than for spins 

in other directions. We performed theoretical modeling and, by fitting the resonance positions for all 

field, we determined a single anisotropy parameter 

for this system. The model also described the 

observed strong field dependence in the intensity 

of the resonance.

Interestingly, the model predicted two resonances 

at finite fields, but the other one (green line in 

Figure 3) was much weaker. We suspected that 

the instrument we used was not sensitive enough 

to see this other line, and we sent the sample 

back to EPFL, (Lausanne, Switzerland), where 

Bálint Náfrádi did more ESR measurements. The 

spectrometer in Lausanne operates at a few fixed 

frequencies, and it cannot be used to create a full 

two-dimensional map of absorption intensity seen 

in Figure 3, but it is much more sensitive than 

ours. The resonance line has been found at the 

predicted position, and we witnessed one of the 

rare cases when the theory not only interpreted 

the existing experimental data, but actually predicted the result of a new experiment. 

Figure 3. Upper panel: Absorption due to spin resonance 

as a function of fi eld and frequency. Darker shades indicate 

stronger absorption. The red line is a theoretical fi t to the 

line position. The green line is another resonance predicted 

by the theory. Lower panel: Simulated experimental results, 

based on the calculated intensity of the absorption.

Figure 1. Crystal structure of LiCu2O2. The magnetic Cu2+

ions are dark blue, the non-magnetic copper is green, the 

lithium is light blue and the oxygen is red. The dark blue 

bonds emphasize the triangular spin ladder.

Figure 2. Helical spin order along a triangular ladder in 

LiCu2O2. All spin directions are parallel to the a-b plane, 

and subsequent spins on the same leg of the ladder make 

an angle slightly larger than 60o.
2-44

BEAMLINE 

X23B

PUBLICATION

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).

FUNDING

National Science Foundation

Offi ce of Naval Research

FOR MORE INFORMATION

Vincent Harris

Dept. of Electrical and Computer 

Engineering

Northeastern University

harris@ece.neu.edu

Manganese ferrite (MnFe2O4) is a well-studied 

spinel ferrite that has low magnetic anisotropy 

(Ha) at room temperature (K1 = -33×103 erg/cm3

or Hu = 2|K1|/MS = 175 Oe) arising from the low 

magnetocrystalline anisotropy energy common 

to cubic structures. This low Hu value limits the 

applications of this ferrite, or more generally, most 

cubic spinel ferrites, to frequencies at or below 

the S-band (1-5 GHz). To overcome this limitation, 

large magnetic fields are needed to achieve a high 

ferromagnetic resonance frequency and increase 

the bandwidth of these materials. These large 

magnetic fields do not allow for the miniaturization 

of such potential devices, however. 

The enhancement of the magnetic anisotropy in 

manganese ferrite is related to the oxygen processing pressure used in the pulsed laser deposition process (Figure 1). We measure a large 

growth-induced anisotropy for both low (Hu~5000 

Oe) and high oxygen-processing pressures (~1500 

Oe). The natures of these magnetic anisotropies 

are quite different. For example, at low oxygenprocessing pressures the magnetization aligns in 

the film plane, as one might expect from the influence of the demagnetizing energy. However, at 

high pressures the anisotropy aligns perpendicular 

to the film plane. 

One possible source of this magnetic anisotropy 

derives from the distribution of magnetic cations 

within the unit cell. In order to measure the cation 

distribution, select samples were subjected to 

EXAFS (extended x-ray absorption fine structure) 

measurements. Data collection was performed 

using beamline X23B at the National Synchrotron Light Source in fluorescence yield at room 

temperature. At the time data were collected, the 

storage-ring energy was 2.54 GeV and the ring 

current ranged from 180-250mA. Here, we applied 

a multi-edge refinement using Athena and Artemis 

codes of Ravel and Newville, respectively, to analyze the cation distribution of these samples, which 

were produced under different oxygen pressures. 

Figure 2 is a plot of representative best-fit data for 

both Mn and Fe EXAFS.

With an increase in oxygen pressure used in 

processing, the octahedral site occupancy of the 

manganese ions increases, as measured using 

EXAFS, from 32% to greater than 50%. This is 

compared with the bulk equilibrium distribution of 

LARGE INDUCED MAGNETIC ANISOTROPY IN PULSED

LASER DEPOSITED MANGANESE SPINEL FERRITE FILMS

X. Zuo1, A. Yang1, S.-D. Yoon1, J.A. Christodoulides2, J. Kirkland3, V.G. Harris1, and 

C. Vittoria1

1

Department of Electrical and Computer Engineering, Northeastern University; 2Naval Research 

Laboratory; 3Sachs Freeman Associates

Here, we report the oxygen-pressure dependence of magnetic anisotropy in pulse laser deposited MnFe2O4 films. Magnetic anisotropy fields 

are shown to reach 5 kOe when the films are processed at oxygen 

pressures below 5 mTorr. The bulk values are around 200 Oe. Further, 

the preferred direction of magnetization can be aligned either along 

the film plane (pOx<8 mTorr), as is typical, or perpendicular to it (pOx>8 

mTorr). The ability to induce large perpendicular magnetic anisotropy 

in spinel ferrites allows for new applications above S-band frequencies 

(i.e. phase shifters, filters, isolators, and circulators) to be considered.

Authors (top, from left) Soack Dae Yoon, Carmine 

Vittoria, Aria Yang, and Vince Harris (bottom, from left) 

Joseph Christodoulides, Xu Zuo, and John Kirkland
2-45

CONDENSED MATTER PHYSICS

20%. Correspondingly, the Fe octahedral occupation decreases from 84% to 75%. The difference 

in site distribution may be influenced by the difference in cation valence caused by the oxygen 

pressure, lattice strain from the mismatch in lattice 

constants and thermal expansion coefficients, or 

from the large effective quench rate.

As the oxygen pressure used in processing is 

increased from 1 to 50 mTorr there are significant 

changes in the physical state of the films. We 

envision that at low oxygen pressures (p<5 mTorr), 

anion defects arise from the incomplete oxidation of cations on the surface of the growing film. 

These defects lead to a greater occupation of Fe2+

on the octahedral sites, providing large contributions to the uniaxial anisotropy constant from a 

single ion anisotropy mechanism. At pressures 

greater than 8 mTorr, Hu becomes negative and 

the magnetization aligns perpendicular to the film 

plane. At higher pressures the ions in the ablated 

flux experience more collisions en route to the 

substrate, which reduces their kinetic energy and 

subsequently reduces their mobility on the surface 

of the growing film. This lack of mobility leads to 

the freezing in of cation disorder. In the case of 

MnFe2O4 this results in an increase in the inversion of Mn cations, that is, the distribution of Mn 

on the octahedral sublattice. Another interesting 

trend seen in the EXAFS analysis is the increase 

in the oxygen displacement parameter (commonly 

denoted by u). We speculate that this distortion is 

a direct consequence of the local strain resulting 

from the cation disorder and results in a tetragonal distortion of the unit cell. This breaking of the 

crystal symmetry leads to perpendicular anisotropy via a magnetocrystalline anisotropy mechanism.

Figure 2. Uniaxial magnetic anisotropy fi eld (Hu) and 

saturation magnetization (4πMS) as functions of oxygen 

pressure used in PLD growth. Me is the vector defi ning the 

magnetic easy axis.

Radical Coordinates (Angstrom)

Real Fourier Transform Amplitude 

(Angstrom-3)

Figure 1. EXAFS data as the real part of the Fourier 

transform from Mn (a) and Fe (b) K-edge absorption (solid 

curve) with best fi t data (symbols) for a MnFe2O4 fi lm 

deposited on a (100) MgO substrate at an oxygen pressure 

of 1 mTorr.

ρO2

4πMS (kG) and 

Hu (kOe)
2-46

OBSERVATION OF SURFACE LAYERING IN A

NONMETALLIC LIQUID

H. Mo1, G. Evmenenko1, S. Kewalramani1,K. Kim1, S.N. Ehrlich2, and P. Dutta1

1

Department of Physics & Astronomy, Northwestern University; 2National Synchrotron Light 

Source, Brookhaven National Laboratory

It has previously been reported, on the basis of synchrotron x-ray 

scattering studies, that many liquid metals have oscillatory density 

profiles (i.e. smectic-like layering) at their free surfaces. On the other 

hand, previous x-ray studies of many nonmetallic isotropic liquids have 

detected no such surface ordering. Is this effect due to the electron 

gas and therefore unique to liquid metals? We used x-ray reflectivity to 

study a molecular liquid, tetrakis(2-ethylhexoxy)silane. When cooled to 

227K and below, the bulk remains liquid but density oscillations appear 

at the surface. There is only short-range lateral order, just as in liquid 

metals and unlike surface freezing. Our results confirm theoretical 

predictions that a surface-layered state will appear in any liquid at sufficiently low temperatures, if not preempted by freezing.

BEAMLINE 

X18A

PUBLICATION

H. Mo, G. Evmenenko, S. Kewalramani, K. Kim, S.N. Ehrlich, and 

P. Dutta, "Observation of Surface 

Layering in a Nonmetallic Liquid,"

Phys. Rev. Letts., 96, 096107 

(2006).

FUNDING

National Science Foundation

U.S. Department of Energy

FOR MORE INFORMATION

Haiding Mo

Dept. of Physics and Astronomy

Northwestern University

mo@northwestern.edu

Haiding Mo

The traditional picture of the free surface of a liquid is that the density changes monotonically from 

that of liquid bulk to that of the vapor. This picture 

describes dielectric liquid surfaces near room 

temperature quite well. However, x-ray scattering 

experiments have established that liquid metals 

and metallic alloy surfaces are layered. 

Recently, Chacón et al concluded from simulations that surface layering will appear in any liquid 

below about 0.2Tc, where Tc is the critical temperature, provided that it is not preempted by freezing. 

According to this theory, metallic liquid surfaces 

are found to be layered because they have high 

Tc values and so room temperature is below T/Tc ~ 

0.2, while Tc is low for most dielectric liquids and 

so room temperature corresponds to T/Tc ~ 0.4 - 

0.5. Many dielectric liquids will freeze above T/Tc ~ 

0.2, making the necessary temperatures inaccessible. If one finds a dielectric liquid with relative 

high Tc and low melting point Tm, so that Tm/Tc is 

less than 0.2, one should be able to observe surface layering in this dielectric liquid.

We have studied the surface 

of a molecular 

liquid, tetrakis(2-ethoxyhexoxy)-silane 

(TEHOS), using 

x-ray reflectivity 

and confirmed 

the prediction 

of Chacón. 

TEHOS is an 

isotropic (nonliquid-crystalline) dielectric liquid. The molecule 

consists of one Si and four O atoms in the center, 

surrounded by four saturated branched alkanes, 

forming a “wax coating” that makes the molecules 

nonreactive and roughly spherical. Viscosity 

measurements have shown that it is a fluid down 

to at least 219 K. Using x-ray scattering in transmission, and differential scanning calorimetry, we 

have found no evidence of a bulk phase transition 

down to 190 K. Its Tc is estimated to be ~950 K.

In order to easily cool the liquid, we prepared 

~5000Å films of TEHOS supported on silicon substrates, which were formed by putting a few drops 

of liquid on the substrates, allowing the liquid to 

spread, and then draining the excess. There is 

no interference between the two interfaces of the 

films because the film thickness is much larger 

than the x-ray coherence length. To avoid seeing features in the reflectivity due to solid-liquid 

interface layering, we prepared and used substrates with RMS surface roughness >20Å. We 

have confirmed that the scattering features due to 

interfacial layers can no longer be seen when the 

substrate surface is rough.

Figure 1 shows the specular reflectivity R divided 

by the Fresnel reflectivity RF at several temperatures. At 237 K (and at higher temperatures, not 

shown here), the scans are featureless, similar, 

to those from typical nonlayered dielectric liquids 

surfaces. At lower temperatures, distinct reflectivity oscillations are seen. A peak occurs at about 

0.6 Å-1, which matches precisely the peak position 

of the bulk scattering data, and signifies that the 

layering occurs at the surface. The temperature 

threshold corresponds to T/Tc ≈ 0.25.
2-47

CONDENSED MATTER PHYSICS

Figure 1. Normalized specular refl ectivity for ~5000 

Å TEHOS fi lms on rough silicon wafers at different 

temperatures. Lines are best fi ts using the electron density 

profi les shown in Figure 2. The data are displaced vertically 

for clarity.

Figure 2. The dashed lines show best-fi t electron densities 

as functions of distance from the surface for ~5000 Å 

TEHOS fi lms at different temperatures. The solid lines show 

the density profi les with capillary broadening removed.

We fit the data in Figure 1 by modifying the ‘semiinfinite series of Gaussians’ model frequently used 

to fit reflectivity data from liquid metal surfaces. 

Good fits were obtained as shown as solid curves 

in Figure 1. Figure 2 shows the electron densities obtained from the fit. The dashed lines are 

the best-fit density functions; the solid lines are 

the same functions with the capillary width set to 

zero. In other words, the solid lines show what 

the surface profiles would look like if they had not 

been broadened by thermal capillary waves. The 

profiles show that at high temperature the density 

changes monotonically, but at low temperatures 

there are layers. The in-plane scattering data 

show only liquid-like order, just as at liquid metal 

surfaces.

Our results confirm the theoretical prediction that 

dielectric liquids will show layered structure at the 

surface if cooled down to sufficiently low temperature. In other words, the surface-layered state is a 

general property of the liquid phase, not one that 

is limited to liquid metals.

Z (Å) Z (Å)

ρ/ρbulk

Q (Å-1)

R/RF
2-48

The THz region of the electromagnetic spectrum 

lies between the infrared and the microwave. Only 

over the past decade has this region become more 

available for scientific research and applications 

as moderate intensity sources have emerged. 

Accelerator-based CSR provides a category of 

broadband THz sources with much higher power. 

The stability of radiation flux, familiar to many 

synchrotron radiation users in synchrotron light 

sources, is also a distinguishing characteristic of 

the CSR obtained from a ring-based THz source. 

Source research efforts in past years predict that 

the achievable stable CSR power and spectrum 

of a ring-based source are strongly dependent on 

ring RF frequency and gap voltage. At present, the 

RF frequencies employed in light-source storage 

rings are 500 MHz and below for practical reasons. For example, the BESSY II storage ring, at 

this frequency, has demonstrated CSR in the THz 

region. The MIT-Bates SHR is the only storage 

ring that is equipped with an S-band (2.856 GHz) 

RF system. The system was originally designed 

to facilitate uniform pulse stretching operation for 

nuclear physics. However, it has also been successfully operated in a storage mode for years 

with this RF system. This provides us with an 

excellent opportunity to investigate the potential of 

a ring-based source at its technical limits.

To attain short electron bunch length (~ 1 mm, 

rms), the SHR optics were turned into a low-momentum compaction (α) lattice, in which electrons 

with different momenta would have smaller pathlength differences. As expected with the higher RF 

frequency, a bunch length of about 1mm rms was 

attained with a moderate α value of 0.0006, which 

is favorable for stable operation. 

The CSR radiation was extracted through a 6-

mm-thick fused quartz view port followed by two 

parabolic reflectors that collected the light and 

matched it to a spectrometer. The spectrometer 

was a modified commercial Nicolet Magna 860 

Fourier Transform Infrared (FTIR) Spectroscopy 

interferometer with a liquid-helium-cooled silicon 

composite bolometer as the detector. The spectrometer could sense CSR to wave numbers as 

low as 1 cm-1. The spectrometer assembly was 

carefully tuned and tested at the NSLS. Strong 

CSR signals were detected in the sub-THz region. 

The enhancement of CSR compared to the 300 K 

blackbody radiation background was 10,000 times, 

peaked near a wave number of 3 cm-1, and had 

a very low electron bunch current of 1.1μA. Most 

COHERENT THZ SYNCHROTRON RADIATION FROM A

STORAGE RING WITH HIGH FREQUENCY RF SYSTEM

F. Wang1, D. Cheever1, M. Farkhondeh1, W. Franklin1, E. Ihloff1, J. van der Laan1, 

B. McAllister1, R. Milner1, C. Tschalaer1, D. Wang1, D.F. Wang1, A. Zolfaghari1, T. 

Zwart1, G.L. Carr2, B. Podobedov2, and F. Sannibale3

1

MIT-Bates Linear Accelerator Center; 2National Synchrotron Light Source, Brookhaven National 

Laboratory; 3Lawrence Berkeley National Laboratory 

Coherent synchrotron radiation (CSR) generated in an electron storage 

ring is a promising source for stable, high-intensity terahertz (THz) 

radiation. The achievable CSR power and spectrum depend strongly 

on ring radiofrequency (RF) system parameters, mainly RF frequency 

and gap voltage. We report the initial results of CSR generation in the 

MIT-Bates South Hall storage ring (SHR), which is equipped with a 

unique high-frequency S-band RF system. The CSR enhancement is 

10,000 times above background for wave numbers near 3 cm-1 with a 

bunch current of 1.1 μA. Suppressing beam instabilities emerged as 

the first challenge in pursuing a very brilliant ring-based THz source, 

with further investigations underway.

BEAMLINE 

U12IR

PUBLICATION

F. Wang, D. Cheever, M. Farkhondeh, W. Franklin, E. Ihloff, J. 

van der Laan, B. McAllister, R. 

Milner, C. Tschalaer, D. Wang, 

D.F. Wang, A. Zolfaghari, T. Zwart, 

G.L. Carr, B. Podobedov, and F. 

Sannibale, “Coherent THz Synchrotron Radiation from a Storage Ring with High Frequency 

RF System,“ Phys. Rev. Lett., 96, 

064801 (2006).

FUNDING

U.S. Department of Energy; Massachusetts Institute of Technology 

FOR MORE INFORMATION

Fuhua Wang

MIT-Bates Linear Accel. Center

fwang@mit.edu

Authors (labeled 1-12, respectively): Fuhua Wang, Ernie 

Ihloff, Wilbur Franklin, Defa Wang, Larry Carr, Chris 

Tschalaer, Jan van der Lann, Boris Podobedov, Richard 

G. Milner, Abbi Zolfaghari, Manouchehr Farkhondeh, and 

Dong Wang
2-49

CONDENSED MATTER PHYSICS

of the 1812 RF buckets of the ring were filled, as 

it was the only available SHR injection mode at 

the time. The signal of the incoherent THz radiation with a few mA circulating beam was below the 

detection limit. The coherency tests of the radiation included dependency of the spectrum intensity on the bunch current and bunch length. The 

CSR radiation spectra from electron bunches with 

different bunch lengths, and the quadratic dependency of intensity on bunch current, are shown in 

Figure 1 and Figure 2.

Beam longitudinal instabilities were observed 

in both the radiation spectrum and time domain 

signals as well as in the beam longitudinal profile measurements. The instabilities limited the 

maximum bunch current that could be used for the 

tests and resulted in deteriorated radiation coherency at higher bunch intensities. Preparation for 

further tests is underway to address the technical 

challenges uncovered here. 

Figure 2. Quadratic dependency of spectrum intensity of 

CSR to beam current.

Figure 1. Intensity ratio of CSR to background for different 

bunch lengths. Total stored current I = 2 mA. Measured rms 

bunch length (ps): 7.6, 4.4, 4.0, corresponding to the RF 

peak voltage VRF (kV) of 20, 80, and 134.

Wave number cm-1

CSR Intensity /background

GHz

l

2 (mA2)

Spectrum Intensity (a.u.)
2-50

The Bardeen, Cooper, and Schrieffer (BCS) theory 

of superconductivity showed that, in a classical superconductor, zero electrical resistance is 

a consequence of electrons pairing themselves. 

These “Cooper pairs” have a typical binding energy (2∆) that leads to a gap for unpaired electrons 

at the Fermi energy. However, Cooper pairs can 

be broken into two electrons if they are given an 

energy larger than the gap. One of such possible 

processes is the absorption of a photon of energy 

greater than 2∆. As Cooper pairs are energetically more favorable than electrons, the electrons 

eventually reform the pair. The full relaxation 

process is a bit more complex, as shown in Figure 

1. In equilibrium, all the electrons in a superconductor should form pairs below the Fermi level 

(Figure 1A). The absorption of a photon will excite 

pairs across the gap and produce electrons above 

the Fermi energy (Figure 1B). We then reach a 

BEAMLINES 

U12IR, U10A

PUBLICATION

R.P.S.M. Lobo, J.D. LaVeigne, D.H. 

Reitze, D.B. Tanner, Z.H. Barber, E. 

Jacques, P. Bosland, M.J. Burns, 

and G.L. Carr, "Photoinduced 

Time-resolved Electrodynamics 

of Superconducting Metals and 

Alloys," Phys. Rev. B, 72, 024510-10 

(2005).

FUNDING

U.S Department of Energy; 

Centre National de la Recherche 

Scientifi que (France); City of Paris

FOR MORE INFORMATION

Ricardo Lobo 

LPS-ESPCI and CNRS

lobo@espci.fr

DISTURBING SUPERCONDUCTIVITY WITH LIGHT

R.P.S.M. Lobo1, D.B. Tanner2, and G.L. Carr3

1

CNRS and ESPCI, France; 2Department of Physics, University of Florida; 3National

Synchrotron Light Source, Brookhaven National Laboratory

Superconductors can be sent out of equilibrium by using light to break 

Cooper pairs. Using a pump-probe setup, we studied the time-dependent behavior of thus depleted superconductivity. Laser pulses were 

utilized to break pairs and synchrotron far-infrared (a.k.a. terahertz) 

pulses measured the spectra as a function of time in the sub-nanosecond scale. This measurement allowed us to determine how electrons 

recombine into pairs, bringing the system back to equilibrium. The 

direct observation of the superconducting gap diminution, expected for 

an excited superconductor, was measured for the first time.

situation where the “unstable” excited electrons 

want to recombine into a pair. Energy conservation imposes that the energy gain occurring when 

electrons form a pair must be emitted, usually 

as a crystal lattice vibration (phonon). Nevertheless, phonons can also break pairs; therefore, 

the emitted phonon is able to produce two new 

excited electrons. This subtle competition between 

electrons willing to recombine and phonons trying to break pairs only ends because, eventually, 

phonons become unavailable by either relaxing to 

very low energies or simply escaping the material. 

The whole process of relaxation is schematized in 

Figure 1C.

A collaboration between the University of Florida 

and the NSLS built a pump-probe setup to study 

systems out of equilibrium. The facility consists of 

a Ti:Sapphire pulsed laser synchronized with the 

electron bunches of the VUV-IR ring. We utilized 

the laser pulses to break pairs (pump) in several 

conventional superconductors, including Pb, Nb, 

and NbN, and the far-infrared light from beamlines 

U12IR and U10A to probe the changes in the optical response of the superconductor, which strongly 

depends on the number of Cooper pairs. By delaying the laser pulses with respect to the synchrotron bunches, we can obtain the time-dependent 

optical response for the specimen.

Figure 2 shows the integrated far-infrared transmission for several out-of-equilibrium superconductors as a function of time and temperature. At 

zero delay, both the laser and synchrotron pulses 

arrive at the sample at the same time and the 

changes in the optical transmission are maximum. 

Ricardo Lobo As we push the synchrotron pulses further away 
2-51

CONDENSED MATTER PHYSICS

from the laser, we allow enough time for some 

pairs to recombine and the optical transmission to 

recover its equilibrium value. Finally, we obtained 

the measurement of the non-equilibrium infrared 

spectrum (Figure 3), which is the first direct determination of the superconducting gap shrinkage 

expected for superconductors with excess 

unpaired electrons.

Figure 3. Non-equilibrium far-infrared spectrum for 

superconducting lead (dots) and expected response 

from BCS theory (line). The jump in the curve is a direct 

measurement of the superconducting gap shrinkage 

expected for a superconductor with excess unpaired 

electrons.

This technique is now being used to analyze more 

complex superconductors such as the cuprate 

high critical-temperature materials and the “twosuperconductors-in-one” material MgB2.

Figure 1. Density of states for a BCS superconductor (A) in 

equilibrium and (B) where pairs were broken into electrons. 

Panel (C) shows schematically the processes involved 

when the system relaxes back to equilibrium. Each process 

(recombination, pair breaking, and phonon escape) is 

characterized by a different time scale.

Figure 2. Relative variation in the far-infrared transmission 

of several classical superconductors as a function of 

temperature and time.
2-52

The remediation of radioactive contamination at 

former weapons testing and production sites is a 

costly and protracted legacy of the U.S. post-WWII 

military industrial complex. 90Sr and 137Cs are important contaminants at a number of Department 

of Energy (DOE) sites, and particularly at the 

Hanford (WA) site, because their half-lives fall 

within human timescales (29 and 30 years, respectively), they are potentially mobile in groundwater, and they are bioavailable substituents for 

Ca2+ and K+, respectively, in organisms. Large 

volumes of high-level radioactive waste and contaminant metals were generated from plutonium 

production and separation processes, much of 

which was stored in underground tanks. At least 

67 single-shell tanks containing high-level wastes 

are known to have leaked into vadose zone sediments, where caustic fluids have reacted with 

sediment minerals and groundwater to generate a 

complex history of mineral alteration, fluid evolution, and waste dispersal. 

Our research team has examined the reaction of 

high-pH, high ionic strength synthetic tank-waste 

leachate (STWL) with model clay minerals and 

Hanford sediments in the laboratory to unravel the 

geochemical processes that control subsurface 

contaminant uptake or release. Our approach 

is to link quantitative macroscopic measures of 

contaminant partitioning to the molecular-scale 

mechanisms that mediate the process, particularly 

those that may lead to irreversible sequestration 

of contaminants into a solid phase. This study 

examined temporal changes in solid-phase Sr 

speciation using bulk and microfocused EXAFS 

analyses in samples of STWL containing Sr2+

and Cs+ (at 10-3 m) reacted with the clay mineral kaolinite from 1 to 369 days. Bulk EXAFS 

spectral analyses showed that Sr initially forms a 

precipitate by 7 days with a local structure similar 

to SrCO3(s). At 33 days, the bulk sample spectrum showed few features beyond the first shell of 

oxygen atoms, but microfocused EXAFS of three 

individual particles in the same sample indicated 

distinct differences (Figure 1). Quantitative 

analyses revealed a mixture of hydrated and dehydrated Sr associated with neoformed sodalite-type 

(feldspathoid) phases. At aging times of 93 days 

and longer, bulk EXAFS spectra and supporting 

characterization methods indicated an increasing 

fraction of non-exchangeable Sr with a local structure consistent with incorporation into increasingly 

crystalline aluminosilicate particles, particularly 

sodalite (Figure 2). A combination of spectroSTRONTIUM SPECIATION DURING REACTION OF

KAOLINITE WITH SIMULATED TANK-WASTE LEACHATE: 

BULK AND MICROFOCUSED EXAFS ANALYSIS

S. Choi1,2, P.A. O’Day2,, N.A. Rivera2, K.T. Mueller3, M.A. Vairavamurthy4, 

S. Seraphin5, and J. Chorover1

1

Dept. of Soil, Water and Environmental Science, Univ. of Arizona; 2School of Natural Sciences, 

Univ. of California; 3Dept. of Chemistry, The Pennsylvania State Univ.; 4Brookhaven National 

Laboratory; 5Dept. of Materials Science and Engineering, Univ. of Arizona

Radioactive strontium (90Sr) is an important constituent of complex 

wastes produced from past nuclear weapons production and stored in 

underground tanks at DOE sites (e.g., Hanford, WA). Using bulk and 

microfocused EXAFS spectroscopy, we examined temporal changes 

in solid phase Sr speciation in kaolinite samples reacted for 1 to 369 

days with high-pH, high ionic strength synthetic tank-waste leachate 

containing Sr2+ and Cs+. Our results and supporting characterizations 

show that Sr forms a transient carbonate phase at early reaction times 

that is replaced by incorporation into neoformed, cage-type feldspathoid aluminosilicate minerals, with Sr becoming dehydrated and 

non-extractable with longer reaction times. Formation of feldspathoid 

minerals as products of sediment alteration may help sequester contaminants at sites such as Hanford.

BEAMLINE 

X18B

PUBLICATION

S. Choi, P.A. O’Day, N.A. Rivera, 

K.T. Mueller, M.A. Vairavamurthy, 

S. Seraphin, and J. Chorover, 

“Strontium Speciation During Reaction of Kaolinite with Simulated 

Tank-waste leachate: Bulk and 

Microfocused EXAFS Analysis,” 

Environ. Sci. and Technol., 40, 

2608-2614 (2006).

FUNDING

U.S. Department of Energy

FOR MORE INFORMATION

Peggy A. O’Day

School of Natural Sciences

University of California

poday@ucmerced.edu

Authors Jon Chorover and Sunkyung Choi
2-53

GEOLOGY AND ENVIRONMENTAL SCIENCE

scopic and microscopic characterization studies by 

our group, including NMR, XRD, SEM/TEM, and 

FTIR, indicated the formation of both sodalite and 

cancrinite, with cancrinite forming at the expense 

of sodalite for reaction times longer than 93 days. 

The Sr-EXAFS analysis uniquely identified the 

stronger association of Sr with sodalite-type cage 

structures, rather than cancrinite-type structures, 

in these samples and showed that local dehydration of Sr within the neoformed phases was associated with increasingly irreversible sequestration. Although this experimental system is greatly 

simplified from field conditions, an important 

observation is that trapping of radionuclides can 

occur if they are present as cage-structure aluminosilicates form and age as alteration products of 

local Si-bearing sediment minerals. Sequestration 

of radionuclides by feldspathoid mineral trapping 

may be an important mechanism for retardation 

near waste sources because re-release to solution requires mineral dissolution rather than ion 

exchange.

Figure 1. From left: SEM images, synchrotron Sr x-ray 

microprobe maps, and microfocused Sr K-edge EXAFS of 

three neoformed particles from a kaolinite sample reacted 

for 33 days with synthetic tank-waste leachate. A bulk 

EXAFS spectrum of the sample is shown for comparison. 

The bulk spectrum was collected at the NSLS (beamline 

X18B) and the microfocused spectra were collected at 

the APS (GSECARS beamline 13-ID-C). Particles were 

dispersed on carbon tape and imaged with SEM to identify 

isolated Sr-bearing particles prior to synchrotron analyses. 

X-ray element maps were made prior to EXAFS data 

collection in order to re-locate the Sr-bearing particles.

Figure 2. (A) Atomic structure of basic sodalite, which has 

a single cage and cation site. Sr (yellow atoms) occupies 

the Na site; surrounding anions and water within cages are 

omitted for clarity; (B) Nitrate cancrinite has two distinct 

cation sites in large (sodalite-type) and small (cancrinitetype) cages; Sr is shown occupying Na sites within the 

sodalite cage, nitrate groups occupy the counter-anion 

position in the center of the cage, and Na and water are 

shown in the cancrinite cage. Nearest interatomic cationcation positions in the ideal structures are indicated. 

k (Å R + ∆ (Å) (A) basic sodalite (B) nitrate cancrinite -1)

χ(k) x k3 (arb. units)

Fourier Transform Magnitude
2-54

BEAMLINE 

X19A

PUBLICATION

G. Toevs, M.J. Morra, M.L. Polizzotto, D.G. Strawn, B.C. Bostick, 

and S. Fendorf, “Metal(loid) Diagenesis in Mine-impacted Sediments of Lake Coeur d’Alene, 

Idaho,” Environ. Sci. Technol., 40,

2537-2543 (2006).

FUNDING

Idaho Water Resources Research 

Institute; Idaho Agricultural 

Experiment Station; Inland Northwest Research Alliance; EPA-STAR 

Fellowship Program; NSF-Environmental Molecular Science 

Institute

FOR MORE INFORMATION

Michael J. Morra

Soil & Land Resources Division

University of Idaho

mmorra@uidaho.edu

Lake Coeur d’Alene (CDA) is a natural lake of 

glacial origin located in northern Idaho. As a result 

of mining activity within the region, mine tailings 

and mill slurries contaminated with Pb, As, Cd, 

Zn and other metal(loid)s have accumulated in 

the sediments of Lake CDA. Prior research to 

characterize sediment geochemistry has produced 

inconsistent and contradictory results. Our objective was to characterize Lake CDA sediments 

using spectroscopic techniques combined with in 

situ interstitial water data, thereby identifying the 

dominant solid-phase minerals and diagenetic 

processes controlling interstitial water metal(loid) 

concentrations. Ultimately, our results will facilitate the prediction of contaminant release from the 

sediments to the overlying water column. 

Two sample sites, Harlow Point (HP) and Peaceful 

Point (PP), were located in the southern portion of Lake CDA in an area highly impacted by 

metal(loid)s. An uncontaminated control site, St. 

Joe (SJ), was also established. Interstitial water 

was collected in situ utilizing Plexiglas equilibrium, 

dialysis samplers (peepers) and cores collected in 

polycarbonate tubes. 

Sulfur x-ray absorption near-edge structure 

(XANES) spectroscopy analyses were conducted 

at the National Synchrotron Light Source on 

beamline X19A. Iron XANES and extended x-ray 

absorption fine structure (EXAFS) spectroscopy 

analyses were conducted at the Stanford Synchrotron Radiation Laboratory on beamline 4-3. 

Sediment sulfur was speciated in an attempt to 

identify specific components of the sediment solid 

phase that potentially participate in metal(loid) 

retention. XANES data clearly indicate that 

pyrite was the principle S mineral detected at 

the contaminated sites (Figure 1). Ester-bound 

sulfate decreased with depth at all sites (Figure 

1). Increased pyrite percentages with depth are 

consistently accompanied by a corresponding 

decrease in organic ester sulfate species. Thus, 

diagenetic alteration of ester-bound sulfate is 

likely important in the generation of pyrite in these 

sediments. However, metal(loid) partitioning into 

and on sulfidic minerals in Lake CDA sediments 

must be re-evaluated given the high Fe to S ratios 

of the sediments.

The speciation of sedimentary iron, achieved with 

XAS spectra, offers additional evidence for the 

diagenesis of sedimentary Fe and S. Contaminated sites show an obvious trend in the speciation 

of solid-phase Fe that reflects changes in sediment redox potentials with depth, with both sites 

displaying a decrease in Fe(III) minerals below the 

METAL(LOID) DIAGENESIS IN MINE-IMPACTED

SEDIMENTS OF LAKE COEUR D’ALENE, IDAHO

(

SEDIMENTS OF LAKE COEUR D’ALENE, IDAHO

( )

SEDIMENTS OF LAKE COEUR D’ALENE, IDAHO

)

G.R. Toevs1, M.J. Morra1, M.L. Polizzotto2, D.G. Strawn1, B.C. Bostick2,3, and S. 

Fendorf2

1

Soil & Land Resources Division, University of Idaho; 2Department of Geological and Environmental Sciences, Stanford University; 3

Department of Earth Sciences, Dartmouth College

Mining operations in northern Idaho have resulted in Pb, As, Hg, Cd, 

and Zn contamination of Lake Coeur d’Alene. Unfortunately, limited 

knowledge of sediment biogeochemistry precludes accurate modeling of metal(loid) flux to the water. We characterized the sediments 

to elucidate diagenetic processes potentially controlling contaminant 

release, showing that flood events bury ferric oxides present at the 

sediment-water interface, transitioning them to an anoxic zone where 

reductive dissolution occurs. Insufficient sulfur limits sulfidic mineral 

formation, but high carbonate concentrations promote siderite formation. Metal(loid) sorption and release is thus a dynamic process intimately tied to reactions involving iron minerals within the sediments.

Gordon Toevs
2-55

GEOLOGY AND ENVIRONMENTAL SCIENCE

suboxic boundary and a concomitant increase in 

Fe(II)-containing solids (Figure 2). 

Linear combination of Fe-EXAFS spectra indicated 

the majority of the Fe(II) increase was in the form 

of siderite. Thus, a cycle of Fe-diagenesis is established where Fe(III) minerals buried by depositional events undergo reductive dissolution in the 

suboxic and anoxic sediments, forming Fe(II) that 

precipitates as siderite or diffuses to the oxic zone 

and reprecipitates as an Fe(III) mineral.

Ferric (hydr)oxides at the sediment-water interface restrict contaminant migration, but diagenetic 

reactions that occur during sediment burial and exposure to reducing conditions release metal(loid)s 

into the interstitial water. Metal(loid) cycling 

between the solid and aqueous phases in Lake 

CDA is thus a dynamic process intimately tied to 

diagenetic reactions involving Fe minerals within 

the sediments.

Figure 2. Iron XANES analyses of Lake Coeur d’Alene 

sediments as determined from linear combination fi ttings 

of Fe(II) and Fe(III) proxies and illite. Data are from 

cores collected in May 2002 at the control site (SJ) and 

two contaminated sites (PP and HP) and have a fi tting 

accuracy of ±5%. Iron comprised up to 10% of the sample 

by weight at the contaminated sites.

Figure 1. Comparison of S species as determined by SXANES analyses of Lake Coeur d’Alene sediments at the 

contaminated sites (PP and HP) and the control site (SJ). 

Data shown for each depth are an average of two spectra 

from adjacent cores collected in May 2002 and have a 

fi tting accuracy of ±5%. Maximum total sulfur within all 

sediments was less than 0.5% by weight.
2-56

BEAMLINE 

X19A

PUBLICATION

S. Sato, D. Solomon, C. Hyland, 

Q.M. Ketterings, and J. Lehmann, "Phosphorus Speciation in 

Manure and Manure-Amended 

Soils Using XANES Spectroscopy," Environ. Sci. Technol., 39, 

7485–7491 (2005).

FUNDING

U.S. Department of Agriculture; 

N.Y. Department of Agriculture 

and Markets

FOR MORE INFORMATION

Shinjiro Sato

Dept. of Crop and Soil Sciences

Cornell University

shinjiro@ifas.ufl .edu

Poultry manure is frequently applied to agricultural 

fields to supply essential nutrients to crops, subsequently increasing yields. However, apart from 

plant uptake, manure P can be lost as the result of 

surface erosion and/or leaching. Such losses have 

resulted in the eutrophication of watersheds in the 

past. Soil pH plays a critical role in P retention 

in soils by, for instance, changing the solubility 

of secondary Fe, Al, and CaP minerals in soils. 

Manure is a well-known liming material; however, 

it is unknown how manure application impacts the 

solubility and transformation of these secondary 

P compounds. Our previous studies suggest an 

increase in the proportion of CaP in the total P 

pool in soils with long-term manure application. 

Using P K-edge XANES, this study aims to assess 

the CaP species formed in an originally acidic soil 

in response to high and long-term (up to 25 years) 

manure applications.

We measured standards of inorganic phosphate 

forms for comparison with spectra of the investigated soils (Figure 1). Both the spectra of the 

Fe-oxide strengite (STR) and the Al-oxide variscite 

(VAR) featured a peak at 2156 eV (Figure 1e), but 

were distinguished by the presence and absence 

of a peak at 2146 eV (Figure 1a) for STR and 

VAR, respectively. The most characteristic feature 

for all of the CaP species was a peak at 2159 

eV (Figure 1f) and a shoulder between 2151 eV 

(Figure 1c) and 2152 eV (Figure 1d). A closer observation of the shoulder (Figure 1c-1d) revealed 

this shoulder to be better expressed for CaP species with decreasing solubility. The solubilities of 

these CaP species generally decrease as follows: 

dibasic calcium phosphate dehydrate (DCPD) > 

dibasic calcium phosphate (DCP) > amorphous 

calcium phosphate (ACP) ≈ β-tricalcium phosphate 

(TCP) > octacalcium phosphate (OCP) > hydroxyapatite (HAP).

The manure spectrum showed only two small 

shoulders that are characteristic of CaP species 

(Figure 2Ac-d and 2Af), but the overall spectra rather resembled that for Aq-PO4. The linear 

combination fitting result showed that this manure 

contained 18% DCP, 35% ACP1, and 47% AqPO4. Aq-PO4 in the fitting results is considered 

a group of “free and weakly bound (adsorbed) 

phosphates,” since it is not possible to use XANES 

alone to quantitatively distinguish Aq-PO4 from 

phosphate adsorbed on minerals. The forest soil 

spectrum showed a shoulder (Figure 2Aa) that 

is indicative of FeP but was significantly widened 

compared to STR, suggesting the presence of 

a combination of phosphates in strengite and 

phosphates adsorbed to the surfaces of various 

Fe-oxides. The linear combination fitting resulted 

in 38% ACP1, 32% STR, and 30% Aq-PO4 in the 

forest soil. Spectra of the manure-applied soils 

showed a decrease and disappearance of the FeP 

shoulder (Figure 2A-2Ca) and an increase in the 

PHOSPHORUS SPECIATION IN MANURE AND MANURE- AMENDED SOILS USING XANES SPECTROSCOPY

S. Sato, D. Solomon, C. Hyland, Q.M. Ketterings, and J. Lehmann

Department of Crop and Soil Sciences, Cornell University

It is important to know what inorganic phosphorus (P) species are 

being formed in soils subjected to high, long-term poultry-manure 

application in order to understand P accumulation and release 

patterns. Phosphorus K-edge XANES spectra of fresh manure showed 

no evidence of crystalline P minerals, but did exhibit a dominance 

of soluble calcium phosphates (CaP) and free and weakly bound 

phosphates. Soils with a short-term manure history contained both 

Fe-associated phosphates and soluble CaP. Long-term application 

resulted in a dominance of CaP and a transformation from soluble to 

more stable CaP species. However, none of the amended soils showed 

the presence of crystalline CaP. Maintaining a high pH is therefore an 

important strategy that can be used to minimize P leaching in these 

soils.

Authors (from left) Shinjiro Sato, Johannes Lehmann, and 

Dawit Solomon
2-57

GEOLOGY AND ENVIRONMENTAL SCIENCE

intensity of the CaP shoulder (Figure 2A-2Cc) and 

the CaP peak (Figure 2A-2Cf) as the application 

history increased. In fact, the linear combination 

fitting suggested that long-term manure application resulted in the transformation of relatively 

soluble CaP species (Figure 2A, S2 soil: 8% DCP 

and 19% ACP1) into more crystalline CaP species 

(Figure 2C, L1 soil: 13% ACP1 and 43% TCP) in 

soils over time. Yet, the most crystalline and therefore least soluble CaP form, such as HAP, was 

not found in the studied soils. Since CaP minerals 

are least soluble at high pH, maintaining a high 

pH may be an important strategy for minimizing P 

leaching in these soils.

Figure 1. Phosphorus K-edge XANES spectra for 

different inorganic phosphate standard species. The 

dashed lines show energy levels of importance to indicate 

unique spectra features for different species: (a) STR; (b) 

absorption edge (white line); (c)–(d) CaP species related 

to their solubility; (e) STR and VAR; (f) CaP species; 

(g) oxygen oscillation. Aq-PO4 is H2PO4

–

 species in 0.1 

M NaCl solution. STR: strengite, VAR: variscite, HAP: 

hydroxyapatite, OCP: octacalcium phosphate, ACP: 

amorphous calcium phosphate (phase 1 and 2), TCP: βtricalcium phosphate, DCP: dibasic calcium phosphate, and 

DCPD: dibasic calcium phosphate dehydrate.

Figure 2. Phosphorus K-edge XANES spectra for poultry 

manure, forest, and manure-applied soils with different 

histories of application: (A) manure, forest, and short-term; 

(B) medium-term; (C) long-term; and (D) linear combination 

fi ts of selected spectra. The dashed lines in (A), (B), and 

(C) correspond to those in Figure 1. The dotted lines in 

(D) represent the best fi tted result to respective spectra by 

linear combination fi tting.

Energy (eV)

Normalized absorbance (a.u.)

Energy (eV) Energy (eV)

Normalized absorbance (a.u.) Normalized absorbance (a.u.)

(A) Manure, Forest, Short-term (B) Medium-term

(C) Long-term (D) Linear combination fitting
2-58

Arsenic (As) solid-state speciation is one of the 

most important factors controlling dissolved As 

concentrations at As-contaminated sites. In this 

case study, we utilized a combination of in situ

bulk- and μ-XAS, in situ μ-XRF, and μ-XRD to investigate As solid-state speciation in aged As-contaminated urban soils in the northeastern United 

States. The origin of As in the soils (predominantly 

lead arsenate) is the disposal of former commodity, specialty, and agricultural chemicals. There 

are two distinct sites with average redox potential 

values of approximately 33 and 275 mV in the top 

4 meters. Subsurface samples at 2-4 m depths 

from a semi-reduced site A and an oxic site B 

(thereafter sample A and B), where total As was 

most concentrated (80 and 284 ppm, respectively), were chosen for detailed spectroscopic 

investigation. 

In situ μ-SXRF analyses indicated that elevated 

As counts (regions 1, 2, 4, and 6 in Figures 1A 

and 1B) are similarly distributed with Ba, Ca, and 

Fe in sample A and with Fe in sample B (XRF 

maps of the metals are not shown). Regions 2, 3, 

and 5 (Figures 1A and 1B), where the As concentrations are not elevated, do not seem to be 

co-distributed with elements such as Cu, Ni, Zn, 

Mn, and Ca. The μXANES analyses show 1) a predominant As(V) oxidation state at regions 1, 2, 4 

and 5; and 2) regions 3 and 6 contain As(III)-S and 

As(III), respectively (Figure 2A). Selected diffractograms of the μ-XRD measurements on sample B 

(Figure 2B) show the presence of calcite, rutile, 

and quartz in all 26 diffractograms, and schultenite 

(PbHAsO4) in about half of the diffractograms.

In the bulk EXAFS analyses, results from μ-XRF, 

-XRD and -XANES analyses were considered, and 

coordination numbers of species at low R were 

correlated with the expected proportions of the 

species at high R (e.g., an As-Ca shell with an 

As-As shell). Figures 2C and 2D shows the leastsquare fits of samples A and B. The CN (±30%) 

and R (±0.03Å) of the first and second shells 

(As-O: 4.3 and 1.7 Å, As-S: 3 and 2.27 Å, As-Fe: 2 

and 3.3 Å, As-Ca: 2 and 4.06 Å, As-Pb: 2 and 3.9 

Å and As-As: 1.5 and 4.09 Å) in each sample correspond to surface species that consist of approximately 25% amorphous orpiment (As2S3), 28% 

adsorbed As(V) on iron oxyhydroxide, 46% of CaAs(V) coprecipitates and/or substitution of arsenate into gypsum in sample A, and approximately 

71% As(V) adsorbed species on iron oxyhydroxide 

with approximately 29% residual schultenite.

In this study, multi-scale spectroscopic techniques 

(μ-XANES, -XRF, and -XRD and bulk-XAS) were 

SPATIAL AND TEMPORAL VARIABILITY OF ARSENIC

SOLID-STATE SPECIATION IN HISTORICALLY LEAD

ARSENATE CONTAMINATED SOILS

Y. Arai1, A. Lanzirotti2, S.R. Sutton3, M. Newville2, J. Dyer1, and D.L. Sparks1

1

Department of Plant and Soil Sciences, University of Delaware; 2Consortium for Advanced 

Radiation Sources, University of Chicago; 3Department of Geophysical Sciences, University of 

Chicago

We investigated aging effects on As retention mechanisms in historically lead-arsenate contaminated urban soils using synchrotron-based 

microfocused (μ) XRD, μ-XRF, and μ- and bulk-XAS analyses. Whereas As is predominantly present as As(V) adsorbed onto amorphous 

iron oxyhydroxides with a residue of schultenite (PbHAsO4) at an oxic ) at an oxic 4

site, there is no trace of schultenite from a semi-reduced site. Instead, 

adsorbed As(V) phases on amorphous iron oxyhydroxide, amorphous 

orpiment, and As(V)-Ca co-precipitates were identified. This study 

shows that aging effects can significantly alter the original chemical 

constituent in soils, resulting in multi and site-specific As solid-state 

speciation.

BEAMLINES 

X11A, X26A

PUBLICATION

Y. Arai, A. Lanzirotti, S. Sutton, M. 

Newville, J. Dyer, and D. Sparks, 

"Spatial and Temporal Variability 

of Arsenic Solid-State Speciation in Historically Lead Arsenate 

Contaminated Soils," Environ. Sci. 

Tech., 40, 673-679 (2006).

FUNDING

U.S. Department of Agriculture

FOR MORE INFORMATION

Yuji Arai

Dept. of Plant and Soil Sciences

University of Delaware

yarai@usgs.gov

Yuji Arai
2-59

GEOLOGY AND ENVIRONMENTAL SCIENCE

effectively combined to elucidate As solid-state 

speciation in lead-arsenate contaminated soils. 

Decades of contamination and weathering resulted 

in an alternation of the original As contaminant 

source (lead arsenate). Traditional bulk chemical digestion and the leachate test could possibly 

overestimate the site-specific As solid-state species that significantly control the bioavailability of 

As in soil solutions. The variability in spatial and 

temporal scale may be important in assessing the 

environmental risk and in developing in-situ remediation technologies. 

Figure 1. In situ As Kα and Kβ μ-x-ray fl uorescence maps 

of sample A and B, respectively. Scale of maps in x- and 

y-axis is in mm. Fluorescence counts of each element are 

indicated by color contour bars on the left side of each 

map, and the intensity of each color is proportional to the 

amount of the corresponding element. Regions 1, 2, 3, 4, 

5, and 6 indicate the area where μ-XANES spectra were 

taken. 

Figure 2. (A) Microfocused XANES spectra at regions 

1-6 of selected areas of the As fl uorescence maps shown 

in Figure 1. (B) Microfocused SXRD patterns (λ=0.7598 

Å) of As concentrated areas of sample B. Selected 

diffractograms show 2.8 Å < d-spacing <3.6 Å. (C) Nonlinear least-square fi ts to normalized k3

-weighted EXAFS 

spectra of the reference compounds and samples A and B. 

Raw data and fi ts are shown by solid lines and open circles, 

respectively. (D) Non-linear least-square fi ts to Fourier 

transforms of the reference compounds and samples A 

(bottom) and B (top). Raw data and fi ts are shown in solid 

lines and open circles, respectively.

k (Å R + ∆ (Å) -1)

χ(k)·k3 Normalized Intensity

Energy (keV) nergy (keV) d-spacing(Å) -spacing(Å)

C D

A B

(A)

(B)
2-60

BEAMLINES 

X19A, X26A, X23A2

PUBLICATION

A. Leri, M. Hay, A. Lanzirotti, W. 

Rao, and S. Myneni. "Quantitative 

Determination of Absolute Organohalogen Concentrations in 

Environmental Samples by X-ray 

Absorption Spectroscopy," Anal. 

Chem., 78, 5711-5718 (2006).

FUNDING

U.S. Department of Energy; 

National Science Foundation 

(NSF); NSF Graduate Research 

Fellowships

FOR MORE INFORMATION

Alessandra Leri

Department of Geosciences

Princeton University

aleri@princeton.edu

Halogens undergo complex biogeochemical transformations in terrestrial systems, cycling between 

organic and inorganic forms. Naturally produced 

organohalogens include a diverse array of relatively low molecular weight molecules, as well 

as macromolecules of indeterminate structure. 

Despite the ubiquity of natural organohalogens, 

the processes associated with their formation and 

degradation in the environment remain poorly 

understood, largely due to the inadequacy of available techniques to account for the myriad halogen 

species in heterogeneous soil, sediment, plant, 

and aqueous samples. Established quantitative 

methods require chemical isolation of organohalogen fractions from natural samples and are prone 

to partial recoveries and/or chemical alterations 

of halogens. We have applied synchrotron-based 

x-ray fluorescence (XRF) and x-ray absorption 

near-edge structure (XANES) spectroscopy to the 

in situ determination of Clorg and Brorg concentrations in natural samples. 

Quantification of Cl relies on the absolute fluorescence intensity of Cl 1s XANES spectra (acquired 

at beamline X19A) determined at 2850.8 eV, an 

energy ~20 eV above the Cl K-absorption edge 

(Figure 1A). By this energy, the near-edge oscillations are attenuated and absorption intensity is 

independent of Cl speciation. Polyacrylic acidbased NaCl standards yield calibration curves with 

a strong linear relationship between Cl concentration and absolute Cl fluorescence intensity 

(Figure 1B). X-ray beam absorption and scattering by polyacrylic acid-based standards and 

natural organic matter (NOM) are comparable, 

allowing for direct measurement of Cl concentrations in homogenized NOM sample pellets, which 

minimizes matrix effects. 

Unnormalized Cl 1s XANES spectra of oak leaf 

NOM at progressive stages of decay are shown in 

Figure 2A (a = least degraded; c = most degraded). Comparison of the absolute Cl fluorescence 

intensity values of these spectra with standard 

curves (as in Figure 1B) yields the following total 

Cl concentrations: a, 364 ppm; b, 141 ppm; c, 70 

ppm. The decreasing trend in Cl concentration 

is consistent with leaching of soluble forms of Cl 

from the mulch material as part of the degradation 

process.

In addition to providing Cl concentration measurements, Cl 1s XANES spectra illuminate the 

chemical forms of Cl present in a sample. Clinorg

exhibits a broad absorption maximum (Figure 

2B, x) higher in energy than the more intense 

maxima characteristic of Clorg compounds. These 

sharp peaks denote 1s à π* or σ* transitions and 

differ in energy depending on C-Cl bond length, as 

QUANTITATIVE DETERMINATION OF ABSOLUTE

ORGANOHALOGEN CONCENTRATIONS IN

ENVIRONMENTAL SAMPLES BY X-RAY ABSORPTION

SPECTROSCOPY

A.C. Leri1, M.B. Hay2, A. Lanzirotti3, W. Rao4, and S.C.B. Myneni5,6 

1

Department of Chemistry, Princeton University; 2Department of Civil and Environmental 

Engineering, Princeton University; 3Consortium for Advanced Radiation Sources, The University 

of Chicago; 4Savannah River Ecology Laboratory, University of Georgia; 5Department of Geosciences, Princeton University; 6

Earth Sciences Division, Lawrence Berkeley National Laboratory

A method for quantification of organic and inorganic halogen concentrations in environmental samples using x-ray absorption spectroscopy 

has been developed. Organochlorine (Clorg) and inorganic chloride ) and inorganic chloride

(Clinorg) concentrations are determined from Cl 1s XANES spectra. The ) concentrations are determined from Cl 1s XANES spectra. The

absolute fluorescence intensity of these spectra is linearly dependent 

on Cl concentration. Calibration curves are obtained from NaCl standards in a matrix of uniform bulk density, and Cl concentration in natural samples is estimated from these curves with high precision. The 

fractions of Cl fractions of Clinorg and aliphatic/aromatic Cl and aliphatic/aromatic Cl and aliphatic/aromatic Clorg contributing to the total Cl contributing to the total Cl

1s XANES signal are computed through least-squares spectral fitting 

with representative model compounds. Concentrations of organic and 

inorganic Br (Brorg and Brinorg) in sediment samples are also measured ) in sediment samples are also measured

using a combination of XRF and Br 1s XANES spectroscopy. 

Authors Alessandra Leri and Michael Hay
2-61

GEOLOGY AND ENVIRONMENTAL SCIENCE

becomes evident through comparison of aliphatic 

and aromatic Clorg spectra (Figure 2B, y-z). The 

substantial variations in spectral features depending on the coordination environment of Cl allow 

percentage estimates of Clinorg and aliphatic and 

aromatic Clorg in natural samples to be ascertained 

via least-squares fitting of normalized sample 

spectra with spectra of representative model 

compounds (Figure 2B). Combination of these 

proportions with total Cl concentrations yields the 

concentrations of Clinorg, aromatic Clorg, and aliphatic 

Clorg in NOM samples. 

Total Br concentrations in environmental samples 

have been determined via XRF analysis for decades. The novelty of our application lies in the 

combination of quantitative information from XRF 

(acquired at beamline X26A) with Br speciation 

information from Br 1s XANES spectra (acquired 

at beamline X23A2) to determine absolute concentrations of Brorg and Brinorg in chemically heterogeneous sediments. 

This method provides a rigorous new approach to 

the determination of organohalogen concentrations 

in complex natural samples in situ. Robust, quantitative information about organohalogen fluxes in 

soil and sediment systems will help complete the 

description of natural halogen cycles, potentially 

illuminating the sources and sinks of naturally 

and industrially produced organohalogens in the 

environment.

Figure 2. Determination of Cl speciation and concentration 

in NOM samples from Cl 1s XANES spectra. (A) 

Unnormalized Cl 1s XANES spectra of pulverized oak 

leaves at different stages of decay (a = least degraded; b = 

more degraded; c = most degraded). Arrows illustrate the 

differences in absolute Cl fl uorescence intensity among the 

spectra. (B) Least-squares fi t of background-subtracted, 

normalized spectrum b with representative inorganic (x, 

glycine-HCl), aliphatic (y, chlorodecane), and aromatic (z, 

chlorophenol red) Cl model compounds. Spectrum b data 

are represented by circles and fi t by the solid line; r is the 

residual after the fi t. Estimated Cl speciation by leastsquares fi tting: a, 78% inorganic (284 ppm), 16% aromatic 

(58 ppm), 6% aliphatic (22 ppm); b, 40% inorganic (56 

ppm), 20% aromatic (29 ppm), 40% aliphatic (56 ppm); 

c, 16% inorganic (12 ppm), 42% aromatic (29 ppm), 42% 

aliphatic (29 ppm).

Figure 1. Quantifi cation of Cl concentration from Cl 

1s XANES spectra. (A) Unnormalized Cl 1s XANES 

spectrum of NaCl standard in PAA matrix (200 ppm Cl). 

The difference at 2850.8 eV between splines through the 

pre-edge and post-edge regions is used as a measure 

of absolute Cl fl uorescence intensity. (B) Relationship 

between Cl concentration in PAA-based NaCl standards 

and absolute Cl fl uorescence intensity. Dashed line, 

equation, and R2 value represent linear fi ts to the data.

Photon Energy (eV)

Photon Energy (eV)

Fluorescence yield (FF/I0)

Photon Energy (eV)

Fluorescence yield (FF/I0)

Chlorine concentration (ppm)

Absolute intensity at 2850.8 eV
2-62

Bacteria, like most living organisms, need iron to 

survive. Because of the low bioavailability of iron, 

bacteria synthesize high-affinity, iron-chelating low 

molecular weight compounds called siderophores 

that form metal:siderophore conjugates.

The size of a metal:siderophore conjugate like 

ferrichrome prohibits entry into the bacteria via 

simple diffusion through porin-like channels. 

Alternatively, bacteria have developed uptake 

systems for these conjugates. We study the Ferric 

Hydroxymate Uptake system (Fhu) that works as 

follows (Figure 1): The outer membrane receptor FhuA, a 22-strand β-barrel protein with a cork 

domain, binds iron-bound ferrichrome. TonB that 

has been energized by the ExbB/D cytoplasmic 

membrane complex comes into contact with FhuA 

and allows ferrichrome to pass into the periplasmic space. Once in that space, ferrichrome binds 

to the protein FhuD that brings it to the FhuB/C 

STRUCTURE OF TonB IN COMPLEX WITH FhuA, E. COLI

OUTER MEMBRANE RECEPTOR

P.D. Pawelek1, N. Croteau1, C. Ng-Thow-Hing1, C.M. Khursigara1, N. Moiseeva2, M. 

Allaire2, and J.W. Coulton1

1

Department of Microbiology and Immunology, McGill University, Canada; 2National Synchrotron 

Light Source, Brookhaven National Laboratory

Iron, an essential element for most living organisms, is highly insoluble 

at physiological pH, making it difficult for bacteria to acquire. In order 

to obtain sufficient amounts of iron, bacteria have developed high affinity uptake systems. For the first time, interactions between two proteins of the ferric hydroxymate uptake (Fhu) system are seen at atomic 

resolution. Crystals of a complex of outer membrane receptor FhuA 

and its energizing partner, TonB, give us insights into the mechanism 

by which E.coli acquires iron. Learning about this mechanism could 

help in the development of targeted antibiotics.

complex, an ABC transporter that finally transports 

it into the cytoplasm.

We first showed that upon binding of the ferrichrome-iron conjugate, a conformational change 

is transmitted to the periplasmic side of FhuA, 

resulting in the unwinding of a switch helix, thus 

signaling the ligand-loaded status of the receptor 

(Figure 2A,B). The next step involves the binding 

of TonB to the FhuA receptor; however the molecular mechanism whereby this occurs was unknown. 

By obtaining diffraction-quality crystals of a 1:1 

FhuA:TonB complex and the use of synchrotron 

radiation, we have been able to shed light on how 

ferrichrome enters the periplasmic space.

The resulting crystal structure of this complex 

reveals that residues from the FhuA Ton box form 

a parallel β-interaction with the β3-strand of the 

central β-sheet of the C-terminal domain of TonB 

(Figure 2C). This interaction positions the highly 

conserved TonB residue, Arg166, to contact FhuA 

residue Glu56, which is also located in a conserved motif. From this we are able to predict the 

functional importance of this FhuA-TonB ionic 

interaction. 

What does the crystal structure of the FhuA-TonB 

complex tell us about interactions of TonB with a 

cognate OM receptor and the transport of metalchelated siderophore? From our structural data 

combined with findings from previous studies, 

we propose that the interprotein β-sheet formed 

between the receptor Ton box, and the C-terminal 

domain of TonB is required to position the TonB 

helix close to the receptor cork domain. In the 

FhuA-TonB structure, this results in TonB Arg166 

BEAMLINES 

X6A, X29

PUBLICATION

P.D. Pawelek, N. Croteau, C. 

Ng-Thow-Hing, C.M. Khursigara, 

N. Moiseeva, M. Allaire, and J.W. 

Coulton, " Structure of TonB in 

Complex with FhuA, E. coli 

Outer Membrane Receptor," 

Science, 312, 1399-1402 (2006).

FUNDING

Canadian Institutes of Health 

Research

FOR MORE INFORMATION

James W. Coulton

Department of Microbiology and 

Immunology

McGill University

james.coulton@mcgill.ca

Authors (from left) Natalia Moiseeva, Marc Allaire, 

Nathalie Croteau, and Peter Pawelek
2-63

LIFE SCIENCE

forming an electrostatic interaction with FhuA 

cork residue Glu56. It was recently proposed that 

hydration of the cork domain may render it prone 

to disruption by TonB through transmission of a 

relatively small force perpendicularly applied to it. 

Given its position proximal to the FhuA cork domain, TonB Arg166 is positioned to mediate such 

a mechanical shearing or pulling force to the cork 

domain. This may result in cork disruption, allowing siderophore translocation into the periplasm.

Figure 2. Changes occurring at the periplasmic side of 

FhuA. (A) Prior to iron-ferrichrome conjugate binding on 

the FhuA receptor. (B) Unwinding of the switch helix upon 

iron-ferrichrome conjugate binding. (C) Binding of the CTerminal domain of TonB to the FhuA conserved Ton box.

Figure 1. The Ferric Hydroxymate Uptake system (Fhu)

A

B

C
2-64

We solved the x-ray crystal structure of the repeat 

protein CTPRa8, which contains eight identical 

TPR repeats, at 2.05Å resolution, using single 

wavelength anomalous diffraction data from cadmium. The structure of CTPRa8 (Figure 1) reveals 

that each repeat is comprised of two helices, 

which are arrayed to form a super helix. A key feature of CTPRa8, and of repeat proteins in general, 

is that, in contrast to globular proteins, there are 

no sequentially distant amino acid contacts. This 

pattern of local contacts suggests that a theoretical description based on the classical one-dimensional Ising model might be an appropriate way 

to understand the folding/unfolding behavior of 

repeat proteins, with the repeating units cast as 

Ising spins.

How can we test this hypothesis? Because the 

variation in behavior for different numbers of 

coupled subunits is a textbook signature of collective effects, the possibility of creating CTPRs 

in any multiplicity desired renders them an ideal 

system in which to test this model of repeat 

protein stability. Accordingly, we synthesized a 

series of CTPRs, for which the number of helices 

varied from 5 to 21. The stability of these proteins 

as a function of guanidine hydrochloride (GuHCl) 

concentration (GuHCl is an agent used to induce 

protein unfolding) is shown in Figure 2. The rapid 

change in each profile with increasing GuHCl concentration corresponds to the transition from the 

folded to the unfolded state. The best fits of the 

Ising model to these data are shown as the solid 

lines in Figure 2. Clearly, the model provides an 

excellent description of the folding/unfolding for all 

of the proteins studied. 

We believe that several aspects of this work are 

particularly exciting. First, the Ising model is predictive: Because thermodynamic data from just two 

different CTPRs in a series are sufficient to predict 

the behavior of all additional CTPRs in that series, 

we may view four of the model profiles in Figure 2

as predictions. These are the first examples of 

successfully predicting the stabilities of proteins 

and the shapes of their unfolding curves.

Second, the Ising model requires a new microscopic picture: In the usual two-state transition, 

a protein is essentially always completely folded 

or completely unfolded with only brief transient 

behavior. In contrast, the Ising description implies 

that near the transition midpoint, partially folded 

configurations occur with significant probability. 

Finally, the structure of CTPRa8 reveals both of 

the atomic details of an individual repeat, and the 

arrangement of repeats in the superhelix, and thus 

A NEW FOLDING PARADIGM FOR REPEAT PROTEINS

T. Kajander1, A.L. Cortajarena1, E.R.G. Main2, S.G.J. Mochrie3, and L. Regan2,4 

1

Department of Molecular Biophysics and Biochemistry, Yale University; 2Department of Chemistry, University of Sussex, UK; 3

Departments of Physics and Applied Physics, Yale University; 4

Department of Chemistry, Yale University

Determining how a protein’s amino acid sequence specifies its structure and properties is a grand challenge for biology in the post-genomic era. Repeat proteins, composed of tandem arrays of a basic 

structural motif, account for more than 5% of metazoan proteins in 

the Swiss-Prot database. It is therefore surprising that the folding of 

repeat proteins has been little studied, especially because their modular structures promise a more tractable folding problem than globular 

proteins. Our approach has been to design a consensus tetratricopeptide repeat (CTPRa) and from this construct a series of proteins that 

contain from two to 20 tandem copies of this repeat. We have shown 

that the folding of this family of TPR proteins can be described and 

predicted by the classical one-dimensional Ising model of statistical 

mechanics, which thus represents a new folding paradigm for repeat 

proteins.

BEAMLINE 

X6A

PUBLICATION

T. Kajander, A.L. Cortajarena, 

E.R.G. Main, S.G.J. Mochrie, and 

L. Regan, “A New Folding Paradigm for Repeat Proteins,” J. Am. 

Chem. Soc., 127(29), 10188-10190 

(2005).

FUNDING

Helsingin Sanomat Centennial 

Foundation (Finland) postdoctoral fellowship; Spanish Ministry 

of Culture, Education and Sports 

postdoctoral fellowship

FOR MORE INFORMATION

Simon Mochrie

Departments of Physics and 

Applied Physics

Yale University

simon.mochrie@yale.edu

Authors (from left) Tommi Kajander, Lynne Regan, 

Simon Mochrie, and Aitziber Cortajarena
2-65

LIFE SCIENCE

promises the possibility of being able to assign 

the Ising model parameters to specific structural 

elements. Re-designs are in progress to test such 

ideas. 

In a more general sense, beyond repeat proteins, 

does the behavior of the CTPRa series tell us anything about the folding of globular globular proteins? The proteins? The

folding of several small, single-domain globular 

proteins has been well-studied. As for individual 

repeat proteins, their thermodynamic behavior can 

Figure 1. Crystal structure of CTPRa8. (A) View 

perpendicular to the superhelical axis. Each TPR repeat is 

colored either red or blue. (B) View along the superhelical 

axis. 

usually be well-described by the traditional twostate model. However, in many cases, hydrogenexchange measurements reveal a richer free-energy landscape than simply two free-energy minima, 

hinting that it may be sensible to envision each 

element of secondary structure itself as a degree 

of freedom that can be either folded or unfolded, 

i.e. as an Ising spin. Such observations suggest 

important similarities between the thermodynamics 

of repeat proteins and globular proteins.

Figure 2. Thermodynamics of CTPRa unfolding. Fraction 

folded vs. [GuHCl] for CTPRa2 (squares), CTPRa3 

(crosses), CTPRa4 (triangles), CTPRa6 (diamonds), 

CTPRa8 (crosses), CTPRa10 (inverted triangles) in 50 mM 

sodium phosphate, pH 6.5, 150 mM sodium chloride, 

at -25 °C. Root-mean-square errors of 0.8 millidegrees 

are smaller than the plotting symbols, except (when 

transformed) for the fraction folded of CTPRa2 in (B). 

Solid lines correspond to the best-fi ts to the predictions 

of the one-dimensional N-spin Ising model. Analogously -spin Ising model. Analogously 

to the Ising-Zimm-Bragg treatment of the polypeptide 

helix-coil transition, our model ascribes a reduced stability 

to the endmost helices, relative to those not at the end, 

by incorporating interactions with fi cticious down spins at 

position 0 and N+1. 

A

C

B

Fraction folded

GuHCI concentration [M]

1.0

0.5

0.0

1 2 3 4
BEAMLINE 

X25

PUBLICATION

A. Serganov, A. Polonskaia, 

A.-T. Phan, R.R. Breaker, and D.J. 

Patel, “Structural Basis for Gene 

Regulation by a Thiamine Pyrophosphate-Sensing Riboswitch,” 

Nature, 441, 1167-1171 (2006).

FUNDING

National Institutes of Health

FOR MORE INFORMATION

Alexander Serganov

Structural Biology Program

Memorial Sloan-Kettering 

Cancer Center

serganoa@mskcc.org

RNA molecules, traditionally viewed as passive 

messengers of genetic information, have surprised 

researchers every few years with the discovery of novel functions that they perform. Recent 

studies have shown that some mRNAs - termed 

riboswitches - can sense changes in the levels of 

cellular metabolites and activate or repress genes 

involved in the biosynthesis and transport of these 

metabolites. Riboswitches are now recognized as 

one of the major metabolite-controlling systems 

that account for about 2% of genetic regulation in 

bacteria and that respond to various metabolites 

including co-enzymes, sugars, nucleotide bases, 

amino acids, and cations. 

Riboswitches typically consist of two parts: a 

sensing region recognizing metabolites and an 

expression platform carrying gene-expression signals. Metabolite binding causes alternative folding 

in the sensing domain followed by conformational 

changes in the adjoining expression platform. This 

structural re-organization of the riboswitch results 

in the formation of specific structures that can 

terminate mRNA synthesis or prevent protein biosynthesis (Figure 1). Remarkably, riboswitches do 

not need protein co-factors for recognition of their 

targets or for RNA folding. Though riboswitches 

are made of only 4 nucleotides instead of 20 different amino acids building the proteins, riboswitches 

can choose their target molecules among very 

similar metabolites as well as proteins do.

In order to understand how riboswitches recognize 

their metabolite targets and regulate gene expression, we have determined the three-dimensional 

structure of the complex between thiamine pyrophosphate (TPP) and its cognate E.coli riboswitch 

at 2.05 Å resolution. The TPP riboswitches are 

the most widespread class of metabolite-sensing 

RNAs and the only riboswitches found in all three 

kingdoms of life. The structure shows that the riboswitch consists of two large helical domains and 

a short helix P1 connected by a junction (Figure 

2). The helical domains are parallel and contact 

each other by long-range tertiary interactions. TPP 

binds the riboswitch in an extended conformation 

and positions itself between and perpendicular 

to the helical domains such that opposite ends of 

TPP are bound to a specific RNA pocket. Notably, 

TPP carries negatively charged phosphate groups 

and the structure shows how RNA recruits positively charged metal ions to mediate otherwise 

unfavorable electrostatic interactions. Similar to 

purine riboswitches, TPP is largely enveloped in 

the structure of the complex and, in agreement 

with biochemical experiments, the TPP riboswitch 

folds upon binding to TPP. However, discrimination 

STRUCTURAL BASIS FOR GENE REGULATION BY A

THIAMINE PYROPHOSPHATE-SENSING RIBOSWITCH

A. Serganov1, A. Polonskaia1, A. Tuân Phan1, R.R. Breaker2, and D.J. Patel1

1

Structural Biology Program, Memorial Sloan-Kettering Cancer Center; 2Department of Molecular, Cellular and Developmental Biology and Howard Hughes Medical Institute, Yale University 

Genes are commonly turned on or off by protein factors that respond 

to cellular signals. The recent discovery of riboswitches proved that 

RNA molecules also control genes by directly sensing the presence of 

essential cellular metabolites. We determined the three-dimensional 

structure of the most widespread riboswitch class bound to its target, 

thiamine pyrophosphate, a co-enzyme derived from vitamin B1. These 

findings reveal how riboswitch RNA folds to form a precise pocket for 

its target and how a drug that kills bacteria tricks the riboswitch and 

starves disease-causing organisms of this essential compound. 

Authors Alexander Serganov and Anna 

Polonskaia

2-66
between TPP and related compounds is achieved 

using a principle that is different from purine 

riboswitches. Purine riboswitches distinguish between adenine and guanine ligands via formation 

of Watson-Crick base pairs with either uridine or 

cytosine nucleotides located in strategic positions 

in the riboswitch. The TPP riboswitch, on the other 

hand, can be considered as a molecular ruler 

measuring the length of the ligand. Analogs of 

TPP lacking one or both phosphates cannot reach 

well into both binding pockets of the riboswitch. 

According to biochemical experiments, they cannot stabilize the metabolite-bound architecture 

of the riboswitch, including the key helix P1, and 

cannot effectively control gene expression. The 

central part of TPP is not specifically recognized 

by the riboswitch, and this observation explains 

how the man-made TPP-like drug pyrithiamine 

pyrophosphate, which differs from TPP in the 

middle part, targets the riboswitch and down-regulates expression of thiamine-related genes, thus 

starving microbes of TPP. Given the important role 

of riboswitches in various microorganisms and the 

fact that riboswitches have not yet been detected 

in the human genome, riboswitch structures 

should enable researchers to employ rational drug 

discovery strategies to create novel classes of 

antimicrobial compounds that specifically target 

riboswitches.

Figure 2. Structural models of a TPP riboswitch and its 

ligands. (A) Chemical structures of the natural metabolite 

TPP and the antimicrobial compound pyrithiamine 

pyrophosphate; (B) Crystal structure of the TPP-bound 

sensing domain from E.coli thiM gene in a ribbon 

representation. Structural elements of riboswitch are 

colored according to Figure 1: major helical domains are in 

green and blue, helix P1 in orange and three-way junction 

in gray. TPP and hydrated Mg cations are shown in red and 

yellow, respectively.

Figure 1. Schematic representation of the riboswitch’s 

function exemplifi ed by the thiamine pyrophosphate - 

specifi c riboswitch, which represses the initiation of protein 

biosynthesis in the presence of metabolite. The structural 

elements of the metabolite-sensing domain are colored in 

yellow, blue, green, and gray, and the expression platform 

is in black. In the absence of metabolite, the metabolitesensing domain folds into the structure, which exposes 

the initiation signal of protein synthesis (green asterisk), 

thereby turning gene expression ‘ON’. In the presence of 

metabolite (shown in red), the sensing domain folds into an 

alternative structure and causes the formation of the hairpin 

in the expression platform. As a result, the initiation signal 

becomes engaged in base pairing (red asterisk) and cannot 

function anymore, thereby shutting down gene expression, 

and acting as an ‘OFF’ switch.

A

B

2-67

LIFE SCIENCE
2-68

BEAMLINE 

X26C

PUBLICATION

L.J. Higgins, F. Yan, P. Liu, H.-W. 

Liu, and C.L. Drennan, "Structural 

Insight into Antibiotic Fosfomycin 

Biosynthesis by a Mononuclear 

Iron Enzyme," Nature, 437, 838-

844 (2005).

FUNDING

National Institutes of Health; 

National Institute of Environmental Health Sciences; Searle 

Scholars Program; Alfred P. Sloan 

Foundation; A Lester Wolfe 

Predoctoral Fellowship

FOR MORE INFORMATION

Catherine L. Drennan

Department of Chemistry

Massachusetts Institute of Technology

cdrennan@mit.edu

Mononuclear non-heme iron enzymes use their 

metal cofactor to activate dioxygen (O2) for difficult redox processes. One of these enzymes, 

S-(2)-Hydroxypropylphosphonic acid epoxidase 

(HppE), from Streptomyces wedmorensis (Figure 

1, overall structure), employs its mononuclear iron 

center and molecular oxygen for the two-electron 

oxidation of S-(2)-hydroxypropylphosphonic acid 

(S-HPP) to catalyze the formation of the antibiotic 

(1R,2S)-(1,2-epoxypropyl)phosphonic acid (fosfomycin). This reaction is essentially a dehydrogenation reaction (loss of hydrogen). In order to 

balance the four-electron reduction of oxygen to 

water, we have proposed a putative two-electron 

reductant (or reductase). Fosfomycin is an unusual C-P-bond-containing epoxide that covalently 

modifies UDP-GlcNAc enolpyruvyl transferase, 

consequently inhibiting bacterial cell-wall peptidoglycan biosynthesis and bacterial growth. Since it 

accumulates in the kidneys and bladder, fosfomycin has been used clinically for the treatment 

of lower-urinary-tract infections. The structures 

of the apo-HppE (metal-free), native Fe(II)-HppE, 

tris(hydroxymethyl)aminomethane (Tris)-Co(II)-

HppE complex, S-HPP-Co(II)-HppE complex, and 

two S-HPP-Fe(II)-HppE complexes (form 1 and 

form 2) were solved in order to better understand 

the epoxidation mechanism of this enzyme. It is 

interesting to note that the Tris molecules in the 

Tris-Co(II)-HppE structure result from the Tris buffer used in the crystallization solution.

Selenomethionine (SeMet) derivatization was used 

to obtain phase information for these protein structures. Initial experimental phases were determined 

from an x-ray dataset of Tris-Co(II)-SeMet-HppE 

collected at the wavelength for the Se absorption 

peak (0.9791 Å) on NSLS beamline X26C. This 

dataset was refined to 2.5 Å in space group P6522 

and the resulting model was further refined against 

a 1.8 Å native Tris-Co(II)-HppE dataset that was 

obtained at 0.9791 Å on Advanced Photon Source 

beamline 8BM. All subsequent structures were 

determined from these initial models. 

The structures of S-HPP-Fe(II)-HppE complexes 

(form 1 and form 2) confirm the direct binding of 

the substrate, S-HPP, to the iron and show the 

existence of two binding modes, a monodentate 

mode and a bidentate mode. These two modes 

are explained by a two-step binding process: (i) 

S-HPP first binds in a monodentate fashion via 

the oxygen atom of the phosphonic acid group, 

resulting in displacement of a water molecule; (ii) 

The subsequent rotation of the substrate allows 

for bidentate coordination of S-HPP to Fe(II). A βhairpin-like structure, formed by β-strands 2 and 3, 

acts as a cantilever that responds to the bidentate 

positioning of the substrate and adopts a closed 

catalytic conformation to cover the hydrophobic 

portion of the substrate bound in the active site 

STRUCTURAL INSIGHT INTO ANTIBIOTIC FOSFOMYCIN

BIOSYNTHESIS BY A MONONUCLEAR IRON ENZYME

L.J. Higgins1*, F. Yan2, P. Liu2, H.-W. Liu2, and C.L. Drennan1

1

Department of Chemistry, Massachusetts Institute of Technology; 2Department of Chemistry 

and Biochemistry, University of Texas at Austin; * Currently a Harvard Medical School Fellow

The mononuclear iron enzyme S-(2)-hydroxypropylphosphonic acid 

epoxidase (HppE), from Streptomyces wedmorensis, uses O2 to 

catalyze the formation of the broad-spectrum antibiotic fosfomycin 

(which inhibits bacterial cell-wall peptidoglycan biosynthesis) from 

S-(2)-hydroxypropylphosphonic acid (S-HPP). The reaction is a 

two-electron oxidation and is mechanistically atypical because it 

is independent of any cofactor or co-substrate and results in the 

incorporation of the hydroxyl oxygen of the substrate, rather than an 

atom of O2, into the epoxide ring. The x-ray crystal structures of six 

forms of HppE — apo-HppE, Fe(II)-HppE, tris(hydroxymethyl)amino 

methane-Co(II)-HppE complex, S-HPP-Co(II)-HppE complex, and two 

S-HPP-Fe(II)-HppE complexes — were solved using data collected in 

part at the NSLS. The purpose was to gain insight into the mechanism 

of this unique enzyme. 

Authors Catherine Drennan and Luke Higgins
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LIFE SCIENCE

(Figure 2). The negative charge on the substrate 

is expected to enhance the reactivity of the diiron 

center toward oxygen, a role that co-substrates 

play in other mononuclear iron proteins. The addition of oxygen to the only open coordination site 

on Fe(II) of the bidentate-S-HPP complex appears 

to occur through a very small channel created at 

the interface of the α- and β- domains. Once O2 is 

bound, abstraction of the C1 hydrogen atom could 

occur by a Fe(IV)-oxo intermediate (Scheme 1, 

pathway A) or by a Fe(III)-hydroperoxide intermediate (Scheme 1, pathway B). This results 

in the formation of a transient-substrate radical 

intermediate that undergoes cyclization to yield 

fosfomycin.

Figure 1. Tetrameric structure of HppE. Scheme 1. Possible reaction mechanisms for HppE.

Figure 2. A portion of the structure called the cantilever 

(red) closes over the active site iron (brown) and substrate 

(ball-and-stick).
2-70

Alzheimer’s disease (AD) is a progressive brain 

disorder that gradually destroys a person’s 

memory, ability to learn, reason, make judgments, 

communicate, and carry out daily activities. The 

brain in AD is characterized by the presence of 

amyloid plaques, which consist of small deposits 

of a peptide called amyloid β (Aβ). In vitro evidence suggests that metal ions such as Cu, Zn, 

Fe, and Mn may play a role in the misfolding of Aβ 

in AD. However, the functions of these metal ions 

and Aβ misfolding in the disease process are not 

well understood. The overall aim of this research 

is to obtain an in situ structural and mechanistic 

picture of how metal ions in the brain are involved 

in Aβ formation and plaque aggregation in AD. 

In this work, thin cryosections (~10 μm) of brain 

tissue from patients with neuropathologically 

confirmed AD were studied. The locations of 

the amyloid plaques were visualized by green 

fluorescence using Thioflavin S staining and 

epifluorescence microscopy (Figure 1B). FTIRM 

carried out at NSLS beamline U10B showed that 

the amyloid plaques had elevated β-sheet content, as demonstrated by a strong Amide I absorbance at 1625 cm-1, which was different from the 

FTIR spectrum of Aβ in vitro (Figure 2A). The 

correlation image generated based on peak height 

ratio of 1625 / 1657 cm-1 (Figure 1C) revealed 

that regions of elevated β-sheet content in the AD 

tissue corresponded well with amyloid deposits as 

identified by Thioflavin staining. 

Using XRF microprobe at NSLS beamline X26A 

and Advanced Photon Source beamline 13-ID, 

we found that the background content of Ca, Fe, 

Cu, and Zn in AD vs. control tissue were similar; 

however the metal distribution in AD tissue was 

not uniform. Specifically, “hot spots” of accumulated Ca, Fe, Cu, and Zn ions were observed. The 

SXRF images of Zn and Cu can be seen in Figure 

1D and 1E, respectively. A strong spatial correlation (r2 = 0.97) was found between the locations of 

the Cu and Zn ions. The elevated Zn and Cu in the 

“hot spot” is also evident in representative XRF 

spectra (Figure 2B). 

In order to correlate the misfolded amyloid protein 

and metal distribution in the tissue, an RGB image 

was generated with Zn content in red channel, 

β-sheet protein content in the green channel, and 

Cu content in the blue channel. Results revealed 

the co-localization of Cu, Zn, and β-sheet protein 

in the amyloid plaques in AD human tissue (Figure 

1F). Neither plaques nor accumulated metal hot 

CO-LOCALIZATION OF β-AMYLOID DEPOSITS AND

METAL ACCUMULATION IN ALZHEIMER’S DISEASE

Q. Wang1, T.P. Telivala1, R.J. Smith1, A. Lanzirotti2, J. Miklossy3, and L.M. Miller1

1

National Synchrotron Light Source, Brookhaven National Laboratory; 2Consortium for 

Advanced Radiation Sources, University of Chicago; 3Kinsmen Laboratory of Neurological 

Research, University of British Columbia

Alzheimer’s disease (AD) is the most common age-related neurodegenerative disease. It is characterized by the misfolding and plaquelike accumulation of a naturally occurring protein, amyloid beta (Aβ) 

in the brain. This misfolding process has been associated with the 

binding of metal ions such as Fe, Cu, and Zn in vitro. In this work, the 

secondary structure of the amyloid plaques in human AD brain tissue was imaged in situ using synchrotron Fourier transform infrared 

microspectroscopy (FTIRM). The results were correlated spatially with 

the metal ion distribution in the identical tissue, as determined using 

synchrotron x-ray fluorescence (XRF) microprobe. Results revealed 

“hot spots” of accumulated Zn and Cu ions that were co-localized with 

the elevated regions of β-sheet protein, suggesting that metal ions may 

play a role in amyloid plaque formation in human Alzheimer’s disease.

BEAMLINES 

U10B, X26A

PUBLICATION

L.M. Miller, Q. Wang, T.P. Telivala, 

R.J. Smith, A. Lanzirotti, and J. 

Miklossy, “Synchrotron-based 

Infrared and X-ray Imaging 

Shows Focalized Accumulation 

of Cu and Zn Co-localized with 

β-amyloid Deposits in Alzheimer’s 

Disease,” J. Struct. Biol., 155(1), 

30-3 (2006). 

FUNDING

National Institutes of Health

FOR MORE INFORMATION

Lisa M. Miller

Brookhaven National Laboratory 

NSLS

lmiller@bnl.gov

Authors (From left) Randy Smith, Adele Qi Wang, 

Antonio Lanzirotti, and Lisa Miller
2-71

LIFE SCIENCE

spots were observed in control brain tissue.

In summary, these results provide increasing evidence that the formation of amyloid plaques from 

the Aβ peptide is associated with metal ions in 

the brain. Here we show for the first time a direct 

strong spatial correlation between AD plaques and 

metal ions in the brain, emphasizing the role of 

metal ions in AD etiology. In the future, exploring 

earlier stages of disease and in-situ probing metalprotein binding will be of interest for understanding 

the disease pathogenesis and mechanism.

Figure 2. (A) Infrared spectra of Thiofl avin-positive area 

(red) and Thiofl avin-negative area (blue) of AD tissue. For 

comparison, the FTIR spectrum of purifi ed Aβ peptide in 

vitro is shown (green). (B) SXRF microprobe spectra from 

Thiofl avin-positive area (red) and Thiofl avin-negative area 

(black). 

Figure 1. (A) Bright fi eld and (B) Epifl uorescence image 

of human AD tissue stained with Thiofl avin S. (C) Single 

channel color FTIR correlation image of β-sheet protein 

(green). (D) Single channel color SXRF microprobe image 

of Zn (red). (E) Single channel color SXRF microprobe 

image of Cu (blue). (F) The RGB correlation image. 

Energy (keV)

A

B

Normalized XRF Intensity

Frequency (cm-1)

Absorbance
2-72

Malaria causes an estimated 300-500 million cases and 1-3 million deaths annually, 80% of which 

are in children under the age of five. There are 

four species of malaria parasite, of which Plasmodium falciparum is responsible for the majority of 

deaths associated with the disease. Within 9-14 

days after an organism is infected (via a mosquito 

bite) the parasite has invaded the red blood cells, 

breaking them down and resulting in the clinical 

symptoms of the disease. Therefore, preventing 

binding and invasion of the red blood cells by 

the parasite would be critical in either preventing malaria (through vaccine design) or treating it 

(through drug design). 

Binding of the parasite to the red blood cells requires the interaction between erythrocyte binding 

antigen 175 (EBA-175), a protein on the surface 

of the parasite, and the sugars of glycophorin A 

(GpA) on the red blood cell. One domain of EBA175, region II, has been found to be the essential 

component of the parasite required to bind GpA. 

The structure of RII shows that it is a dimer, and 

that the two molecules interact extensively with 

one another in an anti-parallel fashion resembling 

a handshake. The dimer results in the formation of 

two channels in the center of the molecule 

(Figure 1).

To examine the binding interaction of RII to GpA, 

we cocrystallized RII with the sugar α-2,3-sialyllactose, which contains the essential components 

of GpA required for binding to RII. We found six 

binding sites for the sugar to the RII dimer, all of 

which were located at the dimer interface (Figure 

1). Using a cell-based binding assay, we mutated RII at residues required for dimerization or 

the observed sugar binding sites to confirm that 

dimerization and sugar/RII binding are essential 

for red blood cell binding. These mutations were 

expressed on the surface of COS cells (monkey 

test cells) and we assayed for their ability to bind 

normal human erythrocytes. All dimerization and 

glycan-binding mutants had impaired erythrocytebinding ability, demonstrating the importance of 

dimerization in erythrocyte binding and validating 

the glycan binding sites.

Together these results allowed us to propose 

a model for RII binding to GpA (Figure 2). We 

propose that the RII domain of EBA-175, which 

is present on the surface of the parasite, might 

assemble around the GpA extracellular domains 

of the red blood cells and that dimerization of 

EBA-175 would occur upon receptor binding. The 

GpA extracellular domains may either bind within 

the channels or dock on the outer surface of RII, 

feeding sugars into the channels. Binding of the 

BEAMLINES 

X26C, X25

PUBLICATION

N.H. Tolia, E.J. Enemark, B.K.L. 

Sim, and L. Joshua-Tor, “Structural 

Basis for the EBA-175 Erythrocyte Invasion Pathway of the 

Malaria Parasite Plasmodium 

Falciparum,” Cell, 122(2),183-93 

(2005).

FUNDING

Watson School of Biological 

Sciences Leslie C. Quick Jr. Predoctoral Fellowship; Louis Morin 

Charitable Trust; Department of 

Defense Small Business Innovation Research

FOR MORE INFORMATION

Leemor Joshua-Tor

W.M. Keck Structural Biology 

Laboratory

Cold Spring Harbor Lab

leemor@cshl.edu

STRUCTURAL BASIS FOR THE EBA-175 ERYTHROCYTE

INVASION PATHWAY OF THE MALARIA PARASITE

PLASMODIUM FALCIPARUM

N.H. Tolia1,2, E.J. Enemark2, B. Kim Lee Sim3, and L. Joshua-Tor1,2

1

Watson School of Biological Sciences and 2Keck Structural Biology Laboratory, Cold Spring 

Harbor Laboratory; 3Protein Potential

Invasion of red blood cells by the malaria parasite Plasmodium falciparum marks the commencement of the clinical manifestation of the 

disease. During invasion, erythrocyte binding antigen 175 (EBA-175), a 

protein on the surface of the parasite, binds to glycophorin A (GpA) on 

red blood cells. Of the several domains in EBA-175, region II (RII) is 

necessary and sufficient for binding to GpA. We have solved the crystal structures of RII and RII in complex with a sugar that contains the 

essential components required for the binding of EBA-175 to GpA. This 

study provides insight into the mechanism of erythrocyte binding and 

invasion by the malaria parasite, and understanding this interaction will 

aid in the development of drugs and vaccines.

Authors (from left) Eric Enemark, Leemor Joshua-Tor, 

and Niraj Tolia
2-73

LIFE SCIENCE

Figure 2. The P. falciparum membrane is shown on the top 

and the erythrocyte membrane on the bottom. The receptor 

binding domain of EBA-175, RII, is shown as a surface 

representation (green/purple denotes each sub-domain). 

Blue lines represent portions of EBA-175 backbone not 

included in the crystal structure. The receptor Glycophorin A 

(GpA) is shown in red with the membrane-spanning region 

in detail using the NMR structure and the extracellular 

domain is drawn as a schematic fl exible line. The glycans 

of GpA, modeled based on the position of sialyllactose, 

are shown as space-fi lling models in gold. In the left panel, 

the RII dimer assembles around the GpA dimer, with GpA 

binding within the channels. An alternative model is shown 

on the right, where the GpA monomers dock on the outer 

surface of the protein, feeding glycans into the channels.

Figure 1. Crystal structure of RII with sialyllactose. (A) 

A ribbon representation of the dimeric structure of RII. 

The monomers are shaded in different intensities and are 

composed of two subdomains (green and purple), F1 and 

F2. Two channels are created in the center of the molecule. 

Glycan positions are shown in Fo – Fc electron density 

in red. (B) Close-up views of three of the glycan binding 

sites – 1, 3 and 5, from left to right. Residues from both 

monomers contact each glycan.

malaria parasite to the red blood cell triggers 

many signaling pathways within the red blood cell. 

Therefore, we propose that RII-mediated dimerization of EBA-175 may be the trigger for signaling 

during invasion. 

These structures have broad implications in helping to model other erythrocyte-binding-like (EBL) 

family members required for binding between 

the parasite and red blood cells. Of particular 

interest is the homologous protein PfEMP-1 that 

is responsible for cytoadherence of the parasitized red blood cells to the endothelium, resulting 

in the most fatal form of malaria. Perhaps most 

importantly, the structure, along with the functional 

analysis, presents possibilities for drug and vaccine design.

 (A)

(B)
DISULFIDE TRAPPED STRUCTURE OF A REPAIR ENZYME

INTERROGATING UNDAMAGED DNA SHEDS LIGHT ON

DAMAGED DNA RECOGNITION

A. Banerjee1,3, W. Santos1, and G.L. Verdine1,2

1

Departments of Chemistry and Chemical Biology and 2Molecular and Cellular Biology, Harvard 

University; 3Current address: Rockefeller University

Spontaneous changes to the covalent structure of DNA are a threat 

that living systems battle constantly. Repair of the resulting lesions 

is initiated by enzymes known as DNA glycosylase enzymes, which 

extrude damaged nucleosides from the helical stack, insert them into 

an extrahelical active site pocket, and catalyze cleavage of their glycosidic bond. It is poorly understood how DNA glycosylases search the 

genome to locate the exceeding rare sites of damage embedded in a 

vast excess of normal DNA. Through the use of intermolecular disulfide 

crosslinking and x-ray crystallography, we have trapped and characterized in atomic detail the initial complex formed between a bacterial 

8-oxoguanine (oxoG) DNA glycosylase, MutM, and undamaged DNA. 

The structures represent the earliest stage of DNA interrogation by a 

DNA glycosylase and suggest a kinetic mode of discriminating normal 

nucleobases from damaged ones. 

2-74

The oxidation of guanine by escaped intermediates in aerobic respiration generates 8-oxoguanine, a potent endogenous mutagen that causes 

G:C to T:A transversion mutations. Repairing 

this lesion is initiated by the 8-oxoguanine DNA 

glycosylase, MutM in bacteria, and the structurally unrelated OGG1 in eukaryotes. The mechanistic and structural details of oxoG recognition 

by MutM and human OGG1 (hOGG1) have been 

studied exhaustively. Both enzymes bend DNA 

drastically at the site of damage and extrude the 

substrate oxoG from the helix into the extrahelical 

enzyme active site; a similar strategy is used by 

DNA glycosylases. In previous work, we reported 

the use of intermolecular disulfide crosslinking 

(DXL) to trap and then characterize a complex in 

which hOGG1 was interrogating an undamaged 

extrahelical guanine nucleobase in DNA. Here 

we extend DXL technology to include crosslink 

attachment to the DNA backbone, and we use this 

chemistry to trap complexes of MutM with undamaged DNA having no extrahelical nucleobase. The 

trapping chemistry is based on proximity-directed 

disulfide bond formation between backbone-modified DNA containing a disulfide linker attached via 

a phosphoramidite linkage and a cysteine residue 

engineered into the protein. Of the three different 

positions we tested on MutM and DNA for crosslinking, the Q166C/p6 combination emerged as the 

one that underwent the most efficient crosslinking, 

hence we chose this position for further structural 

work. By varying the sequence of DNA and the position of crosslinking, we solved the structures of 

three different complexes of MutM crosslinked to 

undamaged DNA, namely interrogation complexes 

1, 2, and 3 (IC1, IC2, and IC3, Figures 1, 2). The 

structures of all the complexes reveal, for the 

first time, a DNA glycosylase interrogating a fully 

intrahelical base-paired duplex for damaged sites. 

Although the base-pairing in the duplex is intact, 

MutM severely bends the DNA and actively distorts 

the interrogated base-pair (also referred to as the 

sampled register) by inserting the aromatic ring of 

Phe114 in the duplex, thereby severely buckling 

the base-pair in question. 

The sequence of the DNA in IC1 was designed to 

unravel the details of MutM interrogating a G:C 

base pair being crosslinked to p6. However, when 

we solved the structure of IC1, it became clear 

that instead of sampling the G:C base pair at position 8 (the +2 register), MutM jumps by one basepair position along the duplex and instead samples 

the A:T base pair at position 9 (register +3), 

evincing enough flexibility allowed by the disulfide 

crosslink to allow MutM to adopt the position of 

choice (Figure 1). In an attempt to coax MutM to 

sample a G:C base pair, we moved the crosslinking position from p6 to p5. However, the structure 

BEAMLINES 

X25

PUBLICATION

A. Banerjee, W. Santos and G.L. 

Verdine, “Structure of a DNA Glycosylase Searching for Lesions,” 

Science, 311, 1153-1157 (2006).

FUNDING

National Institutes of Health

FOR MORE INFORMATION

Gregory L. Verdine

Department of Chemistry

Harvard University

gregory_verdine@harvard.edu

Authors (from left) Webster Santos, Gregory L. Verdine, 

and Anirban Banerjee
2-75

LIFE SCIENCE

of the resulting complex revealed that MutM continues to sample the A:T base pair at position 9 at 

the cost of inducing a pronounced distortion in the 

DNA helical structure (not described in this work). 

Next, by keeping the crosslinking position fixed 

at p5 and switching bp8 to an A:T, the resulting 

complex IC2 was found to adopt the same overall 

conformation seen in IC1, except now sampling 

the A:T base pair at position 8 (Figure 1). Thus, 

MutM prefers to sample an A:T base pair over G:C 

and the +3 sampling register over +2 or +4. 

In IC1, IC2, and IC3, the target base pair is intact 

but severely buckled, with Phe114 inserted deeply 

into the helical stack on the 3’-side of the nucleobase targeted for extrusion. The structure differs 

in other significant ways from that of MutM bound 

to an extrahelical oxoG lesion (lesion-recognition 

complex, or LRC). In the LRC, Arg112 occupies 

part of the space vacated by the extruded oxoG 

and makes specific interactions with the partner 

C (Figure 2B). In the ICs, Arg112 curls down and 

makes non-specific backbone contacts with the 

DNA (Figure 2B). MutM makes numerous direct 

contacts to the DNA phosphate backbone in the 

LRC and a number of these contacts are replaced 

by water-mediated contacts in the ICs. It has now 

been shown by single-molecule studies that both 

MutM and hOGG1 rapidly slide along DNA with a 

low overall barrier for translocation from one base 

pair to the next. Presumably these water molecules play the role of “lubricating” the protein-DNA 

interface to allow fast translocation of MutM along 

undamaged DNA, as is required by a fast search 

process. The fast search process coupled to the 

severe distortion caused by the probe residue, 

Phe114 (Figure 2B), suggests a kinetic mode of 

discrimination between normal and damaged base 

pairs where the distortion serves as a means for 

enhancing selective extrusion of damaged bases. 

Although structures of other DNA glycosylases 

with undamaged DNA are not available, a survey 

of existing structures of LRCs reveal a similar 

probe residue, mostly aromatic in nature, involved 

in severe local distortion of DNA by the disruption of local helical π-stacking. Thus, DNA interrogation by an intercalating probe residue akin to 

Phe114 may be a general strategy employed by 

diverse DNA glycosylases in their search for lesions in the genome. 

Figure 2. Comparison of the lesion recognition complex 

with interrogation complex 3. (A) Overall structures of the 

complexes. (B) Close-up view of key interactions between 

the target base-pair and MutM. The protein backbone is in 

a crimson ribbon representation, with the side-chain of key 

residues shown in green. The DNA is in gold. The target 

base-pair is shown with a box in (A) and is colored aqua in 

(B) 

Figure 1. Schematic representation of Q166C MutM-DNA 

complexes. (A) The MutM lesion-recognition complex (LRC) 

used as the basis for the design of the crosslinking system. 

(B – D) Interrogation complexes showing the positioning 

of MutM over the DNA duplex, with the target base-pair in 

aqua. The side-chain of the helix-probe residue Phe114 is 

indicated. The numbering system for the base-pairs and 

backbone phosphates is as indicated. The curved green 

line denotes the thiol-bearing tether engaged in a crosslink 

to Cys166. Each blue box indicates the site of tether 

attachment to DNA, the position of the target base-pair, 

and the separation between them, here referred to as the 

register. Dashed blue lines indicate the lack of order in the 

oxoG-recognition loop.

Lesion-recognition complex Interrogation complex 3

A

B

A. OxoG-Recognition Complex

B. Interrogation Complex 1

C. Interrogation Complex 2

D. Interrogation Complex 3

Protein 

displacement
2-76

Neurons are required to make path-finding decisions throughout their development and are 

guided to their final targets by a variety of environmental cues. Semaphorins are a family of guidance molecules that act as repellents in a variety 

of axon development processes. Repulsive guidance by Semaphorins is mediated through their 

interaction with Plexins, a family of transmembrane receptors. Biochemical and genetic analysis 

indicates that a large multi-domain cytosolic 

protein, MICAL (Molecule Interacting with CasL), is required for the repulsive axon guidance 

mediated by the interaction of Semaphorins and 

Plexins. MICAL proteins contain a large aminoterminal FAD-binding domain (MICALfd), followed 

by a series of protein-protein binding domains. 

MICALfd is of great interest since it offers a novel 

link between redox reactions and an axon guidance response. Using x-ray crystallography, we 

determined the structure of murine MICAL1 FADbinding domain, MICALfd (Figure 1).

MICALfd is a mixed α/β globular protein that contains a Rossmann β-α-β fold, two conserved FADbinding motifs, and a third conserved sequence 

motif. The first conserved GXGXXG dinucleotide 

binding motif resides within the Rossman fold. The 

second conserved GD motif has been observed 

in flavoprotein hydroxylases and forms part of a 

strand and a helix. A search of known structures 

reveals that the MICALfd protein is most similar to 

aromatic hydroxylases, especially the p-hydroxybenzoate hydroxylase (pHBH) from P. fluorescens

(rms 1.79 Å for 199 out of 484 aligned α-Carbons).

The strong structural similarity of MICALfd to PHBH 

suggests that the two proteins might have similar 

enzymatic activities. Since purified MICALfd contains oxidized FAD, reduction of the cofactor was 

tested using either NADH (nicotinamide adenine 

dinucleotide) or NADPH (nicotinamide adenine dinucleotide phosphate). Although no net reduction 

of the FAD was detected, a steady, time-dependent oxidation of reduced nicotinamide dinucleotide was observed (Figure 2). This observation 

suggested that enzyme-bound FADH2 was formed 

but was then reoxidized by oxygen. The resulting 

production of H2O2 was confirmed by monitoring 

its formation with horseradish peroxidase in a 

coupled spectrophotometric assay (Figure 2). The 

rate of the reaction is over 10 times faster with 

200 μM NADPH than with 200 μM NADH, suggesting that MICAL is probably an NADPH-dependent 

enzyme.

 

The observation of this enzymatic activity can be 

explained by one of three cases. First, H2O2 is 

the physiological product of the enzyme and is a 

component of the avoidance signal. Second, as 

with other FAD hydroxylases, in the absence of 

A REDOX REACTION IN AXON GUIDANCE: STRUCTURE

AND ENZYMATIC ACTIVITY OF MICAL

M. Nadella, M.A. Bianchet, S.B. Gabelli, and L.M. Amzel

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of 

Medicine

During development, neurons are guided to their final targets by external cues. MICAL, a large multidomain cytosolic protein, is a downstream signaling molecule required for repulsive axon guidance. We 

have determined the structure of the N-terminal FAD-binding domain 

of MICAL to 2.0 Å resolution. This structure shows that MICALfd is 

structurally similar to aromatic hydroxylases and amine oxidases. We 

obtained biochemical data that show that MICALfd is a flavoenzyme 

that, in the presence of NADPH, reduces molecular oxygen to H2O2. 

We propose that the H2O2 produced by this reaction may be one of the 

signaling molecules involved in axon guidance by MICAL.

BEAMLINE 

X6A

PUBLICATION

M. Nadella, M.A. Bianchet, 

S.B. Gabelli, J. Barrila, and L.M. 

Amzel, "Structure and Activity 

of the Axon Guidance Protein 

MICAL," Proc. Natl. Acad. Sci. 

USA,102(46),16830-5 (2005). 

FUNDING

National Institutes of Health

MORE INFORMATION

L.M. Amzel

Department of Biophysics and 

Biophysical Chemistry

Johns Hopkins University School of 

Medicine

mario@neruda.med.jhmi.edu

Authors (from left) L.M. Amzel, S.B. Gabelli, M.A. Bianchet, 

and M. Nadella
2-77

LIFE SCIENCE

substrate the hydroperoxide form of the enzyme 

(the MICALfd-FADH-O2H intermediate) decomposes, producing hydrogen peroxide and oxidized 

enzyme-bound FAD (Scheme 1). 

Third, the enzyme may actually be an amine 

oxidase in which the FADH2 is reoxidized by molecular oxygen, and the reduction by NADPH is a 

fortuitous, non-specific reaction. Although this last 

case is unlikely, discrimination among these possibilities requires further experimentation. 

The synthesis of a specific metabolite and the 

production of reactive oxygen species have been 

previously proposed as possible mechanisms of 

MICAL signaling. We have shown here that the 

FAD-binding domain of MICAL can generate at 

least the second kind of signals: MICAL reduces 

molecular oxygen using NADPH to produce H2O2.

Figure 1. Ribbon representation of the tertiary structure 

of MICALfd. MICALfd is a mixed α/β globular protein 

composed of two sub-domains of different sizes linked 

by two β-strands. Subdomain-1 is colored in magenta 

and subdomain-2 is colored in light blue. The observed 

FAD molecule is colored in yellow. The large sub-domain 

(subdomain-1; residues 1 to 226 and 373 to 484) contains 

the two known FAD sequence motifs (residues 84 to 114 

and 386 to 416) and a third conserved motif typically found 

in hydroxylases (residues 212 to 225). The fi rst motif is 

part of a Rossmann β-α-β fold (β1-α5-β2 in MICALfd). This 

is a sequence commonly found in FAD and NAD(P)Hdependent oxidoreductases. The second motif, which 

contains a conserved GD sequence in hydroxylases, 

forms part of a strand and a helix. In MICALfd this second 

conserved sequence makes contacts with the ribose 

moiety of FAD.

Figure 2. Kinetics of NADPH oxidation and H2O2

production. The absorbance peak at 340 nm is 

characteristic of reduced NAPDH and the peak at 560 

nm the concentration of H2O2. The experiment ran for fi ve 

minutes after the addition of the enzyme. The inset shows 

the initial rates as a function of NADPH concentration. 

Scheme 1
2-78

Enzymes in the Fe(II)-2-oxoglutarate-dependant 

digoxygenase superfamily use molecular oxygen, 

Fe(II), and the decarboxylation of 2-oxoglutarate 

(2OG) to generate succinate and CO2 while oxidizing organic substrates. This superfamily makes 

up the largest class of non-heme iron-containing enzymes and is responsible for such diverse 

biological reactions as the synthesis of some 

antibiotics and plant metabolites, the hydroxylation of collagen, and the regulation of hypoxia. 

In the reaction catalyzed by AlkB, a methyl adduct 

on a nucleotide base is converted to an unstable 

hydroxymethyl moiety that is spontaneously released as formaldehyde to regenerate the original 

unmethylated base. Several AlkB substrates have 

been identified: 1-methyladenine, 3-methylcytosine, 1-methylguanine, and 3-methylthymine. E. 

coli AlkB has also been demonstrated to remove 

ethyl, propyl, and exocyclic etheno adducts. The 

substrates for AlkB are generated by SN2 (substitution, nucleophilic, bimolecular) alkylating 

reagents preferentially in single-stranded DNA and 

RNA. However, AlkB has been shown to demethylate these bases in both single-stranded and 

double-stranded nucleic acid polymers as well as 

in DNA/RNA hybrids. 

The accumulation of DNA lesions caused by alkyl 

modifications to nucleic acids is associated with 

the development of aging, cancer, and neurodegenerative diseases. However, these same DNA 

modifiers are widely used as chemotherapeutic 

drugs for the treatment of cancer. Consequently, 

a thorough knowledge of how DNA repair mechanisms work could benefit both cancer therapy 

and prevention. Understanding how AlkB repairs 

different nucleic acid bases requires the detailed 

characterization of how substrates are recognized 

and bound in the active site. However, initial attempts to crystallize full-length E. coli AlkB proved 

unsuccessful. High-resolution backbone amide 

1H/2H (H/D) exchange measurements showed that 

the N-terminus of E. coli AlkB is conformationally 

flexible. When repeated in the presence of iron 

and substrates, other internal regions of the protein backbone became significantly more protected 

against H/D exchange, implying that the presence 

of the ligands stabilized the structure. A new construct lacking the first 11 amino acids (AlkB-∆N11) 

was created. Crystallization trials were performed 

in the presence of Fe(II), 2OG, and a model methylated trimer [dT-(1-me-dA)-dT] under anaerobic 

conditions since the presence of oxygen would 

cause enzyme turnover. This new N-terminally 

truncated AlkB produced high-quality crystals under these conditions. Crystals obtained anaerobically were exposed to atmospheric oxygen over a 

number of days to capture the enzymatic reaction 

in progress.

The resulting crystal structures of E. coli AlkB offer 

insights into the DNA repair mechanism catalyzed 

not only by AlkB but by Fe-2OG dioxygenases in 

general. Although the Fe-2OG dioxygenase core 

CRYSTAL STRUCTURES OF CATALYTIC COMPLEXES OF

THE OXIDATIVE DNA/RNA REPAIR ENZYME AlkB

B. Yu1, W.C. Edstrom1, J. Benach1, Y. Hamuro2, P.C. Weber2, B.R. Gibney3, and J.F. 

Hunt1

1

Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia 

University; 2ExSAR Corporation; 3Department of Chemistry, Columbia University

AlkB is a protein whose role in DNA repair has only recently been elucidated. Identified as a member of the Fe(II)-2-oxoglutarate-dependent 

digoxygease superfamily, AlkB directly converts alkylated DNA and 

RNA bases back into their original form. The preferred substrates of 

AlkB are based-modified by Sn2-type alkylating agents, like busulfan, 

an anti-cancer drug widely used in the treatment of chronic myelogenous leukemia. Here we describe the crystal structure of substrate and 

product complexes of E. coli AlkB. Anaerobic crystallization conditions 

were used to obtain structures from a protein construct optimized for 

crystallization based on high-resolution backbone amide 1H/2H exchange measurements.

BEAMLINE 

X4A

PUBLICATION

B. Yu, W.C. Edstrom, J. Benach, 

Y. Hamuro, P.C. Weber, B.R. 

Gibney, and J.F. Hunt, “Crystal 

Structures of Catalytic Complexes of the Oxidative DNA/RNA 

Repair Enzyme AlkB,” Nature, 439, 

879-884 (2006).

FUNDING

National Institutes of Health 

American Heart Association

FOR MORE INFORMATION

John F. Hunt

Department of Biological Sciences and Northeast Structural 

Genomics Consortium

Columbia University

jfhunt@biology.columbia.edu

Authors John Hunt and Bomina Yu
2-79

LIFE SCIENCE

of AlkB-∆N11 matches that in other superfamily 

members, a unique, conformationally flexible subdomain holds a methylated trinucleotide substrate 

into the active site. This subdomain corresponds 

to that region protected by H/D exchange in the 

presence of ligands. The flexibility of this “lid” 

may enable docking of diverse alkylated nucleotide substrates into the active site. The observed 

open and closed states of a tunnel (Figure 1) in 

different crystal structures provide further evidence for a putative O2 diffusion pathway that has 

been suggested for other superfamily members. 

Furthermore, we found that exposing crystals 

of the anaerobic Michaelis complex to air yields 

partial oxidation of 2OG to succinate (Figure 2), 

supporting the theory that oxygen binds to the iron 

ion, which then moves or rotates to catalyze the 

dealkylation reaction.

Figure 2. Stereo pair showing active site stereochemistry 

in the crystal structure in which the anaerobic Micheaelis 

complex was exposed to oxygen for 2 h. Unbiased electron 

density maps support the conclusion that a signifi cant 

amount of the 2OG has been oxidized to succinate but that 

the adenine base remains largely methylated after shortterm in situ oxidation. The alternative ligands are shown in oxidation. The alternative ligands are shown in 

semi-transparent rendering with the degree of transparency 

scaled according to refi ned occupancy.

Figure 1. Stereo pairs showing cavities near the active 

site in (A) the structure of the anaerobic Michaelis complex 

after 2 h of exposure to air and (B) the substrate complex 

with Fe(II) replaced by Co(II) and in which the putative 

O2-diffusion tunnel is closed. The molecular surface of the 

protein is colored according to the subdomain of origin 

(with the nucleotide-recognition lid in blue and the catalytic 

core in green). The sidechain of trp-178 is shown in the 

different conformations observed in these two structures, 

which exhibit the greatest variation in the structure of the 

O2-diffusion tunnel among the 7 crystal structures reported 

in our paper. Trp-178 has been reported to be hydroxylated 

by AlkB in the absence of nucleotide substrate, although no 

evidence of this modifi cation is observed in the any of these 

refi ned crystal structures. 

(A)

(B)
2-80

Arginase is a trimeric binuclear manganese 

metalloenzyme that catalyzes the hydrolysis of 

the amino acid L-arginine to form L-ornithine and 

urea. Two arginase isozymes have been identified in mammals: cytosolic arginase I, which is 

responsible for the nitrogen-elimination step of the 

urea cycle, and mitochondrial arginase II, which 

functions in L-arginine homeostasis. Significantly, 

arginase inhibitors can enhance NO-dependent 

biological processes such as smooth muscle 

relaxation, so arginase is a potential drug target 

for diseases characterized by insufficient NO flux 

in biological signaling pathways. Most recently, 

our laboratory has determined that arginase is a 

potential drug target for the treatment of male and 

female sexual arousal disorders. Arginase also 

plays a role in mediating the effects of nitric oxide 

in the immune response. Notably, macrophage 

arginase I and NO synthase are reciprocally 

regulated at the level of transcription: NO synthase is induced by TH1 cytokines, and arginase 

I is induced by TH2 cytokines. As a modulator of 

NO-dependent macrophage cytotoxicity, arginase I 

is implicated in the suppression of the tumoricidal 

activity of macrophages and T cells. In a murine 

model of multiple sclerosis, arginase I expression 

is up-regulated approximately 300-fold. Administration of the arginase inhibitor ABH improves the 

symptoms of the disease.

In the current study, we demonstrate that the 

boronic acid substrate analogues ABH and BEC 

(Figure 1) are highly potent inhibitors of human arginase I, with Kd values of 5 and 270 nM, 

respectively. Therefore, ABH and BEC may be 

potentially useful for blocking tumor-cell growth or 

treating multiple sclerosis in humans. Analysis of 

the high-resolution structures of human arginase 

I complexed with ABH and BEC reveals that the 

boronic acid moiety of each inhibitor undergoes a 

nucleophilic attack to bind as tetrahedral boronate 

anion (Figure 2). This binding mode mimics that 

expected for the actual tetrahedral intermediate 

and its flanking transition states in catalysis. Thus, 

boronic acid inhibitors such as ABH and BEC are 

reactive substrate analogues that are chemically 

transformed into transition state analogues in the 

enzyme active site. Such reactive substrate analogues are informally known as “reaction coordinate analogues.” 

Nanomolar affinity is a consequence of strong 

boronate-manganese coordination interactions 

as well as hydrogen-bond networks between 

the enzyme and the α-carboxylate and α-amino 

groups of the inhibitor, as illustrated for BEC in 

CRYSTAL STRUCTURE OF HUMAN ARGINASE I AT 1.29

Å RESOLUTION AND EXPLORATION OF INHIBITION IN

THE IMMUNE RESPONSE

L. Di Costanzo1, G. Sabio2, A. Mora2, P.C. Rodriguez3, A.C. Ochoa3, F. Centeno2, 

and D.W. Christianson1

1

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania; 

2

Department de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de 

Extremadura, Spain; 3Tumor Immunology Program, Stanley S. Scott Cancer Center and Department of Pediatrics, Lousiana State University

Human arginase I, an enzyme critical to the urea cycle, is a potential 

drug target for diseases linked to compromised L-arginine homeostasis. Here, we report high-affinity binding of the boronic acid-based 

inhibitors “ABH” and “BEC” to human arginase I. The 1.29 Å resolution 

structure of the complex with ABH yields an unprecedented view of 

arginase I’s binuclear manganese cluster and illuminates the structural 

basis for nanomolar enzyme-inhibitor affinity. This work serves as a 

foundation for studying the structural and chemical biology of arginase 

I in the immune response, and we demonstrate the inhibition of arginase activity by ABH in human and murine myeloid cells (blood cells).

BEAMLINE 

X12B

PUBLICATION

L. Di Costanzo, G. Sabio, A. Mora, 

P.C. Rodriguez, A.C. Ochoa, F. 

Centeno, and D.W. Christianson, 

“Crystal Structure of Human Arginase I at 1.29 Å Resolution and 

Exploration of Inhibition in the 

Immune Response,” Proc. Natl. 

Acad. Sci. USA, 102(37), 13058-

13063 (2005).

FUNDING

National Institutes of Health

FOR MORE INFORMATION

David W. Christianson

Department of Chemistry

University of Pennsylvania

chris@sas.upenn.edu

Authors Luigi Di Constanzo and David 

Christianson
2-81

LIFE SCIENCE

Figure 3. In catalysis, this array of intermolecular interactions ensures specificity for L-arginine 

and disfavors binding and catalysis for L-arginine 

analogues bearing modified α-substituents. These 

structure-affinity relationships are important to 

consider as arginase I is explored as a potential 

target for new therapies directed toward inflammatory and immunological disorders, and especially 

so as boronic acid-based inhibitors ultimately join 

the growing family of enzyme-targeted drugs.

Figure 3. Summary of intermolecular interactions in the 

human arginase I-BEC complex.

Figure 1. Human arginase inhibitors S-(2-boronethyl)-

L-cysteine (BEC, Kd = 270 nM) and 2(S)-amino-6-

boronhexanoic acid (ABH, Kd = 5.0 nM).

Figure 2. Complex between human arginase I and the 

reactive substrate analogue inhibitor S-(2-boronethyl)-

L-cysteine (BEC). The inhibitor binds as the tetrahedral 

boronate anion (green). Coordination interactions with 

the binuclear manganese cluster (magenta) spheres are 

indicated by green dotted lines.
2-82

Response regulators function within two-component systems, signal transduction pathways that 

are highly prevalent in bacteria. They are modular 

switches typically comprised of a conserved regulatory domain that regulates the activities of an 

associated effector domain in a phosphorylationdependent manner. They confer virulence and antibiotic resistance in several pathogenic bacteria, 

making them attractive drug targets. The majority 

of response regulators function as transcription 

factors, and the OmpR/PhoB family is the largest 

among them. 

Phosphorylation at the active-site aspartate residue in the regulatory domain leads to a propagated conformational change from the active site 

to a distant “functional face” of the protein through 

the concerted reorientation of a few key residues. 

How this conformational change in the regulatory 

domain affects the activity of the effector domain 

in the OmpR/PhoB family is unknown. In the two 

published structures of full-length family members 

DrrB and DrrD, the recognition helix is completely 

exposed, unhindered by the regulatory domain, 

suggesting that the mechanism of activation is not 

intra-molecular relief of steric inhibition. We present crystallographic and solution NMR data that 

suggest a mechanism of activation for PhoB, and 

we extend it to other members of the family.

The regulatory domain of PhoB shows distinct 

rotationally symmetric dimers in the inactive and 

active states when crystallized under identical 

conditions. In the inactive state, PhoBN crystallizes 

as a two-fold symmetric dimer using the α1-α5 

interface. The symmetry was confirmed in solution using NMR. Concentration-dependent shifts 

of resonances in NMR experiments and analytical ultracentrifugation studies show that inactive 

PhoBN exists in equilibrium between a monomer 

and a dimer in solution. When the structure of the 

effector domain is docked on the structure of the 

inactive PhoBN dimer using either DrrD or DrrB as 

a model, the effector domains project in opposite 

directions, in an orientation incompatible with 

tandem binding to direct repeat DNA sequences. 

This alternate dimer is not observed for any other 

OmpR/PhoB family member and may be a specific 

feature of PhoB that provides an additional means 

of regulation.

PhoBN was also crystallized in the active state using the non-covalent beryllium fluoride (BeF3

-

)

complex as a phosphoryl analog. In the active 

state, PhoBN forms a two-fold symmetric dimer 

using the α4-β5-α5 interface. The symmetry was 

confirmed in solution using NMR. The dimer interface is composed of highly conserved residues 

MECHANISM OF ACTIVATION FOR TRANSCRIPTION

FACTOR PhoB SUGGESTED BY DIFFERENT MODES OF

DIMERIZATION IN THE INACTIVE AND ACTIVE STATES

P. Bachawat1,2, G.V.T. Swapna1,3,5, G.T. Montelione1,2,3,4,5, and A.M. Stock1,2,5

1

Center for Advanced Biotechnology and Medicine; 2Department of Biochemistry, Robert Wood 

Johnson Medical School, University of Medicine and Dentistry of New Jersey; 3Department of 

Molecular Biology and Biochemistry, Rutgers University; 4Northeast Structural Genomics Consortium; 5

Howard Hughes Medical Institute

We have determined the crystal structures of the regulatory domain 

of response regulator PhoB (PhoBN) in its inactive and active forms, ) in its inactive and active forms, N

which suggest its mechanism of phosphorylation-mediated regulation. The structure of active PhoBN, together with the structure of the 

effector domain bound to DNA, define the conformation of the active 

transcription factor in which the regulatory domains dimerize using 

rotational symmetry while the effector domains bind to DNA tandemly, 

implying a lack of intra-molecular interactions. While this active DNAbound state seems common to all members of the family, the mode of 

dimerization in the inactive state seems specific to PhoB.

BEAMLINE 

X4A

PUBLICATION

P. Bachhawat, G.V.T. Swapna, 

T. Montelione, and A.M. Stock, 

“Mechanism of Activation for 

Transcription Factor PhoB Suggested by Different Modes of 

Dimerization in the Inactive and 

Active States,” Structure, 13, 

1353-1363 (2005).

FUNDING

National Institutes of Health 

Cancer Institute of New Jersey

FOR MORE INFORMATION

Ann M. Stock

Department of Molecular Biology 

and Biochemistry

Rutgers University

stock@cabm.rutgers.edu

Authors (from left) Gaetano T. Montelione, Priti 

Bachhawat, Ann M. Stock, and G.V.T. Swapna
2-83

LIFE SCIENCE

that form a central hydrophobic patch surrounded 

by salt-bridges. The structure of active PhoBN, 

together with the previously solved structure of 

the effector domain bound to DNA, provides a 

model of the active transcription factor in which 

the regulatory domains dimerize with rotational 

symmetry while the effector domains bind to DNA 

using tandem symmetry (Figure 1). The different 

symmetries adopted by the regulatory and effector domains suggest that activation causes a loss 

of intra-molecular orientational constraints on the 

effector domains. The high degree of conservation 

of the α4-β5-α5 interface and a number of other 

similar structures from this family suggest that this 

mode of dimerization is common to all members of 

the OmpR/PhoB family.

Figure 1. Model of phosphorylation-mediated activation for 

transcription factor PhoB
2-84

Unlike animals, plants have no immune system, 

yet they are still able to recover from virus infection and even acquire resistance. This is because 

plants have other innate defense mechanisms. 

RNA silencing, one of the available plant defense 

mechanisms, targets viral RNA for destruction. 

Double-stranded RNAs generated during viral 

replication can be perceived as a signal of virus 

infection by the plant host and diced into smaller 

fragments, called small interfering RNAs (siRNAs). These siRNAs, consisting of duplexes of 

21 nucleotides in length, are critical mediators in 

the silencing process. The siRNAs assemble with 

effector nucleases and instruct them to specifically 

cleave viral RNAs, thereby thwarting the proliferation and propagation of the virus. On the other 

hand, viruses need to evade or suppress this 

defense in order to survive and propagate. Studies 

have shown that many plant viruses do possess 

evolved weapons for counter-defense. The p21 

protein is an RNA silencing suppressor recently 

discovered in Beet yellows virus. Because of its 

siRNA binding ability, p21 is thought to inhibit the 

silencing process by inactivating siRNA. To understand the function and mechanism of p21, we have 

determined its crystal structure in its free state, 

thereby revealing a surprising viral-engineered 

scaffold used in binding siRNA. 

The structure of the p21 monomer is comprised 

entirely of α-helices and folded into amino-terminal (NTD) and carboxy-terminal (CTD) domains 

(Figure 1B). But at the higher structural level, p21 

forms an octameric ring, which adopts a previously unknown topology (Figure 1A). Normally, 

protein ring structures are formed by a single type 

of asymmetric (involving a different part of the 

protein, head-to-tail) association process between 

adjacent subunits. In stark contrast, the eight p21 

monomer subunits associate through two types of 

symmetric alignments, namely via a head-to-head 

(NTD-NTD) and tail-to-tail (CTD-CTD) association. This structure represents a new theme in 

the cyclic oligomerization of proteins. Figure 1C

compares the topology of p21 and other common 

ring structures.

To search for the RNA binding site, we noticed 

that several basic residues, exposed within the 

inner surface of the ring, are highly conserved 

among p21 homologs, suggesting that they might 

be involved in RNA binding through electrostatic 

interactions with negatively charged phosphates in 

RNA (Figure 2). In addition, the large inner cavity 

of the ring (~90 Å in diameter) provides enough 

space for RNA binding. 

The structure of p21 differs significantly from a 

previously characterized suppressor, p19 from 

tombusvirus, which is dimeric and strictly recognizes an siRNA duplex of specific length. These 

RNA SILENCING SUPPRESSOR P21 ADOPTS AN

UNUSUAL siRNA-BINDING OCTAMERIC RING

ARCHITECTURE

K. Ye and D.J. Patel

Structural Biology Program, Memorial Sloan-Kettering Cancer Center

In plants, RNA silencing functions as an innate defense mechanism 

against virus infection, where viral RNA strands are degraded by an 

RNA-guided mechanism. Many plant viruses counter-attack by expressing proteins to inhibit this defense pathway. The p21 protein, a 

RNA silencing suppressor in Beet yellows virus, seems to function by 

binding siRNAs, a critical mediator in the process. The crystal structure 

of p21 reveals an octameric ring architecture involving a new mode of 

protein oligomerization. Putative RNA binding sites inside the ring are 

suggested by the structure. In addition, biochemical assays show that 

p21 binds various RNAs besides the siRNA duplex, suggesting the 

existence of an alternative suppression mechanism.

BEAMLINE 

X12C

PUBLICATION

K. Ye and D.J. Patel, "RNA 

Silencing Suppressor p21 of Beet 

Yellows Virus Forms an RNA Binding Octameric Ring Structure," 

Structure, 13, 1375–1384 (2005).

FUNDING

The Abby Rockefeller Mauze 

Trust; The Dewitt Wallace and 

Maloris Foundations

FOR MORE INFORMATION

Keqiong Ye

National Institute of Biological 

Sciences, Beijing

yekeqiong@nibs.ac.cnio@nerud

Keqiong Ye
2-85

LIFE SCIENCE

structural differences suggest that their RNA 

binding mechanisms might also be different. 

Indeed, biochemical analysis showed that p21 is 

a general nucleic acid binding protein, interacting 

with 21-nt or longer single- and double-stranded 

RNAs (Figure 3). Because RNA silencing involves 

various types of RNA, it is possible that p21 might 

suppress RNA silencing by interacting with RNAs 

besides siRNA.

Figure 3. RNA-binding assay of p21 showing that p21 

forms complexes with various RNAs. Individual RNAs 

migrate slower in the native gel after forming protein 

complex (RNP). 

Figure 1. Crystal structure of p21. (A) The entire octameric 

ring. Neighboring monomers are alternatively colored 

with green and red. (B) Structure of the p21 monomer, 

which consists of two domains. (C) Ring topology of p21 

(left panel) compared with other common hexameric ring 

scaffolds as an example (right panel). Each p21 monomer, 

colored the same as in (A), is represented by a rectangle 

(NTD) and an ellipse (CTD).

Figure 2. A putative RNA-binding surface inside the ring, 

which is (A) positively charged and (B) clustered with 

several conserved residues. 

A

B

A B
2-86

BEAMLINE 

X26C, X29

PUBLICATION

E.J. Enemark and L. Joshua-Tor, 

“Mechanism of DNA Translocation in a Replicative Hexameric 

Helicase,” Nature, 442, 270-275 

(2006).

FUNDING

The National Institutes of Health

FOR MORE INFORMATION

Leemor Joshua-Tor

Cold Spring Harbor Laboratory

leemor@cshl.edu

Papillomaviruses are tumor viruses that cause 

benign and cancerous lesions in their host. Replication of papillomaviral DNA within a host cell 

requires the viral E1 protein, a multifunctional 

protein. E1 initially participates in recognizing 

a specific replication origin DNA sequence as a 

dimer with E2, another viral protein. Subsequently, 

further E1 molecules are assembled at the replication origin until two hexamers are established. 

These hexamers are the active helicases that 

operate bidirectionally in the replication of the 

viral DNA. In order to unwind DNA, helicases must 

separate the two strands while moving along, or 

translocating on the DNA. Based on structures of 

the DNA-binding domain of E1 bound to DNA that 

we determined a few years ago, we suggested a 

mechanism for DNA strand separation. However, 

the mechanism that couples the ATP cycle to DNA 

translocation has been unclear. The E1 hexameric 

helicase adopts a ring shape with a prominent 

central channel that has been presumed to encircle substrate DNA during the unwinding process, 

but the atomic details of this binding have been 

uncertain, including whether the ring encircles one 

or both strands of DNA during unwinding.

Our crystal structure of the E1 hexameric helicase bound to single-stranded DNA (Figure 1) 

demonstrates that only one strand of DNA passes 

through the central channel and reveals the details of the non-specific binding (Figure 2). The 

β-hairpins (DNA-binding hairpins) of each subunit 

sequentially track the sugar-phosphate backbone of the DNA in a one nucleotide per subunit 

increment. This configuration resembles a spiral 

staircase (Figure 2).

ATP-binding (and hydrolysis) sites are located 

at the subunit interfaces, and multiple configurations are observed within the hexamer. These 

have been assigned as ATP-type, ADP-type, and 

apo-type. The configuration of the site for a given 

subunit correlates with the relative height of its 

DNA-binding hairpin in the staircase arrangement. 

The subunits that adopt an ATP-type configuration place their hairpins at the top of the staircase 

while the hairpins of apo-type subunits occupy the 

bottom positions of the staircase. The hairpins of 

the ADP-type subunits are placed at intermediate 

positions.

A straightforward “coordinated escort” DNA-translocation mechanism is inferred from the staircased 

DNA-binding and its correlation with the configuration at the ATP-binding sites. Each DNA-binding 

hairpin maintains continuous contact with one 

unique nucleotide of ssDNA and migrates downward via ATP-hydrolysis and subsequent ADPrelease at the subunit interfaces. ATP-hydrolysis 

MECHANISM OF DNA TRANSLOCATION IN A REPLICA- TIVE HEXAMERIC HELICASE

E.J. Enemark1 and L. Joshua-Tor1

1

W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory

During DNA replication, two complementary DNA strands are separated and each becomes a template for the synthesis of a new complementary strand. Strand separation is mediated by a helicase enzyme, a 

molecular machine that uses the energy derived from ATP-hydrolysis to 

separate DNA strands while moving along the DNA. We determined a 

crystal structure of a viral replicative helicase bound to single-stranded 

DNA and nucleotide molecules at the ATP-binding sites. This structure 

demonstrates that a single strand of DNA passes through the hexamer 

channel and that the DNA-binding hairpins of each subunit collectively 

form a spiral staircase that sequentially tracks the DNA backbone. It 

also demonstrates a correlation between the height of each DNA-binding hairpin in the staircase and the ATP-binding configuration, suggesting a straightforward mechanism for DNA translocation. 

Authors (from left) Leemor Joshua-Tor and Eric Enemark
2-87

LIFE SCIENCE

occurs between subunits located toward the top of 

the staircase, while ADP-release occurs between 

subunits located toward the bottom of the staircase. The hairpin at the bottom of the staircase 

releases its associated ssDNA phosphate to conclude its voyage through the hexameric channel. 

Upon binding a new ATP molecule, this subunit 

moves to the top of the staircase to pick up the 

next available ssDNA phosphate, initiating its 

escorted journey through the channel and repeating the process. For one full cycle of the hexamer, each subunit hydrolyzes one ATP molecule, 

releases one ADP molecule, and translocates one 

nucleotide of DNA through the interior channel. 

A full cycle, therefore, translocates 6 nucleotides 

with associated hydrolysis of 6 ATPs and release 

of 6 ADPs.

Figure 2. Details of DNA coordination viewed (A) parallel 

and (B) perpendicular to the hexamer channel and (C) a 

cartoon depicting the “coordinated escort” mechanism for 

DNA translocation.

Figure 1. Views of the E1 hexamer parallel and 

perpendicular to the central channel with indidual subunits 

are color-coded. Single-stranded DNA is bound discretely 

within the chanel, and nucleotides are present at the 

subunit interfaces.

A

B

A B

C
2-88

BEAMLINES 

X7B, X18B, X19A

PUBLICATION

F. Zhang, J.M. Raitano, C. Chen, 

J.C. Hanson, W. Caliebe, S. Khalid, and S. Chan, “Phase Stability 

in Ceria-Zirconia Binary Oxide 

(1-x)CeO2-xZrO2 Nanoparticles: 

The Effect of Ce3+ Concentration 

and the Redox Envirnment,” J. of 

Appl. Phys., 99, 0843131-0843138 

(2006).

FUNDING

U.S. Department of Energy

National Science Foundation

FOR MORE INFORMATION

Siu-Wai Chan

Dept. of Applied Physics and 

Applied Mathematics

Columbia University

sc174@columbia.edu

Cerium oxide in the cubic fl uorite structure has been 

widely investigated because of its multiple applications, such as catalyst and electrolyte material of 

solid oxide fuel cells. In particular, the structural 

properties of binary oxide system of ceria and 

zirconia (CeO2–ZrO2) are extensively studied 

because it retains the superb redox and oxygen 

storage capacity (OSC) properties, and prevents 

thermal instability against coarsening of CeO2. 

However, its various phases have not been 

discussed in detail, particularly with crystallite 

size. In this study, we aimed to investigate the 

structural properties of its nanoparticles for phase 

information. Specifically, we aimed to address 

two areas: First, we looked for methods that can 

stabilize the c’ phase for a higher zirconia concentration to lessen particle coarsening. Second, we 

ascertained the extent to which particle size affects phase stability. This has a significant impact 

on catalysis. 

Phase information of ceria–zirconia nanoparticles 

observed in air is studied by x-ray diffraction, 

transmission electron microscopy, and Raman 

spectroscopy. Particle size and composition are 

varied. Both the metastable tetragonal t’ phase 

and the monoclinic m phase are not observed. 

The nanoscale of the particles likely stabilizes the 

tetragonal t phase against the formation of the 

monoclinic phase even at 100% zirconia. As the 

particle size decreases, both the c−t” and the c’−t 

phase boundaries shift to higher zirconia concentrations. The zirconia solubility limit increases 

with decreasing particle size such that the c and t” 

phases can be sustained at higher concentrations 

of zirconia before the corresponding formation of 

the t” and t phases. Raman scattering and XRD 

results are consistent in determining the emerging 

compositions of the t phase in the 1200° and the 

800°C samples. The nanoparticles show different 

phases from those of the bulk in the CeO2–ZrO2

binary system. Nanoparticles of 20 nm and smaller 

having 35%–40% zirconia in ceria are 100% c’ and 

stable against coarsening. The t” phase also likely 

contributes to OSC. This shows that the range of 

c’ phase can be extended to high ZrO2 concentrations by decreasing the c’ crystallite size alone.

We observed that the range of the c’ phase can 

extend to high ZrO2 concentrations by decreasing 

the c’ crystallite size alone. Earlier, we used x-ray

absorption near edge spectroscopy (XANES) to 

demonstrate that the Ce3+ concentration in ceria 

nanoparticles increases with a decreasing crystallite size. Here, we investigated the valence state of 

Ce with varying ZrO2 concentration and annealing 

atmosphere to better understand the phase stability in this nanocrystalline binary oxide system.

PHASE STABILITY IN CERIA-ZIRCONIA BINARY OXIDE

NANOPARTICLES

F. Zhang1, C.-H. Chen1, J.M. Raitano1, R.D. Robinson1, I.P. Herman1, J.C. Hanson2, 

W.A. Caliebe2, S. Khalid2, and S.-W. Chan1

1

Department of Applied Physics and Applied Mathematics, Materials Research Science and 

Engineering Center, Columbia University; 2Brookhaven National Laboratory

Cerium oxide has been widely investigated as a key component in 

catalysts and as an electrolyte for solid oxide fuel cells because of its 

ability to release or store oxygen when in its cubic fluorite structure. 

This property, which is the alleged source of the oxygen storage 

capacity (OSC) of ceria, is much enhanced by a large surface area and 

a small particle size. However, at high temperatures, ceria particles are 

coarsened, resulting in a smaller total surface area and a lower catalytic efficiency. Alloying with other metal oxides, particularly zirconia, can 

halt this coarsening process. However, the zirconia content for most 

effective catalysis will cause the binary oxide in micron-sized particles 

to contain a substantial amount of tetragonal phase that does not have 

the OSC properties, In our study, nanoparticles of ceria-zirconia were 

found to have a stable cubic fluorite phase despite what was predicted 

by the normal “bulk” phase diagram. Furthermore, we proved that a 

reducing environment stabilizes the cubic phase to 90% zirconia.

Authors (from left) Syed Khalid, Siu-Wai Chan, 

Jonathan C. Hanson, and Joan M. Raitano
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MATERIALS SCIENCE

We used x-ray absorption near edge spectroscopy 

(XANES), time-resolved high temperature x-ray 

diffraction (XRD), and room temperature XRD to 

study the stability of the cubic phase (c’) of Ce1–xZrx

O2–y nanoparticles. Results from XANES at the 

Ce LIII edge and the Zr LIII edge indicate the same

phase transition point of c’-t for samples prepared 

in air. This is consistent with earlier results of XRD 

and Raman spectroscopy. The results show that 

the stability of the c’ phase is directly related to 

the Ce3+ concentration. The percentage of the 3+ 

oxidation state of cerium was measured from the 

relative Ce3+ peak intensity at the Ce LIII edge in 

XANES. An 11% concentration of the larger Ce3+

ions, coupled with the smaller particle size, helps 

in releasing the local stress induced by the smaller 

Zr4+ ions and stabilizes the c’ phase even under 

high zirconia concentrations of 40%–60%. XANES 

results at the Zr LIII edge supported the cubic 

phase stabilization. Under a reducing environment 

instead of in air, when the homogenization anneal 

was performed, the solubility limit of the cubic 

phase Ce1–xZrxO2–y was extended to above 90% zirconia. The Ce3+ concentration increased, reaching 

94% in Ce0.1Zr0.9O2–y. Thus, the stability of c’ phase 

is extended to higher ZrO2 concentrations not by 

finer crystallite size alone but, more significantly, 

by a reducing environment.

Figure 3. Lattice parameter study from in-situ XRD of 

as-prepared (1-x)CeO2-xZrO2 in a reducing atmosphere as 

temperature increases. Each composition shown exhibits 

the cubic phase, c’.

Figure 1. Phase stability diagram of (1-x)CeO2-xZrO2

samples with various crystal size of the c’ phase. There 

are overlapping symbols to denote XRD and Raman 

techniques in phase identifi cation. Open symbols are from 

the XRD results and the inside symbols are from Raman 

scattering. Open squares (□): 100% c’ phase present from 

XRD, circles (¡): t phase present from XRD, diamonds 

(◊): only t phase present from XRD. Inner symbols, solid 

squares (■): only Raman peak 4 is present; vertical line (│): 

only Raman peaks 3 and 4 are present; crosses (Î): only 

Raman peaks 1, 3 and 4 are present; dots (•): all Raman 

peaks 1-6 are present. At the top of the diagram are the 

phase fi elds identifi ed at 800oC from reduced-quench-reoxidized bulk/micron-size samples.

Figure 2. TEM lattice image of Ce0.8Zr0.2O2-y nanoparticles 

annealed previously at 900 o C.

Particle Size (nm)

ZrO2 Content (mol%)

Temperature (oC)

Lattice Parameter a (Å)
Size-controlled synthesis of nanoparticles less 

than a few nanometers in diameter is a challenge due to the spatial resolution limit of most 

scattering and imaging techniques used for 

their structural characterization. We present a 

self-consistent analysis of the extended x-ray 

absorption fine-structure (EXAFS) spectroscopy 

data of ligand-stabilized metal nanoclusters. Our 

method employs the measurement of the coordination numbers and metal-metal bond-length 

decrease that can be correlated with the average 

diameter and structure of the nanoparticles in 

the framework of the surface tension model and 

different structural motifs. To test the method, we 

synthesized and analyzed a series of dodecanethiol-stabilized gold nanoparticles where the only 

control parameter was the gold/thiol ratio ξ, varied 

between 6:1 and 1:6. 

The dodecanethiolate gold nanoparticles were 

synthesized by the Brust method at the undergraduate chemistry laboratory of Yeshiva University’s 

Stern College for Women. They were analyzed by 

transmission electron microscopy at the National 

Science Foundation Garcia Materials Research 

Science and Engineering Center at Stony Brook 

University. EXAFS data were collected at NSLS 

beamline X16C. It is evident that the particle 

size is reduced by lowering the Au/thiol ratio as 

inferred from the visible changes in the relative 

contributions of Au-Au and Au-S bonds to the Au 

L3 EXAFS (Figure 1A). The contributions of the 

Au-Au or Au-S interactions to EXAFS progressively become less important, or more important, 

respectively, as ξ decreases. Indeed, the particle 

size decrease lowers the amplitude of Au-Au 

EXAFS oscillations due to the truncation effect (atoms on the surface of the particle are surrounded 

by fewer neighbors than those in the bulk and, 

hence, the average coordination numbers of AuAu decrease) and enhances the amplitude of Au-S 

EXAFS due to the larger surface/bulk ratio. 

EXAFS data were analyzed by fitting FEFF6 paths 

to Au-S and Au-Au shells. The particle diameters can be estimated, among other methods, 

by assuming specific polyhedral shapes that Au 

nanoparticles can adopt: The icosahedral, cuboctahedral, and truncated octahedral are among 

the most commonly discussed geometries. In our 

case, the cuboctahedral fcc model was chosen 

due to the similarity between the nanoparticles 

data and bulk Au data (Figure 1A) for all ξ. The 

particle diameters were obtained from their Au-Au 

coordination numbers (Figure 2). 

For all samples, the second quantity, ∆R(ξ) = R0

- R(ξ), where R0 = 2.88 Å in bulk gold and R(ξ) is 

the bond length measured at the certain ξ, monoAuthors (from left) M. Rafailovich, A. Frenkel, I. Pister, 

L. Soussan, S. Nemzer, and T. Harris

2-90

BEAMLINE 

X16C

PUBLICATION

A.I. Frenkel, S. Nemzer, I. Pister, 

L. Soussan, T. Harris, Y. Sun, and 

M.H. Rafailovich, "Size-controlled Synthesis and Characterization of Thiol-stabilized 

Gold Nanoparticles," J. Chem. 

Phys., 123, 184701 (2005). 

FUNDING

U.S. Department of Energy; NSLS 

Faculty/Student Research Support Program

FOR MORE INFORMATION

Anatoly I. Frenkel

Physics Department

Yeshiva University

Anatoly.Frenkel@yu.edu

SIZE-CONTROLLED SYNTHESIS AND CHARACTERIZATION

OF THIOL-STABILIZED GOLD NANOPARTICLES

A.I. Frenkel1, S. Nemzer1, I. Pister1, L. Soussan1,T. Harris1,Y. Sun1, and 

M.H. Rafailovich2

1

Yeshiva University; 2Stony Brook University

We synthesized thiol-protected gold nanoparticles by varying just one 

parameter: the gold-thiol ratio (ξ), within the range from 6:1 to 1:6. 

Their size and structure were analyzed self-consistently using transmission electron microscopy to measure their size distribution and 

EXAFS to measure their coordination numbers and nearest-neighbor 

distances. Surface tension in the framework of the spherical drop 

model was used to interpret apparent bond length shortening as ξ

decreased. The smallest of such particles (16 Å in diameter) were 

obtained for ξ = 1:1 and the average size did not change as ξ was lowered to 1:6. We interpret this behavior in terms of surfactant-mediated 

stabilization of the particle size.
tonically as ξ increases (Figure 1B). Such 1NN 

distance shortening at smaller sizes has a familiar 

ring from the lattice contraction of closely packed 

nanoparticles that has been previously interpreted 

in terms of surface stress by Mays, et al. (1968) 

using electron microscopy. We relate the particle 

diameter d to the relative lattice contraction α = 

∆R/R via the surface stress and compressibility K:

 . 

Using our EXAFS measurements of ∆R (Figure 

1b) as well as the experimentally determined 

values for K andƒ rr, we obtained the particle 

diameters for all ξ (Figure 2). The fact that both 

(independent) techniques of EXAFS data analysis that we employed for the particle diameter 

determination (by using the coordination numbers 

and the distance contraction) obtain very similar 

results (Figure 2) characterizes these results as 

highly reliable.

Our results for the gold-core sizes obtained by the 

new EXAFS analysis procedure are in good agreement with Scherrer analysis and statistical thermodynamic calculations by Leff, et al., which find that 

the thiol-capped gold nanoparticles should reach 

the minimum size of 14.7 ± 3.7 Å for a certain Au/

thiol ratio (ξ0) beyond which, for ξ < ξ0, the thiols 

will be present in solution as monomers instead 

of assembling on the nanoparticle surface. In our 

work, a similar result (the gold-core size stabilizes 

at its minimum value of 16 ± 2 Å at ξ0 ≈ 1:1) was 

obtained by two independent methods of EXAFS 

analysis: the coordination number method and the 

surface tension method in the framework of the 

spherical drop model.

In summary, the size and structure of thiol-coated 

gold nanoparticles can be controlled by a single 

parameter: the Au/thiol ratio. We demonstrated 

that their lattice contraction follows the simplified 

spherical drop model and their size stabilization at 

the lowest Au/thiol ratio can be explained by the 

interplay between Au-thiol and thiol-thiol interactions.

d = 4 ƒ rr Κ

3 α

Figure 1. Particle size decrease and saturation is 

evidenced in EXAFS data of the samples prepared by 

the two-phase method. (A) The coordination numbers of 

the Au-Au bonds decrease and for Au-S increase as ξ

decreases. (B) Size-dependence of the average Au-Au 

distances (relative to the bulk) for the samples prepared by 

the two-phase method.

2-91

MATERIALS SCIENCE

Figure 2. Particle sizes for the samples prepared by the 

Brust methods. The sizes were obtained by EXAFS using 

two analysis techniques: empty squares indicate the 

surface tension technique and fi lled circles were obtained 

from the coordination numbers characteristic for the 

cuboctahedral fcc packing. Particle size (Å)

ξ

∆R(Å)

ξ

(B)PT Magnitude, Å-3

r, Å

(A) Au-Au

Au-S
2-92

BEAMLINE 

X15A

PUBLICATION

Z. Zhang, et al., “Structure of 

Hydrated Zn2+ at the Rutile TiO2

(110)–Aqueous Solution Interface: 

Comparison of X-Ray Standing 

Wave, X-ray Absorption Spectroscopy and Density Functional 

Theory Results,” Geochim. et Cosmochim. Acta, 70, 4039 (2006).

FUNDING

U.S. DOE; Materials Simulation 

Center, a Penn State MRSEC 

facility; U.S. NSF/DOE Environmental Molecular Sciences Inst., 

Center for Environmental Kinetics 

Analysis 

FOR MORE INFORMATION

Zhan Zhang

X-ray Science Division

Argonne National Laboratory

zhanzhang@anl.gov

Ion adsorption and electrical double layer (EDL) 

formation at the oxide-aqueous solution interface are fundamental to a number of processes, 

including contaminant transport in the subsurface, 

mineral dissolution and precipitation rates and 

mechanisms, bioavailability of trace metals, incorporation of trace metals into growing crystals, and 

heterogeneous catalysis. While there have been 

extensive studies of EDL phenomena over the 

past decades, the connection between molecularscale processes and their macroscopic manifestations remains elusive. Recent experimental and 

computational studies led to new insights concerning the adsorption of various mono- di- and 

tri-valent cations at the rutile (α-TiO2) (110)-aqueous interface with excellent consistency between 

studies ranging from macroscopic observations 

to microscopic structures and processes. While 

these previous studies clearly demonstrated that 

the Zn2+ adsorbs in a manner that was distinct 

from other cations, discrepancies between the predicted and observed behavior of Zn2+ suggested 

that its interaction at the rutile-water interface was 

poorly understood. To resolve this gap, we used 

a combination of Bragg-reflection x-ray standing 

waves (XSW), surface x-ray absorption spectroscopy and density functional theory (DFT) to understand the adsorption of Zn2+ at the rutile (α-TiO2) 

(110)–aqueous interface. 

In the current study, we first confirmed with XSW 

imaging that Zn2+ ions adsorbed at two distinct 

surface sites at pH 8, i.e., monodentate above the 

bridging oxygen (BO) site, and bidentate between 

two terminal oxygen (TO) sites (Figure 1), with 

however, a coverage and partitioning of Zn2+ ions 

between the two sites that was found to be sensitive to solution pH. Polarization-dependent surface 

extended x-ray absorption fine structure (EXAFS) 

spectroscopy results revealed a reduced (i.e., 4- 

or 5-fold) first shell coordination environment for 

adsorbed Zn2+ with respect to the 6-fold coordination found for aqueous species at pH 8. Octahedral to tetrahedral coordination geometry changes 

have previously been observed for adsorbed 

Zn2+ ions, although this was not well understood. 

It could, for instance, be due to the interfacial 

charge distribution and reduced interfacial dielectric constant, which might be significant enough to 

overcome the relatively small energy differences 

between the ion’s two coordination environments. 

DFT calculations revealed that this transformation 

was favored energetically and was directly coupled to surface induced hydrolysis of the hydrated 

Zn2+ cation. Very good agreement between all experimental and computational results is achieved 

when comparing the predicted and observed Zn2+

adsorption structures and coverage. Ball-and-stick 

models for the two adsorption geometries based 

on the DFT results are shown in Figure 2. 

STRUCTURE OF HYDRATED Zn2+ AT THE RUTILE TiO2

(110) – (110) – (110) – AQUEOUS AQUEOUS SOLUTION SOLUTION INTERFACE INTERFACE:COMPARI COMPARI- SON OF X-RAY STANDING WAVE, X-RAY ABSORP- TION SPECTROSCOPY AND DENSITY FUNCTIONAL

THEORY RESULTS

Z. Zhang1, P. Fenter1, S.D. Kelly1, J.G. Catalano1, A.V. Bandura2, J.D. Kubicki2, J.O. 

Sofo3, D.J. Wesolowski4, M.L. Machesky5, N.C. Sturchio6, and M.J. Bedzyk1,7

1

Argonne National Laboratory; 2St. Petersburg State University, Russia; 3Pennsylvania State 

University; 4Oak Ridge National Laboratory; 5Illinois State Water Survey; 6University of Illinois at 

Chicago; 7Northwestern University

Adsorption of Zn2+ at the rutile TiO2 (110)-aqueous interface was studied with x-ray standing waves, surface x-ray absorption spectroscopy, 

and density functional theory calculations to understand the interrelated issues of adsorption site, occupancy, ion coordination geometry, 

and hydrolysis. At pH 8, Zn2+ was found to adsorb as an inner-sphere 

complex at two different sites. A 4- or 5-fold first shell coordination 

environment was observed for adsorbed Zn2+ instead of the 6-fold 

coordination found for aqueous species at this pH. DFT calculations 

confirmed the energetic stability of a lower coordination environment 

and revealed that such change is correlated with the hydrolysis of 

adsorbed Zn2+. 

Authors (from left) Neil Sturchio, Paul Fenter, Zhan 

Zhang, Michael Bedzyk, and Jeffrey Catalano
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MATERIALS SCIENCE

These results demonstrated that a multi-technique 

approach, including structural and spectroscopic 

measurements and high-level DFT theory, allow 

for a complete characterization of the adsorption 

of ions at the oxide-water interface, even when the 

actual structure involves numerous complexities, 

including multiple adsorption sites, changes in the 

ion hydration shell structure, as well as hydrolysis of the adsorbed species. Comparison of such 

Figure 1. XSW generated 3D iso-density contour surfaces 

for Zn2+ cations at (A) pH 8, and (B) pH 6. The iso-density 

contour surfaces at 65% of the peak element density are 

plotted overlapping with the reference ball-and-stick model 

of a half rutile surface unit cell terminated at the Ti-O basal 

plane. 

results with macroscopic pH-titration/adsorption 

studies of powder suspensions and large-scale 

molecular dynamics simulations leads to definitive 

information on the molecular structure of sorbed 

species at the oxide-water interface, as well as realistic models to rationalize and accurately predict 

the macroscopic manifestations of ion adsorption 

phenomena.

Figure 2. Adsorption geometry of adsorbed Zn2+ cations 

at the TiO2 rutile (110)-aqueous interface. Two distinct 

adsorption geometries are observed: (A) monodentate 

above the bridging oxygen and (B) bidentate between 

terminal oxygens. Hydrogen bonds are represented with 

dashed lines.

(A) (B) (A) (B)
2-94

Cd1-xZnxTe is an attractive material for fabricating 

crystals for x- and gamma-ray detectors. With its 

large band-gap (i.e., the energy gap determines 

its leakage current), detectors produced from the 

material function well at room temperature, while 

the high atomic numbers of its elements impart 

high quantum efficiency (i.e., sensitivity). In principle, detectors are simple devices that directly 

convert the charge pairs generated by ionizingand gamma-radiation into electrical signals. These 

advantages, combined with very good resolution, 

make CZT detectors suitable for a wide range of 

purposes, such as imaging devices for nuclear 

medical imaging, detectors for measuring the 

movement of radioactive materials, monitors to 

prevent the diversion of stored nuclear weapons 

and components, and applications in astronomy.

Unfortunately, structural defects, such as twins, 

dislocations, inclusions, grain- and tilt-boundaries result in crystals of low quality, which severely 

limit the detectors’ performances. Several groups 

have characterized CZT detectors at the microscale, thereby allowing detailed investigations 

of their spatial responses. These measurements 

delineated the detrimental effects of grain boundaries and twins, but were unable to describe the 

physical mechanisms responsible for the carrier 

trapping. Further, the role of dispersed Te inclusions and precipitates within the single-crystal 

CZT volumes remained unclear. Recently, by 

developing a unique measurement facility affording an order-of-magnitude improvement in spatial 

resolution, we obtained unequivocal evidence correlating regions where the detector’s performance 

was degraded with the presence of dispersed 

Te-rich inclusions. 

This correlation between Te precipitates, visible in 

the IR images of crystals, and the deterioration of 

the devices’ responses was measured for several 

1-mm thick planar CZT detectors. The original 

CZT crystals, grown by the Modified Vertical 

Bridgman method, were supplied by Yinnel Tech., 

Inc. To obtain the measurements, the detectors 

were mounted inside a standard eV-Products device holder and irradiated from the cathode side. 

The output signals were readout and processed 

using standard spectroscopy electronics, including 

a charge-sensitive preamplifier, a shaper, and a 

MCA card to collect pulse-height spectra. To study 

local variations in the device’s response, x-ray 

scans were performed at the NSLS X12A beamline 

employing beams of different sizes; the smallest 

was slightly less than 10x10 μm2. For each X-Y 

EFFECT OF TE PRECIPITATES ON THE PERFORMANCE OF

CDZNTE (CZT) DETECTORS

G.A. Carini1, A.E. Bolotnikov1, G.S. Camarda1, G.W. Wright1, L. Li2, and R.B. James1

1

Department of Nonproliferation and National Security, Brookhaven National Laboratory; 2Yinnel 

Tech, Inc.

Measurements taken at the National Synchrotron Light Source allowed 

us to make detailed comparisons of the microscale responses and 

infrared (IR) microscopy images of CdZnTe Frisch-ring x-ray and gamma-detectors. The data conclusively showed that local deteriorations 

of electron-charge collection and the device’s response to x-rays fully 

correlate with the presence of Te precipitates as revealed in the IR images. These data offer the first experimental evidence of the material 

property limiting the energy resolution of CZT gamma-ray detectors.

BEAMLINE 

X12A

PUBLICATION

G.A. Carini, A.E. Bolotnikov, G. 

S. Camarda, G.W. Wright, L. Li, 

and R.B. James, “Effect of Te 

Precipitates on the Performance 

of CdZnTe (CZT) Detectors,” Appl. 

Phys. Lett., 88, 143515 (2006).

FUNDING

U.S. Department of Energy

FOR MORE INFORMATION

Gabriella Carini

Dept. of Nonproliferation and 

National Security

Brookhaven National Laboratory

carini@bnl.gov

Authors (from left) Giuseppe Camarda, Gabriella 

Carini, and Aleksey Bolotnikov
2-95

MATERIALS SCIENCE

position of the x-ray beam, pulse-height spectra 

were collected, and the peak positions, which are 

proportional to the total collected charge, were 

evaluated using a Gaussian fit. We plotted the 

findings from the scans as two-dimensional maps 

of the devices’ responses (Figure 1)

Comparing the IR micrographs and x-ray scans 

(Figure 2), the Te precipitates in the IR images 

clearly correspond to the dark spots in the x-ray 

maps where the device’s response drops off by up 

to 50% of its average value. Furthermore, several 

similar measurements for different thin devices 

fabricated from CZT crystals grown by different 

techniques showed, for the first time, a 100% correlation between the locations of the precipitates 

and the areas of the detector with poor performance.

In contrast to randomly distributed single-level 

traps, precipitates can be considered as extended 

local defects with a very high local concentration 

of trapping centers. In this case, an unpredictable number of charges will be trapped, and the 

amount of trapping cannot be corrected with current techniques. Here, the fluctuations in charge 

loss are proportional to the total number of such 

defects encountered by the electron cloud. Moreover, any electric-field distortions around these 

defects also can contribute to dispersing the collected charges and to degrading the spectroscopic 

performance.

In the past, CZT detectors underwent x-ray, 

gamma-ray, and alpha-particle scans to investigate the uniformity of their responses; the sizes of 

the beams used in those measurements were 100 

μm or larger. This investigation clarified that the 

size of the x-ray beam used for the scans is an important factor in determining the ability to spatially 

resolve the effects of isolated Te-rich precipitates. 

Figure 3 presents four maps of the same area on 

a device evaluated with different spatial resolutions to simulate different beam sizes. The original 

x-ray map, measured with 10 μm steps in both 

directions with a beam of 10x10 μm2 unambiguously shows the degraded regions due to 10-20 

μm diameter Te inclusions. They are not as clear 

in the 20x20 μm map. No precipitates were observed with a 100x100 μm2 beam, and the crystal 

seems fairly uniform in the 200x200 μm2 map. The 

earlier mapping measurements obtained by many 

groups using larger beams led the CZT detector 

community to incorrectly assume that isolated Te 

precipitates did not adversely affect a detector’s 

quality. Our new measurements, offered in this 

paper, allow researchers to easily discern the effects of precipitates on electron trapping, and they 

highlight the critical need to address the presence 

of isolated Te precipitates and aggregates of them 

within single-crystal CZT detectors.

Figure. 2. Examples of correlations between x-ray and 

IR transmission maps measured for a 1 mm thick CZT 

planar device. The scans were performed by using a 10x10 

μm2 sized, 85 keV x-ray beam. In some cases, the typical 

triangular shapes of precipitates are recognizable in the 

x-ray maps.

Figure 1. Three-dimensional view of an x-ray map. The 

scan was performed by using a 10x10 μm2 sized, 30 keV 

beam.

Figure 3. X-ray maps from the same area of the device 

evaluated with different spatial resolutions: 10x10 μm2, 

20x20 μm2, 100x100 μm2, and 200x200 μm2.
2-96

Using the cationic surfactants CnTACl (Cn = alkyl 

chain with n = 8 to 18, TA = trimethylammonium) 

and divalent metal-halides (including Zn, Cd, Cu, 

Ni, Co, Fe, and Mn) we have found a rich variety of liquid crystalline phases. The amphiphilic 

character of the inorganic/organic hybrid and 

the respective tunability of charge density of the 

inorganic anions are responsible for the observed 

variation in structure. Amphiphilic molecules and 

salts, as well as many diblock copolymers are well 

known to exhibit molecular scale phase segregation that results in the formation of lamellar, 

cubic, hexagonal columnar, and spherical micellar structural organizations depending on the 

nature and volume fraction of each block of the 

amphiphile. The majority of literature reports of 

[Surfactant]2MCl4 salts exhibit a lamellar crystalline structure. However, reducing the relative 

volume of the organic block by reducing the length 

of the surfactant tail to only an eight-carbon chain 

affords significantly increased 

curvature to the 

interface between 

the organic and 

inorganic blocks 

resulting in the columnar crystalline 

structure shown 

in Figure 1A for 

[C8TA]2ZnCl4. In 

this work, we have 

also demonstrated 

that it is possible 

to control structural organization 

by variation of the 

volume fraction, and thus charge density, of the 

inorganic polar-block. The metal-halide fraction of 

these materials may consist of discrete molecular 

anions such as the relatively high charge density 

[MCl4]

2- or low charge density oligomeric anionic 

networks, [MnCl2n+m]

m-, depending on the relative 

concentration of the inorganic component. An early 

stage of such oligomerization is observed in the 

crystal structure of [C16TA]2Zn2Cl6 shown in Figure 

1B, for which the low charge density of the inorganic anion requires a severe canting of the surfactant chains. Any further decrease in the charge 

density of the inorganic anion requires a structure 

with a greater curvature than can be afforded by a 

lamellar structure.

Each of the divalent metal halide systems studied 

exhibit relatively low melting points (below 100°C). 

Furthermore, upon melting systems with surfactant chain lengths greater than C10 exhibit classic 

smectic, bicontinuous cubic, hexagonal columnar 

or spherical cubic liquid crystalline textures as 

observed by both x-ray diffraction, Figure 2A, and 

polarized optical microscopy (see the journal cover 

below). Because of the polymorphic nature of the 

parent binary metal halide, a greater structural 

diversity is observed for the zinc systems than any 

of the other transition metals. The phase diagram 

shown in Figure 2B, compiled by VTXRD, DSC 

and POM measurements demonstrates the diversity of structure based on the molecular scale segregation of surfactant and inorganic blocks of this 

hybrid system. Most of the crystalline phases melt 

congruently and have a relatively narrow homogeneity range. However, for compositions intermediate between crystalline phases, single homogeneous liquid crystalline phases with broad homoMETALLOTROPIC LIQUID CRYSTALS: SURFACTANT

INDUCED ORDER IN MOLTEN METAL HALIDES

J.D. Martin, C.L. Keary, T.A. Thornton, M.P. Novotnak, J.W. Knutson, and 

J.C.W. Folmer

Department of Chemistry, North Carolina State University

Liquid crystals consist of anisotropic molecular units, the majority of 

which are organic molecules. More recently, liquid crystals incorporating metals into anisotropic molecules have been prepared. Generally 

these require at least two long-chain organic ligands per metal center. In order to create liquid crystals with high metal content we have 

investigated the surfactant templated design of anisotropic structure 

in molten inorganic networks. Variable temperature x-ray diffraction 

(VTXRD) in conjunction with differential scanning calorimetery (DSC) 

and polarized light optical microscopy (POM) were used to determine 

the structural variation in metallotropic liquid crystals as the relative 

volume fraction of the inorganic block was increased from 33 to 80 

mole percent. 

BEAMLINE 

X7B

PUBLICATION

J.D. Martin, C.L. Keary, T.A. Thornton, M.P. Novotnak, J.W. Knutson, 

and J.C.W. Folmer, “Metallotropic Liquid Crystals: Surfactant 

Induced Order in Molten Metal 

Halides,” Nat. Mater., 5, 271-275 

(2006).

FUNDING

The National Science Foundation 

Research Corporation-Cottrell 

Scholar

FOR MORE INFORMATION

James D. Martin

Department of Chemistry

North Carolina State University

Jim_Martin@ncsu.edu

Authors (from left) Jim Martin and 

Jaap Folmer
2-97

MATERIALS SCIENCE

geneity ranges are observed with no evidence 

of immiscible liquid crystalline phases except at 

compositions loaded as close to the phase boundary as possible. While the copper (II) system, for 

example, yields somewhat less structural diversity 

than that of the zinc (II) system, the liquid crystalline organization of a relatively high concentration 

of d9 metals in C16TA-CuCl-60 give evidence of 

ferromagnetic coupling between metal centers.

This demonstration of templating anisotropic structure into liquid metal-halides, with length scales of 

organization sufficient to exhibit classic liquid crystalline birefringent optical textures, is a significant 

advance in the emerging field of amorphous materials engineering. The high metal content of these 

liquid crystalline systems significantly advances 

the field of metallomesogens, which seeks to 

combine magnetic, electronic, optical, redox and 

catalytic properties common to inorganic materials, with fluid properties of liquid crystals.

Figure 2. (A) XRD patterns for liquid crystalline C16TAZnCl-# (# is the mole % ZnCl2) recorded at approximately 

100 °C. Each pattern is offset by 0.1Å-1 for clarity. The 

33% and 50% compositions exhibit lamellar structures, the 

55% composition indexes to a Ia3d bi-continuous cubic 

phase, and the 65% composition indexes as a hexagonal 

columnar structure. (B) Phase diagram of the C16TAC/ZnCl2

system. Crystalline phases are identifi ed by solid vertical 

lines. Liquid crystalline phases include lamellar (SmA) 

(also crystal smectic (Sm)), Ia3d bi-continuous cubic (Cub), 

hexagonal non-geometric (Hng), hexagonal columnar (Colh) 

and cubic micelle (Cub’). Dashed lines represent the 

composition boundary above which crystals of ZnCl2 are 

observed. The dotted line indicates the temperature of the 

Hng-Colh transition that is only observed by a change in the 

optical texture upon heating.

Figure 1. Drawing of the crystal structures of (A) 

[C8TA]2ZnCl4, and (B) [C16TA]2Zn2Cl6, showing columnar 

and lamellar organization, respectively.

C16TA-ZnCl

Temperature (°C)

Mol% ZNCl2

(A)

(B)

Q (Å-1) 

(A) (a) (b) (B)
2-98

Marine biofouling refers to the unwanted accumulation of marine organisms on an underwater 

surface. An environmentally benign strategy to 

tackle marine biofouling is the use of non-toxic 

polymer coatings that can resist bioaccumulation. 

Poly(dimethyl siloxane) (PDMS) elastomers are 

widely used as “fouling release” surfaces because 

they enable easy release of colonizing organisms. 

While PDMS surfaces are quite efficient in the release of Ulva, they are ineffective against diatom 

fouling. The green macroalga Ulva and unicellular 

diatoms are the commonly found algae in marine 

biofilms. Their attachment to surfaces is achieved 

through secretion of adhesive glycoproteins, 

polysaccharides or proteoglycans. The attachment 

strength is determined by molecular interaction of 

these adhesives with the surface. Previous studies 

had shown that diatoms attached strongly to hydrophobic PDMS and weakly to hydrophilic glass 

surfaces, while Ulva exhibited an exactly opposite 

behavior. Our goal was to prepare biomaterial 

surfaces that minimized adhesion of extracellular 

adhesive matrices of a wide range of organisms.

Toward this goal, we attached PEGylated fluoroalkyl groups to a polystyrene-block-poly(acrylic acid) 

copolymer synthesized by ATRP. The amphiphilic 

polymers were expected to undergo an environment-dependent reconstruction as shown in 

Figure 1. Despite a slightly higher surface energy 

than polystyrene, we expected the PEG groups 

to segregate to the air-polymer interface because 

they were anchored to the low-energy perfluoroalkyl groups. Surface segregation of the PEGylated 

side chains was confirmed by NEXAFS. Figure 

2 shows the normalized partial electron yield 

NEXAFS spectra for four representative emission angles, φ. The sampling depth is proportional 

to cosφ. Hence, a higher emission angle implies 

that a thinner surface layer is being probed. The 

intensity of the C1sàπ*Φ resonance corresponding 

to the polystyrene block was found to be lower at 

a higher φ (Figure 2). Conversely, the C1sàσ*C–F

resonance intensity was higher at higher φ. Therefore, the polymer surface was enriched in the 

ANTI-BIOFOULING PROPERTIES OF COMBLIKE BLOCK

COPOLYMERS WITH AMPHIPHILIC SIDE CHAINS

S. Krishnan1, R. Ayothi1, A. Hexemer2, J.A. Finlay4, K.E. Sohn2, R. Perry4, 

C.K. Ober1, E.J. Kramer2,3, M.E. Callow4, J.A. Callow4, and D.A. Fischer5

1

Department of Materials Science and Engineering, Cornell University; 2Department of Materials 

and 3Department of Chemical Engineering, University of California at Santa Barbara; 4School of 

Biosciences, The University of Birmingham; 5National Institute of Standards and Technology

Novel polystyrene block copolymers with amphiphilic side chains were 

synthesized and evaluated for their anti-biofouling surface characteristics. The side chain consisted of a hydrophilic poly(ethylene glycol) 

(PEG) segment capped with a hydrophobic perfluoroalkyl segment. 

Surfaces prepared using these polymers showed a depth-dependent 

composition profile that was characterized using NEXAFS at the NSLS 

beamline U7A. The angle between the surface-normal and an in-plane 

electron detector was varied and partial electron yield NEXAFS spectra 

were acquired at each angle. An analytical framework to extract composition profile from the angle-dependent variations in Auger electron 

intensity was developed. The block copolymer surfaces, which showed 

surface segregation of the higher surface-energy PEG groups, were 

found to have promising fouling release properties when evaluated 

against the marine macroalga Ulva and the diatom Navicula.

BEAMLINE 

U7A

PUBLICATION

S. Krishnan, R. Ayothi, A. Hexemer, J.A. Finlay, K.E. Sohn, R. 

Perry, C.K. Ober, E.J. Kramer, 

M.E. Callow, J.A. Callow, and 

D.A. Fischer, “Anti-biofouling 

Properties of Comblike Block Copolymers with Amphiphilic Side 

Chains,” Langmuir, 22, 5075-5086 

(2006).

FUNDING

Offi ce of Naval Research

National Science Foundation

FOR MORE INFORMATION

Christopher K. Ober

Department of Materials Science 

and Engineering

Cornell University

cober@ccmr.cornell.edu

Authors (from left) John Finlay, Ramakrishnan Ayothi, 

and lead researcher Sitaraman Krishnan

Authors (from left) Karen Sohn, Edward Kramer, 

Alex Hexemer, Dan Fischer, Marvin Paik, Sitaraman 

Krishnan, and Christopher Ober
2-99

SOFT CONDENSED MATTER AND BIOPHYSICS

PEGylated fluoroalkyl side chains relative to the 

polystyrene phenyl rings.

We have shown that the normalized intensity of 

the π*Φ resonance at a given emission angle, I

Φ(φ), 

is proportional to the Laplace-transform of the 

concentration profile, f

Φ(z), of the phenyl-ring carbon atoms. Thus, f

Φ(z) could be determined from 

the experimental intensity versus emission angle 

data. Due to surface segregation of the amphiphilic block, only about 25% of the carbon atoms at 

the surface were from polystyrene, a concentration that was significantly lower than the value 

expected based on the block copolymer structure 

(~60%). The surface concentration of polystyrene 

Figure 3. The left-hand side shows removal of Ulva 

sporelings (small, multicelled pregenitors to seaweed) 

and demonstrates that they are most easily removed from 

our new amphiphilic coating compared to PDMS (silicone 

rubber) or even glass. The right-hand side shows that 

Navicula diatoms are also very easily removed from the 

amphiphilic surface as well as glass whereas they adhere 

very strongly to silicone rubber.

decreased further upon water-immersion. The 

surface was immersed in water and the contact 

angle of an air bubble was measured over a period 

of 2 weeks. The captive-bubble contact angle 

decreased from 55° immediately after immersion 

to 31° after 2 weeks. The equilibrium contact angle 

was close to that of a pure PEG surface.

The amphiphilic surfaces showed a higher removal 

of both Ulva and Navicula compared to PDMS 

(Figure 3). It remains to be determined whether 

these surfaces show similar fouling release properties against invertebrate larvae and other marine 

organisms.

Figure 1. The left-hand side of this fi gure shows the 

chemical structure of the surface active block copolymer 

and its amphiphilic side group. In an air or non-polar 

environment, the fl uoroalkyl group is exposed, but in water 

or polar environment, the polar PEG group occupies the 

surface.

Figure 2. Normalized partial electron yield (PEY) NEXAFS 

spectra at different emission angles, φ, between the surface 

normal and the partial electron yield detector.
2-100

Miscible polymer blends have been model systems for investigations of polymer dynamics 

and equilibrium segregation at polymer surfaces 

and polymer/polymer interfaces. They are often 

composed of polymer pairs that have an apparent 

exothermic enthalpy of mixing. Previously investigated miscible blends have included polystyrene 

(PS) in combination with poly(xylenyl ether) (PXE), 

poly(vinylmethyl ether) (PVME), or tetramethylbisphenol-A polycarbonate (TMPC). These systems 

have constituents with highly different glass transition temperatures (Tgs). These asymmetries can 

lead to spatially 

varying Tgs, making accurate 

decoupling of 

various phenomena difficult. The 

need for a model 

miscible blend involving polymers 

with similar Tgs 

and well-defined 

thermodynamic 

parameters has 

motivated this 

investigation.

To analyze the 

PCHMA/PMMA 

bilayers with 

x-ray specular reflectometry (XR), 

single layers 

of PCHMA and 

PMMA were used 

at NSLS beamline X10B to individually measure the dispersion, 

δ, of the two polymers. In the case of XR analysis 

of polymer bilayer systems, difficulties often arise 

in obtaining details regarding polymer-polymer 

interfaces due to the small x-ray contrast, Δδ/δ, 

between the individual polymers, which is typically 

less than 10% for most polymer pairs. In order 

to overcome this difficulty, we used a Fourier 

transformation (FT) analysis method developed 

previously. A four-layer model (a silicon substrate, 

a native oxide layer, a PMMA layer, and a PCHMA 

layer) was used to fit the XR data. Using the measured values for δ, the PCHMA/PMMA bilayers 

were analyzed using the FT method, as shown in 

Figure 1, and the interfacial roughness (Gaussian) was determined to be 0.6 nm. It should be 

noted that the x-ray contrast between PCHMA and 

PMMA is quite small (< 3%), and that this value is 

considered a lower limit. 

In order to investigate segregation, deuterium 

depth profiles were acquired using a CAMECA 

IMS-6f magnetic sector secondary ion mass spectrometer (SIMS) with a 15 nA Cs+ primary beam 

(6.0 keV impact energy) rastered over a 200 μm x 

200 μm area, with detection of negative secondary 

ions from a 60 μm diameter circle at the center. 

The analysis conditions used provided a nominal 

depth resolution (full width at half maximum) of 8 

to 10 nm. From the phase behavior of the three 

polymer pairs, it is known that PS and PCHMA 

are completely miscible with each other, yet PS 

and PCHMA are completely immiscible with PMMA 

under the conditions implemented here. Taking 

advantage of these asymmetries in the thermodynamic interactions between dPS:PMMA and 

PCHMA:PMMA, dPS has been driven to the 

MISCIBILITY IN A TERNARY POLYMER SYSTEM

S.E. Harton1, T. Koga2, F.A. Stevie3, T. Araki4, and H. Ade4

1

Department of Materials Science & Engineering, North Carolina State University; 2Department 

of Materials Science & Engineering, Stony Brook University; 3Analytical Instrumentation Facility, 

North Carolina State University; 4Department of Physics, North Carolina State University

The polymers poly(cyclohexyl methacrylate) (PCHMA) and polystyrene 

(PS) are miscible with each other, but each is highly immiscible with 

poly(methyl methacrylate) (PMMA). Due to their similar glass transition 

temperatures and the ability of PS and PCHMA to be controllably synthesized with a narrow molecular-weight distribution, we anticipate this 

blend to be a model system for future investigations of certain phenomena, such as diffusion in miscible blends and diffusion near surfaces 

and interfaces. As a first step, we have investigated the segregation 

of deuterated PS (dPS) from a miscible blend with PCHMA to a dPS:

PCHMA/PMMA interface. We achieved this by recording real-space 

depth profiles of dPS with secondary ion mass spectrometry (SIMS). 

X-ray reflectometry was used to determine the interfacial roughness 

between PCHMA and PMMA.

BEAMLINE 

X10B

PUBLICATION

S.E. Harton, T. Koga, F.A. Stevie, T. 

Araki, and H. Ade, “Investigation 

of Blend Miscibility of a Ternary 

PS/PCHMA/PMMA System using 

SIMS and Mean-Field Theory,” 

Macromolecules, 38, 10511-10515 

(2005).

FUNDING

National Science Foundation

U. S. Department of Energy

FOR MORE INFORMATION

Harald Ade

Department of Physics

North Carolina State University

harald_ade@ncsu.edu

Authors (top from 

left) Harald Ade, 

Shane Harton, 

(middle from left) 

Tadanori Koga, 

Tohru Araki, 

(bottom) Fred 

Stevie
2-101

SOFT CONDENSED MATTER AND BIOPHYSICS

interface by annealing bilayer films at 150°C for 

42 hours. Using SIMS, the depth profiles were 

measured for initial dPS concentrations of 5, 10, 

and 20% (v/v) in PCHMA, as shown in Figure 2. 

Because of the low interfacial excess (segregated 

dPS at the dPS:PCHMA/PMMA interface) observed, previously implemented techniques used 

to measure these depth profiles, such as forward 

recoil spectrometry or nuclear reaction analysis, 

would not be able to resolve the segregation of 

dPS to the dPS:PCHMA/PMMA interfaces, as their 

depth resolutions range from approximately 30 to 

80 nm. Even with the relatively high depth resolution attainable using SIMS, it is difficult, if not 

Figure 1. XR of PCHMA/PMMA bilayers. (A) The Fourier 

method was used to determine the interfacial roughness 

of this low contrast system. (B) The low contrast is clearly 

observed in the refl ectivity profi le. 

impossible, to measure the interfacial roughness 

for highly immiscible polymer bilayers. In contrast, 

XR can accomplish that, and SIMS and XR are 

excellent complementary tools.

Our work confirmed that PCHMA and PMMA are 

highly immiscible. Prior literature on the degree 

of miscibility of PS/PCHMA was inconsistent and 

large differences are reported for the interaction 

parameter that governs miscibility. Our segregation data agrees with the more highly miscible 

value, indicating that the PS/PCHMA system might 

be indeed an ideal model system for highly miscible polymers.

q2 (nm-1)

Log (Intensity) Log (Fourier Intensity)

Depth/nm

Volume Fraction of dPS

Figure 2. SIMS profi les for bilayers of dPS in PCHMA 

on PMMA with (A) 5, (B) 10, and (C) 20% (v/v) initial 

concentrations of dPS. After depletion of dPS due to 

segregation to the interface during the 42-hour anneal at 

150 °C, the bulk concentration away from the interface was 

reduced to (A) 4.3, (B) 9.2, and (C) 19.2%.

C

B

A A

B
2-102

BEAMLINE 

U10B

PUBLICATION

J. Torre, M. Cortázar, M.A. Gómez, C. Marco, G. Ellis, C. Riekel, 

P. Dumas, “Nature of the Crystalline Interphase in Sheared iPP / 

Vectra Fiber Model Composites 

by Microfocus X-ray Diffraction 

and IR Microspectroscopy using 

Synchrotron Radiation,” Macromolecules, 39, 5564-5568 (2006).

FUNDING

Spanish Ministry of Education and 

Science; European Synchrotron 

Research Facility 

FOR MORE INFORMATION

Gary Ellis

Department of Polymer Physics 

and Engineering

Inst. of Polymer Science and 

Technology

gary@ictp.csic.es

Fiber-reinforcement is one of the most important 

strategies to improve the application properties 

of both commodity and engineering polymers. 

With an annual production of more than 2.5 billion 

pounds, and a spectacular growth rate, the U.S. 

fiber-reinforced polymer (FRP) market is expected 

to surpass the $6-billion mark in the next few 

years. Many everyday items employ FRPs, from 

automobiles, boats, and sports goods to civil engineering structures and biomedical devices. While 

glass fiber thermosets occupy more than 60 percent of the market, one of the main growth areas 

is thermoplastic resins, including polypropylene, 

and the use of alternative fiber types for reinforcement. Thermotropic liquid crystal polymer (LCP) 

fibers are interesting because of their superior 

mechanical properties, excellent melt flow properties, reduced machine wear and processing costs, 

good recyclability, and low density almost half that 

of glass fibers. This is important for the design of 

strong, lightweight components.

LCP fibers can induce heterogeneous nucleation 

in isotactic polypropylene (iPP) with a high density 

of nucleation sites at the fiber surface, and the 

habitual three-dimensional spherulitic growth is 

impeded due to overcrowding. Crystalline growth 

takes place perpendicular to the fiber surface 

generating a transcrystalline (TC) layer around the 

fiber, in which both the elastic and tensile moduli 

are improved. Various crystalline polymorphs can 

be observed in iPP; the thermodynamically more 

stable monoclinic α-modification predominates, 

whereas crystallization of the less stable trigonal 

β-modification requires specific conditions such as 

thermal gradients, shear stresses, or the presence 

of specific β nucleating agents. Generally when 

fiber-reinforcement generates a TC morphology, 

the α-form of iPP is observed, and the TC β-phase 

is rare. However, there is much interest in the 

mechanical properties of the β-phase, particularly 

improved toughness and impact strength, although 

the mechanisms that generate the β-phase and 

the exact relationship between the presence of TC

morphologies and the final properties of the material are still much debated issues.

Shear stress can also generate β-phase TC-like

iPP around fibers, and a cylindritic crystalline 

superstructure is developed, differentiating it from 

TC structures. The most important evidence for 

this comes from polarized thermo-optical light microscopy that, along with morphological data from 

SEM and AFM, support the Varga and KargerKocsis model: shear produced in the melt by 

fiber-pulling generates extended chain geometries 

that give rise to series of α-row nuclei along the 

fiber surface. At the interface of this thin layer of 

oriented α-crystals a transition from the α- to the 

STUDY OF THE MICROSTRUCTURE OF POLYMORPHIC

INTERPHASES IN FIBER REINFORCED POLYPROPYLENE

COMPOSITES BY SYNCHROTRON IR MICROSPECTROS- COPY AND X-RAY MICRODIFFRACTION

G. Ellis1, M.A. Gómez1, C. Marco1, J. Torre2, M. Cortázar2, C. Riekel3 and P. Dumas4

1

Dpto. Física e Ingeniería, Instituto de Ciencia y Tecnología de Polímeros (CSIC), Spain; 2Dpto. 

Ciencia y Tecnología de Polímeros, Facultad de Química, Universidad del País Vasco UPV/

EHU, Spain; 3European Synchrotron Radiation Facility, France; 4Synchrotron SOLEIL, France

The nature of the fiber-matrix interphase conditions the final properties 

of fiber-reinforced semicrystalline polymers. Heterogeneous nucleation 

at the fiber surface can alter the properties of the matrix, thus the 

understanding and control of the crystalline morphology and microstructure of the interphase is fundamental. Spatially resolved information was obtained from an LCP fiber reinforced isotactic polypropylene 

model composite using two synchrotron-based methods; infrared 

microspectroscopy and microfocus x-ray diffraction. The combination of IR microspectroscopy with spatially resolved crystallographic 

information, obtained for the first time from a polymorphic fiber–matrix 

interphase, confirms a generally accepted model based on morphological evidence. 

Gary Ellis
2-103

SOFT CONDENSED MATTER AND BIOPHYSICS

β-phase takes place, giving rise to the formation of 

the β-cylindritic crystalline superstructure. 

Our main goal was to obtain direct structural 

information from the fiber-matrix interphase. We 

have studied samples where fiber-pulling at 140 

oC generated shear in the polymer melt, and after 

isothermal crystallization and subsequent cooling to room temperature, selected regions of 

the samples were examined using both infrared 

microspectroscopy and wide-angle x-ray microdiffraction. 

Mapping relative IR band intensities at specific 

sampling geometries in the highly polarized synchrotron beam allows us to differentiate between 

the two crystalline polymorphs (Figure 1), and 

a false-color image of the marked area clearly 

shows evidence of a layer of α-phase iPP around 

the fiber. Unequivocal identification depends on 

the relative orientation of the polymer chains with 

respect to the polarization axis of the synchrotron 

beam. 

This is confirmed with wide-angle x-ray microdiffraction experiments (Figure 2). A 3 μm diameter 

x-ray beam was scanned through the interphase 

region perpendicular to the fiber axis in 5 μm 

steps. The observation of the β-cylindritic layer 

and a highly ordered α-phase iPP close to the 

fiber (Figure 2C) confirms the spectroscopic evidence.

The presence of a thin layer close to the sheared 

fiber corresponding to the α-phase has been 

unequivocally confirmed by both synchrotron IR 

microspectroscopy and x-ray microdiffraction. We 

hope further high spatial resolution studies of the 

chain geometry in the transition zone will provide 

more information on the mechanisms involved in 

the formation of the highly ordered β-phase.

Figure 2. Synchrotron x-ray microdiffraction. (A) Schematic 

of sampled region showing original position of LCP fi ber, 

(B) integrated intensities of x-ray patterns obtained from 

a 400 μm line-scan, and (C) diffraction patterns from 

positions marked.

Figure 1. Synchrotron infrared microspectroscopy. (A) 

Polarized light microscopy of polymorphic iPP interphase, 

(B) IR spectra recorded through an 8 μm aperture at 

positions marked, and (C) false-color IR imaging of the 

interphase region using relative band intensities indicated. 

The LCP fi ber position is also shown.

(A) (B) (C)

wavenumber, cm avenumber, cm-1 x axis (μm)

spherulitic spherulitic pherulitic

cylindritic ylindritic

spherulitic spherulitic pherulitic

cylindritic ylindritic

diffraction angle, 2θ

diffraction angle, 2θ

diffraction angle, diffraction angle, iffraction angle, 2θ

β−phase

reflections

(A) (B) (C)

distance, distance, μm
2-104

Emerging nanomaterials utilize not only the 

chemical composition but also the size, shape and 

surface-dependent properties of nanoparticles in 

applications with remarkable performance characteristics. As synthesized, aqueous dispersions of 

metal-oxide nanoparticles (e.g. oxides of cerium, 

iron, or zirconium) exhibit some common properties: i) the particles have crystalline structure, ii)

the sols are typically synthesized in extremely 

acidic (or basic) conditions, and iii) the particles 

are stabilized by electrostatics and are extremely 

sensitive to perturbations in pH, ionic strength, 

and concentration. In order to translate the intrinsic properties of nanoparticles to industrially 

relevant uses there is a need for a robust means 

to stabilize nanoparticle dispersions in aqueous 

media for a variety of processing conditions.

This instability of inorganic nanoparticle sols was 

resolved by 

complexation 

with charged 

ion-containing 

polymers. To 

achieve the goal, 

we have developed a two-step 

process, defined 

as the precipitation-redispersion 

(P-R) process. 

In this study 

we address the 

issue of the adsorption and of 

the complexation 

between cerium 

oxide nanoparticles and short poly(acrylic acid) 

(PAA) chains (molecular weight, Mw=2000 g·mol-1). 

We demonstrate that we may considerably extend 

the range of pH and concentration stability of 

cerium nanosols by irreversibly adsorbing weak 

polyelectrolytes on the surface. This process does 

not require mechanical stimulation.

As synthesized, cerium oxide sols at pH 1.4 

consist of monodisperse cationic nanocrystalline 

particles with a hydrodynamic diameter DH = 10 

nm. Interparticle interactions in the form of strong 

van der Waals attraction, electrostatic repulsion, 

and surface chemistry act in concert to make the 

charged nanosol highly sensitive to the electrostatic environment. Any perturbation in pH (>3) results in aggregation and macroscopic precipitation 

of the nanoparticle suspension, severely limiting 

the utility of nanoceria. 

Figure 1 shows that when cerium oxide sols are 

mixed with poly(acrylic acid) solutions (with the 

same concentration c and pH 1.4), the solution 

undergoes an instantaneous and macroscopic 

precipitation. The mixing is characterized by 

XMix=VCeO2/VPAA2K, where VCeO2 and VPAA2K are the 

respective volumes of the cerium and polymer 

solutions. Sedimentation or centrifugation gave 

two distinctly separated phases. Complexation of 

the polymer chains with several particles results 

in precipitation due to colloidal bridging, which is 

reminiscent of classical associative phase separation. As the pH is progressively increased, the suspension spontaneously redisperses into a clear solution. This evolution of the CeO2-PAA2K solutions 

at X=1 and c = 1 wt. % is illustrated in Figure 1A

for the pH range 1.4-10. The precipitation-redisNANOPARTICLE-POLYMER COMPLEXATION: ELECTRO- STATIC SELF-ASSEMBLY AS A ROUTE TO STABLE

DISPERSIONS OF HYBRID NANOCOLLOIDS

A. Sehgal1, Y. Lalatonne1, J.-F. Berret2, and M. Morvan1

1

Complex Fluids Laboratory, CNRS - Cranbury Research Center Rhodia Inc; 2Matière et Systèmes Complexes,Université Denis Diderot Paris-VII, France

The inherent instability of inorganic nanoparticle sols may be resolved 

by complexation with ion-containing polymers at the particle interface. 

We exploit a precipitation-redispersion (P-R) mechanism to achieve 

the complexation of short chain polyelectrolytes with cerium oxide 

nanoparticles in order to extend their stability over a wide pH range. 

Small-angle x-ray scattering in conjunction with static and dynamic 

light scattering reveals that P-R may yield hybrid nanocolloidal complexes with a single inorganic core-charged corona structure. The 

electrostatic self-assembly of ionic stickers anchors the chains onto 

the surface, resulting in a polymeric brush that provides steric and 

electrostatic stabilization. This simple strategy to achieve stable dispersions surmounts the critical limitation in the use of nanoparticles, 

allowing a facile means to translate the intrinsic properties of mineral 

oxide nanoparticles to a range of novel applications. 

BEAMLINE 

X21

PUBLICATION

A. Sehgal, Y. Lalatonne, J.-F. 

Berret and M. Morvan, “Precipitation-Redispersion (P-R) of 

Cerium Oxide Nanoparticles 

with Poly(Acrylic Acid) : Towards 

Stable Dispersions,” Langmuir, 

21(20), 9359 (2005).

FUNDING

U.S. Department of Energy

FOR MORE INFORMATION

Jean-Francois Berret

Matière et Systèmes Complexes

Université Denis Diderot Paris-VII

jean-francois.berret@ccr.jussieu.fr

Authors (clockwise from left) J.-F. 

Berret, Y. Lalatonne, M. Morvan, and 

A. Sehgal 
2-105

SOFT CONDENSED MATTER AND BIOPHYSICS

persion was followed by static and dynamic light 

scattering experiments. DH was found to decrease 

progressively from 18 nm at pH 7.5 to 12.5 ± 1 

nm at pH 10 (Figure 2B). This latter value is approximately 3 nm larger than the diameter of the 

bare particles (DH = 9.8 nm), suggesting that the 

nanoceria are now coated by a PAA corona. 

Figure 2 illustrates the SAXS intensity profiles performed on both bare and PAA2K-coated 

nanoparticles. At low concentration (c < 0.5 wt. 

% and X = 1), where no structure factor is apparent, the scattered intensity is proportional to 

the concentration and the q-dependence of the 

intensity reflects the form factor of the aggregates. 

The form factors for the bare and coated CeO2-

nanoparticles have been shifted vertically so as to 

superimpose the scattering cross-sections at high 

wave-vectors (Figure 2). This result indicates that 

on a local scale (i.e. below 5 nm) both particles 

have the same structure. A slight deviation below 

0.03 Å-1 is ascribed to the PAA corona surrounding 

the particles. This is also illustrated in the inset 

(Figure 2) as intensities in a Guinier representation. The logarithm of the intensity decreases linearly with q2 and from the straight lines we deduce 

a radius of gyration RG = 3.52 ± 0.02 nm for the 

bare particles and RG = 4.8 ± 0.02 for the coated 

CeO2-PAA2K particles. As q → 0, the intensity of 

the coated particles is 1.4 times that of the bare 

nanoceriums. This value can be used to estimate 

the number of adsorbed polymers. We assume 

that a coated nanoparticle is of the core-shell 

type, having electronic densities ρCeO2 and ρPAA. 

The excess of intensity as q → 0, due to the PAA 

shell with respect to that of the bare particles, may 

be estimated: 

where ρS is the electronic scattering density of the solvent, VPAA is the molar volume of is the molar volume of PAA

poly(ammonium acrylate) polymer, and VCeO2 is 

that of the bare particle. We calculate the number of adsorbed polymers nads = 34 ± 6. This was 

corroborated by static light scattering and total 

organic carbon measurements. The final amount 

of 40 – 50 polymers per particle corresponds to 

1/5 of the total weight of the coated particles. 

An insight into the conformation of the adsorbed 

polymeric corona is obtained. With 50 chains per 

particle and a monomer molar volume v0 = 54.8 Å3, 

the radius of the polymer nanoparticles would be 

increased by 0.4 nm. With a fully extended polyelectrolyte corona the hybrid nanocolloid would 

result in DH = 18 nm. With the intermediate redispersed DH ~ 13 nm, the PAA conformation may be 

described as multisite adsorption of –COOH moieties along the contour length with the remainder 

constituting a solvated polyelectrolyte brush.

The P-R process is a simple route to obtain single 

nanoparticles irreversibly coated with PAA chains. 

With a 2 – 3 nm polyelectrolyte brush surrounding the particles, the cerium sols are stable over 

a broad range of pH values and concentrations. 

The process described could easily be extended 

to other nanoparticle systems. This opens new 

opportunities with electrostatic self assembly as 

a means to dramatically improve the stability of 

inorganic nanosols.

I

CeO2-PAA

I

CeO2 q→0

= 





1+nads

ρPAA - ρs VPAA

ρCeO2 - ρs VCeO2







2

Figure 1. (A) Series of CeO2-PAA2K solutions prepared 

at different pH. The mixing of the polymer and cerium 

solutions was made at pH 1.4, and the pH was further 

adjusted with NH4OH. Above pH 7, the precipitate is 

redispersed. (B) Hydrodynamic diameters measured by 

dynamic light scattering on CeO2-PAA2K solutions during the 

P-R (close symbols). At pH 10, the PAA2K-coated cerium sol 

is stable and it can be brought back to pH 6 without noticing 

any change in the dispersion (empty symbols). Below pH 6, 

the nanoparticles start to aggregate.

(A)

(B)

Figure 2. X-ray scattering intensity for bare and PAA2Kcoated nanoparticles in double logarithmic scale. The 

concentrations are in the two cases c = 0.5 wt. %. At such 

low concentrations, the intensities represent the form 

factors of the particles. The deviation below 0.03 Å-1 is due 

to the PAA corona surrounding the particles. Inset: Guinier 

representation of the intensity for the same samples (I(q) 

versus q2). From the straight line, the radius of gyration RG

of the nanoceria (= 3.52 ± 0.02 nm) can be calculated.

pH

DH(nm)

q (Å-1)

intensity (arb. units)
YEAR IN REVIEW
YEAR IN REVIEW

411TH BROOKHAVEN LECTURE

‘SHINING LIGHT ON THE CAUSE OF

ALZHEIMER’S DISEASE’

January 18, 2006

Alzheimer’s disease is a progressive brain disorder that gradually destroys a person’s

memory and ability to learn, reason, communicate, 

and carry out daily activities. An estimated 4.5 million Americans have it, a number that is expected 

to triple over the next 50 years. Today, one in ten 

people aged 65 and half of people over 85 are 

affected.

The cause of Alzheimer’s disease is thought to 

involve the formation of “plaques” — tiny aggregates of a naturally occurring, but misfolded or 

misshapen protein — in the brain. Recently, the 

formation of these plaques has been associated 

with the binding of metal ions such as iron, copper, and zinc. Yet the function of these metal ions 

and the misfolded proteins in the disease process 

is not well understood.

Now, synchrotron infrared and x-ray microscopes 

are used to image the protein structure and metal 

content in the Alzheimer’s-affected brain tissue, 

providing a better understanding of how the disease occurs and potential ways of preventing it in 

the future.

Biophysical chemist Lisa Miller of the National 

Synchrotron Light Source Department (NSLS) 

gave the 411th Brookhaven Lecture on this 

research in her talk “Shining Light on the Cause 

of Alzheimer’s Disease,” on January 18, 2006 in 

Berkner Hall.

Lisa Miller obtained her B.S. in chemistry from 

John Carroll University in 1989, her M.S. degree 

in chemistry from Georgetown University in 1992, 

and her Ph.D. in biophysics from the Albert Einstein College of Medicine in 1995. Rejoining Albert 

Einstein in a faculty position, she worked with BNL 

scientists to develop new tools using synchrotron 

Lisa Miller 

light to study biological and medical problems. 

She joined the NSLS in 1999 and uses x-ray and 

infrared imaging to study diseases such as osteoarthritis, osteoporosis, and Alzheimer’s. She is 

also an adjunct Assistant Professor in the Department of Biomedical Engineering at Stony Brook 

University, and she heads the NSLS Information &

Outreach Office, which communicates NSLS science to other scientists, government officials, and 

the community.

— Liz Seubert

NSLS ONE OF 10 BNL ORGANIZATIONS

TO ACHIEVE OHSAS 18001 REGISTRA- TION

January 19, 2006

Lab Director Praveen Chaudhari and Safety & 

Health Services Division Manager Pat Williams 

held a celebration on January 19, 2006 to show 

BNL’s appreciation to the many dedicated employees who worked for 12 months to prepare seven 

organizations — the Superconducting Magnet 

Division (SMD), Basic Energy Sciences (BES) 

Directorate, Instrumentation Division, Physics 

Department, National Synchrotron Light Source 

(NSLS), Environmental & Waste Management 

Services (EWMS) Division, and Staff Services 

(SS) Division — for successful registration of 

their occupational safety management systems to 

Occupational Health & Safety Assessment Series 

(OHSAS) 18001.

OHSAS 18001 is widely acknowledged as offering one of the best guidelines available for safety 

Among those who celebrated the successful registration 

of seven more BNL organizations to the OHSAS 18001 

safety management standard are hosts Praveen Chaudhari 

(front, second from left) and Pat Williams (front, second 

from right); and, between them, from left: BNL organization 

representatives Tom Kirk, Sally Dawson, John Taylor, 

Robert Casey, Michael Clancy, and Veljko Radeka, with Jeff 

Swenson (front, left).

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management systems and it is a significant enhancement of the Integrated Safety Management 

System that was already in place on site. In addition to the certificates of appreciation presented 

to all those in attendance, framed OHSAS 18001 

Certificates of Registration were presented to 

Chaudhari as representing BNL, and to Tom Kirk 

for SMD, John Taylor for BES, Veljko Radeka for 

Instrumentation, Sally Dawson for Physics, Robert 

Casey for NSLS, Michael Clancy for EWMS, and 

Jeff Swenson for SS.

Together with the three pilot organizations that 

were successfully registered in September

2004 — the Central Fabrication Services Division, 

Collider-Accelerator Department,

and Plant Engineering Division — BNL now has 

a total of 10 organizations’ occupational safety 

management systems that have achieved OHSAS 

18001 registration. 

Regarding future plans for the Lab, Jim Tarpinian, 

Assistant Laboratory Director for Environment, 

Safety, Health, & Quality, explains, “In 2006, we 

will expand the OHSAS 18001 registration to 

include the balance of BNL organizations. The 

important thing for BNL is not the registration 

itself, but the processes of job-risk assessments, 

employee involvement, goals and objectives, 

management review, and continual improvement. 

OHSAS 18001 is a significant enhancement to our 

Integrated Safety Management System.”

— Maria Beckman

3-4

JOINT PHOTON SCIENCES INSTITUTE

ESTABLISHED

January 23, 2006

A new initiative in photon sciences will capitalize 

on the unique capabilities of NSLS-II. 

A partnership between the DOE and New York 

State, the Joint Photon Sciences Institute (JPSI), 

will serve as an intellectual center for development and application of the photon sciences and 

as a gateway for NSLS-II users. It will enhance 

scientific programs that use the powerful photon 

beams by cultivating and fostering collaborative, 

interdisciplinary R&D.

New York State Governor George Pataki recently 

committed to providing $30 million for the JPSI 

building, which will be located next to NSLS-II and 

provide office space, meeting areas, and specialized state-of-the-art laboratories. The operating 

expenses of the institute and its research programs will be covered by funding from the federal 

government, including the Department of Energy, 

the National Institutes of Health, the Department 

of Defense, and others. Research will be focused 

around several multi-year scientifically and technologically relevant research initiatives.

Over the past few decades, the power of photon 

sources has increased dramatically, and they 

are now used for a broad spectrum of research. 

Modern research increasingly requires interdisciplinary work that either spans multiple scientific 

disciplines or falls at the boundaries between 

them. JPSI will be an interdisciplinary institute 

devoted to basic research 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.

JPSI will have great flexibility in making scientific 

appointments, encompassing both Brookhaven 

scientists and faculty from universities. Junior and 

senior fellowships and sabbatical programs will 

draw the best photon scientists from institutions 

worldwide for interactions with the resident staff 

and user communities. An important element of the 

institute’s mission will be training new researchers 

and enabling established researchers to embark 

on new directions in interdisciplinary research. 

JPSI will also host interdisciplinary workshops that 

highlight new opportunities, foster new collaborations, and promote JPSI initiatives in emerging 

areas of photon science.

— Steve Dierker

New York State Capitol Building, Albany

NSLS EXAMINES PIECES OF STAR DUST

January 25, 2006

Launched on February 7, 1999, Stardust’s mission 

was to collect dust and carbon-based compounds 

from a passing comet, as well as tiny amounts of 

interstellar dust streaming toward Earth from deep 
YEAR IN REVIEW

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After the particles 

were extracted 

from the aerogel, 

they were analyzed 

at other beamlines 

using both x-rays 

(X1A1), and infrared light (U10A and 

U10B). At beamline 

X1A1, a powerful 

imaging device 

called a scanning 

transmission x-ray 

microprobe (STXM) 

was used to collect 

detailed images 

of the particles. 

The STXM employs a technique known as x-ray 

absorption near-edge structure (XANES) to gather 

information about the elemental makeup of the 

particles, especially the carbon found in organic 

compounds. Flynn’s studies using the STXM can 

identify organic compounds within some of the 

smallest Stardust particles - compounds that may 

have formed at the birth of our solar system.

In a concurrent set of studies, Flynn and Stardust co-investigator Lindsay Keller used infrared 

light to identify specific minerals within the dust 

particles. Keller, who leads the group of scientists 

who will perform optical studies of the Stardust 

samples, is a lunar and planetary scientist with 

NASA’s Johnson Space Center. The far-infrared 

microscope at beamline U10A, which can sense 

the unique vibrations of atoms in crystalline solids, 

is an excellent tool for identifying specific minerals within the Stardust sample. The mid-infrared 

light produced at beamline U10B was also used 

to characterize any organic material found in the 

particles. Unlike x-ray methods, the information 

collected using these infrared techniques can be 

compared with the astronomical observations of 

distant interstellar dust clouds, including those 

involved with the formation of planetary systems 

like ours.

— Laura Mgrdichian

space. Its delivery of this material marks the first 

time since Apollo 17 that a NASA spacecraft has 

successfully brought back a space-matter sample.

At the NSLS and other synchrotron facilities, portions of that teaspoonful-sized amount of comet 

and star dust was studied to determine its composition and properties. The variety of research techniques available at the NSLS allowed researchers 

to maximize the amount and type of information 

learned about the dust particles. The information 

scientists gather could help answer some very 

important, very fundamental questions about the 

formation of the solar system and the Earth in 

particular.

The initial analysis of these samples, known as 

the Preliminary Examination Period, began in the 

Stardust Laboratory at NASA’s Johnson Space 

Center. Following these first studies, the samples 

were divided, prepared, and distributed to qualified investigators, including those at the NSLS, 

for more intensive studies. These scientists are 

members of the Stardust Preliminary Exam Team.

At the NSLS, analyses took place at beamline 

X26A, led by physicist and Stardust co-investigator George Flynn (SUNY Plattsburgh). Flynn is 

leading a worldwide group of scientists who will 

perform chemical composition measurements on 

the comet samples collected by Stardust. The 

extremely tiny and bright x-ray beams produced at 

beamline X26A are an excellent tool for analyzing 

the particles, which are just 10-20 millionths of a 

meter in diameter (so small that five particles fit 

across the width of a single human hair). Using 

these capabilities, the X26A scientists were able 

to extract chemical and mineralogical information 

from the sample without the need to remove the 

dust particles from the “aerogel” substance used 

to capture them in space.

(From left) George Flynn (SUNY Plattsburgh), Lindsay 

Keller (NASA), Larry Carr (NSLS), and Randy Smith 

(NSLS) examine samples from the Stardust mission at 

beamline U10A.

Stardust particle (crystalline object 

with dark borders), embedded 

in the aerogel collector. (Photo 

courtesy of NASA)

TWO NSLS STAFF MEMBERS AWARDED

FOR JOBS WELL DONE

February 2, 2006

Congratulations are due to Peter Siddons and 

Nick Gmur, who, respectively, recently were honored with a Science & Technology Award and a 

Brookhaven Award at the Fiscal Year 2006 

BNL Employee Recognition Award Ceremony on 

February 2.
3-6

Peter Siddons

Siddons, a physicist at the NSLS, was cited for his 

outstanding contributions to developing detectors 

for use in synchrotron sources. His ideas were 

recognized as innovative and original, resulting in 

new and unique detectors that make new experiments feasible. He is a strong advocate and leader in the U.S. for detector development and has 

made significant advances possible despite the 

lack of funding in this area. Over the last several 

years, Siddons has directed the NSLS detector 

and control group and, in collaboration with BNL’s 

Instrumentation Division, has developed a suite 

of detectors. These included fast photon counting 

detectors for different energy ranges and applications, linear array detectors, and two-dimensional 

detectors. The detectors have been delivered to 

users with great success, and have made significant impact on scientific programs at the NSLS 

and elsewhere. Also, the detector group under 

Siddons’ direction has gained worldwide recognition for the NSLS and BNL. For example, recently 

BNL was awarded a multi-year project to construct 

two imaging detectors for the Linear Coherent 

Light Source project at Stanford Linear Accelerator Center. Facilities in England, Australia and Taiwan as well as at Argonne National Laboratory are 

interested in or already actively collaborating with 

Siddons’ group. He received his Ph.D. in physics 

at Kings College, London, and joined BNL in 1985.

The Science & Technology Award (presented by 

Peter Bond, Deputy Interim Director for Science 

& Technology) recognizes distinguished contributions to BNL’s science and technology mission 

over one or more years. Nominations for the 

Science & Technology Award are made by 

organization heads. The three criteria considered 

for this award are the exceptional nature of the 

employee’s contributions, their level of difficulty, 

and their benefit to BNL.

Nick Gmur

Gmur was cited for his outstanding work as the 

NSLS Environmental Safety & Health (ESH) Coordinator. In this role, he is involved in many activities within the department that carry into 

almost every part of all programs. He has been a 

key contributor to challenging ESH issues at the 

NSLS that include implementing requirements for 

BNL’s Integrated Safety Management program and 

the internationally recognized ISO 14001 and OHSAS 18001 programs. Other major achievements 

included writing, conducting, and coordinating reviews and implementing the accelerator authorization basis documents for the Deep-Ultraviolet-Free 

Electron Laser, the NSLS and Accelerator Test 

Facility, and the NSLS Environmental Assessment 

required by the National Environmental Policy 

Act. In addition, Gmur resolves many smaller issues daily. He is recognized for his leadership, for 

bringing great attention to quality and detail, and 

for always getting the job done on schedule. He 

is widely respected throughout BNL for his efforts 

and is an excellent representative of the NSLS. 

Gmur, who came to BNL in December 1975, has a 

B.S. in zoology and chemistry from McGill University and an M.S. in biology from the University of 

Michigan.

Presented by Laboratory Director Praveen Chaudhari, the Brookhaven Award recognizes key contributors in support functions whose performance 

and achievements represent outstanding service 

to the Laboratory. Nominees for the Brookhaven 

Award are evaluated by the exceptional nature and 

difficulty level of the contributions, their benefit to 

the Laboratory, and the length of time over which 

the contributions were made.

— Laura Mgrdichian

Peter Siddons (second from left) at the BNL Employee 

Recognition Award Ceremony with the other Science & 

Technology Award winners. They are Stephen Schwartz of 

the Environmental Sciences Department (far left), James 

Alessi of the Collider-Accelerator Department (second from 

right), and Peter Vanier of the Nonproliferation & National 

Security Department (far right). Not pictured: Alexei Tsvelik 

of the Condensed Matter Physics & Materials Science 

Department.

Brookhaven Award winner Nick Gmur (second from left) 

at the awards ceremony with the other Brookhaven award 

winners. Also presented with Brookhaven awards were 

(from left) John DiNicola (Plant Engineering Division), 

Raymond Karol (Collider-Accelerator Department), Gerard 

Shepherd (Safety & Health Services Division), and Peter 

Stelmaschuk (Plant Engineering).
YEAR IN REVIEW

3-7

NSLS RESEARCHERS PRODUCE A

PRAISEWORTHY POSTER

March 1, 2006

At the Materials Research Society semi-annual 

meeting, an NSLS research group received a special honor. Its meeting poster, one of hundreds, 

was chosen as one of only six to receive a “best 

poster” award.

The group, which includes scientists from Stony 

Brook University, Brookhaven National Laboratory, 

and the City University of New York, is studying 

“biomineralization,” the process by which organisms create mineralized tissues, such as bones, 

teeth, and shells. The collaboration includes NSLS 

scientist Elaine DiMasi, as well as Karthikeyan 

Subburaman (SBU), Nadine Pernodet (SBU), SeoYoung Kwak (BNL), Shouren Ge (SBU), Nan-Loh 

Yang (CUNY), and Miriam Rafailovich (SBU). They 

presented their poster at the MRS Fall 2005 meeting, held November 27 through December 1 in 

Boston, Massachusetts.

Biominerals are interesting, in part, because they 

are typically much stronger than ordinary minerals. As such, they may one day be used to create 

a new class of nanoscale composite materials. 

First, however, the underlying mechanisms of 

biomineral formation and structure must be better 

understood.

The group’s winning poster is a summary of their 

research on eggshell protein mineralization. They 

use this as a model to study biomineralization in 

general, since the formation of an eggshell can 

be thought of as a process that includes a series 

of steps. First, the shell’s support membrane is 

formed and proteins are deposited onto it. Then, 

the minerals that make up the shell begin to form 

and grow, using the protein deposits as nucleation 

points. Finally, the mineral forms a crystal structure on top of the protein-fiber network.

The researchers studied this process using real 

“extracellular matrix proteins” — the type of proteins that make up skin tissue, for example. They 

used networks of these proteins as the basis of 

the mineralization process and then studied the 

mineralized proteins using a powerful imaging device called an atomic force microscope (AFM).

As described in their poster, their results show 

that, at the eggshell’s early growth stages, only 

the fibrous portions of the proteins accepted 

calcium carbonate, the mineral. The fibers became thicker as the calcium was incorporated and, 

ultimately, large mineral crystals appeared. The 

group hopes to build on these results by learning 

exactly how the proteins induce the mineralization 

process.

— Laura Mgrdichian

Elaine DiMasi (left) and poster presenter 

Karthikeyan Subburaman.

Elastin protein networks imaged by AFM (a) before 

mineralization and after (b) 30, (c) 60, or (d) 120 minutes 

of exposure to mineral. The fi brous parts of the protein 

become thicker and stiffer as they induce calcium 

carbonate mineralization.

GENERAL BARRY MCCAFFREY TOURS

THE NSLS

March 1, 2006

During a visit to BNL on March 1, Barry McCaffrey, a retired four-star general from the U.S. Army, 

toured the NSLS.

McCaffrey came to BNL with a view to using his 

specialized experience to help the Laboratory 

focus on ideas to increase its sponsorship in areas 

related to homeland security and the understanding and treatment of drug addiction.

At the NSLS, he was guided on a tour of the 

beamline floor by NSLS scientist Peter Siddons, 

who explained how the facility works and gave an 

overview of the science done. McCaffrey expressed interest in the range of scientific research 

that is performed at the NSLS, the type of users 

(academic, industry, etc.), and how the NSLS facility is organized.

McCaffrey’s visit also included tours of the Positron Emission Tomography imaging facility, the 

Radiation Detector Testing and Evaluation Facility, 

and labs developing nuclear-detector instrumenta-
3-8

tion. This gave him first-hand contact with several 

BNL scientists and an opportunity to learn more 

about some of the Lab’s research and development programs.

McCaffrey, who served as the Commander inChief of the U.S. Armed Forces Southern Command, coordinating all national security operations 

in Latin America, also served as the Director for 

Strategic Plans and Policy on the Joint Chiefs of 

Staff. In addition, he followed this distinguished 

record by serving as Director of the Office of 

National Drug Control Policy under President Bill 

Clinton from 1996-2001.

— Laura Mgrdichian

From left, General Barry McCaffrey, Ralph James (BNLEENS), Gabriella Carini (BNL-EENS), Peter Siddons (BNLNSLS), and Alexey Bolotnikov (BNL-EENS).

NSLS STUDENT-RESEARCHER TALKS AT

THE MARCH APS MEETING

March 13-16, 2006

Each year, the NSLS hosts several high school 

and college students, who come to the facility to 

perform research using its bright beams of x-ray, 

ultraviolet, and infrared light. This year, four of 

these students presented the results of their 

research at the March meeting of the American 

Physical Society (APS) in 

Baltimore, Maryland.

Michael DiBiccari, a 

senior at Hauppauge High 

School in Hauppauge, New 

York, worked with NSLS 

biophysicist Elaine DiMasi. 

His project was part of a 

wider research effort on 

the study of biomineralization, the process by which living organisms produce minerals, such as shell and bone. He studied 

diatoms — single-celled algae with outer shells 

composed of biosilica, a type of biomineral. DiBiccari used x-rays to identify the atomic structure of 

the biosilica, which he then compared to the structure of synthetic silica. His results showed that 

the structures of both materials were identical. He 

discussed this research and its implications on 

March 16, 2006, at 1:15 p.m. in Room 323 of the 

Baltimore Convention Center.

Two graduate students 

working at the NSLS also 

gave talks on their research. Kathryn Krycka, 

from Stony Brook University, works with NSLS 

scientist and chair ChiChang Kao and Professor 

Sara Majetich of Carnegie 

Mellon University. Using 

an x-ray technique known 

as small-angle resonant 

x-ray scattering, she 

studied the size and internal structure of magnetic 

nanoparticles, which often consist of metal-only 

cores surrounded by thin metal-oxide shells. This 

work is important for understanding the magnetic 

properties of nanoparticle systems. In her talk, on 

March 14, 2006 at 9:24 a.m. in Room 319 of the 

Baltimore Convention Center, she discussed her 

recent work on cobalt-oxide nanoparticles.

Raji Sundaramoorthy, 

a student of NSLS user 

scientist and collaborator Alex Weiss from the 

University of Texas at Arlington, worked with NSLS 

scientist Steve Hulbert. 

She studied photon-stimulated “Auger” decays in 

solids, a type of multielectron decay. In this 

process, an incoming x-ray 

photon creates a “hole,” or 

positively charged electron vacancy, in one of the 

atom’s core levels. The hole then is filled by an 

electron that jumps down from a higher electron 

orbital, which in turn causes an electron (the Auger electron) to be ejected from the solid. An Auger decay often results in a cascade of additional 

decays, leaving the atom ionized. At the NSLS, 

Sundaramoorthy closely studied this process in 

the compound manganese oxide, and compared 

her results to that of silver and palladium. Her talk 

took place at 10:12 a.m. on March 13 in Baltimore 

Convention Center Room 311.

Samantha Palmaccio, another high school student 

Michael DiBiccari working with DiMasi, attends Sachem High School 

Kathryn Krycka

Raji Sundaramoorthy
YEAR IN REVIEW

3-9

in Farmingville, New York. She investigated the 

biomineralization of protein fibers, which is one 

step in the process by which many organisms 

form shells. Recently, she studied the “growth” of 

the mineral calcium carbonate on a protein-fiber 

network. Her results show that the strength of 

the mineral increases over time as it covers the 

fibers. This is unlike stand-alone calcium carbonate. Additionally, using a powerful microscope, she 

was able to study the crystal structure formed by 

the mineral. Palmaccio presented her results on 

March 13, 2006, at 8:24 a.m. in Room 326 of the 

Baltimore Convention Center.

“The NSLS considers education to be an important 

part of its scientific program and mission,” said 

Kao. “As is also evident by these talks, students at 

the NSLS are working on a wide range of exciting 

research topics.”

— Laura Mgrdichian

NEW WRINKLE IN THE MYSTERY OF

HIGH-TC SUPERCONDUCTORS

March 13-16, 2006

In the 20 years since the discovery of high-temperature (Tc) superconductors, scientists have 

been trying to understand the mechanism by 

which electrons pair up and move coherently to 

carry electrical current with no resistance. “We 

are still at the beginning,” says Tonica Valla of 

the Condensed Matter Physics & Materials Science Department (CMPMS), who gave a talk on 

his group’s latest results at the March American 

Physical Society meeting in Baltimore, Maryland. 

“If anything,” he adds, “it looks as if the story is 

getting more complicated.”

The research of Valla and his group, which includes Alexei Fedorov, now of Lawrence Berkeley 

National Laboratory’s Advanced Light Source, and 

Peter Johnson and Genda Gu, both of CMPMS, 

was funded by the Office of Basic Energy Sciences within DOE’s Office of Science. In 1999, 

Valla’s group was the first to observe a “kink” in 

the energy level of electrons in high-Tc superconductors just as they went through the transition 

temperature from their normal to superconducting state. The kink was the first clue to explaining 

what the mechanism of electron pairing might be. 

“The kink gave us the hope that we could identify the interaction that was responsible for the 

electron pairing,” Valla said. Some groups hold 

that the mechanism is the same as in conventional superconductors — that is, that phonons, or 

vibrations in the crystal lattice, are responsible for 

electron pairing.

Tonica Valla

Other scientists believe that changes in the spin 

alignment, or magnetic polarity, of adjacent electrons — known as magnons — are responsible. 

“The problem is that there are both phonons and 

magnons in the crystal with the energy where we 

see the kink, so it is still not clear,” Valla says.

The latest wrinkle uncovered by Valla’s group is 

the observation of similar energy scales and gaps 

in a material that is not a superconductor. The material is a special form of a compound made of lanthanum, barium, copper, and oxygen, where there 

is exactly one barium atom for every eight copper 

atoms. With less or more barium, the material acts 

as a high-Tc superconductor (in fact, this was the 

very first high-Tc superconductor discovered). But 

at the 1:8 ratio, the material momentarily loses its 

superconductivity.

“The fact that this system, which is not a superconductor, has similar properties to the superconducting system is not helping to solve the mystery,” Valla says. But then he notes that 20 years 

since the discovery of high-Tc superconductors is 

still not that long. “For conventional superconductors,” he says, “it took about 50 years to come up 

with a good explanation for the behavior.

”Valla’s talk was part of a session on the use of 

angle-resolved photoemission spectroscopy in 

the study of high-Tc superconductors. It included 

a discussion of advances in this technique. His 

group uses bright beams of ultraviolet light at 

beamline U13UB at BNL’s National Synchrotron 

Light Source to emit electrons from the samples 

they are studying. Using high-resolution spectrometers, the scientists measure the energy and the 

angle at which the electrons exit the crystal, allowing them to reconstruct the electrons’ state while 

in the crystal — their energy level and whether 

they had any interactions with phonons and/or 

magnons.

— Karen McNulty Walsh
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CERIUM OXIDE NANOTUBES GET

NOTICED

March 28, 2006

Chemists and materials scientists often study 

“nanotubes” — capsule-shaped molecules only a 

few billionths of a meter (nanometers) in width. 

In nanotube form, many materials take on useful, 

unique properties, such as physical strength and 

excellent conductivity. Carbon nanotubes are the 

most widely investigated variety. Now, in pioneering research, scientists at Brookhaven National 

Laboratory have created and investigated the 

properties of nanotubes made of a different, yet 

equally interesting material: cerium oxide.

“Cerium oxide nanotubes have potential applications as catalysts in vehicle emission-control 

systems and even fuel cells,” says Brookhaven 

chemist Wei-Qiang Han, the lead scientist involved in the work. “But until very recently, they 

haven’t been studied.”

Han and his colleagues are in the midst of ongoing research into the structure and properties of 

cerium oxide nanotubes. As part of this, they have 

devised a method to synthesize cerium oxide 

nanotubes of high quality. First, they allow the 

compounds cerium nitrate and ammonia hydroxide 

to chemically react. Initially, this reaction forms 

“one-dimensional” nanostructures, such as rods 

and sheets, made of the intermediate product 

cerium hydroxide. The intermediate product is 

then quickly cooled to zero degrees Celsius, which 

freezes those structures into place. By letting the 

chemical reaction proceed over a long period of 

time, a process called “aging,” the hydrogen is 

eventually removed from the intermediate product 

and a large quantity of the desired end product 

— cerium oxide nanotubes — is formed.

Han discussed this synthesis method at the American Chemical Society National Meeting in Atlanta, 

Georgia. During his talk, Han also discussed his 

group’s recent study 

— how cerium oxide 

nanotubes release 

oxygen ions when 

immersed in a lowoxygen environment, 

a process that is 

critical to the nanotubes’ effectiveness 

as catalysts. To do 

this, the researchers 

used several techniques. These include “transmission 

electron microscopy,” a very powerful 

imaging technique, Wei-Qiang Han

FUTURE CRYSTALLOGRAPHERS ATTEND

RAPIDATA 2006 AT NSLS

April 23-28, 2006

Once again, 48 future crystallographers from 

around the world gathered at BNL for RapiData 

2006. This week-long course is designed to introduce students to the best and latest equipment 

and techniques. The students also get to meet and 

learn from the leading developers of software for 

macromolecular x-ray crystallography.

The course has been offered annually since 

1998 by BNL’s Biology and National Synchrotron 

Light Source (NSLS) departments. It reflects the 

educational component of the PXRR (Macromolecular Crystallography Research Resource), 

funded jointly by the National Center for Research 

Resources — a branch of the National Institutes of 

Health (NIH) — and DOE’s Office for Biological & 

Environmental Research. The course’s usefulness 

to the nearly 400 participants since its inception 

is apparent from the constant numbers of new 

students who sign up each year. Many of these 

budding crystallographers are now becoming 

experts in the field and sending others from their 

institutions to BNL to learn the initial steps of this 

highly specialized area of interest. 

This year’s course, which ran from April 23-28, 

The students and instructors, RapiData class of 2006

and two x-ray techniques, which they performed at 

NSLS beamline X19A.

“We’re interested in studying oxygen-atom vacancies in cerium oxide nanotubes because, when 

combined with their other surface features, these 

vacancies may make them more functional and effective in the applications mentioned,” Han said.

This work was funded by the Office of Basic 

Energy Sciences within the U.S. Department of 

Energy’s Office of Science.

— Laura Mgrdichian
YEAR IN REVIEW

3-11

began with three days of lectures and tutorials 

taught by scientists from BNL, industry, academia, 

and other national labs. Then the beamline staff 

and other teachers guided the students through a 

marathon, 60-hour data-collection session, which 

eventually employed six NSLS beamlines for the 

whole time, and three others to help out as needed. At the same time, nine different tutorials were 

underway. As usual, half of the students came with 

their own specimens to analyze, while the other 

half learned as observers.

Said Bob Sweet of Biology, who, with Denise Robertson and Alex Soares, primarily organized the 

course, “This program excites both the students 

and the teachers by providing a short ‘total immersion’ in this technology. Students learn how to 

obtain and process real data, learning how to locate and fix problems as they arise. It’s a gripping 

experience. About half a dozen of the students left 

with potentially publishable results. This is inspiring to everyone in the course.

“The students find that there is always a hands-on 

scientific supervisor available to give expert help, 

so they can set up experiments in the optimal way, 

or find out the next step without wasting time,” 

continued Sweet. “We depend on so many team 

members for the program’s success: many members of the PXRR (the Biology and NSLS Macromolecular Crystallography Research Resource), 

NSLS staff members, and about 18 outside teachers.”

In addition to the DOE and NIH funding, a special 

grant was provided by the International Union for 

Crystallography and the US National Committee 

for Crystallography to assist half a dozen Latin 

American students in attending the course. Additional support is provided by Brookhaven Science 

Associates, the NSLS, and several very generous 

equipment vendors and drug companies. 

— Liz Seubert

STUDENTS EXPERIENCE THE NSLS VIA

WEBCAST

April 25, 2006

More than 20 chemistry and earth-science students from Sayville High School participated in a 

unique data-analysis project at NSLS beamline 

X15B — without ever entering the NSLS. Via 

webcast, they watched as their teachers, assisted 

by scientists from Stony Brook University’s (SBU) 

Geosciences Department and Brookhaven Lab’s 

Environmental Sciences Department, analyzed 

soil samples from a creek near the school. This arrangement, which could become a model for other 

schools nationwide, allowed an entire classroom 

of students to remotely observe and interact with 

their teachers in real time. Thus, they were able 

to share in the research experience without being 

present.

The soil samples were taken from various locations along the creek, from wetlands to uplands, 

and from various depths. The students have studied water and soil samples from the creek in past 

work, but this exercise provided the first molecular-scale information about the soils.

On April 25, as the students watched over the web 

(using VRVS, the Virtual Room Videoconferencing 

System), teachers Adriana Adler and Janet Kaczmarek analyzed the samples at the NSLS to determine what types of sulfur compounds were present 

in the soils, and in what amounts. Adler and Kaczmarek (who teach chemistry and earth science, 

respectively) mounted the samples into the “hutch 

box” located at the beamline and scanned each 

sample with a beam of x-rays. This resulted in a 

set of x-ray absorption “spectra” for sulfur — measurements that show how the sulfur compounds 

in the soils absorbed the x-rays. Since every 

compound absorbs x-rays differently, this analysis 

uncovered the identity and relative amount of each 

sulfur compound present. The proportions of these 

compounds reveal important information about the 

soil samples and the wetlands ecosystem, such 

as how organic matter decays in soils at different 

depths and under different conditions. The sulfur 

compounds can also indicate how environmental 

contaminants will behave in the wetlands.

As Adler and Kaczmarek worked at the beamline, 

they were able to see their students. Simultaneously, their students could see them. Thus, the 

webcast provided valuable two-way interaction.

“The webcast was a fantastic experience for students,” said Adler. “We attempt to provide many 

opportunities for hands-on laboratory exercises for 

our students. Bringing the NSLS beamline ‘into the 

Participants in the X15B webcast, from left: Janet 

Kaczmarek, Paul Northrup, Adriana Adler, Mirza Beg, 

and Jen Clodius.
3-12

classroom’ and allowing students to direct experiments at the NSLS from the classroom opened 

a valuable teaching tool for us at Sayville High 

School.”

Kaczmarek commented, “This was an invaluable 

experience both for myself and the high school 

students involved with the webcast. I don’t think 

many high school students can say that they were 

part of an experiment run at world-known BNL. I 

see much potential with this type of educational 

outreach and the benefits to all parties involved. It 

is all very exciting.”

The webcast stems from a Research Experience 

for Teachers (RET) project called “High School 

Teacher Training in an EMSI: Bringing First-Hand 

Research Experiences from the Lab to the Classroom,” which is being conducted at the Center 

for Environmental Molecular Science (CEMS) 

at SBU. This project is a collaboration between 

CEMS and an initiative within the Brookhaven 

Lab Office of Educational Programs (OEP) called 

“Building Leadership to Expand Participation in 

Environmental Molecular Science.” Both programs 

are funded through National Science Foundation 

(NSF) supplements to CEMS, which is a collaboration between SBU Geosciences and BNL Environmental Sciences departments and is co-funded by 

the NSF and the U.S. Department of Energy. As 

part of the RET program, both Adler and Kaczmarek have undergone research training at CEMS, 

focused on the integration of molecular-scale approaches for studies of environmental chemistry. 

Both teachers also attended an NSLS-sponsored 

introductory seminar on x-ray absorption spectroscopy applications.

The CEMS personnel who enabled this project 

include Richard Reeder (Director of CEMS and 

Professor of Geoscience at SBU), Mirza Beg (Environmental Education Specialist at CEMS), Paul 

Northrup (CEMS Principal Investigator from BNL’s 

Environmental Sciences Department), and Marianna Kissell (a CEMS graduate student conducting research at NSLS beamline X15B). The project 

was also enabled by OEP personnel, including 

Ken White (OEP Manager), Jen Clodius (Senior 

Educational Programs Representative), and Scott 

Bronson (Educational Programs Administrator). 

OEP provided guidance on the use of the VRVS 

technology and made the broadcast successful. 

Clodius coordinated the webcast at the beamline, 

while Bronson managed it at the school.

Northrup, a beamline scientist for X15B, devoted 

beam time, as well as his own time and expertise, 

to the project. His efforts were critical to the project’s success. Northrup, along with Kissell, also 

provided scientific support to the teachers. Administrative support was provided by the chair of the 

Science Department at the Sayville High School, 

Brian Vorwald. Mike Tabor, head of the school’s 

Technology Department, provided computer and 

network support.

The outcome of the webcast was very positive. It 

generated considerable interest among the students. During the experiment they asked questions 

about x-ray absorption spectroscopy, beamline 

operation and safety procedures, the results of the 

analysis, and the NSLS in general. The organizers 

of the webcast are hopeful that this event could 

serve as a pilot for other scientific facilities and 

schools across the country.

Northrup and beamline X15B are supported by the 

Office of Biological and Environmental Research 

(Environmental Remediation Sciences Division) 

within the U.S. Department of Energy’s Office of 

Science, through the BNL EnviroSuite initiative.

— Laura Mgrdichian

NSLS’ YOUNGEST SCIENTISTS LEARN

FROM LIGHT ON 'TAKE OUR DAUGH- TERS AND SONS TO WORK' DAY

April 27, 2006

On April 27, more than 30 daughters and sons 

of NSLS users and staff learned about some of 

the scientific programs at the NSLS, and even 

performed their own scientific experiments. The 

one-day visit was part of the national “Take Our 

Daughters and Sons to Work Day.”

Upon arriving at the NSLS, the children learned 

that the facility produces many types of light, from 

microwaves to x-rays, and that this light has many 

applications in many fields, including electronics, 

catalysis, microscopes, and medicine. Then the 

fun started!

This year’s program focused on liquid nitrogen, 

which is used by most scientists at the NSLS. The 

children were taken down to the NSLS experiStudents tune in to the X15B webcast. mental floor, where they were given 30 minutes 
YEAR IN REVIEW

3-13

to count the number of beamlines that used liquid 

nitrogen. They questioned beamline scientists and 

learned that liquid nitrogen is used for cooling 

samples, detectors, magnets, and monochromators. Upon summing the beamlines at the end of 

the tour, the children were amazed to find that 

more than 40 beamlines use liquid nitrogen on a 

daily basis.

Next, the children experienced the wonders of 

liquid nitrogen first-hand. By immersing an inflated 

balloon in liquid nitrogen, they discovered that the 

air inside of the balloon contracts, and then re-expands when warmed up. The children also learned 

that a tiny pinhole in a ping pong ball will cause 

the ball to spin wildly after being removed from 

liquid nitrogen. Other experiments included making a liquid nitrogen banana-hammer and an “ice 

egg” with a water balloon. They also listened to a 

“boiling” tea kettle and learned about the wonders 

of superconductivity, a phenomenon that becomes 

possible when certain materials are cooled to very 

low temperatures using liquid nitrogen.

But perhaps the most memorable experiment was 

the “grand finale”: The students mixed cream, 

sugar, and strawberries with liquid nitrogen to 

make the fastest (and perhaps tastiest) ice cream 

ever.

— Laura Mgrdichian

NSLS BIOPHYSICIST LISA MILLER

AWARDED TENURE

May 1, 2006

Brookhaven Science Associates (BSA) granted 

tenure effective May 1 to six BNL scientists: Wolfram Fischer, Collider-Accelerator Department; 

Frithjof Karsch, Physics Department; Lisa Miller, 

National Synchrotron Light Source Department; 

Peter Steinberg, Chemistry Department; Daniel 

van der Lelie, Biology Department; and Vitaly 

Yakimenko, Physics.

At the NSLS, Miller was awarded tenure for her 

outstanding research in the application of spectroscopic synchrotron imaging probes in the biomedical field, her leadership in building a new synchrotron user community, and her extensive outreach 

activities.

Miller earned her Ph.D. in biophysics from the 

Albert Einstein College of Medicine, where she is 

still a visiting assistant professor in the Department of Medicine. She joined the NSLS as an assistant biophysicist in 1999, rising to biophysicist 

by 2003. Since then, she has most fully developed 

her research in the areas of mineralization in bone 

and aberrant protein folding, which are of central 

importance respectively in osteoporosis and in 

neurological diseases such as Alzheimer’s and 

scrapie. Concerning the scientific impact of her 

bone research, for example, she is recognized as 

having provided unique insights into the site-specific chemical composition of bone that are important for both industrial and academic researchers.

Said NSLS Chair Chi-Chang Kao, “Lisa has made 

major contributions to research in bone and protein-folding diseases and to the development of 

synchrotron-based biomedical imaging techniques. 

She is widely 

recognized for 

the creativity 

and originality of 

her work, which 

has resulted in 

a superb record 

of publications, 

invited talks, 

and funded 

proposals. The 

very active user 

program in biomedical imaging 

that she has 

developed at infrared beamline 

U10B is being 

emulated at 

other facilities. 

Her leadership, educational supervision, and outreach activities are outstanding, and she is truly a 

valuable member of the NSLS staff.”

Miller was honored in 2002 with a DOE Outstanding Mentor Award and in 2005 by Brookhaven 

Town for outstanding contributions to science and 

the community. She is also an adjunct assistant 

professor in the Department of Biomedical Engineering at Stony Brook University. 

— Liz Seubert

Participants in the 2006 “Take our Daughters and Sons to 

Work Day” at the NSLS

Lisa Miller 
3-14

QUITE A REMARKABLE SPRING:

NOTES FROM THE 2006 NSLS-CFN

JOINT USERS’ MEETING

May 15-17, 2006

A rosy future was forecast for Brookhaven’s user 

facilities at the first-ever joint meeting of the user 

communities for the National Synchrotron Light 

Source (NSLS) and the Center for Functional 

Nanomaterials (CFN), held May 15-17, 2006.

At the main meeting on May 16, held in BNL’s 

Berkner Hall, officials from the Laboratory, the 

Department of Energy’s (DOE) Office of Science, 

and the New York State congressional delegation 

painted an optimistic picture for an audience of 

several hundred current and prospective users 

of Brookhaven’s cutting-edge science facilities 

– those that are currently in operation, planned 

and under construction, 

or eagerly anticipated. 

The Laboratory’s interim 

director, Sam Aronson, 

welcomed the participants 

and outlined Brookhaven’s 

“extremely strong science agenda in terms of 

ongoing research and new 

facilities that will maintain 

Brookhaven as a leader 

in world science.” He said 

meetings like this are 

important places in which to foster new research 

collaborations and get updated on the status of 

work at the Lab. He said that the Laboratory’s 

highest priority is the design and construction of 

the NSLS-II, which, along with the CFN, will give 

Brookhaven a powerful combination of cuttingedge research tools.

Last fall, the DOE granted “Critical Decision 

Zero (CD-0) status to National Synchrotron Light 

Source-II (NSLS-II), the planned world-leading 

2006 NSLS UEC Members and SpIG Representatives 

stand with DOE and BNL management.

Sam Aronson Pat Dehmer

Robert McGrath

successor to the NSLS. 

soon, Critical Decision 

One (CD-1) will yield a 

construction plan and a 

site decision will be made.

“The NSLS-II will allow 

our science to continue to 

flourish and expand, and 

keep the United States 

in the forefront of lightsource science,” Aronson 

said. Citing Brookhaven’s 

expected contribution to energy research, Aronson 

said that work here “will be vital to that effort for 

the U.S. economy and energy security.” He said 

that the DOE’s forward-looking investments in 

user facilities “will eventually change the face of 

the Laboratory. The completion and operation of 

the CFN and NSLS-II will profoundly change the 

balance of research here.”

Following Aronson, Stony Brook University provost 

Bob McGrath gave an update on the search for 

a new Laboratory director. The search committee has created a list of potential candidates and 

is contacting key individuals of interest. McGrath 

said that the committee has a list of 40 people and 

will begin serious interviews with 10 of those candidates. The committee expects to have a recommendation to Brookhaven Science Associates in 

September. 

The American Competitiveness Initiative

Pat Dehmer, director of DOE’s Office of Basic 

Energy Sciences, outlined the chain of events that 

led to the Laboratory’s bright future outlook, which 

she termed “a quite remarkable spring.” Focusing on the rollout of the 

American Competitiveness 

Initiative (ACI) which she 

called “great news for the 

physical sciences,” Dehmer explained that the ACI 

doubles funding for DOE’s 

Office Science over the 

next 10 years. One of the 

ACI’s focus areas is the 

tools of science, described 

as “unique, expensive, 

large-scale tools beyond 

the means of a single organization.”

Dehmer said that she had anticipated that funding for Office of Science programs would be flat 

or would decline slightly, but that when the ACI 

was announced during the President’s State of the 

Union speech in January, “a miracle occurred.” 

Projected funding for the Office of Basic Energy 

Sciences has increased by 25 percent, in large 

part because the Office’s work “aligns almost 100 

percent with the ACI goals.”
YEAR IN REVIEW

3-15

Doon Gibbs

While Dehmer was optimistic about the construction of the NSLS-II, she cautioned that the project 

would have a long construction life, which will be 

filled with unanticipated challenges.

“You are embarking on a wonderful journey,” she 

said. “You should be euphoric...and frightened. 

And you will vacillate between the two.”

She concluded her remarks by urging employees 

and users to contact their congressional representatives to thank them for the support that resulted 

in this “completely unexpected” funding picture.

“You must realize how difficult it was to make that 

happen,” she said, citing the war, last fall’s hurricanes and other budgetary pressures. “Politicians 

are people, too. They deserve your thanks, and 

they need to hear from you.”

Speaking after Dehmer, 

Congressman Tim Bishop 

said that he is “so proud of 

this Lab, the people who 

work here, and the work 

that’s moving America 

forward in so many different ways.” To see the 

administration’s proposed 

investments in science is 

“encouraging indeed,” he 

said. Citing the FY06 budget language stating that 

it is the “sense of the Congress” that NSLS-II be 

built at Brookhaven, Bishop pledged to continue 

pushing for that result.

Bishop said the full funding of the CFN is also a 

testament to the faith that the Office of Science 

has in Brookhaven, as well as to the “strenuous 

advocacy” of the New York congressional delegation.

“We speak with one voice on the importance of 

this Lab,” he said, and urged attendees to stay in 

touch with their representatives.

“Be forceful in your advocacy,” he said. “We value 

your professional expertise, and these are important issues.” 

NSLS-II Update

The morning’s next speaker, Steve Dierker, BNL 

Associate Director for Light Sources, is leading 

the effort to bring the NSLS-II to BNL. Noting that 

“the CFN will be producing materials that will be 

crying out to be characterized,” he said that development of nanoscale materials will be critical for 

the development of future energy technologies.

“NSLS-II will be brighter than any existing light 

source. None of today’s light sources were designed to probe materials with one-nanometer 

spatial resolution and 0.1 

meV energy resolution,” 

he said. “The changes 

that NSLS-II brings will be 

transformative.”

Dierker briefly described 

plans for the Joint Photon 

Sciences Institute (JPSI), 

intended to foster development of new techniques 

and capabilities. He thanked Stony Brook’s Bob 

McGrath for helping to secure a $30 million commitment from New York State for a building to 

house the proposed institute.

“JPSI will serve as an intellectual center for development and application of the photon sciences 

and as a gateway for NSLS-II users,” he said. 

Dierker showed new drawings depicting the proposed facilities, and noted that there have been 

some changes in the design, in particular, the substitution of a full-energy booster for a full-energy 

linac injector. He said that 99 people are currently 

working on NSLS-II, and predicted that the programs would overlap for less than one year before 

both will be fully and independently staffed.

“The NSLS-II will be essential for energy security, 

and important for U.S. industry, “he concluded. 

“It will enable ‘grand challenge’ science in many 

diverse fields.”

The Center for Functional Nanomaterials

Doon Gibbs, Associate Laboratory Director for 

Basic Energy Sciences and Interim Director of the 

CFN, said that an active search is underway for a 

permanent CFN director, and he urged attendees 

to bring promising candidates to the attention of 

the search committee. 

He said a broader search 

effort will begin this fall, 

with an eye to have a permanent director on board 

by October 2007. Gibbs 

observed that the CFN 

building’s structural shell 

is complete, and that more 

than half of the Center’s 

equipment will be ordered 

by the end of May.

The CFN, whose focus will 

be energy security, has added nine new scientific 

and technical staff members, bringing the total 

fulltime staff total to over 20. He added that the 

staff is becoming more collaborative and using 

bigger teams.

Tim Bishop

Steve Dierker
3-16

Chi-Chang Kao

Gibbs said that along with NSLS-II, the CFN will 

“enable the nanoscience revolution,” and he said 

that the joint user meetings should take place 

every year or two.

“It is very significant and gratifying that so many 

users have come here from all over,” he said. “We 

should continue to have such joint workshops because they perform a valuable service and bring 

us together.”

“It really has been fun being interim director,” he 

said. “It’s an exciting time to lead this project.”

NSLS Update

An update on the work of the NSLS was given by 

Chi-Chang Kao, Interim NSLS Chairman. He said 

that FY06 was a “tough year,” but observed that 

no layoffs were necessary, and he said that funding prospects for FY07 

remain very good.

Kao said the NSLS continues to serve some 2,300 

users per year, and announced plans for a BNL 

User Center to give users 

“one-stop shopping,” for 

functions including checkin, badging, and housing. 

The user center will also 

have extended hours on 

nights and weekends. 

He said the NSLS hopes to continue to add more 

staff on the floor, which he termed important for 

both science and safety.

“More staff, then more beamlines,” he said.

Kao addressed the issue of orbit stability at the 

facility, noting that the staff running the 65 operating beamlines is not the same staff that built 

them.

“There has been some lack of understanding of 

the sensitivity of beamline optics to electron beam 

motion,” he said. “The beamlines need regular 

alignment and performance calibration.”

Along with its usual complement of materials science users, Kao noted an “up tick” in the number 

of biomedical imaging users. A technique called 

Diffraction Enhanced Imaging or DEI has been 

developed to image soft tissue samples and 

delivers 8 to 33 times greater contrast than digital 

mammograms.

“This could eventually have a very wide impact in 

the health industry,” he said.

In conclusion, Kao promised both an aggressive 

upgrade plan for the facility and close NSLS-CFN 

coordination.

Building Safe Nanomaterials

As science ventures into the nanoworld, concerns 

will arise over the potential risks involved in producing and working with materials with properties 

that may not have previously been observed. Vicki 

Colvin, a chemistry professor from Rice University, 

spoke about developing nanomaterials with low 

environmental impacts. 

The future of nanotechnology promises answers 

to key questions in science, she said. Of particular interest to Long Islanders and others in 

the northeast United States is a technology to 

remove arsenic from water efficiently and in large 

quantities. But in considering such advances in 

technology, scientists must deal with what Colvin 

termed the “Wow to Yuck Trajectory,” in which 

the environmental impacts of new technology are 

only revealed after the technology is in wide use. 

Examples include DDT, which cured malaria but 

endangered birds, and refrigerants, which cooled 

our houses but led to a hole in the ozone layer.

“Early examination of nanomaterials’ effects will 

create a responsible technology,” Colvin said. “Scientific data and analysis should take the debate 

about the risks of nanotechnology to the highest 

possible technical level.”

Colvin illustrated some of the challenges inherent in attempting to answer questions of risk by 

considering the question: Are single-walled carbon 

nanotubes (SWNTs) toxic? She pointed out that 

there are 20 major types of SWNTs, and four 

manufacturing types. All of these types have different lengths, different purification methods, and 

10 possible surface coatings, for a possible 50,000 

SWNT samples.

“It will be necessary to map out basic structurefunction relationships for nanomaterials and 

biological impacts,” she said. “Fundamental nanostructure will include both chemical and physical 

properties.”

NSLS User Science Talks

Following a lunch break, users heard from several 

scientists who have conducted research at the 

NSLS.

Henry Chapman, a staff scientist at Lawrence 

Livermore National Laboratory, spoke on “Ultrafast 

Coherent Diffraction Imaging with a Soft X-Ray 

Free-Electron Laser.” This vacuum ultra-violet 

free-electron laser is located at the Deutsches 

Elektronen-Synchrotron (DESY) in Hamburg, 

Germany. It generates pulses just 25 femtoseconds in duration with more than a trillion photons 

per pulse, and is the first free-electron laser to 

produce soft x-rays. It is ideal for high-resolution 

holography and imaging, Chapman said, and he 

showed this by displaying diffraction images and 

measurements.
YEAR IN REVIEW

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BOB SWEET, THE 2006 UEC COMMU- NITY SERVICE AWARD RECIPIENT

May 16, 2006

For his extraordinary service, the NSLS Users' 

Executive Committee chose Robert M. Sweet for 

the UEC Community Service Award. 

Biological crystallography has 

emerged as an 

extremely high-profile research area 

with synchrotron 

radiation, and Bob 

has made numerous contributions to 

create and sustain 

a vibrant community of users at the 

NSLS. Bob is the 

Principal InvestigaBob Sweet tor of the MacroNext, a talk on the “Engineering of Carbon Nanotube Structures” was presented by Pulickel M. 

Ajayan from the Department of Materials Science 

and Engineering at Rensselaer Polytechnic Institute. His talk focused on recent developments in 

his laboratory to fabricate carbon-nanotube-based 

structures that are tailored for various applications. Specifically, he discussed how he and his 

group create branched nanotube and nanotubehybrid structures for applications such as sensors, 

electrical interconnects, and filters.

Before the afternoon break, Lawrence Shapiro, an 

associate professor at Columbia University, spoke 

on “Decoding Cell Adhesion with Protein Crystallography.” Cell adhesion – connections that allow 

cells to stick together – is critical to the formation 

of tissues and complex cellular networks, such as 

those that make up the nervous system. These 

connections are made possible by a few cell-surface protein families. Shapiro discussed how, at 

the NSLS and other synchrotrons, high-resolution 

protein-crystal structures are beginning to reveal 

the atomic-level mechanisms of cell adhesion.

Other Notables

Each year, the NSLS Users’ Executive Committee 

(UEC) presents one user with the UEC Community Service Award, which honors hard work and 

dedication toward bettering the experience of users and the user community. At the main meeting, 

UEC Chair Peter Stephens presented this year’s 

award to Bob Sweet (BNL-Biology). More details 

on this year’s award can be found in the following 

article.

At the conclusion of the main meeting, participants 

attended the annual poster session and vendor exhibition. Hors d'oeuvres were served as attendees 

mingled and talked, making for a lively, enjoyable 

event. Awards were presented to the top student 

and postdoc posters, which were on display in the 

NSLS lobby during the month of June. The winners were: Elena Loginova (Rutgers University), 

Seo-Young Kwak (BNL-NSLS), Shuguo Ma (BNLChemistry), Minhua Shao (Stony Brook University), Jae-Hyuk Her (Stony Brook University), and 

Ariane Kretlow (Robert Koch Institute, Germany). 

Each winner received a BNL certificate and a $50 

American Express gift certificate. Additionally, the 

Synchrotron Catalysis Consortium gave out two 

poster prizes of its own. First prize went to Shao, 

and second prize was awarded to Wen Wen (BNLChemistry).

During the two days after the main meeting, workshops were held at locations across the Laboratory. They were "Synchrotron Catalysis Consortium: 

New Opportunities for in-situ XAFS Studies of 

Nanocatalysis," Nanocatalysis," organized by Simon Bare (UOP) organized by Simon Bare (UOP)

and Anatoly Frenkel (Yeshiva University); "Soft 

Matter and Biomolecular Materials: X-ray Scattering Enabled by High Brightness Beamlines,"

organized by Ben Hsiao (Stony Brook University), 

Lin Yang (BNL-NSLS), Elaine DiMasi (BNL-NSLS), 

and Ron Pindak (BNL-NSLS); "Nanoscale Correlations Heterostructures," relations Heterostructures," organized by Jim organized by Jim

Misewich (BNL-Material Sciences) and Tony Heinz 

(Columbia University); “Chemical and Biological 

Applications of X-ray Emission Spectroscopy,"

organized by James Penner-Hahn (University of 

Michigan) and Trevor Tyson (New Jersey Institute 

of Technology); "Platforms for the Integration of 

Biological Systems into Nanomaterials and Interfaces," faces," organized by Oleg Gang (BNL-CFN), Dan- organized by Oleg Gang (BNL-CFN), Daniel Van Der Lelie (BNL-Biology), and Molly Frame 

(Stony Brook University); and "VUV Radiometry,"

organized by Jeff Keister (SFA, Inc).

— Kay Cordtz and Laura Mgrdichian

Poster winners (from left) Shuguo Ma, Minhua Shao, Ariane 

Kretlow, Elena Loginova, Seo-Young Kwak, and Jae-Hyuk 

Her.
3-18

molecular Crystallography Research Resource 

(PXRR), which provides facilities and support at 

the NSLS for the benefit of outside and in-house 

investigators. The PXRR is supported by the 

NIH’s National Center for Research Resources 

and the DOE Office of Biological and Environmental Research in its mission to create optimal 

facilities and environments for macromolecular 

structure determination by synchrotron x-ray 

diffraction. With a staff of about 24, the PXRR 

innovates new access modes such as FedEx crystallography, builds new facilities, develops remote 

participation software, collaborates with outside 

groups, teaches novice users, and supports visiting investigators with seven-day, 20-hour staff 

coverage.

The PXRR includes six beamlines at X8C, 

X12B, X12C, X25, X26C, and X29. Bob’s work 

on developing macromolecular crystallography 

at the NSLS helped in a continual push toward 

improved performance for NSLS beamlines. The 

X25 wiggler provided an early demonstration of 

the potential for insertion devices at NSLS, and 

the mini-gap undulator at X29 has added to that 

innovation, and inspired upgrades to mini-gap 

undulators for other beamlines, notably X25. 

Bob’s efforts have led to the development of 

sample-loading automation techniques at the 

NSLS, software that enables easy user experimental interaction, and the scope of the PXRR 

has established standardization across many 

NSLS beamlines, enabling users to move easily 

from one beamline to the next.

Bob is warm, easy to talk to, and accessible to 

regular users in the community. Through all his 

efforts, Bob has likely been the single most important factor in keeping the NSLS on the cutting 

edge of macromolecular synchrotron crystallography.

It is thus with great pleasure that Bob Sweet was 

given the NSLS Community Service Award for 

2006.

ENERGY SECRETARY, UNDER

SECRETARY FOR ENERGY TOUR NSLS

June 2, 2006

On June 2, BNL welcomed Energy Secretary 

Samuel Bodman and Raymond Orbach, newly 

named Under Secretary for Science at the Energy 

Department. 

During a whirlwind visit, the Secretary and Under 

Secretary met researchers at the NSLS, where 

they talked about current and future research. 

While discussing applications of synchrotron soft 

ALD for Light Sources Steve Dierker shows 

Energy Secretary Samuel Bodman and Under 

Secretary Raymond Orbach posters in the NSLS 

lobby.

x-rays, NIST physicist, Dan Fischer, gave Bodman 

and Orbach a tour of beamline U7A. NSLS biophysical chemist, Lisa Miller, showed the Secretary and Under Secretary infrared beamline U10B 

and described her group’s work on skin melanoma 

while Steve Dierker, Associate Laboratory Director for Light Sources, highlighted the prospects for 

NSLS-II.

Bodman and Orbach also met researchers at the 

Relativistic Heavy Ion Collider’s (RHIC) PHENIX and STAR detectors and the molecular beam 

epitaxy system laboratory, where they heard about 

the Lab’s nanoscience efforts. 

Later, the Secretary gave a standing-room-only 

talk in Berkner Hall to an audience of employees 

and other guests, including Shirley Strum Kenny, 

President of Stony Brook University and Chair of 

the Brookhaven Science Associates (BSA) Board; 

Carl Kohrt, Battelle President, CEO, and BSA 

Vice-Chair; and other members of the Board. His 

purpose in coming to the Lab, the Secretary said, 

was to support the same level of quality in BNL’s 

future work as that of the greatness of its past 

— ensuring that “from RHIC to the new Center for 

Functional Nanomaterials to the preferred siting 

for the NSLS-II, history will be repeated at the 

Lab.”

DOE/BNL Partnership Requires Safety and 

Science

In committing to maintaining that tradition, DOE 

“requires a partnership between you and us,” Bodman said. “We look to this laboratory for excellence in management as well as science.” 

“The most important asset the Department has 

here . . . is all of you,” he continued. “The personal safety of all departmental employees and 

contractors is a top priority for me.” The Secretary 

emphasized that Brookhaven can be proud of its 
YEAR IN REVIEW

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history of scientific achievement and contributions in many fields, “But, in my judgment, your 

safety record requires improvement,” he said. “We 

ask you to take care of each other and think of 

yourselves. Small accidents are the precursors to 

serious accidents.”

Investing in Science

The President understands that we must make investments to ensure that America retains its world 

pre-eminence in science, Bodman said. “That is 

why he has proposed the American Competitiveness Initiative (ACI), the Alternative Energy Initiative, and the Global Nuclear Energy Partnership 

(GNEP). The Energy Department has a major role 

in all three programs.”

Through the ACI, the Office of Science budget is 

expected to increase by 14 percent in 2007, to 

$4.1 billion. This initiative is especially important 

to the NSLS, as the Office of Science will direct 

additional funds to sectors promising breakthroughs, including supercomputers, nanotechnology, energy from biomass, nuclear fusion, and 

high-intensity light sources like the NSLS. 

Another reflection of Washington’s growing awareness of the importance of science, the Secretary 

pointed out, is Congress’ recent confirmation 

of Ray Orbach as “the first Under Secretary for 

Science in the history of our Department. The 

symbolism involved expresses a role for science 

in our country’s government that it has never had 

before, and we will take maximum advantage of 

it.” Over the next 10 years, even more funding will 

come from the ACI — $136-plus billion — to invest 

in research and development, improved math and 

science education, and incentives to encourage 

entrepreneurship and innovation, Bodman said. 

GNEP, meanwhile, is a collaboration among several countries, Bodman said. The aim is to develop 

new technologies to recycle spent nuclear fuel in 

a way that cuts proliferation risks while reducing 

the volume of waste for disposal. Nine DOE labs, 

including Brookhaven, are playing a role in this 

program.

The Alternative Energy Program is also focused 

on developing new technology. With a 22 percent 

increase for FY07, this will translate into more 

support for work on cellulosic ethanol, lithium ion 

batteries for hybrid vehicles, and hydrogen fuel 

cells.

All this effort depends on people, Bodman said, 

and pointed to the ACI call for $380 million to 

improve mathematics, science, and technical 

education in U.S. elementary and high schools. 

He cited the work being done by BNL’s Office of 

Educational Programs as an example of the type 

of program needed to “assure that future generations of scientists and engineers will step forward 

to carry on the work that all of you are doing so 

ably here today.” In conclusion, the Secretary reiterated the “tremendous respect” he had for BNL’s 

achievements and what he expected the Lab to 

achieve in the future. He ended his formal comments by urging Lab employees to e-mail him with 

their concerns at any time.

— Liz Seubert with Peter Genzer and Kendra 

Snyder

NSLS scientist Lisa Miller shows Energy Secretary 

Samuel Bodman infrared beamline U10B.

Energy Secretary Samuel Bodman (front, middle) stands 

at beamline U7A with (from left) NIST physicist Dan 

Fischer, Under Secretary Raymond Orbach, Battelle 

President and CEO Carl Kohrt, Associate Laboratory 

Director for Light Sources Steve Dierker, BNL Interim 

Director Sam Aronson, and scientists Faisal Alamgir and 

Sharadha Sambasivan.

CRYSTAL GROWTH WORKSHOP HAS

CRYSTALLIZING RESULTS

June 12-15, 2006

Hailing from as far as Australia, 40 researchers 

shared the complexity of the protein crystal growth 

process with leaders in the field at the “Crystallization: Focus on Optimization and High Throughput 

Techniques” workshop. The fourth annual course 

took place at the NSLS from June 12-15, 2006. 

Organized by Vivian Stojanoff (NSLS) and Naomi 

Chayen (Imperial College London), with help from 
3-20

FUTURE ‘POETS,’ STUDENTS LEARN

ABOUT NANOSCIENCE AT BNL

June 19, 2006

Whether they want to be speech therapists or 

chemists, all students can benefit from learning 

about nanoscience. That’s the mantra of National 

Synchrotron Light Source user Anatoly Frenkel, 

who taught two courses on the subject this summer leading up to a week of hands-on research at 

BNL for eight students and eight research assistants from Yeshiva University.

The six-week courses, “Discover Nanoscience” 

and “Nanoscience for Poets” attracted students 

scientists Fabiano Yokaichiya (NSLS) and Jean 

Jakoncic (NSLS), East Coast NIGMS Structural 

Biology Research Facility, and Stony Brook intern 

Matthew Worth, the workshop included a recordnumber of 11 hands-on tutorials for participants to 

choose from.

The purpose of the three-day course was to help 

researchers obtain high-quality protein crystals 

through both conventional and non-conventional 

methods including the use of oils, novel nucleating agents, detergents, crystallization in lipid cubic 

phase, crystallization with gels and high throughput techniques. Participants were divided into 

groups of three or four, according to their main 

interests, and followed practical sessions during 

the course. Researchers chose seven of the 11 

sessions to attend, whereas last year’s course offered eight sessions. 

“What’s unique about this course is that it is a real 

hands-on experience,” Stojanoff said. “You really 

get to try these things out yourself.” This unique 

aspect inspired about a third of the participants to 

bring their own proteins on which they tried different methods. A few participants actually produced 

crystals from the proteins they brought, which 

were screened on beamline X6A on the last day of 

the workshop.

Experts in the academic and industrial crystallization field gave a series of talks and tutorials. Neer 

Asherie (Yeshiva University) discussed “Understanding Protein Phase Behavior,” Marie-Claude 

Marchand (Qiagen Inc.) discussed “The Vapor 

Diffusion Method and Optimization,” Gwen Nneji 

(Imperial College of London) discussed “Non-standard Crystallization Techniques,” Pat Loll (Drexel 

University) discussed “Membrane Proteins and 

Detergents,” Peter Nollert (Emerald BioSystems) 

discussed “Micro Crystallization using the Lipidic 

Cubic Phase Methodology,” Ingo Grotjohann 

(Arizona State University) discussed “The Role of 

the Phase Diagram in the Crystallization of PSI 

and PSII,” and Abel Moreno (Universidad Nacional 

Autonoma de Mexico) discussed “Gels and Fields: 

What Can They Say About the Phase Diagram?”

Practical sessions also included talks by Troy 

Burke (GE Healthcare), Marcia Armstrong (Qiagen 

Inc.), Trevor Harvard (Precision Detectors), Craig 

Sterling (Emerald BioSystems), Chris Gawronski 

(Fluidigm), and NSLS Interim Chairman Chi-Chang 

Kao, who gave participants an introduction to the 

light source facility. 

In addition, by request of last year’s participants, 

a special session on cryogenic protection and 

quality assessment of crystals was conducted at 

beamline X6A on the last day of the workshop. 

Seetharaman Jayaraman (Columbia Universtiy) 

introduced the topic and conducted demonstrations in the New York Structural Biology Center 

Laboratory.

The course attracted researchers with all levels of 

crystallization experience, including current NSLS 

users who have previously encountered problems 

with their crystals. “The course brings new people 

and awareness to companies about the NSLS and 

mutual benefits we can have,” Stojanoff said. 

One participant commented on the course survey: 

“It is better than a conference. In a conference, 

people present results, but in this workshop, we 

are shown how to get results.”

Stojanoff stressed her appreciation to the following groups that allowed the use of their labs and 

time: New York Structural Biology Center, Case 

Center for Proteomics, the X19C PRT, X17 PRT, 

X19A PRT, NSLS staff, NSLS User Administration, 

and the NSLS Outreach Office. Major sponsors 

included GE HealthCare, Qiagen, Precision Detectors, Emerald Biosystems, and Fluidigm. Additional support was provided by Hampton Research, 

Douglas Instruments, Anatrace, Millipore, Eppendorf, and New York New Jersey Scientific.

— Kendra Snyder

The participants of the 2006 Crystallization workshop
YEAR IN REVIEW

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with majors ranging from history to computer 

science. “We want them to become aware of the 

most important problems in modern science,” said 

Frenkel, who taught the courses along with fellow 

Yeshiva professors Gabriel Cwilich and Fredy Zypman. 

The students worked in teams on the design, 

synthesis, manipulation, and characterization of 

nanoparticle catalysts, which are key components 

of hydrogen fuel cells. “We designed the course 

around some activities that students could do from 

beginning to end,” Frenkel said.

The courses began in late May with introductory 

lectures and labs at the Yeshiva campus, in New 

York City, in order to get participants up to speed 

with the concepts of nanoscience and nanotechnology. Students then prepared thiol-stabilized Pd 

nanoparticles for their research.

The focal point of both courses was a weeklong 

stay at Brookhaven, which started on June 19. 

On NSLS beamline X11A, students analyzed their 

samples using x-ray absorption fine structure 

(XAFS) spectroscopy. Short trips also were made 

to Stony Brook University, where students characterized their nanoparticles with electron microscopy and atomic force microscopy.

The efficiency of hydrogen fuel cells correlates 

with the ability of their catalysts to absorb and/or 

adsorb hydrogen. The students studied the effect of hydrogenation of fuel cell performance by 

changing the size of their Pd samples. One of the 

most exciting parts of the courses is that actual 

data was collected, Frenkel said. A mini conference with presentations served as the final exam 

for the students, and their results will be presented in Boston this November at the annual meeting 

of the Materials Research Society.

Frenkel held a similar course in 2003 on experiments in modern physics and plans to expand the 

nanotechnology courses in future years.

Participants in the Yeshiva University nanoscience 

courses at the NSLS 

“Some students go into sciences without knowing too much what the day-to-day research is like 

because they didn’t have any opportunity to learn 

how serious research is different from undergraduate work. And then they’re disappointed and find 

out later in their lives that research is not what 

they wanted to do,” Frenkel said. “We can help 

show them what it’s like and help them make a 

decision, no matter what that decision is.”

— Kendra Snyder

IN MEMORIAM: DAVID MURRAY

ZEHNER

June 19, 2006

David Murray Zehner, who helped develop beamline U12B at the NSLS, died on June 19, 2006. He 

was 62.

A native of Philadelphia, Zehner 

received his B.A. at 

Drexel University 

and his Ph.D. in 

physics from Brown 

University. Zehner 

was a research 

scientist for more 

than 30 years in 

the Solid State and 

Condensed Matter 

Physics Divisions at 

Oak Ridge National 

Laboratory, where 

he served as group 

leader and section head for many years. 

He completed his thesis at Brown under famed 

physicist Harrison E. Farnsworth, one of the first 

to use low-energy electron diffraction to study 

metal crystal surfaces. Described by colleagues 

as an “old-school physicist,” Zehner was greatly 

influenced by his mentor and focused most of his 

research on elemental and alloy metal surfaces.

Doon Gibbs, BNL’s Associate Laboratory Director for Basic Energy Sciences, first worked with 

Zehner in the late 70s and early 80s on experiments focused on the structure and phase behavior of gold surfaces. Prior to completion of the 

NSLS, Gibbs’ group used a rotating anode source 

in the Physics Department and the Cornell High 

Energy Synchrotron Source (CHESS) to carry out 

the experiments. After the start-up of the NSLS, 

they transferred their studies to beamline X22C 

and added platinum and iridium surfaces to their 

research. Zehner also conducted research at 

beamline X20.

David Zehner
3-22

IN MEMORIAM: JULIAN DAVID

BAUMERT

June 24, 2006

Julian David Baumert, a Brookhaven physicist 

working on the cutting edge of research on liquid 

surfaces and thin organic films, died of melanoma 

on June 24, 2006. He was 31.

Described as dedicated, bright and caring, 

“David was brutally honest and he liked to do 

things right,” Gibbs said. “He was very precise 

about the little details, from doing the experiment 

to writing the papers. But he also was a lot of fun 

and cared a lot about what people thought and 

how they were doing.”

Zehner helped develop beamline U12B at the 

NSLS in the early 80s along with Ward Plummer, 

now a Distinguished Scientist at Oak Ridge and a 

Distinguished Professor of physics at the University of Tennessee. As a collaboration between Oak 

Ridge and the University of Pennsylvania, beamline U12B researchers used electron scattering to 

determine and understand the structure and chemistry of surfaces. “He was emphatic that he had to 

do it right and he would do it over and over again 

until it was,” said Plummer, who published some 

15 papers with Zehner during their time together 

at the beamline. “That led to a lot of late nights at 

Brookhaven.” 

Colleagues say Zehner’s compassion was evident 

by the way he mentored the graduate students 

and postdoctoral researchers who worked on his 

experiments. “He followed their career with every 

step they made,” Plummer said. “He really cared 

about people. He joked that with his affinity for 

people, he probably missed his calling and should 

have become a real doctor.”

One of those young researchers who Zehner took 

under his wing was Art Baddorf, now a senior 

research staff member at Oak Ridge who worked 

with Zehner and Gibbs at Brookhaven in the 

1990s. “I learned a lot from him,” Baddorf said. 

“He was a lot of fun to be around and he was interested in what everyone else was doing and how 

they were doing it.”

Zehner enjoyed windsurfing, sports, and music, 

and was a member of the American Vacuum Society and the American Physical Society. A resident 

of Lenoir City, TN, Zehner is survived by close 

friend, Donna Watson; and former wife, Theodora 

Zehner.

— Kendra Snyder

Baumert was a relatively new research associate in the Soft Matter and X-ray groups in the 

Condensed Matter Physics and Materials Science 

Department at BNL. “Julian was an exceptionally 

talented, hard-working young researcher, who 

loved his work,” said colleague John Hill. “He 

understood his research at a deep level and it was 

always a pleasure to ask him what he was working 

on and hear his clear, precise, and enthusiastic 

explanations of his latest results and what they 

meant. It is such a tragedy to lose him so early 

in his life and in his career. We will all miss him 

immensely.”

A native of Molfsee, Germany, Baumert was educated at the Institute of Experimental and Applied 

Physics (IEAP) at the University of Kiel and the 

Institute Laue-Langevin (ILL) in Grenoble, France, 

where he studied a compound known as methane 

hydrate, which is found naturally on the sea floor 

and is a major worldwide energy resource. His 

thesis focused on the structure and dynamics of 

this compound using neutron and x-ray scattering 

techniques and numerical simulations. Baumert 

obtained his Ph.D. from the University of Kiel in 

February 2004, receiving the prestigious “Familie-Schindler Foerderungs-Preis” of the Faculty of 

Science in Kiel.

“He was a very cheerful person,” said colleague 

Oleg Gang. “We deal with so many difficult and 

complicated things here, but he created this 

atmosphere around him where everything was 

positive.” 

Baumert came to BNL in July 2004 and conducted 

his research at beamline X22 of the National 

Synchrotron Light Source, where he was part of 

a team of scientists learning to make smaller and 

more powerful molecular-scale circuit components 

that could someday make electronic devices more 

efficient. He was the principal investigator on a 

paper published in February 2006 in the Proceedings of the National Academy of Sciences that 

Julian Baumert
YEAR IN REVIEW

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described the first measurements of the structure 

of a molecular junction at buried interfaces. He 

was working to elucidate how the structural and 

electrical properties of these molecular junctions 

depend on the molecular coverage.

“He had such great promise to be an extremely 

successful scientist,” said Ben Ocko, who hired 

Baumert into his research group. “He was easygoing and friendly, and exhibited a high level 

of creativity, great skills as an experimentalist, 

and the ability to explain complex phenomena in 

simple and elegant terms. He had such a bright 

future ahead of him.”

In the past year, Baumert was diagnosed as having skin cancer and underwent extensive treatment. That didn’t stop him from continuing his 

research at Brookhaven. “Even when his health 

deteriorated, he continued to come to the Lab daily to work on experiments and to discuss science 

with his colleagues,” Ocko said. After an operation last summer, Baumert continued his scientific 

research including travel to the Advanced Photon 

Source last December to investigate how “surface 

freezing” modifies the capillary wave spectrum 

at the surface of long-chain alkane molecules 

using a technique called x-ray photon correlation 

spectroscopy. 

“It was really amazing how he dealt with it,” said 

Baumert’s office mate and colleague Masa Fukuto. “He must have known the odds were against 

him, but he was courageous to the very last minute. He never lost hope.”

A resident of Sound Beach, Julian Baumert is survived by his wife, Maren; his parents, Ingrid and 

Jürgen; and his sisters, Anna and Sophia. 

— Kendra Snyder

IN MEMORIAM: ELIZABETH A. HICKS

July 12, 2006

Elizabeth “Liz” A. Hicks, a Brookhaven systems 

analyst for more than 14 years, died on July 12, 

2006. She was 41.

A native of Syosset, Hicks received a B.S. in computer science from Stony Brook University. She 

joined BNL in May 1990 as a Database Administrator at the National Synchrotron Light Source 

and later became an applications engineer. Hicks 

maintained and developed numerous employee 

databases, assisted the NSLS User Administration 

Office, helped develop the NSLS stockroom database, and provided general support for sections 

throughout the department. 

“She was very competent and very good at what 

she did,” said NSLS Business Operations Manager 

Frank Terrano. “She loved her work, she loved 

to work, and she never shied away from putting 

in extra hours. She had a huge effect across the 

entire department.”

When last-minute jobs came in, Hicks was ready 

to work, said colleague Mary Anne Corwin. “She 

was always there and always helpful,” Corwin 

said. “She was so friendly and really focused on 

doing things the right way.”

Hicks battled multiple illnesses during her time at 

Brookhaven, but she didn’t let that affect her spirits. “She was so strong-willed and optimistic,” said 

colleague Donna Buckley, who worked with Liz to 

develop the NSLS stock room database. “She was 

such a happy person. I don’t think I ever saw her 

angry in all of the days I worked with her.”

Described as daring, humorous, and without a 

“mean bone in her body,” Hicks enjoyed skiing, 

sailing and the annual Mattituck Strawberry Festival, which she attended for the last time with her 

two sons in June. Hicks left the lab on long-term 

disability in July 2004, partly to spend as much 

time as possible with her children, friends said. 

“She knew she wasn’t going to make it to a ripe 

old age,” said colleague Wendy Morrin. “She lived 

for her boys. She was a really good mom.”

Hicks also loved to sing, dance and play the piano. The clanking sound of tap shoes ringing down 

the NSLS hallways could be pinpointed to Hicks’ 

office, where she and Morrin practiced routines 

during lunchtime for their dance classes.

“It was always great to see Liz,” Morrin said. “She 

was always cheerful and smiling. She had so 

much against her health-wise, but she never let it 

show. She lived every day to its fullest. She was 

just a truly beautiful person.”

Liz Hicks with sons Christopher and Adam
3-24

A resident of Mattituck, Hicks is survived by her 

husband, Eugene; her sons, Christopher and 

Adam; her parents, Holmes and Lucy; her brothers, Gary and Kenneth; and her sister, Lee.

— Kendra Snyder

JEAN JAKONCIC WINS ESTEEMED

STUDENT LECTURER AWARD

July 22-27, 2006

National Synchrotron Light Source student 

researcher Jean Jakoncic won the prestigious 

Margaret C. Etter Student Lecturer Award for 

researching the use of high-energy x-rays to prevent crystal damage in diffraction studies. 

He received the award at the American Crystallographic Association national meeting, held in 

Honolulu, Hawaii, on July 22-27, where he also 

gave a talk on the subject. The Etter award, given 

out just once a year, recognizes achievement and 

future potential for scientists at an early stage in 

their independent careers. 

Jakoncic, a graduate student from Joseph Fourier 

University working toward his Ph.D. in structural biology, came to the NSLS four years ago. 

Conducting research primarily at NSLS beamline 

X6A (under the supervision of Vivian Stojanoff), 

in addition to X17B1 and the European Synchrotron Radiation Facility (ESRF) beamline ID15B, 

Jakoncic helped to show that high-energy x-rays 

could be an option for the structural determination of radiation-sensitive proteins. In addition to 

Stojanoff, he worked with NSLS scientist Zhong 

Zhong and ESRF scientists Marco Di Michiel and 

Veijo Honkimaki.

“Traditionally, people use medium- and lowenergy x-rays for diffraction studies of protein 

samples,” Jakoncic said. “At these energies, there 

is a significant amount of energy deposited in the 

crystal and substantially there is radiation damage. We propose to use higher energies, where 

the energy deposition is about 10 to 15 times less 

than at lower-energy x-rays.”

To visualize radiation damage, the group exposed 

lyzozyme crystals, which are standard test protein 

crystals, to high-energy and low-energy x-rays and 

compared the results. “With the same resolution 

limit, we didn’t see any radiation damage at 55 

keV, the high-energy data, while we observed radiation damage at 12 keV,” Jakoncic said, adding 

that plans for additional testing with crystals from 

different proteins are underway. “This is the first 

step,” he said.

Jakoncic describes his efforts associated with the 

high-energy x-ray research as a “satellite project” 

in relation to his other scientific interests. His 

core research at the NSLS focuses on enzymes 

involved in the degradation of toxic compounds, in 

particular polycyclic aromatic hydrocarbons (PAH). 

— Kendra Snyder

Jean Jakoncic

NSLS SUMMER SUNDAY DRAWS 650

VISITORS TO FACILITY

July 30, 2006

Using gumdrops and toothpicks to illustrate 

molecular crystals and Marshmallow Peeps to 

demonstrate the power of a vacuum, about 650 

community members had a sweet time at the 

NSLS Summer Sunday on July 30, 2006. 

For eight consecutive Sundays each summer, the 

Brookhaven National Laboratory Summer Sunday program invites the public to see the popular 

Whiz-Bang Science Show and showcases a different BNL facility every week. 

Visitors who came to the event began their tours 

in Berkner Hall, where Marc Allaire, Lisa Miller, 

A steady stream of visitors fi lled the NSLS Lobby
YEAR IN REVIEW

3-25

Steve Hulbert, Tony Lanzirotti, and Andrew Ackerman explained the concept of a light source and 

gave more detailed information about the facility 

and its research goals. Before boarding a bus for 

the quick drive to the NSLS, visitors learned more 

about nanoscience research at a display set up 

by the Center for Functional Nanomaterials, and 

roamed among several other hands-on exhibits. 

Once at the NSLS, visitors crowded the lobby, 

seminar room, and front patio, where 14 handson displays were set up to demonstrate how the 

light source works and teach visitors about the 

science performed there. Learning about science 

topics ranging from diffraction to liquid nitrogen, 

the NSLS guests floated from display to display, 

asking questions and collecting some goodies 

along the way.

At the “Crystals: Unlocking the Secrets of Life” 

display, many kids, and some adults, assembled 

“crystals” from toothpicks and gumdrops. Another 

popular display was “Sounds of Silence,” where 

guests watched how a vacuum pump caused a 

balloon to expand and the sound of a ringing bell 

to considerably fade. Display volunteers also exposed Marshmallow Peeps to the vacuum, which 

expanded the Peeps when turned on and shriveled them down to a smaller size when turned off. 

Visitors then performed a science experiment of 

their own by popping the de-puffed Peeps in their 

mouths. Their findings: The vacuum didn’t make 

the candies any less tasty.

At “See the Light,” visitors could observe actual 

synchrotron light, guided to the lobby from the 

experimental floor by a fiber-optic. And by using 

a Skee Ball-type backboard and rubber bouncy 

balls, the “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.

Standing at the lobby and second-floor viewing 

windows overlooking the experimental floor were 

scientists Steve Bennett, John Dabrowski, Susila 

Ramamoorthy, Gary Weiner, and Ray Raynis. The 

volunteers pointed out various components of the 

light source to visitors, using large neon numbers 

as reference points. 

The excitement also carried over to the outside, 

where every half hour visitors gathered around the 

building’s front windows or on the patio to watch 

a special water rocket launch in the parking lot 

across the street by Matt Engel, John Kuczewski, 

and Steve Ehrlich. 

Upon entering the building, each guest received a 

quiz with questions that could be answered by visiting each display. Every finished quiz was handed 

in and redeemed for an NSLS orange frisbee, to 

match the volunteers’ orange shirts. In addition, 

one person was selected raffle-style every half 

hour by the enthusiastic MC Gerry Van Derlaske to 

receive one of two prizes – a BNL T-shirt or a tour 

of the experimental floor. This is the first year that 

floor tours were offered during the event, and visitors were excited to see the actual piping, foil and 

wires of the NSLS up close.

The rest of the more than 40 NSLS volunteers 

that made the event possible included: Kimone 

Antoine, Al Borrelli, Jonathan Cheung, Mary 

Anne Corwin, Angelo Dragone, Steve Giordano, 

Sarah Heins, Madeline Hughes, Steve Hulbert, 

Syed Khalid, Steve Kramer, Ariane Kretlow, Tony 

Kuczewski, Brian Kushner, Andreana Leskovjan, 

Sean McCorkle, Corinne Messana, Eileen Morello, 

Payman Mortazavi, Shirin Mortazavi, Kathy Nasta, 

Kumi Pandya, Meghan Ruppel, Cecilia Sanchez 

Hanke, Lenny Santangelo, Yusuf Siddiqui, Randy 

Smith, Kendra Snyder, Marie Van Buren, Adele 

Wang, Matt Worth, Nancye Wright, and numerous 

NSLS family members.

— Kendra Snyder

Visitors gather around the liquid nitrogen display 

outside the NSLS

Summer Sunday visitors look at displays in the 

seminar room
3-26

1,000 INJURY-FREE DAYS... AND

COUNTING

August 14, 2006

NSLS users and 

staff have worked 

more than 1,000 

days without a 

lost-time injury. 

This significant 

safety milestone was 

reached on Monday, 

August 14, 2006 as the tally in the NSLS lobby 

jumped into the quadruple digits. The number 

means that almost three years has passed without 

a person working at the NSLS losing work time or 

incurring restricted duties as the result of an injury 

or exposure on the job. 

The milestone is a major accomplishment for the 

NSLS, considering the complicated work environment and the hundreds of people working within 

the building 24 hours a day, said Bob Casey, the 

NSLS Associate Chair for Environment, Safety, 

Health, and Quality. “This success is the result 

of many people taking care to plan their work 

and making sure that hazards are identified and 

controlled,” Casey said. “A safe work environment 

is good for each of us personally, and it is good for 

the NSLS. I tip my hat to everyone for their efforts 

to keep our workplace safe.”

— Kendra Snyder

HATS OFF TO THE 2006 NSLS SUMMER

STUDENTS

September 1, 2006

Eighteen high school and college students performed summer research projects at the NSLS this 

year, working with scientists and engineers from 

the department in research fields ranging from 

medical sciences to electrical and mechanical 

engineering. In addition to their research projects, 

students had the opportunity to 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. Here’s 

an idea of what they 

did during the sumKimone Antoine mer:

Kobbina Awuah

Jonathan Cheung

Kimone Antoine worked with Lisa Miller to analyze 

differences in the chemical composition between 

children’s and adults’ fingerprints using infrared 

microspectroscopy. Her objective was to reveal 

why children’s fingerprints disappear faster than 

those of adults. Antoine received her Associate’s 

degree in mathematics and natural science from 

Lehigh Carbon Community College in Pennsylvania and attends classes at Hiram College.

Kobbina Awuah 

worked with John 

Skaritka as part of 

the Science Undergraduate Laboratory 

Internship (SULI) 

program at BNL. 

They designed a 

2-in-1 cryogenic 

permanent magnetic 

undulator (CPMU) 

and a superconducting undulator (SCU). The design will help reduce 

project costs associated with switching from one 

kind of undulator to the other (i.e. CPMU to SCU 

and vice versa). Awuah is a junior at Cornell University.

Jonathan Cheung 

worked at the NSLS 

with Syed Khalid and 

Vivian Stojanoff on a 

project related to the 

origin of color from 

natural pigments. 

Cheung collected 

different materials 

that were dyed using 

pigments from vegetables, tree bark, 

and flowers. This dying process involves some 

natural mordants (fixers) such as iron, copper, and 

aluminum. Using spectroscopy, he found the color 

of the finished sample to be dependent on the type 

of material and mordant used. Cheung is a senior 

at Syosset High School.

Sarah Heins spent most of her time was observing administrative staff and scientists while they 

worked on everything from completing travel 

authorization forms to determining the structure 

and magnetism of 

certain elements. 

She worked with 

Stony Brook University graduate student 

Kathryn Krycka to 

learn how much time 

and effort is needed 

in order to conduct 

experiments, write 

Sarah Heins a thesis and earn a 
YEAR IN REVIEW

3-27

John Kuczewski

Elhag Shaban, Marcus Mason and Eric Huey

Shirin Mortazavi

Saka Okyere-Asiedu, 

Christopher Dixon and Robert 

Opila

Dylan Roden

high-level degree in the physics field. She also 

spent a small portion of her time researching 

physical concepts and past experiments done at 

the NSLS. In her spare time, Heins helped the 

secretarial staff to learn about the administrative 

aspects of scientific research. Heins is a freshman at Syracuse University.

John Kuczewski 

worked with Peter 

Siddons at the 

NSLS as part of the 

High School Summer Research Program. He developed 

a graphical user 

interface for the 

Thorlabs OPTODC 

Servo Motor System 

under the GNU/

Linux platform. Modeled from Siddon’s driver and 

kernel patch, Kuczewski’s software package for 

this motor system was programmed using the C 

programming language and the GTK+2.0 libraries for the Debian GNU/Linux operating system. 

GNU/Linux based systems are used at the light 

source for beamline controls and this new software package will integrate seamlessly into the 

present control systems. Kuczewski is a sophomore at Shoreham-Wading River High School.

Marcus Mason and Eric Huey worked with Peter 

Siddons and Elhag Shaban at the NSLS as part 

of the Faculty and Student Team (FaST) program. 

Mason and Huey studied the processes involved 

in the development of a Bulk MicroMegas Detector. They characterized the detector using 

extended x-ray absorption fine structure (EXAFS) 

methodology at beamline X12A They also attempted to reproduce 

stable gains and 

excellent resolutions 

as studied in previous detectors. They 

both are juniors at 

Southern University 

at Baton Rouge.

Shirin Mortazavi 

participated in BNL’s 

High School Research Program. Under the guidance of Lisa Miller, Mortazavi studied the chemical 

composition of children’s and adults’ fingerprints 

using infrared microspectroscopy at beamline 

U10B. The difference between the chemical makeups should explain why the fingerprints of children 

disappear before those of adults. Mortazavi is a 

junior at Bellport High School.

Saka Okyere-Asiedu and Christopher Dixon 

worked under the mentorship of Delaware Materials Science Professor Robert Opila and NSLS 

staff scientist Steve Hulbert at the NSLS as part 

of the Faculty and Student Team (FaST) program. 

They used ultraviolet photoelectron spectroscopy 

at beamline U4A to determine how the chemical 

bonding of materials 

affects the electrical performance 

of materials. They 

investigated how 

the valence bands 

of silicon determine 

the conductivity of 

photovoltaics. The 

team also used the 

system to test for 

electrical properties 

of material with a 

high dielectric constant for application 

in Si circuits. Their 

results will help maximize the efficiency 

of solar cells and help determine which metal 

and dielectric are used in the future generation of 

very highly integrated circuits. Okyere-Asiedu and 

Dixon are undergraduate students at the University of Delaware.

Dylan Roden participated in the Science Undergraduate Laboratory Internship (SULI) program 

at the NSLS under Lisa Miller. Dylan worked with 

photodynamic therapy treatment of human melanoma cells in an effort to discover an effective 

treatment for the disease. He also uses Fourier 

Transform Infrared (FTIR) analysis to assess 

chemical changes within the melanoma cells as a 

function of treatment method. Roden is an undergraduate student at the Massachusetts Institute of 

Technology pursuing a bachelor’s degree in biological engineering 

with hopes to continue his education 

in medical school.

Yusuf Siddiqui 

worked with Syed 

Khalid and Vivian 

Stojanoff as part of 

the Community Summer Science Pro-
3-28

Weisha Zhu

Yusuf Siddiqui

Rodney Snow

NSLS, NSLS-II STAFF CELEBRATE AT PICNIC AND SERVICE AWARDS

September 21, 2006

Pushed back a week because of rain, the 2006 

Light Source Directorate Picnic took place on 

September 21 with beautiful weather. For the first 

time, the annual end-of-year celebration was held 

for both NSLS and NSLS-II employees, hosted by 

NSLS Chair Chi-Chang Kao and Steve Dierker, 

Associate Laboratory Director for Light Sources. 

In addition to the vast amounts of meat, cheese, 

pasta salads and candy, Kao presented a cake to 

celebrate 1,000 injury-free days at the NSLS. The 

cake was cut – carefully – by Jim Tarpinian, Assistant Laboratory Director for Environment, Safety, 

Health and Quality, after he congratulated employees on the significant safety milestone.

Service Awards

Michael Caruso, Richard Freudenberg, Richard 

Heese and Pooran (Boyzie) Singh were honored 

for 25 years of service at Brookhaven Lab, and 

20-year awards went to Scott Buda, Shuchen 

Kate Feng, and Michael Fulkerson. In the 10-year 

category were G. Lawrence Carr, Elaine DiMasi, 

Joan Marshall, Cheo Teng, and John Vaughn III. 

And although it isn’t an officially recognized BNL 

milestone, John Dabrowski was acknowledged for 

an impressive 45 years of service at the Lab.

NSLS and NSLS-II staff enjoy the food at the annual picnic.

gram at the NSLS. 

Siddiqui searched 

for the chemical 

composition of the 

active site of ferritin 

– a protein used in 

anemia prevention 

and early haemochromatosis detection. Ferritin contains a hollow shell 

that can contain a 

significant amount of iron and is therefore of great 

use to doctors treating iron deficiency disorders. 

Small amounts of cadmium, a toxic transition 

metal found to be in ferritin, could shed light on 

the plausibility of ferritin usage as a medical treatment, therefore contributing to further research 

into new treatments for iron deficiency disorders. 

For these experiments Siddiqui used extended 

x-ray absorption fine structure spectroscopy (EXAFS). Siddiqui said he hopes that the work done 

during his internship will contribute to expand general scientific knowledge. He is a junior at Boston 

University Academy.

Rodney Snow 

worked with Peter 

Siddons at the NSLS 

as a GEM National 

Consortium intern. 

Snow was engaged 

with many assignments simultaneously, but his main 

project was assembling, testing, and 

characterizing a spin 

polarization detection chamber. This chamber will 

be used to detect the ballistic transport of low-energy electrons through ultra-thin films with a thickness on the order of 20 to 100 nm. This study can 

ultimately realize a new generation of electronics 

called spin-based electronics. Snow is a secondyear graduate student at Michigan Technological 

University.

Weisha Zhu worked with Babu Manjasetty of the 

Case Center for Synchrotron Biosciences as a Science Undergraduate Laboratory Intern. Their project studied the complex structures of Escherichia 

coli L-Arabinose isomerse, an enzyme 

with potential use for 

tagatose (low-calorie natural sugar) 

production. By 

co-crystallizing the 

enzyme in complex 

with co-factor metal 

ions and candidate 

substrates/inhibitors, 

they were able to understand structure-function 

interactions important for the enzyme’s biological 

mechanism. Crystals of different complexes were 

grown and several diffraction datasets were collected at NSLS-X4C and X6A beamlines. Comparison studies between the native and complex 

forms of crystal structures will provide valuable 

biological information in designing new pathways 

to increase tagatose production. Zhu is an undergraduate student at Cornell University.

— Kendra Snyder
YEAR IN REVIEW

3-29

Spotlight Awards

The Spotlight awards are tributes to NSLS staff 

members who have shown exceptional dedication 

to their jobs during the year. This year, the winners were:

Walter DeBoer: The 

vendor contracted 

to build the X25 

undulator could not 

deliver the completed device on 

schedule, so the 

burden of completing and testing the 

device fell onto the 

NSLS technical staff. 

From August 2005 

through February 

2006, DeBoer took 

on a great amount 

of that responsibility, traveling twice to Lansing, NY, to assemble, 

bake, and vacuum-test the undulator. Working 

unpaid hours on long days and weekends both in 

Lansing and at BNL, DeBoer is a big reason why 

the undulator was installed successfully during the 

winter shutdown. 

David Harder: The original schedule for X25 

undulator development included at least one and 

a half months for magnetic measurement and 

shimming of the device. However, the delivery was 

delayed because of the vendor, and as a result, 

less than two weeks were left to spend on these 

steps. Harder, whose careful examination of the 

Hall probe scanning system enabled a precise 

characterization of the undulator’s magnetic field, 

spent seven days a week for two months on the 

project to compensate for the lost time. 

Mike Lehecka: 

Lehecka also worked 

seven days a week 

for two months to 

make up for lost 

time on the magnetic 

measurement and 

shimming aspect of 

the X25 undulator 

installation. Lehecka, who runs the 

pulsed wire bench 

for the NSLS magnetic measurement 

laboratory, does 

both mechanical and 

intricate vacuumrelated work. He is an expert in setting up pulsed 

wire measurement systems, which vendors don’t 

have the capability to do. Without his effort, the 

X-25 undulator measurements couldn’t have been 

finished in such a short amount of time. 

Ed Losee: In the effort to produce superconducting undulators for the NSLS and NSLS-II, Losee 

undertook the responsibility for prototype undulator magnet fabrication and assembly. The process 

requires special skills and equipment, and such 

devices had never been built in the United States. 

With minimal direction, Losee taught himself how 

to use a complex turntable device to fabricate the 

magnet, and using it, he then produced several 

prototypes. The NSLS can now produce and test 

superconducting magnets and other complex 

components in-house with Losee’s assistance and 

skills. Losee also provided significant support on 

the X17 superconducting wiggler during the winter 

2005-06 shutdown.

Philip Marino and Tom McDonald: Marino and 

McDonald won this shared Spotlight Award for 

upgrading the NSLS beamline safety checklists, 

which were old, difficult to use, and didn’t have 

a system in place to assure periodic review and 

update. Beginning in 2003, Marino and McDonald 

approached each beamline to identify the critical components, meeting with the local contacts 

to assure minimal interruption to operation. They 

then made and connected all the needed labels 

and photos and assembled the new checklists in a 

standard format. The NSLS relies on this system 

for radiological safety, and Marino and McDonald 

spent considerable effort and time completing the 

upgrade. 

Paul Montanez: Montanez served as an engineer, 

supervisor and coordinator during the relocation 

of beamlines X9A and X9B to X3. The series of 

moves was planned and coordinated in a way 

that needed no additional shutdown time for the 

machine and minimized the total disruption to 

the X9 program. The originally proposed spring 

shutdown schedule was cut in half because Montanez figured out ways to do more preparation and 

minimize work. He put in extra hours to ensure this 

relocation was successful while still completing 

projects with beamline X25 and NSLS-II. 

Charlie Nielson and Wayne Rambo: The NSLS 

Controls and Diagnostics groups were tasked with 

integrating the X25 MGU control system, designed 

by an outside contractor, into the NSLS Controls 

System. At the end of 2005 and early part of 2006, 

Rambo and Nielson both put in overtime hours and 

extraordinary effort to accomplish the system pretesting, installation and commissioning within the 

tight schedule. Both men made trips to Advanced 

Design Consulting in Lansing, NY, to check on the 

project’s progress and work around problems as 

they came up during testing and commissioning. 

Mihai Radulescu: The bellows on the VUV-IR 

injection shutter failed during operations in July 

NSLS Chair Chi-Chang Kao

ALD for Light Sources Steve 

Dierker
3-30

2006. A previous failure of this same assembly 

required complete removal and rebuilding of the 

shutter, and fortunately, the about two-week repair 

process happened near a major maintenance 

time. This recent instance, however, would have 

resulted in major downtime if it weren’t thanks to 

Radulescu. He developed a method for removing the actuator while leaving the shutter block in 

place. This whole process was completed in less 

than 60 hours from the time it was discovered.

— Kendra Snyder

CHI-CHANG KAO NAMED CHAIR OF

THE NSLS

October 1, 2006

Chi-Chang Kao, a physicist and leader in synchrotron light research, was named Chair of the NSLS 

Department, effective October 1. Kao served as 

interim NSLS Chair since mid-January 2006, after 

Steve Dierker 

stepped down 

to lead the 

development of 

the NSLS-II. 

“Chi-Chang is 

an internationally recognized 

scientist with 

a remarkable talent for 

bringing people 

together and 

growing scientific programs,” 

said Dierker, 

who is the current Associate 

Laboratory Director for Light Sources. “I can think 

of no better choice than Chi-Chang to lead the 

NSLS forward.”

As Interim Chair, Kao produced a five-year plan 

for the future development of the NSLS. With 

input from the user community, NSLS staff, and 

Brookhaven researchers, the plan identifies a 

number of exciting scientific opportunities, improvements needed for better accelerator operation, and upgrades for beamlines, detectors, and 

infrastructure. As the new NSLS Chair, Kao wants 

to ensure that these initiatives are implemented.

“The next five years will be a very important time 

for the NSLS, because if NSLS-II gets approval, 

we will transition into the new light source at the 

end of that period,” Kao said. “We have developed 

a very aggressive strategic plan that will help 

keep scientific productivity up and also grow new 

scientific communities at the NSLS. In particular, we want to grow in a way that will allow us to 

smoothly transition the user scientific program to 

the NSLS-II.”

Additionally, Kao wants to encourage closer interaction between the NSLS, Brookhaven’s research 

departments, industry, and universities, as well as 

emphasize research related to nanoscience and 

energy. “There are many ways that synchrotron research can make significant contributions to solve 

the energy problems the world is facing today,” 

Kao said. “Using light, we can study and make 

advances in the fields of catalysis, energy storage, 

fuel cells, and solar energy.” 

Kao earned a B.S. degree in chemical engineering in 1980 from National Taiwan University and 

a Ph.D in chemical engineering from Cornell 

University in 1988. Shortly after, he joined BNL as 

a postdoctoral research assistant at the NSLS. His 

research focuses on the development of new experimental techniques using synchrotron radiation, 

and their applications to condensed matter physics 

and material sciences. 

He received tenure as a Brookhaven physicist 

in 1997 and served as the NSLS high-energy 

program coordinator from 1998 to 2001. He was 

promoted to senior physicist in 2001 and was 

named NSLS Deputy Chairman in 2005. Kao also 

is the Associate Chairman for User Science and 

an adjunct professor in the Department of Physics and Astronomy at Stony Brook University. He 

is a member of the American Physical Society and 

the American Association for the Advancement of 

Science.

— Kendra Snyder

Chi-Chang Kao

UPDATE ON THE X27A MICRO- SPECTROSCOPY FACILITY BEAMLINE

October 1, 2006

In 2006, NSLS hard x-ray micro-spectroscopy 

facility beamline X27A became fully operational. A 

smooth transition from commissioning to operations during the fall of 2005 provided immediate 

implementation of a wide and diverse research 

program involving an extensive range of institutions: Stony Brook University, Rutgers University, 

BNL Environmental Sciences Department, Miami 

University, Institute of Nuclear Physics (PAN) 

Poland, University of Western Ontario, Natural 

Resources Canada and IMEC of Belgium. Ongoing 

research areas include the study of manganese 

and arsenic speciation/distribution in a range of 

environmental sensitive samples; the nature of 
YEAR IN REVIEW

3-31

Figure 2. Ta L2 absorption-edge XANES on Ta2N (5 

nm)/Ta (20 nm) blanket fi lm and the Ta2N barrier on a 

Cu interconnect patterned sample, both on and off the 

interconnect lines.

Tantalum L2 Edge XANES on A14, A11 Samples

Energy [keV]

Normalized Ta Lβ 1 Fluorescence

Figure 1. X-ray fl uorescence line scans across 10 um-wide 

copper interconnects spaced at (A) 40 um and (B) 90 um. 

(C) Cu Kd fl uorescence image of a pad structure.

Sample Height [μm] X Distance [mm]

Cu Kα Fluorescence

Y Distance [mm] Y Distance [mm] Sample Height [μm]

Line scan on #5, E=11.142 keV (white-line peak)

Normalized Ta Lβ1 Fluorescence Counts (10 secs)

Line scan on #5, W=10 μm, S=40 μm, E=9.5 keV

Normalized Cu Kα Fluorescence Counts (3 secs)

Sample Height [μm]

Line scan on Line scan on A9, #6, W=10 A9, #6, W=10 μm, S=90 μm, E=9.5 keV

Normalized Cu Kα Fluorescence Counts (3 secs)

B)

A)

C)

1.5x104

1.0x104

5.0x103

1.5x105

1.0x105

5.0x104

2.0x105

1.8x105

1.6x105

1.4x105

1.2x105

1.0x105

0 -50 0 50 100

0 50 100

titanium incorporation through applied creams 

into human skin layers; plutonium and uranium 

distribution/speciation in contaminated soils; 

polarization dependent thorium EXAFS measurements on small apatite single-crystals; understanding strontium incorporation in osteoporotic 

bone; and determining trace-metal distribution in 

diseased brain tissue. The success of implementing these research areas, and the high-quality 

data being collected at this facility, is largely due 

to the good stability of the NSLS x-ray ring, which 

is especially important for microprobe beamlines. 

An example of an area of research initiated at 

X27A is the investigation of tantalum and tungsten 

thin-film diffusion barriers that are used in copper 

interconnect technology. Using the x-ray microbeam, buried thin-film layers beneath copper are 

investigated using fluorescence x-ray absorption 

spectroscopy. The ability to characterize these 

films, which are often amorphous and cannot be 

studied using x-ray micro-diffraction, is an important area of applied research within the semiconductor industry. Currently, preliminary experiments 

on thin-film interconnect test structures have been 

conducted and analyzed, and these encouraging results have initialized the fabrication of 

‘real’ systems for future in-situ measurements. 

Preliminary measurements on passivated 10 μm 

wide, 120 nm thick Cu interconnects, separated 

by 40 μm and 90 μm ‘field’ regions, and with 

a 4 nm thin ALD Ta3N4 barrier layer have been 

performed. Cu Kα fluorescence recorded at an 

incident x-ray energy of 9.5 keV, and Ta Lβ1 fluorescence recorded at the peak of the Ta whiteline at ~11.142 keV, are shown in Figure 1. The 

Ta L2 XANES on a PVD Ta2N (5 nm)/Ta (20 nm) 

blanket film and a 4nm ALD Ta3N4 barrier used in 

a copper interconnect test structure are shown in 

Figure 2. As can be seen, the nitrogen content 

within the Ta 2N barriers is clearly evidenced by 

the spectral signature of the near-edge region 

and the shift in the absorption edge towards 

higher x-ray energies, compared to the Ta2N (5 

nm)/Ta(20 nm) blanket film, which is of predominantly Ta character.

— James M. Ablett

RICHARD BISCARDI WINS SITEWIDE

SAFETY STEWARD AWARD

October 16, 2006

NSLS chief electrical engineer Richard Biscardi 

was one of four BNL employees to win a Sitewide 

Safety Steward (S3) Award as part of a new employee recognition program for safety awareness.

The S3 program recognizes outstanding awareness and implementation of health and safety 

improvements and corrective actions. Biscardi was 

nominated for the award based on his initiative in 

reducing electrical hazards, an important area of 

risk for the NSLS. 

Erik Johnson, Biscardi’s supervisor, noted that his 

job requires him to be more attuned to electrical 

hazards than most staff members, but he has built 

upon his heightened awareness and shared his 

expertise broadly throughout BNL, primarily as a 

member of the Lab’s electrical safety committee. 

“His work has led to the identification of hazards 

and non-compliances as well as possible methodologies for their mitigation that are now being employed across the Laboratory,” Johnson said. “He 

has truly adopted a stewardship role in promoting 

electrical safety for the NSLS and BNL.”

Of particular note is his effort in providing pathways to compliance with the requirements of two 

safety codes: National Fire Protection Association (NFPA) 70E, which describes standards for 

electrical safety in the workplace; and 10CFR851, 

a worker health and safety program.
3-32

On very short notice, Biscardi worked with staff 

across the department to develop a protocol 

for the NSLS to come into compliance with the 

personal protection equipment requirements of 

70E. He also established an equipment inspection program to assure the electrical equipment 

used by staff, vendors, and visitors either meets 

Nationally Recognized Testing Laboratory (NRTL) 

requirements or has been properly inspected and 

tagged. This program is being emulated across 

the Laboratory.

Biscardi also formed a team to investigate 

equipment compliance with the requirements of 

10CFR851. This working group’s findings and 

recommendations are at the heart of the NSLS 

program to come into compliance with 10CFR851.

Biscardi, along with the other S3 award winners, 

runner-ups, and nominees, was recognized in a 

BNL ceremony on October 16.

— Kendra Snyder

At the presentation of the Sitewide Safety Stewardship 

(S3) Award, the winners were: (from left) Richard Biscardi, 

National Synchrotron Light Source Department; Cheryl 

Conrad, Energy Sciences & Technology Department; 

and (right) Richard Scheidet, Plant Engineering Division. 

The fourth award winner, Jeff Gillow, Environmental 

Sciences Department, was not present. A team award was 

also presented to: (third from left) Adele Billups, Laura 

Thompson, and Peter Guida, all of the Medical Department.

418TH BROOKHAVEN LECTURE

‘BRIGHT PHOTON BEAMS: DEVELOPING

NEW LIGHT SOURCES’

October 18, 2006

A world-leading brightness of intense x-ray light 

is needed for scientists to make the next generation of discoveries in a wide range of disciplines, 

from structural biology to nanoscience, from the 

structure and dynamics of disordered materials to 

Timur Shaftan

properties of materials under extreme conditions 

— and more.

To provide this bright light, BNL proposed and 

the DOE approved the National Synchrotron Light 

Source II (NSLS-II), a state-of-the-art medium 

energy machine designed to produce x-rays more 

than 10,000 times brighter than those produced at 

the current NSLS. These powerful beams and the 

advanced instrumentation at NSLS-II will be able 

to probe samples of materials in a wide range of 

sizes and conditions, giving information that could 

lead to advances, for example, in clean and affordable energy, molecular electronics, and the selfassembly of nanomaterials into useful devices.

Developing the machine and its instrumentation 

is not easy, however. Achieving and maintaining 

the needed level of intensity will involve tightly 

focusing the electron beam, providing the optimally matched insertion devices, and achieving 

and maintaining a high electron current. At BNL, 

research and development are ongoing on these 

and other challenges.

Timur Shaftan, a 

scientist in the NSLS 

Department, gave the 

418th Brookhaven 

Lecture on this work 

on October 18, 2006 

during his talk “Bright 

Photon Beams: Developing New Light 

Sources.”

In his talk, Shaftan 

discussed various sub-systems of 

NSLS-II and the 

requirements and key 

elements of their design. He also explained how 

scientists at the NSLS developed a prototype of 

a light source of a different kind — a short-wavelength free electron laser — and reviewed the development of new concepts in the physics of bright 

electron beams in this facility.

Timur Shaftan, who earned his Ph.D. in physics at 

the Budker Institute of Nuclear Physics, Russia, in 

1997, joined BNL in February 2000. Since 2003, 

he has been involved in many areas of the NSLS-II 

project, including lattice design, insertion devices, 

and the design of the injection system. He currently leads the group working on Conceptual 

Design of the NSLS-II injection system. Involved 

in collaborations with a few accelerator facilities 

worldwide, he also serves as a reviewer in Nuclear 

Instruments and Methods in Physics Research 

journal.

— Liz Seubert and Kendra Snyder
YEAR IN REVIEW

3-33

BNL WINS R&D 100 AWARD FOR

X-RAY FOCUSING DEVICE

October 19, 2006

Brookhaven National Laboratory has won a 2006 

R&D 100 award for developing the first device 

able to focus a large spread of high-energy 

x-rays. The device, called a Sagittal Focusing 

Laue Monochromator, could be used in about 100 

beamline facilities around the world to conduct 

scientific research in physics, biology, nanotechnology, and numerous other fields. 

R&D 100 Awards are given annually by R&D Magazine to the top 100 technological achievements 

of the year. Typically, these are innovations that 

transform basic science into useful products. The 

awards were presented in Chicago on October 19. 

NSLS physicist Zhong Zhong led the development 

of the focusing device with help from BNL scientists Chi-Chang Kao, Peter Siddons, Hui Zhong, 

Jonathan Hanson, Steven Hulbert, Dean Connor 

and Christopher Parham; BNL technicians Anthony 

Lenhard, Shu Cheung, and Richard Greene; and 

former BNL scientist Jerome Hastings, who is now 

working at the Stanford Linear Accelerator Center. 

“I congratulate the researchers who have won this 

award, which highlights the power and promise 

of DOE’s investments in science and technology,” Secretary of Energy Samuel W. Bodman 

said about the BNL team. “Through the efforts of 

dedicated and innovative scientists and engineers 

at our national laboratories, DOE is helping to enhance our nation’s energy, economic and national 

security.”

As x-rays are produced at light sources, they 

spread out, or diverge. X-rays produced by a 

beamline with a 5 milliradian divergence, for 

example, will spread to 5 millimeters (mm) by the 

On the left, from front to back: Jonathan Hanson, Steven 

Hulbert, Shu Cheung, Anthony Lenhard, and Zhong Zhong. 

On the right, from front to back: Peter Siddons, Hui Zhong, 

Chi-Chang Kao, Dean Connor, Christopher Parham, and 

Richard Greene. Not pictured: Jerome Hastings.

time they are 1 meter away from their source, and 

to 50 mm when 10 meters away. This is a problem 

for light source scientists, who want the highest 

possible x-ray flux on a small spot, which requires 

a well-focused beam.

Previous x-ray focusing technologies relied on mirror-like surface reflections, but this required large 

surfaces and caused technical difficulties in error 

control and limitations on the energy of the x-rays 

that could be focused. The device developed by 

Zhong’s team, however, doesn’t rely on a crystal 

surface to reflect the beam. Instead, it sends the 

x-rays directly through a set of silicon Laue crystals, named for German physicist Max von Laue. 

The result is a 1,000-fold increase in beam intensity, as well as high-energy resolution, reduced 

costs and ease of operation, Zhong said.

The device consists of two thin bent crystals 

mounted on a slide, with the first one diffracting 

upward and the second one diffracting downward 

to focus the beam horizontally. It is the first device 

that can focus a large divergence of high-energy 

x-rays, handling a beamline with a divergence as 

great as 20 milliradian.

“This is a very elegant solution to an existing 

problem,” said Zhong, who started working on the 

project in 2001. The first version of the device is 

installed at the NSLS beamline X17B1 and is gaining interest from members of other Brookhaven 

beamlines and scientists at light sources around 

the world. Development of the award-winning device was supported by the Office of Basic Energy 

Sciences within the U.S. Department of Energy’s 

Office of Science. 

— Kendra Snyder

SHORT COURSE: XAFS STUDIES OF

NANOCATALYSIS AND CHEMICAL

TRANSFORMATIONS

October 19-21, 2006

The short course in x-ray absorption fine-structure 

(XAFS) analysis, emphasizing problem-solving 

methods in typical catalysis applications, was offered on October 19-21 at the NSLS. It continued 

the annual NSLS tradition of gathering a group 

of scientists, active in the field, who share their 

expertise with those interested in learning about 

the possible use of XAFS in their research as well 

as with those who are relatively advanced. The latest two courses were organized and co-sponsored 

by the U.S. Department of Energy’s Synchrotron 

Catalysis Consortium (SCC) and the NSLS. The 

theme of the latest course was tailored to users 
3-34

Participants in the XAFS Studies of Nanocatalysis and 

Chemical Transformations Short Course

NSLS USERS RECOGNIZED

October 25, 2006

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 

2006 awards:

2006 Alvin Van Valkenburg award

NSLS user Li Li was the 

2006 recipient of the Alvin 

Van Valkenburg award. 

This international award is 

given every second year 

in the name of physicist 

Alvin Van Valkenburg, 

co-inventor of the diamond anvil cell, to honor 

a young scientist whose 

research involves high 

pressure.

Li received her Ph.D. in geophysics from Stony 

Brook University in 2003 and is an adjunct research assistant professor at the Stony Brook 

Mineral Physics Institute. She started using beamline X17B2 as a graduate student in 1998 to study 

the rheology of minerals at high pressures and 

temperatures. 

Rheological properties of materials at high pressure are valuable in many scientific fields, including geoscience, which is Li’s concentration. 

Geoscientists obtain insight about the dynamics of 

the earth by deforming minerals at mantle conditions. Li probes these properties in-situ using 

synchrotron x-rays. She also performs theoretical 

calculations in collaboration with the University 

College London.

The Van Valkenburg award was presented at the 

2006 High Pressure Gordon Conference in Biddeford, Maine, on June 29, 2006.

Li Li

of the SCC who have recently collected data in 

systems of relevance for catalysis applications: 

nanoparticles- mono- and bimetallic (including 

core-shell), supported on different surfaces, studied ex situ or in situ. The latter included real-time 

reactions studied at the SCC facilities by XAFS. 

The course was organized by Anatoly Frenkel 

(Yeshiva University), Syed Khalid (NSLS), and 

Faisal Alamgir (NIST). The format of the course 

consisted of lectures in the morning and data 

analysis sessions in the afternoon. Most lectures 

were designed as tutorials on different aspects of 

XAFS analysis, such as the “Theory of XANES” 

and “Theory of EXAFS” (Josh Kas, University of 

Washington), advanced data analysis methods 

(Principal Component Analysis, by Stephen Wasserman, SGX Pharmaceuticals), and the basics of 

EXAFS data processing and fitting (Scott Calvin, 

Sarah Lawrence College). In addition, lecture topics included the “Concepts of advanced EXAFS 

data modeling” (Anatoly Frenkel), “In situ XAFS 

studies of fuel cell catalysts” (Carlo Segre, IIT), 

“XAFS studies of battery materials” (Faisal Alamgir), and “New opportunities with Quick XAFS at 

the NSLS” (Syed Khalid). 

There were 26 registered participants from academia, industry, and national laboratories, as 

well as 5-10 graduate students from Stony Brook 

University and Yeshiva University who audited the 

course. The lecturers were also the data analysis 

session instructors. During the data analysis session, participants were trained in using the XAFS 

analysis packages IFEFFIT (authors: M. Newville 

and B. Ravel), FEFF8 (authors: J. Rehr, et al) and 

PCA software (author: S. Wasserman). 

Most of the course participants brought their 

own data they recently collected at the NSLS or 

other synchrotrons. The analysis sessions were 

organized by matching instructors to the problems. Instructors rotated between sessions, thus 

sharing their expertise with more than one group 

of participants. For example, all groups benefited 

from Steve Wasserman’s tutorials on the use of 

his Principal Component Analysis program and 

Josh Kas’ tutorials of modeling in-situ XANES 

data in nanoparticles with FEFF8. Scott Calvin, 

Faisal Alamgir, and Carlo Segre advised all those 

interested in adaptation of IFEFFIT programs to 

advanced modeling methods. Anatoly Frenkel 

helped those studying monometallic and bimetallic, including core/shell, nanoparticles.

All course members thoroughly enjoyed friendly 

and professional logistical support by the NSLS 

Users Administration Office: Gretchen Cisco, Liz 

Flynn, Kathy Nasta, and Mercy Baez.

— Anatoly Frenkel
YEAR IN REVIEW

3-35

2005 Hans-Jürgen Engell Prize

The International Society 

of Electrochemistry (ISE) 

awarded the 2005 HansJürgen Engell Prize to 

NSLS user Dev Chidambaram in recognition of 

his scientific work and 

publications in the field of 

electrochemistry. 

The ISE is a professional 

organization for electrochemists, with 1,400 

members from more than 60 countries. Chidambaram received his prize, consisting of a plaque 

and 500 euros, at the organization’s 2006 annual 

meeting, held in Edinburgh, Scotland. Chidambaram delivered a keynote lecture on September 

1, 2006.

Chidambaram joined Brookhaven Lab in 2004 as 

a Goldhaber Distinguished Fellow. His research 

focuses on protecting metals from corrosion and 

remediating toxic metals and radionuclides in the 

environment. In a project funded by the U.S. Air 

Force, Chidambaram found that molybdenum may 

be a viable replacement for chromate coatings, 

which are used to coat metals to prevent corrosion 

but are carcinogenic. Later, this result was used 

as a starting point for a program funded by the 

U.S. Army. Working with a team from Stony Brook 

University, Chidambaram has developed a new 

molybdate-based coating to prevent the deterioration of depleted uranium. Both programs extensively used the analytical techniques at the NSLS 

to study the materials.

Best Paper Award at 2006 EPCOS 

NSLS users Simone Raoux and Jean JordanSweet won one of three "best paper" awards given 

annually at the European Symposium on Phase 

Change and Ovonic Science (EPCOS) for work 

done in part at NSLS beamline X20C.

The award was presented in May at the 2006 EPCOS in Grenoble, France, for the paper “Scaling 

properties of phase change nanostructures and 

thin films.”

Dev Chidambaram

Using time-resolved x-ray diffraction (XRD), the 

researchers studied the thickness and size-dependent behavior of ultra-thin films and nanostructures, which are important for their applications 

in solid-state memory devices that could one 

day replace digital camera flash cards. The goal, 

Raoux said, is to find a small-scale phase change 

material that would allow for faster and cheaper 

technology.

Raoux, from the IBM Almaden Research Center, 

and Jordan-Sweet, from the IBM T.J. Watson 

Research Center, started working on the project at 

the NSLS more than two years ago. Other companies involved in the research included Infineon 

Technologies and Macronix International Co.

2006 Gregori Aminoff prize

Stephen Harrison, a 

former NSLS user, was 

awarded the 2006 Gregori 

Aminoff Prize in Crystallography by the Royal 

Swedish Academy of Sciences. Harrison received 

the prestigious award 

along with Oxford University professor David 

Stuart, “for their remarkable contributions in virus 

crystallography.”

The Aminoff prize is given out annually to scientists or research groups who have made a major contribution to the field of crystallography. It 

consists of a gold medal, a diploma, and a cash 

award, and is named after Swedish crystallographer Gregori Aminoff, the first scientist to introduce crystallography to Sweden. 

Harrison was a regular NSLS user from the mid 

80s through the end of the 90s. He worked mainly 

on beamline X25, studying the structure of DNA 

protein complexes, in particular, those that control 

the process of transcription. He also served on the 

NSLS Science Advisory Committee, which advises 

the NSLS Chair and the Associate Laboratory 

Director for Light Sources on scientific, technical, 

and policy issues related to the optimization of 

the scientific productivity of the NSLS. Harrison, 

a Harvard Medical School professor, used the 

Cornell High Energy Synchrotron Source (CHESS) 

to conduct most of his research in virus crystallography. 

The prize was presented at the Royal Swedish 

Academy of Sciences in Stockholm on June 7, 

2006. A two-day symposium illuminating the latest 

developments and results in the field of structural 

work on viruses was organized to honor the prizewinners.

— Kendra Snyder

 Simone Raoux Jean Jordan-Sweet

Stephen Harrison
3-36

NANOSCIENCE SAFETY HIGHLIGHTED

December 1, 2006

Nanoscience safety requirements at the NSLS 

tightened in 2006, in an effort to ensure that there 

are no harmful health effects from the study and 

handling of nanomaterials. 

The properties of nanoscale materials are known 

to differ from those observed for the same materials in bulk or even microscale configuration, and 

those differences result in uncertainty about the 

potential health effects and environmental concerns these materials could present.

Studies are showing that nanoscale particulates 

can pass through intact skin, are more likely to 

reach the air exchange portion of the lungs when 

inhaled, and can migrate in the body through 

compartments, along nerve pathways, and through 

epithelial barriers. The acute and chronic effects of exposure are not yet defined and, until 

researchers are able to develop a technical basis 

for exposure standards and for assessment of the 

risks presented, nanomaterial work conducted 

at Brookhaven National Laboratory must include 

conservative controls. 

The U.S. Department of Energy (DOE) and BNL 

policy is to use these materials with care and to 

minimize personnel exposures and environmental 

releases. Environmental, Safety and Health (ESH) 

staff working at each of the five DOE nanocenters developed a set of nanoscience safe work 

practices that is posted on the BNL Standards 

Based Management System (SBMS) website: 

https://sbms.bnl.gov/sbmsearch/subjarea/105/

3836d011.pdf. Everyone working with these materials is expected to know and meet the requirements outlined in that document.

The work practices apply to all nanomaterial handling, but focus on control of "free" nano-particulate work as that presents greater risk of exposure 

or release. Included are requirements for working 

in hoods, encapsulating samples, scrubbing gasses that flow over particulates, labeling, transport 

packaging, and waste handling. 

— Andrew Ackerman

CHI-CHANG KAO AMONG FIVE

NAMED APS FELLOWS

December 28, 2006

Five scientists at BNL – Tim Hallman, Chi-Chang 

Kao, Dmitri Kharzeev, William Morse, and Yimei 

Zhu – were named Fellows of the American Physical Society (APS), a professional organization 

with more than 45,000 members. Election to APS 

Fellowship is limited to no more than one half of 

one percent of its membership in a given year, 

and election for this honor indicates recognition 

by scientific peers for outstanding contributions to 

physics. The Brookhaven scientists were among 

212 Fellows elected in 2006. 

Kao, Chair of the NSLS, was recognized “For his 

many contributions to resonant elastic and inelastic x-ray scattering techniques and their application to materials physics.” During his research at 

the NSLS, Kao has developed new x-ray scattering techniques to study the electronic and magnetic properties of magnetic and strongly correlated 

materials. These techniques have led to better 

understanding of the Earth’s interior and materials 

properties under extreme conditions. 

Kao earned his Ph.D. in chemical engineering 

from Cornell University in 1988. Shortly after, he 

joined BNL as a postdoctoral research assistant 

at the NSLS. He was promoted to senior physicist 

in 2001. Kao is also an adjunct professor in the 

Department of Physics and Astronomy at Stony 

Brook University.

— Kendra Snyder

Clockwise from left, Dmitri Kharzeev, Tim Hallman, 

William Morse, Yimei Zhu, and Chi-Chang Kao
YEAR IN REVIEW

3-37

2006 NSLS TOURS

1/4/2006 Karen Agostisi, Congressman Steve Israel's Washington Legislative Aide 

1/24/2006 Alain E. Kaloyeros, Executive Dir., NYS Center for Advanced Technology, Albany NanoTech

2/3/2006 New York Institute of Technology, IEEE Club

2/23/2006 New York City Biology Teachers Association

2/28/2006 Suffolk County Economic Development Agency

3/1/2006 Retired U.S. Army General Barry McCaffrey, President of B.R. McCaffrey Associates, LLC

3/2/2006 The National Institute for Occupational Safety and Health Data Capture Team

3/8/2006 Communications Trust Advisory Panel Committee

3/14/2006 Polytechnic University of Brooklyn

3/15/2006 American Society of Metals/Materials-Long Island Chapter

3/17/2006 City College of New York

3/21/2006 John J. Grossenbacher, Director of Idaho National Laboratory

3/22/2006 Charterhouse School

3/24/2006 York College of CUNY

3/24/2006 National Research Council of Canada, Infotonics of Rochester and Javelin Assoc. Directors

3/27/2006 Stony Brook University - Graduate Students

3/28/2006 Wildlife Genetics Conference

3/29/2006 University of Montenegro and State Department 

3/30/2006 Stars Program and Japanese Exchange Team

3/31/2006 Smithtown Science Teachers - Staff Development Day

4/11/2006 ASHRAE: American Society of Heating, Refrigeration and Air-Conditioning Engineers

4/18/2006 Renaissance Technologies Corporation

4/28/2006 Muhlenberg College 

4/28/2006 Nassau Community College - Radiation Therapy Program

5/4/2006 Queens College of CUNY

5/16/2006 Department of Energy Budget Offi cers

5/18/2006 Brigham Young University 

6/2/2006 Stony Brook University - Summer Undergraduate Program

6/2/2006 U.S. Secretary of Energy Samuel Bodman

6/19/2006 Nuclear Chemistry Summer School

6/22/2006 Sheryl Silberman, Special Assistant to the Director, Idaho National Laboratory

7/11/2006 Columbia University REU Students

7/12/2006 Dr. Mitchell Shapiro - Overview of BNL 

7/13/2006 Laser Safety Offi cer Conference

7/14/2006 Morgan State University

7/14/2006 Queens Hall of Science Ham Radio Club

7/14/2006 Southern University of New Orleans
3-38

2006 NSLS TOURS

7/20/2006 Columbia University - Summer Chemistry Program

7/27/2006 Jose Antonio Brum, Brazilian Synchrotron Light Source Director

7/27/2006 Stony Brook University - REU Chemistry Program

7/31/2006 Stony Brook University - REU Physics Program

8/7/2006 Lauren Hill, Long Island Alliance

8/9/2006 Research Library General Laboratory Tour

8/9/2006 Stony Brook University - Brookhaven Women in Science

8/10/2006 New York State Business Council's Committee on Education

8/11/2006 Dongwha Kum, Korean Institute of Science & Technology (KIST) President

8/22/2006 Northrop Grumman Corporation

8/24/2006 Long Island Chapter of Oil and Heating Service Managers

8/28/2006 Rocky Point Rotary Club

9/8/2006 John Ryan, State University of New York Chancellor

9/21/2006 Brookhaven Women in Science

9/26/2006 Hofstra University

9/28/2006 New York University Graduate School of Journalism Science and Environmental Reporting 

9/29/2006 Wayne Horsley, Chair of Suffolk County Legislature-Committee for Economic Development, 

 Higher Education & Energy

10/2/2006 University of Palermo

10/11/2006 DOE - Library Operations Working Group

10/12/2006 Battelle Commercialization Managers

10/13/2006 Half Hollow Hills School District 

10/16/2006 BNL ESHQ Directors

10/18/2006 United States Merchant Marine Academy

10/18/2006 Brian Foley, Brookhaven Town Supervisor

10/20/2006 City College of New York 

10/20/2006 Korean Institute of Science and Technology for the Center for Nanomaterial Technology

10/20/2006 Borough of Manhatten Community College

10/24/2006 Hofstra University

10/24/2006 Adelphi University

10/27/2006 Eastport Manorville School District

11/1/2006 Fordham University-Society of Physics Students Club 

11/3/2006 Steven H. Stern, Suffolk County Legislator, 16th District

11/15/2006 Edo Corporation

11/16/2006 Sarah Lawrence University

12/4/2006 Suffolk County Community College

12/8/2006 Suffolk County BOCES Staff Workers
YEAR IN REVIEW

3-39

2006 NSLS SEMINARS

1/11/2006 Interim Controls Upgrade for Measuring Noise and Detecting Glitches in Magnet Power 

Supplies at the APS Storage Ring

Surajit Sarkar, Massachusetts General Hospital

1/13/2006 Control and Noise Immunity for High-Resolution Experiments

Jinyang Liu, University of New Mexico 

1/17/2006 Resonant X-ray Magnetic Scattering from Nanoscale Magnetic Materials

Richard M. Osgood, III, Lincoln Laboratory, Massachusetts Institute of Technology

1/18/2006 Shining Light on the Cause of Alzheimer's Disease

Lisa M. Miller, NSLS-BNL 

1/30/2006 Synchrotrons Helping Solve the Magnetic Oxide Semiconductor Puzzle

Ives U. Idzerda, Montana State University

1/31/2006 Atomic Design and Engineering of Spinel Ferrites for RF and Microwave Device Applications

Vincent Harris, Northeastern University

3/10/2006 Progress in the Development of New Optics for Very High Resolution Inelastic X-ray Scattering 

Spectroscopy.

Yuri Shvyd'ko, Argonne National Laboratory

3/13/2006 Adsorption of Protein GlnB of Herbaspirilum Seropedicae on Silicon Using Spin-Coating 

Technique

Adriana Lubambo, Universidade Federal do Parna, Curitiba, Brazil

3/14/2006 New Insights on the Formation of Bone by Synchrotron X-ray Scattering

Christian Burger, Stony Brook University

3/14/2006 High-Throughput Crystallography for Drug Discovery - In Practice

Gyorgy Snell, Syrrx/Takeda, San Diego

3/21/2006 High-Speed Semiconductor Detectors for the Synchrotron Experiments at LCLS and XFEL

Lothar Strüder, Max-Planck-Institut and University of Siegen, Germany

3/21/2006 Subgrain Size, Planar Defects, and Vacancies from X-ray Line Profi le Analysis

Tamas Ungar, Eötvös University, Hungary

3/28/2006 The Art of Scientifi c Project Management - An LBNL Perspective

Kem Robinson, Lawrence Berkeley National Laboratory

3/28/2006 NSLS-II: Challenges and Opportunities

Steve Dierker, Brookhaven National Laboratory

3/28/2006 An Introduction to X-ray Absorption Spectroscopy in Enviro-, Geo-, and Biosciences

Paul Northrup, Brookhaven National Laboratory

3/29/2006 Superconducting Undulator Development

Kem Robinson, Lawrence Berkeley National Laboratory

4/4/2006 Biological Applications of Bench-top and Synchrotron-based Micro-Computed Tomography: 

PIRL’s Twelve-Year Experience

Steve Jorgensen, Mayo Clinic College of Medicine
3-40

2006 NSLS SEMINARS

4/4/2006 The Generation of Short Electron Bunches and Coherent Synchrotron Radiation in the 

BESSY Storage Ring

Godehard Wuestefeld, BESSY, Germany

4/17/2006 Observation of Surface Layering in a Normal Dielectric Liquid 

Haiding Mo, Northwestern University 

4/20/2006 Imaging Magnetic Nanostructures via Resonant Soft X-ray Spectro Holography

Olav Hellwig, Hitachi Global Storage Technologies

4/20/2006 Interpretation of Complex Images in Coherent X-ray Diffraction

Ian Robinson, University College, London, United Kingdom

4/24/2006 Perspectives in meV Resolved Inelastic X-Ray Scattering

Alfred Baron, Harima RIKEN and SPring-8/JASRI, Japan

4/25/2006 Nonintercepting, Time-resolved Imaging Diagnostics for Multi-GeV Beams

Alex Lumpkin, Argonne National Laboratory

4/26/2006 X-ray Imaging at a 3rd Generation Synchrotron

Qun Shen, Argonne National Laboratory

4/27/2006 Status of High Energy X-ray Microfocusing at the ESRF: Pathways for Nanofocusing 

Anatoly Snigirev, ESRF, France

5/2/2006 Resonant Soft X-ray Scattering and Resonant Soft X-ray Refl ectivity: New Tools for the 

Characterization of Organic Materials

Harald Ade, North Carolina State University

5/4/2006 Calculation of Beam Impedance for Long Tapers and Short Bunches

Gennady Stupakov, SSRL, SLAC

5/19/2006 Si-Ge Thin Film Engineering

J. Burnette, North Carolina State University

5/23/2006 Liquid Crystals in Random Environments

Dennis Liang, Johns Hopkins University

5/31/2006 Multilayer Laue Lenses - a Path Towards Nanometer Focusing of X-rays

Jorg Maser, Argonne National Laboratory

6/8/2006 Current State and Fundamental Limitations of Focusing Hard X-rays with Refractive Optics

Christian Schroer, Institute of Structural Physics Dresden, Germany

6/14/2006 Accelerator Physics Aspects of Crab-Cavity-Based Production of Picosecond X-ray Pulses

Michael Borland, Argonne National Laboratory 

6/15/2006 The New PEEM at the Swiss Light Source

Christoff Quitmann, Swiss Light Source, Switzerland

6/21/2006 Surface and Interface Studies Using High Energy X-rays

Harald Reichert, Max Planck Institute, Germany

6/22/2006 Tailoring the Self-assembly of Small Molecules in Complex Structures in Bulk and at Interfaces

Raluca I. Gearba, Institut de Chimie des Surfaces et Interfaces (ICSI), France
YEAR IN REVIEW

3-41

2006 NSLS SEMINARS

6/22/2006 Strategy Towards Nanometer Size Beams with Refl ective Optics 

Olilvier Hignette, ESRF, France

6/27/2006 Hierarchical Self-assembly of Plant Viruses for Materials Development

Qian Wang, University of South Carolina 

7/7/2006 New Generation of Instruments for Spin Polarized Electron Spectroscopy: Ultrafast Compact 

Classical Mott Polarimeter

V.N. Petrov, St. Petersburg State Polytechnical University, Russia

7/10/2006 Upgrading and Improving the HERA ep Collider

Ferdinand Willeke, DESY, Germany

7/11/2006 The Effect of Alloying Ru into Pt on Bonding Electronics of CO on Pt

Eugene Smotkin, University of Puerto Rico

7/25/2006 The Sub-Picosecond Pulse Source: A Retrospective

Dr. Jerome Hastings, SSRL/SLAC

8/1/2006 CAMD Light Source: Recent Challenges and Improvements

Mikhail Fedurin, Louisiana State University

8/4/2006 Dynamical Theory for X-ray Diffraction and Photonic Crystal Diffraction

Xianrong Huang, Stony Brook University

8/4/2006 Blazed Gratings and Minimal Zone Plates

Li Jiang, Louisana State University

9/5/2006 Femtosecond Electron Diffraction: Probing Structural Dynamics on the Fundamental Timescale

Jianming Cao, Florida State University

9/7/2006 Micro-diffraction and Other Novel Probes of Charge Density Wave Transport and Dynamics

Abdel Isakovic, Cornell University

9/7/2006 Implementation and Performance Overview of Orbit Feedback Systems at APS

Om Singh, Argonne National Laboratory

9/8/2006 The Short Bunches for CSR at MIT-Bates Ring

Dong Wang, Massachusetts Institute of Technology

10/6/2006 A Stroboscopic View Inside High-speed Magnetic Materials

William Bailey, Columbia University 

10/10/2006 GM/CA CAT Beamline Control System for Protein Crystallography at the APS

Sergey Stepanov, Argonne National Laboratory

10/18/2006 Bright Photon Beams: Developing New Light Sources

Timur Shaftan, NSLS-BNL

11/16/2006 Flexoelectricity in Nematics and Chiral Nematics: Symmetry, Geometry, and Devices

Robert B. Meyer, Brandeis University

11/27/2006 Studying the Short and Medium Range Order in Amorphous Metal Systems

Stephan Hruszkewycz, Johns Hopkins University
3-42

11/29/2006 The Linac System at LSU CAMD

Yanshan Wang, Louisana State University

11/30/2006 Electronic Reconstruction of the LaMnO3-SrMnO3 Interface

Peter Abbamonte, University of Illinois

12/5/2006 Advanced Accelerator R&D at the A0 Photoinjector

Raymond Fliller, Fermilab

12/14/2006 High Pressure Electronic Properties Investigated by RIXS: From Magnetic Collapse to 

Quantum Criticality

Jean-Pascal Rueff, CNRS / Synchrotron SOLEIL, France

12/19/2006 X-ray Fluorescence Microscopy of Saccharomyces Cerevisiae

Matthew Kidd, University of Michigan

2006 NSLS SEMINARS
YEAR IN REVIEW

3-43

2006 NSLS WORKSHOPS

4/4/2006 X6A Workbench: Advanced Tools for Structural Biology

4/23/2006 RapiData 2006

5/16/2006 Synchrotron Catalysis Consortium: New Opportunities for in situ XAFS Studies of 

 Nanocatalysis

5/16/2006 Soft Matter and Biomolecular Materials: X-ray Scattering Enabled by High Brightness 

 Beamlines

5/16/2006 Nanoscale Correlations Heterostructures

5/17/2006 Chemical and Biological Applications of X-ray Emission Spectroscopy

5/17/2006 Platforms for the Integration of Biological Systems into Nanomaterials and Interfaces

5/17/2006 Vacuum Ultraviolet Radiometry

6/12/2006 Crystallization: Focus on Optimization and High Throughput Techniques

6/19/2006 Discover Nanoscience and Nanoscience for Poets

10/19/2006 Short Course: XAFS Studies of Nanocatalysis and Chemical Transformations
FACILITY REPORT
FACILITY REPORT

NATIONAL SYNCHROTRON LIGHT SOURCE ORGANIZATION

NSLS and NSLS-ll Staff

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4-3
NSLS ADVISORY COMMITTEES

SCIENCE ADVISORY

COMMITTEE

The Science Advisory committee 

(SAC) evaluates science programs at 

the NSLS and makes recommendations to the Chairman.

Simon Bare, UOP LLC 

Joel Brock, Cornell Univ.

Robert Hettel, SSRL/SLAC 

Eric D. Isaacs, ANL

Leemor Joshua-Tor, Cold Spring 

Harbor

Edward Kramer, Univ. of California 

Simon Mochrie, Yale Univ.

James Penner-Hahn (Chair), Univ. of 

Michigan

William Thomlinson, CLS

Chris Jacobsen (UEC Chair), Stony 

Brook Univ.

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

Chris Jacobsen, Stony Brook Univ.

VICE CHAIR

Daniel Fischer, NIST

PAST CHAIR

Peter Stephens, Stony Brook Univ.

MEMBER

Steve Almo, AECOM

MEMBER

Chris Cahill, George Washington 

Univ.

MEMBER

Chris Dvorak, Montana State Univ.

MEMBER

Howard Robinson, BNL-Biology

SPECIAL INTEREST GROUP

REPRESENTATIVES

Special Interest Groups in areas 

of common concern communicate 

with NSLS management through the 

UEC.

BIO. SCATTERING AND DIFFRACTION

Alexei Soares, BNL-Environ. Sci.

HIGH PRESSURE

Jiuhua Chen, Stony Brook Univ.

IMAGING

Jeff Gillow, BNL-Environ. Sci.

INDUSTRIAL USERS

Simon Bare, UOP LLC

UEC members and SpIG representatives: (Standing from left): Chi-Chang Kao 

(BNL-NSLS), Dean Connor, Jr. (BNL-NSLS), Jiuhua Chen (Stony Brook U.), 

Mahbub Khandaker (TJLab), Jiufeng Tu (City College of NY), Jeff Keister (SFA, 

Inc.), Paul Evans (Univ. Wisconsin-Madison), Paul Northrup (BNL-Env. Sci.), Jeff 

Gillow (BNL-Env. Sci.), Michael Dudley (Stony Brook Univ.), Cecilia SanchezHanke (BNL-NSLS), Kathy Nasta (BNL-NSLS), and Lisa Miller (BNL-NSLS). 

(Sit ting from left): John Sutherland (BNL-Biology), Chris Jacobsen (Stony Brook 

University), Joe Dvorak (Montana State U.), Howard Robinson (BNL-Biology), 

Chris Cahill (George Washington Univ.), and Dan Fischer (NIST). Missing from 

photo: Peter Stephens (Stony Brook Univ.), Steve Almo (AECOM), Alexei Soares 

(BNL-Envi. Sci.), and Simon Bare (UOP LLC).

EX-OFFICIO

Chi-Chang Kao, NSLS User Science 

Division

EX-OFFICIO

Kathy Nasta, User 

Administration Offi ce

EX-OFFICIO

Lisa Miller, NSLS Information and 

Outreach Offi ce

INFRARED USERS

Jiufeng Tu, City College of NY

NSLS-II

Paul Evans, Univ. WisconsinMadison

NUCLEAR PHYSICS

Mahbub Khandaker, TJNL

STUDENTS AND POST DOCS

Dean Connor, Jr., BNL-NSLS

TIME RESOLVED SPECTROSCOPY

John Sutherland, BNL-Biology

TOPOGRAPHY

Michael Dudley, Stony Brook Univ.

UV PHOTOEMISSION AND SURFACE

SCIENCE

Jeff Keister, SFA, Inc.

XAFS 

Paul Northrup, BNL-Environ. Sci.

X-RAY SCATTERING AND

CRYSTALLOGRAPHY

Cecilia Sanchez-Hanke, BNL-NSLS

4-4
FACILITY REPORT

NSLS ADVISORY COMMITTEES

GENERAL USER PROPOSAL

REVIEW PANEL

The Proposal Review Panel (PRP) 

reviews and rates General User Proposals. Members are drawn from the 

scientifi c 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

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

Qun Shen, ANL

Nobumichi Tamara, LBNL

IMAGING AND MICROPROBES: 

ENVIRONMENTAL AND GEOSCIENCES

Don Baker, McGill Univ.

David Black, NIST

George Flynn, SUNY @ Plattsburgh

Kenneth Kemner, ANL

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

Alexander Moewes, Univ. of Sask.

Boris Sinkovic, Univ. of Connecticut

Jiufeng Tu, CUNY

Tonica Valla, BNL-Physics

METHODS AND INSTRUMENTATION

Leroy Chapman, Univ. of Sask.

Kenneth Finkelstein, Cornell Univ.

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.

Andrew Fitch, ESRF

Joseph Hrilijac, Univ. of Birmingham

Stefan Kycia, Univ. of Guelph

Peter Lee, ANL

Peter Stephens, Stony Brook Univ.

X-RAY SCATTERING: MAGNETISM/

STRONGLY CORRELATED ELECTRONS/

SURFACE

Kenneth Finkelstein, Cornell Univ.

Peter Hatton, Univ. of Durham

Valery Kiryukhin, Rutgers Univ.

Karl Ludwig, Boston Univ.

George Srajer, ANL

Trevor Tyson, NJIT

X-RAY SCATTERING: SOFT MATTER AND

BIOPHYSICS

Ben Hsiao, Stony Brook Univ.

Huey Huang, Rice Univ.

H. Miriam Rafailovich, Stony Brook 

Univ.

Detlef Smilgies, Cornell Univ.

Helmut Strey, Stony Brook Univ.

X-RAY SPECTROSCOPY: BIOLOGICAL, 

ENVIRONMENTAL, AND GEOSCIENCES

Martine Duff, Westinghouse 

Savannah River

Douglas Hunter, Univ. of Georgia

Kenneth Kemner, ANL

Satish Myneni, Princeton Univ.

X-RAY SPECTROSCOPY: CHEMICAL AND

MATERIAL SCIENCES

Simon Bare, UOP LLC

Uwe Bergmann, SLAC

Anatoly Frenkel, Yeshiva Univ.

Steven Heald, ANL

Jean-Pascal Rueff, Jussieu

Tsun Sham, Univ. of Western Ontario

Trevor Tyson, NJIT

SAC Committee members (standing, from left) Robert 

Hettel, Leemor Joshua-Tor, and Eric Isaacs. Sitting (from 

left) Simon Mochrie, Edward Kramer, James Penner-Hahn, 

and Bill Thomlinson. Missing from photo: Simon Bare, Joel 

Brock, and Chris Jacobsen.

4-5
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 scientifi c 

community and generally serve a twoyear 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

4-6
FACILITY REPORT

Organization and Mission

The NSLS Accelerator Division (AD), headed by 

James B. Murphy, is organized into two sections: 

the Storage Ring & Insertion Device Section 

(SR&ID), headed by Boris Podobedov, and the 

Linear Accel erator (Linac) Section, headed by 

Xijie Wang. In addition to the NSLS accelerator complex, the AD staff operates the Magnetic 

Measurements Laboratory (MML) and the Source 

Development Laboratory (SDL), which are led by 

Toshiya Tanabe and Xijie Wang, respectively.

The NSLS Accelerator Division has a four-part 

mission: 

● To ensure the quality of the electron beam in 

the existing NSLS booster, linear accelerator, 

and x-ray & vacuum ultraviolet storage rings

● To participate in the NSLS-II project, in particular the design of the storage ring and 

injection system

● To operate the MML and the SDL

● To perform fundamental research and 

development in accelerator and free-electron 

laser physics.

2006 Activities

NSLS Accelerator Complex

The AD staff performed studies to improve the efficiency and diagnostics of the NSLS injection system. The studies resulted in identifying a loss region near the extraction septum in the booster and 

led to a better understanding of the injection system performance. Improvements in the diagnostics 

and controls of the injection system provided for 

measurement of the electron beam position in the 

booster at anytime during the booster ramp. During the NSLS May shutdown, the AD staff assisted 

the Operations and Engineering Division (OED) 

staff in replacing a 40-year-old klystron with a 

rebuilt tube resulting in a significant improvement 

in the reliability of the NSLS linac system.

Close cooperation of all the NSLS divisions contributed to the successful commissioning of the 

new X25 mini-gap undulator (MGU) after its installation in the winter shutdown. The commissioning 

included establishing the correct undulator elevation, calculation of the proper trip points for the 

active interlock system, and assessing the impact 

of the new insertion device on the beam dynamics 

and lifetime of the X-ray ring.

The Task Force on Orbit Stability generated its 

final report and concluded that no major problems 

were identified. The feed forward system to compensate for the elliptically polarized wiggler (EPW) 

was significantly improved by the OED staff. A 

procedure to regularly check the performance of 

the beam position monitoring (BPM) receivers with 

an RF calibrator is being explored.

Development of the Middle Layer Toolkit for studying the properties of the VUV and X-ray storage 

rings continued to make progress. Automated 

scripts for the evaluation of accelerator parameters were deployed. The scripts provide for calibration of the correctors and BPMs, restoration of 

the lattice symmetry broken by gradient errors in 

the sextupoles, and estimation of the quadrupole 

gradients in the sextupoles due to closed orbit 

shifts. Studies to determine the minimum emittance coupling in the X-ray ring were very successful, and it was shown that the coupling ratio 

could be reduced to 0.3%. An improved characterization of the X-ray ring lattice at injection energy 

(750 MeV) will be launched in the near future.

NSLS-II Project

The accelerator physics staff of the AD provided 

the core team for the design of the NSLS-II accelerator complex, including the ultra-high brightness 

storage ring and the top-off booster injection system. A conceptual design report was prepared as 

part of the qualification process to achieve Critical 

Decision One (CD-1) approval from the Department of Energy for the NSLS-II project.

While the primary emphasis of the NSLS-II project 

is the production of ultra-high brightness x-rays, it 

is highly desirable to continue to provide for stateof-the-art capabilities in the VUV and IR as well. 

For the IR region in particular, several options 

ACCELERATOR DIVISION REPORT

James B. Murphy

Associate Chair for Accelerators

James Murphy

4-7
were explored, including upgrading the existing 

VUV ring with a superconducting RF system to 

provide short bunches for a coherent mode of 

operation.

Magnet Measurement Laboratory (MML)

The AD staff worked in collaboration with the OED, 

the User Science Division and an outside vendor 

to design, construct, and measure the new X25 

cryo-ready MGU. The team completed the iterative 

process of magnetic measurements, shimming, 

and optimization in time for the December 2005 

installation. Magnetic measurements before and 

after baking at 90°C, as well as before cool down 

to –120°C and after warm-up to room temperature, 

confirmed that the high field quality and very low 

phase error (2.5° RMS) were preserved through 

the thermal cycling. Also proven were the mechanical design features for accommodating differential 

expansion and contraction during the extreme 

temperature excursions, as were the Keyence 

optical micrometers monitoring the actual magnet 

gap. Commissioning took place in February 2006. 

Figure 1A shows the measured brightness spectrum at the minimum gap of 5.6 mm, and the theoretical spectrum computed by the SPECTRA code 

(from SPRING-8) for an ideal undulator; there is 

excellent agreement between the two results. Figure 1B shows the measured tuning curves for the 

3rd through 9th harmonics over the normal range 

of magnetic gap operation. (Figures courtesy of J. 

Ablett & L. Berman, NSLS)

The X25 MGU is operating presently with watercooling only. Cryogenic operation at 150K could 

extend the tuning range of each harmonic downward by about 10%. Potential benefits of the extended tuning are being weighed against the cost 

of the refrigeration system and the lack of magnetic measurements at cryogenic temperatures. 

The BNL Cryogenic Safety Committee approved 

the Phase I configuration of the superconducting 

(SC) undulator Vertical Test Facility (VTF), permitting operation with liquid helium in the pool-boiling 

mode. For the commissioning test, a SC Helmholtz 

coil (for in-situ Hall probe calibration) and a refurbished pair of legacy SC mini-undulator sections 

with 8.8 mm period were used. Field scans were 

taken over a range of currents from 25 to 150 A. 

Figure 2 shows the on-axis field map of the Helmholtz coil and the test SCU at a current of 150 A in 

both devices. The commissioning run successfully 

demonstrated the operation of the cryogenic Hall 

probe mapper and the in-situ calibrator.

In collaboration with BNL Superconducting Magnet 

Division and HTS110, Inc., the MML staff embarked on a technical study of using high-temperature superconductor (HTS) coils to replace the 

existing copper coils used in VUV dipoles. Three 

identifiable benefits from an HTS retrofit are: a 

significant reduction in electrical power requirements to run the dipoles, a simpler and cheaper 

current supply, and an increased aperture for 

beam extraction.

As an LDRD project, the development of cryo-coil 

packs for an X-ray ring sextupole magnet has 

been conducted. Fabrication of the cryo-coil packs 

has been undertaken and a prototype will be 

tested by the end of FY07.

The 2-meter long strong focusing VISA undulator 

magnet was completed and measured as part of 

the Office of Naval Research-funded Free Electron 

Laser program at the SDL. 

Source Development Laboratory (SDL)

The SDL is an ideal platform to conduct R&D on 

high-brightness electron beams and laser-seeded 

free electron lasers (FEL). The SDL consists 

of a Titanium-Sapphire laser, a photoinjector, a 

300-MeV linac and a 10-meter undulator. A second year of funding was obtained from the Joint 

Technology Office (JTO) and the Office of Naval 

Research (ONR) to pursue high-gain free electron 

laser amplifier experiments in the infrared waveFigure 1. (A) Measured (solid curve) and predicted 

(dotted curve) brightness spectra of X25 MGU at minimum 

magnetic gap of 5.6 mm. (B) Measured tuning curves for 

the 3rd through 9th harmonics. Brightness [ph/sec/mm2/mrad2/0.1%BW/235mA] Brightness [ph/sec/mm2/mrad2/0.1%BW/235mA]

X-ray Energy [keV]

X-ray Energy [keV]

(A)

(B)

4-8
FACILITY REPORT

length regime. The JTO/ONR-sponsored program 

included experiments on optical guiding, efficiency 

enhancement and the first observation of superradiance in an FEL.

In addition to the work in the infrared regime, new 

short-wavelength milestones in the ultraviolet 

region (UV) were also established. UV light at 190 

nm was generated by operating the FEL in the 

Self Amplified Spontaneous Emission mode and 

the first lasing of the High Gain Harmonic Generation (HGHG) scheme in 4th harmonic mode at 199 

nm was achieved. Preliminary results on operating the SDL FEL in the Enhanced Self Amplified 

Spontaneous Emission mode (E-SASE) were also 

obtained.

The SDL has the ability to generate very short 

electron pulses (1 ps FWHM) with high charge (~ 

1 nC), which is ideal for the generation of copious 

quantities of coherent terahertz radiation (THz). 

The AD worked in collaboration with the NSLS 

User Science Division and the BNL Instrumentation Division to characterize the high intensity 

(~ 100 μJ/pulse) single cycle THz radiation. The 

high-intensity pulses allowed BNL researchers to 

explore new phenomena such as nonlinear crossphase modulation (XPM) in electro-optic crystals 

and preliminary ideas on using the THz as a pump 

in pump-probe experiments on high-temperature 

superconductors. The development of an ultra-fast 

electron diffraction source based on the SDL photoinjector technology is also being considered.

Figure 2. VTF commissioning run with Helmholtz coil and 

legacy 8.8 mm period SC undulator immersed in LHe. 

Helmholtz coil provides cold Hall probe calibration up to 1.7 

Tesla at 150 A.

Distance (cm)

On-Axis Field (gauss)

VTF Test Article #1 at 150A

4-9
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:

● Operation of the NSLS 24 hours a day, 7 days 

a week, on average 44 weeks a year 

● Design, fabrication, and maintenance of the 

NSLS accelerators, infrastructure, and instru

ments, including upgrades, modifications, and 

proposal development 

● Engineering and technical support for other 

NSLS divisions and the NSLS user community 

The OED staff includes one scientist, 17 engineers, and 53 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 requires us to draw on the 

capabilities of the other NSLS divisions for support, and in turn, provide specialized support for 

their activities. 

2006 Activities

An overview of machine performance summarized 

for calendar year 2006 is provided in Section 5, 

“Facility Facts and Figures.” For Fiscal Year 2006, 

which is the DOE reporting period, overall reliability was 94% for the X-ray ring and 97% for the 

VUV ring. As in previous years, a comparatively 

small number of disruptions longer than four hours 

in duration account for much of the down time. For 

FY 2006, almost half of the x-ray downtime came 

from only 11 events, and on the UV ring, only eight 

faults accounted for more than 80% of the down 

time. This distribution is a continuing indication of 

an effective maintenance program in action; the 

majority of the faults are small and quickly recoverable and many potential “big” events are avoided 

through preventative maintenance. 

The single largest down-time event in 2006 was 

the failure of the bellows on the UV transport line 

shutter. The shutter assembly is actually welded 

into the transport line, so the decision was made 

to replace the failed actuator without removing the shutter housing. This is not as easy as 

it sounds because of mechanical interferences, 

but the innovative approach that made it possible 

kept the down time to less than three days, from 

failure to return to operations. On the one hand, it 

is heartening that the institutional knowledge and 

creativity are still there to respond so effectively to 

a problem of this kind. A “traditional” repair, which 

would have cut out the shutter and welded in the 

spare, could have resulted in more than a week of 

down time. However, it is a concern that we may 

be beginning to see more “age-related” failures in 

Erik Johnson NSLS equipment. 

Group

Area/System Total X- DT U- DT X-ray UV

Total Charges to Down Time

Controls and Diagnostics 140 44 5 61.6 6.9

Power Systems 235 112 27 139.8 74.0

Utilities 80 36 30 53.3 95.1

Miscellaneous 64 42 5 35.7 4.7

519 234 67 290.3 180.7

Significant Disruptions

VUV Transport line shutter 67.2

Modulator 3 Core Bias 54.1 48.7

XRF Micro 20.2

Electron Gun Replacement 15.3

LBQ9 Short 11.5 4.2

BXESH1 6.8

Modulator 3 Thyratron Replacement 6.7

Water Fitting fail at X18/19 Sawtooth 6.1 6.5

XRF 2B 3 kW Amplifier 5.6

UV Trim Micro 5.6

X1 Active Interlock PS 5.1

X25 MGU Cooling 5.1

UV Interlock Security System 4.4

X29 Active Interlock 4.3

X13/14 Water Interlock 4.1

URF Interlocks 4.0

129.5 155.8

Balance to 'Routine' Faults

160.8 24.9

Number of Faults Downtime [hr]

FY06 Summary Fault Analysis

4-10
FACILITY REPORT

The NSLS has an aggressive preventive maintenance program, which has been effective in 

mitigating the effects of normal “wear and tear” on 

machine down time. The system stewards have 

also identified elements of the machine operations 

where failures are deemed to be most likely or to 

have the greatest impact. In those cases, plans 

for spares, upgrades, or replacements have been 

developed. To help validate the planning assumptions, a Machine Operations Reliability Evaluation 

(MORE) was held in 2006. This review was conducted by an external committee that was charged 

to evaluate our allocation of resources and plans 

to secure reliable operations to the 2012 to 2014 

time frame. 

Overall, the committee gave kudos to the NSLS 

staff members and their contributions to delivering high levels of machine availability and performance, and found that “the analysis of machine 

support and development needs is very good and 

that the mechanisms for project planning and prioritization are in place and appear to be effective.” 

However, the committee also expressed the same 

kinds of concerns raised by the staff regarding 

threats to continued reliable operations. These 

included:

● Aging instrumentation, components, and infra

structure

● The possibility of a major breach in security 

and/or safety

● A flat budget in out years

● Staff recruiting, retention, and knowledge 

transfer.

The committee also noted that staffing is a critical concern with the ramp-up of NSLS-II. These 

issues are being factored into the near-term planning for the facility as are the initiatives outlined in 

the NSLS Five Year Plan.

One of the new initiatives described in the plan is 

the construction of a new insertion device beamline at X9. As noted in the 2005 Activity Report, 

initial preparations for this construction began at 

the end of 2005. During 2006, the move of the 

Case Center for Synchrotron Biosciences beamlines from X9 to X3 was successfully completed. 

Preparations are underway for the construction 

and installation of the new insertion device-based 

Small Angle X-ray Scattering (SAXS) beamline 

to support research for the Center for Functional 

Nanomaterials. During the winter 2006 shutdown, 

the original “phase I” storage ring vacuum chamber for the X9/10 dipole and all of the old X9 bending magnet front-end components were removed. 

A new dipole vacuum chamber with a zero-degree 

output port compatible with the new X9 insertion 

device was installed. The design of a new MiniGap Undulator (MGU) and new front-end components compatible with the X9 MGU started in FY06 

and will continue into FY07.

Fabrication efforts for many components of the 

new X9 MGU insertion device have already begun, 

as has layout and fabrication of the new hutch for 

X9 (the largest ever at the NSLS!). During 2007, 

beamline design is to be completed, and the installation of the front end and insertion device are 

planned for the winter 2007 shutdown. 

With many years of NSLS operations ahead, continuous maintenance and upgrades of the facility 

will be vital to ensure that a robust research community is ready to exploit the exciting new capabilities of NSLS-II when it comes online. The OED 

will continue its work to advance the initiatives in 

the NSLS strategic plan to keep our user community one of the most productive anywhere. 

The old phase I chamber removed during the winter 

shutdown, and the chamber that replaced it being prepared 

in the lab prior to its installation.

Old X-9/10 chamber New X-9/10 chamber

4-11
USER SCIENCE DIVISION REPORT

Chi-Chang Kao

Associate Chair for User Science

Chi-Chang Kao

Organization and Mission

The User Science Division (USD) 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 

(Kathy Nasta), 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 2006 are summarized below.

2006 Activities

NSLS Five-Year Plan

The most important activity of the USD in 2006 

was the development of the NSLS Five-Year 

Strategic Plan. We worked closely with the user 

community and the NSLS Science Advisory Committee (SAC) to identify future scientific opportunities, as well as beamline and infrastructure 

upgrades needed to exploit those opportunities. A 

more detailed plan, which includes the resources 

required, funding sources, and schedule to implement these upgrades, also was developed.

Contributing User Proposals

With the assistance from the SAC, the first set of 

nine Contributing User (CU) proposals was approved. The approved CUs include two research 

resources: COMPRES (a National Science Foundation-funded research resource for earth sciences) and PXRR (a National Institutes of Health 

and DOE Office of Biological and Environmental 

Research-funded resource for macromolecular 

crystallography), as well as several groups of 

researchers who bring significant new instrumentation to the NSLS. Although these CU programs 

have only been in operation for a relatively short 

time, they have already made a significant impact 

to the NSLS user science program.

Funding Renewed for X6A

On the scientific program front, we are delighted 

that funding for the East Coast Structural Biology 

Facility, beamline X6A, has been renewed by the 

National Institute of General Medical Sciences 

(NIGMS). X6A is funded for macromolecular crystallography and, in particular, to provide beam time 

access to young scientists in the process of establishing research groups whose primary interest is 

not x-ray crystallography. This grant from NIGMS 

has enabled the NSLS to significantly expand its 

structural biology program, as well as to develop a 

rapid access and remote user program.

NSLS, BNL to Build Linac Coherent Light 

Source Detectors

The NSLS and Brookhaven’s Instrumentation 

Division were awarded a multi-year project to 

construct detectors for the Linac Coherent Light 

Source (LCLS) project at the Stanford Linear Accelerator Center (SLAC). This is a very challenging 

project and an important milestone for the detector 

development effort at the NSLS. It will significantly 

expand the expertise of the detector and control 

group at the NSLS, led by Peter Siddons, which 

has successfully delivered a wide range of detectors to users over the last several years, including 

fast photon counting detectors and linear array detectors. The detectors developed for the LCLS will 

also benefit many scientific programs at the NSLS.

Education and Outreach

We continue to put a large focus on user education, training, and outreach at the NSLS. In the 

area of user training, our annual XAFS short 

course was held in October 2006, with the title 

“Short Course: XAFS Studies of Nanocatalysis 

and Chemical Transformations.” In addition, two 

macromolecular crystallography courses, “RapiData 2006,” and the “X6A Workbench: Advanced 

Tools for Structural Biology,” continued to attract 

a large number of users. We also worked closely 

with users to organize additional focused scien4-12
FACILITY REPORT

tific workshops, including “Synchrotron Catalysis 

Consortium: New Opportunities for in situ XAFS 

Studies of Catalysis,” a workshop on “Soft Matter and Biomolecular Materials: X-ray Scattering 

Enabled by High Brightness Beamlines,” the “Nanoscale Correlations Heterostructures” workshop, 

a workshop on “Chemical and Biological Applications of X-ray Emission Spectroscopy,” a workshop 

on “Platforms for the Integration of Biological 

Systems into Nanomaterials and Interfaces,” a 

“Vacuum Ultraviolet Radiometry” workshop, and 

the workshop “Crystallization: Focus on Optimization and High Throughput Techniques.” These 

short courses and workshops were very effective 

in introducing the use of synchrotron techniques 

in a particular area of science to non-synchrotron 

users. Many new research opportunities and collaborations have resulted from them. Additionally, 

we’ve continued our effort 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 and Performance 

Improvements

We initiated a program this year to characterize beamline performance, including flux, energy 

resolution, and focal spot size, on a regular basis, 

led by Lonny Berman. The goal is to establish a 

performance baseline for all NSLS facility beamlines, and identify areas that need improvement. In 

addition, the three major upgrade projects initiated 

and completed this year by the NSLS and PRTs 

were at X18, X25, and X9. Details are described 

below:

X18B Beamline Upgrade for Quick-EXAFS

A new monochromator drive and data-collection 

scheme have been developed for beamline X18B 

to allow quick measurements of x-ray absorption 

spectra (QEXAFS). The micrometer on the standard NSLS tangent-arm driven monochromator 

has been replaced with a cam, which continuously 

changes the Bragg-angle of the monochromator 

with a simple rotation of a motor. Different positions in the cam result in different angular ranges 

over which the monochromator is rotated, which 

translates into different energy ranges for the 

scans. This allows the user to concentrate on 

either the near-edge structure (XANES), or the 

extended fine structure (EXAFS). The data are 

collected using an analog-to-digital converter, 

which digitizes the voltage from the current amplifier directly. 

During 2006, the QEXAFS setup was used by 

three groups. Switching the X18B monochromator control system from conventional EXAFS to 

QEXAFS mode takes only minutes. The graphical 

user interface (GUI) for QEXAFS data collection 

is now capable of continuous operation with data 

collection duration of one or five minutes, each 

with many cycles. In fast mode, a full EXAFS scan 

with good signal to noise ratio can be collected in 

200 milliseconds. This new capability will enable 

the use of x-ray absorption spectroscopy for fast 

in-situ kinetic measurements, e.g., for catalysis 

and fuel cell research.

X25 Cryo-Capable Mini-Gap In-Vacuum 

Undulator Installed in the X-Ray Ring

At the start of 2004, beamline X25’s programmatic focus shifted completely to monochromatic 

macromolecular crystallography, following 14 

years of operation as a mixed-use high-brightness 

beamline. Thus, the NSLS was presented with an 

opportunity to renovate the beamline, as well as 

the radiation source, to optimize them for a dedicated macromolecular crystallography program. To 

this end, the BNL Macromolecular Crystallography 

Research Resource (PXRR), a collaboration between the BNL Biology Department and the NSLS, 

submitted a funding request in late 2002 as part of 

its proposal to the National Institutes of Health’s 

National Center for Research Resources and the 

Department of Energy’s Office of Biological and 

Environmental Research (DOE BER) to renew its 

five-year grant. The proposal was well received, 

and $2.2M in funds was awarded by DOE BER 

beginning in late 2003, to be dispensed over the 

course of three fiscal years.

The newly installed double crystal monochromator at 

beamline X25 is shown, with its vacuum chamber open. 

The white beam enters from the right and the diffracted 

beam emerges to the left. The fi rst silicon crystal is 

mounted on a copper support that can be cooled to 

cryogenic temperature, and the second crystal is mounted 

in a bender that can curve the crystal sagittally in order 

to focus the beam horizontally. Directly beneath the 

monochromator is the cryocooler and heat exchanger 

assembly which forms part of the new cryogenic refrigerator 

for cooling the fi rst crystal.

4-13
During the December 2005 shutdown, the original hybrid wiggler, which served as the radiation 

source for beamline X25 since its inception in 

1990, was replaced by a custom-designed invacuum miniature-gap hybrid undulator. At a photon energy of 6.3 keV, the new radiation source 

will be 15 times brighter than the old one, and will 

be six times brighter at a photon energy of 10.5 

keV. Its design consists of 0.99 meter-long planar 

hybrid magnet arrays with a period length of 18 

mm (55 periods total) and a minimum attainable 

gap of 5.6 mm, with a corresponding maximum 

deflection parameter, K, of 1.5. The NdFeB-type 

permanent magnet 

material, which 

has been used 

in this insertion 

device, can have 

a higher magnetic 

field and a higher 

radiation resistance simply by 

cooling: Operation 

at 150K will likely 

produce a 13-14% 

higher magnetic 

field (and higher 

K), resulting in a 

larger photon energy tuning range. 

Therefore, this 

undulator design 

also incorporates a provision for cryogenic operation, which might be pursued in the future. Unlike 

previous miniature-gap undulator designs in use 

at the NSLS, the one now implemented for X25 

will be continuously tunable from 2 to 20 keV by 

employing all harmonics up through the 9th. The 

undulator vacuum and gap separation system was 

manufactured by Advanced Design Consulting of 

Lansing, NY. In conjunction with the installation of 

the undulator, certain components in the front end 

of the beamline, and the active interlock system 

that protects the x-ray ring exit chamber, were 

upgraded in order to cope with the much higher 

power density of the undulator beam.

In addition to the new radiation source, upgrades 

to the beamline optics also were implemented in 

order to exploit the properties of the new source. 

The current double crystal monochromator was 

replaced by one that incorporates cryogenic cooling of the first crystal and sagittal bending of the 

second crystal to permit horizontal focusing. It 

was followed by the installation of a new bendable mirror, containing multiple coating stripes, 

to permit vertical focusing. The completion of the 

X25 upgrade, expected in FY07, is essential to the 

macromolecular crystallography program at the 

NSLS.

X9 to X3 Beamline Relocation Complete

In October 2006, beamlines X3A and X3B began 

operating without restrictions after being transferred from X9 in just four and a half months. The 

relocation of the two beamlines was completed in 

advance of original estimates, with deconstruction 

of X9A and X9B beginning in early May and the 

first commissioning beams at X3A and X3B running in late August and early September. 

The Case Center for Synchrotron Biosciences, 

which utilized the former X9 beamlines, moved 

to X3 to make room for a new undulator-based 

beamline at X9. The X9 straight section is curThe new X25 MGU installed in the NSLS x-ray ring.

Beamline X3 before

Beamline X3 after

X-ray burns taken using original 

wiggler (top) and the new 

undulator (bottom), in the same 

location, show that the undulator 

beam is much smaller than the 

wiggler beam, as expected.

4-14
FACILITY REPORT

rently the last one available in the x-ray ring. It 

will be used for a small-angle x-ray scattering 

Facility Beamline with BNL’s Center for Functional Nanomaterials as a Contributing User. The 

new X9 beamline is expected to be operational in 

2008, with commissioning completed during the 

first cycle of the year and full operations starting 

in May or June. 

Although performed quickly, the relocation from 

X9 to X3 wasn’t an easy process. First, the X16C 

beamline was renovated to accept the experimental program that was operating at beamline X3B1. 

Next, the former X3 beamlines and experimental 

equipment were completely removed from the 

X3 floor space. Then, planning, surveying, and 

engineering and design for the relocation of the 

two X9 bending magnet beamlines to counterpart 

locations at X3 were undertaken and the necessary reviews were completed. The X9A hutch was 

modified and re-built in its new location at X3A, a 

new hutch for X3B was constructed, and associated utilities and interlocks were installed. The 

beam pipes for both beamlines, which penetrate 

the shield wall and connect them with the front 

end, were moved from X9 to X3, and the shield 

wall and neighboring lead shields were re-built accordingly. All experimental equipment and controls 

for these beamlines also were moved to their new 

locations at X3.

All of the equipment was in place at X3 by August, 

with the first commissioning beams running shortly 

after. Re-commissioning was completed around 

the end of the 2006 fiscal year. In addition to hosting Participating Research Team (PRT) experiments, both beamlines also are accepting General 

Users.

4-15
NSLS-II REPORT

Steven Dierker

Associate Laboratory Director for Light Sources 

NSLS-II Project Director

Steve Dierker

Introduction

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. The facility will replace the 

NSLS, producing x-rays more than 10,000 times 

brighter than those produced at the NSLS today. 

The design and engineering is expected to begin 

in 2007, construction in 2009, and operations in 

2014.

The superlative character and combination of 

capabilities will have broad impact on a wide 

range of disciplines and scientific initiatives in 

the coming decades, including new studies of 

small crystals in structural biology, a wide range 

of nanometer-resolution probes for nanoscience, 

coherent imaging of the structure and dynamics of 

disordered materials, greatly increased applicability of inelastic x-ray scattering, and properties of 

materials under extreme conditions.

2006 Activities

2006 was an extraordinary year for the NSLS-II 

Project – challenging, exciting, and full of change 

and accomplishment.

The NSLS-II Project organization, which was created in January 2006, grew rapidly and by the end 

of the year a true team of about 100 people were 

working on the project. Jim Yeck, as Deputy Project Director, brings a wealth of prior experience 

with large DOE and NSF construction projects. We 

are also very fortunate to have the able leadership of Satoshi Ozaki, John Hill, Marty Fallier, and 

Diane Hatton, who as Directors of the Accelerator 

Systems, Experimental Facilities, Conventional 

Facilities, and Project Support Divisions, respectively, have guided their development. We are also 

delighted that Ferdinand Willeke, formerly head of 

the complex HERA facility at DESY, will be joining 

the project this coming July to succeed Satoshi 

Ozaki.

In testimony to BNL’s strength as a first-class accelerator laboratory, we have been able to draw 

on expertise from throughout the laboratory, with 

staff from NSLS, CAD, SMD, and many other 

departments contributing to the project. The fulltime NSLS-II staff took up residence in the new 

NSLS-II Project Site Office, Buildings 817 and 

830M. These buildings are now full, and we will be 

expanding into a new building, 817M, in the coming months.

The project also benefited from the continued 

involvement of the scientific community by hosting 

visits of from 1 day to several weeks of more than 

70 international experts in a variety of disciplines. 

Additional community involvement occurred 

through the formation of four external NSLS-II advisory committees, created to guide, and provide 

oversight to, the project. Altogether, we hosted 

more than 10 reviews or workshops on a wide 

range of topics during 2006.

The culmination of these efforts was expressed 

in the NSLS-II Conceptual Design Report, available on the NSLS-II website, which presents the 

conceptual design of a world leading facility that 

will enable the study of material properties and 

Latest NSLS-ll rendering

4-16
FACILITY REPORT

functions, particularly at the nanoscale, at a level 

of detail and precision never before possible.

In December, 2006 the project underwent a very 

successful DOE (“Lehman”) Review. Overall, the 

committee judged the project team to be strong 

and to have the full support of BNL and the design 

as likely to achieve the technical goals. 

2007 promises to be equally challenging. In addition to ramping up our R&D program, our current 

schedule calls for completing Title I, or preliminary 

engineering, design by the end of this year.

In summary, through the hard work and dedication 

of an extremely talented community, both inside 

and outside BNL, we have gotten off to a great 

start. I look forward to continued future success.

4-17
USER ADMINISTRATION REPORT

Kathleen Nasta

User Administrator

The User Administration Office at the NSLS coordinates site access for all of our users, covering everything from processing appointments to 

ensuring safety compliance and issuing badges. 

We also facilitate the general user proposal program, maintain beamline agreements and data, 

record and interpret statistical data, and plan and 

organize meetings and workshops, including the 

annual Users’ Meeting. 

2006 Activities

User Statistics

During Fiscal Year 2006, 2105 users performed 

experiments at the NSLS. Figures 1 and 2 detail 

the affiliations of our users and their areas of 

scientific research, respectively. There were 656 

new users that joined us in 2006, indicating that 

the NSLS user community continues to be very 

dynamic. Roughly half of our users are U.S. citizens, and about 75% are male. A little more than 

half of the users from the 399 unique institutions 

came from U.S. universities. Other institutional 

categories included foreign, academic, BNL (nonNSLS), U.S. industry, U.S. laboratories, federally funded institutions (non-DOE), non-federally 

funded institutions, foreign national laboratories, 

and others. About two-thirds of the users came 

from institutions located in the northeastern United 

States, and one third of those were located in New 

York (Figure 3). Scientists, faculty members, and 

professional staff made up 44% of those users 

performing experiments, while 37% were graduate students and 13% were postdoctoral students. 

Four percent were undergraduate-level students. 

Reviewing users’ fields of research, almost half 

(45%) perform experiments in the life sciences 

area. The next largest group, at 29%, lists materials science as their research area, and 13% of the 

users are in the environmental and geosciences 

fields.

User Access Procedures

The web-based Proposal, Allocation, Safety and 

Scheduling (PASS) system was used for the first 

time for the fall 2004 operations cycle. PASS allows numerous actions to be taken care of in one 

system, including creating and submitting proposals, conducting feasibility and peer reviews, 

allocating and scheduling beam time, performing 

safety reviews, and maintaining beamline information.

During 2006, work began on prerequisites to create a framework for developing a system for Rapid 

Access to beamtime. A Principal Investigator (PI) 

can now name a delegate for a PASS form (for 

example, a professor can name a student). This 

delegate is another PASS user and s/he can prepare, submit, and receive status updates. In addition, a system of Envelope Safety Approval Forms 

(SAFs) was established. At this time, Macromolecular Crystallography users are asked specific 

questions prior to a full SAF. If answers indicate 

the experiment meets the criteria of a predefined 

Safety Envelope, no further SAF information will 

be required, and approval of the SAF is greatly 

expedited. Several meetings were held to gather 

input on the design and flow of the Rapid Access 

system, and it is expected that during FY 2007 the 

Kathy Nasta system will be operational.

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Figure 1. NSLS users by affi liation

4-18
FACILITY REPORT

A new Proposal Oversight Panel (POP) group was 

established prior to the Fall 2006 beamtime cycle. 

The POP is comprised of a small number of scientific personnel with broad subject-matter expertise. 

The first face-to-face meeting of the group was 

held in order to address any general user proposal 

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Figure 2. NSLS users by fi eld of research

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Figure 3. NSLS geographical user distribution

issues, such as appeals based on score differentials resulting from the initial peer review. Work 

is continuing to develop and streamline the role, 

responsibilities, and reporting of the POP. Related 

to this initiative was initial planning to adjust the 

current guidelines for rating proposals in an attempt to create a more efficient, more quantifiable 

way of scoring.

User Satisfaction Survey

The Department of Energy requests that all users 

complete a user satisfaction survey at the close of 

each experimental run. At the NSLS, this is called 

our End-of-Run survey. These surveys revealed 

that more than half of the respondents would communicate their research results through publishing in peer-reviewed open literature. About half 

said they would present findings at a professional 

society meeting, and three users indicated they 

would acquire a patent. Additional benefits gained 

according to feedback from most of our users 

included:

● obtained access to unique facilities

● facilitated collaborative interactions (such 

as stimulated new ideas for future experi

ments, increased multidisciplinary work, or 

enabled a new approach)

● created an opportunity to train students (un

dergraduate through postdoctoral fellows)

The End-of-Run survey form was revised during 2006, and is now available online. Changes 

were made to limit the number of questions and 

simplify the information gathered so that users 

can complete the survey more quickly. Further 

changes are planned to allow access for particular 

beamline staff, through the PASS system, to view 

the responses to the survey directly and as often 

as they wish. Further, a tracking system will be 

created so that users can view the issues brought 

out through End-of-Run surveys, and what is being done to resolve the issues. It is anticipated 

that this will ensure more timely feedback and/or 

resolution for problems identified. The survey will 

continue to remain anonymous, unless a user 

wishes to provide an email address for an individual follow-up response.

BNL Research Support Building

In 2006, plans were created to provide a more 

convenient and simpler check-in process for the 

users and guests of all facilities on the BNL site. 

These plans included moving all users’ services 

to the new Research Support Building. Located 

on Brookhaven Avenue diagonally across from 

Berkner Cafeteria, the Research Support Building 

opened in October 2006 and currently provides 

part of the envisioned “one-stop shopping” model 

for visiting scientists and guests. The housing, 

travel, rental car, and transportation offices as 

well as the Ronkonkoma Train Station Shuttle and 

Teachers Federal Credit Union are already functioning in the new location.

Currently, NSLS users still need to check in at the 

User Administration Office on the second floor of 

the NSLS upon arrival at BNL. But in 2007, the 

new Guests, Users, and Visitors’ (GUV) Center 

will also open in the Research Support Building, 

eliminating the need for NSLS users to visit two 

buildings upon their arrival on site. When the new 

GUV Center becomes operational, it will allow 

all guests, visitors, and scientists (not including 

contractors) to complete their physical check-in 

process and fulfill other needs, such as picking up 

a key for an on-site dorm room, in one location. 

The hope is to provide weekday coverage from 7 

a.m. to 7 p.m. with some later hours on weekdays 

and Sundays to accommodate users and guests 

who cannot arrive during normal working days and 

hours. Once the GUV Center is open, NSLS users 

4-19
The User Administration Group (from left) Kathy Nasta, 

Gretchen Cisco, Mercy Baez, and Liz Flynn

will be able to go there to complete the check-in 

tasks that would normally be done at the NSLS 

User Administration registration desk. After this 

transition, the NSLS User Administration Office 

will remain in place to pre-process registrations 

prior to physical check-in, and for other user functions as mentioned at the beginning of this article.

Meetings and Workshops

The User Administration office has taken a more 

active role in the past year to help plan and organize major meetings and workshops at the NSLS, 

such as the RapiData course held every April 

and the Crystallization workshop, which is held 

in June. Of course, our largest effort in this area 

is the annual Users’ Meeting, which in May 2006, 

was the first held jointly with BNL’s Center for 

Functional Nanomaterials (CFN). Although there 

are always improvements to be made, most of the 

416 participants of the meeting were pleased with 

the joining of the two user communities, the main 

meeting and workshop programs, and logistical 

arrangements. There were six workshops offered: two concentrated on NSLS user interest, 

two focused on CFN interest, and the remaining 

two workshops were of interest to both communities. There were 34 vendors in exhibition and 

47 posters displayed. New ideas brought out by 

participants that we hope to implement for the 

2007 meeting include holding workshops and/or 

special times for NSLS/CFN technical staff to meet 

with vendors for product discussions, and holding 

a working luncheon to gather Proposal Review 

Panel members.

4-20
FACILITY REPORT

Organization and Mission

The NSLS Environment, Safety, Health, and 

Quality Division is managed by Andrew Ackerman and includes contributions from a mixture of 

department and assigned Laboratory personnel. 

The group includes nine professional staff, two administrative assistants, and one technician whose 

combined efforts amount to about seven full-time 

equivalent positions. These personnel manage 

the various ESH, Quality Assurance, and Training 

issues presented by facility and experiment operations.

There is a continued emphasis on integration of 

ESH&Q principles into all work at BNL and the 

NSLS. Laboratory initiatives for 2006 included 

a focus on electrical safety, implementation of 

the DOE Integrated Safety Management (ISM) 

principles, assurance of worker qualification, and 

control of workplace injury. The NSLS ESH&Q Division is committed to advancing those programs 

and managing the risks presented to personnel 

and the environment in support of the department’s scientific program.

2006 Activities

Everyone was busy in 2006 and there was considerable ESH&Q activity throughout the department. 

A few highlights pertinent to the user community 

are as follows:

● The NSLS completed independent registration with the Occupational Health and Safety 

Assessment Series (OHSAS) management 

system, an important goal for the Laboratory.

SAFETY REPORT

Andrew Ackerman

ESH&Q Manager

● The definition of worker qualification through 

training and experience was advanced, allowing improved work planning and a better 

understanding of worker skills.

● Configuration control and equipment identification on the beamlines were improved with 

better checklists, labeling, and photographs.

● Inspection of electrical equipment for compliance with Nationally Recognized Testing 

Laboratory (NRTL) requirements was implemented for user equipment.

● Electrical safety and Lock Out/Tag Out (LOTO) 

training requirements were redefined for 

beamline staff, resulting in a lowered training 

burden and the assignment of courses that 

are most applicable to the work performed.

● Personnel lead exposure resulting from shielding movement was well characterized and 

shown to be low and controlled with existing 

practices.

Several performance measures are tracked to 

follow the effectiveness of the ESH&Q programs. 

Performance in 2006 was excellent.

● There were no “Days Away, Restricted, 

Transferred” (DART) cases during 2006 or 

2005. That means no injuries or illnesses 

resulted in lost or restricted work time. There 

were some minor injuries, but nothing 

severe enough to require personnel to miss 

time at the Laboratory. The significance of 

this result is obvious to those who work at 

the NSLS and is an important parameter as 

these values are reported to and tracked 

carefully by the DOE as a key indicator of 

safety performance.

● There were two incidents that met the criteria 

for reporting within the Occurrence Reporting 

and Processing System (ORPS) – another 

parameter tracked closely by the DOE. One 

involved a chemical spill and the second a 

mistake in cutting an electrically energized 

wire. Neither resulted in injury or significant 

environmental insult. Both were carefully 

investigated and yielded some valuable 

lessons that were disseminated throughout 

the community.

● Training compliance was excellent and 

improved from last year.

● Routine workplace inspections yielded 

fewer findings per inspection and correction 

time was short.

● Numerous internal and external audits 

resulted in few findings, and the department 

Andrew Ackerman response was timely and organized.

4-21
● Waste generation continues to be low and 

well managed. The department’s mercury 

inventory has been significantly reduced 

through the replacement of mercury switches 

with solid-state devices and the elimination of 

mercury thermometer use. That effort resulted

in some extra waste, but also virtually 

eliminated the risk of a significant environ

mental mercury release and helped us meet 

an important DOE initiative.

● Radiation exposure remains very low; the 

measured collective dose this year was less 

than 50 mRem for some 3,000 personnel who 

were monitored.

There is more to report, but the summaries above 

provide an overall picture of the department’s 

activity and performance in ESH&Q for 2006. The 

NSLS programs are acknowledged throughout the 

Laboratory and by the DOE area office as excellent and there is much reason for pride in staff 

and user attention to safety and in keeping the facility a safe place to work. Good performance indicators and well-managed programs are important, 

but what is most important is that we completed 

an enormous amount of science last year without 

significant injuries or environmental insults.

2007 ESH&Q Initiatives

All that was completed last year must continue, 

and we must seek to improve. A brief summary of 

three important initiatives for 2007 is as follows:

Integrated Safety Management (ISM)

The DOE Integrated Safety Management program 

is aimed at assuring that work is planned, risks 

are controlled, and personnel are qualified. These 

principles are well implemented at the NSLS. 

Worker qualification is assured through training and experience, and all work at the facility is 

planned with attention to scoping and evaluating tasks, identifying and implementing pertinent 

controls, and providing feedback mechanisms for 

improvement.

Evaluation of the program in 2006 confirmed that 

overall implementation is good and that improvement efforts should focus on enhancing feedback 

mechanisms and personnel awareness to the application of ISM. That has begun and will continue 

into the next year with an emphasis on completing 

“End of Run” forms to collect better feedback, and 

with continued discussion of the ISM principles to 

assure that everyone understands how they apply 

to work at the NSLS.

10 CFR Part 851

“10 CFR Part 851” refers to a section in the 

federal code rules that incorporates many ESH 

standards into federal law applicable to the DOE. 

The incorporated rules include OSHA requirements and various health and safety “consensus” standards that cover many topics including 

electrical, fire, laser, pressure, chemical, biological, and nano-material safety. Evaluation of this 

new rule has begun. It has uncovered areas where 

improvements can be made and will likely result in 

requirement changes for the upcoming year.

Event and Issues Management

It is valuable to investigate and understand minor 

occurrences and learn from them with the hope to 

avoid a more significant event. That is the basis 

for a renewed focus on event management and 

emphasis on reporting all occurrences and investigating even those that are minor. Everyone is 

asked to help identify issues and resolve concerns 

before they become troublesome by reporting 

unexpected occurrences to the NSLS Operations 

staff. The approach of finding leading indicators to 

more significant events will be emphasized next 

year.

Summary

A continued focus on ESH&Q has obvious importance to everyone. 2006 was a great year and 

everyone’s involvement and commitment to safety 

is much appreciated. That success can continue in 

2007 if we remain vigilant. There will be program 

challenges as we seek to meet new requirements 

and improve on the old. The ESH&Q Division will 

work to assure that changes fit NSLS operations 

and are well communicated. The focus for the 

New Year will be, as always, safe science. Help us 

achieve that by knowing requirements, continuing 

to generate great science, and assuring that all 

the work we do includes evaluation and control of 

risks.

4-22
FACILITY REPORT

Organization and Mission

The NSLS Building Manager, Bob Kiss, coordinates the activities of BNL Plant Engineering 

departments involved in operating and maintaining the building to ensure that the integration and 

execution of facility work is efficiently and effectively managed and controlled, providing a safe, 

comfortable and hazard free environment for the 

NSLS staff and users. He is supported by Plant 

Engineering Trades Staff Supervisors in the maintenance and housekeeping of the NSLS Complex. 

The Mission of the Building Administration consists of multiple disciplines:

● To maintain the housekeeping and ES&H of 

the facilities in a showcase condition

● To ensure the general maintenance of all 

building systems

● To oversee the construction and installation 

of new equipment or facilities

● To ensure the maintenance and function of all 

security systems

● To promote energy awareness and conservation

● To function as the Work Control Coordinator 

for all building systems

● To comply with the Emergency Preparedness 

Program

2006 Activities

Change of Building Managers

2006 has been more than a busy and positive 

“business-as-usual” year for the NSLS. With the 

BUILDING ADMINISTRATION REPORT

Bob Kiss

NSLS Building Manager

NSLS-II project in the spotlight, the NSLS has 

seen many changes in staff. Many of our valued 

staff members are now doing double duty, continuing to provide support to our current facility while 

giving their expertise to the new and bright future 

of the NSLS-II. Several buildings were acquired 

for the NSLS-II to accommodate the transfer of 

staff into a central, convenient location. Gerry Van 

Derlaske has stepped up and become the Facility 

Manager for the NSLS-II and as such has played 

a major role in setting up the new facilities. During 

the past year, this had taken up the majority of 

Gerry’s time, leaving the day-to-day care of the 

NSLS to me, first as the Alternate Building Manager and then as the permanent Building Manager 

when Gerry officially became the NSLS-II Facility 

Manager at the end of 2006. We thank Gerry for 

his many years of leadership in this position and 

wish him well.

Work Planning and Controls 

With the emphasis on safety and work planning 

by DOE and OSHA, the NSLS has become an 

excellent example of Work Planning and Controls. 

Al Boerner, the NSLS Work Control Manager, has 

continued to ensure that all work is completed in 

a safe and complete manner. Under Al’s guidance, 

the number of work permits for tasks completed 

at the NSLS has grown to about 65 Work Permits 

for 2006. These permits range in complexity from 

a simple permit to ensure the safety of a contract 

vendor repairing a copy machine, to a complex 

permit coordinating the tasks of many BNL trades 

and NSLS staff for the installation of RF Cavities. 

With attention to safety, work planning and work 

controls, we have maintained our safety record of 

no lost workdays for more than three years.

Machine Shop Operations

Machine Shop Safety was an area that received 

extensive attention during 2006. BNL issued a new 

SBMS, detailing the updated requirements for the 

training, safe operation, maintenance, and inspections of all machine shops. As the NSLS User 

Machine Shop Manager, I was a member of the 

SBMS review committee and was able to provide 

NSLS Machine Shop Program policies for the 

SBMS. This resulted in the review and changes of 

the training requirements for anyone authorized to 

use the NSLS User Machine Shop and the NSLS 

Tech Shops. Major changes include required periodic retraining and review of all authorized users, 

monthly and yearly inspections of the shop by the 

shop manager, and restricting access to all maBob Kiss chines to only those individuals fully trained for the 

4-23
particular machine. The NSLS User Machine Shop 

was referred to as a prime example of a well-run 

and maintained facility. This past year has seen a 

change in management of the User Machine Shop. 

Since becoming a member of the NSLS in 2000, 

I had been the Shop Manager. With the many 

staffing changes at the NSLS, the responsibility 

of the NSLS User Machine has now been turned 

over to Dennis Carlson. Dennis has many years of 

machine shop experience, having been a member 

of the NSLS Beamline Development and Support 

group for many years. His experience and knowledge of the workings of the NSLS beamlines is a 

very valuable asset for the users of the machine 

shop. 

High Sensitivity Smoke Detector (HSSD)

In early 2006, at the end of last year’s winter 

maintenance period, the new HSSD was finetuned and tested. Having met and passed all the 

expected requirements and tests, the system was 

placed into full service. The testing of the system 

included simulation of various possible maintenance tasks that may trigger the alarms. These 

tasks included the bake-out of a cavity, soldering 

of large pipes, and the idling of a truck outside 

the area roll-up door. The system consists of a 

system of special PVC piping and nozzles located 

directly above the critical equipment in the NSLS 

power supply area. It is a continuous sampling 

system that pulls air samples through the nozzles 

and piping to a computer analyzer, providing early 

detection of any smoke or fire in the area well before it becomes a major issue. This early detection 

provides the operations coordinators with valuable 

extra time to investigate and shut down any equipment necessary to prevent a major incident. 

X9-X3 Transfer

The x-ray experimental floor received a major 

change with groups working together to “Green 

Field” the X3 beamline in 2005. With that portion 

of the project completed, the next phase of the 

project was to modify and relocate the X9 experimental end station enclosure (EESE) to X3. This 

was a major undertaking since the original EESE 

was too tall to fit at X3. The lead-lined panels 

were transported to the Central Fabrication Facility to be modified and then transported back and 

re-assembled in place at the X3 beamline. All the 

X9 beamline components were painstakingly removed and re-assembled at the new X3 location. 

Green Field of X9

With the completion of the X9 to X3 beamline, 

preparations for the new X9 beamline were begun. 

The most visible aspect of this task was to “Green 

Field” the area beginning with the removal and 

disposal of the old EESE. With the help of Plant 

Engineering Carpenter and Riggers, and thorough 

work planning using the BNL Work Permit program, the removal of the EESE was completed 

quickly and safely. Once the EESE was removed, 

work continued to remove all remaining excess 

equipment, clean, and make necessary repairs to 

the floor to prepare for the planning and installation of the new line later this year. 

Library Renovations

After many years of use, the NSLS ChasmanGreen Library was remodeled. With the assistance 

of Plant Engineering, the old carpet and platform 

was removed and new carpets installed. New ceiling tiles were installed and the walls received a 

fresh coat of paint. Bookcases were rearranged, 

excess file cabinets removed, old periodicals were 

scanned to computer files, and many volumes of 

reference books were placed into storage until the 

renovations were complete. 

In 2007, the reference books will be sorted and arranged for easy access and plans for new furniture 

will be finalized. Plans also include the installation 

of a retractable projection screen in the ceiling to 

allow the library to be used as a conference room. 

A small area will be set up and equipped with a 

computer station, and a fax/copy machine for use 

by visiting users. These renovations will result in 

a warm, quiet, and friendly atmosphere to gather 

and relax or just get away from the busy life of 

running an experiment. 

Behind-the-Scenes Accomplishments

Many times during the year there are tasks and 

jobs completed that go unnoticed by the majority 

of staff and users. Most times these are tasks that 

do not affect the everyday workings of the NSLS, 

but once completed, they make life a little safer 

or comfortable for everyone. Most of these do 

not take much effort on the part of the NSLS, but 

require much coordination between building management, Plant Engineering, contractors and other 

BNL departments. Some of this year’s behind-thescenes accomplishments include for following:

● Parking lots outside the east side of the buildThe renovated Green-Chasman Library

4-24
FACILITY REPORT

ing were cleaned, repaired, and painted.

● A ramp was installed outside the east rollup door entrance to eliminate the curb to the 

bicycle rack storage area. This also allows an 

electric vehicle to be parked under the over

hang and charged overnight. This was completed with funding from the BNL Safety 

Solutions (S2) project.

● The NSLS User Administration Office, along 

with several other offices and the ChasmanGreen Library received new carpets.

● The LEGS Helium trailer was removed to 

create space for an LN2 to N2 heat 

exchanger. Removal of the trailer eliminated 

the need to install another concrete pad to the 

system. 

● The XLS trailer was emptied and disconnected in preparation for removal. 

Conclusion

Year after year, thousands of people come to 

the NSLS, some to use the facility for research, 

some to attend research conferences and training 

courses, and others to tour our facility just to find 

out “what do they do there.” Whoever they are, no 

matter where they come from, it is wonderful to 

know that they leave with a better understanding 

and appreciation of science. A large part of their 

appreciation must go to the talented support staff 

that keeps the NSLS facility up and running, and 

showcases the research community. 

4-25
FACTS AND FIGURES
FACTS AND FIGURES

5-3

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, 300 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 2,100 scientists representing almost 400 institutions, 47 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, provided 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 peerreviewed proposal system. 

The NSLS currently has 51 x-ray and 14 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 2006, the NSLS had 18 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. 

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.

BEAMLINE GUIDE ABBREVIATIONS

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

HARMST

HIGH ASPECT RATIO MICROSYSTEMS

TECHNOLOGY

IRMS

INFRARED MICROSPECTROSCOPY

MAD

MULTI-WAVELENGTH ANOMOLOUS DISPERSION

MCD

MAGNETIC AGNETIC CIRCULAR CIRCULAR DICHROISM DICHROISM

NEXAFS

NEAR EDGE X-RAY ABSORPTION

SPECTROSCOPY

PEEM

PHOTO EMISSION ELECTRON MICROSCOPY

SAXS

SMALL ANGLE X-RAY SCATTERING

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 SCATTERING

XAS

X-RAY ABSORPTION ABSORPTION SPECTROSCOPY SPECTROSCOPY

XPS

X-RAY PHOTOELECTRON PHOTOELECTRON

SPECTROSCOPY SPECTROSCOPY

XRD

X-RAY DIFFRACTION DIFFRACTION

XSW

X-RAY DIFFRACTION DIFFRACTION,STANDING STANDING WAVES
5-4

VUV-IR BEAMLINES

Beamline Source Technique Energy Range Type Organization

U1A Bend XAS

EXAFS

NEXAFS

270-900 eV PRT ExxonMobil Research and Engineering Co.

U2A Bend IRMS

High Pressure Research

IR spectroscopy

30-8000 cm-1 FB BNL-NSLS

Carnegie Institution of Washington

COMPRES

U2B Bend IRMS

IR spectroscopy

50-4000 cm-1 PRT Case Western Reserve University

U3C Bend Metrology 50-1000 eV PRT Bechtel Nevada

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

Sandia National Laboratory

U4A Bend UPS 10-250 eV PRT Army Research Laboratory

North Carolina State University

Rutgers University

University of North Carolina

U4B Bend X-ray scattering, resonant

MCD

UPS

X-ray fl uorescence spectroscopy

XPS

20-1200 eV PRT Montana State University

Northeastern University

U5UA Insertion 

Device

ARPES

UPS, spin-resolved

PEEM

15-150 eV FB BNL-CFN

U7A Bend NEXAFS

XPS

180-1200 eV PRT BNL-Chemistry

Dow Chemical Company

NIST

University of Michigan

U9B Bend UV-CD

UV fl orescence spectroscopy

0.8 - 8.0 eV PRT BNL-Biology

U10B Bend IRMS 500-4000 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
FACTS AND FIGURES

5-5

Beamline Source Technique Energy Range Type Organization

X-RAY BEAMLINES

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

X1A2 Insertion 

Device

STXM 0.25-1 keV PRT Stony Brook University

X1B Insertion 

Device

X-ray scattering, coherent

XAS

X-ray fl uorescence spectroscopy

XPS

0.2-1.6 keV PRT Boston University

Thomas Jefferson National Accelerator Facility

University of Illinois

X2B Bend X-ray microtomography 8-35 keV PRT ExxonMobil Research and Engineering Co.

X3A Bend MAD

Macromolecular crystallography

5-15 keV PRT Albert Einstein College of Medicine

Case Western Reserve University

Rockefeller University

Sloan-Kettering Institute

X3B Bend XAS

EXAFS

5-15 keV PRT Case Western Reserve University

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

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
5-6

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 Inst. and State University

X6A Bend MAD

Macromolecular crystallography

6.0-23 keV FB BNL-NSLS

X6B Bend XRD, surface

WAXD

X-ray refl ectivity

SAXS

GISAXS

6.5-19 keV FB BNL-CFN

BNL-NSLS

X7B Bend XRD, single crystal

XRD, time resolved

WAXD

WAXS

5-21 keV PRT BNL-Chemistry

General Electric

X8A Bend Metrology 1.0-5.9 keV PRT Bechtel Nevada

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

Sandia National Laboratory

X8C Bend MAD

Macromolecular crystallography

5-19 keV PRT Biogen Incorporated

Biotechnology Research Institute

Hoffmann-La Roche

National Institutes of Health

X10A Bend XRD, powder

WAXD

SAXS

WAXS

8-11 keV PRT ExxonMobil Research and Engineering Co.

X10B Bend XRD, powder

XRD, surface

WAXD

X-ray refl ectivity

X-ray scattering, surface

WAXS

14 keV PRT ExxonMobil Research and Engineering Co.

X10C Bend XAS

EXAFS

NEXAFS

4-24 keV PRT ExxonMobil Research and Engineering Co.

X11A Bend DAFS

XAS

EXAFS

NEXAFS

4.5-35 keV PRT BNL-Material Science

BNL-Environmental Science

Canadian Light Source

ETH Labs - Zuerich

Natural Resources Canada

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Stony Brook University

Sarah Lawrence College
FACTS AND FIGURES

5-7

Beamline Source Technique Energy Range Type Organization

X11B Bend XAS

EXAFS

NEXAFS

5.0-23 keV PRT BNL-Environmental Science

BNL-Material Science

Canadian Light Source

ETH Labs - Zuerich

Natural Resources Canada

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Stony Brook University

Sarah Lawrence College

X12B Bend MAD

Macromolecular crystallography

5-20 keV PRT BNL-Biology

X12C Bend MAD

Macromolecular crystallography

5.5-20.0 keV PRT BNL-Biology

X13A Insertion 

Device

X-ray scattering, resonant

MCD

0.2-1.6 keV FB BNL-NSLS

X13B Insertion 

Device

Microdiffraction Imaging 4-16 KeV FB BNL-NSLS

BNL-CFN

Columbia University

IBM

X14A Bend MAD

XRD, powder

XRD, single crystal

XRD, time resolved

WAXD

X-ray refl ectivity

5-26 keV PRT Oak Ridge National Laboratory

Tennessee Technological University

University of Tennessee

X15A Bend XSW

DEI

3-25 keV XSW

10-60 keV DEI

FB BNL-NSLS

Northwestern University

X15B Bend XAS

EXAFS

NEXAFS

0.8-15 keV PRT BNL-Environmental Science

Lucent Technologies, Inc.

Stony Brook University

Temple University

University of Texas @ Austin

X16C Bend XRD, powder 4.5-25 keV PRT Stony Brook University

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

X17B2 Insertion 

Device

XRD, powder

XRD, time resolved

High pressure research

20-130 keV FB BNL-NSLS

COMPRES

Stony Brook University
5-8

Beamline Source Technique Energy Range Type Organization

X17C Insertion 

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV FB COMPRES

University of Chicago

X18A Bend XRD, powder

XRD, single crystal

XRD, surface

WAXD

X-ray refl ectivity

X-ray scattering, surface

WAXS

4-19 keV PRT BNL-Chemistry

Indiana University @ Bloomington

Pennsylvania State University

Purdue University

Stony Brook University

University of Missouri @ Columbia

X18B Bend XAS

EXAFS

NEXAFS

4.8-40 keV FB BNL-Chemistry

BNL-Electrochemistry

BNL-NSLS

ORNL

University of Delaware

UOP LLC

Yeshiva University

X19A Bend X-ray scattering, resonant

XAS

EXAFS

NEXAFS

2.1-17 keV FB BNL-Chemistry

BNL-Electrochemistry

BNL-NSLS

ORNL

University of Delaware

UOP LLC

Yeshiva University

X19C Bend XRD, surface

X-ray topography

X-ray refl ectivity

X-ray scattering, liquid

X-ray scattering, surface

6-17 keV PRT Arizona State University

Fairfi eld Crystal Technology, LLC

Kansas State University

Kyushu University

SUNY @ Albany

Stony Brook University

University of Illinois @ Chicago

X20A Bend XRD, single crystal

Microdiffraction Imaging

X-ray refl ectivity

X-ray scattering, surface

4.5-13 keV PRT IBM Research Division

X20C Bend XRD, single crystal

XRD, surface

XRD, time resolved

X-ray refl ectivity

X-ray scattering, surface

4-11 keV PRT IBM Research Division

X21 Insertion 

Device

XRD, single crystal

XRD, surface

X-ray scattering, magnetic

X-ray scattering, resonant

X-ray scattering, surface

SAXS

5-15 keV FB BNL-NSLS

Boston University

University of Vermont

X22A Bend XRD, single crystal

XRD, surface

WAXD

X-ray refl ectivity

X-ray scattering, surface

WAXS

10.7 keV

32 keV

PRT BNL-CMPMSD

BNL-Chemistry
FACTS AND FIGURES

5-9

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-CMPMSD

BNL-CFN

Harvard University

X22C Bend XRD, single crystal

XRD, surface

X-ray refl ectivity

X-ray scattering, magnetic

X-ray scattering, surface

3-12 keV PRT BNL-CMPMSD

Massachusetts Institute of Technology

Rutgers University

X23A2 Bend XRD, powder

DAFS

XAS

EXAFS

NEXAFS

4.7-30 keV PRT NIST

X23B Bend XRD, powder

XAS

EXAFS

NEXAFS

4-10.5 keV PRT Hunter College

Montana State University

Naval Research Laboratory (NRL)

New Jersey Institute of Technology

Sarah Lawrence College

X24A Bend XSW

Auger spectroscopy

EXAFS

X-ray fl uorescence spectroscopy

XPS

1.8-5 keV PRT NIST

X24C Bend X-ray refl ectivity

UV photoabsorption spectroscopy

UPS

XAS

0.006-1.8 keV PRT Naval Research Laboratory (NRL)

Universities Space Research Association

X25 Insertion 

Device

MAD

Macromolecular crystallography

3-28 keV FB BNL-Biology

BNL-NSLS

X26A Bend Microdiffraction Imaging

X-ray microprobe

3-30 keV PRT BNL-Environmental Science

University of Chicago

University of Georgia

X26C Bend MAD

Macromolecular crystallography

5-20 keV PRT BNL-Biology

Cold Spring Harbor Laboratory

Stony Brook University

X27A Bend X-ray microprobe 4.5-20 keV FB BNL-Environmental Science

BNL-NSLS

Stony Brook University

X27B Bend HARMST 8-40 keV PRT BNL-Nonproliferation & National Security

X27C Bend XRD, time resolved

WAXD

SAXS

WAXS

9 KeV PRT Air Force Research Laboratory

Dow Chemical Company

National Institutes of Health

Naval Surface Warfare Center

Stony Brook University
5-10

Beamline Source Technique Energy Range Type Organization

X28C Bend X-ray footprinting White Beam PRT Case Western Reserve University

X29A Insertion 

Device

MAD

Macromolecular crystallography

6-15keV PRT BNL-Biology

Case Western Reserve University
FACTS AND FIGURES

5-11

NSLS LINAC PARAMETERS AS OF DECEMBER 2006

 Injection Energy 100 keV

 Final Energy 120 MeV

 Number of Sections 3

 Number of Klystrons 3

 Frequency 2856 MHz

NSLS BOOSTER PARAMETERS

 Booster Injection Energy 120 MeV

 Booster Extraction Energy 736 MeV

 Circumference 28.35 m

 Number of Superperiods 4

 Dipole Bend Radius 1.91 m

 Nominal Horizontal Tune 2.42

 Nominal Vertical Tune 1.37

 Maximum Horizontal Beta Function 8.63 m

 Minimum Horizontal Beta Function 1.01 m

 Maximum Vertical Beta Function 5.26 m

 Minimum Vertical Beta Function 1.73 m

 Maximum Dispersion Function 1.21 m

 Minimum Dispersion Function 0.41 m

 Momentum Compaction 0.106

 RF Frequency 52.88 MHz

 RF Peak Voltage 25 kV

Momentum Acceptance ±0.0025

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 Qua dru pole 4 68.82 0.3

 Q2 Quadrupole 4 93.60 0.3

 SF Sextupole 4 1223.7 0.2
5-12

VUV STORAGE RING PARAMETERS AS OF DECEMBER 2006

 Stored Electron Beam Energy 0.808 GeV

 Injected Current 1.0 amp (1.06 x 1012e-)

 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 each)

 Magnet Complement 24 Quadrupole (0.3 meters each)

 12 Sextupole in two families (0.2 meters each) 

 STORAGE RING CHARACTERISTICS

 Number of Dipole Ports 18

 Number of Insertion Device Straight Sections 2

 Maximum Length of Insertion Devices 2.25 meters

 Radiated Power 20.4 kW/amp of beam

 Power per Horizontal Milliradian (@ 1A) 3.2 W

 RF Frequency (frf) 52.887 MHz

 B(ρ) 1.41 Tesla (1.91 meters)

 Electron Orbital Period 170.2 nanoseconds

Number of RF Buckets 9

 Typical Bunch Mode 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 kV (20 kV)

 Design RF Power with 52 MHz (with 211 MHz) 50 kW (10 kW)

 Synchrotron Tune (νs) 0.0018

 Natural Energy Spread (σe/E) 5.0 x 10-4 (I

b

< 20 mA)

 Bunch Length (2σ) 10 cm (Ib< 20 mA)

 (2σ with 211 MHZ Bunch Lengthening) 38 cm

 Horizontal Damped Emittance (εx) 1.60 nm-rad

 Vertical Damped Emittance (εy) ≥ 0.35 nm-rad (4nm-rad in normal ops.)*

{

 8 Bending Magnets (1.5 meters each)

 24 Quadrupole (0.3 meters each)

 12 Sextupole in two families (0.2 meters each) 

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 nor mal 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

* εx is adjustable
FACTS AND FIGURES

5-13

X-RAY STORAGE RING PARAMETERS AS OF DECEMBER 2006

 Stored Electron Beam Energy 2.800 GeV

 Maximum Operating Current 300 mA

 Lifetime ~20 hours

 Circumference 170.08 meters

PHOTON CRITICAL WAVELENGTH (ENERGY)

 λc(Ec) 1.36 T 1.75 Å (7.1 keV)

 λc(Ec) at 5.0 T (W) 0.48 Å (26.1 keV)

LATTICE STRUCTURE (CHASMAN-GREEN) SEPARATED FUNCTION, QUAD TRIPLETS

 Number of Superperiods 8

 16 Bending (2.70 meters each)

 Magnet Complement 40 Quadrupole (0.45 meters each)

 16 Quadrupole (0.80 meters each)

 32 Sextupole (0.20 meters each)

STORAGE RING CHARACTERISTICS

 Number Beam Port on Dipoles 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

 Electron Orbital Period 567.2 nanoseconds

 B(ρ) 1.36 Tesla (6.875 meters)

 Damping Times τx=τy= 4 msec; τε = 2 msec

 Nominal Tunes (νx,νy) 9.8, 5.7

 Momentum Compaction 4.10-3

 RF Frequency (frf) 52.88 MHz

 Radiated Power for Bending Magnets 237 kW (300 mA)

 RF Peak Voltage 1120 kV

 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

 Number of RF Buckets 30

 Typical Bunch Mode (fi lled buckets) 25

 Horizontal Damped Emittance (εx) 6.2 x 10-8 m-rad

 Vertical Damped Emittance (εy) 3.4 x 10-10 m-rad

 Power per Horizontal Milliradian (0.3A) 38 W

{ 16 Bending (2.70 meters each)

 40 Quadrupole (0.45 meters each)

 16 Quadrupole (0.80 meters each)

 32 Sextupole (0.20 meters each)

INSERTION DEVICE PARAMETERS

 Betatron Function (βx, βy) 1.16 m, 0.33 m

 Source Size (σx,σy) 307 μm, 11 μm

 Source Divergence (σx′, σy′) 231 μrad, 32 μrad

ARC SOURCE PARAMETERS

 Betatron Function (βx,βy) 1.0 to 3.5 m, 11.4 to 23.6 m

 Dispersion Function (ηx,η′

x

) 0.03 to 0.25, -0.25 to 0.08

 αx,y = -β’ x,y/2 0.38 to 1.65, -2.3 to 3.6

 γx,y =(1 +α2

x,y)/βx,y 1.073 to 1.133 m-1, 0.54 to 0.58 m-1

 Source Size (σx,σy) 260 to 464 μm, 62 to 90 μm

 Source Divergence (σx′,σy′) 261 to 352 μrad, 13.5 to 14.1 μrad
5-14

Note: Delivered hours are only 

those accumulated during 

scheduled operations. 

Unscheduled operations do not 

contribute to this total.

1

 Operations during scheduled time

2

 Operations compared to total 

 scheduled time

 

January 419 98.4% 118.0% 0 - -

February 570 98.6% 108.4% 372 91.8% 100.9%

March 615 99.2% 111.9% 588 98.1% 106.8%

April 597 99.4% 111.1% 557 94.9% 105.9%

May 420 99.8% 121.7% 275 96.7% 106.1%

June 596 98.3% 110.9% 555 89.6% 98.1%

July 467 86.9% 109.6% 428 95.6% 116.5%

August 613 98.5% 111.2% 565 93.8% 106.5%

September 599 90.8% 101.9% 577 86.4% -

October 571 98.9% 114.4% 563 96.5% 108.1%

November 470 96.6% 105.3% 382 97.3% 103.5%

December 0 - - 0 - -

5937 4862

Calendar 2006

Delivered 5756 97.0% 110.9% 4562 93.8% 104.9%

CALENDAR YEAR 2006

PLANNED

MONTH HOURS

PLANNED

HOURS

VUV ACTUAL CY 06

RELIABILITY1 AVAILABILITY2

X-RAY ACTUAL CY 06

RELIABILITY1 AVAILABILITY2

Other Activities UV/IR X-ray

Studies 1.0% 4.4%

Comm/Cond. 2.5% 5.7%

Holiday 2.4% 2.4%

Injection 1.1% 2.1%

Unscheduled Downtime 2.1% 3.4%

Interlock 0.0% 0.6%

CALENDAR YEAR 2006 NSLS MACHINE ACTIVITIES

Key

Scheduled Operations

Unscheduled Operations

Maintenance

Other

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PUBLICATIONS
PUBLICA TIONS

The following pages list all papers published in the 2006 calendar year as reported to the NSLS by February 28, 2007. 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 lists 

the number of publications reported 

to the NSLS during the 2006 fiscal 

year (Oct. 1, 2005 – Sept. 30, 2006) 

and published between 2003 and 

2006. Although some of these publications were published earlier than 

FY 2006, 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 2006 calendar year 

and reported to the NSLS as of 

February 28, 2007. These numbers 

are slightly lower than the fiscal 

year values because they contain 

only publications from 2006 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 peer-reviewed. 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 2003-2006, 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 2006, NSLS users and staff had 921 publications – a record high for the facility. Moreover, 228 

papers were published in premier journals, representing 25% of the total publications from the facility, and 

demonstrating the high impact of NSLS science.

PUBLICATIONS

Reported in 

Fiscal Year 

2006*

Published in 

Calendar Year 

2006**

Journals, peer-reviewed, premier 228 199

Journals, other peer-reviewed 532 489

Journals, non peer-reviewed 33 28

Total Journals and Magazines 793 716

Books/Chapters in Books 4 4

Published Conference Proceedings 79 40

Reports: Technical, Formal, Informal 1 0

Theses/Dissertations 33 25

Patents 11 1

Total Misc. Publications 128 70

Total Publications 921 786

NSLS VUV User Publications 87 67

NSLS X-Ray User Publications 734 627

NSLS Staff Publications 100 92

921 786

*

 Publications reported to the NSLS from Oct 1, 2005 – Sept. 30, 2006 and published 

between 2003 – 2006.

** Publications published in 2006 as reported to the NSLS by Feb. 28, 2007.

6-3
6-4

NSLS USERS

Beamline U1A

S Buzby, M Barakat, H Lin, C Ni, S Rykov, J Chen, S 

Shah, Visible Light Photocatalysis with NitrogenDoped Titanium Dioxide Nanoparticles Prepared by 

Plasma Assisted Chemical Vapor Deposition, J. Vac. 

Sci. Technol., B, 24 (3), 1210 (2006).

G Liu, K Rider, W Nam, S Fonash, S Kim, Dendritic 

Aggregation of Oligothiophene During Desorption 

of 2,5-Diiodothiophene Multilayer and TopographyInduced Alignment of Oligothiophene Nanofi bers, J. 

Phys. Chem. B, 110, 20197-20201 (2006).

M Smith, R Lobo, The Local and Surface Structure 

of Ordered Mesoporous Carbons from Nitrogen 

Sorption, NEXAFS and Synchrotron Radiation 

Studies, Microporous Mesoporous Mater., 92 (1-3), 

81-93 (2006).

Beamline U2A

J Ciezak, T Jenkins, Z Liu, R Hemley, High Pressure 

Vibrational Spectroscopy of Energetic Materials: 

Hexahydro-1,3,5-trinitro-1,3,5-triazine, J. Phys. Chem. 

A, 59-63, 5 (2006).

L Dobrzhinetskaya, Z Liu, P Cartigny, J Zhang, D 

Tchkhetia, R Hemley, H Green, Synchrotron infrared 

and Raman spectroscopy of microdiamonds from 

Erzgebirge, Germany, Earth Planet Sci. Lett., 248, 

325-334 (2006).

S Ho, C Yan, Z Liu, H Mao, R Hemley, Prospects for 

Large Single Crystal CVD Diamonds, Ind. Diamond 

Rev., 66, 28-32 (2006).

G Iezzi, Z Liu, G Ventura, Synchrotron Infrared 

Spectroscopy of Synthetic Na(NaMg)Mg5Si8O22(OH)2 

up to 30 GPa: Insight on a New High-Pressure 

Amphibole Polymorph, Am. Mineral., 91, 479-482 

(2006).

D Klug, J Tse, Z Liu, R Hemley, Hydrogen-bond Dynamics 

and Fermi Resonance in High-pressure Methane 

Filled Ice, Chem. Phys., 125, 154509 (2006).

J Smedley, I Ben-Zvi, A Burrill, X Chang, J Grimes, 

T Rao, Z Segalov, Q Wu, Electron Amplifi cation in 

Diamond, 2006 Workshop on Advanced Accelerator 

Concepts (AAC06), Vol 887, p. 672-4, sponsored by 

Argonne National Laboratory (2006).

H Zhang, B Chen, B Gilbert, J Banfi eld, Kinetically 

Controlled Formation of a Novel Nanoparticulate ZnS 

with Mixed Cubic and Hexagonal Stacking, J Mater. 

Chem., 16 (3), 249-254 (2006).

Beamline U2B

K Jones, H Feng, E Stern, U Neuhausler, J Osan, N 

Marinkovic, Z Song, Properties of New York/New 

Jersey Harbor Sediments, Acta Phys. Pol. A, 109 (3), 

279-286 (2006).

J Smedley, I Ben-Zvi, A Burrill, X Chang, J Grimes, 

T Rao, Z Segalov, Q Wu, Electron Amplifi cation in 

Diamond, 2006 Workshop on Advanced Accelerator 

Concepts (AAC06), Vol 887, p. 672-4, sponsored by 

Argonne National Laboratory (2006).

P Yu, An Emerging Method for Rapid Characterization 

of Feed Structures and Feed Component Matrix at 

a Cellular Level and Relation to Feed Quality and 

Nutritive Value, Arch. Anim. Nutr., 60, 229-244 (2006).

Beamline U3C

G Rochau, J Bailey, G Chandler, T Nash, D Nielsen, 

G Dunham, O Garcia, N Joseph, J Keister, et al., 

Energy Dependent Sensitivity of Microchannel Plate 

Detectors, Rev. Sci. Instrum., 77, 10E323 (2006).

C Sorce, J Schein, F weber, K Widmann, K Campbell, 

E Dewald, R Turner, O Landen, K Jacoby, et al., Soft 

X-ray Power Diagnostic Improvements at the Omega 

Laser Facility, Rev. Sci. Instrum., 77, 10E518 (2006).

Beamline U4A

T Ellis, K Park, M Ulrich, S Hulbert, J Rowe, Interaction of 

Metallophthalocyanines (Mpc, M=Co, Ni) on Au(001): 

Ultraviolet Photoemission Spectroscopy and Low 

Energy Electron Diffraction Study, J. Appl. Phys., 100, 

093515-10 (2006).

A Mathew, Study of Interfacila Phenomena in Thin Films 

using Photoelectron Spectroscopy, M.S. Thesis, 

University of Delaware, Newark (2006).

E Nemanick, P Hurley, L Webb, D Knapp, D Michalak, 

B Brunschwig, N Lewis, Chemical and Electrical 

Passivation of Single-Crystal Silicon(100) Surfaces 

Through a Two-Step Chlorination/Alkylation Process, 

J. Phys. Chem. B, 110, 14770-14778 (2006).

R O’Connor, G Hughes, P Glans, T Learmonth, K Smith, 

X-ray Photoemission and X-ray Absorption Studies of 

Hf-silicate Dielectric Layers, Appl. Surf. Sci., 253 (5), 

2770-2775 (2006).

R O’Connor, S McDonnell, G Hughes, K Smith, 

Photoemission Studies of Pulsed-RF Plasma Nitrided 

Ultra-thin SiON Dielectric Layers, Surf. Sci., 600, 532-

536 (2006).

M Traub, J Biteen, D Michalak, L Webb, B Brunschwig, 

N Lewis, High-Resolution X-ray Photoelectron 

Spectroscopy of Chlorine-Terminated GaAs(111)A 

Surfaces, J. Phys. Chem. B, 110, 15641-15644 

(2006).

M Ulrich, J Rowe, J Keister, H Niimi, L Fleming, G 

Lucovsky, Comparison of Ultrathin SiO2/Si(100) and 

SiO2/Si(111) Interfaces from Soft X-ray Photoelectron 

Spectroscopy, J. Vac. Sci. Technol., B, 24, 2132 

(2006).

Beamline U4B

D Hill, D Arena, R Bartynski, P Wu, G Saraf, Y Lu, 

l Wielunski, R Gateau, J Dvorak, et al., Room 

Temperature Ferromagnetism in MN Ion Implanted 

Epitaxial ZnO Films, Phys. Status Solidi (a), 203 (15), 

3836-3843 (2006).

C Kinane, A Suszka, C Marrows, B Hickey, D Arena, J 

Dvorak, T Charlton, S Langridge, Soft x-ray resonant 

magnetic scattering from an imprinted magnetic 

domain pattern , Appl. Phys. Lett., 89, 092507 (2006).

E Negusse, J Holroyd, M Liberati, J Dvorak, Y Idzerda, 

T Santos, J Moodera, E Arenholz, Effect of Electrode 

and EuO Thickness on EuO-Electrode Interface in 

Tunneling Spin Filter, J. Appl. Phys., 99, 08E507 

(2006).
PUBLICA TIONS

6-5

K Neupane, J Shearer, Infl uence of Amide/Amine vs NisAmide Coordination in Nickel Superoxide Dismutase, 

Inorg. Chem., 45, 10552-10566 (2006).

H Noh, S Yeo, J Kang, C Zhang, S Cheong, S Oh, P 

Johnson, Jahn-Teller Effect in Spinel Manganites 

Probed by Soft X-ray Absorption Spectroscopy, Appl. 

Phys. Lett., 88, 081911 (2006).

P Wu, G Saraf, Y Lu, D Hill, R Gateau, L Wielunski, R 

Bartynski, D Arena, J Dvorak, et al., Ferromagnetism 

in Fe-Implanted a-plane ZnO Films, Appl. Phys. Lett., 

89, 012508 (2006).

S Yoon, Y Chen, A Yang, T Goodrich, X Zuo, D Arena, 

K Ziemer, C Vittoria, V Harris, Oxygen-defect-induced 

Magnetism to 880 K in Semiconducting Anatase TiO2-

delta Films, J. Phys.: Condens. Matter, 18 (27), L355-

L361 (2006).

Beamline U4IR

H Liu, M Quijada, D Romero, D Tanner, A Zibold, 

G Carr, H Berger, L Forro, L Mihaly, et al., Drude 

Behavior in the Far-Infrared Conductivity of Cuprate 

Superconductors, Ann. Phys., 15 (7), 606-618 (2006).

Beamline U5UA

I Baek, W Kim, E Vescovo, H Lee, Effect of Ni 

Concentration on Quantum-well States of the Alloy 

System Ag/Fe1-xNix: A Spin- and angle-Resolved 

Photoemission Study, Phys. Rev. B, 74, 113302 

(2006).

L Colakerol, T Veal, H Jeong, L Plucinski, A DeMasi, 

T Learmonth, P Glans, S Wang, Y Zhang, et al., 

Quantized Electron Accumulation States in Indium 

Nitride Studied by Angle-Resolved Photoemission 

Spectroscopy, Phys. Rev. Lett., 97, 237601 (2006).

H Lee, I Baek, S Kim, E Vescovo, Electronic and 

Magnetic Properties in Fe-Based Fe1-xNix, Fe1-xCox, 

and Fe1-xVx Films on W(110), Surf. Sci., 600, 4137-

4142 (2006).

H Lee, I Baek, E Vescovo, Spin Reorientation Transition 

in Fe-Rich Alloy Films on W(110): The Role of 

Magnetoelastic Anisotropy and Structural Transition, 

Appl. Phys. Lett., 89, 112516 (2006).

E Vescovo, Reply to “Comment on `Oxidation of the 

Fe(110) surface: An Fe3O4(111)/Fe(110) bilayer’ “, 

Phys. Rev. B: Condens. Matter, 74, 26406 (2006).

E Vescovo, Spin-Resolved Photoemission Studies of 

Magnetic Films, Modern Techniques for Characterizing 

Magnetic Materials , p. 600, Kluwer Academic Pub, 

New York (2006).

Beamline U7A

B Clare, K Efi menko, D Fischer, J Genzer, N Abbott, 

Orientations of Liquid Crystals in Contact with 

Surfaces that Present Continuous Gradients of 

Chemical Functionality, Chem. Mater., 18, 2357-2363 

(2006).

D DeLongchamp, Y Jung, D Fischer, E Lin, P Chang, 

V Subramanian, A Murphy, J Frechet, Correlating 

Molecular Design to Microstructure in Thermally 

Convertible Oligothiophenes: The Effect of Branched 

Versus Linear End Groups, J. Phys. Chem. B, 110, 

10645-10650 (2006).

D DeLongchamp, M Ling, Y Jung, D Fischer, M Roberts, 

E Lin, Z Bao, Thickness Dependence of Microstructure 

in Semiconducting fi lms of an Oligofl uorene Derivative, 

J. Am. Chem. Soc., 128, 16579-16586 (2006).

D Fischer, A Moodenbaugh, Q Li, G Gu, Y Zhu, 

J Davenport, D Welch, Soft X-ray Absorption 

Spectroscopy of the MgB2 Boron K Edge in an MgB2/

Mg Composite, Mod. Phys. Lett. B, 20 (19), 1207-1216 

(2006).

J Genzer, K Efi menko, D Fischer, Formation Mechanisms 

and Properties of Semifl uorinated Molecular Gradients 

on Silica Surfaces, Langmuir, 22, 8532-8541 (2006).

B Haines, Catalytic Hydrodechlorination of Chlorinated 

Aromatics on the Pt(111) Surface, Ph.D. Thesis, 

University of Michigan, Ann Arbor (2006).

T Hemraj-Benny, S Banerjee, S Sambasivan, M 

Balasubramanian, D Fischer, D Lowndes, W Han, J 

Misewich, S Wong, et al., Near-Edge X-ray Absorption 

Fine Structure Spectroscopy as a Tool for Investigating 

Nanomaterials, Small, 2 (1), 26-35 (2006).

T Hemraj-Benny, Investigating the Structural and 

Electronic Properties of Carbon Nanotubes upon 

Chemical Functionalization and Purifi cation, Ph.D. 

Thesis, Stony Brook University, Stony Brook (2006).

A Hexemer, Order and Disorder of Block Copolymers 

and Particles on Surfaces with Topology, PhD Thesis, 

UCSB, Santa Barbara (2006).

D Krapchetov, H Ma, A Jen, D Fischer, Y Loo, HighSensitivity Transmission IR Spectroscopy for the 

Chemical Identifi cation and Structural Analysis of 

Conjugated Molecules on Gallium Arsenide Surfaces, 

Langmuir, 22, 9491-9494 (2006).

S Krishnan, R Ward, A Hexemer, K Sohn, K Lee, E 

Angert, D Fischer, E Kramer, C Ober, Surfaces 

of Fluorinated Pyridinium Block Copolymers with 

Enhanced Antibacterial Activity, Langmuir, 22 (26), 

11255-11266 (2006).

S Krishnan, R Ayothi, A Hexemer, J Finlay, K Sohn, 

R Perry, C Ober, E Kramer, M Callow, et al., AntiBiofouling Properties of Comblike Block Copolymers 

with Amphiphilic Side Chains, Langmuir, 22 (11), 

5075-5086 (2006).

S Krishnan, N Wang, C Ober, J Finlay, M Callow, J 

Callow, A Hexemer, K Sohn, E Kramer, D Fischer, 

Comparison of the Fouling Release Properties of 

Hydrophobic Fluorinated and Hydrophilic PEGylated 

Block Copolymer Surfaces, Biomacromolecules, 7 (5), 

1449-1462 (2006).

S Krishnan, C Ober, A Hexemer, E Kramer, D Fischer, 

Compositional Depth Profi ling of Block Copolymer 

Surfaces using NEXAFS, Polym. Mater. Sci. Eng., 94, 

672-673 (2006).

C Lee, P Gong, G Harbers, D Grainger, D Castner, L 

Gamble, Surface Coverage and Structure of Mixed 

DNA/Alkylthiol Monolayers on Gold: Characterization 

by XPS, NEXAFS, and Fluorescence Intensity 

Measurements, Anal. Chem., 78, 3316-3325 (2006).

C Lee, L Gamble, D Grainger, D Castner, Mixed DNA/

Oligo(ethylene glycol) Functionalized Gold Surface 

Improve DNA Hybridization in Complex Media, 

Biointerphases, 1, 82-92 (2006).

L Lewis, D Yoder, A Moodenbaugh, D Fischer, M Yu, 

Magnetism and the Defect state in the Magnetocaloric 

Antiperovskite Mn3GaC1-ä, J. Phys.: Condens. 

Matter, 18, 1677-1686 (2006).
6-6

A Nambu, J Graciani, J Rodriguez, Q Wu, E Fujita, J 

Fdez Sanz , N Doping of TiO2(110): Photoemission 

and Density-Functional Studies, J. Chem. Phys., 125, 

094706 (2006).

L Pattison, A Hexemer, P Petroff, E Kramer, D Fischer, 

NEXAFS Determination of the Orientation of a 

Conjugated Liquid Crystalline Polymer Film on a 

Rubbed Polyimide Alignment Layer, Polym. Mater. 

Sci. Eng., 94, 216-217 (2006).

L Pattison, A Hexemer, E Kramer, S Krishnan, P Petroff, 

D Fischer, Probing the Ordering of Semiconducting 

Fluorene-Thiophene Copolymer Surfaces on Rubbed 

Polyimide Substrates by Near-Edge X-ray Absorption 

Fine Structure, Macromolecules, 39, 2225-2231 

(2006).

V Prabhu, S Sambasivan, D Fischer, L Sunberg, R 

Allen, Quantitative Depth Profi ling of Photoacid 

Generators in Photoresist Materials by Near-edge 

X-ray Absorption Fine Structure Spectroscopy, Appl. 

Surf. Sci., 253, 1010-1014 (2006).

S Rendon, Processing, Structure, and Property 

Relationships in Commercial Thermotropic Liquid 

Crystalline Polymers, Ph. D. Thesis, Northwestern 

University, Evanston (2006).

S Sambasivan, S Shieh, D Fischer, S Hsu, Effect of SelfAssembled Monolayer Film Order on Nanofriction, J. 

Vac. Sci. Technol., A, 24 (4), 1484 (2006).

N Samuel, C Lee, L Gamble, D Fischer, D Castner, 

NEXAFS Characterization of DNA Components 

and Molecular-Orientation of Surface-Bound DNA 

Oligomers, J. Electron. Spectrosc. Relat. Phenom., 

152, 134-142 (2006).

M Smith, J Tong, J Genzer, D Fischer, P Kilpatrick, 

Effects of Synthetic Amphiphilic alpha-Helical Peptides 

on the Electrochemical and Structural Properties of 

Supported Hybrid Bilayers on Gold, Langmuir, 22 (4), 

1919-1927 (2006).

C Xu, S Barnes, T Wu, D Fischer, D DeLongchamp, J 

Batteas, K Beers, Solution and Surface Composition 

Gradients via Microfl uidic Confi nement: Fabrication of 

a Statistical-Copolymer-Brush Composition Gradient, 

Advanced Materials, 18 (11), 1427-1430 (2006).

X Zhao, J Rodriguez, Photoemission Study of Glycine 

Adsorption on Cu/Au (111) Interfaces, Surf. Sci., 600

(10), 2113-2121 (2006).

Beamline U8B

T Owens, K Nicholson, D Fosnancht, B Orr, M 

Banaszak Holl, Formation of Mixed Monolayers of 

Silsesquioxanes and Alkylsilanes on Gold, Langmuir, 

22, 9619-9622 (2006).

Beamline U9B

Y Nie, J Hobbs, S Vigues, W Olson, G Conn, S Munger, 

Expression and Purifi cation of Functional Ligandbinding Domains of T1R3 Taste Receptors, Chem. 

Senses, 31, 505-513 (2006).

Beamline U10A

C Homes, S Dordevic, G Gu, Q Li, T Valla, J 

Tranquada, Charge Order, Metallic Behavior, and 

Superconductivity in La{2-x}Ba{x}CuO{4} with x = 1/8, 

Phys. Rev. Lett., 96, 257002 (2006).

Beamline U10B

M Gallant, M Rak, A Szeghalmi, M Del Bigio, D Westaway, 

J Yang, R Julian, K Gough, Focally Elevated Creatine 

Detected in Amyloid Precursor Protein (APP) 

Transgenic Mice and Alzheimer Disease Brain Tissue, 

J. Biol. Chem., 281 (1), 5-8 (2006).

A Kretlow, Q Wang, J Kneipp, P Lasch, M Beekes, L 

Miller, D Naumann, FTIR-Microspectroscopy of PrionInfected Nervous Tissue, Biochim Biophys Acta, 1758, 

948-959 (2006).

J Miklossy, A Kis, A Radenovic, L Miller, L Forro, R 

Martins, K Reiss, N Darbinian, P Darekar, et al., BetaAmyloid Deposition and Alzheimer’s Type Changes 

Induced by Borrelia Spirochetes, Neurobiol. Aging, 27, 

228-236 (2006).

L Miller, P Dumas, Chemical Imaging of Biological Tissue 

with Synchrotron Infrared Light, Biochim Biophys Acta, 

1758 (7), 846-57 (2006).

L Miller, Q Wang, T Telivala, R Smith, A Lanzirotti, J 

Miklossy, Synchrotron-based Infrared and X-ray 

Imaging Shows Focalized Accumulation of Cu and 

Zn Co-localized With Beta-amyloid Deposits in 

Alzheimer’s Disease, J. Struct. Biol., 155 (1), 30-37 

(2006).

P Ramasamy, Interactions of Proteins in Gels, Solutions 

and on Surfaces, Ph.D. Thesis, State University of 

Newyork at Stony Brook, Stony Brook (2006).

M Ruppel, D Burr, L Miller, Chemical Makeup of 

Microdamaged Bone Differs from Undamaged Bone, 

Bone, 39 (2), 318-324 (2006).

S Sandford, J Aleon, C Alexander, T Araki, S Bajt, G 

Baratts, J Borg, J Bradley, D Brownlee, et al., Organics 

Captured from Comet 81P/Wild2 by the Stardust 

Spacecraft, Science, 314 (5806), 1720-1724 (2006).

S Seaman, E Helfrich, M Dyar, The Role of Water in the 

Growth and Texture of Spherulites in Rhyolitic Lava 

Flows, Geological Society of America Annual Meeting, 

Vol 38, p. 167, sponsored by Geological Society of 

America (2006).

S Seaman, M Dyar, N Marinkovic, N Dunbar, An FTIR 

Study of Hydrogen in Anorthosite and Associated Melt 

Inclusions, Am. Mineral., 91 (1), 12-20 (2006).

F Serrano, L Lopez, M Jadraque, M Koper, G Ellis, 

P Cano, M Martin, L Garrido, A Nd:YAG Lasermicroperforated poly(3-hydroxybutyrate-co-3-

hydroxyvalerate)-basal Membrane Matrix Composite 

fi lm as Substrate for Keratinocytes, Biomaterials, 28

(4), 650-660 (2006).

J Torre, M Cortazar, M Gomez, C Marco, G Ellis, C 

Rickel, P Dumas, Nature of the Crystalline Interphase 

in Sheared IPP/Vectra Fiber Model Composites by 

Microfocus X-ray Diffraction and IR Microspectroscopy 

using Synchrotron Radiation, Macromolecules, 39, 

5564-5568 (2006).

L Xie, J Jacobsen, B Busa, L Donahue, L Miller, C Rubin, 

S Judex, Low-Level Mechanical Vibrations can Reduce 

Bone Resorption and Enhance Bone Formation in the 

Growing Skeleton, Bone, 39 (5), 1059-1056 (2006).

P Yu, An Emerging Method for Rapid Characterization 

of Feed Structures and Feed Component Matrix at 

a Cellular Level and Relation to Feed Quality and 

Nutritive Value, Arch. Anim. Nutr., 60, 229-244 (2006).
PUBLICA TIONS

6-7

Beamline U11

Y Nie, J Hobbs, S Vigues, W Olson, G Conn, S Munger, 

Expression and Purifi cation of Functional Ligandbinding Domains of T1R3 Taste Receptors, Chem. 

Senses, 31, 505-513 (2006).

Beamline U12A

D Mullins, M Robbins, J Zhou, Adsorption and Reaction 

of Methanol on Thin-fi lm Cerium Oxide, Surf. Sci., 600, 

1547-1558 (2006).

D Mullins, Adsorption of CO and C2H4 and Rh-loaded 

Thin-fi lm Dysprosium Oxide, Surf. Sci., 600 (13), 

2718-2725 (2006).

S Senanayake, H Idriss, Photocatalysis and the Origin of 

Life: Synthesis of Nucleoside Bases from Formamide 

on TiO2(001) Single Surfaces, Proc Natl Acad Sci 

USA, 103 (5), 1194-1198 (2006).

J Zhou, D Mullins, Adsorption and Reaction of 

Formaldehyde on Thin-fi lm Cerium Oxide, Surf. Sci., 

600, 1540-1546 (2006).

J Zhou, D Mullins, Rh-Promoted Methanol Decomposition 

on Cerium Oxide Thin Films, J. Phys. Chem. B, 110, 

15994-16002 (2006).

Beamline U12IR

L Mihaly, B Dora, A Vanyolos, H Berger, L Forro, SpinLattice Interaction in the Quasi-One-Dimensional 

Helimagnet LiCu2O2, Phys. Rev. Lett., 97, 067206 

(2006).

S Washburn, Novel Polymer Nanofi lms from a 

Topochemical Deposition/Polymerization Process, 

Ph.D. Thesis, University of Delaware, Newark (2006).

Beamline U13UB

T Valla, T Kidd, J Rameau, H Noh, G Gu, P Johnson, 

H Yang, H Ding, Fine Details of the Nodal Electronic 

Excitations in Bi2Sr2CaCu2O8+gamma, Phys. Rev. B, 

73, 184518 (2006).

Beamline X1A1

M Anderson, T Haraszti, G Peterson, S Wirick, C 

Jacobsen, S John, M Grunze, Scanning Tranmission 

X-ray Microscopic Analysis of Purifed Melanosomes of 

the Mouse Iris, Micron, 37 (8), 689-698 (2006).

A Braun, S Wirick, A Kubatova, B Mun, F Huggins, 

Photochemically Induced Decarboxylation in Diesel 

Soot Extracts, Atmos. Environ., 40 (30), 5837-5844 

(2006).

D Brownlee, P Tsou, J Aléon, C Alexander, T Araki, S 

Bajt, G Baratta, R Bastien, P Bland, et al., Comet 81P/

Wild 2 Under a Microscope, Science, 314 (5806), 1711 

- 1716 (2006).

B DeGregorio, Structure, Bonding and Composition of 

Carbonaceous Material in Precambrian Cherts, Ph.D 

Thesis, Arizon State University, Tempe (2006).

M Denecke, P Panak, M Plaschke, J Rothe, M Weigl, 

Spectroscopic Actinide Speciation for Nuclear Waste 

Disposal, Recent Advances in Actinide Science 

(ACTINIDES 2005), Vol 305, p. 673-679, (2006).

M Denecke, Actinide Speciation using X-ray 

Spectroscopic Methods, Coordin. Chem. Rev., 250, 

730-754 (2006).

M Feser, B Hornberger, C Jacobsen, G De Geronimo, P 

Rehak, P Holl, L Struder, Integrating Silicon Detector 

with Segmentation for Scanning Transmission X-ray 

Microscopy, Nucl. Instrum. Meth. A, 565, 841-854 

(2006).

P Haberstroh, J Brandes, Y Gelinas, A Dickens, S Wirick, 

G Cody, Chemical Composition of the Graphitic 

Black Carbon Fraction in Riverine and Marine 

Sediments at Submicron Scales using Carbon X-ray 

Spectromicroscopy, Geochim. Cosmochim. Acta, 70

(6), 1483-1494 (2006).

B Hornberger, M Feser, C Jacobsen, S Vogt, D Legnini, 

D Paterson, P Rehak, G De Geronimo, B Palmer, 

Combined Fluorescence and Phase Contrast Imaging 

at the Advanced Photon Source, 8th International 

Conference on X-ray Microscopy, Vol IPAP 

Conference Series 7, p. 396-398, sponsored by S Aoki 

et al. (2006).

J Kinyangi, D Solomon, B Liang, M Lerotic, S Wirick, 

J Lehmann, Nanoscale Biogeocomplexity of the 

Organomineral Assemblage in Soil: Application of 

STXM Microscopy and C 1s-NEXAFS Spectroscopy, 

Soil Sci. Soc. Am. J., 70 (5), 1708-1718 (2006).

B Liang, J Lehmann, D Solomon, J Kinyangi, J Grossman, 

B O’Neill, J Skjemstad, J Thies, F Luizão, et al., Black 

Carbon Increases Cation Exchange Capcity in Soils, 

Soil Sci. Soc. Am. J., 70, 1719-1730 (2006).

M Lu, Nanofabrication of Fresnel zone plates for soft 

X-ray imaging at carbon edge, Ph.D Thesis, SUNY at 

StonyBrook, StonyBrook (2006).

M Lu, D Tennant, C Jacobsen, Orientation Dependence 

of Linewidth Variation in sub-50-nm Gaussian e-beam 

Lithography and its Correction, J. Vac. Sci. Technol., 

B, 24 (6), 2881 (2006).

L Lucai, H Nanko, A Rudie, D Mancosky, S Wirick, The 

Use of C-near Edge X-ray Absorption Fine Structure 

Spectroscopy for the Elaboration of Chemistry in 

Lignocellulosics, 2006 TAPPI International Conference 

on Nanotechnology, Vol 2006, p. 8, sponsored by 

TAPPI (2006).

A Naber, M Plaschke, J Rothe, H Hofmann, T Fanghänel, 

Scanning Transmission X-ray and Laser Scanning 

Luminescence Microscopy of the Carboxyl Group 

and Eu(III) Distribution in Humic Acid Aggregates, 

J. Electron. Spectrosc. Relat. Phenom., 153, 71-74 

(2006).

S Sandford, J Aleon, C Alexander, T Araki, S Bajt, G 

Baratts, J Borg, J Bradley, D Brownlee, et al., Organics 

Captured from Comet 81P/Wild2 by the Stardust 

Spacecraft, Science, 314 (5806), 1720-1724 (2006).

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J Majzlan, A Navrotsky, B McCleskey, C Alpers, 

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S Wishkerman, J Bernstein, P Stephens, Polymorphism 

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C Mandel, D Gebauer, H Zhang, L Tong, A Serendipitous 

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E Martinez-Hackert, N Anikeeva, S Kalams, B Walker, 

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H Park, H Wu, Crystal Structure of RAIDD Death Domain 

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Y Hsiao, G Jogl, V Esser, L Tong, Crystal Structure of Rat 

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J Khan, X Tao, L Tong, Molecular Basis for the Inhibition 

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T Holyoak, S Sullivan, T Nowak, Structural Insights into 

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H Hong, D Patel, L Tamm, B van den Berg, The Outer 

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J Jakoncic, Y Jouanneau, C Meyer, V Stojanoff, 

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N Pashkova, Y Jin, S Ramaswamy, L Weisman, 

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Y Wang, Y Zhang, Y Ha, Crystal Structure of a Rhomboid 

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Beamline X7A

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Beamline X7B

E Anokhina, Y Go, Y Lee, T Vogt, A Jacobson, Chiral 

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N Sutin, D Szaida, R van Eldik, Transition State 

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E Johnson, J Post, Water in the Interlayer Region of 

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PUBLICA TIONS

6-13

J Martin, C Keary, T Thornton, M Novotnak, J Knutson, 

J Folmer, Metallotropic Liquid Crystals Formed by 

Surfactant Templating of Molten Metal Halides, Nat. 

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A Martinez-Arias, D Gamarra, M Fernandez-Garcia, X 

Wang, J Hanson, J Rodriguez, Comparative Study on 

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M Nyman, A Celestian, G Holland, T Alam, J Parise, 

Solid-state Structural Characterization of a Rigid 

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J Pike, S Chan, F Zhang, X Wang, J Hanson, Foramtion 

of Stable Cu2O from Reduction of CuO Nanoparticles, 

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S Ruebush, G Icopini, S Brantley, M Tien, In Vitro 

Enzymatic Reduction Kinetics of Mineral Oxides by 

Membrane Fractions from Shewanella oneidensis 

MR-1, Geochim. Cosmochim. Acta, 70 (1), 56-70 

(2006).

A Setlur, W Heward, Y Gao, A Srivastava, R Chandron, 

M Shankar, Crystal Chemistry and Luminescence of 

Ce3+ -Doped Lu2CaMg2(Si,Ge)3O12 and Its Use in 

LED Based Lighting, Chem. Mater., 18, 3314-3322 

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X Shen, Y Ding, J Hanson, M Aindow, S Suib, In 

situ Synthesis of Mixed-Valent Manganese Oxide 

Nanocrystals: An In situ Synchrotron X-ray Diffraction 

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T Szailer, J Kwak, D Kim, J Hanson, C Peden, J Szanyi, 

Reduction of Stored NOx on Pt/Al2O3 Catalysts with 

H2 and CO, J. Catal., 239, 51-64 (2006).

W Yoon, J Hanson, J McBreen, X Yang, A Study on the 

Newly Observed Intermidate Structures During the 

Thermal Decomposition of Nickel-Based Layered 

Cathode Materials using Time-Resolved XRD, 

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F Zhang, C Chen, J Raitano, J Hanson, W Caliebe, 

S Khalid, S Chan, Phase Stability in Ceria-Zirconia 

Binary Oxide Nanoparticles: The Effect of the Ce3+ 

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F Zhang, C Chen, J Hanson, I Herman, S Chan, Phases 

in ceria-zirconia binary oxide (1-x)CeO2-xZrO2 

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Beamline X8A

G Rochau, J Bailey, G Chandler, T Nash, D Nielsen, 

G Dunham, O Garcia, N Joseph, J Keister, et al., 

Energy Dependent Sensitivity of Microchannel Plate 

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C Sorce, J Schein, F weber, K Widmann, K Campbell, 

E Dewald, R Turner, O Landen, K Jacoby, et al., Soft 

X-ray Power Diagnostic Improvements at the Omega 

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M Austin, T Saito, M Bowman, S Haydock, A Kato, B 

Moore, R Kay, J Noel, Biosynthesis of Dictyostelium 

Discoideum Differentation-Inducing Factor by a Hybrid 

Type I Fatty Acid A-Type III polyketide synthase , Nat. 

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X Chu, W DePinto, D Bartkovitz, S So, B Vu, K Packman, C 

Lukacs, Q Ding, N Jiang, et al., Discovery of [4-Amino2-(1-methanesulfonylpiperidin-4-ylamino)pyrimidin-5-

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E Crouch, B McDonald, K Smith, T Cararella, B Seaton, 

J Head, Contributions of Phenylalanine 335 to Ligand 

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A Faravelli, N Dimasi, Expression, Refolding and 

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D Fong, V Yim, M D’elia, E Brown, A Berghuis, Crystal 

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M Hung, E Rangarajan, C Munger, G Nadeau, T Sulea, 

A Matte, Crystal Structure of TDP-Fucosamine 

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N Ishiyama, C Creuzenet, W Miller, M Demendi, E 

Anderson, G Harauz, J Lam, A Berghuis, Structural 

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A Kim, J Rylett, B Shilton, Substrate Binding and Catalytic 

Mechanism of Human Choline Acetyltransferase, 

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G Kozlov, P Maattanen, J Schrag, S Pollack, M Cygler, 

B Nagar, D Thomas, K Gehring, Crystal Structure of 

the bb’ Domains of the Protein Disulfi de Isomerase 

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S Ku, P Yip, P Howell, Structure of Escherichia Coli 

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C Lukacs, N Oikonomakos, R Crowther, L Hong, R 

Kammlott, W Levin, S Li, C Liu, D Lucas-McGady, et 

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A Lyubimov, P Lario, I Moustafa, A Vrielink, Atomic 

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T Modoveanu, Q Liu, A Tocilj, M Watson, G Shore, K 

Gehring, The X-ray Structure of a BAK Homodimer 

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677-688 (2006).
6-14

T Moldoveanu, Q Liu, J Tocilj, M Watson, G Shore, K 

Gehring, The X-ray Structure of a BAK Homodimer 

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S Mrkobrada, L Boucher, D Tyers, F Sicheri, Structural 

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J Payandeh, E Pai, A Structural Basis for Mg(2+) 

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J Payandeh, E Pai, Crystallization and Preliminary X-ray 

Diffraction Analysis of the Magnesium Transporter 

CorA, Acta Cryst. F, 62, 148-152 (2006).

J Pedelacq, S Cabantous, T Tran, T Terwilliger, G Waldo, 

Engineering and Characterization of a Superfolder 

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88 (2006).

E Rangarajan, A Proteau, J Wagner, M Hung, A Matte, 

M Cygler, Structural Snapshots of Escherichia coli 

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B Rho, L Hung, J Holton, D Vigil, S Kim, M Park, T 

Terwilliger, j Pedelacq, Functional and Structural 

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C Shao, F Zhang, M Kemp, R Lindhardt, D Waisman, J 

Head, B Seaton, Crystallographic Analysis of Calciumdependent Heparin Binding to Annexin A2, J. Biol. 

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D Shaya, A Tocilj, Y Li, J Myette, G Venkatarman, 

R Sasisekharan, M Cygler, Crystal Structure of 

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E Sickmier, K Frato, H Shen, S Paranawithana, M Green, 

C Kielkopf, Structural Basis for Polypyrimidine Tract 

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S Singh, D Christendat, Structure of Arabidopsis 

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45, 7787-7796 (2006).

M Suits, N Jaffer, Z Jia, Structure of the Escherichia 

coli O157:H7 heme oxygenase ChuS in complex with 

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Q Ye, X Li, A Wong, Q Wei, Z Jia, Structure of Calmodulin 

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Beamline X9A

A Hoelz, J Janz, S Lawrie, B Corwin, A Lee, T Sakmar, 

Crystal Structure of the SH3 Domain of beta PIX in 

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A Ketkar, A Shenoy, U Ramagopal, S Visweswariah, K 

Suguna, A Structural Basis for the Role of Nucleotide 

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V Lamour, B Hogan, D Erie, S Darst, Crystal Structure 

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Y Leduc, C Phenix, J Puttick, K Nienaber, D Palmer, L 

Delbaere, Crystallization, Preliminary X-ray Diffraction 

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M Lilic, M Vujanac, C Stebbins , A Common Structural 

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I Lorenz, J Marcotrigiano, T Dentzer, C Rice, Structure 

of the catalytic domain of the hepatitis C virus NS2-3 

protease, Nature, 442 (7104), 831-5 (2006).

B Manjasetty, M Chance, Crystal Structure of Escherichia 

coli L-Arabinose Isomerase (ECAI), The Putative 

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B Manjasetty, K Bussow, M Fieber-ErdMan, Y Roske, J 

Gobam, C Scheich, F Gotz, F Niesen, U Heinemann, 

Crystal Structure of Homo Sapiens PTD012 Reveals 

a Zinc-Containing Hydrolase Fold, Protein Sci., 15, 

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S Margarit, W Davidson, L Frego, F Stebbins, A Steric 

Antagonism of Actin Polymerization by a Salmonella 

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E McManus, B Luisi, R Perham, Structure of a 

Putative Lipoate Protein Ligase from Thermoplasma 

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S Patel, C Ciatto, C Chen, F Bahna, M Rajebhosale, N 

Arkus, I Schieren, T Jessell, B Honig, Type II Cadherin 

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Cadherin Specifi city, Cell, 124 (6), 1255-1268 (2006).

G Prehna, M Ivanov, J Blisha, C Stebbins, Yersinia 

Virulence Depends on Mimicry of Host Rho-Family 

Nucleotide Dissociation Inhibitors, Cell, 126, 869-880 

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M Roden, D Brims, A Fedorov, T DiLorenzo, S Almo, 

s Nathenson, L Anovitz, D Wesolowski, Structural 

Analysis of H2-Db Class I Molecules Containing 

Two Different Allelic Forms of the type 1 Diabetes 

Susceptibility Factor beta-2 Microglobulin: Implications 

for the Mechanism Underlying Viriations in Antigen 

Presentation, Mol. Immunol., 43 (9), 1370-1378 

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T Schwartz, D Schmidt, S Brohawn, G Blobel, 

Homodimerization of the G Protein Srbeta in the 

Nucleotide-Free State Involves Proline cis/trans 

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V Singh, W Shi, S Almo, G Evans, R Furneaux, P Tyler, G 

Painter, D Lenz, S Mee, et al., Structure and Inhibition 

of Quorum Sensing Target from Streptococcus 

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W Yew, A Fedorov, E Fedorov, J Rakus, R Pierce, S 

Almo, J Gerlt, Evolution of Enzymatic Activities in the 

Enolase Superfamily: L-Fuconate Dehydratase from 

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W Yew, A Fedorov, E Fedorov, B Wood, S Almo, 

J Gerlt, Evolution of Enzymatic Activities in the 

Enolase Superfamily: D-Tartrate Dehydratase from 

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14608 (2006).
PUBLICA TIONS

6-15

Beamline X9B

J Bielnicki, Y Devedjiev, U Derewenda, Z Dauter, A 

Joachimiak, Z Derewenda, B. subtilis ykuD Protein at 

2.0 Angstrom Resolution: Insights into the Structure 

and Function of a Novel, Ubiquitous Family of Bacterial 

Enzymes, Proteins: Struc. Func. Bioinformatics, 62, 

144-151 (2006).

K Boeshans, F Liu, G Peng, W Idler, S Jang, L Marekov, 

L Black, B Ahvazi, Purifi cation, Crystallization and 

Preliminary X-ray Diffraction Analysis of the Phage 

T4 Vertex Protein Gp24 and its Mutant Forms, Protein 

Expr. Purif., 49 (2), 235-243 (2006).

J Cook, K Bencze, A Jankovic, A Crater, C Busch, 

P Bradley, A Stemmler, M Spaller, T Stemmler, 

Monomeric Yeast Frataxin is an Iron-Binding Protein, 

Biochemistry, 45, 7767-7777 (2006).

A Costello, G Periyannan, K Yang, M Crowder, D Tierney, 

Site Selective Binding of Zn(ll) ot Metallo-b-Lactamase 

L1 from Stenotrophomonas Maltophilia, J. Biol. Inorg. 

Chem., 11, 351-358 (2006).

A Costello, N Sharma, K Yang, M Crowder, D Tierney, 

X-ray Absorption Spectroscopy of the Zinc-Binding 

Sites in the Class B2 Metallo-B-lactamsase ImiS 

from Aeromonas veronii bv. sobria, Biochemistry, 45, 

13650-13658 (2006).

E Eren, D Kennedy, M Maroney, J Arguello, A Novel 

Regulatory Metal Binding Domain is Present in the C 

Terminus of Arabidopsis Zn2+ -ATPase HMA2, J. Biol. 

Chem., 281, 33881-33891 (2006).

R Franzini, R Watson, G Patra, R Breece, D Tierney, 

M Hendrich, C Achim, Metal Binding to BipyridineModifi ed PNA, Inorg. Chem., 45, 9798-9811 (2006).

B Frost, C Bautista, R Huang, J Shearer, Manganese 

Complexes of 1,3,5-triaza-7-phosphaadamantane 

(PTA): The First Nitrogen Bound Transition Metal 

Complex of PTA, Inorg. Chem., 45, 3481-3483 

(2006).

J Grembecka, T Cierpicki, Y Drvedjiev, U Derewenda, 

B Kang, J Bushweller, Z Derewenda, The Binding 

of the PDZ Tandem of Syntenin to Target Proteins, 

Biochemistry, 45, 3674-3683 (2006).

K Gunter, M Aschner, L Miller, R Eliseev, J Salter, K 

Andersen, T Gunter, Determining the Oxidation States 

of Manganese in NT2 Cells and Cultured Astrocytes, 

Neurobiol. Aging, 27 (12), 1816-26 (2006).

T Ju, R Beaulieu Goldsmith, S Chai, M Maroney, S Sondej 

Pochapsky, T Pochapsky, One Protein, Two Enzymes 

Revisited: A Structural Entropy Switch Interconverts 

the Two Isoforms of Acireductone Dioxygenase, J. 

Mol. Biol., 363 (4), 823-834 (2006).

J Kaste, B Bostick, A Friedland, A Schroth, T Siccama, 

Fate and Speciation of Gasoline-Derived Lead in 

Organic Horizons of the Northeastern USA, Soil Sci. 

Soc. Am. J., 70, 1688-1698 (2006).

F Larsen, A Boisen, K Berry, B Moubaraki, K Murray, 

V McKee, R Scarrow, C McKenzie, Identifi cation 

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G Periyannan, A Costello, D Tierney, K Yang, b Bennett, 

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Que, Jr., Nonheme Oxoiron(IV) Complexed of Tris(2-

pyridylmethyl)amine with cis-Monoanionic Ligands, 

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K Sekar, M Yogavel, S Kanaujia, A Sharma, D 

Velmurugan, M Poi, Z Dauter, M Tsai, Suggestive 

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Krishna, M Poi, Z Dauter, M Dauter, M Tsai, Atomic 

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6-16

Beamline X10A

A Cisneros, G Mazzanti, R Campos, A Marangoni, 

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D Dorset, S Weston, S Dhingra, Crystal Structure 

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J Calla, M Bore, A Datye, R Davis, Effect of Alumina and 

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Beamline X11A

A Argo, J Odzak, J Goellner, F Lai, F Xiao, B Gates, 

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S Lee, J Dyer, D Sparks, N Scrivner, E Elzinga, A MultiScale Assessment of Pb(II) Sorption on Dolomite, J. 

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6-17

S Maeng, L Axe, T Tyson, L Gladczuk, M Sosnowski, 

Corrosion Behavior of Magnetron Sputtered Alpha 

Ta Coatings on Smooth and Rough Steel Substrates, 

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S Maeng, L Axe, T Tyson, P Cote, Corrosion Hehaviour 

of Electrodeposited and Sputtered Cr Coatings and 

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L Menard, H Xu, S Gao, R Twesten, A Harper, Y Song, G 

Wang, A Douglas, J Yang, et al., Metal Core Bonding 

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S Morrison, C Cahill, E Carpenter, V Harris, Production 

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S Park, K Kang, W Yoon, A Moodenbaugh, L Lewis, T 

Vogt, Magnetic Spin Glass Properties of the Bi-layer 

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E Peltier, R Allada, A Navrotsky, D Sparks, Nickel 

Solubility and Precipitation in Soils: A Thermodynamic 

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(2006).

A Scheinost, A Rossberg, D Vantelon, I Xifra, R 

Kretzschmar, A Leuz, H Funke, C Johnson, 

Quantitative Antimony Speciation in Shooting-Range 

Soils by EXAFS Spectroscopy, Geochim. Cosmochim. 

Acta, 70 (13), 3299-3312 (2006).

M Shultz, E Carpenter, S Morrison, S Calvin, Cation 

Occupancy Determination in Manganese Zinc Ferrites 

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R Swaminathan, J Woods, S Calvin, J Huth, M McHenry, 

Microstructural Evolution Model of the Sintering 

Behavior and Magnetic Properties of NiZn Ferrite 

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J Wong, E Larson, P Waide, R Frahm, Combustion Front 

Dynamics in the Combustion Synthesis of Refractory 

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Y Xu, T Boonfueng, L Axe, S Maeng, T Tyson, Surface 

Complexation of Pb(II) on Amorphous Iron Oxide and 

Manganese Oxide: Spectroscopic and Time Studies, 

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Beamline X11B

B Ravel, Y Kim, P Woodward, C Fang, Role of Local 

Disorder in the Dielectric Response of BaTaO2N, 

Phys. Rev. B: Condens. Matter, 73, 184121 (2006).

A Ryser, D Strawn, M Marcus, S Fakra, J JohnsonMaynard, G Moller, Microscopically Focused 

Synchrotron X-ray Investigation of Selenium 

Speciation in Soils Developing on Reclaimed Mine 

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P Shanthakumar, M Balasubramanian, D Pease, A 

Frenkel, D Potrepka, V Kraizman, J Budnick, W 

Hines, X-ray Study of the Ferroelectric [Ba0.6Sr0.4] 

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M Si, V Zaitsev, M Goldman, A Frenkel, D Peiffer, E Weil, 

J Sokolov, M Rafailovich, Self-extinguishing Polymer/

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Y Xu, T Boonfueng, L Axe, S Maeng, T Tyson, Surface 

Complexation of Pb(II) on Amorphous Iron Oxide and 

Manganese Oxide: Spectroscopic and Time Studies, 

J. Colloid Interface Sci., 299 (1-3), 28-40 (2006).

Beamline X12A

A Bolotnikov, G Camarda, G Carini, M Fiederle, L Li, D 

McGregor, W McNeil, G Wright, R James, Performance 

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W Caliebe, I So, A Lenhard, D Siddons, Cam-driven 

Monochromator for QEXAFS, 20th International 

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Vol 75, p. 1962-1965, sponsored by University of 

Melbourne (2006).

W Caliebe, I So, A Lenhard, D Siddons, Cam-Driven 

Monochromator for QEXAFS, Radiat. Phys. Chem., 

75 (11), 1962-1965 (2006).

G Camarda, A Bolotnikov, G Carini, R James, L Li, 

Effects of Tellurium Precipitates on Charge Collection 

in CZT Nuclear Radiation Detectors, Nato Conference 

on Countering Nuclear and Radiological Terrorism, p. 

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G Camarda, A Bolotnikov, G Carini, Y Cui, K Kohman, 

L Li, R James, High Spatial-Resolution Imaging of Te 

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Hard X-ray and Gamma-Ray Detector Physics VIII, 

Vol 6319, p. 63190Z-1, sponsored by SPIE (2006).

G Carini, A Bolotnikov, G Camarda, Y Cui, H Jackson, 

A Burger, K Kohman, L Li, R James, Te Inclusions 

and Their Relationship to the Performance of CdZnTe 

Detectors, In Proceedings of SPIE Hard X-ray and 

Gamma-Ray Detector Physics VIII, Vol 6319, p. 

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G Carini, A Bolotnikov, G Camarda, G Wright, R James, 

Y Li, Effect of Te Precipitates on the Performance 

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(2006).

G Carini, Development of CdZnTe Radiation Detectors, 

Ph.D. Thesis, University of Palermo, Palermo (2006).

M Chu, S Terterian, G Carini, G Camarda, A Bolotnikov, 

R James, D Xu, Z He, Effects of Material Improvement 

on CZT Detectors, In Proceedings of SPIE Hard X-ray 

and Gamma-Ray Detector Physics VIII, Vol 6319, p. 

631905-1, sponsored by SPIE (2006).

A Mavroudis, A Avgeropoulos, N Hadjichristidis, E 

Thomas, D Lohse, Synthesis and Morphological 

Behavior of Model 6-Miktoarm Star Copolymers, 

PS(P2MP)5, of Styrene (S) and 2-Methyl-1,3-

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Beamline X12B

M Adams, Z Jia, Modulator of Drug Activity B from 

Escherichia Coli: Crystal Structure of a Prokaryotic 

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D Copeland, A Soares, A West, G Richter-Addo, Crystal 

Structures of the Nitrite and Nitric Oxide Complexes of 

Horse Heart Myoglobin, J. Inorg. Biochem., 100 (8), 

1413-1425 (2006).

M Groves, M Singh, G Beydaghyan, M Muller, E 

Sheridan, D Schneider, Design and Implementation of 

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6-18

S Kamtekar, R Ho, M Cocco, W Li, S Wenwieser, 

M Boocock, N Grindley, T Steitz, Implications of 

Structures of Synaptic Tetramers of gamma delta 

Resolvase for the Mechanism of Recombination, Proc 

Natl Acad Sci USA, 103 (28), 10642-10647 (2006).

J Mao, S Mukherjee, Y Zhang, R Cao, J Sanders, Y Song, 

Y Zhang, G Meints, Y Gao, et al., Solid-State NMR, 

Crystallographic, and Computational Investigation 

of Bisphosphonates and Farnesyl Diphosphate 

Synthase-Bisphosphonate Complexes, J. Am. Chem. 

Soc., 128, 14485-14497 (2006).

M McDonough, V Li, E Flashman, R Chowdhury, C Mohr, 

B Lienard, J Zondlo, N Oldham, I Clifton, et al., Cellular 

Oxygen Sensing: Crystal Structure of HypoxiaInducible Factor Prolyl Hydroxylase (PHD2), Proc Natl 

Acad Sci USA, 103 (26), 9814-9819 (2006).

S Mylavarapu, M Furgason, D Brewer, M Munson, 

The Structure of the Exocyst Subunit Sec6p Defi nes 

a Conserved Architecture with Diverse Roles, Nat. 

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H Pinkett, K Shearwin, S Stayrook, I Dodd, T Burr, A 

Hochschild, J Egan, M Lewis, The Structural Basis 

of Cooperative Regulation at an Alternate Genetic 

Switch, Mol. Cell, 21, 605-615 (2006).

C Simmons, Q Liu, Q Huang, Q Hao, T Begley, P 

Karplus, M Stipanuk, Crystal Structure of Mammalian 

Cysteine dioxygenase: A Novel Mononuclear Iron 

Center for Cysteine Thiol Oxidation, J. Biol. Chem., 

281, 18723-18733 (2006).

M Swan, D Bastia, C Davies, Crystal Structure of pi 

Initiator Protein-iteron Complex of Plasmid R6K: 

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Proc Natl Acad Sci USA, 103 (49), 18481-18486 

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J Thompson, Z Ryan, J Salisbury, R Kumar, The Structure 

of the Human Centrin 2-Xeroderma Pigmentosum 

Group C Protein Complex, J. Biol. Chem., 281, 18746 

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Z Wang, C Li, M Ellenburg, E Soistman, J Ruble, B 

Wright, J Ho, D Carter, Structure of Human Ferritin L 

Chain, Acta Cryst. D, 62, 800-806 (2006).

Beamline X12C

R Agarwal, J Bonanno, S Burley, S Swaminathan, 

Structure Determination of an FMN Reductase 

from Pseudomonas aeruginosa PA01 using Sulfur 

Anomalous Signal, Acta Cryst. D, 62, 383-391 (2006).

S Bajaj, A Schmidt, S Agah, M Bajaj, K Padmanabhan, 

High Resolution Structures of p-Aminobenzamidineand Benzamidine- VIIa/Soluble Tissue Factor: 

Unpredicted Conformation of the 192-193 Peptide 

Bond and Mapping of Ca2+, Mg2+, Na+ an Zn2+ 

Sites in Facto VIIa, J. Biol. Chem., 281, 24873-24888 

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A Balakrishna, Y Tan, H Mok, A Saxena, K Swaminathan, 

Crystallization and Preliminary X-ray Diffraction 

Analysis of Salmonella typhi PilS, Acta Cryst. F, 62, 

1024-1026 (2006).

M Barreras, M Bianchet, L Ielpi, L Tong, Crystallization and 

Preliminary Crystallographic Characterization of GumK, 

A Membrane-Associated Gluocuronosyltransferase 

from Xanthomonas campestris Required for Xanthan 

Polysaccharide Synthesis, Acta Cryst. F, 62, 880-883 

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M Bewley, V Graziano, J Jiang, E Matz, F Studier, A 

Pegg, C Coleman, J Flanagan, Structures of WildType and Mutant Human Spermidine/Spermine 

N1-acetyltransferase, a Potential Therapeutic Drug 

Target, Proc Natl Acad Sci USA, 103, 2063-8 (2006).

M Botuyan, J Lee, I Ward, J Kim, J Thompson, J Chen, G 

Mer, Structural Basis for the Methylation State-Specifi c 

Recognition of Histone H4-K20 by 53BP1 and Crb2 in 

DNA Repair, Cell, 127 (7), 1361-1373 (2006).

D Ceccarelli, H Song, F Poy, M Schaller, M Eck, Crystal 

Structure of the FERM Domain of Focal Adhesion 

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W Franks, B Wylie, S Stellfox, C Rienstra, Microcrystalline 

U-15N-Labeled Protein by 3D Dipolar-Shift Solid-State 

NMR Spectroscopy, J. Am. Chem. Soc., 128, 3154-

3155 (2006).

H Gennadios, D Christianson, Binding of Uridine 

5’-Diphosphate in the “Basic Patch” of the Zinc 

Deacetylase LpxC and Implications for Substrate 

Binding, Biochemistry, 45, 15216-15223 (2006).

Q Huai, Structure of Human Urokinase Plasminogen 

Activator, Science, 311, 656 (2006).

S Kamtekar, R Ho, M Cocco, W Li, S Wenwieser, 

M Boocock, N Grindley, T Steitz, Implications of 

Structures of Synaptic Tetramers of gamma delta 

Resolvase for the Mechanism of Recombination, Proc 

Natl Acad Sci USA, 103 (28), 10642-10647 (2006).

B Kelly, B Howard, H Wang, H Robinson, W Sundquist, 

C Hill, Implications for Viral Capsid Assembly from 

Crystal Structures of HIV-1 Gag1-278 and CAN133-

278, Biochemistry, 45 (38), 11257 -11266 (2006).

D Kumaran, J Bonnano, S Burley, S Swaminathan, 

Crystal Structure of Phosphatidylglycerophosphat

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Phosphatase, Reveals a Novel Binuclear Metal 

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Func. Bioinformatics, 64, 851-862 (2006).

C Lawson, B Yung, A Barbour, W Zuckert, Crystal 

Structure of Neurotropism-Associated Variable 

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S Lee, Y Tsai, R Mattera, W Smith, M Kostelansky, A 

Weissman, J Bonifacino, J Hurley, Structural Basis 

for Ubiquitin Recognition and Autoubiquitination by 

Rabex-5, Nat. Struct. Mol. Biol., 13, 264-271 (2006).

Y Liu, J Wu, J Song, J Sivaraman, C Hew, Identifi cation 

of a Novel Nonstructural Protein, VP9, from White Spot 

Syndrome Virus: Its Structure Reveals a Ferredoxin 

Fold with Specifi c Metal Binding Sites, J. Virology, 80

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Y Liu, J Sivaraman, C Hew, Expression, purifi cation and 

crystallization of a novel nonstructural protein VP9 

from white spot syndrome virus., Acta Cryst. F, 62 (8), 

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S Ni, F Forouhar, D Bussiere, H Robinson, M Kennedy, 

Crystal Structure of VC0702 at 2.0 Angstrom: 

Conserved Hypothetical Protein from Vibrio Cholerae, 

Proteins: Struc. Func. Bioinformatics, 63 (4), 733-741 

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S Park, P Borbat, G Gonzalez-Bonet, J Bhatnagar, A 

Pollard, J Freed, A Bilwes, B Crane, Reconstruction 

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PUBLICA TIONS

6-19

K Rao, J Bonanno, S Burley, S Swaminathan, 

Crystal Structure of Glycerophosphodiester 

Phosphodiesterase from Agrobacterium tumefaciens 

by SAD with a Large Asymmetric Unit, Proteins: Struc. 

Func. Bioinformatics, 65, 514-518 (2006).

J Seetharaman, D Kumaran, J Bonanno, S Burley, S 

Swaminathan, Crystal Structure of a Putative HTHType Transcriptional Regulator yxaF from Bacillus 

subtilis, Proteins: Struc. Func. Bioinformatics, 63, 

1087-1091 (2006).

J Seetharaman, K Rajashankar, V Solarzano, R Kniewel, 

C Lima, J Bonanno, S Burley, S Swaminathan, Crystal 

Structures of Two Putative Phosphoheptose, Proteins: 

Struc. Func. Bioinformatics, 63, 1092-1096 (2006).

N Silvaggi, C Zhang, Z Lu, J Dai, D Dunaway-Mariano, K 

Allen, The X-ray Crystal Structures of Human {alpha}-

Phosphomannomutase 1 Reveal the Structural Basis 

of Congenital Disorder of Glycosylation Type 1a, J. 

Biol. Chem., 281 (21), 14918-14926 (2006).

S Sunita, H Zhenxing, J Swaathi, M Cygler, A Matte, J 

Sivaraman, Domain organization and crystal structure 

of the catalytic domain of E.coli RluF, a pseudouridine 

synthase that acts on 23S rRNA, J. Mol. Biol., 359 (4), 

998 - 1009 (2006).

F Xue, R Burnett, Capsid-like Arrays in Crystals of 

Chimpanzee Adenovirus Hexon, J. Struct. Biol., 154

(2), 217-221 (2006).

Y Yuan, Y Pei, H Chen, T Tuschl, D Patel, A Potential 

Protein-RNA Recognition Event Along the RISCLoading Pathway from the Structure of A. aeolicus 

Argonaute with Externally Bound siRNA, Structure, 14

(10), 1557-1565 (2006).

Beamline X13A

B Kirby, J Borchers, J Rhyne, K O’Donovan, S Velthuis, 

S Roy, C Sanchez-Hanke, T Wojtowicz, X Liu, et al., 

Magnetic and Chemical Nonuniformity in Ga1-xMnxAs 

Films as Probed by Polarized Neutron and X-ray 

Refl ectometry, Phys. Rev. B, 74, 245304 (2006).

C Sanchez-Hanke, R Gonzalez-Arrabal, J Prieto, E 

Andrzejewska, N Gordillo, D Boerma, R Loloee, 

J Skuza, R Lukaszew, Observation of Nitrogen 

Polarization in Fe-N Using Soft X-ray Magnetic Circular 

Dichorism, J. Appl. Phys., 99, 08B709 (2006).

Beamline X13B

G Cargill, III, L Moyer, G Wang, H Zhang, C Hu, W Yang, B 

Larson, G Ice, Thermal and Electromigration-Induced 

Strains in Polycrystalline Films and Conductor Lines: 

X-ray Microbeam Measurements and Analysis, AIP 

Conference Proceedings, Vol 817, p. 303, sponsored 

by AIP (2006).

G Wang, H Zhang, G Cargill III, C Hu, L Ge, A Maniatty, 

Thermal and Electromigration-Induced Strains 

in Copper Conductor Lines: X-ray Microbeam 

Measurements and Analysis, Materials Research 

Society Spring 2006 Meeting, Vol 914, p. 0914-F06-

06, sponsored by Materials Research Society (2006).

H Yan, I Noyan, Measurement of Stress/Strain in SingleCrystal Samples using Diffraction, J. Appl. Cryst., 39, 

320-325 (2006).

Beamline X14A

J Biernacki , C Parnham, T Watkins, C Hubbard, J Bai, 

Phase-Resolved Strain Measurements in Hydrated 

Ordinary Portland Cement Using Synchrotron X-rays, 

J. Am. Ceram. Soc., 89 (9), 2853-2859 (2006).

M Deleon, Structural, Magnetic, and Transport 

Characteristics of Strained Lanthanum Defi cient 

Manganite Films, Ph. D. Thesis, New Jersey Institute 

of Technology, Newark (2006).

S Jaradat, H Gleeson, N Roberts, Y Wang, The Effects of 

Highly Chiral Dopants on the Smectic Phases of Liquid 

Crystals Remarkably Wide Intermediate Phases, J 

Mater. Chem., 16, 3753 (2006).

S Kewalramani, G Dommett, K Kim, G Evmenenko, H 

Mo, B Stripe, P Dutta, Aggregation-governed Oriented 

Growth of Inorganic Crystals at an Organic Template, 

J. Chem. Phys., 125 (22), 224713 (2006).

H Sheng, W Luo, F Alamgir, J Bai, E Ma, Atomic Packing 

and Short-to-Medium-Range Order in Metallic 

Glasses, Nature, 439, 419-425 (2006).

Beamline X15A

A Antunes, A Safatle, P Barros, S Morelhao, X-ray 

Imaging in Advanced Studies of Ophthamic Diseases, 

Med. Phys., 33 (7), 2338-2343 (2006).

J Brankov, M Wernick, Y Yang, J Li, C Muehleman, 

Z Zhong, M Anastasio, A Computed Tomography 

Implementation of Multiple-Image Radiography, Med. 

Phys., 33 (2), 278 (2006).

D Connor, D Sayers, D Sumner, Z Zhong, Diffraction 

Enhanced Imaging of Controlled Defects Within Bone, 

Including Bone-Metal Gaps, Phys. Med. Biol., 51 (12), 

3283-3300 (2006).

M Kelly, R Beavis, D Fourney, E Schultke, C Parham, B 

Juurlink, Z Zhong, L Chapman, Diffraction-enhanced 

Imaging of the Rat Spine, Can. Assoc. Radiol. J., 57, 

204-210 (2006).

G Khelashvili, J Brankov, D Chapman, M Anastasio, 

Y Yang, Z Zhong, M Wernick, A Physical Model of 

Muliple-Image Radiography, Phys. Med. Biol., 51 (2), 

221-236 (2006).

C Kim, M Bourham, J Doster, A Wide-Beam X-ray Source 

Suitable for Diffraction Enhanced Imaging Applications, 

Nucl. Instrum. Meth. A, 566 (2), 713-721 (2006).

C Muehleman, J Li, Z Zhong, J Brankov, M Wernick, 

Multiple-Image Radiography for Human Soft Tissue, J. 

Anatomy, 208, 115-124 (2006).

C Muehleman, J Li, Z Zhong, Preliminayr Study on 

Diffraction Enhanced Radiographic Imaging for a 

Canine Model of Cartilage Damage, Osteoarthr. 

Cartilage, 14 (92), 882-888 (2006).

M Wernick, Y Yang, I Mondal, D Chapman, M Hasnah, 

C Parham, E Pisano, Z Zhong, Computation of Mass 

Density Images from X-ray Refraction-Angle Images, 

Phys. Med. Biol., 51, 1769-1778 (2006).

Z Zhang, P Fenter, L Cheng, N Sturchio, M Bedzyk, M 

Machesky, L Anovitz, D Wesolowski, Zn2+ and Sr2+ 

Adsorption at the TiO2 (110)-Electrolyte Interface: 

Infl uence of Ionic Strength, Coverage, and Anions, J. 

Colloid Interface Sci., 295 (1), 50-64 (2006).
6-20

Z Zhang, P Fenter, S Kelly, J Catalano, A Bandura, 

J Kubicki, J Sofo, D Wesolowski, M Machesky, et 

al., Structure of Hydrated Zn2+ at the Rutile TiO2 

(110)-Aqueous Solution Interface: Comparsion of Xray Standing Wave, X-ray Absorption Spectroscopy, 

and Density Functional Theory Results, Geochim. 

Cosmochim. Acta, 70 (16), 4039-4056 (2006).

Beamline X15B

H Sheng, W Luo, F Alamgir, J Bai, E Ma, Atomic Packing 

and Short-to-Medium-Range Order in Metallic 

Glasses, Nature, 439, 419-425 (2006).

M Vittadello, P Stallworth, F Alamgir, S Suarez, S 

Abbrent, C Drain, V Di Noto, S Greenbaum, Polymeric 

gamma-MgCl2 Nanoribbons, Inorg. Chim. Acta, 359

(8), 2513-2518 (2006).

Beamline X16C

J Kim, G Korshin, A Frenkel, A Velichenko, 

Electrochemical and XAFS Studies of Effects of 

Carbonate on the Oxidation of Arsenite, Environ. Sci. 

Tech., 40, 228-234 (2006).

P Lyman, V Shneerson, R Fung, S Parihar, H JohnsonSteigelman, E Lu, D Saldin, Structure and Stability of 

Sb/Au(110)-c(2x2) Surface Phase, Surf. Sci., 600 (2), 

424-435 (2006).

L Menard, H Xu, S Gao, R Twesten, A Harper, Y Song, G 

Wang, A Douglas, J Yang, et al., Metal Core Bonding 

Motifs of Monodisperse Icosahedral Au13 and Larger 

Au Monolayer-Protected Clusters as Revealed by 

X-ray Absorption Spectroscopy and Transmission 

Electron Microscopy, J. Phys. Chem. B, 110, 14564-

14573 (2006).

K Pokhodnya, M Bonner, J Her, P Stephens, J 

Miller, Magnetic Ordering (Tc=90K) Observed for 

Layered [Fell(TCNE-)(NCMe)2]+[FelllCl4]- (TCNE = 

Tetracyanoethylene), J. Am. Chem. Soc., 128, 15592-

15593 (2006).

M Sachan, N Walrath, S Majetich, K Krycka, C Kao, 

Interaction Effects Witin Langmuir Layers and ThreeDimensional Arrays of E-Co Nanoparticles, J. Appl. 

Phys., 99, 08C302 (2006).

K Sugimoto, R Dinnebier, T Schlecht, Chlorartinite, A 

Volcanic Exhalation Product Also Found in Industrial 

Magnesia Screed, J. Appl. Cryst., 39, 739-744 (2006).

Y Sun, A Frenkel, H White, L Zhang, Y Zhu, H Xu, 

J Yang, T Koga, V Zaitsev, et al., Comparison of 

Decanethiolate Gold Nanoparticles Synthesized by 

One-Phase and Two-Phase Methods, J. Phys. Chem. 

B, 110, 23022-23030 (2006).

Beamline X17B1

D Anschel, B Foerster, T Yuasa, H Benveniste, Z Zhong, 

J Heinfeld, A Dilmanian, 9.4 T MRI Characterization of 

a Focal Lesion in the Rat Brain Induced by Interlaced 

Microbeam Radiation, Epilepsia, Vol 46, p. 280-

281, sponsored by American Epilepsy Society and 

American Clinical Neurophysiology Society (2006).

G Carini, Development of CdZnTe Radiation Detectors, 

Ph.D. Thesis, University of Palermo, Palermo (2006).

G Carini, C Arnone, A Bolotnikov, G Camarda, R De 

Wames, J Dinan, J Markunas, B Raghothamachar, S 

Sivananthan, et al., Material Quality Characterization 

of CdZnTe Substrates for HgCdTe Epitaxy, J. Electron. 

Mater., 35 (6), 1495-1502 (2006).

T Chen, A Neville, K Sorbie, Z Zhong, Using Synchrotron 

Radiation Wide Angle X-Ray Scattering (WAXS) to 

Study the Inhibition Effect of DiEthyleneTriaminePenta 

(MethylenePhosphonic acid) (DETPMP) on CaCO3 

Scale Formation , SPE Eighth International Symposium 

on Oilfi eld Scale, p. Paper 100440, sponsored by SPE 

(2006).

T Chen, A Neville, K Sorbie, Z Zhong, Using Synchrotron 

Radiation Wide Angle X-Ray Scattering (WAXS) to 

Study the Inhibiting Effect of Polyphosphonocarboxylic 

Acid (PPCA) on CaCO3 Scale Formation, 

CORROSION/2006, p. Paper 06386, sponsored by 

NACE (2006).

T Chen, New Insights into the Mechanisms of Calcium 

Carbonate Mineral Scale Formation and Inhibiton, 

Ph.D Thesis, Heriot-Watt University, Edinburgh 

(2006).

F Dilimanian, Z Zhong, T Bacarian, H Benveniste, P 

Romanelli, R Wang, J Welwart, T Yuasa, E Rosen, 

D Anschel, Interlaced X-ray Microplanar Beams: A 

Radiosurgery Approach with Clinical Potential, Proc 

Natl Acad Sci USA, 103 (25), 9709-9714 (2006).

G Gwanmesia, J Zhang, K Darling, J Kung, B Li, L Wang, 

D Neuville, R Liebermann, Elasticity of Polycrystalline 

Pyrope (Mg3Al2Si3O12) to 9 GPa and 1000 degrees 

C, Phys. Earth Planet. Interiors, 155 (3-4), 179-190 

(2006).

K Hirota, S Wakimoto, D Cox, Neutron and X-ray Studies 

of Relaxors, J. Phys. Soc. Japan, 75 (11), 111006-1 to 

13 (2006).

J Jakoncic, M Di Michiel, Z Zhong, V Honkimaki, Y 

Jouanneau, V Stojanoff, Anomalous Diffraction at 

Ultra-High Energy for Protein Crystallography, J. Appl. 

Cryst., 39, 831-841 (2006).

B Noheda, D Cox, Bridging Phases at the Morphotropic 

Boundaries of Lead Oxide Solid Solutions, Phase 

Transit, 79 (1-2), 5-20 (2006).

A Phelippeau, S Pommier, T Tsakalakos, M Clavel, C 

Prioul, Cold Drawn Steel Wires—Processing, Residual 

Stresses and Ductility—Part I: Metallography and 

Finite Element Analyses, Fatigue Fract. Eng. Mater. 

Struct., 29, 201-208 (2006).

A Phelippeau, S Pommier, I Zakharchenko, R LevyTubiana, T Tsakalakos, M Clavel, M Croft, Z Zhong, C 

Prioul, Cold Drawn Steel Wires—Processing, Residual 

Stresses and Ductility Part II: Synchrotron and Neutron 

Diffraction, Fatigue Fract. Eng. Mater. Struct., 29, 255-

265 (2006).

C Stock, D Ellis, I Swainson, G Xu, H Hiraka, Z Zhong, H 

Luo, X Zhao, D Viehland, et al., Damped Soft Phonons 

and Diffuse Scattering in 40% Pb(Mg1/3Nb2/3))3-60% 

PbTiO3, Phys. Rev. B, 73, 064107 (2006).

T Tsakalakos, M Croft, N Jisrawi, R Holtz, Z Zhong, 

Measurement of Residual Stress Distributions by 

Energy Dispersive X-ray Diffraction Synchrotron 

Radiation, Int. J. Offshore Polar Eng., 16, 358-366 

(2006).

G Xu, Z Zhong, Y Bing, Z Ye, G Shirane, Electric-FieldInduced Redistribution of Polar Nano-Regions in a 

Relaxor Ferroelectric, Nat. Mater., 5, 134-140 (2006).
PUBLICA TIONS

6-21

Beamline X17B2

J Chen, L Li, T Yu, H Long, D Weidner, L Wang, M 

Vaughan, Do Reuss and Voigt Bounds Really Bound 

in High-Pressure Rheology Experiments?, J. Phys.: 

Condens. Matter, 18, S1049-1059 (2006).

G Gwanmesia, J Zhang, K Darling, J Kung, B Li, L Wang, 

D Neuville, R Liebermann, Elasticity of Polycrystalline 

Pyrope (Mg3Al2Si3O12) to 9 GPa and 1000 degrees 

C, Phys. Earth Planet. Interiors, 155 (3-4), 179-190 

(2006).

J Kung, B Li, R Liebermann, Ultrasonic Observations of 

Elasticity Changes Across Phase Transformations in 

MgSiO3 Pyroxenes, J. Phys. Chem. Solids, 67 (9-10), 

2051-2055 (2006).

W Liu, B Li, Thermal Equation of State of 

(Mg0.9Fe0.1)2SiO4 Olivine, Phys. Earth Planet. 

Interiors, 157 (3-4), 188-195 (2006).

V Solozhenko, O Kurakevych, E Solozhenko, J Chen, J 

Parise, Equation of State of Graphite-like BC,, Solid 

State Commun., 137 (5), 268-271 (2006).

Beamline X17B3

R Aksoy, Y Ma, E Selvi, M Chyu, A Ertas, A White, 

Equation of State Measurement of Molybdenum 

Disulfi de, J. Phys. Chem. Solids, 67, 1914-1917 

(2006).

V Levitas, Y Ma, J Hashemi, M Holtz, N Guven, Straininduced disorder, phase transformations and TRIP 

in hexagonal boron nitride under compression and 

shear in a rotational diamond anvil cell: in-situ X-ray 

diffraction study and modeling, J. Chem. Phys., 125, 

044507 (2006).

Y Ma, J Liu, C Gao, A White, W Mei, J Rasty, Highpressure X-ray diffraction study of the giant dielectric 

constant material CaCu3Ti4O12: evidence of stiff 

grain surface, American Physical Society Spring 

meeting, p. #Q1.152, sponsored by American Physical 

Society (2006).

Y Ma, V Levitas, J Hashemi, X-ray Diffraction 

Measurements in a Rotational Diamond Anvil Cell, J. 

Phys. Chem. Solids, 67, 2083-2090 (2006).

Y Ma, E Selvi, V Levitas, J Hashemi, Effect of Shear 

Strain on the α-ε Phase Transition of Iron: a New 

Approach in the Rotational Diamond Anvil Cell, J. 

Phys.: Condens. Matter, 18, 1075 (2006).

Y Ma, J Liu, C Gao, W Mei, A White, J Rasty, Highpressure X-ray Diffraction Study of the Giant Dielectric 

Constant Material CaCu3Ti4O12: Evidence of Stiff 

Grain Surface, Appl. Phys. Lett., 88, 191903 (2006).

E Selvi, Y Ma, R Aksoy, A Ertas, A White, J Sandhu, High 

pressure x-ray diffraction study of tungsten disulfi de, J. 

Phys. Chem. Solids, 67, 2183-2186 (2006).

Beamline X17C

R Aksoy, Y Ma, E Selvi, M Chyu, A Ertas, A White, 

Equation of State Measurement of Molybdenum 

Disulfi de, J. Phys. Chem. Solids, 67, 1914-1917 

(2006).

N Conil, A Kavner, Elastic Behavior and Strength of 

Al2O3 Fiber/Al Matrix Composite and Implications for 

Equation of State Measurements in the Diamond Anvil 

Cell, J. Appl. Phys., 100, 043517 (2006).

G Gatta, Y Lee, On the Elastic Behaviour of Zeolite 

Mordenite: a Synchrotron Powder Diffraction Study, 

Phys. Chem. Miner., 32, 726-732 (2006).

D He, T Duffy, X-ray Diffraction Study of the Static 

Strength of tungsten to 69 Gpa, Phys. Rev. B, 73, 

134106 (2006).

J Hu, H Mao, J Shu, Q Guo, H Liu, Diamond Anvil Cell 

Radial X-ray Diffraction Program at the National 

Synchrotron Light Source, Workshop on Synergy of 

21st Century High-Pressure Science and Technology, 

Vol 18, p. S1091-S1096, sponsored by HPcat, APS, 

ANL (2006).

J Hu, H Mao, J Shu, Q Guo, H Liu, Diamond Anvil Cell 

Radial X-ray Diffraction Program at the National 

Synchrotron Light Source, J. Phys.: Condens. Matter, 

18 (25), S1091-S1096 (2006).

F Jiang, S Speziale, T Duffy, Single-crystal Elasticity of 

Brucite, Mg(OH)2, to 15 Gpa by Brillouin Scattering, 

Am. Mineral., 91, 1893-1900 (2006).

Y Lee, J Hriljac, J Parise, T Vogt, Pressure-induced 

Hydration in Zeolite Tetranatrolite, Am. Mineral., 91, 

247-251 (2006).

V Levitas, Y Ma, J Hashemi, M Holtz, N Guven, Straininduced disorder, phase transformations and TRIP 

in hexagonal boron nitride under compression and 

shear in a rotational diamond anvil cell: in-situ X-ray 

diffraction study and modeling, J. Chem. Phys., 125, 

044507 (2006).

M Lufaso, W Gemmil, S Mugavero, Y Lee, T Vogt, H zur 

Loye, Compression mechanisms of symmetric and 

Jahn–Teller distorted octahedra in double perovskites: 

A2CuWO6 (A 1⁄4 Sr, Ba), Sr2CoMoO6, and La2LiRuO6, 

J. Solid State Chem., 179, 3571-3576 (2006).

M Lufaso, R Macquart, Y Lee, T Vogt, H zur Loye, 

Pressure induced octahedral tilting distortion in 

Ba2YTaO6, Chem. Commun., 168, 168-170 (2006).

Y Ma, J Liu, C Gao, A White, W Mei, J Rasty, Highpressure X-ray diffraction study of the giant dielectric 

constant material CaCu3Ti4O12: evidence of stiff 

grain surface, American Physical Society Spring 

meeting, p. #Q1.152, sponsored by American Physical 

Society (2006).

Y Ma, V Levitas, J Hashemi, X-ray Diffraction 

Measurements in a Rotational Diamond Anvil Cell, J. 

Phys. Chem. Solids, 67, 2083-2090 (2006).

Y Ma, E Selvi, V Levitas, J Hashemi, Effect of Shear 

Strain on the α-ε Phase Transition of Iron: a New 

Approach in the Rotational Diamond Anvil Cell, J. 

Phys.: Condens. Matter, 18, 1075 (2006).

Y Ma, J Liu, C Gao, W Mei, A White, J Rasty, Highpressure X-ray Diffraction Study of the Giant Dielectric 

Constant Material CaCu3Ti4O12: Evidence of Stiff 

Grain Surface, Appl. Phys. Lett., 88, 191903 (2006).

A Papandrew, M Lucas, R Stevens, I Halevy, B Fultz, M 

Hu, P Chow, R Cohen, M Somayazulu, Absence of 

Magnetism in Hcp Iron-Nickel at 11K, Phys. Rev. Lett., 

97, 087202 (2006).

S Park, Y Lee, M Elcombe, T Vogt, Synthesis and 

Structure of the Bilayer Hydrate Na0.3NiO2.1.3D2O, 

Inorg. Chem., 45 (9), 3490-3492 (2006).

J Provis, Modelling the Formation of Geopolymers, Ph.D. 

Thesis, University of Melbourne, Melbourne (2006).

W Qiu, P Baker, N Velisavljevic, Y Vohra, S Weir, 

Calibration of an isotopically enriched carbon-13 layer 

pressure sensor to 156 GPa in a diamond anvil cell, J. 

Appl. Phys., 99, 064906 (2006).
6-22

E Selvi, Y Ma, R Aksoy, A Ertas, A White, J Sandhu, High 

pressure x-ray diffraction study of tungsten disulfi de, J. 

Phys. Chem. Solids, 67, 2183-2186 (2006).

S Sen, S Gaudio, B Aitken, C Lesher, Observation of a 

Pressure-Induced First-Order Polyamorphic Transition 

in a Chalcogenide Glass at Ambient Temperature, 

Phys. Rev. Lett., 97, 025504 (2006).

S Speziale, S Shieh, T Duffy, High-Pressure Elasticity 

of Calcium Oxide: A Comparison Between Brillouin 

Scattering and radial X-ray Diffraction, J. Geophys. 

Res., 111, B02203 (2006).

F Zhang, J Lian, U Becker, R Ewing, L Wang, L Boatner, J 

Hu, S Saxena, Pressure-induced Structural Transitions 

and Phase Decomposition in the Cd2Nb2O7 

Pyrochlore, Phys. Rev. B, 74, 174116 (2006).

Beamline X18A

A Braun, F Huggins, K Kelly, B Mun, S Ehrlich, G 

Huffman, Impact of Ferrocene on the Structure of 

Diesel Exhaust Soot as Probed with Wide-Angle X-ray 

Scattering and C(1s) NEXAFS Spectroscopy, Carbon, 

44 (14), 2904-2911 (2006).

X Chen, K Tenneti, C Li, Y Bai, R Zhou, X Wan, X Fan, 

Q Zhou, Design, Synthesis, and Characterization 

of Bent-Core Mesogen-Jacketed Liquid Crystalline 

Polymers, Macromolecules, 39, 517-527 (2006).

K Chung, H Lee, W Yoon, J McBreen, X Yang, Studies 

of LiMn2O4 Capacity Fading Mechanism at Elevated 

Temperature Using In Situ Synchrotron X-Ray 

Diffraction, J. Electrochem. Soc., 153, A774 (2006).

G Liu, K Rider, W Nam, S Fonash, S Kim, Dendritic 

Aggregation of Oligothiophene During Desorption 

of 2,5-Diiodothiophene Multilayer and TopographyInduced Alignment of Oligothiophene Nanofi bers, J. 

Phys. Chem. B, 110, 20197-20201 (2006).

L Martinez-Miranda, Y Hu, Temperature and Depth 

Dependence of Order in Liquid Crystal Interfaces, J. 

Appl. Phys., 99, 113522 (2006).

H Mo, G Evmenenko, S Kewalramani, K Kim, S 

Ehrlich, P Dutta, Observation of Surface Layering in 

a Nonmetallic Liquid, Phys. Rev. Lett., 96, 096107 

(2006).

G Wang, Y Ji, X Huang, X Yang, P Gouma, M Dudley, 

Fabrication and Characterization of Polycrystalline 

WO3 Nanofi bers and Their Application for Ammonia 

Sensing, J. Phys. Chem. B, 110, 23777-23782 

(2006).

W Yoon, K Chung, J McBreen, X Yang, A Comparative 

Study on Structural Changes of LiCo1/3Ni1/3Mn1/3O2 

and LiNi0.8Co0.15Al0.05O2 During First Charge using 

in situ XRD, Electrochem. Commun., 8 (8), 1257-1262 

(2006).

Beamline X18B

M Afeworki, D Dorset, G Kennedy, K Strohmaier, 

Synthesis and Characterization of a New Microporous 

Material. 1. Structure of Aluminophosphate EMM-3, 

Chem. Mater., 18, 1697-1704 (2006).

O Alexeev, A Siani, G Lafaye, C Williams, H Ploehn, 

M Amiridis, EXAFS Characterization of DendrimerPT Nanocomposites Used for the Preparation of 

Pt/gamma-Al2O3 Catalysts, J. Phys. Chem. B, 110, 

24903-24914 (2006).

B Anderson, J Fierro-Gonzalez, K Ramesh, C Vinod, 

J Niemantsverdriet, B Gates, Tricarbonyls of LowCoordinated Au(0) Atoms in Zeolite-Supported Gold 

Nanoparticles: Evidence from Infrared and X-ray 

Absorption Spectroscopies, Langmuir, 22, 4310-4314 

(2006).

S Bare, G Mickelson, F Modica, A Ringwelski, N Yang, 

Simple Flow Through Reaction Cells for in situ 

Transmission and Fluorescence X-ray Absorption 

Spectroscopy of Heterogeneous Catalysts, Rev. Sci. 

Instrum., 77, 023105 (2006).

S Beauchemin, J Kwong, Impact of Redox Conditions 

on Arsenic Mobilization from Tailings in a Wetland with 

Neutral Drainage, Environ. Sci. Tech., 40, 6297-6303 

(2006).

V Bhirud, J Ehresmann, P Kletnieks, J Haw, B Gates, 

Rhodium Complex with Ethylene Ligands Supported 

on Highly Dehydroxylated MgO: Synthesis, 

Characterization, and Reactivity, Langmuir, 22, 490-

496 (2006).

W Caliebe, I So, A Lenhard, D Siddons, Cam-driven 

Monochromator for QEXAFS, 20th International 

Conference on X-Ray and Inner-Shell Processes, 

Vol 75, p. 1962-1965, sponsored by University of 

Melbourne (2006).

S Chin, O Alexeev, J Amiridis, Structure and Reactivity 

of Pt-Ru/SiO2 Catalysts for the Preferential Oxidation 

of CO Under Excess H2, J. Catal., 243 (2), 329-339 

(2006).

S Choi, P O’Day, N Riveria, K Mueller, S Seraphin, J 

Chorover, Strontium Speciation During Reactin of 

Kaolinite with Simulated Tank-Waste Leachate: Bulk 

and Microfocused EXAFS Analysis, Environ. Sci. 

Tech., 40, 2608-2614 (2006).

S Chotisuwan, J Wittayakun, B Gates, Pt3Ru6 

Clusters Supported on gamma-Al2O3: Synthesis 

from Pt3Ru6(Cu)21(u3-H)(u-H)3, Structural 

Characterization, and Catalysis of Ethylene 

Hydrogenation and n-Butane Hydrogenolysis, J. Phys. 

Chem. B, 110, 12459-12469 (2006).

A Ganjoo, G Chen, H Jain, Photoinduced Changes in the 

Local Structure of a-GeSe2 by in-situ EXAFS, Phys. 

Chem. Glasses, 47 (2), 177-181 (2006).

F Huggins, G Huffman, Comment on and addenda to 

“Arsenic in coal: a review” by Yudovich and Ketris., Int. 

J. Coal Geol., 66, 148-150 (2006).

R Hull, L Li, Y Xing, C Chusuei, Pt Nanoparticle Binding 

on Functionalized Multiwalled Carbon Nanotubes, 

Chem. Mater., 18, 1780-1788 (2006).

G Hutchings, M Hall, A Carley, P Landon, B Solsona, 

C Kiely, A Herzing, M Makkee, J Moulijn, et al., Role 

of Gold Cations in the Oxidation of Carbon Monoxide 

Catalyzed by Iron Oxide-Supported Gold, J. Catal., 

242 (1), 71-81 (2006).

G Jacobs, S Ricote, B Davis, Low Temperature WaterGas Shift: Type and Loading of Metal Impacts 

Decomposition and Hydrogen Exchange Rates of 

Pseudo-stabilized Formate over Metal/ceria Catalysts, 

Appl. Catal. A, 302, 14-21 (2006).

G Jacobs, R Keogh, B Davis, Steam Reforming of 

Ethanol over Pt/ceria with Co-fed Hydrogen, J. Catal., 

245, 326-337 (2006).

M Keane, G Jacobs, P Patterson, Ni/SiO2 Promoted 

Growth of Carbon Nanofi bers, J. Colloid Interface Sci., 

302, 576 (2006).
PUBLICA TIONS

6-23

D Kim, B Dunn, F Huggins, G Huffman, M Kang, J Yie, E 

Eyring, SBA-15-Supported Iron Catalysts for FischerTropsch Production of Diesel Fuel, Energ. Fuel, 20, 

2608-2611 (2006).

M Kissell, An X-ray Absorption Spectroscopy Study 

of Arsenic Uptake and Oxidation-Reduction in the 

Arsenic Hyperaccumulating Fern, Pteris cretica, M.S. 

Thesis, Stony Brook University, Stony Brook (2006).

F Larsen, A Boisen, K Berry, B Moubaraki, K Murray, 

V McKee, R Scarrow, C McKenzie, Identifi cation 

of the Dinuclear and Tetranuclear Air-Oxidized 

Products Derived from Labile Phenolate-Bridged 

Dimanganese(II) Pyridyl-Chelate Compounds, Eur. J. 

Inorg. Chem., 2006, 3841-3852 (2006).

K Lee, S Oyama, Bifunctional Nature of a SiO2-

Supported Ni2P Catalyst for Hydrotreating: EXAFS 

and FTIR Studies, J. Catal., 239 (2), 376-389 (2006).

E Maris, W Ketchie, V Oleshko, R Davis, Metal Particle 

Growth During Glucose Hydrogenation over Ru/SiO2 

Evaluated by X-ray Absorption Spectroscopy and 

Electron Microscopy, J. Phys. Chem. B, 110 (15), 

7869-7876 (2006).

S Nemana, B Gates, Surface-Mediated Synthesis and 

Spectroscopic Characterization of Tantalum Clusters 

on Silica, Langmuir, 22, 8214-8220 (2006).

S Nemana, B Gates, Redox Chemisty of Tantalum 

Clusters on Silica Characterized by X-ray Absorption 

Spectroscopy, J. Phys. Chem. B, 110, 17546-17553 

(2006).

S Overbury, V Schwartz, D Mullins, W Yan, S Dai, 

Evaluation of the Au Size Effect: CO Oxidation 

Catalyzed by Au/TiO2, J. Catal., 241 (1), 56-65 

(2006).

S Pandey, A Kumar, S Khalid, A Pimpale, Electronic 

States of LaCoO3: Co K-edge and La L-edge X-ray 

Absorption Studies, J. Phys.: Condens. Matter, 18, 

7103-7113 (2006).

S Pandey, S Khalid, N Lalla, A Pimpale, Local Distortation 

in LaCoO3 and PrCO03: Extended X-ray Absorption 

Fine structure, X-ray Diffraction and X-ray Absorption 

Near Edge structure Studies, J. Phys.: Condens. 

Matter, 18, 10617 (2006).

S Pandey, R Bindu, A Kumar, S Khalid, A Pimpale, 

Doping and Bond Length Contributions to Mn Kedge Shift in La1-xSrxMnO3 (x = 0 - 0.7) and Their 

Correlation with Electrical Transport Properties, 

International Workshop on the Physics of Mesoscopic 

and Disordered Materials-December 4-8, 2006, p. 88, 

sponsored by Indian Institute of Technology (2006).

M Pena, X Meng, G Korfi atis, C Jing, Adsorption 

Mechanism of Arsenic on Nanocrystalline Titanium 

Dioxide, Environ. Sci. Tech., 40, 1257-1262 (2006).

C Reed, Y Lee, S Oyama, Structure and Oxidation State 

of Silica-Supported Manganese Oxide Catalysts and 

Reactivity for Acetone Oxidation with Ozone, J. Phys. 

Chem. B, 110, 4207-4216 (2006).

S Ricote, G Jacobs, M Milling, Y Ji, P Patterson, B Davis, 

Low temperature Water-Gas Shift: characterization 

and Testing of Binary Mixed Oxides of Ceria and 

Zirconia Promoted with Pt, Appl. Catal. A, 303, 35 

(2006).

A Rouff, E Elzinga, R Reeder, The Effect of Aging and 

pH on PB(II) Sorption Processes at the Calcite-Water 

Interface, Environ. Sci. Tech., 40, 1792-1798 (2006).

X Wang, J Rodriguez, J Hanson, D Gamarra, A MartinezArias, M Fernandez-Garcia, In Situ Studies of the 

Active Sites for the Water Gas Shift Reaction over 

Cu-CeO2 Catalysts: Complex Interaction Between 

Metallic Copper and Oxygen Vacancies of Ceria, J. 

Phys. Chem. B, 110, 428-434 (2006).

J Ziegelbauer, D Gatewood, A Gulla, D Ramaker, S 

Mukerjee, X-Ray Absorption Spectroscopy Studies 

of Water Activation on an RhxSy Electrocatalyst for 

Oxygen Reduction Reaction Applications, Electrochem. 

Solid-State Lett., 9 (9), A430-A434 (2006).

Beamline X19A

S Chaudhuri, J Graetz, A Ignatov, J Reilly, J Muckerman, 

Understanding the Role of Ti in Reversible Hydrogen 

Storage as Sodium Alanate: A Combined Experimental 

and Density Functional Theoretical Approach, J. Am. 

Chem. Soc., 128, 11404-11415 (2006).

W Feng, E Borguet, R Vidic, Sulfurization of a Carbon 

Surface for Vapor Phase Mercury Removal-II: Sulfur 

Forms and Mercury Uptake, Carbon, 44 (14), 2998-

3004 (2006).

C Jing, S Liu, G Korfi atis, X Meng, Leaching Behavior of 

Cr(III) in Stabilized/Solidifi ed Soil, Chemosphere, 64

(3), 379-385 (2006).

D Kim, J Szanyi, J Kwak, T Szailer, J Hanson, C Wang, 

C Peden, Effect of Barium Loading on the Desulfation 

of Pt-BaO/Al2O3 Studied by H2 TPRX, TEM, Sulfur Kedge XANES, and In Situ TR-XRD, J. Phys. Chem. B, 

110, 10441-10448 (2006).

A Leri, M Hay, A Lanzirotti, W Rao, S Myneni, 

Quantitative Determination of Absolute Organohalogen 

Concentrations in Environmental Samples by X-ray 

Absorption Spectroscopy, Anal. Chem., 78, 5711-5718 

(2006).

Z Liu, S Wang, B McCoy, A Cady, R Pindak, W Caliebe, 

K Takekoshi, K Ema, H Nguyen, C Huang, Smectic-C* 

alpha-smectic-C* Phase Transition and Critical Point in 

Binary Mixtures, Phys. Rev. E, 74, 030702(R) (2006).

R Maguire, D Hesterberg, A Gernat, K Anderson, M 

Wineland, J Grimes, Liming Poultry Manures to Kill 

Pathogens and Decrease Soluble Phosphorus, J. 

Environ. Qual., 35, 849-857 (2006).

G Murray, D Hesterberg, Iron and phosphate dissolution 

during abiotic reduction of ferrihydrite-boehmite 

mixtures, Soil Sci. Soc. Am. J., 70, 1318-1327 (2006).

V Poltavets, K Lokshin, S Dikmen, M Croft, T Egami, M 

Greenblatt, La2Ni2O6: A New Double T’-type Nickelate 

with Infi nite Ni1=/2=O2 Layers, J. Am. Chem. Soc., 

128, 9050-9051 (2006).

V Poltavets, M Croft, M Greenblatt, Charge Transfer, 

Hybridization and Local Inhomogeneity Effects in 

NaxCo02 Center Dot yH(2)O: An X-ray Absorpton 

Spectroscopy Study, Phys. Rev. B, 74 (12), 125103 

(2006).

A Shober, D Hesterberg, J Sims, S Gardner, 

Characterization of Phosphorus Species in Biosolids 

and Manures Using XANES Spectroscopy, J. Environ. 

Qual., 35, 1983-1993 (2006).

U Skyllberg, P Bloom, J Qian, C Lin, W Bleam, 

Complexation of Mercury(II) in Soil Organic Matter: 

EXAFS Evidence for Linear Two-Coordination with 

Reduced Sulfur Groups, Environ. Sci. Tech., 40, 4174-

4180 (2006).
6-24

Y Suh, M Carroll, R Levy, G Bisognin, D Salvador, 

M Sahiner, Implantation and Activation of High 

Concentrations of Phosphorus and Boron in 

Germanium, Materials Research Society Fall Meeting 

2005, Vol 891, p. EE 7.20.1, sponsored by Materials 

Research Society (2006).

G Toevs, M Morra, M Polizzotto, D Strawn, B Bostick, 

S Fendorf, Metal(loid) Diagenesis in Mine-Impacted 

Sediments of Lake Coeur d’Alene, Idaho, Environ. 

Sci. Tech., 40, 2537-2543 (2006).

X Wang, J Rodriguez, J Hanson, D Gamarra, A MartinezArias, M Fernandez-Garcia, In Situ Studies of the 

Active Sites for the Water Gas Shift Reaction over 

Cu-CeO2 Catalysts: Complex Interaction Between 

Metallic Copper and Oxygen Vacancies of Ceria, J. 

Phys. Chem. B, 110, 428-434 (2006).

S Wang, Z Liu, B McCoy, R Pindak, W Caleibe, H 

Nguyen, C Huang, Optical and Resonant X-Ray 

Diffraction Studies Confi rm a SmC*F12-SmC* Liquid 

Crystal Sequence Reversal, Phys. Rev. Lett., 96, 

097801 (2006).

L Whaley, M Lobanov, D Sehptyakov, M Croft, K 

Ramanujachary, S Lofl and, P Stephens, J Her, G 

Van Tendeloo, et al., Sr3Fe5/4Mo3/4O6.9, an n = 2 

Ruddlesen-Popper Phase: Synthesis and Properties, 

Chem. Mater., 18, 3448-3457 (2006).

W Yoon, K Chung, J McBreen, K Zaghib, X Yang, 

Electronic Structure of the Electrochemically 

Delithiated Li1-xFePO4 Electrodes Investigated by P 

K-edge X-ray Absorption Spectroscopy, Electrochem. 

Solid-State Lett., 9, A415 (2006).

F Zhang, C Chen, J Raitano, J Hanson, W Caliebe, 

S Khalid, S Chan, Phase Stability in Ceria-Zirconia 

Binary Oxide Nanoparticles: The Effect of the Ce3+ 

Concentration and the Redox Environment, J. Appl. 

Phys., 99, 084313 (2006).

F Zhao, J Lehmann, D Solomon, M Fox, S McGrath, 

Sulphur Speciation and Turnover in Soils: Evidence 

from Sulfur K-Edge XANES Spectroscopy and Isotope 

Dilution Studies , Soil Biol. Biochem., 38 (5), 1000-

1007 (2006).

Beamline X19C

G Carini, C Arnone, A Bolotnikov, G Camarda, R De 

Wames, J Dinan, J Markunas, B Raghothamachar, S 

Sivananthan, et al., Material Quality Characterization 

of CdZnTe Substrates for HgCdTe Epitaxy, J. Electron. 

Mater., 35 (6), 1495-1502 (2006).

G Dhanaraj, M Dudley, D Bliss, M Callahan, M Harris, 

Growth and Process Induced Dislocations in Zinc 

Oxide Crystals, J. Cryst. Growth, 297 (1), 74-79 

(2006).

P Konkapaka, B Raghothamachar, M Dudley, Y Makarov, 

M Spencer, Crystal Growth and Characterization of 

Thick GaN Layers Grown by Oxide Vapor Transport 

Technique, J. Cryst. Growth, 289 (1), 140-144 (2006).

S Malkova, R Stahelin, S Pingali, W Cho, M Schlossman, 

Orientation and Penetration Depth of MonolayerBound p40phox-PX, Biochemistry, 45, 13566-13575 

(2006).

S Pingali, T Takiue, G Luo, A Tikhonov, N Ikeda, M 

Aratono, M Schlossman, X-ray Studies of Surfactant 

Ordering and Interfacial Phases at the Water-Oil 

Interface, J. Dispersion Sci. Technol., 27, 715-722 

(2006).

B Raghothamachar, G Dhanaraj, J Bai, M Dudley, Defect 

Analysis in Crystals using X-ray Topography, Microsc. 

Res. Tech., 69, 343-358 (2006).

J Ruggles, G Foran, H Tanida, H Nagatani, Y Jimura, 

I Watanabe, I Gentle, Interfacial Behavior of 

Tetrapyridylporphyrin Monolayer Arrays, Langmuir, 22, 

681-686 (2006).

A Tikhonov, Water Density in the Electric Double Layer 

at the Insulator/Electrolyte Solution Interface, J. Phys. 

Chem. B, 110, 2746-2750 (2006).

A Tikhonov, X-ray Study of the Electric Double Layer at 

the n-Hexane/Nanocolloidal Silica Interface, J. Chem. 

Phys., 124 (16), 164704 (2006).

A Tikhonov, H Patel, S Garde, M Schlossman, Tail 

Ordering Due to Headgroup Hydrogen Bonding 

Interactions in Surfactant Monolayers at the WaterOil Interface, J. Phys. Chem. B, 110, 19093-19096 

(2006).

M Volz, M Schweizer, B Raghothamachar, M Dudley, 

J Szoke, S Cobb, F Szofran, X-ray Characterization 

of Detached-Grown Germanium Crystals, J. Cryst. 

Growth, 290 (2), 446-451 (2006).

Beamline X20A

S Gaudet, C Detarvernier, A Kellock, P Desjardins, C 

Lavoie, Thin Film Reaction of Transition Metals with 

Germanium, J. Vac. Sci. Technol., A, 24 (3), 474-485 

(2006).

Y Gong, H Yan, I Kuskovsky, Y Gu, I Noyan, G Neumazrk, 

M Tamargo, Structure of Zn-Se-Te System with 

Submonolayer Insertion of ZnTe Grown by Migration 

Enhanced Epitaxy, J. Appl. Phys., 99, 064913 (2006).

I Kuskovsky, Y Gu, Y Gong, H Yan, J Lau, I Noyan, G 

Neumark, O Maksimov, X Zhou, et al., Mechanism for 

Increasing Dopant Incorporation in Semiconductors 

Via Doped Nanostructures, Phys. Rev. B, 73, 195306 

(2006).

S Larochelle, M Ramazanoglu, R Birgeneau, Effects of 

Disorder on a Smectic-A-nematic Phase Transition, 

Phys. Rev. E, 73, 060702 (2006).

H Yan, I Noyan, Measurement of Stress/Strain in SingleCrystal Samples using Diffraction, J. Appl. Cryst., 39, 

320-325 (2006).

Beamline X20C

S Gaudet, C Detarvernier, A Kellock, P Desjardins, C 

Lavoie, Thin Film Reaction of Transition Metals with 

Germanium, J. Vac. Sci. Technol., A, 24 (3), 474-485 

(2006).

S Gaudet, C Lavoie, C Detavernier, P Desjardins, 

Germanide Phase Formation and Texture, SiGe 

Technology and Device Meeting, 2006, ISTDM 2006, 

International, p. 18-19, sponsored by IEEE (2006).

S Gaudet, C Detavernier, C Lavoie, P Desjardins, 

Reaction of Thin Ni Films with Ge: Phase Formation 

and Texture, J. Appl. Phys., 100, 034306 (2006).

C Lavoie, C Detavernier, C Cabral, Jr. , F d’Heurle, A 

Kellock, J Jordan-Sweet, J Harper, Effects of Additive 

Elements on the Phase Formation and Morphological 

Stability of Nickel Monosilicide Films, Microelectron. 

Eng., 83 (11-12), 2042-2054 (2006).
PUBLICA TIONS

6-25

W Leroy, C Detavernier, R van Meirhaeghe, A Kellock, 

C Lavoie, Solid-State Formation of Titanium Carbide 

and Molybdenum Carbide as Contcts for CarbonContaining Semiconductors, J. Appl. Phys., 99, 

063704 (2006).

D Mitzi, S Raoux, A Schrott, M Copel, A Kellock, J 

Jordan-Sweet, Solution-Based Processing of the 

Phase-Change Material KSb5S8, Chem. Mater., 18, 

6278-6282 (2006).

K Park, Y Sung, M Toney, Structural Effect of PtRu-WO3 

Alloy Nanostructures on Methanol Electrooxidation, 

Electrochem. Commun., 8, 359-363 (2006).

S Raoux, C Rettner, J Jordan-Sweet, V Deline, J 

Philipp, H Lung, Scaling properties of phase change 

nanostructures and thin fi lms, European Symposium 

on Phase Change and Ovonic Science, p. 127-134, 

sponsored by CEA, France (2006).

H Schubert, C Hill, Structure of ATP-Bound Human ATP:

Cobalamin Adenosyltransferase, Biochemistry, 45, 

15188-15196 (2006).

M Toney, E Marinero, J Hedstrom, Microstructural Origin 

of Orientation Ratio in Magnetic Recording Media, J. 

Appl. Phys., 99, 033907 (2006).

Y Wang, A Ozcan, k Ludwig, A Bhattacharyya, 

T Moustakas, L Zhou, D Smith, Complex and 

Incommensurate Ordering in Al0.72Ga0.28N Thin 

Films, Appl. Phys. Lett., 88 (18), 181915 (2006).

Beamline X21

N Aliouane, D Argyriou, J Strempfer, I Zegkinoglou, 

S Landsgesell, M von Zimmermann, Field-Induced 

Linear Magnetoelastic Coupling in Multiferroic 

TbMnO3, Phys. Rev. B: Condens. Matter, 73, 020102 

(2006).

F Ashish, R Garg, J Anguita, J Krueger, Binding of 

Full-Length HIV-1 gp120 to CD4 Induces Structural 

Reorientation around the gp120 Core, Biophys. J., 91, 

L69-71L (2006).

R Daimant, R Sharon, W Caliebe, C Kao, M Deutsch, 

Structure of the Co and FeK alpha(3,4) Satellite 

Spectra, J. Phys. B: At., Mol. Opt. Phys., 39 (3), 651-

667 (2006).

R Diamant, Multiple Electron Excitations in Medium-Z 

Atoms , Ph.D. Thesis, Bar-Ilan Univesrity, Ramat-Gan 

(2006).

R Diamant, S Huotari, K Hämäläinen, R Sharon, C Kao, 

M Deutsch, The Evolution of Inner-shell Multielectronic 

X-ray Spectra from Threshold to Saturation for Low- to 

High-z Atoms, Radiat. Phys. Chem., 75, 1434 (2006).

M Foldvari, I Badea, S Wettig, R Verrall, M Bagonluri, 

Dicationic Gemini Surfactant Gene Delivery 

Complexes Contain Cubic-lamellar Mixed Polymorphic 

Phase, NSTI Nanotechnology Conference and Trade 

Show, 2006, Vol 2, p. 400-403, sponsored by Nano 

Science and Technology Institute (2006).

M Foldvari, I Badea, S Wettig, R Verrall, M Bagonluri, 

Structural Characterization of Novel Gemini Non-viral 

DNA, J. Exp. Nanoscience, 1 (2), 165-176 (2006).

V Graziano, W McGrath, L Yang, W Mangel, SARS CoV 

Main Proteinase: The Monomer-Dimer Equilibrium 

Dissociation Constant, Biochemistry, 45, 14632-

14641 (2006).

M Misner, Solvent Enhanced Block Copolymer 

Ordering in Thin Films, Ph. D Thesis, University of 

Massachusetts, Amherst (2006).

Z Niu, M Bruckman, V Kotakadi, J He, T Emrick, T 

Russell, L Yang , Q Wang, Study and Characterization 

of Tobacco Mosaic Virus Head-to-tail Assembly 

Assisted by Aniline Polymerization, Chem. Commun., 

2006 (28), 2019-3021 (2006).

A Ozcan, Y Wang, G Ozaydin, K Ludwig, A Bhattacharyya, 

T Moustakas, D Siddons, Real-time X-ray Studies of 

Gallium Adsorption and Desorption, J. Appl. Phys., 

100 (8), 084307 (2006).

M Paine, Calcium-Induced Conformational Changes 

in Gelsolin and Actin-Bound Gelsolin Using SmallAngle X-Ray Scattering, M. S. Thesis, UNC Charlotte, 

Charlotte (2006).

D Pan, W Wang, W Liu, L Yang, H Huang, Chain Packing 

in the Inverted Hexagonal Phase of Phospholipids: A 

Study by X-ray Anomalous Diffraction on BromineLabeled Chains, J. Am. Chem. Soc., 128, 3800-3807 

(2006).

W Wang, D Pan, Y Song, W Liu, L Yang, H Huang, 

Method of X-ray anomalous diffraction for lipid 

structures, Biophys. J., 91 (2), 736-743 (2006).

Y Wang, A Ozcan, G Ozaydin, K Ludwig, Jr., A 

Bhattacharyya, T Moustakas, H Zhou, R Headrick, 

P Siddons, Real-Time Synchrotron X-ray Studies of 

Low- and High-temperature Nitridation of c-plane 

Sapphire, Phys. Rev. B, 74, 235304 (2006).

Beamline X22A

K Alvine, Nanoparticle Assembly and Liquids on 

Nanostructured , Ph.D. Thesis, Harvard University, 

Cambridge (2006).

S Dourdain, Structural, Porous and Mechanical 

Characterization of Mesoporous Silica Thin Films. 

Functionalization infl uence., Ph.D Thesis, Universite 

du Maine, Le Mans (2006).

A Gibaud, S Dourdain, G Vignaud, Analysis of 

Mesoporous Thin Films by X-ray Refl ectivity, Optical 

Refl ectivity and Grazing Incidence Small Angle X-ray 

Scattering, Appl. Surf. Sci., 253 (1), 3-11 (2006).

X Guo, M Myers, S Xiao, M Lefenfeld, R Steiner, G 

Tulevski, J Tang, J Baumert, F Leibfarth, et al., 

Chemoresponsive Monolayer Transistors, Proc Natl 

Acad Sci USA, 103 (31), 11452-11456 (2006).

F He, B Wells, Lattice Strain in Epitaxial BaTiO3 Thin 

Films, Appl. Phys. Lett., 88 (15), 152908 (2006).

G Kim, S Wang, A Jacobson, Z Yuan, W Donner, C Chen, 

L Reimus, P Brodersen, C Mims, Oxygen Exchange 

Kinetics of Epitaxial PrBaCo2O5+delta Thin Films, 

Appl. Phys. Lett., 88 (2), 024103 (2006).

S Larochelle, M Ramazanoglu, R Birgeneau, Effects of 

Disorder on a Smectic-A-nematic Phase Transition, 

Phys. Rev. E, 73, 060702 (2006).

M Lefenfeld, J Baumert, E Sloutskin, I Kuzmenko, P 

Pershan, M Deutsch, C Nuckolls, B Ocko, Direct 

Structural Observation of a Molecular Junction by 

High-Energy X-ray Refl ectometry, Proc Natl Acad Sci 

USA, 103 (8), 2541-2545 (2006).

I Misirlioglu, S Alpay, F He, B Wells, Stress Induced 

Monoclinic Phase in Epitaxial BaTiO3 on MgO, J. Appl. 

Phys., 99, 104103 (2006).

C Nelson, R Kolagani, M Overby, V Smolyaninova, 

R Kennedy, Charge Order in Photosensitive 

Bi0.4Ca0.6MnO3 Films, J. Phys.: Condens. Matter, 

18, 997-1004 (2006).
6-26

S Park, E DiMasi, Y Kim, W Han, P Woodward, T Vogt, The 

Preparation and Characterization of Photocatalytically 

Active TiO2 Thin Films and Nanoparticles using 

Successive-Ionic-Layer-Adsorption-and-Reaction, 

Thin Solid Films, 515 (4), 1250-1254 (2006).

G Xu, J Li, D Viehland, Ground State Monoclinic (Mb) 

Phase in (110)c BiFeO3 Epitaxial Thin Films, Appl. 

Phys. Lett., 89 (22), 222901 (2006).

Beamline X22B

K Alvine, Nanoparticle Assembly and Liquids on 

Nanostructured , Ph.D. Thesis, Harvard University, 

Cambridge (2006).

E DiMasi, S Kwak, F Amos, M Olszta, D Lush, L Gower, 

Complementary Control by Additivies of the Kinetics 

of Amorphous CaCO3 Mineralization at an Organic 

Interface: In-Situ Synchrotron X-ray Observations, 

Phys. Rev. Lett., 97, 045503 (2006).

S Dourdain, Structural, Porous and Mechanical 

Characterization of Mesoporous Silica Thin Films. 

Functionalization infl uence., Ph.D Thesis, Universite 

du Maine, Le Mans (2006).

M Fukuto, O Gang, K Alvine, P Pershan, Capillary Wave 

Fluctuations and Intrinsic Widths of Coupled Fluid-fl uid 

Interfaces: An X-ray Scattering Study of a Wetting Film 

on Bulk Liquid, Phys. Rev. E, 74, 031607 (2006).

A Gibaud, S Dourdain, G Vignaud, Analysis of 

Mesoporous Thin Films by X-ray Refl ectivity, Optical 

Refl ectivity and Grazing Incidence Small Angle X-ray 

Scattering, Appl. Surf. Sci., 253 (1), 3-11 (2006).

S Kim, M Misner, L Yang, O Gang, B Ocko, T Russell, 

Salt Complexation in Block Copolymer Thin Films, 

Macromolecules, 39 (24), 8473-8479 (2006).

L Martinez-Miranda, Y Hu, Temperature and Depth 

Dependence of Order in Liquid Crystal Interfaces, J. 

Appl. Phys., 99, 113522 (2006).

M Maye, D Nykypanchuk, D van der Lelie, O Gang, A 

Simple Method for Kinetic Control of DNA-Induced 

Nanoparticle Assembly, J. Am. Chem. Soc., 128, 

14020-14021 (2006).

M Misner, Solvent Enhanced Block Copolymer 

Ordering in Thin Films, Ph. D Thesis, University of 

Massachusetts, Amherst (2006).

E Ofer, E Sloutskin, L Tamam, B Ocko, M Deutsch, 

Surface Freezing in Binary Alkane-Alcohol Mixtures, 

Phys. Rev. E, 74, 021602 (2006).

O Shpyrko, R Streitel, V Balagurusamy, A Grigoriev, M 

Deutsch, B Ocko, M Meron, B Lin, P Pershan, Surface 

Crystallization in a Liquid AuSi Alloy, Science, 313, 77 

(2006).

E Sloutskin , R Lynden-Bell, S Balasubramanian, M 

Deutsch, Comparing Simulated and X-ray-measured 

Surface Structure: The Case of Ionic Liquids, J. Chem. 

Phys., 175, 174715 (2006).

J Strzalka, T Xu, A Tronin, S Wu, I Miloradovic, I 

Kuzmenko, T Gog, M Therien, K Blasie, Structural 

Studies of Amphiphilic 4-Helix Bundle Peptides 

Incorporating Designed Extended Chromophores for 

Nonlinear Optical Biomolecular Materials, Nano Lett., 

6 (11), 2395-2405 (2006).

J Wang, J Leiston-Belanger, J Sievert, T Russell, 

Grain Rotation in Ion-Complexed Symmetric Diblock 

Copolymer Thin Films under an Electric Field, 

Macromolecules, 39, 8487-8491 (2006).

Beamline X22C

A Borissov, X-ray Scattering Study of Inhomogeneous 

Charge-ordered States of Colossal Magnetoresistance 

Manganites and Chalcogenide Spinel Compounds, 

Ph.D. Thesis, Rutgers University, New Brunswick 

(2006).

F He, B Wells, Lattice Strain in Epitaxial BaTiO3 Thin 

Films, Appl. Phys. Lett., 88 (15), 152908 (2006).

M Hucker, M Zimmermann, R Klingelar, S Kiele, J Geck, 

S Bakehe, J Zhang, J Hill, A Revcolevschi, et al., 

Undirectional Diagonal Order and Three-Dimensional 

Stacking of Charge Stripes in Orthorhombic 

Pr1.67Sr0.33NiO4 and Nd1.67Sr0.33NiO4, Phys. 

Rev. Lett., 74, 085112 (2006).

M Hucker, V Zimmermann, R Klingeler, S Kiele, J Geck, 

S Bakehe, J Zhang, J Hill, A Revcolevschi, et al., 

Unidirectional Diagonal Order and Three-Dimensional 

Stacking of Charge Stripes in Orthorhombic 

Pr1.67Sr0.33Ni)4 and Nd1.67Sr0.33NiO4, Phys. Rev. 

B, 74, 085112 (2006).

G Kim, S Wang, A Jacobson, Z Yuan, W Donner, C Chen, 

L Reimus, P Brodersen, C Mims, Oxygen Exchange 

Kinetics of Epitaxial PrBaCo2O5+delta Thin Films, 

Appl. Phys. Lett., 88 (2), 024103 (2006).

V Kiryukhin, Y Horibe, Y Hor, H Noh, S Cheong, 

Incommensurate Structural Correlations in the 

Disordered Spin-Dimer State Induced by X-Ray and 

Electron Irradiation in CuIr2S4, Phys. Rev. Lett., 97, 

225503 (2006).

P Lyman, V Shneerson, R Fung, S Parihar, H JohnsonSteigelman, E Lu, D Saldin, Structure and Stability of 

Sb/Au(110)-c(2x2) Surface Phase, Surf. Sci., 600 (2), 

424-435 (2006).

C Nelson, R Kolagani, M Overby, V Smolyaninova, 

R Kennedy, Charge Order in Photosensitive 

Bi0.4Ca0.6MnO3 Films, J. Phys.: Condens. Matter, 

18, 997-1004 (2006).

Y Uozu, Y Wakabayashi, Y Ogimoto, N Takubo, 

H Tamuru, N Nagaosa, K Miyano, Intrinsic 

Colassol Magnetoresistance Effect in Thin-Film 

Pr0.5Sr0.5MnO3 Through Dimensionally Switching, 

Phys. Rev. Lett., 97, 037202 (2006).

Beamline X23A2

I Levin, E Cockayne, M Lufaso, J Woicik, J Masler, Local 

structures and Raman spectra in the Ca(Zr,Ti)O3 

perovskite solid solutions, Chem. Mater., 18, 854 

(2006).

M Shao, T Huang, P Liu, J Zhang, K Sasaki, M Vukmirovic, 

R Adzic, Palladium Monolayer and Palladium Alloy 

Electrocatalysts for Oxygen Reduction, Langmuir, 22, 

10409-10415 (2006).

Beamline X23B

M Altman, A Shukla, T Zubkov, G Evmenenko, P Dutta, M 

van der Boom, Controlling Structure from the BottomUp: Structural and Optical Properties of Layer-by-Layer 

Assembled Palladium Coordination-Based Multilayers, 

J. Am. Chem. Soc., 128, 7374-7382 (2006).

G Evmenenko, H Mo, S Kewalramani, P Dutta, 

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for Enzyme Function and Drug Developement, J. Biol. 

Chem., 281, 21469 (2006).

Y Xu, Y Xing, Y Chen, Y Chao, Z Lin, E Fan, J Yu, 

S Strack, P Jeffrey, Y Shi, Structure of the Protein 

Phosphatase 2A Holoenzyme, Cell, 127, 1239-1251 

(2006).

W Yew, A Fedorov, E Fedorov, J Rakus, R Pierce, S 

Almo, J Gerlt, Evolution of Enzymatic Activities in the 

Enolase Superfamily: L-Fuconate Dehydratase from 

Xanthomonas campestris, Biochemistry, 45, 14582-

14597 (2006).

Y Yuan, Y Pei, H Chen, T Tuschl, D Patel, A Potential 

Protein-RNA Recognition Event Along the RISCLoading Pathway from the Structure of A. aeolicus 

Argonaute with Externally Bound siRNA, Structure, 14

(10), 1557-1565 (2006).

H Zhu, J Nandakumar, J Aniukwu, L Wang, M 

Glickman, C Lima, S Shuman, Atomic Structure 

and Nonhomologous End-Joining Function of the 

Polymerase Component of Bacterial DNA Ligase D, 

Proc Natl Acad Sci USA, 103 (6), 1711-1716 (2006).

Beamline X29B

H Wang, Y Liu, Q Huai, J Cai, R Zoraghi, S Francis, 

J Corbin, H Robinson, Z Xin, et al., Multiple 

Conformations of Phosphodiesterase-5: Implications 

for Enzyme Function and Drug Developement, J. Biol. 

Chem., 281, 21469 (2006).

NSLS STAFF

J Ablett, C Kao, R Reeder, Y Tang, A Lanzirotti, X27A 

- A New Hard X-ray Micro-Spectroscopy Facility at the 

National Synchrtron Light Source, Nucl. Instrum. Meth. 

A, 562, 487-494 (2006).

D Anschel, B Foerster, T Yuasa, H Benveniste, Z Zhong, 

J Heinfeld, A Dilmanian, 9.4 T MRI Characterization of 

a Focal Lesion in the Rat Brain Induced by Interlaced 

Microbeam Radiation, Epilepsia, Vol 46, p. 280-

281, sponsored by American Epilepsy Society and 

American Clinical Neurophysiology Society (2006).
PUBLICA TIONS

6-35

D Arena, E Vescovo, C Kao, Y Guan, W Bailey, Weakly 

Coupled Motion of Individual Layers in Ferromagnetic 

Resonance, Phys. Rev. B, 74, 064409 (2006).

I Baek, W Kim, E Vescovo, H Lee, Effect of Ni 

Concentration on Quantum-well States of the Alloy 

System Ag/Fe1-xNix: A Spin- and angle-Resolved 

Photoemission Study, Phys. Rev. B, 74, 113302 

(2006).

J Beaujour, J Lee, A Kent, K Krycka, C Kao, 

Magnetization Damping in Ultrathin Polycrystalline Co 

Films: Evidence for Nonlocal Effects, Phys. Rev. B, 

74, 214405 (2006).

J Bengtsson, A Control Theory Approach for Dynamic 

Aperture, Proceedings of EPAC 2006, Edinburgh, 

Scotland, p. 3478-3480, sponsored by EPAC (2006).

A Blednykh, Trapped Modes in Tapered Vacuum 

Chambers for a Mini-Gap Undulator Magnet, Nucl. 

Instrum. Meth. A, 565 (2), 380-393 (2006).

A Blednykh, S Krinsky, B Podobedov, J Wang, 

Transverse Impedance of Small-gap Undulators for 

NSLS-II, EPAC2006, p. 2970, sponsored by EPAC 

(2006) (2006).

J Brankov, M Wernick, Y Yang, J Li, C Muehleman, 

Z Zhong, M Anastasio, A Computed Tomography 

Implementation of Multiple-Image Radiography, Med. 

Phys., 33 (2), 278 (2006).

L Brewer, M Othon, Y Gao, B Hazel, W Buttrill, Z Zhong, 

Comparison of Diffraction Methods for Measurement 

of Surface Damage in Superalloys, J. Mater. Res., 21

(7), 1775-1781 (2006).

Y Cai, P Chow, O Restrepo, Y Takano, H Kito, H Ishii, C 

Chen, K Liang, C Chen, et al., Low-Energy ChargeDensity Excitations in MgB2: Striking Interplay 

Between Single-Particle and Collective Behavior 

for Large Momenta, Phys. Rev. Lett., 97, 176402-4 

(2006).

W Caliebe, I So, A Lenhard, D Siddons, Cam-driven 

Monochromator for QEXAFS, 20th International 

Conference on X-Ray and Inner-Shell Processes, 

Vol 75, p. 1962-1965, sponsored by University of 

Melbourne (2006).

W Caliebe, I So, A Lenhard, D Siddons, Cam-Driven 

Monochromator for QEXAFS, Radiat. Phys. Chem., 

75 (11), 1962-1965 (2006).

B Chapman, A Checco, R Pindak, T Siegrist, C Kloc, 

Dislocations and Grain Boundaries in Semiconducting 

Rubrene Single-Crystals, J. Cryst. Growth, 290 (2), 

479-484 (2006).

D Connor, D Sayers, D Sumner, Z Zhong, Diffraction 

Enhanced Imaging of Controlled Defects Within Bone, 

Including Bone-Metal Gaps, Phys. Med. Biol., 51 (12), 

3283-3300 (2006).

R Daimant, R Sharon, W Caliebe, C Kao, M Deutsch, 

Structure of the Co and FeK alpha(3,4) Satellite 

Spectra, J. Phys. B: At., Mol. Opt. Phys., 39 (3), 651-

667 (2006).

G Decker, M Borland, D Horan, A Lumpkin, N Sereno, B 

Yang, S Krinsky, Transient Bunch Compression using 

Pulsed Phase Modulation in High-Energy Electron 

Storage Rings, Phys. Rev. ST AB, 9, 120702 (2006).

F Dilimanian, Z Zhong, T Bacarian, H Benveniste, P 

Romanelli, R Wang, J Welwart, T Yuasa, E Rosen, 

D Anschel, Interlaced X-ray Microplanar Beams: A 

Radiosurgery Approach with Clinical Potential, Proc 

Natl Acad Sci USA, 103 (25), 9709-9714 (2006).

E DiMasi, S Kwak, F Amos, M Olszta, D Lush, L Gower, 

Complementary Control by Additivies of the Kinetics 

of Amorphous CaCO3 Mineralization at an Organic 

Interface: In-Situ Synchrotron X-ray Observations, 

Phys. Rev. Lett., 97, 045503 (2006).

T Ellis, K Park, M Ulrich, S Hulbert, J Rowe, Interaction of 

Metallophthalocyanines (Mpc, M=Co, Ni) on Au(001): 

Ultraviolet Photoemission Spectroscopy and Low 

Energy Electron Diffraction Study, J. Appl. Phys., 100, 

093515-10 (2006).

R Fiorito, A Shkvarunets, T Watanabe, V Yakimenko, 

D Snyder, Interference of Diffraction and Transition 

Radiation and Its Application as a Beam Divergence 

Diagnostic, Phys. Rev. ST AB, 9 (5), 052802 (2006).

Y Guan, W Bailey, C Kao, E Vescovo, D Arena, 

Comparison of Time-Resolved X-ray Magnetic 

Circular Dichroism Measurements in Refl ectino 

and Transmission for Layer-Specifi c Precessional 

Dynamics Measurements, J. Appl. Phys., 99, 08J305 

(2006).

K Gunter, M Aschner, L Miller, R Eliseev, J Salter, K 

Andersen, T Gunter, Determining the Oxidation States 

of Manganese in NT2 Cells and Cultured Astrocytes, 

Neurobiol. Aging, 27 (12), 1816-26 (2006).

D Hill, D Arena, R Bartynski, P Wu, G Saraf, Y Lu, 

l Wielunski, R Gateau, J Dvorak, et al., Room 

Temperature Ferromagnetism in MN Ion Implanted 

Epitaxial ZnO Films, Phys. Status Solidi (a), 203 (15), 

3836-3843 (2006).

J Hu, C Foerster, J Skaritka, D Waterman, Novel 

Chamber Design for An In-Vacuum Cryo-Cooled 

Mini-Gap Undulator, 4th International Workshop 

on Mechanical Engineering Design of Synchrotron 

Radiation Equipment & Instrumentation, Vol 1, p. 8, 

sponsored by Japan Synchrotron Radiation Research 

Institute and MEDSI-06 (2006).

J Jakoncic, Y Jouanneau, C Meyer, V Stojanoff, 

The Catalytic Pocket of the Ring-hydroxylating 

Dioxygenase from Sphingomonas CHY-1, Biochem. 

Biophys. Res. Commun., 352, 861-866 (2006).

J Jakoncic, M Di Michiel, Z Zhong, V Honkimaki, Y 

Jouanneau, V Stojanoff, Anomalous Diffraction at 

Ultra-High Energy for Protein Crystallography, J. Appl. 

Cryst., 39, 831-841 (2006).

Y Jouanneau, C Meyer, J Jakoncic, V Stojanoff, J Gaillard, 

Characterization of a Naphthalene Dioxygenase 

Endowed with an Exceptionally Broad Substrate 

Specifi city Toward Polycyclic Aromatic Hydrocarbons, 

Biochemistry, 45, 12380-12391 (2006).

M Kelly, R Beavis, D Fourney, E Schultke, C Parham, B 

Juurlink, Z Zhong, L Chapman, Diffraction-enhanced 

Imaging of the Rat Spine, Can. Assoc. Radiol. J., 57, 

204-210 (2006).

G Khelashvili, J Brankov, D Chapman, M Anastasio, 

Y Yang, Z Zhong, M Wernick, A Physical Model of 

Muliple-Image Radiography, Phys. Med. Biol., 51 (2), 

221-236 (2006).

C Kinane, A Suszka, C Marrows, B Hickey, D Arena, J 

Dvorak, T Charlton, S Langridge, Soft x-ray resonant 

magnetic scattering from an imprinted magnetic 

domain pattern , Appl. Phys. Lett., 89, 092507 (2006).

B Kirby, J Borchers, J Rhyne, K O’Donovan, S Velthuis, 

S Roy, C Sanchez-Hanke, T Wojtowicz, X Liu, et al., 

Magnetic and Chemical Nonuniformity in Ga1-xMnxAs 

Films as Probed by Polarized Neutron and X-ray 

Refl ectometry, Phys. Rev. B, 74, 245304 (2006).
6-36

D Koller, G Ediss, L Mihaly, G Carr, Infrared 

Measurements of Possible IR Filter Materials, Int. J. 

Infrared Millimeter Waves, 27 (6), 835-846 (2006).

S Kramer, S Krinsky, J Bengtsson, Comparison of Double 

Bend and Triple Bend Achromatic Lattice Structures 

for NSLS-II, Proceedings of EPAC 2006, Edinburgh, 

Scotland, p. 3484-3486, sponsored by EPAC (2006).

S Kramer, J Bengtsson, Optimizing the Dynamic Aperture 

for Triple Bend Achromatic Lattices, Proceedings 

of EPAC 2006, Edinburgh, Scotland, p. 3481-3483, 

sponsored by EPAC (2006).

A Kretlow, Q Wang, J Kneipp, P Lasch, M Beekes, L 

Miller, D Naumann, FTIR-Microspectroscopy of PrionInfected Nervous Tissue, Biochim Biophys Acta, 1758, 

948-959 (2006).

S Krinsky, J Bengtsson, S Kramer, Consideration 

of a Double Bend Achromatic Lattice for NSLS-II, 

Proceedings of EPAC 2006, Edinburgh, Scotland, p. 

3487-3489, sponsored by EPAC (2006).

S Krinsky, Y Li, Statistical Analysis of the Chaotic Optical 

Field from a Self-Amplifi ed Spontaneous-Emission 

Free-Electron Laser, Phys. Rev. E, 73, 066501 

(2006).

H Lee, I Baek, E Vescovo, Spin Reorientation Transition 

in Fe-Rich Alloy Films on W(110): The Role of 

Magnetoelastic Anisotropy and Structural Transition, 

Appl. Phys. Lett., 89, 112516 (2006).

H Lee, I Baek, S Kim, E Vescovo, Electronic and 

Magnetic Properties in Fe-Based Fe1-xNix, Fe1-xCox, 

and Fe1-xVx Films on W(110), Surf. Sci., 600, 4137-

4142 (2006).

Z Liu, S Wang, B McCoy, A Cady, R Pindak, W Caliebe, 

K Takekoshi, K Ema, H Nguyen, C Huang, SmecticC* alpha-smectic-C* Phase Transition and Critical 

Point in Binary Mixtures, Phys. Rev. E, 74, 030702(R) 

(2006).

H Liu, M Quijada, D Romero, D Tanner, A Zibold, 

G Carr, H Berger, L Forro, L Mihaly, et al., Drude 

Behavior in the Far-Infrared Conductivity of Cuprate 

Superconductors, Ann. Phys., 15 (7), 606-618 (2006).

J Miklossy, A Kis, A Radenovic, L Miller, L Forro, R 

Martins, K Reiss, N Darbinian, P Darekar, et al., BetaAmyloid Deposition and Alzheimer’s Type Changes 

Induced by Borrelia Spirochetes, Neurobiol. Aging, 27, 

228-236 (2006).

L Miller, P Dumas, Chemical Imaging of Biological Tissue 

with Synchrotron Infrared Light, Biochim Biophys Acta, 

1758 (7), 846-57 (2006).

L Miller, Q Wang, T Telivala, R Smith, A Lanzirotti, J 

Miklossy, Synchrotron-based Infrared and X-ray 

Imaging Shows Focalized Accumulation of Cu and 

Zn Co-localized With Beta-amyloid Deposits in 

Alzheimer’s Disease, J. Struct. Biol., 155 (1), 30-37 

(2006).

H Mo, G Evmenenko, S Kewalramani, K Kim, S 

Ehrlich, P Dutta, Observation of Surface Layering in 

a Nonmetallic Liquid, Phys. Rev. Lett., 96, 096107 

(2006).

C Muehleman, J Li, Z Zhong, J Brankov, M Wernick, 

Multiple-Image Radiography for Human Soft Tissue, J. 

Anatomy, 208, 115-124 (2006).

C Muehleman, J Li, Z Zhong, Preliminayr Study on 

Diffraction Enhanced Radiographic Imaging for a 

Canine Model of Cartilage Damage, Osteoarthr. 

Cartilage, 14 (92), 882-888 (2006).

C Nelson, R Kolagani, M Overby, V Smolyaninova, 

R Kennedy, Charge Order in Photosensitive 

Bi0.4Ca0.6MnO3 Films, J. Phys.: Condens. Matter, 

18, 997-1004 (2006).

Z Niu, M Bruckman, V Kotakadi, J He, T Emrick, T 

Russell, L Yang , Q Wang, Study and Characterization 

of Tobacco Mosaic Virus Head-to-tail Assembly 

Assisted by Aniline Polymerization, Chem. Commun., 

2006 (28), 2019-3021 (2006).

A Ozcan, Y Wang, G Ozaydin, K Ludwig, A Bhattacharyya, 

T Moustakas, D Siddons, Real-time X-ray Studies of 

Gallium Adsorption and Desorption, J. Appl. Phys., 

100 (8), 084307 (2006).

S Pandey, A Kumar, S Khalid, A Pimpale, Electronic 

States of LaCoO3: Co K-edge and La L-edge X-ray 

Absorption Studies, J. Phys.: Condens. Matter, 18, 

7103-7113 (2006).

S Pandey, S Khalid, N Lalla, A Pimpale, Local Distortation 

in LaCoO3 and PrCO03: EXAFS, X-ray Diffraction and 

X-ray Absorption Near Edge structure Studies, J. 

Phys.: Condens. Matter, 18, 10617 (2006).

S Pandey, R Bindu, A Kumar, S Khalid, A Pimpale, 

Doping and Bond Length Contributions to Mn Kedge Shift in La1-xSrxMnO3 (x = 0 - 0.7) and Their 

Correlation with Electrical Transport Properties, 

International Workshop on the Physics of Mesoscopic 

and Disordered Materials-December 4-8, 2006, p. 88, 

sponsored by Indian Institute of Technology (2006).

S Park, E DiMasi, Y Kim, W Han, P Woodward, T Vogt, The 

Preparation and Characterization of Photocatalytically 

Active TiO2 Thin Films and Nanoparticles using 

Successive-Ionic-Layer-Adsorption-and-Reaction, 

Thin Solid Films, 515 (4), 1250-1254 (2006).

P Pawelek, N Croteau, C Ng-Thow-Hing, C Khursigara, 

N Moiseeva, M Allaire, J Coulton, Structure of TonB 

in Complex with FhuA, E. Coli Outer Membrane 

Receptor, Science, 312, 1399-1402 (2006).

A Phelippeau, S Pommier, T Tsakalakos, M Clavel, C 

Prioul, Cold Drawn Steel Wires—Processing, Residual 

Stresses and Ductility—Part I: Metallography and 

Finite Element Analyses, Fatigue Fract. Eng. Mater. 

Struct., 29, 201-208 (2006).

A Phelippeau, S Pommier, I Zakharchenko, R LevyTubiana, T Tsakalakos, M Clavel, M Croft, Z Zhong, C 

Prioul, Cold Drawn Steel Wires—Processing, Residual 

Stresses and Ductility Part II: Synchrotron and Neutron 

Diffraction, Fatigue Fract. Eng. Mater. Struct., 29, 255-

265 (2006).

I Pinayev, T Shaftan, Synchrotron Radiation Monitor 

for NSLS Booster, Beam Instrumentation Workshop 

2006: Twelfth Beam Instrumentation Workshop, Vol 

868, p. 428-434, sponsored by AIP (2006).

I Pinayev, Lepton Beam Emittance Instrumentation, 

Beam Instrumentation Workshop 2006: Twelfth Beam 

Instrumentation Workshop, Vol 868, p. 112, sponsored 

by AIP (2006).

B Podobedov, S Krinsky, Transverse impedance of 

elliptical cross-section tapers, EPAC2006, p. 2973, 

sponsored by EPAC (2006).

B Podobedov, S Krinsky, Transverse Impedance of 

Axially Symmetric Tapered Structures, Phys. Rev. ST 

AB, 9 (5), 054401 (2006).

J Prada, R Haire, M Allaire, J Jakoncic, V Stojanoff, J 

Cannon, G Litman, D Ostrov, Ancient Evolutionary 

Origin of Diversifi ed Variable Regions Demonstrated 

by Crystal Structures of an Immune-Type Receptor in 

Amphioxus, Nat. Immunol., 7 (8), 875-882 (2006).
PUBLICA TIONS

6-37

M Ruppel, D Burr, L Miller, Chemical Makeup of 

Microdamaged Bone Differs from Undamaged Bone, 

Bone, 39 (2), 318-324 (2006).

A Rusydi, P Abbamonte, H Eisaki, Y Fujimaki, G 

Blumberg, S Uchida, G Sawatzky, Quantum Melting 

of the Hole Crystal in the Spin Ladder of Sr14-

xCaxCu24O41, Phys. Rev. Lett., 97, 016403 (2006).

C Ryan, D Siddons, G Moorhead, P Dunn, R Kirkham, 

A Dragone, G De geronimo, R Hough, B Etschmann, 

The Next Generation of Synchrotron Fluorescence 

Imaging for Geological Applications, Geochim. 

Cosmochim. Acta, 70 (18), A550 (2006).

M Sachan, N Walrath, S Majetich, K Krycka, C Kao, 

Interaction Effects Witin Langmuir Layers and ThreeDimensional Arrays of E-Co Nanoparticles, J. Appl. 

Phys., 99, 08C302 (2006).

G Sainz, J Jakoncic, L Sieker, V Stojanoff, N Sanishvilli, 

M Asso, P Bertrand, J Armengaud, Y Jouanneau, 

Structrue of a [2Fe-2S] Ferredoxin from Rhodobacter 

capsulatus likely Involved in Fe-S Cluster Biogenesis 

and Conformational Changes Observed upon 

Reduction, J. Biol. Inorg. Chem., 11, 235-246 (2006).

C Sanchez-Hanke, R Gonzalez-Arrabal, J Prieto, E 

Andrzejewska, N Gordillo, D Boerma, R Loloee, 

J Skuza, R Lukaszew, Observation of Nitrogen 

Polarization in Fe-N Using Soft X-ray Magnetic Circular 

Dichorism, J. Appl. Phys., 99, 08B709 (2006).

T Shaftan, J Bengtsson, S Kramer, Control of Dynamic 

Aperture with Insertion Devices, Proceedings of EPAC 

2006, Edinburgh, Scotland, p. 3490-3492, sponsored 

by EPAC (2006).

W Shi, H Robinson, M Sullivan, D Abel, J Toomey, L 

Berman, D Lynch, G Rosenbaum, G Rakowsky, et 

al., Beamline X29: A Novel Undulator Source for X-ray 

Crystallography, J. Synch. Rad., 13, 365-372 (2006).

V Struzhkin, H Mao, J Lin, R Hemley, J Tse, Y Ma, M 

Hu, P Chow, C Kao, Valence Band X-Ray Emission 

Spectra of Compressed Germanium, Phys. Rev. Lett., 

96, 137402 (2006).

K Subburaman, N Pernodet, S Kwak, E DiMasi, S Ge, 

V Zaitsev, X Ba, N Yang, M Rafailovich, Templated 

Biomineralization on Self-Assembled Protein Fibers, 

Proc Natl Acad Sci USA, 103 (40), 14672-14677 

(2006).

T Tanabe, J Ablett, L Berman, D Harder, S Hulbert, M 

Lehecka, G Rakowsky, J Skaritka, A Deyhim, et al., 

X-25 Cryo-ready In-vacuum Undulator at The NSLS, 

International Conference on Synchrotron Radiation 

Instrumentation, Vol 879, p. 283-286, sponsored by 

PAL/JASRI (2006).

T Tsakalakos, M Croft, N Jisrawi, R Holtz, Z Zhong, 

Measurement of Residual Stress Distributions by 

Energy Dispersive X-ray Diffraction Synchrotron 

Radiation, Int. J. Offshore Polar Eng., 16, 358-366 

(2006).

E Vescovo, Reply to “Comment on ‘Oxidation of the 

Fe(110) Surface: An Fe3O4(111)/Fe(110) Bilayer’”, 

Phys. Rev. B, 74, 026406 (2006).

E Vescovo, Reply to “Comment on `Oxidation of the 

Fe(110) surface: An Fe3O4(111)/Fe(110) bilayer’ “, 

Phys. Rev. B: Condens. Matter, 74, 26406 (2006).

E Vescovo, Spin-Resolved Photoemission Studies of 

Magnetic Films, Modern Techniques for Characterizing 

Magnetic Materials , p. 600, Kluwer Academic Pub, 

New York (2006).

F Wang, D Cheever, M Farkhondeh, W Franklin, E Ihloff, 

J van der Laan, B McAllister, R Milner, C Tschalaer, 

et al., Coherent THz Synchrotron Radiation from a 

Storage Ring with High-Frequency RF System, Phys. 

Rev. Lett., 96, 064801 (2006).

S Wang, Z Liu, B McCoy, R Pindak, W Caleibe, H 

Nguyen, C Huang, Optical and Resonant X-Ray 

Diffraction Studies Confi rm a SmC*F12-SmC* Liquid 

Crystal Sequence Reversal, Phys. Rev. Lett., 96, 

097801 (2006).

W Wang, D Pan, Y Song, W Liu, L Yang, H Huang, 

Method of X-ray anomalous diffraction for lipid 

structures, Biophys. J., 91 (2), 736-743 (2006).

Y Wang, A Ozcan, G Ozaydin, K Ludwig, Jr., A 

Bhattacharyya, T Moustakas, H Zhou, R Headrick, 

P Siddons, Real-Time Synchrotron X-ray Studies of 

Low- and High-temperature Nitridation of c-plane 

Sapphire, Phys. Rev. B, 74, 235304 (2006).

T Watanabe, D Liu, J Murphy, J Rose, T Shaftan, T 

Tsang, X Wang, L Yu, P Sprangle, Experimental 

Characterization of Seeded FEL Amplifi er at the NSLS 

SDL, The 27th International Conference on Free 

Electron Lasers, Vol , p. 98, sponsored by APS, LBNL, 

LNL, LCLS, SLAC and UCLA (2006).

T Watanabe, D Liu, J Murphy, J Rose, T Shaftan, T 

Tanabe, T Tsang, X Wang, L Yu, et al., Design Study 

of a Compact Megawatt Class FEL Amplifi er Based on 

the VISA Undulator, The 27th International Conference 

on Free Electron Lasers, Vol , p. 320, sponsored by 

APS, LBNL, LNL, LCLS, SLAC and UCLA (2006).

T Watanabe, D Liu, J Murphy, J Rose, T Shaftan, T 

Tsang, X Wang, L Yu, Y Shen, et al., An Experimental 

Test of Superradiance in a Single Pass Seeded FEL, 

The 27th International Conference on Free Electron 

Lasers, Vol , p. 526, sponsored by APS, LBNL, LNL, 

LCLS, SLAC and UCLA (2006).

M Wernick, Y Yang, I Mondal, D Chapman, M Hasnah, 

C Parham, E Pisano, Z Zhong, Computation of Mass 

Density Images from X-ray Refraction-Angle Images, 

Phys. Med. Biol., 51, 1769-1778 (2006).

P Wu, G Saraf, Y Lu, D Hill, R Gateau, L Wielunski, R 

Bartynski, D Arena, J Dvorak, et al., Ferromagnetism 

in Fe-Implanted a-plane ZnO Films, Appl. Phys. Lett., 

89, 012508 (2006).

D Xiang, S Park, J Park, Y Parc, X Wang, Reduction 

of Thermal Emittance by using P-polarized Laser at 

Oblique Incidence, Nucl. Instrum. Meth. A, 562 (1), 

48-52 (2006).

L Xie, J Jacobsen, B Busa, L Donahue, L Miller, C Rubin, 

S Judex, Low-Level Mechanical Vibrations can Reduce 

Bone Resorption and Enhance Bone Formation in the 

Growing Skeleton, Bone, 39 (5), 1059-1056 (2006).

G Xu, Z Zhong, Y Bing, Z Ye, G Shirane, Electric-FieldInduced Redistribution of Polar Nano-Regions in a 

Relaxor Ferroelectric, Nat. Mater., 5, 134-140 (2006).

S Yoon, Y Chen, A Yang, T Goodrich, X Zuo, D Arena, 

K Ziemer, C Vittoria, V Harris, Oxygen-defect-induced 

Magnetism to 880 K in Semiconducting Anatase TiO2-

delta Films, J. Phys.: Condens. Matter, 18 (27), L355-

L361 (2006).

F Zhang, C Chen, J Raitano, J Hanson, W Caliebe, 

S Khalid, S Chan, Phase Stability in Ceria-Zirconia 

Binary Oxide Nanoparticles: The Effect of the Ce3+ 

Concentration and the Redox Environment, J. Appl. 

Phys., 99, 084313 (2006).