Natio

nal

Synchrotron

Light Source Activity

Report 2004

 BNL 73577 National Synchrotron Light Source Activity Report 2004
BNL-73577-2005

UC400

(General Energy Research)

DISCLAIMER

This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any 

agency thereof, nor any of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes 

any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents 

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manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any 

agency, contractor, or subcontractor thereof. The views and opinions of authors express herein do not necessarily state or reflect those of the United States

Government or any agency, contractor, or subcontractor thereof.

Printed in the United States of America

Available from

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Springfield, VA 22161

Cover image from the Science Highlight by A.J. Celestian, J.B. Parise, C. Goodell, A. Tripathi, J. Hanson,“Time-Resolved 

Diffraction Studies of Ion Exchange: K+ and Na+ Exchange into Synthetic Aluminogermanate Molecular Sieve with the 

Gismondine Topology,” page 2-54.
National Synchrotron Light Source

2004 Activity Report

Lisa M. Miller

managing editor

Laura Y. Mgrdichian

science editor

Nancye A. Wright, Stephen A. Giordano & Theresa A. Esposito

design & layout

managed for the U.S. Department of Ene gy 

by Brookhaven Science Associates, a coy m

founded by Stony Brook University and Ba

The National Synchrotron Light Source Department is supported by the

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

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

Under contract no. DE-AC02-98CH10886
ii

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 Sciences.........................................................................................................................................2-28

 Condensed Matter Physics.........................................................................................................................2-44

 Geology and Environmental Sciences....................................................................................................2-54

 Life Sciences.....................................................................................................................................................2-66

 Soft Condensed Matter and Biophysics.................................................................................................2-92

 

Year in Review

 Brookhaven Town Supervisor John Jay LaValle Visits BNL ................................................................3-3

 Brookhaven Lab Expects $30 Million to Support Life Sciences.......................................................3-3

 The DUV-FEL Workshop.................................................................................................................................3-4

 NSLS-II Workshop Lights Brookhaven National Laboratory .............................................................3-6

 Cullie Sparks: In-Memoriam .........................................................................................................................3-8

 New Technology Turns Dredged Material into Cement.....................................................................3-9

 NSLS Hosts More Than 100 Children on "Take Our Sons and Daughters to Work" Day .......3-10

 2004 RapiData Crystallography Course .................................................................................................3-11

 2004 NSLS Annual Users' Meeting Caps Off Another Successful Year........................................3-12

 Better Ways to See the Light: Advanced Detectors for Synchrotron Radiation Workshop .3-14

 Anatomy of a Virus Workshop ...................................................................................................................3-15

 Grazing Incidence Small X-ray Scattering Workshop........................................................................3-16

 Pharmaceutical Applications of Synchrotron Radiation Workshop.............................................3-18

 Advanced Optical Systems for High Power and Coherent Beamlines Workshop...................3-19

 Applications of Synchrotron-Based Methods to Hydrogen Storage Materials Workshop..3-21

 Nanoprobes for Nanosciences Workshop.............................................................................................3-22

 Crystallization: Focus on Membrane Proteins Workshop................................................................3-23

 UEC Community Service Award Presented to Sue Wirick ...............................................................3-24

 The PASS System Arrives.............................................................................................................................3-25

 NSLS EXAFS Data Collection and Analysis Short-Course "Graduates" 32 Students...............3-26
iii

 NSLS Visiting Scientist Mehmet Aslantas Wins Prestigious Lecturer Award.............................3-26

 Summer Sunday Visitors Battle the Weather for a Great Day at NSLS.........................................3-27

 Summer Student Research at the NSLS.................................................................................................3-28

 Parney Albright, DHS, Visits BNL...............................................................................................................3-29

 Awards and Good Times at the 2004 NSLS Barbeque ......................................................................3-30

 The Hill Comes to the Lab...........................................................................................................................3-31

 Remembering Dale Sayers.........................................................................................................................3-32

 The Gregori Aminoff Prize Goes to Prominent NSLS User David Mao........................................3-33

 Zhong Zhong Explains Diffraction Enhanced Imaging at the 399th Brookhaven Lecture...3-34

 NSLS Visitors and Tours in 2004 ................................................................................................................3-35

NSLS Organization

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

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

 

Facility Report 

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

 Operations and Engineering Division Report....................................................................................... 5-6

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

 User Administration Report ......................................................................................................................5-17

 Safety Report..................................................................................................................................................5-20

 Building Administration Report...............................................................................................................5-22

Facts and Figures

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

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

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

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

 2004 Ring Performance and Usage........................................................................................................6-13

Publications

 NSLS Users......................................................................................................................................................... 7-3

 NSLS Staff.........................................................................................................................................................7-24

Introduction
INTRODUCTION 1-3

Chairman’s Introduction

Steven Dierker

Chairman, National Synchrotron Light Source

The NSLS remains a viable and productive facility, as can be seen by the rich and diverse science produced in 

2004. In one of these exciting research projects published in Nature, researchers detected a rare “hole crystal” in a 

cuprate superconductor, which may provide insight into high-temperature superconductivity. In another Nature 

publication, the crystal structure of a segment of RNA was determined, opening a new window of knowledge into 

that crucial molecule. These are just a couple of the science highlights of 2004, and many others are displayed in 

the pages of this report. All told, more than 700 publications resulted from NSLS research this year, the facility 

hosted 2,299 users, and the number of experiments performed rose from 1,145 in 2003 to 1,374—clear indications that the NSLS continues to thrive.

As the NSLS accelerator complex enters its third decade of operations, it continues to perform very well. For 

2004, the overall reliability of the VUV-IR ring was excellent at 99 percent. The reliability of the x-ray ring was 

just shy of 92 percent, primarily due to the need to replace the injection septum vacuum chamber, which developed a leak during the middle of the year. The Operations Division did a tremendous job of installing our spare 

chamber in minimal time, despite the complexity of the job and the inaccessibility of its location in the ring, as 

well as keeping downtime to a minimum throughout the rest of the year.

In order to continue to meet the needs of users, several key 

beamline upgrades took place this year that will enrich our 

scientific programs, including upgrades to beamlines U12IR, 

X1A, X13A, and X21. We are very excited about two brand-new 

beamlines that were commissioned in 2004: X29 and X27A. X29 

is the new mini-gap undulator beamline designed for macromolecular crystallography, and it will meet the growing demand of 

NSLS users who perform research in that area. The establishment of an x-ray microprobe at beamline X27A, optimized for 

the environmental science community, is also very important, 

as it will help to satisfy the large over subscription rate for this 

technique at the NSLS. Two other important upgrades that were 

initiated this past year are the replacement of the X25 wiggler 

with an undulator and the construction of the X9 undulator 

beamline for small-angle scattering, with an emphasis on nanoscience research.

Another key activity that will benefit all users was the restoration 

of the x-ray ring lattice symmetry, which reduced the horizontal 

emittance and made the operational lattice more robust. Similarly, all users will benefit from the introduction of the PASS (Proposal Allocation Safety Scheduling) system this past year, which 

has greatly improved the process of proposal submission, review, 

allocation, and scheduling. This coming year we will work to add 

Rapid Access to the capabilities of PASS. Overall, the success of 
1-4 NSLS ACTIVITY REPORT 

these and the many other projects that space does not permit listing is a testament to the dedication, hard work, and 

skill of the NSLS staff.

Safety has always been an important issue at a large, complex scientific facility like the NSLS and in 2004 it received 

renewed attention. Safety is our highest priority and we spent a great deal of time reviewing and refining our safety 

practices and procedures. A new “Safety Highlights” web page was created for safety news, and a large number of safety 

meetings and discussions were held. These reviews and meetings generated many ideas on how the NSLS might improve its safety practices, and we are committed to putting these in place and improving our already very good safety 

program. We had no lost-time accidents in 2004, which is a notable accomplishment. Our goal is to be best in class 

and I’m confident that by working together we can achieve that status.

Several activities took place this past year to advance our proposal to replace the NSLS with a new National Synchrotron Light Source-II facility. These included a major workshop in support of the proposed facility in March, a mail 

review of our proposal outlining the scientific opportunities enabled by NSLS-II, and a technical review of the preconceptual design of the machine. The feedback from the reviews has been positive and indications are promising that 

NSLS-II will become a reality. The scientific opportunities enabled by NSLS-II are incredibly exciting and it is a critically needed addition to the nation’s scientific infrastructure. It will ensure that we remain world leaders in synchrotron 

science for decades to come.
INTRODUCTION 1-5

Notes from the UEC

Larry Shapiro

Columbia University

I’d like to take this opportunity to discuss the relatively difficult environment currently faced by the DOE synchrotron facilities, and our response to it. The problem has two primary origins. First is the budgetary environment, and second are rising concerns about safety that require attention from all of us. Both the UEC and the 

NSLS administration are taking concerted action on these issues, and I’d like to describe some of these efforts.

The short-term funding environment for science in the United States is highly tenuous. Even programs with such 

high public exposure as the Hubble space telescope are in danger of being cut, and we must be greatly concerned 

about the level of funding for the NSLS in the near future. It’s difficult to know what to expect, but a continuation of tight budgets seems likely. This difficulty is further compounded by the expectation of cost increases, 

including a potential hike in electric power rates, and new DOE rules on infrastructure expenditures that may 

divert some funding away from operations. It’s not yet clear where we’ll be next year, but odds are we won’t see 

much improvement in the near term.

The UEC has taken steps to help our political representatives understand the importance of the NSLS to the 

status of science in the Northeast, and NSLS-II to the continuation of great science here in the future. In anticipation of the budgetary process unfolding in Washington this month and next, I met with Long Island Congressman 

Tim Bishop to stress the importance of NSLS and ask for his active support. Congressman Bishop understands the 

importance of BNL to Long Island and New York, and understands that the NSLS is extremely important to the 

Lab. He will be a strong supporter in this year’s budgetary process, and hopefully in those to come. The UEC has 

also started to arrange a trip to Washington, scheduled for April, in order to meet with legislators and legislative 

staff. This trip, as is the custom, will be made jointly with user representatives from the other DOE synchrotron 

facilities, and will attempt to underscore the national importance of synchrotron research.

Safety issues continue to demand attention at the NSLS and other facilities. An accident at SPEAR3, which 

caused serious injury to an electrician in mid-October, resulted in an extended shutdown of that facility. In the 

wake of this accident, safety measures at the NSLS may sometimes seem draconian, but increased attention to 

maintaining safe operations is absolutely necessary. The UEC, NSLS 

administration, and the NSLS Scientific Advisory Committee are 

committed to both augmenting safety guidelines and insuring that 

they are implemented fairly. Despite the challenges we face now, I 

think the community is effectively dealing with these issues, and I 

hope you share my confidence that the NSLS will continue in its 

long history of great scientific achievement.
Science Highlights
SCIENCE HIGHLIGHTS 2-3

Science at the NSLS

Laura Mgrdichian

NSLS SCIENCE WRITER

As the Information and Outreach Office wraps up 2004 with this report, so have I recently completed my first full 

year at the NSLS. I am happy to write that it’s been a good year.

Being the NSLS science writer, as it turns out, is an education unto itself. Over the course of the year, we select 

about 50 scientific papers to appear on the NSLS homepage out of almost 700 hundred published by NSLS users in 

many journals. This means that, each month, I read numerous papers, spanning research in chemistry, soft and condensed matter physics, materials science, nanoscience, and the life sciences. As a result, I have learned about polymers, proteins, and minerals—to name just a few topics. I learn new things every week, in fact, and I feel fortunate 

to be immersed in such a diverse and rich scientific atmosphere.

However, choosing those 50 is one of the most difficult aspects of what I do, as each experiment at the NSLS helps 

to answer an interesting scientific question. How, for example, do certain catalysts affect the growth of carbon nanotubes? How does synchrotron light damage protein samples? What causes high-temperature superconductivity in 

certain materials?

Thus, while the pages beyond this introduction display only a small 

fraction of the science performed at the NSLS, they will show you 

how these and other fundamental questions are being answered. The 

“Science Highlights” are summaries of research papers and are written 

by users, for users; the “Feature Highlights,” aimed at non-scientists, 

are written by me.

I thank the scientists I’ve worked with this year for helping me to 

understand their work and bring it to others, and I look forward to 

the year ahead. 
2-4 NSLS Activity Report

Science Highlights

 Feature Highlights

 NSLS Users Determine the Structure of a Protein “Gateway” in Cells......................................................................................... 2-8

 Tackling Water Pollution by Tracking Phosphorus in Soils...........................................................................................................2-10

 Evidence of Ancient Water on an Asteroid.........................................................................................................................................2-12

 New Brookhaven Laser Facility Captures Molecules in Action....................................................................................................2-14

 Scientists Create and Manipulate Nanoscale “Water Wires”.........................................................................................................2-16

 Unlocking the Secrets of Titanium, a “Key” that Assists Hydrogen Storage............................................................................2-18

 NSLS Users Help Decode RNA.................................................................................................................................................................2-19

 New Physics Law Unifies Several Superconducting Compounds..............................................................................................2-20

 First Glimpse of DNA Binding to Viral Enzyme..................................................................................................................................2-22

 Under Pressure, Zirconium is a “Glass” Act..........................................................................................................................................2-24

 Research on “Holes” May Unearth Causes of Superconductivity................................................................................................2-26

 A Brain Cell Gateway...................................................................................................................................................................................2-27

Chemical Sciences

 The Structure and Unusual Hydration/Dehydration Behavior 

 of the New Aluminophosphate SSZ-51 .............................................................................................................2-28

 A. Burton, R. Morris, L.M. Bull, and S.I. Zones

 Effects of Shear Flow on Interfacial Ordering in Liquids: X-ray Studies....................................................................2-30

C. Yu, G. Evmenenko, J. Kmetko, and P. Dutta

 Chemistry of SO2 on Ce1-xZrxO2 Nanoparticles and Ce1-xZrxO2(111) Surfaces.........................................................2-32

J.A. Rodriguez, X. Wang, G. Liu, J. Hanson, J. Hrbek, C.H.F. Peden, A. Iglesias-Juez, and M. Fernández-García

 Peering Into the Self-Assembly of Surfactant Templated Thin-Film Silica Mesophases..................................2-34

D.A. Doshi, A. Gibaud, V. Goletto, M. Lu, H. Gerung, B. Ocko, S.M. Han, and C.J. Brinker

 Structures and Properties of Supramolecular Assembled 

 Fullerenol/Poly(dimethylsiloxane) Nanocomposites...................................................................................2-36

 S. Zhou, J. Ouyang, and S.H. Goh

 Vapor Phase Self-Assembly of Electrooptic Thin Films Via Triple Hydrogen Bonds...........................................2-38

P. Zhu, H. Kang, A. Facchetti, G. Evmenenko, P. Dutta, and T.J. Marks

 Growth of Controlled Diameter Single-Walled Carbon Nanotubes............................................................................2-40

D. Ciuparu, Y. Chen, S. Lim, G.L. Haller, and L. Pfefferle

 Structural Characterization of Self-Assembled Monolayer Films of (α–Quarterthiophene) 

 Phosphonate Bonded to the Silicon Native Oxide Surface........................................................................2-42

 E.L. Hanson, J. Schwartz, B. Nickel, N. Koch, and M.F. Danisman
Science Highlights 2-5

 Condensed Matter Physics

 XAS Study of Au Supported on TiO2: Influence of Oxidation State and 

 Particle Size on the Catalytic Activity .................................................................................................................2-44

 V. Schwartz, D.R. Mullins, W. Yan, B. Chen, S. Dai, and S.H. Overbury

 High Anisotropy CoPtCrB Magnetic Recording Media.......................................................................................................2-46

 M.F. Toney, E.E. Marinero, M.F. Doerner, and P.M. Rice 

 Orbital and Spin Correlations in a Manganite Probed With Soft X-ray Resonant Diffraction.......................2-48

K.J. Thomas, J.P. Hill, S. Grenier, Y.-J. Kim, P. Abbamonte, L. Venema, A. Rusydi, Y. Tomioka, Y. Tokura, 

D.F. McMorrow, G. Sawatzky, and M. van Veenendaal

 Melting Point Enhancement of a Self-Assembled Monolayer Induced by a 

 Van-Der-Waals-Bound Capping Layer................................................................................................................2-50

 F. Schreiber, M.C. Gerstenberg, H. Dosch, and G. Scoles

 Measurement of Ti, Ta and Sc Off-Center Displacements in Relaxor Ferroelectric PST-PT...........................................2-52

A.I. Frenkel, D.M. Pease, J. Giniewicz, E.A. Stern, D.L. Brewe, M. Daniel, and J.Budnick

 Geological and Environmental Sciences

 Time-Resolved Diffraction Studies of Ion Exchange: K+ and Na+ Exchange into Synthetic 

Aluminogermanate Molecular Sieve with the Gismondine Topology................................................................2-54

A.J. Celestian, J.B. Parise, C. Goodell, A. Tripathi, and J. Hanson

 Localization and Speciation of Chromium in Subterranean Clover Using XRF, XANES, and EPR Spectroscopy ......2-56

 J.A. Howe, R.H. Loeppert, V.J. DeRose, D.B. Hunter, and P.M. Bertsch

 Quantifying Hazardous Species in Particulate Matter Derived from Fossil-Fuel Combustion.........................................2-58

F.E Huggins, G.P. Huffman, W.P. Linak, and C.A. Miller

 Arsenic Speciation and Reactivity in Poultry Litter .................................................................................................................................. 2-60

Y. Arai, A. Lanzirotti, S. Sutton, J.A. Davis, and D.L. Sparks

 Natural Occurrence and Synthesis of Two New Post-Spinel Polymorphs of Chromite.................................................2-62

 M. Chen, J. Shu, H-k. Mao, X. Xie, and R.J. Hemley

 The Origin of Organic Matter in the Solar System: Evidence from the Interplanetary Dust Particles...........................2-64

 G.J. Flynn, L.P. Keller, M. Feser, S. Wirick, and C. Jacobsen

 Life Sciences

 X-ray Structure Analysis of a Designed Oligomeric Miniprotein Reveals a Discrete 

Quaternary Architecture ...................................................................................................................................................................... 2-66

M.H. Ali, E. Peisach, K.N. Allen, and B. Imperiali

 Structure of the ClpB Molecular Chaperone............................................................................................................................................... 2-68

S. Lee, M.E. Sowa, and T.F. Tsai
2-6 NSLS Activity Report

 Crystal Structure of Human α-Tocopherol Transfer Protein Bound to its Ligand: Implications for 

 Ataxia with Vitamin E Deficiency ............................................................................................................................... 2-70

 K.C. Min, R.A. Kovall, and W.A. Hendrickson

 The Mutant Proteins of a Neurodegenerative Disorder..................................................................................................................2-72

J. Stine Elam, A.B. Taylor, R. Strange, S. Antonyuk, P.A. Doucette, J.A. Rodriguez, S.S. Hasnain, 

L.J. Hayward, J. Selverstone Valentine, T.O. Yeates, and P.J. Hart

 The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme........................... 2-74

F. Berkovitch, Y. Nicolet, J.T. Wan, J.T. Jarrett, and C.L. Drennan

 Structure of a Specific Alcohol-Binding Site Defined by the Odorant Binding Protein LUSH 

 from Drosophila Melanogaster..................................................................................................................................................2-76

 S.W. Kruse, R. Zhao, D.P. Smith, and D.N.M. Jones

 Crystal Structure of LeuA from Mycobacterium Tuberculosis, a Key Enzyme in Leucine Biosynthesis ..................... 2-78

 N. Koon, C.J. Squire, and E.N. Baker

 Structural Basis of the α1−β Subunit Interaction of Voltage-Gated Ca2+ Channels..............................................................2-80

Y.-h. Chen, M.-h. Li, Y. Zhang, L.-l. He, Y. Yamada, A. Fitzmaurice, Y. Shen, H. Zhang, L. Tong, and J. Yang

 Structure of Mammalian Protein Geranylgeranyltransferase Type-I..........................................................................................2-82

T.S. Reid, J.S. Taylor, K.L. Terry, and L.S. Beese

 Structural Effects of Radiation Damage and its Potential for Phasing............................................................................. 2-84

 S. Banumathi, P.H. Zwart, M. Dauter, and Z. Dauter

 Amphiphilic 4-Helix Bundles Designed for BioMolecular Materials Applications................................................................2-86

 S. Ye, J.W. Strzalka, S. Zheng, T. Xu, J.K. Blasie, B.M. Discher, D. Noy, and P.L. Dutton

 The Crystal Structure of Activated Protein C-Inactivated Bovine Factor Va: Implications 

for Cofactor Function ............................................................................................................................................................................ 2-88

T.E. Adams, M.F. Hockin, K.G. Mann, and S.J. Everse

 An Asymmetric Complex of Restriction Endonuclease MspI on its Palindromic DNA Recognition Site ......................2-90

Q.S. Xu, R.B. Kucera, R.J. Roberts, and H.-C. Guo

 Soft Condensed Matter and Biophysics

 Orientation and Crystallization of Natural Rubber Network as Revealed by WAXD Using 

 Synchrotron Radiation..........................................................................................................................................................................2-92

 M. Tosaka, S. Murakami, S. Poompradub, S. Kohjiya, Y. Ikeda, S. Toki, I. Sics, and B.S. Hsiao

 Tuning Substrate Surface Energies for Blends of Polystyrene and Poly (Methyl Methacrylate) .....................................2-94

 D.A. Winesett, S. Story, J. Luning, and H. Ade

 Block Copolymer Domain Reorientation in an Electric Field: An In-Situ Small-Angle X-ray Scattering Study ..........2-96

T. Xu, J. DeRouchey, T. Thurn-Albrecht, T.P. Russell, and R. Kolb
Science Highlights 2-7

 Time-Resolved Small-Angle X-ray Scattering Study of the Kinetics of Disorder-Order Transition in a 

Triblock Copolymer in a Selective Solvent for the Middle Block..................................................................................2-98

H. Nie, R. Bansil, K. Ludwig, M. Steinhart, C. Konak, and J. Bang

 Low-Density Polymer Thin Film Formation in Supercritical Carbon Dioxide.......................................................................2-100

T. Koga,Y.-S. Seo, J.L. Jerome,S. Ge, M.H. Rafailovich, J.C. Sokolov, B. Chu, O.H. Seeck, M. Tolan, and R. Kolb

 Shear-Induced Crystallization Precursor Studies in Model Polyethylene Blends by In-Situ

Rheo-SAXS and Rheo-WAXD ................................................................................................................................................2-102

L. Yang, R.H. Somani, I. Sics, B.S. Hsiao, R. Kolb, H. Fruitwala, andC. Ong

 Influence of Crystallization Conditions on the Microstructure and Electromechanical Properties of 

Poly(Vinylidene Fluoride-Trifluoroethylene-Chlorofluoroethylene) Terpolymers........................ 2-104

R.J. Klein, J. Runt, and Q.M. Zhang
2-8 NSLS ACTIVITY REPORT 

NSLS Users Determine the Structure of a Protein “Gateway” in Cells

Scientists working at the Brookhaven National Laboratory have determined the structure of a tiny “gateway” protein 

on the surface of cells that allows other proteins to exit the cell. This structure, determined at the National Synchrotron Light Source (NSLS), is a significant scientific achievement that may provide insight into the complex mechanisms of several essential cellular functions. The structure is described in the January 1, 2004 issue of Nature.

These pore-like gateways are situated within the cell’s protective, greasy outer “skin,” called 

the membrane. The membrane contains thousands of pores, known as channels, which allow only certain substances, such as nutrients and energy sources, to enter and exit the cell. 

There are many types of channels, and each type is constructed to permit the passage of 

specific molecules.

The channel studied in this research is a protein-conducting channel. It permits “secretory 

proteins” to leave the cell by passing straight through the membrane and allows “membrane 

proteins” to integrate into the membrane so that parts of the protein appear on the outer 

side of the membrane. This passage system, called protein translocation, allows the proteins 

to perform many of an organism’s essential functions: For example, secretory proteins, such 

as digestive enzymes and antibodies, leave the cell to help digest food and fight off disease, 

respectively, while membrane proteins are needed at the cell surface to fire off nerve signals 

or trigger the immune system.

Understanding precisely how the proteins traverse the channel – a question many scientists would like to answer – first 

requires determining the channel’s intricate molecular structure. This task was successfully completed at the NSLS by a 

collaboration of scientists from Harvard Medical School, the Max Planck Institute of Biophysics in Frankfurt, Germany, and the University of Luebeck in Luebeck, Germany.

“The structure tells us much more than we ever hoped to be able to get out of it,” said Tom Rapoport, a cell biologist 

at Harvard and the team’s lead scientist. “We can now propose mechanisms for how the channel is opened, how other 

molecules are prevented from crossing the membrane, and other processes. The structure initiates a new era of more 

directed research into the mechanism of protein translocation.”

At the NSLS, Rapoport and his colleagues slowly imaged and pieced together the components of the channel’s overall 

structure. The final product is a huge step in the field of cell biology: a channel imaged to a degree of detail that had 

previously only been achieved for channels that transport much smaller molecules, such as water and ions.

The channel is shaped like an hourglass, but behaves quite differently, thanks to certain features. For example, the bottom region of the channel is separated from the top region by a molecular “plug” that swings open to allow the passage 

of outbound proteins and forms a barrier between the inside of the cell and the external aqueous environment. At the 

narrow “neck” connecting the top and bottom parts of the hourglass, the channel is lined by a gasket-like “pore ring” that forms 

a seal around exiting proteins. This keeps smaller molecules from 

sneaking in or out of the cell.

The channel also consists of a component that acts somewhat like 

two molecular “hands” clasped around a cup. By tightening or 

releasing their grip, the hands narrow or widen the pore, allowing 

it to admit a wide variety of proteins and shut away unwanted molecules. The hands can also unclasp at the point where their “fingertips” meet. This release mechanism permits proteins to slip sideways out of the channel and become integrated into the membrane. 

Assembling this biological puzzle was a great challenge for the 

researchers. “This is the culmination of 25 years of work on the 

mechanism of protein translocation, and so it’s rewarding to finally From left, William Clemons, Jr., Tom Rapoport, and Bert van 

den Berg
FEATURE HIGHLIGHTS 2-9

see its three-dimensional structure,” Rapoport said. “This is a dream for me.”

The first step in that long process, selecting the organism that would produce the best sample to study, was a 

major hurdle. “We had to go through 10 different bacterial species,” said Rapoport. “Finally, we found that a 

complex derived from an archaebacterium, a primitive organism, was the most stable. Altogether, it took us about 

five years.”

The researchers trapped the protein channel in a crystal form, a process 

that is like taking a three-dimensional “snapshot.” Then, working at NSLS 

beamline X25 and Argonne National Laboratory, they studied the crystals 

using a technique known as x-ray crystallography: They placed the crystals 

in the path of an x-ray beam and recorded the pattern the rays created as 

they scattered and bounced off its molecules. Then, they used a computer to 

analyze the pattern and determine the structure of the protein in the crystal.

“The next big goal is to crystallize the channel in action,” Rapoport concluded.

The other members of the research collaboration are Bert van den Berg, 

William Clemons, Jr., Yorgo Modis, and Stephen Harrison, all from 

Harvard Medical School; Ian Collinson, from the Max Planck Institute of 

Biophysics; and Enno Hartmann, from the University of Luebeck.

Laura Mgrdichian

A top view of the protein-conducting channel, 

looking down into it. The channel's "plug" is 

shown in green.
2-10 NSLS ACTIVITY REPORT 

Tackling Water Pollution by Tracking Phosphorus in Soils

At the National Synchrotron Light Source (NSLS), scientists have determined how the element phosphorous, a plant 

fertilizer and surface water contaminant, adheres to two common soil minerals. This study will help to determine 

how phosphorus migrates from soils to water bodies and which types of soil are better at holding phosphorus – findings that may help to define future soil management policies and decrease the environmental impacts of phosphorous 

contamination.

The results appeared as the cover article in the March-April 2004 issue of the Soil Science Society of America Journal.

“Studying how soils hold phosphorus is necessary because soils are critical for food production and for removing environmental contaminants from water that flows into streams, 

rivers, lakes, and estuaries,” explained Dean Hesterberg, a soil chemist from North Carolina 

State University who led the study. “However, soils are made up of very complex mixtures 

of minerals, and it is difficult to determine exactly how plant nutrients and contaminants 

bind in the soil.”

“Therefore, preventing water pollution by managing soil phosphorous levels is often based 

on indirect approaches that measure how easily a portion of phosphorus can be pulled out 

of the soil, rather than on an understanding of how the phosphorus is chemically bound in 

the soil. Knowing the latter helps in more accurately predicting how environmental changes 

affect phosphorus release.”

Phosphorus is commonly added to soils as fertilizers for agricultural crop production. “Phosphorus becomes an environmental concern when it is applied to soils in excessive amounts, as sometimes occurs when waste materials, such 

as animal waste, are used to fertilize crop soils,” Hesterberg said. If the amount of phosphorus added to soils exceeds 

the plants’ needs and the soil’s holding capacity, he explained, then excess phosphorus migrates to rivers and lakes via 

runoff waters, and abnormally stimulates the growth of aquatic plants. The boom in plant growth depletes the waters’ 

oxygen content, endangering fish and other aquatic plants, and deteriorating water quality. 

“This work was important because it showed that we can use x-rays to obtain more exact information on how phosphorus binds to different minerals that occur together, and to better understand how each mineral contributes to holding phosphorus in soils,” he said. “This is necessary for developing better ways to manage many different soils so that 

phosphorus movement to waterways is minimized, and we can better evaluate how much phosphorus can be added to 

soils without causing environmental problems.”

Phosphorus occurs at different concentrations in different types of soil, but soils rich in iron (iron oxide) and aluminum (aluminum oxide) minerals can hold more phosphorous. In this research, two such minerals, iron oxide-based 

ferrihydrite and aluminum oxide-based boehmite, were 

investigated to determine how phosphorus (in the form of 

phosphate, a phosphorus compound) is adhered, or “adsorbed,” onto them, and to understand how phosphorus is 

distributed between both types of minerals in soils.

Working at NSLS beamline X19A, the scientists tracked 

how much phosphate was held by each mineral. They 

determined how phosphate adsorbed onto ferrihydrite and 

boehmite by shining x-rays at soil samples containing just 

ferrihydrite, just boehmite, and mixtures of both. By looking at the unique patterns created as the x-rays emerged 

from each sample, the scientists were able to determine how 

much phosphate had adsorbed onto each mineral in the 

mixture based on data for the individual minerals.

The results show that, at low phosphate concentrations, Clockwise (From left, top): Nidhi Khare, Dean Hesterberg, Shan-Li Wang, 

and Suzanne Beauchemin 
FEATURE HIGHLIGHTS 2-11

ferrihydrite holds phosphate more strongly than boehmite. The researchers 

also found that at intermediate concentrations, each of these minerals adsorbs 

phosphate about equally well. This information will help determine how 

phosphate dissolves and migrates within different soils, which may contribute 

to the development of soil management policies aimed at minimizing the effect of phosphorus on the environment.

The other researchers who participated in this study are Dr. Nidhi Khare, a 

former Ph.D. student in Hesterberg’s lab and the lead author, now a postdoctoral researcher at the University of Wyoming; Dr. Suzanne Beauchemin, 

from Natural Resources Canada; and Dr. Shan-Li Wang, now an Assistant 

Professor at National Chung Hsing University in Taichung, Taiwan.

This research was funded by the U.S. Department of Agriculture’s National 

Research Initiative (Soils and Soil Biology Program) and the North Carolina 

Agricultural Research Service.

Laura Mgrdichian Transmission electron microscope image 

(50,000X magnification) of a mixture of ironand aluminum-oxide minerals: hexagonal 

gibbsite [α-Al(OH)3

] platelets and aggregated, 

lathe-shaped goethite (α-FeOOH) particles. 

Iron and Al-oxides are considered the most 

important minerals for retaining phosphate 

in soils, but their relative importance as they 

coexist in soils is unclear.
2-12 NSLS ACTIVITY REPORT 

Evidence of Ancient Water on an Asteroid

May help lead to new information on the formation of Earth

Working in part at the National Synchrotron Light Source (NSLS), scientists have discovered evidence of ancient 

water on a large asteroid previously thought to lack water. The findings indicate that water was most likely deposited 

onto the asteroid, suggesting it came from an outside source, such as a collision with an icy comet. The discovery may 

give scientists new insight into the rules governing the mobility and availability of water in the solar system at the time 

Earth was formed.

The results appear in the March 15, 2004 issue of Earth and Planetary Science Letters.

The scientists learned about the asteroid, named 4 Vesta, which orbits the Sun in our solar system, by studying a 

meteorite that is believed to have once been part of it, due to the two bodies’ very similar chemical compositions. The 

meteorite, called Serra de Magé, fell to Earth in 1923. When analyzing Serra de Magé, the researchers discovered a 

sign that water had once been present: threads, or “veinlets,” of quartz, a mineral that is often deposited onto rocks by 

liquid water solutions. The appearance and condition of the veinlets suggested that water existed on the meteorite long 

ago, and could only have been deposited before Serra de Magé broke away from 4 Vesta.

Allan Treiman, a geologist from the Lunar and Planetary Institute and the study’s lead scientist, explained, “The veinlets are quite old – 4.5 billion years – so they formed when the solar system was quite young. Because Vesta is now so 

dry, our best guess is that the veinlets’ water came from an outside source, such as comets or water-rich meteorites that 

hit Vesta.”

According to Treiman, this hypothesis has some important potential implications. “Scientists have theorized water 

delivery by comets for the early solar system, especially for how the Earth got enough water to make our oceans. 

However, gathering evidence for or against this theory has been difficult, because few Earth rocks (or Moon rocks) are 

old enough. But this ancient meteorite from Vesta appears to show that it received water somehow, which suggests that 

water could have been delivered to Earth in a similar way.”

To analyze Serra de Magé, the researchers bombarded it with x-rays at NSLS beamline X26A. In this method, called 

x-ray micro-diffraction, the x-rays entered the sample, scattered off its molecules, and emerged from the sample in a 

distinct pattern. A camera created an image of the diffracted x-rays, and, from this, the scientists were able to determine what materials make up the sample based on known diffraction patterns of many different substances. This is 

how they identified the quartz veinlets.

4 Vesta is the third-largest asteroid in the Main Asteroid Belt – the ring of cosmic debris that orbits the Sun outside 

Mars’ orbit and inside Jupiter’s. The asteroid is 320 miles in diameter, or about as wide as the state of Iowa, and is 

roughly spherical in shape. Its chemical composition is unique: Unlike other large asteroids, Vesta appears to have once 

contained a hot molten center, as Earth does. This finding contradicts conventional ideas that asteroids are cold, rocky remnants of the early days of planet 

formation. Studying Vesta may help scientists learn how Earth formed, as the 

asteroid has other characteristics similar to terrestrial planets, such as evidence of 

ancient lava eruptions. Its surface is pocked with impact craters – which is most 

likely how Serra de Magé was knocked loose.

In the future, Treiman and his colleagues plan to study other meteorites from 4 

Vesta and look for similar quartz veinlets. They will also study them for more definitive signs of water on the asteroid, such as actual water – very small droplets 

trapped in the quartz – or water-bearing minerals. Another approach is to look 

for excess hydrogen in Serra de Magé as compared to meteorites without quartz 

veinlets, which would indicate that water, a hydrogen-oxygen compound, may 

have been present. This could be done using the infrared rays produced at the 

NSLS vacuum ultra-violet (VUV) ring.

Allan Treiman The collaboration that performed this research also includes Antonio Lanzirotti, 
FEATURE HIGHLIGHTS 2-13

of the University of Chicago’s Consortium for Advanced 

Radiation Sources at Brookhaven National Laboratory and 

Dimitrios Xirouchakis, of the National Aeronautic and Space 

Administration’s (NASA) Johnson Space Center.

The work is funded by NASA, the Lunar and Planetary Institute, and the U.S. Department of Energy’s (DOE) Geosciences 

Research program within the Office of Basic Energy Sciences 

in DOE's Office of Science.

Laura Mgrdichian

The largest quartz veinlet in the meteorite (V), surrounded by 

the minerals pyroxene (Px) and plagioclase (Pl).
2-14 NSLS ACTIVITY REPORT 

New Brookhaven Laser Facility Captures Molecules in Action 

Scientists at Brookhaven National Laboratory have released results from the first experiment at Brookhaven’s Deep 

Ultraviolet Free Electron Laser (DUV-FEL), a facility that produces powerful ultraviolet laser light for research applications. The researchers investigated how gas molecules break apart when they are highly energized by the laser light 

– research that may offer insight into many fundamental chemical and physical processes that are based on moleculelight interactions, such as photosynthesis, radiation damage, and ozone formation. 

“This experiment has helped us to understand the specifics of what happens when we excite molecules with energetic 

ultraviolet light,” said Brookhaven chemist Arthur Suits, the experiment’s lead scientist. The results are described in the 

February 27, 2004 issue of Physical Review Letters. 

“We also learn, more generally, how electrons rearrange in molecules in response to the light, the nature of chemical 

bonds, and the dynamics of bond-breaking processes,” he said. 

The gas used in this experiment is called methyl fluoride. Each molecule can be thought of as the sum of two parts: a 

negatively charged fluorine atom, or fluorine ion, and a positively charged methyl ion containing three hydrogen atoms bonded to one carbon atom. When Suits and his group aimed the ultraviolet beam from the DUV-FEL at a beam 

of methyl fluoride gas, the gas molecules each absorbed a single energetic photon, or tiny “packet,” of light, which 

caused them to separate, or dissociate, into their positive and negative fragments, called ion pairs. 

This dissociation is a special case, Suits explained. When a molecule absorbs a great deal of energy, normally it will spit 

out an electron and become a positive ion. But sometimes, molecules can temporarily exist in “superexcited” states, 

absorbing enough energy to ionize, but without doing so. Instead, they can dissociate into fragments. By studying the 

parts, scientists can gain information about the whole molecule and the details of the bond-breaking process. 

In this experiment, Suits and his collaborators used a technique called “ion pair imaging” to learn about methyl 

fluoride’s reaction to the light. After breaking the molecules into ion pairs, they tracked the motion of the fluorine ions 

by causing them to strike a screen that records each ion’s impact location. The resulting pattern gives the scientists information about the speed and trajectory of the fluorine ions. By working backward, they can learn about the properties of the entire methyl fluoride molecule and its interaction with the light. 

“Methyl fluoride was a good test case to use in the first FEL experiment, 

but we hope to study other dissociation processes,” said Suits. “We have 

yet to take full advantage of the DUV-FEL’s many unique features and 

capabilities, which will help us learn more about how electrons move in 

molecules as chemical bonds are changed and broken.”

Understanding the DUV-FEL 

The DUV-FEL is located at the National Synchrotron Light Source 

(NSLS), which produces light by accelerating electrons in a circular 

path at very high speeds, but it does not work the same way. Instead, the 

electrons are first accelerated in a straight line down a linear accelerator 

(linac). They then pass through a “wiggler,” a device that uses a series of 

permanent magnets to force them to “wiggle” in a wavy path. This wiggling motion causes the electrons to emit light. 

At this point, the electrons need a little help in order to produce light 

with the qualities DUV-FEL scientists need to perform their experiments 

– a steady wavelength and frequency, and very short pulses. Thus, as they 

traverse the wiggler, the electrons are simultaneously coupled with light 

from a “seed laser.” The seed laser light gives the electrons a boost by regulating their motion so that they emit more concentrated, laser-like light. 

Wen Li (left) and Arthur Suits Next, the electrons enter a “bunch compressor” device, where they are 
FEATURE HIGHLIGHTS 2-15

grouped into tiny clusters. Finally, the electrons are sent into 

a second, longer wiggler, where 

they emit light pulses that can be 

used for experiments.”

“The DUV-FEL is a very 

intense source of high-energy 

light pulses,” Suits said. “But 

the FEL light has other unique 

properties. It is very coherent, or 

steady, and each pulse lasts less than one trillionth of a second. These short, intense 'flashes' allow us to make very 

rapid ‘snapshots’ of brief molecular processes, such as chemical reactions, using the light. These are the kinds of 

experiments we hope to perform in the future.” 

The research was funded by the Office of Basic Energy Sciences in the Department of Energy’s Office of Science, 

the National Science Foundation, and the Robert A. Welch Foundation.

Laura Mgrdichian

Images of fluorine ions from the ion pair dissociation of methyl fluoride. The images show the changing 

anisotropy of the ions with increasing excitation energy (eV = electron volts).
2-16 NSLS ACTIVITY REPORT 

Scientists Create and Manipulate Nanoscale “Water Wires”

Scientists working at the National Synchrotron Light Source (NSLS) have caused tiny strands of water, each less than 

one nanometer (a billionth of a meter) in width, to form inside a common mineral. These nanoscale “water wires” 

give the scientists a new opportunity to study the properties of very small quantities of water, such as that found inside 

cells, which behave differently than water at the macro-scale.

The results are published in the March 17, 2004 issue of Nano Letters. 

Brookhaven physicist Tom Vogt led the research, performed with collaborators Yongjai Lee of Brookhaven Lab; Joe Hriljac of the University 

of Birmingham, United Kingdom; and C. Dave Martin and John B. 

Parise, both of Stony Brook University.

“Water in cells is distinct from bulk water as we know it,” explained 

Vogt. “For instance, it can take the form of long chains of single water 

molecules, which we call ‘water wires’ or ‘water polymers.’ But scientists 

know very little about water in this form.” 

They do know, however, that water wires are responsible for proton 

transport across cell membranes, which is one step in the fundamental 

process by which most organisms produce energy. Scientists understand 

how proton conduction occurs in bulk water, but not yet in water at the 

nanoscale. Studying water wires may shed light on the mechanism.

“In order to understand the biological role of water wires, we must relate their structure to the properties they display, 

such as their stability and how they transport protons,” Vogt said. “Confining very small amounts of water inside minerals and glasses is a good way to model and thus learn about water polymers.”

Lee and Martin placed a sample of the mineral natrolite (Figure 1) inside a diamond anvil cell, a device that applies 

very high pressure to a sample using the polished faces of two diamonds. In this case, the pressure was applied after the 

researchers first surrounded the natrolite sample with a water/alcohol solution. As the high pressure altered the natrolite structure, it also forced water molecules into its empty spaces – a process called pressure-induced hydration. Like 

tennis balls inserted into a canister, the water molecules nestled one-by-one within the structural framework, forming 

water wires.

As pressure was continually applied, it nudged the oxygen atoms in adjacent water molecules closer together than 

oxygen atoms in bulk water. This suggests that the wires may be good proton 

conductors, since protons travel in water by “hopping” from one molecule to 

the next, choosing the path of least water-to-water distance.

Next, Vogt and his group heated the sample to 200 degrees Celsius (Figure 2). 

Under pressure and heat, the natrolite structure expanded non-uniformly, i.e. 

more in one direction than the other. As a result, some water molecules moved 

closer together while others moved farther apart. This shifted the direction of 

the shortest water-to-water distance, creating a new preferred hopping route 

for protons. Because the direction of proton hopping is what defines the water 

wires, this shift also changed the wires’ orientation.

Understanding proton transport at the nanoscale in water wires could be useful in the development of applications such as hydrogen fuel cell technology, 

which also involves proton transport. It may also help scientists better understand biological processes that depend on proton transport, such the production of adenosine triphosphate, the compound that provides the energy for 

many cellular functions.

The scientists followed the natrolite’s structural changes at NSLS beamline 

Tom Vogt

Figure 1. The orientation of the waterwires 

(water molecules are shown as red balls) as they 

exist within the natrolite structure at room 

temperature. The yellow balls represent sodium 

ions.
FEATURE HIGHLIGHTS 2-17

X7A. They focused a beam of x-rays at the sample as they increased the 

diamond anvil cell pressure. The x-rays entered the sample, bounced off 

its atoms, and emerged in a distinct pattern, creating a “signature” of the 

sample. By analyzing its changing signature, the scientists tracked the 

sample’s changing structure.

This research was funded by a grant from Brookhaven’s Laboratory Directed Research and Development (LDRD) program.

Laura Mgrdichian

Figure 2. The waterwires within the natrolite 

structure, heated to 200 degrees Celsius. Upon 

heating, the wires change direction.
2-18 NSLS ACTIVITY REPORT 

Unlocking the Secrets of Titanium, a “Key” that Assists Hydrogen Storage 

New research may lead to better catalysts for hydrogen fuel cells 

Scientists at Brookhaven National Laboratory and the New Jersey Institute of Technology have taken steps toward 

understanding how a titanium compound reacts with a hydrogen-storage material to catalyze the release and re-absorption of hydrogen. Their results, appearing in the July 19, 2004, issue of Applied Physics Letters, may help scientists 

learn how similar catalysts work, improve their performance, and possibly develop more efficient storage materials for 

hydrogen fuel cells. 

In the late 1990s, scientists discovered that adding, or “doping,” a small amount 

of titanium to sodium aluminum hydride, a hydrogen storage compound (also 

known as sodium alanate), allows it to reversibly release and re-absorb hydrogen. In a sense, the titanium acts like a molecular “key” that facilitates hydrogen 

absorption and allows the reaction to proceed more rapidly. Until now, however, 

the nature of that reaction was not well understood. 

“We found that the titanium resides on the surface of sodium alanate as a titanium aluminum compound called titanium aluminide, rather than entering the 

bulk material and replacing other atoms or occupying empty spots within the 

lattice,” said the study’s lead author, Brookhaven physicist Jason Graetz. 

Graetz and his collaborators first prepared two titanium-doped samples by mixing titanium chloride and sodium alanate using a planetary mill, a device that 

grinds substances together using marble-sized metal spheres. They then prepared two samples from each doped sample 

(for a total of six): a dehydrided sample (containing no absorbed hydrogen) and a hydrided sample. By working with 

both types, the researchers were able to study the titanium’s properties before and after hydrogen absorption. This gave 

them one more way to determine the titanium’s role in the reaction. 

The group probed the samples with high-energy x-rays at the National Synchrotron Light Source (NSLS) beamline 

X19A. Because every substance absorbs x-rays differently, having a unique “signature,” the researchers were able to 

compare the six sample signatures to those of different titanium compounds and pure titanium. From this, they determined that the titanium chloride reacted with sodium alanate to form titanium aluminide. 

“Our finding is the first step toward an even more interesting discovery: determining exactly how titanium aluminide 

helps the hydride release and re-absorb hydrogen,” Graetz said. “Understanding that mechanism may help us identify 

better catalysts for the sodium alanate system and help us find dopants for new compounds that are currently impractical energy-storage materials, due to the high temperatures and pressures required to release and re-absorb hydrogen.” 

Sodium alanate is one of several metal-based hydrogen storage materials, called metal hydrides, being investigated for 

use in hydrogen fuel cells. A fuel cell works like a battery: Hydrogen atoms enter the negative terminal and split into 

their constituent particles, protons and electrons. The protons pass through the cell to the positive terminal, while the 

electrons leave the cell as a stream of electric current. The electrons then re-enter 

the cell at the positive terminal and reunite with the protons and oxygen to form 

water molecules. 

The known hydrides are impractical for fuel cells because they are quite heavy 

and have relatively low storage capacities (less than five percent hydrogen by 

weight). However, they have more potential than compressed hydrogen gas or 

liquid hydrogen, which pose explosion and freezing risks. These forms of hydrogen must be stored in tanks under very high pressure or at temperatures cold 

enough to liquefy the oxygen in air. 

This research was funded by a Brookhaven Laboratory Directed Research and 

Development grant and the National Science Foundation. 

Laura Mgrdichian

Jason Graetz

Scanning electron microscope image of Tidoped sodium aluminum hydride.

5 μm
FEATURE HIGHLIGHTS 2-19

NSLS Users Help Decode RNA

Working at the National Synchrotron Light Source (NSLS), scientists from Yale University have determined the 

crystal structure of a section of ribonucleic acid (RNA), the molecule in cells that uses the information contained 

in deoxyribonucleic acid (DNA) to synthesize proteins. The work, described in the July 1, 2004 issue of Nature, 

illuminates a piece of RNA never seen before, and may lead to many discoveries, ranging from new information 

on how proteins behave to new ways to prevent or treat genetic disorders.

“The structure contains a number of features that have not been seen before in any 

structurally-determined macromolecule,” said Scott Strobel, the lead author of the 

paper. “This is very exciting, since there is substantially less known about RNA than 

protein.”

The structure contains an RNA segment called an “intron” flanked by two additional 

segments called “exons.” Exons are the information-carrying pieces of RNA, while 

introns do not carry information. The process of putting exons together and removing introns is called RNA splicing, and it is a process performed on almost all RNA 

molecules before they are used by cells.

Until now, however, knowledge of how splicing occurs, and what the splicing site 

looks like, was limited. Usually, RNA splicing is performed by a large RNA-protein 

complex called the spliceosome, but, in some RNA molecules, the introns can selfsplice by removing themselves without the help of proteins. Strobel and his group 

crystallized an RNA molecule of this type to learn more about the splicing process. 

“We determined the crystal structure of one of these self-splicing introns that includes both of the exons that are 

about to be joined, or ligated, together,” Strobel said. “This configuration displays a splicing intermediate step, 

where one of the exons has been severed from the intron and is about to be ligated to the second exon, which 

results in the release of the intron.”

Self-splicing, essentially a chemical reaction in which the intron is the catalyst, is the same reaction as that catalyzed by the spliceosome. Although self-splicing involves a much simpler mechanism than that carried out by 

the spliceosome, this self-splicing “snapshot” is useful because it is likely to reveal how the spliceosome removes 

introns during exon ligation. This, in turn, may have implications for human health 

and medicine, since splicing defects are responsible for many genetic disorders.

Using the structure, Strobel and his colleagues were also able to closely study the 

splicing site, or “active” site. They discovered that the site contains two metal ions, 

whose role is to promote the splicing reaction. This is very similar to the metal ions 

found within the active sites of the protein enzymes that catalyze the formation of 

RNA and DNA chains. Thus, studying the behavior of these ions may explain how 

these protein enzymes “learned” to perform their function.

The RNA structure was determined at NSLS beamline X25 using a technique called 

macromolecular crystallography, which uses intense x-rays to “see” the molecular 

structure of different materials. The x-rays are scattered, or diffracted, by atoms in the 

crystal, forming a unique pattern on a detector screen when they emerge from the 

sample. By analyzing this pattern, the researchers were able to determine the location 

of each atom in their RNA crystal.

Strobel and his group plan to continue their research by investigating how the metal 

ions in the active site promote the splicing reaction. They would also like to learn 

more about how the intron is rearranged during splicing. This research was funded by 

the National Science Foundation and the National Institutes of Health. 

Laura Mgrdichian

The crystal structure of the RNA 

section, with the exons (red) 

attached to the intron (orange, 

blue, and green). The intron 

catalyzes a reaction in which the 

red segments are joined together 

and the blue segment is released.

Scott Strobel
2-20 NSLS ACTIVITY REPORT 

New Physics Law Unifies Several Superconducting Compounds 

A research group led by a scientist at Brookhaven National Laboratory has discovered a simple relationship that mathematically links the properties of a class of high-temperature superconductors, materials that, below a certain temperature, conduct electricity with no resistance. This new, unexpected law applies to superconductors with very different 

structures and compositions, and may provide clues to understanding the mechanism of high-temperature superconductivity. It is discussed in the July 29, 2004 issue of Nature. 

“Because this law unifies many different materials, it may allow us to predict the behavior of other superconductors, 

giving us deeper insight into how these systems work,” said Brookhaven Lab physicist Christopher Homes, who led 

the research. 

Homes focused on several members of a class of high-temperature superconductors known as cuprates, which are 

characterized by layers of copper oxide. He found a relationship between three of each cuprate’s physical properties: 

direct current, or dc, conductivity (how much direct current it conducts); critical temperature (the temperature below 

which it superconducts); and the “superfluid density” in the superconducting state. This last property refers to how 

many current carriers  electrons or “holes” (which are spaces in the electron sea that act positively charged)  are in 

the superconductor. 

The new law, called a scaling relation, states that the superfluid density is proportional to the dc conductivity multiplied by the critical temperature. When the researchers plotted this relationship on a graph for each material and 

compared the shape of these plots, they observed that the overall result is a straight line. 

“The interpretation of this result and exactly what it says about the nature of the superconductivity in these materials is a source of ongoing debate,” Homes said, “but it should provide insight into the origins of superconductivity in 

these materials, or even give us a way to predict the behavior of other superconductors.” 

The scaling relation applies regardless of each cuprate’s crystal structure, doping level (the amount of other elements, 

such as calcium or strontium, added to improve their performance), and type of disorder (how the crystal lattices are 

distorted by impurities). The relation also works regardless of the direction in which the properties are measured  

parallel to the copper oxide planes or perpendicular to them. This is significant because, in a cuprate, the electric current only runs parallel to the copper oxide planes. Perpendicular to the planes, the cuprate acts much like an insulator, 

with very little current flowing. 

“The fact that this scaling law makes a connection between the superconductivity in both directions, where the properties are very different, was surprising,” said Homes. 

Homes and his group studied each material using a wide range of light, from 

microwaves to ultraviolet rays. In some cases, they worked at the National 

Synchrotron Light Source infrared beamline U10A. They measured how 

much light is reflected away from each sample, a value called absolute reflectance. From this measurement, they calculated the properties used to determine the scaling relation. 

“The beauty of this technique is that this simple measurement allows both 

the conductivity and the superfluid density to be measured without touching 

the material,” Homes said. “It is amazing what you can learn about a material 

just by looking at how it reflects light.” 

Homes also applied the scaling law to two conventional superconductors, the 

metals lead and niobium, using known measurements from literature. He 

and his group will continue this research by studying certain other conventional superconductors, to see if they obey the scaling law. 

This research is the result of a collaboration between researchers at 

Christopher Homes Brookhaven Lab, the University of British Columbia, the Central Research 
FEATURE HIGHLIGHTS 2-21

Institute of Electric Power Industry (Japan), Stanford University, 

the Stanford Synchrotron Radiation Laboratory, the University 

of California at San Diego, and McMaster University. 

The research was funded by the Office of Basic Energy Sciences 

within the U.S. Department of Energy's Office of Science, the 

National Science Foundation, the Natural Sciences and Engineering Research Council of Canada, and the Canadian Institute 

for Advanced Research. 

Laura Mgrdichian

The log-log plot of the superfluid density (y-axis) versus the 

product of the dc conductivity (measured just above the 

transition temperature) and the critical temperature (x-axis) for a 

variety of cuprates, using data taken perpendicular to the copperoxide planes. Within error (dotted lines), all the data for the 

cuprates are described by the dashed line.
2-22 NSLS ACTIVITY REPORT 

First Glimpse of DNA Binding to Viral Enzyme 

May serve as new target for antiviral drugs 

Scientists at Brookhaven National Laboratory and the Albert Einstein College of Medicine have produced the first molecular-scale images of DNA binding to an adenovirus enzyme — a step they believe is essential for the virus to cause 

infection. The images, which appear on the cover of the October 2004 issue of Molecular and Cellular Proteomics, show 

how binding to DNA may stimulate the enzyme and are already being used to design new antiviral drugs to block this 

interaction. 

“We were quite surprised to see that DNA actually stimulated the activity of the enzyme,” 

said Brookhaven biologist Walter Mangel, a co-author on the paper. “If we can block this 

interaction, we should be able to prevent the virus from replicating, and thereby thwart 

infection.” 

Adenoviruses cause respiratory, gastrointestinal, and eye infections, including highly 

contagious viral pink eye. Some adenovirus eye infections lead to blindness. Respiratory 

epidemics of adenovirus are often prevalent on army bases. In patients with compromised 

immune systems, such as those infected with human immunodeficiency virus (HIV), an 

opportunistic adenovirus infection can be deadly. 

During infection, adenovirus makes an enzyme called a protease, which cleaves or degrades viral “scaffolding” proteins to complete the maturation of newly synthesized virus 

particles. Mangel and others have been working to understand all the steps necessary for this enzyme’s function, looking for new ways to stop its action and, therefore, block an adenovirus infection. 

The scientists didn’t expect the viral DNA to bind to the protease, but they figured they should look just to rule out 

such an interaction. “It was something we had to do, to make sure they did not interact,” Mangel said. The discovery that the viral DNA interacts with the protease was unprecedented and led them to characterize the interaction in 

detail. The scientists now believe that inside the virus particle the protease uses the DNA as a guide wire, sliding along 

the genetic material to remove the internal “scaffolding” proteins, all located near the DNA. 

The team used a technique called synchrotron x-ray footprinting, which was pioneered by paper co-author Mark 

Chance and his colleagues at the Albert Einstein College of Medicine to show where DNA binds on the adenovirus 

protease. 

“Synchrotron footprinting is a technique recently developed at Einstein that allows structural information on the 

contacting surfaces of biological molecules to be precisely mapped. These contact points are regions providing critical communication in the cell,” Chance 

explained. “In this study, the footprinting approach provided information on 

the DNA binding region of the adenovirus protease that has not been solved by 

other techniques and can be used in drug design.” 

At the National Synchrotron Light Source, beamline X28C Einstein’s Sayan 

Gupta, the study’s lead author, bombarded different solutions of the adenovirus 

protease and DNA with x-rays and characterized the changes that occurred on 

the surface of the protein. With this technique, the team was able to deduce the 

location of the DNA binding site based upon the changes in accessible surface 

area. 

“There is extensive contact between the enzyme and the DNA,” Gupta said. 

“The DNA wraps around more than half the enzyme molecule. It appears like 

a strap, holding two parts of the protease together.” 

Since the DNA binding site is quite long, there are numerous locations along 

Walter Mangel it that could be used as targets for drugs to block the interaction and act as 
FEATURE HIGHLIGHTS 2-23

Two views of the adenovirus protease, an enzyme required for 

viral replication. DNA, depicted by the white “sticks,” is shown 

binding to the enzyme on the right. Drugs that prevent the DNA 

from binding should prevent the virus from replicating and stop an 

infection.

antiviral agents, Mangel said. The scientists have already 

begun looking for such drugs and hope to have the National 

Institutes of Health test some of them for anti-viral activity 

within a year. 

This work was funded by the Office of Biological and Environmental Research within the U.S. Department of Energy’s 

Office of Science, the Biotechnology Resource Centers 

Program of the National Institute of Biomedical Imaging and 

Bioengineering of the National Institutes of Health, and by 

the National Institute of Allergy and Infectious Diseases of 

the National Institutes of Health.

Karen McNulty Walsh
2-24 NSLS ACTIVITY REPORT 

Under Pressure, Zirconium is a “Glass” Act

By working in part at the National Synchrotron Light Source (NSLS), scientists from Los Alamos National Laboratory have produced a new glass material by squeezing the metal zirconium under very high pressures. This glass may 

be stronger and more resilient than traditional glasses, and has the potential to be a better material for medical, sports, 

and electronics products. The research is published in the July 15, 2004, issue of Nature.

“This is the first time that this type of glass has been formed from a single element or pure metal,” said Jianzhong 

Zhang, one of the two scientists who performed the research. “Moreover, because of its single-element nature and high 

stability at extreme temperatures, this zirconium glass has many exciting, potential applications.”

Unlike conventional metals and metal alloys, which are made of 

tiny crystalline grains and are thus prone to breakage, metallic 

glasses made from a single element have a uniform, non-granular 

structure. These “bulk” glasses have many desirable properties, 

such as a high resistance to breaking, shattering, and distortion. 

In this way, bulk metallic glasses behave like a plastic yet are much 

stronger than other metal materials. These characteristics make 

them attractive engineering materials, for example.

At the NSLS and Argonne National Laboratory (ANL), Zhang 

and Zhao created the glass by placing a crystalline sample of pure 

zirconium in a device that subjected it to extreme conditions – up 

to 80,000 times atmospheric pressure and 1,300 degrees Fahrenheit. These factors caused the zirconium atoms in the crystal 

to change their positions and bond to each other differently, producing a material that is still made of zirconium, 

but takes on a different form: glass. As opposed to other pressure production methods, which produce microscopic 

samples, this method creates millimeter-sized samples of bulk glass and can even create inch-sized pieces large enough 

to be used in industry.

Bulk metallic glasses are being used in an increasing number of practical applications, such as to make electronics components, jewelry, and 

sports equipment. Scientists believed that bulk metallic glasses can only 

be alloys. But alloy glasses are not as stable as glasses made from pure 

metals, and are conventionally produced by melting the alloy metal and 

rapidly cooling it in water.

This research has dispelled these conventions. “We’ve broken new 

ground by showing that metallic glasses do not have to be alloys, and 

can be produced using an alternate method,” said Yusheng Zhao, 

Zhang’s colleague and the paper’s co-author.

Zhang and Zhao used x-rays at NSLS beamline X17B2 and ANL to 

watch how the zirconium changed from a metal to a glass as the pressure 

and temperature increased. When shined at the sample, the x-rays acted 

like tiny probes. They bounced off the zirconium atoms and then exited 

the sample, forming a pattern recorded by a detector. When analyzed, 

the pattern yielded information about how the structure of the zirconium crystal changed as it was squeezed and heated.

In ongoing follow-up research, Zhang and Zhao will work with commercial-grade zirconium, which is not as pure and, therefore, is less 

expensive. They want to create a similar glass, but have found that 

even higher temperatures and pressures are required, and yield a glass 

Jianzhong Zhang (courtesy of Los Alamos National Laboratory)

Glass-forming conditions and stability of amorphous 

zirconium. Circles in red refer to pressures and 

temperatures at which crystalline zirconium metal 

transformed into an amorphous phase upon heating. 

Arrows indicate the selected experimental P-T paths 

along which no precipitation of any crystalline phase was 

observed after the formation of amorphous zirconium. 

Circles in blue refer to a portion of data collected along 

the paths. The hexagon symbol corresponds to the 

conditions where the reversed transformation from glass 

to ω phase was observed upon cooling. Temperature °C

Pressure, GPa
FEATURE HIGHLIGHTS 2-25

with lesser quality than that produced using pure zirconium. The 

researchers hope to remedy this with future experiments.

This work is funded by the Office of Basic Energy Sciences within 

the U.S. Department of Energy’s Office of Science and a Laboratory Directed Research and Development grant from Los Alamos 

National Laboratory. 

Laura Mgrdichian

An x-ray scattering image recorded in a CCD detector for a 

zirconium specimen recovered at ambient conditions. The 

pattern is characteristic of an amorphous phase and does 

not reveal any diffraction lines of crystalline zirconium 

metal.

Columns

Rows

0 500 1000 1500 2000 2500 3000

0 500 1000 1500 2000 2500 3000

3000

2500

2000

1500

1000

500

0

3000

2500

2000

1500

1000

500

0
2-26 NSLS ACTIVITY REPORT 

Research on “Holes” May Unearth Causes of Superconductivity

Working at the National Synchrotron Light Source (NSLS), scientists have uncovered another possible clue to the 

causes of high-temperature superconductivity, a phenomenon in which the electrical resistance of a material disappears 

below a certain temperature. In a superconducting compound, they found evidence of a rarely seen arrangement of 

“holes” – locations where electrons are absent. The results appear in the October 28, 2004, issue of Nature.

The researchers were studying a compound made of strontium, copper, and oxygen (which they’ve dubbed SCO) that 

is one of the “cuprates,” a family of compounds that contain copper oxide. In SCO, the scientists found evidence of 

a “hole crystal” – a rigid, ordered arrangement of holes. Holes are positively charged and, like electrons, may interact 

with each other to produce a superconducting current.

“A hole crystal is a very unusual phenomenon,” said NSLS physicist 

Peter Abbamonte, the study’s lead researcher. “Its existence is a direct 

result of the correlations between holes, which are believed to produce 

superconductivity in other cuprates.”

SCO consists of one layer of strontium atoms sandwiched by two 

sheets of different copper oxides. In one sheet, the copper-oxide molecules form long, parallel chains. The other copper-oxide layer, which 

contains the hole crystal, has a ladder structure, resembling chains 

that are linked horizontally.

A hole crystal is just one type of arrangement of electric charge in a 

material. These arrangements are important because some researchers 

believe that superconductivity is the result of a particular arrangement, or occurs when a superconductor approaches a boundary 

between two arrangements. In other cuprates, for example, scientists 

are studying a charge arrangement in which ribbons of holes and magnetic regions form alternating “stripes.”

“We believe the hole crystal and stripes may be linked,” said Abbamonte. “Specifically, the hole crystal in SCO may be 

a ‘low-dimensional’ precursor to stripes, meaning it exists only along the copper-oxide ladders, rather than in an entire 

copper-oxide plane.”

He and his collaborators studied SCO using x-rays. They placed an SCO sample in the path of an x-ray beam, varied 

the wavelength of the beam, and watched how the x-rays reflected away from the sample.

At a particular energy, the sample reflected back the x-rays very intensely. The research group discovered that this reflection was caused by the holes, which led them to determine that the holes formed an ordered lattice since randomly 

placed holes could not have produced such a strong reflection.

Abbamonte and his collaborators plan to continue this research by varying 

the chemical composition of SCO to see if it changes the hole crystal. 

They will also examine another cuprate to see if its stripes are related to 

the crystal.

“Clearly, more research needs to be done to study these phases and their 

possible link to superconductivity,” said Abbamonte.

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

the U.S. Department of Energy’s Office of Science, the National Science 

Foundation, Bell Laboratories, the Dutch Science Foundation, and the 

Netherlands Organization for Fundamental Research on Matter.

Laura Mgrdichian

Peter Abbamonte (bottom) and student researcher Andrivo 

Rusydi

The peak intensity and ladder position (LL

) of the hole 

crystal reflection.

Photon energy (eV)

LL (r.l.u.)
FEATURE HIGHLIGHTS 2-27

A Brain Cell Gateway

New protein structure may lead to therapies for neural conditions

At the National Synchrotron Light Source (NSLS), scientists from Columbia University have determined the crystal structure of a cell membrane protein that transports glutamate, a chemical essential for normal human brain 

development and function, in and out of brain cells. This structure has helped them explain how glutamate enters 

and exits brain cells, which may help researchers develop treatments for neural conditions based on glutamate 

dysfunction, such as Alzheimer’s disease and depression.

“Until now, there was no information on the three-dimensional structure of a glutamate transport protein or the 

mechanisms it uses,” said Columbia biochemist Eric Gouaux, 

who led the study. “This structure gives us a very good idea 

of how the transporter functions.”

Glutamate is one of the most important signaling molecules 

that is transmitted between brain cells, or neurons. These 

chemical “messengers,” called neurotransmitters, enter and 

exit a neuron by crossing the membrane, a cell’s outer skin, 

via a transporter protein situated within the membrane. 

To understand how these transporters function, scientists 

must first determine their three-dimensional structures. The 

researchers determined that the glutamate transport protein’s structure – the first-ever structure of a neurotransmitter transporter – is bowl-shaped. The bowl, which is filled with a watery solution, is nestled into the membrane 

such that the basin dips about midway into the membrane and the rim rises just above it.

The bowl’s major structural elements are three wedge-shaped segments. The wide ends of each wedge form the rim 

of the bowl, while the pointy ends meet to form the basin. Each wedge has an intricate sub-structure, composed 

of multiple helix-shaped protein strands, called “alpha-helices,” that are folded and twisted together. These include 

two helical, hairpin-shaped substructures (hairpins 1 and 2) that are key players in the transport mechanism.

Hairpin 1 is located at the bottom of the basin. Positioned approximately vertical, it spans the thickness of the 

bowl such that its curved end points up. Hairpin 2 is closer to the rim of the bowl and is connected to hairpin 1 

horizontally, with the two curved ends touching, forming a hinge with an inverted “L” shape. Additionally, a large 

portion of hairpin 2’s surface area touches the solution inside the basin.

Gouaux and his team think that hairpin 1 can unhinge from hairpin 2 and swing away from it, like a gate. When 

glutamate from a neighboring neuron enters the basin and diffuses down through the solution, the gate opens and 

the glutamate molecule slips through. Together, the three gateways – one in each wedge – make up the glutamate 

passage system.

“We now have a much better idea of how glutamate is transported into a cell, which gives us more information on 

how neurons communicate,” said Gouaux. “In turn, we may be able to use this information to help find treatments for neural diseases and conditions that are based on glitches in 

glutamate transport.”

The researchers made these findings at NSLS beamlines X4A, X6A, X25, 

and X26C. Using a method called protein crystallography, they scattered 

x-rays off a crystal sample of the transport protein. The scattered x-rays 

were collected by a detector and then analyzed by a computer, yielding a 

three-dimensional model of the protein. This research is funded by the 

Howard Hughes Medical Institute and the National Institutes of Health.

Laura Mgrdichian

Columbia Researchers Olga Boudker, Yan Jin, and Dinesh Yernool

The structure of the cell membrane protein, from 

a view parallel to the cell membrane.
2-28 CHEMICAL SCIENCES 

BEAMLINE X7A

Funding

The Royal Society; National 

Science Foundation; U.S 

Department of Energy – Division of Materials Sciences, 

Division of Chemistry

Publication

R.E. Morris, A. Burton, L.M. 

Bull, and S.I. Zones, "SSZ51-A New Aluminophosphate 

Zeotype: Synthesis, Crystal 

Structure, NMR, and Dehydration Properties," Chem. 

Mater., 16(15), 2844-2851 

(2004). 

Contact information

Russell E. Morris

School of Chemistry, University of St. Andrews

Email: rem1@st-and.ac.uk

The Structure and Unusual Hydration/Dehydration 

Behavior of the New Aluminophosphate SSZ-51

A. Burton, R. Morris, L.M. Bull, and S.I. Zones

School of Chemistry, University of St Andrews and ChevronTexaco Energy Research and Technology 

Company

The aluminophosphate SSZ-51 is a novel molecular “sieve” prepared using 4-(dimethylamino) pyridine as a structure-directing agent in aluminophosphate gels containing 

fluoride. We studied the calcination and dehydration behaviors of SSZ-51 using powder 

x-ray diffraction at beamline X7A. We found that the as-made structure changes only 

slightly when heated to 300°C. However, at 400°C, there are dramatic changes in both 

the peak diffraction positions and intensities as the organic structure-directing agent 

and the fluoride are removed from the structure. As water is adsorbed, reversible structural changes occur within the framework of SSZ-51.

The aluminophosphate mineral SSZ-51 is a novel molecular “sieve” prepared using 

4-(dimethylamino) pyridine as a structure-directing agent in aluminophosphate 

gels containing fluoride. The SSZ-51 unit cell is monoclinic, with a = 21.759, b

= 13.821, c = 14.224 Å, and β = 98.85°. The structure of SSZ-51 (Figure 1) is 

closely related to the silicoaluminophosphate SAPO-40. Both structures possess 

intersecting 12- and 8-ring channels.

The powder diffraction pattern of SSZ-51 changes dramatically after calcination, which removes the occluded organic template and fluoride ions (Figure 2). 

Except for the low-angle 110 and 200 peaks, the diffraction pattern of the calcined 

material shows little resemblance to the as-made form, suggesting perhaps that the 

material is decomposing during calcination. However, it was quite puzzling that 

SSZ-51 possessed an appreciable microporosity, and that adsorption measurements 

were consistent with the presence of 12- and 8-rings in the calcined structure. 

We therefore decided to collect variable temperature powder diffraction data at 

beamline X7A on the as-made sample, to monitor structural changes as SSZ-51 

was heated in air.

The sample was placed in a glass capillary and heated in open air in 100°C increments up to 800°C. After completing the initial series of experiments to remove 

the organic component, the material was placed over a beaker containing water. 

After hydrating for a day, the sample was loaded into another capillary and data 

were again collected in 100°C increments. 

Figure 3 shows the effect of 

temperature on the powder 

diffraction pattern of the 

as-made sample of SSZ-51. 

As the material is heated 

to 300°C, there are only 

slight changes in the x-ray 

Authors (left to right) 

(front) Ignatius Chan, Allen Burton, 

Saleh Elomari, Lucy Bull, and CongYan Chen; (back) Stacey Zones, Steven 

Vittoratos, Charlie Wilson, and Chuck 

Kibby
 SCIENCE HIGHLIGHTS 2-29

diffraction (XRD) pattern. However, at 400°C there are dramatic changes in 

both the peak positions and intensities as the organic structure-directing agent 

and the fluoride are removed from the structure. The shifts are readily apparent 

in the positions of the 110, 200, and 310 reflections. This XRD pattern can be 

indexed by a C-centered monoclinic cell with lattice parameters of a = 22.471, 

b = 13.735, c = 14.052, and β = 98.5°. While the other lattice parameters show 

little change, the a lattice parameter increases by 3.3%. This change seems 

mostly due to the relaxation of the framework as the fluoride bonds with the 

framework are broken. 

After 400°C, there is little variation in the pattern. At 800°C the XRD pattern 

shows some disparity near 9.43 and 11.98 °2θ, likely due to structural changes 

in the berlinite impurity, which exhibits a phase transition near 600°C. 

We were surprised that the material survived calcination to 800°C. We then 

thought that the changes we initially observed in the XRD pattern might be 

due to adsorption of water rather than to thermal instability. If we allowed the 

sample to hydrate for a day, would we then obtain the grotesque XRD pattern 

we observed in our calcined samples? If so, could we reheat the sample and recover a nice “crystalline” diffraction pattern? Figure 4 shows that the answer to 

both questions is “Yes.” In fact, at 100°C, most of the expected reflections from 

the unit cell are distinctly visible.

So how do we explain these reversible structural changes induced by water? It 

appears the adsorbed water removes the long-range order from the otherwise 

crystalline structure. Water is known to coordinate with aluminum atoms in the 

frameworks of aluminophosphate zeotypes to produce octahedrally coordinated 

aluminum species. In some cases water may even hydrolyze the framework 

bonds to destroy the structure. If the water molecules do not bond to each 

crystallographically equivalent aluminum atom in the same manner, the longrange symmetry of the structure is lost and a diffraction pattern is obtained with 

features similar to the one at the bottom of Figure 2.

Figure 4. Dehydration of calcined 

SSZ-51.

Figure 1. Structure of the novel 

aluminophosphate SSZ-51.

Figure 2. XRD (CuKa) patterns 

of SSZ-51 taken before and after 

calcination.

Figure 3. Calcination of the as-made 

form of SSZ-51.

a

c

a

b P

Al

F

O

two-theta (degrees)

Intensity (CPS) Intensity

* - indicates berlinite peaks

2 4 6 8 10 12 14

Intensity

2 Theta (°)

2 4 6 8 10 12 14 16
2-30 CHEMICAL SCIENCES 

Effects of Shear Flow on Interfacial Ordering in 

Liquids: X-ray Studies

C. Yu, G. Evmenenko, J. Kmetko, and P. Dutta

Northwestern University, Department of Physics and Astronomy

We have directly observed shear-induced structural changes in two interfacial liquids 

using x-ray reflectivity. The liquids are tetrakis (2-ethylhexoxy) silane (TEHOS) and 

polydimethylsiloxane (PDMS). Both are insulating, nonpolar liquids, but TEHOS 

molecules are spherical (non-entangling), while PDMS molecules are linear (entangling). The static interfacial structure of TEHOS, approximately three layers at the 

interface, was gradually destroyed as the shear rate increased. PDMS, which has no 

observable interfacial layers when unsheared, developed approximately four layers at 

the interface at the shear rate of about 104 units/second (s-1), applied for 1.5 minutes. 

We suggest possible correlations between our observations and unusual shear responses 

reported by other researchers.

Classical hydrodynamics assumes isotropic, continuous media, but this assumption is likely to fail near interfaces, and there is considerable evidence that it does 

fail. Many experiments have showed a non-classical shear response in interfacial 

liquids, but the relation between this response and structural changes in the interfacial liquid is not clear. We have directly observed structural changes in interfacial 

liquids under shear. We used the liquids tetrakis(2-ethylhexoxy)silane (TEHOS) 

and polydimehylsiloxane (PDMS) in this study. These materials are chemically 

similar (both are insulating, nonpolar, nonreactive van der Waals liquids), but 

the molecules are geometrically very different (TEHOS is spherical and PDMS is 

spaghetti-like).

Surface Force Apparatus (SFA) experiments on nanoscopic round-molecule 

liquids confined between two smooth solid surfaces have showed shear thinning 

(reduction of shear viscosity) above a threshold shear rate about 108

 times smaller 

than that for bulk liquids. The reduction follows a power law. Computer simulations indicate that shear thinning occurs only in the interfacial region. While our 

experiments used much thicker liquid films than the SFA experiments, we applied 

the same shear rates and looked at the structure in the interfacial region. For this 

purpose we fabricated a shearing apparatus that maintains micrometer-thick liquid 

films while rotational shear is applied (Figure 1). 

When no shear is applied, TEHOS is known to develop layers (density oscillations) near hard surfaces. Our shear-dependent x-ray reflectivity data show that 

these density oscillations are gradually lost above a threshold shear rate, as indicated by the loss of scattering peak 

height. The relaxation time of the 

interfacial TEHOS, 0.01 s, can be 

estimated from the inverse of the 

threshold shear rate. However, we 

observed that the disrupted diffraction peak did not significantly 

redevelop for at least a few hours. 

We attribute this discrepancy to 

BEAMLINE X18A

Funding

National Science Foundation

Publication

C.J. Yu, G. Evmenenko, J. 

Kmetko, and P. Dutta,“Effects 

of Shear Flow on Interfacial 

Ordering in Liquids: X-ray 

Studies,” Langmuir, 19, 9558 

(2003).

Contact information

Pulak Dutta 

Department of Physics & 

Astronomy, Northwestern 

University

Email: pdutta@northwestern.edu

Authors (left to right) 

Chungjong Yu and Guennady Evmenenko
 SCIENCE HIGHLIGHTS 2-31

the fact that the shear rate we quote is based on the bulk viscosity of TEHOS, 

while near the interface a far higher viscosity is likely to exist. The anomalous 

increase of viscosity at the solid-liquid interfaces has been observed experimentally and is supported by computer simulations.

A very different behavior was observed for PDMS. Unsheared PDMS has a 

featureless reflectivity pattern (no layering). After shear of 104 s

-1 was applied for 

1.5 minutes, a peak developed corresponding to a spacing equal to the backbone 

diameter of PDMS. This ordering persisted after the shear was no longer being 

applied, returning to the unsheared state in approximately three hours. The peak 

is probably a consequence of the disentanglement of PDMS molecules (Figure 

2).

Figure 1. Schematic diagram of the 

experimental setup. The outer housing 

and attached kapton window are 

rotated to apply shear.

Figure 2. Schematic representation 

of the effect of shear stress near an 

interface on (a) TEHOS and (b) 

PDMS 

(a)

(b)
2-32 CHEMICAL SCIENCES 

Chemistry of SO2 on Ce1-xZrxO2 Nanoparticles and 

Ce1-xZrx

O2(111) Surfaces

J.A. Rodriguez1, X. Wang1, G. Liu1, J. Hanson1, J. Hrbek1, C.H.F. Peden2, A. IglesiasJuez3, and M. Fernández-García3 

1Brookhaven National Laboratory; 2Pacific Northwest National Laboratory; 3Instituto de Catálisis y 

Petroleoquímica, Spain

A major effort in environmental cleanup is controlling the emission of toxic pollutants 

produced during the combustion of fuels in factories, power plants, and automotive 

engines. Cerium oxide (CeO2

) -based materials are utilized as catalysts for the destruction of one of these pollutants, sulfur dioxide (SO2

), and are also used to prevent acid 

rain. High-resolution photoemission, time-resolved x-ray diffraction (TR-XRD), and 

x-ray absorption near-edge spectroscopy (XANES) were used to investigate the chemistry 

of SO2

 on cerium oxide zirconium (Ce1-xZrxO2) nanoparticles and Ce1-xZrxO2(111) 

surfaces (x ≤ 0.5). Sulfur K-edge XANES spectra pointed to sulfate (SO4

) as the main 

product of the adsorption of SO2

 on these mixed-metal oxides. Full SO2 dissociation was 

seen on the nanoparticles, but not on the Ce1-xZrx

O2(111) surfaces. The metal cations at 

corner or edge sites of the Ce1-xZrx

O2 nanoparticles probably play a very important role 

in interactions with the SO2

 molecules.

The Ce1-xZrx

O2 system is one of the most studied mixed-metal oxides in the 

literature. Typically, the Ce and Zr cations are randomly distributed in a fluoritetype structure. The focus has been on examining possible correlations between the 

CeO2

:ZrO2 interactions and differences in the behavior of Ce1-xZrxO2 and CeO2. 

Oxide nanostructures can have special chemical properties due to size-induced 

structural distortions and the presence of corner sites and oxygen vacancies. Recent 

studies have shown that Ce1-xZrx

O2 nanoparticles can be prepared by a novel 

microemulsion method that leads to materials with highly homogenous chemical 

compositions (i.e. Ce, Zr distribution) and a narrow distribution of particle sizes. 

Following this approach, we synthesized nanoparticles with sizes between 4 and 7 

nm. We investigated their reactivity, and the reactivity of Ce1-xZrx

O2(111) surfaces, 

towards SO2

.

Figure 1 shows the structure of an ideal Ce1-xZrx

O2(111) surface (x < 0.4). The 

top layer consists of O atoms, but within this layer there are holes that expose the 

Ce or Zr cations in the second layer. This well-defined surface allows the detailed 

study of O↔SO2

 and Ce,Zr↔

SO2

 interactions. For the Ce1-xZrx

O2 nanoparticles, the results of 

transmission electron microscopy 

show rough surfaces that can be 

O-or cation-terminated and have a 

high density of edge or corner sites. 

These different structural properties affect the chemical reactivity of 

these mixed-metal oxides.

The top of Figure 2 shows S 

K-edge XANES spectra for the adBEAMLINES

U7A, X7B, X19A

Funding

U.S. Department of Energy; 

Interministerial Committee 

on Science and Technology 

(Cicyt, Spain)

Publication

G. Liu et al, “Adsorption and 

Reaction of SO2 on Model 

Ce1-xZrxO2(111) Catalysts,” J. 

Phys. Chem. B, 108, 2931 

(2004). 

Contact information

José A. Rodriguez

Chemistry Department, 

Brookhaven National 

Laboratory

Email: rodrigez@bnl.gov

Authors (left to right)

(standing) Xiaqin Wang and Jose A. Rodriguez 

(sitting) Jon Hanson and Jan Hrbek
 SCIENCE HIGHLIGHTS 2-33

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sorption of SO2 on CeO2(111) and Ce0.7Zr0.3O2(111) surfaces at room temperature. A comparison to the corresponding peak positions for sulfates and sulfites 

indicates that SO4

 is the main species formed on the oxide surfaces, with a minor concentration of SO3

 (SO2,gas + nOlattice →SO3,ads or SO4,ads). The cations in 

the second layer have all of their O neighbors (eight in total), and interact very 

weakly with an adsorbed SO2

 molecule. One must introduce O vacancies in 

CeO2

(111) and Ce0.7Zr0.3O2(111) to see the interaction of SO2 with the metal 

cations and the subsequent dissociation of the molecule.

Figure 2 also shows S K-edge XANES spectra taken after exposing nanoparticles 

of CeO2

, Ce0.66Zr0.33O2 and Ce0.66Ca0.33O2-y to SO2 at 25oC. Again, we found 

that SO4

 is the main sulfur-containing species present on the oxides, but, in 

addition, we saw features at photon energies between 2470 and 2472 eV that 

denote the existence of metal-S bonds as a consequence of full SO2

 dissociation. Thus, the nanoparticles have metal cations at corner or edge sites that can 

interact well with the SO2

 molecule. In addition, there may be O vacancies in 

the surface of the Ce0.66Zr0.33O2

 and Ce0.66Ca0.33O2-y nanoparticles that facilitate 

S-O bond cleavage.

Figure 3 shows the effect of temperature on the SO4

 signal for the CeO2 and 

Ce1-xZrx

O2 systems in Figure 2. As the temperature is raised, SO4 decomposes. 

The SO4

 adsorbed on the nanoparticles is somewhat more stable than that present on the (111) surfaces. For both types of systems, the presence of Zr seems to 

induce an increase in the thermal stability of the adsorbed sulfate.

Figure 3. Effect of temperature on the XANES signal for the SO4 formed on the CeO2

and Ce1-xZrx

O2 systems shown in Figure 2. The top panel shows the results for the 

(111) surfaces, while the bottom panel contains the corresponding results for the 

nanoparticles.

Figure 1. Top and side views of an 

oxygen-terminated Ce1-xZrx

O2(111) 

surface (x < 0.4). The large spheres 

represent O atoms, and the small 

spheres correspond to Ce or Zr atoms 

in a solid solution.

Figure 2. S K-edge spectra taken 

after dosing SO2

 to CeO2(111) 

and Ce0.7Zr0.3O2

(111) surfaces, and 

nanoparticles of CeO2

, Ce0.66O0.33O2

and Ce0.66Ca0.33O2-y. The samples were 

exposed to 0.1 Torr of SO2

 for five 

minutes at 25o

C.

top view

side view

Ce,Zr O

Normalized fluorescence yield (arb units)

Temperature ( Photon Energy (eV) oC)

XANES So4 signal (arb units)

XANES So4 signal (arb units)

Temperature (oC)
2-34 CHEMICAL SCIENCES 

BEAMLINES

X22B, X22A

Funding

University of New Mexico; 

National Science Foundation; 

French ACI “Nanostructure”; 

Department of Energy’s 

Office of Basic Energy 

Sciences;Air Force Office 

of Scientific Research; A 

Laboratory Directed Research 

and Development (LDRD) 

grant from Sandia National 

Laboratories

Publication

D.A. Doshi, A. Gibaud, V. 

Goletto, M.C. Lu, H. Gerung, 

B. Ocko, S.M. Han, SM, and 

C.J. Brinker, “Peering Into the 

Self-Assembly of Surfactant 

Templated Thin-Film Silica 

Mesophases,” J. Am. Chem. 

Soc., 125(38), 11646-11655 

(2003).

Contact information

C.J. Brinker

Advanced Materials 

Laboratory 

Email: cjbrink@sandia.gov

Peering Into the Self-Assembly of Surfactant Templated 

Thin-Film Silica Mesophases

D.A. Doshi1,£, A. Gibaud2,3, V. Goletto4, M. Lu1,*, H. Gerung1, B. Ocko5, S.M. Han1, and 

C.J. Brinker1,2

1Department of Chemical and Nuclear Engineering and Center for Micro-Engineered Materials, University of New Mexico; 2Sandia National Laboratories; 3Université du Maine, Faculté des Sciences, 

France; 4Chimie de la Matière Condensée, Université Pierre et Marie Curie, France; 5Department 

of Physics, Brookhaven National Laboratory; £Currently at Los Alamos National Laboratories; *Currently at Intel Corporation, Portland Technology Development

In this study, time-resolved grazing incidence small angle x-ray scattering (GISAXS) 

was combined with gravimetric analysis and infrared spectroscopy to structurally and 

compositionally characterize in situ the evaporation-induced self-assembly (EISA) of a 

homogeneous silica/surfactant/solvent solution into a highly ordered surfactant-templated mesostructure. Using detergent-like molecules of cetyl trimethyl ammonium bromide 

(CTAB) as the structure-directing agents, a two-dimensional hexagonal thin film with 

cylinder axes oriented parallel to the substrate surface forms from an incipient lamellar (layered) mesophase through a correlated micellar intermediate. A comparison with 

the corresponding CTAB/water/alcohol system (prepared without silica) shows that the 

hydrophilic and non-volatile silicic acid components actively participate in self-assembly 

and, along with the presence of solid-liquid and liquid-vapor interfaces, significantly 

influence the self-assembly pathway.

It is now recognized that self-assembly is a powerful synthetic approach to the fabrication of nanostructures with feature sizes smaller than achievable with state-ofthe-art lithography, and with a complexity approaching that of biological systems. 

For example, recent research has shown that silica/surfactant self-assembly can 

direct the formation of porous and composite thin film mesostructures characterized by precise periodic arrangements of inorganic and organic constituents on the 

scale of one to 50 nanometers in size. Despite the potential utility of these films for 

a diverse range of applications, such as sensors, membranes, catalysts, waveguides, 

lasers, nano-fluidic systems, and low dielectric constant insulators, the mechanism 

of thin film self-assembly remains largely unexplored. Understanding and ultimately controlling self-assembly is critical in order for it to transition from largely a 

laboratory practice to a reliable ‘tool’ for nanofabrication.

In this study we used time-resolved GISAXS combined with gravimetric analysis 

to structurally and compositionally characterize in situ the EISA process. Solutions 

were dispensed onto a silicon substrate positioned horizontally on the platform 

of a weighing balance that was confined within a cell, allowing controlled solvent 

evaporation. The liquid spectrometer at beamline X22B allowed the 

x-rays to impinge upon the surface 

at grazing incidence, and the scattering was continuously collected 

onto a charge-coupled device camera. In situ stress and attenuated 

total reflection-Fourier transform 

infrared spectroscopy (ATR-FTIR) 

measurements, performed using 

Authors (left to right) 

Dhaval Doshi and Jeffrey Brinker
 SCIENCE HIGHLIGHTS 2-35

the identical horizontal geometry and x-ray reflectivity analysis of the final selfassembled films, enabled further structural interpretation of the GISAXS results, 

providing greater insight into the self-assembly pathway.

Figure 1 shows the temporal evolution of starting weight percentage for the 

0.12 sample (where 0.12 is the CTAB-to-Si molar ratio), along with that 

calculated for the surfactant, CTAB. The self-assembly pathway comprises four 

successive stages: (I) isotropic, (II) lamellar, (III) correlated micellar, and (IV) 

hexagonal, where each is characterized quantitatively by the d-spacing observed 

normal to the substrate, and, for the hexagonal phase, the in-plane spacing afcr 

(where fcr is the face-centered rectangular lattice representation of the hexagonal 

lattice). Figure 2 maps the evaporation-induced compositional trajectories of 

the three CTAB/silica systems onto the bulk water/ethanol/CTAB phase diagram. Also plotted is the trajectory for the sample prepared without silica (WS). 

Selected corresponding GISAXS patterns obtained after the specified times, t

(seconds), are presented. 

The formation of the lamellar phase (Region II in Figure 1, inset b in Figure 

2) is completely unexpected from the bulk phase diagram and is not observed 

in the WS system. Based on orientation, we attribute its appearance to the local 

enrichment of the sol (the silica/surfactant/solvent solution) at the liquid-vapor 

interface. We also observe a continuous reorganization of both the mesostructure and the lattice dimension within Regions II-IV (Figure 1) that results from 

the reorganization of the surfactant molecules within the lamellar or micellar 

structures due to ethanol evaporation. For all samples of CTAB and the other 

surfactant systems that were studied, we find that the presence or absence of 

hydrophilic silica species dramatically influences mesophase development. Generally, without silica, the evaporation of solutions like WS results in a crystalline 

surfactant product without forming the mesophase(s) anticipated from the bulk 

phase diagram. This apparent kinetic effect presumably results from the evaporation of water. We suppose that such kinetic barriers are avoided for silica-containing systems because the silicic acid species serve as non-volatile fluids that 

are as hydrophilic as water. 

As a result of this study, we now recognize the opportunity to controllably interrupt EISA to derive novel intermediate sandwich-like structures or fine-tune the 

d-spacing and its associated properties, such as surface area, refractive index, and 

dielectric constant.

Figure 1. The temporal evolution of 

structure and composition for the 0.12 

sample.

Figure 2. Bulk and thin-film ternary 

phase diagram. The evaporationinduced compositional trajectories 

of the three CTAB/silica systems 

(0.10, 0.12, and 0.16) and the WS 

systems are mapped onto the bulk 

water/ethanol/CTAB phase diagram, 

considering the hydrophilic silicic acid 

precursors to be equivalent to water. 

For the 0.12 sample (a) corresponds to 

the isotropic phase, (b) the lamellar, 

(c & d) the correlated micellar, and 

(e & f) the hexagonal. For the WS 

sample, (g) corresponds to isotropic, 

(h) correlated micellar, (i & j) lamellar 

and correlated micellar, and (k) to 

crystalline CTAB.
2-36 CHEMICAL SCIENCES 

Structures and Properties of Supramolecular Assembled 

Fullerenol/Poly(dimethylsiloxane) Nanocomposites

S. Zhou1, J. Ouyang1, and S.H. Goh2 

1Department of Chemistry, The College of Staten Island and the Graduate Center, The City University of New York; 2Department of Chemistry, National University of Singapore

We prepared supramolecular assembled fullerenol/poly (dimethylsiloxane) nanocomposites by solution-casting the complexes of fullerenol and poly (dimethylsiloxane) (PDMSdi-NH2

) at different molar ratios. The results from our small-angle x-ray scattering 

(SAXS) study of the nanocomposites indicate that nanodomains of fullerenol aggregates 

are confined homogeneously in the PDMS matrix and grow in size when fullerenol 

molecules are gradually added. This novel structural feature, together with the unique 

molecular properties of fullerenol, gives these nanocomposites superior thermal and 

thermal mechanical stability, excellent elastic response, and attractive dielectric properties  i.e., one can enhance the permittivity but dramatically decrease the loss factor of 

the materials.

Fullerene-based nanomaterials are popular research targets due to their unique 

electrical and optical properties. However, the low solubility of fullerenes in polar 

media and the difficulty of controlling their aggregation states have prevented these 

materials from being fabricated into novel materials for advanced applications. 

One strategy for overcoming these obstacles is to modify fullerenes, such as C60, 

and incorporate them into polymer matrixes. Poly(dimethylsiloxane) (PDMS-diNH2

) is an ideal polymer candidate to host C60 due to its many useful properties, 

such as its flexibility, low glass transition temperature, very low surface energy, 

good thermal stability, and biocompatibility. Making novel materials that combine 

the outstanding properties of C60 fullerene and PDMS is thus desirable.

Recently, we prepared a series of freestanding C60-containing PDMS nanocomposite films via the strong hydrogen bonding interactions between the hydroxyl 

(-OH) groups of fullerenol and the terminal NH2

 groups of PDMS. Figure 1

shows the small-angle x-ray scattering (SAXS) profiles of pure PDMS-di-NH2

and the fullerenol/PDMS nanocomposite films formed at different molar ratios of 

OH/NH2

. While the bulk PDMS-di-NH2 has no scattering peaks, the fullerenol/

PDMS composites exhibit a single scattering peak, as a result of the homogeneous 

embedding of fullerenol domains in the PDMS matrix. The gradual addition of 

fullerenol into the nanocomposites not only sharpens and intensifies the peaks, but 

also shifts the peak positions to lower q values, indicating a gradual increase in the 

inter-distances of fullerenol nanodomains. In our design, the fullerenol molecules 

are constrained by the end-functionalized PDMS chains, which means that the 

distance between neighboring fullerenol nanodomain surfaces should be equivalent 

to the PDMS chain length. Therefore, the increase in the inter-distances of fullerenol nanodomains could only be explained by an increase in the size of individual 

fullerenol nanodomains.

Figure 2 depicts the formation and expansion process 

of fullerenol nanodomains 

in fullerenol/PDMS 

BEAMLINE X27C

Funding

National Science Foundation 

Division of Chemistry, 

Organic and Macromolecules

Publication

J. Ouyang, S. Zhou, F. Wang, 

and S. Hong Goh, “Structures 

and Properties of Supramolecular Assembled Fullerenol/

Poly(dimethylsiloxane) 

Nanocomposites,” J. Phys. 

Phys. Chem. B, 108(19), 

5937-5943 (2004).

Contact information

Shuiqin Zhou

Department of Chemistry, 

The College of Staten Island 

and Graduate Center, The 

City University of New York

Email: Zhoush@mail.csi.cuny.edu

Authors (left to right) 

Shuiqin Zhou and Jianying Ouyang
 SCIENCE HIGHLIGHTS 2-37 Intensity (a.u.)

q/nm-1

Temperature (°C) Temperature (°C)

-180 -150 -120 -90 -60 -30 0 30 60

0.20

0.15

0.10

0.05

0.00

ε'ε"

nanocomposites upon a gradual addition of fullerenol molecules. This threedimensional network structure, with fullerenol nanodomains homogeneously 

confined in the PDMS matrix, gives the material superior thermal and thermal 

mechanical stability, a strongly suppressed crystalline phase, and excellent elastic 

mechanical properties. More importantly, the controllable size of these fullerenol 

nanodomains enables us to adjust the dielectric constants of the nanocomposite 

films. Figure 3 shows the temperature dependence of dielectric permittivity 

(ε') and loss factor (ε") of PDMS-di-NH2

 and the fullerenol/PDMS composite 

film, formed at a molar ratio of OH/NH2

 = 2:1 under several frequencies. The 

strong interactions between fullerenol and PDMS-di-NH2

 can severely restrain 

the dipole mobility, resulting in very low ε' and ε" values. On the other hand, 

the unrestricted, highly polar fullerenol molecules possess very high ε' values 

due to their direct current conductivity. For relatively large fullerenol nanodomains, only those OH groups located on the domain surface were linked with 

the PDMS chains. Thus, the unrestricted interior fullerenol molecules could enhance the ε' value for the nanocomposites, which explains the higher ε' value of 

the nanocomposite film than that of PDMS-di-NH2

 (Figure 3A). This unique 

dielectric property of Fol/PDMS-di-NH2

 nanocomposites has the potential to 

lead to novel materials with high ε' values and much lower ε" values.

Figure 3. Temperature dependence of ε' and ε" of PDMS-di-NH2 (star symbols) 

and fullerenol/PDMS composite film formed at a molar ratio of OH/NH2

 = 2:1 

(solid symbols). ε'= 0.3 kHz (square), 3 kHz (up triangle), and 30 kHz (circle). ε"=

0.3 kHz. 

Figure 1. SAXS profiles of pure 

PDMS-di-NH2

 and fullerenol/PDMS 

nanocomposite films formed at 

different molar ratios of OH/NH2

groups.

Figure 2. Structural model for the 

formation of fullerenol/PDMS 

nanocomposites and the expansion 

of fullerenol nanodomains upon the 

continuous addition of fullerenol 

molecules.

PDMS-di-NH2

Fullerenol

C60-(OH)22

Continuous

addition

-180 -150 -120 -90 -60 -30 0 30 60

3.6

3.3

3.0

2.7

2.4

2.1
2-38 CHEMICAL SCIENCES 

BEAMLINE X23B

Funding

Defense Advanced Research 

Projects Agency/Office of 

Naval Research; National 

Science Foundation’s Materials Research Science and 

Engineering Centers

Publication

P. Zhu, H. Kang, A. Facchetti, 

G. Evmenenko, P. Dutta, and 

T.J. Marks, “Vapor Phase SelfAssembly of ElectroOptic Thin 

Films Via Triple Hydrogen 

Bonds”, J. Am. Chem. Soc.,

125(38), 11496 (2003).

Contact information

Tobin J. Marks

Department of Chemistry, 

Northwestern University

Email: t-marks@northwestern.edu

Vapor Phase Self-Assembly of Electrooptic Thin Films 

Via Triple Hydrogen Bonds

P. Zhu1, H. Kang1, A. Facchetti1, G. Evmenenko2, P. Dutta2, and T.J. Marks1

1Department of Chemistry and 2Department of Physics and Astronomy, Northwestern University

Microstructural acentricity – the alignment of molecular dipole moments in a material – is one of the basic requirements for creating electrooptic (EO) materials useful 

for high-speed optical telecommunications. A new molecular chromophore, DTPT 

(5-{4-[2-(4,6-diamino-[1,3,5]triazin-2-yl)-vinyl]-benzylidene}-pyrimidine-2,4,6-trione), was designed and synthesized to create a precursor for the vapor phase growth of 

a high-response organic EO film. Triple H-bonding interactions between neighboring 

molecules direct self-assembled chromophore alignment in a head-to-tail orientation using a straightforward vapor-phase thin-film deposition process. Angle-dependent Second 

Harmonic Generation (SHG) interference patterns and the quadratic dependence of the 

output light intensity on the film’s thickness demonstrate high, reproducible film quality 

and uniformity. Synchrotron x-ray diffraction (XRD) demonstrates long-range order in 

the film and yields a molecular tilt angle in good agreement with polarized SHG data. 

This shows that out-plane ordering of chromophore molecules – i.e. ordering perpendicular to the substrate – has been achieved.

Organic EO materials represent a promising direction in the quest to develop 

novel technologies for increased optical data network speed, capacity, and bandwith. Achieving microstructural acentricity is a key, yet synthetically daunting 

challenge for developing such materials. To date, the principle EO active films that 

have been developed are electric-field poled polymers, Langmuir-Blodgett films, 

and covalent self-assembled superlattices (SASs) formed layer by layer. In addition 

to advantages, each approach also poses challenges – ranging from the inherent 

thermodynamic instability of poled polymers, to the inefficiency of SAS growth 

techniques, to the fragility of amphiphilic (having both water-loving and waterhating components) lattices enforced principally by van der Waals interactions.

 We reported an alternative, vapor phase approach that utilizes robust patterns of 

directed triple H-bonds to assemble microstructurally acentric, EO-active films in 

an expedited growth process. This approach utilizes specifically designed intermolecular longitudinal triple H-bonding interactions to align chromophore molecules 

head-to-tail and preferentially perpendicular to the substrate, forming thin solid 

films from the vapor phase. Out-plane non-centrosymmetric microstructures are 

thereby achieved in smooth, optically clear, thermally robust films, which can be 

grown in hours. Theoretical work shows that such head-to-tail orientations also 

produce intermolecular cooperative effects, which substantially enhance the effective molecular hyperpolarizability of the films. The chromophore DTPT (5-{4-[2-

(4,6-diamino-[1,3,5]triazin2-yl)-vinyl]-benzylidene}-

pyrimidine-2,4,6-trione), 

containing H-bond + 

electron donor and H-bond 

+ electron acceptor modules, 

Authors (left to right) 

Peiwang Zhu, Antonio Facchetti, 

Tobin J. Marks, and Hu Kang
 SCIENCE HIGHLIGHTS 2-39

was synthesized and characterized using conventional analytical/spectroscopic 

techniques. The pyrimidine-2,4,6-trione and 4,6-diamino-1,3,5,-trizine-2-yl 

moieties of DTPT form longitudinally directed donor-acceptor triple H-bonds 

between neighboring molecules (Figure 1).

 In this process, a melamine template was first anchored to a glass or Si (100) 

substrate. A Denton Vacuum DV-502 deposition apparatus (10-5 ~ 10-6 Torr) 

was then used to fabricate films at 100 o

C at a growth rate of 0.5 – 2.0 Å/s. The 

film growth rate and thickness was monitored with a quartz crystal sensor. The 

resulting films are optically transparent (α ~ 10 cm-1 at 640 – 1800 nm) and 

smooth, as measured using atomic force microscopy (AFM) (rms roughness = 

1.7 nm over a 25 μm2 area for a 1.22 μm-thick film). Polarized transmission 

SHG measurements were carried out at λo

 = 1064 nm. Angle-dependent interference patterns for glass substrates coated on both sides (Figure 2a, inset) demonstrate that identical film quality and uniformity on both sides of the substrate 

is achieved. The quadratic dependence of the 532 nm light output intensity (I2ω)

on film thickness (Figure 2a) further demonstrates the uniformity of the chromophore orientation. Calibrating the data (Figure 2a, inset) vs. quartz yields 

nonlinear optical coefficients of d33 = 0.15 pm/V (picometers per volt) and d31

= 0.25 pm/V. Using standard assumptions, the SHG analysis yields an average 

chromophore tilt angle of ~61.3o

 with respect to the substrate normal.

Synchrotron XRD techniques were employed to probe film microstructural 

regularity. The data reveal a specular (mirror-like) feature at 0.69 Å-1, which corresponds to a repeat distance of 9.1 Å (Figure 2b). Molecular modeling shows 

that the repeat distance between DTPT molecules in a H-bonded chain is ~16.8 

Å, which, combined with the XRD data, yields a molecular tilt angle relative to 

the substrate normal of ~57o (Figure 2b, inset). This result is in good agreement 

with the tilt angle derived from SHG data and shows that out-plane ordering of 

chromophore molecules has been achieved. Importantly, these results demonstrate that appropriately designed molecule precursors can be used in gas phase 

film growth processes to produce smooth, robust, EO-active films with high 

microstructural acentricity.

Figure 2a. Square-root of second 

harmonic generation response (I2ω)

1/2

as a function of DTPT film thickness. 

Inset: I2ω as a function of fundamental 

beam incident angle. The dashed line 

is drawn as a guide to the eye. The 

solid line is the fitting result.

Figure 1. Scheme for DTPT selfassembly.

Figure 2b. Specular synchrotron x-ray 

diffraction pattern for a DTPT film 

grown on a template-functionalized 

Si(100) substrate. Inset: Proposed 

molecular alignment in film. (l2ω)1/2 (a.u.)

Film thickness (nm)

R (a.u.)

qz(Å-1)
2-40 CHEMICAL SCIENCES 

BEAMLINE X23A2

Funding

Defense Advanced Research 

Projects Agency; Defense 

Sciences Office Department 

of Energy; Office of Basic 

Energy Sciences

Publication

D. Ciuparu et al., “UniformDiameter Single-Walled Carbon Nanotubes Catalytically 

Grown in Cobalt-Incorporated 

MCM-41,” J. Phys. Chem. B, 

108(2), 503-507 (2004).

Contact information

Dragos Ciuparu

Department of Chemical 

Engineering, Yale University

Email: dragos.ciuparu@yale.edu

Growth of Controlled Diameter Single-Walled Carbon 

Nanotubes

D. Ciuparu, Y. Chen, S. Lim, G.L. Haller, and L. Pfefferle

Department of Chemical Engineering, Yale University

The electronic properties of single-walled carbon nanotubes (SWNTs) depend on their 

diameter and the chiral angle along which a single graphene sheet is rolled in a cylinder. The selective growth of SWNTs of predetermined diameters allows the synthesis of 

SWNTs with uniform electronic properties, which are required for electronic applications. We have shown that SWNTs can be produced with a narrow distribution of diameters centered at different discrete values. The average size of the cobalt (Co) clusters 

used as catalysts for SWNT growth has been determined by extended x-ray absorption 

fine structure (EXAFS) spectroscopy at beamline X23A2.

Catalytic processes that provide more than 90% selectivity to single-walled carbon 

nanotubes (SWNTs) have been developed, but catalysts that allow the engineered 

control of the mean diameter of SWNTs are not available. Since the properties of 

SWNTs depend on the tube diameter, a catalyst that selectively produces a given, 

preselected size is technologically important. Here we demonstrate that the cobaltbased catalyst Co-MCM-41 (where MCM stands for “mobil crystalline material”) 

can be used to control the cluster size of cobalt metal in the pores. This, in turn, 

catalytically produces SWNTs with a narrow distribution of diameters (± 0.05 nm) 

in the 0.5 to 0.8 nm range. 

We chose Co as the catalytic material because it has been demonstrated to be a 

selective catalyst for SWNTs, especially when stabilized against total reduction. We 

hypothesized that if Co were isomorphously substituted for silicon (Si) in MCM41, the MCM-41 matrix would stabilize the Co against total reduction and sintering. Since catalyst metal particle size has been hypothesized to control tube diameter, we studied whether catalyst pore size could be used to control Co cluster size 

and, thus, SWNT diameter. Four catalysts with pore diameters of about 1.9, 2.2, 

2.6, and 2.9 nm (as determined by the classical Barrett-Joyner-Halenda method) 

were prepared hydrothermally using C10, C12, C14, and C16 organic templates, 

where 10, 12, 14, and 16 denote the number of carbon atoms in the alkyl chain 

of the template. The diameters of the SWNTs (synthesized by the disproportionation of carbon monoxide, i.e. the Boudouard reaction) were estimated from the 

nitrogen adsorption isotherms and high-resolution transmission electron microscope (TEM) imaging, with the former occurring after hydrofluoric acid purification and the latter occurring before the removal of the SWNTs from the catalysts. 

These estimates were consistent with data from UV-visual/near-infrared absorption 

spectroscopy, multiple excitation 

wavelength Raman, and fluorescence (the last two techniques 

were only used for the C16 

template).

In Figure 1 the average SWNT 

diameter, determined from niAuthors (left to right) 

Dragos Ciuparu, Lisa Pfefferle, Sangyun 

Lim, Yuan Chen, and Gary Haller
 SCIENCE HIGHLIGHTS 2-41

trogen isotherms, is plotted against the Co-MCM-41 pore size (also determined 

from nitrogen desorption isotherms) and compared with the inner diameter of 

the SWNT, which was estimated from TEM. A remarkable linear correlation 

between the synthesized SWNT and the Co-MCM-41 pore size is observed. It 

is apparent, however, that the SWNT diameter control is not a result of simple 

geometric or mechanical constraint by the pore walls.

We hypothesize that the actual sites for SWNT growth are Co metal clusters, 

which is consistent with previously proposed growth mechanisms, and that the 

diameters of the SWNTs are controlled by the Co metal cluster size. The metal 

cluster size, in turn, is determined by the stability of the Co2+ ions in the MCM41 silica wall. Controlling the cluster size is done using the metal precursor as a 

cation constituent of the MCM-41 pore wall, which stabilizes the metal against 

reduction and migration/sintering during catalyst preparation. The smaller the 

pore diameter of the Co-MCM-41, the more resistant is the Co2+ against reduction, and the smaller is the Co metal cluster that is formed. We have confirmed 

this hypothesis using the temperature-programmed reduction method. We used 

EXAFS to measure the Co cluster size in variable-diameter Co-MCMC-41 

samples exposed to the Boudouard reaction under identical conditions. The 

EXAFS results indicate increased Co cluster sizes in MCM-41 with larger pore 

diameters, as shown in Figure 2.

Figure 2. Size of metallic Co clusters 

determined from Co-Co coordination 

number estimated determined by 

fitting the EXAFS spectra recorded for 

Co-MCM-41 samples reacted with 

CO under identical conditions. The 

cluster sizes were calculated assuming 

a (111) truncated hemispherical 

cuboctahedron model for the cobalt 

clusters. The TEM image inset shows 

a SWNT bundle in a closed hexagonal 

packing characteristic only for uniform 

diameter nanotubes.

Figure 1. SWNT diameters determined 

by nitrogen physisorption and HRTEM for samples produced using 

catalysts with different pore sizes.

Co Cluster diameter (nm)

First shell C0-C- coordination number

Pore size (nm)

SWNT mean diameter (nm)
2-42 CHEMICAL SCIENCES 

BEAMLINE X10B

Funding

National Science Foundation

Publication

E. Hanson, J. Schwartz, 

B.Nickel, N. Koch, and M. 

Danisman, "Bonding Self-Assembled, Compact Organophosphonate Monolayers to 

the Native Oxide Surface of 

Silicon," J. Am. Chem. Soc., 

125, 16074-16080 (2003).

Contact information

Jeffrey Schwartz 

Department of Chemistry, 

Princeton University

Email: jschwartz@princeton.edu

Structural Characterization of Self-Assembled Monolayer Films of (α–Quarterthiophene) Phosphonate 

Bonded to the Silicon Native Oxide Surface

E.L. Hanson, J. Schwartz, B. Nickel, N. Koch, and M.F. Danisman

Department of Chemistry, Princeton University

Electron transport across an interface might be controllable by chemically bonding 

monolayer films to a substrate surface; one possible application is in organic field effect 

transistors (OFETs), which necessitate a film that is dense and ordered. α-Quarterthiophene-2-phosphonate (4TP) has a band gap comparable to α-sexithiophene, which 

has been examined as a semiconducting layer in OFETs. A self-assembled monolayer 

(SAM) film of 4TP was grown on SiO2

/Si. Atomic force microscopy (AFM) showed a 

comprehensive film with no pinholes over large areas. Film thickness measurements were 

made by section analysis. An x-ray reflectivity study confirmed this measurement, which 

was calculated to be 1.8 nm, indicating that the 4TP units are nearly perpendicular 

to the surface. The profile for 4TP/SiO2

/Si is not as abrupt as that for clean SiO2/Si, 

indicating some microscopic disorder within the 4TP film.

Electron transport across or at interfaces might be controllable by chemically 

bonding monolayers to a substrate surface, which themselves could be modified to 

further enhance device function. One such possible application of surface-bound 

monolayers is for organic field effect transistors (OFETs), for use in “next generation” electronic devices. An interesting observation for OFETs is that most of the 

charge transport occurs through the first few electroactive organic monolayers. 

We were therefore interested in determining if such films might be prepared from 

phosphonate derivatives of oligoaromatic species via self assembly on the native 

oxide surface of silicon (SiO2

/Si). α-Quarterthiophene-2-phosphonate (4TP) 

would be an attractive example of an oligoaromatic phosphonate for use in such a 

film, since this material would be easy to process and quarterthiophene (4T) has a 

band gap comparable to α−sexithiophene, which has been examined previously as 

a semiconducting layer in OFETs.

α-Quarterthiophene-2-phosphonic acid (4TPA) was prepared from 4T and was 

used to grow a self-assembled monolayer (SAM) film on SiO2

/Si using our “TBAG” (Tethering By Aggregation And Growth) method. Atomic force microscopy 

(AFM) showed a comprehensive monolayer on the surface (Figure 1a). The absence of pinholes in large (20 

μm x 20 μm, Figure 1b) sections revealed the high degree 

of homogeneity in the SAM. 

Film thickness measurements 

therefore had to be made by 

section analysis (Figure 1c), 

based on the 4TP/SiO2

/Si 

film edge; this indicated the 

thickness to be 2.0 ± 0.2 nm. 

Because the estimated length 

Authors (left to right) 

(Top) Eric L. Hanson, Jeffrey Schwartz, 

(bottom) Norbert Koch, Mehmet Fatih 

Danisman, and (far right) Bert Nickel
 SCIENCE HIGHLIGHTS 2-43

of 4TP is approximately 1.9 nm, this measurement suggests only a small deviation, if any, of the 4T moiety from vertical. The surface loading of the 4TP 

SAM was measured using quartz crystal microgravimetry (QCM) to be 0.66 ± 

0.03 nmol/cm2

. This corresponds to a molecular cross-sectional area of 25.1 ± 

0.4 Å2

/molecule, which is in the range reported for crystalline 4T (23.4-25.6 

Å2

/molecule).

An x-ray study was undertaken using beamline X10B. Measurements were 

performed in reflectivity mode (ν-2ν), resulting in a momentum transfer, qz

, 

along the surface normal (qz

 = 4π/λ sin ν). Analyses of films of 4TP bonded 

to chemically reoxidized Si (HNO3

 oxidation of H-terminated Si; rms roughness 0.21 nm) were performed in air, and both rinsed and unrinsed samples of 

4TP/SiO2

/Si were used. Data were analyzed using dynamical scattering theory. 

Various parameterizations for electron density profiles (n) were used to model 

the reflectivity from the organic layer.

X-ray reflectivities were measured for 4TP/SiO2

/Si after the film was prepared, 

thermally set on the surface (Figure 2a; ο) (both before and after rinsing to 

remove any multiplayer material)(Figure 2a; ), and were plotted against the 

momentum transfer, qz

. Intensities were multiplied by q4 to compensate for 

overall decay. As shown in Figure 2a, measurements made for the 4TP-covered 

surface before rinsing show intensity variations in the range qz ≈ 0.1 Å-1. These 

data indicate a structural feature in direct space on the order of about 2π/0.1 = 

70 Å, indicative of multilayer formation. Reflectivity data from this multilayered structure could not be modeled. In contrast, reflectivity data obtained after 

rinsing (Figure 2b; ) were well-modeled; the solid line in Figure 2b represents 

a best fit based on the inset electron density profile (normalized to the density 

of SiO2

). The striped area in this profile is due to the organic film, which is 

calculated to be 1.8 nm thick. Furthermore, the profile shape for 4TP/SiO2

/Si 

indicates some microscopic disorder exists within the 4TP film.

Figure 2. (a) X-ray reflectivity of 

unrinsed vs. rinsed 4TP/SiO2

/Si and 

(b) profile of rinsed 4TP/SiO2

/Si.

Figure 1. Both (a) and (b), Atomic 

Force Microscopic (AFM) images of 

4TP/SiO2

/Si, and (c) section analysis 

of a film edge.

μm

nm

(a)

(b)

(c)
2-44 CONDENSED MATTER PHYSICS 

XAS Study of Au Supported on TiO2: Influence of Oxidation State and Particle Size on the Catalytic Activity

V. Schwartz, D.R. Mullins, W. Yan, B. Chen, S. Dai, and S.H. Overbury

Chemical Sciences Division, Oak Ridge National Laboratory

We investigated the effect of synthesis, pre-treatment, and reaction conditions on the 

structure, activity, and oxidation state of Au clusters supported on nanocrystalline and 

mesoporous TiO2

. X-ray absorption spectroscopy was applied to correlate the particle size 

and oxidation state with several parameters, such as the pH of the precursor solution, 

Au loading, pre-treatment, and support structure. Catalytic CO oxidation activity data 

were obtained and correlated with the particle size, indicating a decrease of activity 

with particle growth. In-situ studies of Au supported on different allotropic forms of 

TiO2

 revealed that the high activity state corresponds to Au in a fully reduced state. 

Catalysis by small gold particles has been the object of considerable attention in 

the past few years. The reactivity of gold (Au) was found to be tunable for many 

important reactions, such as CO oxidation, through the control of particle size 

and the selection of support materials. It is generally accepted that the Au particle 

structure and the consequent catalytic properties depend on the support used, 

Au loading, the synthesis method, and pre-treatment conditions. Among various supports, reducible oxides, such as TiO2

, are perhaps the most popular due to 

the expected strong metal-support interaction phenomena they exhibit. Our goal 

was to vary many of these factors and characterize the gold supported on titania, 

during preparation and the working state, using x-ray absorption spectroscopy 

(XAFS). We scrutinized Au supported on different allotropic nanocrystalline forms 

of titania and on mesoporous titania material. The XAFS data at the Au LIII-edge 

were collected at beamline X18B in transmission and fluorescence mode using a 

channel cut Si (111) monochromator.

The effect of Au loading on the particle size and reducibility of Au clusters was 

studied using mesoporous TiO2

 as a support. The most important observation was 

that lower Au loadings resulted in bigger Au aggregates with lower reducibility. 

The x-ray absorption near-edge structure (XANES) provided information regarding changes in the Au oxidation state during in-situ pre-treatment and reaction 

conditions. Varying the titania crystalline structure does not seem to affect the 

redox behavior of the Au clusters. 

For instance, during the study of 

Au supported on anatase, a gradual 

reduction of the Au precursor was 

clearly observed when the reaction 

mixture, 1% CO/air, was present at 

room temperature (Figure 1a), even 

though the concentration of oxygen 

is 20 times higher than the reductant. Once fully reduced in H2

, no 

re-oxidation occurs under reaction 

conditions, even after flowing air at 

higher temperatures (Figure 1b). 

BEAMLINE X18B

Funding

U.S. Department of Energy 

Office of Basic Energy 

Sciences

Publication

V. Schwartz, D.R. Mullins, 

W. Yan, B. Chen, S. Dai, and 

S.H. Overbury, "XAS Study 

of Au Supported on TiO2: 

Influence of Oxidation State 

and Particle Size on Catalytic 

Activity," J. Phys. Chem. B,

108, 15782-15790 (2004).

Contact information

Viviane Schwartz 

Surface Science and Catalysis 

Group, Chemical Sciences 

Division, Oak Ridge National 

Laboratory

Email:schwartzv@ornl.gov

Authors 

David Mullins and Viviane Schwartz
SCIENCE HIGHLIGHTS 2-45

These observations imply that reaction conditions also drive the sample irreversibly towards the fully reduced state. Furthermore, a comparison of lightoff 

curves after exposing a single sample to a sequence of pretreatment steps demonstrated that Au is in a highly active state, in the form of Au0

, after treatment in 

H2

 at 150oC. This indicates that oxidized Au is not necessary for high activity.

A comparison of the activity for CO oxidation and the mean particle size 

determined by extended x-ray absorption fine structure (EXAFS) is provided 

in Figure 2. The activity is described using T50, the temperature at which the 

conversion reaches 50%. The particle size is estimated using the hemispherical 

cuboctahedron model given the Au-Au first shell coordination number, which is 

obtained directly from the EXAFS. By these measures, we see that there is a correlation between the Au particle size in the range studied and the activity. Data 

are given for each sample following the treatment in H2

 at 150oC and following 

treatment in O2

 at 300oC. Although the catalytic activities of Au supported on 

these different allotropic forms of titania are comparable after low temperature 

treatments, the stability of the Au-catalysts at higher temperatures is dependent 

upon the TiO2

 structure-type. Au on brookite exhibited no significant particle 

agglomeration and was the most active catalyst after treatment at 300o

C.

Figure 2. Relationship between activity 

on CO oxidation and particle size.

Figures 1A and 1B. XANES of the Au 

supported on anatase after different 

pretreatment protocols.

Photon Energy /eV

Edge Jump /A.U. Edge Jump /A.U.

Photon Energy /eV

R(nm)

T50 (oC)

(A)

(B)
2-46 CONDENSED MATTER PHYSICS 

High Anisotropy CoPtCrB Magnetic Recording Media

M.F. Toney1, E.E. Marinero2, M.F. Doerner3, and P.M. Rice4

1Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center; 2Hitachi San Jose 

Research Center; 3Hitachi Global Storage Technologies; 4IBM Almaden Research Center

Scientists from the Stanford Synchrotron Radiation Laboratory, Hitachi Global Storage Technologies, and the IBM Almaden Research Center have used x-ray diffraction 

(XRD) at the National Synchrotron Light Source to understand the microstructure of 

advanced magnetic recording media and to relate this physical structure to the magnetic 

properties of the media. The studies were conducted on thin film CoPtCrB media with 

platinum (Pt) concentrations varying from 10 to 43 percent. We find that the magnetic 

anisotropy and coercivity of the media, which determine the media’s stability and the 

strength of the field needed to flip the media’s magnetization, increase as Pt concentration increases to about 30 percent, plateau, and then decrease for concentrations greater 

than 40 percent Pt. The x-ray diffraction data show that, with increasing Pt, a facecentered cubic (fcc) cobalt (Co)-alloy phase is progressively formed at the expense of the 

hexagonal close-packed (hcp) Co-alloy, and that this fraction becomes significant for Pt 

concentrations greater than 35 percent. The formation of the fcc phase likely causes the 

behavior in the anisotropy.

The development of thermally stable, small-grain recording media is pivotal to 

achieving magnetic recording densities beyond 200 Gbits/in2

, in accordance with 

consumer demands for better and better recording devices. This requires media 

with high magnetic anisotropy (which determines its stability) and coercivity 

(field-flipping strength). There are several alternative materials under investigation 

that provide adequately high anisotropy, including chemically-ordered alloys, such 

as FePt and CoPt, and rare-earth transition-metal alloys. Another way to achieve 

this goal is to increase the magnetocrystalline anisotropy of current state-of-the-art 

CoPtCrB alloys. The anisotropy is enhanced by substituting Pt atoms for the Co 

atoms in the hexagonal-close packed (hcp) structure. This approach is advantageous because it only requires a relatively small change in the disk manufacturing 

process.

The disk structures consisted of a glass or nickel-phosphorus substrate, followed by 

thin films of a seedlayer, a chromium (Cr)-based underlayer, the 

CoPtCrB media, and a protective carbon coating. The media 

films were 10 to 20 nanometers 

thick, with 10 to 43 percent Pt, 

15 to 17 percent Cr, and nine to 

11 percent boron (B). Figures 

1a and b show, respectively, the 

magnetic anisotropy (Hk) and 

coercivity (Hc) as a function of 

Pt concentration. Large Hk and 

Hc are needed for stable media. As is evident, Hk increases 

BEAMLINES

X20C, X20A

Funding

U.S. Department of Energy 

Office of Science

Publications

M.F. Toney, E.E. Marinero, 

M.F. Doerner, P.M. Rice, “High 

Anisotropy CoPtCrB Magnetic 

Recording Media," J. Appl. 

Phys., 94, 4018 (2003).

M.F. Doerner et al., “Demonstration of 35 Gbit/in2

Media on a Glass Substrate,” 

IEEE Trans. Magn., 37, 1052 

(2001).

Contact information

Mike Toney

Stanford Synchrotron Radiation Laboratory, SLAC

Email:mftoney@slac.stanford.edu

Authors (left to right) 

(top) Mike Toney and Mary Doerner

(bottom) Philip Rice and Ernesto Marinero 
SCIENCE HIGHLIGHTS 2-47

nearly linearly up to about 30 percent Pt, then plateaus, and finally drops above 

about 40 percent Pt; Hc follows a similar trend. The thermal decay rate of our 

CoPtCrB media decreases with increasing Pt (from about 15 percent per decade 

to about one percent per decade), which is consistent with the increase in Hk.

To understand the structural origins of this behavior, x-ray diffraction measurements were done to determine the lattice parameters, the film texture, the 

stacking fault densities and the fraction of fcc regions in the media. An example 

of diffraction scans that pass through the fcc(200) and hcp(1011) peaks are 

shown in Figure 2 for media with 10, 17, 36, and 41 percent Pt. As is evident, 

the intensity of the fcc(200) peak, and hence the amount of fcc CoPtCrB alloy, 

increases significantly with increasing Pt concentration. However, since x-ray 

diffraction is performed over the entire volume of the media, we cannot determine if the fcc regions form isolated grains or are inter-granular. 

The fcc concentration was quantified from the integrated intensity of the 

fcc(200) peak to that of the hcp(1011) peak. This is shown in Figure 1c. From 

these data, it is apparent that the fcc fraction is approximately linear until about 

35 percent Pt. Above this Pt concentration, the fcc fraction increases more 

quickly. The fcc phase of Co has a much lower magnetic anisotropy than the 

hcp phase, suggesting that the increasing presence of the fcc phase with increasing Pt causes the plateau, and then the drop, in Hk that is shown in Figure 1.

Interestingly, for all Pt concentrations studied, both the growth and deformation fault densities (specific defects in the way atoms stack in an fcc crystal) do 

not show a significant trend with increasing Pt concentration, except, perhaps, 

for a slight increase in the growth faults above about 35 percent Pt. This lack of 

an increase in fault density with increasing Pt concentration is rather surprising, 

since high fault concentrations are found in Co-alloys near the fcc-hcp transition region.

Figure 2. Radial diffraction scans 

for several media with varying Pt 

concentration. These diffraction scans 

pass through the fcc(200) and hcp

(1011) peaks. To facilitate comparison, 

the intensity is plotted relative to 

the position of the hcp peak (QB), 

the background scattering has been 

subtracted, and the intensities have 

been normalized to the peak intensity 

of the hcp(1011) peak. The peak 

near Q-QB = -0.2 Å-1 is the media 

fcc(111) diffraction peak overlapping 

the under/seed layer (110) diffraction 

peak, while the peak near -0.4 Å-1

corresponds to hcp(1010).

Figure 1. Anisotropy field (Hk), 

coercivity (Hc), and fcc concentration 

as a function of Pt concentration in (a), 

(b), and (c), respectively. Present media 

have Hc ≈ 4 kilo-Oersteds (kOe) and 

Hk ≈ 20 kOe, while Hk for pure, bulk 

Co is 6.4 kOe. Intensity

Q - QB [Å-1]
2-48 CONDENSED MATTER PHYSICS 

Orbital and Spin Correlations in a Manganite Probed 

With Soft X-ray Resonant Diffraction

K.J. Thomas1, J.P. Hill1, S. Grenier1,2, Y.-J. Kim1, P. Abbamonte3, L. Venema4, A. Rusydi3, 

Y. Tomioka5, Y. Tokura5,6,7, D.F. McMorrow8,9, G. Sawatzky10, and M. van Veenendaal11,12

1Department of Physics, Brookhaven National Laboratory; 2Department of Physics and Astronomy, 

Rutgers University; 3National Synchrotron Light Source, Brookhaven National Laboratory; 4Materials Science Centre, University of Groningen, Netherlands; 5Correlated Electron Research Center, 

National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan; 6Department 

of Applied Physics, University of Tokyo; 7Spin Superstructure Project, ERATO, Japan Science and 

Technology Corporation, Tsukuma, Japan; 8London Centre for Nanotechnology, London, UK; 9Department of Physics and Astronomy, University College London, London, UK; 10University of British 

Colombia, Vancouver, Canada; 11Northern Illinois University; 12Argonne National Laboratory

Soft x-ray resonant diffraction was used to directly probe spin and orbital correlations 

in a near-half doped manganite. The diffraction was performed at the manganese (Mn) 

LII and LIII absorption edges, providing a sensitive spectroscopy method for studying the 

Mn 3d states in the spin and orbitally ordered phases. These measurements suggest that 

the established “checkerboard” model for charge ordering of the Mn3+ and Mn4+ ions 

is too simplistic, and reveal a surprising discrepancy between the orbital and magnetic 

correlation lengths.

In doped manganites of the form RE1-xAx

MnO3 (where RE is a rare earth and A is a 

divalent element), the magnetic coupling between Mn sites depends on the overlap 

of the Mn 3d electron orbitals. Therefore, a complex behavior arises in these materials when the direction of the highest occupied Mn 3d orbital is itself a degree of 

freedom. For example, the Mn 3d orbitals can undergo long-range order, usually 

in association with cooperative distortions of the oxygen octahedra that surround 

the Mn sites. Understanding how the orbital physics drives the overall ground state 

necessitates a direct probe of both orbital and magnetic order.

We used resonant x-ray diffraction to directly probe the magnetic and orbital order 

in the near half-doped manganite Pr0.6Ca0.4MnO3

, for which the proposed spin, 

charge, and orbital ground state is shown in Figure 1. The incident energy at a 

magnetic, (1⁄2 0 0), or orbital, (0 1⁄2 0), Bragg peak was tuned through the Mn LII

and LIII atomic absorption edges (~ 650 eV). At the L-edges, core Mn p1/2 and p3/2

electrons are resonantly excited into unoccupied 3d levels, which enhances the 

Mn sites’ contribution to the diffracted intensity. The strength of the 2p → 3d

resonance at a Mn site depends on the local charge distribution of the occupied 

3d orbitals. This leads to a large contrast between the resonant scattering factors 

on sites 1 and 2 (Figure 1) and a large enhancement of the orbital (0 1⁄2 0) Bragg 

peak. The resonance matrix element also depends on the direction of the spin in 

the 3d levels, resulting in 

magnetic resonant scattering at the antiferromagnetic 

Bragg peak, (1⁄2 0 0). The 

magnetic enhancement at the 

L-edges is truly enormous 

– off resonance, the magnetic 

scattering is too weak to be 

BEAMLINE X1B

Funding

Department of Energy, Division of Materials Science; 

The Netherlands Organization 

for Scientific Research (NWO) 

Spinoza program

Publication

K.J. Thomas, J.P. Hill, S. Grenier, Y-J. Kim, P. Abbamonte, 

L. Venema, A. Rusydi, Y. 

Tomioka, Y. Tokura, D. F. McMorrow, G. Sawatzky, and M. 

van Veendendaal, "Soft X-ray 

Resonant Diffraction Study 

of Magnetic and Orbital Correlations in a Manganite Near 

Half-Doping," Phys. Rev. 

Letts., 92, 237204 (2004).

Contact information

Jessica Thomas

Department of Physics, 

X-ray Scattering Group,

Brookhaven National 

Laboratory

Email:jessica@bnl.gov

Authors (clockwise from left)

John Hill, Peter Abbamonte, Jessica 

Thomas, Young-June Kim, Andrivo 

Rusydi, and Stephane Grenier
SCIENCE HIGHLIGHTS 2-49

observed in these materials – and thus provides a unique opportunity to directly 

compare the orbital and magnetic correlations in a manganite.

Figure 2a shows the orbital and magnetic resonant line shapes (energy scans at 

fixed Q). The features in the line shapes are the different excited states in the 3d

band, which are probed with increasing incident energy. The 3 eV shift in spectral weight and the large difference in intensity between the orbital and magnetic spectra suggests that the checkerboard charge-ordered picture in Figure 1

is too simple. Furthermore, longitudinal scans through the orbital and magnetic 

Bragg peaks show that the orbital peak is approximately two times wider than 

the magnetic peak (Figure 2b). This suggests that the orbital correlations are 

shorter-ranged than the magnetic correlations, a result that appears at odds with 

orbitally driven magnetic order.

Figure 2. (a) Resonant diffraction 

line shapes at fixed Q at the orbital (0 

1⁄2 0) position (black curve) and the 

magnetic (1⁄2 0 0) (red curve). Note 

that the magnetic resonant line shape 

is peaked ~ 3 eV below the orbital 

line shape. (b) Longitudinal Q scans 

through the magnetic and orbital 

Bragg peaks, at the same energy. 

Figure 1. Schematic of the ground state 

exhibiting charge-orbital-magnetic 

order in Pr0.6Ca0.4MnO3

, showing only 

the Mn sites in the Mn-O plane. In 

Pr0.6Ca0.4MnO3

, the charge order is 

modeled as a checkerboard of Mn3+

and Mn4+ ions and only the Mn3+ ions 

have the orbital degree of freedom. 

(The symmetry of the highest occupied 

electron orbital is indicated by a blue 

lobe). The orbital zig-zag chains couple 

the Mn sites ferromagnetically along 

the chain and antiferromagnetically 

between the chains. The orbital order 

doubles the unit cell along b, leading 

to (0 1⁄2 0) type reflections, while the 

spin order doubles the unit cell along a, 

leading to (1⁄2 0 0) reflections.

Highest Occupied 3d orbital

Resonant line shapes

Normalized Counts

Energy (eV)

Q-scans (E = 645 eV)

Normalized Counts

H/K (r.l.u.)

0.48 0.49 0.50 0.51 0.52 0

0.6

1.2

0

0.4

1.2

630 640 650 660 670 680

(a)

(b)

0.8
2-50 CONDENSED MATTER PHYSICS 

Melting Point Enhancement of a Self-Assembled 

Monolayer Induced by a Van-Der-Waals-Bound 

Capping Layer

F. Schreiber1,2, M.C. Gerstenberg2, H. Dosch1, and G. Scoles2

1Max Planck Institut für Metallforschung and Institut für Theoretische und Angewandte Physik at 

the Universität Stuttgart; 2Princeton Materials Institute, Princeton University

Using in-situ surface x-ray diffraction, the temperature dependence and thermal 

stability of a self-assembled monolayer (SAM) of decanethiol, sandwiched between the 

Au(111) substrate and a van-der-Waals-bound capping layer of PTCDA (3,4,9,10-

perylenetetracarboxylic dianhydride), are measured. While the bare SAM on Au(111) 

undergoes a melting transition at 100°C, this transition temperature is raised to 115°C 

if the SAM is capped by PTCDA. Possible mechanisms and implications of this capping-layer-mediated melting point enhancement are discussed.

Phase transitions in reduced geometry are a very fundamental issue in condensed 

matter science, and even the seemingly simple case of hard discs in two dimensions 

continues to be a matter of discussion. A particularly interesting situation arises if a 

thin film is subject to interactions on both the bottom and top interfaces. 

For phase transitions in complex low-dimensional organic materials, the internal 

degrees of freedom of the molecules, which are an important characteristic of organics, have to be considered and a very rich phase behavior, as seen, for example, 

in Langmuir films (on liquid surfaces), can be found. Among the well-defined, 

crystalline two-dimensional organic thin films chemisorbed on a solid substrate, 

self-assembled monolayers (SAMs) are probably the best characterized systems, and 

the phase behavior of the archetypal SAM system (alkanethiols on Au(111)) as a 

function of coverage and temperature has been thoroughly studied.

Here we present the case of rather soft boundary conditions for an organic monolayer, namely a SAM of decanethiol on Au(111) capped by a van-der-Waals-bound 

crystalline multilayer of PTCDA, a model compound for organic molecular beam 

deposition (Figure 1).

The SAM melting curve is obtained from the area under a Bragg reflection as a 

function of temperature, T. Compared to the uncapped SAM, we found that the 

melting temperature of the PTCDA-capped SAM is enhanced by about 15°C, 

while the character of the transition appears unaltered (Figure 2). Note that 

PTCDA remains solid to well above 200°C – i.e., at the SAM melting T it is still a 

solid capping layer.

Since the PTCDA layer is only coupled 

to the SAM itself, it cannot directly 

exert a significant pressure on the SAM. 

Therefore, we believe that the mechanism for the melting point enhancement 

observed here is different from a pressure-induced scenario. We note that the 

system studied here does not correspond 

to a confined-melting phenomenon in 

BEAMLINE X10B

Funding

Deutsche 

Forschungsgemeinschaft 

(DFG); Max-PlanckGesellschaft; Air Force 

Office of Scientific Research; 

National Science Foundation

Publication

F. Schreiber, M.C. 

Gerstenberg, H. Dosch, 

and G. Scoles, "Melting 

Point Enhancement of a 

Self-Assembled Monolayer 

Induced by a Van-DerWaals-Bound Capping Layer," 

Langmuir (Letters), 19, 

10004 (2003).

Contact information

Frank Schreiber 

Physical and Theoretical 

Chemistry Laboratory, 

University of Oxford

Email:frank.schreiber@chem.ox.ac.uk

Frank Schreiber
SCIENCE HIGHLIGHTS 2-51

the conventional sense of a hard confinement, since the capping layer is connected only to the SAM and thus is not at a fixed height above the substrate. In 

fact, one way for the SAM to gain space and thus reduce its density during the 

phase transition is to reduce the tilt angle of the chains, and thereby increase 

the effective chain-to-chain distance in the plane. The exact need for this extra 

volume is not known, but it is clear that the capping layer would not impose 

serious restrictions on this change of the SAM’s effective height, due to the weak 

interaction of the capping layer with the substrate over this distance. Nevertheless, one should expect that the PTCDA layer at least tends to reduce the 

fluctuations along the surface normal, which may have an impact on the phase 

transition.

In addition, the capping layer can have an effect on the lateral interactions within the SAM, in that it tends to “clamp” the chain termina to certain positions in 

the corrugated potential of the flat-lying PTCDA molecules and, thereby, effectively stabilizes a certain chain-to-chain distance. In this context, it is important 

to note that PTCDA grows with a well-defined epitaxial relationship, implying 

that the lateral variation of the PTCDA-SAM interaction potential does not 

average out. While it is difficult to quantify these interactions, the impact of the 

capping layer on the fluctuations both along the normal and on the (indirect) 

in-plane interaction appear to be plausible mechanisms for the melting point 

enhancement.

Figure 1. Schematic of the layered 

structure of the sample (Au(111) 

substrate / SAM / PTCDA).

Figure 2. Melting curve as determined 

from the temperature dependence of 

the Bragg intensity (integral of the 

hexagonal in-plane reflection) of the 

SAM with and without the PTCDA 

capping layer. For the capped SAM, 

the melting temperature is enhanced 

by ~ 15 K.
2-52 CONDENSED MATTER PHYSICS 

Measurement of Ti, Ta and Sc Off-Center Displacements in Relaxor Ferroelectric PST-PT

A.I. Frenkel1, D.M. Pease2, J. Giniewicz3, E.A. Stern4, D.L. Brewe4,5, M. Daniel2, and 

J.Budnick2

1Yeshiva University; 2University of Connecticut; 3Indiana University of Pennsylvania; 4University of 

Washington; 5Advanced Photon Source, Argonne National Laboratory

We probed titanium (Ti), tantalum (Ta), and scandium (Sc) environments in the 

(1-x)Pb(Sc,

Ta)O3 – xPbTiO3 relaxor ferroelectric (PST-PT), which displays variable 

order–disorder, relaxor, a mixed phase region, and normal ferroelectric behaviors as x 

is increased. The abrupt structural phase transition from rhombohedral to tetragonal is 

observed by x-ray diffraction at x = 0.45. According to x-ray absorption fine structure 

(XAFS) studies, the structure around Ta, Sc, or Ti atoms changes differently with x and 

there are no abrupt changes at any concentration. No displacements of Ta or Sc atoms 

from their oxygen octahedron centers were observed. But surprisingly, we find that 

Ti is displaced along the (111) direction for x = 0.05. However, it gradually changes 

direction from (111) to (001) as x increases. We suggest that PST-PT consists of mixed 

regions, some characterized by a (111) Ti displacement and others by a (001) displacement. The displacement averaged over all regions becomes more weighted toward (001) 

as x increases. 

Relaxor ferroelectrics display a diffuse temperature dependence of their polarization-related macroscopic properties. The origin of this behavior lies in the interactions of polarized entities at the nanoscale. Relaxors typically belong to a class of 

“oxygen-octahedra compounds,” in which six oxygen ions surround a particular 

transition metal ion, such as Ti, Ta, or Sc (Figure 1). The unique characteristics of 

the relaxor ferroelectric (1-x) Pb(Sc1/2Ta1/2)O3 – x PbTiO3

 (PST-PT) are revealed 

when one traverses a variety of compositions, x. A variety of thermally “adjustable” 

states of structural ordering, Curie temperatures, and material properties are accessible for these materials. PST-PT is attractive for device applications, and also as a 

model to explore the nature of relaxor ferroelectrics.

The structure determined by x-ray diffraction (XRD) was rhombohedral for low x

values, but abruptly becomes tetragonal for x = 0.45. The Ta L3

-edge XAFS data of 

the same samples were measured at beamline X11A. The Sc and Ti K-edges were 

measured at the Pacific Northwest Consortium - Collaborative Access Team beamlines at the Advanced Photon Source. 

At low x values, an energy dispersive 

detector is required to separate Ti 

Kα fluorescence photons from the 

Sc Kα photons that dominate the 

fluorescence background. We used 

a log-spiral of revolution analyzer 

designed by Doug Pease and Joe 

Budnick, recently improved by the 

addition of the annular ion chamber, 

designed by Ed Stern. We know of 

no other detector setup that could 

BEAMLINE X11A

Funding

U.S. Department of Energy

Publication

A.I. Frenkel et al., “Concentration-Dependent Short 

Range Order in Relaxor Ferroelectric (1-x)Pb(Sc,Ta)O3

- xPbTiO3,” Phys. Rev. B, 70, 

014106 (2004).

Contact information

Anatoly I. Frenkel

Physics Department 

Yeshiva University

Email:Anatoly.Frenkel@yu.edu

Anatoly Frenkel
SCIENCE HIGHLIGHTS 2-53

successfully separate the dilute Ti fluorescence from the otherwise overwhelming 

Sc fluorescence photons without saturating the detector, and with much more 

intensity than any other crystal monochromator.

Ti K-edge x-ray absorption near-edge structure (XANES) data of all the samples 

(Figure 2, left) have a feature “A” located in the region corresponding to the 

dipole-forbidden 1s-3d transition. In order to contribute to the XANES data, 

the p-character of the final state of the photoelectron has to be added in the 

solid. That may occur due to, for example, hybridization between Ti 3d and O 

2p orbitals that is enhanced if Ti is displaced away from the inversion symmetry 

center. The presence of a large peak “A” is, therefore, a signature of the off-center displacements of Ti atoms. The area under the peak can be used to quantify 

the off-center displacement d of the Ti atom (A ∝ d2

 ). In the Ti K-edge XANES 

data of all the samples (Figure 2, left), the intensity of the signal in this region 

is much larger than in the reference cubic EuTiO3

 system. For all x < 1, we 

obtained d ~ 0.23(2) Å. We found that this large Ti atom displacement is in 

marked contrast with Ta and Sc atom behaviors, where no measurable displacement from the oxygen octahedron centers (Figure 1A) was found by their 

EXAFS or XANES (Figure 2, left (inset)) analyses. 

The EXAFS analysis (Figure 2, right) revealed that Ti atoms were displaced 

along the (111) cubic direction from x = 0.05 (Figure 1B). However, this 

displacement gradually changes direction from (111) to (001) as x increases 

(Figure 1C). 

These results allow two interpretations. First, the Ti atom displacement direction changes gradually from (111) to (001) as x increases, going through the 

intermediate orientations. The second interpretation, supported by Maaskant 

and Bersuker (MB) theory, allows no intermediate orientation between the 

(111) and (001) directions. In the framework of the MB model, we propose that 

the PST-PT system consists of mixed regions, some having (111) Ti displacement and others having (001) displacement. The displacement averaged over all 

regions becomes more weighted toward (001) as x increases. 

Our work resulted in the atomic-level scenario of the structural transformations 

in PST-PT. We found that the changes in the local structure could not be simply 

interpolated from the average structure data: The independent, element-specific 

measurements were required to elucidate the structure around each atomic species. Our results give the first experimental observation of the 111-displacement 

direction of a Ti atom in the ferroelectric perovskite system.

Figure 1. Perovskite pseudo-cubic 

ABO3

 unit cell (A=Pb, B=Ta, Sc,Ti). 

(A) The Ta and Sc atoms were shown 

to be approximately in the cell center. 

Arrow shows different directions of Ti 

atom displacements obtained by XAFS 

for (B) x=0.05 and (C) x=1.

Figure 2. Left: XANES spectra of 

Ti K-edge in (PST)1-x(PT)x

 samples. 

Feature A denotes the energy region of 

the dipole-forbidden 1s-3d transition. 

(A) The inset shows the featureless 

1s-3d transition region in Sc K-edge 

XANES. Right: the Ti K-edge EXAFS: 

Fourier transform magnitudes of 

kχ(k) in (PST)1-x(PT)x

 samples. 

Shown by arrows are groups of Ti-O 

distances that correspond to either 

(111) or (001) displacement of the 

Ti atom from the center of the TiO6

octahedron, depicted schematically in 

Figure 1 (B) or (C), respectively.

(A)

(B)

(C)

Energy, eV r, Å

Normalized absorption coefficient

FT Magnitude, Å-2
2-54 GEOLOGY AND ENVIRONMENTAL SCIENCES 

Time-Resolved Diffraction Studies of Ion Exchange: K+

and Na+

 Exchange into Synthetic Aluminogermanate 

Molecular Sieve with the Gismondine Topology

A.J. Celestian1, J.B. Parise1,2, C. Goodell1, A. Tripathi3, and J. Hanson4

1Stony Brook University, Department of Geosciences; 2Stony Brook University, Department of 

Chemistry; 3Texas A&M, Department of Chemistry; 4Brookhaven National Laboratory, Department 

of Chemistry

Time-resolved in situ x-ray diffraction was used to determine how ions are exchanged in 

the potassium (K+

) and sodium (Na+) forms of the aluminogermanate molecular “sieve” 

(AlGe-GIS) with the topology of the gismondine (GIS) family of zeolite minerals. The 

AlGe-GIS structure is of particular interest due to its highly flexible framework and its 

use in industrial processes. This study illustrates the ion site-selective exchange pathways 

that are created during the substitution process and also determines possible ion exchange mechanisms. Bond valence calculations indicated that the preferred charge-balancing cation in the GIS structure is K+

, due to its larger framework bonding coordination. Experiments were conducted at beamline X7B.

Zeolites are nanoporous minerals built from a fully corner-shared framework of 

tetrahedra. In the gismondine (GIS) family of zeolites, the synthetic aluminogermanate (AlGe-GIS) framework is composed of aluminum (Al3+) and germanium 

(Ge4+) ions, resulting in a net negative (-1) charge for every Al3+ ion in the framework. Therefore, extra-framework cations must be incorporated to charge-balance 

the structure and maintain electro-neutrality (Figures 1 and 2). These extraframework cations are found in the large channels of the zeolitic framework and 

can be substituted for other cations. Due to the size, shape, and composition of 

the zeolitic channels, these materials behave as molecular “sieves” that selectively 

absorb and desorb cations – a property often used in environmental and industrial 

applications.

The information obtained from time-resolved in situ x-ray diffraction measurements enables us to directly follow the ion exchange process. The exchange of potassium ions (K+

) into Na-AlGe-GIS proceeded to 90% (± 1%) completion within 

the time frame of the experiment (Figures 3 and 4). During the first 10% of K+

substitution, K+

 only entered the [-101] channel (Figures 1 and 4) of the NaAlGe-GIS structure. After 10%, exchange site-specific substitution could no longer 

be followed. In the reverse exchange (Na+

 into K-AlGe-GIS; data not shown), a 

gradual growth of the Na-AlGe-GIS phase was observed and stopped after approximately 10% substitution (Figure 4) in the time frame of the experiment. Sitespecific ion exchange was not 

observed during the substitution 

of Na+

 into K-AlGe-GIS.

The affinity of the GIS framework for the K+

 ion can be 

explained through bond valence 

analysis. In K-AlGe-GIS, K conducts most of its bond valence 

electrons to the O2- framework 

BEAMLINE X7B

Funding

National Science Foundation Division of Materials 

Research

Publication

A.J. Celestian, J.B. Parise, 

C. Goodell, A. Tripathi, 

and J. Hanson, "Time 

Resolved Diffraction Studies of Ion Exchange: K+

and Na+ Exchange into 

(Al, Ge) Gismondine (GIS) 

Na24Al24Ge24O96•40H2O and 

K8Al8Ge8O32•8H2O," Chem. 

of Mat., 16(11), 2244-2254 

(2004).

Contact information

Aaron J. Celestian

Center for Environmental and 

Molecular Sciences, Department of Geosciences, Stony 

Brook University

Email: aaron.celestian@stonybrook.edu

Authors (left to right) 

John Parise and Aaron Celestian
SCIENCE HIGHLIGHTS 2-55

Figure 4. Plot of K+ occupancy as a function of time during 

forward and reverse ion exchanges in AlGe-GIS. Open circles 

represent structure refinements where site-specific occupancies 

were refined. Time is normalized due to different experimental 

time frames.

(approximately 51% of its total valence), thus achieving direct framework 

charge balancing. In Na-AlGe-GIS, Na+

 conducts most of its bond valence 

electrons through interstitial water molecules (approximately 71% of its total 

valence). This effectively reduces the amount of direct charge balancing that Na+

can accomplish and results in a less stable bonding configuration relative to the 

K+

 bonding environment.

Figure 1. Crystal structure of Na-AlGeGIS Na24Al24Ge24O96•40 H2

O in the 

C2/c space group. The 8-member ring 

channel is filled with Na+

 (yellow) and 

water molecules (blue). Unit cell drawn 

in black. View is down the [-1 0 1] 

direction.

Figure 2. Crystal structure of K-AlGeGIS K8

Al8Ge8O32•8H2O in the I 

2/a space group. The 8-member ring 

channels are filled with K+

 (orange) and 

water molecules (blue). The unit cell is 

drawn in black. View is down [0 0 1].

Figure 3. In situ time resolved diffraction patterns (selected 2-theta 

range shown for clarity). Each diffraction pattern is collected for 60 

sec with 2.5 min between each pattern. The onset of ion exchange 

is seen approximately 60 min from the start of the experiment. 

New peak growth at 2-theta 16° and 16.75° indicate the K-AlGeGIS phase forming. Top right insert shows the Iterative Targeted 

Transformation Factor Analysis (ITTFA), which follows peak 

position and intensity over all the diffraction patterns. ITTFA 

serves as an indicator of when subtle changes in the diffraction 

patterns occur and identifies those patterns for subsequent 

structure refinements.

Normalized Time

fractional occupancy of K+

2-theta (*)

Intensity

Estimated Peak Evolution

Time (min)
2-56 GEOLOGY AND ENVIRONMENTAL SCIENCES 

Localization and Speciation of Chromium in 

Subterranean Clover Using XRF, XANES, and EPR 

Spectroscopy

J.A. Howe1, R.H. Loeppert1, V.J. DeRose2, D.B. Hunter3, and P.M. Bertsch3

1Department of Soil and Crop Sciences, Texas A&M University; 2Department of Chemistry, Texas 

A&M University; 3Advanced Analytical Center for Environmental Sciences, Savannah River Ecology 

Laboratory, University of Georgia

Scientists from Texas A&M University and the University of Georgia have used x-ray 

absorption near edge spectroscopy (XANES) and synchrotron x-ray fluorescence (SXRF) 

microprobe spectroscopy at beamline X26A, as well as electron paramagnetic resonance 

(EPR) spectroscopy, to investigate the absorption, localization, and transport of chromium (Cr) in plants. These studies have shown that the reduction of Cr(VI) to Cr(III) 

and the immobilization or compartmentalization of Cr are important detoxification 

mechanisms used by the plant. 

The industrial use and release of chromium compounds into the environment has 

led to the contamination of water and soil, and therefore to associated environmental and health concerns. In soils, Cr occurs predominately in the +3 and +6 

oxidation states. The more soluble and more toxic +6 state presents the greater 

environmental concern. In efforts to remediate soils contaminated with low levels 

of Cr(VI), the use of plants to extract or immobilize the metal (phytoremediation) 

has been proposed. But before phytoremediation can be performed effectively and 

safely, it is necessary to understand the mechanisms of Cr uptake, translocation, 

tolerance, and bonding by plants, and the conditions under which Cr is absorbed 

and/or immobilized. 

Nondestructive techniques, such as electron paramagnetic resonance (EPR) spectroscopy, x-ray absorption near edge spectroscopy (XANES), and synchrotron x-ray 

fluorescence (SXRF) microprobe spectroscopy, are useful for the chemical investigation of Cr, to minimize changes in the metal’s chemistry that might occur with 

destructive techniques. The objectives of this study were to localize Cr in the leaf 

using SXRF microprobe spectroscopy, determine the oxidation state of Cr in the 

plant using EPR and XANES, and evaluate possible modes of Cr complexation in 

the plant using EPR. These analyses were performed on subterranean clover plants 

exposed to various concentrations of inorganic Cr(III), Cr(VI), and Cr(III)-organic 

complexes.

Localization of the translocated 

Cr in leaves using SXRF microprobe spectroscopy indicated two 

distinct Cr accumulation patterns. At the low Cr(VI) treatment concentration (0.04 mM), 

Cr accumulated primarily at leaf 

margins with some slight accumulation in the veins (Figure 

1A). This result corresponded 

BEAMLINE X26A

Funding

U.S. Department of Energy, 

Environmental Remediation Sciences Division in the 

Office of Biological and Environmental Research; U.S. 

Department of Energy and 

the University Research Alliance, formerly the Amarillo 

National Research Center 

Publication

J.A. Howe, R.H. Loeppert, 

V.J. DeRose, D.B. Hunter, and 

P.M. Bertsch, "Localization 

and Speciation of Chromium 

in Subterranean Clover using XRF, XANES, and EPR 

Spectroscopy," Environ. Sci. 

Technol., 37, 4091 (2003).

Contact information

Richard H. Loeppert

Soil and Crop Sciences 

Department, Texas A&M 

University

Email: r-loeppert@tamu.edu

Authors (left to right) 

Vickie DeRose, Julie Howe, and Richard 

Loeppert
SCIENCE HIGHLIGHTS 2-57

with visual observations of red pigmentation at the leaf margin. At the high 

Cr(VI) treatment concentration (1.6 mM), Cr accumulation was observed in 

or around the veins (Figure 1B). This accumulation corresponded to regions 

of brown coloration and tissue damage along the leaf veins. The high Cr(VI) 

concentration resulted in the death of the plants within seven to 10 days. 

The oxidation state of Cr in the plant was determined using both EPR and 

XANES. This combination of techniques was used because the +6 oxidation 

state is not detectable using EPR, but is easily identifiable as a pre-edge peak in 

the Cr K-edge XANES spectrum. In plants grown with the low Cr(VI) treatment concentration and with various Cr(III) treatments (i.e., CrCl3

, Cr(III)-

EDTA, Cr(III)-citrate, and Cr(III)-oxalate), the Cr in the plant was only 

observed in the +3 oxidation state. Furthermore, the EPR spectra indicated the 

occurrence of Cr(III)-organic complexes, except in the case of the plants grown 

in CrCl3

 and the low Cr(VI) treatment. The EPR spectra from these two treatments indicated the presence of a precipitated Cr(OH)3

 phase in or on the roots. 

EPR spectra of both the roots and shoots of plants grown in a high Cr(VI) 

treatment concentration revealed distinct Cr(V) signals and additional signals of 

Cr(III)-organic complexes in the leaf. Using XANES, Cr(VI) was only positively 

identified in the roots of plants grown with the high Cr(VI) treatment concentration (Figure 2). Successive scans revealed the rapid disappearance of this 

peak, indicating the rapid reduction of Cr(VI) (Figure 2F, 2G). 

Results from this study provide information on how plants tolerate Cr(VI). This 

tolerance must involve the complete reduction of highly toxic Cr(VI), Cr(V), 

or Cr(IV) to the considerably less toxic Cr(III), and either the immobilization 

or compartmentalization of Cr(III). Three processes of immobilization and 

compartmentalization were identified: (i) the precipitation of a Cr(III) hydroxide phase at the root, (ii) the complexation of Cr(III) and its probable storage as 

Cr(III)-organic complexes, and (iii) the transport of Cr(III)-organic complexes 

to the leaf margins, where the Cr is less disruptive to plant metabolic processes.

Figure 1. SXRF microprobe images 

of the relative Cr concentrations in 

transects of subclover leaves grown 

in (A) 0.04 mM Cr(VI) for 21 days 

and (B) 1.6 mM Cr(VI) for 4 days. 

The rectangle on the subclover leaflet 

at the top of the figure indicates the 

approximate location of the transect.

Figure 2. XANES Cr K-edge spectra of 

5% (w/w) standards of (A) Cr(VI) and 

(B) Cr(III), fresh subclover (C) leaf and 

(D) root tissue grown with 0.04 mmol 

L-1 Cr(VI), fresh subclover (E) leaf and 

(F, G) root tissue grown with 1.6 mM 

Cr(VI). Spectra F and G are successive 

scans at the same position on the 

root indicating the rapid reduction of 

Cr(VI).

Subclover leaflet

X-ray energy relative to pre-edge (eV)

Normalized intensity of Cr Kα counts
2-58 GEOLOGY AND ENVIRONMENTAL SCIENCES 

Quantifying Hazardous Species in Particulate Matter 

Derived from Fossil-Fuel Combustion

F.E Huggins1, G.P. Huffman1, W.P. Linak2, and C.A. Miller2

1Consortium for Fossil Fuel Science, Department of Chemical and Materials Engineering, University 

of Kentucky; 2National Risk Management Research Laboratory, U.S. EPA

X-ray absorption fine structure (XAFS) spectroscopy at beamlines X18B and X19A was 

used to investigate and assess the hazards posed to human health from the presence of 

potentially toxic species in airborne particulate matter (PM) released during the combustion of fossil fuels. XAFS spectroscopy was combined with a leaching protocol and 

used to quantify the oxidation states of As and Cr in PM from coal combustion and the 

presence of Ni sulfides in PM from residual oil combustion. Such speciation information 

is needed in order to assess the potential bioavailability and health hazards posed by 

metals and other species in airborne PM. 

In 1997 the U.S. Environmental Protection Agency (U.S. EPA) promulgated new 

regulations regarding exposure to fine airborne particulate matter, based on the 

results of several major epidemiological studies that demonstrated an association 

between the amount of fine particulate matter (PM) in the ambient atmosphere 

and various respiratory and cardiovascular health problems in humans. The new 

regulations propose keeping existing limits on emissions of particulate matter less 

than 10 μm in size (PM10) and including new limits on finer PM, viz., the fraction less than 2.5 μm in size (PM2.5). The additional regulations place increased 

emphasis on particle emissions from combustion processes that typically generate 

very fine particles (0.01 – 2.5 μm) in comparison to mechanical processes based on 

comminution and fracture processes, 

which tend to generate coarser particles, 

usually greater than 2.5 μm in size. 

Major combustion processes thought 

to contribute significantly to ambient PM2.5 include fossil-fuel (e.g. coal, 

residual oil) combustion for electrical 

power generation, biomass combustion (e.g. crop-clearing fires, forest fires, 

wood-stove combustion), and internal 

combustion engines powered by liquid 

(diesel, gasoline) fuels.

Although the link between the PM2.5

content of the atmosphere and adverse health effects is well established, 

the actual mechanism of injury is still 

poorly understood and a multitude of 

different theories are being pursued. 

Another important research area is how 

to determine the relative proportions 

of different source contributions to the 

ambient PM2.5 fraction.

BEAMLINES

X18B, X19A

Funding

National Science Foundation 

Publication

F.E. Huggins, G.P. Huffman, 

W.P. Linak, and C.A. Miller, 

“Quantifying Hazardous 

Species in Particulate Matter 

Derived from Fossil-Fuel 

Combustion,” Environ. Sci. 

and Tech., 38, 1836-1842 

(2004).

Contact information

Frank E. Huggins

Research Professor, CME/

CFFS University of Kentucky

Email: fhuggins@engr.uky.edu

Authors (left to right) 

(top) Frank Huggins and Jerry Huffman 

(bottom) Bill Linak and Andy Miller
SCIENCE HIGHLIGHTS 2-59

In this work, we used XAFS spectroscopy at beamlines X18B and X19A to investigate the speciation of hazardous metals in PM2.5 derived from the combustion of coal and residual oil. Coal and residual oil samples were combusted in 

large laboratory-scale combustion units at the U.S. EPA’s National Risk Management Research Laboratory, and two fractions of PM – a coarse PM2.5+ fraction and a fine PM2.5 fraction – were separated using a cyclone with a cut-point 

of 2.5 μm. The PM samples were then subjected to leaching in deionized water 

and hydrochloric acid, and both bulk samples and residues from the leaching 

experiments were investigated by XAFS spectroscopy. The combination of XAFS 

spectroscopy and leaching studies not only provides the means for quantifying the presence of various toxic species in PM samples, but can also provide 

important information regarding the solubility, and hence potential bioavailability, of such species. For coal combustion, the oxidation states of As and Cr 

in PM are important issues, whereas, for residual oil combustion, it is important 

to be able to establish the presence or absence of nickel sulfides. Our results 

show that the toxic species are distributed unequally among PM samples from 

different sources. For example, in coal PM, the toxic oxidation state of Cr, viz. 

Cr(VI), comprises between 10% and 40% of the total Cr in PM2.5 derived from 

low-sulfur, lower-rank coals from the western United States. However, it is not 

usually detected (<5% of the total Cr) in PM2.5 from the combustion of higher 

sulfur coals from the eastern United States. In PM from residual oil combustion, 

nickel sulfides were more prevalent in coarse PM2.5+ than in fine PM2.5 fractions 

(Figure 1). Similar information regarding the occurrence of individual hazardous species in PM samples collected for epidemiological or toxicological studies 

should be of significance for testing specific mechanisms of injury arising from 

exposure to PM.

The study summarized here is just one aspect of a large NSF-supported effort, 

involving groups at the Universities of Kentucky, Missouri and Utah in collaboration with groups at U.S. EPA, Ford Motor Company, EPRI, the Lovelace 

Respiratory Research Institute, etc., that is designed to provide detailed characterization of PM derived from combustion of fossil fuels in both stationary and 

mobile combustion processes.

Figure 1. Ni XANES spectra for fine 

(PM2.5) and coarse (PM2.5+) particulate 

matter fractions from combustion of 

a low-sulfur No. 6 residual oil and 

for the residues obtained from them 

by aqueous leaching. The spectra are 

dominated by nickel sulfate in the 

original, as-received state, but, as a 

result of aqueous leaching, the Ni 

spectra have dramatically changed 

and indicate that the insoluble Ni is 

predominantly present as a nickelbearing spinel in the PM2.5 leaching 

residue and as a nickel sulfide in the 

coarse PM2.5+ leaching residue. The 

zero-point of energy corresponds to 

8333 eV.

Energy, eV

Normal Absorption
2-60 GEOLOGY AND ENVIRONMENTAL SCIENCES 

Arsenic Speciation and Reactivity in Poultry Litter

Y. Arai1, A. Lanzirotti2, S. Sutton2,3, J.A. Davis1, and D.L. Sparks4

1

U.S. Geological Survey, Water Resource Division; 2Consortium for Advanced Radiation Sources, 

University of Chicago; 3

Department of Geophysical Sciences, University of Chicago; 4Department of 

Plant and Soil Sciences, University of Delaware

Recent U.S. government action to lower the Maximum Concentration Levels of total 

arsenic (As) in drinking water (currently 10 parts per billion) has raised serious concerns about the agricultural use of As-containing biosolids such as poultry litter (PL). 

Microfocused (μ) synchrotron x-ray fluorescence (SXRF) and μ-x-ray absorption near 

edge structure spectroscopic (XANES) analyses showed that As(III and V) was always 

concentrated in abundant needle-shaped microscopic particles (approximately 20 μm 

x 850 μm) that are associated with Ca, Cu, and Fe, and to a lesser extent with S, 

Cl, and Zn. Post-edge XANES features of litter particles are dissimilar to those of the 

organo As(V) compound in poultry feed (i.e. roxarsone), suggesting possible degradation/

transformation of roxarsone in the litter and/or in poultry digestive tracts. Our research 

results raise concerns about long-term PL amendment effects on As contamination in 

surrounding soil-water environments.

In the last four decades, the poultry industry has become one of the major livestock 

operations in the middle Atlantic states of the U.S. While PL has been recycled 

on agricultural lands as an N amendment, much of the trace metal(loid) input 

(total annual As inputs between 20 and 50 metric tons) into the environments has 

been neglected. The origin of As in PL is an organo-As(V) compound (3-nitro-4-

hydroxyphenylarsonic acid (roxarsone)) for coccidiosis control in the poultry feed 

(approximately 25 - 50 mg of roxarsone is mixed per kilogram of feed). Feed spillage and digested materials have increased the mean total As concentration in PL to 

14 - 76 mg kg-1. At present, annual total metal(loid) inputs on agricultural lands 

via PL amendments are not specifically regulated at either the state or federal levels, 

and continuous PL amendment effects on As contamination in Atlantic coastal 

plain soil/water environments remain virtually unknown. To better understand the 

reactivity of As from PL to surface and ground water, the As solid-state speciation 

in the PL was investigated using SXRF and μ-XANES at beamline X26A and the 

Advanced Photon Source. 

A photomicrograph of one of 17 As-rich particles (approximately 20 x 850 μm) 

found in an approximately 200 mm2

 area (Figure 1) shows the distinctive elongated particle morphology. The XRF analyses at the center of this particle (indicated 

by a black open square) show that elevated As levels are associated with Ca, Fe, and 

Cu, and to a lesser extent with Zn, Ti, Cl, and S (Figure 1). A total of 17 similar 

particles were found in nearly half of the 

thin section (about 200 mm2

). Elemental 

maps (Figure 2) generated from the region 

in the white open square in Figure 1 also 

show that the distribution of As is highly 

associated with Cl and Cu. Assuming no 

significant changes in the sample thickness and the density of the particle, the 

flux-normalized fluorescence counts in 

BEAMLINE X26A

Funding

National Science Foundation 

U.S. Department of Energy

Publication

Y. Arai, A. Lanzirotti, S. 

Sutton, J.A. Davis, and D. 

L. Sparks, “Arsenic Speciation and Reactivity in Poultry 

Litter,” Environ. Sci. & Tech., 

37, 4083–4090 (2003).

Contact information

Yuji Arai

U.S. Geological Survey, 

Water Resource Division

Email: yarai@usgs.gov

Yuji Arai
SCIENCE HIGHLIGHTS 2-61

Figure 2 can be correlated to relative elemental concentrations for each element. It is possible that the formation of mixed metal-As, As-S precipitates, 

and/or As sorption complexes on metal oxide precipitates were occurring in 

the litter and/or during poultry digestion. Our preliminary microfocused x-ray 

diffraction analyses at the NSLS showed no distinctive diffraction patterns on 

these particles, indicating the amorphous nature of the As-containing particles.

The μ-XANES measurements were performed on the particle in Figure 1 (i.e. 

particle A in Figure 3b) and several additional As-containing particles (only 

particles B and C are shown in Figure 3a and 3b). They all produce similar 

XRF spectra as particle A (data not shown). Wide whiteline peaks are consistently observed in particles A-C (Figure 3a and 3b), indicating the presence of 

mixed As(III and V) oxidation states in these particles. Although the absorption 

energy position at ≈11871 eV might indicate the presence of the orpiment-like 

As(III)-sulfide species, the exact As(V) species are difficult to elucidate based 

on the absorption edge LC fit, since the energy positions for different As(V) 

standards closely occur within 0.8 eV (Figure 3a). Post-edge XANES features of 

the particles (indicated by a dotted circle in Figure 3b) are dissimilar to those of 

the organo-As(V) compound in poultry feed, suggesting possible degradation/

transformation of roxarsone in the litter and/or in poultry digestive tracts. 

Figure 3 (to right). (a) Short-range normalized XANES spectra of As reference materials (sodium arsenate 

(Na2

HAsO4), sodium m-arsenite (NaAsO2), Cu3(AsO4)

2

·27H2O, orpiment (As2S3), and roxarsone) and 

As- rich particles in poultry litter are shown. The open circles overlying the sample spectra are the best fit 

from the linear combinations of model compounds. Spectra contribution (%) of roxarsone and As2

S3 are 

54 and 46 for particle A, 64 and 36 for particle B, and 53 and 47 for particle C, respectively. Three vertical 

dashed lines are at the absorption edge energy positions of orpiment (As2

S3 ≈11869 eV), sodium m-arsenite 

(Na-As(III)≈11871 eV), and sodium arsenate salt (Na-As(V)≈11874 eV), respectively. (b) Long-range 

normalized XANES spectra are shown for roxarsone and As-rich particles A, B, and C. 

Figure 1. A photographic image of 

a thin section of poultry litter and 

a synchrotron-based microfocused 

x-ray fluorescence spectrum of an 

arsenic-rich particle inside the black 

open square region. The white open 

square (approximately 600 x 600 

μm) indicates the selected area for 

microfocused x-ray fluorescence maps 

shown in Figure 2. 

Figure 2. Synchrotron-based microfocused x-ray fluorescence maps (600 x 600 μm) of the white open 

square area in the photographic image in Figure 1. Flux-normalized fluorescence counts / 20 sec are shown 

for each element.

Energy (eV)

Normalized Intensity

Energy (eV)

Normalized Intensity

X-ray Energy (keV)

Fluorscence Counts

(a)

(b)
2-62 GEOLOGY AND ENVIRONMENTAL SCIENCES 

Natural Occurrence and Synthesis of Two New PostSpinel Polymorphs of Chromite

M. Chen1, J. Shu2, H-k. Mao2, X. Xie1, and R.J. Hemley2

1Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, China; 2Geophysical Laboratory, Carnegie Institution of Washington

Chromite is a common accessory mineral occurring in most meteorites and in many 

mantle rocks. A high-pressure polymorph of chromite, the first natural sample with 

the calcium ferrite structure, has been discovered in the shock veins of the Suizhou 

meteorite. Synchrotron x-ray diffraction analyses reveal the sample has an orthorhombic CaFe2

O4-type (CF) structure. The unit-cell parameters are a = 8.954(7) Å, b = 

2.986(2) Å, c = 9.891(7) Å, and V (volume) = 264.5(4) Å3 (Z, the number of molecules per unit cell, = 4), with space group Pnma. The new phase has a density of 5.62 

g/cm3

, which is 9.4 % denser than the chromite-spinel phase. Laser-heated diamond 

anvil cell experiments were performed to establish that chromite-spinel transforms to CF 

at 12.5 GPa and then to the recently-discovered CaTi2

O4-type (CT) structure above 20 

GPa. With the ubiquitous presence of chromite, the CF and CT phases may be among 

the more important index minerals for tracking the natural transition sequence and PT conditions in mantle rocks, shock-metamorphosed terrestrial rocks, and meteorites. 

Chromite is a common accessory mineral that is a member of the spinel group of 

minerals, a group of oxides that have very similar structures. Chromite occurs in 

most meteorites and in many mantle rocks. The experimentally calibrated CF and 

CT polymorphs of chromite could therefore be ideal pressure gauges, not only for 

shock-metamorphosed terrestrial rocks and meteorites, but also for mantle rocks 

covering the important pressure range throughout the transition zone.

Spinel structure is the most important type of structure occurring in minerals 

in Earth's mantle. CaFe2

O4-type (CF) and CaTi2O4-type (CT) structures were 

proposed as the top candidates for "post-spinel" transitions in the deep mantle 

(Figure 1). However, no dense post-spinel polymorphs have been discovered in nature. A preliminary examination of the shock-metamorphosed Suizhou meteorite 

has recently revealed a CT polymorph of chromite (Fe,Mg)(Cr,Al)2

O4. This study 

reports another new CF-type polymorph of chromite in the same meteorite.

Synthesis experiments were performed at pressures from 7.5 to 25 GPa at a 

temperature of 2000o

C, using laser-heated diamond anvil cells. Our experiments 

indicate that chromite-spinel transforms to the CF structure above 12.5 GPa, and 

to the CT structure above 20 GPa (Figure 

2). The x-ray diffraction pattern of the 

quenched CF polymorph was indexed to 

give lattice parameters a = 8.955(7)Å, b = 

2.985(2)Å, c = 9.909(7)Å, V = 264.9(4)Å3 

(Z=4), density (ρ) = 5.61 g/cm3, and space 

group Pnma. For the CT polymorph, 

the parameters are a = 9.467(5) Å, b = 

9.550(7) Å, c = 2.905(2) Å, V = 262.6(4) 

Å3

 (Z=4), ρ = 5.65g/cm3, and space group 

Cmcm. The densities of synthetic CF and 

BEAMLINE X17C

Funding

Chinese Academy of Sciences; National Science 

Foundation of China; National 

Science Foundation (U.S.); 

U.S. Department of Energy

Publication

M. Chen, J. Shu, H.K, Mao, X. 

Xie, and R.J. Hemley, "Natural Occurrence and Synthesis 

of Two New Post-Spinel Polymorphs of Chromite," Proc. 

Nat. Acad. Sci. USA, 100

(25), 14651-14654 (2003).

Contact information

Dr. Ming Chen

Guangzhou Institute of Geochemistry, Chinese Academy 

of Sciences, China 

Email: mchen@gig.ac.cn

Ming Chen
SCIENCE HIGHLIGHTS 2-63

CT polymorphs are 9.4 % and 10.1 % denser, respectively, than that of chromite.

Some chromite grains in the Suizhou meteorite covered a shock-induced pressure gradient. These grains show three zones of distinct densities corresponding 

to the pressure gradient - a CT phase zone close to the shock vein, a chromite 

zone relatively apart from the vein, and a lamella-rich (layered) zone between 

the CT phase zone and the chromite zone (Figure 3). These three zones have a 

uniform chromite chemical composition. We used a synchrotron x-ray beam to 

probe the shock chromite grain in situ in the thin section mount of the meteorite, and confirmed that a zone in contact with the shock vein, ranging from 20 

to 30 μm in width, had transformed into a fine-grained polycrystalline aggregate with a CT-type structure identical to the CT phase that was synthesized 

experimentally. We also confirmed that the clear zone at the low-pressure end 

has the usual chromite-spinel structure.

We focused the x-ray microprobe on the lamella-like zone between the CT and 

spinel zones and obtained distinct diffraction patterns for the CT phase, which 

are consistent with a mixture of the CF and spinel phases, and a trace amount 

of the CT phase, with the fraction of spinel decreasing toward the shocked 

vein and the CT phase increasing toward the shocked vein. The x-ray patterns 

collected from different orientations of the sample show that the lamellae-like 

slices are polycrystalline in nature. X-ray reflections from the CF phase were 

indexed to an orthorhombic cellwith parameters a = 8.954(7) Å, b = 2.986(2) 

Å, c = 9.891(7) Å, and V = 264.5(4) Å3

 (Z=4). The structure is identical to the 

synthetic CF phase in our high-pressure experiment. The calculated density of 

the natural CF phase is ρ = 5.62 g/cm3

, which is 9.4 % denser than that of the 

chromite-spinel phase. This is the first natural occurrence of a dense FeCr2

O4

polymorph displaying the CF structure.

Figure 3. Back-scattered electron images 

(BSE) of shock-metamorphosed chromitespinel grains in the Suizhou meteorite. 

A chromite grain was transformed to a 

CaTi2

O4-type phase zone (CT) contacting 

with the shock vein, and partially to a 

CaFe2

O4-type phase zone (CF) between the 

CT phase zone and the chromite zone (Ch) 

apart from the shock vein. The CF phase 

occurs as lamella-like slices associating with 

a chromite matrix, and two to three sets 

of slices are observed. On the image, both 

the CT and CF phases are brighter than 

chromite. Pyx = pyroxene. 

Figure 1. Schematic view of the (A) 

spinel, (B) CaFe2

O4 , and (C) CaTi2O4

type structures. The spinel structure 

has octahedral and tetrahedral sites. In 

the CF and CT structures, a compact 

three-dimensional network is formed 

by edge- and corner-sharing octahedra, 

with hollow channels parallel to the 

b axis (CF structure) and the a axis 

(CTstructure), respectively, where the 

large Ca cations are located. These 

two structures contain dodecahedral 

and octahedral sites; the difference 

between the two structures lies in 

slight modifications of the polyhedral 

linkage. There are two types of FeO6

octahedral sites in the CF structure, 

and one type of FeO6

 octahedral site in 

the CT structure.

Figure 2. X-ray diffraction patterns from 

the natural chromite-spinel, synthesized 

CaFe2

O4-type, and CaTi2O4-type phases. 

The peaks labeled with 'CH' from the 

residue of the starting material, chromitespinel. * = escape peaks. 

(a)

(b)

(c)

Energy (KeV)

Intensity
2-64 GEOLOGY AND ENVIRONMENTAL SCIENCES 

BEAMLINES

X1A, U10B

Funding

NASA Exobiology Research 

Program

Publication

G.J. Flynn, L.P. Keller, M. Feser, S. Wirick, and C. Jacobsen, "The Origin of Organic 

Matter in the Solar System: 

Evidence from the Interplanetary Dust Particles," Geochim. et Cosmochim. Acta, 

67(24), 4791-4806 (2003).

Contact information

George J. Flynn

Department of Physics, 

SUNY-Plattsburgh

Email: george.flynn@plattsburgh.edu

The Origin of Organic Matter in the Solar System: 

Evidence from the Interplanetary Dust Particles

G.J. Flynn1, L.P. Keller2, M. Feser3, S. Wirick3, and C. Jacobsen3

1Department of Physics, SUNY-Plattsburgh; 2NASA Johnson Space Center; 3Department of Physics, 

Stony Brook University

Researchers from SUNY-Plattsburgh, the NASA Johnson Space Center, and Stony 

Brook University measured the types and abundances of organic matter in interplanetary dust particles, originating from asteroids and comets, that NASA research aircraft 

collected from the Earth’s atmosphere. They found the same amount and types of organic 

matter in both anhydrous and hydrated interplanetary dust particles. This suggests that 

aqueous processing, long believed to have played an important role in the production of 

organic matter, was much less important, and that most of the pre-biotic organic matter 

in the Solar System formed at about the same time as the first dust that condensed from 

the Solar Nebula. It is also possible that this matter formed even earlier, in circumstellar 

or interstellar space. 

Extraterrestrial materials, including asteroids, comets, and grains in interstellar 

space, contain organic compounds that may have been important starting materials for the origin of life. How this pre-biotic organic matter formed is not known, 

but a wide variety of processes, ranging from catalyzed reactions on the surfaces of 

grains to reactions involving liquid water, have been proposed. If this organic matter was produced by the aqueous alteration of elemental carbon, which is believed 

to happen on wet asteroids, then we would expect to see organic matter occurring 

preferentially in interplanetary materials that exhibit evidence of aqueous activity, such as the presence of hydrated silicates. If the organic matter were produced 

either during the nebula phase of Solar System evolution or in the interstellar 

medium, we would expect this organic matter to be incorporated into the dust as 

it formed, so that it would be present in the anhydrous interplanetary materials as 

well. Earlier studies of meteorites showed abundant organic matter in the hydrated 

meteorites, but mostly amorphous carbon, with little or no organic matter, in 

the anhydrous meteorites. This suggested aqueous activity was important in the 

production of the pre-biotic organic matter. However, all the anhydrous, carbonrich meteorites show significant depletions of the moderately volatile elements in a 

pattern that indicates these meteorites were once exposed to temperatures as high 

as 1200 degrees Celsius, hot enough to destroy any organic matter initially present. To make a proper comparison, we were forced to examine interplanetary dust 

particles (IDPs) like the one shown in Figure 1, which are fragments from asteroids and comets, approximately 10 micrometers in size, 

that NASA collects from the Earth’s stratosphere. These 

particles are so small that we required the high sensitivity of the synchrotron-based instruments at the National 

Synchrotron Light Source to perform the analyses. We 

mapped the carbon distribution in approximately 100 

nanometer (nm) thick slices of seven anhydrous and 

four hydrated IDPs, determining the carbon abundance, 

and we performed carbon x-ray absorption near-edge 

structure (XANES) and infrared spectroscopy, both of 

George Flynn
SCIENCE HIGHLIGHTS 2-65

which identify specific carbon functional groups. The carbon-XANES spectra 

of the hydrated and anhydrous IDPs (Figure 2) are very similar, with strong 

absorptions at about 285 electron volts (eV), identifying C=C, and at about 

288.5 eV, identifying C=O. The infrared spectra of the hydrated and anhydrous 

IDPs are also very similar (Figure 3), with the pair of features near the 2926 

and 2854 cm-1 wavelengths identifying aliphatic CH2

, and the feature near 2960 

cm-1 identifying aliphatic CH3

 (where ‘aliphatic’ refers to organic compounds 

containing short-chain arrangements of carbon atoms). In some anhydrous 

IDPs the individual mineral grains are coated with this carbonaceous material, 

apparently the “glue” holding the aggregate particle together. We found that 

organic matter is present in similar types and abundances in both the anhydrous 

and the hydrated IDPs, indicating that the bulk of the pre-biotic organic matter 

in the Solar System did not form by aqueous processing. Instead, this organic 

matter had already formed at the time that primitive, anhydrous dust was being 

assembled. The hydrated meteorite, Murchison, has a higher ratio of aliphatic 

CH3

 to CH2 (indicating a shorter mean aliphatic chain length) and Murchison 

also contains more aromatic C-H (the broad absorption at approximately 3050 

cm-1 in Figure 3) than either type of IDP, consistent with Murchison being 

more thermally processed than the hydrated IDPs.

Figure 3. Infrared spectra of typical 

anhydrous and hydrated IDPs and 

the organic residue extracted from the 

Murchison hydrated meteorite.

Figure 1. Scanning electron microscope 

image of an approximately 10 

micrometer-diameter interplanetary 

dust particle, showing many small 

grains that aggregated to form the 

particle. (NASA photo)

Figure 2. Carbon XANES spectra of 

typical anhydrous and hydrated IDPs 

and the organic residue extracted from 

the Murchison hydrated meteorite.

Wavelength (cm-1)

Energy (eV)

Optical density
2-66 LIFE SCIENCES 

X-ray Structure Analysis of a Designed Oligomeric 

Miniprotein Reveals a Discrete Quaternary 

Architecture

M.H. Ali1, E. Peisach2, K.N. Allen2, and B. Imperiali1

1Department of Chemistry, Massachusetts Institute of Technology; 2Department of Physiology and 

Biophysics, Boston University School of Medicine

Oligomerization, or noncovalent association, is a fundamental strategy for determining 

protein structural and functional complexity in nature. In this research, miniproteins 

adopting a defined oligomeric state were designed to study the advantages of protein 

oligomerization. Peptide 1 is a discretely folded, mixed α/β, homo-oligomeric miniprotein motif with only 21 amino acids. The x-ray crystal structure of peptide 1 at 1.2 Å 

resolution reveals that it associates as a tetramer (a four-unit oligomer), in which α and 

β components form a tightly-packed and well-defined hydrophobic core. The miniprotein is thermally stable and shares many of the characteristics of larger proteins. 

Miniproteins are short peptide sequences that adopt a discrete protein-like fold 

in aqueous solution. Therefore, they are valuable minimal models for studying 

natural proteins. Oligomeric miniproteins, in particular, are good model systems 

for quaternary structure formation in proteins. Moreover, they are appropriate 

platforms for determining whether more complex oligomeric structures might 

ultimately support function. 

A homo-oligomeric ββα miniprotein was derived from a monomeric precursor by 

a strategy inspired by “domain swapping,” an important evolutionary mechanism 

for protein oligomerization. The monomeric ββα motif includes intramolecular 

interactions between α and β secondary structural elements, where α is a helix and 

ββ is a hairpin. We introduced a bias towards oligomerization by shortening the 

length of the hinge region between the α and β elements, thereby precluding intermonomer interactions. A fluorescence-screening assay yielded a homo-oligomeric 

miniprotein composed of 21 amino acids, with eight residues in the β hairpin 

and 12 residues in the α helix. 

Biophysical studies revealed that 

this miniprotein forms a defined 

oligomer in solution and has 

many of the features of larger 

proteins, including cooperative 

folding and a solvent-protected 

core. However, the exact nature 

of the miniprotein structure 

and the forces contributing to 

the native-protein-like stability 

remained unknown. We thus 

set out to determine the crystal 

structure of peptide 1, a more 

stable analog of the original 

homo-oligomer. 

BEAMLINE X12C

Funding

National Science Foundation 

National Institutes of Health

Publication

M.H. Ali, E. Peisach, K.N. Allen, and B. Imperiali, "X-ray 

Structure Analysis of a Designed oligomeric miniprotein 

reveals a discrete quaternary 

architecture," Proc. Natl. 

Acad. Sci., USA, 101(33), 

12183-8 (2004).

Contact information

Prof. Karen Allen

Department of Physiology 

and Biophysics, Boston University School of Medicine

Email: allen@med-xtal.bu.edu

Authors (left to right) 

(top) Mayssam H. Ali and Barbara 

Imperiali

(bottom) Karen N. Allen and Ezra Peisach
SCIENCE HIGHLIGHTS 2-67

The nature of oligomerization in peptide 1 was revealed by the 1.2 Å x-ray crystal structure, determined using multi-wavelength anomalous diffraction (MAD) 

phasing. The tetramer consists of four monomers arranged in an antiparallel 

topology (Figure 1), with each monomer flanked by two others oriented in the 

opposite direction. The tetramer possesses approximate four-fold symmetry: 

Each monomer is slightly closer to one neighbor than the other. The well-defined central hydrophobic core of the tetramer is formed by residues from one 

monomer in proximity to core residues from the other three monomers. Those 

residues on the periphery of the hydrophobic interface interact with residues of 

the antiparallel monomer nearest them, while the polar residues are solvent-exposed. 

Each tetramer is enveloped by a sheath of waters of crystallization with a demarcated water-exclusion zone in the central core region, indicating that no waters 

can pass into this hydrophobic core. The tetrameric structure is highly proteinlike in terms of the degree of complexity and the tight packing of side chains. 

In fact, the relationships between surface area, volume, and molecular weight fit 

well to a series of empirical relationships for monomeric and oligomeric proteins 

of varying sizes. The hydrophobic core is defined by five palindromic layers 

(Figure 2) composed of residues from the α-helix and the β-sheet. The packing “register” between monomers might be determined by the conformationally 

restricted aromatic residues of the core or the interactions made by the hairpin 

region. The tight packing of the hydrophobic core accounts for the cooperative 

unfolding and high melting temperatures of peptide 1. This packing is remarkable in light of the very short linear sequence. Overall, this “miniprotein” structure provides a view of the forces that contribute to oligomerization and a model 

for understanding quaternary structure in large natural proteins.

Figure 2. The hydrophobic core of tetrameric peptide 1. At left, a side view of the tetramer, 

highlighting the positions of the five palindromic core layers. At right are cross-sectional slices 

through layers A (Ile-3/DapBz-20), B (Phe-8/Leu-16), and C (Leu-12/Leu-12). Residues 

comprising the core are in bold. 

Figure 1. Tetrameric structure of 

peptide 1. (A) Ribbon diagram of 

tetramer, side view. (B) Topology 

diagram. Dashed line indicates 

inter-monomer interaction. (C) 

Crystallographic waters, with void in 

the shape of the tetramer. (D) CPK 

model of peptide 1 indicating space 

occupied by tetramer.

A

B

C

D
2-68 LIFE SCIENCES 

Authors (left to right) 

Francis T.F. Tsai, Mathew E. Sowa, and Sukyeong Lee

BEAMLINE X25

Funding

Baylor College of Medicine

American Heart Association 

Robert A. Welch Foundation

Publications

J.S. Lee, M.E. Sowa, Y. Watanabe, P.B. Sigler, W. Chiu, M. 

Yoshida, and F.T.F. Tsai, "The 

Structure of ClpB: A Molecular Chaperone that Rescues 

Proteins from an Aggregated 

State," Cell, 115, 229-240 

(2003a)

S. Lee, M. Hisayoshi, M. Yoshida, and F.T.F. Tsai, "Crystallization and Preliminary Xray Crystallographic Analysis 

of the Hsp100 Chaperone 

ClpB from Thermus Thermophilus," Acta Crystallogr., 

D59, 2334-2336 (2003b).

Contact information

Dr. Francis T.F. Tsai

Department of Biochemistry 

& Molecular Biology, Baylor 

College of Medicine

Email: ftsai@bcm.tmc.edu

Structure of the ClpB Molecular Chaperone

S. Lee, M.E. Sowa, and T.F. Tsai

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of 

Medicine

Molecular chaperones are cellular proteins that assist other proteins in the folding and 

assembly of higher order structures without being components of these final structures. 

ClpB is an essential protein of the bacterial heat-shock response, but unlike other chaperones, has the remarkable ability to rescue proteins from an aggregated state. The 3.0 

angstrom (Å) resolution crystal structure of ClpB reveals that the ClpB middle region 

forms an 85 Å-long, mobile coiled-coil structure, which resembles the shape of a twobladed propeller. The conformation and motion of this coiled-coil are critical for ClpB’s 

chaperone function. The coiled-coil is located on the outside of the ClpB hexamer, 

where it can interact with aggregated proteins. This suggests that the long coiled-coil 

may function as a “molecular crowbar” that mediates protein disaggregation.

Bacterial ClpB is a molecular chaperone that requires adenosine triphosphate 

(ATP) for function. Members of the ClpB family form large ring structures and 

contain two ATP-binding domains. Moreover, ClpB has a longer middle region, 

known as the ClpB-linker, and, unlike other Clp proteins, does not direct the 

degradation of its substrate proteins. Instead, ClpB has the remarkable ability to 

rescue stress-damaged proteins from an aggregated state.

Despite the wealth of biochemical and genetic data, the mechanism by which 

ClpB disaggregates stress-damaged proteins has remained elusive. To investigate 

this structure-function relationship, we have determined the 3.0 Å-resolution crystal structure of ClpB bound to adenosine 5’-(β,γ-imido)triphosphate (AMPPNP), 

an ATP analog. We have also determined the structure of the physiological assembly at approximately 21 Å resolution using electron cryomicroscopy (cryo-EM). 

Our crystal structure reveals that ClpB consists of five domains (Figure 1A). The 

most remarkable structural feature is its 85 Å-long coiled-coil that consists of the 

ClpB-linker. There are three independent representations of ClpB in the asymmetric unit of our crystal. The three molecules are arranged in a manner that gives rise 

to a helical assembly (Figure 2A), which extends throughout the crystal and forms 

a hexameric ring structure when viewed in projection (Figure 2B). Interestingly, 

each ClpB molecule adopts a different conformation even though they are in the 

same nucleotide-bound state. This suggests 

that ClpB is a dynamic molecule that can 

undergo large conformational rearrangements. Using a combination of structurebased targeted mutagenesis and biochemical 

experiments, we have further demonstrated 

that the conformation and motion of the 

long coiled-coil are critical for chaperone 

activity.

The structure of the functional ring assembly was determined using cryo-EM and 

single-particle reconstruction techniques 
SCIENCE HIGHLIGHTS 2-69

Figure 2. Molecular arrangement of six ClpB molecules as seen in our crystal 

structure. The figure illustrates the molecular contents of two asymmetric units, 

which are related by a crystallographic two-fold screw axis. Each ClpB monomer is 

colored differently. To depict the relative orientation of ClpB in our crystal, one of the 

six molecules has been highlighted and color-coded as shown in Figure 1A.

Figure 1. (A) Ribbon drawing of the 

ClpB monomer. The N-terminal 

domain is colored in yellow, the 

D1-large domain or NBD1 in cyan, 

the D1-small domain in purple, the 

D2-large domain or NBD2 in green, 

and the D2-small domain in pink. The 

bound AMPPNP molecules have been 

omitted for clarity. (B) Single-particle 

reconstruction of the ClpB hexamer. 

The cryo-EM map is contoured 

as a yellow mesh, with the atomic 

coordinates of an N-terminal domain 

truncated ClpB hexamer docked in. 

The N-terminal domains and part of 

the ClpB-linker are not visible in the 

reconstruction because they are mobile.

of ClpB-AMPPNP complexes. Our three-dimensional reconstruction shows 

that ClpB is a hexamer and that both of its ATP-binding domains are required 

for hexamer formation in the AMPPNP-bound state (Figure 1B). An atomic 

model of the ClpB hexamer was generated by fitting the crystal structure of 

ClpB into the cryo-EM density map (Figure 1B). Our model reveals that the 

ClpB-linker is located on the outside of the hexamer, where it can interact with 

large aggregated substrate proteins. Taken together, our structural and biochemical studies support a mechanism in which the long coiled-coils function as 

“molecular crowbars” that pull apart large aggregates, thereby mediating protein 

disaggregation.

(A)

(B)
2-70 LIFE SCIENCES 

Crystal Structure of Human α-Tocopherol Transfer Protein 

Bound to its Ligand: Implications for Ataxia with Vitamin E 

Deficiency

K.C. Min1,2,3, R.A. Kovall3, and W.A. Hendrickson1,3

1Howard Hughes Medical Institute, 2Department of Neurology, and 3Department of Biochemistry

and Molecular Biophysics, Columbia University

Human α-tocopherol transfer protein (ATTP) plays a central role in vitamin E homeostasis, preventing the degradation of α-tocopherol (α-T), a lipophilic molecule, by 

routing it for secretion by hepatocytes (liver cells). Mutations in the gene that encodes 

ATTP have been shown to cause a severe deficiency in α-T, which results in a progressive neurodegenerative spinocerebellar ataxia, a disorder of neurons primarily in 

the brainstem and spinal cord, known as ataxia with vitamin E deficiency (AVED). 

We have determined the high-resolution crystal structure of human ATTP with (2R, 

4'R, 8'R)-α-T in the binding pocket. One mutation associated with human disease is 

located directly in the binding pocket, likely disrupting binding to α-T.

Ataxia with Vitamin E Deficiency (AVED) is a recessively inherited condition in 

which afflicted individuals develop problems with balance, typically starting in 

the late teen years. As the disease progresses, many individuals are limited to a 

wheelchair, lose sensation in their hands and feet, and have difficulties with slurred 

speech. Some develop retinitis pigmentosa, a blinding condition caused by the degeneration of the retina. Mutations in α-tocopherol transfer protein (ATTP) have 

been shown to cause AVED.

ATTP exists in the fluid portion of a cell’s cytoplasm and is expressed mainly in 

the liver. The heterologous expression of ATTP in cell culture confers its ability to 

secrete α-T by a non-Golgi pathway, preventing the degradation of α-T. Patients 

with AVED absorb α-T from their diets normally, but have nearly immeasurable 

steady-state plasma levels due to the defective incorporation of α-T for transport 

with very low density lipoprotein. A transgenic mouse in which the ATTP gene 

was deleted replicated the phenotype of the human disease.

There are eight forms of vitamin E (including α-δ tocopherol and α-δ tocotrienol), which differ in two structural features: the degree of methylation (decreasing 

from α-T to δ-T) of the chroman ring and saturation of the phytyl tail. All forms 

are potent lipophilic antioxidants, but α-T is the most biologically potent due to 

the action of ATTP. Of the eight possible stereoisomers, i.e. variations, of α-T, 

only (2R, 4′R, 8′R)-α-T occurs naturally. Synthetic vitamin E supplements are 

racemic mixtures, but ATTP is sensitive to stereochemistry and particularly so at 

the C2 stereocenter.

The high-resolution 1.5Å structure of ATTP in a complex with 

(2R, 4′R, 8′R)-α-T was determined from multiwavelength 

anomalous diffraction (MAD) 

data measured at beamline X4A 

using a selenomethionyl recomBEAMLINE X4A

Funding

Howard Hughes Medical 

Institute; Leukemia and 

Lymphoma Society; National 

Institutes of Health

Publication

K.C. Min, R.A. Kovall, and 

W.A. Hendrickson, "Crystal 

Structure of Human AlphaTocopherol Transfer Protein 

Bound to its Ligand: Implications for Ataxia with Vitamin 

E Deficiency," Proc. Natl. 

Acad. Sci. USA., 100(25), 

14713-8 (2003).

Contact information

Wayne A. Hendrickson, 

Howard Hughes Medical Institute, Columbia University

Email: wayne@convex.hhmi.

columbia.edu

Authors (left to right) 

R.A. Kovall, K.C. Min, and W.A. 

Hendrickson
SCIENCE HIGHLIGHTS 2-71

binant protein crystal. The structure of ATTP is composed of two domains: an 

N-terminal all-helical domain and a C-terminal domain, which at its core is 

composed of a βαβαβαβ fold and contains the binding pocket for α-T (Figure 

1). The most striking feature of the structure is the buried, solvent-inaccessible 

binding pocket, which would require significant conformational changes to 

release α-T. Most of the interactions between ATTP and α-T are through van 

der Waals contacts, although there are three well-ordered water molecules that 

appear to form a hydrogen bonding network with the hydroxyl group of α-T 

(Figure 2A).

In ATTP, a number of missense mutations – which occur when one DNA base 

pair is substituted for another – have been associated with AVED. One mutation, L183P – a change from one amino acid, leucine, to another, proline – was 

found to map directly to the binding pocket (Figure 2A). The sidechain of 

L183 has extensive van der Waals contacts with α-T, and a change to proline 

at this position would not only be expected to disrupt these interactions, but 

would also affect the residues in the nearby α-helix that also form contacts with 

α-T. When expressed in E. coli, the L183P mutant was insoluble and could not 

be further characterized.

Three other missense mutations, R59W (arginine-to-tryptophan), R192H (arginine-to-histidine), and R221W, involve a change in positively charged residues, 

which help to form a prominent positively charged surface on ATTP (Figure 

2B). Although the function of this region is not understood, it seems unlikely 

to affect binding to α-T directly. We have proposed that it may represent a site 

of protein-protein or protein-lipid interaction that regulates the release of α-T 

from the binding pocket of ATTP. Interestingly, a similar mutation (R233W) 

in a related protein, cellular retinaldehyde binding protein, causes a hereditary 

retinopathy, suggesting that this region of the protein may have a conserved 

function across multiple members of this family of lipophilic transfer proteins.

Figure 2. (A) Close-up view of the 

ligand binding pocket. Side chains (in 

green) that form van der Waals contacts 

with α-T (in yellow) or participate 

in hydrogen-bonding networks in 

the ligand-binding pocket are shown. 

Three well-ordered water molecules 

located in the binding pocket are 

shown as red spheres. The protein 

backbone is shown as a worm model, 

excluding residues 216-220 and 249-

275 for clarity. Electron densities that 

cover the residues of interest, α-T, and 

three water molecules are drawn as 

mesh at 1σ. Dashed red lines indicate 

hydrogen bonds. (B) Electrostatic 

potential surface map of ATTP. A 

positively charged cleft indicates where 

a number of disease-causing mutations 

are located.

Figure 1. Ribbon diagram of ATTP 

viewed down the β-sheet. α-T is 

colored in yellow. The N-terminal 

domain helices are indicated in green, 

and the C-terminal domain’s helices 

are in blue and its strands in red. The 

electron density that covers α-T is 

drawn as a blue mesh at 1σ.

(A)

(B)
2-72 LIFE SCIENCES 

Authors (left to right) 

Nick Criscimagna, Stephen Holloway, 

P. John Hart, Jennifer Stine Elam, Lisa 

Whitson, Alex Taylor, and Ahmad 

Galaleldeen

BEAMLINE X8C

Funding

National Institutes of 

Health’s National Institute 

of Neurological Disorders 

and Stroke (NIH-NINDS); 

Robert A. Welch Foundation; Amyotrophic Lateral 

Sclerosis (ALS) Association; 

the Council for the Central 

Laboratory of the Research 

Councils (CCLRC) Daresbury 

Laboratory

Publication

J.S. Elam, A.B. Taylor, R. 

Strange, S. Antonyuk, P.A. 

Doucette, J.A. Rodriguez, 

S.S. Hasnain, L.J. Hayward, 

J.S. Valentine, T.O. Yeates, 

and P.J. Hart, "Amyloid-Like 

Filaments and Water-Filled 

Nanotubes Formed by SOD1 

Mutants Linked to Familial 

ALS," Nat. Struct. Biol., 10, 

461-467 (2003).

Contact information

P. John Hart, Ph.D. 

Associate Professor of 

Biochemistry, Director of the 

X-ray Crystallography Core 

Laboratory ,The University of 

Texas Health Science Center 

at San Antonio

Email: pjhart@biochem.uthscsa.edu

The Mutant Proteins of a Neurodegenerative Disorder

J. Stine Elam1, A.B. Taylor1, R. Strange2, S. Antonyuk2, P.A. Doucette3, J.A. Rodriguez3, 

S.S. Hasnain2, L.J. Hayward4, J. Selverstone Valentine3, T.O. Yeates3, and P.J. Hart1

1Department of Biochemistry and the X-ray Crystallography Core Laboratory, The University of 

Texas, Health Science Center at San Antonio; 2CCLRC Daresbury Laboratory; 3Department of 

Chemistry and Biochemistry, University of California; 4Department of Neurology, University of 

Massachusetts Medical School

Mutations in copper-zinc superoxide dismutase (SOD1) proteins cause the neurodegenerative disorder familial amyotrophic lateral sclerosis (FALS). In human spinal 

cord neurons and in transgenic mice expressing these proteins, proteinaceous inclusions 

(aggregates) containing pathogenic SOD1 are observed. These aggregates are believed to 

interfere with a variety of cellular processes, eventually leading to motor neuron death. 

We discovered that several metal-deficient, pathogenic SOD1 proteins can undergo

conformational changes that do not occur in non-pathogenic (native) SOD1. This 

promotes a “gain-of-interaction” between the molecules, causing them to “stick” to each 

other. In turn, this leads to the formation of extensive helical and linear, or “amyloidlike,” arrays of SOD1. Such non-native protein-protein interactions, leading to larger, 

or “higher order,” SOD1 assemblies, could thus represent a toxic property that is common to mutants of SOD1 linked to FALS.

Amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig’s disease or motor 

neuron disease) is a neurodegenerative condition characterized by the loss of motor 

neurons in the spinal cord and brain. The disorder results in paralysis, leading to 

the death of the afflicted individual within two to five years of diagnosis. A subset 

of ALS cases are familial (FALS), and most of these are associated with dominantly 

inherited mutations in copper-zinc superoxide dismutase (SOD1). SOD1 is an 

antioxidant enzyme that is 32 kilodaltons (kDa) in size (where one Da is equal 

to one atomic mass unit), and is homodimeric, meaning it consists of two identical molecules. Initial hypotheses suggested that SOD1-linked FALS comes from 

extensive oxidative damage in the neurons, arising from diminished SOD1 activity. However, mice without SOD1 appear normal and live to adulthood without 

developing motor neuron disease. In contrast, transgenic mice expressing human 

FALS SOD1 mutants become paralyzed, even though they possess normal levels 

of SOD1 activity from their own endogenous SOD1. Together, these observations 

strongly suggest that pathogenic SOD1 molecules act by gaining the ability to kill 

other cells (becoming “cytotoxic”) and not by losing their enzymatic function.

There has been increasing support for the concept that this “toxic gain of function” of pathogenic SOD1 is due to the propensity of these proteins to misfold 

and aggregate. This is supported by the manifestation of aggregates containing 

pathogenic SOD1 in human spinal cord neurons and in transgenic mice expressing these proteins. These pathogenic SOD1 aggregates (or their 

soluble precursors) could play 

a role in pathogenesis, either 

by occupying the neurons’ heat 
SCIENCE HIGHLIGHTS 2-73

Figure 2. The gain-of-interaction in zinc-loaded H46R (Zn-H46R) SOD1, giving rise to 

water-filled helical nanotubes. The GOI interface between Zn-H46R dimers is boxed, and 

buries approximately 550 Å2

 of solvent-accessible surface area per polypeptide. (A) and (B)

One-half of the helical Zn-H46R filament is represented by two dimers, shown from top 

to bottom in green and gold, respectively. Image B is related to the left half of image (C) 

by a rotation of 90 degrees. (C) The approximate location of the crystallographic two-fold 

axis, which runs along the diagonal in the tetragonal unit cell, is indicated by a black line 

without arrows and a 180-degree rotation symbol. Applying this two-fold operator generates 

one complete turn of the helical filament. One-half of each SOD1 β-barrel is shown in 

red. Residues of the zinc loop undergo a conformational change and form a short β-strand 

(shown in blue) that reciprocally adds to this sheet in neighboring Zn-H46R dimers, 

stabilizing the GOI interface. Zinc ions are shown as magenta spheres. (D) A schematic 

representation of SOD1 dimers in the helical filaments in the same orientation as in image 

(C). The GOI interfaces are represented by red patches.

Figure 1. The gain-of-interaction 

(GOI) interfaces in pathogenic SOD1 

give rise to cross-β fibers (or filaments) 

in two different crystal systems. 

Two orthogonal views of the linear, 

amyloid-like apo-H46R filament are 

represented by three dimers, shown 

from top to bottom in green, gold, and 

blue, respectively. Because the overall 

architecture and GOI interfaces in the 

S134N filament and the metal-free 

H46R filament are nearly identical, 

both filaments are represented by the 

single filament shown in this panel. 

The GOI interface is boxed, and buries 

approximately 640 square angstroms 

(Å2

) of solvent-accessible surface area 

per polypeptide. (A) A schematic 

representation of SOD1 dimers in 

the amyloid-like filaments (in the 

same orientation as in image (D). The 

GOI interfaces are represented by red 

patches. (B) and (C) Space filling and 

ribbon representations of the filaments, 

respectively. These are rotated 90o

relative to the images in (A) and (D). 

In (B), the naturally occurring interface 

between SOD1 monomers is also 

indicated and buries approximately 

660 Å2

 of solvent-accessible surface 

area per polypeptide. (D) One-half of 

each SOD1 β-barrel, shown in red. (E) 

The long axes of the red strands run 

perpendicular to the long axis of the 

filament, an architecture similar to the 

“cross-β” structure observed in amyloid 

fibrils.

shock proteins and preventing them from doing their jobs, which leaves the 

neuron vulnerable, and/or interfering with the way the neurons transport materials along their length (or along their axons) and get rid of unwanted proteins.

However, the molecular basis underlying the formation of pathogenic SOD1 

oligomers has remained undefined.

To partially address this issue, we determined the crystal structures of the pathogenic SOD1 mutants H46R and S134N, which are members of a larger class of 

“metal-binding region mutants.” As the name suggests, members of this class of 

pathogenic SOD1 cannot properly bind either copper or zinc, or both. In the 

absence of the proper complement of these metal ions, structural features normally involved in metal binding, called loop elements, undergo conformational 

changes that allow H46R and S134N to polymerize into two types of higher-order filamentous arrays. Figure 1 shows that both metal-free H46R and metaldeficient S134N (which crystallize in different crystal systems) form nearly identical linear, amyloid-like fibers. A variation on this theme can be seen in Figure 

2(D), which shows that copper-free, but zinc-loaded H46R engages in slightly 

different pathogenic SOD1-SOD1 interactions, leading to the formation of 

helical, rather than linear, filamentous arrays. From the perspective in Figure 

2(D), the interactions (which occur in the red patches) form a donut shape. 

Thus, propagating them leads to hollow, water-filled nanotubes. Importantly, 

when native SOD1 dimers are structurally aligned with the pathogenic SOD1 

dimers in these linear and helical arrays, it is obvious that the native variety cannot participate in filamentous assembly. This is due to clashes and unfavorable 

electrostatic interactions between the loop elements described above.

In summary, the filamentous arrangement of mutant, metal-deficient SOD1 

proteins provides justification for a specific and testable hypothesis that links 

various pathogenic SOD1 mutations to protein aggregation, thereby making it 

possible to draw a parallel between ALS and other established amyloid diseases.

(A) (B)

(C) (D) (E)

(A) (B) (C) (D)
2-74 LIFE SCIENCES 

The Crystal Structure of Biotin Synthase, an 

S-Adenosylmethionine-Dependent Radical Enzyme

F. Berkovitch1, Y. Nicolet1, J.T. Wan2, J.T. Jarrett2, and C.L. Drennan1

1Department of Chemistry, Massachusetts Institute of Technology; 2Johnson Research Foundation 

and Department of Biochemistry and Biophysics, University of Pennsylvania

The crystal structure of biotin synthase addresses how “AdoMet radical” enzymes, also 

called “Radical SAM” enzymes, use an Fe4

S4 cluster and S-adenosyl-L-methionine to 

generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of 

sulfur into dethiobiotin (DTB) to form biotin (vitamin B8

). The structure places the 

substrates, i.e. DTB and AdoMet, between the Fe4

S4 cluster (essential for radical generation) and the Fe2

S2 cluster (postulated to be the source of sulfur), with both clusters 

in unprecedented coordination environments.

Biotin is an essential vitamin that plays a ubiquitous role in human growth and 

metabolism. Biotin deficiency results in skin lesions, abnormal fat distribution, 

neurological symptoms, and immunodeficiency. A low biotin level has also been 

correlated to an increased incidence of type II diabetes mellitus. Biotin is a valuable 

commercial commodity, used as an additive in food, health, and cosmetic products, and as a research tool in the biochemical sciences. 

We recently reported the crystal structure of E. coli Biotin Synthase (BioB), which 

belongs to the emerging “AdoMet radical” or “radical SAM” enzyme superfamily. 

The superfamily is characterized by the presence of a conserved CX3

CX2C motif, 

(“C” is the amino acid cysteine and “X” is any amino acid), and the requirement 

of a 4Fe-4S cluster and S-adenosyl-L-methionine (AdoMet or SAM) to perform 

carbon-based radical chemistry. Enzymes that utilize radical chemistry are able to 

catalyze challenging and unusual reactions, but are difficult to work with because 

of their aberrant reactivity and oxygen sensitivity. We were able to grow crystals of 

BioB in an anaerobic chamber and, over a 17-month period, obtained crystals of 

high-enough quality to solve the structure of this fascinating protein (Figure 1).

BioB activates DTB, a biotin precursor, for sulfur (S) insertion between two nonactivated carbon atoms, forming biotin (Figure 2). The molecular basis for this 

remarkable chemistry lies in a novel reactivity of AdoMet in the presence of unique 

Fe-S clusters. BioB is a homodimer (i.e. formed by two identical molecules), with 

one active site per protomer and no interactions between the two active sites. 

Each protomer adopts a common protein structure known as the “TIM barrel,” 

and contains two Fe-S clusters, both of which have unprecedented coordination 

environments. At the C-terminal end 

of the TIM barrel, a 4Fe-4S cluster is 

coordinated by the three cysteines of 

the CX3

CX2C motif, and a unique Fe of 

this cluster is coordinated by the amino 

and carboxyl groups of AdoMet. Buried 

deep in the center of the TIM barrel, a 

2Fe-2S cluster is coordinated by three 

cysteines and one arginine, each of 

which is absolutely conserved. DTB is 

BEAMLINE X25

Funding

National Institutes of Health; 

Searle Scholars Program; 

Cecil and Ida Green Career 

Development Fund; Lester 

Wolfe Predoctoral Fellowship; 

Cellular, Biochemical, and 

Molecular Sciences training 

grant; U.S. Department of 

Energy; National Institute of 

General Medical Sciences

Publication

F. Berkovitch, Y. Nicolet, 

J.T. Wan, J.T. Jarrett, and 

C.L. Drennan, "The Crystal 

Structure of Biotin Synthase, 

an S-AdenosylmethionineDependent Radical Enzyme," 

Science, 303, 76-79 (2004).

Contact information

Catherine Drennan 

Department of Chemistry, 

Massachusetts Institute of 

Technology

Email: cdrennan@mit.edu

Fred Berkovitch
SCIENCE HIGHLIGHTS 2-75

bound between AdoMet and the 2Fe-2S cluster (Figure 3). 

The coordination of the 4Fe-4S cluster by AdoMet ensures efficient electron 

transfer from the cluster to the cofactor. The donation of one electron by the 

4Fe-4S cluster to AdoMet results in reductive cleavage of the carbon-sulfur 

bond, generating the high-energy 5’-deoxyadenosyl radical (Ado•), an intermediate that has historically been associated with adenosylcobalamin (AdoCbl)-dependent radical enzymes. Ado• removes hydrogen atoms from DTB, preparing 

it for sulfur insertion. The unique 2Fe-2S cluster is proposed to be the S donor 

in the BioB reaction, and the close linear arrangement of AdoMet, DTB, and 

the 2Fe-2S cluster supports this hypothesis. It is possible that the arginine ligand 

plays a role in the reaction mechanism, or helps stabilize the 2Fe-2S cluster after 

sulfur insertion. 

The structures of BioB and diol dehydratase, an AdoCbl-dependent radical 

enzyme, show remarkable similarities. Both deploy the TIM barrel fold to bind 

their radical-generating cofactors. Moreover, the active sites of BioB and diol 

dehydratase show that the positions of the substrate, cofactors, essential metals, 

and secondary structural elements coincide. These structural similarities point to 

the evolutionary relationship between the AdoMet-dependent and AdoCbl-dependent radical enzymes.

Figure 3. The unique Fe-S clusters of 

BioB. The 4Fe-4S cluster is shown, 

coordinated by the CX3

CX2C motif 

and by the amino and carboxyl groups 

of AdoMet. The 2Fe-2S cluster is 

coordinated by three cysteines and one 

arginine. All ligands to both clusters 

are absolutely conserved.

Figure 1. The BioB dimer. BioB is a 

homodimer, composed of two TIM 

barrel protomers (colored different 

shades of green). The 4Fe-4S cluster, 

which is present in all AdoMet radical 

proteins, is located at the C-terminal 

end of the cluster. AdoMet (red sticks) 

coordinates a unique Fe of this cluster. 

The substrate, DTB (black sticks), is 

located between AdoMet and a 2Fe-2S 

cluster, which is buried in the core of 

the barrel and is proposed to be the S 

donor in the BioB reaction. Fe and S 

atoms are represented by brown and 

yellow spheres, respectively.

Figure 2. Reaction of BioB
2-76 LIFE SCIENCES 

Authors (left to right) 

Schoen Kruse and David Jones

Structure of a Specific Alcohol-Binding Site Defined by 

the Odorant Binding Protein LUSH from Drosophila 

Melanogaster

S.W. Kruse1, R. Zhao2, D.P. Smith3, and D.N.M. Jones1,4

Departments of 1Pharmacology, 2Biochemistry and Molecular Genetics, and the 4Program in Biomolecular Structure, University of Colorado Health Sciences Center; 3Department of Pharmacology and 

Center for Basic Neuroscience, University of Texas Southwestern Medical Center

LUSH is a non-enzymatic alcohol-binding protein that is required for a normal chemosensory response to alcohols, such as ethanol in the fruit fly Drosophila melanogaster. 

We have recently solved the structures of LUSH in complex with ethanol, n-propanol, 

and n-butanol to 1.49 angstroms (Å), 1.45Å, and 1.25Å, respectively. From these 

structures we have identified a set of inter-molecular interactions that act in concert 

with each other and may help to increase the binding affinity of alcohol to the protein, 

and thereby defines a specific alcohol-binding site. We propose that this structure may 

represent a general alcohol-binding motif that is believed to exist in a number of 

alcohol-sensitive ion channels in mammalian cells.

There is substantial evidence that many of the biochemical effects of alcohol are 

linked to changes in the structure and dynamics of a number of receptors in the 

central nervous system, including the gamma-amino butyric acid (GABA) and 

nicotinic acetylcholine (nAChR) receptors. Alcohol appears to bind to these receptors at specific sites, but the details of this interaction remain unclear because of 

the lack of structural information about these membrane-associated proteins. Our 

goal is to determine the molecular architecture of specific alcohol-binding sites 

through structural studies of a model protein, LUSH, from the fruit fly Drosophila 

melanogaster. In insects, odorant binding proteins are key components of the 

insect sensory system and bind to odor molecules from various sources, including those from food or other insects. LUSH is an odorant binding protein that is 

required for the normal behavioral response to alcohols. Adult flies have an active 

avoidance mechanism that responds to high concentrations of short chain alcohols, 

but this mechanism is defective in flies that lack the lush gene. LUSH was given its 

name because fruit flies without the corresponding gene are attracted to alcohol. 

From the high-resolution structures of LUSH determined by Miyazawa et al., we 

identified a structural motif that may provide a high-affinity alcohol-binding site. 

An essential part of this study was the availability of the “Mail-in Data Collection” 

program at the NSLS. Since we work 

in a laboratory that traditionally uses 

nuclear magnetic resonance (NMR) 

spectroscopy to analyze protein 

structures, this service gave our group 

rapid access to synchrotron beam 

time, which would have otherwise 

been difficult to obtain through a 

conventional application. In addition, 

we received expert assistance from 

NSLS staff, in particular Dr. Howard 

Robinson. LUSH protein labeled with 

BEAMLINE X12C

Funding

National Institutes of Health 

(National Institute on Alcohol 

Abuse and Alcoholism); 

American Heart Association

Publication

S.W. Kruse, R. Zhao, S.P. 

Smith, and D.N.M. Jones, 

"Structure of a Specific Alcohol-Binding Site Defined by 

the Odorant Binding Protein 

LUSH from Drosophila melanogaster," Nat. Struct. Biol., 

9, 694-700 (2003).

Contact information

David N.M. Jones

University of Colorado Health 

Sciences Center

Email: David.Jones@uchsc.edu
SCIENCE HIGHLIGHTS 2-77

seleno-methionine was crystallized at the University of Colorado Health Sciences Center and sent to the NSLS for data collection. As a result, we were able 

to solve the structure in a matter of weeks, rather than several months.

The structure of LUSH consists of six α-helices and a short segment of a 310-

helix that surround a central cavity that is hydrophobic (does not like aqueous 

environments) and contains the alcohol-binding site. The hydroxyl group of the 

alcohol forms hydrogen bonds (H-bonds) to two amino acids in LUSH, serine 

(Ser52) and threonine (Thr57), at one end of this cavity (Figure 1). The structure was solved in the presence of 30 to 50 millimolar (mM) alcohol, and under 

these conditions we only observe the one alcohol-binding site, suggesting that 

the chemistry within this site may have evolved to specifically bind alcohols. We 

hypothesize that this is a result of the side-chain hydroxyl of Ser52 making an 

H-bond to the main-chain oxygen of Thr48, another amino acid, increasing the 

ability of the side chain of Ser52 to accept a H-bond from the alcohol. The positioning of Thr57 as a H-bond donor to the alcohol may simultaneously make 

the alcohol a better H-bond donor to Ser52. 

The recent structure of the nAChR from the Torpedo Ray suggests the possibility that serine and threonine residues could be positioned within the protein 

interior to make a set of concerted interactions with alcohol in a manner analogous to that seen in LUSH. If so, then as the acetylcholine receptor is the archetypal model for several receptors implicated in the effects of alcohol consumption. We suggest that the alcohol-binding site defined in LUSH may represent a 

general model for alcohol binding in other proteins. We are now testing the role 

that individual amino acids play in binding alcohol by solving the structure of 

proteins that have undergone amino acid substitutions. We believe these structures will provide further insights into the nature of alcohol-binding sites.

Figure 1. A surface representation of 

key residues in the LUSH alcoholbinding pocket. The pocket is lined 

with hydrophobic residues with the 

exception of Thr57 and Ser52, which 

form concerted hydrogen bonds with 

the alcohol. Ethanol is shown in a stick 

representation. The hydrogen bonds 

between the alcohol and the hydroxyl 

groups of Thr57 and Ser52 are shown 

as yellow dotted lines.
2-78 LIFE SCIENCES 

Crystal Structure of LeuA from Mycobacterium 

Tuberculosis, a Key Enzyme in Leucine Biosynthesis

N. Koon1,2, C.J. Squire1,2, and E.N. Baker1,2,3

1Centre for Molecular Biodiscovery; 2School of Biological Sciences; and 3Department of Chemistry, 

University of Auckland

The leucine biosynthetic pathway is essential for the growth of Mycobacterium tuberculosis, and is a potential target for the design of new anti-tuberculosis drugs. We have 

used multiwavelength anomalous diffraction (MAD) phasing to determine the highresolution crystal structure of α-isopropylmalate synthase, the product of the leuA gene. 

The structure reveals a tightly associated dimer comprised of an (α/β)

8

 barrel catalytic 

domain joined by flexibly-hinged linker domains to a C-terminal regulatory domain. 

The structure shows how the substrate, the leucine precursor α-ketoisovalerate, binds to 

an essential zinc atom in the catalytic domain, and a potential mechanism of feedback 

inhibition by leucine binding in the regulatory domain.

Tuberculosis (TB) is responsible for more deaths worldwide than any other infectious disease – more than two million each year, with an estimated one third of the 

world’s population infected. The problem is compounded by the length of current 

treatments and by the ability of Mycobacterium tuberculosis, the causative agent, to 

survive in a dormant state inside activated macrophages in the lung for long periods of time, emerging many years later as active infections. Multi-drug resistance 

is also a growing problem. The genome sequence of M. tuberculosis, completed in 

1998, has stimulated new approaches, including the formation of the TB Structural Genomics Consortium. Our goals, as part of this consortium, are to determine 

the three-dimensional structures of proteins that are potential new targets for TB 

drug development or that will help to understand TB biology.

The biosynthetic pathways for the branched-chain amino acids leucine, isoleucine 

and valine (i.e. the series of enzyme reactions that produce these amino acids) are 

essential for the survival of the TB organism. These pathways are not present in 

humans, indicating that inhibitors targeted against enzymes from them could be 

useful as anti-TB drugs. We chose the enzyme α-isopropylmalate synthase (αIPMS), the product of the leuA gene, for structural analysis. This enzyme catalyzes 

the first step in leucine biosynthesis, in which an acetyl group is transferred from 

acetyl-coenzymeA to the substrate α-ketoisovalerate (α-KIV), the leucine precursor. The enzyme was known to be dimeric (2 x 70 kDa), metal ion-dependent, and 

subject to feedback inhibition by the end product leucine, but its three-dimensional structure was unknown.

The structure was solved using multiwavelength anomalous diffraction (MAD) 

data from a selenomethioninesubstituted α-IPMS crystal, 

which was frozen and sent from 

New Zealand to beamline X8C 

(FedEx crystallography) for data 

collection. The data quality 

was such that 70% of the 1288 

residues in the dimer could be 

BEAMLINE X8C

Funding

Health Research Council of 

New Zealand

Publication

N. Koon, C. J. Squire, and E. 

N. Baker, "Crystal Structure 

of LeuA from Mycobacterium 

Tuberculosis, a Key Enzyme 

in Leucine Biosynthesis," 

Proc. Natl. Acad. Sci. USA, 

101, 8295-8300 (2004).

Contact information

Edward N. Baker

School of Biological Sciences, 

University of Auckland, New 

Zealand

Email: ted.baker@auckland.ac.nz

Authors (left to right) 

Ted Baker, Chris Squire, and Nayden Koon
SCIENCE HIGHLIGHTS 2-79

immediately traced and autobuilt. The structure was then completed and refined 

at 2.0 Å resolution. Α spherical peak for a bound metal ion, marking the active 

site of each monomer, was identified by a fluorescence scan as zinc. We also 

subsequently prepared complexes with α-KIV (substrate) and leucine (feedback 

inhibitor).

The α-IPMS monomer is folded into three domains (Figure 1), an (α/β)

8

 barrel 

catalytic domain, a helical linker domain, and a C-terminal domain of novel 

fold. Two α-IPMS monomers form a domain-swapped dimer in which the 

linker domain of one monomer sits over the catalytic domain of the other. This 

domain swapping makes the active site almost completely enclosed, except for a 

tunnel that allows the entry of substrates. In the crystal structure, the substrate 

α-KIV is bound to the zinc (Figure 2A), and although acetyl-CoA is not present, two water molecules mark where the acetyl group would sit, adjacent to αKIV. With this information we can propose a catalytic mechanism for α-IPMS, 

based on that of malate synthase, an enzyme that is evolutionarily unrelated but 

carries out a very similar reaction on a very similar substrate.

Several features make the α-IPMS structure suitable for drug development: 

the zinc ion as a template for inhibitor binding and surrounding invariant side 

chains inside the enclosed active site cavity. The structure also reveals an intriguing mechanism for feedback inhibition. Leucine binds in the regulatory 

C-terminal domain (Figure 2B) 70 Å away from the nearest active site, but this 

binding must be signalled via the flexible linker domain, which inserts two key 

residues into the active site.

Figure 2. Close-up of the ligand 

binding sites. (A) The α-KIV substrate 

(shown in its electron density as a 

blue mesh), bound to zinc. Two water 

molecules (small red spheres) mark 

where the acetyl group of acetyl-CoA 

would bind. The side chains of His379 

and Tyr410 are from helix α10 of 

the other monomer, which covers the 

active site. (B) A leucine molecule 

bound in the regulatory domain with 

its carboxyl group between two helices.

Figure 1. Ribbon diagram of the LeuA 

dimer. One monomer is in green. The 

other is colored to show the three 

domains: the N-terminal catalytic 

domain (light blue), the central linker 

domain (shown as red and yellow 

subdomains), and the C-terminal 

regulatory domain (dark blue). The 

active site of each monomer is shown 

by the zinc atom (magenta sphere) and 

bound α-KIV substrate. Each active 

site is covered by helix α10 from the 

other monomer of the dimer. A leucine 

molecule is shown bound in the 

regulatory domain.
2-80 LIFE SCIENCES 

BEAMLINE X4A

Funding

National Institutes of Health; 

The McKnight Foundation; 

The EJLB Foundation; The 

American Heart Association

Publication

Y-h. Chen, M-h. Li, Y. 

Zhang, L-l. He, Y. Yamada, 

A. Fitzmaurice, Y. Shen, H. 

Zhang, L. Tong, and J. Yang. 

“Structural Basis of the α1−β

Interaction of Voltage-Gated 

Ca2+ Channels,” Nature, 429, 

675-680 (2004).

Contact information

Prof. Jian Yang

Department of Biological Sciences, Columbia University

Email: Jy160@columbia.edu

Yu-hang Chen

Structural Basis of the α1−β Subunit Interaction of 

Voltage-Gated Ca2+ Channels

Y.-h. Chen, M.-h. Li, Y. Zhang, L.-l. He, Y. Yamada, A. Fitzmaurice, Y. Shen, H. Zhang, 

L. Tong, and J. Yang

Department of Biological Sciences, Columbia University

High voltage-activated (HVA) Ca2+ channels in cell membranes control diverse biological processes, such as muscle contraction and hormone release. They are composed of α1

, 

α2-δ, β, and sometimes γ, subunits. The proper expression and function of HVA Ca2+

channels are critically dependent on the β subunit, which binds directly to the α interaction domain (AID) in α1

, presumably through the β interaction domain (BID). We 

have solved the crystal structure of the conserved core region of β3

, alone and in complex 

with AID, and of β4

 alone. The structures show that the β core contains two common 

protein-interacting domains (an Src homology 3 (SH3) domain and a guanylate kinase 

(GK) domain) and that AID does not bind to BID. These represent the first crystal 

structures of a Ca2+ channel subunit or domain and suggest that β may be a multifunctional protein.

There are four subfamilies of Ca2+ channel β subunits (β1

-β4). Each β subunit contains five regions, with the three middle regions forming a core that can perform 

most functions of full-length β. The crystal structure of the β3

 core in complex 

with a 49-amino acid segment of α1

, which contains the 18-amino acid α interaction domain (AID) (at 2.6 Å-resolution), shows that the three regions comprising the β core are: an Src homology 3 (SH3) domain, a guanylate kinase (GK) 

domain, and a “HOOK” region that connects them (Figure 1A). The SH3 and 

GK domains interact intramolecularly. The AID forms an α-helix and binds to a 

hydrophobic (water-fearing) groove in the GK domain. The interactions between 

AID and β are extensive, involving hydrophobic interactions, hydrogen bonds, 

and an ion pair (Figure 1B). These interactions form the basis for the high-affinity 

binding between α1

 and β. Most of the amino acids involved in the interactions 

are conserved in both subunits. The structure also reveals that the β interaction 

domain (BID) spans all three regions of the SH3-HOOK-GK motif and is thus 

crucial for the intramolecular interaction between the SH3 and GK domains, as 

well as their structural integrity. But, it is not directly involved in binding AID 

(Figure 1A). 

The overall structure of the unliganded (unbound) β3

 core is very similar to that of 

the β3

 core bound to AID, indicating that AID binding does not change the β subunit structure. Also, as predicted by the high amino acid similarity, the structure of 

the β4

 core is nearly identical to that of the β3 core.

The β subunit SH3 domain (β-SH3) 

is structurally similar to canonical SH3 domains, but, unlike the 

continuous configuration of the latter, 

β-SH3 is split, with a separate, flexible HOOK region inserted between 

the first four β strands and the last 

one. Furthermore, although β-SH3 
SCIENCE HIGHLIGHTS 2-81

Figure 2. Structural and functional comparisons of β with PSD95. (A) 

Whole-oocyte current measured in oocytes injected with Cav2.1 (α1

) and 

α2

-δ only (β−) or together with the indicated construct. β3_GK represents 

amino acids M177-G366 of β3

; PSD95_SHG represents the SH3-HOOKGK motif (amino acids G473-L767) of PSD95; and PSD95_GK represents 

the GK domain (amino acids H575-S755) of PSD95. The current was 

normalized using the mean current obtained with wild-type β3

. (B) 

Superposition of the GK domain of unliganded β3

 (green) and PSD95 

(1KJW, pink). Only the region around the AID binding site is shown. 

Secondary structures are labeled only for β3

. 

Figure 1. Crystal structure of the β3

core in complex with its α1

 binding 

partner (AID). (A) The β3

 core can 

be divided into three regions: an 

SH3-domain (gold), a HOOK region 

(purple), and a GK domain (green). 

The AID and BID are colored in 

orange and blue, respectively. (B) 

Close-up of the interface between β3

and AID. Most residues involved in the 

interactions are shown.

possesses several amino acids critical for binding PXXP motifs (molecules that 

typically bind to SH3 domains), it is unlikely to interact with PXXP-containing 

proteins because the binding site is shielded by part of the HOOK. Likewise, 

although the overall structure of the β subunit GK domain (β-GK) is similar to 

that of the yeast GK domain, it is catalytically inactive. Thus, the function of the 

β subunit SH and GK domains remains to be determined. 

Interestingly, the SH3-HOOK-GK motif is also a common structural signature 

of a family of proteins called membrane-associated guanylate kinase homologs 

(MAGUKs). Many members of this family, including PSD95, are concentrated 

at the boundaries between neurons, or “synapses,” as are HVA Ca2+ channels, 

and play a central role in clustering and organizing both pre- and post-synaptic 

ion channels and neurotransmitter receptors. Electrophysiological studies indicate that the PSD95 SH3-HOOK-GK and PSD95_GK do not interact with 

HVA Ca2+ channels (Figure 2A). A comparison of the structure of PSD95_GK 

and β_GK clearly reveals why: The AID-binding pocket is completely blocked 

in PDS95_GK (Figure 2B). Our study thus provides a structural basis for the 

specificity of Ca2+ channel β subunits and MAGUK proteins.

(A)

(B)

(A) (B)
2-82 LIFE SCIENCES 

Structure of Mammalian Protein Geranylgeranyltransferase Type-I

T.S. Reid, J.S. Taylor, K.L. Terry, and L.S. Beese

Department of Biochemistry, Duke University Medical Center

Protein geranylgeranyltransferase type-I (GGTase-I) is an essential enzyme in eukaryotes. GGTase-I catalyzes an essential reaction in which a specific lipid group, acting as 

a substrate, becomes covalently attached to proteins involved in cell growth and differentiation, allowing these proteins to associate with the cell membrane. We present the 

first structural information for mammalian GGTase-I, including a series of substrate 

and product complexes that delineate the path of the chemical reaction. These structures reveal that all protein prenyltransferases share a common reaction mechanism and 

identify specific amino acid residues that play a dominant role in selecting the correct 

lipid substrate. Protein prenyltransferase inhibitors are under evaluation in phase III 

clinical trials for the treatment of cancer and show promise for the treatment of parasitic 

infections, including malaria.

Over 100 proteins involved in cell growth and differentiation require the covalent 

attachment of an iosprenoid lipid, a process called prenylation, for membrane 

association and proper function. The three known enzymes that catalyze protein 

prenylation are GGTase-I, protein farnesyltransferase (FTase), and Rab GGTase. 

GGTase-I performs the bulk of cellular prenylation, and inhibiting its function has 

dramatic biological effects, such as blocking cell growth and promoting apoptosis, 

the natural death of a cell. 

The structure of GGTase-I was determined by a method called single isomorphous 

replacement with anomalous scattering (SIRAS). There are six GGTase-I molecules 

(each is 91 kilo-Daltons in size), or approximately 33,000 non-hydrogen atoms, 

in each asymmetric unit. The overall structure of GGTase-I is shown in Figure 

1A. The α subunit is composed of α-helical pairs, forming a crescent that wraps 

around the compact α-α barrel of the β subunit, and the active site opens into 

the central funnel-shaped cavity of the β subunit. At the rim of the active site is a 

catalytic zinc ion.

We have captured four crystal structures representative of the GGTase-I reaction 

cycle (Figure 2). The first step in the reaction cycle is the binding of the 20-carbon 

(20-C) lipid substrate geranylgeranyl diphosphate (GGPP, Figure 1B). GGPP 

binds in the GGTase-I active site with the first three isoprene units of the lipid 

group arranged along a straight line and the fourth isoprene unit turned approximately 90 degrees relative to this axis (Figure 1C). This structure permitted us to 

identify residues that are responsible for selecting the correct lipid substrate. To 

test this hypothesis, a single point 

mutation was constructed, which 

converted the lipid specificity 

of FTase (15-C lipid substrate) 

to that of GGTase-I (20-C lipid 

substrate) (Figure 1C). Following GGPP binding, the next step 

in the reaction cycle is substrate 

Authors (left to right) 

Lorena Beese, Kimberly Terry, and Scott Reid

BEAMLINES

X12B, X25

Funding

National Institutes of Health; 

Postdoctoral Fellowship from 

the American Heart Association

Publication

J.S. Taylor, T.S. Reid, K.L. 

Terry, P.J. Casey, and L.S. 

Beese, "Structure of Mammalian Protein Geranylgeranyltransferase Type-I.," EMBO 

J., 22, 5963-5974 (2003).

Contact information

Lorena S. Beese

Department of Biochemistry, 

Duke University

Email: lsb@biochem.duke.edu
SCIENCE HIGHLIGHTS 2-83

peptide binding (Figure 2-2). GGTase-I recognizes peptides that contain a Cterminal Ca1

a2X box, defined by the cysteine (C), two aliphatic residues (a1a2), 

and a variable C-terminal residue (X), which determines whether the protein is 

a substrate for GGTase-I, FTase, or both. The Ca1

a2X box binds in an extended 

conformation, with the cysteine coordinating the catalytic zinc and hydrogen 

bonds that anchor the carboxyl-terminus. After catalysis, the peptide-prenyl 

product is retained by the enzyme (Figure 2-3). Comparing complexes 2 and 

3 illustrates that the lipid substrate undergoes a conformational change during 

the transition state that brings it in-line for catalysis. GGPP binding partially 

displaces the product from the active site: The Ca1

a2X peptide adopts an alternate conformation, and the product lipid group translocates (to make room for 

the incoming GGPP) into a shallow, solvent-accessible groove, called the “exit 

groove” (Figure 2-4). The dissociation of the product, which is accelerated by 

fresh substrate peptide, allows the reaction cycle to repeat. 

The structural snapshots of the GGTase-I reaction cycle are consistent with the 

unusual reaction mechanism proposed for FTase, thereby indicating that this 

cycle is a common feature of the protein prenyltransferase family. Overall, these 

structures, when contrasted with FTase, reveal the dominant structural features 

responsible for substrate selectivity. Protein prenyltransferases are promising 

targets for chemotherapy drugs, but further development may require designing 

drugs that are highly selective for one enzyme. This work, along with our earlier 

work on FTase, provides a foundation for structure-based design and the optimization of drugs that are specific to a particular protein prenyltransferase.

Figure 1. (A) GGTase-I ternary 

substrate complex. The GGTase-I 

consists of a 48 kilo-Dalton (kDa) α

subunit (red) and a 43 kDa β subunit 

(blue). The non-reactive 3’azaGGPP 

(cyan) binds similarly to GGPP in the 

active site. The Ca1

a2X portion of the 

KKKSKTKCVIL peptide substrate 

(yellow) binds against the isoprenoid, 

with the cysteine sulfur coordinating 

the catalytic zinc ion (magenta). (B) 

Geranylgeranyl diphosphate (GGPP) 

has four isoprene units; farnesyl 

diphosphate (FPP) has three. (C) 

Comparison of lipid substrate binding 

in FTase (blue) and GGTase-I (red). In 

FTase, the larger tryptophan residue 

fills the space where the additional five 

carbons of GGPP bind in GGTase-I 

and is one of the prime determinants 

of lipid substrate specificity. Mutation 

of the tryptophan residue to the 

equivalent GGTase-I threonine residue 

resulted in an FTase mutant that 

prefers the 20-C GGPP as a lipid 

substrate over the typical 15-C FPP 

lipid substrate.

Figure 2. Structures of the GGTase-I 

reaction cycle. The GGTase-I active 

site is shown in stereo as a molecular 

surface, with the α subunit colored 

red, the β subunit blue, and the exit 

groove highlighted in cyan. Complex 

1: The enzyme with bound GGPP. 

Complex 2: Ternary complex with 

3’azaGGPP analog and Ca1

a2X 

peptide substrate (only CVILCOOH

shown). Complex 3: Prenylated 

peptide product complex. Complex 4: 

Displaced prenylated peptide product 

and GGPP.

(A)

(B)

(C)
2-84 LIFE SCIENCES 

BEAMLINE X9B

Funding

National Institutes of Health 

National Cancer Institute

Publication

S. Banumathi, P.H. Zwart, 

U.A. Ramagopal, M. Dauter, 

and Z. Dauter, "Structural 

Effects of Radiation Damage 

and its Potential for Phasing," 

Acta Cryst., D60, 1085-1093 

(2004).

Contact information

Zbigniew Dauter

Argonne National Laboratory

Email: dauter@anl.gov

Structural Effects of Radiation Damage and its 

Potential for Phasing

S. Banumathi1, P.H. Zwart2, M. Dauter2, and Z. Dauter1

1Synchrotron Radiation Research Section, MCL, National Cancer Institute, Brookhaven National 

Laboratory; 2SAIC Frederick, Inc., Basic Research Program, Brookhaven National Laboratory

We have carried out a detailed analysis on the structural effects of radiation damage on 

the model protein thaumatin. The most pronounced structural changes observed were 

disulfide bond breakage and the associated main and side chain movements, as well 

as the decarboxylation of the aspartate and glutamate residues. The structural changes 

induced on the sulfur atoms were used successfully to solve the structure via a Radiationdamage Induced Phasing (RIP) procedure.

Radiation damage has been a curse of macromolecular crystallography from its 

early days. Until the 1990s all diffraction data were collected from macromolecular 

crystals mounted in glass or quartz capillaries and kept at ambient temperature, in 

the range of 4-20°C. Initially, collecting data from protein crystals using precession 

cameras or multi-circle diffractometers took a very long time. The introduction of 

the screenless rotation method considerably sped up this process by recording more 

reflections simultaneously. Still, only the most robust crystals were able to deliver 

all the necessary data from one specimen, and very often a complete data set had to 

be combined from data measured on several crystals. Although the advent of cryocooling techniques, where diffraction data is obtained from crystals cooled down to 

approximately 100K, substantially alleviated the problem of radiation damage, the 

obvious deterioration of cryo-cooled crystals at bright undulator beamlines revived 

interest and prompted several investigations into the effects of radiation damage.

Whereas previous structural radiation damage studies have been carried out at 

third-generation synchrotron sources, the effects of radiation damage on protein 

crystals can be also observed after prolonged exposures at second-generation bending magnet synchrotron beamlines. We have analyzed the effects of radiation damage on crystals of thaumatin, a medium-sized protein containing 207 amino acids, 

including eight disulfide bridges. We collected twenty high-resolution data sets 

that allowed us to perform a detailed 

investigation of the structural changes 

induced by x-ray irradiation. 

The structural changes induced by 

radiation damage can be visualized using difference Fourier maps that reveal 

the appearance or disappearance of 

electrons on and around the molecular model. The most striking features 

our analyses revealed are the breakage 

of disulfide bonds and the associated 

main and side chain movements, as 

shown in Figure 1. Less prominent, 

but still significant, structural changes 

Authors (clockwise from top left) 

Peter Zwart, Mirka Dauter, Zbigniew Dauter, and 

Banumathi Sankaran 
SCIENCE HIGHLIGHTS 2-85

involve the decarboxylation of side chains and water molecule movements.

As can be seen from Figure 1, the amount of electrons relocated over the course 

of the experiment is quite large. This suggests that the observed changes in 

the diffraction intensities are dominated by this structural change and that the 

disulfide bridges can be located using the isomorphous difference only. When 

this so-called substructure is located, standard procedures can be used to obtain 

an image of the three-dimensional electron density of the protein, which finally 

results in an atomic model of the protein under investigation. Normal phasing 

techniques use chemical or biochemical methods in order to generate a so-called 

derivative. In this case, the interaction of the x-rays with the protein produces 

a derivative suitable for phasing, hence the name Radiation-damage Induced 

Phasing (RIP). In the investigated case, the electron density estimates that result 

from various standard crystallographic computations are of such a high quality 

that they can be easily interpreted, as indicated in Figure 2.

Figure 2. An electron density map calculated with solvent flattened 

RIP phases overlaid on the final model.

Figure 1. Positive and negative 

difference Fourier maps showing 

the disappearance of electrons in 

red and the appearance of electrons 

in green over the course of the data 

collection. The pattern of negative 

(red) and positive (green) peaks 

suggests that, upon the breakage of 

the disulfide bond CYS134-CYS145, 

the sulfur atoms ‘swing out’ while 

the surrounding main and side chain 

positions are affected.
2-86 LIFE SCIENCES 

Amphiphilic 4-Helix Bundles Designed for 

BioMolecular Materials Applications

S. Ye, J.W. Strzalka, S. Zheng, T. Xu, J.K. Blasie, B.M. Discher, D. Noy, and P.L. Dutton

Department of Chemistry, University of Pennsylvania

Artificial peptides previously designed to possess α-helical bundle motifs have been either 

hydrophilic (soluble in polar media) or lipophilic (soluble in non-polar media) in their 

overall character. The realization of these bio-inspired bundles has led to the reproduction of a variety of biomimetic functions within the appropriate media. To translate 

this functionality into useful biomolecular devices, the bundles must be oriented in a 

macroscopic ensemble, e.g., at an interface. This goal has been achieved in a new family of α-helical bundle peptides that are amphiphilic, meaning they have well-defined 

hydrophilic and hydrophobic domains. This peptide family binds metallo-porphyrin 

prosthetic groups at selected locations within these domains to impart functionality.

Bundles of α-helices provide a robust scaffold for binding prosthetic groups (nonamino acid portions of proteins) at selected locations within the structure, which 

is necessary in order to mimic the functions exhibited by biological proteins. To 

be used in device applications, the peptide bundles must be vectorially oriented 

in an ensemble, e.g., at an interface. In order to generate vectorial function across 

an interface, we have investigated two approaches that are designed to render the 

4-helix bundles themselves amphiphilic such that they possess both a hydrophilic 

and a hydrophobic domain along the length of each bundle. 

In the first approach, each α-helix is designed to be amphipathic, i.e. having polar 

and non-polar faces. However, the amino acid sequence was oriented such that 

when the non-polar faces of each amphipathic helix were apposed in the 4-helix 

bundle over the first m-residues of each helix, the polar faces were apposed over 

the last n-residues. Thus, a 4-helix bundle with parallel (or syn) topology would 

possess a charged-polar exterior with a non-polar interior over the first m-residues, 

thereby forming the hydrophilic domain of the bundle, and a non-polar exterior 

with an uncharged-polar interior over the last n-residues, thereby forming the hydrophobic domain. The first of these amphiphilic 4-helix bundles was designated 

Amphiphilic Protein zero (AP0). AP0 can possess bis-histidyl metalloporphyrin 

binding sites at two positions of the sequence, which are separated by fourteen 

residues within the larger hydrophilic portion of the 4-helix bundle. 

Alternatively, these amphiphilic peptides (the second case) can possess a hydrophobic domain that utilizes a sequence of exclusively non-polar amino acids. Like 

AP0, these amphiphilic peptides 

can possess bis-histidyl metalloporphyrin binding sites within 

the hydrophilic portion of the 

4-helix bundle. Importantly, 

they can also possess bis-histidyl 

metalloporphyrin binding sites in 

the hydrophobic portion of the 

bundle. These two new types of 

amphiphilic 4-helix bundles now 

BEAMLINE X22B

Funding

National Science Foundation 

U.S. Department of Energy

Publication

S. Ye, B.M. Discher, J.W. 

Strzalka, D. Noy, S. Zheng, 

P.L. Dutton, and J.K. Blasie, 

"Amphiphilic 4-Helix Bundles 

Designed for BioMolecular 

Materials Applications," Langmuir, 20(14), 5897-5904 

(2004).

Contact information

Prof. J. Kent Blasie

Department of Chemistry, 

University of Pennsylvania

Email: jkblasie@sas.upenn.edu

Authors (left to right) 

Ting Xu, Shixin Ye, and Joseph Strzalka
SCIENCE HIGHLIGHTS 2-87

allow for the positioning of prosthetic groups on either side or both sides of the 

interface. This is essential for the vectorial electron transfer across the interface, 

which creates an electrochemical potential. This transforms a designed molecular property at the microscopic level into a material property of the interface at 

the macroscopic level.

Figure 1. (A) Fresnel-normalized x-ray reflectivity data collected from a Langmuir monolayer of pure 

AP0 at surface pressures (π) of 10, 20, 30, and 45 mN/m. The data were collected on the liquid surface 

spectrometer on beamline X22B. The continuous curves are calculated from the box-refinement solution 

to the phase problem, thus providing the gradient electron density profiles (not shown). (B) The 

autocorrelation function of the monolayer gradient electron density profile (computed from the data in 

(A)) without phase information at π = 10 (long dash), 20 (short dash), 30 (dot), and 45 mN/m (solid). 

(C) The absolute electron density profiles for the monolayer at each pressure (same symbols as in (b)), 

computed by analytic integration of a sum of Gaussian functions that best fit the gradient profiles from box 

refinement. (D) A schematic illustration of the surface pressure-dependent orientational transition of AP0 

at the air-water interface; the air-water interface is indicated by the plane. At lower surface pressures of 10, 

20, and 30 mN/m, both the autocorrelation functions and the electron density profiles indicate that the 

long axis of the helices lies parallel to the interface, although the plane of the di-helices rotates from parallel 

to perpendicular to the interface with increasing pressure. When the pressure reaches 45 mN/m, both the 

autocorrelation function and the electron density profile indicate that all of the AP0 helices are oriented 

with their long axis normal to the plane of the air/water interface. However, the packing of the molecule 

along the surface cannot be derived from the electron density profile. An analysis of grazing-incidence 

x-ray diffraction from these monolayers, collected at Sector 09 at the Advanced Photon Source using a 

new version of the liquid surface spectrometer (developed by Ben Ocko and Scott Coburn, BNL Physics 

Department) and an undulator source, has shown that the bundles are indeed comprised of four helices and 

that the arrangement within the bundle cross-section is square rather than close-packed.

Figure 2: The amphiphilic 4-helix bundles can bind not only metallo porphyrin prosthetic groups, but 

also non-biological prosthetic groups possessing much more extended π-electron systems. These nonbiological groups have the advantage of including the electron donor and the electron acceptor within the 

same prosthetic group, which is bound to the 4-helix bundle via only a single bis-histidyl site. An example 

of such a prosthetic group (synthesized and characterized by Prof. Michael Therien’s research group in the 

Chemistry Department at the University of Pennsylvania) is shown, symmetric in this instance, with its 

anticipated location within AP0; the hydrophobic domain of the bundle is shown in green. The changes 

(red-shifts) in the rich electronic spectrum of this prosthetic group upon binding to the peptide are also 

shown. In addition, the vectorial incorporation of this symmetric prosthetic group into the amphiphilic 4-

helix bundle via a single bis-histidyl site breaks the symmetry, which should result in an exceptionally large 

molecular hyperpolarizability, as exhibited by closely related asymmetric, extended π-electron systems. The 

vectorial orientation of the 4-helix bundles in a two-dimensional ensemble at an interface between polar 

and non-polar media should then allow large second-order non-linear optical phenomena to be generated at 

the interface.

R/Rρ

q'z

(Å-1)

P(z)=<dρ(z)/dz>*<dρ(-z)/dz>

Z(Å)

ρ/ρ water

Z(Å)

Intensity (a.u)

Wavelength (nm)

(A)

(B)

(C)

(D)
2-88 LIFE SCIENCES 

The Crystal Structure of Activated Protein 

C-Inactivated Bovine Factor Va: Implications for 

Cofactor Function

T.E. Adams1, M.F. Hockin2, K.G. Mann2, and S.J. Everse1

1Department of Biochemistry, University of Vermont; 2Department of Human Genetics, Howard 

Hughes Medical Institute, University of Utah

Within the blood coagulation cascade, the process by which blood clots, factor Va serves 

as an essential protein cofactor for the efficient generation of thrombin, the primary 

blood-clotting enzyme. Upon the formation of the prothrombinase complex with factor Xa on a membrane surface, factor Va increases the catalytic efficiency of factor Xa 

300,000-fold. The crystal structure of activated protein C (APC)-inactivated factor 

Va (Vai

) is the first view of this multi-domain cofactor and begins to address questions 

regarding its mechanism, including membrane binding, chain association, and complex 

assembly.

The majority of deaths throughout the world can be either directly or indirectly 

attributed to an imbalance in hemostasis, which leads to thrombosis – a blood clot. 

Under normal circumstances hemostasis is defined as the process that stops bleeding by activating the blood coagulation cascade. An action central to this cascade 

is the catalytic acceleration of each step through the assembly of the vitamin Kdependent enzyme complexes. This culminates in the conversion of prothrombin, 

an inactive zymogen in blood plasma, to its enzyme counterpart, thrombin, by the 

prothrombinase complex.

Factor V circulates in the plasma as a pro-cofactor comprised of six domains (A1-

A2-B-A3-C1-C2). Thrombin activates factor V by excising the B domain, forming 

the heterodimer factor Va, composed of a heavy chain (A1-A2) and a light chain 

(A3-C1-C2) associated in a calcium-dependent manner. During the initial stages 

of coagulation, factor Va actively recruits the enzyme, factor Xa, and the substrate, 

prothrombin, to the membrane surface of activated platelets. Condensation of 

this enzyme-substrate pair on a surface contributes to the explosive generation of 

thrombin observed in vivo. The reaction is regulated through the inactivation of 

factor Va by APC, which removes the A2 domain, forming factor Vai

 and shutting 

down thrombin production. A common polymorphism in which a single APC 

cleavage site is removed, factor VLeiden, significantly increases the risk of thrombosis 

by sustaining factor Va activity.

We recently solved the crystal structure of bovine factor Vai

. This structure reveals 

a novel domain architecture that suggests a new mechanism for cofactor function (Figure 1). Our structure 

includes two A domains (A1 & 

A3), each encompassing two 

plastocyanin-like folds, and 

two C domains (C1 & C2) 

with weak homology to the 

discoidin family of lipid-binding proteins. In fact, historical 

BEAMLINES

X12C, X25

Funding

National Institutes of 

Health; American Society of 

Hematology Scholar Award; 

U.S. Department of Energy 

EPSCoR Fellowship; HHMI 

Support Program for Medical 

Schools

Publication

T.E. Adams, M.F. Hockin, 

K.G. Mann, and S.J. Everse, 

"The Crystal Structure of Activated Protein C-inactivated 

Bovine Factor Va: Implications for Cofactor Function," 

Proc. Natl. Acad. Sci. USA, 

101(24), 8918-23 (2004).

Contact information

Stephen J Everse

Department of Biochemistry, 

University of Vermont

Email: Stephen.Everse@uvm.edu

Authors (left to right)

Kihachiro Umezaki, Stephen J. Everse, 

Sara K. Briggs, and Ty E. Adams
SCIENCE HIGHLIGHTS 2-89

data concerning the membrane binding ability of factor V has been localized 

to the C domains, primarily the C2 domain, and previous hypothetical models 

have proposed that membrane interaction is mediated strictly by the C2 domain. However, we found that the C domains in factor Vai

 are oriented in such 

a way that both domains may potentially interact with the membrane. 

At the base of each C domain, several loops adopt an extended conformation 

and expose several hydrophobic residues at the apex of these loops (Figure 2). In 

the literature, these loops are referred to as “spikes” and have been postulated to 

be critical phospholipid-binding sites. Indeed, mutations of these loops within 

the C2 domain have been shown to reduce or knockout cofactor activity. Recent 

information has also shown that mutation of key hydrophobic residues within 

the spikes of the C1 domain decreases the membrane binding potential and activity of the cofactor. Along with our structure, this suggests that the C1 domain 

is important for membrane interaction and cofactor function.

Our structure provided the first glimpse into how this cofactor, as well as the 

homologous cofactor factor VIII, functions in coagulation. We can now use this 

information to develop improved methods of controlling coagulation in vivo for 

the treatment of thrombosis in such cases as factor VLeiden and explain hemophilia in various factor VIII mutations.

Figure 2. Membrane binding domains. 

The three loops that compose the 

“spikes” in each domain are marked 

with arrows. Residues important for 

membrane interaction are shown as 

ball-and-stick.

Figure 1. Ribbon diagram of the 

structure of bovine factor Vai

 (PDB 

ID code 1SDD). The domains are 

colored as follows: A1 (red), A3 (blue), 

C1 (green), and C2 (yellow). The two 

metal ions, calcium and copper, are 

shown as magenta and green spheres, 

respectively. The five carbohydrates are 

shown in grey as ball-and-stick.
2-90 LIFE SCIENCES 

An Asymmetric Complex of Restriction Endonuclease 

MspI on its Palindromic DNA Recognition Site

Q.S. Xu1, R.B. Kucera2, R.J. Roberts2, and H.-C. Guo1

1Department of Physiology and Biophysics, Boston University School of Medicine; 2New England 

Biolabs 

Most well-known restriction endonucleases recognize palindromic DNA sequences 

and are classified as Type IIP. Due to the recognition and cleavage symmetry, Type IIP 

enzymes are usually found to act as homodimers in forming two-fold symmetric enzyme-DNA complexes. Now we find an asymmetric complex of the Type IIP restriction 

enzyme MspI in complex with its cognate recognition sequence. Unlike any other type 

IIP enzyme reported to date, a MspI monomer and not a dimer binds to a palindromic 

DNA sequence. The enzyme makes specific contacts with all four base pairs in the recognition sequence. This MspI-DNA structure represents the first example of asymmetric 

recognition of a palindromic DNA sequence by two different structural motifs in one 

polypeptide.

Restriction endonucleases (REases) are enzymes that recognize specific DNA 

sequences and cleave at the sugar-phosphate backbone of DNA. They are components of restriction-modification systems that protect bacteria from invasive foreign 

DNA. However, REases are best known for their roles in recombinant DNA technology and genetic manipulation. More than 3,570 REases with 240 unique specificities have been biochemically characterized. Of the 588 commercially available 

REases, a great majority recognize double-strand DNA sequences of 4-8 base-pairs 

with a dyad axis of symmetry, called palindromes. In the presence of Mg2+, these 

REases cleave both strands of the DNA at fixed symmetrical locations to generate 

cohesive or blunt ends suitable for molecular cloning. These symmetrically cleaving 

enzymes are grouped into a subtype, called Type IIP. Biochemical and structural 

evidence for several Type IIP prototype enzymes indicate that they form symmetric 

dimers or tetramers to recognize their palindromic recognition sequences. One of 

these Type IIP Reases, known as MspI, 

produces a different cleavage pattern from 

those of known structures. It recognizes 

the palindromic tetranucleotide sequence 

5’-CCGG and cleaves between the first 

and second nucleotides, leaving two-base 

cohesive 5’ overhangs.

We recently reported the crystal structure 

of an MspI-DNA complex at 1.95 Å resolution, using a combination of multiple 

isomorphous replacement with anomalous 

scattering (MIRAS) and multiwavelength 

anomalous diffraction (MAD) methods. 

This represents the first crystal structure 

of a restriction enzyme that recognizes 

a tetranucleotide sequence. Unexpectedly, MspI interacts with the palindromic 

BEAMLINES

X4A, X12C

Funding

National Institutes of Health

Publication

Q.S. Xu, R.B. Kucera, R.J. 

Roberts, and H.-C. Guo, 

"An Asymmetric Complex 

of Restriction Endonuclease 

MspI on its Palindromic DNA 

Recognition Site," Structure,

12, 1741-1747 (2004).

Contact information

Hwai-Chen Guo

Department of Physiology 

and Biophysics, Boston University School of Medicine

Email: hcguo@bu.edu

Authors (from top)

Qian Steven Xu and Hwai-Chen Guo
SCIENCE HIGHLIGHTS 2-91

recognition sequence as a monomer (Figure 1). As a result, two symmetric 

half-sites of DNA are recognized asymmetrically by the MspI monomer (Figure 

2). Together, there are six direct and five water-mediated hydrogen bonds from 

the MspI monomer to the four base-pair recognition sequence, which nearly 

saturates the hydrogen-bonding potential in the major groove of the recognition 

site. In addition, the two dyad-related half-sites on DNA make asymmetric van 

der Waals contacts with different motifs in one MspI polypeptide. Although 

homodimers had been previously reported to bind pseudo-palindromic DNA 

sequences asymmetrically, the MspI-DNA complex represents the first structure 

of a palindromic DNA sequence bound by an asymmetric protein monomer.

The observation of a monomeric MspI-DNA complex in crystals (where MspI 

is in 18 mM concentration) suggests that such a unique DNA recognition by 

MspI is likely to occur in an optimal reaction solution where MspI concentrations are much lower (in the sub-μM range). Since there is only one catalytic site 

in an MspI monomer, some kind of enzyme dimerization or flipping is necessary 

to cleave both strands of DNA at the recognition site. It is thus plausible that 

MspI binds to its recognition sequence through the monomer-DNA intermediate captured in the crystals, and then proceeds to a final homodimer-DNA 

complex (Figure 3) responsible for symmetrical cleavage of both strands of 

DNA. Alternatively, MspI may achieve double-strand DNA cleavage by bringing together two monomers bound on two separate recognition sites, similar to 

the model proposed for the Type IIS REase FokI that recognizes a specific asymmetric DNA sequence. A third possibility is that MspI undergoes some conformational rearrangements to use a single active site to sequentially cut both DNA 

strands, similar to that proposed for BfiI, another Type IIS REase.

Figure 1. The tertiary structure of the 

MspI-DNA complex. The enzyme is 

represented as ribbons and the DNA 

as a brown stick model. Secondary 

structure elements of MspI are labeled 

and the conserved structural core is 

colored in red for N-terminal helices, 

green for the five-stranded central 

β-sheet, and yellow for the β-sheet 

involved in DNA recognition. Side 

chains of the catalytic site residues 

(Asp99, Asn117, and Lys119) are 

shown as ball-and-stick representations 

with carbons in black, nitrogens in 

blue, and oxygens in red. 

Figure 2. Schematic diagram of 

hydrogen bonding between MspI 

and DNA. The DNA recognition 

sequence is shaded in gray, with the 

scissile phosphate (C4-C5) circled in 

red. One DNA base pair (G10:C11) is 

omitted in the final model. Blue and 

pink represent amino acids that bind 

to DNA bases in the major and minor 

groove, respectively. Amino acids that 

bind to the phosphate backbone of 

DNA are colored in black. Solid and 

dotted lines represent direct and watermediated hydrogen bonds, respectively.

Figure 3. The relationship between 

a putative MspI dimer and the 

crystallographic dimer in the MspIDNA cocrystal. The enzymes are 

represented as ribbons and the DNAs 

as stick models. In the crystal, two 

MspI monomers (green and red) 

bind to two separate recognition 

sequences (brown and blue). To 

generate a putative dimer (gold 

and red), the red monomer was 

rotated 180o

 along the dyad axis 

(perpendicular to the paper plane) of 

the palindromic DNA (blue).
2-92 SOFT CONDENSED MATTER AND BIOPHYSICS 

Orientation and Crystallization of Natural Rubber 

Network as Revealed by WAXD Using Synchrotron 

Radiation

M. Tosaka1, S. Murakami1, S. Poompradub1, S. Kohjiya1, Y. Ikeda2, S. Toki3, I. Sics3, and 

B.S. Hsiao3

1Institute for Chemical Research, Kyoto University, Japan; 2Kyoto Institute of Technology, Matsugasaki, Japan; 3Department of Chemistry, Stony Brook University

The tough elastic properties of natural rubber (NR) are thought to originate from its 

ability to crystallize rapidly upon stretching, which has been known since the 1920s. 

However, the growth mechanism of the strain-induced crystallites for cross-linked NR 

has only been revealed by our recent in-situ x-ray study of NR under uniaxial deformation. On the basis of these results, a new mechanism for strain-induced crystallization 

has been proposed. 

Natural rubber (NR) is a biomass produced from Hevea trees. It is an indispensable material for many industrial and household applications, due to its outstanding tensile strength and crack growth resistance, which can be attributed to its 

ability to rapidly crystallize upon elongation. The main constituent of NR is 

cis-1,4-polyisoprene, which has a near-perfect sequence of cis structures – only one 

or two trans structures are found at both ends of a molecular chain (where cis and 

trans are the two types of polymer configurations). On the other hand, synthetic 

cis-1,4-polyisoprene (IR) always contains a few percent of trans structures, which 

are randomly positioned along the molecular chains. As a result, IR is not as strong 

as NR.

The x-ray diffraction pattern of stretched NR was reported in the1920s, prior to 

the acknowledgment of “macromolecules” or polymers. Though the knowledge 

of NR strain-induced crystallization was recognized long ago, the crystal growth 

mechanism in NR that is cross-linked (i.e. includes an additive that bridges the 

NR chains, giving the material the ability to retrieve its original shape after large 

deformation) has not been clear for the past eight decades.

In our study, the morphological features of strain-induced crystallites in NR were 

studied in real time. A series of NR samples with different crosslinking densities 

were continuously deformed using a custom-made stretching machine. We recorded two-dimensional wide-angle x-ray diffraction (WAXD) patterns during the 

deformation process with a MAR-CCD camera at beamline X27C. 

By analyzing the WAXD patterns along with the tensile response of the NR 

samples, we recognized several 

interesting new features. First, 

even at the onset of crystallization, the NR crystallites 

were highly oriented. On the 

other hand, a strong isotropic 

amorphous halo persisted even 

when the sample was elongated up to eight times the initial 

BEAMLINE X27C

Funding

Japan Society for the Promotion of Science; National 

Science Foundation; U.S. 

Department of Energy 

Publication

M. Tosaka, S. Murakami, S. 

Poompradub, S. Kohjiya, Y. 

Ikeda, S. Toki, I. Sics, and 

B. Hsiao, “Orientation and 

Crystallization of Natural 

Rubber Network as Revealed 

by WAXD using Synchrotron 

Radiation,” Macromolecules, 

37(9), 3299-3309 (2004).

Contact information

Masatoshi Tosaka

Instructor, Institute for 

Chemical Research Kyoto 

University, Uji, Japan

Email: tosaka@scl.kyoto-u.ac.jp

Authors (left to right) 

Igors Sics, Shigeyuki Toki, Syozo 

Murakami, and Masatoshi Tosaka
SCIENCE HIGHLIGHTS 2-93

length. The onset strain of crystallization upon elongation was almost independent of the cross-linking density. We also observed that the sample with the 

higher cross-linking density showed the smaller lateral crystallite size and that 

the crystal lattice was almost linearly deformed in response to nominal stress.

Based on these results, we proposed a model for the strain-induced crystallization (Figure 1). When the rubber sample is stretched, some molecular chains 

are highly extended, while most of the chains remain in the almost randomly 

coiled state. Upon further elongation, the melting temperature of the sample 

increases due to entropic changes, and is independent of the cross-linking 

density. When the melting temperature exceeds the ambient temperature, the 

system enters a supercooled state and oriented crystallites form immediately 

on the stretched chains. The molecular chains that are consumed by the crystal 

growth are supplied by the surrounding coiled chains. In this way, the higher the 

cross-linking density, which results in dense crystallites, the smaller the lateral 

crystallite size. As a result of crystallization, an elongated macromolecule coil 

would be converted into a series of crystalline portions comprised of straight 

chain segments, and an amorphous portion comprised of coiled chain segments. The entropy of the amorphous portion will increase, while the degree of 

supercooling (the difference between the ambient temperature and the melting 

temperature) will decrease. However, further crystallization would be hindered 

without increasing the supercooling by additionally elongating the sample. The 

persistence of an almost isotropic amorphous halo in the WAXD pattern of 

highly strained NR samples can be explained by this model.

The deformation of the crystal lattice indicates that the crystalline portion can 

bear the stress and act as a nanometer-sized reinforcing filler. As the crystallites 

appear in response to the mechanical load on NR, the strain-induced crystallization can be regarded as “smart in-situ nanocompounding.”

Figure 1. A model of the straininduced crystallization in vulcanized 

NR. Relatively short chains are drawn 

as blue lines. Filled circles represent 

crosslinks. (a) Before deformation. 

(b) After deformation: Short chains 

are fully stretched. (c) Crystallites are 

grown from the stretched chains (green 

parts).
2-94 SOFT CONDENSED MATTER AND BIOPHYSICS 

BEAMLINE X1A

Funding

National Science Foundation 

Publication

D.A. Winesett, S. Story, J. 

Luning, and H. Ade,“Tuning 

Substrate Surface Energies 

for Blends of Polystyrene and 

Poly (Methyl Methacrylate),” 

Langmuir, 19, 8526-8535 

(2003).

Contact information

Harald Ade

Dept. of Physics, North 

Carolina State University

Email: harald_ade@ncsu.edu

Tuning Substrate Surface Energies for Blends of 

Polystyrene and Poly (Methyl Methacrylate)

D.A. Winesett1, S. Story1, J. Luning2, and H. Ade1

1Dept. of Physics, North Carolina State University; 2Stanford Synchrotron Radiation Laboratory

We have developed and characterized three simple and inexpensive ways to make substrate surfaces that are neutral, i.e. that have the same interfacial energy, for polystyrene 

(PS), a common hard plastic, and poly (methyl methacrylate) (PMMA), a commercial 

plastic. In the first two of these surface treatment methods, two different high molecular-weight copolymers made of styrene and methyl methacrylate were absorbed onto 

hydroxylated silicon oxide. In another method, octyltrichlorosilane (OTS), a highly 

hydrophobic material, was covalently bonded onto hydroxylated silicon, a highly hydrophilic surface. A fourth method covalently attached hydroxyl-terminated, miscible, low 

molecular-weight homopolymers of PS and PMMA to the substrate. We found that the 

OTS treatment is advantageous because a gradient of continuous interaction can be created. Nonetheless, the principles of each method should be applicable to other polymer 

systems.

The ability to adjust the interactions between a material or a molecule and a 

substrate is desirable for a number of applications. This includes nano-patterning, 

sensing, and the dewetting and phase segregation in two-dimensional systems of 

polymer blends at elevated temperatures. In polymer blends, differences in interfacial energies, which reflect a preferential interaction, generally cause one polymer 

to segregate to the substrate or air interface. This segregation has to be avoided in a 

number of applications, and is prevented by tuning the polymer/substrate interfacial properties.

Homopolymer blends of polystyrene (PS) and poly (methyl methacrylate) 

(PMMA) of relatively low molecular weight (10,000 to 200,000 g/mol) make 

excellent model systems for a number of studies. Both polymers exhibit comparable glass transition temperatures (temperatures below which a polymer becomes 

hard and brittle) of approximately 102 to 120 degrees Celsius (°C) and are readily codissolved in a common solvent. Moreover, for typical annealing temperatures (140°C to 180°C), the interfacial tension between PS and PMMA is larger 

than the absolute value of the difference 

between the surface energies of PS and 

PMMA. Hence, neither polymer can 

spread onto the other at an air interface. A 

polymer-air interface might thus be one of 

two “neutral” interfaces that can be used 

to produce a two-dimensional system. A 

“neutral” substrate surface will provide the 

second defining interface.

Thin polymer films are often cast on silicon substrates. At elevated temperatures, it 

is well established that the PMMA in a PS/

PMMA blend will quickly segregate to the 

Authors (clockwise from top left) 

Harald Ade, Steve Story, Andy Winesett, and Jan Luning
SCIENCE HIGHLIGHTS 2-95

native silicon oxide (SiOx) interface to form a wetting layer. In order to avoid 

and/or control this segregation, the effectiveness of several simple surface energy 

tuning methods has been tested. Using a standard UV/O3

 process, in which 

ultraviolet light is used to produce ozone and oxygen radicals in the air that removes carbon from surfaces, silicon substrates were cleaned and simultaneously 

activated to produce –OH groups on their surfaces. They were subsequently 

treated with either a commercial random copolymer, P(S-ran-MMA), an alternation copolymer, P(S-alt-MMA), a partial or gradient n-octyltrichlorosilane 

(OTS) self-assembled monolayer, or a brush of a hydroxyl (–OH)-terminated 

low molecular-weight PS/PMMA blend with varying PS/PMMA composition. 

The relative effectiveness of all four methods was characterized using optical 

microscopy, Near Edge X-ray Absorption Fine Structure (NEXAFS) microscopy 

and spectroscopy, atomic force microscopy, and contact angle measurements.

The optical micrographs in Figure 1 clearly show that very different morphologies develop, depending on the surface treatment. The P(S-ran-MMA)-treated 

surface shows a semi-bicontinuous morphology, wherein the two material phases 

are partially continuous across the whole sample. However, the untreated SiOx

surface and the P(S-alt-MMA)-treated surface show large droplets. Therefore, 

the P(S-alt-MMA) treatment clearly failed. To verify that the P(S-ran-MMA) 

treatment was successful, NEXAFS microscopy was used to quantitatively map 

the thickness of the PS and PMMA phases on P(S-ran-MMA)-treated silicon 

nitride (Si3

N4) membranes (Figure 2). The results show that the morphology is 

essentially two-dimensional in nature, with a relatively uniform film thickness 

and domains of PS and PMMA that span the entire film thickness.

Our specific interests and studies on “neutral” surfaces were restricted to surfaces 

that would have the same interfacial energy for PS and PMMA. Hydroxy-terminated PS and PMMA is the most novel approach investigated. Except for 

the P(S-alt-MMA) treatment, all of the methods yielded neutral or near-neutral 

surfaces. The OTS treatment has the advantage that a gradient of continuous 

interaction ranging from preferential PMMA to preferential PS interactions can 

be created. However, the principles of all the methods developed should be applicable to other polymer systems.

Figure 1. Optical micrographs of a 

PS21k/PMMA22k blend film, spun to a 

thickness of 500 nm and annealed in 

vacuum at 170°C for 250 minutes on 

three types of surfaces: (a) SiOx

 -OH 

surface treated with 270,000 g/mol 

P(S-ran-MMA), (b) SiOx

-OH surface 

treated with 108,000 g/mol P(S-altMMA), (c) Si-OH surface with no 

polymer treatment. The field of view 

in all three micrographs is 100 μm x 

100 μm.

Figure 2. Quantitative STXM 

thickness maps of equal weight percent 

blend of PS21k/PMMA22k annealed at 

153°C for 1 hour on Si3

N4 treated 

with 270,000 g/mol P(S-ran-MMA). 

(a) PS map (b) PMMA map (c) PS + 

PMMA map (d) The line profile of the 

thickness maps.

(a)

(b)

(c)

(a) (b) (c)

(d)
2-96 SOFT CONDENSED MATTER AND BIOPHYSICS 

Block Copolymer Domain Reorientation in an Electric 

Field: An In-Situ Small-Angle X-ray Scattering Study

T. Xu1, J. DeRouchey1, T. Thurn-Albrecht1, T.P. Russell1, and R. Kolb2

1Department of Polymer Science and Engineering, University of Massachusetts; 2Exxon Mobil Research

The electric field alignment of block copolymer thin films from an orientation nearly 

parallel to the substrate to an orientation normal to the substrate was investigated using 

in-situ small angle x-ray scattering (SAXS). An analysis of the scattering patterns indicated that, during alignment of the lamellar microdomains, the material goes through 

an intermediate state with substantially reduced order. After orientation, the sample 

consists of many small grains with the lamellae oriented parallel to the electric field and 

a random orientation in the plane perpendicular to the field.

Block copolymers, comprised of two chemically distinct polymers covalently linked 

at one end, self-assemble into well-ordered arrays of nanoscopic elements, ranging from spheres to cylinders to lamellae, depending on the volume fraction of the 

components. The size of the domains can be easily tuned by varying the molecular 

weight of the copolymer. However, it is imperative to control the orientation of 

these self-assembled morphologies, and the use of an external electric field has 

proven to be an effective method to achieve this. Nanoporous films with aspect ratios in excess of 300 have been successfully made by orienting the domains in thin 

block copolymer films and selectively removing one component. The subsequent 

electrodeposition of metal into these nanopores produces arrays of high-aspect ratio nanowires that are attracting substantial attention as candidates for high-density 

magnetic storage media. Understanding the mechanism by which the nanoscopic 

domains are aligned by an electric field is the key to optimizing their use. 

Figure 1 shows the orientation of cylindrical domains of a diblock copolymer 

under an applied electric field. Starting from an ordered state with cylinders parallel to the surface, the applied electric field enhances fluctuations at the interfaces 

between the domains and at the matrix where the fluctuations have a wavelength 

comparable to Lo

, the center-to-center distance between the cylindrical domains. 

The enhancement in the fluctuations leads to a disruption of cylindrical domains, 

the formation of spherical domains, the deformation of these spherical domains 

into ellipsoids, and the eventual reformation of nanoscopic cylinders highly oriented in the field direction. In-situ small angle x-ray scattering (SAXS) provides 

an ideal means of characterizing 

the orientation of the domains and 

elucidating the mechanism by which 

the orientation occurs. Two different 

copolymers were studied: one with 

cylindrical domains and the other 

with lamellar nanoscopic domains. 

Here, we discuss the orientation of 

lamellae due to geometric simplicity.

Figure 2 shows the azimuthal 

angular (Ω) dependence of the 

BEAMLINE X10A

Funding

U.S. Department of Energy, 

Office of Basic Energy Sciences; Army Research Lab; 

National Science Foundation 

– Materials Research Science 

and Engineering Center

Publication

J. DeRouchey, T. Thurn-Albrecht, R. Kolb, and T.P. Russell, 

“Block Copolymer Domain 

Reorientation in an Electric 

Field: An in-Situ Small-Angle 

X-ray Scattering Study”, 

Macromolecules, 37(7), 

2538 (2004).

Contact information

Thomas P. Russell

Department of Polymer 

Science and Engineering, 

University of Massachusetts

Email: russell@mail.pse.umass.edu

Authors (left to right) 

Thomas Russell and Ting Xu
SCIENCE HIGHLIGHTS 2-97

time-resolved SAXS pattern of an ordered, symmetric diblock copolymer, polystyrene-b-polyisoprene film (~ 80-120μm in thickness), that was heated above 

the glass transition temperature of both blocks under an applied electric field. 

Four distinct SAXS patterns were seen in the experiments that characterized 

different stages of the orientation. The sequence of patterns (A-D) arises from 

the re-orientation of the lamallar domains from nearly parallel to the substrate 

(A, B) to normal to the substrate (D). Curve C, however, revealed an unexpected result in which the azimuthal dependence of the SAXS was lost. This, 

coupled with a shift in the peak to higher scattering vectors (smaller spacing) 

and a broadening of the peak, suggests, contrary to the results from simulations, 

that the block copolymer domains disorder or are broken-up, and then reform 

in the presence of the field. These reformed domains are highly oriented in the 

direction of the applied field. Thus, the time-resolved SAXS pattern revealed an 

unexpected disordering of the copolymer.

Figure 2. Azimuthal angular 

dependence of the scattering 

pattern integrated over the full width 

of the Bragg reflection of a lamellar PSb-PI film under an 18 V/μm applied 

field. The film is tilted at a 45o

 angle. 

Four distinct SAXS patterns (A-D) are 

shown.

Figure 1. Simulation of the alignment 

of cylindrical microdomains under 

an electric field based on the dynamic 

self-consistent field (courtesy of A. 

Zvelindovsky). Intensity [a.u]

Ω (Degrees)

E

↓

E

↓
2-98 SOFT CONDENSED MATTER AND BIOPHYSICS 

BEAMLINE X27C

Funding

National Science Foundation 

Division of Materials 

Research; National Science 

Foundation U.S.-Czech 

Collaborative Research 

Grants; Grant Agency of 

the Academy of Sciences of 

the Czech Republic; Grant 

Agency of the Czech Republic

Publication

H. Nie, R. Bansil, and K. 

Ludwig, “Time-Resolved 

Small-Angle X-ray Scattering Study of the Kinetics of 

Disorder-Order Transition in 

a Triblock Copolymer in a Selective Solvent for the Middle 

Block,” Macromolecules, 36, 

8097-8106 (2003).

Contact information

Rama Bansil

Department of Physics, 

Boston University

Email: rb@bu.edu

Time-Resolved Small-Angle X-ray Scattering Study of 

the Kinetics of Disorder-Order Transition in a Triblock 

Copolymer in a Selective Solvent for the Middle Block

H. Nie1, R. Bansil1, K. Ludwig1, M. Steinhart2, C. Konak2, and J. Bang3

1Department of Physics, Boston University; 2Institute of Macromoleculear Chemistry, Academy of 

Sciences of the Czech Republic; 3Department of Chemical Engineering & Materials Science, University of Minnesota

Solutions of block copolymers in solvents that selectively dissolve one of the component 

polymers form micelles with the insoluble component in the cores. These complex fluid 

or gel states exhibit a rich phase diagram with many different ordered structures. Understanding the phase behavior and kinetics of these materials is of considerable importance to controlling their properties. We reported the first time-resolved small angle x-ray 

scattering (SAXS) study on the kinetics of the formation of a bcc ordered state from a 

disordered micellar fluid in solutions of Kraton, a commercial triblock copolymer. Our 

studies reveal a two-stage process that shows significant change of the micelle’s size at the 

onset of ordering. 

Solutions of multi-block copolymers exhibit rich phase diagrams and novel morphologies, and can form clusters, networks, and gels. These properties determine 

their numerous applications, such as detergents, adhesives, elastomers, bio-mimetic 

vesicles, and templates for nanomaterials. The phase behavior and properties of 

these materials can be tuned by varying the number of component polymers and 

blocks, the chemical composition and length of the blocks, and the blocks’ interactions with solvents. For example, an ABA triblock copolymer solution in a solvent 

that is good for the outer (A) block forms isolated micelles with cores containing 

the B block. On the other hand, in a solvent that is good for the middle B block, 

loops or bridges will be formed and the middle block can tether two adjoining 

micelles, eventually forming a network. The micelles, which can be either spherical or cylindrical, either exist as a complex fluid or form ordered structures, such as 

cubic or hexagonal. Our focus is to understand the kinetics of the phase transitions 

between the different disordered and ordered states of the micellar phases of these 

solutions. Since the micellar cores are on nanometer-length scales and the phase 

transitions occur on the time scale of minutes, synchrotron based time-resolved 

small angle x-ray scattering (SAXS) is an ideal tool for examining their structure 

and kinetics. 

A few SAXS studies of the kinetics of order-order and order-disorder transitions 

in melts of block copolymers have been reported. To the best of our knowledge, 

our recent publication 

is the first temperature 

jump study of isothermally evolving kinetics in 

solutions of triblocks. We 

examined the disorderorder transition kinetics 

of a styrene (S) ethyleneco-butylene (EB) triblock 

Authors (left to right) 

Milos Steinhart, Rama Bansil, 

Minghai Li, and Huifen Nie
SCIENCE HIGHLIGHTS 2-99

copolymer, SEBS, in mineral oil, which preferentially dissolves the middle EB 

block. This commercial thermoplastic elastomer from Shell, known as Kraton®, 

is used in footwear, adhesive sealants and coatings, roofing, and packaging. 

Using the high flux monochromator at beamline X27C and a one-dimensional 

wire detector, we were able to measure the scattered intensity I(q) as a function 

of the wavenumber, q, with a time resolution of 10 seconds over the q-range 

0.01 to 0.3 Å-1, and thus follow the kinetics of the micellar fluid’s ordering 

onto a bcc lattice. The transition was typically followed either by ramping the 

temperature over a wide range (Figure 1) or by rapidly quenching the sample 

temperature into the ordered phase (Figure 2). The temperature ramp experiment identifies the phase transition temperature, while the temperature quench 

experiment provides the isothermal kinetics. A model based on interacting hard 

spheres was used to analyze the data and provide detailed information about the 

time evolution of the micellar structural parameters during the ordering process. 

For example, the results showed that the core radius decreased sharply at the 

onset of the ordering process (Figure 3a). The kinetics exhibits two stages corresponding to temperature equilibration and supercooling of the micellar fluid, 

followed by the nucleation and growth of the ordered state (Figure 3b). The 

induction-time for the onset of the second stage shows a minimum around the 

glass transition temperature of the polystyrene cores.

Figure 3. (a) The time evolution of the core radius Rc

of the micelles following the quench from 140 o

C to 96 o

C shows a sudden decrease in the size of the micelle 

at the onset of ordering, at around 1000 seconds. (b) 

Temporal evolution of the primary peak’s intensity 

following quenches from 140°C to different final 

temperatures, as indicated on the graph. The data 

reveal two stages in the ordering process. Note that the 

data are offset by different constants for visual clarity.

Figure 1. The development of Bragg 

peaks in the scattering intensity I(q)

versus q during a cooling ramp from 

140 to 60o

C show a transition from 

a disordered micellar fluid at high 

temperatures to a bcc structure below 

about 120o

C. The primary peak in the 

high-temperature data is due to the 

interacting micellar cores in the fluid 

phase.

Figure 2. The time evolution of the 

scattering intensity I(q) versus q

following a rapid jump from 140o

C 

to 96o

C shows the isothermal growth 

kinetics of the ordered bcc structure 

at the final temperature of 96o

C. The 

delayed appearance of the higher Bragg 

peaks indicates a two-stage process. 

Note that the temperature of the 

sample equilibrates within 60 seconds 

following the jump.
2-100 SOFT CONDENSED MATTER AND BIOPHYSICS 

BEAMLINE X10B

Funding

National Science Foundation

Publication

T. Koga, Y.-S. Seo, J.L. Jerome, S. Ge, M.H. Rafailovich, J.C. Sokolov, B. Chu, 

O.H. Seeck, M. Tolan, and R. 

Kolb, "Low-Density Polymer 

Thin Film Formation in Supercritical Carbon Dioxide," 

Appl. Phys. Letts., 83, 4309 

(2003).

Contact information

Dr. Tadanori Koga

Department of Materials 

Science and Engineering, 

Stony Brook University 

Email: tkoga@notes.cc.sunysb.edu

Low-Density Polymer Thin Film Formation in 

Supercritical Carbon Dioxide

T. Koga1, Y.-S. Seo1, J.L. Jerome1, S. Ge1, M.H. Rafailovich1, J.C. Sokolov1, B. Chu1, 

O.H. Seeck2, M. Tolan3, and R. Kolb4

1Stony Brook University; 2FZ Juelich GmbH, Institut fuer Festkoerperforschung, Germany; 3Universitaet Dortmund, Experimentelle Physik I, Germany; 4ExxonMobil Research and Engineering 

Company

We have developed a method for producing stable low-density polymer films using 

supercritical carbon dioxide (scCO2

). Two different molecular-weight polystyrene films 

with various thicknesses were exposed to scCO2

 along the density fluctuation ridge in a 

phase diagram. The swollen structures could be then frozen via the flash evaporation of 

CO2

 without forming additional large voids. X-ray reflectivity data clearly showed that 

exposure to scCO2

 could be used to produce uniform low-density films about 2Rg thick 

or less, where Rg is the radius of polymer gyration. 

Increased miniaturization in the electronics industry has produced a need for 

highly uniform ultrathin polymer coatings with well-controlled optical and dielectric properties. Often the thickness of these films is commensurate with a few radii 

of gyration (Rg

) of the polymer, and tight clearances impose very strict tolerances 

on surface roughness. This high degree of confinement therefore makes it difficult 

to satisfy the stringent uniformity requirements if we modify the electronic properties using standard gas foaming methods or blending it with other polymers or 

inorganic additives. Here we show a novel approach for producing stable, uniform, 

low-density polymer films using supercritical carbon dioxide (scCO2

).

ScCO2

 has long been known to be a “green” medium for polymer chemistry or 

material science. Unfortunately, its potential benefits have not been fully exploited 

since only a limited class of polymers can be dissolved in it. Recently, we have 

shown that a wide variety of polymer thin films can swell by as much as 30 to 

60% when exposed to scCO2

 within a narrow temperature and pressure regime, 

known as the “density fluctuation ridge,” even when the bulk miscibility of the 

films with scCO2

 is poor. In addition, we found that the in situ film quality, i.e. 

density, roughness, and film thickness, could be frozen via the flash evaporation of 

CO2

. We report x-ray reflectivity measurements in which the density profile of the 

vitrified films is measured directly and correlated with other properties, such as the 

dielectric constant, index of refraction, and surface glass transition. 

Two kinds of polystyrene (PS), corresponding to molecular weights (Mw) of 

2.0×105

 and 6.5×105 g/mol, were used in this study. Thin films spun cast on 

cleaned Si substrates were placed in a high-pressure chamber containing scCO2

 at 

T = 36oC and P = 8.2 MPa, i.e. the ridge condition, for two hours and then quickly depressurized to atmospheric 

pressure within 10 seconds. The 

films were then characterized 

by x-ray reflectivity at beamline 

X10B. As shown in Figure 1, 

we found that the density of the 

films, which is obtained from a 

Authors (left to right) 

Miriam Rafailovich and Tadanori Koga

2-100 SOFT CONDENSED MATTER AND BIOPHYSICS
SCIENCE HIGHLIGHTS 2-101

dispersion value in the x-ray refractive index, decreased from 23% to 13% by 

varying the thickness of both PS films. Furthermore, the data could be collapsed 

on a universal curve when the initial film thickness (L0

) was scaled byRg (Figure 1 inset). Hence, when confined as a thin film on a surface, thickness and 

molecular structure influence the density of the materials. 

The reduction in density has several consequences affecting the material properties of the films. First, there is a decrease in its optical index of refraction (or 

dielectric constant). Figure 2 shows the refractive indices (nf

) of the PS (Mw = 

6.5×105 g/mol) films for the unexposed and two exposed films measured using 

spectroscopic ellipsometry. From the figure we can clearly see that the nf

 values 

for the exposed films decreased with decreasing Lo

 values over the wide wavelength range. Second, there is a decrease in the glass transition temperature (Tg

). 

In the Figure 2 inset, we plot the modulation amplitude vs. T for unexposed 

and exposed PS thin films obtained using the Shear Modulation Force Microscopy technique. From the figure we can see that the discontinuity in the plot, 

which corresponds to Tg

, occurs at T = 100oC for the unexposed film. The Tg

value for the exposed film decreases by 10oC compared to that of the unexposed 

PS film.

Figure 1. Density (ρ) vs. L0 for the 

exposed films: PS (Mw = 2.0×105

) (ο), 

PS (Mw=6.5×105

) ( ). In the inset, 

L0

/Rg dependence of ρ is shown. 

Figure 2. Index of refraction for PS 

(Mw = 6.5×105

): before (∆) and after 

(L0 = 2Rg (ο) and L0 = 1.3Rg ( )). 

In the inset, X vs. T curves for PS 

films: exposed films L0

=1.3Rg (ο) and 

unexposed film ( ). 
2-102 SOFT CONDENSED MATTER AND BIOPHYSICS 

Shear-Induced Crystallization Precursor Studies in 

Model Polyethylene Blends by In-Situ Rheo-SAXS and 

Rheo-WAXD

L. Yang1, R.H. Somani1, I. Sics1, B.S. Hsiao1, R. Kolb2, H. Fruitwala2, and C. Ong3

1Department of Chemistry, Stony Brook University; 2ExxonMobil Research and Engineering Company; 3ExxonMobil Chemical Company

The development of the shear-induced crystallization precursor structure of crystallizing, high molecular-weight binary polymer blends and non-crystallizing, low molecular-weight polyethylenes was investigated by in-situ rheo-small-angle x-ray scattering (SAXS) and wide-angle x-ray diffraction (WAXD) techniques. A “shish-kebab” 

structure, detected by both SAXS and WAXD, was observed in the blend containing 

the non-crystalline matrix of relatively higher viscosity, while only a twisted lamellar 

structure was seen in the rest of the blends. These results suggest that the matrix viscosity 

plays an important role in the formation of the crystallization precursor structure from 

the high molecular-weight chains under flow.

Prior to crystallization, the initially formed precursor structures, with a molecular 

orientation induced by flow during polymer processing – such as extrusion, injection molding, fiber spinning, and film blowing – can often dictate the subsequent 

morphology and, thus, the final properties of the polymer. Although extensive 

research on orientation-induced crystallization has been conducted, the nature of 

the earliest events during crystallization under flow is still not fully understood. In 

this study, a unique polymer blend system, inspired by studies of dilute polymer 

solutions under flow, was used to simulate the formation of precursor structures at 

the initial stage of flow-induced crystallization. In these blends, two low molecular-weight polyethylene copolymers, containing 2 mol % of hexene, with average 

molecular weights (Mw) of 50,000 (MB-50k) and 100,000 (MB-100k) and a polydispersity of 2, were used as the 

matrix material of different viscosity. A high molecular-weight 

polyethylene homopolymer 

with a Mw of 250,000 (MB250k) and a polydispersity of 2, 

which is miscible with both low 

molecular-weight polyethylene 

matrices, was used as the crystallizing minor component. Two 

series of model blends, MB-50k/

MB-250k and MB-100k/MB250k, each containing weight 

ratios of 100/0, 97/3, 95/5, and 

90/10, were prepared by solution blending to ensure thorough 

mixing at the molecular level. 

A Linkam CSS-450 high-temperature shear stage, modified for 

BEAMLINE X27C

Funding

National Science Foundation

ExxonMobil Company

Publication

L. Yang, R.H. Somani, I. 

Scis, B.S. Hsiao, R. Kolb, 

H. Fruitwala, and C. Ong, 

“Shear-Induced Crystallization Precursor Studies in 

Model Polyethylene Blends by 

In Situ Rheo-SAXS and RheoWAXD,” Macromolecules, 

37(13), 4845-4859 (2004).

Contact information

Benjamin S. Hsiao

Stony Brook University

Email: bhsiao@notes.cc.sunysb.edu

Authors (left to right) 

(top) Igors Sics and Rajesh Somani, 

(bottom) Benjamin S. Hsiao and Ling Yang

2-102 SOFT CONDENSED MATTER AND BIOPHYSICS
SCIENCE HIGHLIGHTS 2-103

in-situ x-ray scattering measurements, was used to control the shear conditions 

of the polymer samples. Two-dimensional WAXD and SAXS measurements 

(not measured simultaneously) were carried out at beamline X27C using a MAR 

CCD x-ray detector.

At the chosen shear conditions (rate = 60 s-1, duration = 5 s, T = 120oC, which 

is greater than the melting point of the matrix), while no flow-induced structures were seen in pure MB-50k and MB-100k melts, the blends in both series 

showed distinct but different shear-induced structures. Our results indicate that 

the high molecular-weight MB-250k chains are responsible for the formation of 

crystallization precursor structures in the blend under shear, which can act as a 

template for further crystallization. A “shish-kebab” structure, detected by both 

WAXD (Figure 1A) and SAXS (Figure 1B), was observed in the MB-100k/

MB-250k (90/10) blend, while only a twisted lamellar structure was seen in the 

rest of the blends under the same shear conditions. These findings suggest that 

the matrix viscosity plays an important role in influencing the formation of the 

crystallization precursor structure from the high molecular-weight chains under 

flow. The evolution of the shish-kebab structure from SAXS, consistent with the 

appearance of two equatorial (110) reflection peaks in WAXD, can be explained 

by the coil-stretch transition that is induced by flow. The observed “shish” is due 

to the extended chain crystallization of the stretched chains, whereas the kebabs 

are due to the folded chain crystallization of the coiled chains. In other blends, 

because the stretched chains could not aggregate rapidly, no detectable shish was 

observed. In the MB-100k/MB-250k (90/10) blend, the length of the shish was 

estimated from the equatorial streak in SAXS, and showed a noticeable decrease 

with time, possibly due to the relaxation of stress distribution or the overall 

crystal orientation.

Figure 1. Selected two-dimensional 

(A) WAXD and (B) SAXS patterns, 

which illustrate the development of the 

“shish-kebab” morphology in the MB100k/MB-250k (90/10) blend under 

shear (rate = 60 s-1, duration = 

5 s, T = 120 oC).

WAXD

SAXS

kebab

shish

t =30 s t =135 s

kebab

shish

(A)

(B)
2-104 SOFT CONDENSED MATTER AND BIOPHYSICS 

BEAMLINE X8A

Funding

The Office of Naval Research

Publication

R.J. Klein, J. Runt, and 

Q.M. Zhang, "Influence of 

Crystallization Conditions 

on the Microstructure and 

Electromechanical Properties 

of Poly(vinylidene fluoridetrifluoroethylene-chlorofluoroethylene) Terpolymers," 

Macromolecules, 36, 7220-

7226 (2003).

Contact information

Rob Klein

Penn State University

Email: rjk255@psu.edu

Influence of Crystallization Conditions on the 

Microstructure and Electromechanical Properties of 

Poly(Vinylidene Fluoride-TrifluoroethyleneChlorofluoroethylene) Terpolymers

R.J. Klein1, J. Runt1,2, and Q.M. Zhang1,2,3

1Materials Research Institute; 2Department of Materials Science and Engineering; and 3Department 

of Electrical Engineering, The Pennsylvania State University

The crystallization process and its influence on the microstructure, ferroelectric, and 

electromechanical properties of a poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene) (PVDF-TrFE-CFE) terpolymer were investigated. By varying the isothermal 

crystallization temperature Tx

 of this terpolymer, the ratio of ferroelectric crystal concentration to the concentration of relaxor ferroelectric crystal (a defect-modified class of 

ferroelectrics exhibiting strong electrostrictive behavior) can be determined. The higher 

Tx

 samples show an increased polarization hysteresis and reduced electric field-induced 

strain response. In addition, the experimental results, in combination with other 

reported results, indicate that CFE units are included in the crystalline lattice. Consequently, the influence of CFE on the ferroelectric behavior of the polymer is through the 

defects it induces in the crystal lattice.

Polymers for electromechanical applications offer many unique and inherent 

advantages when compared with other materials, being lightweight, flexible, and 

relatively easy to process and form into complicated shapes or large areas. We have 

examined one of these terpolymers, P(VDF-TrFE-CFE), and investigated how 

its ferroelectric and electromechanical responses are influenced by polymer crystallization processes in tandem with corresponding microstructure changes. We 

found that, by varying the crystallization temperature Tx

, we can selectively vary 

the fraction of polar and non-polar crystallites in the crystalline phase. Crystallites 

formed during long periods of time at Tx exhibit less polar behavior. Crystallites 

formed during the rapid cooling process between Tx and room temperature exhibit 

stronger polar behavior. This is established most quantitatively by wide-angle x-ray 

diffraction (WAXD) and reinforced by Fourier transform infrared (FT-IR) spectroscopy, polarization loop, and electromechanical strain measurements. As will be 

shown, crystallizing the terpolymer at higher Tx values has an adverse effect on its 

electromechanical strain response.

X-ray data were collected in order to interrogate interchain spacing and, via x-ray 

peak width, the crystalline order perpendicular to the chain direction. For PVDFTrFE copolymers in the ferroelectric phase, this peak corresponds to the (110, 200) 

reflection. The data were acquired at selected temperatures between room temperature and Tx (taken on heating) 

in order to follow the evolution 

of the microstructure. The xray data in the 2θ range of the 

(110, 200) reflection acquired 

at room temperature for terAuthors (left to right)

Kailiang Ren, Xuezhen Li, Yanyun Ma, 

Feng Xia, Sabrina Choudhury, Rob Klein, 

Qiming Zhang, and Cheng Huang

2-104 SOFT CONDENSED MATTER AND BIOPHYSICS
SCIENCE HIGHLIGHTS 2-105

polymer films with different Tx are shown in Figure 1a.

For the terpolymer films with Tx at 112, 122, and 127°C, the x-ray data are relatively well characterized by a single peak at 14.7°, which represents the non-polar phase. The data fitting can be improved, however, by including a small peak 

at 15.3°, which is close to the position of the diffraction peak expected for the 

polar phase of the terpolymer’s corresponding copolymer, PVDF-TrFE. As Tx

is raised to 132 °C, this higher angle shoulder increases quite markedly, and the 

best fitting to the data is achieved by including two peaks, one near 15° and the 

other at 15.4°. Figure 1b summarizes the evolution of the x-ray peak positions 

as Tx is raised from 112 to 142°C. In comparison with the x-ray data for PVDFTrFE, we deduced that the peak at the lower angle arises from the non-polar 

phase while the peaks at 15° and 15.4° indicate the presence of the polar phase 

component in the crystallites. 

The importance of these x-ray peak assignments is seen in the electromechanical strain data for samples at the extremes of the Tx

 range. As shown in Figure 

2, the terpolymer sample with a Tx of 112°C exhibits a field-induced strain of 

-5.9% at 133 MV/m (megavolts per meter), while for the sample with Tx

 of 

142°C, the strain is reduced to -4.2% under the same field. The lower fieldinduced strain is due to existing ferroelectric domains that do not undergo the 

local conformation change upon application of the electric field. Thus, for better 

performance, a sample should be annealed near 112o

C.

Figure 2. Thickness strain of the 

terpolymer as a function of the applied 

field for the terpolymer samples with 

Tx = 112 and 142 °C. The data were 

acquired at room temperature and 1 

Hz AC field.

Figure 1. (a) X-ray data in the angular 

range of the (110, 200) reflection 

taken at room temperature for the 

terpolymers with different Tx

, from 

which lattice constants are determined. 

(b) Lattice constants for the nonpolar (4.9 Å) and polar (triangles and 

squares) components of the (110, 

200) reflection measured at room 

temperature as a function of Tx

. The 

data for the copolymer of similar 

composition are also shown. The x-ray 

wavelength is 1.2399 Å.

(a)

(b)

Lattice spacing (Å)

Tx(°C)

2θ(°)

-Strain (%)

Electric Field (MV/m)
YEAR IN REVIEW
 YEAR IN REVIEW 3-3

Brookhaven Town Supervisor 

John Jay LaValle Visits BNL

January 9, 2004

To learn more about research being done at BNL, which is 

one of Brookhaven Town’s largest employers, Brookhaven 

Town Supervisor John Jay LaValle visited the Lab for the 

first time on December 15, 2003.

Laboratory Director Praveen Chaudhari welcomed LaValle 

and his office staffer Christopher Nuzzi, who both also met 

Michael Holland, DOE’s Brookhaven Area Office Manager; 

Marge Lynch, Assistant Laboratory Director for Community, Education, Government & Public Affairs (CEGPA); 

and Jeanne D’Ascoli, CEGPA Community Relations 

Representative.

The visitors then toured part of the Lab, with a first stop 

at the National Synchrotron Light Source (NSLS). There, 

Associate Laboratory Director for Light Sources and NSLS 

Chair Steven Dierker gave an overview of how Lab scientists and some 2,500 researchers from across the nation and 

overseas who visit BNL annually use x-rays and ultraviolet and infrared light to make discoveries in biology and 

physics, chemistry and geophysics, materials science and 

medicine.

At the next stop, Bill Christie of the Physics Department 

talked about the massive STAR detector, where about 450 

researchers are among the approximately 1,000 scientists, 

engineers, and technicians from the U.S. and abroad who 

work at the Relativistic Heavy Ion Collider to replicate 

conditions at the dawn of time to gain a better understanding of how the universe evolved.

Then, at the Positron Emission Tomography (PET) facility, the visitors learned from scientist David Schlyer of the 

Chemistry Department about BNL’s work in probing the 

brain chemistry of addiction, mental illness, and aging, and 

recent work to find effective treatments. 

—Liz Seubert

At beamline U10B at the National Synchrotron Light Source, researcher 

Lisa Miller explains to Brookhaven Town Supervisor John Jay LaValle how 

she uses infrared light to study bone composition in osteoporosis.

Brookhaven Lab Expects $30 Million to 

Support Life Sciences

February 12, 2004

The Biology Department at Brookhaven National 

Laboratory announced that it expects to receive more 

than $30 million over the next five years, which will 

renew financing to support structural biological research, 

including studies of disease and genomics. 

The funding, administered by the Office of Biological 

and Environmental Research within the U.S. Department of Energy's (DOE) Office of Science and by the 

National Center for Research Resources within the 

National Institutes of Health, will support a group of six 

beamlines at the (NSLS). 

“The large size of the grant is a tribute to the strong 

infrastructure within the NSLS and Brookhaven Lab,” 

said Robert Sweet, a structural biologist in the Biology 

Department at Brookhaven and spokesperson for the 

research group that maintains the beamlines. “It also reflects how valuable we are to a large number of powerful 

Northeastern U.S. research groups that use our facility.” 

For example, researcher Roderick MacKinnon of The 

Rockefeller University received the 2003 Nobel Prize 

in Chemistry for his research, performed in part at the 

NSLS, on how nerve signals are propagated through the 

body. 

“We’re very proud of our ability to identify and support 

Nobel-quality projects like MacKinnon’s work,” Sweet 

said. “These funds will allow other important projects to 

move forward.” 

A research group from Yale University has used NSLS 

light to study the structure of ribosomes – cellular “machines” that assemble the proteins cells need to function. 

Also, scientists from Harvard University determined the 

structure of a type of tiny opening on the surface of cells 

that allows proteins to pass in and out of the cell. Their 

results may provide valuable insight into several basic 

cellular activities. The grants will also further the work 

of scientists from local Long Island institutions, such as 

Stony Brook University and Cold Spring Harbor Laboratory. 

Ari Patrinos, Associate Director of Science for DOE’s Office of Biological and Environmental Research within the 

Office of Science, welcomed the renewal of funding for 

the beamlines. “The Brookhaven scientists are addressing two major objectives of the Lab’s structural biology 

program: developing state-of-the-art technologies for 

solving the most difficult molecular structure problems, 

and providing access to this major facility, which is used 

by more than 2,500 scientists each year,” he stated. 
3-4 NSLS ACTIVITY REPORT 

Above are the staff of the Protein Crystallography Research Resource 

(PXRR), the Biology Department and National Synchrotron Light Source 

(NSLS) Department scientists, engineers, machinists, and technicians

who operate six NSLS beamlines for macromolecular crystallography. 

The DUV-FEL Workshop

February 19-20, 2004

The Deep Ultra Violet Free Electron Laser (DUV-FEL), a 

laser linac facility at Brookhaven National Laboratory, is the 

world’s only facility dedicated to laser-seeded FEL research 

and development (R&D) and its applications. To explore 

opportunities for future experiments on free electron laser 

and beam physics at the DUV-FEL, the DUV-FEL Beam 

Physics and FEL Research and Development Workshop was 

held on February 19-20, 2004.

Representatives from seven countries and 14 institutions 

– including Lawrence Berkeley National Laboratory, the 

Massachusetts Institute of Technology, BESSY, and Pohang 

Accelerator Laboratory – participated in the workshop. 

More than 20 talks were presented, covering a broad 

spectrum of beam physics and FEL topics, such as cascaded 

high-gain harmonic generation (HGHG) FEL, ultra-short 

FEL generation techniques, electron-beam optimization, 

bunch compression, and femtosecond electron-beam 

instrumentation. The presentations revealed that the seeded 

FEL, especially the HGHG type, will play a critical role in 

the proposed x-ray FEL facility.

Brookhaven’s Xijie Wang and Li Hua Yu began the workshop with presentations on the DUV-FEL facility and its 

current FEL R&D program. The facility’s main components are a high-brightness electron accelerator, a HGHG 

FEL, a chemical science endstation, and sophisticated 

electron and photon beam instrumentation.

The DUV-FEL accelerator system consists of a 1.6 cell 

photo injector driven by a Ti:Sapphire laser system, and a 

four-section 2856 MHz SLAC-type traveling wave linac 

that is capable of producing a 200 MeV electron beam. The 

facility’s magnetic chicane bunch compressor produces subpicosecond-long electron bunches with a peak current of a 

few hundred amperes. The high-brightness electron beam 

travels down the 10 meter-long undulator to generate UV 

light with a fundamental wavelength of 266 nm.

Past DUV-FEL Activity

One of the most important milestones at the DUV-FEL 

last year is the initialization and completion of the first 

DUV-FEL user experiment by Arthur Suits and his collaborators from BNL’s Chemistry Department.

This first chemical science experiment – on ion pair imaging – used the HGHG’s third harmonic beam (89 nm) to 

study the super excited states of methyl fluoride, a highly 

flammable gas. Velocity-mapped ion images of the fluoride 

ion, obtained using intense, coherent, sub-picosecond pulses of 86-89 nm light, revealed a low translational energy, 

implying a very high internal excitation in the molecule’s 

methyl cation cofragment [W. Li et al, PRL 92, 083002-1 

(2004)].

This type of research is part of a field of biology called 

macromolecular crystallography, which uses x-rays to 

determine the structure of various proteins and nucleic 

acids, the molecular engines that control the functions of 

all living cells. Because abnormalities and malfunctions in 

macromolecules, especially proteins, are often the root of 

many diseases, an important step toward developing drug 

treatments is learning about these molecules’ structures. 

The funds will cover the expenses of improving and 

maintaining the beamlines, which is carried out by Sweet’s 

research group – a team of nine scientists and fourteen 

engineers and technicians. It also will cover the costs of 

training and assisting researchers in performing their measurements. 

One of the beamlines supported by the grants is brand-new, 

and will produce the brightest x-ray light at the NSLS. 

Another, the beamline where MacKinnon performed his 

research, will be upgraded to produce even brighter light. 

Lonny Berman, an NSLS physicist, will manage the upgrade. 

In addition, Sweet’s group will use the funds to develop 

techniques that allow experimenters to work more quickly 

and efficiently. They have already pioneered a sophisticated 

service managed by Howard Robinson, a biophysicist, 

which allows crystal samples to be sent to NSLS researchers 

through the mail. In another project, managed by biophysicist Dieter Schneider, they are building a robot that will 

automatically change the specimens that are studied during 

NSLS experiments.

—Laura Mgrdichian
 YEAR IN REVIEW 3-5

In response to the requests of many users to study chemical 

science at the facility, the DUV-FEL linac is being upgraded 

from 200 to 300 MeV to enable the HGHG FEL to produce 100 μJ pulses of 100 nm light. This will help establish 

the DUV FEL as a premier user facility for ultraviolet radiation, and will enable state-of-the-art gas phase photochemistry research.

After successfully lasing at 266 nm with 800 nm laser seeding in late October 2002 [L.H. Yu et al, PRL 91, 074801-1 

(2003)], experiments were carried out at the DUV-FEL to 

further characterize the properties of the HGHG FEL and 

to demonstrate its stability and controllability. The narrower spectrum and better stability of the HGHG, compared to a Self-Amplified Spontaneous Emission (SASE) 

FEL, were observed. Both the second and third harmonic 

HGHG FEL beams were experimentally characterized using a vacuum monochromator. The pulse energy for both 

harmonics (133 and 89 nm, respectively) was measured to 

be about 1 μJ, which is about one percent of the fundamental value at 266 nm.

A two-photon absorption auto-correlator with 100 femtosecond (fs) resolution was developed to characterize the 

HGHG output pulse length. It was experimentally demonstrated that the HGHG can produce output pulses with 

lengths from one picosecond down to 250 fs by varying the 

seed laser pulse length.

Experiments to investigate a chirped HGHG FEL were also 

initialized in 2003. The preliminary results are very promising, and the chirped FEL could lead to even shorter HGHS 

output pulses. The possibility of achieving HGHG output 

tuning via electron beam energy chirping was discussed 

by Timur Shaftan of BNL. Brian Sheehy, also of BNL, 

discussed various FEL output manipulation techniques and 

their limitations.

DUV-FEL in the Future

One of the main goals of FEL R&D at the DUV-FEL is to 

continue developing key technologies for a future x-ray 

FEL that will be based on the HGHG. For example, a 

cascaded HGHG and a higher harmonic (n>5) HGHG 

are critical for the realization of the HGHG x-ray FEL. 

Additionally, multi-laser electron beam synchronization 

and timing jitter reduction are very important technologies that will enable ultra-fast science at all future x-ray 

FEL facilities.

Paul Emma of SLAC discussed a technique that uses 

an emittance spoiler to achieve ultra-short FEL pulses. 

Computer simulations have shown that, by using a cleverly placed piece of slotted foil, the Linac Coherent Light 

Source (LCLS) at SLAC will be able to produce brilliant 

x-ray pulses that are extremely short – a few femtoseconds. This pulse length, which is more than 200 times 

shorter than the LCLS baseline design, will dramatically increase that facility’s x-ray time resolution, giving 

scientists the ability to study the movement of matter 

at atomic scales and observe the structural changes that 

occur when chemical bonds are made or broken. To test 

the feasibility of an emittance spoiler at the DUV-FEL, 

Emma proposed a demonstration experiment. This could 

reduce the FEL output pulse length by a factor of four.

Beam physics during the electron-beam bunch compression was extensively discussed during the workshop. Zhirong Huang of SLAC gave an overview on microbunching instability during electron-beam compression and 

its impact on the future x-ray FEL. The LCLS proposes 

using a laser heater or superconducting undulator to 

mitigate microbunching instability. Michael Borland of 

the Advanced Photon Source discussed the latest developments in electron-beam bunch compression simulation. 

Experimental investigation of microbunching instability 

and validation of computer predictions will be the major 

part of beam physics R&D at the DUV-FEL.

To take advantage of the DUV-FEL’s unique capabilities, 

other possibilities in beam physics and FEL R&D will 

continue to be explored, such as coherent terahertz generation and a femtosecond electro-optical bunch detector.

The workshop ended with a lively discussion on the 

possible future FEL and beam physics experiments at the 

DUV-FEL. The workshop participants ranked possible 

future experiments according to the following criteria:

1. What are likely critical beam physics and FEL experi- 

 ments for future linac-based light sources? Can the 

 DUV-FEL make an impact? 

2. What is the best way to carry out those experiments? 

 How can we take advantage of the unique features of 

 the DUV-FEL? 

—Xijie Wang and Laura Mgrdichian

An enthusiastic group of DUV-FEL workshop attendees, (from left) Xijie 

Wang (BNL), June-Rong Chen (NSRRC), Gwo-Huei Luo (NSRRC), Bill 

Weng (BNL), Li-Hua Yu (BNL), Rene Bakker (Trieste), and Jong Oh (PAL), 

enjoying dinner after a successful workshop.
3-6 NSLS ACTIVITY REPORT 

NSLS-II Workshop Lights Brookhaven 

National Laboratory

March 15, 2004

On March 15, 2004, approximately four hundred registered attendees participated in the NSLS-II Workshop at 

Brookhaven National Laboratory to support the proposed 

facility, a world-leading synchrotron that will facilitate 

cutting-edge research in the biological, material, chemical, 

environmental, and physical sciences.

The current National Synchrotron Light Source (NSLS) 

is one of the world’s most widely used scientific facilities. 

Each year, about 2,400 researchers from more than 400 

universities, government laboratories, and companies use 

its x-rays, ultraviolet light, and infrared light for research. 

The scientific productivity of the NSLS user community is 

very high and has widespread impact, with approximately 

800 publications per year, of which some 130 appear in socalled premier scientific journals.

Though the current NSLS has been continually updated 

since its commissioning in 1982, today the practical limits 

of machine performance have been reached. In order for 

the productivity of its user community to continue, and 

in order to tackle the ‘grand challenge’ scientific problems 

of tomorrow, plans to upgrade the NSLS are under way. 

The centerpiece of the proposed NSLS-II will be a state-ofthe-art, medium-energy electron storage ring designed to 

deliver world-leading x-ray brightness and flux, more than 

10,000 times brighter than the current NSLS. This facility, 

which will also include full-energy injection for constant 

intensity as well as a dedicated infrared ring, is expected to 

have profound impact on a wide range of scientific disciplines and initiatives and lead to many exciting discoveries 

in the coming decades.

The NSLS-II workshop kicked 

off with opening remarks from 

Steve Dierker, the Associate 

Laboratory Director for Light 

Sources, Chair of the National 

Synchrotron Light Source 

(NSLS), and the workshop’s 

host. “The design of NSLS-II 

has surpassed anything that 

has ever been built,” said Dierker, setting the tone for the 

enthusiasm and interest that 

NSLS-II has generated. “The 

science that will come out of 

this will be very, very exciting.”

Dierker then introduced the 

morning’s first speakers: Brookhaven Lab Director Praveen 

Chaudhari and the Department of Energy’s Brookhaven 

Area Office Manager, Michael Holland, who matched 

Dierker’s enthusiasm for the days ahead. The stage was then 

turned over to the workshop’s invited distinguished guests.

Addressing a packed auditorium, the morning speakers 

at the workshop – including NY Congressman Sherwood 

Boehlert, Chairman of the House Committee on Science, 

Patricia Dehmer, Associate Director of the DOE Office 

of Basic Energy Sciences, NY Congressman Tim Bishop, 

and Battelle President and CEO Carl Kohrt – praised and 

pledged their support for the proposed NSLS-II facility.

In addition, the two scientific speakers, the 2003 Nobel 

Prize in Chemistry recipient, Professor Roderick MacKinnon of Rockefeller University, and Dr. Paul Horn, the Vice 

President for Research and Development at IBM, gave 

stimulating talks that hinted at the new, exciting science 

NSLS-II will enable.

Their enthusiasm was shared by Boehlert, the keynote 

speaker, who said, “One doesn’t need a degree in physics 

to understand the value of a scientific tool that furthers 

human understanding of matter while answering practical 

questions in materials science and biology; a tool that is of 

use to both academic and industrial researchers; a tool that 

attracts the best researchers from throughout the world.” 

“The U.S. simply must invest to upgrade its capabilities in 

this area, building on the expertise that Brookhaven and the 

researchers who use its facilities have developed over the last 

few decades,” he continued.

“NSLS-II is something we need to do,” Dehmer agreed in 

her talk. “I want you to know that I give you my commitment that NSLS-II will happen. Never doubt my resolve, 

never doubt your own power, never doubt the power of a 

great idea.”

Bishop imparted a similar message. “We have such confiSpeakers at the NSLS-II Workshop at BNL included: (from left) BNL 

Director Praveen Chaudhari; Battelle President and CEO and current 

BSA Chair Carl Kohrt; Nobel Prize-winner Roderick MacKinnon of 

Rockefeller University; DOE Brookhaven Area Office Manager Michael 

Holland; DOE’s Office of Basic Energy Sciences Associate Director 

Patricia Dehmer; Associate Laboratory Director for Light Sources and 

National Synchrotron Light Source Department Chair Steven Dierker; 

and IBM Senior Vice President and Director of Research Paul Horn.

Associate Laboratory Director for 

Light Sources and NSLS Chair 

Steve Dierker enthusiastically 

welcomed the workshop 

participants and speakers.
 YEAR IN REVIEW 3-7

dence in what this Lab can 

do and what the scientists in 

this Lab can do. And the best 

scientists in the world deserve 

the best equipment,” he said.

Kohrt, who is also the Board 

Chair of Brookhaven Science Associates, the company 

formed by Battelle and Stony 

Brook University to manage 

Brookhaven Lab, also spoke 

enthusiastically about the 

new facility. “Thank you to 

the DOE and the visionaries 

that started this,” he said of 

NSLS-II. “The journey has 

just begun.”

But Boehlert also reminded the workshop participants of 

some very real issues, including the financial constraints 

that are involved. His main 

message: Nothing is certain in 

politics, and the realization of 

NSLS-II largely depends on 

the ability of its potential users 

to express why the facility is 

necessary. “I will do everything I can to help you, but 

I can’t do it alone,” he said. 

“Lawmakers need to hear from 

you, and especially from those 

of you in industry and your 

CEOs, why a light source, or 

any other piece of equipment 

or area of research, is important. They - we - need to learn 

from you what the nation will actually be giving up if you 

aren’t able to succeed.”

Seeming to answer this challenge, Horn gave examples 

of how his company would 

benefit from NSLS-II. In his 

presentation on nanoscience, 

Horn discussed why progress 

in improving the performance of silicon transistors 

has slowed, and how NSLS-II 

could open doors to new materials that may replace silicon 

transistors.

The silicon transistor, Horn 

explained, has developed into 

a nanodevice. But any further 

miniaturization has all but 

halted because researchers 

can’t solve the problem of transistor cooling. As a result, 

technology development companies have moved in a 

different direction, and are trying to gain better transistor 

performance without scaling them down. This involves 

researching new materials, which, Horn said, is where 

NSLS-II would step in as a valuable research tool.

“We are at a paradigm shift, where the physics that comes 

from synchrotrons like NSLS-II is absolutely critical,” he 

said. “We can use x-rays to 

look at new materials and 

their features at an incredibly fine scale.”

Horn hailed NSLS-II as a 

gateway into cutting-edge 

nanoscience research, a field 

that is expected to become a 

major engineering discipline 

that will integrate many 

fields – physics, materials science, chemistry, and 

biology – reduce the cost 

of manufacturing, ultimately reducing costs for 

the consumer, and generally 

revolutionize the information technology and electronics 

industries.

In his talk, MacKinnon also clearly explained how 

NSLS-II would further his work, which he said would 

be “impossible” with the 

current NSLS. He described 

his Nobel prize-winning 

research involving the structural determination of cell 

membrane proteins called 

ion channels, which was 

performed, in part, at the 

existing NSLS. 

In the meantime, however, 

there are still many other 

membrane proteins to study, 

which, according to MacKinnon, make up between 

25 and 30 percent of all 

proteins. “We know almost 

nothing about this important class of proteins,” he said, 

and emphasized the role that NSLS-II would play in 

changing that fact. “There is no other way to study these 

proteins at the level a synchrotron allows.”

“We’re behind,” he added. “Our need is getting severe.”

MacKinnon also stressed the importance of the facility’s 

location in the northeastern United States. NSLS-II 

would service the many research institutions in the rePatricia Dehmer, Associate 

Director of the Office of Basic 

Energy Sciences, gave an 

inspiring and positive speech in 

support of NSLS-II.

Carl Kohrt, the President and 

CEO of Battelle and the current 

chair of Brookhaven Science 

Associates, also offered his 

support for NSLS-II.

NY Congressman Tim Bishop 

spoke about the importance of 

NSLS-II to Brookhaven Lab and 

the scientific community.

NY Congressman Sherwood 

Boehlert, Chairman of the House 

Committee on Science, the 

workshop’s keynote speaker and 

distinguished guest.

IBM Vice President for Research 

Paul Horn, who gave an excellent 

talk on how NSLS-II could 

help revive the silicon transistor 

industry.
3-8 NSLS ACTIVITY REPORT 

gion, he said, and it is essential 

for researchers whose work 

requires frequent visits to have 

local access to the facility.

During the afternoon, the 

workshop participants divided 

into seven breakout sessions, 

giving them a chance to 

provide input and feedback 

on the design and parameters of NSLS-II. The topics 

were spectroscopy, scattering, 

small angle x-ray scattering 

and x-ray photon correlation 

spectroscopy (SAXS/XPCS), 

nanoprobe/imaging, macromolecular crystallography, infrared, and inelastic x-ray scattering.

—Laura Mgrdichian

Roderick MacKinnon, winner 

of the 2003 Nobel Prize in 

Chemistry, discussed how NSLSII would enable further research 

on ion channels.

Cullie Sparks: In-Memoriam

March 19, 2004

Cullie Sparks, a charter member of the NSLS users group 

and one of the first Chairmen of the Users Executive 

Committee, died March 19, 2004. Dr. Sparks made major 

contributions to materials science, x-ray physics, and synchrotron science that continue to have a worldwide impact. 

He was a particularly enthusiastic supporter of synchrotron 

radiation and threw himself wholeheartedly into developing 

beamline X14 at the NSLS when the NSLS was still on the 

drawing board. 

After earning a metallurgical Ph.D. from the University 

of Kentucky, Sparks joined Oak Ridge National Laboratory in 1957. In the mid 60’s Sparks and his group leader, 

Bernard Borie, used symmetry to interpret variations in 

the weak so-called diffuse x-ray scattering from crystalline 

alloys. By quantitatively 

studying patterns in the 

diffuse x-ray scattering, 

they found that local 

structural fluctuations 

could be measured with 

unprecedented sensitivity. This early research 

explored the tendency 

for some materials to 

have a long-ranged average structure but with 

important nanoscale 

fluctuations about 

the average. Later this 

research led to elegant experiments at the NSLS that measured chemically specific bond distances to less than a tenth 

of a picometer (<0.001 Å).

Their Borie-Sparks method for analyzing diffuse x-ray 

and neutron scattering is still used worldwide to interpret 

diffuse neutron scattering and forms the basis for modern 

diffuse x-ray techniques. Research based on their pioneering 

work continues at major Department of Energy facilities 

including the Advanced Photon Source, National Synchrotron Light Source, and ORNL’s High Flux Isotope Reactor.

Also in the 60’s, Dr. Sparks recognized the potential of 

artificial graphite crystals for high-performance x-ray and 

neutron monochromators. He worked with researchers at 

Union Carbide Corporation to perfect the manufacture and 

performance of graphite monochromators and became the 

world’s expert on mosaic graphite optics. By combining the 

natural tendency of mosaic graphite crystals to focus in the 

plane-of-scatter with out-of-plane focusing based on curved 

surfaces, he created powerful doubly-focusing crystal optics. 

Carbide continues to make a range of graphite monochromators that are used worldwide both for x-rays and neutrons. 

Armed with a vastly more powerful way to produce intense 

x-ray beams, Sparks began a systematic search for inelastic 

x-ray scattering contributions that might have contributed 

background in his diffuse scattering measurements. His 

careful research uncovered an unsuspected resonant-inelastic scattering mechanism. Although a respected reviewer 

from Bell Labs, who specialized in inelastic x-ray scattering, 

could find no fault in Sparks’ 1974 Physical Review Letters 

paper, the reviewer personally performed definitive synchrotron experiments at Stanford Synchrotron Radiation Laboratory (SSRL) to check Sparks’ results—and verified, much 

to his surprise, that Sparks was correct! Resonant raman 

x-ray scattering or “Sparks scattering” is still widely used to 

study the dynamics of x-ray-induced atomic transitions.

In 1976, proton microprobe measurements on monozite 

inclusions with anomalously large halos in micas from 

Madagascar indicated the presence of primordial superheavy elements. This “discovery” reverberated throughout 

the scientific community, as the presence of primordial 

superheavy elements suggested that the earth might be only 

a few thousand years old, a compact atomic weapon might 

be made of these unusual elements, and even the shape of 

the nucleus might differ from standard materials.

In a crash program to settle the issue, Sparks designed the 

first synchrotron-based x-ray fluorescence microprobe and 

led a team of distinguished scientists that installed and 

executed the critical test at the SSRL. Sparks and his team 

convincingly showed that primordial superheavy elements 

do not exist in these micas. As a result, the U.S. and other 

governments avoided the enormous resources that might Cullie Sparks aligning a sample on beamline X14.
 YEAR IN REVIEW 3-9

otherwise have been expended to understand something 

for which there is no evidence. This experiment clearly illustrated the critical need for intense synchrotron radiation 

sources.

In the summer of 1979, during a sabbatical at BNL, Sparks 

began studying how to focus x-rays with bent perfect 

crystals. He was motivated by the fact that crystals, with 

roughly a 20 times larger scattering angle than mirrors, 

can collect much larger divergences and focus them onto a 

sample. Although Sparks was greatly challenged by computer programming, he worked with scientists at BNL and 

ORNL to study ways to utilize the potential of crystal focusing. He discovered that in a nondispersive geometry, the 

Bragg angle of each ray reflected from a flat crystal is virtually the same off a crystal bent to focus at magnification=1/

3. This discovery opened the possibility of dynamically bent 

sagittal focusing optics. Despite major technical challenges 

and a general consensus that the method could not work, 

sagittal focusing optics were demonstrated, paving the way 

for beamline X14. Sagittal focusing optics are now installed 

in multimillion-dollar facilities around the world providing 

20 times greater x-ray intensity than alternative focusing 

methods. 

Not only were the sagittal focusing optics widely adopted 

by the worldwide synchrotron community, but the efficiency and flexibility of sagittal focusing optics on beamline 

X14 also led to numerous exciting collaborations. First or 

early measurements included fluorescence tomography, 

resonant magnetic scattering, multiple wavelength holography, anomalous powder and diffuse x-ray scattering, nuclear 

resonant scattering, glancing angle scattering from lipids, 

scattering from liquid crystals, quasi crystals, and other 

experiments.

In addition to his other contributions at the NSLS, in 1985 

Sparks and three associates contributed the after-dinner 

show at the NSLS users meeting. This legendary performance of bluegrass songs with synchrotron themes was 

topped off with a round of authentic moonshine for those 

NSLS users and staff brave enough to try.

In short, Sparks was a gifted experimentalist and a good 

Cullie (left on banjo) and the Earsore Quartet playing at the 1985 NSLS 

Users' Meeting. 

friend of the NSLS. His scientific legacy continues to this 

day through advanced x-ray optics, new fields of atomic 

physics, materials, and synchrotron science.

—Gene Ice, ORNL

New Technology Turns Dredged Material 

into Cement

April 7, 2004

In research performed in part at the NSLS, scientists at 

Brookhaven National Laboratory have helped develop a 

new technology that converts material dredged from the 

bottoms of harbors and waterways into a substance that 

can be made into construction-grade cement. The technology, called Cement-Lock, was developed in collaboration with the U.S. Environmental Protection Agency 

(EPA), the State of New Jersey, and other government 

and public groups.

“This technology will greatly help to increase the health 

of many U.S. harbors and waterways, such as the Port of 

New York and New Jersey,” said Keith Jones, an environmental scientist at Brookhaven who took part in CementLock’s development. “These waterways are contaminated 

by metals and pollutants from many human activities, 

such as sewer overflow systems and discharges from 

industrial operations.”

To ensure that the port can continue to service large container ships, which need deep water, it must be dredged 

regularly, Jones explained. But because the dredged material is contaminated, there are very strict restrictions on 

where and how it can be disposed of.

“This is one of several promising technologies that have 

the power to solve the problem of dredged material,” 

said EPA Regional Administrator Jane M. Kenny at an 

event in Bayonne, New Jersey on November 24, 2003. 

“It enables us to treat contaminated material and use it 

The kiln in Bayonne, New Jersey
3-10 NSLS ACTIVITY REPORT 

beneficially, instead of 

adding tons of material to landfills that are 

already short on space.”

According to Eric Stern, 

the EPA Regional 

Contaminated Sediment Program Manager, 

“Sediment decontamination is a component 

of an overall dredged 

material/contaminated 

sediment management 

strategy. What sets this program apart from typical remediation is that beneficial use products – cement, lightweight 

aggregates, bricks, and soils – are the end result. These 

products then serve as economic drivers for the restoration and revitalization of impacted waterways, ports, and 

harbors around the entire world.”

Brookhaven Lab has been involved in the development of 

sediment decontamination strategies since 1994, when it 

began collaborating on a decontamination program for the 

Port of New York and New Jersey, called the New York/

New Jersey Harbor Sediment Decontamination Project, led 

by Stern. The collaboration also includes the EPA, the U.S. 

Army Corps of Engineers, and the New Jersey Department 

of Transportation (NJDOT) Office of Maritime Resources, 

which joined the collaboration in 1998. 

Many researchers at Brookhaven Lab participated in that 

project, and began by performing basic research on contamination chemistry. For example, using x-rays and infrared 

light at NSLS beamlines U2B, X1A, X26A, and X27A, the 

scientists closely studied how contaminants are bound to 

sediment particle grains.

Brookhaven researchers also determined which experimental treatment methods would be tested and selected several 

technology companies to perform bench and pilot-scale 

tests, which can treat a few gallons and several cubic yards 

of sediment, respectively. 

Once those test results were completed, the Brookhaven 

group reviewed the results and selected several treatment 

methods for fullscale demonstrations. As a result, 

Brookhaven and 

the EPA awarded 

contracts for the 

construction and 

operation of two 

large-scale sediment 

treatment facilities that can treat 

thousands of cubic yards of material. The Gas Technology 

Institute (GTI) in Des Plaines, Illinois, which developed 

Cement-Lock during the initial testing phases, is one of the 

two winning companies. GTI is an independent company 

that develops energy and environmental technologies.

“The GTI group developed a process that can treat all types 

of sediment, and highly contaminated ones, in particular,” 

said Jones, who is also the project’s technical manager. “The 

facility has potential for use on major problem spots in the 

region.”

GTI is now carrying out a large-scale demonstration of the 

Cement-Lock process with a specially constructed 10-foot 

diameter by 30-foot long rotary kiln melter that they built 

for the demonstration in Bayonne. In the process, dredged 

material and modifying minerals are loaded into the kiln 

and heated to between 2,400 and 2,600 degrees Fahrenheit, 

creating a molten material. The high temperature causes 

some contaminants in the material to break down into environmentally safe components that are vented to the atmosphere, while the contaminants that do not break down are 

incorporated into the melt. The resulting treated material, 

called “Ecomelt,” is then ground to a powder and blended 

with cement. The Ecomelt takes part in the hardening process of concrete, which is a mixture of cement, sand, gravel, 

and water. Further, Ecomelt reduces the quantity of other 

raw materials that are typically used in cement manufacturing, such as shale.

After the testing phase, which will treat 400 cubic yards 

of dredged material from New Jersey’s upper Newark Bay, 

EPA and NJDOT will work with GTI to develop a commercial kiln that can treat up to 500,000 cubic yards of 

sediment per year.

The research is funded by EPA, the NJDOT Office of 

Maritime Resources, GTI, and Unitel Technologies.

—Laura Mgrdichian

A view into the kiln as it operates

Grains of Ecomelt

NSLS Hosts More Than 100 Children on 

“Take Our Sons and Daughters to Work” 

Day

April 24, 2004

On April 24, more than 100 BNL daughters and sons 

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 Sons and 

Daughters to Work Day.” 

At the NSLS, the children learned that the facility produces 

many types of light, from microwaves to x-rays, which have 

many applications in many fields, including computers, 
 YEAR IN REVIEW 3-11

2004 RapiData Crystallography Course

April 25-30, 2004

From April 25 to 30, budding crystallographers from 

around the world gathered at Brookhaven Lab for 

RapiData 2004, a week-long course run by Brookhaven’s 

Biology and National Synchrotron Light Source (NSLS) 

Departments. The course introduces students to the field 

of macromolecular x-ray crystallography by giving them 

access to advanced equipment, the latest crystallography 

techniques, and the instruction of experienced crystallographers.

The course, “Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular 

X-Ray Diffraction Measurement,” consisted of two days 

of lectures and tutorials taught by scientists from BNL, 

industry, academia, and other national labs. This was 

followed by a marathon sixty-hour data-collection and 

analysis session at the NSLS, in which the same instructors and volunteers acted as hands-on advisors. Several of 

the course’s 48 students left with solved structures, which 

will likely result in publications.

The course, which helps to train the next generation of 

NSLS users, is mostly organized by Bob Sweet and Denise Kranz of Biology, but they emphasize that its success 

depends on enthusiastic help from most of the twenty 

members of the PXRR (the Biology and NSLS Macromolecular Crystallography Research Resource), plus a 

dozen or so outside teachers. 

Major funding for the course was provided by the National Institutes of Health through the National Center 

for Research Resources, and the Office of Biological & 

Environmental Research within the U.S. Department 

of Energy’s Office of Science. Additional support comes 

from the NSLS, as well as equipment vendors and drug 

companies.

—Karen McNulty Walsh and Laura Mgrdichian

Some of the participants at the NSLS "Take Our Sons and Daughters Work 

Day"

catalysis, microscopes, and medicine. Synchrotron light was 

contrasted with more familiar forms of light as the children 

played a game that tested their knowledge of everyday light 

sources, such as laser pointers, cell phones, radios, and TV 

remote controls.

The daughters and sons then toured the experimental 

floor, where NSLS Control Room Operator Gary Weiner 

explained how synchrotron light is made. NSLS scientists 

Marc Allaire, Lisa Miller, Cecilia Sanchez-Hanke, and 

Vivian Stojanoff then showed the students a few x-ray and 

infrared beamlines, where they discovered how synchrotron 

light is used to study the composition of rocks and minerals 

and, using protein crystallography, to develop new drugs. 

After the tour, the daughters and sons had the chance to 

perform their own scientific experiments. Marc Allaire, 

NSLS student Tejas Telivala, and NSLS postdoc Adele Qi 

Wang demonstrated the refraction of light through a prism, 

and each child had the opportunity to test their skills with 

their own prism. 

NSLS beamline 

scientist Randy 

Smith showed the 

students how a 

vacuum is created 

using a bell jar and 

vacuum pump. The 

children observed 

the effect of vacuum 

on balloons, a bell, 

a candle, and soda 

water. But perhaps 

the most memorable 

experiment was the effect of vacuum on marshmallow Peeps 

candies, which dramatically expanded under vacuum, but 

then shriveled to half their size when re-exposed to air. 

Regardless, the final product was still tasty.

—Lisa Miller

The children observed the effect of vacuum 

on a marshmallow Peep.

2004 RapiData Crystallography course attendees
3-12 NSLS ACTIVITY REPORT 

2004 NSLS Annual Users’ Meeting Caps 

Off Another Successful Year

May 17-20, 2004

Almost 400 participants at the 2004 NSLS Annual Users’ 

Meeting, held May 17-20 at Brookhaven National Laboratory (BNL), came together for a successful event full of 

interesting talks and important messages for the future. The 

meeting affirmed that the NSLS continues to be a facility 

that produces important science.

In his welcoming remarks at the 

main meeting on May 18, the new 

Users’ Executive Committee (UEC) 

Chair, Larry Shapiro, discussed the 

continuing excellence of NSLS research, such as the cellular ion channel structure determined by user 

Roderick MacKinnon, performed 

at the NSLS and the Cornell High 

Energy Synchrotron Source. This 

work earned MacKinnon the 2003 

Nobel Prize in Chemistry.

Steve Dierker, NSLS Chairman and 

Associate Laboratory Director for 

Light Sources, described another 

important crystal structure, a cellular protein channel, recently determined here and featured on the cover of Nature

in January 2004.

He also described other research highlights – a new liquid 

crystal phase in polar ordered materials, featured on the 

cover of Science in August 2003; a new material texture 

type, appearing in Nature in December 2003; and a new 

way to store hydrogen in molecular compounds, published 

in January 2004 in the Proceedings of the National Academy 

of Sciences.

“These give you a flavor of the diversity and quality of science that continues at this facility,” he said. “The NSLS has 

a well-deserved reputation for outstanding productivity.”

The main meeting’s scientific talks focused on user research 

from a more in-depth perspective. Chris Jacobsen, of Stony 

Brook University (SBU), gave an overview of the many xray and infrared imaging techniques 

available to users at the NSLS. 

Mark Croft, from Rutgers University, described his research on strain 

fields in macroscopic materials, in 

which he uses an energy dispersive 

x-ray diffraction method.

Simon Billinge, of Michigan State 

University, presented his work on 

the structures of complex materials 

that display order on the nanoscale, 

using the rapid acquisition pair distribution function technique he developed with his group. Brookhaven 

Lab’s John Hill discussed how he 

uses soft x-ray scattering to probe the behavior of electrons 

in solids.

Another speaker, Cornell University’s Lois Pollack, described an apparatus designed by her research group, which 

allows them to observe, using small angle x-ray scattering 

(SAXS), how an RNA chain molecule compacts and folds 

into a three-dimensional structure. Following this, Yvonne 

Akpalu, of Rensselaer Polytechnic Institute, presented her 

work, which investigates how to solve the crystal structure 

of a copolymer using SAXS.

On the days before and after the main meeting, users divided up to listen to additional talks on specific topics. These 

talks were organized into the following workshops: “Better 

Ways to See the Light: Advanced Detectors for Synchrotron 

Radiation,” organized by Peter Siddons (BNL) and Gianluigi De Geronimo (BNL); “Anatomy of a Virus,” organized 

by Marc Allaire (BNL) and Paul Freimuth (BNL); “Grazing Incidence Small Angle Scattering,” organized by Ben 

Ocko (BNL) and Detlef Smilgies (Cornell University); 

“Pharmaceutical Applications of Synchrotron Radiation,” 

organized by Evgenyi Shalaev (Pfizer Inc.), Raj G. Suryanarayanan (College of Pharmacy), and Peter Stephens (SBU); 

“Advanced Optical Systems and Metrology for High Power 

and Coherent Beamlines,” organized by Peter Takacs (BNL) 

and Steve Hulbert (BNL); “Applications of Synchrotron 

Based Methods to Hydrogen Storage Materials,” organized 

by Trevor Tyson (New Jersey Institute of Technology) and 

Wolfgang Caliebe (BNL); “Nanoprobes for Nanoscience,” 

Among the main meeting speakers at the Annual NSLS Users' Meeting 

were (from left): Bob Casey (BNL-NSLS), Pedro Montano (DOE), Mark 

Croft (Rutgers University), Steve Dierker (BNL-NSLS), John Hill (BNLPhysics), Lois Pollack (Cornell University), Simon Billinge (Michigan 

State University), and Chris Jacobsen (Stony Brook University).

Yvonne Akpalu (RPI) 

discussed the use of light 

and x-ray scattering on 

copolymers.

The new NSLS Users’ 

Executive Committee 

Chair, Larry Shapiro, gave 

welcoming remarks at the 

main meeting.
 YEAR IN REVIEW 3-13

organized by Cecilia Sanchez-Hanke (BNL) and Peter 

Sutter (BNL); and “Crystallization, Membrane Proteins,” 

organized by Naomi Chayen (Imperial College of Science, 

Technology & Medicine) and Vivian Stojanoff (BNL).

Now and Ahead

On the performance front, Dierker said the facility did well 

overall in the last year, with the VUV ring achieving 98 percent reliability and 108 percent availability. The x-ray ring 

didn’t perform quite as well, operating at 89 percent reliability and 99 

percent availability. He noted that 

more than 60% of the downtime 

on the x-ray ring was due to three 

unusual major events, including the 

Northeast electrical power blackout 

last August. 

In a message users are very familiar 

with, he stressed that the NSLS, 

designed 30 years ago and the only 

remaining second-generation DOE 

light source, is now performing at 

the limits of its capabilities. Pedro 

Montano, manager of the X-ray 

and Neutron Scattering Facilities 

program within the Department of 

Energy’s Office of Basic Energy Sciences, acknowledged this 

in his talk, referring to the NSLS as the “working horse” of 

the DOE light sources.

Dierker and Montano repeated the need and excitement for 

NSLS-II, the proposed third-generation light source that 

would replace the NSLS.

Currently, Montano said, an international panel of 

scientists is reviewing the proposal – the first step in the 

process. He urged the prospective users of NSLS-II to 

contact their representatives in Congress and tell them 

how vital the facility is.

“I think NSLS-II is necessary,” Montano said. “There are 

a huge number of scientists in the Northeast that would 

benefit from it.”

All of the day’s speakers affirmed this idea – that NSLS-II 

is needed to broaden and enrich 

their research.

BNL and the NSLS

In his “CFN Update” talk, Robert 

Hwang, director of the upcoming 

Center for Functional Nanomaterials (CFN) facility, discussed 

how the CFN will be “an interdisciplinary environment for 

nanoscience research,” performed 

in conjunction with several BNL 

departments, including the current NSLS and NSLS-II.

In this way, the research the CFN 

will enable promises to be very 

exciting. “The Northeast is becoming a hotbed for nanoscience,” said Dierker. “Brookhaven is becoming a focal 

point for much of that research.”

The future of Brookhaven Lab was the subject of Lab 

Director Praveen Chaudhari’s talk. In his vision for the 

Laboratory in the next 20 years, Chaudhari said NSLS-II 

plays a significant part in his desire to see more integration between departments, and the emergence of a new 

culture and way of thinking at the Lab.

“In a research lab, departmentalizing can be a hindrance,” 

he said. “To reach the frontiers in the life, physical, and 

environmental sciences, we need to find the major challenges at these interfaces between disciplines, and begin 

to address them.”

Another Lab-wide initiative – safety – was discussed by 

Bob Casey, the NSLS Associate Chair for Environment, 

Health, Safety, and Quality. While the NSLS safety 

record hovers around the DOE average, “We’re being 

asked to really improve,” Casey said. “We want to be best 

in class.”

The types of accidents that occur at the NSLS are 

sometimes considered routine, such as slips and muscle 

strains, but, as Dierker said in his talk, “Accidents have 

consequences.” Additionally, there have been near misses 

at BNL in the special-hazard category, which include 

more serious electrical, radiation, and laser accidents. 

Members of the 2004 planning committee for the NSLS Users' Meeting 

include: (from left) Larry Shapiro (Columbia University), Liz Flynn 

(BNL-NSLS), Mary Anne Corwin (BNL-NSLS), Tony Lanzirotti 

(University of Chicago), Gretchen Cisco (BNL-NSLS), Lisa Miller 

(BNL-NSLS), Vivian Stojanoff (BNL-NSLS), Paul Stevens (Exxon Mobil 

Research & Engineering Company), and Dan Fischer (National Institute 

of Standards & Technology).

Brookhaven National 

Laboratory Director 

Praveen Chaudhari 

discussed his vision for the 

Laboratory in the next 20 

years.

Center for Functional 

Nanomaterials (CFN) 

Director Robert Hwang 

gave the "CFN Update" at 

the main meeting.
3-14 NSLS ACTIVITY REPORT 

Casey made it clear that these must also be avoided, ending 

his talk with a series of photographs showing obvious safety 

violations in several areas of the NSLS. The pictures made 

it clear that safety really is an issue everybody must take 

seriously.

Honorable Mentions

Numerous honors and awards were presented at the close of 

the meeting. Outgoing UEC chair Tony Lanzirotti presented the UEC Community Service Award to Sue Wirick 

of Stony Brook University. Additionally, Lisa Miller, the 

meeting’s poster session and publicity chair, gave out awards 

for the best posters. The winners were Dario Arena (BNLNSLS), Mehmet Aslantas (BNL-NSLS), Alexei Grigoriev 

(Harvard University), Marianna Kissel (SBU), Meghan 

Ruppel (SBU), and Xianqin Wang (BNL-Chemistry).

At the evening banquet, Shapiro presented the meeting’s organizers – Mary Anne Corwin, Liz Flynn, Gretchen Cisco, 

and Melissa Abramowitz – with framed letters of appreciation. This year’s banquet was reggae-themed, complete with 

a reggae band, colorful hats, and island fare.

—Laura Mgrdichian

Poster prize winners at the 2004 NSLS Users’ Meeting were (from left 

to right): Dario Arena (BNL-NSLS), Xianqin Wang (BNL-Chemistry), 

Marianna Kissell (SBU), Mehmet Aslantas (BNL-NSLS), and Alexei 

Grigoriev (Harvard University). Not pictured: Meghan Ruppel (SBU).

Tuesday night’s Reggae Banquet was enjoyed by all including (from left 

to right): Gene Ice (ORNL), Pedro Montano (DOE), Peter Siddons 

(BNL-NSLS), Chi-Chang Kao (BNL-NSLS), and Chris Ryan (CSIRO, 

Australia).

Better Ways to See the Light: Advanced 

Detectors for Synchrotron Radiation 

Workshop

May 17, 2004

The workshop attracted 62 registrants, who enjoyed a wide 

range of talks about the latest in detector developments for 

synchrotron radiation (SR) applications. The following is a 

very brief resumé of the talks presented.

Many people think the center of this activity is in Europe 

these days, and to bring us up to date with what is happening over there, we heard Dr. Gareth Derbyshire (from the 

Rutherford-Appleton Laboratory in the UK) talk about 

“Detector Developments for Synchrotron Radiation in 

Europe.” He described work underway at the Daresbury 

and Rutherford laboratories, as well as work being pursued 

by the Swiss Light Source in collaboration with the Centre Européenne pour la Recherche Nucléaire (CERN). In 

particular, he stressed the need to provide advanced detector systems to the UK’s Diamond Light Source, currently 

under construction, ready for use on ‘day 1.’

There are many interesting detector developments happening in fields other than SR. The next speaker, Dr. Oswald 

Siegmund, was from the Space Sciences Laboratory at the 

University of California Berkeley. In his talk, “Microlithographic Silicon-Based Microchannel Plates and Readout 

Techniques for Photon and Particle Detection,” he told us 

of some interesting developments in microchannel electron 

multiplier device technology, in particular the use of micromachining techniques to make precision microchannels in 

silicon wafers. Such devices offer much improved uniformity and reduced noise over conventional drawn-glass 

structures. He also described readout electronics they are 

capable of providing good spatial resolution in one and two 

dimensions, for use with these new channel plates.

There is a real lack of detector technologies that are suitable 

for hard x-ray detection. Perhaps the most promising at the 

moment is cadmium-zinc telluride (CZT). This material is 

not ideal, but the use of special signal processing techniques 

can be helpful. Gabriella Carini (Brookhaven National 

Laboratory) spoke about “A New Integrated Circuit for 

Coplanar-grid Detector Readout.” The coplanar grid detector has a special electrode structure which can mitigate the 

poor hole mobility in these room-temperature semiconductor detectors. The talk described a new microcircuit designed by the BNL microelectronics group, which provides 

enhanced capabilities for such devices.

A key part of any detector system is the software used 

to control the detector and analyze the data produced. 

Dr. Chris Ryan, from the Commonwealth Scientific & 

Industrial Research Organization (CSIRO) in Australia, 

has developed “A New Technique for Real-Time Spectral 
 YEAR IN REVIEW 3-15

Deconvolution of Energy-resolving Detector Data,” which 

can generate quantitative elemental maps from fluorescence microprobe data, in real-time. Simple methods using 

pulse-height windows can lead to serious errors in elemental 

identification due to strong peak overlaps. Chris’ technique 

is able to account for all these overlaps, together with other 

artifacts such as escape peaks, and build up an elemental 

map photon-by-photon.

An exciting development that is beginning to become 

more accessible is that of very high-resolution x-ray detectors based on cryogenic superconducting technology. Kent 

Irwin (National Institute of Standards and Technology, 

Boulder, CO) in his talk “Cryogenic Microbolometer X-ray 

Detectors,” brought us up-to-date on these devices. They 

can reach single-digit eV resolution in the x-ray region, a 

remarkable achievement. The disadvantage of these detectors is that they are rather slow, and Kent described how 

his group is working to overcome this limitation by making 

large arrays of detectors, and how superconducting quantum interference device (SQUID) technology used to read 

them out can be integrated into such an array device.

Even the best detectors sometimes need help, and in the 

field of absorption spectroscopy this is particularly true. In 

his talk “Multilayer Optics for Fluorescence Detectors,” Ke 

Zhang (BioCAT, Argonne National Laboratory) described 

the development and application of multi-element analyzer 

systems based on synthetic multilayer optical elements. The 

instrument he presented provides an efficient filter that only 

allows a particular spectral line to pass to the detector. The 

multiple elements provide enhanced solid angle and hence 

efficiency.

Perhaps the most powerful driver for advanced detector 

development in the synchrotron community has been the 

demands of macromolecular crystallography. The talk by 

Dr. Edwin Westbrook (Molecular Biology Consortium Inc.) 

titled “Silicon Pixel Array Detectors for Protein Crystallography,” described some new ideas for fabricating detectors 

using non-traditional processing techniques. The result is 

a technology that can produce efficient arrays of detectors 

with excellent properties. One point that is unique to this 

technology is that the arrays do not have any dead area 

around the edges, so detectors can be easily tiled together to 

make large area systems without any lost image regions.

Tae Joo Shin (NSLS) then told us about his work using 

2-D position-sensitive proportional counters (PSPCs) 

for x-ray speckle experiments. Present speckle experiments typically use either a single-point detector and 

photon-counting with high time resolution, or a CCD 

area detector, which has a readout time of, at best, tens 

of milliseconds. PSPCs have the potential to combine 

the advantages of a photon counting detector and an area 

detector. Preliminary experiments to characterize and 

improve the performance of such detectors to make them 

suitable for speckle were described.

The final talk was to have been given by Dr. Mark Rivers 

(University of Chicago). Although circumstances prevented him from giving the talk at that time, it was rescheduled for a few days later. It also concerned the software 

implications of advanced detector systems. This area of 

development is extremely important, and the difficulties 

and required effort are frequently underestimated. Mark 

told us about the software solutions he has developed for 

interfacing area detectors, in particular CCD devices, to 

data acquisition systems based on the EPICS framework.

The breadth and depth of these talks only scratch the 

surface of what we believe is the last remaining barrier to 

the full utilization of our powerful synchrotron facilities. 

We look forward to hearing much more of these developments at future meetings.

—D. Peter Siddons and Gianluigi De Geronimo

Better Ways to See the Light: Advanced Detectors for Synchrotron Radiation 

Workshop attendees

Anatomy of a Virus Workshop

May 17, 2004

It was a memorable day at the workshop, “Anatomy of a 

Virus,” where prominent experts in the field got together 

to talk about their favorite subject. Sponsored by the User 

Executive Committee at the National Synchrotron Light 

Source, the National Institute of Health (National Institute of Allergy and Infectious Diseases, National Institute 

of General Medical Sciences, and National Center for 

Research Resources) and Area Detector System Corporation (Poway, CA), this full day workshop highlighted the 

frontiers in the study of viral structure and the future 

needs in structural virology. With the impressive list of 

speakers that were present on that day (front row of the 

picture), we all had the feeling that the future of structural virology was already there.

The workshop started with no less than a historical perspective given by Donald Caspar (Florida State 

University), which was elegantly introduced by Dieter 

Schneider. Don related the important factors that were 

required for the success and the birth of structural studies 
3-16 NSLS ACTIVITY REPORT 

of viral capsids. The next speaker was Denis Leclerc (Laval 

University), who reported on his progress on the assembly 

of nucleocapsid-like particles of hepatitis C virus. Their 

results suggest that the first N-terminal half of the core protein would be sufficient for the formation of viral particles. 

Michael Chapman (Florida State University) presented 

his work on structural studies of a gene therapy vector, the 

adeno-associated virus. From their atomic x-ray structure, it 

was possible to predict the viral site where it attaches to the 

cellular receptor. Huilin Li (Brookhaven National Laboratory) talked about genomic RNA packaging in the vesicular 

stomatitis virus. By single-particle cryo-electron microscopy, a ring of density was revealed on the inner surface, 

and the density is proposed to be the RNA. Stacy Benson 

(the Wistar Institute) followed and reported on structural 

studies of the lipid-containing bacteriophage PRD1. The 

x-ray crystal structure of its major coat protein has revealed 

a molecule that contains two viral jelly rolls and appears 

to link PRD1 evolutionarily with the human adenovirus. Michael Rossmann (Purdue University) talked about 

“Membranes and Motors: Where Electron Microscopy 

Meets Crystallography.” He described a variety of examples 

in which crystallography and cryoEM were combined to 

construct detailed atomic models of large complexes. A 

striking example was the structure of the bacteriophage T4 

base plate assembly in two different states. High-resolution 

structures of component proteins, combined with cryoEM 

reconstructions of the entire base plate complex in the 

extended and contracted states, revealed the extraordinary 

dynamic character of this complex and the large-scale motions of individual proteins. 

The afternoon session started with Philip Dormitzer 

(Harvard Medical School) describing the structural rearrangements during rotavirus cell entry. His group's recent 

structure of the membrane penetration domain of VP4 

reveals a fold-back rearrangement reminiscent of the enveloped virus fusion proteins that mediate enveloped virus cell 

entry. Wayne Hendrickson (Columbia University) gave his 

presentation on the structural biology of HIV attachment 

and entry into cells. His studies suggest that the flexibility 

of the glycoprotein GP120 of HIV is implicated in the 

escape to the immune response. The next talk, “Motors 

and Membranes: Where Crystallography Meets Electron 

Microscopy,” was given by David Stuart (Oxford University). He presented his extensive work on the x-ray crystal 

structure analysis of the entire 66 MDa bacteriophage 

PRD1. These viral particles contain approximately 2000 

protein subunits from 18 different protein species including integral membrane proteins associated with an internal 

lipid bilayer. Their crystal structure reveals, among other 

things, an ordered membrane structure that allows specific 

interactions with the genome and the coat proteins. John 

Johnson (The Scripps Research Institute) then closed the 

workshop with a lively talk about structure-based studies 

of auto-catalytic chemistry in virus particles. He described 

auto-catalytic cleavages that occur in the maturation of 

non-enveloped RNA insect viruses and proposed mechanisms based on atomic models from crystallography. The 

talk concluded with the description of a unique auto-catalytic ligation of a lysine side chain with an asparagine side 

chain to create catenated subunit rings that “chain-link” the 

capsid of HK97, a dsDNA bacteriophage.

—Marc Allaire

Anatomy of a Virus Workshop attendees

Grazing Incidence Small X-ray Scattering 

Workshop

May 17, 2004

A workshop on Grazing Incidence Small-Angle X-ray 

Scattering was held on May 17, 2004 as part of the 2004 

National Synchrotron Light Source (NSLS) Users Meeting. This technique, commonly referred to by the acronym 

GISAXS, is the surface analogue of Small-Angle X-ray 

Scattering (SAXS). Scientific topics discussed included thin 

polymer films, nanoparticles at interfaces, and semiconductor nanostructures. GISAXS measurements are sensitive to 

both the surface morphology and the internal structure of 

films, and provide information both lateral and normal to 

the surface on length scales extending from 1-100 nm. As a 

result, GISAXS provides an excellent complement to more 

conventional nanoscale structural probes such as atomic 

force microscopy and transmission electron microscopy. 

Moreover, GISAXS lends itself to in-situ and real-time 

studies. Eleven speakers presented their results, followed by 

a discussion on ways to improve the technique and access to 

GISAXS facilities.

The first speaker was Detlef Smilgies from the Cornell High 

Energy Synchrotron Source (CHESS). Detlef presented 

a short introduction on the history and applications of 

GISAXS. He reviewed the rapid development of the technique, starting with the pioneering measurements of Levine 

and coworkers in the U.S. and Naudon and coworkers in 

France during the late 1980s. Detlef provided a perspective 

on how three different x-ray communities, SAXS, diffuse 
 YEAR IN REVIEW 3-17

reflectivity, and Grazing Incidence Diffraction (GID), 

were converging through GISAXS. In the following talk, 

a youthful Sunil Sinha from the University of California 

presented an intriguing and mesmerizing talk on the underlying scattering theory associated with GISAXS with a focus 

on the Distorted Wave Born Approximation (DWBA). 

Examples were presented in which wave-guiding effects, 

induced by the film interfaces, significantly enhanced the 

small-angle scattering from the particulate matter inside 

or on the surface of the film. In the third presentation, 

Ian Robinson from the University of Illinois presented a 

stimulating talk on coherent GISAXS investigations of 

granular micro-structures in thin metal films, performed at 

the Advanced Photon Source (APS). Speckled diffraction 

patterns were reported for gold nanoparticles prepared by 

the dewetting of a thin gold film on a solid support. The 

shapes of the speckle patterns were used to investigate the 

changing geometry associated with different parts of the 

diffraction pattern.

After a short break, Till Hartmut Metzger from the European Synchrotron Radiation Facility (ESRF) presented a 

captivating review on combined GISAXS and GID studies 

of semiconducting nanostructures, so-called quantum dots, 

performed at HASYLAB and the ESRF. Particular emphasis 

was placed on the role of strain, size, and chemical composition and their relationship to growth, which are the 

crucial input parameters for the understanding the electronic and optical properties of the quantum dots. Specific 

examples included InAs islands on GaAs and Ge pyramids 

on Si, for which detailed maps of strain and composition 

within the quantum dots were obtained. The following 

speaker, Alain Gibaud from the Université du Maine, 

presented a visually stimulating talk on in-situ studies of 

surfactant-templated silica thin films at the NSLS, which 

included the premier of several “reciprocal space” movies. In these studies, time resolved GISAXS measurements 

were carried out simultaneously with gravimetric studies 

during the slow evaporation of ethanol from a film containing surfactant (CTAB), silica precursor (TEOS), and 

water to obtain silica mesostructures. The time evolution 

was exploited to probe the mechanism of the self-assembly 

process. Prior to lunch, Thomas Russell from the University 

of Massachusetts gave a lively and animated presentation 

on the assembly of nanoparticles at the interface of two immiscible fluids. Tom noted that the nanoparticles mediate 

the interactions between the two fluids, thereby reducing 

the interfacial energy. 

After lunch, Christine Papadakis from the Technical 

University of Munich awoke the audience with an enlightening presentation on the inner structure of lamellar 

diblock copolymer thin films, as studied at CHESS and 

ESRF. Christine showed how poly(styrene-b-butadiene) 

films undergo a morphological transition from parallel lamellae for short chains to perpendicular lamellae 

for long chains. Complementary in-situ time-resolved 

GISAXS measurements were presented after the injection of toluene into the sample cell, which revealed both 

changes in the sample thickness and the lamella orientation on a timescale of minutes. Continuing the polymer 

theme, Matthew Misner from Prof. Russell’s group at the 

University of Massachusetts presented an informative talk 

on real-time studies of block copolymer thin films at the 

NSLS. Results for two different systems were examined: 

polystyrene-block-poly(ethylene oxide) diblock copolymers, where the orientation of the micro domains was 

normal to the surface, and poly(ethylene-alt-propyleneb-lactic acid), where the orientation was parallel to the 

substrate. Analysis of the time-resolved GISAXS provided 

information on the size, morphology, and orientation of 

the films during solvent evaporation. In the final polymer talk, Phong Du, a student from Cornell University 

working with Prof. Ober and Prof. Wiesner, presented 

an intriguing overview of their GISAXS studies at the 

CHESS. Poly(styrene-b-ethylene oxide) structures were 

exploited to create silica nanostructures, making use of 

the silica precursor being readily concentrated in the 

poly(ethylene oxide) block and successive calcination. In 

a second project, nanosieves were prepared from cylindrical diblock copolymer films by selective photoreactions, 

in order to remove one block, while cross-linking the 

other for stability. To close out the session, Oleg Gang 

from Brookhaven National Laboratory presented a fascinating talk on liquid films on nano-sculptured surfaces. 

By varying the chemical potential difference between the 

liquid-vapor coexistence, small nanometer pits were filled 

with an organic liquid. By combining GISAXS and x-ray 

reflectivity at the NSLS, detailed information could be 

obtained on both the liquid in the pits and the thin wetting film above the surface.

After a short break, Gilles Renaud from the Commissariat à l’Energie Atomique (CEA) in Grenoble an inspiring 

whirl wind presentation of their work on real-time in-situ 

investigations of the morphology, organization, and internal structure of growing metal nanoparticles on oxide 

surfaces in ultra-high vacuum at ESRF. Results were presented for palladium, silver, and platinum on MgO(001) 

as well as for copper on alumina, gold on TiO2

, and copGrazing Incidence Small Angle Scattering Workshop attendees per and silver on ZnO. Combined GISAXS and wide-
3-18 NSLS ACTIVITY REPORT 

angle x-ray scattering provided a wealth of information on 

the growth modes and particle morphology. Quantitative 

information could be extracted by theoretical modeling 

within the framework of DWBA. In the final presentation, Jin Wang from Argonne National Laboratory gave a 

thought-provoking talk on the kinetics of nanocomposites 

obtained from both SAXS and GISAXS measurements at 

the APS. Jin showed that the motion of the nanoparticles is 

highly anisotropic. 

Following the talks there was an enthusiastic discussion on 

the future of GISAXS methods, including the needs of the 

emerging community. There was wide agreement that one 

of the key features of GISAXS is the ability to carry out 

real-time, in-situ measurements. While there are currently 

few dedicated GISAXS beamlines, GISAXS capabilities can 

often be implemented on existing SAXS or GID beamlines through the addition of a 2D detector. There was a 

lively discussion on CCD detectors including the need for 

faster readout times. For soft matter applications, it was 

noted that it is often desirable to combine GISAXS with 

reflectivity and SAXS measurements. Simultaneous optical 

measurements of the film thickness can be very useful for 

in-situ experiments. For hard-matter applications, it was 

noted that it is essential to combine GISAXS measurements 

with GID studies, in order to obtain shape and internal 

structural information. Finally, it was remarked that future 

GISAXS facilities should be user-friendly and well supported in order to open up the technique to non-specialists.

—Ben Ocko and Detlef Smilgies

Pharmaceutical Applications of Synchrotron Radiation Workshop

May 17, 2004

The workshop “Pharmaceutical Applications of Synchrotron Radiation” was held as part of the 2004 Annual Users’ 

Meeting of the National Synchrotron Light Source (NSLS) 

on May 17th. The main goal was to bring together people 

working in the pharmaceutical industry with those familiar with synchrotron radiation techniques. The workshop 

focused on issues related to later stages of the drug development cycle, i.e., polymorphism, selection of salts and 

hydrates, quantification of crystallinity, partial states of 

crystallinity, etc. Research in drug discovery, such as protein 

crystallography, was not covered, although that has grown 

to a very large user base at synchrotron facilities worldwide.

One of the co-organizers, Evgenyi Shalaev of Pfizer, opened 

the discussion with an overview of the drug development 

cycle. Of several million candidates screened, only one 

or two will be reduced to a profitable new drug, after a 

development period of approximately fifteen years. X-ray 

techniques are crucial to many of the steps along the way, 

as well as the protection of intellectual property during the 

marketing lifetime of the drug.

Peter Stephens of Stony Brook University and the NSLS 

(also a workshop co-organizer) discussed the differences between laboratory and synchrotron x-ray sources, first from 

the standpoints of source properties and later in terms of 

access issues. He showed several comparisons of laboratory 

vs. synchrotron powder diffraction patterns and concluded 

that the additional information available was often dramatic 

in its ability to solve technical problems. He also emphasized that synchrotron sources are strongly motivated to 

attract new users, and while there may be some barriers to 

a new user getting a synchrotron research program started, 

they are generally fewer than popularly assumed, and the 

rewards are substantial.

Bill David and Kenneth Shankland, both of Rutherford 

Appleton Laboratory (UK), discussed many aspects of 

structure determination of small molecules from powder xray data. David emphasized the value of detailed structural 

crystallography, illustrated with the structure determination of a transient phase that existed for only one minute 

during the hydration of paracetamol (acetaminophen). He 

also showed the remarkable detail of information available, 

primarily through changes in diffraction peak shapes, of 

the transformation process in a dehydration reaction of the 

hypnotic zopiclone (see figure below). Shankland discussed 

the importance of various steps taken in experimental 

design and data collection to ensure the accurate solution of 

structures, emphasizing that these techniques, both experimental data collection and analysis through simulated annealing methods, are widely available to those who care to 

use them. His message is that you can solve, from powder 

diffraction, structures that represent the typical complexity 

The molecular conformation of the hypnotic drug zopiclone in its 

monoclinic anhydrous form, solved from powder diffraction data taken at 

ESRF BM16. The puzzle alluded to in the illustration, that of significant 

batch-to-batch variation in the physical properties of commercially prepared 

zopiclone tablets, was solved only when XRPD was brought to bear. The 

experiments revealed the structural relationships between the previously 

unsolved monoclinic anhydrous form, the monoclinic dihydrate form, 

and the stable orthorhombic anhydrous form. Picture courtesy of Alastair 

Florence and Kenneth Shankland.
 YEAR IN REVIEW 3-19

of most pharmaceutical compounds.

Mike Pikal of the University of Connecticut discussed the 

degradation of pharmaceutical compounds, such as freezedried proteins in the form of glassy solids. The stability of 

pharmaceutical solids can be extremely sensitive to formulation, and the relationship between thermodynamic measurements and structural relaxation is an important topic 

of research. The current state of understanding is largely 

empirical, and the development of other methods to characterize the state of glassy solids is an important challenge. 

Shalaev discussed the nature of the disordered states, such 

as amorphous states, and crystalline mesophases, of pharmaceutically relevant solids. Amorphous solids can have advantages in solubility and bioavailability, but disadvantages 

in stability; amorphous phases can also arise during certain 

standard processing techniques such as milling, drying, and 

compaction. He challenged the audience to help to clarify 

the possible existence of more than one amorphous phase 

of a given system, so-called polyamorphism, and the extent 

to which nominally amorphous solids, e.g., protein/sugar 

mixtures, may be heterogeneous. Another important issue 

is the relationship between local structure of amorphous 

solids and the structure of crystalline phases of the same 

compounds.

The third co-organizer, Raj Suryanarayanan of the University of Minnesota, discussed x-ray measurements of the 

degree of crystallinity of pharmaceuticals, especially from 

the standpoint of monitoring the physical instability of 

products that are prepared as non-crystalline phases. He 

discussed in situ measurements of the crystallization of 

amorphous sucrose, performed with synchrotron radiation 

and an area detector. These experiments avoid the difficulties associated with the preparation of a large number 

of mixtures required for the traditional preparation of a 

calibration curve.

Satyendra Kumar, of Kent State University, discussed model 

systems related to the issue of delivering water-insoluble 

drugs. Such materials may be physically encapsulated in 

micelles or at the level of individual molecules, which then 

have interesting mesophases. He reported on synchrotron 

x-ray scattering studies of aqueous solutions of cyclodextrin and small molecule dyes, which have a variety of 

self-organized structures with varying degrees of orientational and structural order. He demonstrated how the use 

of external electric, magnetic, or mechanical (shear) fields 

can reveal important new structural details that otherwise 

cannot be obtained.

The final talk of the session was given by Heinz Amenitsch of the Austrian Institute of Biophysics and X-ray 

Structure Research outstation at the ELETTRA synchrotron source in Trieste. His topic was the use of simultaneous small- and wide-angle x-ray scattering to study 

nanostructural features of relevant solids. The size of 

domains of the different components of a pharmaceutical 

formulation, the nature of the internal surfaces, and the 

degree of dispersion are all accessible to these techniques. 

He showed that these measurements can be made with 

sub-millisecond time scales, allowing real-time study of 

the relevant structural changes during such processes as 

spray-drying.

At the end of the workshop, Bruno Hancock of Pfizer 

moderated a round-table discussion of collaboration 

between pharmaceutical scientists and facilities such as 

the NSLS. Some participants expressed concerns that the 

federal government might claim ownership of intellectual property derived from experiments at synchrotron 

sources, even if the user follows procedures for proprietary access. Obviously, this is a matter to be addressed by 

lawyers, not scientists, but the large investment in protein 

crystallography by major drug companies at synchrotron 

sources indicates that this might not be a serious impediment to the commercial use of these facilities. Participants who are not experienced with synchrotron radiation as a research tool probably came away thinking of 

synchrotron sources as valuable commodities, not heroic 

investments. And synchrotron experts should have seen 

that their expertise may be of real value to some important practical problems.

—Peter Stephens

Pharmaceutical Applications of Synchrotron Radiation Workshop attendees

Advanced Optical Systems and Metrology 

for High Power and Coherent Beamlines 

Workshop

May 19, 2004

Future light source beamline instrumentation will 

challenge users and instrument designers to take full 

advantage of the brightness and coherence of the x-rays 

delivered by the new sources. Since Brookhaven National 
3-20 NSLS ACTIVITY REPORT 

Laboratory has a strong tradition in the development of 

metrology instrumentation in support of synchrotron 

radiation optics, it is appropriate that this session on optical 

systems and metrology reviewed the current state-of-the-art 

in optical technology and metrology, and explored avenues 

that may lead to improved capabilities for the future. 

Chris Jacobsen from Stony Brook University, who has 

extensive experience in the generation and use of coherent 

x-rays with existing sources, provided a summary of the 

capabilities of various groups around the world to produce 

small spot sizes from present sources of coherent x-rays. A 

Japanese group at SPring8 has demonstrated 90nm spot 

sizes with Kirkpatrick-Baez focusing optics, and 15nm line 

spacing in zone plates have been reported by workers at the 

Center for X-ray Optics at Berkeley. 

Following Jacobsen’s introduction to coherent imaging at 

x-ray wavelengths, the workshop heard from two speakers 

who are primarily involved with normal incidence UV and 

visible optics for large programs at Lawrence Livermore 

National Laboratory (LLNL) and at NASA Marshall Space 

Flight Center. The surface figure and finish requirements 

on normal incidence optics for DUV (Deep Ultraviolet) 

and EUV (Extreme Ultraviolet) lithography and for large 

space telescopes are nearly the same as those for grazing 

incidence optics, so it was appropriate to hear from John 

S. Taylor of LLNL and from Phil Stahl of NASA about 

mirror fabrication and metrology technologies that are 

being supported by these projects. Taylor discussed the 

development of diffraction-limited multilayer-coated optics 

for normal incidence EUV lithography systems that have 

been developed over the past several years by the Virtual 

National Laboratory consortium of three national laboratories and three companies involved in developing tools for 

the semiconductor manufacturing industry. Slope errors 

on these optical components are in the 200 nrad range, 

which is where synchrotron optics will need to be for effective utilization of the next generation of high-brightness 

x-ray sources. Stahl gave an overview of future NASA space 

telescope missions and the technology that will be required 

to build large, lightweight mirrors and structures. Over 

the past few years he has organized a symposium, “NASA 

Tech Days,” for NASA contractors and university grant 

recipients to present progress in technology development 

programs funded by government agencies. Of interest to 

the Synchrotron Radiation (SR) community are the various 

materials-development projects investigating the use of Be, 

SiC, and other ceramic and composite materials as high 

power mirror substrates, and the fabrication technologies 

that accompany these new materials. 

Don Golini from QED Technologies in Rochester, NY, 

gave a presentation on a new surface finishing technique 

that looks quite promising as an alternative to conventional pitch polishing for the production of spherical and 

aspherical surfaces. His company has developed various 

polishing machines that use magnetorheological fluids as 

the polishing medium. These fluids change viscosity by 

orders of magnitude when a magnetic field is applied and 

can conform to exotic surface shapes not possible with hard 

laps, such as ellipsoids and toroids. A great deal of research 

has gone into characterizing the polishing process, which 

is highly deterministic. With the appropriate metrology, it 

is possible to quickly correct for figure errors and converge 

rapidly to the desired surface shape.

Refractive optics for focusing x-ray beams are a new addition to the techniques available to users for producing small 

spot sizes. Ken Evans-Lutterodt (National Synchrotron 

Light Source) gave an overview of the subject and discussed 

the production of the optimum elliptical hole shape with 

an e-beam writer and the use of diamond as a substrate for 

high heat load situations. Ali Khounsary, Argonne National 

Laboratory, followed with a discussion of high heat load 

optics. He emphasized the need for a systematic approach 

to the design of optical systems that incorporate knowledge 

of the source parameters, mirror substrate characteristics, 

mechanical design, and testing. 

Following the lunch break, Peter Takacs (BNL/

Instrumentation) discussed metrology issues related to 

the Long Trace Profiler (LTP). The LTP is widely used to 

measure the surface quality of large aspheric x-ray optics. 

In order to reach the 100 nrad measurement accuracy level, 

improvements are needed in the quality of the internal optical components in the system. Custom-made glass prisms 

with superpolished surfaces will be needed to reduce the 

systematic error to below the current 1 μrad level. Wayne 

McKinney (Advanced Light Source, Lawrence Berkeley National Laboratory) followed with a discussion of issues that 

are driving the direction of SR metrology. Although the 

LTP has served well in the past, other alternative metrology 

techniques need to be explored, such as stitching interferometry, Hartmann sensors, and multi-beam autocollimator techniques such as those proposed by Polack’s group 

at SOLEIL in France and by Weingärtner’s group at the Advanced Optical Systems and Metrology for High Power and Coherent 

Beamlines Workshop attendees
 YEAR IN REVIEW 3-21

Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany.

The final session of the day began with a description 

of Kirkpatrick-Baez (KB) mirror nanofocusing systems 

by Gene Ice from Oak Ridge National Laboratory. The 

practical limit to the focal spot size is in the range of 10 

to 30 nm, which can be produced by highly demagnifying (~1000:1) elliptical cylinders. These mirrors need to 

have slope error tolerances of less than 200 nrad in order to 

perform correctly. The technique of differential deposition, 

which he has pioneered, appears to be a promising tool 

for converting cylindrical surfaces into accurate elliptical 

shapes. 

The final two talks were presented jointly by Riccardo 

Signorato (ACCEL, France) and Daniel Hausermann (Advanced Photon Source, Argonne National Laboratory) as 

they related to the fabrication and use of modular piezoelectric bimorph mirrors as adaptive optics. The piezoelectric 

bimorph has been developed by Signorato and is currently 

in use at a number of sites, including beamlines at the APS. 

Hausermann uses a pair of bimorphs in a KB configuration 

to focus a 500μm x 500μm hard x-ray beam down to a 10 

μm spot. The longest size currently available is 1050 mm in 

length with N=33 actuator segments. Signorato is looking 

into adding a Shack-Hartmann wavefront analyzer to the 

system to enable automated closed-loop focus control for 

the mirror. 

Following the final talk, a quick tour of the Optical Metrology Laboratory in the NSLS Instrumentation Division was 

offered to those participants who remained. The workshop 

was successful in bringing together members of several different communities, including conventional optics fabricators, end users, and metrology specialists, to share thoughts 

and ideas on the current state of optical component technology, and to chart a course toward future capabilities. 

—Peter Z. Takacs and Steven Hulbert

Applications of Synchrotron-Based Methods to Hydrogen Storage Materials 

Workshop

May 19, 2004

A workshop on “Applications of Synchrotron-based Methods to Hydrogen Storage Materials” was held in conjunction with the 2004 National Synchrotron Light Source 

(NSLS) Users’ Meeting on May 19, 2004. The purpose of 

the workshop was to bring together scientists who synthesize materials with applications in hydrogen storage and 

scientists with expertise in the application of synchrotron 

radiation methods, who currently study these materials. 

The workshop was opened by Doon Gibbs, the Associate Laboratory Director for Basic Energy Sciences at 

Brookhaven National Laboratory (BNL). He emphasized 

the importance of the Hydrogen Energy Project (production, storage, utilization) as one of the missions of the 

Department of Energy (DOE), and encouraged collaborations between scientists within BNL and with outside 

groups by utilizing facilities like the NSLS and the Center for Functional Nanomaterials (CFN) for research.

John Petrovic, from the Hydrogen Storage Team in the 

DOE Office of Hydrogen, Fuel Cells, and Infrastructure Technology, described in his talk titled “The DOE 

National Hydrogen Storage Project: Addressing Key Performance Targets for Materials-based Hydrogen Storage 

Systems” the targets for automotive research over the next 

15 years, and the funding efforts by the DOE to reach 

these targets. He presented different projects and Centers 

of excellence that actively work in the field of hydrogen 

storage and that pursue different paths trying to create 

a successful system. Currently, none of the proposed 

hydrogen storage systems achieves the proposed targets 

for 2005! 

James Reilly from the Department of Energy Science and 

Technology at BNL described in his talk “The Application of Hydrogen Driven Metallurgical Reactions to 

Prepare Reactive Nanoscale/Nanocomposite Materials” 

several ways to create nano-composite metal-hydrides, 

and discussed their properties. By doping some materials 

with fairly large amounts of different metals, the storage 

capacity can be increased, and the temperature for release 

is lowered.

Zafar Iqbal of the Department of Chemistry and Environmental Science at the New Jersey Institute of Technology talked about “Electrochemically-Induced Hydrogen 

Storage in Metal-Functionalized Carbon Nanotubes.” 

He described different ways to synthesize single-wall 

nanotubes (SWNTs), ways to functionalize the SWNT 

with metals, and their properties. Experimental investigation with Raman and Fourier Transform Infrared (FTIR) 

spectroscopy indicate a chemisorption process in CoApplications of Synchrotron Based Methods to Hydrogen Storage 

Materials attendees
3-22 NSLS ACTIVITY REPORT 

doped SWNT, while (weaker) physisorption is present in 

undoped nanotubes. 

Tom Vogt of the CFN talked about “Hydrogen Storage and 

Nano-Structure.” He emphasized the importance of clearly 

characterizing the materials to better understand their 

storage and release mechanisms. High-brightness synchrotron radiation sources like the proposed NSLS-II are ideal 

sources for real-space and dynamical imaging. Also, probes 

at the CFN, such as proximal probes, are well suited for 

studying SWNTs, for example. 

Alexander Ignatov of the Department of Physics at the 

New Jersey Institute of Technology presented in his talk 

“X-ray Absorption Studies of Hydrogen Storage Materials 

– Strength and Limitations” experimental results of EXAFS 

and XANES experiments studying the Ti K-edge in Tidoped NaAlH4

. The data indicate that Ti does not substitute Na in the lattice. Instead, amorphous TiAl3

 is formed, 

and H is found in the first coordination sphere about Ti. 

The EXAFS-analysis allows extraction of the position of H, 

but the H coordination numbers have large errors. 

Yan Gao from the GE Global Research Center talked 

about “Characterization of NaAlH4

 by High-Pressure X-ray 

Diffraction and in-situ EXAFS.” He presented the first 

powder-diffraction data of the re-hydrogenation process 

measured with high time resolution. The data clearly indicate that two steps in the dehydrogenation and re-hydrogenation process have to be completed individually before the 

next step can start. He also observed an increase in particle 

size, which slows down the reactions. His Ti XAS-data also 

indicate the formation of TiAl3

, and the growth of TiAl3-

crystals with the number of cycles. 

The final speaker, Najeh Jisrawi from the Department of 

Physics and Astronomy at Rutgers University, discussed 

“Synchrotron XRD Studies of Hydrogen Absorption in 

Metallic Multilayers and Nano-Particles.” He applied surface x-ray diffraction to study charge-discharge curves of Pd 

and Nb/Pd/Nb thin films, and of polyhedral clusters with 

magic-number sizes. Molecular dynamics calculations support his experimental results and demonstrate that a cluster 

with a size of 8 nm shows similar behavior to a thin film.

The workshop was concluded with a brief discussion of 

techniques and equipment that are required for further successful studies of hydrogen storage materials at the NSLS.

—Wolfgang Caliebe and Trevor Tyson

Nanoprobes for Nanosciences Workshop

May 19, 2004

A workshop on synchrotron-based nanoprobes was held on 

May 19th, 2004 as part of the National Synchrotron Light 

Source (NSLS) and Center for Functional Nanomaterials 

(CFN) annual users’ meetings. The goal of the workshop 

was to explore the scientific opportunities offered by synchrotron-based nanoprobes, with emphasis on combined 

low-energy/photo-electron microscopy (LEEM/PEEM), 

soft x-ray microscopy, and x-ray micro-diffraction.

Bob Hwang, director of the CFN at Brookhaven National 

Laboratory (BNL), opened the workshop by giving an 

overview talk about the status of the CFN, current CFN capabilities that are open for users, including scanning probes, 

transmission electron microsocopy (TEM) and NSLS 

beamlines, and the plan to establish close collaborations 

with other BNL research departments. He also outlined 

the vision to provide the nanoscience user community 24/7 

access to a broad range of “off the shelf” instruments, as 

well as develop new and novel characterization methods in 

conjunction with partner users to achieve a more efficient 

transfer of information and technology. 

After the introduction, the workshop was divided into three 

dedicated sessions. In the soft x-ray microscopy session, 

Harald Ade from North Carolina State University presented 

an extensive review of his work on the characterization of 

polymers using soft x-ray transmission microscopy (XTM). 

The chemical sensitivity in near edge x-ray absorption fine 

structure (NEXAFS) and linear dichroism are exploited 

to provide a unique contrast mechanism to discriminate 

different components in the sample as well as characterize 

the crystallinity and morphology of the sample. The second 

speaker of the session was Chris Jacobsen from Stony Brook 

University. Chris first gave an excellent review of x-ray microscopy using zone-plates as well as the advances made in 

recent years in the fabrication of high-resolution x-ray zoneplates. In the second half of his talk, Chris talked about 

diffraction imaging, a new technique that has attracted a 

great deal of attention recently because the possibility of 

achieving higher spatial resolution than that of zone-platebased x-ray microscopy. The key in diffraction imaging is, 

of course, recovering the phase information that is lost in 

the measurement. Chris gave a detailed account of a very 

efficient iterative algorithm recently developed.

Nanoprobes for Nanosciences Workshop attendees
 YEAR IN REVIEW 3-23

After a short break, Cev Noyan from IBM and Columbia 

University started the session on hard x-ray micro-spectroscopy and micro-diffraction. Cev presented a study of 

strain in SiGe crystals grown on Si crystals. It was a very 

nice demonstration of the power of micro-diffraction. In 

this case, he was able to map out the strain in both the SiGe 

layer as well as that of the substrate. He also discussed in 

some length the challenges in finding and focusing on a 

single grain using x-ray microbeams. The second talk in the 

session was given by Barry Lai from the Advance Photon 

Source (APS) at Argonne National Laboratory. Barry talked 

about the applications of micro-fluoresence and x-ray absorption near edge spectroscopy (XANES) spectroscopy to 

life science problems, in particular the role of trace amounts 

of metals and metal oxides in immunology and intracellular 

processes. At the 2ID at the APS, x-rays down to 200 nm x 

200 nm, with intensities up to 2 x 109

 ph/sec, are achieved 

using a hard x-ray zone-plate. These hard x-ray zone-plates 

are extremely difficult to produce because of the narrow 

width and the height/width aspect ratio required. Barry also 

shared his experience in how to accurately align optics and 

position samples, a very challenging problem as the spatial 

resolution of the experiment improves to sub-micron level.

The third speaker of the session was Ken Evans-Lutterodt 

of NSLS. Ken gave an overview of the microdiffraction 

project at the X13B beamline at the NSLS. The project is 

funded by the Department of Energy to serve the increasing needs of nanoscience users. The instrument, taking 

advantage of the small source size at the X13 straight section of the ring, is designed to perform sub-micron x-ray 

micro-diffraction and imaging. It has the unique capability 

of allowing experimenters to choose the focusing optics to 

optimize their measurement. The beamline will also serve 

as a test bench for new emerging focusing optics and x-ray 

imaging techniques.

The third session, focused on LEEM/PEEM, began after 

lunch. Rudolph Tromp from IBM gave a broad overview of 

the history, current state-of-the-art, and future possibilities 

of this powerful technique. For example, structural information with 4 nm spatial resolution can be achieved with 

LEEM today. There are also a variety of contrast mechanisms that can be exploited in LEEM, for example, using 

bright and dark field imaging, as well as work function and 

electron energy dependence. A LEEM instrument can also 

be combined with a photon source to perform PEEM to 

obtain chemical contrast. The potential of combining the 

structural information from LEEM and chemical information from PEEM is extremely exciting. Finally, by using a 

spin-polarized electron source, LEEM can be used to study 

magnetic surfaces and interfaces (SPLEEM). Time-resolved 

study of magnetization dynamics has also been demonstrated. Stefan Heun from ELETTRA Trieste/Italy presented the 

capability and results from the X-PEEM instrument located 

at Synchrotrone Trieste. The unique feature of the instrument is the energy filtering of photoelectrons. It enhances the chemical sensitivity significantly. The session ended 

with a talk on the next generation of PEEM developed at 

the Advanced Light Source by Jun Feng from Lawrence 

Berkeley National Laboratory (LBNL). Jun talked about 

the design of the PEEM3 project at LBNL. The goal of 

PEEM3 is to achieve spatial resolution down to 5 nm, 

almost an order of magnitude better than the PEEMs 

currently operating at various synchrotron facilities. Jun 

discussed in detail the critically important aberration 

correction system, including an electronmirror aberration 

corrector and an aberration-free magnetic beam separator.

Following the three focused sessions, there was a lively 

discussion period, chaired by Peter Sutter of CFN/BNL, 

Ken Evans-Lutterodt, and Chris Jacobsen. These valuable ideas will be taken into consideration in the design 

of the new LEEM/PEEM end station and for the future 

upgrade of the x-ray microscopy programs at the NSLS.

—Cecilia Sanchez-Hanke

Crystallization: Focus on Membrane 

Proteins Workshop

May 19-20, 2004

The Crystallization workshop organized in conjunction 

with the 2004 National Synchrotron Light Source Annual Users’ Meeting focused this year on crystallization 

techniques available to membrane proteins. This two-day 

workshop covered different crystallization methods from 

the most standard vapor diffusion to more advanced 

techniques. A morning of introductory talks was followed 

by five practical sessions, of two hours each, where participants had the opportunity to carry out different crystallization methods in the laboratory. The main purpose 

of this workshop was to bring the practical aspects of the 

crystallization methods to the participants, the exchange 

of experiences and ideas being its essence. 

Naomi Chayen, Imperial College London, in her talk 

“Tackling the bottleneck of protein crystallization: PractiCrystallization: Focus on Membrane Proteins Workshop attendees
3-24 NSLS ACTIVITY REPORT 

cal techniques with a difference,” introduced the phase 

diagram and discussed the several different crystallization 

techniques developed for soluble proteins and the necessary 

modifications for crystallization of membrane proteins. The 

laboratory practical sessions included setting up microbatch 

and vapour diffusion trials using oils as a tool to aid crystal 

growth. Participants had the opportunity to try several different crystallization configurations. 

Peter Nollert, deCODE Genetics, in his talk “Miniaturization of the cubic phase,” introduced the cubic lipid phase 

method and discussed the difficulties of membrane protein 

crystallization. The cubic lipid phase method was demonstrated in the laboratory and participants were able to set 

up crystallization trials for bacteriorhodopsin. The application to soluble proteins was also introduced. A number of 

participants tried the method with their own proteins with 

success.

Petra Fromme, Arizona State University, talked about 

“Overcoming the Crystallization Problems of PSI and 

PSII.” She discussed the importance of the phase diagram to the crystallization of PSI and PSII proteins. The 

contribution of the dialysis method was introduced and 

participants were able to assemble their own crystallization 

reactors. Most experiments lead to the crystallization of PSI 

within 24 hours and by the end of the workshop participants were able to harvest some of the crystals. 

Marie Claude Marchand, NEXTAL Biotechnologies, in her 

presentation on “The Vapour Diffusion Method,” discussed 

the vapour diffusion method, as well as seeding, derivatization, and optimization of the phase diagram. Some participants were able to screen for the best crystallization 

conditions of their own protein. 

Ana Belen Moradela Merlo, University of Granada, discussed “Protein Crystallization by the Counter,” diffusion, 

and introduced the counter diffusion method. Participants 

were able to set up crystallization trials of soluble proteins 

in the “Granada Box.” Possible applications to membrane 

proteins were discussed.

The demand for the course was overwhelming. It was 

oversubscribed by over 100%. At the end of the workshop 

students were asked to evaluate the course and suggest 

changes and additions; two thirds responded to the survey. 

Overall the course was rated as extremely useful as reflected 

in one of the answers to the survey: “I learned a great deal 

about crystallization methods. Most importantly I now 

understand the more practical aspects of each method that I 

was not aware of. These ideas cannot be gained from other 

formats.” All participants who answered the survey thought 

that the workshop should be offered again. 

—Vivian Stojanoff and Naomi Chayen

UEC Community Service Award Presented 

to Sue Wirick

May 20, 2004

The National Synchrotron Light Source Users’ Executive 

Committee (UEC) presented the 2004 UEC Community 

Service Award to Sue Wirick of Stony Brook University’s 

Physics Department. Sue is a beamline scientist for the X1A 

insertion device beamline. This award is given for service, 

innovation, and dedication to users of the NSLS, and she is 

well deserving of that honor.

Members of the NSLS user community nominated Sue 

for this award. Here are some of the comments users made 

about her wonderful contributions:

• “Since joining the X1A effort more than a decade ago, 

Sue Wirick has played a central role in the development of 

the scientific program and in supporting user access to the 

spectromicroscopy facilities. Quite simply put, she is the 

key to outside users’ ability to carry out experiments.”

• “Our research team owes very much to the assistance 

that Sue Wirick was able to give us. She was available day 

and night, gave excellent advice, steered us through the 

experimental process with ease, and provided a positive and 

friendly environment that made it a pleasure to work at the 

beamline.”

• “Sue Wirick actively participates in meetings of the 

user community to improve the user support at the NSLS. 

She contributed heavily in the past to making the annual 

user meeting a success by helping in the planning and 

chairing of sessions. Sue is known by users for helping with 

technical problems even for beamlines that are not her 

responsibility.”

• “Sue Wirick has been a godsend to the NSLS community. She is one of the rare people who will help anyone, 

including the most difficult personalities, when they have 

UEC Chair Tony Lanzirotti presents the award to Sue Wirick.
 YEAR IN REVIEW 3-25

a problem. She will do this anytime, even on weekends 

and evenings. She is the person that I recommend first 

to outside users who want to find out more about NSLS 

and Brookhaven. She always provides detailed and concise 

advice on instrumental capabilities, and also on the more 

mundane aspects of how to get beam time, availability, etc.”

Tony Lanzirotti, the Chair of the UEC, presented the award 

to Sue at the NSLS Users’ Meeting banquet on the evening 

of Tuesday, May 18th. Sue receiveed a $250 gift certificate 

and her name was engraved on the plaque on display in the 

NSLS lobby. Congratulations Sue and well done!

—Tony Lanzirotti

The PASS System Arrives

June 23, 2004

We are very happy to announce the arrival of the new Proposal, Access, Safety and Scheduling (PASS) system, which 

debuted in May for the submission of general user proposals for the fall cycle.

PASS was developed to facilitate the submission and review 

of general user and proprietary proposals and the allocation 

and scheduling of beamtime at the NSLS. To meet DOE 

reporting requirements and to ensure safety compliance, the 

safety approval form is also incorporated into the system.

The first phase of development (proposal submission, safety 

approval, and the scheduling of general user proposals) is 

complete and online. Proposals (and Px Forms when appropriate) are submitted online in one system and routed 

for beamline review for feasibility and safety purposes. 

PASS then routes the form to proposal review panel (PRP) 

members for peer review and ratings, to allocation panel 

members for beamtime allocations, to NSLS safety staff for 

review and approval, and finally for beamtime scheduling. 

Each principal investigator and reviewer is granted individual access according to permissions assigned.

Instructions and frequently asked questions are provided 

throughout the system to ensure user friendliness and accessibility. The production version will soon include a link to 

send comments or report functionality issues or problems.

Further development will take place over the next few 

months to integrate proprietary proposals, safety approval 

for Participating Research Team (PRT) experiments, to 

further develop scheduling for all experiments, and to add 

more functionality and capabilities. The final phase will 

incorporate a reduced lead-time to provide for rapid access.

Some proposal process changes introduced in the PASS 

system are:

• PASS randomly assigns each proposal to three PRP 

reviewers who have reviewed the lowest number of 

proposals for the given cycle to date. This ensures that 

all reviewers review approximately the same number of 

proposals and that members are not overburdened with 

requests, and plans are in place to increase the pool of 

reviewers. PASS does not assign proposals to a PRP member whose institution is the same as the PI.

• PASS notifies PRP members by email immediately 

after submission of the proposal by the PI, allowing 

reviews to take place as soon as the PRP member is able.

• PRP reviews are completed independently of other 

PRP members and all ratings are averaged for a final rating.

• Lifetime days are no longer requested. The PI 

requests the number of days needed in a given cycle, and 

this is the information that is vital for review, allocation 

and scheduling.

• Penalties for canceling beamtime after allocation 

have been eliminated. Our goal is to re-assign canceled 

beam time to other users who were not allocated due to 

high demand.

• The one-half point credit given for one cycle to 

lower-rated proposals not allocated beam time is no 

longer given. Alternatives available are for the PI to 

submit a new proposal based on an existing one and to 

thereby address concerns or questions that were raised by 

reviewers in the previously submitted proposal. Another 

planned capability is to provide PRTs the ability to offer 

PRT beamtime to rated proposals that did not receive an 

allocation of beam time since higher-rated proposals filled 

up the general user obligation for that beamline.

• PIs must assign a lead experimenter to serve as lead 

person for the experimental team while present on the 

NSLS experimental floor, who will in turn receive an 

email with links to his/her roles and responsibilities.

—Mary Anne Corwin
3-26 NSLS ACTIVITY REPORT 

NSLS EXAFS Data Collection and Analysis 

Short-Course “Graduates” 32 Students 

June 22-25, 2004

A hands-on EXAFS Data Collection and Analysis ShortCourse was held June 22-25, 2004 at the NSLS. The course 

was co-organized by Bruce Ravel (Naval Research Laboratory) and Simon Bare (UOP LLC), with excellent administrative support by Lisa Tranquada (SFA, Inc.) and Melissa 

Abramowitz from User Administration. 

Thirty-two eager participants (graduate students, postdocs, 

and institution and industrial scientists), representing 

universities, national laboratories, research institutes, and 

industry, attended the four-day course. 

Among the 32 participants, 15 were new users to the 

NSLS. The participants had diverse research interests across 

a broad spectrum of scientific fields, including materials 

science, geological and environmental sciences, catalysis, 

and biology. 

The four-day course was divided into morning lectures, 

with two afternoons of hands-on data collection using 

seven different NSLS spectroscopy beamlines (X9B, X11A, 

X11B, X18B, X19A, X23B, and X26A), and two afternoons of data analysis. The instructors on the beamlines 

were Faisal Alamgir, Wolfgang Caliebe, Scott Calvin, Syed 

Khalid, Tony Lanzirotti, Nebojsa Marinkovic, and Kaumudi Pandya.

The eight morning lectures were: “Introduction to XAFS” 

and “Basics of sample preparation” by Matt Newville 

(CARS, University of Chicago), “XANES Measurements 

and Interpretation” by Simon Bare (UOP LLC), “Detectors 

and Synchrotron Radiation” by Peter Siddons (BNL), “Basics of Data Processing” by Scott Calvin (Sarah Lawrence 

College), “A Practical Introduction to Multiple Scattering Theory” by Bruce Ravel (Naval Research Laboratory), 

“Introduction to Data Analysis” by Shelly Kelly (Argonne 

National Laboratory), and “Incorporating XAFS into a Research Program” by Vince Harris (Northeastern University). 

The morning lectures included ample time for stimulating 

questions and discussion.

For the first two afternoons the participants were divided 

up into small groups in order to spend time on the NSLS 

floor at an EXAFS beamline. There, they learned first hand 

how to collect high quality EXAFS data. Each student became familiar with beamline operation and sample preparation while collecting EXAFS data on representative samples 

from their own individual research projects. It was fascinating to see the diverse array of samples and projects in which 

EXAFS was being used.

During the last two afternoons the participants learned EXAFS data analysis techniques using the data they had collected the prior two days. The participants enjoyed informal 

discussions during coffee breaks, lunches, and the dinners 

that were included in the course fee.

There was a tremendous amount of information disseminated over the four days. All the participants left the course 

with new friends and armed with the basic tools to apply xray absorption spectroscopy to their own research programs. 

The organizers thank all those who made the course the 

great success that it was! 

We plan to offer the course again in 2005. Please check the 

NSLS website for updated information.

The course was sponsored by the NSLS, with support from 

the Center for Environmental Molecular Science at Stony 

Brook University.

—Simon Bare

Participants in the 2004 NSLS EXAFS course

NSLS Visiting Scientist Mehmet Aslantas 

Wins Prestigious Lecturer Award

July 18-22, 2004

National Synchrotron Light Source visiting scientist 

Mehmet Aslantas won the prestigious Margaret C. Etter 

Student Lecturer Award for a talk on his recent work: how 

to reduce the effects of radiation damage to protein crystals 

during synchrotron x-ray studies.

He received the award at the American Crystallographic 

Association national meeting, held in Chicago, Illinois, on 

July 18-22, 2004. The Etter award, given out just once a 

year, recognizes achievement and future potential for scientists at an early stage in their independent careers.

Aslantas, who initially came to the NSLS for six months 

through a U.S. Department of Energy Cooperative Research program, received an extension that allowed him to 

stay for over a year. “The NSLS is a great place to work, and 

I couldn’t have completed my research or won this award 

without the research extension I received,” said Aslantas. “I 
 YEAR IN REVIEW 3-27

would like to thank the NSLS Chairman, Steve Dierker, the 

Associate Chair for User Science, Chi-Chang Kao, Vivian 

Stojanoff, and the User Administration office for their support.”

Aslantas worked under Stojanoff’s supervision at NSLS 

beamlines X6A and X17B1. In his talk, titled “Radiation 

Effects on Biological Samples,” he described his work at the 

beamlines. At X6A, he studied the effect of low-energy xrays on 'Lyzozyme' crystals, which are standard test protein 

crystals. At X17B1, the sample was subjected to high-energy x-rays.

“My experimental results show that, with lower-energy 

x-rays, the sample absorbs more radiation than at higher 

energies, in which it 

absorbs less energy 

and sustains no 

significant damage,” 

he said. “This is 

because the lowenergy x-ray beam 

interacts with the 

inner shell electrons 

in the atoms of the 

protein, causing an 

overall higher dose 

to the sample. This 

leads to structural 

damage and limits 

the structural information we can learn 

about the sample. 

However the high 

energy x-rays interact with the outer shell electrons in the 

atom of the protein. This interaction, known as Compton 

scattering, plays a role in causing the overall dose deposited 

to the sample to be less significant. The sample will have a 

longer life time, too.”

Aslantas’ work was funded by a U.S. Department of Energy 

Cooperative Research program, which allowed him to work 

at the NSLS as part of a scientific exchange program with 

another synchrotron, SESAME (Synchrotron-light for 

Experimental Science and Applications in the Middle East). 

SESAME is under construction.

Aslantas prepared three manuscripts describing his work 

at the NSLS. His experience will help him form a protein 

crystallography group at his home institution, Hacettepe 

University in Ankara, Turkey. In turn, this group will be 

working with SESAME to develop a protein crystallography beamline at the facility. After his return to Hacettepe 

University, Aslantas expects to keep in close contact with 

the NSLS and will continue his research. 

—Laura Mgrdichian

Mehmet Aslantas holds a ball-and-stick model 

of the test protein he used in his research.

Summer Sunday Visitors Battle the 

Weather for a Great Day at NSLS

August 1, 2004

Despite the rainy, humid weather, NSLS Summer 

Sunday, held August 1, still pulled in over 450 members 

of the community and was one of the most enjoyable 

Sundays yet.

For eight consecutive Sundays each summer, the 

Brookhaven National Laboratory Summer Sundays program welcomes the public to see the popular Whiz-Bang 

Science Show and several hands-on science exhibits. Each 

Sunday also showcases a different BNL facility.

Visitors wishing to see the NSLS began the tour in 

Berkner Room B, where there were NSLS-specific exhibits and posters, manned by NSLS staff volunteers Steve 

Ehrlich, Nick Gmur, Payman Mortazavi, Eva Rothman, 

and Marty Woodle, and student volunteers Meghan 

Ruppel and Jyoti Tibrewala. The visitors then saw a short 

“Introduction to the NSLS” overview film before boarding a bus for the facility.

Upon arrival, they went upstairs to see a presentation by 

an NSLS scientist, who welcomed them and gave more 

detailed information on the facility and the research 

performed here. They also discussed how they use synchrotron light to perform their individual research. Many 

guests were very curious about the NSLS, and the speakers answered several questions. This year’s speakers were 

Marc Allaire, Elaine DiMasi, Tony Lanzirotti, Lisa Miller, 

Peter Siddons, and Vivian Stojanoff.

Visitors then filed down to the NSLS lobby and patio, 

where more activities awaited them, such as the “What 

am I looking at?” picture window that provides an impressive view of the VUV-IR experimental floor, a sight 

that is always fascinating for guests. NSLS staff members 

Steve Bennett, Mike Buckley, Susila Ramamoorthy, and 

Larry Fareria explained the view and answered questions, 

such as the common query, “What’s the aluminum foil 

Student volunteer Angela Padilla shows a group of young Sunday 

visitors how to build a protein crystal model from gumdrops.
3-28 NSLS ACTIVITY REPORT 

for?” This year, for the first time, large neon numbers were 

placed on beamline components, which made it easier for 

guests to see the features described to them.

The lobby also contained several exhibits, such as “See the 

Light,” in which volunteers Randy Smith and Ted Feldman 

showed how a fiber optic cable siphoned actual NSLS light 

into the lobby, and “Flowing Lasers,” in which Tom Dickinson and Raji Sundaramoorthy made a laser beam “flow” 

down a stream of water. The children watched the laser 

light fill the water and sparkle when they put their hands 

under the stream. Other displays were hosted by additional 

NSLS scientists, staff, and students: Peter Abbamonte, 

Marc Allaire, Alec Bernston, Brandon Chapman, Ed Haas, 

Amubhav Jain, Payman Mortazavi, Angela Padilla, Vivian 

Stojanoff, Tejas Telivala, Adele Wang, and Zhong Zhong.

On the patio, the visitors saw how superconductivity can 

“levitate” a magnet and how boiling liquid nitrogen sends a 

sprinkler spinning. Scientists Wolfgang Caliebe and Cecilia 

Sanchez-Hanke kept watch over the outdoor activities.

A fun, new event this year was the quiz/raffle, which turned 

out to be quite successful. Each visitor received a yellow 

quiz card with questions, which could only be answered by 

visiting each exhibit. This encouraged them to stop at each 

one and also made the day more interactive. Every 20 minutes, the quiz cards were collected and Gerry Van Derlaske, 

the enthusiastic quiz/raffle MC, picked a winning name. 

Each winner received an NSLS flashlight.

Additionally, at several points during the day, Caliebe 

braved the rain to launch a giant water rocket in the parking lot across from the NSLS – a hit with all the guests.

The day was made possible by several additional volunteers, 

who served as tour guides, escorts, and support personnel: 

Melissa Abramowitz, Diane Hatton, Madeline Hughes, 

Laura Mgrdichian, Eileen Morello, Wendy Morrin, Gina 

Paveglio, Lydia Rogers, Nancye Wright, and Emil Zitvogel.

—Laura Mgrdichian

NSLS scientist Zhong Zhong (right) shows several Summer Sunday 

guests how a monochromator divides visible light into a rainbow of 

colors.

Summer Student Research at the NSLS

August 10, 2004

Each summer, many high school and college students 

perform summer research projects at Brookhaven National 

Laboratory. Many of the students work at the NSLS, teaming up with an NSLS scientist, as part of Laboratory-sponsored research internship programs.

The students work with scientists and engineers in a wide 

range of research fields, including medical sciences, geology 

and environmental sciences, chemistry, materials science, 

physics, and electrical and mechanical engineering. In addition to their research projects, students have the opportunity to attend scientific lectures, tour Brookhaven research 

facilities, and participate in numerous social activities.

The following are summaries of programs that NSLS summer students participated in, and short profiles of some of 

the students that performed research here this summer.

Community Summer Science Program (CSSP)

This program invites high school students who have 

completed their junior or senior year to come to BNL for 

a six-week period, where they attend morning lectures and 

demonstrations by BNL scientists, workshops, and afternoon internships. Volunteer BNL mentors guide the interns 

in individual research projects.

Science Undergraduate Laboratory Internships (SULI)

The SULI program is sponsored by the U.S. Department of Energy (DOE), and offers internships for college 

students in the spring, summer, and fall terms. Participants 

are paired with a member of the BNL staff to perform a 

research project in chemistry, physics, engineering, biology, 

nuclear medicine, applied mathematics, particle accelerators, or science writing.

Michael Dibiccari, a junior at Hauppauge 

High School, worked at beamline X22B 

with Elaine DiMasi as part CSSP. After 

growing mineral crystals, he studied 

the x-ray diffraction patterns they 

created in order to determine how the 

crystals formed. This research will help 

scientists understand the process of 

biomineralization.

Dina Halajian is a senior a Half Hollow 

Hills High School East. Participating in 

CSSP, she also worked with NSLS scientist 

Elaine DiMasi. They investigated the 

growth process of minerals by growing 

calcium crystals and studying them 

at beamline X22B with a microscope. 

Their results will add to the field of 

biomineralization.
 YEAR IN REVIEW 3-29

Also involved in research at the NSLS this summer were 

SULI participants Patrick Lynch (Bucknell University) 

and Matthew Teng (Cornell University), who worked with 

NSLS mentors John Skaritka and Zhong Zhong, respectively. Lynch worked on a “Mechanical Design of a FiveMeter Superconducting Undulator” and Teng’s project was 

titled “Use of Diffraction Enhanced Imaging to Determine 

Refractive Indices of Various Tissues at Select Energies.”

Participating in PST, Angela Padilla 

worked with Vivian Stojanoff to 

study samples from a native American 

17th century artifact, using different 

spectroscopy and diffraction techniques. 

Their research may help anthropologists 

understand the social and economic 

relationships between native Americans.

Pre-Service Teacher program (PST)

In this program, a collaboration with the National Science Foundation and sponsored by the DOE Office of 

Science, teachers in training are paired with scientist 

mentors and a professional teacher, and immersed in a 

research environment. The pre-teachers perform scientific 

research, which helps them learn how to better explain 

scientific concepts in a classroom environment.

Faculty and Student Teams (FaST)

The FaST program pairs a student/professor team from 

a university or college with limited research capabilities 

with a BNL scientist. For 10 weeks, the faculty/student 

team performs research they cannot do at their home 

institution, which not only helps the BNL researcher, but 

also gives the team experience while building a relationship between the institution and BNL.

At the NSLS, FaST program summer visitors from 

Southern University in Louisiana were faculty member 

Elhag Shaban and students Clifford Williams and Shayla 

Wilkinson. They worked with NSLS scientist Peter Siddons on new electron multiplier structures for synchrotron x-ray detector systems.

—Laura Mgrdichian

Parney Albright, DHS, Visits BNL

August 27, 2004

Parney Albright, Assistant Secretary of Homeland Security, Science & Technology Division of the Department 

of Homeland Security, came to BNL on August 27. After 

a welcome by BNL Director Praveen Chaudhari, Interim 

Deputy Director for Science & Technology Peter Bond, 

Brookhaven Site Office Manager Michael Holland, and 

Associate Laboratory Director for Energy, Environment 

& National Security Ralph James, Albright and his 

executive assistant Leslie Stone toured facilities and met 

with several scientists over lunch.

During a visit to the Radiation Detector Testing & 

Evaluation Center, James discussed portal monitors and 

hand-held monitoring devices and the results of BNL’s 

Alec Bernston is a sophomore at 

Cornell University, where he studies 

computer science. This summer, in 

the SULI program with NSLS mentor 

Vivian Stojanoff, he participated in the 

development of a software package for 

protein crystallography diffraction analysis. 

The software will help speed up the 

diffraction process.

Meghan Ruppel is a senior at Stony Brook 

University, and will soon earn her degree in 

Materials Science and Engineering. In the 

SULI program, she worked with Lisa Miller 

at beamline U10B, using infrared light to 

study the chemical composition of bone 

and calcified cartilage in osteoarthritis. 

This work will help them understand how 

the makeup of bone in knee joints plays a 

role in cartilage breakdown.

Ted Feldman is a sophomore at Stony 

Brook University. As part of Stony Brook’s 

Interdisciplinary Biomedical Research 

Program, Ted worked with Lisa Miller 

to study the chemical and mechanical 

properties of bone that has been 

mineralized. This work will help increase 

scientists’ understanding of bone quality, 

which may help predict osteoarthritis.

Jyoti Tibrewala is a graduating senior at 

MIT and this summer she worked with 

Lisa Miller as a SULI participant. They 

studied the effects of pressure on the 

chemical composition of bone mineral 

using infrared spectroscopy at beamine 

U2A. Their results will help explain 

bone loss in post-flight astronauts and 

osteoporosis patients.

Anubhav Jain, a SULI participant, worked 

with Vivian Stojanoff, designing computer 

software that will automatically position 

crystal samples in the path of an x-ray 

beam for diffraction studies. This task is 

currently done manually by researchers 

– thus, this new software will decrease the 

time needed to collect data and allow the 

researchers to solve more crystal structures 

in less time.
3-30 NSLS ACTIVITY REPORT 

At BNL’s Radiation Detector Testing & Evaluation Center are: (from left) 

Leslie Stone, Department of Homeland Security (DHS); Peter Bond, BNL; 

Ralph James, BNL; Parney Albright, DHS; and Joseph Indusi, BNL.

Awards and Good Times at the 2004 NSLS 

Barbeque

September 24, 2004

On September 24, a crowd of National Synchrotron Light 

Source staff members joined the recipients of the 2004 

Spotlight and Service awards to celebrate the winners’ careers and accomplishments, and to enjoy food, drinks, and 

the early autumn weather. NSLS Chairman Steve Dierker 

led the ceremony.

Service Awards

This year, the following staff members were 

honored with 25 years 

of service: Steve Bennett, 

Rich Biscardi, Conrad 

Foerster, Tony Lenhard, 

Bill Newburgh, Gary 

Ninztel, Stefan Palo, Sal 

Pjerov, Susila Ramamoorthy, Bob Scheuerer, and 

Jiunn-ming Wang.

Receiving the 20-year service awards were Bob Best, 

Pete Ratzke, Ray Raynis, 

and John Skaritka, and Qing-yi Dong received the 10-year 

award.

Spotlight Awards

The Spotlight awards, which commend deserving NSLS 

staff members for exceptional performance during the year, 

were presented to Laura Miller, recommended by Steve 

Dierker; Bob Best and Tony Santiago, both recommended 

by John Gallagher; and two groups (each group shares 

one award). The first group, nominated by Steve Hulbert, 

was Dennis Carlson, Michael Caruso, Shu Cheung, Rick 

Greene, Tony Lenhard, and Gary Nintzel. The second, 

nominated by Ed Haas, was Walter deBoer, Mike Radulescu, and Bob Scheuerer.

Bob Best: Bob received his award for building, testing, and 

NSLS Chairman Steve Dierker

testing and evaluation of commercial, off-the-shelf radiation 

detectors for homeland security applications.

In touring the Instrumentation Division, the party learned 

about BNL’s advanced detectors: Peter Vanier, Instrumentation, described the xenon gamma detector; Creighton 

Wirick, Department of Environmental Sciences (ES) Chair, 

spoke on the standoff detection capabilities of the Raman 

Mini-LIDAR chemical and biological sensor system; and 

Graham Smith, Instrumentation, explained how advanced 

neutron detectors and low-noise electronics for nuclear 

spectroscopy and imaging can be used to further national 

security.

A visit to the National Synchrotron Light Source (NSLS) 

was also on the agenda. NSLS scientist Peter Siddons gave 

an overview of the wide range of research in biology and 

physics, chemistry and geophysics, materials science and 

medicine, performed by Lab scientists and some 2,200 researchers from the U.S. and overseas at this facility. Aleksey 

Bolotnikov of the Nonproliferation & National Security 

Department discussed the expectations made possible by 

another kind of radiation detector utilizing cadmium zinc 

telluride crystals.

At the Lab’s Relativistic Heavy Ion Collider (RHIC), the 

visitors saw another example of how basic research results 

in breakthrough detector capabilities. Tim Hallman of the 

Physics Department described the RHIC program and the 

giant STAR detector, conceived and developed with three 

other detectors to track instantaneously thousands of subatomic particles formed when two beams of heavy ions are 

crashed together at nearly the speed of light, to recreate and 

reveal what happened in the earliest stages of the universe.

In the environmental sciences area, Albright learned about 

BNL’s contribution to the urban dispersion program and 

work on consequence management for radiological dispersal devices, topics discussed by Michael Reynolds, and 

Paul Kalb and Jeff Gillow, all of ES, respectively. The Lab’s 

forefront research in areas involving biological security was 

represented by John Dunn of the Biology Department, 

who displayed real-time DNA sequencing for agriculturalbiological terrorism counter measures, and Subramanyam 

Swaminathan, also of Biology, who described his work on 

ultra-sensitive assays for botulinum toxins. 

— Liz Seubert
 YEAR IN REVIEW 3-31

debugging the laser interlock/controllers system at beamline 

X17B3. This required extensive planning and coordination 

between the other electricians at the NSLS. If not for Bob’s 

hard work, one of two costly alternatives to controlling 

the inner cavity shutter at the beamline would have been 

explored, resulting in long delays to the program at X17B3.

Tony Santiago: Tony was honored for modifying the 

Source Development Laboratory’s (SDL) laser interlock 

system, a task that required extensive electrical work and 

rearrangment. With direction from Scott Buda and John 

Gallagher, he worked through breaks, lunches, and put in 

overtime to complete the project, and managed to do so 

without impacting the operations of the SDL.

Laura Miller: Presented as a surprise, Laura received this 

award for organizing and planning many of the details of 

the NSLS-II Workshop. Her hard work, involving extended 

hours and even weekends, helped to make the workshop 

incredibly successful. In turn, this success is vital to helping 

ensure that NSLS-II becomes a reality.

Dennis Carlson, Michael Caruso, Shu Cheung, Rick 

Greene, Tony Lenhard, and Gary Nintzel: This group 

was recognized for their exceptional service to the NSLS 

during the May 2004 shutdown. During this time, three 

major beamline upgrades were performed in addition to 

the increased beamline maintenance during that period. 

At X21, the largest of the upgrades, where two nested 

wiggler beamlines had to be fabricated and installed, 

the group performed much of this work during the 

shutdown, and faced several problems that popped up 

during the process. At the same time, they worked on 

the upgrades at X13A and X1A1, which both required 

unexpected work.

Walter deBoer, Mike Radulescu, and Bob Scheuerer: 

Just before the NSLS May shutdown, a vacuum leak was 

found in the x-ray ring that worsened until x-ray operations were significantly affected. Walter, Mike, and Bob 

successful dealt with the problem and the intricate details 

surrounding it without impacting the x-ray schedule. 

Walter repeatedly came in after hours and on short notice 

to temporarily fix the leak. His repairs allowed operations to continue until he could properly fix the problem. 

From start to finish, Walter performed above and beyond 

the call of duty.

The leak forced the spring shutdown schedule to be 

changed, demanded that new work plans be reviewed and 

approved rapidly, required new hardware to be ordered, 

and necessitated the location, check, and approval of new 

fixtures. These details required coordinating many parties 

across varying time frames. Bob proved instrumental in 

making it happen.

Mike was the chief technician who performed the repair; 

he worked flawlessly and quickly, and put in long hours 

to complete it. His excellent, efficient work helped result 

in the quick-fix of a complex repair job – finished ahead 

of schedule with no significant errors.

—Laura Mgrdichian

From left: Rodger Hubbard, Bob Best, Don Davis, Jim Newburgh, 

and Bob Scheuerer.

Clockwise, from left: Michael Appel, Jim Rose, Timur Shaftan, 

Alexei Blednykh, Li-Hua Yu, and Randy Smith.

The Hill Comes to the Lab

Energy & Water Development Appropriations 

Subcommittee personnel visit BNL 

October 26, 2004 

Visiting the Lab on Tuesday, October 26, were Kevin 

Cook, Majority Clerk of the Energy & Water Development Appropriations Subcommittee (EWDAS) and 

Dixon Butler, EWDAS Minority Professional Staff 

Member. Welcomed by BNL Director Praveen Chaudhari, DOE Brookhaven Site Office Manager Michael 

Holland, Deputy BNL Director for Operations Michael 

Bebon, and Assistant Lab Director for Community, Education, Government & Public Affairs Marge Lynch, the 

visitors, with Jack Bagley of Battelle’s Washington Office, 

toured selected facilities to see more of BNL’s research 
3-32 NSLS ACTIVITY REPORT 

Standing near the viewing window in the NSLS lobby are Brookhaven 

Lab Director Praveen Chaudhari; Steve Dierker, NSLS Chairman 

and Associate Laboratory Director for Light Sources; Kevin Cook, 

Majority Clerk of the Energy & Water Development Appropriations 

Subcommittee (EWDAS); and Dixon Butler, EWDAS Minority 

Professional Staff Member. Elaine Lowenstein, of Brookhaven’s 

Community Relations group (foreground), led the group on a tour 

of the facility.

Remembering Dale Sayers

November 25, 2004

On November 25, 2004, Dale Sayers, a founder of the 

extended x-ray absorption fine structure (EXAFS) technique and a prominent NSLS user and advisor, passed away 

from complications due to a heart attack. He was 60 years 

old. He is remembered for his immense impact on NSLS 

science and operations, and his commitment to the field of 

synchrotron science. 

Dale’s part in developing EXAFS began in 1968 when he 

was a graduate student at the 

University of Washington. 

He was a student of Edward 

Stern, a UW faculty member 

and a consultant for the Boeing Scientific Research Laboratories (BSRL) in Seattle. 

Stern knew BSRL researcher 

Farrel Lytle and learned of his 

work on what would be the 

early theory of EXAFS. He 

decided that further work on 

the subject would be a good thesis project for Dale. 

Dale began working with Lytle at his laboratory, measuring 

the EXAFS of various materials. By the end of the 1970 

spring semester, the major parts of the theory were established, but one task was left: determining how to obtain 

structural information from the EXAFS equation they had 

formulated. The three decided that inverting the equation 

would be the way, and, in 1971, Dale tried applying the 

Fourier integral theorem to the equation. Success! 

In a 1999 Journal of Synchrotron Radiation paper, Lytle 

wrote, “In a defining moment, I can still visualize Dale’s excitement as he ran down the hall to greet me with the first 

plot of the first Fourier transform of the EXAFS function 

Dale Sayers

capabilities and learn about site infrastructure. 

At the National Synchrotron Light Source (NSLS), which 

draws annually more than 2,200 researchers from the U.S. 

and overseas to join Lab scientists in studying physics, 

chemistry, materials science, biochemistry, geophysics, and 

medicine, Associate Laboratory Director for Light Sources 

and NSLS Chair Steve Dierker gave an overview of the 

facility and plans for its upgrade as well as for the proposed 

NSLS-II. Doon Gibbs, Associate Laboratory Director for 

Basic Energy Sciences, and Robert Hwang, Director of 

the Center for Functional Nanomaterials, discussed BNL’s 

thriving nanoscience program. 

The STAR detector at BNL’s Relativistic Heavy Ion Collider (RHIC) provided another stop on the agenda. Derek 

Lowenstein, Collider-Accelerator Department Chair, and 

STAR spokesperson Timothy Hallman of the Physics Department described the RHIC facility and explained some 

of the physics being explored there. At RHIC, more than 

1,000 researchers are working on four experimental teams 

to recreate and analyze conditions believed to have occurred 

during the earliest stages of the universe. 

On a tour to look at site infrastructure, Bebon showed the 

visitors the recent improvements to the Materials Sciences 

Department in Building 480 and talked about near- and 

long-term plans being made for the needs of various areas 

of the Lab. 

Lowenstein, with Betsy Sutherland of the Biology Department, outlined the National Aeronautics & Space Administration (NASA) and BNL research on the possible risks to 

humans exposed to space radiation. These studies, which 

use proton and ion beams that simulate the cosmic rays 

found in space, are done at the NASA Space Radiation 

Laboratory, known as the NSRL, operational at BNL since 

July 2003. 

Another high-profile BNL initiative, medical imaging, was 

the focus of a stop at the Positron Emission Tomography 

(PET) facility. There, Helene Benveniste, who, at the time, 

was the Associate Laboratory Director for Life Sciences, and 

PET Program Director Joanna Fowler, Chemistry Department, described the Lab’s pioneering work in probing the 

brain chemistry of addiction, mental illness, and aging, and 

other recent work to find effective treatments and on imaging awake animals. 

—Liz Seubert 
 YEAR IN REVIEW 3-33

of germanium!” The EXAFS technique is now used at every 

synchrotron across the globe. 

During his time as a NSLS user, beginning in the early days 

of the facility, Dale was a physicist with the North Carolina 

State University (NCSU) but spent a great deal of time 

here. He was the chair of the NSLS Users Executive Committee in the early 1980’s, at a time when the NSLS was 

an “unrefined” scientific workplace, and often a difficult 

environment in which to perform research. Dale established 

trust between the NSLS and the user community, culminating in an excellent users’ meeting in 1985 that included 

an especially memorable dinner event. He also chaired the 

UEC in 1987 and ’88. 

Dale’s work at the NSLS led him to establish and operate 

beamline X11A. Under his leadership, X11A has been one 

of the most scientifically productive beamlines at the NSLS. 

He established a participating research team (PRT) at X11 

(the longest-lived PRT beamline) and was its spokesperson 

from 1983 until 2001. 

In the 1990’s, Dale initiated a mammography project at 

the NSLS, working with former NSLS staff physicists Bill 

Thomlinson and Dean Chapman, and current NSLS physicist Zhong Zhong. The project led to the development of 

diffraction-enhanced imaging (DEI), a technique now used 

around the world to image bone and soft tissue in a way 

not possible using conventional x-rays. Dale became the 

co-spokesperson for beamline X15A after a dedicated DEI 

system was established there in 1998. He was leading efforts 

to apply DEI to a clinical setting and, for the past few years, 

had been working with graduate students Dean Connor 

and Miklos Kiss to characterize bone and reconstruct DEI 

images using computerized tomography (CT). 

While Dale was renowned internationally for his research, 

his influence extended far beyond raw science. Astute and 

determined, he was committed to the successful operation of synchrotron facilities and the success of the 

field of synchrotron radiation research. This led him to 

become a trusted advisor to many facilities, and he sat on 

many scientific advisory committees. 

Dale was known as a tough, yet fair, advisor, but his personal experiences were filled with laughter and frequent 

interactions with family, friends, and colleagues. He 

enjoyed traveling abroad with his wife, Anne, and did so 

often. 

Dale earned his bachelor’s degree from the University 

of California at Berkeley, his master’s and Ph.D. degrees at the University of Washington, and then joined 

the NCSU physics department in 1976. He received 

many awards over the course of his career, including the 

American Crystallographic Association’s Bertram Warren Award, Case Western Reserve University’s Centennial 

Scholar Award, and the Outstanding Achievement Award 

of the International XAFS Society.

—Laura Mgrdichian

Contributors: Bill Thomlinson, Zhong Zhong, and Kumi 

Pandya

From left, Edward Stern, Dale Sayers, and Farrel Lytle accept the 

American Crystallographic Association’s Bertram Warren Award 

in 1979, for their development of EXAFS.

The Gregori Aminoff Prize Goes to 

Prominent NSLS User David Mao

December 1, 2004

David Mao, a frequent NSLS user, was awarded the 

2005 Gregori Aminoff Prize in Crystallography by the 

Royal Swedish Academy of Sciences. Mao received this 

prestigious award “for pioneering research of materials at 

ultrahigh pressures and temperatures.” 

 “I am very honored to 

receive this award for my 

work using high-pressure 

diamond anvil cell devices,” 

said Mao, a researcher with 

the Geophysical Laboratory 

at the Carnegie Institution 

of Washington. “We are at 

the exciting moment when 

high-pressure research 

may emerge as a major 

branch of modern science. 

Groundbreaking high-pressure experiments reveal 

numerous new phenomena 

of revolutionary importance for a wide range of problems in the physical sciences. Fortunately, with modern 

David Mao
3-34 NSLS ACTIVITY REPORT 

Zhong Zhong Explains Diffraction Enhanced Imaging at the 399th Brookhaven 

Lecture

December 15, 2004

To look below the surface of the human body in search of 

deep-seated injury or disease, today’s radiologists use an alphabet-soup of imaging techniques: computerized tomography, or CT; magnetic resonance imaging, or MRI; positron 

emission tomography, 

or PET; single photon 

emission computed 

tomography, or SPECT; 

whole body scanners; and 

ultrasound. 

Despite the advancements in non-invasive 

medical imaging, 80 

percent of radiology still 

involves the well-known 

x-ray. But x-ray imaging technology has not 

changed very much over 

the past 100-plus years, mostly showing bone much more 

clearly than soft tissue, such as ligaments, cartilage, or blood 

vessels. 

Zhong Zhong

synchrotron light sources, these phenomena can be directly 

probed and studied at extreme pressure conditions.” 

He continued, “There are so many colleagues at the Geophysical Laboratory to whom I am in debt for this development, particularly Larry Finger and Charlie Prewitt, from 

whom I learned structural crystallography; and Bill Bassett, 

Peter Bell, and Rus Hemley, who I joined in developing this 

new high-pressure field. I must also thank Chi-Chang Kao 

at the NSLS, who taught me how to study electron and 

phonon dynamics of crystals by inelastic x-ray scattering 

spectroscopy.” 

The Aminoff prize is given out annually to scientists or 

research groups (of three people or fewer) who have made 

a major contribution to the field of crystallography. It 

consists of a gold medal, a diploma, and a $10,000 cash 

award, and is named after Swedish crystallographer Gregori 

Aminoff, the first scientist to introduce crystallography to 

Sweden. 

Mao will formally accept the prize from His Majesty King 

Carl XVI Gustaf, the king of Sweden, at the Royal Swedish Academy’s annual meeting, to be held June 8, 2005. 

Following the ceremony, Mao will present a lecture on his 

work.

—Laura Mgrdichian

Now, thanks to researchers working at BNL, x-rays from 

the National Synchrotron Light Source (NSLS) are being 

employed in a new, low-dose experimental technique to 

visualize not only bone, but also soft tissue, in a way that is 

not possible using conventional x-rays. Called diffraction 

enhanced imaging (DEI), the technique provides all the information provided by conventional x-rays, plus additional 

data on soft tissues that were previously accessible only using alternative methods such as MRI or ultrasound.

Zhong Zhong, a physicist at the NSLS and the co-inventor of DEI, has been developing the technique for nine 

years. He discussed the imaging technique at the 399th 

Brookhaven Lecture, “Diffraction Enhanced Imaging: Seeing X-Rays as One Sees the Light,” at 4 p.m. on Wednesday, December 15, 2004 in Berkner Hall. Zhong was 

introduced by Steve Dierker, NSLS Chair and Associate 

Laboratory Director for Light Sources.

Zhong is currently responsible for the DEI program and 

the high-energy x-ray scattering facility at NSLS beamlines 

X15A and X17B1, respectively. 

Zhong earned his B.S. in physics from Beijing University, 

China, in 1990; received an M.S. in applied physics from 

Michigan Technological University in 1992; and, in 1996, 

received his Ph.D. in physics from Stony Brook University.

—Laura Mgrdichian
 YEAR IN REVIEW 3-35

2004 NSLS Tours

1/13/2004 House Committee on Science

1/13/2004 New York Power Authority

2/26/2004 William Faulk, Suffolk County Legislature

2/27/2004 New Jersey Institute of Technology

3/9/2004 Stony Brook University - African Students

3/12/2004 CCNY of New York IEEE Chapter

3/15/2004 University of Louisville, Kentucky

3/19/2004 University of Connecticut, Storrs

3/25/2004 Charterhouse School

3/26/2004 New York University

3/29/2004 SUNY at Farmingdale

3/29/2004 Brian Davison, Director of Life Sciences Division at ORNL

3/30/2004 Defense Threat Reduction Agency

4/14/2004 Representatives from Historically Black Colleges and Universities

4/16/2004 Senator Charles Schumer Staff 

4/16/2004 Nassau Community College

4/20/2004 Adult Program of the Great Neck Public Schools

4/20/2004 Johns Hopkins University 

4/20/2004 Brookhaven Women In Science (BWIS) High School Career Day

4/22/2004 Take Our Daughters and Sons to Work Day

4/22/2004 Stony Brook University Research Executives

4/30/2004 Small Business Fair

5/5/2004 United Federation of Teachers 

5/6/2004 The Roundtable at Stony Brook University

5/14/2004 SUNY at Farmingdale Information Club

6/4/2004 Stony Brook University Research Experience for Undergraduate (REU) Students

6/8/2004 Miller Place School District 

6/9/2004 Nonproliferation and National Security (NNS) Workshop

6/25/2004 11th Advanced Accelerator Concepts Workshop

6/28/2004 Department of Homeland Security

7/16/2004 Stony Brook University Alliance for Graduate Education and the Professiorate 

(AGEP) Program

7/19/2004 Stony Brook University REU Students

7/21/2004 Columbia University REU Students 

7/22/2004 Columbia University Summer Chemistry Program
3-36 NSLS ACTIVITY REPORT

2004 NSLS Tours

7/26/2004 BNL-Hofstra-Stony Brook University

7/28/2004 Stony Brook University Taiwanese Students

8/11/2004 Korean Institute of Science & Technology, KIST

8/19/2004 Property Management Association - Long Island Chapter

9/9/2004 Stony Brook University Foundation Trustees 

9/13/2004 Congressman Tim Bishop's Staff

9/22/2004 Dr. Thomas Jourdan - FBI Liaison to the National Laboratories

9/23/2004 Retired Vice Admiral Grossenbacher

9/24/2004 Battelle NanoTechnology Alliance Group

9/29/2004 Stony Brook University - Biomedical Engineering Program

10/1/2004 United States Merchant Marine Academy

10/20/2004 English as a Second Language Program

10/22/2004 Stony Brook University Engineering Department

10/26/2004 House Appropriations Subcommittee on Energy and Water Development

10/27/2004 The Minister of the Science and Technology Ministry of the Republic of Korea 

10/27/2004 Joint US-Japan Workshop

10/28/2004 Japanese Society for the Promotion of Science Group 

11/5/2004 New York University

11/16/2004 Brookhaven Women In Science (BWIS) High School Career Day

11/17/2004 Adult Program of the Great Neck Public Schools

11/19/2004 Stony Brook University - Black Engineers Student Club

11/23/2004 Stony Brook University - Physics Department

11/30/2004 SUNY at Farmingdale - Institute of Retirement and Learning

12/7/2004 Columbia University Chemistry Department
Organization
 ORGANIZATION 4-3

National Synchrotron Light Source Organization

Members of the NSLS Staff

NSLS Organization Chart

Associate Laboratory Director

for Light Sources

S. Dierker

Beamline Support

S. Hulbert Linac

X. Wang

ESH Coord. N. Gmur

QA Rep. M. Buckley

Operations and

Engineering Division

Associate Chair

for Operations

E. Johnson

Accelerator

Division

Associate Chair

for Accelerators

J. Murphy

User Science

Division

Associate Chair

for User Science

C. Kao

ESH

Division

Associate Chair

for ESH/Q

R. Casey

Science Advisory Committee (SAC)

J. Penner-Hahn

Users Executive Committee (UEC)

L. Shapiro

Proposal Study Panels (PSPs)

Allocation Panels

General Users Oversight Comm. (GUOC)

NSLS Chair

S. Dierker

Assistant to Chair

for Administration

F. Terrano

Administrative

Services

F. Terrano

Science Program Support

R. Pindak

Controls & Detectors

P. Siddons

R. Biscardi

Electrical Systems

Mechanical Engineering

E. Haas

Operations

R. Heese

ESH/Q

R. Casey

Storage Ring

and Insertion Device

B. Podobedov

User Administration

M. Corwin

Information and Outreach

L. Miller
4-4 NSLS ACTIVITY REPORT 

NSLS Advisory Committees

SCIENCE ADVISORY

COMMITTEE

The Science Advisory committee 

(SAC) evaluates science programs 

at the NSLS and makes recommendations to the Chairman.

Mario Amzel, Johns Hopkins Medical 

School

Joel Brock, Cornell Univ.

Thomas Ellenberger, Harvard Medical 

School

Eric D. Isaacs, Argonne National Lab.

Edward Kramer, Univ. of California, 

Santa Barbara

Simon Mochrie, Yale Univ.

James Penner-Hahn, Univ. of Michigan

Larry Shapiro, Columbia Univ., 

Ex-Officio, UEC Chair

William Thomlinson, Canadian Light 

Source, Inc.

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

Larry Shapiro, Columbia Univ.

PAST CHAIR

Antonio Lanzirotti, Univ. of Chicago

MEMBER

Daniel Fischer, NIST

MEMBER

Dean Hesterberg, NCSU

MEMBER

Trevor Tyson, NJIT

MEMBER

Hao Wu, Cornell Univ.

VICE CHAIR

Peter Stephens, Stony Brook Univ.

EX-OFFICIO

Chi-Chang Kao, NSLS User Science 

Division

EX-OFFICIO

Mary Anne Corwin, User 

Administration Office

EX-OFFICIO

Lisa Miller, NSLS Information and 

Outreach Office

SPECIAL INTEREST GROUP

REPRESENTATIVES

Special Interest Groups in areas of common concern communicate with NSLS 

management through the UEC

BIO. SCATTERING AND DIFFRACTION

Tom Hollis, Wake Forest Univ.

INDUSTRIAL USERS

Laura Silvian, Biogen Inc.

IMAGING

Jeff Fitts, BNL-Environmental 

Sciences Department 

INFRARED USERS

Randy Smith, BNL-NSLS

NUCLEAR PHYSICS

Mahbub Khandaker, Thomas 

Jefferson National Lab.

STUDENTS AND POST DOCS

Meghan Ruppel, BNL-NSLS

XAFS 

Simon Bare, UOP LLC

X-RAY SCATTERING AND

CRYSTALLOGRAPHY

Valery Kiryukhin, Rutgers Univ.

TIME RESOLVED SPECTROSCOPY

John Sutherland, BNL-Biology 

TOPOGRAPHY

Michael Dudley, Stony Brook Univ.

UV PHOTOEMISSION AND SURFACE

SCIENCE

Elio Vescovo, BNL-NSLS
 ORGANIZATION 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 scientific community 

and generally serve a two-year term.

VUV

Laszlo Mihaly, Stony Brook Univ. 

Elio Vescovo, BNL-NSLS

X-RAY

Marc Allaire, BNL-NSLS

Annie Heroux, BNL-Biology 

Jean Jordan-Sweet, IBM

Elaine DiMasi, BNL-Physics

Syed Khalid, BNL-NSLS 

Wolfgang Caliebe, BNL-NSLS

NSLS Advisory Committees

GENERAL USER PROPOSAL

REVIEW PANEL

The Proposal Review Panel (PRP) 

reviews and rates General User Proposals. Members are drawn from the 

scientific community and generally 

serve a two-year term.

IMAGING AND MICROPROBES: 

BIOLOGICAL AND MEDICAL

Max Diem, City Univ. of New York

Paul Dumas, Centre National de La 

Recherche Scientifique

Kathleen Gough, Univ. of Manitoba

Lindsay Keller, NASA-Johnson Space 

Center

Irit Sagi, Weizmann Institute of 

Science

IMAGING AND MICROPROBES: 

CHEMICAL AND MATERIALS

SCIENCES

Harald Ade, NCSU

Barry Lai, Argonne National Lab.

I. Noyan, Columbia Univ.

IMAGING AND MICROPROBES: 

ENVIRONMENTAL AND GEOSCIENCES

Jeffrey Fitts, BNL-Environmental 

Sciences

George Flynn, SUNY @ Plattsburgh

Lindsay Keller, NASA-Johnson Space 

Center

Kenneth Kemner, Argonne National 

Lab.

David Wetzel, Kansas State Univ.

IR/UV/SOFT X-RAY SPECTROSCOPY: 

CHEMICAL SCIENCES/SOFT MATTER/

BIOPHYSICS

Jingguang Chen, Univ. of Delaware

Daniel Fischer, NIST

Jan Genzer, North Carolina State 

Univ.

David Mullins, Oak Ridge National 

Lab.

Michael White, BNL-Chemistry

IR/UV/SOFT X-RAY SPECTROSCOPY: 

MAGNETISM/STRONGLY CORRELATED

ELECTRONS/SURFACE

Robert Bartynski, Rutgers Univ.

Hong Ding, Boston College

Boris Sinkovic, Univ. of Connecticut

Jiufeng Tu, City Univ. of New York

Barrett Wells, Univ. of Connecticut

METHODS AND INSTRUMENTATION

Kenneth Finkelstein, Cornell Univ.

Albert Macrander, Argonne National 

Lab.

Ralf-Hendrik Menk, Univ. of Siegen

Peter Takacs, BNL-Instrumentation

MACROMOLECULAR CRYSTALLOGRAPHY

Alex Bohm, Tufts Univ.

Brain Crane, Cornell Univ.

DaXiong Fu, BNL-Biology

Daniel Leahy, John Hopkins Univ.

Brenda Schulman, St. Jude Children's 

Research

Da Neng Wang, New York Univ.

Joshua Warren, Duke Univ.

POWDER/SINGLE CRYSTAL CRYSTALLOGRAPHY

Simon Billinge, Michigan State Univ.

Thomas Duffy, Princeton Univ.

John Parise, Stony Brook Univ.

Patrick Woodward, Ohio State Univ.

X-RAY SCATTERING: MAGNETISM/

STRONGLY CORRELATED ELECTRONS/

SURFACE

Sean Brennan, Stanford Linear Accelerator Center

Kenneth Finkelstein, Cornell Univ.

Valery Kiryukhin, Rutgers Univ.

Karl Ludwig, Boston Univ.

George Srajer, Argonne National Lab.

X-RAY SCATTERING: SOFT MATTER AND

BIOPHYSICS

Paul Heiney, Univ. of Pennsylvania

Ben Hsiao, Stony Brook Univ.

Huey Huang, Rice Univ.

Robert Leheny, Johns Hopkins Univ.

H. Miriam Rafailovich, Stony Brook 

Univ.

Detlef Smilgies, Cornell Univ.

Helmut Strey, Stony Brook Univ. 

X-RAY SPECTROSCOPY: BIOLOGICAL, 

ENVIRONMENTAL, AND GEOSCIENCE

Dean Hesterberg, North Carolina 

State Univ.

Douglas Hunter, Savannah River 

Technology Center

Kenneth Kemner, Argonne National 

Lab.

Satish Myneni, Princeton Univ.

James Penner-Hahn, Univ. of 

Michigan

X-RAY SPECTROSCOPY: CHEMICAL

AND MATERIAL SCIENCES

Uwe Bergmann, Stanford Linear Accelerator Center

Simon Bare, UOP

Anatoly Frenkel, Yeshiva Univ.

Vincent Harris, Northeastern Univ.

Trevor Tyson, NJIT
Facility Report
 FACILITY REPORT 5-3

NSLS Accelerator Division

James B. Murphy

ASSOCIATE CHAIR FOR ACCELERATORS

Organization and Mission

The NSLS Accelerator Division (AD), headed by James B. Murphy, is organized into two sections: the Linear 

Accelerator (Linac) Section, headed by Xijie Wang, and the Storage Ring & Insertion Device Section (SR&ID), 

headed by Boris Podobedov. The AD staff consists of eleven accelerator physicists, two engineers, three technicians, and two postdocs.

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 (VUV) storage rings

• To participate in the NSLS-II project, in particular the design of the storage ring and injection system

• To operate the Magnet Measurement Lab (MML) and the Deep Ultra Violet Free Electron Laser (DUV- 

 FEL) Laboratory

• To perform fundamental research and development (R&D) in accelerator and free-electron laser physics

2004 Activities

Injection System & Storage Ring Improvements

In 2004, the activity with the most direct benefit to the NSLS user community was the restoration of the x-ray 

ring lattice symmetry, which resulted in a reduction of the horizontal emittance (Figure 1) and a more robust 

operational lattice.

The basic eight-fold symmetry of the x-ray ring magnet lattice can be broken due to gradient errors in the ring 

quadrupoles and changes in the reference closed orbit. The quadrupole errors can be partially mitigated by the installed trim coils available in the x-ray ring for one of the quad families. In studies that took place over the summer 

and fall of 2004, these gradient errors were determined through a series of orbit-response matrix measurements 

and an elaborate analysis that included fitting a ring model to a suitable set of parameters. The mathematical 

model was later confirmed by a direct measurement of the dispersion function of the eight-fold symmetric lattice. 

The optics system was commissioned before the winter shutdown and is now in routine operation. 

Another important activity regarding the storage rings was the implementation of the so-called “middle layer” software interface on the NSLS 

control system. The middle layer was originally developed at the Advanced 

Light Source (ALS) to interface between the EPICS control system and the 

high-level MATLAB-based accelerator physics applications. It is currently 

used at a number of operating and future light sources, such as SPEAR-3, 

the Canadian Light Source, SOLEIL, and DIAMOND. The NSLS uses 

a real-time control system that is different from EPICS. However, due to 

the clever layered client-server architecture of the NSLS control system, the 

SR&ID staff, together with Operations and Engineering Division (OED) 

staff, were able to adapt the middle layer so that it could “hook into” the 

NSLS control system. This allowed us to port about five man-years worth 

of high-level accelerator physics and control tools development to the 

NSLS control system. One of the tools, a MATLAB-based version of the 

LOCO program, was used for the x-ray ring lattice symmetry restoration. 

To ensure the smooth operation of the NSLS injection system, we per-
5-4 NSLS ACTIVITY REPORT 

formed a thorough review of its operational principles and hardware systems. Aging electron and photon beam instrumentation was refurbished and new synchrotron-light monitors were added. This focused effort has led to a significant 

increase in the reliability of the injection system. An industrial partner was also identified to rejuvenate old klystrons 

for the linac injector.

A number of important contributions to the present facility came through the efforts of the magnet-measurement lab 

(MML) staff with support for the O&ED personnel. A vertical beam scraper assembly, built in the MML in 2003, was 

installed in the X13 straight section of the x-ray ring during the winter 2003/04 shutdown. Controls for the device 

were installed and calibrated during the May 2004 shutdown. The measurements of beam losses versus scraper position allow one to better understand the x-ray ring beam dynamics. In particular, it is possible to validate the minimum 

allowed vertical aperture, and hence the minimum magnetic gap, of future insertion devices planned for the x-ray ring, 

such as the X25 mini-gap undulator (MGU).

The magnetic design of the one-meter-long X25 MGU was finalized in 2004. The hybrid-permanent magnet design 

uses the newest high-field, high-temperature-capable magnets developed for hybrid/electric vehicle motors. The design 

is based on room temperature operation, but includes the option of cooling the magnet arrays to as low as -120o

 C to 

gain an additional 13% in field strength and a wider tuning range. Specifications for magnets and poles were developed, bids were received from three vendors, and NEOMAX America Inc. was selected. The mechanical support 

structure and vacuum chamber specifications were also developed and bids for construction were received from several 

U.S. and foreign vendors. The contract was awarded to Advanced Design Consultants Inc. A preliminary design 

review was held in December 2004. Delivery of the magnets, poles, and the mechanical structure are scheduled for 

summer 2005 and installation in the x-ray ring is planned for the winter 2005 shutdown.

It should be mentioned that the X29 MGU (designed and installed by the MML staff in collaboration with the O&E 

Division) and its new protein crystallography beamline were successfully commissioned in 2004 by NSLS user science 

and biology staff members. Optical measurements proved the X29 MGU to be performing “brilliantly” and this is 

currently the brightest insertion device in the NSLS complex. 

NSLS-II Design Work

The NSLS-II storage ring will provide unprecedented high brightness to the NSLS user community. As such, the 

NSLS-II design presents challenges in the areas of lattice design, collective effects, superconducting insertion devices, 

and choice of injector.

Lattice: In Spring 2004 the NSLS-II lattice design team hosted visitors from the ALS, DIAMOND, the European 

Synchrotron Radiation Facility, KEK, and the Swiss Light Source, with the purpose of acquiring input from world-renowned experts on light source design. In the following summer, intensive effort was placed on developing improved 

lattice and tracking tools for addressing the higher-order nonlinear effects in the high-performance lattice. Work is continuing to optimize 

the baseline 24-cell triple-bend achromat lattice and we are considering the merits of other candidate lattices.

Collective Effects: The combination of very low emittance (~ 1.5 

nm), medium energy (3 GeV), and high single-bunch charge (I ~ 1 

ma) makes the NSLS-II design challenging from the point of view of 

collective effects. To properly assess the impact of collective effects, an 

impedance budget is being developed, starting with the most critical 

components, such as MGUs, radio-frequency (RF) cavities, and beam 

position monitors. Much progress has been made in analyzing the 

impedance of vacuum chambers for the superconducting insertion 

devices, in particular the taper sections from the main ring vacuum 

chamber to the small-gap insertion devices. 

Thresholds of various instabilities have been found and analyzed. In 

particular, the transverse mode coupling instability (TMCI) threshold 

driven by the resistive chamber of MGUs was estimated by comparCorrected

Uncorrected

740 μm h 170 μm v

522 μm h 162 μm v

Figure 1. The x-ray ring photon beam spot size before and 

after the correction of the lattice symmetry.
 FACILITY REPORT 5-5

ing the resistive wall tune shift to the synchrotron tune, and confirming the estimate with computer simulations. 

Other important findings were related to the beam-induced heat in the mini-gap undulators, which provided 

concrete estimates for the cryo-designers. It was also found that employing a third-harmonic RF system will lessen 

the problems associated with collective effects and significantly improve the beam lifetime.

Superconducting Undulator Development: Compared to conventional permanent-magnet MGUs, superconducting undulators (SCUs) can provide higher brightness and continuous photon coverage. 

However, one of the most significant challenges to building an SCU for NSLS-II is the ability 

to measure and correct the undulator field errors. Other challenges are heat management and 

removal. To address these challenges head-on, we are constructing a state-of-the-art cryogenic 

vertical test facility (VTF) for taking magnetic and calorimetric measurements of SCU test 

models (Figure 2). The VTF will allow precise magnetic field mapping of short SCU models 

up to 0.4 m long, using a motorized Hall probe field mapper. The mapper, which includes an 

NSLS-built six-element cryogenic Hall probe, has fast on-the-fly field mapping capabilities and 

has been bench-tested on an existing permanent magnet undulator. A superconducting Helmholz coil is under construction to provide an in-situ calibration check of the Hall sensors in 

liquid helium. A pulsed-wire insert, interchangeable with the Hall probe mapper, is also under 

construction, to provide a complementary magnetic measurement technique. Initial bench 

tests of the pulsed wire insert have been successfully completed. A cryogenic safety review of 

the VTF is planned for January 2005. The VTF will then be installed and commissioned at the 

BNL Superconducting Magnet Division’s facilities in 2005.

Both a booster synchrotron and full-energy linear accelerator were explored as possible injectors 

for the NSLS-II project.

The Deep Ultra Violet Free Electron Laser (DUV-FEL) Laboratory

The DUV-FEL is a dedicated platform for single-pass high-gain FEL R&D and applications. 

After successfully lasing at 266 nm with 800 nm laser seeding in late October 2002, experiments were carried out at the DUV-FEL last year to further explore laser-seeded high-gain 

harmonic generation (HGHG) FEL and improve its tunability. We also continued to provide 

significant support for users to explore the potential of the DUV-FEL for chemical science applications. 

The chirped pulse amplification (CPA) experiments made significant progress in the last year with the development of a VUV SPIDER diagnostic apparatus and a pulse compressor. We demonstrated that by imposing a chirp 

on both the electron bean energy and the seed laser wavelength, a linear chirp could be detected on the HGHG 

FEL output. These results demonstrate the potential to generate short pulses through CPA. Another major 

achievement at the DUV-FEL was the successful characterization of half-cycle coherent THz pulses using an electro-optical technique. 

The electron beam energy upgrade project was successfully completed with support from NSLS Engineering and 

Environment, Safety, and Health divisions in the last year. The DUV-FEL linac energy was upgraded from 200 

to 300 MeV to enable the HGHG FEL to produce 100 μJ pulses of 100-nm light. This will establish the DUVFEL as a premier source of ultraviolet radiation and will enable state-of-the-art gas phase photochemistry research. 

Furthermore, the upgraded facility will also enable future critical R&D experiments, such as multi-stage cascaded 

HGHG FELs and higher-harmonic HGHG (n > 5). The MML continued to support the DUV-FEL program in 

2004 by rebuilding and recalibrating the modulator wiggler and adding a new dispersion magnet.

Figure 2. VTF
5-6 NSLS ACTIVITY REPORT 

Operations and Engineering Division

Erik D. Johnson

ASSOCIATE CHAIR FOR OPERATIONS AND ENGINEERING

Organization and Mission

The Operations and Engineering Division (OED) has three sections: Operations, which is led by Richard Heese; 

Electrical Systems, led by Richard Biscardi; and Mechanical Engineering, led by Ed Haas. To serve the NSLS user 

community, our mission falls into three main areas:

• Operating the NSLS 24 hours a day, seven days a week, and, on average, 44 weeks a year 

• Designing, fabricating, and maintaining the NSLS accelerators, infrastructure, and instruments, including 

 upgrades, modifications, and proposal development

• Providing engineering and technical support for other NSLS divisions and the NSLS user community

The OED staff includes one scientist, 21 engineers, and 57 technicians, making it the largest of the NSLS 

divisions. In addition to its own staff, the division coordinates the activities of seven skilled tradesmen from 

Brookhaven Lab. The breadth of our mission is such that we need to draw on the capabilities of the other NSLS 

divisions for support and, in turn, provide specialized support for their activities. 

2004 Activities

Maintenance and upgrade activities continue to be important factors in achieving high performance for the NSLS, 

a facility that is now entering its third decade of operations. For fiscal year 2004, overall reliability was above 90% 

for the x-ray ring and 99% for the VUV ring. An overview of machine performance is provided in this report’s 

“Facility Facts and Figures” section. The facility continued to operate well throughout most of the year, with a few 

rough patches in April/May and July/August on the x-ray ring, which accounted for much of the year’s downtime. 

On April 21, with the May shutdown already set and fully scheduled, the x-ray ring injection septum vacuum 

chamber began to fail. It quickly became evident that the most complex vacuum chamber on the x-ray ring would 

need to be replaced as part of the shutdown. Fortunately, the last time the septum was replaced, in 1987, a spare 

was built that was available for this emergency repair (see photos on next page). Nonetheless, the installation is extremely difficult because the chamber is deeply buried in shielding and is captured by two of the large quadrupole 

magnets. As the scope of the task became clear, we advised the user community to expect at least a week delay in 

operations. Through careful planning and execution, as well as some very long hours, the actual installation only 

took four days longer than the originally scheduled shutdown. An additional four days went into conditioning the 

machine, which was also not part of the original plan. 

Routine operations were established on June 1, which was, overall, just eight 

days later than planned in January when the schedule was released. Without 

the hard work and dedication of the staff, as well as the existence of the spare 

chamber, this problem could well have stretched into the summer and beyond. The whole activity emphasizes the importance of preparing for surprises, no matter how improbable they seem.

The injection septum chamber replacement overshadowed a significant body 

of other shutdown work. The power distribution maintenance on May 8 

revealed problems in each of the three substations, which were resolved. None 

of these issues would have resulted in unsafe conditions, but they could have 

led to failures that would have caused substantial operations downtime. 

No less significant were several major activities by the Utilities Group, aimed 

at improving the reliability of the NSLS cooling systems. One involved the 

addition of a third pump to act as a rotating spare for the low-pressure cop-
 FACILITY REPORT 5-7

(A) Upstream before replacement: This photograph shows the injection point into the x-ray ring. It is a heavily shielded area because there can be 

significant losses on injection. The failing injection septum chamber is buried within this part of the ring. Replacing it required removing all of the 

shielding visible in the photograph, parting two large quadrupole magnets, removing the kicker magnet and supply, and removing the trims and all of 

the diagnostics attached to the injection septum. An activity of this magnitude would normally be reserved for a winter shutdown. (B) Upstream during 

replacement: This photo was taken during the installation process on May 11. The extent of the disruption of the machine is quite obvious. To protect 

against inadvertent damage as the machine components were reinstalled, the ceramic chamber was covered in bubblewrap. (C) Replacement Chamber: 

The spare Injection Septum Chamber is shown during preparations for the installation. The small port in the foreground is where the injected beam 

enters the machine. The ceramic chamber has a copper sleeve inside of it that surrounds the circulating beam to shield it from the field of the pulsed 

magnet that steers the injected beam into the ring. The replacement chamber dimensions were checked against the pulsed magnet (BXISH) and the ring 

girder to assure smooth installation. The entire assembly was prebaked before installation, which was a significant factor in the fast commissioning of the 

machine.

(A) (B) (C)

per system that provides cooling for the machine power systems. Cleaning the high-pressure copper system heat 

exchangers was also required to bring the efficiency of that system back to specification. 

Since 2003, when a failure on the site chilled-water system dislodged debris from the distribution piping, we have 

been experiencing significant difficulty keeping these systems clear and fully functional. This fine silt-like material 

has been migrating to the low point of the system (the NSLS) ever since, clogging equipment strainers (see photo 

below), and fouling the heat exchangers for the machines. To head off continuing fouling, full-flow strainers were 

installed on the 12” lines from the site central chilled-water supply to the machine cooling equipment.

Although the unanticipated replacement of the x-ray injection ceramic 

in May was the single largest contributor of downtime for the year, we 

also experienced a swarm of small system failures from late July into 

August that accrued more than 45 hours of downtime, almost twice the 

average for a whole month. These two types of failures illustrate several 

important points. 

From the user's perspective, the summer episode of unrelated equipment failures was more disruptive than the single large failure in May. 

In the case of the injection ceramic, we knew the magnitude of the 

problem and were able to provide the user community with advance 

notice. The series of problems we encountered this summer resulted in 

downtime scattered throughout a three-week period of scheduled operations, impacting many more user experiments than the extension of the May shutdown (see table). 

While a few large events can dominate the reliability statistics for any given year, the impact of small-duration but 

more frequent failures can be devastating for a single user’s experimental run. Recognizing this problem, the NSLS 

has, for many years, run a preventive maintenance program to minimize equipment failures. Downtime faults and 

system failures that do occur are carefully monitored to look for trends and address problems where possible. The 

observed trends can result in significant investment by the NSLS in machine improvement efforts.

Both the Accelerator Division and the Operations and Engineering Division devoted a great deal of effort to 

NSLS machine improvements this year. Digital closed-orbit feedback has now been implemented in both planes 

on the x-ray ring, the culmination of several years work on orbit stabilization. New machine improvement activities have also been initiated. The injection system, including the linac, booster, and transport lines to the rings, has 

been the subject of an active study to characterize and improve the system’s performance and reliability. Diagnos-
5-8 NSLS ACTIVITY REPORT 

Group

Area/System Total X- DT U- DT X-ray UV

Total Charges to Down Time

Controls and Diagnostics 103 38 14 29.3 9.5

Power Systems 218 109 15 106.9 22.0

Utilities 77 42 20 258.9 24.5

Miscellaneous 69 37 9 37.1 1.2

467 226 58 432.2 57.2

Major Events

Water Leak damaged Ion Pump feedthrough 24.0

Persistent XRF1 Faults 17.3

XRF1 Tube and Socket Replacement 13.4

XQD trim failure 20.2

BXESH1 failures 17.6

BXISH Chamber Replacement 192.0

284.5 0.0

Balance to 'Routine' Faults

147.6 57.2

Number of Faults Downtime [hr]

tics are being added to the transport lines and booster ring to monitor and improve the injection efficiency into the 

storage rings. 

High-level accelerator modeling software developed over the last five years at the Advanced Light Source and SPEAR 

was successfully ported to the NSLS for use in machine studies of the storage rings. These MATLAB-based tools are 

linked to the NSLS control system and were used to restore the eight-fold symmetry of the x-ray ring lattice. Trim 

supplies on the ‘D’ family of quadrupoles are required to implement the lattice corrections. Significant effort was invested by the Electrical Systems Section to make sure the QD-trim supplies would be sufficiently robust to provide the 

required corrections and operate reliably. More about the lattice symmetrization work can be found in the Accelerator 

Division article in this report.

The winter 2004 shutdown schedule was originally 

planned with the goal of completing the radio frequency (RF) cavity upgrades on the x-ray ring. Unfortunately, we entered the fiscal year with a very austere 

budget under a continuing resolution. Although the 

new cavity is ready for installation, we deferred the 

task to mitigate the risk of damage to the machine 

that could draw on contingency funds. The shutdown was instead dedicated to routine maintenance 

and compelling installation tasks. One such task was 

the replacement of another injection ceramic for the 

BXIFB1 bump on the x-ray ring, which had begun 

to leak over the summer. Since this work required 

venting superperiod 8, the water-cooled ‘speedbump’ 

downstream of X1 was also removed. The water-cooling had been removed some time ago due to a leak, 

and with the advent of the active interlock system it 

was no longer required. 

A number of activities to support initiatives from 

other divisions were also undertaken during the year. A major upgrade of the X25 wiggler to a one-meter-long minigap undulator (MGU) was initiated. The program’s justification and coordination are provided by the User Science 

Division, the magnetic design is being undertaken by the Accelerator Division, and the mechanical and electrical 

design for the MGU, its controls, and the vacuum system is being performed by the Operations and Engineering Division. A bit further out, but following a similar path, is the development of a new insertion device program at beamline 

X9. Engineering design and analysis are also being provided to support several end station development projects, and 

significant support was provided for the energy upgrade of the Deep Ultra-Violet Free Electron Laser (DUV-FEL). 

The details of these activities can be found in the Accelerator Division article in this report.

Although not directly visible to the user community, substantial investment was made this year in safety programs. 

This included design reviews for new systems, documenting existing equipment, and developing procedures for 

maintenance and troubleshooting that address the heightened safety expectations of the Department of Energy. These 

activities are really investments for the future that keep our staff and users safe and, in the long run, will pay dividends 

in continued robust operations of the NSLS.

In fact, the vast majority of what the OED does is transparent to our user community, something we diligently strive 

to achieve. Through the hard work and dedication of the staff, most of the operational issues are headed off before 

they become problems. When problems do arise, we make every effort to minimize their impact on our users’ research. 

In this way, we continue to work with the other NSLS divisions to ensure that our user community continues to be 

one of the most productive.
 FACILITY REPORT 5-9

User Science Report

Chi-Chang Kao

ASSOCIATE CHAIR FOR USER SCIENCE

Organization and Mission

The User Science Division coordinates major facility activities related to users so that we can be more effective in 

communicating with the user community, strengthening existing scientific programs, fostering the growth of new 

scientific programs, and raising the visibility of the exciting science produced by our users. The division consists 

of five sections: User Administration (Mary Anne Corwin), Information and Outreach (Lisa Miller), Beamline 

Development and Support (Steve Hulbert), Scientific Program Support (Ron Pindak), and Detectors and Controls (Peter Siddons). The major initiatives and accomplishments of the User Science Division and the NSLS user 

community for 2004 are summarized below.

2004 Activities

With the help of a large number of users and staff, a major NSLS-II workshop was organized in March 2004 to 

summarize the outcome of more than a dozen focused workshops where the grand challenges in the individual 

fields of research, and the impact of NSLS-II on those challenges, as well as the technical challenges in the accelerator, insertion devices, optics, and detectors, were discussed. The workshop was well attended and provided 

additional support to the NSLS-II scientific case. Following the workshop, the NSLS-II proposal was officially 

submitted to the Department of Energy (DOE).

The general user proposal system was switched to the new online proposal system (PASS) in the May-August cycle 

of 2004, after extensive testing by the User Administration office and representative users. The transition has been 

very smooth, with only minor problems. Additional new features, in particular rapid access, will be implemented 

in 2005. As always, we welcome comments and input from users to continue improving the system. 

This year was also a particularly busy year because, as part of the overall plan to enhance the experimental capabilities at the NSLS, we have completed a large number of beamline construction and upgrade projects, including 

beamline upgrades for the U12IR beamline, the X1A undulator beamline, the X13A elliptically polarizing wiggler 

beamline, and the X21 wiggler beamline, as well as the construction of the X27A x-ray microprobe beamline and 

the X29 undulator beamline. Some of the highlights are described below, and more detailed descriptions can be 

found in the pages following this article.

• U12IR beamline upgrade: The U12IR far-infrared beamline was upgraded to accommodate a Bruker IFS- 

 125HR spectrometer with a resolution capability of 0.001 cm-1 (125 nV or 30 MHz), making U12IR the 

 highest resolution IR beamline of any synchrotron facility. This new capability, in combination with the ex 

 isting high-field magnet and Ti-sapphire laser, provides a unique facility for the study of THz spectroscopy, 

 electron spin resonances, and time-resolved magneto-spectroscopy.

• X1A beamline upgrade: The X1A1 beamline is dedicated 

 to scanning transmission soft x-ray spectromicroscopy 

 in the 200-600 eV range, which includes the carbon, 

 nitrogen, and oxygen K-edges. A new four-position in 

 terchangeable grating chamber with state-of-the-art 

 soft x-ray laminar gratings optimized for specific portions 

 of the X1A1 photon energy range was implemented to 

 improve the throughput and energy resolution of the 

 beamline. 

• X13A beamline upgrade: A new motorized and water- 

 cooled mirror system was installed in the X13A elliptically 

 polarizing wiggler beamline. The larger collecting angle 

 and improved mirror figure have resulted in an order of 
5-10 NSLS ACTIVITY REPORT 

 magnitude increase in flux. The increased flux and temperature stability of the mirror will be particularly import- 

 ant for the detection of small magnetic circular dichroism signals.

• X21 beamline upgrade: The X21 wiggler beamline was upgraded for research programs in materials sciences, 

 including x-ray scattering studies of materials under high magnetic fields, in-situ study of materials growth, 

 and small angle x-ray scattering. An important feature of the new beamline is the non-dispersive double silicon 

 crystal or multilayer monochromator, which contains selectable pairs of silicon crystals or multilayer elements that 

 can be chosen in-situ to suit the experiment at hand.

• X27A beamline construction: A new hard x-ray microprobe beamline, X27A, has been completed to provide 

 much-needed additional x-ray microprobe capacity and enhanced x-ray microspectroscopy capabilities to the 

 NSLS. In particular, the beamline is optimized for the environmental science user community. 

• X29 beamline construction: A new mini-gap in-vacuum undulator beamline, X29, dedicated for macromolecular 

 crystallography, has been completed. The beamline was funded by various divisions of DOE (Offices of Basic 

 Energy Sciences and Biological and Environmental Research within the Office of Science) and the National Insti 

 tutes of Health (National Center for Research Resources, National Institute for Biomedical Imaging and Bioengi- 

 neering, and National Institute of General Medical Sciences) in order to meet the increasing demand at the NSLS 

 for high-brightness x-ray beamlines for the study of the most challenging problems in macromolecular crystallog- 

 raphy.

In the areas of computer control and detector development, the major effort in the development of a multi-element Si 

detector was completed this year. Extensive testing of the detector with users has begun. Using the same technology, a 

linear array Si detector was constructed and used by users in real-time x-ray scattering experiments with great success. 

In addition, we have extended the fast avalanche photodiode (APD) detector-electronics unit to soft x-ray scattering 

experiments, and are working with outside vendors to make NSLS-designed APD-based detectors commercially available. We also continued the upgrade of EPICS-based beamline control system and PLC-based user interlock system on 

NSLS and PRT beamlines.

Finally, we continue to take more immediate steps to enhance user science, education, and outreach at NSLS. The annual short course on EXAFS “graduated” 32 students this summer. This hands-on workshop was organized by NSLS 

users Bruce Ravel (Naval Research Laboratory), Simon Bare (UOP LLC), and Lisa Tranquada (SFA, Inc.), and provided both new and experienced users with exposure to EXAFS theory, data collection, and analysis. A regular series 

of science highlight articles is now published on the NSLS website to help inform the NSLS user community and the 

broader scientific community of the exciting scientific results obtained at NSLS. The symposium series continues at 

the NSLS to give staff and users an opportunity to hear about cutting-edge synchrotron research that is performed 

worldwide. Upcoming seminars are listed on the NSLS homepage for easy access to the schedule. Finally, outreach 

events such as the NSLS Summer Sunday, “Take Our Sons and Daughters to Work” Day, and tours (more than 50 

tours of the facility were conducted in 2004) continue to bring hundreds of members of the community to the NSLS 

to hear about the exciting science ongoing at the NSLS and how this research impacts their everyday lives.
 FACILITY REPORT 5-11

 X13A Magnetic Circular Dichroism Beamline Upgrade

Two insertion devices are installed in the X13 straight section: the mini gap undulator (MGU) and the fast-switching 

(22 Hz) elliptically polarizing wiggler (EPW). The X13A beamline, which utilizes the EPW source, is dedicated to the 

study of magnetic materials and their properties. The EPW provides alternately left- and right-handed elliptically polarized soft x-rays, which enables magnetic circular dichroism (MCD) measurements to be performed at a fixed magnetic 

field on the sample. The fast-switching capability simplifies the detection of small magnetic signals via the use of lock-in 

techniques. 

The first optical element in the X13A beamline is a horizontally deflecting mirror (M0) that collects the central ~1 mrad 

of the EPW source, directs it to the X13A branch, and focuses 

it horizontally at the entrance slit of a horizontally dispersing 

spherical grating monochromator (SGM). The original (1980s) 

M0 mirror was too short, not well cooled, and suffered from 

mechanical stability problems and inadequate adjustment controls. We have replaced this mirror with a new one that remedies 

all of these problems. The new M0 mirror has twice the length 

of the old one, is integrally water-cooled, and is outfitted with 

a robust mounting and motor-driven mirror alignment system. 

These features have significantly improved the stability of the 

signal ratio between left and right elliptically polarized soft 

x-rays. Very often, the magnetic signals measured at X13A are 

quite small, such that an improvement in beam stability results 

in a significant improvement in data quality. In order to maximize beamline performance for demanding soft x-ray MCD 

measurements, the M0 mirror position for X13A operations has 

been centered on the EPW beam fan. This geometry necessarily blocks any output from the MGU, and results in a 50/50 

scheduling split of X13 beamtime between X13A and X13B 

operations.

The new position of the X13A M0 mirror, both horizontally 

and along the beamline, required realigning the entire X13A 

beamline: the X13A SGM monochromator, I0 chamber, 22 Hz 

chopper, and diffractometer endstation. During initial commissioning of the newly rebuilt X13A beamline, it became 

clear that the EPW beam was not quite level, so we requested a vertical orbit correction for X13A. The new orbit bump 

was eventually made permanent, and contributed most of the factor-of-ten increase in intensity measured at the sample 

in the X13A endstation. (The doubled mirror length contributed only a factor of two.) The stability of the new mirror 

mounting system has also resulted in an improvement in stability of the left/right signal ratio. The flux and stability 

improvements combine to provide a significant increase in sensitivity, i.e. the ability to detect small magnetic signals. 

The newly renovated X13A beamline was tested by users during the fall 2004 scheduling cycle.

Principal thanks for the installation of this mirror, including the large amount of lead shielding required around the 

mirror chamber, go to the User Science Division technical group led by Tony Lenhard. In particular, Shu Cheung 

performed most of the mechanical assembly and installation work on this mirror chamber, once the vendor (Advanced 

Design Consulting, Lansing, NY) completed delivery. Thanks also go to the Operations and Engineering Division for 

mechanical survey work and control-room assistance during commissioning, as well as to the Accelerator Division for 

the X13 orbit bump work. —Cecilia Sanchez-Hanke, BNL-NSLS

The new X13A M0 mirror before installation at the beamline. Only 

the bottom flange of the ultra-high vacuum chamber is shown in 

this photograph. The flexible bellows behind the mirror surrounds 

and vacuum-isolates the water-cooling plumbing. The mirror itself 

is gold-coated electroless nickel deposited on glidcop, which is 

explosion-bonded to a stainless steel substrate. The water-cooling 

channels are milled in the stainless steel/glidcop substrate, and then 

a stainless steel plate containing mechanical and plumbing fittings 

is welded to the mirror substrate. The three bellows underneath the 

mirror allow motor-driven adjustments of the mirror in the x and 

z translations and in rho and tilt rotations, while the surrounding 

chamber remains fixed. 
5-12 NSLS ACTIVITY REPORT 

 A Unique Spectrometer for High-Resolution Inelastic X-ray Scattering

A nine-element, two-dimensional crystal array 

analyzer system for inelastic x-ray scattering 

(IXS) has been designed and built at the NSLS. 

Each individual crystal analyzer is aligned with 

an inverse joystick goniometer. The energy 

of the scattered photons is measured with a 

conventional double-circle goniometer mounted 

on a translation stage, which allows the maintenance of the sample, analyzers, and detector 

in a Rowland-circle geometry. The spherically 

bent crystal analyzers play the key role in this 

spectrometer. We chose a diameter of about 10 

cm for a 500 μm thick Si(440) wafer, and bent 

it to radius of 1 m. We realized an adequate 

compromise between energy resolution (1.5 eV) and the solid angle (about 4% with nine analyzer crystals). At a Bragg-angle 

close to backscattering (θ= 88°

), we obtained an energy resolution of 0.5 eV.

The instrument can be used to probe the metal site valence, spin polarized charge density, and local magnetic ordering in 

transition-metal systems. In addition, it can be used to obtain light-element x-ray absorption spectra by the use of inelastic 

scattering with bulk sensitivity without the need for vacuum conditions. The light-element sensitivity utilizing a hard x-ray 

incident beam makes the spectrometer useful for studying in-situ processes. The multi-element analyzer development was 

funded by a National Science Foundation Instrumentation for Materials Research (NSF-IMR) grant.

For more information on applications of this instrument see: Qian, Q., Tyson, T., Savrassov, S., Kao, C., and Croft, M., 

Phys. Rev. B, 68, 014429 (2003). —Trevor Tyson, NJIT

(Top) Picture of the IXS-spectrometer. The nine individual inverse joystick goniometers for 

each analyzer crystal are mounted on a two-circle goniometer, which in turn is mounted on a 

translation stage. The detector mounted on the two theta can move along the two-theta arm 

to stay on the Rowland circle. (Bottom) A close-up picture of the nine-crystal (10 cm each) 

analyzer array. 

 A Renovated X-Ray Wiggler Beamline for Materials Science

The X21 hybrid wiggler x-ray beamline and its endstations are devoted to inelastic x-ray scattering for materials science research. To meet the increasing needs of 

these programs, the beamline optics and endstations have been upgraded.

The first optical component is a new non-dispersive double silicon crystal or 

multilayer monochromator, which contains selectable pairs of silicon crystals or 

multilayer elements that can be chosen in-situ to suit the experiment at hand. 

The first silicon crystal and multilayer element are mounted side-by-side on a 

helium-gas-cooled cryogenic support that suppresses thermal distortions of the 

crystal or multilayer when subjected to the 500 W wiggler beam. 

The monochromatic beam that emanates can be used as is, or can be further 

conditioned by the original high-resolution four-reflection Si(220) monochromator, which remains installed in the beamline, if high energy resolution is 

desired. 

Finally, the beam is then focused and delivered to the appropriate experimental 

setup by one of two bent cylindrical mirrors, each of which is shaped to focus the 

beam into one of the two experimental stations.

The X21 experimental endstations have been rebuilt to accommodate new 

experimental programs that address elastic x-ray scattering studies of materials 

under high magnetic fields, thin films grown in-situ, and materials studied with 

small angle x-ray scattering, with appropriate setups permanently installed in the 

endstations. The renovated beamline and both experimental endstations, including their dedicated instruments, are now in operation.

The new X21 monochromator internal assembly 

contains silicon crystal and multilayer pairs that 

can be selected in-situ via transverse alignment of 

the appropriate pair in the beam path. The first 

pair is mounted on a cryogenic copper support. 

The second silicon crystal and multilayer element 

are mounted on their own motor-driven kinematic 

supports. The entire assembly is mounted on a 

rotary vacuum feedthrough, which is driven by the 

motorized assembly shown behind the mounting 

flange.
 FACILITY REPORT 5-13

 X1A Monochromator and Laser Interferometer Upgrades

The X1A1 beamline received a new monochromator in May 2004. The purpose of 

this monochromator upgrade was to provide for exchangeable gratings with higher 

calculated diffraction efficiency, integrated water-cooling (such as will be required 

for NSLS-II), and improved vacuum performance to minimize carbon contamination. Due to constraints of the beamline length, the optical configuration could 

not be changed; it continues to be a spherical grating with a fixed exit arm and a 

resolving power of about 5000 at 290 eV. The monochromator was specified by 

Steve Hulbert of the NSLS, and manufactured by Physical Science Laboratories. 

It was installed by NSLS personnel during the May shutdown, and the electronic 

interfacing and alignment was done by the Stony Brook X1A group in late May 

and early June. The monochromator offers a significant improvement in ease of 

alignment, and the possibility of extending the operating energy range of X1A1. 

Two of the new gratings (Horiba Jobin-Yvon, Inc., Edison, NJ) are optimized for 

operation near the carbon K-edge (calculated diffraction efficiency 16% at 290 eV) 

and one is optimized for the oxygen K-edge (calculated diffraction efficiency 27% 

at 505 eV). At present it has been used primarily for carbon edge studies, and as 

the vacuum gradually improves we hope to see a reduction in the rate of carbon 

contamination. Thanks to Chi-Chang Kao, Steve Hulbert, Qing-Yi Dong, Gary 

Nintzel, and Dennis Carlson, along with many others from the NSLS, as well as 

Bjorg Larson, Mirna Lerotic, and Sue Wirick from Stony Brook, for their efforts 

with this system.

We are also in the middle of installing a laser interferometer upgrade to the scanning transmission x-ray microscope at X1A2, and then, at a later date, the one at 

X1A1. This will follow impressive developments at the Advanced Light Source by 

David Kilcoyne and others to use laser interferometer information on scanning stage position in a closed-loop feedback 

system to improve position stability in spectromicroscopy. The laser interferometer upgrade is also accompanied by a 

complete redesign of the control electronics and software, which will improve throughput of the microscope. This effort 

has included Holger Fleckenstein, Dan Flickinger, Benjamin Hornberger, and Mirna Lerotic from Stony Brook, and it 

is a key element to NASA-funded research performed by George Flynn of SUNY Plattsburgh in partnership with Stony 

Brook. —Chris Jacobsen, Stony Brook University

The new monochromator at beamline 

X1A1. It will provide for exchangeable 

gratings with higher diffraction efficiency, 

integrated water-cooling, and improved 

vacuum performance to minimize carbon 

contamination. It includes four selectable 

in-situ side-cooled grating holders, and 

provides for micro-radian angular precision 

and repeatability.

The ultrahigh resolution infrared 

spectrometer at beamline U12IR.

 Ultrahigh Resolution Infrared Spectroscopy Moves In at Beamline U12IR

In a collaboration between Stony Brook and UCLA researchers and funded by the 

Defense Advanced Research Projects Agency (DARPA), a new high-resolution infrared 

spectrometer has been acquired for the U12IR beamline. It is hard to miss the long 

vacuum box next to the entrance to the NSLS VUV-IR floor, running approximately 

parallel to the walkway. 

The key component of the instrument is a mirror that is mounted on a high precision 

motion stage and runs inside the box. The exceptionally long range of motion results 

in a high spectral resolution (on the order of 0.001 cm-1); in fact, this Bruker Instruments spectrometer (Bruker IFS-125HR) has the highest possible resolution available 

today. 

The spectrometer will be used to investigate low energy (<1 eV) vibrational and electronic excitations in gases, liquids, and solids. A particularly unique application is the 

study of electron spin resonance (ESR) with infrared light; this becomes possible when 

the light from the spectrometer is fed to the 16 Tesla superconducting magnet at the 

beamline, purchased earlier with support from the National Science Foundation.

—Laszlo Mihaly, Stony Brook University
5-14 NSLS ACTIVITY REPORT 

This is an example of the central region 

of a diffraction pattern recorded at X29. 

One can see that the undulator, the x-ray 

optics, and the detector provide excellent 

sensitivity and resolution. The system will 

work quite well for study of the largest and 

most difficult molecular systems.

The new diffractometer and detector system in the 

X29 x-ray hutch. This device is equipped with a 

high-speed and high-precision crystal axis suitable 

for operation with a robotic specimen changer.

 A New X-ray Undulator Beamline for Macromolecular Crystallography

A new experimental station dedicated to macromolecular crystallography has been 

completed and has commenced operation at beamline X29. The mini-gap in-vacuum 

undulator beamline was built in a collaboration between the BNL Biology Department, 

the Center for Synchrotron Biosciences at Albert Einstein College of Medicine, and the 

NSLS.

The funding for construction and operation comes from the Department of Energy’s 

offices of Basic Energy Sciences and Biological & Environmental Research, and the 

National Institutes of Health (specifically, the National Center for Research Resources, 

the National Institute for Biomedical Imaging and Bioengineering, and the National 

Institute of General Medical Sciences).

The beamline was constructed especially to meet the increasing demand at the NSLS 

for a high-brightness x-ray beam for stateof-the-art macromolecular crystallography 

research, which had previously been served 

by a single beamline, X25.

The x-ray optics for the beamline consists 

of a Si(111) double crystal monochromator, with the first crystal being cryogenically cooled and second crystal bendable to provide sagittal focusing of the 

horizontal beam fan, followed by a vertically focusing mirror. The experimental 

station includes a Crystal Logic diffractometer, an ADSC Q315 CCD x-ray area 

detector, and an Oxford Instruments Cryojet sample conditioner. Already in 

heavy use by conventional means, the focus of this facility will be automation 

and high throughput operation. A fraction of this new beamline’s use will be 

devoted to both “FedEx” (mail-in) crystallography and structural genomics.

High-pressure, high-energy research 

occupies beamlines X17B2 and X17B3. 

 Two New Facilities for High-Pressure Research

The X17 wiggler is the only high-energy x-ray insertion device at the NSLS. Over the years, user demand in high pressure, 

materials, and medical research has increased significantly. In order to meet the needs of these growing user communities, 

two new experimental hutches (X17B2 and X17B3), funded by the NSLS and NSF through COMPRES (Consortium for 

Materials Properties Research in Earth Sciences), were built and commissioned this year. In addition, a beam splitter/filter 

unit was installed in the upstream X17 transport hutch to allow x-ray beams to be 

relayed through the B1, B2, and B3 hutches in a manner that allows experiments to run 

in the three hutches simultaneously. 

The new hutches are dedicated to high-pressure, earth, and mineral science research. 

The X17B2 hutch is utilized by the COMPRES consortium from Stony Brook University, led by Professor Don Weidner, to accommodate a multi-anvil large-volume 

press. White beam is currently used for experiments on this press. A multi-element Ge 

detector is used to collect energy-dispersive x-ray diffraction data. Radiographic imaging 

of the sample in the press can also be taken during all experiments. The development of 

a sagittal-focusing, side-diffracting Laue monochromator and a separate new large-volume press is underway for angle-dispersive diffraction. The X17B3 hutch, downstream 

of X17B2, is utilized by the diamond anvil cell group led by Dr. David Mao (Carnegie 

Institution of Washington, also a member of COMPRES). In this beamline, white 

beam is focused by Kirkpatrick-Baez mirrors onto the sample in the diamond anvil cell. 

Ongoing projects include the commissioning of an in-hutch, sagittal-focusing, 30 keV 

monochromator at X17B1 to provide monochromatic beam to X17B3, and safety and 

interlock approvals to include laser-heating capabilities.

—Zhong Zhong, BNL-NSLS
 FACILITY REPORT 5-15

 X27A: A New Hard X-Ray Microprobe Beamline for Environmental Research

A new and advanced hard x-ray microprobe facility has been installed at NSLS 

bending-magnet beamline X27A. This beamline was constructed to meet the 

increasing demand of environmental molecular science users for state-of-the-art 

x-ray microprobe research, only previously served by the highly productive X26A 

beamline. Operated as a microprobe since 1986 by the University of Chicago’s 

Consortium for Advanced Radiation Sources, the Savannah River Ecology Laboratory, and BNL’s Environmental Sciences Department, X26A’s research mission 

has been to provide a national facility for micro-spectroscopy to the environmental sciences and geosciences community. However, as the only dedicated hard 

x-ray microprobe at the NSLS, beamline X26A has been consistently oversubscribed. X27A will allow the NSLS to meet the demand of this ever increasing 

and vibrant user base. 

The new X27A microprobe facility consists of a newly designed monochromator and slit system, which is installed between the X27A & X27B hutches and 

enables both monochromatic and white-beam modes of operation. Si(111) and 

Si(311) channel-cut crystals are employed, enabling an energy accessible range 

from below 4 keV up to 32 keV. To micro-focus the incoming x-rays, a Kirkpatrick-Baez (K-B) bender system is used to form the required elliptical shapes from 

flat tapered rhodium-coated trapezoids. The x-ray beam is focused to a spot size 

of ~ 5 μm [vertical] x 15 μm [horizontal] at the sample location, which is ~ 9 cm from the end of the helium-filled mirror enclosure box. A 13-element, liquid-nitrogen cooled germanium detector is used to collect the fluorescence photons 

emitted from the sample. Transmission is collected with a photodiode. Spatially resolved information is obtained by 

raster-scanning the sample through the micro-focused x-ray beam with a 

high-resolution motorized sample stage.

Beamline control is VME-based EPICS through the SPEC and IDL (using 

X26A IDL routines) software programs.

The X27A microprobe facility involves a collaboration between the NSLS, 

EnviroSuite, and CEMS. EnviroSuite is a strategic initiative within BNL’s 

Environmental Sciences Department that facilitates environmental molecular 

science research at the NSLS, and CEMS is the Center for Environmental Molecular Science, based at Stony Brook University. The funding for 

construction of the X27A facility, the detector system, and operation comes 

from the Offices of Basic Energy Sciences and Biological & Environmental 

Research within the Department of Energy's Office of Science, and CEMS is 

supported by grants from the National Science Foundation and the Department of Energy. —James Ablett, BNL-NSLS

The new X27A hard x-ray microprobe shown 

within the experimental hutch.

Close-up of the microprobe setup: The K-B 

mirror system is located towards the top center, 

the high-resolution sample stage is towards the 

bottom center, and the 13-element fluorescence 

detector is on the right of the photograph.

Ge 

detector

K-B mirrors

Sample Stage
5-16 NSLS ACTIVITY REPORT 

 A New Micro-Focused Branch is Added to the U5UA Beamline

The U5UA beamline is an intense undulator beamline operating in the 15 to 200 eV 

photon energy range. It can excite valence bands electrons as well as shallow core levels 

from solid surfaces, and is also equipped with a four-reflection circular polarizer that 

operates in the 15 to 70 eV range.

U5UA has been upgraded with a new branch (#2) added downstream from the existing 

branch (#1). The new branch consists of a pair of ellipsoidal mirrors that demagnify 

the U5UA #1 sub-mm-sized beam by a factor of approximately 10, forming a microfocused spot.

The new micro-focused branch is therefore particularly appropriate because it can be 

used as an intense excitation source in LEEM/PEEM experiments. 

Furthermore, even conventional VUV spectroscopy techniques, such as angle-resolved 

photoemission, are currently spot-size limited in their quest for better and better energy 

resolution. 

The U5UA beamline optics are capable of delivering very high photon energy resolution light. For example, a resolving power of 10,000 has been demonstrated at ~30 eV. 

However, in order to match this source ideally to a high-resolution electron spectrometer, a micro-focused light spot is required.

The new branch was constructed to meet the increasing demand of nanoscience users. 

The small spot will be of major importance in microscopy studies, such as LEEM/

PEEM, where combining a small spot size with tunable synchrotron photon energy 

enables VUV spectromicroscopy experiments to be performed. The micro-spot will also 

benefit ultra-high resolution photoemission and emission experiments.

The new branch is now operational and available to users. Presently the performance of 

the new beamline is being characterized, and preliminary results indicate a spot-size of 

approximately 25 microns in diameter at fwhm.

The new micro-focused branch at the 

U5UA undulator beamline meets the 

increasing demand of nanoscience users. 

The small spot will be of major importance 

in microscopy studies. In the figure the 

calculated spot-size is compared with direct 

measurements, obtained by scanning the 

light-beam with a 5 μm pinhole.

Real-time sample characterization is now 

available at beamline X21. 

 A New Facility for Real-Time X-Ray Studies of Materials Processing

Formation of the advanced materials that are at the forefront of science and technology requires increasingly sophisticated 

thin film growth techniques and surface modification regimens. To better understand in real time the atomic-level changes 

occurring during such processing, a new facility is being developed at beamline X21 

– the X-ray Studies of Materials with Analysis in Real Time (XSMART) facility. Funded 

with the National Science Foundation (NSF) Major Research Instrumentation (MRI), 

and Instrumentation for Materials Research (IMR) support to Boston University (K. 

Ludwig and T. Moustakas) and the University of Vermont (R. Headrick), the XSMART 

collaboration also includes C. Eddy of the Naval Research Laboratory. To promote 

flexibility, the x-ray spectrometer is designed so that modest-sized processing/vacuum 

chambers can be rolled onto a base diffractometer system. This design allows multiple 

specialized chambers to be constructed, optimized for processing, and then moved onto 

the diffractometer for x-ray experimentation. Thus, the base diffractometer system will 

be available for scientists in the community to design processing chambers to meet their 

individual needs.

Initially, two UHV chambers have been constructed. First studies with these are focusing on surface evolution during several distinct processes: ion bombardment and plasma 

processing, growth of novel thin films by pulsed laser deposition (PLD), formation of 

ultra-thin silicide films, and growth of III-V nitrides by molecular beam epitaxy (MBE).

—Karl Ludwig, Boston University
 FACILITY REPORT 5-17

User Administration Report

Mary Anne Corwin

USER ADMINISTRATOR

Administrative Services

User Administration provides many services for our new and continuing users. Our primary goals are to facilitate 

site access, process user appointments, ensure safety training compliance, oversee the general user proposal process, 

organize the annual Users’ Meeting, assist the Users’ Executive Committee in its efforts, maintain beamline-specific information, and generate statistical reports. 

Thanks to our applications developer Brian Bindert, the User Administration staff, and more than 30 NSLS staff and users, we proudly announced 

the debut of the new web-based Proposal, Allocation, Safety and Scheduling (PASS) system in May for general user proposals for the fall 2004 

cycle.

PASS provides a single, web-based source for proposal submissions, feasibility and peer review, allocation and 

scheduling of beam time, safety review, and maintenance of beamline information. The proposal review panel 

(PRP) structure has changed and is now more closely associated with the synchrotron technique and field of 

research for the proposed experiment. A new safety measure incorporated into the system requires assignment of a 

lead experimenter during onsite experimental work. 

Priorities for 2005 are to integrate proprietary proposals, provide rapid access to beamtime, and improve scheduling capabilities.

User Statistics

In FY04, 2,299 users from academia, government, industry, and other institutions performed experiments at the 

NSLS. More than a third were first-time users.

During the registration process, users select their primary field of science. In FY04, the majority of users came 

from the materials and life sciences arenas. Slight increases in applied science/engineering and in geosciences/

ecology were noticed between FY03 and 04. At the same time, life sciences and non-specific areas decreased 

slightly. Other areas remained stable.

Education and employment levels vary. Over 44% of users are scientists, faculty members, or other professionals. 

Graduate students account for 36% and post-docs make up 13% of our population. Age levels vary, with 34% in 

the 20-29 age bracket and 33% in the 30-39 age bracket. In FY04, 383 unique academic, government, non-government laboratory, and industrial institutions sent users to the NSLS. Nearly 240 were academic institutions.

Experimental Statistics

During FY04, 1,374 experiments were performed, up from 1,145 in FY03. 

Just over 32% were materials science experiments; life sciences accounted 

for slightly under 32%. Funding comes primarily from the Office of Basic 

Energy Sciences within the DOE Office of Science, the National Science 

Foundation, and the National Institutes of Health.

Paperless Office

A milestone was achieved this year in converting User Administration into 

a paperless office. Over the last three years, as time and resources permitted, 

existing records were scanned. New records are now generated electronically. This accomplishment resulted in an $8K budget savings and eliminated 

the need for 280 cubic feet of office space. We exceeded DOE and BNL’s 
5-18 NSLS ACTIVITY REPORT 

goals in reducing consumption and waste and are at the forefront 

in electronic records retention, significantly facilitating audits. 

Factors that helped us to achieve this goal include the web-based 

development of BNL’s Guest Information System, the End of Run 

Form, and the PASS System.

Conferences & Workshops

Thanks to a tremendous effort by Gretchen Cisco, this year’s Users’ 

Meeting was as administratively successful as the last, with nearly 

400 attendees and eight workshops. Limited funds for meals, 

entertainment, and other unallowable expenses come primarily 

from corporate vendor and sponsor support. To provide up-to-date 

information on allowable and unallowable funds to the Users’ Executive Committee and for simplified maintenance and reporting, 

we entered all financial data into Microsoft Money. Though vendor 

space is very limited, User Administration staff worked diligently to 

accommodate six additional vendors, increasing revenue by $5.6K 

(our special thanks to Liz Flynn).

User Administration also handled the registration process for the 

NSLS-II Workshop in March. In May, we assisted with the coordination of and processed registrations for the CFN Users’ Meeting, 

which occurred back-to-back with the NSLS Users’ Meeting. With 

Liz’s efforts, $30K was secured through vendor contributions to 

cover meals and related expenses.

Badge Scanning for Site Access

Site access policies require that users produce valid BNL identification badges or have active or pending appointments. 

A badge-scanning system notifies the officer at the gate of problems with a user’s appointment or visa status. These 

users are asked to check in at User Administration and work cannot begin until the user has done so. However, though 

approved for site access, some users had difficulty on arrival. Our office was instrumental in providing feedback for 

improvements to several laboratory systems to ensure access. We have seen significant improvements since that time.

Check-In/Check-Out System

To minimize problems getting onsite, users are asked to complete BNL’s check-in/check-out online form in advance. 

User Administration generates daily reports to verify users have arrived, have valid appointments, are in visa status, and 

to input user departure dates. Check-in at User Administration is only necessary when the report indicates a problem 

or the departure date is missing. In FY05, the check-in/check-out system will be upgraded to notify users of expiring 

appointments and visas.

Visas for Foreign Nationals

Foreign national users must possess work-type visas. Users who obtain B2 and WT visas are not permitted to perform 

experiments and are required to return to the port of entry within 24 hours to get corrected documents.Visa lengths 

vary from 90 days to several years. As a convenience, users are issued two-year appointments, sometimes extending 

beyond their visa expiration date, but must provide a new visa each time the documents we have on file expire. Users 

with short-term visas should schedule beam time during the workweek to ensure they will be permitted to work on 

arrival. We urge all foreign national users to bring valid passports, visas, and supporting documents during each visit. 

Several users have had to return home to retrieve their documents before starting their experiment.

Instances of non-compliance resulted from users who were out of visa status and began their experiments without 

checking in at User Administration, after being informed by BNL officers that they needed to do so. To minimize 

NSLS Users by Affiliation FY 2004

OTHER

9%

INDUSTRY

6%

FEDERAL

(non-DOE)

4%

DOE

(non-BNL)

2%

BNL

10% ACADEMIC

69%

NSLS Users by Field of Research FY 2004

24.23%

35.06% 7.74%

5.35%

5.18%

12.44%

10.00%

Chemical Sciences Materials Sciences

Life Sciences Geosciences and Ecology

Applied Science and Engineering Optical/Nuclear/General Physics

None Specified
 FACILITY REPORT 5-19

these problems, User Administration recommended 

modifications to the Guest Information System to inform 

foreign national guests of their expiration dates by email. 

Implementation is tasked for FY05.

In June, DOE issued a new Foreign Visits and Assignments order for which all laboratories must comply. Most 

requirements mimic those previously issued, but BNL is 

required to implement additional requirements in FY05.

Experimental Floor Access

We found instances of safety non-compliance where users 

accessed the experimental floor with expired or no training. To eliminate these problems, as well as non-compliances by foreign nationals, User Administration now 

provides “timed-access” to expire with the first expiration of training, ID badge, passport, or visa status dates. 

Modifications to the PASS system were made to ensure that experimenters are listed on safety approval forms and 

are in compliance. And, the laboratory’s training record database (BTMS) now generates automatic emails to users 

whose training has expired.

On-Site Housing for Foreign Nationals

Last year’s change in housing policies made it impossible for foreign national users with pending appointments 

to make reservations. User Administration worked with BNL Housing to correct a misconception that such users 

had not yet received approval to visit BNL. We have seen significant improvements since that time.

Vehicle Identification

New security policies require all users to obtain vehicle stickers or placards. To eliminate an unnecessary trip to 

Security for our users, User Administration received permission to acquire the stickers and placards in the same 

manner that we obtain identification badges.

Benefits to Compliance

With limited resources, we’re very grateful to our users who help us maintain compliance with DOE directives. By 

eliminating non-compliances, we can focus more on user-related quality-of-life issues. We encourage our users to 

contact User Administration at (631) 344-USER (or nslsuser@bnl.gov) with any additional recommendations to 

eliminate non-compliances or with any questions.

The User Administration Group (from left): Mary Anne Corwin, Liz 

Flynn, Melissa Abramowitz, and Gretchen Cisco.
5-20 NSLS ACTIVITY REPORT 

Safety Report

Bob Casey

ASSOCIATE CHAIR FOR ESH

Organization and Mission

Environmental, Safety, and Health (ESH) performance within the NSLS and at BNL in general remains an important 

issue for all NSLS staff, PRT members, and general users. 

2004 Activities

There is a great emphasis at Brookhaven Lab on reducing the frequency of injuries and incidents, and this emphasis 

resulted in heightened visibility for all matters relating to safety during 2004. So how are we doing at the NSLS?

In many factors we are doing very well.

1. We had no injuries that met recording criteria or resulted in lost or restricted time during 2004. BNL and 

DOE weight this parameter heavily in judging safety performance — we can all take pride in that accomplishment.

2. Radiation exposure remains very low. The total recorded committed dose equivalent to NSLS staff and users 

for 2004 was less than 50 mRem. Fewer than 10 badges for the year had any recordable exposure.

3. Generation of hazardous and industrial wastes continues near all-time lows. Inspections of work sites indicate 

a high degree of compliance with hazardous waste and environmental requirements.

4. Responsiveness to inspection and audit findings was prompt and complete in general. 

5. Compliance with safety and training requirements as evidenced through numerous audits is viewed as high.

These factors indicate a very satisfactory program. However, this year two events involving electrical safety raised 

concerns about that part of our program and have resulted in a considerable emphasis on improving electrical safety 

practices. For example, two significant incidents occurred this year: An NSLS technician received a high-voltage shock 

while working on a component at a beamline, and visiting researchers improperly modified a high-voltage power supply, leaving a shock hazard for subsequent groups. Detailed information on these incidents is available on the NSLS 

website. 

Following Up with Concerns

In 2004, a key issue that emerged is ensuring that all electrical devices requiring lockout prior to maintenance or servicing have been identified. A major effort has been devoted to establishing this 

inventory and clearly labeling these devices. A second major effort has been on 

analyzing the adequacy of our work planning to ensure that hazards are identified 

and controlled prior to the start of work. Both of these efforts will continue to be 

a major focus in 2005. 

Key Work-Planning Points for Electrical Safety for 2005

• Make sure that all work on electrical components is adequately screened for 

hazards by the supervisor or other knowledgeable person before the work 

begins — make no assumptions. If you are not knowledgeable of the equip

ment and its potential hazards, find someone who is.

• All work involving exposed electrically energized surfaces, including troubleshooting measurements, must be planned and conducted in accordance with 

NSLS work planning requirements. In general, working with exposed energized circuits is not allowed unless explicitly authorized by the NSLS Electrical 

Safety Officer and the supervisor through a “working hot” permit.
 FACILITY REPORT 5-21

NSLS User Training 

Programs

Eva Rothman

TRAINING COORDINATOR

NSLS user safety training has been 

available on the web for some time. 

Now, the vast majority of our users take 

advantage of this convenience to complete training before arrival. This year 

saw some further enhancements. The 

User Safety Module was converted from 

simple web pages to the format used 

by the other BNL web courses. During 

this conversion process, the course was 

edited page-by-page and pared down 

by about 30%, resulting in, hopefully, a 

more concise and memorable presentation. The new format allows the quiz to 

be automatically graded and the results 

returned to the trainee immediately. 

The safety module used for scientific 

and technical staff was also converted to 

this format.

The NSLS has discontinued using its 

own version of GERT, or General Employee Radiological Training, and has 

adopted the BNL version. Historically, 

GERT had only been available as a 

weekly classroom session that was inadequate for a 24-7 facility with aroundthe-clock arrivals. The NSLS used a 

videotape presentation of GERT as 

part of the safety training administered 

in the User Office and Control Room. 

Later, we implemented a web version, 

which, because we wanted to keep it 

short, was only applicable to the NSLS 

(not transferable to other BNL departments or other DOE facilities). In early 

2004, BNL introduced GERT as a web 

course and the NSLS is now able to 

offer that to its users. The NSLS continues to have a reciprocal relationship 

with other DOE labs regarding GERT 

and now the GERT training obtained at 

BNL should be fully accepted by other 

DOE facilities.

• Unless specifically authorized by the responsible supervisor and the 

NSLS Electrical Safety Officer under the conditions of a “working 

hot” permit, all work that involves exposed electrical conductors 

less than 50 volts must be initiated by securing the electrical power 

source in accordance with the BNL lock-out/tag-out procedure.

• Proper protective clothing and gloves must be worn by all workers 

servicing or trouble-shooting electrical equipment until it has been 

verified that all electrical voltages have been secured and the equip

ment is in a zero-energy state.

Adherence to these procedures will permit work with electrical components to be safely performed. 

Conclusion

The NSLS Safety Program is based on the principles of safety that the 

U.S. Department of Energy refers to as Integrated Safety Management (ISM). The intent of this program is to ensure that all work 

is effectively performed by trained and qualified personnel and that 

hazards associated with the work have been fully identified and properly controlled. These concepts are embodied in the safety program 

requirements established for all users and staff. 

We all take justifiable pride in the world-class research that is performed at the NSLS. We need a sharp focus on working safely and 

taking steps to ensure that our research programs fully capture the 

requirements of the NSLS safety program and the essence of ISM. It 

is clear that world-class research will not proceed without world-class 

safety.
5-22 NSLS ACTIVITY REPORT 

Building Administration Report

Gerry Van Derlaske

NSLS BUILDING MANAGER

Facing new safety initiatives, curtailed budgets, and a new emphasis on adhering to National Fire Protection Association electrical safety programs, the NSLS continued to be a vibrant beehive of activity in 2004. Scientists, technicians, support staff, and in-house service personnel worked together to establish a safe and healthy work environment 

for scientific research. Beamline X29 was fully commissioned and began data-taking runs, overhead projectors were 

installed in select conference rooms, maintenance programs in conjunction with the BNL Plant Engineering Division 

were undertaken, and several in-house workshops were held. These factors all contributed to another very active and 

productive year at the NSLS.

Safety

First and foremost on staff and users’ minds these days is performing everyday duties in a manner that promotes a 

culture of safety and a safe working environment at the NSLS. Seasoned subject matter experts (SMEs) are available to 

answer questions relating to all aspects of industrial safety. Combined with a fully staffed Environment, Safety, Health, 

& Quality (ESH&Q) Division, these SMEs are conveniently located on the experimental floor, adjacent to the main 

control room. No one should feel that answers on how to proceed safely are far from hand. Stop-work orders may be 

invoked when observing operations that may place personnel in imminent danger. Numerous review avenues have 

been established that assist personnel with work being planned and carried out, such as hazard analyses, which are 

performed and reviewed by the appropriate SME. Everyone should take advantage of these services whenever a task is 

planned that may involve hazards, know or yet unknown.

During the past year, after a site-wide visit by the Occupational Safety and Health Administration (OSHA) inspection 

team in October 2003, the operative words for work performance within the laboratory continued to be “safety” and 

“compliance.” Various NSLS and BNL support, safety, and technical groups corrected many findings of the various 

OSHA inspection teams. A small percentage of the findings were grouped with similar findings from other laboratory 

departments/divisions and will be tracked for future closeout by the BNL Plant Engineering Division. Tier 1 facility and beamline inspections by NSLS ESH&Q staff will continue to search for other possible safety concerns, and 

will record and forward these findings to the appropriate individuals or groups for remediation. Once notification is 

received, a data-based system will track the findings, which will either be repaired in a timely fashion or corrected immediately. After mitigation, the Tier 1 contact is notified to close out the finding.

Simultaneously, we have reacted to other Lab-wide directives as they surfaced. 

One area of concern revolved around material-handling equipment and hoisting and lifting equipment. The NSLS point of contact for such issues is Bob 

Kiss. A new training program that Bob has been instrumental in developing 

is tailored to fit the requirements of the type and frequency of lifts performed 

within the NSLS facility. As a result of this directive, all cranes have been assigned a padlock, with limited key distribution to those individuals deemed 

“responsible” for the operations of a particular crane or overhead-lifting device. 

Feel free to contact Bob if you have any questions pertaining to lifts, hoists, 

cranes, and all of the “below the hook” lifting devices that you may encounter. An ongoing effort to capture all such devices in our inventory will assure 

that the proper inspections take place within the yearly time frame. If, at your 

workplace, you have any below-the-hook lifting devices, such as slings, shackles, strong backs, etc., that are not inspected on a yearly basis, please have Bob 

inspect these items. Any lifting device, such as portable lifters/engine hoists, 

hoists, chain falls, slings, shackles, etc., brought to BNL and used on-site must 

be inspected prior to use. This includes new and used items, even if the item 

will only be used once. All inspected items will carry a color-coded identification tag, alerting the user that a proper inspection took place and that the item 
 FACILITY REPORT 5-23

has been recorded in our inventory system. Of course, each below-the-hook item must be checked by the end user 

each time it is used, to assure that no damage has occurred to the device while in storage, or by the previous user.

A new worker qualification and training list for users and beamline staff was implemented and presented to the 

user community. The list outlines tasks considered to be “skill of the worker.” Tasks were divided into three levels, 

with the rigor of training and enhanced work planning corresponding to the difficulty of the assigned tasks or 

systems being modified or impacted. In all cases, if the scope of the task has changed or new hazards have been 

introduced, stop, reassess, and get qualified assistance before returning to complete the task.

A new automated external defibrillator (AED) has been installed in the main lobby of Building 725 and another 

has been installed in Building 729 near the west doorway. A number of NSLS personnel have taken BNL’s training 

course in CPR and AED use. Additional AEDs will be purchased and installed during FY05. 

Maintenance/Upgrades

In a continuing program, the BNL Plant Engineering Division once more provided both material and manpower 

resources to address various roof leaks detected in areas above the experimental floor. Areas that received considerable attention were sections above the VUV ring, the vehicle ramp leading to the center of the x-ray ring, and the 

area above beamline X29. The proof testing of the repairs will be how well they survive the frost-thaw cycles of the 

winter season.

The main lobby stairwell leading to the User Administration reception area received a new coat of paint. New 

labeling schemes in the stairwell help direct visitors to the Chairman’s office and conference rooms. New overhead 

digital projectors were installed in both the Seminar Room and Conference Room A.

A full inspection of the facility revealed some concerns with the interior seals and gaskets on several windows, 

installed during later phases of building construction. Those windows deemed to be in suspect condition were 

removed and replaced. The driver for this inspection was a pane of glass that separated itself from the vacuum 

seal on one of the double-pane insulating windows. When a vacuum seal deteriorates, moisture seeps between the 

panes of glass, causing the glue to weaken. Inspections will continue to look for windows with voided seals, and 

these units will be scheduled for replacement.

The annual stripping and waxing of the experimental floor was 

completed in mid-December. This coordinated effort requires much 

planning and logistical deployment of several custodial crews, working 

under the guidance of Plant Engineering Custodial Services supervisors and the NSLS alternate building manager to complete the tasks 

with as minimal an impact on beamline operations as possible. Two 

custodial supervisors, a lead custodian, and a crew of nearly 20 custodians refinished the beamline areas, hallways, and perimeter walkways 

on both the x-ray and VUV experimental floors.

In late December, the south elevator in the main lobby had to be shut 

down to repair leaky packing on the main lift cylinder. Concurrently, 

the flow valve, which allows the oil in the cylinder to return to the 

reservoir, was replaced. In the future, the Lab plans to fund a complete 

overhaul of the electrical drive components of this elevator, as the present logic system is driven by an outdated method using solenoids and 

relays. Installing solid state, up-to-date logic drive components will 

occur as funding becomes available. 

Bicycles

The BNL Quality of Life Office has turned over bicycle management 

to department building managers. The NSLS maintains a fleet of seven 

NSLS Administration Group bicycles that may be loaned out for both long and short terms. Once 
5-24 NSLS ACTIVITY REPORT

signed out, the “owner” is responsible for maintaining the bicycle, keeping it protected from theft, and returning the 

bike in good condition at the end of the term. It is necessary to follow all applicable road-use rules when biking onand off-site, and wearing a helmet is required when biking on-site.

Going Wireless

The x-ray and VUV floors now boast wireless capabilities, running at broadband speeds, with coverage extending to all 

areas within points of normal user access. Common areas, such as the library, conference rooms, and the main lobby 

are covered. This wireless connection is outside the BNL firewall, therefore, one would need to use virtual private network (VPN) software to enter the BNL intranet. Additional future planning includes installing wireless access points 

inside the firewall.

User Moves

A concerted effort between Plant Engineering, NSLS, Exxon, and the New York Structural Biology Center was undertaken during the summer, culminating in the relocation of machine tools and user shop equipment to Building 

801. As a result, dedicated interior building space was allocated to the last user staff members being housed in portable 

structures in the NSLS trailer park, located east of Building 727. 

Holiday Merrymaking

In our year-end event to celebrate the holiday season, the Budget group hosted a festive party. They transformed the 

main lobby with hanging snowflakes and created intimate bistro-style seating on the mezzanine overlooking the lobby. 

The decorations brightened the spirits of all in attendance. After feasting on a potluck buffet and tables of desserts, 

a staff “talent” show was held in the Seminar Room, hosted by Al “Donnie Osmond” Boerner, with accompaniment 

from Al Almasy on keyboard. There were singers, musical performers, a “hunters and reindeers” act, a tale of budget 

woes parodied to The Night Before Christmas, and an amusing show by the “Don Ho Hula Guys.” All in all, it was a 

day to remember.

Conclusion

The multi-faceted NSLS facility, where each year thousands of users carry out their research, is alive and well. With 

assistance from many talented, behind-the-scene individuals, who work so diligently to make our time here a bit more 

pleasant, my thanks. We continue to pace ourselves, but we are moving forward steadily. There is brightness on the 

horizon, as the future holds plans for larger and more powerful tools to explore the mysteries of our surroundings.
Facts & Figures
FACTS & FIGURES 6-3

Facility Facts & Figures

The National Synchrotron Light Source (NSLS) is a national user research facility funded by the U.S. 

Department of Energy’s Offi ce of Basic Energy Science. The NSLS operates two electron storage rings: an x-ray 

ring (2.8 GeV, 280 mA) and a vacuum ultraviolet (VUV) ring (800 meV, 1.0 A), which provide intense light 

spanning the electromagnet spectrum from the infrared through x-rays. The properties of this light, and the 

specially designed experimental stations, called beamlines, allow scientists in many fi elds of research to perform 

experiments not otherwise possible at their own laboratories.

Over 2,200 scientists representing more than 350 institutions, more than 50 of them corporations, come to 

Brookhaven National Laboratory annually to conduct research at the NSLS. The facility operates seven days a 

week, 24 hours a day throughout the year, except during periods of maintenance and studies.

As a national user facility, the NSLS does not charge for its beamtime, providing that the research results are 

published in the open literature. Proprietary research is conducted on a full cost recovery basis.

There are two ways to obtain beamtime at the NSLS: either as a General User or as a member of a Participating Research Team (PRT). General Users are independent investigators interested in using the NSLS for their 

research. Access is gained through a peer-reviewed proposal system. All operational beamlines at the NSLS 

reserve at least 25% of their available beamtime for General Users. PRTs are groups of researchers with related 

interests from one or more institutions. Membership in a PRT is open to all members of the scientifi c community who can contribute signifi cantly to the program of the PRT, (i.e., funding, contribution of equipment, 

scientifi c program, design and engineering, operations manpower, etc).

The NSLS currently has 54 x-ray and 16 VUV-IR operational beamlines for performing a wide range of experiments. The following pages list the operational beamlines at the NSLS and their unique characteristics. 

BEAMLINE GUIDE

TECHNIQUE DESCRIPTION TECHNIQUE DESCRIPTION TECHNIQUE DESCRIPTION

ARPES

UV PHOTOELECTRON SPECTROSCOPY, 

ANGLE-RESOLVED

DAFS

X-RAY DIFFRACTION ANOMALOUS FINE

STRUCTURE

DEI 

DIFFRACTION-ENHANCED IMAGING

EXAFS

X-RAY ABSORPTION SPECTROSCOPY, 

EXTENDED FINE STRUCTURE

IRMS

INFRARED MICROSPECTROSCOPY

MAD

MULTI-WAVELENGTH ANOMOLOUS

DISPERSION

MCD

MAGNETIC CIRCULAR DICHROISM

NEXAFS

NEAR EDGE X-RAY ABSORPTION

SPECTROSCOPY

SAXS

SMALL ANGLE X-RAY SCATTERING

SPARPES

UV PHOTOELECTRON SPECTROSCOPY, 

SPIN- AND ANGLE-RESOLVED

STXM

SCANNING TRANSMISSION X-RAY

MICROSCOPY

UPS

UV PHOTOELECTRON SPECTROSCOPY

UV-CD

ULTRAVIOLET CIRCULAR DICHROISM

WAXD

WIDE-ANGLE X-RAY DIFFRACTION

WAXS

WIDE-ANGLE X-RAY SCATTERING

XAFS

X-RAY ABSORPTION SPECTROSCOPY, FINE STRUCTURE

XANES

X-RAY ABSORPTION SPECTROSCOPY, NEAR EDGE STRUCTURE

XAS

X-RAY ABSORPTION

SPECTROSCOPY

XPS

X-RAY PHOTOELECTRON

SPECTROSCOPY

XRD

X-RAY DIFFRACTION

XSW

X-RAY STANDING WAVES
6-4 NSLS ACTIVITY REPORT 

BEAMLINE SOURCE TYPE OF RESEARCH ENERGY RANGE ORGANIZATION

U1A Bend XAS

XAFS

NEXAFS

XANES

270-900 eV ExxonMobil Research and Engineering Co.

U2A Bend IRMS

High pressure research

IR spectroscopy

30-8000 cm-1 Carnegie Institution of Washington

U2B Bend IRMS

IR spectroscopy

50-4000 cm-1 Albert Einstein College of Medicine

U3C Bend XPS 50-1000 eV Bechtel Nevada

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

Sandia National Laboratory

U4A Bend UPS 10-250 eV Army Research Laboratory

Boston University

BNL-NSLS

North Carolina State University

Rutgers University

University of North Carolina

U4B Bend X-ray scattering, resonant

MCD

UPS

X-ray fluorescence spectroscopy

XPS

20-1200 eV BNL-NSLS

Montana State University

U4IR Bend IRMS 50-700 cm-1 BNL-Chemistry

BNL-NSLS

U5UA Insertion

Device

Magnetospectroscopy

UPS

ARPES

SPARPES

15-150 eV BNL-NSLS

U7A Bend NEXAFS

XANES

XPS

180-1200 eV BNL-Chemistry

BNL-Physics

Dow Chemical Company

National Institute of Standards & Technology

Rutgers University

Texas A&M University

University of Michigan

U9B Bend UV-CD

UV fluorescence spectroscopy

0.8 - 8.0 eV BNL-Biology

BNL-NSLS

U10A Bend IR spectroscopy 30-20000 cm-1 BNL-NSLS

BNL-Physics

U10B Bend IRMS

IR spectroscopy

500-4000 cm-1 BNL-NSLS

U11 Bend UV photoabsorption spectroscopy

UPS

UV photoionization spectroscopy

3-30 eV BNL-Biology

BNL-NSLS

U12A Bend XAS

XPS

100-800 eV BNL-NSLS

Oak Ridge National Laboratory

U12IR Bend IR spectroscopy

THz / millimeter wave spectroscopy

Time-resolved spectroscopy

6-600 cm-1 BNL-NSLS

Stony Brook University

University of Florida

U13UB Insertion

Device

UPS

ARPES

3-30 eV Boston University

BNL-NSLS

BNL-Physics
FACTS & FIGURES 6-5

BEAMLINE SOURCE TYPE OF RESEARCH ENERGY RANGE ORGANIZATION

X1A1 Insertion

Device

STXM .25-.50 keV BNL-Environmental Science

BNL-NSLS

ExxonMobil Research and Engineering Co.

SUNY @ Plattsburgh

Stony Brook University

University of Texas @ Houston

X1A2 Insertion

Device

STXM .25-1 keV Stony Brook University

X1B Insertion

Device

X-ray scattering, coherent

XAS

X-ray fluorescence spectroscopy

XPS

.2-1.6 keV Boston University

BNL-NSLS

University of Groningen

X2B Bend X-ray microtomography 8-35 keV ExxonMobil Research and Engineering Co.

X3B1 Bend XRD, powder 6-30 keV Stony Brook University

X4A Bend MAD

Macromolecular crystallography

3.5-20 keV 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 for Cancer Research

Wadsworth Center

X4C Bend MAD

Macromolecular crystallography

7-20 keV 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 for Cancer Research

Wadsworth Center

X5A Bend Laser backscattering 150-420 MeV BNL-Physics

Forschungszentrum Juelich (KFA)

James Madison University

Norfolk State University

Ohio University

University of Paris

University of Rome II

University of South Carolina

University of Virginia

Virginia Polytechnic Institute and State University

X6A Bend MAD

Macromolecular crystallography

6.0-23 keV BNL-NSLS

National Institutes of Health

X6B Bend MAD

Macromolecular crystallography

7-19 keV BNL-NSLS

X7A Bend XRD, powder 5-45 keV BNL-Physics

ChevronTexaco Energy Research and Technology Co.

Ohio State University

Stony Brook University

University of Birmingham

University of California @ Santa Barbara

University of Pennsylvania

X7B Bend XRD, single crystal

XRD, time resolved

WAXD

WAXS

5-21 keV BNL-Chemistry
6-6 NSLS ACTIVITY REPORT 

BEAMLINE SOURCE TYPE OF RESEARCH ENERGY RANGE ORGANIZATION

X8A Bend Metrology 1.0-5.9 keV Bechtel Nevada

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

Sandia National Laboratory

X8C Bend MAD

Macromolecular crystallography

5-19 keV Biogen Incorporated

BNL-Biology

Hoffmann-La Roche

National Research Council of Canada

X9A Bend MAD

Macromolecular crystallography

5-15 keV Albert Einstein College of Medicine

Rockefeller University

Sloan-Kettering Institute for Cancer Research

X9B Bend XAS

EXAFS

XAFS

NEXAFS

XANES

5-15 keV Albert Einstein College of Medicine

X10A Bend XRD, powder

XRD, time resolved

WAXD

X-ray reflectivity

SAXS

WAXS

6-15.2 keV ExxonMobil Research and Engineering Co.

X10B Bend XRD, powder

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

14 keV ExxonMobil Research and Engineering Co.

X10C Bend XAS

EXAFS

XAFS

NEXAFS

XANES

4-24 keV ExxonMobil Research and Engineering Co.

X11A Bend DAFS

XAS

EXAFS

XAFS

NEXAFS

XANES

4.5-35 keV BNL-Environmental Science

Canadian Light Source

Hunter College

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Northeastern University

Paul Scherrer Institute

U.S. Environmental Protection Agency

Virginia Union University

X11B Bend DAFS

XAS

EXAFS

XAFS

NEXAFS

XANES

5.0-23 keV BNL-Environmental Science

Canadian Light Source

Hunter College

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Northeastern University

Paul Scherrer Institute

U.S. Environmental Protection Agency

University of Connecticut

Virginia Union University

X12B Bend MAD

Macromolecular crystallography

5-20 keV BNL-Biology

X12C Bend MAD

Macromolecular crystallography

5.5-20.0 keV BNL-Biology

X13A Insertion

Device

X-ray scattering, resonant

MCD

Magnetospectroscopy

.2-1.8 keV BNL-NSLS
FACTS & FIGURES 6-7

BEAMLINE SOURCE TYPE OF RESEARCH ENERGY RANGE ORGANIZATION

X13B Insertion

Device

Microdiffraction Imaging 4-16 KeV BNL-NSLS

X14A Bend MAD

XRD, powder

XRD, single crystal

XRD, time resolved

WAXD

X-ray reflectivity

5-26 keV Oak Ridge National Laboratory

Tennessee Technological University

University of Tennessee

X15A Bend XSW

DEI

3-25keV XSW

10-60keV DEI

Argonne National Laboratory

BNL-NSLS

Canadian Light Source

Illinois Institute of Technology

North Carolina State University

Northwestern University

University of North Carolina

University of Saskatchewan

X15B Bend XAS

EXAFS

XAFS

NEXAFS

XANES

0.8-15 keV BNL-Environmental Sceinces

Lucent Technologies, Inc.

Stony Brook University

Temple University

University of Texas @ Austin

X16C Bend XRD, powder

XAS

XAFS

4.5-25 keV BNL-NSLS

Yeshiva University

X17B1 Insertion

Device

XRD, powder White Beam

55-80 keV

BNL-Medical

BNL-NSLS

X17B2 Insertion

Device

XRD, powder White Beam

55-80 keV

Stony Brook University

X17B3 Insertion

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV BNL-NSLS

Carnegie Institution of Washington

X17C Insertion

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV Carnegie Institution of Washington

Lawrence Livermore National Laboratory

Naval Research Laboratory (NRL)

University of Chicago

X18A Bend XRD, powder

XRD, single crystal

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

4-19 keV BNL-Department of Materials Sciences

BNL-NSLS

General Electric

Indiana University @ Indianapolis

Pennsylvania State University

Purdue University

University of Maryland

University of Missouri @ Columbia

X18B Bend XAS

EXAFS

XAFS

NEXAFS

XANES

5.7-40 keV BNL-Chemistry

BNL-NSLS

General Electric

Natural Resources Canada

North Carolina State University

Rutgers University

UOP

University of Kentucky

X19A Bend XAS

EXAFS

XAFS

NEXAFS

XANES

2.1-17 keV BNL-NSLS

BNL-Chemistry Department

General Electric

Natural Resources Canada

North Carolina State University

Rutgers University

UOP

University of Kentucky
6-8 NSLS ACTIVITY REPORT 

BEAMLINE SOURCE TYPE OF RESEARCH ENERGY RANGE ORGANIZATION

X19C Bend XRD, surface

X-ray topography

X-ray reflectivity

X-ray scattering, liquid

X-ray scattering, surface

6-17 keV Army Research Laboratory

Carnegie Mellon University

Dartmouth College

Johns Hopkins University

Kansas State University

National Aeronautics and Space Admin. (NASA)

Stony Brook University

University of Chicago

University of Illinois @ Chicago

University of Wisconsin

X20A Bend XRD, single crystal

XRD, surface

Microdiffraction Imaging

X-ray reflectivity

X-ray scattering, surface

4.5-13 keV IBM Research Division

X20B Bend XRD, single crystal

XRD, surface

X-ray reflectivity

X-ray scattering, surface

17.4 keV IBM Research Division

X20C Bend XRD, single crystal

XRD, surface

XRD, time resolved

X-ray reflectivity

X-ray scattering, surface

4-11 keV IBM Research Division

X21 Insertion

Device

XRD, single crystal

X-ray scattering, magnetic

X-ray scattering, resonant

SAXS

5-15 keV BNL-NSLS

X22A Bend XRD, single crystal

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

10 keV, 32 keV BNL-Environmental Science

BNL-Physics

Rutgers University

University of Maryland

X22B Bend XRD, surface

X-ray scattering, liquid

X-ray scattering, surface

6.5-10 keV BNL-Physics

Harvard University

Rutgers University

X22C Bend XRD, single crystal

XRD, surface

X-ray reflectivity

X-ray scattering, magnetic

X-ray scattering, surface

3-12 keV BNL-Physics

Rutgers University

University of Maryland

X23A2 Bend XRD, powder

DAFS

XAS

EXAFS

XAFS

NEXAFS

XANES

4.7-30 keV National Institute of Standards & Technology
FACTS & FIGURES 6-9

BEAMLINE SOURCE TYPE OF RESEARCH ENERGY RANGE ORGANIZATION

X23B Bend XRD, powder

XAS

EXAFS

XAFS

NEXAFS

XANES

3-10.5 keV BNL-Environmental Science

Canadian Light Source

Hunter College

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Northeastern University

Paul Scherrer Institute

U.S. Environmental Protection Agency

Virginia Union University

X24A Bend XSW

Auger spectroscopy

EXAFS

X-ray fluorescence spectroscopy

XPS

1.8-5 keV National Institute of Standards & Technology

X24C Bend UV photoabsorption spectroscopy

XAS

.006-1.8 keV Naval Research Laboratory (NRL)

X25 Insertion

Device

MAD

Macromolecular crystallography

3-28 keV BNL-Biology

BNL-NSLS

X26A Bend Microdiffraction Imaging

X-ray microprobe

3-30 keV BNL-Environmental Science

University of Chicago

University of Georgia

X26C Bend MAD

Macromolecular crystallography

5-20 keV BNL-Biology

Cold Spring Harbor Laboratory

Stony Brook University

X27C Bend XRD, time resolved

WAXD

SAXS

WAXS

9 keV Basell USA, Inc. ( formerly Montell)

National Institute of Standards & Technology

National Institutes of Health

Naval Surface Warfare Center

New Jersey Institute of Technology

Stony Brook University

U.S. Air Force

X28C Bend X-ray footprinting White Beam Albert Einstein College of Medicine

X29A Insertion

Device

MAD

Macromolecular crystallography

6-15 keV Albert Einstein College of Medicine

BNL-Biology
6-10 NSLS ACTIVITY REPORT 

NSLS LINAC PARAMETERS AS OF DECEMBER 2004

 Electron Gun Injection Energy 100 keV

 Linac Final Energy 120 MeV

 Number of Accelerating Sections 3

 Number of Klystrons 3

 Linac Frequency 2856 MHz

 Horizontal Emittance into Booster (εx) 7.6 x 10-1 m-rad

 

NSLS BOOSTER PARAMETERS

 Booster Injection Energy 120 MeV

 Booster Extraction Energy 750 MeV

 Circumference 28.35 m

 Number of Superperiods (Ns

) 4

 Dipole Bend Radius (ρ) 1.91 m

 Nominal Tunes (νx,νy) 2.42, 1.37

 Betatron Function (βx,βy) 8.63 to 1.01, 5.26 to 1.73 m

 Dispersion Function (ηx,η′x) 1.21 to 0.41 m

 Momentum Compaction (α) 0.106

 RF Frequency (frf) 52.88 MHz

 RF Peak Voltage (Vrf) 25 keV

 Horizontal Acceptance 1.66 x 10-4 m-rad

 Vertical Acceptance 6.11 x 10-5 m-rad

 Momentum Acceptance ±0.0025

 Horizontal Emittance at Extraction (εx) 7.6 x 10-7 to 1.0 x 10-7 m-rad

 Energy Spread at Extraction (σE/E) 1.4 x 10-4

 Bunch Length at Extraction 110 mm

BOOSTER MAGNETIC ELEMENTS (FIELDS AT 750 MEV)

 Name Type Quantity B (kG) B’ (kG/m) B” (kG/m) Effective Length (m)

 BB Dipole 8 13.099 -7.97 -125 1.5

 Q1 Quadrupole 4 68.82 0.3

 Q2 Quadrupole 4 93.60 0.3

 SF Sextupole 4 1223.7 0.2
FACTS & FIGURES 6-11

VUV STORAGE RING PARAMETERS AS OF DECEMBER 2004

 Stored Electron Beam Energy 0.808 GeV

 Injected Current 1.0 amp

 Lifetime @ 200 mA unstretched (stretched) ~6 (9.8) hr

 Circumference 51.0 meters

PHOTON CRITICAL WAVELENGTH (ENERGY)

 Dipole Source 1.41 T λc

(Ec) 19.9 Å (622 eV)

LATTICE STRUCTURE (CHASMAN-GREEN) SEPARATED FUNCTION, QUAD DOUBLETS

 Number of Superperiods (Ns) 4

 8 Bending Magnets (1.5 meters long each)

 Magnet Complement 24 Quadrupole (0.3 meters long each)

 12 Sextupole in two families (0.20 meters long each) 

 

STORAGE RING CHARACTERISTICS

 Number of Dipole Ports 18

 Number of Insertion Device Straight Sections 2

 Maximum Length of Insertion Devices 2.25 meters

 Dipole Bend Radius 1.91 meters

 Radiated Bending Magnet Power (I= 1A) 20.4 kW

 Power per Horizontal Milliradian (I= 1A) 3.2 W

 RF Frequency (frf) 52.887 MHz

 Electron Orbital Period 170.2 nanoseconds

Number of RF Buckets 9

 Typical Bunch Mode (filled buckets) 7

 Damping Times τx=τy= 13 msec; τε = 7 msec

 Nominal Tunes (νx,νy) 3.14, 1.26

 Momentum Compaction 0.0235

 RF Peak Voltage with 52 MHz (with 211 MHz) (Vrf) 80 keV (20 keV)

 Design RF Power with 52 MHz (with 211 MHz) 50 kW (6 KW)

 Synchrotron Tune (νs) 0.0018

 Natural Energy Spread [Ib< 20 mA] (σE/E) 5.0 x 10-4

Natural Bunch Length[Ib< 20 mA]52 MHZ(211 MHZ)(2σ) 9.7 mm (360 mm)

 Horizontal Damped Emittance (εx) 1.6 x 10-7 m-rad

 Vertical Damped Emittance (εy

) 3.5 x 10-10 m-rad (4 x 10-9 in normal ops.)*

{

INSERTION DEVICE PARAMETERS

 Betatron Function (βx,βy) 11.1 m, 5.84 m

 Source Size (σx,σy) 1240 μm, >45 μm (220 μm in normal ops.)*

 Source Divergence (σ′x, σ′y) 112 μrad, >7.7 μrad (22 μrad in normal ops.)*

 Betatron Function (βx,βy) 1.18 to 2.25 m, 10.26 to 14.21 m

 Dispersion Function (ηx,η′x) 0.500 to 0.062 m, 0.743 to 0.093 m

 αx,y = -β’ x,y/2 -0.046 to 1.087, 3.18 to -0.96

 γx,y =(1 +α2

x,y)/βx,y 0.738 to 0.970 m-1, 1.083 to 0.135 m-1

 Source Size (σx,σy) 536 to 568 μm, >60 to >70 μm (170-200 μm in normal ops.)*

 Source Divergence (σ′x,σ′y) 686 to 373 μrad, 19.5 to 6.9 μrad (55-20 μrad in normal ops.)*

ARC SOURCE PARAMETERS
6-12 NSLS ACTIVITY REPORT 

X-RAY STORAGE RING PARAMETERS AS OF DECEMBER 2004

 Stored Electron Beam Energy 2.800 GeV

 Injected Current 0.3 A

 Lifetime ~20 hours

 Circumference 170.1 meters

PHOTON CRITICAL WAVELENGTH (ENERGY)

 Dipole Source 1.36 T λc

(Ec) 1.75 Å (7.1 keV)

 Wiggler Source 5.0 T λc(Ec) 0.48 Å (26.1 keV)

LATTICE STRUCTURE (CHASMAN-GREEN) SEPARATED FUNCTION, QUAD DOUBLETS

 Number of Superperiods (Ns) 8

 16 Bending (2.7 meters long each)

 Magnet Complement 40 Quadrupole A,C and D type (0.45 meters each)

 16 Quadrupole B type (0.8 meters long each)

 32 Sextupole in two families (0.20 meters long each)

STORAGE RING CHARACTERISTICS 

 Number of Dipole Ports 30

 Number of Insertion Device Straight Sections 6

 Maximum Length of Insertion Devices 4.50 meters

 Dipole Bend Radius 6.875 meters

 Radiated Bending Magnet Power (1=0.25A) 198 kW

 Power per Horizontal Milliradian (1=0.25A) 32 W

 RF Frequency (frf) 52.88 MHz

 Electron Orbital Period 567.2 nanoseconds

Number of RF Buckets 30

 Typical Bunch Mode (filled buckets) 25

 Damping Times τx=τy= 4 msec; τε = 2 msec

 Nominal Tunes (νx,νy) 9.8, 5.7

 Momentum Compaction 4.1 x 10-3

 RF Peak Voltage (Vrf) 1120 keV

 Design RF Power 450 kW 

 Synchrotron Tune (νs) 0.0023

 Natural Energy Spread (σE/E) 9.2 x 10-4

 Natural Bunch Length (2σ) 87 mm 

 Horizontal Damped Emittance (εx

) 7.5 x 10-8 m-rad

 Vertical Damped Emittance (εy) 1.5 x 10-10 m-rad 

{

INSERTION DEVICE PARAMETERS

 Betatron Function (βx, βy) 1.60 m, 0.35 m

 Source Size (σx,σy) 300 μm, 6 μm 

 Source Divergence (σx

′, σy′) 260 μrad, 35 μrad

ARC SOURCE PARAMETERS

 Betatron Function (βx,βy) 1.0 to 3.8 m, 7.9 to 26.5 m

 Dispersion Function (ηx,η′x) 0.47 to -0.11, -0.39 to 0.22

 αx,y = -β’ x,y/2 -0.49 to 1.62, -3.4 to 4.5

 γx,y =(1 +α2

x,y)/βx,y 0.952 to 0.962 m-1, 0.81 to 0.52 m-1

 Source Size (σx,σy) 371 to 612 μm, 27 to 53 μm

 Source Divergence (σx

′,σy′) 476 to 324 μrad, 9 to 7 μrad
FACTS & FIGURES 6-13

FISCAL YEAR 2004

Note: Delivered hours are only those 

accumulated during scheduled operations. Unscheduled operations do not 

contribute to this total.

 

October 605 99.5% 115.0% 561 92.3% 105.9%

November 499 99.0% 114.0% 403 91.1% 110.3%

December 0 - - 0 - -

January 409 97.7% 125.8% 335 93.0% 95.2%

February 570 98.8% 108.5% 511 98.1% 106.0%

March 620 99.7% 110.5% 510 98.2% 109.2%

April 592 99.9% 111.3% 583 97.3% 100.9%

May 348 98.6% 127.1% 238 22.5% 22.5%

June 551 98.9% 122.3% 528 98.5% 109.0%

July 500 99.8% 112.5% 448 94.9% 103.3%

August 615 98.6% 108.4% 509 89.2% 98.7%

September 597 98.4% 109.8% 525 96.5% 108.6%

 5906 5151

Fiscal 2004

Delivered 5871 99.0% 114.2% 4725 91.7% 101.1%

PLANNED

MONTH HOURS

PLANNED

HOURS

VUV ACTUAL FY 04

RELIABILITY1 AVAILABILITY2

X-RAY ACTUAL FY 04

RELIABILITY1 AVAILABILITY2

FY 2004 NSLS MACHINE ACTIVITIES

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1

 Operations during scheduled time

2

 Operations compared to total sched-

 uled time

Other Activities UV/IR X-ray

Studies 2.3% 8.4%

Comm/Cond. 2.3% 3.5%

Holiday 2.4% 2.4%

Injection 1.2% 2.4%

Unscheduled Downtime 0.7% 4.9%

Interlock 0.0% 0.7%
Publications
 PUBLICATIONS 7-3

NSLS Users

Beamline U1A

H Hwu, B Fruhberger, J Chen. Different Modification Effects 

of Carbidic and Graphitic Carbon on Ni Surfaces. J. Catal..

221 (1), 170-177 (2004). 

J McCormick, B Zhao, S Rykov, H Wang, J Chen. Thermal

Stability of Flame-Synthesized Anatase TiO2

Nanoparticles. J. Phys. Chem. B. 108, 17398-17402

(2004).

S Xiao, S Brunner, M Wieland. Reactions of Surface Amines 

with Heterobifunctional Cross-Liners Bearing Both

Succinimidyl Ester and Maleimide for Grafting 

Biomolecules. J. Phys. Chem. B. 108, 16508-16517

(2004).

M Zellner, J Chen. Synthesis, Characterization and Surface

Reactivity of Tungsten Carbide (WC) PVD Films. Surf. Sci..

569, 89-98 (2004). 

Beamline U2A

D Klug, J Tse, Z Liu, X Gonze, R Hemley. Anomalous

Transformations in Ice VIII. Phys. Rev. B. 70, 144113

(2004).

J Kung, B Li, T Uchida, Y Wang, D Neuville, R Liebermann. In

Situ Measurements of Sound Velocities and Densities

Across the Orthopyroxene-High-Pressure Clinopyroxene

Transition

in MgSiO3 at High Pressure. Phys. Earth Planet. Interiors.

147, 27-44 (2004). 

H Liu, J Hu, J Xu, Z Liu, J Shu, H Mao, J Chen. Phase

Transition and Compression Behavior of Gibbsite under

High-Pressure. Phys. Chem. Miner.. 31, 240-246 (2004). 

C Slebodnick, J Zhao, R Angel, B Hanson, Y Song, Z Liu, R 

Hemley. High Pressure Study of Ru3(CO)12 by X-ray

Diffraction, Raman, and Infrared Spectroscopy. Inorg.

Chem.. 43 (17), 5245-5252 (2004). 

D Wetzel. Recent Analytical Synchrotron Infrared

Microspectroscopy and Imaging. Microsc. Microanal.. 10

(suppl 2), 1354-1355 (2004). 

The following pages list all papers published in the 2004 calendar year as reported to the NSLS by February 28, 

2005. Citations are listed in order of beamline number and then alphabetically by the last name of the first author. This 

list contains reported citations for journal articles, published conference proceedings, books, chapters in books, formal 

reports, informal reports, technical 

reports, theses, dissertations, and 

patents. For citation submissions where 

research was performed on more than 

one beamline, the citation is listed 

under each beamline. However, each 

citation was only counted once.

The first column in the table 

(right) lists the number of publications 

reported to the NSLS during the 2004 

fiscal year (Oct. 1, 2003 – Sept. 30, 

2004) and published between 2001 

and 2004. Although some of these 

publications were published earlier than 

FY 2004, 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 2004 calendar year and reported to 

the NSLS as of Feb. 28, 2005. These 

numbers are slightly lower than the 

fiscal year values because they contain 

only publications from 2004 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. Premier 

journals include: Physical Review 

Letters, Science, Nature, Cell, EMBO 

Journal, Nature Structural Biology, 

Proceedings of the National Academy 

of Sciences, Structure, and Applied 

Physics Letters.

Reported in 

Fiscal Year 

2004*

Published in 

Calendar Year 

2004**

Journals, peer-reviewed, premier 100 102

Journals, other peer-reviewed 506 487

Journals, non peer-reviewed 35 28

Total Journals and Magazines 641 617

Books/Chapters in Books 4 4

Published Conference Proceedings 40 40

Reports: Technical, Formal, Informal 3 3

Theses/Dissertations 15 15

Patents 0 0

Total Misc. Publications 62 62

Total Publications 734 679

NSLS VUV User Publications 71 57

NSLS X-Ray User Publications 549 537

NSLS Staff Publications 114 85

734 679

* Publications reported to the NSLS from Oct 1, 2003 – Sept. 30, 2004 and published 

between 2001 – 2004.

** Publications published in 2004 as reported to the NSLS by Feb. 28, 2005.
7-4 NSLS ACTIVITY REPORT 

Beamline U2B

E Chouparova, A Lanzirotti, H Feng, K Jones, N Marinkovic, C 

Whitson, P Philp. Characterization of Petroleum Deposits

Formed in a Producing Well by Synchrotron RadiationBased Microanalyses. Energ. Fuel. 18 (4), 1199-1212

(2004).

S Lappi, S Franzen. Eigenvector Mapping: A Method for

Discerning Solvent Effects on Vibrational Spectra.

Spectrochim. Acta A. 60, 357-370 (2004). 

D Wetzel, J Striova, D Huggins, M Collinson. Synchrotron

Infrared Microspectroscopy Reveals Localized

Heterogeneities in an Organically Modified Silicate Film.

Vib. Spectrosc.. 35 (1-2), 153-158 (2004). 

P Yu, J McKinnon, C Christensen, D Christensen. Applications 

of Synchrotron Technology (SR_FTIR) to Feed Analysis

and Utilization: A Novel Approach. Proceeding of the 25th 

Western Nutrition Conference - Nutrient Requirement and 

Ingredient Evaluation in 21st Century, Vol Sept 28-30, p. 

98-112, sponsored by University of Saskatchewan.

(2004).

P Yu, J McKinnon, C Christensen, D Christensen. Using

Synchrotron Transmission FTIR Microspectroscopy as a

Rapid, Direct and Nondestructive Analytical Technique to 

Reveal Molecular Microstructural-Chemical Features within 

Tissue in Grain Barley. J. Agr. Food Chem.. 52, 1484-

1494 (2004). 

P Yu, J McKinnon, C Christensen, D Christensen. Using

Synchrotron-Based FTIR Microspecscopy to Reveal

Chemical Features of Feather Protein Secondary

Structure: Comparison with Othe Feed Protein Sources. J.

Agr. Food Chem.. 52, 7353-7361 (2004). 

Yu, J McKinnon, C Christensen, D Christensen. Imaging

Molecular Chemistry of Pioneer Corn. J. Agr. Food Chem..

52, 7345-7352 (2004). 

P Yu. Application of Advanced Synchrotron-Based Fourier

Transform Infrared Microspectroscopy (SR-FTI) to Animal 

Nutrition and Feed Sciences: A Novel Approach. Brit. J.

Nutr.. 92, 869-885 (2004). 

P Yu, J McKinnon, C Christensen, D Christensen, N

Marinkovic. Chemical Imaging of Microstructures of Plant 

Tissues within Cellular Dimension using Synchrotron

Infrared Microspectroscopy. J. Agr. Food Chem.. 51,

6062-6067 (2004). 

Beamline U4A

A Chan, W Chen, H Wang, J Rowe, T Madey. Methanol

Reactions Over Oxygen-Modified Re Surfaces: Infleuence 

of Surface Structure and Oxidation. J. Phys. Chem. B.

108, 14643-14651 (2004). 

L Fleming, M Ulrich, K Efimenko, J Genzer, A Chan, T Madey, 

S Oh, O Zhou, J Rowe. NEXAFS and UPS Studies of

Aligned Single-walled Carbon Nanotubes on Si(100). J.

Vac. Sci. Technol., B. 22 (4), 2000-2005 (2004). 

M Gladys, I Ermanoski, G Jackson, J Quinton, J Rowe, T

Madey. A High Resolution Photoemission Study of CoreLevel Shifts (SCLS) in Clean and Oxygen. J. Electron.

Spectrosc. Relat. Phenom.. 135, 105-112 (2004). 

Beamline U4B

J Holroyd, Y Idzerda, S Stadler. Properties of thin film

europium oxide by x-ray magnetic circular dichroism. J.

Appl. Phys.. 95 (11), 6571 (2004). 

A Lussier, J Dvorak, Y Idzerda, S Ogale, S Shinde, T

Venkatesan. Comparative X-ray Absorption Spectroscopy 

Study of Co-Doped SnO2 and TiO2. J. Appl. Phys.. 95

(11), 7190-7191 (2004). 

D Resnick, K Gilmore, Y Idzerda, M Klem, E Smith, T

Douglas. Modeling of the Magnetic Behavior of GammaFe[sub 2]O[sub 3] Nanoparticles Mineralized in Ferritin. J.

Appl. Phys.. 95 (11), 7127 (2004). 

S Stadler, Y Idzerda, J Dvorak, J Borchers. Using Circularly

Polarized Soft X-rays to Probe antiferromagnetically

correlated Co/Cu multilayers. J. Appl. Phys.. 95 (11),

6672 (2004). 

P Wu, G Saraf, Y Lu, D Hill, R Bartinski, D Arena, R Mee-Yi, A 

Raley, K Yung. Ion-Beam-Induced Sharpening of ZnO

Nanotips. Appl. Phys. Lett.. 85, 1247 (2004). 

Beamline U4IR

L Keller, S Messenger, G Flynn, S Clemett, S Wirick, C

Jacobsen. The Nature of Molecular Cloud Material in

Interplanetary Dust. Geochim. Cosmochim. Acta. 68 (11), 

2577-2589 (2004).

Beamline U5UA

H Jeong, R Skomski, C Waldfried, T Komesu, P Dowben, E 

Vescovo. The Effective Spin Dependent Debye

Temperature of Gd(0001). Phys. Lett. A. 324, 242

(2004).

Beamline U7A

L Andruzzi, A Hexemer, X Li, C Ober, E Kramer, G Galli, E

Chiellini, D Fischer. Control of Surface Properties Using

Fluorinated Polymer Brushes Produced by SurfaceInitiated Controlled Radical Polymerization. Langmuir. 20,

10498-10506 (2004). 

S Banerjee, T Hemraj-Benny, M Balasubramanian, D Fischer, 

J Misewich, S Wong. Ozonized Single-Walled Carbon

Nanotubes Investigated using NEXAFS Spectroscopy.

Chem. Commun.. 7 (7), 772-773 (2004). 

S Banerjee, T Hemraj-Benny, M Balasubramanian, D Fischer, 

J Misewich, S Wong. Surface Chemistry and Structure of 

Purified, Ozonzied, Multiwalled Carbon Nanotubes Probed 

by NEXAFS and Vibrational Spectroscopies.

ChemPhysChem. 5, 1416-1422 (2004). 

D Burnett, A Capitano, A Gabelnick, A Marsh, D Fischer, J

Gland. In-situ Soft X-ray Studies of CO Oxidation on the 

Pt(111) Surface. Surf. Sci.. 564, 29-37 (2004). 

D Burnett, A Gabelnick, A Marsh, D Fischer, J Gland.

Comparisons of Propylene and Propyne Catalytic

Oxidation on a 100 Å Pt/Al2O3 Thin Film using in situ Soft 

X-ray Fluorescence Methods. Surf. Sci.. 553, 1-12

(2004).

D Burnett, A Gabelnick, A Marsh, H Lewis, S Yalisove, D

Fischer, J Gland. Defect Enhanced Carbon Monoxide

Oxidation at Elevated Oxygen Pressures on a Pt/Al2O3. J.

Phys. Chem. B. 108, 5314-5323 (2004). 

D Fischer, K Efimenko, R Bhat, S Sambasivan, J Genzer.

Mapping Surface Chemistry and Molecular Orientation

with Combinatorial Near-edge X-ray Absorption Fine

Structure. Macromol. Rapid Commun.. 25, 141-149

(2004).

E Jablonski, V Prabhu, S Sambasivan, D Fischer, E Lin, D

Goldfarb, M Angelopoulos, H Ito. Surface and bulk

chemistry of chemically amplified photoresists:. Advances

in Resist Technology and Processing, Vol XXI, p. 31,

sponsored by SPIE. (2004). 

J Lenhart, S Fischer, D Sambasivan, E Lin, C Soles, R Jones, 

W Wu, W Goldfarb, M Angelopoulos. Utilizing Near Edge

X-ray Absorption Fine Structure to Probe interfacial issues 

in Photolithography. Polymers for Microelectronics and

Nanoelectronics, Vol 874, p. 98-117, sponsored by ACS. 

(2004).

G Liu, J Rodriguez, Z Chang, J Hrbek. Adsorption and

Reaction of SO2 on Model Ce1-xZrxO2(111) Catalysts. J.

Phys. Chem. B. 108, 2931-2938 (2004). 

A Marsh, D Burnett, D Fischer, J Gland. In-Situ Soft X-ray

Studies of Toluene Catalytic Oxidation on the Pt(111)

Surface. J. Phys. Chem. B. 108, 605-611 (2004). 
 PUBLICATIONS 7-5

R Petrie, T Bailey, C Gorman, J Genzer. Fast Directed Motion 

of "Fakir" Droplets. Langmuir. 20, 9893-9896 (2004). 

J Rodriguez. Gold Nanoparticles on Titania: Activation and

Behavior. Dekker Encyclopedia of Nanoscience and

Nanotechnology, p. 1297-1304, Marcel Dekker, New York. 

(2004).

J Rodriguez, P Liu, J Dvorak, T Jirsak, J Gomes, Y Takahashi, 

K Nakamura. The Interaction of Oxygen with TiC(001):

Photoemission and First-Principles Studies. J. Chem.

Phys.. 121, 465-474 (2004). 

J Rodriguez, P Liu, J Dvorak, T Jirsak, J Gomes, Y Takahashi, 

K Nakamura. Adsorption of Sulfur on TiC(001):

Photoemission and First-Principles Studies. Phys. Rev. B.

69, 115414-1,10 (2004). 

S Sambasivan, D Fischer, M Shen, S Hsu. Molecular

Orientation of Ultrahigh Molecular Weight Polyethylene. J.

Biomed. Mater. Res. B. 70B (2), 278-285 (2004). 

W Yoon, C Grey, M Balasubramanian, X Yang, D Fischer, J 

McBreen. A Combined NMR and XAS Study on the Local

Environments and Electronic Structures of the

Electrochemically Li-ion deintercalated

LiCo1/3Ni1/3Mn1/3O2 electrode System. J. Electrochem.

Soc.. 7 (3), A53 (2004). 

W Yoon, M Balasubramanian, X Yang, Z Fu, D Fischer, J

McBreen. Soft X-Ray Absorption Spectroscopic Study of a 

LiNi0.5Mn0.5O2 Cathode during Charge. J. Electrochem.

Soc.. 151 (2), A246 (2004). 

K Zhang, G Rosenbaum, C Liu, D Fischer. Development of

Multilayer Analyzer Array Detectors for X-ray Fluorescence 

at the Third Generation Synchrotron Source. Synchrotron

Radiation Instrumentation: Eighth International, Vol 8th,

p. 957-960, sponsored by AIP. (2004).

Beamline U7B

M Fernandez-Garcia, A Martinez-Arias, J Hanson, J

Rodriguez. Nanostructured Oxides in Chemistry:

Characterization and Properties. Chem. Rev.. 104 (9),

4063-4104 (2004). 

Beamline U8B

T Owens, B Ludwig, K Schneider, D Fosnacht, B Orr, M

Banaszak Holl. Oxidation of Alkylsilane-Based Monolayers 

on Gold. Langmuir. 20 (22), 9636-9645 (2004). 

T Owens, B Ludwig, D Fosnacht, J Bartolin, N Homann, N

Wells, B Orr, M Banaszak Holl. Octylgermane on Gold:

Synthesis, Oxidation, and Pattern Formation. Langmuir.

20, 11422-11427 (2004). 

T Owens. Formation and Reactivity of Alkylsilane-Based

Monolayers on Gold. Ph.D. Thesis. University of Michigan, 

Ann Arbor. (2004). 

Beamline U9B

J Lees, B Smith, F Wien, A Miles, B Wallace . CDtool - an

Intergrated Software Package for Circular Dichroism

Spectroscopic Data Processing, Analysis, and Archiving.

Anal. Biochem.. 332, 285-289 (2004). 

Beamline U10A

C Homes, S Dordevic, M Strongin, D Bonn, R Liang, W

Hardy, S Komiya, Y Ando, G Yu, et al.. A Universal Scaling 

Relation in High-Temperature Superconductors. Nature.

430, 539-541 (2004). 

A Zimmers, N Bontemps, R Lobo, C Hill, M Barr, R Greene, C 

Homes, A Millis. Infrared Signature of the

Superconducting State in Pr(2-x)Ce(x)CuO(4). Phys. Rev. 

B. 70, 132502 (2004). 

Beamline U10B

D Chidambaram, G Halada, C Clayton. Synchrotron

Radiation Based Grazing Angle Infrared Spectroscopy of

Chromate Conversion Coatings Formed on Aluminum

Alloys. J. Electrochem. Soc.. 151 (3), B160 (2004).

M Diem, M Romeo, C Matthaus, M Miljkovic, L Miller, P

Lasch. Comparison of Fourier Transform Infrared (FTIR)

Spectra of Individual Cells Acquired using Synchrotron

and Conventional Sources. Infrared Phys. Technol.. 45,

331-338 (2004). 

P Dumas, N Jamin, J Teillaud, L Miller, B Beccard. Imaging

Capabilities of Synchrotron Infrared Microspectroscopy.

Faraday Discuss. 126, 289-302 (2004). 

G Flynn, L Keller, C Jacobsen, S Wirick. An Assessment of

the Amount and Types of Organic Matter Contributed to

the Earth by Interplanetary Dust. Adv. Space Res.. 33

(1), 57-66 (2004). 

G Flynn, L Keller, C Jacobsen, S Wirick. The Origin of

Organic Matter in the Solar System: Evidence from the

Interplanetary Dust Particles . Bioastronomy 2002: Life

Among the Stars, Vol 213, p. 275-280, sponsored by

International Astronomical Union. (2004). 

L Keller, S Messenger, G Flynn, S Clemett, S Wirick, C

Jacobsen. The Nature of Molecular Cloud Material in

Interplanetary Dust. Geochim. Cosmochim. Acta. 68 (11), 

2577-2589 (2004).

J Kneipp, L Miller, S Spassov, F Sokolowski, P Lasch, M

Beekes, D Naumann. Scrapie-infected Cells, Isolated

Prions, and Recombinant Prion Protein: A Comparative

Study. Biopolymers. 74 (1-2), 163-7 (2004). 

L Miller, J Tetenbaum Novatt, D Hamerman, C Carlson.

Alteractions in Mineral Composition Observed in

Osteoarthritic Joints of Cynomologus Monkeys. Bone. 35

(2), 498-506 (2004). 

D Wetzel, J Striova, D Huggins, M Collinson. Synchrotron

Infrared Microspectroscopy Reveals Localized

Heterogeneities in an Organically Modified Silicate Film.

Vib. Spectrosc.. 35 (1-2), 153-158 (2004). 

D Wetzel. Recent Analytical Synchrotron Infrared

Microspectroscopy and Imaging. Microsc. Microanal.. 10

(suppl 2), 1354-1355 (2004). 

P Yu. Application of Advanced Synchrotron-Based Fourier

Transform Infrared Microspectroscopy (SR-FTI) to Animal 

Nutrition and Feed Sciences: A Novel Approach. Brit. J.

Nutr.. 92, 869-885 (2004). 

Beamline U12A

S Linic, H Piao, K Adib, M Barteau. Ethylene Epoxidation on 

Ag: Identification of the Crucial Surface Intermediate by 

Experimental and Theoretical Investigation of its

Electronic Structure. Angew. Chem. Int. Ed.. 43 (22),

2918-2921 (2004). 

D Mullins. Adsorption of CO and C2H4 on Rh-Loaded ThinFilm Praseodymium Oxide. Surf. Sci.. 556 (2-3), 159-170

(2004).

H Piao, K Adib, M Barteau. A Temperature-Programmed Xray Photoelectron Spectroscopy (TPXPS) Study of Chlorine 

Adsorption and Diffusion on Ag(111). Surf. Sci.. 557 (1-

3), 13-20 (2004). 

Beamline U12IR

L Mihaly, D Talbayev, L Kiss, J Zhou, T Feher, A Janossy. 

Field-frequency Mapping of the Electron Spin Resonance

in the Paramagnetic and Antiferromagnetic States of

LaMnO3. Phys. Rev. B. 69, 024414 (2004). 

D Talbayev, L Mihaly, J Zhou. Antiferromagnetic Resonance 

in LaMnO3 at Low Temperature. Phys. Rev. Lett.. 93 (1), 

017202-1 (2004). 
7-6 NSLS ACTIVITY REPORT 

Beamline U13UB

T Valla, A Fedorov, P Johnson, P Glans, C McGuinness, K

Smith, E Andrei, H Berger. Quasiparticle Spectra, ChargeDensity Waves, Superconductivity, and Electron-Phonon

Coupling in 2H-NbSe(2). Phys. Rev. Lett.. 92 (8), 086401 

(2004).

S Wang, H Yang, A Sekharan, H Ding, J Engelbrecht, X Dai, 

Z Wang, A Kaminski, T Valla, et al.. The Quasiparticle

Lineshape of Sr(2)RuO(4) and its Relation to Anisotropic

Transport. Phys. Rev. Lett.. 92, 137002 (2004).

Beamline X1A1

T Beetz. Soft X-ray Diffraction Imaging With and Without

Lenses and Radiation Damage Studies. Ph.D. Thesis.

SUNY at StonyBrook, StonyBrook. (2004). 

C Boyce, M Zwieniecki, G Cody, C Jacobsen, S Wirick, A

Knoll, N Holbrook. Evolution of Xylem Lignification and

Hydrogel Transport Regulation. Proc Natl Acad Sci USA.

101 (50), 17555-17558 (2004). 

A Braun, N Shah, F Huggins, G Huffman, S Wirick, C

Jacobsen, K Kelly, A Sarofim. A Study of Diesel PM with Xray Microspectroscopy. Fuel. 83, 997-1000 (2004). 

G Flynn, L Keller, C Jacobsen, S Wirick. An Assessment of

the Amount and Types of Organic Matter Contributed to

the Earth by Interplanetary Dust. Adv. Space Res.. 33

(1), 57-66 (2004). 

G Flynn, L Keller, C Jacobsen, S Wirick. The Origin of

Organic Matter in the Solar System: Evidence from the

Interplanetary Dust Particles . Bioastronomy 2002: Life

Among the Stars, Vol 213, p. 275-280, sponsored by

International Astronomical Union. (2004).

H Geckeis, T Schäfer, W Hauser, T Rabung, T Missana, C

Degueldre, A Möri, J Eikenberg, T Fierz, W Alexander.

Results of the Colloid and Radionuclide Retention

Experiment (CRR) at the Grimsel Test Site (GTS),

Switzerland - Impact of Reaction Kinetics and Speciation

on Radionuclide Migration. Radiochim. Acta. 92, 765-774

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P Abbamonte, G Blumberg, A Rusydi, A Gozar, P Evans, T

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Sr14Cu24041. Nature. 431, 1078 (2004). 

J Downes, C McGuinness, P Glans, T Learmonth, D Fu, P

Sheridan, K Smith. Electronic Structure Near the Fermi

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O Kugeler, E Rennie, A Ruedel, M Meyer, A Marquette, U

Hergenhahn. N2 valence Photoionization Below and Above 

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K Thomas, J Hill, S Grenier, Y Kim, P Abbamonte, L Venema, 

A Rusydi, Y Tomioka, Y Tokura, et al.. Soft X-Ray

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K Fiese, M Panthofer, G Wu, M Jansen. Strategies for the

Structure Determination of Endohedral Fullerenes Applied

to the Example of Ba@C74.Co(octaethylpophyrin).2C6H6. 

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R Poulsen, A Bentien, T Graber, B Iverson. Synchrotron

Charge-Density Studies in Materilas Chemistry: 16K X-ray

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A Reich, M Panthofer, H Modrow, U Wedig, M Jansen. The

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A Nogales, G Broza, Z Roslaniec, K Schulte, I Sics, B Hsiao, 

A Sanz, M Garcia-Gutierrez, D Rueda, et al.. Low

Percolation Threshold in Nanocomposites Based on

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L Sun, L Zhu, Q Ge, R Quirk, C Xue, S Cheng, B Hsiao, C

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L Sun, Y Liu, L Zhu, B Hsiao, C Avila-Orta. Path-dependent

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L Yang, R Somani, I Sics, B Hsiao, R Kolb, H Fruitwala, C

Ong. Shear-Induced Crystallization Precursor Studies in

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S Zhou, C Xu, J Wang, P Golas, J Batteas. Phase Behavior of 

Cationic Hydroxyethyl Cellulose-Sodium Dodecyl Sulfate

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Side Chain Length of Polymers. Langmuir. 20, 8482-8489

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S Zhou, C Xu, J Wang, W Gao, R Akhverdiyeva, V Shah, R 

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D Balzar, N Audebrand, M Draymond, A Fitch, A Hewat, I

Langford, A Le Bail, D Louer, O Masson, N Popa. SizeStain Line Broadening Analysis the Ceria Round-Robin

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C Botez, P Stephens, O Omotoso. Crystal Structure of

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E Caspi, M Avdeev, S Short, J Jorgensen, M Lobanov, Z

Zeng, M Greenblatt, P Thiyagarajan, C Botez, P Stephens.

Structural and Magnetic Phase Diagram of the TwoElectron-Doped [Ca(1-x)Ce(x)]MnO3 System: Effects of

Competition Among Charge, Orbital, and Spin Ordering.

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A Hoennerscheid, L van Wuellen, R Dinnebier, M Jansen, J

Rahmer, M Mehring. Evidence for C60 Dimerisation in the 

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M Lobanov, M Greenblatt, E Caspi, I Jorgensen, D

Sheptyakov, B Toby, C Botez, P Stephens. Crystal and

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C Muehle, R Dinnebier, L van Wuellen, G Schwering, M

Jansen. New Results in the Field of

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C Nunes, R Suryanarayanan, C Botez, P Stephens.

Characterization and Crystal Structure of D-Mannitol

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J Readman, P Barker, I Gameson, J Hriljac, W Zhong, P

Edwards, P Anderson. An Ordered Array of Cadmium

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Y Soo, S Kim, Y Kao, A Blattner, B Wessels, S Khalid, C

Sanchez-Hanke, C Kao. Local Structure Around Mn Atoms 

in Room-Temperature Ferromagnetic (In,Mn) As Thin

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T Vos, Y Liao, W Shum, I Her, P Stephens, W Reiff, L Miller. 

Diruthenium Tetracarboxylate Monocation,

[RuII/III2(O2CR)4]+, Building Blocks for 3-D Moleculebased Magnets. J. Am. Chem. Soc.. 126, 11630-11639

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W Blankenfeldt, A Kuzin, T Skarina, Y Korniyenko, L Tong, P 

Bayer, P Janning, L Thomashow, D Mavrodi. Structure and 

Function of the Phenazine Biosynthetic Protein PhzF from 

Pseudomonas Fluorescens. Proc Natl Acad Sci USA. 101,

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C Brautigam, Y Chelliah, J Deisenhofer. Tetramerization and 

ATP Binding by a Protein Comprising the A, B, and C

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J Buglino, K Onwueme, J Ferreras, L Quadri, C Lima. Crystal

Structure of PapA5, a Phthiocerol Dimycocerosyl

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M Bukhtiyarova, K Northrop, X Chai, D Casper , M Karpusas, 

E Springman. Improved Expression, Purification, and

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B Chakravarty, Z Gu, S Chirala, S Wakil, F Quicocho. Human 

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Y Chen, M Li, Y Zhang, L He, Y Yamada, A Fitzmaurice, Y

Shen, H Zhang, L Tong, J Yang. Structural Basis of the

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Y Cheng, D Patel. Crystallographic Structure of the Nuclease 

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J Dai, J Liu, Y Deng, T Smith, M Lu. Structure and Protein 

Design of a Human Platelet Function Inhibitor. Cell. 116,

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H Dvir, M Harel, S Bon, W Liu, M Vidal, C Garbay, J

Sussman, J Massoulie, I Silman. The Synaptic

Acetylcholinesterase Tetramer Assembles Around a

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C Fabrega, S Hausmann, V Shen, S Shuman, C Lima.

Structure and Mechanism of the mRNA (guanine-N7) cap 

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F Forouhar, I Lee, J Benach, K Kulkarni, R Xiao, T Acton, G 

Montelione, L Tong. A Novel Nad-Binding Protein Revealed 

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S Galdiero, E Gouaux. High Resolution Crystallographic

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D Gebauer, J Li, G Jogl, Y Shen, D Myszka, L Tong. Crystal

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S Goldsmith-Fischman, A Kuzin, A Edstrom, J Benach, R

Shastry, R Xiao, T Acton, B Honig, G Montelione, J Hunt. 

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M Gu, C Fabrega, D Liu, H Liu, M Kiledjian, C Lima. Insights

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B Hamaoka, C Dann III, B Geisbrecht, D Leahy. Crystal

Structure of Caenorhabditis elegans HER-1 and

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C Ho, L Wang, C Lima, S Shuman. Structure and Mechanism 

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Y Hsiao, G Jogl, L Tong. Structural and Biochemical Studies 

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C Huang, M Venturi, S Majeed, M Moore, S Phogat, M Zhang, 

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G Jogl, L Tong. Crystal Structure of Yeast Acetyl-Coenzyme

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J Khan, E Brint, L O'Neill, L Tong. Crystal Structure of the

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R Kovall, W Hendrickson. Crystal Structure of the Nuclear

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J Liu, W Yong, Y Deng, N Kallenbach, M Lu. Atomic Structure 

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S Olsen, O Ibrahimi, A Raucci, F Zhang, A Eliseenkova, A

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S Patel, M Rajala, L Rossetti, P Scherer, L Shapiro. DisulfideDependent Multimeric Assembly of Resistin Family

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S Prigge, B Eipper, R Mains, L Amzel. Dioxygen Binds EndOn to Mononuclear Copper in a Precatalytic Enzyme

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D Reverter, C Lima. A Basis for SUMO Protease Specificity

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Y Shen, S Volrath, S Weatherly, T Elich, L Tong. A

Mechanism for the Potent inhibition of Eukaryotic Acetyl

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I Shumilin, R Bauerle, J Wu, R Woodard, R Kretsinger.

Crystal Structure of the Reaction Complex of 3-Deoxy-Darabino-heptulosonate-7-phosphate Synthase from

Thermotoga maritima Refines the Catalytic Mechanism

and Indicates a New Mechanism of Allosteric Regulation.

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Y Wang, R Coulombe, D Cameron, L Thauvette, M Massariol, 

L Amon, D Fink, S Titolo, E Welchner, et al.. Crystal

Structure of the E2 Transactivation Domain of Human

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H Ye, T Chen, X Xu, M Pennycooke, H Wu, C Steegborn.

Crystal Structure of the Putative Adapter Protein

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D Yernool, O Boudker, Y Jin, E Gouaux. Structure of a

Glutamate Transporter Homologue From Pyrococcus

Horikoshii. Nature. 431, 811 (2004). 

H Zhong, B Tweel, L Tong. Molecular Basis for the Inhibition 

of the Carboxyltransferase Domain of Acetyl-coenzyme-A

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H Zhong, B Tweel, J Li, L Tong. Crystal Structure of the

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X Wei, C Bade, A Caracappa, T Dageya, F Lincoln, M Lowry, 

J Mahon, A Sandorfi, C Thorn, et al.. New Improvements 

Leading to Higher Polarization Frozen Spin HD targets at 

the LEGS Facility. Nucl. Instrum. Meth. A. 526, 157

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S Gabelli, M Bianchet, H Azurmendi, Z Xia, V Sarawat, A

Mildvan, L Amzel. Structure and Mechanism of GDPMannose Glycosyl Hydrolase, a Nudix Enzyme that

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N Moiseeva, M Allaire. Crystals of Family 11 Xylanase II from 

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I Kim, E DiMasi, J Evans. Identification of Mineral Modulation 

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G Bonilla, I Diaz, M Tsapatsis, H Jeong, Y Lee, D Vlachos.

Zeolite (MFI) Crystal Morphology Control Using Organic

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M Colligan, P Forster, A Cheetham, Y Lee, T Vogt, J Hriljac. 

Synchrotron X-ray Powder Diffraction and Computational

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M Hucker, K Chung, M Chand, T Vogt, J Tranquada, D

Buttrey. Oxygen and Strontium Codoping of La2NiO4:

Room Temperature Phase Diagrams. Phys. Rev. B:

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I Jeong, T Darling, M Graf, T Proffen, R Heffner, Y Lee, T

Vogt, J Jorgensen. Role of the Lattice in the gamma arrow 

alpha Phase Transition of Ce: A High-Pressure Neutron

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P Juhas, I Grinberg, A Rappe, W Dmowski, T Egami, P

Davies. Correlations between the Structure and Dielectric 

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B Kennedy, L Li, Y Lee, T Vogt. Pressure Induced Valence

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J Lai, K Shafi, A Ulman, K Loos, N Yang, M Cui, T Vogt, C

Estournes, D Locke. Mixed Iron-Manganese Oxide

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Y Lee, C Martin, J Parise, J Hriljac, T Vogt. Formation and

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Y Lee, J Hriljac, A Studer, T Vogt. Anisotropic Compression

of Edingtonite and Thomsonite to 6 GPa at Room

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R Morris, A Burton, L Bull, S Zones. SSZ-51-A New

Aluminophosphate Zeotype: Synthesis, Crystal Structure, 

NMR, and Dehydration Properties. Chem. Mater.. 16,

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H Xu, M Nyman, T Nenoff, A Navrotsky. Prototype Sandia

Octahedral Molecular Sieve (SOMS) Na2Nb2O6.H2O:

Synthesis, Structure and Thermodynamic Stability. Chem.

Mater.. 16, 2034-2040 (2004). 

H Xu, A Navrotsky, M Nyman, T Nenoff. Crystal Chemistry

and Energetics of Pharmacosiderite-Related Microporous

Phases in the K2O-Cs2O-SiO2-TiO2-H2O System.

Microporous Mesoporous Mater.. 72, 209-218 (2004). 

X Yang, M Camblor, Y Lee, H Liu, D Olson. Synthesis and

Crystal Structure of As-Synthesized and Calcined Pure

Silica Zeolite ITQ-12. J. Am. Chem. Soc.. 126, 10403-

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S Antao, I Hassan, J Parise. Tugtupite: High-Temperature

Structures Obtained from in situ Synchrotron Diffraction

and Rietveld Refinements. Am. Mineral.. 89 (4), 492-497

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S Antao, I Hassan, J Parise. Chromate Aluminate Sodalite,

Ca8[Al12O24](crO4)(2): Phase Transitions and HighTemperature Structural Evolution of the Cubic Phase. Can.

Mineral. 42 (4), 1047-1056 (2004).

K Barkigia, M Renner, M Senge, J Fajer. Interplay of Axial

Ligation, Hydrogen Bonding, Self-Assembly, and

Conformational Landscapes in High-Spin Ni(II) Porphyrins. 

J. Phys. Chem. B. 108, 2173-2180 (2004). 

A Celestian, J Parise, C Goodell, A Tripathi, J Hanson. Time 

Resolved Diffraction Studies of Ion Exchange: K+ and

Na+ Exchange into (Al, Ge) Gismondine (GIS)

Na24Al24Ge24O96.40H2O and K8Al8Ge8O32&.8H2O.

Chem. Mater.. 16 (11), 2244-2254 (2004). 

A Christensen, T Jensen, N Scarlett, I Madsen, J Hanson.

Hydrolysis of Pure Sodium Substituted Calcium

Aluminates and Cement Clinker Compents Investigated by 

In Situ Synchrotron Powder Diffraction. J. Am. Ceram.

Soc.. 87 (8), 1488-1493 (2004). 

A Christensen, T Jensen, J Hanson. Formation of Ettringite, 

AFT and in Hydrothermal Hydration of Portland Cement

Studied by in situ Synchrotron X-ray Powder Diffraction. J.

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P Chupas, S Chaudhuri, J Hanson, X Qui, P Lee, S Shastri, S 

Billinge, C Grey. Probing Local and Long-Range Structure 

Simultaneously: An in situ Study of the High-Temperature

Phase Transtion of Alpha-ALF3. J. Am. Chem. Soc.. 126,

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M Fernandez-Garcia, A Martinez-Arias, J Hanson, J

Rodriguez. Nanostructured Oxides in Chemistry:

Characterization and Properties. Chem. Rev.. 104 (9),

4063-4104 (2004). 

A Guiltieri, P Norby, C Grey, J Hanson. Sorbate

Rearrangement and Cation Migration in HFC-134 Loaded 

NaY Zeolite; A Temperature Dependent Synchrotron

Powder Diffraction Study. Mater. Sci. Forum. 443-4, 295-

298 (2004). 

X Guo, P Devi, B Ravi, J Parise, S Sampath, J Hanson. Phase

Evolution of Yttrium Aluminium Garnet (YAG) in a Citratenitrate Gel Combustion Process. J Mater. Chem.. 14 (8), 

1288-1292 (2004). 

I Hassan, S Antao, J Parise. Phase Transition and HighTemperature Structures Obtained from Synchrotron

Radion and Rietveld Refinements. Miner. Mag.. 68 (4),

499-513 (2004). 

I Hassan, S Antao, J Parise. HighTemperature Structures

Obtained from Synchrotron Radition and Rietveld

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J Kim, J Hanson, A Frenkel, P Lee, J Rodriguez. Rduction of 

CuO with Hydrogen Studied by using Synchrotron-Based

X-ray Diffraction. J. Phys.: Condens. Matter. 16, s3459-

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D Mahajan, C Marshall, N Castagnola, J Hanson. Sono

Synthesis and Characterization of Nanophase

Molybdenum-Based Materials for Catalytic

Hydrodesulfurization. Appl. Catal. A. 258, 83-91 (2004). 

D Medvedev, A Tripathi, A Clearfield, A Celestian, J Parise, J 

Hanson. Crystallization of Sodium Titanium Silicate with

Sitinakite Topology: Evolution from the Sodium

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O Rotthaus, L Le Roy, A Tomas, K Barkigia, I Artaud.

Synthesis, Structure and Catalytic Activity of Low-Spin

Dicyano iron(III) Complexes of N,N Œbis(quinolyl)malonamide Derivatives. Inorg. Chim. Acta.

357 (8), 2211 (2004). 

Z Song, T Cai, J Grey, J Rodriguez, J Hrbek. Structure and 

Reactivity of Ru Nanoparticles Supported on Modified

Graphite Surfaces: A Study of the Model Catalysts for

Ammonia Synthesis. J. Am. Chem. Soc.. 126, 8576-8584

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X Wang, J Hanson, A Frenkel, J Kim, J Rodriguez. Timeresolved Studies for the Mechanism of Reduction of Coper 

Oxides with Carbon Monoxide: Complex Behavior of Latice 

Oxygen and Formation of Suboxides. J. Phys. Chem. B.

108 (36), 13667-13673 (2004). 

X Wang, J Hanson, G Liu, J Rodriguez, A Iglesias-Juez, M

Fernandez-Garcia. the Behavior of Mixed-Metal Oxides:

Physical and Chemical Properties of Bulk Ce(1-

x)Tb(x)O(2) and Nanopatricles of Ce(1-x)Tb(x)O(y). J.

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X Wang, J Hanson, J Szanyi, J Rodriguez. Interaction of H2O 

and NO2 with BaY Faujasite: Complex Contraction

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K Backbro, A Roos, E Baker, V Arcus. Crystallization and

Preliminary X-ray Analysis of a Conserved Hypothetical

Protein PAE2754 from Pyrobaculum aerophilum and of a

Double Leu arrow Met Mutant Engineered for MAD

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M Bar, G Golan, M Nechama, G Zolotnitsky, Y Shoham, G

Shoham. A New Crystal Form of XT6 Enables a Significant 

Improvement of its Diffraction Quality and Resolution.

Acta Cryst. D. 60, 545-549 (2004). 

S Chan, B Segelke, T Lekin, H Krupka, U Cho, M Kim, M So, 

C Kim, C Naranjo, et al.. Crystal Structure of the

Mycobacterium tuberculosis dUPTase: Insights into the

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Beamline X17C

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Beamline X18A

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and Molecular Dynamics Simulations. Phys. Status Solidi

(a). 201 (10), 2375-2380 (2004). 
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Beamline X18B

J Bang, D Hesterberg. Dissolution of Trace Element

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of a Water Cover on the Stability of Arsenic in a

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S Beauchemin, J Fiset, T Mackinnon. Stability of Arsenic in

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J Guzman, B Gates. Catalysis by Supported Gold:

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J Guzman, S Kuba, J Fierro-Gonzales, B Gates. Formation of 

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A Rouff, E Elzinga, R Reeder. X-ray Absorption Spectroscopic 

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W Yoon, C Grey, M Balasubramanian, X Yang, D Fischer, J 

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Beamline X19A

S Beauchemin, J Fiset, T Mackinnon. Stability of Arsenic in

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CANMET Mining and Mineral Sciences Laboratories,

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of a Water Cover on the Stability of Arsenic in a

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S Beauchemin, D Hesterberg, J Nadeau, J McGeer.

Speciation of Hepatic Zn in Trout Exposed to Elevated

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W Caliebe, S Cheung, A Lenhard, D Siddons. Fixed Exit

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7-18 NSLS ACTIVITY REPORT 

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F Huggins, G Huffman. How do Lithophile Elements Occur in 

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F Huggins, G Huffman, W Linak, C Miller. Quantifying

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K Mondal, N Sathitsuksanoh, M Croft, S Lalvani. X-ray

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J Ramallo-Lopez, E Lede, F Requejo, J Rodriquez, J Kim, R

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J Rodriguez. Gold Nanoparticles on Titania: Activation and

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A Sahiner, C Magee, D Downey, E Arevalo, J Woicik. The

Role of Ge in Cluster Formation in B and BF2 Implanted Si 

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Society Fall 2003 Meeting, Vol 792, p. R7.3.1-7,

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Materials Research Society Spring 2004 Meeting, Vol 810, 

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Y Suh, M Carroll, R Levy, A Sahiner, C King. Phophorus and 

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G Veith, M Lobanov, T Emge, M Greenblatt, M Croft, F

Stowasser, J Hadermann, G Van Tendelo. Synthesis and

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X Wang, J Hanson, G Liu, J Rodriguez, A Iglesias-Juez, M

Fernandez-Garcia. the Behavior of Mixed-Metal Oxides:

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Beamline X19C

F Akin, I Jang, M Schlossman, S Sinnott, G Zajac, E Fuoco, 

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J Bai, G Dhanaraj, P Gouma, M Dudley, M Mynbaeva. Porous 

SiC for HT Chemical Sensing Devices: An Assessment of

its Thermal Stability. International Conference on Silicon

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J Bai, M Dudley, B Raghotamachar, P Gouma, B Skromme, L 

Chen, P Hartlieb, E Michaels, J Kolis. Correlated Structural 

and Optical Characterization of Ammonothermally Grown

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X Huang, M Dudley, W Cho, R Okojie, P Neudeck.

Characterization of SiC Epitaxial Structures using HighResolution X-ray Diffraction Techniques. International

Conference on SiC and Related Materials 2003, Vol 457-

460, p. 157-162, sponsored by CNRS et al. (2004). 

X Ma, M Dudley, T Sudarshan. Nondestructive Defect

Characterization of SiC Epilayers and its Significance for

SiC Device Research. International Conference on Silicon 

Carbide and Related Materials 2003, Vol 457-460, p. 601-

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A Tikhonov, S Pingali, M Schlossman. Molecular Ordering

and Phase Transitions in alkanol Monolayers at the Water–

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Beamline X20A

E Bernard, R Boltnev, V Khmelenko, V Kiryukhin, S Kiselev, 

D Lee. Impurity - Helium Solids: Chemistry and Physics at 

1.5 K. J. Low Temp. Phys.. 134 (1/2), 133-143 (2004). 

H Chen. Microscale Laser Shock Peening-- Experiment,

Modeling and Spatially Resolved Material Characterization. 

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of Residual Stress Induced by Micro Scale Laser Shock

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H Chen, J Kysar, Y Yao. Characterization of Plastic

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M Ramazanoglu, P Clegg, R Birgeneau, C Garland, M

Neubert, J Kim. First Order Isotropic-Smectic-A transition 
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Beamline X20C

J Baglin, S Sun, A Kellock, T Thomson, M Toney, B Terris, C 

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C Detavernier, C Lavoie, R Van Meirhaeghe. CoSi2 Formation 

in the Presence of Ti, Ta or W. Thin Solid Films. 468, 174-

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S Fritz, S Martin, C Frisbie, M Ward, M Toney. Structural

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H Kim, C Lavoie, M Copel, V Narayanan, D Park, S

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A Ozcan, K Ludwig, Jr., C Lavoie, S Basu, C Coia, C Cabral, 

Jr., K Rodbell, J Harper. Evolution of Microstructure in TiTa Bilayer Thin Films on Polycrystalline-Si and Si(001).

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W Prater, E Allen, W Lee, M Toney, J Daniels, J Hedstrom. 

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Terris. Structural and Magnetic Model of Self-assembled

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T Thomson, B Terris, M Toney, S Raoux, J Baglin, S Lee, S

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Synchrotron X-Ray Beams. Second International

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Institute. (2004).

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of Magnet Epoxy at NSLS X-Ray Ring. Mech. Engng.

Design of Synch. Radiation Equipment & Inst. (MEDSI),

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J Hu, R Reciniello, N Holden. Optiminzation of the Epithermal 

Neutron Beam for Boron Neutron Capture Therapy at the 

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one Liquid-Crystal Compound Exhibiting the No-LayerShrinkage Effect Near the SM-a-Sm-/sup*/Transition.

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