National Synchrotron Light Source

Brookhaven National Laboratory

Upton, NY 11973

www.nsls.bnl.gov
Kathleen Nasta

Managing Editor

Kendra J. Snyder

Science Writer

Tiffany A. Gagnon

Graphic Designer

Nancye Wright

Editorial Assistant

National Synchrotron Light Source

2008 Activity Report

The National Synchrotron Light Source Department is supported by the Offi ce of Basic Energy Sciences,

United States Department of Energy, Washington, D.C.

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

Under contract no. DE-AC02-98CH10886
BNL-81989-2008

UC400

(General Energy Research)

Printed in the United States of America

Available from

National Technical Information Service

U.S. Department of Commerce

5285 Port Royal Road

Springfi eld, VA 22161

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 that its use would not infringe privately owned rights. Reference herein to any specifi c commercial 

product, process, or service by trade name, trademark, 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 expressed herein do not necessarily state or refl ect those of the United States Government or any agency, contractor, or subcontractor 

thereof.

On the Cover

Model of the atomic structure of the enzyme telomerase, which was solved by a group of researchers from the Wistar Institute 

at NSLS beamline X6A. Telomerase plays a major role in the development of nearly all human cancers and has implications for 

the creation of therapies to combat aging and other age-related diseases. 

The 2008 Activity Report has gone green. This year's book uses 100 percent recycled paper, a move that saves about 120 

trees compared to last year's publication. In addition, the paper band wrapped around this book is embedded with wild 

flower seeds. To use: thoroughly soak the paper with water, plant it one-eighth inch below the surface of your soil, water 

generously, and watch it bloom!
Table of Contents | 3

Welcome 4

Chairman's Introduction 4

A Beacon for Research 6

A New Light on the Horizon 7

Science Highlights 8

Physical and Chemical Sciences Introduction 8

Condensed Matter Physics 10

Materials Science 12

Chemical Sciences 18

X-Ray Optics and Accelerator Physics 20

Life and Environmental Sciences Introduction 22

Earth and Environmental Sciences 24

Life Sciences 29

Soft Condensed Matter and Biophysics 34

Year in Review 36

Staff Photo 36

January - April 38

May - August 40

September - December 42

Facility Report 44

Safety 44

The Accelerator Complex 46

Experimental Systems 52

Facility Facts and Figures 58

Introduction 58

Machine Parameters 60

2008 Publications 60

User Statistics 61

Beamline Status 62

Beamline Guide 63

Advisory Committees 68
4 | Chairman’s Introduction

After 20 years at the National Synchrotron Light Source 

(NSLS), I’m still excited to learn about the wide range of science conducted here and to meet users from around the 

world. In 2008, even with an additional shutdown due to 

budgetary constraint, the NSLS attracted almost 2,200 individual users. These researchers produced a collective 964 

publications – more than 20 percent of which appeared 

in premier publications. A few examples of this research, 

which ranges from exploring the mysteries of high-temperature superconductors to finding an inhibitor of botulinum neurotoxin, can be found in the following pages of 

this Activity Report. 

We will continue to facilitate this world-leading research by 

providing our users with first-class tools in response to the 

ever-changing needs of science. One of our major upgrade 

projects, now near completion, is the construction of beamline X9, a new undulator-based beamline jointly developed 

by the NSLS and the Center for Functional Nanomaterials. X9 

will host the small-angle x-ray scattering program that currently exists at beamline X21 and will provide much-needed 

beam time for the soft condensed matter physics, life sciences, and nanoscience communities. You can read about 

all of our recent upgrades in the “Facility Report” at the end 

of this book. 

As we continue to make upgrades to beamlines, their performance must be fully characterized so that users can design and plan their experiments better. With that in mind, 

we started an effort this year to measure the performance 

of NSLS beamlines and work with staff members to solve 

any problems that are identified. The Experimental Systems 

Division began by comparing the actual flux of the facility’s 

x-ray spectroscopy beamlines to theoretical values. Next, we 

will focus on other types of beamlines as well as develop 

tools to measure energy resolution and spot size.

We’ve also made great strides this year to diversify our user 

base. We’ve launched an initiative to work closely with industrial researchers to identify and exploit new opportunities in industrial applications using synchrotron light. In addition, our second annual NSLS Historically Black Colleges 
Chairman’s Introduction | 5

“After 20 years at the NSLS, I’m still excited to learn

about the wide range of science conducted here

and to meet users from around the world.”

Chi-Chang Kao

Chairman, National Synchrotron Light Source

and Universities Workshop was again a success, attracting 

17 participants from nine institutions for tutorials about synchrotron science and techniques and a chance to form research collaborations with our staff. I hope we can continue 

to strengthen their ties to our facility and staff members.

Although basic funding continued to present challenges 

this year, we also received some encouraging news: funding 

for the Synchrotron Catalysis Consortium (SCC) was renewed 

through the U.S. Department of Energy’s (DOE) Office of Basic Energy Sciences. The SCC, which promotes the utilization 

of synchrotron techniques to perform cutting-edge catalysis research, operates two – and soon, three – beamlines at 

the NSLS and has been extremely successful in its first years 

of operation. We also received grants totaling $28 million 

from DOE’s Office of Biological and Environmental Research 

and the National Institutes of Health’s National Center for 

Research Resources to support the X-ray Crystallography 

Research Resource (PXRR) at the NSLS. The grants will fund 

five years of operations and research for the PXRR, which has 

received about 800 visits from 150 university, industrial, and 

national laboratory research groups in the last year. In addition, we were awarded a three-year DOE grant to develop 

new x-ray detectors with unprecedented capabilities. Members of our Detector Group, in collaboration with staff from 

Brookhaven’s Instrumentation Department, will use the 

funding to explore the use of three-dimensional integration 

technology, pioneered in the semiconductor industry, to 

develop x-ray detectors with a higher level of functionality 

than is possible with current technologies. 

Finally, as we get closer to the groundbreaking for the National Synchrotron Light Source II, we are paying a great deal 

of attention to planning for transition to this new, worldleading facility. Toward that end, one of our major activities this year was a series of planning workshops hosted in 

collaboration with NSLS-II. The workshops were divided 

into two types: those that focus on specific scientific communities and those that focus on experimental techniques. 

The community input collected during these sessions will 

be used to guide the scientific strategic plans and beamline 

development for both facilities.
6 | A Beacon for Research

Funded by the U.S. Department of Energy’s Office of Basic Energy Sciences, the National Synchrotron Light Source 

(NSLS) is a national user facility that operates two electron 

storage rings: X-Ray (2.8 GeV, 300 mA) and Vacuum Ultraviolet (VUV) (800 mev, 1.0A). These two rings provide intense 

light spanning the electromagnetic spectrum — from very 

long infrared rays to ultraviolet light and super-short x-rays 

— to analyze very small or highly dilute samples. The properties of this light, and the specially designed experimental 

stations, called beamlines, allow scientists in many diverse 

disciplines of research to perform experiments not possible at their own laboratories.

Each year, about 2,200 scientists from more than 400 universities and companies use the NSLS for research in such 

diverse fields as biology, physics, chemistry, geology, 

medicine, and environmental and materials sciences. For 

example, researchers have used the NSLS to examine the 

minute details of computer chips, decipher the structures 

of viruses, probe the density of bone, determine the chemical composition of moon rocks, and reveal countless other 

mysteries of science. The facility has 65 operating beamlines, with 51 beamlines on the X-Ray Ring and 14 beamlines on the VUV-Infrared Ring. It runs seven days a week, 

24 hours a day throughout the year, except during periods 

of maintenance and studies. Researchers are not charged 

for beam time, provided that the research results are published in open literature. Proprietary research is conducted 

on a full-cost-recovery basis. 

With close to 1,000 publications per year, the NSLS is one 

of the most prolific scientific facilities in the world. Among 

the many accolades given to its users and staff, the NSLS 

has won nine R&D 100 Awards for innovations ranging 

from a closed orbit feedback system to the first device able 

to focus a large spread of high-energy x-rays. In addition, 

a visiting NSLS researcher shared the 2003 Nobel Prize in 

Chemistry for work explaining how one class of proteins 

helps to generate nerve impulses.
A New Light on the Horizon | 7

Since its first operations in 1982, the NSLS has continually 

updated its technology and expanded its scientific capabilities. However, as the boundaries of scientific discovery have 

been expanded, many researchers are looking for capabilities beyond those provided by the NSLS. And while newer 

synchrotrons surpass the performance of the present NSLS, 

no synchrotron anywhere in the world will enable scientists 

to image and characterize materials down to billionth-of-ameter (nanometer) resolution.

To address this need, Brookhaven is building — the National 

Synchrotron Light Source II (NSLS-II). The new facility, which 

will replace the NSLS, will be a medium-energy storage ring 

designed to deliver world-leading brightness and flux. It will 

provide advanced tools for discovery-class science in condensed matter and materials physics, chemistry, and biology. 

For example, major advances in energy technologies — such 

as the use of hydrogen as an energy carrier, the widespread, 

economical uses of solar energy, or the development of the 

next generation of nuclear power systems — will require scientific breakthroughs in developing new materials with advanced properties.

The combination of capabilities at NSLS-II will have broad 

impact on a wide range of disciplines and scientific initiatives in the coming decades, including new studies of 

small crystals in structural biology, the development of 

probes for nanoscience, coherent imaging of the structure 

and dynamics of disordered materials, greatly increased 

applicability of inelastic x-ray scattering, and properties of 

materials under extreme conditions. This high-brightness 

light source will also foster research in areas such as structural genomics and drug design as well as extend the studies of early disease detection.

The leading-edge ability of NSLS-II to analyze materials will 

help guide the development of new materials at Brookhaven’s 

Center for Functional Nanomaterials. The synergy of these 

two facilities is expected to lead to breakthroughs in the use 

of renewable energy through improved energy conversion, 

transmission, and storage — science that ultimately will enhance national and energy security and help drive abundant, 

safe, and clean energy technologies.
8 | Science Highlights

Physical and Chemical Sciences Introduction

Ron Pindak

Physical and Chemical Sciences Division Head

While developing future plans for NSLS-II, NSLS staff and users 

continued to apply existing beamline facilities to advance both 

new and on-going research programs. In the physical and chemical sciences, dominate research themes were the study of nanoparticles for energy applications, the study of high-temperature 

superconductivity in copper- and iron-based compounds, and 

the study of materials under extreme conditions. Key discoveries 

for each research area are listed below and described more fully 

in the science highlights that follow.

In hard condensed matter physics, researchers from Brookhaven 

Lab took a significant step in advancing our understanding of 

high-temperature superconductors by showing that electron 

pairs emerge before superconductivity sets in, but only in a 

particular direction. This observation required the researchers 

to improve the resolution of their angle-resolved photoemission spectroscopy measurements so they could look at weak 

signals from above the Fermi level in finer detail. A second 

important avenue of research conducted this year involved 

understanding how misfit strains in thin films can modulate 

their structure and impact their transport properties. A team 

from the Max-Planck-Institut demonstrated how Sr-doped lanthanum manganite films have unexpected one-dimensional 

structural motifs that evolve from a twinning modulation wave 

in thin films to laterally coherent tilt domains in thicker films. 

In materials science, researchers from the University of Minnesota used a gas-condensation technique to fabricate nanoparticles with an iron-cobalt core and gold cladding. Using x-ray 

magnetic circular dichroism, the researchers found that the 

iron-cobalt core had magnetic moments three to four times 

higher than traditional iron oxide nanoparticles. These nanoparticles are of potential interest for enhancing contrast in 

magnetic resonance imaging, for advanced data storage, and 

further down the road, in spintronic devices. Another active 
Science Highlights | 9

area of research in materials science was the study of materials under high pressure. A team led by researchers from the 

Carnegie Institution of Washington used synchrotron infrared 

spectroscopy to observe metallic behavior in silane when compressed to over 60 GPa. This was the first observation of metallization in a hydrogen-rich IVa hydride and represented a significant step toward ultimately observing metallic behavior in 

molecular hydrogen, which is predicted to occur at significantly 

higher pressures and is believed to exhibit unique properties 

that could be useful for developing new methods of energy 

production. The high pressure created in a diamond-anvil cell 

was also used to provide new information on the recently discovered iron-based superconductors. Measurements on this 

new class of superconductors, using angle-dispersive x-ray 

diffraction, revealed that, as pressure was increased, there was 

an abrupt change in lattice parameters followed by an unusual 

negative relationship between pressure and the superconducting transition temperature. 

In the chemical sciences, a wide range of different synchrotron 

techniques were applied to advance our understanding of 

catalytic activity. Using a combination of x-ray photoemission 

spectroscopy, scanning tunneling microscopy, and modeling, 

Brookhaven researchers identified the mechanism underlying 

the water-gas shift reaction catalyzed by cerium oxide and 

titanium oxygen nanoparticles on gold. The water-gas-shift 

reaction is important in preventing carbon monoxide from 

degrading the performance of the platinum electrode used in 

fuel cells. Another team of researchers from Utrecht University 

demonstrated, for the first time, how synchrotron infrared microspectroscopy could be applied to study catalytic reactions 

in-situ within zeolite crystals in a space- and time-resolved manner. Finally, a team of researchers who are members of the Synchrotron Catalysis Consortium used a combination of extended 

x-ray absorption fine structure, x-ray diffraction, and density 

functional theory to demonstrate how a galvanic replacement reaction could be used to form palladium-gold nanoparticles from palladium nanowires. The researchers showed that 

at different stages of the reaction, the palladium-gold in the 

nanoparticle evolved from being a non-random alloy with a 

gold-rich core to a random alloy. Non-random bimetallic nanoparticles have been shown to have enhanced catalytic activity, 

so this was an important advance.

Physical and Chemical Sciences Introduction

“In the chemical sciences, a wide range of different

synchrotron techniques were applied to advance our

understanding of catalytic activity.”
10 | Science Highlights

Condensed Matter Physics

Formation and Thickness Evolution of Periodic Twin Domains in Manganite Films

Since the discovery of colossal magnetoresistance in perovskites containing lanthanides, alkaline earth metals, and 

magnesium oxide, there has been enormous interest in their 

bulk and thin-film forms because of their unusual physical 

properties that lend to potential applications such as magnetic field sensors, computer read heads, infrared detectors, 

and microwave active components. Because future applications will extensively exploit thin-film geometries, the associated transport properties will strongly be determined by 

the strain misfit as caused by the microscopic clamping of 

the film to the substrate.

Conventional film material adjusts its lattice parameters to 

the substrate by stretching or compressing its bond lengths. 

But a perovskite film may use tilting of its oxygen octahedral for strain accommodation at relatively low energy costs. 

Single crystals are naturally microtwinned indicating a low 

energy cost for domain boundaries. Exploiting both aspects, 

manganite films are able to grow epitaxially on a perovskite 

substrate even for large lattice misfits. Thus, by a microscopic understanding of this misfit strain relaxation mechanism, 

one may get a tool at hand for tuning the electronic properties of manganite films.

At NSLS beamline X22A, researchers from the Max-PlanckInstitut conducted a systematic x-ray diffraction study of 

the strain relaxation behavior of a strontium-doped lanthanum manganite film on a strontium titanate substrate. They 

revealed a new kind of misfit strain relaxation process that 

emerges as unexpected one-dimensional structural motifs 

that evolve from a twinning modulation wave in thin films to 

laterally coherent tilt domains in thicker films. 

U. Gebhardt, N.V. Kasper, A. Vigliante, P. Wochner, H. Dosch, F.S. Razavi, 

and H.-U. Habermeier, “Formation and Thickness Evolution of Periodic 

Twin Domains in Manganite Films Grown on SrTiO3(001) Substrates,” 

Phys. Rev. Lett., 98, 096101 (2007).

(a) Real-space sketch to show which motifs of the film structure, grown on average pseudomorphically on top of a rigid, 

cubic substrate (STO), are dominant in the case of a thin 

(left) and a thick manganite film (right). The difference in 

variance of the TD length for the two cases is not illustrated 

in the picture. (b) Temperature dependence of the structure 

(integrated intensity of the central peak and the 1st and 2nd 

order satellite peaks of the (004) Bragg reflection) and transport of the 26 nm LSMO film. The inset shows the (00L) 

associated film (solid symbols) and substrate (open circle) 

peak positions.

From left, Nikolai Kasper, Assunta Vigliante, and Peter Wochner
Science Highlights | 11

Condensed Matter Physics

Electron Pairs Precede High-Temperature Superconductivity

Brookhaven physicists have found ways to sharpen images of 

the energy spectra in high-temperature superconductors — 

materials that carry electrical current effortlessly when cooled 

below a certain temperature. These new imaging methods 

confirm that the electron pairs needed to carry current emerge 

above the transition temperature, before superconductivity 

sets in, but only in a particular direction.

To search for pre-formed electron pairs, the Brookhaven team 

bombarded a copper-oxide material, held at temperatures 

above and below the transition temperature, with beams of 

light from NSLS beamline U13UB, and analyzed the energy 

spectrum of electrons emitted from the sample. This method, 

known as angle-resolved photoemission spectroscopy, ordinarily gives a clear picture of only half of the energy spectrum — all 

the levels electrons can occupy below the so-called Fermi level. 

To glimpse the other half, above the Fermi level, the scientists 

devised ways to sharpen the resolution of their images. 

Seeing both sides of the Fermi level is important because, 

when a material becomes a superconductor, there is an energy gap surrounding the Fermi level. A perfectly symmetrical gap is a strong indication that electrons are paired up. 

But scientists had previously observed a second gap, or 

pseudogap, in some high-temperature materials, well above 

the transition temperature. If this pseudogap exhibited the 

same symmetry around the Fermi level, the researchers reasoned, it would be definitive evidence of paired electrons 

above the transition temperature. Using their new image-enhancing techniques, the Brookhaven team demonstrated that 

the pseudogap does indeed exhibit this same symmetry.

Another interesting observation: The pairing occurs only 

along certain directions in the crystalline lattice of atoms 

making up the material — along those in which copper atoms are bonded with oxygen atoms.

H. Yang, J. Rameau, P. Johnson, T. Valla, A. Tsvelik, and G. Gu, “Emergence of Preformed Cooper Pairs from the Doped Mott Insulating 

State in Bi2Sr2CaCu2O8+δ,” Nature, 456, 77-80 (2008).

Map of the spectral intensity of photoelectrons emitted from a high-Tc superconductor in the superconducting state as a function of energy and momentum. a) The spectral intensity as measured and b) the spectral intensity after 

Peter Johnson analysis showing states both above and below the Fermi level (vertical line).
12 | Science Highlights

Materials Sciences

Determining the Dislocation Sense of Closed-Core Screw Dislocations 

Defects existing in semiconductor single-crystal materials 

adversely affect the device performance fabricated on them. 

Understanding the defect characters plays a critical role in 

designing strategies to eliminate or reduce their negative 

effect. At the NSLS, researchers from Stony Brook University used x-rays to reveal details about a particular defect in 

silicon carbide, an abrasive material used in everything from 

grinding wheels to semiconductor equipment. 

Single-crystal materials have pre-existing boundaries between regions that are displaced relative to one another. 

These boundaries, called dislocations, come in several forms. 

One form, called a screw dislocation, features planes that are 

connected in a manner similar to a spiral parking ramp. Currently, no technique is able to reveal the dislocation sense 

(left- or right-handed) of closed-core screw dislocations in 

commercial silicon carbide wafers in a simple, unambiguous, 

and non-destructive way. But the researchers demonstrated 

two new techniques that might be able to do just that.

Using grazing-incidence synchrotron white beam x-ray topography at NSLS beamline X19C, the team observed and 

differentiated the sense of screw dislocations in their sample 

silicon carbide wafers. In order to confirm these dislocation 

senses, small Bragg angle back-reflection topography was 

used in the same region of the crystal. The results were 

consistent, showing that screw dislocations can be unambiguously and non-destructively revealed using either technique. Revealing the sense of these dislocations can provide 

critical information regarding their formation mechanism 

and these techniques can possibly be used in other singlecrystal materials.

Y. Chen and M. Dudley, “Direct Determination of Dislocation Sense of 

Closed-Core Threading Screw Dislocations Using Synchrotron White 

Beam X-Ray Topography in 4H Silicon Carbide,” Applied Physics Letters, 

91, 141918 (2007).

(a) A highly magnified x-ray topograph 

showing the images of 1c TSDs in 4HSiC. (b) Ray-tracing simulation of lefthanded 1c TSD. (c) Ray-tracing simulation of right-handed 1c TSD.

Yi Chen (left) and Michael Dudley
Science Highlights | 13

Materials Sciences

Response of Pyrochlore to Extreme Conditions

At the NSLS, a team of researchers from the University of Michigan and Rensselaer Polytechnic Institute demonstrated the 

effect of composition on the stability and response of the 

pyrochlore structure under high pressure and high radiation. 

This study lays the foundation for understanding how complex 

ceramics will respond to the extreme environments, such as 

those in advanced nuclear reactors.

Pyrochlore has a flexible structure, which can exist in more than 

500 compositions that have a wide variety of chemical and 

electronic properties with many technological applications. 

Some pyrochlores can also incorporate actinides, such as plutonium, so there is great interest in their use as nuclear waste 

forms or as inert matrix fuels.

In order to investigate the effects of high pressures and irradiation on pyrochlore, two closely related compositions — a gadolinium titanate oxide and a gadolinium zirconate oxide — were 

compressed with up to 45 gigapascals (GPa) of pressure, roughly 

more than six million pounds per square inch. That, by comparison, is almost 200,000 times the pressure in a car tire and more 

than the weight of a space shuttle on one’s fingertip. 

The structure of gadolinium titanate oxide remained relatively 

stable under the highest pressures tested (45 GPa), but the 

gadolinium zirconate oxide only maintained stability up to 23 

GPa, above which it structurally distorted. When the pressure 

was released, the zirconate pyrochlore further disordered into a 

very stable defect-fluorite structure.

Under ion-beam radiation, however, the behaviors of the two pyrochlores changed. The zirconium pyrochlore was more resistant 

to radiation damage, and therefore remained crystalline. In contrast, the titanate pyrochlore transformed into disordered structure at low doses and finally became stable at higher doses.

After using Raman scattering, calculations, and angle dispersive x-ray diffraction at NSLS beamline X17C, the researchers 

concluded that the performance of these materials in extreme 

environments is directly related to the energetics of the disordering process. 

F. X. Zhang, J. W. Wang, J. Lian, M. K. Lang, U. Becker, and R. C. Ewing, 

“Phase stability and pressure dependence of defect formation in Gd2

Ti2O7 and Gd2Zr2O7 pyrochlore,” Phys. Rev. Lett., 100(4): 045503 (2008).

X-ray diffraction images for Gd2Ti2O7 at (a) 22.2 

GPa, (b) 45.0 GPa, (c) 0 GPa (recovered sample 

and measured immediately), (d) 1 bar, 5 h after 

release of pressure; Gd2Ti2O7at (e) 16.0, (f) 44.0, 

(g) 0 GPa (recovered sample and measured immediately) and (h) 1 bar, 10 h after releasing 

pressure.

From left, Maik Lang, Jianwei Wang, Udo Becker, Fuxiang Zhang and Rod Ewing (holding Sofia)
14 | Science Highlights

Materials Sciences

Through the Wire: A New Nanocatalyst Synthesis Technique

Materials containing bimetallic nanoparticles are attractive 

in vast technological fields because of their unique catalytic, 

electronic, and magnetic properties. One of the most promising of the bunch is made from palladium and gold, an alloy that could be used in a wide variety of catalytic activities 

including the water-gas shift reaction and the oxidation of 

carbon dioxide – both important steps in alternative energy 

applications like fuel cells. This alloy has the highest catalytic 

activity when its structure is “non-random,” with a core made 

predominantly of gold nanoparticles and a shell made mostly 

of palladium. However, creating the material with traditional 

chemistry techniques is tricky and difficult to control. 

Recently, though, a team of researchers from Brookhaven, 

Yeshiva University, and the University of Delaware demonstrated an alternative, highly efficient method based on galvanic replacement – the principle behind the technology of 

batteries. The driving force for galvanic replacement is the 

electrical potential difference between two metals, with one 

metal acting principally as the cathode and the other metal 

as the anode. The reaction was set up between palladium 

nanowires just about 2.5 nanometers thick – one of the 

thinnest wires reported in the scientific community – and 

a solution of gold chloride in toluene. The researchers then 

“watched” the reaction take place through multiple techniques, including electron microscopy and UV-vis absorption at Brookhaven’s Center for Functional Nanomaterials, 

x-ray diffraction at NSLS beamline X7B, and extended x-ray 

absorption fine structure at beamline X18B. 

In the early stages of the reaction, the alloy was, indeed, 

non-random, with a gold-rich core and palladium-rich shell. 

The subsequent addition of the compound alkylamine stabilized palladium to the surface and kept the non-random 

form intact. However, if the reaction was allowed to continue, a random alloy was formed, with uniformly mixed gold 

and palladium atoms inside the particles.

X. Teng, Q. Wang, P. Liu, W. Han, A. Frenkel, W. Wen, N. Marinkovic, J. 

Hanson, J. Rodriguez, “Formation of Pd/Au Nanostructures from Pd 

Nanowires via Galvanic Replacement Reaction,” J. Am. Chem. Soc., 

130: 1093-1101 (2008).

Schematic side view (top) and cross section (bottom) of as-made Pd, Pd68Au32, 

Pd45Au55, and Au nanomaterial during the 

galvanic replacement reaction.

From left, Wen Wen, Xiaowei Teng, Nebojsa Marinkovic, 

Jonathan Hanson, Weiqiang Han, Qi Wang, and Anatoly 

Frenkel
Science Highlights | 15

Materials Sciences

Putting the Pressure on Iron-Based Superconductors

Traditionally, magnetism and superconductivity don’t mix. 

For more than 20 years, the only known superconductors 

that worked at so-called “high” temperatures (above 30 K, 

or about -406 degrees Fahrenheit) were almost all based on 

copper. Materials with strong magnetism, scientists thought, 

would disrupt the pairing of electrons that is key to achieving 

the frictionless flow of superconductivity. So when a group 

of researchers recently found high-temperature superconductivity present in a class of iron-based materials, their discovery shocked and excited the scientific community. 

Made from conducting layers of iron, arsenic, and various 

other elements, this new class of materials could lead to 

applications such as more-efficient power transmission. 

However, iron-based superconductors are still in the early 

stages of experimentation and implementation. That’s why 

researchers from the Harbin Institute of Technology, the Chinese Academy of Sciences, and the NSLS set out to study 

the characteristics of a specific iron-and-arsenic-based, neodymium-containing superconductor.

The main objective for scientists in the field is to find superconductors with the highest transition temperature (Tc). To find 

out how Tc is affected by high pressure in the iron-based neodymium arsenide superconductor system, the research team 

subjected their samples to more than 30 GPa with NSLS beamline X17B3’s diamond-anvil cell. High pressure can compress the 

crystalline structure of the material and force its layers closer 

together, which might increase the material’s Tc by improving 

charge transfer between the layers. To measure this effect, the 

researchers used angle-dispersive x-ray diffraction. 

Their results didn’t turn out exactly as expected: As pressure 

increases from 0 to 15 GPa, the spacing decreases and Tc 

increases marginally. But as the pressure increases further, 

one of the other lattice parameters abruptly increases and 

the Tc drops. These new findings could offer insight on how 

to design and create other superconducting systems.

J. Zhao, L. Wang, D. Dong, Z. Liu, H. Liu, G. Chen, D. Wu, J. Luo, N. 

Wang, Y. Yu, C. Jin, and Q. Guo, “Structure Stability and Compressibility of Iron-Based Superconductor Nd(O0.88F0.12)FeAs Under High 

Pressure,” JACS, 130 (42), 13828-13829 (2008).

An iron-based superconductor under pressure.

From left, Jinggeng Zhao, Dawei Dong, Zhiguo Liu, Haozhe 

Liu, and Luhong Wang
16 | Science Highlights

Materials Sciences

Squashing Silane into Metal

Squeeze it hard enough and hydrogen, the most abundant 

and lightest element in our Universe, strangely takes on a metallic nature. During this state, as it loses hold of its electrons, 

hydrogen is believed to display unique characteristics including high-temperature superconductivity and properties that 

could be useful in developing new methods of energy production using nuclear fusion and alternative fuels. Creating 

this drastic phase change, however, is extremely difficult. As a 

result, efforts to form and detect solid metallic hydrogen have 

been elusive. Recently, though, a team of researchers from the 

Carnegie Institution of Washington, South China University of 

Technology, and the University of Western Ontario, used the 

NSLS to study silane, a hydrogen-rich compound, to learn 

more about the leader of the period table.

Most scientists believe that the recipe for creating metallic 

hydrogen involves heating it to 3,000 degrees Kelvin (a little 

hotter than 2,700 degrees Celsius) and exposing it to about 

1.4 million atmospheres of pressure (140 GPa). By comparison, the pressure inside the core of the Earth is 380 GPa. 

However, these conditions are very difficult to reach and record in a laboratory.

Using two silane samples, the researchers found far less demanding pressure requirements for metallization: about 60 

GPa. Their experiment offers the first example for the metallization of an IVa hydride.

In order to conduct the experiment, the researchers placed 

their silane samples in a diamond anvil cell, a device that 

uses the polished faces of two diamonds to apply extremely 

high pressure. By applying a range of pressures and measuring the results through infrared reflectivity experiments at 

beamline U2A, the group found that silane undergoes three 

phase transitions before becoming opaque at 27-30 GPa. 

Above 60 GPa, the material shows an increase in reflectivity, 

indicating pressure-induced metallization.

X. Chen, V. Struzhkin, Y. Song, A. Goncharov, M. Ahart, Z. Liu, H. Mao, 

R. Hemley, “Pressure-Induced Metallization of Silane,” Proc. Natl. Acad. 

Sci., 105(1), 20-23 (2008).

Room-temperature infrared reflectivity spectra of SiH4 at selected pressures up to 67.2 GPa. The blue squares are the 

measurement results. The solid lines represent model fits to 

the data. The small gap in the spectrum near 2000 cm-1 is 

due to diamond anvil absorption.

Back, from left, Zhenxian Liu, Russell Hemley, Alexander 

Goncharov, and Ho-kwang Mao. Front, from left, Muhtar 

Ahart, Viktor V. Struzhkin, and Xiaojia Chen
Science Highlights | 17

Materials Sciences

Creating Highly Sought Magnetic Nanoparticles in One Step

Researchers from the University of Minnesota demonstrated 

a one-step technique for producing a class of magnetic nanoparticles that could be used in everything from biomedical 

applications to data storage. 

In the medical realm, single magnetic nanoparticles might 

someday be used to deliver anticancer drugs to a targeted 

area of the body, or to enhance the contrast in magnetic resonance imaging (MRI). The particles also could assist in the 

development of advanced computers, and further down the 

road, in spintronic devices. In general, the higher the nanoparticle’s magnetic moment – the measure of a material’s magnetic strength – the more valuable it is for these applications.

The research group studied nanoparticles made of iron-cobalt (the core) and gold (shell), which have a magnetic moment three to four times higher than traditional iron oxide 

nanoparticles. Their study is the first to show how these particles can be created in a simpler and more efficient manner 

than conventional chemical methods, which are limited by 

the solvent’s extremely high boiling temperature and the risk 

of corrosion due to air exposure. In their one-step, gas-condensation technique, a sputter gun bombards a solid metallic 

target made of iron, cobalt, and gold with energetic ions. This 

all happens within a heat bath of high-pressure gas, which 

transforms the high-energy atoms into the desired nanoparticles.

The resulting nanocrystals were analyzed with high-resolution 

transmission electron microscopy and energy-dispersive x-ray 

spectroscopy, as well as with x-ray magnetic circular dichroism 

at NSLS beamline U4B. Their findings suggest that the nanoparticles are very promising for biomedical applications: the 

resulting cubic crystals are very pure; the shell is thick enough 

to prevent oxidation of the iron-cobalt core for more than four 

months of air exposure; and the nanoparticles’ magnetic moments are close to the values in bulk iron-cobalt alloy. 

Y. Xu, J. Wang, “FeCo-Au Core-shell Nanocrystals,” Appl. Phys. Lett., 91: 

233107 (2007).

(Right): Structure of FeCo-Au nanocrystals. (a) CBED of the nanocrystal in (b), the two distorted hexagons (dot and dot-dash line) indicating two perpendicular Au [011]s. (b) a TEM bright field image of 

a nanocrystal. (c) illustration of the epitaxial relationship between 

the bcc FeCo (dotted line) and fcc Au (solid line) (smaller atom, Fe 

or Cu; larger atom, Au). (d) the perpendicular relationship between 

the two Au (110)s (indicated by arrows) at two neighboring facets 

of FeCo {100}, with a twinning at the rim. (e) a 3D illustration of a 

corner of the FeCo-Au nanocrystal. (f) HRTEM image of a corner of 

a nanocrystal with the same angle between the Au (111)s from the 

neighboring Au.

(Above): Hysteresis loop of Fe in FeCo-Au nanocrystals (measured at Fe-L edge by XMCD).
18 | Science Highlights

Chemical Sciences

Experiments Reveal Unexpected Activity of Purifying Catalysts

A group of Brookhaven-led researchers unveiled important 

details about a class of catalysts that could help improve the 

performance of fuel cells. With the goal of producing “clean” 

hydrogen for fuel cell reactions in mind, the researchers determined why two next-generation catalysts including gold, 

cerium, titanium, and oxygen nanomaterials exhibit very 

high activity. 

A major problem facing fuel cell technology is that the 

hydrogen-rich materials feeding the reaction often contain 

carbon monoxide (CO), which deteriorates the expensive 

platinum-based catalysts that convert hydrogen into electricity. That’s where the “water-gas shift” (WGS) reaction 

comes in, combining CO with water to produce additional 

hydrogen gas and carbon dioxide. The ultimate goal is to 

find the catalysts that will help convert nearly 100 percent 

of the CO into carbon dioxide, an important step toward 

achieving a hydrogen-based economy. 

Toward this effort, the researchers, from Brookhaven’s chemistry department, the Center for Functional Nanomaterials, and 

the Central University of Venezuela, examined the nanoscale 

catalysts gold-cerium oxide and gold-titanium oxide. These 

catalysts usually consist of gold nanoparticles dispersed on 

a ceria or titania surface. But to get a better idea of how the 

catalysts work, the researchers studied the “inverse models,” 

ceria or titania nanoparticles on gold. 

Using x-ray photoelectron spectroscopy at NSLS beamline 

U7A, in addition to scanning tunneling microscopy and calculations, the group found that although pure gold is inert for 

the WGS reaction, it becomes extremely active when combined with ceria or titanium. This high activity is due to the 

catalysts’ nanosized oxides, which are able to break apart water molecules – the most difficult part of the WGS reaction. 

J.A. Rodriguez, S. Ma, P. Liu, J. Hrbek, J. Evans, and M. Pérez, “Activity 

of CeOx and TiOx Nanoparticles Grown on Au(111) in the Water-Gas 

Shift Reaction,” Science, 318: 1757-1760 (2007).

A scanning tunneling microscopy (STM) image 

taken of ceria nanoparticles on a gold surface. 

Size: 40 x 40 nanometers.

From left, Jose Rodriguez, Jan Hrbek, and Ping Liu
Science Highlights | 19

Chemical Sciences

Watching Catalytic Reactions from Within

Researchers from Utrecht University, in The Netherlands, have 

demonstrated a new way to get a real-time, microscopic view 

of the inner workings of catalytic reactions.

Catalysis, a natural and manmade way to accelerate and direct chemical reactions, is a common process used in everything from the production of gasoline, electronic devices, and 

clothing, to the development of clean and renewable energy 

technologies. Traditionally, catalysts are studied using a synchrotron technique called x-ray absorption spectroscopy 

(XAFS), during which samples are bombarded with beams of 

high-energy x-rays.

But XAFS is not always capable of giving clear details about 

the chemical transformation that reactant molecules undergo 

on the catalyst’s surface. To get a better idea of the inner happenings of these molecules, the research team used a unique 

setup at NSLS beamline U10B, where an infrared spectrometer 

is coupled with an optical microscope to create a powerful 

technique called infrared microspectroscopy.

IR microspectroscopy offers unprecedented chemical sensitivity and spatial resolution and gives researchers direct insight into the chemical nature of the reactant molecules, the 

potential intermediates, and the resulting products as the catalytic reaction occurs. The method is one of just a few techniques capable of analyzing the internal surfaces of catalyst 

materials during the course of a reaction, and it’s the first to 

be done using infrared light. 

The researchers tested the technique on a zeolite – a powerful catalyst used in the petrochemical industry that contains 

aluminum, silicon, and oxygen. Specifically, the researchers 

looked at the transformation of the organic compound, styrene, within the zeolite crystals. They were able to determine 

the principal reaction intermediate and identify important 

structure-function relationships within the material.

E. Stavitski, M.H. Kox, I. Swart, F.M.F. de Groot, B.M. Weckhuysen, “In 

Situ Synchrotron-Based IR Microspectroscopy To Study Catalytic Reactions in Zeolite Crystals,” Angew. Chem., 47(19) 3543–3547, (2008).

Molecules formed during a catalytic reaction in the zeolite micropores are identified using synchrotron infrared light.From left, Tom Visser, Eli Stavitski, and Marianne Kox
20 | Science Highlights

X-Ray Optics and Accelerator Physics

Creating an Electron Avalanche without Electronics

Dilute elements – those with low concentrations in a material – are extremely hard to pinpoint using synchrotron 

radiation. However, a team of scientists from the NSLS and 

Southern University is testing a way to amplify these small 

signals, creating a signal stronger than those produced by 

traditionally used detectors.

Extended x-ray absorption fluorescence spectroscopy (EXAFS) is a powerful technique used often in the environmental and geological sciences for measuring trace element 

concentrations in a sample. Conventional devices such as 

passivated implanted planar silicon (PIPS) and Lytle detectors are generally used in EXAFS experiments to pinpoint 

weak signals. Neither is perfect: Lytle detectors produce 

noise that can further hide the already weak dilute element 

signals, and PIPS detectors are sensitive to light and temperature changes.

That’s why the research group explored the use of a detector based on a gas electron multiplier (GEM), which amplifies 

a signal without electronics, and therefore, virtually without noise. Like a single chunk of snow that grows into an 

avalanche, the amplification technique accelerates a small 

group of electrons in a field, which hits and excites other 

atoms until the signal is very strong. 

Using an arbitrary tree leaf as a sample on NSLS beamline 

X19, the research team tested its GEM detector in the search 

for the dilute element iron. They found that the GEM resulted 

in an improvement in signal amplitude by a factor of 20 and 

a factor of 2 when compared to the Lytle and PIPS detectors, 

respectively.

E.H. Shaban, D.P. Siddons, A. Kuczewski, “Gas Electron Multiplier (GEM) 

Enhanced Ionization Chamber for Fluorescence Detector,” Nuclear Instruments and Methods in Physics Research, 582, 185-186 (2007).

μ(E) for the detectors SUBRSAB, PIPS, and Lytle

Elhag Shaban (left) at Brookhaven with Southern University 

students Marcus Walker and Vontrelle Collins
Science Highlights | 21

X

Ray Optics and Accelerator Physics

Efficiency Doubling in a Laser-Seeded Free Electron Laser Amplifier

As scientific research continues to explore the limits of smaller (nanometer and sub nanometer) and faster (femtosecond 

and attosecond) phenomena, light pulses are commonly 

used as probing tools. Free electron lasers (FELs) are capable 

of generating light levels that exceed those of conventional 

synchrotron sources by many orders of magnitude. However, by simply relying on the FEL instability, x-ray FEL emission can have good transverse (spatial) coherence, but lacks 

longitudinal (temporal) coherence. A proposed solution 

is seeded FEL emission, in which the instability is initiated 

by a coherent seed laser pulse. Recently, researchers from 

Brookhaven and Science Applications International Corp. 

used the NSLS Source Development Laboratory to demonstrate the doubling of FEL efficiency without degradation of 

its quality. This is the first direct experimental demonstration 

of the FEL spectral stability in a laser-seeded FEL.

In the detuning experiment, a 800 nm Ti:sapphire laser was 

used as the seed, and the FEL output energy and spectrum 

were measured as the electron beam energy was scanned. 

When the electron beam energy was tuned to about 0.7 

percent higher than resonance, the FEL energy more than 

doubled. Instead of the 1.4 percent spectral shift predicted 

by the resonance condition, no FEL spectral shift was observed within the spectrometer resolution (0.05 percent) as 

the electron beam energy was scanned. An increase in the 

FEL gain length was also observed with energy detuning.

The experiment not only demonstrated for the first time 

a simple technique to improve the FEL efficiency, but also 

showed that the coherent seed laser determines FEL central 

wavelength, hence FEL spectral is insensitive to the electron 

beam energy jitter.

X.J. Wang, T. Watanabe, Y. Shen, R.K. Li, J.B. Murphy, T. Tsang, and H.P. 

Freund, “Efficiency Enhancement Using Electron Energy Detuning in 

a Laser Seeded Free Electron Laser Amplifier,” Applied Physics Letters, 

91, 181115 (2007).

The FEL output as a function of electron beam energy. The 

graph shows that electron beam energy detuning can improve the FEL efficiency by more than a factor of two.

From left, Takahiro Watanabe, James Murphy, Thomas Tsang, 

Xijie Wang, Yuzhen Shen and Boyzie Singh at the Source Development Lab
22 | Science Highlights

Life and Environmental Sciences Introduction

Lisa Miller

Life and Environmental Sciences Division Head

2008 was another exciting and productive year for NSLS users 

and staff research in the fields of structural biology, biomedical 

imaging, geological and environmental sciences, and soft condensed matter and biophysics. The community represents more 

than 60 percent of the NSLS users and its publications continue 

to be of high impact in premier scientific journals like Science, 

Nature, Physical Review Letters, and PNAS. This year’s Activity Report briefly describes some of the highlights of 2008, while many 

more highlights can be found on the NSLS website.

In the fields of soft condensed matter and biophysics, the 

mechanisms behind the ordering and self-assembly of materials 

were studied in a wide range of systems in 2008. Selected as an 

“Editors’ Favorite” in Nature in 2008, a team of Brookhaven Lab researchers used DNA to guide the creation of three-dimensional, 

ordered, crystalline structures of nanoparticles (Nykypanchuk, et 

al.). The ability to engineer such 3-D structures is essential to producing functional materials that take advantage of the unique 

properties that may exist at the nanoscale – for example, enhanced magnetism, improved catalytic activity, or new optical 

properties. In another study, Jaradat, et al. used resonant x-ray 

scattering to measure orientational order in layered liquid crystal 

phases. Depending on how the direction of the in-plane polarization varies between layers, an applied electric field can induce 

changes in orientation, which can be utilized in applications 

from high-resolution camera viewfinders to large-area monitors. 

In earth and geosciences, the high brightness of synchrotron 

light shined in 2008 when Lehmann, et al. used x-rays to illustrate, 

for the first time, the nanoscale heterogeneity of organic carbon 

soils from countries around the world including the United States, 

Panama, Brazil, Kenya, and New Zealand. Since the presence of 

natural organic matter in soils is a sensitive indicator of environmental stresses such as climate change, it is important to under-
Science Highlights | 23

Life and Environmental Sciences Introduction

stand the fate of natural organic matter worldwide. A further understanding of this process in nutrient-poor lakes was gleaned 

by Schafer, et al. when they used transmission electron microscopy (TEM), scanning transmission x-ray microscopy (STXM), and 

Fourier transform infrared micro-spectroscopy (μFTIR) to show 

that natural organic matter adsorbs to inorganic particles in the 

lakes, reducing their bioavailability.

Synchrotron applications yielded further progress toward improved environmental remediation in 2008 when x-ray fluorescence microprobe studies of plutonium (Kaplan, et al.) and 

uranium (Tokunaga, et al.) showed how the mobility of these 

contaminants in the environment is heavily dependent upon 

their oxidation state. These findings have important implications 

for the disposal and remediation scenarios for long-lived radioisotopes. In addition, Ndiba, et al. used extended x-ray absorption 

fine structure (EXAFS) to show that other metals and toxins can 

be immobilized in dredged sediments through phosphate and 

thermal treatment, making them safer and reusable for things 

like road-based construction.

Finally, it was another impressive year for the structural biologists 

in the field of macromolecular crystallography. As an example, 

this year’s Activity Report highlights work by Kumaran, et al. that 

identifies a highly efficient inhibitor of the botulinum neurotoxin, 

which is a promising drug target for the most deadly neurotoxin 

known to humans. We also feature four important crystal structures published in Nature this year that provide atomic resolution 

images that describe enzyme functions including: how the p300/

CBP enzyme regulates gene function through acetylation (Liu, 

et al.); how AMP-activated protein kinase (AMPK) regulates the 

intracellular ratio of AMP:ATP (Amodeo, et al.); how telomerase 

works to replicate the ends of chromosomes – a process critical 

to both tumor development and the aging process (Gillis, et al.); 

and how calpastatin can inhibit calcium-bound calpain without 

being cut and destroyed in the process (Hanna, et al.). But this selection of highlights barely touches the surface of the hundreds 

of crystal structures solved at the NSLS in 2008 and I encourage 

you to visit the NSLS website for more details on these important 

discoveries.

“The life and environmental science community represents

more than 60 percent of the NSLS users and its publications

continue to be of high impact in premier scientific journals.”
24 | Science Highlights

Earth and Environmental Sciences

Experimental and linear combination fitting reconstructed χ(k)·k3

spectra for dredged and treated sediments. Only spectra with 

more than 10% contributions are included. The fitting factor R 

= ∑[(k3χexp-k3χmodel)/k3χexp]

2 where χmodel refers to spectra reconstruction with PCA decomposed components. Zn-HFO and 

Zn-MnO refer Zn sorbed to hydrous iron oxide and hydrous manganese oxide, respectively.

Authors Peter Nbida (left) and Lisa Axe

Heating Up Dredged Sediment

Historically, dredged materials – often contaminated with 

heavy metals and toxins from industrial and urban activities 

– were dumped in open waters, rivers, estuaries, or wetlands. 

But heightened environmental regulations and increasing 

costs for land deposition have presented a major challenge 

for dredging projects. As an alternative, attention has turned 

to the treatment and reuse of sediments, a move that would 

reduce costs and conserve resources. Most of these alternative technologies involve heating the sediment to extreme 

temperatures in order to eliminate its toxic nature and make 

it environmentally safe for products such as cement, lightweight bricks, and ceramic and glass tiles. However, few existing technologies are actually commercially used, stressing 

the need for further development.

Toward that effort, a group of researchers from the New Jersey Institute of Technology investigated a specific thermal 

technique that incorporates the addition of phosphate. 

After obtaining sediment from waterways in Belgium, the 

group added phosphoric acid to their samples and then 

heated them to 700 degrees Celsius. Next, they used x-ray 

absorption spectroscopy at NSLS beamline X11A to study 

the heavy metals’ speciation, which primarily determines 

how easily they leach from the sediment and into the surrounding environment. 

Looking primarily at zinc – found in abundance in contaminated sediment from both the United States and Europe – the group discovered that the thermal phosphate 

treatment transformed the metal into more stable phases, 

phosphate minerals and spinels. The result was an 89 percent reduction in zinc leachability.

Their findings suggest that even if zinc does leach in its 

final form, it probably won’t be at a measureable level.

P. Ndiba, L. Axe, T. Boonfueng, “Heavy Metal Immobilization through 

Phosphate and Thermal Treatment of Dredged Sediments,” Environ. 

Sci. Technol., 42, 920-926 (2008).
Science Highlights | 25

Earth and Environmental Sciences

Lake Brienz 1 m depth 

sample (July 2005). From 

left to right: absorption 

image at 280 eV, distribution of aromatics, and 

distribution of organics. 

Shades of bright grey 

indicate high concentrations of organic functionality.

Vincent Chanudet (left) and Montserrat Filella

Characterization of Natural Organic Matter in a Low-Nutrient Lake

Low-nutrient, or oligotrophic, alpine lakes showing very small 

quantities of natural organic matter (NOM) have attracted increased interest recently as they are sensitive indicators for a 

wide variety of anthropogenic stressors (those derived from 

human activities). To investigate the role of mineral colloids 

and organic macromolecules in creating and/or maintaining 

severe oligotrophic conditions, a team of researchers from 

the Institut für Nukleare Entsorgung, the University of Geneva, and the Bureau de Recherches Géologiques et Minières 

used a combination of microscopic and spectroscopic tools 

on samples from Switzerland’s Lake Brienz and its tributaries, 

the Aare and Lütschine Rivers.

Data were gathered from transmission electron microscopy, 

scanning transmission x-ray microscopy (STXM) at NSLS beamline X1A1, and ultra-Fourier transform infrared (FTIR) spectroscopy at NSLS beamline U10B. Combining these methods with NOM 

measurements made it possible, for the first time, to quantify the 

types, functionalities, sources, and fate of submicron NOM present in the lake and tributaries. 

The group found that NOM concentrations remained extremely 

low throughout the year, melting snow was responsible for about 

32 percent of the lake's annual refractory organic matter input 

(ROM), and about 25 percent of ROM was lost within the lake that 

is not accounted for by lake flushing.

In particular, all organics in a Lake Brienz sample taken at a 100-meter depth showed an association to potassium-rich minerals and 

very comparable organic functionality to the mineral-associated 

organic matter of the surface waters. This suggests that sedimentation of organic material is one of the major organic removal processes in the lake, thus supporting conclusions that NOM sorption 

onto inorganic settling particles mainly causes the elimination of 

NOM in the lake. Their results prove that STXM and FTIR are suitable to characterize colloidal and particulate organic material and 

its functionality in very low organic carbon systems.

T. Schäfer, V. Chanudet, F. Claret, and M. Filella, “Spectromicroscopy 

Mapping of Colloidal/Particulate Organic Matter in Lake Brienz, Switzerland,” Environmental Science & Technology, 41, 7864-7869 (2007). 

V. Chanudet and M. Filella, “Submicron Organic Matter in a Peri-Alpine, 

Ultra-Oligotrophic Lake,” Organic Geochemistry, 38, 1146-1160 (2007).
26 | Science Highlights

Earth and Environmental Sciences

Micro-SXRF elemental map 

images of sediment next 

to the PuIV(NO3)

4-amended 

filter disc. Relative concentrations on these maps 

increase from black (least 

concentrated), blue, red, 

and yellow (most concentrated).

Daniel Kaplan

Investigating Plutonium Oxidation State Transformations

Plutonium (Pu) is an element of concern in disposal and remediation scenarios because of its radiotoxicity and very 

long half-lives for several isotopes. Once released into the 

environment, the movement of Pu is strongly related to its 

oxidation state. In aqueous solutions, Pu can exist in oxidation states III, IV, V, and VI, with two or three of these oxidation states commonly present at equilibrium. Pu(V) and 

Pu(VI) are typically two orders of magnitude more mobile 

than Pu(III) or Pu(IV). To further investigate Pu oxidation state 

transformations in its natural environment, a team of researchers from the Savannah River National Laboratory and 

Clemson University used x-ray techniques at the NSLS. 

First, the researchers established a series of lysimeters on 

the Savannah River Site located in Aiken, South Carolina, to 

evaluate the long-term transport of Pu through vadose zone 

sediments – the region below the root zone and above the 

underlying water table where radioactive waste in the U.S. is 

disposed. Five lysimeters, planted for 11 years, were evaluated for this study: an unamended control and four lysimeters 

amended with varying oxidation states of Pu.

Micro- x-ray fluorescence studies at NSLS beamline X26 revealed that Pu was very unevenly distributed on the sediment and manganese concentrations were too low and 

perhaps of the wrong mineralogy to influence Pu distribution. X-ray absorption near-edge structure of the Pu(III) and 

Pu(IV)-amended lysimeters contained essentially identical 

Pu distributions, suggesting steady state had been achieved. 

This is likely the first observation of steady state Pu(III) in association with natural sediments.

D.I. Kaplan, B.A. Powell, M.C. Duff, D.I. Demirkanli, M.E. Denham, R.A. 

Fjeld, and F.J. Molz, “Plutonium Source Solubilities and Oxidation 

State Transformations in Vadose Zone Sediments,” Environ. Sci. Technol., 41(21): 7417–7423 (2007).

Martine Duff Brian Powell Miles Denham

Pu Fe Mn
Science Highlights | 27

Earth and Environmental Sciences

Distribution of carbon contents and molecular forms 

in a soil microassemblage 

from Nandi Forest (Kenya) 

determined by NEXAFS in 

combination with STXM. a) 

Total carbon. b) Aromatic 

carbon. c) Aliphatic carbon. 

d) Carboxyl carbon. e) Phenolic carbon. f) Cluster map 

of carbon forms.

First Nanoscale Image of Soil Reveals an ‘Incredible’ Variety

A handful of soil is a lot like a banana, strawberry, and apple 

smoothie: Blended all together, it is hard to tell what’s in there, 

especially if you have never tasted the fruits before.

But when you look at soil’s organic carbon closely, it has an 

incredible variety of known compounds. And looking closely 

is exactly what Cornell researchers did for the first time – at 

a scale of 50 nanometers (1 nanometer equals the width of 

three silicon atoms). Until now, handfuls of soil humus (or the 

organic component of soil, formed by the decomposition 

of leaves and other plant material by soil microorganisms) 

looked remarkably similar.

Knowing the structure and detailed composition of soil carbon could provide a better understanding of the chemical 

processes that cycle organic matter in soil. For example, the 

research may help scientists understand what happens when 

materials in the soil get wet, warm or cool and how soils sequester carbon, which has implications for climate change.

The soil measurements were made at NSLS beamline X1A1 using near-edge x-ray fine structure spectroscopy coupled scanning transmission x-ray microscopy – a method developed by 

physicists at Stony Brook University. Using this technique, the 

researchers found that while the composition of organic carbon in soils from North America, Panama, Brazil, Kenya or New 

Zealand proved remarkably similar within each sample, within 

spaces separated by mere micrometers, soils from any of these 

locations showed striking variation in their compositions. 

The researchers were also able to identify the origins of some 

of the nano-sized compounds, determining that some of 

them, for example, were microbe excretions and decomposed 

leaves. 

This method can now be used to break soil down, separate 

compounds, conduct experiments on individual compounds 

and better understand the interactions.

— Krishna Ramanujan, NSF

J. Lehmann, D. Solomon, J. Kinyangi, L. Dathe, S. Wirick, C. Jacobsen, “Spatial Complexity of Soil Organic Matter Forms at Nanometre 

Scales,” Nature Geosci., 1: 238-242 (2008).
28 | Science Highlights

Researchers Identify Problems in the Uranium Bioremediation Avenue

Uranium found in soil and groundwater takes billions of years 

to decay radioactively. In addition, traditional clean-up methods involving pumping of contaminated water are useless 

against uranium because it sticks to soil, making it tricky to find 

a treatment option that is both efficient and cost-effective. To 

help narrow the search, a team of researchers from Lawrence 

Berkeley National Laboratory, the University of California, the 

University of Chicago, and the Savannah River Ecology Laboratory set out to question a popular potential bioremediation 

method involving the infusion of organic carbon. 

The overall mobility of uranium in the environment is determined by its oxidation state, which is either hexavalent – U(VI), 

soluble and travels with water – or tetravalent – U(IV), insoluble 

and practically immobile. The goal for researchers is to reduce 

uranium and keep it stabilized in its tetravalent state. 

Using uranium-contaminated sediments from Oak Ridge National Laboratory, the research team previously studied the 

effect of adding various levels of organic carbon to samples, 

which encourages the reduction of uranium. 

Their results were surprising: Rapid reduction of U(VI) to 

U(IV) was shortly followed by the reoxidation of uraniuam. 

The researchers guessed that this reoxidation could be due 

to one of the other predominant elements coexisting in the 

contaminated samples – iron or manganese. The challenge 

for the team in the most recent study was to determine the 

true culprit. 

While treating sediment samples with varying amounts of 

organic carbon, scientists used micro-x-ray absorption nearedge spectroscopy at NSLS beamline X26A to determine the 

oxidation states of uranium, iron, and manganese in real time. 

The data showed that as the uranium switched to its tetravalent state under the influence of organic carbon, manganese 

also reduced while most of the iron remained in its Fe(III) state 

– evidence that it’s the likely reoxidizing agent. 

T.K. Tokunaga, J. Wan, Y. Kim, S.R. Sutton, M. Newville, A. Lanzirotti, 

W. Rao, “Real-Time X-ray Absorption Spectroscopy of Uranium, Iron, 

and Manganese in Contaminated Sediments During Bioreduction,” 

Environ. Sci. Technol., 42(8), 2839-2844 (2008).

Uranium contaminated sediment column during micro-XAS 

data collection at beamline X-26A. Examples of XANES 

spectra for determining oxidation states of (a.) manganese, 

(b.) iron, and (c.) uranium.

Tetsu Tokunaga (left) and Tony Lanzirotti

Earth and Environmental Sciences
Science Highlights | 29

Life Sciences

Enzyme Discovery May Lead to Better Heart and Stroke Treatments

A Queen’s University study sheds new light on the way a 

specific cell enzyme, implicated in causing tissue damage 

after heart attacks and strokes, is normally kept under control. The research team’s discovery will be useful in developing new drug treatments that can aid recovery in stroke and 

heart disease, as well as lessen the effects of Alzheimer’s and 

other neurologically degenerative diseases.

In remodeling proteins needed for cell growth and movement, cells use the enzyme calpain to break off pieces from 

other proteins. Calpain is activated when the cell releases 

short bursts of calcium. During heart attacks or strokes, however, blood supply to cells is interrupted. When the blockage 

is re-opened, the influx of blood causes calcium levels in the 

cell to become dangerously high, and the calpain activity to 

increase. The result is significant damage to tissues.

The researchers’ study shows how another protein, calpastatin, binds and blocks calpain once it has been activated by 

calcium. Because the crystals grown in the lab at Queen’s 

were too small to be used for x-ray diffraction data collection on the university’s diffractometer, the group booked 

time at NSLS beamline X6A. Using x-ray crystallography, the 

researchers were able to determine the structure of the calcium-bound calpain and discover how calpastatin can inhibit calpain without being cut and destroyed in the process. 

That information will be useful in designing drugs to protect 

against the damage caused by over-activation of calpain.

— Nancy Dorrance, Queen’s University

R. Hanna, R. Campbell, and P. Davies, “Calcium-Bound Structure of 

Calpain and its Mechanism of Inhibition by Calpastatin,” Nature, 456, 

409-412 (2008).

Queen’s University Biochemistry Ph.D. student Rachel Hanna checks data from one of the university’s diffractometers 

(on the left) while professors Peter Davies and Rob Campbell 

look on. (Stephen Wild for Queen’s University)

The 27-residue B-peptide is colored as follows: the residues 

that make the loop out of the active site are yellow, the residues N-terminal to the loop are purple, and the residues Cterminal to the loop are green. Other calpastatin residues 

are dark grey. Hydrogen-bond interactions of calpastatin 

with calpain are shown by black dashed lines. O and N atoms 

are red and blue, respectively. a) Overview of calpain binding 

at the active site of calpain. b) Close-up view of the calpastatin at the unprimed side of the active site. c) Close-up view of 

calpastatin looping away from the catalytic residue. d) Closeup view of calpastatin at the primed side of the active site.
30 | Science Highlights

Life Sciences

Cracking the Structure of a Key Cancer-Related Protein

A team of researchers from The Wistar Institute, the University of Pennsylvania, and Johns Hopkins University used xray crystallography at NSLS beamline X6A to solve the threedimensional structure of a an enzyme whose mutations are 

linked to a variety of deadly human cancers, including pancreatic, colon, and lung cancer.

The protein, p300/CBP, belongs to a family of enzymes known 

as histone acetyltransferases (HATs) that activate genes by 

attaching chemicals called acetyl groups to chromosomes, 

altering gene function. A substance that selectively inhibits 

the protein might be the basis for an anticancer drug.

After 10 years of work, the researchers cracked the structure 

of p300/CBP bound to a small molecule that inhibits its activity. They found that although other HATs are built quite 

differently than p300/CBP, the central region of the protein is 

very similar. The study also shows how the binding site and 

chemical mechanism of the enzyme enable it to regulate a 

range of genes: p300/CBP has a binding pocket that is able 

to link with a wide variety of substrates; and the protein uses 

a “hit-and-run” mechanism to attach acetyl groups to chromosomes. Other HATs tend to hang on to both the acetyl 

group and chromosome until the transfer is made. These 

characteristics are well suited for designing cancer drugs 

capable of targeting p300/CBP without causing unwanted 

side effects.

X. Liu, L. Wang, K. Zhao, P.R. Thompson, Y. Hwang, R. Marmorstein, 

P.A. Cole, “The Structural Basis of Protein Acetylation by the p300/CBP 

Transcriptional Coactivator,” Nature, 451, 846-850 (2008).

Structure of the histone acetyltransferase domain of p300 

bound to the Lys-CoA bisubstrate inhibitor. The protein is 

shown as a cartoon with α-helices, β-strands and loops shown 

in red, yellow and green, respectively. The Lys-CoA inhibitor 

is shown in CPK coloring (carbon in blue) as a stick figure.

The Marmorstein laboratory. Bottom, from left, Michael 

Brent, Kimberly Malecka, Jasna Maksimoska, Brandi Sanders, Zhenyu Zhao; middle, from left, Dario Segura Pena, 

Ronen Marmorstein, Katie Meeth, Peng Xie, Daniela Fera, 

Manqing Hong; top, Yong Tang
Science Highlights | 31

Life Sciences

Landmark Study Opens Door to New Cancer, Aging Treatments

Researchers at The Wistar Institute deciphered the structure 

of the active region of telomerase, an enzyme that plays a major role in the development of nearly all human cancers. The 

achievement opens the door to the creation of new, broadly 

effective cancer drugs, as well as anti-aging therapies.

Telomerase is a complex structure made up of multiple protein domains and a stretch of RNA, which contains the template the enzyme uses to synthesize telomeres. Last year, the 

Wistar team solved the structure of a key segment of the 

molecule — the so-called TRBD domain, where RNA binding 

occurs. However, the complexity of telomerase has proved a 

roadblock to determining the enzyme’s overall architecture 

— a goal pursued by researchers worldwide for more than 

15 years.

First, the researchers needed to find sufficient quantities of 

the enzyme for the study. They looked beyond commonly 

relied-on sources such as humans and yeast and discovered that a gene from the red flour beetle could produce 

telomerase in copious amounts, and in a stable form. The 

researchers then used x-ray crystallography at NSLS beamline X6A, a technique that analyzes the diffraction patterns 

of x-rays aimed at crystals of a molecule, to determine the 

first three-dimensional structure of the enzyme’s active region — the catalytic component called telomerase reverse 

transcriptase protein, or TERT.

The study revealed surprising details, at the atomic level, 

including the fact that the molecule’s three domains are organized into a doughnut shape. Knowledge of the structure 

allowed the researchers to create a model of the enzyme’s 

function, in particular, how it works to replicate the ends of 

chromosomes — a process critical to both tumor development and the aging process.

— Abbey J. Porter, The Wistar Institute

A Gillis, A Schuller, E Skordalakes, “Structure of the Tribolium castaneum Telomerase Catalytic Subunit TERT,” Nature, 455, 633-637 (2008).

Model of the atomic structure of telomerase, solved by Emmanuel Skordalakes, 

a researcher at The Wistar Institute. 

Shown are the molecule’s protein component (in green) in complex with RNA 

(in beige) and DNA (in red).
32 | Science Highlights

Life Sciences

Scientists Determine Drug Target for the Most Potent Botulinum Neurotoxin

Botulinum neurotoxin – responsible for the deadly food 

poisoning disease botulism and for the beneficial effects of 

smoothing out facial wrinkles – can also be used as a dreaded biological weapon. Although experimental vaccines administered prior to exposure can inhibit the destructive action of this neurotoxin – the most deadly protein known to 

humans – no effective pharmacological treatment exists.

However, scientists at Brookhaven National Laboratory and 

the U.S. Army Medical Research Institute of Infectious Diseases have taken the first step toward designing an effective 

antidote to the most potent form of the toxin. 

To cause its deadly effects, the botulinum neurotoxin first 

binds to a nerve cell membrane and eventually cleaves specific proteins, thereby blocking the release of neurotransmitters – chemicals nerve cells use to communicate with one 

another and with muscles. Blockage of this communication 

paralyzes muscles, including those that enable breathing.

To block the toxin’s action, the researchers designed four 

“decoy” protein fragments that mimic the structure of the 

protein to which the toxin ordinarily binds. The toxin attaches itself to the decoy fragments instead of to the cell’s protein, which allows neurotransmitters to keep functioning.

The scientists used x-ray diffraction at NSLS beamline X29 to 

see how the toxin binds to the protein inhibitors. They found 

that all four decoy proteins are efficient at inhibiting the toxin’s binding to the cell’s protein, but one of them in particular is by far the best of any known inhibitors. The scientists’ 

next step in this process is to transform the most effective of 

the four protein fragments into a drug-like molecule before 

clinical testing is done.

D. Kumaran, R. Rawat, M.L. Ludivico, S.A. Ahmed, and S. Swaminathan, “Structure and Substrate Based Inhibitor Design for Clostridium 

Botulinum Neurotoxin Serotype A,” J. Biol. Chem., 283, 27, 18883-18891 

(2008).

From left, Subramanyam Swaminathan, Desigan Kumaran, 

and Richa Rawat

Substrate analogs binding to the active site of Balc424. Superposed models of RRGC, RRGM, RRGL, and RRGI are shown 

in green, cyan, gold, and magenta, respectively. Balc424 is 

represented in ribbons embedded on the surface model.
Science Highlights | 33

Life Sciences

Revealing the Crystal Structure of an AMPK Homologue Core

Adenosine monophosphate-activated protein kinase (AMPK) 

is a crucial enzyme for maintaining energy homeostasis in eukaryotes (nucleus-containing organisms ranging from yeast to 

humans). It is regulated by the intracellular ratio of AMP: adenosine triphosphate (ATP). When this ratio is high, indicating 

a low-energy state, AMPK is activated, whereas, it is inhibited 

when the ratio is low. Upon activation, AMPK up-regulates a 

number of catabolic processes while simultaneously downregulating energy-consuming processes. Because of this, 

AMPK is an attractive drug discovery target for obesity and 

type II diabetes, among other diseases. Using the NSLS, a 

group of Columbia University researchers were able to determine the structure of the core of the AMPK homologue SNF1 

from S. cerevisiae, a species of budding yeast. 

AMPK consists of three proteins (subunits α, β, and γ) that together make a functional enzyme by taking on specific roles 

related to stability and activity. To find out more about the interactions between these subunits, researchers used x-ray diffraction at NSLS beamlines X29A and X4C on samples of SNF1. 

Their findings confirm biochemical and genetic data indicating a direct subunit interaction that probably regulates the 

kinase domain, which plays an important role in numerous 

cellular processes, including division, proliferation, apoptosis, 

and differentiation. 

Specifically, they discovered that the α-subunit has a regulatory sequence that might control both the inhibition and the 

activation of SNF1: inhibition could be caused by the regulatory sequence binding to the active site or interacting with a 

lobe of the kinase domain. Once SNF1 is activated, this inhibition is removed by sequestration of the regulatory sequence 

by the γ -subunit, which might represent the activated core 

of S. cerevisiae SNF1. The authors propose that mammalian 

AMPK might use a similar regulatory mechanism.

G.A. Amodeo, M.J. Rudolph, and L. Tong, “Crystal Structure of the 

Heterotrimer Core of Saccharomyces cerevisiae AMPK Homologue 

SNF1,” Nature, 449, 492 (2007).

Structure of the SNF1 heterotrimer core

From left, Liang Tong, Gabriele A. Amodeo, and Michael J. 

Rudolph
34 | Science Highlights

Soft Condensed Matter and Biophysics

DNA Technique Yields 3-D Crystalline Organization of Nanoparticles

An interdisciplinary team of Brookhaven researchers, for the 

first time, used DNA to guide the creation of three-dimensional, ordered, crystalline structures of nanoparticles (particles 

with dimensions measured in billionths of a meter). The ability to engineer such structures is essential take advantage of 

the unique properties that may exist at the nanoscale – for 

example, enhanced magnetism, improved catalytic activity, 

or new optical properties. 

The new assembly method relies on the attractive forces between complementary strands of DNA – the molecule made 

of pairing bases known by the letters A, T, G, and C that carries 

the genetic code of living things. First, the scientists attach to 

nanoparticles hair-like extensions of DNA with specific “recognition sequences” of complementary bases. Then they mix 

the DNA-covered particles in solution, during which the recognition sequences bind together to link the nanoparticles.

To achieve ordered crystals, the scientists heat the samples of 

DNA-linked particles and then cool them back to room temperature. This allows the nanoparticles to unbind, reshuffle, 

and find more stable binding arrangements. The team also 

alters the properties of DNA in order to find a “sweet spot” 

where a stable, crystalline form would appear.

Small angle x-ray scattering at NSLS beamline X21 and dynamic light scattering and different types of optical spectroscopies and electron microscopy at the Center for Functional 

Nanomaterials were combined to reveal the detail of the ordered structures and the underlying formation processes. 

The resulting crystals are extraordinarily sensitive to thermal 

expansion and remarkably open, which leaves room for future 

modifications that would enhance nanoscale properties and 

reveal new classes of applications.

D. Nykypanchuk, M.M. Maye, D. van der Lelie, O. Gang, “DNA-Guided Crystallization of Colloidal Nanoparticles,” Nature, 451, 549 – 552 

(2008).

“Body-centered-cubic” unit cells of the 3-D nanoparticle 

crystals. One type of nanoparticle occupies each corner of 

the cube and a second type of nanoparticle is located centrally inside. These unit cells, measuring tens of nanometers, 

form a repeating lattice that extends more than a micron 

(1,000 nanometers) in three dimensions.

From left, Mathew Maye, Niels van der Lelie, Oleg Gang, and 

Dmytro Nykypanchuk
Science Highlights | 35

Soft Condensed Matter and Biophysics

Investigating Orientational Order of Liquid Crystals

Orientational order enables technological applications for liquid crystals as positional order does for crystals. Electric-fieldinduced reorientation of the large optical anisotropy of the 

molecules has been utilized in applications from high-resolution camera viewfinders to large-area monitors. In order to 

learn more about the behavior of these intriguing phases, three 

groups, headed by the University of Minnesota, The University 

of Manchester, and Bordeaux University, collaborated with 

NSLS scientists to use resonant x-ray scattering to measure orientational order in various layered liquid crystal phases. 

Because of the chirality or banana-shape of the molecules, the 

tilted, layered, liquid-crystal phases lack a mirror symmetry, 

which allows the existence of an in-plane polarization. Depending on how the direction of the in-plane polarization varies, the 

phases can be ferro-, ferri-, heli-, or antiferroelectric and an applied electric field can induce changes in orientation or phase.

Each research group made significant discoveries in this field using NSLS beamlines X6B and X19A: while using chiral additives 

to extend the temperature range of the rod-shaped molecule 

phases, the Manchester group made an unexpected discovery 

of a five-state switching sequence for one of the phases under 

applied fields; the Minnesota group showed a continuous evolution of the incommensurate helical pitch (INHP) through the fourlayer lock-in region in agreement with theory, but also showed a 

significant change in curvature at INHP=four layers, which is not 

explained by any theory; and the Bordeaux group made progress 

in determining the structure of the non-helical, B2 liquid crystal 

phase that is comprised of fluid layers of achiral banana-shaped 

molecules stacked in an antiferro-electric sequence.

S. Jaradat, P. Brimicombe, C. Southern, S. Siemianowski, E. DiMasi, 

M. Osipov, R. Pindak, and H. F. Gleeson, “Unexpected Field-Induced 

Phase Transitions Between Ferrielectric and Antiferroelectric Liquid 

Crystal Structures,” Phys. Rev. E, 77: 010701, (2008). 

Z.Q. Liu, B.K. McCoy, S.T. Wang, R. Pindak, W. Caliebe, P. Barois, P. Fernandes, H.T. Nguyen, C.S. Hsu, and C.C. Huang, “The Unique Pitch Evolution in the Smectic-C * Phase,” Phys. Rev. Lett., 99: 077802 (2007). 

P. Fernandes, P. Barois, S.T. Wang, Z.Q. Liu, B.K. McCoy, C.C. Huang, R. 

Pindak, W. Caliebe, and H.T. Nguyen, “Polarization Studies of Resonant 

Forbidden Reflections in Liquid Crystals,” Phys. Rev. Lett., 99: 227801 

(2007).

(a) View of the SmC* phases along their layer normal showing the molecular projections in sequential layers labelled 

1,2,3,... The in-plane polarization direction is shown by the 

green arrows for the SmC* and SmCA* phases. (b) Side view 

of the SmC*α phase, the green arrows indicate the heli-electric polarization. (c) Schematic showing the dependence of 

the induced SmC* phases on applied electric field and temperature. Insert shows the change in resonant x-ray scattering features for increasing electric field at a fixed temperature indicated in the phase diagram by an arrow.

From left, Ron Pindak, Suntao Wang, Paulo Fernandes, and 

Philippe Barois

From left, Zengqiang Liu, Helen Gleeson, Winnie Wang, Nicholas Roberts, and Shaden Jaradat
36 | Year in Review

NSLS and NSLS-II staff gather at the Light Sources Directorate 

Annual Awards Barbeque.
Year in Review | 37

The Light Sources Directorate grew to more than 300 people in 2008, 

including scientists, engineers, technicians, and support staff.
38 | Year in Review

January February

NSLS Black Diamond Research 

Among Discover Magazine’s 2007 Tops

The discovery of the origin of Earth’s so-called black diamonds at the 

NSLS is ranked 60th among the top 100 scientific stories of 2007 by 

Discover Magazine. The article, which details “the trends and events 

that most changed our understanding of our world,” appears in the 

magazine’s January 2008 issue.

NSLS, NSLS-II Strategic Planning Workshops 

Draw User Input from Hundreds

About 330 current and prospective users from around the world

attend a series of Scientific Strategic Planning Workshops sponsored 

by NSLS and NSLS-II meant to help guide the future of light sources 

at Brookhaven. Divided into six fields – life sciences, materials science 

and engineering, earth and environmental sciences, chemical and 

energy sciences, hard condensed matter and materials physics, and 

soft and biomolecular materials – the workshops were coordinated 

with a related string of seven NSLS-II workshops based on experimental techniques. Together, input gathered during the sessions will 

be used to steer the scientific strategic plans and beamline development for both facilities.

432nd Brookhaven Lecture: Jim Murphy

NSLS Deputy Chairman for Accelerators & Operations Jim Murphy 

gives the 432nd Brookhaven Lecture, “At the Cutting Edge of Bright 

Beams: The NSLS Source Development Laboratory,” focusing on the 

next generation of light sources being pursued at the Laboratory.

(Above) A black, or carbonado, 

diamond. 

(left) Jim Murphy

Materials Science and Engineering group at the NSLS and NSLS-II Strategic Planning 

Workshop

“The series of Light Source Directorate planning workshops

hosted by the NSLS and NSLS-II were very well attended and

received. The users and organizers I’ve talked to were pleased

with the quality of the talks given and the resulting input from

current and new users.”

—Chi-Chang Kao, NSLS Chair 
Year in Review | 39

March April

Historically Black Colleges and Universities Faculty, 

NSLS Staff Collaborate to Develop Synchrotron 

Curriculum

Professors from the NSLS Historically Black Colleges and Universities 

(HBCU) User Consortium meet to further the involvement of HBCU 

students and faculty at the NSLS. In addition to planning for the second annual HBCU-NSLS workshop and touring the experiment floor, 

the group developed the framework for a National Science Foundation proposal to create a new curriculum that emphasizes synchrotron research and instrumentation for HBCUs.

NSLS Users Earn Prestigious Honors

Four users are honored for scientific achievement, including: University of Delaware professor Jingguang Chen, winner of the 2008 Award 

for Excellence in Catalysis from the Catalysis Society of Metropolitan 

New York; Florida State University researcher Linda Hirst, recipient 

of a National Science Foundation Faculty Early Career Development 

grant for research involving cell membranes; Carnegie Institution of 

Washington researcher Ho-kwang (Dave) Mao, winner of the American Geophysical Union’s Inge Lehmann Medal; and Brookhaven 

chemist José Rodriguez, who received HENAAC’s Outstanding Technical Achievement Award.

RapiData Celebrates 10 Years of Teaching 

Crystallography Skills

One of the most widely recognized courses at the NSLS – RapiData – 

turns 10. The weeklong crash course, which attracted 52 students, is 

designed to introduce participants to the best and latest equipment 

and techniques for macromolecular x-ray crystallography.

Al Boerner, Mike Buckley Receive 

Team Sitewide Safety Stewardship Award

NSLS employees Al Boerner and Mike Buckley receive a team 2007 

Sitewide Safety Stewardship Award for their efforts to ensure that 

Laboratory suppliers follow proper Integrated Safety Management 

practices. 

NSLS Sons, Daughters Become 

Materials Science Detectives

Scouring the experiment floor for clues, about 50 children of NSLS users and staff members take on the role of scientific detectives as part 

of the national Take our Sons and Daughters to Work Day.

Brookhaven Scientists Receive Hall of Fame 

Award for Microbeam Radiation Therapy

Brookhaven scientists F. Avraham Dilmanian and James F. Hainfeld, together with Gerard M. Morris, a guest researcher at Brookhaven from 

Morvus Technology Ltd., Wales, win The Long Island Technology Hall 

of Fame award for the most innovative patent in the category of innovation for the individual. The patent is for microbeam radiation 

therapy, which, as first implemented, uses the NSLS to produce arrays 

of parallel, very thin x-ray beams to irradiate and destroy malignant 

tumors, while keeping normal adjacent tissues free from harm.

The HBCU User Consortium professors explore the NSLS 

experimental floor.

Participants in the NSLS Take our Sons and Daughters to 

Work Day
40 | Year in Review

May June

Eli Sloutskin Receives 2008 Julian Baumert Award

Harvard University physicist Eli Sloutskin receives the 2008 Julian 

Baumert Ph.D. Thesis Award for his work on liquid surfaces and the 

nanometer-thin layers that cover them. The prize is given to a researcher who has recently conducted a thesis project that included 

measurements at the NSLS.

Annual Crystallization Course 

Draws More Than 40 Participants

Forty-five researchers from across the country and the world gather 

at the NSLS to discuss and learn about membrane protein crystallization from leaders in the field at the annual “Crystallization: Focus 

on Membrane Proteins” workshop. Carried out by about 20 crystallization experts and volunteers, the sixth annual course includes 10 

hands-on tutorials for participants to choose from.

BioCD-2008: Synchrotron Radiation Circular Dichroism 

Spectroscopy of Proteins and other Biomolecules

A weeklong workshop focusing on circular dichroism (CD) spectroscopy using both conventional and synchrotron sources brings 12 students to the NSLS. CD is particularly useful for studying the structure 

of proteins, DNA, RNA and other biopolymers in solution, and this 

was a major focus of the workshop.

Gabriella Carini Wins IEEE Young Engineer Award

NSLS researcher Gabriella Carini wins the 2008 Institute of Electrical 

and Electronics Engineers (IEEE) Long Island Section’s Outstanding 

Young Engineer Award for “outstanding contributions to the advancement of semiconductor detectors for x-ray spectroscopy.”

UEC Community Service Awards go to Jingzhu Hu, 

Randy Smith

The NSLS Users Executive Committee presents two Community 

Service Awards: one to Stony Brook University’s Jingzhu Hu and the 

other to NSLS science associate Randy Smith. The awards are given 

for service, innovation, and dedication to users of the NSLS.

2008 NSLS-CFN Joint Users’ Meeting 

Stresses Strategic Planning

About 400 people attend the third joint meeting of the NSLS and 

Center for Functional Nanomaterials user communities, which focused on defining the role of synchrotron science and research at the 

nanoscale for Brookhaven and the nation at large. Plenary speakers 

included: BNL Director Sam Aronson, DOE Office of Science Deputy 

Director for Science Programs Pat Dehmer, Associate Laboratory Director for Light Sources Steve Dierker, CFN Director Emilio Mendez, 

and NSLS Chair Chi-Chang Kao. 

Participants in the 2008 “Crystallization: 

Focus on Membrane Proteins” workshop

Participants in the 2008 Joint NSLS/CFN Users’ Meeting mingle at the 

poster and vendor session.
Year in Review | 41

July August

NSLS Summer Sunday Draws 

Record Number of Visitors

More than 800 community members attend the NSLS Summer Sunday for scientific demos, tours, and freebies – a record high for the 

facility. The NSLS was the first of five facilities to be showcased in 

the lab-wide program, during which the public is invited to explore 

some of Brookhaven’s most exciting science.

NSLS Synchrotron Catalysis Consortium 

Receives 3-Year Funding Renewal

Funding for the Synchrotron Catalysis Consortium – an organization 

meant to improve and expand catalysis research by taking advantage 

of the unique investigation tools available at the NSLS – is renewed 

through the U.S. Department of Energy’s Office of Basic Energy Sciences. The $1 million award lasts for three years.

NSLS Users Rack Up Numerous Awards

Six NSLS users win a number of prestigious honors. They include: 

Brookhaven chemist Radoslav Adzic, winner of a 2008 DOE Hydrogen 

Program R&D Award; Cold Spring Harbor researcher Leemor JoshuaTor, who was named a Howard Hughes Medical Institute Investigator; 

National Center for Scientific Research (CNRS) scientist Ricardo (Ric) 

Lobo, recipient of the Ludwig-Genzel-Prize; Carnegie Institution of 

Washington researcher Ho-kwang (Dave) Mao, who was elected as a 

foreign member of the Royal Society of London; adjunct Stony Brook 

professor David Sayre, who won the 2008 Ewald Prize; and Bar-Ilan 

University doctoral student Lilach Tamam, who received one of two 

best poster awards at the international conference on Surface X-ray 

and Neutron Scattering.

NSLS Hosts 2nd Annual Historically Black Colleges 

and Universities Workshop

Expanded in both attendance and duration, the 2nd annual NSLS 

Historically Black Colleges and Universities Workshop focuses on 

strengthening existing research ties between Brookhaven and minority-serving schools as well as establishing new relationships. The 

workshop attracted 17 participants from nine institutions to learn 

how to transform themselves and their students into successful synchrotron users.

Participants in the 2008 NSLS HBCU Workshop

Summer Sunday visitors peruse the hands-on 

displays set up in the NSLS lobby.

“The hands-on aspect to this course is what makes it such a success. 

We want to provide a basic background for beginners in the field, but 

then give them the opportunity to develop skills in the lab.”

— Vivian Stojanoff, NSLS physicist & crystallization workshop organizer 
42 | Year in Review

September October

DOE Awards NSLS $2.2 Million 

for Advanced X-ray Detector Development

The NSLS receives a $2.2 million, three-year, renewable grant from 

the Department of Energy’s Office of Basic Energy Sciences to develop the next generation of advanced x-ray detectors for synchrotron 

radiation. The grant will allow the NSLS Detector Group to explore 

the possibility of applying three-dimensional integration techniques 

for “smart” two-dimensional detectors.

Nobel Prize in Chemistry Linked 

to NSLS Protein Work

Two American scientists and a Japanese researcher win the 2008 

Nobel Prize in Chemistry for their discovery and development of a 

protein that has become a ubiquitous tool in bioscience. Their work 

centered on a protein, found in a type of jellyfish, that glows green 

under ultraviolet light. Known as green fluorescent protein (GFP), this 

protein has become an extremely popular tool for probing the insides of living cells or whole animals and watching molecules interact in real time. The structure of GFP was first reported in the journal 

Science in 1996, partially as the result of x-ray studies at the NSLS.

International Collaborations, Funding Help Open 

the Secrets of Radiation-Protective Drugs

Gulgun Cakmak, a graduate student from the Middle East Technical 

University, uses the NSLS to study the molecular effect of a popular 

radioprotective agent on samples of irradiated brain tissue from rats. 

To conduct her research, she received support from numerous sources, including: a $9,000 scholarship from the Scientific and Technical 

Research Council of Turkey; a $2,000 grant from the U.S. Department 

of Energy’s Cooperative Research Program for SESAME, which stands 

for Synchrotron-light for Experimental Science and Applications in 

the Middle East; and $2,500 from the NSLS.

Employees Enjoy Food, Recognition 

at Light Sources Directorate Awards Barbeque

The annual Light Sources Directorate Awards picnic, hosted by NSLS 

Chair Chi-Chang Kao and Steve Dierker, Associate Laboratory Director for Light Sources, includes a barbeque, clambake, and awards to 

honor NSLS and NSLS-II employees for another year of smooth and 

productive operation.

NSLS Summer Student Projects Range 

from Crystallography to Detector Development

Eleven college students perform summer research projects at the 

NSLS, working with scientists and engineers from the department in 

research fields ranging from medical sciences to electrical and mechanical engineering. In addition to their research projects, students 

had the opportunity to attend scientific lectures, tour Brookhaven’s 

research facilities, and participate in numerous social activities.

Three of the 11 college students who worked at the NSLS in 

summer 2008 pictured with NSLS physicist Vivian Stojanoff.

Light Sources Directorate employees celebrate another 

year of accomplishments at the annual awards barbeque.

"This grant will allow us to explore threedimensional integration techniques for 

smart two-dimensional detectors. That 

translates into higher detector sensitivity,

superior image quality, and lower

acquisition times."

— Pete Siddons, Head of the NSLS Detector Group
Year in Review | 43

November December

442nd Brookhaven Lecture: Elaine DiMasi

NSLS physicist Elaine DiMasi gives the 442nd Brookhaven Lecture, 

“Which Came First, the Eggshell or the Egg? – Answering Riddles 

About Biomineralization,” which focuses on the process by which 

organisms form sturdy materials such as bones, mollusk shells, and 

other structures.

Introduction to XAFS: Experiment, 

Theory, Data Analysis

The short course in x-ray absorption fine-structure spectroscopy 

brings 30 participants to the NSLS. The course, geared toward beginners, included beamline experiments, lectures by experts in the field, 

tutorials, and data analysis sessions. 

Chi-Chang Kao Named Founding Director 

of New Photon Science Institute

Chi-Chang Kao, a physicist and Chair of the National Synchrotron 

Light Source, is named founding Director of Brookhaven’s Joint Photon Sciences Institute (JPSI), an interdisciplinary research institute 

meant to exploit the properties of advanced light sources to address 

challenging problems in science and technology. Kao, who will continue to serve as Chair of the NSLS, will be responsible for developing the scientific programs within JPSI as well as for overseeing the 

construction of the building.

“Naturally Obsessed” Documentary 

Wows NSLS, BNL Crowd

Brookhaven employees and community members are treated to two 

showings of “Naturally Obsessed,” a one-hour documentary filmed in 

part at the NSLS. Recorded over a three-year span, the documentary 

features Columbia University student crystallographers mentored by 

NSLS user Larry Shapiro as they study a protein known as AMP-activated protein kinase (AMPK), which could reveal a new path toward 

the treatment of diabetes and obesity. 

High-Pressure Workshop Highlights Advances 

in Field, Beamline Scientists’ Dedication

An NSLS-held workshop on “Advances in High-Pressure Science Using Synchrotron X-Rays” is attended by more than 50 scientists, postdoctoral fellows, and students from the high-pressure and synchrotron x-ray research fields. 

Site Preparation Work Begins 

For NSLS-II Ring Building

Site preparation work for construction of NSLS-II begins. The project, 

expected to be completed over the next six years, will include the 

construction of conventional facilities, installation of the accelerator 

and experimental equipment and the startup, testing, and commissioning of all systems.

NSLS Beamline Used as Test Bed for NASA Detector

Using powerful x-rays produced by the NSLS as a calibration tool, a 

team of researchers from NASA’s Goddard Space Flight Center tests 

a time projection chamber – a special instrument meant to probe 

deep space phenomena such as gamma rays and black holes.

Elaine DiMasi

Carole Rifkind (left) and Richard Rifkind 

(second from left) talk to local students 

before the screening of their film, “Naturally Obsessed,” in Brookhaven’s Berkner 

Auditorium.

Counter clockwise, from back, 

researchers Syed Khalid (NSLS), C.J. 

Martoff (Temple University), Kevin 

Black (Rock Creek Scientific), Michael 

Dion (Temple University), and Joe Hill 

(NASA).
44 | Facility Report

Safety

Andrew Ackerman

Environment, Safety, Health, and Quality Division Head

Everyone was busy in 2008 and there was considerable Environment, Safety, Health, and Quality (ESH&Q) activity throughout the NSLS. A summary of some of those activities follows:

•	 The NSLS maintained independent registration with the 

Environmental Management System (ISO 14001) and 

the Occupational Health and Safety Assessment Series 

(OHSAS) – an important goal for the Laboratory.

•	 An audit of the management of nanoscience risks was 

completed by a Department of Energy (DOE) Environmental, Safety, Security, and Health team. The NSLS 

scores were excellent and the department program was 

recognized as the best at the Laboratory.

•	 Personnel protective equipment requirements for work 

with cryogens were defined through a detailed risk assessment and regulatory analysis that has become the 

basis for these requirements throughout the Laboratory.

•	 A detailed oxygen-deficiency hazard analysis was completed for work with cryogens within the macromolecular crystallography hutches, yielding recommendations 

for important control improvements and allowing for 

proper risk classification of these facilities.

•	 Training in “Human Performance” principles was initiated 

and completed for more than 90 percent of the staff. 

Incorporation of these principles to work operations has 

begun and an implementation team has been created.

•	 Inspection of electrical equipment for compliance with 

Nationally Recognized Testing Laboratory requirements 
Facility Report | 45

Safety

“The NSLS safety programs are acknowledged throughout

the Laboratory and by the DOE as excellent, and there is much

reason for pride in staff and user attention to keeping the facility

a safe place to work.”

was advanced for facility and user equipment. The 

department is on schedule for completing the remaining required inspections and a robust process to capture 

equipment entry as part of the user experiment program 

is established.

•	 The management safety observation program was much 

improved with excellent involvement from the department 

management.

•	 The NSLS wet chemistry laboratories were cleared of 

excess or legacy equipment and a program for completing detailed experiment safety review documents was 

established.

Several performance measures are tracked to follow the 

effectiveness of the ESH&Q programs. In 2008:

•	 A detailed ESH Improvement Plan was generated with 

39 targets assigned to individuals and tracked within 

the electronic NSLS Family Assessment Tracking System. 

Progress on all was good.

•	 Training compliance was excellent and emphasis on 

Human Performance training was met with staff support 

and cooperation.

•	 Numerous internal and external audits resulted in few 

findings and the department response was timely and 

organized.

•	 Waste generation continues to be low and well managed.

•	 Personnel exposure to chemical and physical hazards 

was well controlled and well below allowable limits.

•	 Radiation exposure remains very low with a collective 

dose of approximately 70 mRem for the year measured 

through use of some 2,300 personnel dosimeters.

•	 A greater number of routine workplace inspections were 

completed than last year, with each inspection resulting in some findings, efficient staff response, and timely 

correction.

•	 Injuries were all minor, with no “days away, restricted, 

transferred” (DART) cases, only one “recordable” case, 

and seven first-aid cases.

•	 And three events — two that involved equipment failure 

and resulted in smoke conditions, and one that involved 

poor transfer of liquid helium with a first-aid injury — 

were analyzed for cause and lessons to be learned. 

There is more to report, but the summaries above provide 

a good overall picture of the department's activity and performance in ESH&Q. The NSLS programs are acknowledged 

throughout the Laboratory and by the DOE as excellent, and 

there is much reason for pride in staff and user attention to 

keeping the facility a safe place to work. Good performance 

indicators and well-managed programs are important, but 

what is most important is that we completed an enormous 

amount of science last year without significant injury or environmental insult.
46 | Facility Report

The Accelerator Complex

James B. Murphy

Deputy Chairman for Accelerators and Operations

“In 2008, our users enjoyed continued robust operation

of our two storage rings. The Vacuum Ultraviolet Ring remained

strong at 97.5 percent reliability and the X-Ray Ring reliability

came in at 93.2 percent. Both statistics handily beat our Department 

of Energy requirement of greater than 90 percent reliability.”

In calendar year 2008 (CY08), our users enjoyed continued 

robust NSLS operation of our two storage rings. The Vacuum 

Ultraviolet Ring (VUV) remained strong at 97.5 percent reliability and the X-Ray Ring reliability came in at 93.2 percent. 

Both statistics handily beat our Department of Energy (DOE) 

requirement of greater than 90 percent reliability. In addition, our users also benefited from our excellent availability 

in both rings (VUV 110.5 percent, X-Ray 105.7 percent). Availability is a result of unscheduled hours coming from early 

return to operations from other activities such as maintenance. 

The budgetary continuing resolution enacted by the federal 

government impacted the NSLS funding profile, which resulted in an additional shutdown period starting in August 

and ending in late September. The NSLS staff took advantage 

of this shutdown period to install the X9 mini-gap undulator 

(MGU) and replace two kicker drivers responsible for bumping the electron beam into the Booster and out to the X-Ray 

transport line. To provide additional beam time to the user 

community, we extended operations past the Thanksgiving 

holiday and started the winter shutdown in both rings on 

December 8.
Facility Report | 47

The Accelerator Complex

Injection System

Many of the activities in the operations group have been 

centered on improvements of the reliability of the injection 

system. In response to an issue raised in the 2006 Machine 

Operations Reliability Evaluation (MORE) review, a considerable effort was directed toward redesign and replacement 

of four pulsed magnet drivers in the Booster. Kicker magnets 

are required to offset the orbit of the electrons as they are 

injected into and extracted from the accelerators. Pulsed 

magnet drivers provide the kicker magnets with a current on 

the order of a thousand amperes (A) in pulses lasting several 

tens of microseconds to generate fields of a few kilogauss 

that deflect the electron bunches into the Booster synchrotron and then out of the Booster into the extraction transport lines at the precise moment in time. Four drivers were 

identified in the MORE review as a vulnerability for reliable 

operations due to their age and the difficulty to repair them. 

Our operations team designed and built the first kicker driver, which is actually two drivers in one cabinet, and installed 

it in the Booster Ring during the August-September shutdown period. One half of the driver is responsible for kicking the electron beam into the Booster from the Linac and 

the other half kicks the beam out of the booster and into 

the X-Ray transport line. The careful design, fabrication, and 

testing proved worthy, giving us a very swift and smooth XRay start-up in September. The remaining two kicker drivers, 

both responsible for kicking the beam from the Booster into 

the VUV transport line, were installed during the 2008 winter shutdown. Since the Booster provides electron beams to 

both rings, we all benefit from these important upgrades to 

our equipment.

Since timing of the kicker magnet pulses is so critical to 

successful storage ring injection, a kicker timing monitor 

system was developed and put into operation just prior to 

the spring 2008 shutdown. Because errors both in timing 

and pulse shape can cause a failure to inject electrons, the 

new LabView-based system allows for monitoring of the 

kicker pulses themselves as well as their relation to each 

other. The new system also gives us the ability to store all 

kicker pulse waveforms for comparison to live waveforms, 

which will prove extremely valuable for troubleshooting 

injection timing. The display and control of this new tool 

has become part of the center operator console for use by 

our staff of machine operators.

63.5%

8.5%

6.9%

8.6% 16.2%

VUV-IR X-Ray

19.4% 51.5%

25.4% Scheduled Operations

Unscheduled Operations

Maintenance

Other - Studies, Com/Con, Holiday,

Injection, Unscheduled downtime, 

Interlock

Calendar year 2008 machine activities
48 | Facility Report

The Accelerator Complex

As a hedge against future klystron failures, we took proactive steps to develop a procedure that allows us to fill the 

two storage rings with only two of the three klystrons in operation. The injection energy from the Linac to the Booster 

was lowered from 120 mega-electron volts (MeV) to 80 MeV. 

Magnet settings in the Linac-to-Booster transport line were 

scaled down proportionally to the beam energy, the Linac 

timing was moved 15 milliseconds (ms) earlier and the low 

energy part of the Booster ramps, trims, and injection kickers 

were modified. We were able to obtain a current of 15 mA in 

the Booster at the top energy and extracted it efficiently to 

the transport line. The successful development of this procedure will minimize the downtime due to a failed klystron 

in the future. This effort goes in concert with another effort 

being undertaken in 2009 to install new radiofrequency (RF) 

windows in the waveguide between each klystron and the 

corresponding Linac tank. With these windows in place, the 

Linac can still operate while the failed klystron is replaced 

and conditioned.

Our efforts to maintain a stock of spare Linac klystrons continued in 2008. At the end of the year, a new vendor capable 

of rebuilding our klystron tubes was identified. The new 

vendor has promised a much quicker turn-around than we 

have ever experienced in the past. Thanks to this very quick 

turn-around, we look forward to the receipt and testing of 

the rebuilt klystron tube in the first quarter of 2009.

We used the Methodical Accelerator Design (MAD) tools to 

optimize the extraction parameters, and achieved a more 

than 10 percent reduction on the extraction loss and about 

a 50 percent reduction on the shot-to-shot fluctuation in 

the Booster-to-X-Ray transport line. It has been established 

that a significant amount of Booster beam is lost in a 2-meter region around the extraction area, where we have limited steering ability. To address this, we designed, built, and 

tested a compact C-frame trim magnet that provides about 

1 milliradian (mrad) kick in both the horizontal and vertical 

directions that last for about 10 ms during the X-Ray extraction. This has been installed at the very beginning of the 

Booster-to-X-Ray transport line during the winter 2008 shutdown and has been undergoing commissioning.

VUV Ring

A series of VUV Ring feasibility studies to provide beamline 

Peter Zuhoski (left) and Ken Pedersen flanking their innovative new booster kicker power supply.
Facility Report | 49

The Accelerator Complex

U4B users with fast-switching, elliptically polarized radiation has been performed. Polarization was controlled by 

moving the vertical orbit at the U4B source point (dynamic 

orbit bump), thus effectively moving the beamline detector in and out of the bend plane. Control of the bump was 

performed by extending the algorithm used in the VUV 

Ring digital orbit feedback. Achieving the required levels 

of polarization requires rather substantial (about 1 mm) orbit variation at the U4B source point. At the same time, a 

much stricter tolerance on allowable orbit motion exists 

through the rest of the ring. Meeting these requirements 

turns out to be a challenging control systems problem. Initial results and user feedback were very encouraging; up to 

5 hertz switching rates appear possible without significant 

hardware modifications. These studies will continue as the 

beamline is being equipped with additional photon beam 

position diagnostics. 

X-Ray Ring

Another important project planned and carried out by our 

operations staff in 2008 was the replacement of an aging 

tube-based pre-amplifier with a solid-sate 3-kilowatt amplifier that drives the final 125-kilowatt amplifier in one of 

our four RF systems. The tube-based amplifier was burdened with multiple bias power supplies as well as a 100-

watt preamplifier of its own. The difficulty and expense 

required to maintain the tube amplifier was eliminated 

with the installation of the solid-state amplifier. The new 

amplifier reduces our equipment count and its modular 

design allows for a speedy swap-out of defective modules. 

All of these factors will contribute to improved machine 

reliability. The newfound physical space will be filled with 

an updated 125-kilowatt plate supply, which is planned for 

a May 2009 installation.

The NSLS operations staff played critical roles in the success 

of the new X9 MGU. A well-designed and implemented bakeout controller helped ensure that the temperature of the 

permanent magnets did not exceed a maximum level. This 

controller performed flawlessly during both the lab pre-installation bake-out as well as the in-situ bake-out following ring 

installation in August. Other vital systems contributing to the 

success of the X9 MGU include an active interlock system and 

a motor control system based on updated computer boards 

that will serve as a model for future motor control systems.

Michael Lehecka (left) and George Rakowsky setting up the 

X9 MGU for Hall probe field mapping in the Magnetic Measurement Lab.
50 | Facility Report

The Accelerator Complex

Overall Improvements

NSLS diagnostics routinely used in operations do not 

have capabilities to measure a single-turn electron 

beam orbit that could greatly help in optimization injection process into both the X-Ray and VUV Rings. In CY08, 

we started installation and commissioning of a new diagnostic system, a so-called Libera Brilliance receiver, 

allowing real-time observations of turn-by-turn beam 

dynamics. Each ring has so far been equipped with one 

test system, and initial results have been very encouraging. The new system has already allowed us to carry out 

beam-based measurements of the temporal profiles of 

the fast-injection kickers in the VUV Ring. Commissioning and studies are continuing and additional systems 

are being considered. 

Magnetic Measurement Lab (MML)

In 2008, a new in-vacuum MGU was completed and 

installed at X9 to serve the new Center for Functional 

Nanomaterials beamline. This MGU is similar to the X29 

MGU in that it just fits between a pair of RF cavities. However, it has a longer period length (14.5 mm vs. 12.5 mm), 

achieves a higher peak field (1.28 tesla (T) vs. 0.96 T), and 

provides a wider tuning range (2:1 vs. ~1.4:1), which gives 

full spectral coverage from 2.2 keV to over 20 keV without gaps, using both odd and even harmonics up to the 

7th. A redesigned support structure accommodates the 

75 percent higher magnetic load. A new model-based 

magnet sorting algorithm was developed and implemented to determine an optimal magnet sequence that 

minimized the effect of magnetization errors on trajectory straightness. As a result, the MGU produced a 

straight trajectory with phase error less than 2.2 degrees 

root mean square with no post-assembly shimming.

Installation of X9 MGU had been planned for the December 2007 shutdown. However, the NdFeB magnets (the 

same grade used successfully in the X25 MGU) failed to 

withstand a key “pre-bake” test at elevated temperature. 

This prompted us to conduct a series of destructive thermal tests on a short prototype model, which determined 

that the safe limit for these magnets in-situ is only 90 

Left, the X9 MGU between RF accelerating 

cavities. Right, tuning 

curves for X9 MGU. 

Odd harmonics shown; 

range of 2nd harmonic 

is indicated, showing 

full coverage from 2.2 

to over 20 keV.
Facility Report | 51

The Accelerator Complex

degrees Celsius, but that ultra-high vacuum can be 

achieved at this temperature, albeit with a much longer duration bake. Consequently, an elaborately instrumented and temperature-limited bakeout scheme was 

implemented, first in the MML and again in the ring, to 

protect the magnets from permanent demagnetization. 

The MGU was re-measured after the first bake and verified that no magnetic changes had occurred, although 

mechanical “creep” had introduced some gap taper and 

systematic phase error. More taper adjustments and 

thermal cycling of the frame were required to settle the 

structure before the MGU was deemed ready for installation. A special short shutdown in August was dedicated 

to installation and final bakeout in the X-Ray Ring.

R&D efforts in the area of cryogenic permanent magnet undulators included: characterizing PrFeB magnets; 

optimally sorting and assembling them in a test MGU; 

installing the MGU in the superconduting undulator Vertical Test Facility and mapping it at room temperature; 

and preparing a Cryogenic Safety Review for measurements at 77 degrees Kelvin.

Source Development Laboratory

The Source Development Laboratory (SDL) is a linear accelerator and laser-based R&D facility dedicated to the 

exploration of new radiation sources and high brightness electron beams. In 2008, the scientific program emphasized three key themes:

•	 High-gain laser-seeded free electron laser (FEL

amplifiers

•	 High-intensity terahertz (THz) radiation

•	 Ultrafast electron diffraction (UED)

The high-gain laser-seeded FEL amplifier program is 

funded by the Joint Technology Office (JTO) and the 

Office of Naval Research (ONR). The scientific results 

from the THz source development and characterization 

program were published in Physical Review Letters and 

Physical Review A. The hardware for the ultrafast electron 

diffraction source is being assembled and should be operational in the coming year.

The X9 mini-gap undulator bakeout 

monitor
52 | Facility Report

Experimental Systems

“Design and R&D efforts on behalf of the NSLS-II

project beamlines commanded a significant fraction

of time on the part of Beamline R&D Section members 

as well as members of other NSLS sections – as much 

as 50 percent in some cases.”

The major activities, projects, and accomplishments of the Experimental Systems Division in 2008 are summarized below.

Beamline R&D

During 2008, members of the Beamline R&D Section, led by 

Lonny Berman, were heavily engaged in NSLS beamline and 

endstation construction and upgrade projects, as well as in 

NSLS-II project beamline design preparation and R&D.

At the NSLS, construction of the new X9 beamline and endstation for small angle x-ray scattering (SAXS)/wide angle 

x-ray scattering (WAXS) moved closer to completion. The 

undulator and front end for this beamline were installed in 

2008, as were major components of the beamline and the 

endstation, and the beamline is on track for commissioning 

and startup of operation during 2009. Construction of the 

new X13A endstation for soft x-ray scattering made further 

advances through the construction of its vacuum chamber 

and rotary feedthrough, sample transfer system, and superconducting magnet, and will proceed through the end of 

2009. Projects that began in 2007 and were completed in 

2008 included an upgrade of the X7B monochromator based 

on bent Laue diffracting silicon crystals optimized for high 

x-ray energies and an upgrade of the X18A beamline based 

Steven Hulbert on replacement of its monochromator and mirror with newExperimental Systems Division Head
Facility Report | 53

Experimental Systems

er ones optimized for tunability and operation to high x-ray 

energies. Both of these projects were intended to uphold 

new experimental programs at these beamlines; namely, 

high x-ray energy powder diffraction and pair distribution 

function measurements at X7B and combined diffraction/

extended x-ray absorption fine structure (EXAFS), including 

time-resolved, at X18A. These new programs are currently 

serving users. Finally, groundwork was laid for a new X17A 

beamline and endstation, which will employ a single double-focusing bent Laue diffracting silicon crystal delivering 

a fixed high energy x-ray beam to an endstation instrument 

that will be devoted to pair distribution function measurements. The project is expected to be completed in 2010.

Design and R&D efforts on behalf of NSLS-II project beamlines commanded a significant fraction of time on the part 

of Beamline R&D Section members as well as members of 

other NSLS sections – as much as 50 percent in some cases. 

NSLS staff members led the preparation of the preliminary 

designs for four out of the six NSLS-II project beamlines: the 

coherent hard x-ray beamline, the coherent soft x-ray beamline, the hard x-ray nanoprobe beamline, and the powder 

diffraction beamline. These designs were subjects of the 

CD-2 review of NSLS-II, which occurred in November 2007. 

Efforts by these NSLS staff members, working together with 

NSLS-II project beamline staff, continued on behalf of these 

designs through the remainder of the year, leading up to 

the CD-3 review in September 2008. In addition, NSLS staff 

members helped organize workshops held on behalf of the 

project beamlines and conducted associated R&D for the 

beamlines’ optics and diagnostics.

Two infrared projects were undertaken at diagnostic & instrumentation beamline U4IR in 2008. The NSLS, in collaboration 

with the City College of New York, completed the installation of a 10 T split-coil superconducting magnet for use with 

far- and mid-infrared synchrotron radiation. The system will 

be redeployed at beamline U12IR once the optics have been 

restored to their original conditions and the magnet cryostat’s 

windows have been upgraded from quartz to polypropylene 

to expand the spectral range. The second project was optimization of the optical interface of the National Institutes of 

Health-funded infrared focal plane array (FPA) microspectrometer system for use at a large-horizontal-collection infrared beamline. The system will be moved from U4IR to a permanent location at infrared beamline U10 in 2009.

Turning to x-ray focusing optics R&D, diamond offers several 

distinct advantages as an optic material for producing hard 

x-ray (E > 4 keV) focusing lenses, including its relatively large 

decrement in refractive index, relatively low absorption, 

and high thermal conductivity. Current trends in beamline 

(Right) One of 

the crystal assemblies of the 

new X7B bent 

Laue diffracting 

double crystal 

monochromator

(Right) View of a kinoform lens fabricated from diamond polycrystalline material. The prototype lens was functional, but future lenses will need to have deeper etches in order to have 

more useful larger-sized apertures (taken from A. Isakovic et al., 

J. Synchrotron Rad. 16, 8-13 (2009)).
54 | Facility Report

Experimental Systems

design are to preserve the coherence of the source, and a 

practical way to do this is to minimize the number of optical 

elements in a beamline, and to use only optical elements 

that are perfect enough to preserve the source coherence. A 

good choice for fabricating such a phase-preserving single 

optic that can withstand the direct beam from a synchrotron is a kinoform fabricated from diamond. A prototype was 

made by the Beamline R&D Section. While this lens displayed 

focusing behavior, there is much that remains to be done. 

For example, the prototype optic was fabricated from the 

polycrystalline material, and it is expected that the performance of the optic will be dramatically improved by using 

single-crystal material. Additional improvements will come 

from larger apertures to collect more light as the fabrication 

technique is improved.

A relatively new focus of the Beamline R&D Section is to 

track the performance of NSLS beamlines. Toward this effort, 2008 activities centered on taking performance measurements for all of the x-ray spectroscopy beamlines and 

building a new instrument that can measure various aspects 

of the beam resolution function. A summary of the x-ray 

spectral flux findings for the x-ray spectroscopy beamlines 

reveals that those beamlines whose performance falls farthest below expectation tend to be those that use mirrors 

(with one exception). Several of these mirrors are of old vintage and have poor reflectivity, and these findings indicate 

that replacement of these may be a useful upgrade pathway 

for improved performance of these beamlines. 

The newest member of the Beamline R&D Section arrived 

during the latter part of 2008 and is leading a program to 

coordinate and grow industrial research at the NSLS. Work 

started with General Electric to develop and use a hightemperature furnace for powder diffraction to study ceramic 

materials, and continues with IBM on developing a remoteaccess capability for beamline X20B.

Detectors

The mission of the Detector Group, headed by Peter Siddons, is threefold: to develop and implement new detectors 

for synchrotron applications, to support these systems for 

beamline use at the NSLS, and to support those systems provided to other labs as necessary.

During 2008, the Detector Group successfully tested prototypes of the x-ray imaging detector designed by NSLS 

for the Linac Coherent Light Source (LCLS) project at the 

SLAC National Accelerator Laboratory. The 64 x 64 pixel 

prototype shows that the requirements of the LCLS pumpprobe experiment can be met. These successful tests also 

Measured spectral flux at various x-ray spectroscopy beamlines (dotted lines), compared with 

simulations (solid lines)

A close-up of the 64 x 64 sensor with its wire-bonds connecting it to the custom chip for readout 
Facility Report | 55

Experimental Systems

demonstrate that this detector will be extremely valuable 

for normal synchrotron applications, such as protein crystallography (PX). The prototype has been used to record PX 

diffraction spots in fine-slicing mode. With the full-scale 

version of this detector, a 1,000-frame dataset could be collected in less than 10 seconds (assuming sufficient x-ray 

intensity). Current PX detectors require a time on the order 

of seconds to read a single frame.

A new opportunity for the Detector Group has been provided by a Department of Energy (DOE) grant to study the 

application of a new circuit fabrication technology to x-ray 

detectors: 3D circuit integration. This is a technology currently being explored by the semiconductor industry to extend the circuit density of systems by expanding in the third 

dimension, i.e. upwards. This circuit technology is achieved 

by bonding complementary metal-oxide semiconductor 

(CMOS) integrated circuits one atop the other, with micronscale interconnections between layers. One could imagine 

putting the floating-point processor directly above the CPU 

in a microprocessor, thus greatly reducing the number of 

long wires required in a planar geometry to connect these 

two units. Similarly, detectors can be built using the appropriate technology for each type of circuit. For example, 

low-noise analog circuits have a sweet spot around 0.3 μm, 

whereas digital circuits can be effective down to tens of 

nanometers. 3D integration could allow both technologies 

to coexist in the same device, and be bonded directly to the 

thick x-ray-sensitive detector. This could open the doors for 

developing detectors with more “intelligence” in each pixel; 

for example, energy-resolving imaging detectors or detectors with time-correlation calculations performed in real 

time. Under this three-year DOE grant, awarded in August 

2008, the possibilities of using 3D circuit integration for synchrotron x-ray detector applications will be explored.

Mechanical Systems

The Mechanical Systems Section, led by Payman Mortazavi, 

provides mechanical engineering, design, and technical 

support to all NSLS divisions, both for operations and for 

project upgrades, large and small. The largest undertaking 

for the Mechanical Section this year was completion of the 

X9 project, described below, which involved significant 

mechanical section engineering, design, and technical efforts. The Mechanical Section also continued preventative 

maintenance and emergency repair efforts on all accelerator and storage ring systems and components with the 

goal of better than or equal to 95 percent reliability delivered to NSLS users. As part of this effort, numerous components subject to wear and degradation were replaced 

(hoses, fittings, valves, and connectors), rebuilt (e.g. the X17 

Image and histograms corresponding to a reflection of a sample of 

thaumatin taken at X6A at 12.2 keV with a beam size at the sample of 

200 x 200 mm2. The rotation speed was 0.5°/ s and data integration 

time 32 ms. The pixel size is 90 x 90 mm2.
56 | Facility Report

Experimental Systems

cryogenic refrigerator/liquefier), and calibrated (e.g. gauges and instruments) during 2008.

The major NSLS projects for which the Mechanical Systems 

Section provided significant support during 2008 include:

Accelerator

Injection System: Good progress was madeon a project to 

identify spare and missing transfer line magnet coils. The 

scope was first expanded to include the identification of 

redundant magnets and magnet coil protections and later 

again to include the booster, X-Ray, and VUV Ring magnets. 

Booster Ring: Three ion pumps in the NSLS Booster Ring 

were replaced to improve vacuum. Replacement of two 

of these parts was planned, owing to their age and condition, while the third was replaced following discovery that 

it was leaking.

X9 undulator: Engineering, detailed design, and construction of the X9 mini-gap undulator (MGU) began in-house in 

2007 and continued throughout 2008. The project included 

installation of upstream and downstream pick-up electrodes 

for straight-section beam-position monitoring. The X9 MGU 

project culminated in early September 2008 when installation of the X9 MGU into the X-Ray Ring was completed. 

RF cavities near X9: Two new all-copper radio frequency (RF) 

cavities XRF1 and XRF2 that “bookend” the new X9 undulator 

in the X9 insertion device straight section of the X-Ray Ring 

were installed during past shutdowns.

X9 front end: Design, fabrication, and installation of the 

new X9 front end required a total of three shutdown periods, all of 2008, to accomplish. The first was to remove all of 

the old X9 bending magnet components and take the necessary measurements for design, and the second and third 

were to install and precisely align the new front-end components. The X9 front end components were engineered 

and designed to handle the undulator power, including a 

specially designed differential ion pump that provides windowless vacuum isolation between the front end and the 

rest of the X9 beamline.

Utilities

Installation was completed of the Automated Process and 

Control Software (APACS), industry-standard software that 

collects inputs from numerous temperatures, pressures, 

valve positions, and fluid flow sensors so that troubleshooting information can be analyzed and corrective actions determined remotely. The assessment of the need for additional sensors to provide a more complete set of control inputs 

and enhance the capabilities of the system will continue.

XRF1 and XRF2 cavities X9 front end configuration
Facility Report | 57

Experimental Systems

Beamlines

In addition to the mechanical engineering, design, and 

technical development and support for the beamline activities described earlier in this report, several additional 

efforts were undertaken by the Mechanical Section:

•	 Engineering, fabrication, and installation support for a 

new beamline at X9 occurred throughout 2008, including a new experimental end station enclosure. Most of 

the fabrication work was completed by Central Fabrication Services, but many smaller items were made by 

Mechanical Section technicians, who also undertook 

much of the installation work and all of the survey and 

alignment work.

•	 Implementation of new external exhaust capabilities at 

X18, X19, X21, and X22 were undertaken. Extensive new 

design and modifications were needed to supply highefficiency particulate air (HEPA)-filtered external exhaust capabilities to the participating research teams at 

X18A, X18B, and X19A for nanoscience work. Additionally, external exhaust capabilities were added at X21A 

and X22B. The added capability for X21 will vent a new 

gas cabinet and a class IV excimer laser that will be added within the X21 Experimental End Station Enclosure 

(EESE) to pulsed laser deposition growth of thin films 

for in-situ x-ray diffraction studies. These new exhaust 

system connections should be completed early in 2009.

•	 The engineering and design work for the addition of a 

new beamline at X17A was another large undertaking. 

The design work for this effort started late in 2008. A 

single-bounce sagittal bent Laue monochromator (511 

Si reflection, Zhong optical design) will take photons 

from the X17A shutter and diffract, focus, and deflect 

them into the new X17A beamline. Adding the X17A 

beamline to the existing X17B,C beamline suite will require expansion of the small and large X17 transport 

enclosures on the outboard side. A new X17A EESE will 

be engineered, designed, and specified for procurement. The beamline design layout work for this project is ongoing and sketches/statements of work for the 

new X17A EESE and X17 transport enclosure modifications will be written and sent out for quotes in 2009. 

A novel monochromator design is being undertaken, 

which will utilize two-axis bending to simultaneously 

focus x-ray photons in two axes. In order to prove out 

this novel approach, a test fixture design is being undertaken to determine the limits of two-axis bending 

for this new device.

X9 beamline
58 | Facility Facts and Figures

Introduction

The NSLS is a facility open to researchers, called "users," that 

operates around the clock throughout the year, except during 

pre-announced maintenance and studies periods. In 2008, 51 

x-ray and 14 vacuum ultraviolet-infrared operational beamlines were available for a wide range of experiments utilizing 

a variety of techniques. There are two types of beamlines at 

the NSLS: Facility Beamlines (FBs), of which there are 18; and 

Participating Research Beamlines (PRTs), currently totaling 47. 

FBs are operated by the NSLS staff and reserve a minimum of 

50 percent of their beam time for users from various institutions outside the NSLS, called general users. Some FBs also 

host Contributing Users (CUs), who enhance endstation capabilities and provide generalized support to general users. PRT 

beamlines are operated by user groups with related interests 

from one or more institutions. PRT beamlines reserve 25 percent of their beam time for general users, although they can 

grant additional time at their own discretion. Membership in 

a PRT or CU program is open to all members of the scientific 

community who can contribute significantly to the program 

of the beamline. For example, this can include funding, contribution of equipment, scientific program, design and engineering, or operations staffing. The following pages provide 

details on the NSLS operational beamlines, including their 

unique characteristics.

Users at the NSLS primarily are awarded beam time by 

submitting a “General User” proposal through our peerreviewed, web-based proposal system. The proposal is 

rated based on various scientific criteria, and can remain 

active for up to six cycles of operations (or about two 

Kathleen Nasta

Manager, Information, Outreach, & User Administration
Facility Facts and Figures | 59

Introduction

years). In fiscal year 2008, more than 1,000 requests for 

beam time were submitted, nearly half of those requests 

on new proposals. Beam time is given without charge, as 

long as the research results are published in open literature. Work that is proprietary in nature is charged on a 

full-cost recovery basis according to U.S. Department of 

Energy (DOE) guidelines. 

During the calendar year 2008, hundreds of visitors attended 

the many workshops, short courses, seminars, reviews, and 

tours offered at the NSLS. In addition to the annual Joint NSLS/

Center for Functional Nanomaterials (CFN) Workshop in May 

and the second triennial review of the NSLS by the U.S. Department of Energy, 14 other workshops were held, as well as 

6 beamline reviews, 133 seminars, and 70 tours of the facility.

In fiscal year 2008, about 400 different institutions sent close 

to 2,200 users to the NSLS to conduct their research. Of this 

number, about 600 were new users. The majority (74%) of 

users comes from academic institutions, and a steady 7 percent of users were from industry.

The users who visited in 2008 were characterized by their 

fields of research in different ways. The greatest number 

works in the life sciences field, with materials sciences studies following closely. Considering the number of days spent 

on experiments – based on running times gathered from 

experimental Safety Approval Forms, which are required for 

every experiment – materials sciences studies make up the 

greatest portion of beam time used. 

About half of our users are U.S. citizens, and nearly 30 percent are women. Nearly one-third of our users are from within New York State, and another third come from locations 

nearby in the northeastern states.

In 2008, nearly 40 percent of the researchers working at the 

NSLS were students in undergraduate or graduate studies. 

Almost 22 percent of the users were post-doctoral researchers, with faculty members, professional staff, or research scientists making up the balance.

Just about equal to last year’s record-breaking number, NSLS 

users and staff published 964 articles in FY 2008. Of these, 

nearly 21 percent were published in premier journals. A publication is considered premier if the journal has an impact factor 

of 6 or greater (from Journal Citation Report 2005, Thomson 

Institute for Scientific Information). The table shown on page 

60 summarizes publications during the past year. The first column in the table lists the number of publications reported to 

the NSLS during the 2008 fiscal year (October 1, 2007 through 

September 30, 2008) and published between 2005 and 2008. 

Although some of these publications were published earlier 

than FY 2008, they were not reported to the NSLS until this 

fiscal year. Thus, they have not been counted in prior years’ 

reports. The second column in the table lists the number of 

papers published in the 2008 calendar year and reported to 

the NSLS as of February 27, 2009. These numbers are slightly 

lower than the fiscal year values because they contain only 

publications from 2008, and it often takes many months or 

years to account for user and staff publications.

“Visits to the NSLS were brisk business in 2008! In addition to our

annual Users’ Meeting and the triennial review by the U.S. Department 

of Energy, the NSLS hosted 14 workshops, 6 beamline reviews, 133 

seminars, and 70 tours.”
60 | Facility Facts and Figures

Parameters / Publications

X-Ray VUV-IR

Energy 2.800 GeV 0.808 GeV

Maximum Current 300 mA 1.0 A 

Photon Critical Wavelength

(Energy) for Dipole 1.75 Å (7.1 keV) 19.9 Å (622 eV)

Photon Critical Wavelength

(Energy) for X17 wiggler at 0.57 Å (22 keV) 

Horizontal Emittance 62 nm-rad 160 nm-rad

Vertical Emittance 0.34 nm-rad ≥ 0.35 nm-rad (4 nm-rad in normal ops.)

Electron Orbital Period 567.2 nanoseconds 170.2 nanoseconds

Number of RF Buckets 30 9

Typical Bunch Mode 25 7

Natural RMS Energy Spread 9.2 x 10-4 5.0 x 10-4 ( Ib< 20 mA)

RMS Bunch Length 44 mm 5 cm (Ib< 20 mA)

X-Ray and VUV-IR Parameters

2008 Publications

Reported in FY08* Published in CY08**

Journals, peer-reviewed, premier 202 163

Journals, other peer-reviewed 603 509

Journals, non peer-reviewed 25 16

Books/Chapters in Books 17 9

Published Conference Proceedings 69 32

Reports: Technical, Formal, Informal 4 4

Theses/Dissertations 43 26

Patents 1 6

Total Publications 964 765

NSLS VUV-IR User Publications 104 76

NSLS X-Ray User Publications 729 600

NSLS Staff Publications 131 89

Total Publications 964 765

* Publications reported to the NSLS from Oct. 1, 2007 - Sept. 30, 2008 and published between 2005 - 2008.

** Publications published in 2008 as reported to the NSLS by Feb. 27, 2009.
Facility Facts and Figures | 61

User Statistics

Users by Field of Research

Fiscal Year 2008

Geographical User Distribution

Fiscal Year 2008

Users by Affiliation

Fiscal Year 2008

Beamtime Used*

Fiscal Year 2008

44%

Life Sciences

Life Sciences

New York Only

Northeast

(not New York)

Academic

BNL Employees

Industry/Corporate

Other Labs and Affiliations

Non-Northeast

Foreign

Geosciences and Ecology

Environmental and Geosciences

Optical/Nuclear/General Physics

3% - Applied Sciences and Engineering

Applied Sciences and Engineering

2% - Unknown

Optical/Nuclear/General Physics

Chemical Sciences

Chemical Sciences - 4%

DOE Employees (non-BNL) - 2%

Federal Agencies (non-DOE) - 2%

Other

Materials Sciences

Materials Sciences

13%

5%

4%

29%

31%

46%

74%

9%

7%

6%

15%

12%

5%

7%

9%

33%

22%

14%
62 | Facility Facts and Figures

Beamline Status

Diraction

& Scattering 0 20

Macromolecular

Crystallogrophy 0 20

Microspectroscopy 3 8

Spectroscopy 9 10

Other 1 4

Insertion Devices

VUV-IR X-Ray

X-Ray Ring

VUV-IR Ring

U9 B U7 A

U5 UA

U4 B

U3 C

U2 A,B

U1 A

U13 UB

X21

X25

U11

U12 A

U12 IR

U10 B

X1 A1, A2, B

X4 A,C

X6 A, B

X7 B

X8 A, C

X10 A, B, C

X11 A, B

X12 B, C

X13 A, B

X17 B1, B2, B3, C

X14 A

X15 A, B

X16 C X18 A, B

X19 A, C

X20 A, C

X22 A, B, C

X23 A2, B

X24 A, C

X26 A, C

X27 A, B, C

X28 C

X29 A

X3 A, B

X2 B

Diraction

& Scattering 0 20

Macromolecular

Crystallogrophy 0 20

Microspectroscopy 3 8

Spectroscopy 9 10

Other 1 4

Insertion Devices

VUV-IR X-Ray

X-Ray Ring

VUV-IR Ring

U9 B U7 A

U5 UA

U4 B

U3 C

U2 A,B

U1 A

U13 UB

X25

U11

U12 A

U12 IR

U10 B

X1 A1, A2, B

X4 A,C

X6 A, B

X7 B

X8 A, C

X10 A, B, C

X11 A, B

X23 A2, B

X24 A, C

X26 A, C

X27 A, B, C

X28 C

X29 A X3 A, B

X2 B

ARPES Photoelectron Spectroscopy, Angle-Resolved SAXS Small Angle X-Ray Scattering

DAFS X-Ray Diffraction Anomalous Fine Structure STXM Scanning Transmission X-Ray Microscopy

DEI Diffraction-Enhanced Imaging UPS UV Photoelectron Spectroscopy

EXAFS X-Ray Absorption Spectroscopy, Extended Fine Structure UV-CD Ultraviolet Circular Dichroism

Beamline Guide Abbreviations

Beamline Status
Facility Facts and Figures | 63

Beamline Guide

HARMST High Aspect Ratio Microsystems Technology WAXD Wide-Angle X-Ray Diffraction

IRMS Infrared Microspectroscopy WAXS Wide-Angle X-Ray Scattering

MAD Mulit-Wavelength Anomolous Dispersion XAS X-Ray Absorption Spectroscopy

MCD Magnetic Circular Dichroism XPS X-Ray Photoelectron Spectroscopy

NEXAFS Near Edge X-Ray Absorption Spectroscopy XRD X-Ray Diffraction

PEEM Photo Emission Electron Microscopy XSW X-Ray Diffraction, Standing Waves

Beamline Source Type of Research Energy Range Type Organization

VUV-IR Beamlines

U1A Bend

XAS

EXAFS

NEXAFS

270-900 eV PRT ExxonMobil Research and

 Engineering Co.

U2A Bend

IRMS

High pressure research

IR spectroscopy

30-10000 cm-1 FB

COMPRES

Carnegie Institution of Washington

BNL-NSLS

U2B Bend IRMS 500-4000 cm-1 PRT Case Western Reserve University

U3C Bend Metrology 50-1000 eV PRT

Lawrence Livermore National Laboratory

Los Alamos National Laboratory

National Security Technologies

Sandia National Laboratory

U4B Bend

X-ray reflectivity

X-ray scattering, magnetic

X-ray scattering, resonant

MCD

XAS

X-ray fluorescence spectroscopy

20-1200 eV FB Montana State University 

BNL-NSLS

U5UA Insertion 

Device

ARPES

UPS, spin-resolved 15-150 eV FB BNL-NSLSBNL-CFN

U7A Bend NEXAFS

XPS 180-1200 eV PRT

BNL-Chemistry

Dow Chemical Company

National Institute of Standards &

 Technology

U9B Bend

Time-resolved spectroscopy

UV-CD

UV florescence spectroscopy

0.8 - 8 eV PRT BNL-Biology

U10B Bend IRMS 500-4000 cm-1 FB BNL-NSLS

U11 Bend UV-CD 3-10 eV PRT BNL-Biology

U12A Bend XAS

XPS 100-800 eV PRT Oak Ridge National Laboratory

U12IR Bend

IR spectroscopy

Magnetospectroscopy

THz / millimeter wave spectroscopy

Time-resolved spectroscopy

8-600 cm-1 FB BNL-NSLS

U13UB Insertion 

Device

UPS

ARPES 3-30 eV PRT

Boston College

Boston University

BNL-Physics

Columbia University
64 | Facility Facts and Figures

Beamline Guide

Beamline Source Type of Research Energy Range Type Organization

X-Ray Beamlines

X1A1 Insertion 

Device

STXM

NEXAFS 0.25-0.50 keV PRT

BNL-Environmental Sciences

ExxonMobil Research and

 Engineering Co.

Stony Brook University

SUNY @ Plattsburgh

University of Texas @ Houston

X1A2 Insertion 

Device STXM 0.25-1 keV PRT Stony Brook University

X1B Insertion 

Device

XAS

X-ray fluorescence spectroscopy

XPS

0.2-1.6 keV PRT

Boston University

Thomas Jefferson National Accelerator 

 Facility

University of Illinois

X2B Bend X-ray microtomography 8-35 keV PRT ExxonMobil Research and

 Engineering Co.

X3A Bend MAD

Macromolecular crystallography 4.6-15.1 keV PRT

Case Western Reserve University

Rockefeller University

Sloan-Kettering Institute for Cancer 

 Research

X3B Bend XAS

EXAFS 5-13.7 keV PRT Case Western Reserve University

X4A Bend MAD

Macromolecular crystallography 3.5-20 keV PRT

Albert Einstein College of Medicine

City University of New York (CUNY)

Columbia University

Cornell University

Mount Sinai School of Medicine

New York Structural Biology Center

New York University

SUNY @ Buffalo

Sloan-Kettering Institute for Cancer 

 Research

Wadsworth Center

X4C Bend MAD

Macromolecular crystallography 7-20 keV PRT

Albert Einstein College of Medicine

City University of New York (CUNY)

Columbia University

Cornell University

Mount Sinai School of Medicine

New York Structural Biology Center

New York University

Rockefeller University

SUNY @ Buffalo

Sloan-Kettering Institute for Cancer 

 Research

Wadsworth Center

X6A Bend MAD

Macromolecular crystallography 6.0-23 keV FB BNL-NSLS

X6B Bend

XRD, surface

WAXD

X-ray reflectivity

6.5-19 keV FB BNL-CFN

BNL-NSLS

X7B Bend

XRD, single crystal

XRD, time resolved

WAXD

WAXS

25-50 keV PRT BNL-Chemistry

General Electric

X8A Bend Metrology 1.0-5.9 keV PRT

Lawrence Livermore National

 Laboratory

Los Alamos National Laboratory

National Security Technologies

Sandia National Laboratory
Facility Facts and Figures | 65

Beamline Guide

Beamline Source Type of Research Energy Range Type Organization

X8C Bend MAD

Macromolecular crystallography 5-19 keV PRT

Biogen Incorporated

Biotechnology Research Institute

Hoffmann-La Roche

National Institutes of Health

X9 Bend SAXS

WAXS 10-20 keV

X10A Bend

XRD, powder

WAXD

SAXS

WAXS

8-11 keV PRT ExxonMobil Research and

 Engineering Co.

X10B Bend

XRD, powder

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

14 keV PRT ExxonMobil Research and

 Engineering Co.

X10C Bend

XAS

EXAFS

NEXAFS

4-24 keV PRT ExxonMobil Research and

 Engineering Co.

X11A Bend

DAFS

XAS

EXAFS

NEXAFS

4.5-35 keV PRT

BNL-Material Sciences

BNL-Environmental Sciences

Canadian Light Source

ETH Labs - Zuerich

Natural Resources Canada

Naval Research Laboratory (NRL)

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Sarah Lawrence College 

Stony Brook University

X11B Bend

XAS

EXAFS

NEXAFS

5.0-23 keV PRT

BNL-Environmental Sciences

BNL-Material Sciences

Canadian Light Source

ETH Labs - Zuerich

Natural Resources Canada

Naval Research Laboratory

Naval Surface Warfare Center

New Jersey Institute of Technology

North Carolina State University

Sarah Lawrence College

Stony Brook University

X12B Bend MAD

Macromolecular crystallography 5-20 keV PRT BNL-Biology

X12C Bend MAD

Macromolecular crystallography 5.5-20 keV PRT BNL-Biology

X13A Insertion 

Device

X-ray scattering, magnetic

X-ray scattering, resonant

MCD

0.2-1.6 keV FB BNL-NSLS

X13B Insertion 

Device Microdiffraction Imaging 4-16 keV FB Columbia UniversityBNL-NSLS

X14A Bend

MAD

XRD, powder

XRD, single crystal

XRD, time resolved

WAXD

X-ray reflectivity

5-26 keV PRT

New York State College of Ceramics

Oak Ridge National Laboratory

Tennessee Technological University

University of Tennessee

X15A Bend XSW

DEI

3-25 keV XSW

10-60 keV DEI FB BNL-NSLS
66 | Facility Facts and Figures

Beamline Guide

Beamline Source Type of Research Energy Range Type Organization

X15B Bend

XAS

EXAFS

NEXAFS

0.8-15 keV PRT

BNL-Environmental Sciences

Lucent Technologies, Inc.

Stony Brook University

Temple University

University of Texas @ Austin

X16C Bend XRD, powder 6.5-25 keV PRT Stony Brook University

X17B1 Insertion 

Device XRD, powder 55-80 keV mono20-150 keV white FB BNL-NSLSRutgers University

X17B2 Insertion 

Device

XRD, powder

XRD, time resolved

High pressure research

20-130 keV FB

COMPRES

BNL-NSLS

Stony Brook University

X17B3 Insertion 

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV FB

COMPRES

BNL-NSLS

Princeton University

Stony Brook University

X17C Insertion 

Device

XRD, powder

XRD, single crystal

High pressure research

5-80 keV FB

COMPRES

BNL-NSLS

Princeton University

Stony Brook University

X18A Bend

XRD, powder

XRD, single crystal

XRD, surface

WAXD

X-ray reflectivity

X-ray scattering, surface

WAXS

XAS

5-25 keV PRT

BNL-Chemistry

BNL-Electrochemistry

BNL-NSLS

Oak Ridge National Laboratory

UOP LLC

University of Delaware

University of Massachusetts

Yeshiva University

X18B Bend

XAS

EXAFS

NEXAFS

4.8-40 keV FB

BNL-Chemistry

BNL-Electrochemistry

BNL-NSLS

ORNL

UOP LLC

University of Delaware

Yeshiva University

X19A Bend

X-ray scattering, resonant

XAS

EXAFS

NEXAFS

2.1-17 keV FB

BNL-Chemistry

BNL-Electrochemistry

BNL-NSLS

ORNL

UOP LLC

University of Delaware

Yeshiva University

X19C Bend

XRD, surface

X-ray topography

X-ray reflectivity

X-ray scattering, liquid

X-ray scattering, surface

6-17 keV PRT

Fairfield Crystal Technology, LLC

Kansas State University

Stony Brook University

SUNY @ Albany

University of Illinois @ Chicago

X20A Bend

XRD, single crystal

WAXD

Microdiffraction Imaging

X-ray reflectivity

X-ray scattering, surface

4.5-13 keV PRT IBM Research Division

X20C Bend

XRD, single crystal

XRD, surface

XRD, time resolved

X-ray reflectivity

X-ray scattering, surface

4-11 keV PRT IBM Research Division
Facility Facts and Figures | 67

Beamline Guide

Beamline Source Type of Research Energy Range Type Organization

X21 Insertion 

Device

XRD, single crystal

XRD, surface

WAXD

X-ray scattering, magnetic

X-ray scattering, resonant

X-ray scattering, surface

WAXS

5-15 keV FB

Boston University

BNL-NSLS

University of Vermont

X22B Bend X-ray scattering, liquid 8 keV PRT BNL-CMPMSD

BNL-CFN

X22C Bend

XRD, single crystal

XRD, surface

X-ray reflectivity

X-ray scattering, magnetic

X-ray scattering, surface

3-12 keV PRT

BNL-CMPMSD

Massachusetts Institute of Technology

Rutgers University

X23A2 Bend

DAFS

XAS

EXAFS

NEXAFS

4.7-30 keV PRT National Institute of Standards

 & Technology

X23B Bend

XRD, powder

XAS

EXAFS

NEXAFS

4-10.5 keV PRT

Hunter College

National Institute of Standards

 & Technology

Naval Research Laboratory

Naval Surface Warfare Center

New Jersey Institute of Technology

Northeastern University

Sarah Lawrence College

X24A Bend

XSW

Auger spectroscopy

EXAFS

X-ray fluorescence spectroscopy

XPS

1.8-6 keV PRT National Institute of Standards

 & Technology

X24C Bend

X-ray reflectivity

UV absorption spectroscopy

XAS

0.006-1.8 keV PRT

Naval Research Laboratory

SFA, Inc.

Universities Space Research

 Association

X25 Insertion 

Device

MAD

Macromolecular crystallography 5-20 keV FB BNL-BiologyBNL-NSLS

X26A Bend Microdiffraction Imaging

X-ray microprobe 3-30 keV PRT

BNL-Environmental Sciences

University of Chicago

University of Kentucky

X26C Bend MAD

Macromolecular crystallography 5-20 keV PRT

BNL-Biology

Cold Spring Harbor Laboratory

Stony Brook University

X27A Bend X-ray microprobe 4.5-32 keV FB

BNL-Environmental Sciences

BNL-NSLS

Stony Brook University

X27B Bend HARMST 8-40 keV PRT BNL-Nonproliferation & National Security

X27C Bend

XRD, time resolved

WAXD

SAXS

WAXS

9 keV PRT

Air Force Research Laboratory

National Institutes of Health

Naval Surface Warfare Center

Stony Brook University

X28C Bend X-ray Footprinting Focused White 

 Beam PRT Case Western Reserve University

X29A Insertion 

Device

MAD

Macromolecular crystallography 6-15 keV PRT BNL-BiologyCase Western Reserve University
68 | Facility Facts and Figures

Advisory Committees

Users’ Executive Committee

The NSLS regularly consults with the Users’ Executive Committee 

(UEC). This committee provides a forum for ongoing, organized discussions between representatives from the NSLS user community in 

various research disciplines and the management and administration 

at the NSLS and Brookhaven National Laboratory. The purpose is to 

communicate current and future needs, concerns, and trends, and to 

disseminate information about future plans for the NSLS and BNL.

Chair John Parise, Stony Brook University

Vice Chair Bruce Ravel, National Institute of Standards 

and Technology

Past Chair Daniel Fischer, National Institute of Standards 

and Technology

General Member Peter Abbamonte, University of Illinois at

Urbana-Champaign

General Member Jean Jordan-Sweet, IBM

General Member George Flynn, SUNY at Plattsburgh

General Member Don Weidner, Stony Brook University

General Member Peter Stephens, Stony Brook University

Ex-Officio Chi-Chang Kao, NSLS Chair, BNL

Ex-Officio Kathleen Nasta, Manager, NSLS Information 

Outreach & User Administration, BNL

Special Interest Group Representatives

Special Interest Group (SpIG) Representatives are listed below; these 

groups in areas of common concern communicate with NSLS management through the UEC.

Bio. Crystallography 

& Diffraction

Annie Heroux, BNL/ Biology 

High Pressure Michael Vaughan, Stony Brook University

Imaging Dawit Solomon, Cornell University

Industrial Users Gary Mitchell, The Dow Chemical Company

Infrared Users Jiufeng Tu, City University of New York

Magnetism Cecilia Sanchez-Hanke, BNL/NSLS

NSLS-II Daniel Fischer, National Institute of

Standards and Technology

Students & Post Docs Andreana Leskovjan, Stony Brook University

Time Resolved

Spectroscopy

John Sutherland, BNL/Biology

Topography Michael Dudley, Stony Brook University

UV Photoemission & 

Surface Science

Jeff Keister, SFA, Inc.

XAFS Faisal Alamgir, Georgia Institute of Technology

X-ray Scattering & 

Crystallography

Helmut Strey, Stony Brook University

Scientific Advisory Committee

The NSLS Scientific Advisory Committee (SAC) advises the NSLS Chair 

and the Associate Laboratory Director for Light Sources on scientific, 

technical, and policy issues related to the optimization of the scientific productivity of the NSLS.

Mario Amzel, Johns Hopkins University

Simon Bare, UOP, LLC

Joel Brock, Cornell University 

Tony Heinz, Columbia University

Robert Hettel, Stanford Synchrotron Radiation Laboratory/ 

Stanford Linear Accelerator Center

Eric Isaacs, Argonne National Laboratory

Leemor Joshua-Tor, Cold Spring Harbor Laboratory

James Kaduk, INEOS Technologies

Edward Kramer, University of California, Santa Barbara

Simon Mochrie, Yale University

James Penner-Hahn (Chair), University of Michigan

William Thomlinson, Canadian Light Source

Daniel Fischer (UEC Chair), National Institute of Standards 

and Technology

Proposal Review Panels

As part of the peer-review process of GU proposals, the Proposal Review Panels (PRPs) at the NSLS review and rate the proposals within 

their scientific area. Members are drawn from the scientific community and usually serve a two-year term. Each PRP has an appointed 

Chair, who is part of the Proposal Oversight Panel (POP), established 

to review any proposals that might need special attention due to use 

of multiple techniques or conflicts in scores. The POP has additional 

appointed members, listed below after the PRP membership.

* = Chair of PRP

Imaging and Microprobes: Biological and Medical 

Leroy Chapman, University of Saskatchewan

Paul Dumas, Soleil Synchrotron

Kathleen Gough, University of Manitoba

Barry Lai*, Argonne National Laboratory

Carolyn Larabell, Lawrence Berkeley National Laboratory

Irit Sagi, Weizmann Institute of Science

Stefan Vogt, Argonne National Laboratory

Users’ Executive Committee
Facility Facts and Figures | 69

Advisory Committees

 Imaging and Microprobes: Chemical and Materials Sciences 

Harald Ade*, North Carolina State University

David Black, Topographix

Paul Evans, University of Wisconsin

Ismail Noyan, Columbia University

Nobumichi Tamura, Lawrence Berkeley National Laboratory 

Imaging and Microprobes: Environmental and Geosciences

Don Baker, McGill University

David Black, Topographix

George Flynn, SUNY at Plattsburgh

Matthew Ginder-Vogel, University of Delaware

Keith Jones*, BNL

Mark Rivers, University of Chicago

Donald Ross, University of Vermont

IR/UV/Soft X-ray Spectroscopy: Chemical Sciences/Soft Matter/

Biophysics

Daniel Fischer*, National Institute of Standards & Technology

Jan Genzer, North Carolina State University

Robert Lodder, University of Kentucky

Gary Mitchell, The Dow Chemical Company

IR/UV/Soft X-ray Spectroscopy: Magnetism/Strongly Correlated 

Electrons/Surface

Robert Bartynski*, Rutgers University

Di-Jing Huang, Synchrotron Radiation Research Center

Jeffrey Keister, SFA, Inc.

Alexander Moewes, University of Saskatchewan

David Mullins, Oak Ridge National Laboratory

Boris Sinkovic, University of Connecticut

Jiufeng Tu, City University of New York

Tonica Valla, BNL

Methods and Instrumentation

Leroy Chapman, University of Saskatchewan

Kenneth Finkelstein, Cornell University

Jeffrey Keister, SFA, Inc.

Ralf Hendrik, Menk Sincrotrone Trieste

Peter Takacs*, BNL

Macromolecular Crystallography

Alex Bohm*, Tufts University

Ashley Deacon, Stanford Synchrotron Radiation Lab

Xiangpeng Kong, New York University

Nicolas Nassar, Stony Brook University

Brenda Schulman, St. Jude Children’s Research Hospital

Hao Wu, Cornell University

Powder/Single Crystal Crystallography

Andrew Campbell, University of Maryland

Thomas Duffy*, Princeton University

Andrew Fitch, European Synchrotron Radiation Facility

Volker Kahlenberg, University of Innsbruck

Stefan Kycia, University of Guelph

James Martin, North Carolina State University

Wendy Panero, Ohio State University

X-Ray Scattering: Magnetism/Strongly Correlated Electrons/Surface

Peter Abbamonte, University of Illinois at Urbana-Champaign

Kenneth Finkelstein*, Cornell University

Peter Hatton, University of Durham

Karl Ludwig, Boston University

Christopher Marrows, University of Leeds

George Srajer, Argonne National Laboratory

Trevor Tyson, New Jersey Institute of Technology

Gerrit Van Der Laan, Diamond Light Source

X-Ray Scattering: Soft Matter and Biophysics 

Masafumi Fukuto, BNL

Randall Headrick, University of Vermont

Benjamin Hsiao*, Stony Brook University

Huey Huang, Rice University

Thomas Russell, University of Massachusetts

Detleff-Matthias Smilgies, Cornell University

Lei Zhu, University of Connecticut

X-Ray Spectroscopy: Biological, Environmental and Geosciences

Suzanne Beauchemin, Natural Resources Canada

Martine Duff, Westinghouse Savannah River Co.

Graham George, University of Saskatchewan

Douglas Hunter, Westinghouse Savannah River Co.

Satish Myneni*, Princeton University

Matthew Newville, University of Chicago

X-Ray Spectroscopy: Chemical and Material Sciences

Simon Bare, UOP

Scott Calvin, Sarah Lawrence College

Anatoly Frenkel , Yeshiva University

Steve Heald, Argonne National Laboratory

Bruce Ravel, National Institute of Standards & Technology

Jean-Pascal Rueff, Synchrotron SOLEIL

Trevor Tyson*, New Jersey Institute of Technology

Proposal Oversight Panel Members

Antonio Lanzirotti, University of Chicago

Jonathan Hanson, BNL

Stephen Shapiro, BNL

Peter Stephens, Stony Brook University

Subramanyam Swaminathan, BNL

Scientific Advisory Committee

National Synchrotron Light Source

Brookhaven National Laboratory

Upton, NY 11973

www.nsls.bnl.gov