Pdf - Cornell High Energy Synchrotron Source - Cornell University

On the Cover: 

New testing for small size scales 

Professor Matthew Miller and his group from the Sibley School 

of Mechanical and Aerospace Engineering standing in front of the load 

frame / diffractometer system located in Rhodes Hall, Cornell University. 

Back row (left to right): Michael Ross, Kevin McNelis, and Jay Schuren. 

Front row (left to right): Jon Acquaviva, Zachary Peeples, Ben Oswald, 

and Professor Miller. The system was designed and built for their high 

energy diffraction work at CHESS - Complete article on page 37. 

Contents 

Staff in Focus 

John Kopsa 

from the Staff 

Welcome the new 

Chae Un Kim 

Facility Upgrades 

Chris Conolly 

Facility Highlights 

Education & Outreach 

Lora Hine 

MacCHESS Advances 

Marian Szebenyi 

2 CHESS Director’s Report 

Sol Gruner 

3 G-line Director’s Report 

Joel Brock 

4 MacCHESS Director’s Report 


6 CHESS Assistant Director’s Report 

Ernie Fontes 

8 User and Student Highlights 

Ernie Fontes and Kathy Dedrick 

11 Staff in Focus 

Laura Houghton 

13 Facility Upgrades, Networking and Computing 

Chris Conolly 

17 C-line Upgrades and New Capabilities 

Ernie Fontes and Ken Finkelstein 

19 D-line Upgrades and New Science Capabilities 

Ernie Fontes and Detlef Smilgies 

22 Education & Outreach 

Lora Hine 

25 MacCHESS Advances: Microcrystallography & More 


27 Station F3 

Ulrich Englich 

28 XPaXS: Improved Data Acquisition & Real-Time Analysis at CHESS 

Darren Dale 

30 CHESS High-pressure B1/B2 Update 

Zhongwu Wang 

31 The Cornell Energy Recovery Linac: 

update on a future source of coherent hard x-rays 

Don Bilderback, Bruce Dunham, Georg Hoffstaetter, 

Alexander Temnykh, and Sol Gruner 

CHESS News Magazine 2009

The Cornell High Energy Synchrotron Source (CHESS)... 

CHESS - Cornell University 

Rt 366 & Pine Tree Road 

Ithaca, NY 14853 

phone: 607-255-7163 

fax: 607-255-9001 

...is a user-oriented National Facility to provide state-of-the-art synchrotron radiation facilities to the 

scientific community. 

Supported by grants from the Division of Materials Research of the National Science Foundation, CHESS 

encompasses a multifaceted research and development program which is partly in-house and partly 

collaborative, with a wide spectrum of experimental groups from Universities, National Laboratories 

and Industry. 

Research Highlights 

Mechanical Testing 

Matt Miller 

Citrine Structure 

Sol Gruner 

Super BioSAXS 

Richard Gillilan 

Topography 

Richard Jones 

Nanoparticles 

John Hart 

37 New Mechanical Testing Methods for Structural 

Materials at Small Size Scales 

Matthew P. Miller 

43 Alteration of Citrine Structure by Hydrostatic Pressure 

Sol Gruner, Buz Barstow, Nozomi Ando, 

and Chae Un Kim 

45 Putting Color into Surface Diffraction 

Detlef Smilgies 

48 Self-Assembled Nano-Checkered Thin Films Studied 

by Reciprocal Space Mapping at CHESS 

Sean O’Malley, Peter Bonanno, Keun hyuk Ahn, 

Andrei Sirenko, Alex Kazimirov, Soon-Yong Park, 

Yoichi Horibe, and Sang-Wook Cheong 

50 Structures from Solutions: Biomolecular Small-Angle 

Solution Scattering at MacCHESS 


54 Development of X-ray Pixel Array Detectors 

Sol Gruner 

56 Exploring New Physics of Nanoparticle Supercrystals 

by High Pressure Small Angle X-ray Diffraction 

Zhongwu Wang, Ken Finkelstein, 

and Detlef Smilgies 

58 Topography of Diamonds at CHESS helps Nuclear 

Physics Program at JLAB 

Richard Jones, Franz Klein, and Ken Finkelstein 

60 Nanoparticle-block Copolymer 

Ulrich Wiesner, Laura Houghton, and Sol Gruner 

61 Heat-bump Measurements at CHESS 

A2 Wiggler Beam 

Peter Revesz, Alex Kazimirov, Ivan Bazarov, 

Jim Savino, Emmett Windisch, and Christopher 

MacGahan 

63 Advances in X-ray Microfocusing with Monocapillary 

Optics at CHESS 

Sterling Cornaby, Thomas Szebenyi, 

Heung-Soo Lee, and Don Bilderback 

67 Watching Carbon Nanotube Forest Growth 

using X-rays 

Eric Meshot, Mostafa Bedewy, Sameh Tawfick, 

K. Anne Juggernauth, Eric Verploegen, Yongyi 

Zhang, Michael De Volder, and John Hart 

71 Phase Behavior of Water inside Protein Crystals 

Chae Un Kim, Buz Barstow, Mark Tate, 

and Sol Gruner 

Other Information 

The Cornell High Energy Synchrotron Source is 

supported by the National Science Foundation and the 

National Institutes of Health/National Institute of 

General Medical Sciences under grant DMR 0225180. 

MacCHESS is supported by NIH 5 P41 RR001646-24. 

Editor: Laura Houghton, lab49@cornell.edu 

Co-editor: Marian Szebenyi, dms35@cornell.edu 

Layout and design: 

Laura Houghton - CHESS, Cornell University 

Special thank you to David Schuller 

CHESS News Magazine 2009 Page 1

CHESS Director’s Report 

Sol Gruner 

Artist’s rendition of Wilson Lab showing CESR under the present 

Upper Alumni Athletic field. 

Synchrotron radiation (SR) science is evolving rapidly. When 

CHESS started in 1979, synchrotron radiation was largely a 

niche area populated by a small number of condensed matter 

physicists who worked parasitically at high energy physics 

facilities. Today, SR is part of the essential infrastructural fabric 

of scientists from many disciplines, who would have been 

shocked to know that they would be working productively at 

large-scale accelerator-based facilities. For example, modern 

biological science stands on the two legs of molecular 

structural determination and genetic engineering; the former 

is totally dependent on SR protein structure determination. In 

consequence, many new dedicated SR storage rings are coming 

on-line around the world to serve a growing and incredibly 

diverse user community. The size of this community is difficult 

to estimate, but certainly numbers in the tens of thousands. 

CHESS has contributed greatly to the evolution of SR. The 

question we ask ourselves daily is: “How can we best continue 

to serve the community and to have a unique impact” 

Historically, SR science cut its teeth at three laboratories: 

Cornell (where SR was first systematically studied in the early 

1950’s), DESY in Hamburg, Germany, and SLAC in California. 

In each case SR started as a parasitic activity to elementary 

particle physics accelerators. Within the last few years all three 

labs have undergone a transition to primary use of the on-site 

accelerators for photon science. These three laboratories have 

historically led the way in SR for user applications, in training 

accelerator physicists and SR facility scientists who go on to 

populate other facilities, and as incubators for new technology. 

So, for example, DESY and SLAC are now commissioning hard 

X-ray Free Electron Lasers (as is SPring-8 in Japan), whereas 

Cornell is developing a hard x-ray Energy Recovery Linac (ERL) 

x-ray source. 

Cornell has arguably trained more accelerator physics and 

beamline scientist leaders than any other laboratory in the 

world. Along the way, much of the technology in use at 

accelerator-based facilities was developed. Recent NSF reviews 

about the future of SR science at Cornell have emphatically 

pointed out that these three core missions -- serving SR 

users, training SR facility scientists and accelerator physicists, 

and development of new SR and accelerator technology – 

are continuing strengths of Cornell’s SR activity and offer a 

uniquely useful and important future for Wilson Lab. 

In 2006, Wilson Synchrotron Laboratory, consisting of CHESS 

and the Laboratory for Elementary-Particle Physics (LEPP), was 

formed into a single administrative umbrella called the Cornell 

Laboratory for Accelerator-based ScienceS and Education 

(CLASSE). Proposals for continued operation of CHESS and ERL 

R&D through 2014 have been extremely favorably reviewed; 

we are very optimistic that these activities will continue. These 

continuing awards will be very positive steps in our hoped 

for evolutionary path, namely, to continue to operate the 

storage ring for CHESS while completing ERL R&D. Eventually 

we’d like to build a full-scale ERL facility that incorporates and 

supersedes the existing facility as the world’s first continuousduty, 

coherent hard x-ray source. 

The Facility Highlights section of this News Magazine shines 

a spotlight on many CLASSE activities. At the same time, user 

science is as productive as ever, as highlighted in the Research 

Highlights section of the News Magazine. Enjoy. 

Page 2 CHESS News Magazine 2009

G-Line Director’s Report 

Joel Brock 

G-line has had another banner year, both in terms of the 

exciting forefront science that has been accomplished and in 

the truly excellent graduate students who have been trained 

and performed their research there. For example, the Cornell 

Center for Materials Research’s Interdisciplinary Research 

Group studying the growth of thin-films of chemically 

complex materials is operating both pulsed laser and 

supersonic molecular beam (SMB) deposition systems in the 

G3 experimental station. They are using them to perform in 

situ, real-time x-ray structural studies of the growth processes 

occurring during deposition. These research programs involve 

several Cornell faculty research groups (faculty, post-docs, 

graduate students, and undergrads) and several of the CHESS 

staff scientists. The program studying the growth of thin 

films of organic semiconductors via SMB deposition provides 

an excellent example of the value of both in situ studies and 

the immersion of post-docs and graduate students in the 

G-line facility. Supervised by Professors George Malarias 

(Materials Science), James Engstrom (Chemical Engineering), 

Joel Brock (Applied Physics) and Arthur Woll (CHESS/G-line), 

post-doctoral research associates Aram Amassian and Sukwon 

Hong and graduate students Vladimir Pozdin, Tushar Desai, 

and John Ferguson deposited thin films of pentacene onto 

SiO 2 

a gate dielectric, treated with hexamethyldisilazane 

(HMDS) and fluorinated octyltrichlorosilane (FOTS). The 

morphology of pristine, as-deposited thin films was 

determined during growth by in situ real-time X-ray reflectivity 

and was measured again, ex situ, by atomic force microscopy 

(AFM) following aging at room temperature in vacuum, in 

N 2 

atmosphere, and in ambient air. The films deposited on 

HMDS and FOTS undergo significant reorganization under 

vacuum or in N 2 

atmosphere1. The changes observed indicate 

a de-wetting behavior. This work highlights the propensity of 

small-molecule thin films to undergo significant molecularscale 

reorganization at room temperature when kept in 

vacuum or in N 2 

atmosphere after deposition, and provides 

a cautionary note to anyone investigating the behavior of 

organic electronic devices and the relationship of ex situ 

studies to the initial growth of ultra-thin molecular films. 

The SMB deposition system was designed and built over 

the past several years by graduate students in the Engstrom 

research group. The data collection was a collaboration led 

by Drs. Amassian and Hong with intensive involvement by 

the graduate students. Arthur Woll’s development of the 

analytical tools necessary to extract reliable coverage data 

from the time-dependent x-ray reflectivity data was crucial to 

the success of this project. Dr. Amassian has recently accepted 

a faculty position at the brand new King Abdullah University of 

Science and Technology (KAUST) but continues to collaborate 

with G-line through the KAUST center at Cornell. 

References 

1. A. Amassian, V.A. Pozdin, T.V. Desai, S. Hong, A.R. Woll, J.D. 

Ferguson, J.D. Brock, G.G. Malliaras, and J.R. Engstrom; 

“Post-deposition Reorganization of Pentacene Films 

Deposited on Low-Energy Surfaces”, Journal of Materials 

Chemistry 19, 5580-5592 (2009) 

AFM images (3×3 μm 2 ) obtained ex situ 

from ~8 ML pentacene thin films deposited 

from a supersonic source (E i 

= 2.5 eV) on 

(a) bare SiO 2 

and on SiO 2 

treated with (b) 

HMDS and (c) FOTS. The continuous (color 

filled) curves were calculated directly from 

the AFM images. The (hollow) bars were 

calculated from the X-ray measurements. 

(a) and (b) were obtained after aging 12 

hours in vacuum and 30 days in air, (c) was 

obtained after 6 hours in vacuum and 60 

days in air. Figure from Ref. [1]. 


MacCHESS Director’s Report 


“MacCHESS” stands for “Macromolecular 

Diffraction at CHESS” (or “son of CHESS” 

if one is Scots like Keith Moffat, the 

founder of MacCHESS). It was founded 

more than 20 years ago, when the 

potential of synchrotron sources for 

macromolecular structure determination 

was just becoming apparent, and was 

one of the first organizations dedicated 

to welcoming structural biologists into 

what had heretofore been a physicists’ 

domain. Funding was obtained, and has 

continued to this day, from the National 

Institutes of Health under its National 

Center for Research Resources program, 

which mandates both service and 

R&D activities by supported facilities. 

MacCHESS has been among the leaders 

in the development and implementation 

of the beamline hardware – detectors, 

goniometers, cooling systems, cameras 

– and software – for alignment, data 

collection, processing – that have made 

synchrotron work so routine that users 

can concentrate on biology and not 

details of the structure determination 

process. Today, MacCHESS continues 

to provide excellent user support, while 

its research activities have branched 

out into new paths which will enhance 

opportunities for structural investigation 

beyond the traditional crystallographic 

experiment. 

Support is provided by MacCHESS for all 

biological crystallography at CHESS, i.e. 

almost all experiments at stations A1, F1, 

and F2, and about half the use of F3, as 

well as occasional experiments at other 

stations. The typical MacCHESS user 

visits for a 24-hour period and collects 

5-20 data sets during this time. In the 

last year for which statistics are available 

(April 2007 – March 2008), there were 

approximately 500 badges issued 

to MacCHESS users and nearly 100 

MacCHESS-related publications released. 

Important work by users includes Eddy 

Arnold’s ongoing studies of drugs to 

treat AIDS 1 , Kate Ferguson’s investigation 

of anti-cancer drugs 2 , Gino Cingolani’s 

study of how a bacteriophage punctures 

a cell membrane 3 , and many more. 

Our facilities for crystallographic data 

collection are always being improved; 

some recent upgrades include: 

motorized CCD detector motion, 

enhanced crystal centering interface, 

private networks at each station for 

data transfer, and robust automatic 

safety shields. More details are given 

in the report on page 25. Mail-in data 

collection is available; it has been 

used roughly half a dozen times per 

year and is working well. A number 

of collaborations between MacCHESS 

scientists and other investigators are 

active and have produced excellent work 

such as the elucidation of the active site 

structure in the multifunctional enzyme 

CD38 4 . Additionally, experiments that 

are not standard crystallography can 

now be carried out at CHESS: 

• Small angle x-ray scattering (SAXS) 

and wide-angle x-ray scattering 

(WAXS) of solutions, at G1 (or F2) 

and F1, respectively. A new sample 

cell with a disposable insert, and 

temperature control between 4 

ºC and 60 ºC, is available. Staff are 

knowledgeable in data collection 

and processing techniques. 

• Pressure cryocooling of crystals 

or other samples. This technique 

can produce better quality crystals 

than those cryocooled at ambient 

pressure, and can also stabilize 

ligands which are otherwise 

disordered. Apparatus for 

pressurizing samples with helium, 

and cooling them to liquid nitrogen 

temperature under pressure, is 

installed at CHESS, and trained 

staff will process users’ samples, on 

request. Pressure-cooling using 

other gases is also possible using 

equipment in the Gruner lab, located 

in nearby Clark Hall. 

• Microbeam, produced by focusing 

x-rays with a glass capillary. 

Capillaries with focal spot sizes of 18 

and 5 μm are routinely available, and 

custom capillaries can be produced if 

needed. Microbeams have been used 

to examine small crystals, small good 

regions on heterogeneous crystals, 

and non-crystalline samples such as 

plant fibers. 

Research projects at MacCHESS 

are focused on 5 initiatives: 

Microcrystallography, Pressure 

Cryocooling, SAXS and Envelope 

Phasing, X-ray Optics (at F3), and 

Automation. More detailed reports are 

found elsewhere in this Newsmagazine; 

here I will just mention a few highlights: 

• Dan Schuette (a graduate student 

of Sol Gruner) and MacCHESS staff 

demonstrated that a prototype Pixel 

Array Detector (PAD; one of several 

being developed by the Gruner 

group) could be used to collect 

crystallographic data, of a quality 

comparable to that from a CCD, but 

with a much shorter readout time. 

This PAD is small compared to current 

CCD and image plate detectors, but 

work is in progress at Area Detector 

Systems Corp. to produce a large, 

tiled, device for crystallographic use. 

See report on detectors on page 54. 


• Xinguo Hong, Visiting Scientist, designed and constructed the improved sample cell for SAXS experiments, and also 

developed a method for avoiding radiation damage by stepwise translation of the cell between exposures. Moreover, he 

has demonstrated the feasibility of combining SAXS and WAXS data to obtain information about the internal structure of 

macromolecules. 

• Sterling Cornaby (a graduate student of CHESS Associate Director Don Bilderback) collaborated with MacCHESS staff to show 

that Laue data collected from many small crystals, using a tailored 30% bandpass beam, could be used to solve structures. See 

full report on page 63. 

• Chae Un Kim has used the pressure-cryocooling technique, and lots of beamtime, to collect data on samples cooled at various 

pressures and examined at various temperatures, to improve our understanding of that most common but most complex 

material – water. See page 71. 

In a recent competitive renewal process, the MacCHESS proposal received an excellent rating from NIH, and funding is assured 

through 2013. MacCHESS personnel tend to stay with the organization for a long time, but there have been some changes 

in recent years. Quan Hao, Director since 2001, has moved on to a faculty position at Hong Kong University; he continues a 

connection with MacCHESS as a collaborator. Marian Szebenyi has taken over as Director. Xinguo Hong has been in residence as 

a Visiting Scientist for the last few years and has been a great asset to the MacCHESS SAXS program; he is now at Brookhaven Lab. 

Long time technical support person Chris Heaton has retired to the sunny South and been replaced by Scott Smith as the local 

CompuMotor expert (among other talents). We welcome Chae Un Kim as a new Staff Scientist; as the principal developer of the 

pressure cryocooling technique, he is uniquely qualified to advance research in this area. 

References: 

1. K. Das, J.D. Bauman, A.D. Clark, Jr., Y.V. Frankel, P.J. Lewi, A.J. Shatkin, S.H. Hughes, and E. Arnold; “High Resolution Structures of 

HIV-1 Reverse Transcriptase/TMC278 Complexes: Strategic flexibility explains potency against resistance mutations”, PNAS 105, 

1466-1471 (2008) 

2. J. Schmiedel, A. Blaukat, S. Li, T. Knöchel, and K. M. Ferguson; “Matuzumab Binding to EGFR Prevents the Conformational 

Rearrangement Required for Dimerization”, Cancer Cell 13, 365-373 (2008) 

3. A. S. Olia, S. Casjens, and G. Cingolani; “Structure of Phage P22 Cell Envelope-penetrating Needle”, Nature Struct. Mol. Biol. 14, 

1221-1226 (2007) 

4. Q. Liu, I. A. Kriksunov, H. Jiang, R. Graeff, H. Lin, H. C. Lee, and Q. Hao; “Covalent and Noncovalent Intermediates of an NAD 

Utilizing Enzyme, CD38”, Chemistry & Biology 15, 1068-1078 (2008) 

MacCHESS is pleased to welcome Staff Scientist, Chae Un Kim 

Chae Un Kim hails from South Korea, 

where he majored in physics at Seoul 

National University and graduated summa 

cum laude in 1999. Following a 2-year 

stint in the Korean army, he arrived at 

Cornell in 2001 as a graduate student in 

Sol Gruner’s lab. After completing the 

required coursework, he quickly became 

interested in proteins under pressure, 

an interest of Gruner’s for many years, 

but one that involved tricky experiments 

whose results were not widely applicable. 

Together with fellow grad student 

Raphael Kapfer, Chae Un developed a new 

apparatus (much easier to use than the 

old one) for cryocooling crystals under 

pressure, and determined that crystals 

cooled in this way, and subsequently 

handled at room pressure, were often of 

better quality than those cooled in the 

normal way. After Raphael’s untimely 

death in a bicycle accident, Chae Un 

continued as the principal developer of 

pressure cryocooling, and proceeded 

to elaborate a series of extensions to 

the technique. Publications reporting 

these developments, beginning with the 

initial report in 2005, have generated 

great excitement in the crystallographic 

community. Chae Un is now recognized 

as the number one expert in pressure 

cryocooling, and has made numerous 

presentations on the topic. In 2005, he 

received the Oxford Cryosystems Prize for 

his poster, “High Pressure 

Cooling of Protein Crystals 

without Cryoprotectants”, 

presented at the Annual 

Meeting of the American 

Crystallographic 

Association. In 2007, 

he received the Ph.D 

degree in the Field 

of Biophysics, with a 

thesis entitled “High 

Pressure Cryocooling 

for Macromolecular 

Crystallography”. 

Wishing to continue 

working with Gruner, and CHESS, Chae 

Un stayed on at Cornell, first as a postdoc, 

and now as a MacCHESS Staff 

Scientist. He is continuing to explore the 

ramifications of pressure cooling, and the 

advances that it makes possible in protein 

crystallography and the understanding of 

the physics of proteins, water, and other 

materials in cryocooled crystals. Besides 

conducting exciting research, which he is 

always willing to explain to anyone who 

is interested, Chae Un is a very helpful 

guy: when people heard 

about the pressurecooling 

technique, many 

of them were eager to 

try it; since the method 

requires special high 

pressure apparatus and 

is a little tricky to learn, 

Chae Un volunteered to 

pressure-cool (many!) 

collaborators’ crystals. 

When a pressure-cooling 

apparatus was installed 

at CHESS, it was he who 

approved its design and 

trained MacCHESS staff in operating it. 

MacCHESS is pleased to welcome Chae Un 

Kim as its newest Staff Scientist. 


CHESS Assistant Director’s Report 

Ernie Fontes 

Some sort of “rough waters” analogy is 

needed to describe activities at CHESS 

over the past year. The CHESS staff 

kept as even a keel as possible despite 

two external forces. First, uncertainty 

about science funding affected the 

laboratory (as well as researchers across 

the United States). Budget constraints 

heavily throttled capital spending we 

had planned for the 2008-2011 renewal 

period. This slowed – but did not 

stop – progress to improve x-ray user 

facilities, as the reader can learn from 

other articles in this magazine. Second, 

CHESS was directly impacted by the end 

of the High-Energy Physics (HEP) data 

collection program and the start of an 

accelerator physics program called CESR- 

TA – or CESR Test Accelerator. The CESR- 

TA project is a jointly-funded NSF-DOE 

project to use the Cornell accelerator 

(CESR) as a test development model for 

the damping rings that will ultimately be 

part of the International Linear Collider 

(ILC). Alterations to CESR caused some 

loss of x-ray running days, though the 

hardware improvements resulting 

from the project will yield long-term 

benefits to x-ray users in terms of better 

reliability, better alignment and better 

stability of x-ray beams. 

The quality of the CHESS facilities and 

depth of user support depend critically 

on the staff. This past year saw three 

longtime staff members depart from 

the CHESS team. Jeff White took an 

early retirement and was excited 

to dedicate himself to upgrading 

his own home to be a model of 

environment-friendly energy 

efficiency. Jeff had worked at 

CHESS for over 23 years in many 

formative roles, among them 

leading the operations team, liaison 

to the accelerator staff, developer of 

the E-line diagnostic beamline, and 

head of the CHESS and ERL safety 

committees. Holly Manslank was 

a CHESS operator for 4 years and 

moved on to a technical position 

closer to her new home in Geneva 

NY. Holly brought to CHESS a keen 

sense of organization and logic that 

helped the staff see the benefits of 

well-organized and documented 

Page 6 CHESS News Magazine 2009 

procedures for chemical room use, signal 

monitoring, cable mapping and labeling. 

And last but certainly not least, Virginia 

Bizzell retired after 30 years as CHESS 

business manager and staff “memory.” 

Virginia served both CHESS Directors, 

Batterman and Gruner, and all the CHESS 

and MacCHESS staff and users with 

sincere respect, nurturing and care over 

the entire life of the facility. Her service 

is sorely missed and we wish her, Jeff, 

and Holly all the best. 

The CHESS staff strives to constantly 

improve the quality of the x-ray user 

facility and user support at CHESS. 

Those who visit CHESS periodically have 

noticed that the running modes of the 

facility have changed dramatically over 

the past few years. From its inception, 

x-ray users had always collected data 

while the HEP program was running 

the accelerator and collecting particle 

physics data. While in this “parasitic 

mode,” the accelerator needed 

considerable performance tuning and 

the x-ray beam positions and stability 

were sometimes compromised. This 

running mode changed over the past 

few years so that CHESS users now 

have a dedicated machine during “x-ray 

running.” With dedicated running, 

accelerator conditions can be optimized 

for the best combination of small source 

size, long-term stability, and long beam 

lifetime. Our goals are to realize as few 

interruptions as possible during x-ray 

Fig. 1: Historical data 

for hours spent per visit 

for macromolecular 

crystallography users 

and, for all users, the 

success rate of receiving 

scheduled x-ray beamtime. 

For non-crystallographic 

users, the hours per visit 

has consistently averaged 

between 4-5 days, over 

three times longer than 

for crystallographic data 

collection. 

data collection. We have seen that when 

the machine is well conditioned – a 

process we improve upon each day – 

interruptions for re-injections should be 

limited to once every 8-12 hours or more. 

We expect this to improve in the future. 

To hasten these improvements, we have 

formed a study group of both x-ray and 

accelerator experts who will identify and 

tackle issues related to beam alignment 

and stability. 

The reliability and use of CHESS have 

changed over time. Figure 1 shows 

historical trends for the amount of time 

that each visiting research group has 

spent collecting x-ray data. Also shown 

is the reliability during those visits. 

Among the many conclusions that can 

be drawn the most obvious is that the 

reliability of user beamtime has grown 

– at or above 95% - which is similar 

to other state-of-the-art synchrotron 

facilities across the United States. This 

is quite an accomplishment given that 

the Cornell accelerator was designed to 

serve the HEP program and continues 

to store both electrons and positrons 

simultaneously. The flexible design of 

the CESR source affords some benefits, 

though, allowing the laboratory to 

explore creative accelerator physics 

development programs such as CESR-TA 

and also test novel undulator designs. 

Speaking of novelty, other articles in this 

magazine highlight exciting upgrades to 

CHESS beamlines and instruments over

the recent past. Updating the x-ray beamline front-ends and optics helps improve x-ray performance and add new capabilities 

that users should appreciate. For instance, both the F3 and C1 beamlines have newly-installed 800 millimeter-long white beam 

mirrors. These help collimate and/or focus x-ray beams in the vertical direction, while at the same time reducing heat loads and 

higher-order harmonic content of downstream monochromator optics. The downstream optics for both stations are still not 

ready to reap the full benefits, but this will improve as our budget and resource situation improve over the next year. D-line is 

the first-ever CHESS beamline that can now operate without any beryllium windows. Traditionally, beryllium windows serve to 

separate downstream x-ray optics environments, typically helium volumes, from the delicate ultra-high vacuum of the accelerator 

storage ring. Adding a new vacuum optics box to D-line and removing the windows makes it possible for researchers to use highintensity, 

low-energy x-ray beams when needed. 

Looking forward to continued funding from the NSF, we have plans for scientific and technical initiatives that will benefit users 

in many ways. The next year should show progress on many fronts, including designing and building new high-energy, vertical 

focusing optics to increase the x-ray intensity by a factor of forty or so for high-pressure research at the upgraded B2 station. This 

will dramatically decrease exposure times for angle-dispersive diamond-anvil high-pressure experiments. We would also like 

to roll out horizontal-focusing synthetic multilayer optics at a few stations. Best of all would be to engineer a flexible, tunable 

substrate for multilayers that would provide a very rare capability – the ability to adjust and optimize the horizontal focus of a 

wide-energy-bandpass x-ray beam. The corresponding x-ray intensity increase would enable much more rapid scanning x-ray 

fluorescence imaging at the F3 station, for example. We also expect to see many new applications of fast pixel-array detectors, in 

collaboration with developments from the Gruner laboratory. 

Sol Gruner - CHESS Director 

Sol M. Gruner was raised on a farm in Southern New Jersey. He received his undergraduate physics degree from M.I.T. and his Ph.D., 

also in physics, from Princeton University. Following receipt of his Ph.D. in 1977, Sol remained in Princeton as a member of the physics 

department faculty. He moved to Ithaca in 1997 as Director of the Cornell CHESS facility and as a faculty member in the physics 

department and the Laboratory of Applied and Solid State Research (LASSP). He presently holds the post of The John L. Wetherill 

Professor of Physics. In addition to his work at CHESS, he has an active, independently funded research group in the physics department. 

He is a member of the graduate fields of Physics, Applied Physics, Biophysics, and Materials Science and Engineering. 

Sol characterizes himself as working across the continuum between biological and condensed matter physics, with a heavy emphasis 

on instrumentation and technique development. Areas of particular interest include the biophysics of lipid membranes, the effects 

of pressure on biomacromolecules and assemblies, the physical properties of block copolymers and the development of x-ray 

instrumentation and methods. He has been involved in the introduction of liquid crystal methods to the study of membrane lipid phases, 

and the discovery of a number of block copolymer phases. His group develops x-ray detectors, and much of the technology for the CCD 

detectors now used at synchrotrons throughout the world has come from this effort. The group is presently developing silicon-based 

detectors for time-resolved x-ray experiments. 

Don Bilderback - CHESS Associate Director 

After receiving his PhD in physics (with 

R. Collella, Purdue, 1975) Don Bilderback 

came to Cornell and shortly thereafter 

became the first CHESS employee under 

Bob Batterman, the first CHESS director. 

He has pursued a career in x-ray research, 

developing x-ray sources (CHESS and 

now the Energy Recovery Linac), x-ray 

detectors (first real-time back-reflection 

Laue camera when in Materials Science 

and Engineering, see www.multiwire. 

com), the first transmission x-ray mirror 

and the first bendable mirror with table 

legs underneath that you push apart to 

accomplish the bending. In 1993, he was a 

co-winner of an R&D 100 Award, an honor 

given annually to the one hundred most 

significant technical innovations of the 

year, in recognition of the development 

of tapered capillaries for producing 

micron-sized x-ray beams. The capillary 

work is ongoing and last year resulted in 

the excellent thesis by Sterling Cornaby 

(Applied and Engineering Physics PhD, 

2008) entitled “The Handbook of X-ray 

Single-bounce Monocapillary Optics”. 

Don has also been concerned with highheat-load 

x-ray optics over the last 20 

years. His idea of cryo-cooling the silicon 

optics has been widely adopted by other 

synchrotron laboratories and resulted 

in the Compton Award of 1998 to Don 

Bilderback, Andreas Freund, Gordon 

Knapp and Dennis Mills. Don recently 

set the goal (from the backdrop of ERL 

development) of making x-ray optics reach 

a one nanometer hard x-ray beam size. 

The APS/NSLS II community has picked up 

this goal and is rapidly developing Laue 

lenses that might be one of the first kinds 

of optical component that might reach this 

goal. This is very exciting! 

Don is a member of the ACA, the AAAS, 

and is a fellow of the American Physical 

Society. He often serves as a consultant to 

APS, ESRF and other synchrotron sources. 

He is a member of the Photon Science 

Committee for the Deutsches Elektronen- 

Synchrotron (DESY) and of the Nanoprobe 

Beam-line Advisory Committee at the 

NSLS II project. And Don is currently 

the Cornell University correspondent for 

Synchrotron Radiation News and a Coeditor 

for World Publishing Co. for a book 

series on Synchrotron Radiation. 

Don Bilderback is married to Becky, his 

wife and sweetheart of 39 years. He 

has one son, Doug, and a 2½ year-old 

grandson, Ian, who live in Seattle. Don 

loves to travel, commute to work on his 

bicycle, swim, and cross-country ski. He 

recently was involved (with many other 

Ithacans) in settling 53 refuges from 

Burma in the Ithaca area. One young lady 

from the group, Wimber Pha, lived with 

the Bilderbacks five days a week, where 

she received tutoring in English, math, 

driving a car, etc and moved up to English 

as a Second Language in her studies. Don 

also enjoys discussing science and faith 

issues. 


User and Student Highlights 

Ernie Fontes and Kathy Dedrick 

Although it may be impossible to 

capture the excitement and breadth 

of research done by visitors to 

CHESS, it is fun trying! With a bias 

towards the most recent half year 

or so, this brief article will show 

some of the rich flavor of work done 

by established scientists as well as 

aspiring undergraduates. CHESS 

“shows off” the successes of our 

users in a number of ways, using this 

magazine (of course), short highlights 

posted on the CHESS web site, 

editorial coverage on official Cornell 

news outlets, and in international 

arenas using highlights posted at 

www.lightsources.org. We frequently 

stream highlights to the National 

Science Foundation, and some of the 

more colorful stories get posted on 

their web site and news channels. 

Please keep us informed about your 

successes so that we can to spread 

information to our wide CHESS 

community of users and supporters. 

This past January Debashis Ghosh’s 

lab at the Hauptman-Woodward 

Medical Research Institute 

(HWI) in Buffalo, 

New York 

published the three-dimensional structure of aromatase, the key enzyme required for 

the body to make estrogen 1 . This structure plus those of two other enzymes involved 

in controlling estrogen levels provide the first means to visualize the mechanism of 

synthesizing estrogen; the enzymes also offer targets for drugs to treat some types 

of breast cancer. Ghosh added 2 ; “Now that we know the structures of all three key 

enzymes implicated in estrogen-dependant breast cancers, our goal is to have a 

personalized cocktail of inhibitors customized to the specific treatment needs of each 

patient. Our knowledge about these three enzymes will enable us to develop three 

mutually exclusive inhibitors customized to each patient’s needs which will work in 

harmony together with minimal side effects.” 

Media channels lit up February 17th with a stunning image (fig. 1) and story about a 

three year project by Rice University scientist Jane Tao and collaborators, who mapped 

out the coat of the PsV-F virus, one of very few viruses containing double-stranded 

RNA to be studied at the atomic level. Many diffraction images were needed to create 

this detailed picture, which appeared online Feb. 25 in the journal Proceedings of the 

National Academy of Sciences 3 . The packing of molecules in the PsV-F coat proved to 

be surprisingly different from that in related viruses, a finding that will ultimately help 

researchers to understand the structure and function of viruses and uncover ways 

to fight viral infections 4-6 . Rice University press said: “If a picture is worth a thousand 

words, then Rice University’s precise new image of a virus’ protective coat is seriously 

undervalued. More than three years in the making, the image... could help scientists 

find better ways to both fight viral infections and design new gene therapies. The 

stunning image…was painstakingly created from hundreds of high-energy X-ray 

diffraction images and paints the clearest picture yet of the viruses’ genome-encasing 

shell called a ‘capsid’.” 

Changing channels to metallurgy and mechanical engineering, Matt Miller (Cornell) 

has been selected to receive the ASM Henry Marion Howe Medal for 2009 for 

his publication 7 , “Measuring Stress Distributions in Ti-6 Al-4V Using 

Synchrotron X-ray Diffraction.” This award honors the author 

whose paper has been selected as the best of those 

published in the journal Metallurgical and Materials 

Transactions for the prior year. Miller, who reports on 

his group’s many efforts in the cover article of this 

newsmagazine, points out that the paper cited for 

the award covers some of the first titanium data 

taken at CHESS and was the basis of the third 

chapter of graduate student Joel Bernier’s Ph.D. 

thesis. Now that work is responsible for him 

having to rent a tuxedo! 

Fig. 1: High-energy x-ray diffraction was 

used to reveal the structure of the protective 

protein coat of PsV-F. 

Credit: J. Pan & Y.J. Tao/Rice University 1 


The end of August saw news channels 

saturated with stories about a discovery 

of a “hidden treasure” in the art world. 

Jennifer Mass, chemist and senior scientist 

at Delaware’s Winterthur Museum and 

Country Estate, gave a keynote presentation 

on x-ray fluorescence to study buried 

painting layers at the August 19th, 2009 

American Chemical Society (ACS) meeting 

symposium, “Practical Applications of 

Surface Chemistry: Art and Sensing 

Applications.” Her presentation recounted 

work enabled by a collaboration with CHESS 

scientists Arthur Woll, Don Bilderback and 

Sol Gruner to develop a confocal x-ray 

fluorescence (CXRF) microscope to examine 

the chemistry – and ultimately see the 

color palette – of layers of paint buried 

beneath a later portrait. X-radiography 

of an N. C. Wyeth family portrait (c. 

1922-1924) revealed the presence of a 

second painting buried underneath the 

surface. CXRF was able to identify the 

chemistry of the buried paint layers and, 

ultimately, help Mass reconstruct the color 

palette. Mass added: “to date, there have 

been no published studies on N.C. Wyeth’s 

painting materials and methods, and so this 

research will not only elucidate a buried 

painting but also contribute to the extant 

N.C. Wyeth art historical scholarship and 

attribution decisions. The Cornell University 

synchrotron source is currently the only 

facility for the joint confocal XRFand XRF 

intensity mapping of buried paintings.” This 

story received streaming video coverage of 

the ACS press meeting and was the topic 

of the NPR Science Friday radio interview 

as well as print coverage by the Cornell 

Chronicle, CHESS and lightsources.org 8-12 . 

This summer saw a particularly large (and 

welcomed!) group of undergraduate 

student research interns at Wilson 

Laboratory. CHESS and MacCHESS hosted 7 

students in research projects, who filled out 

an unusually large summer community of 41 

undergraduates including 11 participating 

in the CLASSE Research Experiences for 

Undergraduates (REU) program, 18 students 

in a CMS program in high-energy physics 

and 6 students providing technical support 

and upgrades for the CESR-TA program. 

One REU student, Elizabeth Brost, worked 

with scientists Peter Revesz and Don Hartill 

on “Vibration Studies at CHESS.” Liza, a 

Physics major at Grinnell College, configured 

a test station using a seismic accelerometer 

with fast-fourier-transform analysis to 

characterize mechanical vibrations and 

component stability at a number of critical locations – e.g. x-ray optics and 

beam position monitors - around the lab. Peter Melich and Adam Putzer 

formed a “dynamic duo” working with Arthur Woll to upgrade the confocal x-ray 

fluorescence scanning stage to perform “topographic” measurements. Peter and 

Adam, both Cornell juniors majoring in Applied and Engineering Physics, wrote 

Labview programs and machined and configured translation stages, encoders, 

and automated dial indicators to create topographic-like scans of 3-dimensional 

objects, similar to skimming across a surface as an atomic-force microscope does. 

Their hope is to dramatically speed up x-ray fluorescence scans of surfaces by 

following the interfacial surface directly, rather than having to scan an entire 3D 

volume (fig. 2). 

Fig. 2: Rapid, “topographic-like” x-ray fluorescence imaging involves following the 

surface (below) instead of having to scan the full 3D volume of the specimen (top). 

Michael Lyons, a Cornell junior majoring in Electrical and Computer Engineering, 

worked with Phil Sorensen, Bob Seeley and Ernie Fontes to help design and 

build a computer-automated apparatus that will be used to carefully control 

the heating and cooling process of vacuum equipment. The so-called “bakeout” 

process is used to heat vacuum equipment to high temperatures to accelerate 

the removal of adsorbed or trapped water from vacuum vessels and parts. Mike 

made progress using the EPICS control system to automate heating and reading 

temperatures and pressures. Paul Grigas, a junior studying Operations Research 

at Cornell, worked with Laura Houghton, Kathy Dedrick, Phil Sorensen and Ernie 

Fontes to examine ways to improve web-enabled databases to track the user 

community at CHESS. CHESS uses databases to keep track of the hundreds 

of student and scientist visitors each year who share dozens of scientific 

instruments. Paul explored modern software options and identified three 

candidate packages that are being considered for a next generation system. 

Gavrielle Untracht, a Cornell junior majoring in Applied and Engineering 

Physics, worked with Tom Szebenyi and Don Bilderback to improve the 

fabrication of tapered-glass capillary x-ray optics. She learned how to run the 

computerized glass puller that makes x-ray optics for CHESS use (the optics 

make micron diameter x-ray beams for our staff and our users). She has also 

spent a considerable amount of time writing Labview code to analyze the farfield 

x-ray intensity patterns formed by imperfect glass capillaries, hoping that 


those patterns can be used to pinpoint the sources of error in the figure and surface perfection of the glass. Rachel Pauplis, a 

Cornell junior in Physics and Asian studies, worked with Irina Kriksunov, Chae Un Kim and Marian Szebenyi to study the process of 

pressure freezing protein crystals using a new apparatus being commissioned for MacCHESS users. Pressure freezing crystals is a 

fairly new technique that often results in better protein crystallography data by avoiding the need to use cryoprotectant additives, 

among other benefits. Rachel, a neophyte at the start, helped pinpoint necessary improvements to the apparatus and procedures 

which should, ultimately, make it easier to apply pressure cooling to users’ crystals on a routine basis. 

As you can see, this year we had a sizable group of productive 

Cornell students working on research projects. For the coming 

years, CHESS has requested support for programs that would allow 

us to continue to recruit Cornell students as well as those from 

wider regional and national pools. We look forward to continuing 

our summer tradition of working with enthusiastic young 

scientists in training. 

References: 

1. Debashis Ghosh, Jennifer Griswold, Mary Erman, and Walter 

Pangborn; “Structural Basis for Androgen Specificity and 

Oestrogen Synthesis in Human Aromatase”, Nature 457 (7226), 

219-223 (2009) 

2. The original news release can be found at: http://www.hwi. 

buffalo.edu/newsroom/Press_Release_09/January/1_8_09.pdf 

3. Published online before print February 25, 2009, doi: 10.1073/ 

Rachel Pauplis 

pnas.0812071106; PNAS 106 no. 11, 4225-4230 March 17, 2009 

4. Read the original Rice Report here: http://www.media.rice.edu/media/NewsBot.aspMODE=VIEW&ID=12128 

5. Visit the Tao research group for more information: http://www.bioc.rice.edu/~ytao/index.html 

6. See an interesting video explanation of virus structure and function 

that includes quotes from eminent CHESS user Michael Rossmann: http://www.livescience.com/health/090217-virus-coat. 

html 

7. J.V. Bernier, J.-S. Park, A.L. Pilchak, M.G. Glavicic, and M.P. Miller; “Measuring Stress Distributions in Ti-6Al-4V Using Synchrotron 

X-Ray Diffraction”, Metallurgical And Materials Transactions A 39a, 3120 (2008) 

8. The ACS meeting archived video news conference is here: http://www.ustream.tv/recorded/2009896 

9. NPR Science Friday radio interview with Jennifer Mass: http://www.npr.org/templates/story/story.phpstoryId=112105590 

10. Coverage of the development of the technique is here: http://news.chess.cornell.edu/articles/2007/WollWyeth.html 

11. Science writer Anne Ju of the Cornell Chronicle wrote the following summary (PDF): http://www.news.cornell.edu/stories/ 

Aug09/WyethColor.html 

12. Lightsources.org coverage (PDF): http://www.lightsources.org/cms/pid=1003645 


Staff in Focus - John Kopsa 

In March of 1988 John Kopsa, CHESS 

Machinist, began working at the Cornell 

Plantations mowing the grass and 

planting trees. A year later, a call was 

placed to John, asking him if he would 

come and hang some lead/steel panels 

for x-ray shielding of the experimental 

hutches over at Wilson Lab, to help 

build a new “East” research area for the 

Cornell High Energy Synchrotron Source 

(CHESS). He agreed. 

After the panels were done, Boris 

Batterman (Director Emeritus), offered 

John a permanent position at CHESS. 

By the time the East area was completed 

it was time to rebuild the West section; 

that was in 1993. John was involved 

with the plumbing and vacuum work. 

John Kopsa working in the CHESS Machine Shop. 

Laura Houghton 

When the construction was finally 

done, John moved into the machine 

shop with Basil Blank and Walt Protas 

(Equipment Machinist). It was there that 

he began to do machine work. On April 

20th, 2000 he became a Journeyman 

Toolmaker. Through a correspondence 

course and hands on training, John 

completed the New York State 

Department of Labor requirements for a 

Tool and Die Maker. 

Except for a period of time spent 

assisting with the build of G-line, the 

machine shop is where John can still be 

found. His time in the machine shop 

has been spent building the equipment 

to fill the East, West, and G-line stations. 

He has touched almost every aspect 

of the experimental equipment 

throughout the lab. 

According to John, “The best part of the 

job has been keeping the Staff Scientists 

humble, especially Ken Finkelstein”. 

He told me that he is also looking 

forward to seeing what the ERL (Energy 

Recovery Linac) will bring and how the 

lab will change. 

“I met my wife at Wilson lab. We got 

married in 2000 and have a fantastic 

young daughter on the high honor roll 

who loves Math & Science”, John states 

proudly. “We live in a big farmhouse 

spending a lot of time taking care of the 

yard and over two acres of flower gardens. 

Shell, my wife, and I are looking forward 

to riding our bikes this summer”. 

John enjoys many different genres 

of music which can almost always be 

heard when entering the machine shop. 

He is a diehard fan of the Grateful Dead 

as well as Johnny Cash. How’s that for a 

combination 

He takes great pride in his work, is 

dedicated, and is a well respected 

member of the CHESS team. 

1999 

2007 

... a few words from John’s supervisor, Dana Richter ... 

John has been involved in most of the 

large projects in the lab over the past 20 

years. He started out putting together our 

experimental hutches when he first came 

here in 1989. The work involved putting 

up large shielding panels and forming 

and placing concrete shielding blocks. 

He has also installed cooling and exhaust 

systems. John is our expert at fabricating and 

assembling optical tables and translation stages. 

Many people do not realize that John and 

the hutch assembly crew often would put 

little notes inside the hutch walls as they 

put them up and we have found some of 

them as we have upgraded beam lines. 

He now spends most of his time in the 

machine shop where he has become 

proficient with the numerically controlled 

milling machine. John makes many of 

the parts used throughout Wilson Lab. 


Facility Upgrades, Networking and Computing 

Chris Conolly 

C-line Upgrades and New Capabilities 


D-line Upgrades and New Science Capabilities 


Education & Outreach 

Lora Hine 

MacCHESS Advances: Microcrystallography & More 

Station F3 



XPaXS: Improved Data Acquisition & Real-Time Analysis at CHESS 

Darren Dale 

CHESS High-pressure B1/B2 Update 

Zhongwu Wang 

The Cornell Energy Recover Linac: 

update on a future source of coherent hard x-rays 

Don Bilderback, Bruce Dunham, Georg Hoffstaetter, Alexander Temnykh, and Sol Gruner 

Facility Highlights 


Facility Upgrades, Networking and Computing 

Chris Conolly 

Cornell High Energy Synchrotron Source, Cornell University 

Transparent upgrades 

“We have done so much with so little for so long 

we can do anything with nothing” 

-- author unknown 

While not completely true, here at CHESS, 

sometimes it feels that way. I like to think we 

could do almost anything with what we have, and 

sometimes we do. As I have looked over the list 

of projects over the past few years, a surprising 

number of upgrades have taken place, improving 

the capabilities of almost every experimental 

station. Some are quite obvious to the casual 

user of the lab, but many are not and deserve 

to be mentioned. Driven to innovate, the CHESS 

Operations staff, through a collaborative effort, 

make ideas into a reality. In the following article, 

I will describe some of the upgrades that you may 

or may not have heard about and who made them 

into a reality. 

Video, driving motors, racks that roll, and 

(hopefully) no more floods 

Upgrades can take on many forms and affect 

users in many different ways. One that improves 

the quality of x-rays directly is the installation of 

additional video beam position monitors (VBPMs) 

at F1 and C1 stations, which were designed and 

installed by operator and designer Tom Krawczyk. 

Viewing the F-line wiggler beam directly after it is 

reflected off the collimating mirror, the F1 VBPM 

speeds tuning by eliminating the laborious process 

of taking burns, which process involves opening 

the helium chamber, overriding the equipment 

protection system, and running back and forth 

from the cave to the control area numerous times. 

Diamonds have become our best friends at 

CHESS lately. The move towards more UHV 

monochromators has created a need for VBPM’s 

that do not rely on visible light fluorescence of 

helium. To the rescue are movable, thin diamond 

foils that can be moved into the beam as needed. 

They use the same video cameras and processing 

software, and they have proven very useful for 

beam alignment and even position monitoring, if 

the experiment can tolerate a slight loss of flux. 

Current systems have been installed on the D- and 

G-beam lines. 

Former CHESS Operator and current electronics 

designer, Eric Edwards, 

has made a revolutionary 

upgrade to how we move 

motors throughout the 

lab. In designing what he 

terms the MDCP -- which 

stands for motor drive, 

control, and power -- Eric has 

simultaneously reduced the 

size and cost to drive a motor 

while increasing the reliability 

and usability of the system. 

Now, many sets of long cables 

and separate components 

have been reduced to a 

single chassis, a set of motor 

cables, Ethernet, and power. 

Eric packaged a Galil motor 

controller and eight Gecko 

brand motor drives coupled 

to an in-house designed 

circuit board, all sandwiched 

into a 2U electronics chassis. 

Installations on optical tables 

and diffractometers have significantly 

decreased the time required to move 

experiments around the laboratory 

floor and get them running again. 

Through the efforts of Ernie Fontes, 

Ellen Kathan, Phil Sorenson and 

many others the beam line front 

end electronics have been slowly 

evolving over the past few years. 

Gone are the days of electronics 

scattered into any space 

available under the beam lines. 

Lead-shielded rolling electronics 

racks have been installed in the 

CESR tunnel near each front end. 

Each rack is the nerve center for its 

beam line -- containing ion pump 

controls, thermocouple monitors, 

motor drives, position monitor 

supplies, and computer networking. 

Tethered to the front end by a thick 

bundle of cables and wires, the 

wheels allow the rack to swing out 

of the way of activities and repairs 

taking place on CESR. Although staff 

must still crawl around under the 

The F3 XRF optical table setup can roll into 

place in minutes and be fully operational 

a short time later with its own on-board 

MDCP motor drives. 

A typical rolling rack which serves 

as the nerve center for each front 

end. This particular rack belongs 

to A-line and houses PE monitor 

electronics, ion pump controllers, a 

thermocouple local monitor, patch 

panels, a networking switch, a 

multiport serial to Ethernet adapter 

and power conditioning. 


eam lines we no longer have to troubleshoot electronics 

while we are there. 

A detector system recently installed by Ted Luddy, one 

of our long-time CHESS Operators, is one which users 

will, hopefully, never get to experience -- the flood 

detection system. In the past, whenever there was 

a breach in any of the five different water systems 

around the lab, the first indication of a problem 

was an alarm from a water sensor in the CLEO pit, the 

lowest point in the lab. As one can imagine, the probability 

that equipment damage would occur was high, leading 

to machine down time and experiments being delayed. 

The CHESS 

Flood Alarm. 

Green lights indicate 

that all CHESS areas are dry. 

Now a series of sensors have been installed in critical areas -- such as beam line front ends, optics caves, and station roofs 

-- to give advanced warning. The system pages the CHESS Operator directly and also sounds an alarm in the CESR control 

room whenever the slightest drip is detected. The system uses an off-the-shelf continuity sensor coupled with a relay box 

designed and built by Ted in our own electronics shop. We all sleep a little better knowing that thousands of gallons of 

water from one of our many water systems has less of a chance of flooding our experimental floor. Thank you for that, Ted. 

Another behind the scenes upgrade is a gas flow monitoring system installed by Operator Dave Jones. You may have 

wondered how a CHESS Operator knew you had set the gas flow to your flight tube or ion chamber a bit too high. Simply 

put, units have been installed for CHESS East, West, and G-line to log the pressure and flow of the helium and argon 

distributed gases. For example, a quick glance at the signal-monitoring web page tells the Operator whether the lab’s 

helium usage is normal or excessive, and then he or she can easily and efficiently make the proper adjustment. The system 

helps us to see trends develop and allows us to reduce usage, when necessary, saving thousands of dollars a year in costs. 

The compact F3 white beam mirror. Notice the 

external bender mechanism at the top indicating 

the mirror has a bounce down configuration. 

It’s all done with mirrors 

Operators Tom Krawczyk and Aaron Lyndaker traveled to the APS to use the 

long-trace profilometer to characterize three newly-fabricated glidcop white 

beam mirrors. C1 and F3 each now have an 800mm-long mirror installed in 

their front ends. Compact new benders for them have been designed, which 

locate the motor driven actuator on the exterior of the UHV mirror chamber 

to facilitate ease of installation and repair, if ever needed. The UHV chambers 

have been designed to 

take up the minimum 

of volume to be able 

to fit into the tight 

space available on the 

respective front ends. A 

spare for the aging A1 

collimating mirror has 

also been fabricated and 

is standing by. 

The F3 monochromator 

second optics cart as 

model and in reality. 

CHESS Engineer Alan Pauling has redesigned the F3 monochromator 

for better stability and increased capabilities to accept beam from 

the new F3 white beam mirror. The re-fit includes a new set of white 

beam slits located in their own upstream chamber and a longer second 

crystal travel stage. Ever creative, Alan used an existing port on the 

monochromator chamber to support the first crystal stages to allow 

overlap with the second crystal stage for low energy experiments. The 

new monochromator can use silicon or multilayer optics over an energy 

range of 1keV to 135keV and bandwidths up to 0.6%. 

Sharing space with the F3 monochromator in the large helium 

coffin, the F1 monochromator required some re-design to avoid an 

interference with the first crystal mount of the F3 monochromator. Alan 

designed a new compact cooled crystal bender which incorporates a 

more reliable bending mechanism coupled to a new copper block with 


e-routed cooling lines. During the project, the helium 

chamber and all its internal components were cleaned to 

near UHV standards and all radiation-damaged stepper 

motor wiring was replaced. The complete motor drive 

system for the 56 motors located in the F-cave was replaced 

with MDCPs and re-located from the cave roof to a leadshielded 

rack inside the F-cave. Overall, the re-fit has 

proven to be reliable and the additional capabilities have 

been put to good use. 

Alan Pauling and Aaron Lyndaker put the finishing 

touches on the C-line front end before the CESR 

dipole magnet is slid back into place. 

A phased reconstruction of C-line began during the 2009 

winter down period. Replacement of a section of CESR 

beam pipe required the removal of the CESR dipole magnet 

next to C-line and afforded CHESS the luxury of space for 

one short week to complete the installation of a new front 

end. A new copper-flared chamber and CESR X-ray Beam 

Size Monitor optics chamber were installed along with the 

previously mentioned white beam mirror. The C1 mono 

box was raised up a few inches to be able to accept the 

mirror reflected beam. This required the monochromator 

offset to change, which led to a complete overhaul of the 

existing monochromator, followed by motor rewiring and 

plumbing. Additional pink and white beam safety bricks 

were also installed in the coffin. Completion of phase one 

of this project reduces the number of beryllium windows in 

the beam line down to one, which will be removed in phase 

2 to allow the x-ray beam-size monitor (xBSM) project to 

gather data at low energy. The final phase will be new UHV 

optics, which will allow C1 to utilize low energy x-rays and 

continued xBSM data collection. 

Vacuum goes for a walk 

The CHESS Vacuum group, under the direction of group 

leader Bob Seeley, has endured many changes of venue 

over the past few years. Bumped from their long-time home 

just off the CHESS control area by the ERL project, the group 

has become mobile. A small fraction of the CESR vacuum 

lab has been turned over to CHESS for general vacuum 

processing needs, but larger fabrication projects have had 

to take place elsewhere. An additional space has been 

carved out of Room 128 -- a clean room built specifically for 

ERL development -- for clean UHV assembly work. Many of 

the stockpile of flanges, controls, and spare parts are now 

shared with the CESR group. CHESS specific components 

and tools now share space with the CHESS Glass Puller in 

RM 180. Although nomadic, productivity has increased 

significantly for this group with many difficult installations 

under their belt. The group should be commended for 

being flexible enough to work in this unusual situation. 

Multiple networks and processors 

On the computing front, a new private control network 

has been installed that is isolated from the general CHESS 

laboratory network. A need developed for a secure network 

for devices controlled over Ethernet. The implementation of 

Parker Compumotor motor drives and later the new MDCP 

drives forced the computer group to look seriously at a 

separate secure network. Each station has been connected 

to the private network to accommodate motor drive 

upgrades, present and future. MacCHESS has also joined 

the trend, installing its own local networks at A1, F1, F2 and 

F3. Keeping the flow of data local to each station will also 

have the benefit of keeping network issues localized and 

speeding data transfers. 

Out in the CESR tunnel, each beam line front end has 

been configured utilizing the private network to allow 

remote management of motor drives, ion pump controls, 

and, potentially, thermocouple and position monitors. By 

using multiport serial to Ethernet converters, devices can 

communicate bi-directionally with an EPICS display located 

at the CHESS 

control area, which 

allows operations 

staff to view status, 

trends, and even 

control the devices. 

One advantage of 

this system is to 

allow access to the 

hardware located 

in the CESR tunnel, 

without calling 

for a machine 

access; this reduces 

downtime for user 

experiments. 

Operator Ellen Kathan 

completed wiring one 

of the rolling racks in 

the CESR tunnel. This 

rack contains all of the 

pump controllers for 

the F hard bend and 

wiggler front ends. 

Consolidation of the computers that process the VBPM 

signal to a central location has been led by Operator Lee 

Shelp. Using USB converters to bring the many video signals 

back to the CHESS control area eliminates the need for 

individual computers taking up space throughout the lab, 

and also minimizes the potential for failure from multiple 

computer systems running multiple programs. 


The design group has seen many upgrades to the popular AutoCAD Inventor CAD suite over the past few years. CAD 

workstations have all been upgraded to dual-processor machines running 64-bit Windows to utilize all of the functionality 

of the program. This upgrade also benefits ANSYS users, who are now able to churn out simulations at an ever-increasing 

rate. 

Smaller is always better in the CHESS world. This is certainly the case when it comes to diagnosing and testing motor 

problems quickly. Operations staff now have a few netbooks available to allow one person to single-handedly move 

motors locally rather than requiring a second person to run them remotely. Using an ssh session over the wireless 

network, operators can quickly locate and repair motor problems in the caves and CESR tunnel. These basic machines are 

inexpensive, lightweight, and run a variety of operating systems. They have also found a use running RGAs and viewing 

signals using a specially developed fast-monitoring windows program. 

New Blood 

The changes around the lab aren’t simply with systems upgrades and 

modifications. We have added some new faces to our staff as well. 

Within the past year, we have hired two new CHESS Operators. Rich Jayne 

jumped right in with both feet to design, fabricate, and install a MAR345 

detector cradle in the B2 station. The overhead rail system gives ample 

clearance for experiments, while allowing effortless motion in the x, y, 

Operator Rich Jayne inspects 

the MAR 345 detector in the 

B2 station. 

and z directions as well as in rotation. 

Solenoid actuated brakes lock the 

detector firmly in place. A less involved 

mount for our other MAR345 detector 

was requested for the A2 station on short 

notice and Rich delivered -- cobbling 

together a motorized table from spare 

parts found around the lab. Alignment time of the detector for the Miller 

group has decreased by an order of magnitude and allowed the group to 

collect data sooner in their allotted beam time. A positive outcome for all. 

Our other new Operator, Aaron Lyndaker, has brought excellent design skills 

to the group. Beam line front-end design at CHESS requires that we be able 

to think and work in very tight spaces. In most cases, removing components 

from a beam line makes this easier, but when removing beryllium windows this 

isn’t the case. Once the beryllium windows are removed, a differential-pumping 

section must be installed to protect CESR from the higher pressure at the experiment. 

Differential pumping requires additional valves, pumps, and apertures to work. Aaron was able to incorporate all of these 

into a clean design for D-line. So far, our first foray into windowless beam lines has been a success, allowing the CESR xBSM 

experiment to happen in a very short time frame. As part of this project, the old D-line monochromator was scrapped 

and a new UHV set of optics, designed by Tom Krawczyk, was installed. The detector used by the xBSM experiment is not 

UHV compatible, so a single, very thin 5 micron diamond window was purchased to separate the detector chamber from 

accelerator vacuum. Using a complex pressure-balancing system, designed by Engineer Jim Savino, the pump-down and 

venting of the xBSM detector chamber has been automated using a PLC. A single button press allows the user to access 

the detector at any time while protecting the UHV vacuum system connected directly to the accelerator vacuum. 

There is also a new face in the computer group, Shijie Yang, who will help with hardware and software maintenance and 

system administration. He will also help train and supervise staff, students, and visitors in the many software packages 

used around the lab. 

These are but a few of the upgrades CHESS has seen over the past few years. Many thanks for the countless hours spent by 

the tireless CHESS staff that has resulted in less downtime and increased capabilities. Who knows what future upgrades are 

in store for CHESS but one thing is certain, the CHESS staff will be there with creativity and a drive to make them a reality. 


C-line Upgrades and New Capabilities 



This article will highlight developments at C-line, including recent upgrades, new science capabilities and long-term plans. 

Recall that C-line is a bend-magnet-source beamline that features very flexible x-ray optics and has one of the smallest x-ray 

beam source sizes of any CHESS beamlines. Primary use of the beamline has been for energy dependent resonant (anomalous) 

scattering including 4-circle diffraction, anomalous SAXS, EXAFS and XANES. In addition the station is used for x-ray topographic 

studies, multiple beam diffraction, high pressure x-ray spectroscopy, and specialized x-ray optics development. See article on 

page 58 by Richard Jones – Topography of Diamonds at CHESS helps Nuclear Physics Program at JLAB. 

Several years ago, while writing a proposal for CHESS 

funding starting in 2008, the scientific staff identified 

research capabilities that were missing from CHESS and 

new scientific communities they would benefit. At the top 

of the list was the need to extend the x-ray beam energy 

range down to 2 keV to accommodate low energy x-ray 

applications. This will open new opportunities in biology, 

condensed matter and environmental sciences and give 

the CHESS staff invaluable experience in a new spectral 

region. A unifying theme of the new scientific capabilities 

was the need to perform resonant elastic x-ray scattering, 

anomalous SAXS, crystallographic phasing, solution x-ray 

absorption (XANES), and to study quantum correlations by 

gaining access to low-energy absorption edges. If C-line 

could reach down to 2 keV, figure 1 shows the elemental K, 

L, and M edges which would then become accessible. 

In the past, CHESS has not supported x-ray applications 

below 6 keV because our beamline designs traditionally 

Fig. 1: Periodic table showing low-energy absorption edges that will become 

newly accessible at the C1 station after technical upgrades. Blue, red, and green 

indicate K,L,M edges, respectively. 

included two beryllium vacuum windows, typically 0.01 

inch ultrapure foils. The engineering purpose of these windows was to separate the downstream x-ray optics box atmosphere, 

typically helium, from the sensitive upstream ultra-high-vacuum environment needed for the particle accelerator. While 

providing vacuum protection, these windows also dramatically attenuate photons with energies below 6 keV, making it 

impractical to collect data at light element absorption edges, for example. To overcome this limitation and improve the 

capabilities of C line, the engineering staff outlined a plan summarized in figure 2. It involves upgrading the beamline front-end, 

beam transport, x-ray optics, and experimental hutch components to be compatible with (clean) vacuum equipment and to 

include differential pumping segments, and fast-acting sensors and valves to protect against component failures. With upgraded 

pumping and protective valves in place, we can remove all windows during normal x-ray operations. 

Fig. 2: Schematic plan view of the major 

upgrades proposed for the C-line beamline 

and C1 station. At left, a new white beam 

vertical-focusing 800 millimeter glidcop mirror 

was installed and used. Placeholders for a 

low-energy mirror and new high-vacuum x-ray 

optics box are show. Long term we hope to 

extend the length of the hutch: shielding wall 

positions indicate “old” (dashed) and “new” 

positions. The new positions would extend the 

hutch approximately two meters so that the 

diffractometer could be located at a 1:1 focusing 

arrangement. Not shown off the left side is a 

small vacuum box to hold the CESR-TA pinhole 

camera optics. 


In addition to new capabilities for low-energy x-ray 

experimentation, removing windows from the beamline also 

makes it possible for a group of accelerator physicists to study 

the operation of the storage ring at lower beam energy, e.g. 

2.0 GeV. The CESR-TA group, as they are called, is using CESR 

as a test accelerator and model of the positron damping ring 

proposed for the International Linear Collider project 1 . In their 

studies, the C beamline and station will be used to create a pinhole 

camera to view the electron bunches stored in CESR. The 

pin-hole camera is formed by putting a small slit or pin-hole in 

the tunnel, upstream of the C-line shielding wall, and placing a 

diode array detector in the downstream-most station position. 

Since the work is done with a low-energy particle beam (2 

GeV) the windowless arrangement of the beamline is needed 

to maximize the photon flux for their measurements. These 

measurements will be done outside the x-ray run schedule, and 

so will not affect x-ray users at C1. A similar beam-size monitor 

was commissioned last year on D-line to study positron beams; 

see the discussion of the D-line upgrades in a separate article. 

The C-line upgrades included an extensive rearrangement and 

replacement of upstream vacuum components over the course 

of two CESR down periods. In the upstream-most position, 

a new copper-flared chamber was installed to contain and 

aperture the x-ray beam when it first exits the storage ring. 

Just downstream, a new small vacuum chamber was added to 

allow the CESR-TA group to install apertures and pinholes for 

source imaging experiments. During x-ray running periods, 

this pinhole optics is completely withdrawn and does not 

interfere with the x-ray user beam. Downstream of the main 

line beamstops, pieces were installed to accommodate a new 

white beam vertical focusing mirror. Fabricated by CHESS 

with help from LBNL, this new 800 millimeter-long glidcop 

mirror is internally-cooled and located for 1-to-1 focusing of 

the CESR source at the center of the C1 diffractometer in the 

experimental hutch. This mirror will improve C line in four 

ways: 1) focusing will increase flux density (photons/second/ 

area) at the sample by about 3 times, without increasing 

angular divergence or reducing energy resolution. 2) The mirror 

can be used for (vertical) angle collimation to produce a more 

parallel x-ray beam. This reduces vertical beam size at the 

sample and increases spectral flux density (photons/second/ 

unit bandwidth). 3) The mirror also reduces total power on the 

monochromotor first crystal, typically by a factor of 2. 4) It can 

be adjusted to remove high energy harmonics of the primary 

beam. 

To satisfy all the goals of the project we need to completely 

replace the x-ray optics box, but for the running periods in 2009 

we only had time to modify existing parts to accommodate 

variable height of mirror reflected beam. These modifications 

included redesigning the monochromator to permit height 

adjustment of the first crystal, and installation of a novel beam 

viewer system downstream of the crystals. The viewer uses 

a 40 micron thick, 100 mm diameter silicon wafer to convert 

x-rays to visible light. Light from the crystal is reflected by a 

mirror to a video camera. The thin crystal will be a very useful 

diagnostic and alignment tool because it can intercept filtered 

white beam, mirror reflected “pink beam” and/or image Laue 

diffraction from the first crystal. These capabilities allow us 

to use the x-ray beam for precise positioning of the mirror 

and mono first crystal. We have also added “phi-adjustment” 

(rotation about the surface normal) to the first crystal. Phiadjustment 

is critical when using asymmetrically cut crystals 

(diffraction planes NOT parallel to the surface), for example 

to expand the beam for topography studies (as was needed 

during the topography work by Richard Jones). The support 

structure for the second mono crystal has also been rebuilt for 

greater stability and for operation at fixed height above the 

white beam. To accommodate these improvements we have 

also rebuilt the white beam slit system for the wider range of 

vertical beam position, raised up the optics box to match the 

new range of beam positions, built new apertures to ensure 

safe handling of white and pink beams, and added a capability 

for white beam use in C-hutch by the accelerator physics group. 

Work is also ongoing to design new instruments for the 

experimental hutch to meet goals to expand science 

capabilities at C line. One project involves design of an x-ray 

emission spectrometer for collecting x-ray fluorescence 

with high energy resolution over a large solid angle 2 . This 

capability is being built in collaboration with Serena DeBeer 

George 3 , a new Cornell chemistry professor who is interested 

in development and application of x-ray based spectroscopies 

to probe electronic structure in biological and chemical 

catalysis. In particular, she studies transition metal active 

sites that are often centers of catalytic activity. Active sites 

provide inspiration for biomimetic model chemistry and for 

understanding homogeneous catalysis. Once the emission 

spectrometer is perfected it will become available to all CHESS 

users. The present design will collect about 10 times more solid 

angle than is possible with our large aperture single element 

solid state detectors (e.g Vortex), and it will provide energy 

resolution matched to the width of emission 

lines (see figure 3). This will allow collection of: 

weak emission, closely spaced lines, and lines 

that are very close in energy to the incident 

beam. We plan to couple this spectrometer 

to a fast readout, low noise position sensitive 

detector to permit simultaneous data collection, 

over a range of energy sufficient for line shape 

analysis. 

Continued on pg. 21 


Fig. 3: Schematic design for the high-efficiency triple-crystal x-ray fluorescence 

detector. The incident x-ray beam (from left) excites fluorescence in the specimen, and 

that light is collected by three spherically-bent silicon crystals and focused to a highcount-rate 

photon counting detector. Shielding and helium flight paths are not shown.

D-line Upgrade and New Science Capabilities 



CHESS’s popular D1 station, utilizing synchrotron radiation 

from a hard-bend dipole magnet and a multilayer 

monochromator, has both a versatile optical system and a 

5-meter long hutch (Figure 1). Sharing the smallest x-ray 

source size at CHESS with C-line, D1 has been extensively 

used for small and wide angle scattering as well as 

microbeam experiments with glass capillaries to create x-ray 

beams on the scale of 50 nanometers to 50 microns. Recent 

applications include grazing-incidence small- and wideangle 

x-ray scattering on thin films of soft materials such 

as block copolymers 1 , conjugated polymers 2 , nanocrystal 

assemblies 3 and nanoporous films 4 as well as high-energy 

small-angle scattering in conjunction with diamond anvil 

cells 5 , and microbeam SAXS and WAXS studies 6 . D1 has also 

supported a development program for new experimental 

techniques such as an evaluation of the potential of 

Laue diffraction for structure determination of protein 

microcrystals 7 or fluorescence imaging of large-scale 

paintings 8 and Roman tombstones 9 . 

At about the same time the accelerator physics 

group was proposing to use the CESR storage ring 

as a “test accelerator” (TA) for part of the R&D aimed 

at the international linear collider (ILC). Using the 

flexible lattice of CESR the TA group wanted to 

create a prototype ultralow emittance positron 

Fig. 1: Conceptual plan to improve the D1 experimental program by lengthening 

the user space by 2 meters (old wall position shown). The new high-vacuum x-ray 

optics box is already installed and commissioned, and D1 has delivered a total of 

12 weeks of user operation within the old experimental hutch (dashed). 

A few years ago, during an exercise to identify strategic 

long-term plans to improve CHESS stations and beamlines, 

it became clear that the size and scope of the soft-matter 

science program being supported at D1 was “bursting at 

the seams.” For example, new demand has been growing 

steadily to study thin-films either in static specimens or 

in-situ during solvent vapor conditioning. Technically, 

the beamline front-end and optics had not been 

upgraded in almost two decades. In particular, the helium 

monochromator box that housed the synthetic multilayer 

mirrors was in poor shape and the unclean environment 

led to carbon-like deposits on the multilayer surfaces that 

needed to be cleaned off periodically. 

This exercise resulted in replacing the old helium optics 

box with a high-vacuum enclosure and a conceptual design 

to lengthen the experimental hutch (see figure 1). The 

extra space became available with the demise of the high- 

energy physics program at the decommissioned 

CLEO detector. The longer hutch would allow 

access to SAXS studies with higher resolution 

and/or at higher beam energies. A new optics 

box was designed to provide rapid changeover 

between multiple multilayer optics with different 

wavelength ranges, thus cutting down on set-up 

and realignment time. 

and electron damping ring of the sort that might become part of 

the injector system for the ILC. In this study they needed to setup 

a pinhole camera to image the electron and positron bunches, 

using the CHESS x-ray beamlines C1 and D1 close to the former 

interaction region. Using a fast detector, the group hoped to 

be able to measure the size and shape of individual bunches of 

charged particles, with photons emanating from a single pass 

of the bunches through the bend magnet source. Because this 

work would be done with a machine energy of 2.0 GeV, where the 

x-ray flux is peaked at 1 keV, the accelerator physicists requested 

that the targeted beamlines have all beryllium vacuum windows 

removed, in order to avoid absorption of low-energy x-rays 

coming down the line. 

Marrying the needs for better x-ray science capabilities with the 

accelerator group requests, the CHESS design, technical and 

vacuum groups designed an upgrade plan to accomplish these 

goals. Pictured in figure 2, the upstream D beamline was almost 

completely replaced with ultra-high-vacuum compatible flight 

tubes, apertures, a differential pumping stage to separate storage 

CESR hard bend dipole magnet 

quadrupole 

CESR-TA 

optics box 

D1 optics box 

Fig. 2: The new windowless D1 front-end. The x-ray beam enters from the right, traveling 

downstream to the left through a series of beamstops, a beam viewer, and differential 

pumping chambers. The D1 optics box is described in more detail in the text and in Figure 3. 


ing ultra-high vacuum from the high vacuum typically achieved 

in optics boxes, as well as removable thin diamond foil x-ray 

beam viewers to assist line-up. 

For the CESR-TA project a small vacuum optics box as close to 

the storage ring as possible was added. This small box is used 

by the accelerator group to hold a small pinhole, Fresnel zone 

plate, or coded aperture that will create an image of the positron 

source. During these special “TA” runs, all D1 hutch equipment 

(two full CHESS optical tables) is removed and the CESR-TA 

group rolls into the x-ray station a large vacuum detector box 

that has an ultra-thin diamond window with a pressure balance 

system designed by CHESS. This box houses a high-speed pindiode 

linear array detector that measures the projected size of 

the x-ray source. 

The old D1 x-ray optics box was replaced by a high-vacuum 

chamber with all vacuum-compatible motors, a large 

turbomolecular pump, gate valves before and after the optics 

for isolation of vacuum cells, a set of adjustable white beam 

slits, and a second downstream thin diamond foil x-ray beam 

viewer (figures 2 and 3). When the x-ray beam passes through 

the diamond foil beam viewer it creates a visible light image that 

is recorded by a video camera. Coupled with custom software 

designed by CHESS scientist Peter Revesz, the in-situ video 

images of the x-ray beam are extremely helpful for diagnostics 

on beam shape, position, and stability. 

The new D1 multicrystal monochromator contains three pairs 

of multilayers of varying properties. The first set is the tried and 

true 30Å Mo:B 4 

C multilayer made by the APS optics group that 

has been D1’s workhorse monochromator over the past four 

years 10 . Although somewhat damaged by prolonged operation 

in the old helium box, there are still good parts left. In the last 

running period of Spring 2009, the x-ray beam remained at a 

beam 

limiting 

slit set 

optional 

mirror 

long translation 

x table 

multi 

layer 2 

multi 

layer 1 

single spot, and it showed no signs of degradation over an 

initial four week user-mode operations period. Typically this 

multilayer covers the 8 keV to 15 keV energy range, but can 

get as low as 6 keV at increased offset. The second multilayer 

set is again a matched set, 21Å W:B 4 

C by Osmic. This 

multilayer was chosen to cover the hard x-ray range from 15 

keV to 30 keV. Originally conceived for fluorescence imaging, 

it is now also being tested for high-pressure SAXS and GIWAXS 

for an extended scattering range. 

The third multilayer set is an experimental one for exploring 

new optics configurations. The d-spacings of the Mo:B 4 

C 

multilayers were purposely mismatched with 21 Å for the 

upstream multilayer and 25 Å for the downstream multilayer, 

resulting in a beam that is somewhat bent down from the 

horizontal. A third optical element, a rhodium-coated mirror, 

is used to bend the beam back up to the horizontal plane, 

working close to the Rh critical angle. Since multilayer 

scattering angles and the critical angle of the mirror both 

scale inversely proportional with energy, this configuration 

can be maintained throughout the energy range of 10-20 keV. 

The Pd mirror generates an appropriate energy cut-off for 

higher harmonics, so that the third and higher orders cannot 

pass. This will result in a D1 beam with much less higherenergy 

contamination. 

As an additional option, the mirror can be slightly detuned 

towards lower incident angles, resulting in a slightly bent 

down beam that could enable grazing incidence experiments 

from liquid surfaces. Again, as multilayer Bragg angles and 

relevant critical angles have the same energy dependence, 

this mode can be maintained throughout the energy range. A 

future upgrade could add a bender to this mirror to increase 

flux on the samples at the cost of a small extra angular 

divergence, while maintaining a well-defined incident angle 

on samples. The advanced mirror options still remain to be 

commissioned at the time of writing. 

The multilayer set-up rests on a solid internal x-translation 

table so that different multilayers can be brought into the 

beam via remote computer control. This avoids the problem 

of having to re-align the optical tables in the hutch after 

changing multilayers. All monochromator motions use 

vacuum-compatible motors and bearings. Vacuum of better 

than 10 nanoTorr was maintained under beam and motor 

moving after careful conditioning. The whole monochromator 

assembly can be leveled by an external 3-point actuator set. 

Additional optical elements are a set of white beam slits 

limiting the incident beam to the beam that is needed. 

These internally water-cooled slits are controlled by external 

actuators via bellows, and maintain a clean vacuum even 

under heat load. Finally, a set of fixed slits behind the 

multilayer optics will be used to clean up the beam exiting 

the monochromator; in particular, to remove small amounts 

of diffuse scattering from the multilayers. This slit set, to be 

installed before the upcoming run, is also controlled through 

an external actuator via bellows. 

3-point mount for leveling 


Fig. 3: Inside detail of the new D1 vacuum multicrystal 

monochromator. Details given in text.

One aspect of the upgrade that has not yet been tackled is to lengthen the experimental hutch. This will require a significant 

restructuring of the thick and heavy shielding walls, as well as moving some quantity of wiring. Short of moving those walls, 

though, the downstream-most wall of the hutch had a 12-inch hole bored through it. This was done as an optional, alternate 

means to locate the “TA” beam size detector as far as possible from the storage ring source. This option has not yet been exploited. 

Another option under discussion is adding a full second D-line hutch at the far end of the CLEO enclosure, that would serve for 

USAXS, microbeam scattering, or coherent scattering applications as well as for CESR-TA at higher resolution. 

We thank the members of the CHESS Mechanical Design Group headed by Jim Savino, the Operations Group headed by Chris 

Conolly, and the Vacuum Group headed by Bob Seeley for all their great work. Particular thanks to Aaron Lyndaker who designed 

the bulk of the vacuum system including the new monochromator box, and Tom Krawczyk who designed, assembled, and 

commissioned the complex insides of the multi-crystal monochromator. 

References: 

1. Christine M. Papadakis, Zhenyu Di, Dorthe Posselt, and Detlef-M. Smilgies; “Structural Instabilities in Lamellar Diblock Copolymer 

Thin Films During Solvent Vapor Uptake”, Langmuir 24, 13815-13818 (2008) 

2. Mingqian He, Jianfeng Li, Michael L. Sorensen, Feixia Zhang, Robert R. Hancock, Hon Hang Fong, Vladimir A. Pozdin, 

Detlef-M. Smilgies, and George G. Malliaras; “Alkylsubstituted Thienothiophene Semiconducting Materials: Structure – Property 

Relationships”, J.Am. Chem. Soc. online (2009) 

3. Danielle K. Smith, Brian Goodfellow, Detlef M. Smilgies, and Brian A. Korgel; “Self-Assembled Simple Hexagonal AB2 Binary 

Nanocrystal Superlattices: SEM, GISAXS and Substitutional Defects”, J. Am. Chem. Soc. 131, 3281–3290 (2009) 

4. Sivakumar Nagarajan, Mingqi Li, Rajaram A. Pai, Joan K. Bosworth, Peter Busch, Detlef-M. Smilgies, Christopher K. Ober, 

Thomas P. Russell, and James J. Watkins; “An Efficient Route to Mesoporous Silica Films with Perpendicular Nanochannels”, Adv. 

Mater. 20, 246–251 (2008) 

5. Zhongwu Wang, Ken Finkelstein, and Detlef Smilgies; “Exploring New Physics of Nanoparticle Supercrystals by High Pressure 

Small Angle X-ray Diffraction”, CHESS News Magazine, pg 56 (2009) 

6. Jessica S. Lamb, Sterling Cornaby, Kurt Andresen, Lisa Kwok, Hye Yoon Park, Xiangyun Qiu, Detlef M. Smilges, Donald H. 

Bilderback, and Lois Pollack; “Focusing Capillary Optics for use in SAXS Solution Scattering”, J. Appl. Cryst. 40, 193–195 (2007) 

7. S. Cornaby, D.M.E. Szebenyi , D.-M. Smilgies , D.J. Schuller , R. Gillilan , Q. Hao, and D.H. Bilderback; “Feasibility of One-Shot-per- 

Crystal Structure Determination using Laue Diffraction”, (to be published) 

8. A.R. Woll, J. Mass, C. Bisulca, M. Cushman, C. Griggs, T. Wazny, and N. Ocon; “The Unique History of the Armorer`s Shop: an 

application of confocal x-ray fluorescence microscopy”, Studies in Conservation 53, 93-109 (2008) 

9. J. Powers, N. Dimitrova, R. Huang, D.-M. Smilgies, D.H. Bilderback, K. Clinton, and R.E. Thorne; “Recovering Ancient Inscriptions 

by X-ray Fluorescence Imaging”, Zeitschrift für Papyrologie und Epigraphik (Bonn, Germany) 152, 221-227 (2005) 

10. Alexander Kazimirov, Detlef-M. Smilgies, Qun Shen, Xianghui Xiao, Quan Hao, Ernest Fontes, Don H. Bilderback, Sol M. Gruner, 

(continued from pg 18) 

In conclusion, during this upcoming Fall 2009 x-ray running period the technical and scientific staff at CHESS will 

commission new beamline, optics and station equipment that promise to significantly update and enhance the scientific 

capabilities of the flexible C-line experimental station. Our ambitious plans to produce low-energy x-ray optics and expand 

the size of the experiment hutch are still being developed. Look for more innovations during the coming year and contact 

the station scientist, Ken Finkelstein, with any questions or suggestions. 

References: 

1. See for CESR-TA: http://www.news.cornell.edu/stories/Aug09/cesrTA.html 

2. U. Bergmann et.al., Chem.Phys.Lett. 302, 119 (1999) 

3. http://www.chem.cornell.edu/faculty/index.aspfac=70 


Education and Outreach 

Lora K. Hine 

Cornell Laboratory for Accelerator-based Sciences and Education, 

Cornell University 

I have the best job in the entire laboratory. Hands down. I have never 

made that proclamation out loud or even dared to whisper it to anyone 

sitting next to me; I am afraid people will finally catch on and realize 

that the work I do is much more enjoyable than what they are doing. 

Here’s why: I do not have to follow any taxing laboratory protocol; my 

instrumentation does not require fine-tuning; my results seldom (okay, 

never) end up in any peer-reviewed publications. My office resembles a 

toy store, where visitors spend more time scanning the shelves crammed 

full of useful materials (i.e. equipment) than they do maintaining eyecontact. 

My trip record forms display regional travel destinations 

that end in the words “school district” versus distant, more expensive, 

locations ending with “national laboratory”. My calendar is peppered 

with a variety of exciting events; camps, tours, teacher workshops, lab 

activities/demonstrations, and even the much anticipated student field 

trips. My work day includes interactions with a range of people as young 

as third grade school children to as senior as emeritus faculty members. 

My job, directing outreach activities at CLASSE and helping fulfill the 

broader impact criterion established by the NSF, is a truly remarkable 

appointment. 

One of the most rewarding aspects of this position is the time I get to 

spend with young children. They are so anxious to learn something, just 

about anything, about science. Before reaching puberty, children are 

blessed with a sense of awe and wonder; their minds are wide open and 

waiting to be filled. To a ten year old, nothing is cooler than looking at 

clusters of dead skin cells underneath a microscope! Discovering that 

Middle school science teachers Mary Anne Ritinski (IS 234 

Brooklyn) and Crisan Berina (IS 126 Queens) work together 

during the Summer Institute to build their own light bulb to 

observe the effects of resistance in a wire. 

you can blow a bubble using a toilet-paper tube is 

sheer ecstasy. Donning safety goggles to witness 

the shattering of a flower after being submerged in 

liquid nitrogen is, to an elementary student, as good 

as life will ever get. After visiting with Wilson Lab as 

part of a class field trip, I have no doubt in my mind 

that these children run home and enthusiastically 

tell their family members about all of the fascinating 

science stuff they saw (and did!) that day. And, more 

importantly, they tell their parents and themselves 

that they want to learn more. 

During the last year, the laboratory has provided 

after-school enrichment programming for 

nearly 100 elementary school students. That’s 

a lot of kids receiving one-on-one, hands-on 

science programming outside of school hours! 

This programming is provided free of charge to 

any school within a sixty-mile radius of Ithaca. 

Many schools have children from disadvantaged 

backgrounds; their families live in remote, rural 

areas and they haven’t even heard of Cornell 

University. Most programs run one hour a week 

after school for six weeks, which is just enough time 

for me to get to know the kids, figure out what they 

want to learn more about, and (hopefully!) inspire 

them to seek out science and be comfortable with 

it - not scared of it. The most popular program we 

deliver to schools on a regular basis is “Atoms for 

Kids!”, but “The Science of Bubbles” comes in a close 

second. During the Atoms program, students get 

to operate light microscopes, investigate crystal 

formation, study light spectra, and witness what 

happens to atoms inside of a bell jar. All of which is 

extremely cool stuff when you are a 3-5th grader…. 

and still cool stuff when you are an adult. 

If only we could bottle the excitement of a fifth 

grade class and pass it along to class of high school 

students. By the time a typical high school physics 

class makes a trip to Wilson Lab, they are less 

enthralled by the wonders of science and are more 

concerned with grades, college, dating and a host 

of other distractions. This is not to say that these 

students are disinterested in science, but they are 

less enamored by its mysteries and more concerned 

with completing college applications! Some 

students have a genuine interest in conducting 

research, and it is the Lab’s good fortune to be able 

to provide some research experiences for high 

school students. During the past year, a number 


of high school students have worked alongside our laboratory’s 

scientists, involved in projects of value to their mentors. One 

CHESS researcher, Richard Gillilan, worked with Ithaca High 

School student Sohyun (Sarah) Kim during the summer of 2007 

to help her write a Java program to analyze 100,000 digital 

images of crystal growth. This past summer, she gave a poster 

presentation on her work at the CHESS user meeting. Currently 

Sarah is volunteering in MacCHESS’s lab growing protein crystals 

for use in beam-line testing. 

In addition to structured internships, the laboratory hosts a large 

number of visiting high school students as part of class field trips 

to Wilson. Many science teachers, from as far away as Buffalo NY, 

visit the lab as part of their one (and usually only) field trip during 

the school year. On average, 250 high school students each year 

amble along the passageways of the laboratory, gawking at the 

massive collection of electronic gadgetry, dodging the occasional 

drip of tunnel-juice, and timidly asking questions about the 

scope of the research being done here. A tour of the facility just 

can’t but help some high school students feel a sense of awe 

and wonder about the opportunities that lie in store for them as 

budding young scientists. 

Having spent six years as a middle school science teacher, I have 

grown comfortable interacting with children at this age level 

and even more at ease with the teachers who choose to make a 

profession out of educating this age-group. Consequently, the 

bulk of the professional development opportunities available 

to teachers through the outreach program at the Laboratory 

are geared towards 6-8th grade science teachers. Contrary to 

popular belief, middle school students are wonderful to have in 

the science classroom. They are capable, curious and internally 

motivated to “do science”. They adore hands-on activities and 

investigations; they benefit tremendously from interactive 

experiences, and are not yet afraid to propose an explanation 

for observed phenomena. Much anecdotal evidence suggests 

that middle school is the time when students decide, somewhat 

subconsciously, that they enjoy or despise science. Knowing this, 

it is important that adults, especially teachers, fuel a student’s 

passion for science before they leave middle school. If not 

properly fueled, that passion may not ever be reignited. 

One can see how important it is that middle school science 

teachers have the capacity and training to confidently teach their 

students. The outreach program at Wilson lab has taken an active 

role in helping to provide science teachers with the professional 

Lincoln Street Elementary School 

(Waverly, NY) 

Students have a good time learning about 

surface tension and experimental 

design by blowing bubbles with various 

house-hold objects. 

African Road Elementary School 

(Vestal, NY) 

Students look through the spectroscopes they built 

to observe the different colors of light released by 

heated gas bulbs. 

development training they need by hosting the Cornell Physical Science Summer Institute for Middle School Science Teachers 

during the summer of 2008. The theme for the week-long institute was “Making Connections: What Science Research and Your 

Middle School Curriculum Have in Common”. The Institute was partially funded through grant money received from the New York 

State Education Department; the other funding came from money devoted to Outreach at CLASSE. The Institute, held at Cornell 

for a week in July, provided eleven middle school science teachers from New York City with the opportunity to gain content 

knowledge aligned with NY State learning standards. It also provided teachers with the chance to interact with scientists who 

are conducting cutting-edge research and allowed participants to learn about state-of-the-art technology in the unique setting 

of a world-class research university. All participants earned one unit of graduate credit in Physics for the five days they spent on 

campus. A quote from one participant asked to reflect upon the week states; “My experience at the Physics Summer Institute was 

very exciting and informative. The hands-on explanations and the lectures from various experts in the field of physics can assist 

me in enhancing my knowledge in science as well as in delivering more research-based activities.” 

In addition to working with K-12 teachers and students, I am given the opportunity to interact with undergraduate students 

who spend time conducting research at our laboratory. These students, from diverse backgrounds and experience levels, 

are competent, motivated and frequently amaze me with their intellectual maturity. The science and engineering students 

participating in the Research Experience for Undergraduate (REU) program are selected from a large pool of applicants from 


throughout the country and come to Wilson Lab to work with faculty, research associates, and graduate students on a broad 

selection of research projects. These projects contain important elements of the overall research program at CLASSE; topics 

range from accelerator physics to microwave superconductivity to applications of synchrotron radiation in scientific research. 

During their final presentations delivered during the last week of the program, students showcase the complex research 

they have done and reveal the advanced level of thought and understanding required to work on projects alongside their 

Cornell mentors. Although these students work hard, they also play hard and take advantage of many social opportunities 

made available to them as part of the summer program. These college students live at the same dorm and hang out with REU 

students from other nationally sponsored programs at Cornell. REU’ers can be found playing soccer, bowling, dining, riding 

bikes, or sightseeing in downtown Ithaca with their colleagues throughout the summer months. 

During the summer of 2008, seven of the ten REU students worked for ten weeks on substantive ERL-related research projects, 

the efforts of which will be referenced and utilized by future staff and students. For instance, REU student Justin Hugon worked 

with research scientist Don Bilderback and technician Tom Szebenyi to reduce the vibration that occurs during current x-ray 

capillary optics fabrication. Improvements in capillary design will be necessary to take full advantage of the synchrotron 

radiation generated by the ERL. Upon completion of the program Justin, currently a physics major at Rhodes College, stated 

that his experience at CLASSE was beneficial and rewarding; it helped convince him to pursue a doctoral degree instead of a 

bachelors or masters degree. For many REU students, the time spent in the program and on campus has encouraged them to 

seriously consider applying for graduate school at Cornell University. Seven students from past REU programs at Wilson Lab 

have continued their graduate work at Cornell and have enrolled in PhD programs or have pursued STEM (Science, Technology, 

Engineering, and Mathematics) teaching careers. 

Having a particle accelerator facility in the neighborhood is not only a unique attribute of the Ithaca community (how many 

cities advertise tours of a particle accelerator in their Visitor’s Guide), but it also offers remarkable opportunities for people 

throughout central New York to learn more about physics and other fields of science. Through the outreach program at CLASSE 

and nearly a dozen other STEM Outreach programs on campus, Cornell provides informal science education opportunities 

through a number of different of venues. A glimpse into the outreach program at the lab reveals staff involved in the following 

events: hosting informative, hands-on activity booths at local and state-wide science fairs; funding and offering workshops 

for campus-wide events such as Expanding Your Horizons and Career Explorations; participating in regional events to 

promote science literacy such as NanoDay and CCC Math Day; providing professional development training to educators from 

underperforming schools in New York City through the Science Sampler Series and Science Leadership Academy; escorting 

groups of community members through the tunnel that houses one of the most powerful tools for studying the atomic world; 

and many other examples. Through these volunteer efforts, and through the hard work of the outreach staff at CLASSE, 

thousands of people throughout the state of New York have been exposed to the many wonders of science. And hopefully, 

these people and others will recognize the important role that science research plays in their own lives and the lives of their 

children’s children. 

So, if you happen to be walking by my office 

and quickly glance at the vast collection of 

materials stacked on the shelves, see me 

carting tubs full of science equipment to and 

from the parking lot, or you see me escorting 

a young group of visitors throughout the 

Lab, ask me what I am doing and how you 

can help. The secret is out: I have the best 

job in the entire lab. And I will be more than 

delighted to share it with you! 

At the New York State Fair, Lora Hine explains to a visitor how 

potatoes create an electrochemical reaction between two probes 

in a Two Potato Clock which powers the digital clock. Visitors are 

invited to test various fruits and vegetables for themselves. 


MacCHESS Advances: 

Microcrystallography and More 


Macromolecular Diffraction Division of 


Microcrystallography 

Crystals of proteins and other biological macromolecules 

never grow very big, due to the “soft” nature of the 

molecules and the weakness of the forces holding them 

together. At CHESS and other synchrotron sources, it is 

routine to deal with crystals that are ~100 μm across, but 

how often do we need to work with even smaller crystals 

Ithaca High School student Sarah Kim, under the direction 

of MacCHESS staffer Richard Gillilan, surveyed thousands of 

crystallization attempts (Fig. 1), and concluded that about 

50% of initial crystals were in the “micro” category, 

and that many larger crystals have “good” 

and “bad” regions and would benefit 

from use of a microbeam to isolate 

the better regions. 

• Mike Cook, Scott Smith, and Bill Miller have installed 

rear-mounted, piezo-based motors for crystal centering 

at F2. Using these, the runout error of spindle rotation 

can be reduced below 1 μm, as verified using a LabView 

program developed by Cornell student Ivan Temnykh 

(Fig. 3). 

Fig. 1: Sarah Kim and 

the crystal-scoring 

Java interface that 

she designed almost 

completely by herself, 

with some help from 

R. Gillilan. 

MacCHESS provides users with an x-ray beam as small 

as 5 μm, using a focusing capillary (see p. 63), excellent 

crystal-viewing optics to center a microcrystal in the beam, 

and a very precise rotation stage to keep it there. Users 

have determined important 

structures from “difficult” 

crystals using this equipment, 

e. g. the SAM riboswitch 

reported by Ailong Ke’s group 1 

(Fig. 2). Seeking to enhance the 

microcrystallography facility, 

• Don Bilderback’s group is 

working to reduce slope errors, 

and hence improve focusing, of 

X-ray capillaries. 

Fig. 2: The SAM riboswitch 

structure, rendered using Jmol 2 . 

Fig. 3: Piezomotor-equipped rotation stage 

installed in F2, Ivan Temnykh, plot of runout 

error using the modified stage. 

• Dave Schuller has upgraded the crystal-centering 

software to be more robust, and to include computer 

control of crystal illumination, as well as auto-centering 

using the XREC software 3 (Fig. 4). 

• Marian Szebenyi has added to the ADX data collection 

software an option for automated scanning of a crystal to 

identify the best-diffracting regions. 

A new experiment using an old technique 

With the very intense beam that would be produced by 

future sources such as an ERL, very tiny samples could 

produce diffraction patterns, but radiation damage would 

severely limit the amount of useful data that could be 

obtained from each sample. An experiment at D1, led by 

graduate student Sterling Cornaby, investigated the use of 

Laue diffraction to record a few images from each of several 

crystals mounted together (Fig. 5). With the Laue technique, 

many diffraction data are recorded simultaneously, with no 

need to rotate the sample; hence it is ideal for obtaining as 

much data as possible in a very short time. The experiment 

demonstrated the feasibility of collecting Laue data from 

a group of crystals and obtaining a structure from them 


Fig. 4: Java-based crystal-centering user interface, incorporating 

excellent video quality, automated centering, computer control 

of camera and light settings, easy recording of images of crystal, 

singly, as a rotation series or as a video stream. 

shown that modifications to the standard technique may 

be useful, and have also furthered understanding of what 

is going on inside cryocooled crystals. Matt Warkentin, 

from Rob Thorne’s lab, demonstrated that a faster cooling 

rate, obtained by blowing away the cold gas layer above 

the surface of liquid nitrogen before plunging a crystal 

into the liquid, is often advantageous 5 (Fig. 6). A pressure 

cryocooling technique developed primarily by Chae Un 

Kim (first a graduate student of Gruner’s, now a MacCHESS 

scientist) can also improve the quality of cryocooled 

crystals; see pages 43 and 71 for recent interesting 

results using pressure-cooling. Warkentin and Kim have 

also considered cooling crystals in capillaries, and have 

looked at the behavior of cryocooled crystals when the 

temperature is varied; this is an active area of research that 

will enhance our understanding of what is going on inside 

cold crystals, and may lead to better data from crystals 

which do not take kindly to routine cryopreservation. 

(see p. 63 for more details); further studies are planned to 

ascertain the limits of the technique. 

Detectors 

As in the past, MacCHESS has served as a test bed for 

new x-ray detectors. The first of the latest generation 

of CCD-based detectors from Area Detector Systems 

Corp. (ADSC), the Q-270, was installed at CHESS in 2006 

for testing; a few problems (mostly in software) were 

discovered and corrected, and the detector was made 

available to users later that year. Generally similar to the 

earlier Q-210 and Q-315, the new detector differs in having 

increased sensitivity, for accurate measurement of weak 

reflections. ADSC is also collaborating with the Gruner 

group in developing a tiled pixel array detector (PAD) for 

crystallographic use. A prototype PAD was tested at CHESS 

in 2007, with promising results 4 . Modifications to ADX 

allowed easy switching between CCD and PAD devices, 

as well as collection of a series of PAD images at different 

detector locations, which could subsequently be 

assembled into a large image. The sensitivity of 

the PAD proved to be similar to that of the Q-210 

CCD, but the dynamic range is much higher 

and the readout time much less. No geometric 

distortion corrections are necessary for the 

PAD, and background subtraction is easily done 

with existing software; yet to be developed are 

corrections for edge effects, and procedures to 

scale and combine multiple small PAD images 

into one in real time. See p. 54 for the latest on 

PAD’s. 

Temperature and pressure 

Typically, macromolecular crystals are 

cryocooled by plunging into a container of liquid 

nitrogen, and then maintained at about 100 K 

for data collection. Recent experiments have 


Fig. 5: Collection of microcrystals on a MicroMesh mount, for 

use in Laue experiment at D1. 

SAXS and SAD 

Over the last few years there has been increasing interest 

by structural biologists in conducting small angle x-ray 

scattering (SAXS) studies, and CHESS now offers facilities 

for SAXS including a new temperature-controlled sample 

cell, helium-filled flight paths, and expert 

advice. See the article on p. 50 for a full 

report on bioSAXS. The SAD (singlewavelength 

anomalous diffraction) 

technique, using the signal from heavy 

atoms such as Se or Hg, is the most 

common way to phase structures when 

no appropriate model is available for 

molecular replacement. At CHESS, A1 is 

suitable for Se-SAD and F1 for Br-SAD, 

and F2 can be tuned to accommodate 

a number of elements with absorption 

edges between 7 and 14 keV. For 

elements with edges at lower energies, 

Fig. 6: Simple “hyperquenching” device for 

blowing away cold gas above the surface of 

a liquid nitrogen bath.

down to slightly below 6 keV, the F3 

station, with multilayer optics, presents 

another option; see sidebar. 

Station upgrades 

A number of changes have been made to 

improve users’ productivity and comfort: 

Station F3 




• Robust safety shields which open and 

close automatically. 

• Motorized detectors which roll back 

automatically when a hutch is opened, 

and which can be moved using ADX. 

• Up-to-date computing hardware 

and software, including an extensive 

collection of standard crystallographic 

software. 

References: 

1. C. Lu, A.M. Smith, R.T. Fuchs, F. 

Ding, K. Rajashankar, T.M. Henkin, 

and A. Ke; “Crystal Structures of the 

SAM-III/S(MK) Riboswitch Reveal the 

SAM-dependent Translation Inhibition 

Mechanism”, Nat. Struct. Mol. Biol. 15, 

1076-1083 (2008) 

2. “Jmol: an open-source Java viewer 

for chemical structures in 3D”, http:// 

www.jmol.org 

3. “Crystal Recognition” , http://www. 

embl-hamburg.de/XREC 

4. W. Vernon, M. Allin, R. Hamlin, T. 

Hontz, D. Nguyen, F. Augustine, S.M. 

Gruner, Ng.H. Xuong, D.R. Schuette, 

M.W. Tate, and L.J. Koerner; “First 

Results from the 128x128 Pixel Mixedmode 

Si X-ray Detector Chip”, SPIE 

Optics & Photonics Conference, San 

Diego, CA (August 26-30, 2007) 

5. M. Warkentin, V. Berejnov, 

N.S. Husseini, and R.E. Thorne; 

”Hyperquenching for Protein 

Crystallography”, J. Appl. Cryst. 39, 

805-811 (2006) 

The F3 station is shared between CHESS (e.g. x-ray topography studies, 

x-ray imaging, x-ray fluorescence) and MacCHESS (macromolecular 

crystallography). Darren Dale, the responsible scientist for CHESS, 

maintains all beamline components up to the hutch and is currently 

working on further enhancements. The station supports a variety of 

monochromators: Si or Ge crystals as well as multilayers of various 

bandwidths. For macromolecular experiments the new 0.22% multilayers 

are used. Recent improvements in the monochromator box now allow 

users to tune the energy between 5.9 and 15.4 keV (2.1Å – 0.81 Å). This 

range spans the K and L edges of most commonly used elements for 

anomalous dispersion experiments. 

In the hutch CHESS and MacCHESS have rolling setups on separate 

optical tables for quick and easy switch-over. A new 1.5m optical 

table has been designed for crystallographic purposes; it supports all 

experimental components on one platform. This greatly facilitates 

alignment procedures and overall stability. It also gave CHESS the 

opportunity to install a new “integrated motion controller and drivers 

unit” for the table motors, which is much more compact than the old 

controller. In addition, the 32 bit workstation for data collection and 

processing has been replaced with a modern 64 bit Linux based system 

similar to those at other MacCHESS beamlines. 

The station has been used mainly by MacCHESS personnel, the Crane 

group from Cornell and the Cingolani group from Upstate Medical 

University. Recent experiments at the station examined samples that 

contain anomalous scatterers, e. g. Xe, Fe and S. The results show that 

we can obtain an anomalous signal from an element as weak as sulfur, 

with data collected at 7.1 keV. Due to the increase in flux with the 0.22 

% multilayer monochromator, data collection times were significantly 

shorter (~ 5 times) compared to a data set taken from a similar sample at 

the F2 beamline. As an example of the quality of anomalous data from 

F3, the figure shows an anomalous difference Fourier map from horse 

hemoglobin, after refinement, contoured at 4 σ. The region depicted 

includes both heme groups and their protein surroundings. Large 

positive peaks (blue) appear at the positions of the iron atoms in the 

center of the hemes, and smaller peaks are visible for sulfurs, e. g. in the 

disulfide bond located slightly above and to the right of the left-hand Fe. 


XPaXS: Improved Data Acquisition 

and Real-Time Analysis at CHESS 

The Scanning X-ray Fluorescence Microscopy (SFXM) capability at CHESS draws users from diverse fields, including Environmental 

Science, Soil Science, Anthropology and Native American Studies, Dendrochronology and Classics. When I inherited responsibility 

for the F3 beamline, two of the elements essential for the success of this research program were already available: wide-bandpass 

multilayers to provide the intense monochromatic flux required for detection of elements in trace quantities; and singlebounce 

capillary x-ray optics capable of yielding microbeams at the sample position. In the past three years we have completely 

refurbished the F3 station and upgraded all of the sample manipulation hardware, which is now capable of scanning areas 30 cm 

wide by 30 cm tall and 5 cm deep, with step sizes below 1 micrometer if necessary. 

Scanning large areas with high resolution presents some new experimental challenges. To give a sense of scale, scanning an area 3 

mm by 3 mm with a 15 µm step size requires 40,000 independent measurements, and if integrated for 1 second per point the scan 

will take more than 11 hours to finish (development of new multi-element 

detectors will improve the throughput in the near future). We use the “spec” 

command-line program for data acquisition, which is familiar to seasoned 

synchrotron researchers but frustrating to many newcomers, see figure 1. 

When I first took over F3, we would use “spec” to start a scan, and then watch 

raw data scroll across the screen for 11 hours. The experience was similar to 

watching the screens of encrypted data in the movie “The Matrix”, where a 

willful suspension of disbelief is required to accept that the data are somehow 

meaningful. 

Many experiments required recording the full fluorescence spectrum at each 

point. The datasets were growing in size and becoming difficult to work with. 

Some peak-fitting routines were available to process the data after collection 

was complete, but on several occasions we discovered problems with a 

Fig. 1: Everybody’s first experience with the command line. 

dataset weeks after the experiment had ended. Clearly what we needed was 

an improved analysis capability, one that could fit fluorescence spectra with many overlapping peaks, determine the elemental 

concentrations from the peak areas, and update an element map in a graphical user interface in real time while the experiment 

is ongoing. We also wanted the ability to interact with the data in real time without disrupting the acquisition, for example by 

selecting a single pixel or region of interest in the image map and inspecting the raw fluorescence spectra and fit results or 

performing some kind of statistical analysis such as Principle Components Analysis or cluster analysis. 

In order to foster development of the multidisciplinary research program at F3, we have begun augmenting the flexible 

command-line interface with just such an intuitive graphical user interface for experimental controls and data processing (see 

figure 2). Working with Cornell undergraduate students, we have begun to develop XPaXS, an extensible set of packages for x-ray 

science. These packages are written in Python, which is an established, powerful cross-platform scripting language that allows 

scientists to focus more on science than 

the minutiae of computer programming. 

Python is emerging as the standard language 

for systems integration, in part due to its 

permissive open-source license (it can be 

used for both free and commercial projects), 

simple and elegant syntax and wide variety 

of scientific libraries, all of which enable 

rapid development of powerful, large and 

yet maintainable projects. Our software 

development work is done in cooperation 

with other successful free software projects. 


Darren Dale 


Fig. 2: Graphical user interface for HDF5 files 

and spec scan controls.

For example, SpecClient provides a 

python interface to the “spec” data 

acquisition program, and PyMca is 

used for advanced spectral fitting and 

composition analysis, both of which were 

developed at the European Synchrotron 

Radiation Facility. 

The graphical user interface and 

improved data handling allow us to 

develop flexible and powerful tools for 

data inspection and analysis. Experiments 

that once provided only lines of text on 

the command line as feedback during the 

measurement now provide capabilities 

for real-time analysis and interactive 

inspection of data in a form that is most 

meaningful to the experimenter. The 

program is multithreaded, so it is possible 

to interact with the data even while both 

data acquisition and analysis are ongoing. 

It is possible to select a single point in 

a map, or drag out a region of interest, 

and inspect the fluorescence spectra to 

identify anomalies or bad data points, or 

to average over a heterogeneous sample 

in order to calibrate the measurement 

to a NIST standard. In the example 

illustrated in figure 3, all the spectra 

in a region of interest specified in the 

calcium mass fraction map are passed 

to PyMca for peak fitting 

and concentration 

determination, and 

the averaged results 

are compared with the 

accepted values. 

This acquisition and 

analysis package is 

developed with the hope 

that many will find it 

useful, and that many 

will contribute to — and 

take credit for — its 

development. Working 

with colleagues at the 

European Synchrotron 

Radiation Facility, we have 

settled upon a simple 

common file format based 

upon the freely available 

HDF5 technology suite, 

which supports the 

compressed, binary 

HDF5 format developed 

specifically for scientific 

applications. HDF5 allows 

us to efficiently work 

with arbitrarily large and 

complicated datasets, 

loading only small subsets of the data 

into memory at any given time. We take 

advantage of computers with multiple 

processors and even computing clusters 

to process data in parallel, as quickly as 

possible. Many synchrotron techniques 

can be significantly enhanced by the 

ability to analyze and inspect relatively 

large datasets in various ways, both in 

real time during the acquisition and 

off-line after acquisition is complete. 

The software is designed to be easily 

extended and applied to other kinds of 

experiments and analyses, has already 

been used for analysis of EXAFS data, 

and is currently being extended to other 

kinds of experiments at CHESS as well. 

Users can revisit or reprocess their data 

after leaving the lab using the Python 

packages which are freely available on 

the internet. XPaXS and its dependencies 

are free, open-source projects that can be 

used on Linux, Windows and Macintosh 

OS-X. The source code is also available for 

download, so anyone can add whatever 

additional features they need, regardless 

of platform. Everyone is encouraged 

to contribute and take credit for their 

contributions. 

Documentation is a major focus of our 

project. A Users’ Guide is currently being 

developed, along with a Developers’ 

Guide and Application Programming 

Interface reference to help those 

interested in adding new features. 

The documentation is created using 

modern documentation generation 

tools. The library documentation, online 

html and printable pdf documents 

are all generated from a common 

origin, so the entire documentation 

suite can easily be kept up to date. 

The documents are searchable, crossreferenced, 

and automatically indexed. 

The documentation in its current form 

is available at http://www.chess.cornell. 

edu/software/xpaxs. 

The documentation is a central and 

ongoing effort. The users guide for 

the SXFM program will be the primary 

focus in the near future, in order to 

provide users who wish to work more 

independently with the means of 

doing so. A comprehensive set of unit 

tests will be assembled to aid in future 

development and ensure trouble-free 

operation. We are developing several new 

features, such as a network-based video 

monitoring capability which is currently 

being developed to allow 

remote observation of the 

experiment and its progress. 

We are also planning to 

incorporate existing code 

with features similar to 

those available at the CXRO 

website for calculations 

of x-ray transmission, 

anomalous form factors, 

index of refraction, etc. 

The long range goal is to 

provide a framework such 

that additional packages 

can be added over time to 

provide all the components 

necessary for imaging, 

spectroscopy and scattering 

experiments, optics design 

and characterization, 

characterization of x-ray 

sources, and most likely 

other areas we have not yet 

considered. 

Fig. 3: (Top) Calcium mass fracton 

distribution in NIST citrus leaves 

standard reference. (Bottom) Spectrum 

averaged over a region of interest 

selected from the Calcium map and the 

fit produced by PyMca. 


CHESS High-pressure Stations (B1/B2) Update 

Zhongwu Wang 


High pressure coupled with synchrotron x-ray diffraction is one powerful technique for discovering novel 

physics and chemistry with a wide spectrum of applications. CHESS has long been playing a significant role 

in the development of high pressure synchrotron facilities. To expand our research abilities, particularly in 

nanoscience and nanotechnology, we have made an effort to improve and update our high pressure facilities, 

to be capable of a series of new in-situ measurements of materials, including wide and small angle x-ray 

diffraction and Raman measurements at extreme conditions of pressure and temperature. Here, we highlight 

several modifications and developments at CHESS: 

1. 

2. 

3. 

4. 

Two beam lines for energy-dispersive and angle-dispersive x-ray diffraction are combined and 

merged into one versatile station. This modification not only keeps all experimental capabilities 

- energy-dispersive or angle-dispersive x-ray diffraction can be selected by repositioning two 

monochromator crystals - but also expands the hutch space, enabling introduction of a series of 

fixed and portable instruments for development of new techniques. The improved capabilities 

include a three-dimensional rotating stage for side x-ray diffraction, laser-excited Raman 

spectroscopy, a detector control system, a high temperature tuning system etc. 

Four-dimensional control for movement of the Mar345 detector is implemented. Slightly tilting and 

rotating the Mar345 detector enables an accurate calibration of the sample-to-detector distance 

and associated parameters. Most importantly, a new in-situ technique has been developed allowing 

measurement of both small and wide angle x-ray diffraction at various pressures and temperatures 

without multiple calibrations. Easy optimization of x-ray energy and sample-to-detector distance 

makes the two types of measurements possible during one single pressure run. 

Switching the x-ray source to white beam and using a large area image plate detector enable single 

crystal Laue diffraction under pressure. 

A series of side instruments become operational for users. These include two portable 

spectrometers for Raman, reflectivity and transmission spectra, mechanical and Electrical Discharge 

Machining (EDM) drillings, a high pressure gas loading system, optical microscopes, etc. 


The Cornell Energy Recovery Linac: 

update on a future source of coherent hard x-rays * 

Don Bilderback 1,2 , Bruce Dunham 3 , Georg Hoffstaetter 3 , 

Alexander Temnykh 3 , and Sol Gruner 1,4 

1 


2 

School of Applied Physics, Cornell University 

3 

Laboratory of Elementary-Particle Physics, Cornell University 

4 

Physics Department, Cornell University 

* 

For the Cornell ERL Team, Cornell University 

Synchrotron radiation research is still growing, with newer and more capable x-ray sources being constructed. Petra III 

in Hamburg, Germany and the NSLS II in Upton, NY are examples of storage rings under construction that are nearing 

the expected limits of storage ring performance. In contrast, linac-based sources such as energy recovery linacs (ERLs) 

and x-ray free electron lasers (XFELs) are still at an early stage of development, and have great potential for steady 

improvements in performance for many years to come. 

The ERL upgrade to the CESR ring described below 

promises to generate ultra-bright electron beams, and 

thus ultra-bright x-ray beams with dramatically smaller 

emittances and shorter pulse durations than those available 

from storage rings 1 . The high coherence and temporal 

properties of the ERL will have transformative, broad 

impact across the sciences and engineering by enabling 

numerous experiments that are now not feasible at even 

the most modern 3 rd generation storage ring sources; 

nor would many of these experiments be suitable for 

x-ray free electron lasers. Enabled science includes many 

types of imaging of materials and biological structures, 

macromolecular structure determination without 

crystals, effective nanoprobes for matter at higher static 

pressures than are presently feasible, and detailed studies 

of the structure of glasses, disordered materials, and 

polycrystalline materials. The ERL would be especially 

useful in cases where structure needs to be determined on 

objects for which structural details vary from one specimen 

to another, which is the case for most nanoparticles and 

biological cells and organelles. It would also allow the 

recording of extremely rapid events, so researchers 

can “visualize” rapid physical, catalytic and 

biological processes taking place on times scales 

down to 50 femtoseconds. Societal impacts 

will come in numerous areas such as life-saving 

medicines and drugs, new materials for better 

batteries, more efficient catalysts for fuel cells, 

better composite materials, smarter electronics, etc. 

The transverse emittance of the electron bunches 

used to generate x-rays determines the spectral 

brilliance and transverse coherence of the x-ray 

beams. Ideally, the emittance should be small 

enough to produce full transverse coherence of the 

x-rays, i.e., to produce a diffraction-limited x-ray 

beam. The underlying basis of an ERL is that, in 

principle, very low emittance electron beams can 

be generated from a laser-driven photocathode, 

and accelerated to high (GeV) energies without 

substantial emittance growth in linear accelerators. 

High brightness, highly coherent x-ray beams can then 

be generated from these electrons as they pass through 

undulators. Since the electron beam carries several 

hundred megawatts of beam power, this is feasible only 

if the electron beam energy is recovered after the x-rays 

are generated. Using a superconducting (SC) RF linac, 

essentially all the electron energy may be recovered by 

passing the beam through the linac a second time, 180 o 

out of phase with the accelerated beam, hence, the name 

Energy Recovery Linac. Although the basis of the ERL idea 

was suggested many years ago by Maury Tigner 2 , it only 

became practical for x-ray generation in the mid-1990’s, 

due to advances in superconducting linac technology and 

photoemission electron sources 3 . 

Phase 1a & 1b: Testing the first stages of the ERL accelerator 

The ERL group at CLASSE is in the midst of prototyping 

the technology that will be needed for a 5 GeV ERL facility. 

The most difficult and critical component in need of R&D 

is the injector; a full-scale prototype injector has now been 

assembled in the L0 area of Wilson Laboratory (Figure 1). 

The injector generates a beam of high average current, lowemittance 

electrons using a laser-driven photo-cathode and 

then accelerates them to relativistic energies up to 15 MeV. 

Fig. 1: Floor layout of the ERL test area in L0 of Wilson Laboratory, just south 

of CHESS East. From right to left: DC photocathode, superconducting linac, 

branch lines for diagnostics, and finally, a high power beam dump. 


A consequence of special relativity is that the mutual charge repulsion that tends to blow apart a bunch of electrons at low 

energy is counteracted at relativistic speeds. Thus, the difficult task of the injector is not only to generate a low emittance 

electron beam, but to preserve the emittance until relativistic energies are achieved. Figure 1 shows the layout of the test 

accelerator designed to generate ultra-low emittance bunches of electrons at a 1.3 GHz rate with up to 100 mA average 

current. This injector is now in the commissioning stage. 

The electrons are produced in a special cathode material using the photoelectric effect. A precisely shaped laser pulse is 

directed at the cathode, giving the electrons enough energy to escape. The ejected electrons are then accelerated across 

a small gap using a high voltage power supply. The cathode material is gallium arsenide (GaAs), which is commonly used 

for high speed electronics, in photomultiplier tubes, and in night vision goggles. To obtain efficient electron emission, the 

surface of the GaAs wafer must be as clean as possible and maintained at a vacuum level below 10 -11 torr. After cleaning, 

Fig. 2: Photocathode gun area. A vacuum of better than 10 -11 Torr 

has to be maintained around the photocathode to avoid ion back 

bombardment of the photocathode, which would spoil the lifetime of 

the photocathode by ruining the monolayer of Cs on the surface. A 

load-lock chamber facilitates quick change of the cathodes for testing 

and for renewing the Cs monolayer needed for the cathode to work well. 

Fig. 3: The superconducting (SC) linac consists of 5 SC cells 

in series. Each cell uses a waveguide to conduct 1.3 GHz 

microwave power from associated klystron transmitters on the 

mezzanine floor above. The cavities are cooled by liquid helium 

at 1.8 K from a closed-cycle refrigeration system. The linac is 

now functional. 

it is coated with very thin layers of cesium and fluorine, which act to reduce the work function, making it easier for the 

electrons to escape (Figure 2 shows the cathode preparation system). The properties of GaAs have been extensively 

measured 4,5 , demonstrating that it is currently the best cathode choice for obtaining low beam emittance and high average 

current. 

A very sophisticated laser system is required to produce bunches of electrons with the correct shape, power and time structure. It 

turns out that the shape of the outgoing electron pulse closely matches the shape of the incoming laser pulse, and the electron 

beam emittance can be reduced by choosing the correct shape. The spacing (frequency) of the pulses must also match the 

frequency of the RF accelerating cavities, which operate at 1.3 GHz. There are no commercial laser systems available to meet all of 

the needs for an ERL injector, thus we have built a custom laser using ytterbium (Yb) doped optical fibers. 

After the electron bunches are produced 

at the cathode and given an initial 

acceleration by the electron gun, they are 

boosted to high energy using a series of 

5 superconducting RF cavities (Figure 3). 

Each cavity can transfer up to 100 kW of 

microwave energy to the electron beam, for 

a total of 500 kW (1/2 of a million watts!). 

Superconducting cavities are used to 

overcome the heating problems that would 

occur with such large power. Figure 4 

shows the five high-power microwave tubes 

that provide the energy to the accelerating 

cavities. 

Fig. 4: Microwave generators 

produce the power needed to 

drive the superconducting linac. 


The final parts of the test set-up are diagnostic tools to measure the emittance of the electron bunches and its pulse duration 

before the beam is sent to a 0.5 MW beam dump. 

We are now starting the second phase of the ERL R&D program. The proposed research program addresses five critically important 

technology areas: 

1. Superconducting linac development. The ERL requires linacs capable of continuous duty (CW) operation at high current with 

short bunch lengths while preserving emittance and dealing effectively with higher order modes. A full linac cryomodule 

(somewhat similar to the injector linac, but with longer cavities and with much weaker power couplers because in the 

ERL it is the decelerated beam that fills the cavity with energy, not the power coupler) will be designed and fabricated at 

Cornell. Cryomodule component testing will be done collaboratively with several other institutions. The program includes 

development of requisite cavities, higher-order-mode absorbers, beam position monitors, in-vacuum cryomagnets, RF 

amplifiers and power couplers, and cool-down procedures. 

2. High brightness photoinjector development. Continued development will be performed on laser driven photoinjectors capable 

of delivering requisite current at high brightness and long photocathode lifetime. This includes R&D on new photocathodes, 

high voltage electron sources, drive lasers, and advanced beam simulation tools. Further R&D on the HV insulator is needed 

to reach the required 500 to 750 kV energy level from the electron gun. 

3. High-brightness electron beam physics and diagnostics. The program will address challenges of emittance preservation from 

the electron source, through the injector, merger, and transport loop sections via experiments and simulations on the Cornell 

injector. Beam diagnostics to monitor bunch timing and position will be advanced, both for beam stability at the x-ray source 

points, and for simultaneously accelerating and decelerating bunches in the linacs. 

4. Beam dynamic effects will be investigated, such as ion trapping, short bunch behavior and other possible sources of instability. 

Beam loss mechanisms, impedance issues, failure modes and beam abort strategies will all be studied through overall system 

modeling. In each case, methods of mitigation and control will be studied. 

5. X-ray beamline components necessary to exploit ERL capabilities will be developed. These include novel undulators to exploit 

the identical horizontal and vertical emittances of an ERL, x-ray optics for high specific heat loads, coherence monitors, and 

detectors to effectively utilize the temporal possibilities of a coherent ERL source. 

Fig 5: Low-energy electrons are produced and accelerated to 5-10 MeV at the injector. They are raised to 2.5 GeV in the North Linac by traveling “on-crest” 

through the RF fields produced by the SRF cavities, turned around and raised to 5 GeV after passing through the South Linac. X-rays will be produced in 

undulators in the position of the blue arrows, mostly in a new building to be added to the east of Wilson laboratory. Electrons returning to the North Linac 

are shifted 180 degrees out of accelerating phase (by adjusting the path length) so that the electrons are now “off-crest” and their energy is recovered in 

both linacs before the spent electron beam is sent to the dump. There is room in the layout for a non-energy-recovered, fast-pulse beamline as shown by 

the red arrow. 

Phase II: the full-energy, 5 GeV machine 

The work of the Phase I development (described above) is designed to provide confidence and costing for a 5 GeV ERL that we 

would hope to build at Wilson Laboratory. 

The CESR tunnel and Wilson laboratory infrastructure will be reused for the ERL facility. Much of the ERL would consist of new 

construction to the East (above, in Figure 5) of the present CESR and Wilson Lab complex. A new partially-underground laboratory 

will be added to increase the number of x-ray beamlines and new tunnels will be bored to house the new linacs required. We 

already have a first round of plans and costing from ARUP, an internationally-based architectural and engineering company 

that has been contracted to develop plans for the civil engineering (buildings and tunnels) of the project. The present plans are 


for conceptual design purposes. We are presently optimizing the layout of tunnels, buildings and the machine to fit campus, 

performance, and cost constraints. For example, we are evaluating layouts with twin linacs in the same tunnel as well as versions 

in separate tunnels. When this work is completed, we plan to submit a conceptual design proposal to the NSF for a full-scale 

5 GeV ERL facility, including x-ray beamlines. 

The ERL design group is working on a 

Conceptual Design Report containing the 

following parameters table which shows 

various ERL operating modes. An ERL is 

more flexible than a storage ring, which 

opens new opportunities and a plethora 

of operating modes. 

There is a long list of items that are being 

worked on in parallel with work on the 

injector and the 5 GeV facility layout, 

including electron beam machine design, 

shielding wall design, collimators ahead 

of undulators, exit crotch design, etc. 

The x-ray group has begun planning for 

5 to 25 m long undulators and beamlines 

that extend outward to 70 m from the 

source. We have established preliminary 

working groups to conceive of beamlines 

in the following areas: 

1. Diffraction-limited x-ray scattering 

beamline suitable for soft-matter 

using SAXS, USAXS, WAXS and 

GISAXS techniques; 

2. Short-pulse repetitive pump-probe timing beamline for 100 femtosecond pulse work at a repetition rate of 100 kHz and a 2 

picosecond pulse length at a 1.3 GHz repetition rate. This will be useful for ultrafast time-resolved experiments; 

3. A beamline for coherent diffractive imaging and dynamic studies of bulk materials, interfaces and biological samples 

including techniques of intensity fluctuation spectroscopy, ptychography. Examples of application areas are dynamics of 

magnetic materials and the glass transition; 

4. Inelastic x-ray scattering (IXS) with meV resolution will be used to study the dynamical properties of materials at atomic to 

mesoscopic length scales. An ERL IXS facility has the potential to outperform all existing facilities, their proposed upgrades, 

and sources under construction by one order of magnitude more flux; 

rd 

5. A nanoprobe for making a 1 nm diameter x-ray beam at 10 keV with as much flux per square nm as most 3 generation light 

sources put into a square micron. This will make possible x-ray experiments on even a single atom, which might be useful 

for studying the in-situ doping properties (atom clusters that are electrically inactive) of the smallest line-width transistors or 

performing x-ray experiments in the smallest possible volumes. 

New undulator designs are underway: 

ERLs offer opportunities to use insertion devices 

that take advantage of long, small, round bores (5 

mm). This is very different than in a storage ring, 

where a much wider horizontal bore is needed to 

provide orbital room for electron injection. The small 

sized bore feasible with an ERL allows design of very 

compact magnetic structures that can generate 

larger magnetic fields than the planar undulators 

used in 3 rd generation storage rings. 

Figure 6 shows a novel “Delta” undulator that was 

designed to utilize the unique properties of ERL 

electron beams 6 . As opposed to conventional 

undulators, it provides full control of x-ray 

polarization and a stronger magnetic field that 


Fig. 6: Prototype of 

the Delta undulator 

made from small 

triangular blocks of 

NdFeB material with 

a remnant field of 

1.26 Tesla. The central 

hole for the electron 

beam is only 5 mm in 

diameter.

translates to high x-ray flux. In addition, it is 

much more compact and cost-efficient. To 

demonstrate the new design principles, a 30 

cm long model has been built and recently 

tested with a Hall probe, Figure 7. 

Testing of the very first Delta-type undulator 

prototype revealed a 1.25T peak field in planar 

mode and 0.85T in helical (Figure 8) that is 

approximately 90% of the design value. 

The field profile analysis indicates that the field 

errors cause less than a 3% loss of the x-ray 

photon flux in the helical mode and 20% loss 

in the planar mode. These very favorable test 

results have confirmed the basic principles of 

the Delta-style design. 

Fig. 7: Delta undulator model 

on magnetic field measurement 

bench, complete with coils for 

compensating for background 

magnetic fields. The center 

ceramic tube guides the Hall 

probe down the bore of the 

undulator during the magnetic 

profile measurement. 

Fig. 8: The measured 

magnetic field components 

in planar and in helical mode 

of operation corresponding 

to linear and circular x-ray 

polarization. Plots are from 

reference [7]. 

Presently we are working on the next, fully-functioning model. It will have an improved mechanical design which should increase 

peak field up to the full design value and reduce magnetic field errors still further. The next model will be UHV compatible and will 

be tested with a small diameter electron beam at a linac test facility. 

Conclusion: 

A 5 GeV ERL facility would be a great advance to synchrotron radiation science and would have numerous benefits to society. R&D 

on necessary ERL components is well underway. Plans for a full-scale, 5 GeV hard x-ray ERL are in an advanced stage of planning. 

We intend to deliver a conceptual design for the full-energy ERL within the next year. 

References: 

1. C. Sinclair, and S. Gruner; “ERL Developments”, CHESS News Magazine, pg 9 (2005) 

2. M. Tigner; Nuovo Cimento 37, 1228 (1965) 

3. B. Aune et al.; Phys. Rev. ST-AB 3, 092001 (2000); G. R. Neil et al., Phys. Rev. Lett. 84, 662 (2000); C. K. Sinclair, 

Proceedings of the 2003 Particle Accelerator Conference, p. 76 

4. I. Bazarov et al.; “Thermal Emittance and Response Time Measurements of NEA Photocathodes”, J. Appl. Phys. 103, 05490 

(2008) 

5. I. Bazarov, B. Dunham, and C. Sinclair; “Maximum Achievable Brightness from Photoinjectors:, Phys. Rev. Lett. 102, 

104801 (2009) 

6. A. Temnykh; “Delta Undulator for Cornell Energy Recovery Linac”, Phys. Rev. ST Accel. Beams 11, 120702 (2008) 

URL: http://link.aps.org/doi/10.1103/PhysRevSTAB.11.120702 

7. A. Temnykh; “Evaluation of Magnetic and Mechanical Properties of Delta Undulator Model”, Reprint CBN 09-1,Cornell 

(2009) URL: http://www.lns.cornell.edu/public/CBN/2009/ 


New Mechanical Testing Methods for Structural Materials at Small Size Scales 

Matthew Miller 

Alteration of Citrine Structure by Hydrostatic Pressure 

Sol Gruner, Buz Barstow, Nozomi Ando, and Chae Un Kim 

Putting Color into Surface Diffraction 

Detlef Smilgies 

Self-Assembled Nano-Checkered Thin Films Studied by Reciprocal Space Mapping at 

CHESS 

Sean O'Malley, Peter Bonanno, Keun hyuk Ahn, Andrei Sirenko, Alex Kazimirov, Soon-Yong Park, Yoichi Horibe, 

and Sang-Wook Cheong 

Structures from Solutions: Biomolecular Small-Angle Solution Scattering at MacCHESS 


Development of X-ray Pixel Array Detectors 

Sol Gruner 

Exploring New Physics of Nanoparticle Supercrystals by High Pressure Small Angle 

X-ray Diffraction 

Zhongwu Wang, Ken Finkelstein, and Detlef Smilgies 

Topography of Diamonds at CHESS Helps Nuclear Physics Program at JLAB 

Richard Jones, Franz Klein, and Ken Finkelstein 

Nanoparticle-block Copolymer 

Ulrich Wiesner, Laura Houghton, and Sol Gruner 

Heat-bump Measurements at CHESS A2 Wiggler Beam 

Peter Revesz, Alex Kazimirov, Ivan Bazarov, Jim Savino, Emmett Windisch, and Christopher MacGahan 

Advances in X-ray Microfocusing with Monocapillary Optics at CHESS 

Sterling Cornaby, Thomas Szebenyi, Heung-Soo Lee, and Don Bilderback 

Carbon Nanotube and Crystalline Silicon Structures 

Eric Meshot, Mostafa Bedewy, Sameh Tawfick, K. Anne Juggernauth, Eric Verploegen, Yongyi Zhang, Michael De Volder, 

and John Hart 

Phase Behavior of Water inside Protein Crystals 

Chae Un Kim, Buz Barstow, Mark Tate, and Sol Gruner 

Research Highlights 


New Mechanical Testing Methods for Structural 

Materials at Small Size Scales 

Matthew P. Miller 

Sibley School of Mechanical and Aerospace Engineering, Cornell University 

Abstract 

This paper describes new experiments 

designed to characterize the 

micromechanical response of structural 

materials. As a way to calibrate 

microscale constitutive models and to 

understand grain scale elastic-plastic 

deformation, our group worked closely 

with CHESS personnel to develop a high 

energy x-ray method for measuring 

lattice Strain Pole Figures (SPFs) in 

situ in the A2 experimental station at 

CHESS. Results from experiments and 

crystal-based finite element simulations 

on copper are presented in the paper. 

The distribution of stresses predicted 

by the model closely compares to 

the experimental result. Motivated 

by our success at CHESS, we have 

begun conducting experiments at 

the Advanced Photon Source (APS) to 

characterize individual grains within a 

deforming polycrystal. We show results 

for crystals in two processed states 

of a titanium alloy,Ti-7Al. The stress 

states change with deformation-likely 

due to translation of the stress state 

along the single crystal yield surface. A 

complicated residual stress state was 

present in each grain upon unloading. 

By highly resolving individual diffraction 

spots within each crystal, we were 

able to understand the character of 

dislocation structure formation in 

each alloy state. These experiments 

show huge potential as a means of 

characterizing engineering materials in 

general. We also believe the experiments 

– coupled with a crystal-based stress 

state representation methodology – 

bring a new measurement capability to 

the important problem of residual stress. 

Introduction 

Structural materials play a key role in 

the products we use every day. From the 

titanium of a bicycle frame to the nickelbased 

super alloy that makes up a jet 

engine component, structural materials 

are selected for their strength, stiffness, 

density, corrosion resistance and a 

myriad of other properties. Mechanical 

properties are always related to some 

idealization of material behavior referred 

to as a constitutive model. From Young’s 

modulus to yield strength and fracture 

toughness, mechanical properties 

arise naturally when the response of 

a structural material to thermal and 

mechanical loading is viewed from the 

perspective of a constitutive model. 

Mechanical properties are measured 

by applying thermo-mechanical loads 

to a test specimen then monitoring 

its response. By knowing both the 

stimulus and response functions, the 

properties can be determined. With 

the mechanical properties known, 

these experiments – which are referred 

to as mechanical tests – can also be 

used to monitor the performance 

characteristics of a structural material. 

The fidelity of the constitutive model 

can be verified by subjecting the 

material to more complicated loading 

scenarios. The simplest test is uniaxial 

monotonic loading – pull or compress 

the specimen past the yield strength to 

failure. Multiaxial loading experiments, 

such as tension-torsion tests, can be 

used to understand material behavior 

and the validity of the model under 

complicated stress states, which more 

closely mimic service conditions. High 

temperature, corrosive conditions, 

cyclic loading and loading rate variation 

can be employed to create a veritable 

“gauntlet” of service conditions for the 

material and the model. Success in 

correlating experimental behavior builds 

confidence that a constitutive model 

can be trusted in the actual conditions 

an engineering component will be 

subjected to – conditions that cannot be 

replicated in the laboratory. 

Constitutive model development for 

structural applications has moved 

down scale for several reasons. Microelectromechanical 

systems, MEMS, are 

the same size as the microstructure. 

MEMS design requires an understanding 

of material response on the scale of the 

microstructure. More importantly, there 

is a growing need to model deformation 

– induced microstructure evolution 

within large scale components. The hope 

for these microscale formulations– from 

models of atomic behavior to dislocation 

models to crystal plasticity – is that some 

of the behaviors that are mysterious and 

practically random on the macroscale 

will become tractable and predictable 

when the microstructural response 

is being modeled. These processes 

include fatigue microcrack initiation, 

plasticity, recrystallization and phase 

transformations. Enormous growth 

has taken place in the general field of 

multiscale material modeling over the 

past 10-15 years. The ever-increasing 

capacity of computing facilities has 

encouraged theoreticians to model 

behaviors on increasingly smaller size 

scales with the hope of creating truly 

predictive links between material 

structure, thermo-mechanical properties 

and measures of performance. These 

links will eventually enable designers 

to base allowable (operating loads 

and temperatures, for instance) on 

micromechanical properties and 

analyses. From an experimental 

perspective, the question becomes 

whether or not we can reproduce 

mechanical tests on the microscale. 

One approach is to conduct traditional 

mechanical tests on subsized specimens 

constructed from the microstructure or 

from components of a micromechanical 

machine. Another approach is to 

employ microscopic mechanical 

instruments such as nanoindentation 

devices to probe microscale stress-strain 

behavior. High energy synchrotron 

x-ray diffraction methods represent 

a formidable alternative to subscale 

experiments. Modern area detectors and 

impressive depths of penetration have 


made it possible to probe a metallic 

crystal that lies far beneath the surface 

of a test specimen and make diffraction 

measurements quickly. By conducting 

carefully designed mechanical tests 

in situ during an x-ray diffraction 

experiment, the crystal lattice plays 

the role of the engineering strain gage 

on the macroscale, with the added 

bonus that the strains indicated by the 

lattice are elastic. The challenge is the 

deconvolution of the diffraction data - 

pulling it apart in order to understand 

its origin and significance – then 

recombining it to draw conclusions 

regarding the deformation of the 

polycrystalline aggregate. 

Our group at Cornell began using high 

energy x-rays at the A2 experimental 

station at CHESS to understand 

the behavior of polycrystalline 

structural materials and to validate 

micromechanical constitutive models. 

Working closely with beamline 

personnel, we designed and fabricated 

our own mechanical loading stage 

and have had significant success 

interrogating polycrystalline aggregates 

for distributions of lattice strain and 

stress 1,2 . Since that time, we have 

moved farther downscale to probe 

individual crystals within an aggregate 

at the Advanced Photon Source (APS). 

This paper describes our experiment 

developed at A2 designed to measure 

lattice strain distributions within a 

loaded polycrystalline aggregate. By 

determining the lattice strain tensor 

at each orientation, we are able to use 

Hooke’s law to calculate the orientationaveraged 

stress tensor distribution. 

Coupled with crystal-based simulations, 

these data have proven invaluable 

for improving our understanding 

of deformation partitioning in 

polycrystalline alloys. The second type 

of experiment, in which the deformation 

of individual crystals within the 

aggregate is tracked, is part of the High 

Energy Diffraction Microscopy (HEDM) 

suite of experiments at beamline 1-IDC 

at the APS. When full spatial resolution 

is attained, the HEDM experiment will 

likely become the “gold standard” for 

microscale stress measurements. 

Stress State Distributions in 

Loaded Polycrystals 

In this "powder" experiment , we 

interrogate an entire polycrystalline 

aggregate simultaneously. As with 

traditional mechanical tests, each 

continuum point within the sample 

is identical. Each diffraction volume 

that defines a continuum point must 

contain a statistically relevant number of 

grains - usually several thousand. In this 

way, we are not restricted to tracking 

a particular set of crystals during the 

in situ deformation. This condition is 

crucial for this experiment and dictates 

the grain size / beam size relationship. 

We acquire bands of diffraction data for 

each family of lattice planes, {hkl}, by 

rotating the loadframe using its builtin 

goniometer 3 . At A2 we typically use 

a beam of 50 KeV x-rays with 0.5mm x 

0.5mm slits. A set of lattice Strain Pole 

Figures (SPFs) are measured at discrete 

loads; then the lattice strain distribution 

tensor, є(R), at each lattice orientation, 

R, is determined 4 . Lattice strains are 

elastic so the stress distribution is 

calculated using Hooke’s law, σ(R) = 

C(R)є(R), where C are the single crystal 

moduli. We know that orientation as 

well as crystallographic neighborhood 

contribute to the mechanical response of 

an individual crystal within an aggregate. 

Therefore σ(R) has the interpretation of 

being the most likely state of stress at a 

particular orientation. The σ(R) data are 

ideal for use with a crystal-based modeling 

framework, such as an elastic-plastic finite 

element formulation, for understanding 

the distribution of deformation within 

the aggregate. One way to evaluate the 

distribution of each stress component over 

orientation space - both measured and 

computed - is by an expansion of spherical 

∞ 

harmonic functions, σij(R) = Ʃ H l T l (R). 

l=0 

Here the T l (R) are generalized spherical 

harmonics functions (modes) that satisfy 

relevant symmetry conditions and form 

an orthonormal basis over orientation 

space. The coefficients, H l , prescribe the 

contribution of each mode to the stress. 

Fig. 1 depicts two spherical harmonic 

modes plotted over orientation space. 

Fig. 1 also depicts the spherical harmonics 

coefficients for the shear stress, σ xy , over 

orientation space from a polycrystalline 

copper sample loaded in tension to a 

macroscopic stress of S zz = 180 MPa. Based 

upon the coefficients, we see that both the 

experiment and simulation have “chosen” 

mode 7 as the dominant mode. Even 

though this component of stress must 

necessarily integrate to zero over the cross 

section to match the boundary conditions 

of the experiment, shear stress values as 

large as 75-80 MPa are present. The close 

comparison between the simulation and 

experiment creates confidence in both, 

and builds additional trust in the model 

as it is applied beyond the reach of the 

experiments. Similar comparison was made 

(a) mode 3 (b) mode7 (c) σ xy 

Fig. 1: (Left and Center)Two spherical harmonic modes shown distributed over the cubic fundament region of orientation space parameterized using the 

Rodrigues representation of orientation. The surface of the region along with orthogonal slices through the origin are depicted. (Right) Spherical Harmonics 

(SH) coefficients vs. mode number for the shear stress component, σ xy as determined from the experimental data (EXP) and computed from the crystalbased 

finite element simulations (SIM) at a uniaxial stress of S zz = 180 MPa. Three finite element mesh sizes for the virtual test specimen were employed, 

1,098, 2,916 and 10,976 crystals. Each crystal contained 48 finite elements. 


for other components of stress 5 . From 

these experiments and simulations, 

we learned that the microscale stress 

state can be very different than the 

macroscopically applied stress. There 

are many situations (such as fatigue) 

when an assumption of uniaxial stress 

is nonconservative. These data enable 

us to implement the finite element 

modeling formulation with greater 

confidence. 

Individual Crystal Experiments 

The stress distribution data from the 

in situ SPF experiments described 

in the previous section provide an 

orientation dependent, statistically 

relevant approximation of the 

micromechanical partitioning of the 

elastic-plastic deformation over a 

polycrystalline aggregate. As described 

above, the stress distribution data 

are an excellent match for the current 

generation of crystal based simulation 

formulations. In reality, the response 

of each crystal within the aggregate 

is a function of both its orientation 

and the surrounding crystals that 

supply the boundary conditions for 

its deformation. Measurement of the 

stress state within individual crystals 

will enable us to eventually quantify the 

neighborhood effect. The 3DXRD suite 

of interrogation experiments were first 

developed by Risoe researchers at the 

European Synchrotron Radiation Facility 

(ESRF) 6 . One of the 3DXRD capabilities 

made it possible to measure lattice 

strains within an individual crystal 

within a loaded aggregate 7 . Our group 

has collaborated with APS sector 1 

personnel to further develop this in situ 

lattice strain measurement capability 

as a part of the beamline 1-IDC suite 

of experiments called High Energy 

Diffraction Microscopy (HEDM). Fig. 2 

depicts a configuration for conducting 

two HEDM experiments: individual 

crystal lattice strain measurements 

for understanding crystal stress states 

and high resolution interrogation of 

individual reflections within the crystal 

to understand deformation-induced 

dislocation substructure formation 8 . 

Titanium Alloys 

With their high strength to density 

ratio and excellent corrosion resistance 

and temperature range, titanium 

alloys have enabled some of the most 

important aircraft design innovations 

over the past several decades 9 . Single crystal property anisotropies make processing of 

titanium alloys difficult and create challenging design conditions, however. Our group 

has conducted a number of studies on titanium. Fig. 2 also depicts the macroscopic 

stress strain curves for experiments on an α phase (hcp) Ti-7Al alloy in two states. The 

slow cooling rate that the AC (Air Cooled) material experiences from α / ß transus 

temperature produces an ordering of the titanium and aluminum atoms over short 

length scales. Dislocation glide within this Short Range Order (SRO) material results in 

planar slip and increased strain hardening and greatly affects the room temperature 

creep behavior of Ti-7Al 10 . When the Ti-7 was quenched quickly in the IWQ (Ice Water 

Quenched) state, the SRO does not form and the slip is more isotropic. We conducted 

HEDM experiments - lattice strain measurements and high resolution reflection 

decomposition - on samples from both material states. The stress strain curves shown 

in Fig. 2 also depict the macroscopic stress levels where diffraction experiments were 

conducted. We tracked the deformation of several grains in each specimen but only 

collected high resolution data on one each. While identical orientations would have 

been preferred, we chose the subject grains based mostly on the number of clear 

reflections we were able to capture. The angles between the c axis and the loading 

axis in the IWQ and AC grains was 28.7°and 81.0°, respectively. Monochromatic 52 KeV 

x-rays were employed with a beam size of 300 μm x 150 μm (horizontal x vertical) for 

detector A and 100 μm x 100 μm for detector B. Additional experimental details can be 

found in 11 . 

Fig. 2: (Left) HEDM setup at APS beamline 1-IDC. Different detectors were used for the lattice strain 

measurements and for the high resolution experiments. Each experiment requires a rotation of Φ about 

the y axis to interrogate relevant scattering vectors. Detector A (approximately 1m from the sample) 

captures many discrete diffraction spots from multiple {hkl}s and the lattice strains are used to determine 

the full lattice strain tensor for the grain. A single reflection is captured on detector B - very high resolution 

is possible. The B detector is approximately 8m from the sample. The x', y', z' laboratory and q x', q y', q z' 

reciprocal space coordinate systems are indicated. The y' axis coincides with the sample y direction, 

the sample x and z directions rotate with Φ. The insert indicates diffraction from a selected bulk grain. 

(Right) Macroscopic stress-strain response for the AC and IWQ Ti-7Al samples during the in situ loading 

experiment. The symbols indicate stress levels where diffraction experiments were conducted. 

Stress State Evolution 

Fig. 3 depicts the evolution of the three dimensional stress state within the AC and 

IWQ grains. Each grain begins with a stress state that very nearly matches the applied 

uniaxial state. As the load increases and the grains yield, the stress states change. 

The largest change in each grain’s stress state occurs between points 2 and 3, when 

fully developed plasticity occurs. The stress states become multiaxial - which is very 

interesting from an elastic-plastic deformation perspective and validates, at least 

in a qualitative manner, the trends that we observed in the aggregate experiments 

described above. The direction associated with the largest principal stress is near 

the macroscopic loading direction, but the other two principal components are not 

zero, which they would be for a uniaxial stress state. Each specimen was unloaded to 

400 MPa, which corresponds to the first stress level. The residual stress state in each 

grain can be understood by comparing 400el values to 400un values. Even “simple” 

macroscopic loading conditions like uniaxial tension can produce complex, threedimensional 

residual stress states on the crystal scale that evolve with straining. Since 

most residual stress measurement capabilities require an assumption of stress state 12 , 

this indicates a real need for a more sophisticated measurement capability. Processinginduced 

residual stresses are a huge issue in titanium parts used in aerospace 


applications. For instance, it is nearly impossible to predict the fatigue life of a titanium part that contains significant residual 

stresses. 

Resolved Shear Stress 

Dislocation glide (yielding on the crystal scale) occurs when the shear stress on one or more of the slip systems (slip plane + slip 

direction) reaches a critical value. One of the primary hcp slip systems is the basal, {0001} 〈1120〉. 

− 

Calculation of the resolved shear 

stress, τ , involves projecting the stress state onto the slip plane in the slip direction. The typical approach is to assume uniaxial 

tension as the macroscopic stress state. We have measured the full stress tensor so we do not need to assume a uniaxial stress 

state. To understand the possible error that might arise with a uniaxial assumption, we calculated τ in the AC grain two ways. First 

we employ the usual approach: project the macroscopic stress, S yy , onto the slip system. Then we calculate τ using the entire stress 

tensor. The results are depicted in Fig. 3. The biggest difference is seen between 595 MPa and 630 MPa where fully developed 

plasticity ensues and the stress state jacks in Fig. 3 are seen to rotate. We actually see a drop in τ between 595 MPa and 630 MPa for 

two of the three slip systems, even though the macroscopic stress increases by 35 MPa. This seemingly inconsistent result arises 

due to the topology of the single crystal yield surface. Metallic crystals are restricted to plastic straining only on the prescribed slip 

systems. To accommodate a general plastic strain rate, therefore, it has been hypothesized that the crystal stress state will actually 

rotate to activate more slip systems 13,14 . Certainly this evolution can involve a decrease in the value of stress projected onto a slip 

system. The decrease seen in Fig. 3 is entirely consistent with this rotation of the stress state. To our knowledge, this is the first 

measurement of the yield surface-induced stress rotation for a crystal embedded within a polycrystalline aggregate. The rotation 

of the stress state should not be confused with the crystal rotation, which is discussed in the next section. 

Fig. 3: (Left)Principal axis triads or 

”jacks” depicting the orientation 

of the principal stress state at the 

four indicated macroscopic stress 

levels (in MPa) for the IWQ (top) 

and AC (bottom) specimen. The 

legs of the jacks correspond to 

the principal directions relative to 

the specimen Loading Direction 

(LD), Transverse Direction (TD) 

and Normal Direction (ND). The 

colors of each leg and accompanying color scale indicate the principal value. (Right) Resolved shear stress, τ for the 3 basal slip systems of the AC grain as a 

function of the applied load. The box symbols were calculated assuming a uniaxial stress and the macroscopic stress value. The X symbols were calculated 

using the full stress tensors shown in the figure on the left. 

High Resolution Reflection Decomposition 

We hypothesized that the SRO-induced differences between AC and IWQ would be visible in the high resolution data. Using 

detector B, we analyzed individual reflections (spots) associated with the AC and IWQ grains. Basically this study is an extension of 

traditional peak broadening analysis. The detailed geometric information that can be obtained with high brilliance synchrotron 

radiation and large sample to detector distances however, enable increased understanding of the deformation-induced 

dislocation substructure formation that occurs within metallic crystals. 

Fig. 4 depicts reciprocal space representations of intensity and lattice strain distribution for individual reflections in the AC 

and IWQ grains. Fig. 4(a) are intensity maps. An interesting feature of the AC map is the extended “tail” which is consistent with 

inhomogeneous grain rotation. The intensities integrated over the peak and tail region are roughly the same; hence, the volumes 

are similar 15 . This would indicate significant dislocation structure formation, which is consistent with TEM micrographs of the 

material 11 . The intensity distribution for the IWQ reflection is consistent with relatively small grain rotation and homogeneous 

deformation and distribution of dislocations. Fig. 4(b) depicts the “centroid” of the axial distributions, q y' . The centroid values 

represent the lattice strain in the direction of q y' averaged over the orientation fiber specified by the q x' and q z' coordinates. There 

is a broader spread in centroid over the AC grain than the IWQ grain. Fig. 4(c) depicts intensity vs. q y' for the maximal values in the 

centroid maps and the peak intensity point from the azimuthal map. The multiple peaks (black, red and blue) in the AC data are 

consistent with heterogeneous straining within the grain. From the profiles, the IWQ grain appears to be deforming uniformly. 

Additional data from multiple diffraction peaks would be necessary to quantify the exact distribution of orientations within the 

grain - an intragrain Orientation Distribution Function, but the information from the reflections shown here is consistent with 

the hypothesis regarding short range order and planar slip. From the TEM analysis, we determined that the dislocation density 

in the AC grain was comparable to that in the IWQ 11 . We used the IWQ integrated profile (green curve) and the restricted random 

dislocation model developed by Wilkins 16 to confirm the dislocation density. However, an estimate of the AC grain dislocation 

density from its integrated peak information would grossly overestimate the dislocation density in the AC grain. The broadening 

in this case comes primarily from the larger structures associated with heterogeneous straining within the grain. 


Fig. 4: Reciprocal space maps 

and intensity profiles for 

individual reflections from the 

AC and IWQ crystal. (a) Azimuthal 

map of diffracted intensity in 

reciprocal space. The reciprocal 

space coordinates are depicted in 

Fig. 2. The dashed lines and Miller 

indices indicate the directions of 

the smallest and largest widths 

at half maximum. (b) Azimuthal 

map of the centroid of the q y' 

(d −1 ) distribution. (c) Normalized 

intensity vs. q y' for points 1 and 2 

in (b) and for the peak intensity 

value in (a). 

A: AC (1212) 

− − B: IWQ (0220) 

− 

Summary and Future Directions 

Motivated by traditional mechanical 

tests, we have conducted experiments 

that combine mechanical loading 

with synchrotron x-ray diffraction 

to understand the micromechanical 

response of metallic alloys. 

• The aggregate-based experiments 

that we developed at CHESS A2 have 

become our standard mechanical 

test. We have characterized copper, 

titanium, aluminum and nickel 

alloys. In addition to building a more 

complete understanding of our error 

bars and resolution, we are continuing 

to develop data reduction schemes 

that have greatly streamlined the SPF 

experiments and made them more 

user friendly. In general, any success we 

have enjoyed with these experiments 

is due in large part to the environment 

of encouragement that exists at CHESS 

and the excellent working relationship 

we have with CHESS personnel. Our 

graduation to other techniques and 

facilities has come about by the 

confidence we have gained from our 

CHESS experience. 

• In addition to understanding elasticplastic 

deformation behavior within a 

polycrystalline aggregate, we foresee the 

combined suite of distribution-based 

SPF diffraction experiments and crystalbased 

micromechanical representations 

as a way to understand residual stresses in 

a way that has never been done. Residual 

stress plays a major role in the processing 

and performance of wrought metallic 

alloys. As demonstrated in this paper, 

the state of stress within an aggregate is 

a function of macroscopic loading and 

microscopic mechanical properties. In 

order to accurately quantify and predict 

a residual stress state, one must have 

a way for accounting for both. Our 

experiments and simulations represent a 

potential framework capable of such an 

accounting. 

• In addition to monotonic loading, 

we conduct cyclic experiments - 

determining SPFs after a certain number 

of cycles. In collaboration with Peter 

Revesz at CHESS, we have also developed 

an experiment for measuring lattice 

strains in real time using a custom built 

x-ray shutter system 17 . 

• The potential of the HEDM experiments 

is enormous. We are currently working 

with other 1-IDC users to transform the 

experimental suite from “heroic efforts”, 

capable of measuring the response of 

a handful of grains, to methodologies, 

capable of characterizing large 

polycrystalline aggregates of grains. 

Creating robust data acquisition and 

reduction software is at the heart of 

this effort. Plans include combining the 

lattice strain measurements described 

above with grain reconstruction 

experiments 18 to characterize spatially 

resolved stress fields over a statistically 

relevant number of grains. Again, the 

exciting part of this plan is combining 

such datasets with micromechanical 

modeling formulations. 

Acknowledgments 

The results presented here form parts 

of the Ph.D. dissertation research of Dr. 

Joel V. Bernier and Dr. Jun-Sang Park. 

Other members of the group include 

Ph.D. students Jay C. Schuren and Kevin 

P. McNelis and post-doctoral associate Dr. 

Christos Efstathiou. The simulations were 

conducted by Professors Paul Dawson of 


Cornell and Tong Han of Yonsei, Korea. The collaborations with beamline scientists Dr. Alexander Kazimirov (CHESS) and Dr. Ulrich 

Lienert (APS) were crucial to this research. Our external collaborators on the Ti-7Al experiments were Professor Michael Mills of 

The Ohio State University and Dr. Matthew Brandes of the Naval Research Laboratory. The research has been supported financially 

by the Air Force Office of Scientific Research, #F49620-02-1-0047, the National Science Foundation, grant #CMS0301615 and the 

Office of Naval Research, grant # N00014-05-1-0505. 

References 

1. M.P. Miller, J.V. Bernier, J.-S. Park, and A. Kazimirov; "Lattice Strain Pole Figure Measurements using Synchrotron X-rays", CHESS 

News Magazine, pages 44–47 (2005) 

2. M.P. Miller, J.V. Bernier, J.-S. Park, and A. Kazimirov; "Experimental Measurement of Lattice Strain Pole Figures using Synchrotron 

X-rays", Review of Scientific Instruments 76:113903 (2005) 

3. J.C. Schuren, S. Watts, J.-S. Park, and M.P. Miller; "A System for Measuring Crystal Level Stresses in Deforming Polycrystals", In 

Proceedings of the 2007 SEM Annual Conference and Exposition on Experimental and Applied Mechanics, sec. 82 p4, Bethel, 

Connecticut, Society for Experimental Mechanics, Inc. (2007) 

4. J.V. Bernier and M.P. Miller; "A Direct Method for the Determination of the Mean Orientation Dependent Elastic Strains and Stresses 

in Polycrystalline Alloys from Strain Pole Figures", Journal of Applied Crystallography, 39:358–368 (2006) 

5. M.P. Miller, J.-S. Park, P.R. Dawson, and T.-S. Han; "Measuring and Modeling Distributions of Stress State in Deforming Polycrystals", 

Acta Materialia, 56:3827–3939 (2008) 

6. H. Poulsen; "Three-Dimensional X-Ray Diffraction Microscopy", Springer, Heidelberg, U.K. (2004) 

7. L. Margulies, H.F. Poulsen T. Lorentzen, and T. Leffers; "Strain Tensor Development in a Single Grain in the Bulk of a Polycrystal 

Under Loading", Acta Materialia, 50(7):1771–1779 (2002) 

8. B. Jacobsen, H.F. Poulsen, U. Lienert, J. Almer, S.D. Shastri., H.O. Sorensen, C Gundlach, and W. Pantleon; "Formation and 

Subdivision of Deformation Structures During Plastic Deformation", Science, 312:889–912 (2006) 

9. G. Lutjering and J. Williams; "Titanium (Engineering Materials and Processes)", Springer Verlag, Berlin (2003) 

10. T. Neeraj and M.J. Mills; "Short-Range Order (sro) and Its Effect on the Primary Creep Behavior of a ti – 6wt", Materials Science and 

Engineering A, A319-321:415–419 (2001) 

11. U. Lienert, M. Brandes, J.V. Bernier, J. Weiss, S. Shastri, M.J. Mills, and M.P. Miller; "In-situ Single Grain Peak Profile Measurements 

on ti-7al During Tensile Deformation", Materials Science A, In press (2009) 

12. Society of Experimental Mechanics. Handbook of Measurement of Residual Stresses. Fairmont Press, Lilburn, Georgia, USA 

(1996) 

13. U.F. Kocks; "The Relation Between Polycrystal Deformation and Single Crystal Deformation", Metallurgical Transactions, 

1:1121–1143 (1970) 

14. H.R. Ritz, P.R. Dawson, and T. Marin; "Analyzing the Orientation Dependence of Stresses in Polycrystals using Vertices of the Single 

Crystal Yield Surface", Journal of the Mechanics and Physics of Solids, page In Review (2009) 

15. B.D. Cullity; "Elements of X-Ray Diffraction", Addison-Wesley, Reading, MA, 2nd edition (1978) 

16. M. Wilkins; "The Determination of Density and Distribution of Dislocations in Deformed Single Crystals from Broadened X-ray 

Diffraction", Physical Status Solidi (A), 2:359–370 (1970) 

17. J.-S. Park, P. Revesz, A. Kazimirov, and M.P. Miller; "A Methodology for Measuring in situ Lattice Strain of Bulk Polycrystalline 

Material under Cyclic Load", Review of Scientific Instruments, 78:023910 (2007) 

18. R.M. Suter, C.M. Heffernan, S.F. Li, D. Hennessy, and C. Xiao; "Probing Microstructure Dynamics with X-ray Diffraction 

Microscopy", Journal of Engineering Materials and Technology, 130:021007 (2008) 


Alteration of Citrine Structure by Hydrostatic Pressure 

Sol M. Gruner 1,2,3 , Buz Barstow 1 , Nozomi Ando 2 , and Chae Un Kim 2,3 

1 


2 

Department of Physics, Cornell University 

3 


In 1914 Percy Bridgman, the Nobel 

prize winning father of high pressure 

physics, squeezed hen egg white at high 

pressure and found that it coagulated, 

as though it had been hard-boiled 1 . He 

had discovered that proteins denature 

under pressure, resulting in a coagulated 

state reminiscent of what happens when 

proteins are thermally denatured. Since 

Bridgman’s pioneering observation 

many hundreds of papers have reported 

on the effects of high pressures on 

biomolecular systems: Proteins unfold, 

enzymatic rates change, multimeric 

assemblies have greatly altered 

stabilities, viral infectivities are greatly 

different, etc. Frequently, the changes 

are of very large magnitude and occur at 

pressures encountered in the biosphere. 

Yet proteins are very incompressible, 

typically 10 times stiffer than water, 

so the actual change in volume is 

very small, even at a few thousand 

atmospheres pressure. What are the 

mechanisms of the pressure effects 

What do these mechanisms teach us 

about protein function 

Little is known about structural changes 

in proteins in response to pressure and 

the way the resultant changes affect 

function. The main reason for this 

lack of understanding is that very few 

protein structures have been solved as 

a function of pressure. Another reason 

is a cultural bias that pressure effects 

are esoteric and have little relevance to 

understanding proteins. This thinking is 

misguided for two reasons: First, there 

are significant pressure effects observed 

in the biosphere. For example, certain 

essential enzymatic processes adapted 

for deep sea life fail at atmospheric 

pressure, and vice versa. Second, 

pressure is another thermodynamic 

“knob” that can be turned by the 

experimenter to gain insight about 

protein function. Put another way, the 

free energy that governs molecular 

reactions is related to d(PV – TS), where P 

is pressure, V is volume, T is temperature 

and S is the entropy. In many protein systems, a change in pressure of a thousand 

atmospheres is comparable in magnitude to a change of many tens of degrees in 

temperature. 

In recent years we have developed methods of data acquisition and analysis 

to perform protein crystallography at pressures ranging to several thousand 

atmospheres in order to study pressure-induced structural changes 2,3,4 . The studies 

have provided a wealth of information on phenomena, including pressure-induced 

protein unfolding 5 , water penetration into proteins 4,6 , and conformational changes 

that affect function 2,7 . A general theme that emerges is that pressure induces a host 

of structural displacements at the level of a few tenths of an angstrom. Although 

these displacements are well below typical resolution limits for observation of single 

atoms in proteins, they are readily observed for collections of protein residues and 

secondary structures by observing changes in the center of mass of the protein parts. 

This should not be surprising – recall that changes in displacements of atomic force 

microscope cantilevers are routinely observed at the fraction of an angstrom level, 

even though the resolution of the visible light optical systems involved is only a few 

tenths of a micron. 

Why are these small changes significant Most enzymatic reactions involve 

conformational changes of only a few tenths of an angstrom at active sites. Therefore, 

changes of this magnitude can distort active sites resulting in big effects on reaction 

rates. Observation of the structural changes and consequent effects on reaction 

rates provides important insight on the detailed structural requirements of enzyme 

reactive sites. 

A recent study at CHESS used high pressure crystallography to understand the 

pressure sensitivity of fluorescence in the protein Citrine 7 . Citrine is a modified 

green fluorescent protein (GFP) whose peak fluorescent wavelength is known to 

shift with pressure. All proteins in the GFP family have a β-barrel structure with a 

fluorescent chromophore at the center, formed by the autocatalytic fusion of three 

amino acid residues (Fig. 1). In Citrine, an additional tyrosine ring is stacked upon 

the chromophore. The fluorescence peak of Enhanced GFP (MEGFP) is not pressure 

dependent to at least a few thousand atmospheres (Fig. 2) (wild type GFP does 

Fig. 1: Ribbon diagram of 

Citrine showing the residues 

that make up the chromophore 

in the core of the protein 7 . 

Fig. 2: Change of the peak fluorescent 

wavelength with pressure for Citrine (red 

squares) and a modified GFP (blue diamonds) 7 . 


display pressure sensitive behavior, for 

reasons that are related to the reduction 

in fluorescence intensity of Citrine rather 

than the shift in fluorescence peak). 

Basic quantum chemistry suggests that 

the peak fluorescent wavelength of a 

stacked aromatic system would be very 

sensitive to the detailed coupling, e.g., 

the relative positions of the π-bonds 

of the aromatic rings. Since GFP has a 

single aromatic chromophore, it would 

be relatively insensitive to movements 

of the chromophore with pressure. On 

the other hand, Citrine, with a stacked 

aromatic chromophore, would be very 

sensitive to small displacements of one 

aromatic ring relative to the other. Our 

study sought to observe if there is a 

relative displacement of the expected 

magnitude with pressure. If so, this may 

be taken as generally analogous for 

what happens in active sites in enzymes. 

That is to say, comparable distortions 

of active sites can be expected to alter 

reaction rates, thereby explaining in a 

general way why enzymes are pressure 

sensitive. 

The relative motions versus pressure 

of the two aromatic rings are shown 

in Fig. 3. What gives rise to these 

displacements The two aromatic rings 

that make up Citrine’s chromophore 

are connected to very different parts 

of the single polypeptide chain from 

which Citrine is folded. One of the rings 

hangs off the inside of the β-barrel 

while the other is in another part of the 

polypeptide chain that threads through 

the axis of the barrel. Thus, distortions 

of the overall structure are sensitively 

coupled to relative displacements 

between the stacked rings. Specifically, 

the residues that make up Citrine can 

be grouped into two clusters. Cluster 

1 makes up one side of the barrel 

and Cluster 2 includes the threading 

polypeptide chain. A careful analysis of 

the changes in overall Citrine structure 

with pressure shows that Cluster 1 

contracts, resulting in a bending motion 

relative to residues of Cluster 2. The 

relative motions of the two clusters 

result in relative motions of the two 

rings. 

This study illustrates how collective 

distortions of the overall structure of a 

protein are conveyed to critical parts of 

the structure necessary for “function”, 

“function” in this case being peak 

fluorescent wavelength. Citrine was 

chosen for this study because there 

is good fundamental understanding 

of how distortions of the stacked 

aromatic rings should affect the peak 

fluorescence. In enzymes, however, 

the detailed structural requirements 

of active sites are frequently less 

well understood. The Citrine study 

also suggests how pressure studies 

on proteins may guide mutagenic 

engineering to optimize enzymatic 

function. Given the observed distortions 

of the chromophore required to achieve 

a given peak fluorescence shift, can 

these be used to guide programmed 

mutations to generate the shift at 

room pressure The study suggests 

that insertion of smaller residues in 

the barrel side of Cluster 1 might 

result in the same kind of contraction 

needed to mimic the shift seen at 

high pressure. This experiment has yet 

to be performed, but it suggests an 

overall strategy to optimize enzymes 7 : 

As noted earlier, many enzymes have 

pressure-dependent catalytic rates. The 

strategy would involve observation of 

the structural changes that result in 

increased activity with pressure. Once 

these are identified, one would attempt 

Fig. 3: Movement of one part of the chromophore relative to the other with pressure 7 . 

to perform targeted mutagenesis to 

mimic the structural deformations. 

The Citrine study has shown that 

the pressure-dependence of protein 

function can be understood in 

terms of straightforward collective 

displacements of protein structure. 

Prediction of the exact conformational 

changes that occur is beyond 

the present state-of-the-art, but 

experimental observation of the 

changes has been demonstrated. 

In the future these may be used to 

engineer protein activity. 

References: 

1. P.W. Bridgman; “The Coagulation 

of Albumen by Pressure”, Journal 

of Biological Chemistry, 19(4): p. 

511-512 (1914) 

2. P. Urayama, G.N. Phillips Jr, and S.M. 

Gruner; “Probing Substates in Sperm 

Whale Myoglobin Using High-pressure 

Crystallography”, Structure 10: p. 

51-60 (2002) 

3. C.U. Kim, and S.M. Gruner; “High 

Pressure Cooling of Protein Crystals 

without Cryoprotectants”, Acta Cryst. 

D61: 881-890 (2005) 

4. M.D. Collins, M.L. Quillin, G. Hummer, 

B.W. Matthews, and S.M. Gruner; 

“Structural Rigidity of a Large Cavitycontaining 

Protein Revealed by Highpressure 

Crystallography”, J. Mol. Biol. 

367: p. 752-763 (2007) 

5. N. Ando, B. Barstow, W.A. Baase, 

A. Fields, B.W. Matthews, and 

S.M. Gruner; “Structural and 

Thermodynamic Characterization 

of T4 lysozyme Mutants and The 

Contribution of Internal Cavities to 

Pressure Denaturation”, Biochemistry 

47(42): p. 11097-11109 (2008) 

6. M.D. Collins, G. Hummer, M.L. 

Quillin, B.W. Matthews, and S.M. 

Gruner; “Cooperative Water Filling of 

a Nonpolar Protein Cavity Observed 

by High-pressure Crystallography 

and Simulation”, PNAS 102(45): p. 

16668-16671 (2005) 

7. B. Barstow, N. Ando, C.U. Kim, and 

S.M. Gruner; “Alteration of Citrine 

Structure by Hydrostatic Pressure 

Explains the Accompanying Spectral 

Shift”, Proc. Natl. Acad. Sci. USA 105: 

p. 13362-13366 (2008) 


Putting Color into Surface Diffraction 

Detlef-M. Smilgies 


Surface X-Ray Diffraction (SXRD), also called Grazing-Incidence Diffraction (GID) is a well-established powerful tool for structure 

determination of surfaces 1,2 , monolayers 3 , and thin films 4,5 . Moreover, surface phase transitions 1,2 and time-dependent effects, such 

as growth kinetics 6 , have been studied in depth with this method. However, SXRD/GID also acquired a reputation of being highly 

esoteric with very refined representations of scattering data in unusual units. 

Since molecular thin films have come into focus, be it for organic electronics device-grade films, self-organized functional 

coatings, or biophysical membranes, this spartan picture has begun to change. While in close-to-perfect inorganic structures all 

information is contained along the diffuse scattering rods perpendicular to the substrate surface, soft materials inherently have 

a larger amount of disorder. Hence, rather than just scanning the rods, now full reciprocal space maps (RSM) have become of 

interest, in order to determine structure and distinguish different types of disorder at the same time. Along with the reciprocal 

space maps has come the color. 

While we originally started out working in the conventional 

way of characterizing molecular films by hunting for molecular 

Bragg reflections along the symmetry directions of the 

substrate 4 , it soon became apparent that this was not the most 

efficient route to find all sufficiently strong film reflections, in 

order to collect as much structural information as obtainable. 

Moreover molecular films are often characterized by lowsymmetry 

lattices such as monoclinic and triclinic, which 

complicates this search even more. 

Hence we started combining the linear detection scheme 

from liquid surface diffraction 3 with the oscillation method 

from protein crystallography. The oscillation range could 

be set either narrow for proper integration of all reflections 

along a single scattering rod 7 or wide enough to cover the full 

irreducible range of rotation as given by substrate symmetry 8 . 

The latter “survey scans” provided the desired efficient method 

to identify all strong film reflections. In combination with 

azimuth scans around the surface normal at specific q-values 

to measure the scattering rods, all available information can be 

efficiently collected. We called our method GI-RSM 7 . 

GI-RSM proved to be also an effective method for uniaxial 

powders. These are organic thin films that are grown on 

amorphous substrates such as native or thermal oxides of 

silicon wafers, glass, or indium-tin oxide (ITO) coatings. In such 

cases there often is a well-defined orientation of the molecular 

layers with respect to the surface, however, crystallites are 

oriented at random in the surface 

plane. The Bragg condition is met 

easily, where the ring-like Bragg 

reflections oriented parallel to 

the surface intercept the Ewald 

sphere. Hence 2D powders in 

grazing incidence geometry 

produce discrete spots in the 

scattering images, and the 

overlap problem of conventional 

powder diffraction is much 

reduced. The resulting diffraction 

patterns closely resemble fiber 

diffraction patterns. 

Fig. 1: Radial scan with 

oscillation along the [110] 

high-symmetry plane of 

the KCl substrate (top) and 

azimuth scan revealing the 

fine structure of the (11L) rod 

(bottom). The boomerangshaped 

BP1T molecule 

containing both phenyl and 

thiophene rings and related 

molecules can be used 

in organic light-emitting 

devices covering the color 

range from red to blue 7 . 

Fig. 2: First incarnation of 

the GI-RSM set-up at G2, still 

using the horizontal four-circle 

diffractometer 7 . After upgrading 

the instrument to a six-axis 

psi-circle diffractometer 9 the 

detector arm can now also 

scan in the vertical direction 

extending the access to 

higher exit angles β, which 

was previously limited by the 

aperture of the linear detector. 


A first success for the Resel group was collecting 

enough information from a pentacene film to 

compare the structure of the thin film phase 

predicted by first principles methods with 

these low-resolution diffraction data 10 . By 

now we have refined data collection further 

with the new kappa diffractometer 9 so that 

angular ranges of up to 60° in Ψ and 50 ° in β 

can be collected by merging several 6-8° strips, 

collected with the linear detector 11 , at a time. 

An even more subtle kind of organization was 

found for Ru-bpy molecules deposited onto 

ITO in device-like samples. Ru bpy, a Ru ++ - 

bipyridine 3 

complex with two PF - counterions, 

is known as an ionic conductor which produces 

efficient red light emission in organic lightemitting 

devices (OLED). In previous work it had 

been concluded that such Ru-bpy films were 

amorphous, as no discernable scattering was 

obtained with lab-based x-ray generators. 

Using GI-RSM we found subtle broad ring-like 

scattering features, after we optimized the 

scattering geometry to suppress scattering 

from the substrate. We could correlate the 

weak powder rings with a known crystalline 

structure and concluded that Ru-bpy forms 

nanoscale domains of only a couple of lattice 

constants in diameter. In addition we traced 

back our observation, that occasionally films 

featured higher order, to water contamination 

in the glove box. This first proof of GI-RSM 

being able to reveal the medium range order 

in a nominally amorphous organic film was 

recognized in an inside cover of Journal of 

Materials Chemistry 12 and Daniel Blasini was 

awarded the CHESS Thesis Prize for this work 

and his other results at G2 station 13 . 


Fig. 3: GI-RSM of 

thermally grown 

pentacene on 

a silicon wafer. 

This data set was 

used in Nabok et 

al. 10 to identify 

the structure of 

the pentacene 

thin film phase 

in comparison 

to first principles 

calculations. 

Fig. 4: Ru-bpy 

based-light 

emitting device 

and Ru bpy 

molecule depicted 

on top of the 

scattering map 

obtained at G2 12 . 

Molecular monolayers are the ultimate 

challenge in surface diffraction. The Allara 

group at Penn State has developed a wetchemistry 

procedure of preparing thiol 

monolayers on GaAs surfaces. In Fouriertransform 

infrared (FTIR) spectra the thiols 

appeared well aligned, so the question was, 

whether these thiols would form well-ordered 

monolayers, as known for thiols on gold 14 . 

Christine McGuinness’ and coworkers’ paper 

in ACS Nano 15 ended a ten year quest of optimizing and characterizing the order in thiol layers on GaAs(100). It turned out that 

thiols on GaAs(100) only form nanoscale domains, even under the best preparation conditions. These nanoscale domains show 

some preferential alignment along the [100] substrate azimuth, which we ascribed to alignment of thiol crystallites parallel to step 

edges. Moreover, the lattice spacing in the thiol domains shows a subtle variation as a function of the substrate azimuth. This indepth 

study with about 30 samples became the most-cited paper in ACS-Nano in the first year of its introduction. 

As the flux and stability of the beam at G-line has continuously improved, we have been increasingly facing the problem that the 

limited dynamic range of the ORDELA linear gas detector has become the bottleneck that limits the speed of data acquisition, 

since intense peaks need to be rescanned with attenuation. A couple of years ago, we started talking to Peter Siddons at NSLS 

about the possibility of obtaining one of his prototype diode array detectors. In such an advanced detector, each diode element 

samples a comparable solid angle like the corresponding MCA channel of the gas detector. However, as each element has its 

own electronics, it can handle a dynamic range from single photon counting to a couple of 10 5 counts/sec, while the gas detector 

shows signs of saturation already at 10 3 counts/sec/channel.

At the time of writing we have just obtained such a high 

performance diode array and it is currently being set up at 

G2 by Abruña student Michael Lowe and G2 scientist Arthur 

Woll. State-of-the-art extended GI-RSMs, such as the one 

shown in Fig. 5, can thus be scanned in future without beam 

attenuation or fear of saturation of the brightest peaks. 

The new detector should help us to overcome many of the 

restrictions imposed by the limited dynamic range of the 

linear gas detector, promising a bright future for the GI-RSM 

system at G2. 

Acknowledgements 

I am indebted to many colleagues and coworkers, first of all 

Daniel Blasini, Cornell Chemistry, who built the reciprocal 

space mapping system at G2 with me. The list continues with 

Hector Abruña, Cornell Chemistry, Christine McGuinness and 

Fig. 5: Extended 

GI-RSM map of a 

pentacene film 

in the thin film 

phase. Several 8° 

strips, obtained 

by offsetting 

the delta arm of 

the G2 kappa 

diffractometer, 

were merged to a 

map spanning 40° 

in each direction of 

the detector arm 11 . 

David Allara, Penn State Chemistry, George Malliaras and 

Aram Amassian, Cornell Materials Science, Roland Resel and his merry men from the Technical University in Graz, Austria, Hisao 

Yanagi at Kobe University, Japan, Ed Kintzel, Jr., now at Western Kentucky University, as well as the other G2 students Dave Nowak, 

Yi Liu, and Aaron Vodnick. In the name of the G2 user community, we are most grateful to Pete Siddons, NSLS, for supplying us 

with a new diode array detector. Finally we thank the CHESS and G-line staff, in particular Arthur Woll and Ernie Fontes, for the 

good working conditions at G2 and all the technical help provided. 

References 

1. R. Feidenhans’l; “Surface Structure Determination by X-ray Diffraction”, Surf. Sci. Rep. 10, 105-188 (1988) 

2. I.K. Robinson, and D.J. Tweet; “Surface X-ray Diffraction”, Rep. Prog. Phys. 55, 599-651 (1992) 

3. J. Als-Nielsen, D. Jacquemain, D. Kjaer, F. Leveiller, and L. Leiserowitz; Phys. Rep. 246, 252 (1994); V. Kaganer, H. Mohwald, and 

P. Dutta; "Structure and Phase Transition in Langmuir Monolayers", Rev. Mod. Phys. 71, 779 (1999) 

4. D.-M. Smilgies, N. Boudet, B. Struth, Y. Yamada, and H. Yanagi; “Highly Oriented POPOP Film Grown on the KCl(001) Surface”, J. 

Cryst. Growth 220, 88-95 (2000); D.-M. Smilgies, N. Boudet, and H. Yanagi; “In-plane Alignment of Para-sexiphenyl Films Grown 

on KCl(001)”, Appl. Surf. Sci. 189, 24-30 (2002) 

5. S. Schiefer, M. Huth, A. Dobinevski, and B. Nickel; “Determination of the Crystal Structure of Substrate-induced Pentacene 

Polymorphs in Fiber Structured Thin Films”, J. Am. Chem. Soc. 129, 10316 (2007) 

6. A.C. Mayer, R. Ruiz, H. Zhou, R.L. Headrick, A. Kazimirov, and G.G. Malliaras; “Growth Dynamics of Pentacene Thin Films: Real-time 

synchrotron x-ray scattering study”, Phys. Rev. B. 73, 205307 (2006) 

7. D.-M. Smilgies, D.R. Blasini, S. Hotta, and H. Yanagi; “Reciprocal Space Mapping and Single-Crystal Scattering Rods”, J. 

Synchrotron Rad. 12, 807–811 (2005) 

8. D.-M. Smilgies, and D.R. Blasini; “Indexation Scheme for Oriented Molecular Thin Films Studied with Grazing-incidence Reciprocalspace 

Mapping”, J. Appl. Cryst. 40, 716-718 (2007) 

9. D.E. Nowak, D.R. Blasini, A.M. Vodnick, B. Blank, M.W. Tate, A. Deyhim, D.-M. Smilgies, H. Abruña, S.M. Gruner, and S.P. Baker; 

“Six-circle Diffractometer with Atmosphere- and Temperature-controlled Sample Stage and Area and Line Detectors for use in the 

G2 Experimental Station at CHESS”, Rev. Sci. Instrum. 77, 113301 (2006) 

10. D. Nabok, P. Puschnig, C. Ambrosch-Draxl, O. Werzer, R. Resel, and D.-M. Smilgies; “Crystal and Electronic Structures of Pentacene 

Thin Film from Grazing-incidence X-ray Diffraction and First-principles Calculations”, Phys. Rev. B. 76, 235322 (2007) 

11. D.-M. Smilgies, A. Amassian, S. Hong, S. Bhargava, J.R. Engstrom, and G.G. Malliaras; unpublished. 

12. D.R. Blasini, J. Rivnay, D.-M. Smilgies, J.D. Slinker, S. Flores-Torres, H.D. Abruña, and G.G. Malliaras; “Observation of Intermediaterange 

Order in a Nominally Amorphous Molecular Semiconductor Film”, J. Mater. Chem. (Hot Commun.) 17, 1458–1461 (2007) 

13. D. Blasini; “Dan’s Big Adventure”, CHESS News Magazine, p. 39 (2005) 

14. P. Fenter, P. Eisenberger, and K.S. Liang; “Chain-length Dependence of the Structures and Phases of Ch3(Ch2)N-1sh Self-assembled 

on Au(111)”, Phys. Rev. Lett. 70, 2447-2450 (1993) 

15. C.L. McGuiness, D. Blasini, J.P. Masejewski, S. Uppili, O.M. Cabarcos, D.-M. Smilgies, and D.L. Allara; “Molecular Self-Assembly at 

Bare Semiconductor Surfaces: Characterization of a Homologous Series of n-Alkanethiolate Monolayers on GaAs(001)”, ACS-Nano 

1, 30–49 (2007) 


Self-Assembled Nano-Checkerboard Thin Films 

Studied by Reciprocal Space Mapping at CHESS 

Sean M. O'Malley 1 , Peter Bonanno 1 , Keun hyuk Ahn 1 , Andrei A. Sirenko 1 , 

Alex Kazimirov 2 , Soon-Yong Park 3 , Yoichi Horibe 3 , and Sang-Wook Cheong 3 

1 

Dept. of Physics, New Jersey Institute of Technology 

2 


3 

Rutgers Center for Emergent Materials and Dept. of Physics and Astronomy, Rutgers University 

Material systems that can self-assemble into nano-structures are of great interest because of their ability to form 

compositionally and spatially distinct regions otherwise unattainable through traditional materials processing techniques 

such as optical or electron beam lithography. The spinel oxide ZnMnGaO 4 

(ZMGO) was recently discovered to undergo a selfassembly 

process during slow annealing of bulk samples 1 . Nano-structure formation in ZMGO occurs during the annealing 

process and is driven by a combination of spinoidal decomposition between Jahn-Teller-active and -inactive ions and spatial 

separation through diffusion processes 1-4 . The bulk ZMGO crystals end up comprising Mn-rich and Mn-poor nanorods 

forming a checkerboard (CB) pattern within the a-b plane that is accompanied by a herringbone (HB) arrangement along the 

c-direction. 

For the purpose of future device fabrication, nano-scale structures should be available in thin-film form, whereby the material 

properties can be enhanced through the overall reduction in volume and by the strain associated with heteroepitaxial 

growth. Our ZMGO thin films were grown using pulsed laser deposition by the research team at Rutgers University Center for 

Emergent Materials 5 . The target material was a homogenous high-temperature quenched form of ZMGO, with a tetragonal 

lattice (a = 0.82 nm, c = 0.87 nm); the substrate was single crystal cubic MgO (0 0 1) with lattice constant a = 0.4212 nm. 

Transmission electron microscopy (TEM) revealed that the films indeed contain an in-plane CB pattern with suppression of 

the out-of-plane HB formation. The typical nanorod dimensions in the epitaxial films increased to 4×4×700 nm 3 compared 

with 4×4×70 nm 3 for the bulk material. Portions of this work have been published in References 5,6 . 

Experiment 

To determine structural parameters and strain-accommodating distortions for the CB 

films we utilized reciprocal space mapping at the A2 x-ray diffraction (XRD) beamline 

of Cornell High Energy Synchrotron Source (CHESS). The incident x-ray beam was 

conditioned using a double-bounce Si (1 1 1) monochromator passing photons with 

an energy of 10.531 keV (λ=1.1775 Å). High angular resolution was achieved by using 

a single-bounce Si (1 1 1) analyzer crystal. Reciprocal space mapping of the ZMGO 

checkerboard structures were measured for several symmetric and asymmetric 

reflections: (0 0 2), (−2 0 2), (−2 −2 2), (0 0 4), (0 4 4), (−2 2 6). The Miller index L 

corresponds to the film growth direction, while H and K represent the in-plane 

parameters of the structure. The integer values of H, K, and L correspond to reciprocal 

lattice points (RLP) of a cubic spinel structure with lattice parameter a S 

= 0.8424 nm 

(i.e., twice the corresponding value for the cubic MgO substrate). 

Results 

Figure 1 depicts a 3-dimensional construct of 

H−K, H−L, and K−L cross sectional maps measured 

around the asymmetric (0 4 4) RLP. The map is 

dominated by several peaks, associated with 

different phases within the CB film. The four broad 

peaks labeled α, ß, γ, and δ correspond to two 

conversely rotated tetragonal (ß and γ) and two 

perpendicularly-oriented orthorhombic (α and 

δ) phases, respectively. The four diagonal peaks 

(ρ, σ, τ, υ) correspond to the structural distortions 

originating from domain boundaries between 

checkerboard phases. The average in-plane 

lattice parameter of the two rotated tetragonal 

phases are lattice-matched to the substrate, i.e. 

the tetragonal phase is elastically strained with 

in-plane lattice constant of a tet 

= 0.841 

nm. These tetragonal phases of the 

ß and γ peaks are rotated by ±2.55° 

around the (0 0 L) reciprocal lattice 

vector. The orthorhombic phases α and 

δ have short and long in-plane lattice 

parameters a otho 

= 0.814 nm and b otho 

= 

0.898 nm, respectively, and are therefore 

inelastically strained. The diffraction 

peak intensities of the structural phases 

were integrated over their volume in 

reciprocal space in order to determine 

the prevalence of each phase within 

the film. The total intensity of the four 

α, ß, γ, and δ peaks is ~6 times that of 

the central tetragonal phase (A). This 

Fig. 1: (a) The H−K, H−L, and K−L cross-sectional 

RSM measured around the asymmetric (0 4 

4) reflection, with L = 4.08. The α and δ peaks 

are orthorhombic phases, while the ß and γ 

peaks are rotated tetragonal phases associated 

with the CB structure. The elastically strained 

tetragonal phase is labeled A. Signal originating 

from domain boundaries, highlighted by the 

radial lines emanating from the central (0 4 

4) RLP, are labeled ρ, σ, τ and υ. The central 

figure is a 3D reconstruction of experimentally 

determined FWHMs of the corresponding peaks. 

Reprinted figure with permission from Reference 

[6]. Copyright (2008) by the American Physical 

Society. (b) TEM image of the CB film on MgO 

substrate. 


atio is consistent with results from TEM 

images, and supports the assumption 

that this central peak A originates from 

the elastically strained transition layer 

between the CB layer and MgO substrate. 

Discussion 

The CB epilayer therefore contains four 

structurally different spinel phases: two 

conversely rotated tetragonal (Mnpoor, 

JT inactive) and two orthogonally 

oriented orthorhombic (Mn-rich, JTactive) 

phases. Each of the 4×4×750 

nm 3 nano-rod domains is formed 

by one of these four distorted 

unit cell phases as depicted in 

Fig. 2(a). The dashed lines in 

Fig. 2(b) define the CB supercell, 

which through translational 

operations can produce the entire 

CB film. The orthorhombic and 

rotated tetragonal phases are separated 

by domain boundaries (DB) closely 

aligned along the and 

directions. These domain walls should 

accommodate structural distortions 

between the α, ß, γ, and δ phases and 

provide a means for their coherent growth 

along both the film growth direction and 

in the a−b plane. Comparing the in-plane 

domain size (4×4 nm 2 ) and the in-plane 

footprint of the spinel lattice (~ 0.8×0.8 

nm 2 ), we determined that the fraction of 

distorted unit cells at the DB is significant 

(~30%) in comparison to the number of 

undistorted cells within each phase, see 

Fig. 2(b). Hence, these DBs should also 

produce a significant contribution to the 

total diffraction picture as illustrated by 

the prominent diagonal streak in the (0 4 

4) RSM. 

The symmetry of the lattice distortions at 

the domain boundaries of the CB pattern 

Fig. 2: (a) Illustration of the four structural 

unit cell phases present within the CB layer 

with arrows pointing to the appearance with 

the asymmetric (0 4 4) RSM. (b) Illustration 

of the CB arrangement of tetragonal and 

orthorhombic domains with DB along the 

and directions. The dashed 

lines define the CB super-cell (SC) by which 

translational operations can repeat the 

entire CB film. 

can be described in terms of distortions 

with respect to a 2D square lattice with 

monoatomic basis 7 . These distortions can 

be represented as a linear combination of 

e 3 

, r, and two other modes, either t + 

and 

s + 

or t – 

and s – 

. For example, distortions 

at the interface between the γ and δ 

domains, as illustrated in Fig. 3, can be 

characterized by a combination of the 

–e 3 

+ r + t + 

+ s + 

distortion modes with 

amplitudes of e 3 

= –ε/2, r = ε/2, t + 

= ε/2, 

and s + 

= ε/2. 

Fig. 3: Representation of the linear combination 

of distortion modes at the domain boundary τ. 

Squares γ and rectangles δ correspond to the rotated 

tetragonal and orthorhombic lattices, respectively. 

The role that the substrate plays in 

establishing and stabilizing the CB 

structure should not be overlooked as 

its influence can be seen in a number 

of aspects, e.g., the suppression of the 

out-of-plane herringbone formation. 

In the case of ZMGO thin films grown 

on MgAl 2 

O 3 

substrates (a S 

= 0.8083 nm) 

the film is under a compressive strain 

in contrast to the previously described 

case of growth on MgO, where the 

film is under stabilizing tensile strain. 

Results from TEM and RSM reveal that 

ZMGO samples grown on MgAl 2 

O 3 

have 

regressed back to forming the out-plane 

herringbone structure. Evidence of the HB 

structure can be seen in Fig. 4(a), where 

the signal originates from a pair of tilted 

inelastic tetragonal phases and two tilted 

elastically strained tetragonal phases, 

which appears around the symmetric 

(0 0 4) reflection. The elastic tetragonal 

phases are accompanied by rotations 

around K and H axes by about ±0.9° 

and the inelastic tetragonal phases 

are tilted by about ±1.4°. The long 

diagonal strikes originate from the 

canted nanorod interfaces, similarly to 

the data shown in Fig. 1 for the CB 

films. 

Conclusion 

The use of synchrotron radiation-based 

reciprocal space mapping (RSM) was 

paramount in investigating the complex 

structural properties of epitaxially grown 

ZnMnGaO 4 

thin films on single crystal 

MgO (0 0 1) substrates. The ZnMnGaO 4 

films consist of a self-assembled 

CB structure of highly aligned and 

regularly spaced vertical nano-rods. 

Reciprocal space mapping revealed 

the strain-accommodating interaction 

between the phases of the CB structure 

through lowering of the volume strain 

energy, while maintaining long-range 

commensurability of the structure with 

the MgO substrate. Such a planar CB 

surface could be utilized as a template 

for the subsequent growth of 

ferromagnetic material and the 

possible construction of highdensity 

magnetic recording 

devices. Work at NJIT and Rutgers 

was supported by the DE- 

FG02-07ER46382 and the NSF- 

DMR-0546985. 

Fig. 4: (a) crosssectional 

H-L 

RSM taken of the 

symmetric (004) 

reflection from ZMGO 

thin film grown on 

MgAl 2 

O 3 

. (b) TEM 

image showing HB 

structure. 

References 

1. S. Yeo, Y. Horibe, S. Mori, C.M. Tseng, C.H. 

Chen, A.G. Khachaturyan, C.L. Zhang, and 

S-W. Cheong; App. Phys. Lett. 89, 233120 

(2006) 

2. C.L. Zhang, S. Yeo, Y. Horibe, Y.J. Choi, S. 

Guha, M. Croft, S-W. Cheong, and S. Mori; 

Appl. Phys. Lett. 90, 133123 (2007) 

3. Y. Ni, Y. M. Jin, and A. G. Khachaturyan; 

Acta Mat. 55, 4903 (2007) 

4. M.A. Ivanov, N. K. Tkachev, and A. Ya. 

Fishman; Low Temp. Phys. 25, 459 (1999) 

5. S. Park, Y. Horibe, T. Asada, L.S. Wielunski, 

N. Lee, P. L. Bonanno, S.M. O’Malley, A.A. 

Sirenko, A. Kazimirov, M. Tanimura, T. 

Gustafsson, and S-W. Cheong; Nano Lett. 

8, 720 (2008) 

6. S.M. O’Malley, P.L. Bonanno, K.H. Ahn, 

A.A. Sirenko, A. Kazimirov, M. Tanimura, T. 

Asada, S. Park, Y. Horibe, and S-W. Cheong; 

Phys. Rev. B 78, 165425 (2008), http://link. 

aps.org/abstract/PRB/v78/p165424 

7. K.H. Ahn, T. Lookman, A. Saxena, and A. R. 

Bishop; Phys. Rev. B 68, 092101 (2003) 


Structures from Solutions: Biomolecular 

Small-Angle Solution Scattering at MacCHESS 

Richard E. Gillilan 



Fig. 1: Scattering profiles of 

a lysozyme standard taken 

on both G1 and F2 stations. 

For approximately the 

same sample-to-detector 

distances and energies, 

G1 performs better in the 

low-angle range, while F2 

yields wider-angle data. The 

inset shows a typical protein 

solution scattering pattern 

and the triangular region 

used to produce the profile. 

Protein crystallography continues to 

be the prime source of high-resolution 

molecular structural information in 

biology. Its success depends totally 

upon the ability of proteins and other 

biomolecules to form well-ordered 

crystalline lattices under the right 

conditions. Many important biological 

molecules, however, are not well 

behaved in this regard, a fact that is 

becoming more apparent as biologists 

focus their investigations on new and 

more challenging systems. Molecular 

order is handy, but it isn't everything. As 

it turns out, there is valuable structural 

information to be found even in dilute 

solutions where proteins are randomly 

oriented. 

The two-dimensional scattering pattern 

of a solution is perfectly symmetrical 

but the intensity falls off in a Gaussian 

fashion from the beamstop outward. 

In practice, 2D images thus collected 

are integrated into one-dimensional 

scattering intensity profiles, I(q), 

parameterized by q = 4π sin(θ)/λ, with 

2θ being the scattering angle (see Figure 

1). The inset in Figure 1 shows a typical 

biological small-angle x-ray scattering 

(BioSAXS) image collected at CHESS's 

G1 line. Several important particlespecific 

parameters are derived from 

these scattering curves. The famous 

Guinier relation connects the width of 

the Gaussian falloff observed at small 

q to the radius of gyration Rg of the 

particle, a useful geometric parameter 1 . 

The absolute scattered intensity at 

the beamstop, I(0), is related directly 

to molecular mass. Particle volume 

and maximum diameter can also be 

obtained. 

Historically, much x-ray 

solution scattering work has 

involved comparison to models. 

Experimental scattering curves 

can be used very effectively to 

select from among different 

competing structural hypotheses 

by comparison with computed 

curves. Because solutions 

can be examined under near 

physiological conditions, it 

becomes possible to study such 

phenomena as concentrationdependent 

changes in 

oligomeric state as well as 

large conformational changes. Even 

structurally-disordered systems give 

characteristic scattering profiles; 

consequently much use of x-ray solution 

scattering has been made in the study 

of protein unfolding 2 . 

Just how much information solution 

scattering yields is still open to debate, 

but modern advances in synchrotron 

technology and computer algorithms have 

produced some very surprising results 

and the popularity of BioSAXS has grown 

dramatically in recent years as a result. Due 

largely to the software tools developed by 

Sohyun (Sarah) Kim, is now a senior 

at Ithaca High School, Ithaca NY. She 

started working for Richard Gillilan 

during the Summer of 2007 writing 

a Java program to analyze 100,000 

digital images of crystal growth. This 

past summer, she gave a poster on her 

work at the CHESS user meeting 

(pictured above). Currently, she is 

volunteering in MacCHESS's lab 

over in the Biotech building located 

on the Cornell University campus, 

growing protein crystals for use by 

MacCHESS staff in beamline testing. 

One set of crystals she grew were used 

in a recent x-ray microbeam study by 

MacCHESS that is currently under 

review for publication. Sarah is also 

now working on a project to isolate 

purple membranes from a species of 

salt loving bacteria as a standard for 

several MacCHESS experiments. 


Svergun and coworkers (www.emblhamburg.de/ExternalInfo/Research/ 

Sax/software.html), reconstruction of 

actual low-resolution biomolecular 

shapes from simple scattering profiles 

has become routine. But how is 

it possible to derive a meaningful 

three-dimensional structure from an 

orientationally-averaged scattering 

pattern that is inherently onedimensional 

The answer lies in how additional 

constraints are applied to help limit the 

number of potential solutions. Consider, 

for example, the widely-used GASBOR 

method of reconstruction 3 . Intensity is 

modeled by applying the Debye formula 

to a set of N "dummy residues" and firstlayer 

solvent atoms: 

Each g i 

(q) can be either a form factor 

for an average amino acid residue (a 

"dummy residue"), or the form factor 

for a solvent atom. The r ij 

are distances 

between dummy residues. Good 

configurations of dummy residues 

should minimize the mean square 

difference χ 2 between calculated and 

measured intensities: 

The sum runs over the number of 

sample points m in the scattering profile 

and σ 2 is the standard deviation of the 

measurements at each point. † But the 

problem is that there are too many 

nonphysical arrangements of 

dummy residues that 

minimize χ 2 . Additional constraints must 

be considered to limit the solution space. 

GASBOR defines a penalty function P(r) 

that rejects unphysical configurations 

of residues by insisting that models 

have a realistic distribution of nearest 

neighbors, that they be connected 

regions, and that the center of mass be 

close to the origin. GASBOR seeks to 

minimize the goal function E = χ 2 +αP, for 

some fixed positive weight α. Random 

movements of residues are accepted 

or rejected based on their E values 

according to a simulated annealing 

protocol. 

Typically 10 or more independent 

simulated annealing calculations 

are performed so that results can be 

compared. The degree of consensus 

between different solutions is an 

indicator of confidence. GASBOR 

attempts to incorporate wide 

angle data and is more effective 

at modeling structural detail. 

For very large complexes, 

the programs DAMMIN and 

DAMMIF, which use a related 

"dummy atom" approach, are 

more appropriate 4 . 

Volkov and Svergun have 

reconstructed a variety of 

ideal model shapes such as 

rods, disks, hollow spheres, 

and cylinders as a means of 

validation for these methods, 

but this classic paper on the 

subject also serves as a useful guide 

to the kinds of intensity profiles to 

expect and what kind of fidelity can be 

achieved in reconstructions 5 . A typical 

low-resolution shape reconstruction is 

shown in Figure 2 as a transparent 

surface superimposed 

on a crystal structure of a zinc transport 

protein solved by Cherezov et al. 6 . 

BioSAXS at CHESS 

While SAXS measurements are done at 

a number of CHESS beamlines, several 

time slots on G1 station are regularly 

dedicated to BioSAXS during each run. 

Typically running at 9-10 keV for SAXS, 

the multilayer optics feeding G1 deliver 

a very high flux with approximately 1% 

bandwidth. Disposable sample cells, 

custom manufactured by ALine Inc. 

(Redondo Beach, CA) require only 10 µl 

of sample and are produced with a layer 

of pressure-sensitive adhesive on the 

outside to accommodate a wide variety 

of (adhesive-free) window materials such 

as mica or ultra-thin polyimide (Fig. 3). A 

temperature-regulated housing for the 

sample cells has been fabricated which 

allows easy access for refilling. 

Fig. 3: Disposable sample cell for biological 

small-angle scattering (right). On-cell 

adhesive allows a wide variety of choices 

for thin-window material. The copper 

sample cell mount (left) can be easily 

removed from the temperature-controlled 

housing for refill. 

Fig. 2: Low resolution molecular shape 

reconstruction (transparent blue surface) 

compared with one of the known 

structures of the zinc transport protein 

CzrB from Thermus thermophilus. 

† 

For simplicity, scaling and correction factors have been omitted. 

Interested readers should consult Ref [3] for details. 


The beamstop in a SAXS 

experiment is placed as far 

from the sample as possible 

in order to capture scattering 

at the smallest angles. This 

necessitates using a vacuum 

or helium flight path to 

eliminate air scatter from 

the direct beam that would 

otherwise drown out the faint 

SAXS signals. The beamline 

configuration for BioSAXS is 

shown in Figure 4. G1 utilizes 

interchangeable vacuum pipes 

of various lengths containing 

an internally-mounted 

beamstop with integral PIN 

diode for monitoring direct 

beam counts. Sample-to-detector distances 

on the order of 850 mm are commonly used 

for proteins, yielding a practical q range from 

about 0.02 to 0.4 (300 Å - 15 Å), though G1 can 

accommodate significantly longer distances if 

necessary for large complexes. 

The Shannon sampling theorem holds that 

SAXS scattering profiles are fully determined 

by a relatively small number of parameters † ; 

consequently detector resolution needs are 

modest (i.e. the curves are gradual and have 

no real sharp features) 1 . Because additional 

physical constraints are always imposed when 

solving for molecular shapes (as illustrated 

above in the case of GASBOR), there is actually 

more information to be extracted from the 

data than one might expect on the basis of 

the sampling theorem. Nonetheless, 1k x 1k 

CCD detectors are usually more than adequate 

for BioSAXS needs. CHESS's unique FLICAM 

detector is routinely used for this purpose. 

While the number of pixels on state-of-theart 

crystallography detectors far exceeds the 

requirements for SAXS, they have been used 

quite effectively for BioSAXS on other stations 

and offer a potentially wider angle range for a 

single experiment. 

CHESS F2 station is now available for 

BioSAXS. F2's gentler flux, easy tunability, 

and high energy resolution are actually very 

well-suited for SAXS work. The increased 

flexibility in scheduling and access means 

that crystallography users can potentially 

collect BioSAXS and crystallographic data 

during the same visit. The same sample 

cell and temperature-control enclosure 

used in G1 can be used in F2; consequently 

there is no difference in sample handling. 

Fig. 4: BioSAXS beamline configuration at G1 station. Beam is collimated by 

a series of slits (right) and passes into the cooled sample cell enclosure. Both 

scattered radiation and direct beam travel through the vacuum flight tube 

where direct beam is stopped just prior to the detector. Scattering profiles 

are recorded on the FLICAM CCD detector at left. 

For convenience, a helium-filled flight path has been used in F2 with beam 

provided by a standard 300 µm collimator. Comparisons between G1 and F2 

using a lysozyme standard show excellent agreement (Figure 1). G1 reaches 

smaller angles q min 

and gives slightly better results in that region than F2, while 

F2 captures significantly wider angles q max 

than G1. Only a single quadrant of 

the Quantum 210 detector in F2 was used for these tests. Future improvements 

in beam collimation and beamstop design as well as planned extensions of 

sample-to-detector distance may well close the low-angle gap between the 

stations for most proteins, but G1 will remain the station of choice for the very 

largest complexes. 

Preparing for a run 

While BioSAXS is probably more tolerant of impurity than protein 

crystallography, good sample preparation is essential to success. Protein 

solutions should be monodisperse and as concentrated as possible. A total 

sample volume of 50 µl is the minimum advisable volume to prepare. This will 

allow enough for a series of dilutions, tests to determine the best exposure time, 

and any possible sample loading problems. Lysozyme gives an ideal signal at 

25mg/ml, but still gives a reasonable small-angle signal at 1 mg/ml. For much 

larger proteins, lower concentrations may be permissible since larger particles 

scatter more strongly. Concentrations of lysozyme stronger than 25 mg/ml 

will exhibit concentration-related distortions of the small-angle part of the 

scattering curve. It is advisable to collect data at several different concentrations 

and extrapolate to infinite dilution if possible. Often, as in the case of 10-25mg/ 

ml lysozyme, a single dilute measurement is enough for good data, but 

concentration effects are heavily sample dependent and should be checked in 

each case. 

Users must also provide a matched buffer solution for background subtraction. 

This should be the exact same buffer used in the original sample preparation if 

possible. It is good to change buffer if you don't know the original composition 

exactly. Prepare plenty of extra buffer for sample dilutions and for rinsing 

sample cells. 

Users often wonder how many samples to bring and how long sample 

collection takes. Typically exposure times on G1 can be as short as one second 

(even with attenuation). Exposure times on F2 are commonly 20 sec or more. 

† 

Theoretically there are D max 

(q max 

-q min 

)/π parameters, where D max 

is the maximum diameter of the protein. By this criterion, 

measuring profiles down to q min 

< π/ D max 

is recommended. Often, the criterion q min 

< 1.3 ⁄ Rg is used in direct Guinier analysis. 


A complete dataset, however, may involve the collection of several 

protein concentrations along with matched buffers at several 

different exposure times. Most users need less than 24 hours to 

collect their data. New users are advised to bring only 2-6 proteins 

at first, preferably some with known structures that can be used 

to judge how well SAXS will work on their particular system. 

Experienced users have been able to collect data on dozens of 

proteins during that time, generating several gigabytes of images. 

Each protein responds differently to radiation damage. Preliminary 

data quality is assessed by looking at the flatness of the buffer 

subtraction and the linearity of Guinier plots. While MacCHESS does 

not yet offer microfluidic sample cells, Hong and Hao have recently 

demonstrated that scanning the x-ray beam within sample cells can 

significantly reduce radiation damage 7 . 

While BioSAXS can make definitive statements about disordered 

systems, potential users should be advised that shape reconstruction 

is only as good as the degree of order in the sample. Samples 

existing in more than one conformational or oligomeric state require 

special treatment and may prove difficult to process. 

Preliminary processing can and should be performed onsite during 

data collection. Lower-resolution shape reconstructions using 

the recently released DAMMIF program 4 are quite fast, but final 

reconstructions may require multiple independent calculations 

using slower algorithms, such as GASBOR 3 , that can take one or more 

days. Users can take advantage of MacCHESS's fast multiprocessor 

computers, cf105 and Feynman, to run processing jobs on site. 

Because BioSAXS involves the measurement of relatively few 

parameters to reconstruct complex shapes, and because it is 

sensitive to multiple complicating factors, such as aggregation, 

concentration effects, non-uniformity of sample cells and so forth, 

it is important to use it in conjunction with other techniques. In 

BioSAXS, much more so than in crystallography, it is important to 

recognize when data are not good and to utilize known standards 

when possible to assess the success of data collection and the 

fidelity of reconstructions. 

BioSAXS offers a comparatively simple and rapid means of learning 

about the size, low-resolution shape and oligomeric state of 

biomolecular complexes under near-physiological conditions. It has 

become an important tool in the reconstruction of large complexes 

for which only some parts are known. A number of groups have 

recently taken advantage of BioSAXS data collected on G1 station to 

complement their crystallographic studies and to resolve important 

questions on solution-state behavior. Zoltowski et al. investigated 

conformational switching in the fungal light sensor VIVID and were 

able to observe conformational changes between light and dark 

states in solution 8 . Wedekind et al. produced a model of catalyticallyactive 

APOBEC3G (a cytidine deaminase active on HIV singlestranded 

DNA) using BioSAXS data which has been further validated 

by recent experimental work 9 . Wang et al. studied calcium sensing by 

GCaMP2, a protein used in studying Ca 2+ flux in vivo in the heart and 

vasculature of mice 10 . Yuan et al. were able to identify the dimeric 

solution state of a serine integrase catalytic domain 11 . Hong and 

Hao have recently used wide-angle solution scattering data to help 

phase crystal structures 12 . 

Users interested in trying BioSAXS may apply for time through the 

express-mode proposal mechanism by specifying "Other" under 

"Choice of experimental technique" and by typing "standard 

BioSAXS" in the box provided for "Special experimental 

and facility needs." More information is available on the 

MacCHESS web site www.macchess.cornell.edu under the 

BioSAXS link. 

References 

1. D.I. Svergun, and M.H.J. Koch; "Small-angle Scattering 

Studies of Biological Macromolecules in Solution", 

Reports on Progress in Physics 66(10): p. 1735-1782 

(2003) 

2. N. Ando, et al., "Structural and Thermodynamic 

Characterization of T4 Lysozyme Mutants and 

the Contribution of Internal Cavities to Pressure 

Denaturation", Biochemistry 47(42): p. 11097-11109 

(2008) 

3. D.I. Svergun, M.V. Petoukhov, and M.H.J. Koch; 

"Determination of Domain Structure of Proteins from 

X-ray Solution Scattering", Biophysical Journal 80(6): p. 

2946-2953 (2001) 

4. D. Franke, and D.I. Svergun; "DAMMIF, a program for 

rapid ab-initio shape determination in small-angle 

scattering", Journal of Applied Crystallography, 42(2) 

(2009) 

5. V.V. Volkov, and D.I. Svergun; "Uniqueness of ab initio 

Shape Determination in Small-angle Scattering", 

Journal of Applied Crystallography 36: p. 860-864 

(2003) 

6. V. Cherezov, et al.; "Insights into the Mode of Action 

of a Putative Zinc Transporter CzrB in Thermus 

Thermophilus", Structure 16(9): p. 1378-1388 (2008) 

7. X.G. Hong, and Q. Hao; "Measurements of Accurate 

X-ray Scattering Data of Protein Solutions using 

Small Stationary Sample Cells", Review of Scientific 

Instruments 80(1): (2009) 

8. B.D. Zoltowski, et al.; "Conformational Switching in 

the Fungal Light Sensor Vivid", Science 316(5827): p. 

1054-1057 (2007) 

9. R.P. Bennett, et al.; "APOBEC3G Subunits Self-associate 

via the C-terminal Deaminase Domain", Journal of 

Biological Chemistry 283(48): p. 33329-33336 (2008) 

10. Q. Wang, et al.; "Structural Basis for Calcium Sensing by 

GCaMP2", Structure 16(12): p. 1817-1827 (2008) 

11. P. Yuan, K. Gupta, and G.D. Van Duyne; "Tetrameric 

Structure of a Serine Integrase Catalytic Domain", 

Structure 16(8): p. 1275-1286 (2008) 

X. Hong, and Q. Hao; 

12. "Combining Solution Wide-angle 

X-ray Scattering and Crystallography: determination of 

molecular envelope and heavy-atom sites", Journal of 

Applied Crystallography, 42(2): p. 259-264 (2009) 


Development of X-ray Pixel Array Detectors 

Sol M. Gruner 1,2 

1 


2 


X-ray detector development has not 

kept pace with the exponentially 

increasing brightness and capability of 

synchrotron sources. The result is that 

experiments at synchrotron sources 

are very frequently more limited by 

the detector than the source. The 

reason detector development has not 

kept pace is because responsibility 

for detector development has 

traditionally been somewhere 

between the sources and the users: 

Detectors have most commonly 

been viewed as the responsibility 

of the user end of a facility. In 

consequence, the large resources that 

have been devoted to developing 

new synchrotron facilities have not 

involved adequate development of 

new detectors. But it takes the better 

part of a decade, a dedicated team 

of detector designers, and millions 

of dollars to develop a new detector 

technology. This requires resources 

and a commitment that are very 

unusual for user groups. At the same 

time, the market is sufficiently small, 

and the commitment of resources 

is sufficiently large, that it isn’t very 

attractive to industry. 

A CHESS goal has been to break 

this cycle in order to catalyze 

the introduction of new detector 

technologies for synchrotron 

experiments. In the mid-1980’s CHESS 

teamed with Kodak (Rochester, 

NY) to install a novel image plate 

detector system. In the early 1990’s 

CHESS teamed with my group, then 

at Princeton University, to install 

the first fiber-optically coupled CCD 

detectors for routine macromolecular 

crystallography. This evolved into 

a collaboration with Area Detector 

Systems Corp (ADSC; Poway, CA) and 

resulted in ADSC’s very successful line 

of CCD detectors. Since the mid 1990’s, 

my group, now at Cornell, has been 

developing x-ray Pixel Array Detectors 

(PADs), a next generation detector 

technology. 

In a phosphor-coupled CCD detector 

x-rays are absorbed in a thin phosphor 

layer resulting in visible light emission. 

The phosphor is deposited on fiber 

optics that conveys the light image 

to a CCD. This type of detector, 

while having many advantages, still 

suffers from a number of drawbacks: 

Phosphors are slow and have limited 

resolution, fiber optics distort the 

image, each x-ray results in a signal 

in the CCD that is barely above the 

intrinsic noise, the CCD read time 

is long, and the technology allows 

limited in-detector processing of 

information. 

PADs can overcome all these 

limitations. In this context, a PAD 

consists of two silicon integrated 

circuits (ICs) bonded together (Fig. 1). 

The front layer, called the detective 

layer, is divided into pixels and is 

sufficiently sensitive throughout 

its ~500 μm thickness to stop 

most x-rays below roughly 20 keV. 

Each pixel of the detective layer is 

individually connected to its own 

Diode Detection Layer 

• Fully depleted, high resistivity 

• Direct x-ray conversion in Si 

Connecting Bumps 

• Solder, 1 per pixel 

CMOS Layer 

• Signal processing 

• Signal storage & output 

pixel of processing electronics in 

the back, or CMOS layer, via a small 

solder connection, or bump. Modern 

IC fabrication methods allow an 

incredible amount of processing 

power to be squeezed into each pixel. 

In a well designed PAD signals are 

conveyed to the processing layer in 

nanoseconds with amplitudes well 

above inherent noise, and with no 

signal spread beyond neighboring 

pixels. The processing layer can be 

designed not only to process signals, 

but also to read the information out 

very quickly. 

PADs are of two general types: photon 

counters and integrators. Each type 

has advantages and disadvantages, 

depending on the experiment at 

hand. Photon counters process 

photons one at a time, generally 

taking a few tenths of a μs to do so. 

Consequently, photons that arrive at 

a pixel faster than the time required 

to process the signal from an x-ray 

suffer counting losses. In other words, 

photon counters are locally count-rate 

limited. At the same time, they can 

provide some level of photon energy 

X-rays 

Fig. 1: A PAD, here shown in an exploded view, consists of two silicon ICs bonded 

together, pixel-by-pixel, with solder connecting bumps. 


discrimination. Integrators sum the signal 

from arriving x-rays for later digitization and 

can, thus, avoid local count rate limitations, 

but they do not discriminate between 

photons of different energies. Our focus is 

on integrators, in part because there are 

competent efforts in Europe (such as the 

PILATUS PAD developed at the Swiss Light 

Source (now being vended by DECTRIS, 

Switzerland) focused on photon counters. 

Specifically, we have developed two distinct 

integrating PADs. 

The first is a PAD made in collaboration with 

ADSC. It is designed to deliver images at up 

to a 1 kHz rate, with no dead time and with 

an extraordinarily large dynamic range per 

pixel (~2 x 10 7 x-rays/pixel/msec). Design of 

this detector was the principal focus of Dan 

Schuette’s Ph.D. thesis when he was at Cornell 

(Dan was one of the first recipients of a 

Cornell G-line Fellowship. He is now a scientist 

at Lincoln Laboratory in Massachusetts.) 

Figure 2 shows an x-radiograph of a Canadian 

dime taken with this PAD. Figure 3 shows the 

extraordinary dynamic range and sharp point 

spread function (e.g., per pixel resolution) of 

this PAD. 

Fig. 2: 

X-radiograph 

of a Canadian 

dime. The 

back was 

sanded off to 

thin the coin. 

Both PADs are now operational as single chip detectors about an inch 

across. Future work on both projects will be to make mosaics of chips 

to cover larger areas. In the meantime both PADs are being used for 

a variety of user x-ray experiments at CHESS and the APS, including 

coherent x-ray microscopy, time-resolved pulsed laser deposition 

growth of complex oxides, protein solution scattering, and timeresolved 

growth studies of carbon nanotube forests. 

The future of PADs is very bright, indeed. 

Fig. 3: (top) Diffraction 

from a large grain 

aluminum sample. The 

four panels are all of a 

single image taken at the 

CHESS F2 station at various 

display magnifications. No 

beam stop was used, which 

is why there is a large 

central peak. (bottom) 

A graph of intensity 

through the single image 

diffraction pattern. Note 

the logarithmic ordinate. 

Also note the small peaks 

about 10 pixels to the left 

and right of the central 

main beam peak. These peaks are 25,000 times weaker than the central peak 

and less than a mm removed from it. This type of extraordinary dynamic range 

and sharp point spread behavior is not possible with a phosphor coupled CCD 

detector. From W. Vernon, M. Allin, R. Hamlin, T. Hontz, D. Nguyen, F. Augustine, 

S.M. Gruner, Ng.H. Xuong, D.R. Schuette, M.W. Tate, and L J. Koerner; “First 

Results from the 128x128 Pixel Mixed-mode Si X-ray Detector Chip”, Proc. SPIE, 

Conference 6706, paper 29, U-1 to U-11 (2007). 

The second PAD is being designed for 

the coherent imaging station at the Linac 

Coherent Light Source (LCLS) at SLAC. X-rays 

from diffraction patterns from the LCLS 

arrive at the detector with the time structure 

of the x-ray laser, e.g., ~100 fs. It would be 

impossible to count photons at these rates. 

So the PAD was designed to have very good 

single photon sensitivity, but to integrate the 

signal. In other words, the PAD will clearly 

be able to see signals as small as 1 x-ray per 

pixel, yet can receive up to 3000 x-rays per 

pixel. The entire detector will frame at the 

LCLS repetition rate of 120 Hz. Figure 4 shows 

a radiograph of part of U.S. dollar bill taken in 

Cu Kα radiation. The contrast in the image is 

provided by the ink in the dollar bill. Pull out 

a dollar and look at the relevant feature to 

note the resolution. 

Fig. 4: Cu Kα radiograph of part of 

U.S. dollar bill. The display of the 

radiograph data has been adjusted 

to zoom in on the contrast variation 

coming from the green ink in the 

dollar. 

Acknowledgements: 

The PAD developments described in this article have been carried out by 

members of the Cornell detector group in my lab in the Cornell Physics 

Department, including Mark Tate, Hugh Philipp, Marianne Hromalik, 

Lucas Koerner, Kate Green and Dan Schuette (now at Lincoln Labs in 

Massachusetts). Darol Chamberlain (CHESS) has also been involved. PAD 

research in our lab is supported by DOE Office of Biological Research 

via grant DE-FG02-97ER62443. The ADSC project is a collaboration with 

Area Detector Systems Corporation via NIH grant RR-014613. LCLS PAD 

development is supported by the Department of Energy. 


Exploring New Physics of Nanoparticle Supercrystals 

by High Pressure Small Angle X-ray Diffraction 

Zhongwu Wang, Ken Finkelstein, and Detlef-M. Smilgies 


Superlattices built from self-assembled 

nanoparticles (NPs) combine the 

size-tuned unique properties of single 

crystals with the collective properties 

of newly created (one- two- and threedimensional) 

ordered arrays and promise 

the next generation of devices spanning 

a variety of applications 1-4 . For example, 

in nature, a colorless opal is a disordered 

aggregate of silica particles. When the 

silica particles are ordered, the opal 

changes to a color correlated with the 

size of the self-assembled particles 3 . 

In the laboratory, several approaches, 

including templating, soft lithography 

and supramolecular chemistry, 

have enabled creation of numerous 

superlattices comprising NP building 

blocks 3,5-7 . These NP nanobuilding blocks 

fall mostly into three types of order 

displaying variable packing densities 

and properties: Face-Centered-Cubic 

(FCC), Hexagonal-Centered-Packing 

(HCP) and Body-Centered-Cubic (BCC) 

or Body-Centered Tetragonal (BCT) (Fig. 

1) 4 . To facilitate custom engineered 

applications for NP superlattices 

requires understanding the structural 

and mechanical stabilities, inter-NP 

interaction and tuning mechanisms. 

In order to explore the structure and 

dynamic behavior at atomic resolution as 

NPs evolve into ordered building blocks 

and are tuned for stable structures and 

novel properties, we have developed 

a powerful in-situ synchrotron x-ray 

technique. Our window capable of 

peeking into the mysterious nanoworld 

utilizes small and wide angle x-ray 

diffraction under varying pressure and 

temperature for the exploration of 

the new physics and chemistry of NP 

supercrystals. 

Probing a wide spectrum of information 

of NP superlattice formation covering 

the atomic scale and the nanoscale 

requires monitoring x-ray diffraction 

from NP supercrystals in the small and 

the wide angle range. The complexity of 

measurement increases with application 

of pressure and involves several key 

experimental components: a pressure 

cell with transparent x-ray windows, 

x-ray energy tuning and position control 

of a large area detector. The diamond 

anvil cell (DAC) is certainly the primary 

option to reach extreme pressure, but 

strong absorption of low energy x-rays 

by diamond limits the measurement 

of small angle x-ray scattering. We 

circumvent these problems by tuning 

x-ray energy and sample-to-detector 

distance. At a wavelength optimized 

to avoid significant weakening of the 

scattering signal, we optimize detector 

position for collection of both firstorder 

small angle and wide angle x-ray 

diffraction by taking several exposures at 

different detector positions (but without 

multiple calibrations of sample-todetector 

distance). 

Our DAC has a large downstream 

angular opening that covers the wide 

angle x-ray diffraction. For a supercrystal 

sample made up of nanoparticles with 

known size, we roughly estimate the 

angle and corresponding position of the 

first order small angle x-ray diffraction 

peaks at different x-ray wavelengths, 

and then tune the x-ray energy to the 

optimum value at one intermediate 

sample-to-detector distance. After a 

quick check of the diffraction image, we 

move the detector to a long distance 

from the sample, enabling observation of 

small angle x-ray diffraction rings. After 

one calibration of sample-to-detector 

distance, we move the detector off the 

beam center. A one-dimensional plot 

generated from the collected x-ray 

diffraction pattern can then cover both 

small and wide angles, and processing 

of the two-dimensional pattern on the 

image requires only a simple definition 

of the beam center. Due to a significant 

reduction of the beam intensity at a low 

energy, the optimization of experimental 

conditions for collection of high quality 

images at short exposure times uses 

the following approach: the higher the 

x-ray energy, the smaller the beam stop 

and the shorter the sample-to-detector 

distance. 

The key component in this scheme is 

the development of a four dimensional 

control system for our Mar345 detector. 

As shown in Fig.2, tracks attached to 

the B2 hutch roof are used to move the 

detector, effectively eliminating detector 

vibration during data collection. Buttons 

2 and 3 control the movement of the 

detector horizontally, perpendicular 

and parallel to the beam, whereas 

knobs 4 and 5 control detector vertical 

position and rotation. At 25 keV, when 

the detector is ~450 mm from the 

sample, the small angle x-ray rings 

diffracted from a NP supercrystal are 

almost entirely blocked by the beam 

stop (Fig.2a). With x-ray energy tuned to 

20 keV, the first-order small angle x-ray 

Fig. 1: Schematic illustrating the 

positioning of nanobuilding blocks into 

periodic crystallographic arrays and 

corresponding small angle x-ray diffraction 

patterns. Top left shows a spherical 

nanobuilding block, top right a superlattice 

comprising nanobuilding blocks located 

at face centred cubic (FCC) lattice points. 

Adapted partially from Ref [4]. 


diffraction rings are fully observable 

(Fig.2b), allowing refinement of the NP 

superstructure to BCT symmetry. In a 

FCC ordered supercrystal composed of 

slightly larger NPs, the full small angle 

x-ray diffraction pattern was observed by 

moving the detector distance to ~1200 

mm. 

Fig.3 shows one example of how well 

this technique worked for high pressure 

studies of NP supercrystals. By tuning 

the x-ray energy to several wavelengths 

at ambient conditions, the small angle 

and wide angle x-ray diffraction images 

of In 2 

O 3 

NP supercrystals 8 were collected 

and shown in Fig.3 (left). Small angle 

x-ray diffraction images (Figs.3a, 3b) 

confirm that 15 nm octahedral-shape 

NPs assemble into an ordered simple 

BCT superstructure. In addition, In 2 

O 3 

supercrystals display a noticeable 

lamellar structure that may be caused 

by a preferred orientation. Fig 3a was 

obtained using the small-angle setup 

at D1 with an energy of 10 keV and a 

sample to detector distance of 700 mm 

for comparison, and Fig 3b shows that 

our current set up at B2 can detect all 

SAXS rings with the exception of the first 

order. 

The wide angle x-ray diffraction image 

and integrated pattern (Fig.3c) indicate 

that each single In 2 

O 3 

NP crystallizes 

into a cubic atomic structure. A pressure 

induced hexagonal phase has been 

observed at 10 GPa in bulk materials, 

but it does not appear in this NP 

supercrystal. However, small angle x-ray 

diffraction (Fig.3d) clearly reveals that 

the intermediate distance between NPs 

expands at pressures above 10 GPa. This 

Fig. 2: (left) Four dimensional control of mar345 

detector: 1) Mar345 Detector; 2) side-to-side (x); (3) 

Back-forward (y); (4) Vertical (z); (5) Rotation (x-y); 

(6) Moving tracks. (Right) small angle images of 

supercrystal with same particle size: a) 25 keV for 

BCT at short distance; b) 20 keV for BCT at long 

distance; c) 20 keV for FCC with slightly larger NPs 

at long distance. 

enhanced structural stability could be 

attributed to combined effects of particle 

size, morphology and NP order; the 

pressure-induced expansion of inter-NP 

distance mostly results from a series 

of subtle surface structure variations. 

Additional examples have also been 

tested (Fig.1), and we observed several 

novel phenomena including: mechanical 

stability, phase transformation and 

associated changes in surface structure 

and nanoparticle interaction. 

This unique capability opens a window 

for exploring new phenomena and 

tuning mechanisms for different NPs and 

NP building blocks under pressure. The 

collected information enables not only 

understanding the mechanical stability, 

multiple interactions, processes and 

resulting mechanism of nanoparticles 

Fig. 3: Small and wide angle x-ray diffraction patterns of In 2 

O 3 

nanoparticle supercrystals at ambient and 

pressurized conditions. Panels a and b, small angle x-ray patterns at 0 pressure at different energies; c, 

wide angle x-ray image and integrated pattern; d, high pressure small angle x-ray scattering. 

and packed building blocks [9], but also 

clarifying the development of surface 

properties upon pressure-induced phase 

transformation in single nanoparticles. 

We appreciate technical assistance 

and discussions from all CHESS staff 

that made this high pressure technique 

feasible. Special thanks go to several 

collaborators including Prof. J. Fang 

(SUNY), Dr. H. Fan (SNL), Prof. D. C. 

Sayle (UK), Prof. T. Hyeon (Korea), Dr. R. 

Hoffmann (Cornell) for sample syntheses 

and valuable discussions. 

References: 

1. M.A. Meyers, A. Mishra,. and D.J. 

Benson; “Mechanical Properties of 

Nanocrystalline Materials”, Prog. Mater. 

Sci. 51, 427-556 (2006) 

2. A.P. Alivisatos; “Semiconductor Clusters, 

Nanocrystals, and Quantum Dots”, 

Science 271, 933-937 (1996) 

3. M.P. Pileni; “Self-assembly of Inorganic 

Nanocrystals: Fabrication and collective 

intrinsic properties”, Acc. Chem. Res. 40, 

685-693 (2007) 

4. D.C. Sayle, S. Seal, Z. Wang, et al; 

“Mapping Nanostructure: A systematic 

enumeration of nanomaterials by 

assembling nanobuilding blocks at 

crystallographic positions”, ACS Nano 2, 

1237-1251 (2008) 

5. B.D. Gates, Q.B. Xu, M. Stewart, et al; 

“New Approaches to Nanofabrication: 

molding, printing and other techniques”, 

Chem. Rev. 105, 1171-1196 (2005) 

6. Y.N.Xia and G.M. Whitesides; “Soft 

Lithography”, Ann. Rev. Mat. Sci. 28, 

153-184 (1998) 

7. J. Aizenberg, J.C. Weaver, M.S. 

Thanawala, V.C. Sundar, D.E. Morse, 

and P. Fratzl; “Skeleton of Euplectella sp.: 

Structural hierarchy from the nanoscale 

to the macroscale”, Science 309, 

275-278 (2005) 

8. W.Q. Lu, Q.S. Liu, Z.Y. Sun, J.B. He, C. 

Ezeolu, and J.Y. Fang; “Supercrystal 

Structure of Octahedral c-In 2 

O 3 

Nanocrystals”, J. Am. Chem. Soc. 130, 

6983-6991 (2008) 

9. D.K. Smith, B. Goodfellow, D.M. 

Smilgies, and B.A. Korgel; “Selfassembled 

Simple Hexagonal Ab2 Binary 

Nanocrystal Superlattices; SEM, GISAXS 

and Defects”, JACS, DOI: 10.1021/ 

ja8085438, http://pubs.acs.org/doi/ 

abs/10.1021/ja8085438 


Topography of Diamonds at CHESS 

Helps Nuclear Physics Program at JLAB 

Richard Jones 1 , Franz Klein 2 , and Ken Finkelstein 3 

1 

University of Connecticut 

2 

Catholic University of America 

3 


Our group at the University of Connecticut, with 

collaborators from Catholic University of America and 

Glasgow University, is in charge of construction of the 

photon source for Hall D at Jefferson Laboratory (JLAB). 

This source of polarized high-energy photons is an 

essential part of the GlueX experiment [1] – a key scientific 

motivation for the 12 GeV Upgrade of CEBAF at JLAB and 

the highest priority in the 2007 NSAC Long Range Plan for 

Nuclear Science. GlueX requires a 9 GeV photon beam with 

a high degree of linear polarization that will be produced 

by passing 12 GeV electrons through a thin oriented 

diamond crystal radiator, using the process of coherent 

bremsstrahlung (CB). 

selection for diamond radiators. We were unable to 

identify any x-ray diffraction end station at major US 

facilities with the capability to do whole-crystal rocking 

curves on samples of dimensions 10 mm with arc-second 

resolution, but we were advised to contact CHESS to discuss 

our specialized requirements. CHESS staff member Ken 

Finkelstein agreed to collaborate with us on a feasibility 

study; first measurements of diamond radiators took place 

at CHESS in November 2006. During that run we obtained 

rocking curve images of several used diamond radiators. 

These whole-crystal rocking curves were taken with 100 

micron spatial resolution using a CCD detector - the first 

time these whole crystals had been examined with such 

high spatial resolution. 

Figure 2 illustrates our first topographic rocking curve 

setup that provided ~100 micron spatial resolution. The 

asymmetric Si(111) monochromator (green) operating at 

15KeV (b = 8) expanded the beam and gave sample (gold) 

rocking curve angle resolution not better than 150mrad 

(FWHM). Adding a second, symmetric Si(220) mono (pink) 

improved resolution to 30mrad. Photo shows sample & lenscoupled 

CCD mounted on C-line 4-circle diffractomator. 

Figure 3 displays transmission topographs of several 

diamond samples. Localized light regions near the center 

Fig. 1: Illistration of the relative position of the source 

of polarized photons (diamond wafer), GlueX target, and 

surrounding components making up the high energy 

physics detector. [image from www.gluex.org] 

The creation of CB makes very stringent demands on the 

thickness and mosaic spread of the diamonds. We start with 

the very best monocrystals available from the diamond 

industry and thin them to the required thickness while 

subjecting them to a thorough quality control process. The 

unprecedented intensity of the GlueX source demands a 

better understanding of radiation damage rates in diamond 

than is currently available. Because the “coherent scattering 

vertex” (scattering process) in CB has the same form as 

elastic scattering in x-ray diffraction, the later method is an 

essential tool for diamond radiator diagnostics. 

The ability to do whole-crystal rocking curves with arcsecond 

angular resolution is essential to raw material 

Figure 2 


in two images show damage caused by 

exposure to high energy electron beams at 

JLab. Near upper left corner are ink spots 

added by the manufacturer for identification. 

GlueX requires diamond radiators of thickness 

no more than 20 microns - the thinnest ever 

used in a CB source. The diamond we studied 

during this visit had been produced for use 

in Hall B, but never put into production 

because it appeared to be unstable in 

alignment. The measurements at CHESS 

provided an explanation for this instability: 

Figure 3 

the rocking curves demonstrated that the 

diamond was severely warped. This result was 

very significant because it pointed to a problem with the thinning and mounting techniques used for past CB sources. 

Uncovering this problem early in the R&D phase of the GlueX experiment has enabled us to put in place a mitigation plan 

that will help avoid project delays and additional costs that would result if not uncovered until beamline commissioning. 

Following this initial success, we returned for a second run in 2007. The purpose was primarily to help in the upgrade and 

testing of new C-line optics designed to obtain arc-second resolution in the rocking curves. This was an essential element 

of the original feasibility proposal, and would yield an order of magnitude improvement over what was obtained in 2006. 

The improvement was made possible by fabrication of a custom asymmetric silicon (311) mono crystal pair that provided 

nearly perfect dispersion matching to the diamond (220) reflection. The optics were designed and simulated by our 

group, and machined, etched & installed at C-line by CHESS specifically for our measurements. Subsequent measurements 

demonstrated the customization meets all requirements put forward for CB diamond radiator diagnostics. 

Figure 4, a photo taken in Nov. 2007, shows the new C-line asymmetric monochromator. 

It uses two asymmetric Si (311) reflections with b=14 at 15KeV, and provides a large 

beam that is dispersion matched to diamond 220 planes so dispersion broadening under 

10μrads was expected. 

Figure 5 shows results from a quantitative analysis of a series of topographs from a 

nearly perfect diamond. The indicated pixel range corresponds to a 3 square mm area. 

Vertical surface height variation shows the range of angle required for peak rocking curve 

intensity. The angular resolution obtained shows the new monochromator is working as 

expected. 

A follow-up run was conducted in May 2009 to take advantage of instrument upgrades 

at C-line (see p. 17) that enabled switchover to our custom monochromator more quickly 

and efficiently. In a related development, our group has benefited from 

parallel developments in thin diamond monocrystal fabrication and 

mounting taking place at the Instrumentation Division of Brookhaven 

National Lab. From this group, we obtained, on loan, a diamond 

monocrystal produced using the latest CVD diamond technology. We 

characterized the mosaic structure at CHESS during our trip in May. 

Figure 4 

Access to unique facilities at CHESS is essential to carry out diamond 

thinning and mounting studies for GlueX during the next three years. 

Once those goals have been met, we anticipate there will be an ongoing 

need for radiator diagnostics that will enable us to provide a continuous 

source of top-quality radiators to guarantee continuous operation 

of the source throughout the data-taking lifetime of GlueX. CHESS 

occupies a unique place among X-ray user facilities in the US as a place 

where specialized needs can be accommodated. As non-specialists 

in the techniques of X-ray optics and measurements, our group has 

greatly benefited and learned from our collaboration with CHESS staff. 

Figure 5 

Our experience demonstrates how CHESS has a critical impact in other areas of scientific exploration. 

[1] A goal of the GlueX experiment is to provide critical data needed to address one of the outstanding and fundamental challenges in physics – the 

quantitative understanding of the confinement of quarks and gluons in quantum chromodynamics (QCD). For more info see http://portal.gluex.org/. 


Complex Porous Metal Nanostructures: 

self-assembled from block copolymers 

Uli Wiesner 1 , Laura Houghton 2 , and Sol M. Gruner 2,3 

1 

Department of Materials Science & Engineering, Cornell University 

2 


3 


Uli Wiesner (Dept. of Materials Science & 

Engineering, Cornell University) and coworkers 

have pioneered a novel way to use block 

copolymers to make nanoporous structures 

for catalyst, battery and fuel cell applications. 

The self-assembly of nanoparticles using 

block copolymers depends largely on the 

ability to design the right polymers and 

ligand-stabilized nanoparticles. Ligands can 

be used to achieve a high solubility in an 

organic solvent and allow particles to flow 

at high density. The layer of ligand needs to 

be thin around each particle so that the final 

structure has a volume of metal large enough 

to maintain a microstructural shape when the 

organic materials are removed 1 . The metal 

particles may then be sintered or calcined into 

a metal or metal oxide framework that has 

structure directed by the parent copolymer 

system and high porosity. 

A structure made of platinum, which is 

the best catalyst for fuel cells, can now be 

created with uniform hexagonal pores. The 

neatly ordered pores create a large surface area within a very small volume of 

material. Fuel cells and solar cells also both benefit from nanoscale pores: For 

a fuel cell, pores offer increased surface area at which a fuel can interact with 

a catalyst, making it more efficient. Similarly in certain types of solar cells, 

more surface area means that more light can be absorbed and generated 

charge carriers can be collected, converting more of the incident light energy 

into electricity. Porous films of titanium oxide, used in Grätzel-type solar 

cells, and niobium oxide, a fuel cell catalyst support, are obtained by mixing 

the chemicals that react to form the metal oxides with a polymer solution of 

Pl-b-PEO (poly isoprene-block-polyethylene oxide). As the reaction proceeds, 

the Pl portion of the copolymer forms cylinders surrounded by metal oxides. 

Subsequent heat treatments leave uniform, crystalline metal oxide with 

cylindrical pores 2 . The exceptional properties make them excellent candidates 

for solar cells but also valuable in many other areas. 

In addition to making porous materials, this technique could be used to create 

finely structured surfaces. In the field of plasmonics, waves of electrons move 

across the surface of a conductor with the information-carrying capacity of 

fiber optics, but in spaces small enough to fit on a chip. The self-assembly of 

nanoparticles with block copolymers may enable the formation of porous 

materials made of a range of elements, alloys, or intermetallics. This may 

enable mixtures of distinct metal nanoparticles to be combined into a single 

nanoporous material. Nanoporous metals made from nanoscopic particles 

of distinct compositions may have unique electrical, optical, and catalytic 

properties. There is great promise for future energy 

applications. Control over the structure of metals is crucial 

for energy conversion, sensing, and information processing. 

Self-assembly of nanoparticles with block copolymers 

provides a natural entry point to materials structured on 

this length scale 3 . 

Related information by the Wiesner Research Group, 

Department of Materials Science at Cornell University can 

be found at http://people.ccmr.cornell.edu/~uli/. CHESS 

was used to characterize the nanoporous structures at 

various steps along the processing sequence in order to 

understand the formation process, thereby enabling future 

materials improvements. 

References: 

Computer simulated image of how platinum 

nanoparticles fuse into a structure with tiny pores 

after the polymers that guided them into position 

are removed. Figure from the Wiesner Lab. 

1. B.Steele; "In ‘novel playground’, metals are formed into porous 

nanostructures for better fuel cells and microchips", Cornell 

Chronicle Online (June 26, 2006) 

2. B.Steele; "‘One-pot’ process can make more efficient materials 

for fuel cells and solar cells", Cornell Chronicle Online (January 

28, 2008) 

3. S.C. Warren, and U. Wiesner; “Self-assembled Ordered 

Mesoporous Metals”, Pure Appl. Chem 81(1), pp. 73-84 (2009) 


Heat-bump Measurements at CHESS A2 Wiggler Beam 

Peter Revesz 1 , Alex Kazimirov 1 , Ivan Bazarov 4 , Jim Savino 1 , 

Emmett Windisch 2 , and Christopher MacGahan 3 

1 


2 

Wayne State University 

3 

Applied Engineering and Physics, Cornell University 

4 


Thermal distortion of the first crystal due to high heat load can significantly reduce the throughput of a 

monochromator. An in-situ optical technique has been developed to measure the resulting crystal distortion (heatbump). 

We have investigated the effect of the heat load from the CHESS A2 wiggler on crystals and multilayers. A 

computer algorithm has been developed to calculate the depth distribution of the absorbed power in a format that 

can be used by ANSYS. Calculations performed using this approach are in good agreement with the experimental 

profiles measured by the optical technique. 

Experimental Technique and Results 

The CHESS A-line 49 pole wiggler produces a total power of 6.6 kW when 

operating at 5.3 GeV and 200 mA current. Although only a portion of this 

power reaches the monochromator due to the apertures and upstream 

filters, still, the heat load can produce a considerable deformation of the 

first crystal, leading to the deterioration of the monochromatic beam 

(a) 

and the loss of x-ray flux throughput. Different approaches have been 

developed to deal with the heat load problem. They include internal 

and external cooling of Si crystals, including cryo-cooling, to minimize 

the thermal expansion 1 , using diamond instead of Si 2 and, in the case 

of multilayer optics, using SiC as a substrate material instead of Si 3 . 

Traditionally, the effect of the heat-bump is assessed by measuring 

a monochromator rocking curve. The widening of the rocking curve 

characterizes the deterioration of the Bragg reflection averaged over the 

beam footprint area. 

Our direct method of a heat-bump measurement gives an in-situ 3D map 

of the surface distortion. The main idea of the method proposed by P. 

Revesz et al. 4,5 is as follows: We use an array of light source dots viewed as 

(b) 

reflected from the monochromator crystal surface. As the surface heatbump 

is formed and the reflecting surface becomes distorted, the image measurement. The image of an array of light-dots is 

Fig. 1: (a) Principal scheme of the heat-bump 

of the regular dots pattern will also be distorted. More accurately, the 

captured with a CCD camera as reflected from the crystal. 

image of the individual dots will shift their positions according to the local The position of the dots in the image shifts as the crystal 

becomes deformed as a result of a beam heating. (b) Slope 

slope error developed on the crystal surface. The principal setup of the 

gradient field produced by a heat load and captured by 

experiment is shown in Figure 1a. The array of light dots was formed by 

a heat-bump measuring program. Each line represents 

a flat panel light source covered with a thin metal mask with an array of 

a shift of a centroid position of each light dot relative 

small holes. This assembly was mounted on the downstream crystal holder to its original non-distorted centroid position. The X 

and Y components for each dot represent the g 

of the monochromator. The CCD camera was mounted on the top of the 

x 

and g y 

components of the gradient vector fields 

monochromator box to observe through a viewport the image of the light 

dots as reflected off the first monochromator crystal. The CCD images were 

captured and analyzed in-situ by a special program based on a modified version of the program Centroid, described earlier in ref. 

6. In Figure 1b, the change of the centroid positions of the light dots is shown as a result of the surface distortion. The shift of each 

dot characterizes the slope error vector as ∆g= ∆r/L, where ∆r is the shift of a dot’s virtual position and L is the distance between 

the virtual image of the light dot and the CCD camera. It is easy to see that the x and y components of the centroid shifts give the 

gradient field {g x 

, g y 

} of the distorted surface. 

The reconstruction of the surface from the gradient field has been studied extensively as it is the central issue for a number of 

applications; for instance, it is known as the “shape-from-shade” problem. Reconstruction of the shape from the gradient is not a 

problem in one dimension but in two dimensions; in this case, the experimentally measured gradient field does not necessarily 

satisfy the integrability requirement. An elegant solution of the problem was proposed by A. Agrawal et.al. 7 , by solving the 

Poisson equation with the Neumann boundary condition. 

An example of the heat-bump formed on the Si(111) crystal, as reconstructed from the measured gradient field, is shown in Figure 

2a. In this case, the white x-ray beam from the CHESS A-line wiggler was incident on the monochromator crystal at an angle of 


9°. The beam was defined by the 1x6 mm slit (vertical/ 

horizontal) and the total X-ray power impinging on the Si 

crystal was ~ 90 W as measured by a bolometer. In Figure 

2b and c, the section of the heat-bump and the slope error 

are shown, respectively, along the beam direction through 

the heat-bump maximum. The solid lines show the heatbump 

and the slope error as derived from the reconstructed 

surface, and the crosses are the measured data. The 1D 

heat-bump height shown in Figure 2b was obtained by a 

simple integration of the experimental slope values. In [8], 

this technique has been applied to multilayer optics and 

proved that the multilayers on SiC substrates develop a 

factor of two smaller heat-bumps than the same multilayers 

on traditional Si substrates. 

To verify our experimental data we developed a computational algorithm to calculate 

the heat-bump. The algorithm is based on the characteristics of the x-ray source, 

material characteristics of the first crystal, and the cooling scheme included in the 

finite element analysis routine. First, a three-dimensional representation of the x-ray 

power absorbed in the Si crystal was calculated by using a Matlab based program. 

The program uses the wiggler characteristics and beam-line parameters, including 

absorbers and slits, to approximate the 3D power absorption in the crystal by a 

number of staggered “bricks” along the beam’s path. Next, a mechanical model of the 

Si crystal, plus the copper crystal holder with water cooling, was created in the ANSYS 

workbench. Then the 3D heat-load data from the Matlab program were imported 

into the ANSYS workbench and the steady-state thermal distribution was calculated 

followed by a static structural simulation. 

In Figure 3a, the result of the structural simulation is shown. In Figure 3b the 

comparison of the heat-bump profile obtained by the ANSYS simulation (black) and 

the measured data are shown. Note that the measured data covers only a part of the 

Si crystal, determined by the field of view of the optical setup, whereas the ANSYS 

simulation generates the profile over the whole Si crystal. The measured and the 

simulated results are in a good agreement and they show that the crystal distortion 

extends well beyond the beam footprint. We found that the slope error profile obtained 

from the ANSYS simulation, and the experimentally measured slope error profile, are 

also in a good agreement. 

References: 

1. D.H. Bilderback, A.K. Freund, G.S. Knapp, and D. M. Mills; “The Historical Development 

of Cryogenically Cooled Monochromators for Third-generation Synchrotron Radiation 

Sources“, J. Synchrotron Rad. 7, 53-60 (2000) 

2. L.E. Berman, J.B. Hastings, D.P. Siddons, M. Koike, V. Stojanoff, and M. Hart; 

“Diamond Crystal X-ray Optics for High-power-density Synchrotron Radiation Beams”, 

Nucl. Instr. & Methods A329, 555-563 (1993) 

3. A. Kazimirov, D.-M. Smilgies, Q. Shen, X. Xiao, Q. Hao, E. Fontes, D.H. Bilderback, and 

S.M. Gruner; “Multilayer X-ray Optics at CHESS “, Journal of Synchrotron Radiation, 

13, 204-210 (2006) 

Fig. 2: The heat-bump surface reconstructed from 

the measured gradient vector field using the Poisson 

method (a). The heat-bump (b) and the slope error 

profile (c) along the beam direction. The solid line 

is obtained from the reconstructed surface, and the 

red markers represent the measured data. 

8. A. Kazimirov, P. Revesz, and R. Huang; “Multilayer Optics under CHESS A2 Wiggler Beam”, Proceedings of SPIE, v. 7077, 

707702-1-8 (2008) 


(a) 

beam footprint 

(b) 

Fig. 3: (a) ANSYS simulation of heat-bump 

and (b) the comparison between the 

simulated (black) and the measured (red) 

heat-bump profiles for the 90W X-ray power 

from the CHESS A2 wiggler impinging at 9° 

on the Si monochromator crystal. 

4. P. Revesz, A. Kazimirov, and I. Bazarov; “In-situ Visualization of Thermal Distortions of Synchrotron Radiation Optics under Wiggler 

Beam”, Nucl. Instr. & Methods A576, 422-429 (2007) 

5. P. Revesz, A. Kazimirov, and I. Bazarov; “Optical Measurement of Thermal Deformation of Multilayer Optics under Synchrotron 

Radiation“, Nucl. Instr. & Methods A582, 142-145 (2007) 

6. P. Revesz, and J. A. White; “An X-ray Beam Position Monitor Based on the Photoluminescence of Helium Gas”, Nucl. Instr. & 

Methods A540, 470-479 (2005) 

7. A. Agrawal, R. Chellappa, and R. Raskar; “An Algebraic Approach to Surface Reconstruction from Gradient Fields”, IEEE 

International Conference on Computer Vision (ICCV), (2005)

Advances in X-ray Microfocusing with 

Monocapillary Optics at CHESS 

Sterling W. Cornaby 1,2,3 , Thomas Szebenyi 1 , Heung-Soo Lee 4 , 

and Donald H Bilderback 1,2 

1 


2 

Applied and Engineering Physics, Cornell University 

3 

Currently at Moxtek Inc., Orem, UT 

4 

Pohang Accelerator Laboratory, Pohang, Korea 

Single-bounce monocapillary optics are ellipticallyshaped 

hollow glass tubes which are capable of 

focusing x-ray beams at CHESS to a spot size between 

5 and 50 µm, with intensity gains ranging from 

10 to 1000, and divergences ranging from 1 to 10 

milliradians (mr) 1,2,3 . Experiments at CHESS using 

x-ray microbeams created with these optics include 

high pressure powder diffraction, high resolution 

micro-diffraction (µXRD) 4,5 , micro-x-ray fluorescence 

(µXRF) 6,7 , micro-XANES 8 , confocal x-ray fluorescence 

on antique paintings (confocal µXRF) 9 , micro-protein 

crystallography 10 , Laue protein crystallography 11 , 

micro-small angle x-ray scattering (µSAXS) 12 , timeresolved 

powder diffraction of reactive multilayer 

foils 13 , miniature toroidal mirrors for grazing-incidence 

SAXS 14 , micro-X-ray standing waves 18 , and others 15 . 

Over the past few years, experiments using 

microbeams on various stations at CHESS have 

increased greatly. Between 2005 and the present, 

CHESS has increased its hardware to accommodate 

from one to five simultaneous capillary setups, with 

specialty setups for protein crystallography and 

μSAXS. The increase in x-ray microbeam capacity 

has been fueled by user requests. During a typical 

run, one or two x-ray microbeam setups are in use 

continually throughout the run, with a peak of four 

of CHESS’s twelve stations using x-ray microbeams 

simultaneously in November 2007. 

Single-bounce monocapillaries are shaped like a small 

section of a very eccentric ellipsoid. Rays emitted 

from an x-ray source at one focus of an ellipse are 

directed to the opposite focus where the sample 

under study is placed, as the rays undergo a single 

specular reflection from the inner capillary wall. The 

ellipsoidal shape is designed to satisfy the grazing 

incidence requirement needed for total external 

reflection of x-rays. This basic premise allows for 

many potential shapes for optics that depend on 

the maximum divergence chosen, spot size required 

and working length from capillary tip to focus. For 

synchrotron applications, the source is typically 

located many meters away from the optic and the 

incident radiation has a low glancing angle on the 

glass wall of order 0.2°. 

We evaluate the quality of our drawn optics with 4 kinds of tests. 

First, we evaluate the departure of the observed glass figure 

from the ideal design shape. This is accomplished using optical 

metrology to evaluate the rms slope errors and rms centerline 

deviations from a straight line. Second, we observe a far-field 

image on a fluorescent screen to measure the divergence of the 

capillary and to see if it has the proper ring structure. The farfield 

x-ray image is viewed on a high quality fluorescent screen 

about 25 to 100 cm downstream from the focus. This far-field 

image is used to align the optic with the x-ray beam and contains 

information regarding the straightness and the slope errors of 

the optic. Third, we take a pinhole scan at the focus of the optic 

to see that it makes a small spot. The spot size is measured by 

scanning a 5 to 10 μm diameter pinhole across the focus. Fourth 

and last, we measure the x-ray beam intensity through the small 

pinhole with an ion chamber, with and without a capillary. The 

gain is simply the ratio of the two intensity numbers. 

Figure 1 shows both a pinhole scan and a far-field image from a 

single-bounce monocapillary optic. 

Fig 1: A schematic cut away of a single-bounce monocapillary 

is in the lower left corner. The positions of the reflected rays are 

in dark blue and positions of the non-reflected rays are in light 

blue. In the upper left corner is a pinhole scan across the focus 

of an optic, with a spot size of 5 μm FWHM, determined after 

deconvoluting the data with the 5 μm pinhole size. A far-field 

image is on the right side. In the schematic, the far-field screen 

is represented by the red line, which is normal to the x-ray 

beam. Both the scan and the far-field image are from capillary 

f1b_mr9f20_01. Note that the outer ring is not perfectly round. 

The strands of concentric intensity arise from several periods of 

slight oscillations that develop around the desired figure, most 

likely imprinted during the drawing process itself. The diagram 

was taken from reference [1]. 


Single-bounce monocapillaries have a Fig. 2: A diagram of the 

number of attributes, listed below. 

setup for two total-reflection 

mirrors and a single 300 nm 

The positive attributes: 

thick transmission mirror 

• They are achromatic. They reflect all used to create a tunable, 

large-bandwidth beam for 

x-ray energies to the same focal spot crystallography. The diagram 

position. 

was redrawn from reference [1]. 

• They are optically and mechanically 

robust. For example, they are not 

particularly fragile and they are 

typically operated in air. 

• They are 90% to 99% efficient. Almost 

all the x-rays that hit the surface of the 

optic are reflected, if the condition of 

total external reflection is satisfied. 

• The divergence and focal length can 

be designed. 

The limiting monocapillary attributes are: 

• They have profile and slope errors, 

which currently limit the spot size to 5 

µm or larger, at CHESS, with the present glass drawing technology. 

• They are not imaging optics, they simply focus the beam. 

• They have finite aperture size of about 1 mm or less and divergence 

of about 12 mrad or less. The small numerical aperture limits the 

amount of x-ray light that the optic can collect. 

Being achromatic, however, is an exceptionally important advantage of 

the monocapillary optics. This means the focal spot size, the focal spot 

location, and the divergence of the focused beam do not change with 

the x-ray photon energy. Thus these optics focus a 0.01% bandwidth 

beam as effectively as a 50% bandwidth beam. The reflection efficiency 

remains high over the entire x-ray energy range as long as the x-rays do 

not exceed the critical angle. 

A recent example of using this achromatic principle to good advantage can be 

seen in a Laue diffraction experiment whose purpose is to determine the 3D 

crystal structure of protein microcrystals 1,16 . This experiment used a combination 


Fig. 3: A graph showing the predicted 

efficiency and measured spectrum of the 

30% bandwidth (FWHM) created from two 

rhodium reflection mirrors and one Si 3 

N 4 

transmission mirror combination. The pink 

curve is calculated, and the blue-green curve 

is measured. They compare favorably. The 

bandwidth is peaked at 12 keV (λ=1.24 Å) 

with half-height values at 9.6 keV (λ=1.29 Å) 

and 13.4 keV (λ=0.93 Å). In the measured 

Compton scattering curve (green), the several 

sharp fluorescence peaks originate from trace 

contaminants within the Kapton® tape; they 

are not present in the incident X-ray beam. 

The diagram was taken from reference [1]. 

Fig. 4: Right, Laue diffraction pattern from a 

lysozyme crystal. Left, magnified view of the area 

in the magenta box, showing well-separated, 

acceptably-shaped spots. 

of two rhodium coated reflection mirrors and a silicon nitride x-ray transmission mirror to generate a 30% bandwidth beam 

peaked at 12 keV, Figures 2 and 3. 

The wide-bandwidth beam was then focused with a single-bounce monocapillary optic to a 10(H)x13(V) µm 2 spot, with a 

divergence of ~ 5(H)x2(V) mrad 2 and resulted in a total flux of 4.4×10 10 photons/s (~3.4×10 8 photons/s/µm 2 over the 30% 

bandwidth). This experiment was performed at the D1 bending magnet station whose critical energy is about 10 keV. 

The flux density achieved using the bending magnet is close to what you would expect for a 1-2% bandwidth microfocused beam 

on a wiggler station. This small beam was then used to take Laue diffraction images of small protein crystals, mostly lysozyme, but 

also of a few thaumatin crystals, Figure 4. 

The crystals were a few tens of microns in size. In the short term, we believe that this approach will lead to a new avenue for 

solving protein structures using less than 10 µm sized crystals at CHESS. In the longer term at an ERL source of x-rays, we hope to 

push crystal sizes down into the hundreds of nanometers range with this approach - an approach that will be more limited by the 

radiation damage of crystals than by any beam qualities. 

Another important advantage of single-bounce monocapillary optics is that the divergence and focal length can be designed. 

CHESS has a glass capillary puller which has been set up to make a number of different optics 1 . Two examples show the power 

of having this in-house tool for constructing specialized monocapillary optics. We have been able to fabricate “football” shaped 

optics with very short focus-to-focus distances of 20 to 30 cm 1 . We have also been able to make a bifocal miniature toroidal mirror 

that horizontally and vertically focuses to two different locations 14 . 

The need for a football monocapillary optic arose within the Confocal X-Ray Fluorescence (CXRF) project, led by CHESS staff 

scientist Arthur Woll and his collaborators, to investigate buried paint layer structures of antique paintings 9 . CXRF uses x-ray

optics to define a small viewable volume 

in free space that the XRF detector can see. 

By limiting the volume of the detection 

region with two separate x-ray optics, the 

third dimension (the depth) of the sample’s 

elemental composition can be resolved, 

such as in a painting’s underlying layers. At 

CHESS, a single-bounce monocapillary optic 

is used to focus the x-ray beam and an XOS 

polycapillary optic is used to collect XRF 

events for the detector, Figure 5. 

We decided to try CXRF with two crossed 

monocapillary optics. The second collection 

optic needed to have a very short focus-tofocus 

distance of 30 cm or less. We 

made this second football-shaped 

optic and were able to use it in a 

CXRF experimental setup to test 

the confocal resolution, Figure 6. 

The football-shaped optic is a 

good fit for x-ray tube sources, 

where short focus-to-focus 

distances improve the total usable 

x-ray flux from the tube. We are 

presently looking further into other 

applications using this kind of 

optic. 

We have also made a non-elliptically shaped 

single-bounce monocapillary optic at CHESS. 

A special dual-focal length toroidal mirror 

Fig. 5: The left diagram shows how a small detection volume in space is created at the intersection 

of a beam produced by the monocapillary and accepted by the polycapillary optic. The confocal 

volume is green in color in the inset. The diagram on the right shows how this small volume can 

be used to resolve a layered structure. Since the confocal volume is about the same dimension as a 

typical paint layer on an oil painting, the composition of the different layers can be resolved in three 

dimensions. The diagram was taken from reference [9]. 

Fig. 6: The left diagram shows 

a sketch of the CXRF test 

made with two monocapillary 

optics. The confocal volume 

was measured with an XRF 

detector, as a 6 µm thin lead 

foil was passed through 

the confocal volume. Spot 

defining slits at the second 

focus of the football shaped 

collection optic controlled the 

viewable size of the confocal 

volume. The graph on the 

right shows the resolution as a function of the slit opening. A resolution of ~120 µm FWHM was 

achieved with a 300 µm slit setting, and a resolution of ~50 µm FWHM was achieved with a 50 µm 

slit setting. The diagram was taken from reference [1]. 

was designed to focus vertically at the sample’s position 50 mm from the capillary tip and to horizontally focus at the detector’s 

position, 150 mm from the capillary tip. This mirror was made to provide a smaller vertical footprint of beam for grazing incidence 

wide-angle scattering (GIWAXS), while at the same time producting better angular resolution in the horizontal direction. No other 

capillary has been designed to date with such separate focal distances! 

This optic, however, is very similar in concept to the elliptically-shaped single-bounce monocapillary optics. This miniature 

toroidal mirror was designed to decouple the sagittal and meridional focusing of the traditional single-bounce monocapillary 

optic, Figure 7. 

Essentially, the normal ellipsoidal shape is modified by increasing its inner diameter, changing the sagittal focus, and at the same 

time not modifying its meridional curvature, leaving the meridional focusing capability unchanged. 

Using the entire inner optical surface will not produce the needed horizontal line focus at the sample position and a vertical line 

focus at the detector position. In order to create a line focus, only a small section of the optic’s full inner surface is exposed to 

x-rays. Slits are set upstream of the optic to block most of the optical surface illumination as only about 10% of the inner optical 

surface area is used. [If the full surface of the optic is exposed to an x-ray beam, a narrow ring of intensity will be observed at the 

location of the meridional focus, and a 

semi-large spot will appear at the sagittal 

focused position.] X-ray tests were 

made with this optic, Figure 8. 

Improvements have been made to the 

capillary drawing process. Parts are now 

drawn under constant pressure (rather 

than constant tension) and the furnace 

moves in the opposite direction to the 

upward drawing of glass out of the 

heating zone, Figure 9. 

These changes, instituted by Heung-Soo 

Lee when he was a visiting scientist with 

Fig. 7: This sketch outlines the morphing of a ellipsoidal shape (left) into a toroidal shape (right). The 

diameter of the optic is changed, thereby decoupling, the sagittal and meridional focal points. The 

meridional focus position is unchanged, but the sagittal focusing is moved further away from the tip of 

the optic. The diagram was taken from reference [14]. 


us last year, have contributed 

to drawing better optics. 

In addition, H-S. Lee also 

worked on making far-field 

simulations from the slope 

errors measured from the 

on-board Keyence optical 

metrology, Figure 10. 

In conclusion, micro-focusing 

single-bounce monocapillary 

optics will continue to be an integral part of the capabilities of CHESS. 

Work will continue to perfect the monocapillary optics by reducing 

slope and figure errors in the fabrication process. With improvements 

in slope and figure errors, these optics should make smaller beam 

sizes and will be very useful for both 3rd generation x-ray sources and 

the ERL. 

Fig. 8: The beam was observed (with 5 micron 

diameter pinhole scans) to be horizontally focused 

150 mm from the capillary tip and vertically focused 

only 50 mm from the tip, proof that the dual-focal 

lengths had been produced. Some structure can 

be seen in the vertical scan, showing that more 

perfecting work is needed to turn this prototype 

into a usable optic. Nonetheless, this is an excellent 

demonstration that a new type of capillary optic 

has been created! The diagram was taken from 

reference [14]. 

Fig. 9: Capillary drawing tower 

showing AB Tech air-bearing 

in the background, tensionproducing 

stage on the left, 

furnace and optical metrology 

in the foreground (with 

suspended glass tube) and a 

load cell at the bottom of the 

apparatus. 

Fig. 10: Far-field capillary image (including direct beam in center). 

Circular strands of intensity are due to small slope errors remaining 

from the glass drawing process. The simulation on the right shows 

similar ring structure and is approaching the circular structures seen 

at left when realistic slope-error values are included in the calculation. 

Acknowledgement: 

We wish to acknowledge that our work was supported by CHESS 

through the NSF & NIH/NIGMS via NSF award DMR-0225180 and by the 

MacCHESS resource through NIH/NCRR award RR-01646. One of us, SC, 

was also supported by a Cornell University supported G-line fellowship. 

References: 

1. S. Cornaby; The Handbook of X-ray Single-Bounce Monocapillary 

Optics, Including Optical Design and Synchrotron Applications, 

Dissertation, Cornell University 2008. Available at http://glasscalc. 

chess.cornell.edu/Cornaby_Capillary_Handbook_2008.pdf. 

2. S. Cornaby, T. Szebenyi, R. Huang, and D.H. Bilderback; “Design 

of Single-Bounce Monocapillary X-Ray Optics”, 55th Denver X-ray 

Conference, Advances in X-ray Analysis Vol. 50 (2006) 

3. R. Huang and D. H. Bilderback; “Single-bounce Monocapillaries 

for Focusing Synchrotron Radiation: modeling, measurements and 

theoretical limits”, J. of Synchrotron Radiation 13, 74-84 (2006) 

4. A.A. Sirenko, A. Kazimirov, S. Cornaby, D.H. Bilderback, B. Neubert, 

P. Brueckner, F. Scholz, V. Shneidman, and A. Ougazzaden; 

“Microbeam High Angular Resolution X-ray Diffraction in InGaN/GaN 

Selective-area-grown Ridge Structures”, Applied Physics Letters 89 

(18): Art. No. 181926 (Oct. 30 2006) 

5. A. Kazimirov, A.A. Sirenko, D.H. Bilderback, Z.-H. Cai, and B. 

Lai; “Microbeam High Angular Resolution Diffraction Applied to 

Optoelectronic Devices”, AIP Conference Proceeding CP879, 

Synchrotron Radiation Instrumentation: Ninth International 

Conference 1395-1397 (2007) 

6. K. Limburg, R. Huang, and D.H. Bilderback; “Fish Otolith Trace 

Element Maps: new approaches with synchrotron microbeam X-ray 

fluorescence”, X-ray Spectrometry, 36, 336-342 (2007) 

7. C. Schmidt, K. Rickers, D.H. Bilderback, and R. Huang; “In situ 

Synchrotron-radiation XRF Study of REE Phosphate Dissolution in 

Aqueous Fluids to 800°C”, Lithos 95, 87-102 (2007) 


8. R.A. Barrea, R. Huang, S. Cornaby, D.H. Bilderback, and T.C. 

Irving; “High-flux Hard X-ray Microbeam using a Single-bounce 

Capillary with Doubly Focused Undulator Beam”, J. of Synchrotron 

Radiation 16, 76-82 (2009) 

9. A.R. Woll, J. Mass, C. Bisulca, R. Huang, D.H. Bilderback, S. Gruner, 

and N. Gao; “Development of Confocal X-ray Fluorescence (XRF) 

Microscopy at the Cornell High Energy Synchrotron Source”, Applied 

Physics A 83 (2), 235-238 (2006) 

10. R. Huang and D.H. Bilderback; “Secondary Focusing for Micro- 

Diffraction using One-Bounce Capillaries”, Eighth International 

Conference on Synchrotron Radiation Instrumentation, AIP 

Conference Proceedings, 712-715 (2004) 

11. Ibid ref. 1 

12. J.S. Lamb, S. Cornaby, K. Andresen, L. Kwok , H.Y. Park, X. Qiu, 

D.M. Smilgies, D.H. Bilderback, and L. Pollack; “Focusing Capillary 

Optics for use in SAXS”, Journal of Applied Crystallography 40, 

193-195 (2007) 

13. J.C. Trenkle, L.J. Koerner, M.W. Tate, S.M. Gruner, T.P. Weihs, and 

T.C. Hufnagel; “Phase Transformations during Rapidly Propagating 

Reactions in Nanolaminate Foils”, App. Phy. Lett. vol. 92 (2008) 

14. S. Cornaby, D. Smilgies, and D. Bilderback; “Bifocal Miniature 

Toroidal Shaped X-ray Mirrors”, 57th Denver X-ray Conference, 

Advances in X-ray Analysis Vol. 52 (in print, 2009) 

15. D.H. Bilderback, A. Kazimirov, R. Gillilan, S. Cornaby, A. Woll, 

C-S Zha, and R. Huang; “Optimizing Monocapillary Optics 

for Synchrotron X-ray Diffraction, Fluorescence Imaging, and 

Spectroscopy Applications”, AIP Conference Proceeding CP879, 

Synchrotron Radiation Instrumentation: Ninth International 

Conference, 758-763 (2007) 

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Gillilan, Q. Hao, and D.H. Bilderback, Acta Cryst. D. (submitted) 

17. S. Cornaby and D.H. Bilderback; “Silicon Nitride Transmission X-ray 

Mirrors”, Journal of Synchrotron Radiation 15, 371-373 (2008) 

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Ougazzaden; “Microbeam High-resolution Diffraction and X-ray 

Standing Wave Methods Applied to Semiconductor Structures”, J. 

Phys. D: Appl. Phys. 37, 3L9-L12 (2004)

Watching Carbon Nanotube Forest Growth 

using X-rays 

Eric R. Meshot 1 , Mostafa Bedewy 1 , Sameh Tawfick 1 , K. Anne Juggernauth 1 , 

Eric Verploegen 2 , Yongyi Zhang 1 , Michael De Volder 1 , and A. John Hart 1 

1 

Department of Mechanical Engineering, University of Michigan 

2 

Department of Materials Science and Engineering, MIT 

Carbon nanotubes (CNTs) have many 

potential applications due to their atomic 

structure and consequent mechanical 1 , 

electrical 2 and thermal 3 properties. 

CNTs can be classified into two distinct 

structural forms: (i) a single seamless 

cylindrical shell of sp 2 -bonded carbon 

atoms arranged in a honeycomb lattice 

constituting a single-wall CNT (SWCNT) 

which typically has a diameter ranging 

from 0.4 nm to 3nm; (ii) several concentric 

seamless shells with 0.34 nm interwall 

spacing, forming a multi-wall CNT 

(MWCNT) which can have diameters 

ranging from 1.4 nm to 100 nm. An 

infinitely long assembly of aligned, 

continuous, and densely packed CNTs 

would constitute the ultimate of synthetic 

fibers, and could have several times the 

strength of piano wires at one-fourth 

the density, along with thermal and 

electrical conductivity exceeding copper. 

However, before this dream is realized, 

many smaller-scale configurations of CNTs 

are potentially useful for next-generation 

transistors, flexible and transparent 

electronics, and multifunctional interface 

layers. Specifically, vertically aligned CNT 

“forests”, consisting of tens of billions 

of CNTs per square centimeter on a flat 

substrate, are widely sought as highperformance 

electrical, thermal, and 

mechanical interface layers, as well as 

filtration membranes 4-10 . 

Although CNTs can be synthesized 

by many methods involving hightemperature 

decomposition and 

reorganization of solid carbon, the most 

popular and scalable means of CNT 

synthesis is catalytic chemical vapor 

deposition, where CNTs “grow” from metal 

catalyst nanoparticles that are typically 

placed on a substrate or floated in a 

carbon-containing gas atmosphere. The 

process of CNT forest growth by thermal 

CVD typically involves multiple stages: (1) 

the catalyst is prepared on a substrate, 

such as a silicon wafer; (2) the catalyst is heated and treated chemically, such as by 

exposure to a reducing atmosphere that causes agglomeration of a thin film into 

nanoparticles; (3) the catalyst is exposed to a carbon-containing atmosphere, which 

causes formation and “liftoff” of CNTs from the nanoparticles on the substrate; and 

(4) CNT growth continues by competing pathways between accumulation of “good” 

(graphitic) and “bad” (amorphous) carbon 11 . To engineer the functional properties 

of CNT materials such as forests, we must develop reaction processes that not only 

treat these stages independently, but that are also accompanied by characterization 

techniques that enable mapping of the forest characteristics for large sample sizes 

and populations. Despite extensive study of aligned CNT forest production 12-27 , 

including recent advances using water and oxygen as additives to increase reaction 

yield and catalyst lifetime, the limiting mechanisms of forest growth are not fully 

understood, and CNT forest heights are typically limited to several millimeters. 

In Figure 1, we show an AFM image of nanoparticles arranged for CNT forest 

growth, as well as images of a vertically aligned multi-wall CNT forest at different 

magnifications. 

Fig. 1: (a) 500 nm AFM scan of Fe nanoparticles formed on an 

Al 2 

O 3 

support layer by heating in H 2 

for 2 minutes at 825 °C; and 

vertically aligned multi-wall CNTs at different magnifications: (b) 10 X, 

(c) 140,000 X (SEM) and (d) 7,000,000 X (TEM). 

At CHESS, we use ex situ and in situ small-angle X-ray scattering (SAXS) to investigate 

growth of CNT forests, and work closely with Dr. Arthur Woll, Prof. Sol Gruner, and 

colleagues. In order to elucidate the dynamics of catalyst particle coarsening, forest 

self-organization, temperature- and reactant-driven CNT structure evolution, and 

growth termination in realtime, a custom-built atmospheric-pressure CVD reactor 

featuring a resistively heated substrate platform 28 , shown in Figure 2, is mounted 

directly in the G1 beamline at CHESS, enabling in situ grazing incidence (GI-SAXS) 

and transmission (SAXS, WAXS) scattering studies, as shown in Figure 3. Simultaneous 

laser measurement of the forest height captures the growth kinetics, the 

heated platform enables rapid temperature changes (200 °C/s) during annealing 

and growth, and the reactant gas is independently heated to create a population of 

active carbon species that cause efficient CNT growth. Further, Figure 3 summarizes 

the different techniques and resulting data for both GI and transmission modes: we 

show schematics of our setups, examples of scattering intensities collected by the 

FLICAM detector, and data demonstrating temperature effects on nanoparticle and 

CNT formation. 


Fig. 2: Photograph of CNT 

growth apparatus mounted 

in the G1 Beamline. 

Fig. 3: Schematic and data 

for both grazing incidence 

(a-c) and transmission (d-f) 

SAXS configurations. For 

GI mode: (a) schematic 

shows X-rays glancing off 

substrate-bound particles; 

(b) scattering intensity 

from a population of Fe 

nanoparticles forming in 

real time as temperature 

increases; (c) I vs. q profiles 

showing real-time evolution 

of the structure factor peak 

for the Fe nanoparticles. 

For transmission mode: (d) schematic shows X-rays passed directly through a CNT forest; (e) 

representative scattering intensity from a CNT forest; (f) I vs. q profiles with curve fits showing the 

dependence of the CNT form factor peak on growth temperature – the shift of the peak position 

to lower q indicates larger CNT mean diameter. 

After growth, we also carry out ex situ characterization of the CNT forests in order to spatially map their bulk morphology 29 . Using 

SAXS we can investigate the spatial variations in MWCNT orientation. In addition we use SAXS to measure a locally averaged spatial 

variation in CNT diameters within our films. CNT diameters obtained by fitting the scattering results were confirmed by TEM 

imaging, which establishes SAXS as an attractive non-destructive technique for precisely examining CNT materials 29,30 . 

Starting with a catalyst thin-film of Fe/Al 2 

O 3 

on Si, we observe rapid coarsening of Fe at temperatures as low as 650 °C (Figure 

3c) 31 . CNT diameter and growth rate are directly proportional to the substrate temperature (Figure 3f) 30 , and tuning of annealing 

and growth conditions using SAXS-derived diameter measurements reveals that CNT forests with mean diameters ranging from 

4-20 nm can be grown from the same starting catalyst film thickness (not shown here) 31 . Growth self-terminates abruptly, accompanied 

by a sudden loss of alignment at the CNT-substrate interface (Figure 4); this appears to be a universal chemical and/or 

mechanical signature in our experiments 32 . Our apparatus and investigative technique offer significant potential to further understand 

the limiting mechanisms of CNT forest growth, and for rapid tuning of process conditions to engineer application-oriented 

structural characteristics of nanotubes and nanowires. 

Figure 4a shows in situ measurements of the height evolution of a forest that self-terminates, and of forests which are terminated 

prematurely by rapidly cooling the substrate or stopping the flow of the carbon containing gas while maintaining the substrate 

temperature 33 . As seen in Figure 4b, the orientation (quantified by the Hermans orientation parameter) increases sharply at the 

top of a forest, representing the transition from tangled to vertically aligned morphology during the first stage of growth. The 

orientation then remains approximately constant as growth proceeds, and then it decays steeply toward zero before growth 

terminates, indicating the onset of disordered CNTs. In agreement with the morphological evolution indicated by the calculated 

Hermans values, SEM images (Figure 4c) show that the self-terminated forest exhibits disorder at its base, yet the intentionally 

terminated forests exhibit strong alignment at the base. This demonstrates that the loss of alignment is a signature of growth 

self-termination, and is not caused by cooling the reactor or by an abrupt decrease in the carbon concentration in the CVD atmosphere. 


Based on our in situ and ex situ results, we explain the evolution and termination 

of CNT forest growth based on a collective model consisting of four stages 33 , as 

illustrated in Figure 5: 

I. nucleation and self-assembly of randomly oriented CNTs into a 

vertically aligned forest structure; 

II. steady growth, wherein the number density of growing CNTs 

remains constant with time; 

III. density decay, wherein the number density of CNTs within the forest 

decreases with time; and 

IV. abrupt termination, wherein forest growth ceases suddenly, and is 

accompanied by a loss of CNT alignment at the interface between 

the CNTs and the substrate. 

Fig. 4: (a) Growth kinetics for 3 CNT forests 

for different growth times under otherwise 

identical conditions are plotted along with 

theoretical quadratic and exponential decay 

curves. (b) Relative alignment within each 

forest is quantified, and (c) corresponding 

SEM images verify the CNT morphology. 

In conclusion, we have employed nondestructive X-ray techniques for rapid 

characterization of CNT forests, revealing dynamics of their growth and termination 

processes and enhancing our ability to better engineer the characteristics 

of these forests (i.e., length, density, CNT diameter). Further, we have developed 

in situ GI methods with our custom CVD apparatus for probing the dynamics 

of catalyst particle formation from thin films for CVD of CNTs. By observing the 

agglomeration and coarsening of these particles in real time, we elucidate this 

rapid process as we move toward understanding the different chemical states 

and transitions of the particles as well as the prerequisites for stabilizing populations 

of small particles for small-diameter CNT growth. These applied techniques 

may also be adapted for comprehensive studies of other systems of 1-dimensional 

(nanotubes, nanowires) and 0-dimensional (nanoparticles) structures, 

demonstrating the impact and versatility of such characterization methods for 

understanding how to create new materials and nanostructures. 

The Mechanosynthesis Group’s X-ray team (Figure 6) makes the following acknowledgements. 

This work was funded by the University of Michigan Department 

of Mechanical Engineering and College of Engineering, and the National 

Science Foundation (CMMI-0800213). E. R. Meshot and S. Tawfick are grateful 

for University of Michigan Mechanical Engineering Departmental Fellowships. 

E. A. Verploegen is grateful to the Institute for 

Soldier Nanotechnologies at MIT, funded by the U.S. 

Army Research Office (DAAD-19-02-D0002). Some 

studies (Figure 3f) based from methods developed 

at CHESS were conducted at the National Synchrotron 

Light Source, Brookhaven National Laboratory, 

which is supported by the U.S. Department of 

Energy Office of Basic Energy Sciences (DE-AC02- 

98CH10886). Otherwise, X-ray scattering was performed 

at CHESS, which is supported by the National 

Science Foundation and the National Institutes 

of Health under Grant No. DMR-0225180. SEM and 

TEM were performed at the University of Michigan 

Electron Microbeam Analysis Laboratory (EMAL). 

We thank Jong G. Ok, Sangwoo Han, Myounggu 

Park, Arthur Woll, Mark Tate, Hugh Philipp, Marianne 

Hromalik, and Sol Gruner for assistance with X-ray 

scattering experiments and analysis. 

Fig. 5: Collective growth mechanism of a CNT forest: 

(a) growth stages; and SEM images of the tangled 

crust at top of forest, aligned morphology at bottom 

during steady growth, and the randomly oriented 

morphology at bottom, induced by density decay 

and abrupt self-termination; (b) time evolution of 

Hermans orientation parameter for forests grown for 

different durations in a “hot wall” tube furnace.. 


Fig. 6: Mechanosynthesis Group’s X-ray team in the 

hutch at G1 line. 

From left to right: Mostafa Bedewy, Michael de Volder, 

Eric Verploegen, John Hart, Penguin, Yongyi Zhang, 

Eric Meshot, and Sameh Tawfick. 

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Phase Behavior of Water inside Protein Crystals 

Chae Un Kim 1 , Buz Barstow 2 , Mark W. Tate 3 , and Sol M. Gruner 1,3,4 

1 

Macromolecular Diffraction Division of Cornell High Energy Synchrotron Source, 

Cornell University 

2 


3 

Laboratory of Atomic and Solid State Physics, Cornell University 

4 


Protein crystals typically consist of ≈ 40 - 60 % water. The internal water forms solvent channels (≈ 2 - 4 nm in 

diameter) inside the crystals. We have studied the phase behavior of water inside protein crystals using a novel 

crystal freezing method: high-pressure cryocooling. Using x-ray diffraction, we demonstrated that the high-density 

amorphous (HDA) ice induced inside the high-pressure cryocooled protein crystal undergoes a phase transition to 

low-density amorphous (LDA) ice as the crystal is warmed from 80 to 170 K. We also found evidence for a liquid state 

of water during the ice transition. These results have significant implications for the understanding of the anomalous 

behavior of supercooled water. 

Protein crystals used in x-ray protein 

crystallography have properties that 

distinguish them from typical inorganic 

crystals. An important difference is that protein 

crystals contain internal water, typically 

amounting to 40 to 60 % of the volume of 

the crystal. This internal water forms solvent 

channels inside protein crystals, as shown in 

Figure 1, and fills the significant void volume 

between the folded protein molecules that 

make up the crystal. 

We have recently studied the phase behavior 

of water confined inside protein crystals 1 

using a crystal freezing method, high-pressure 

cryocooling 2 , which was originally developed 

for protein cryoprotection and diffraction 

phasing 3,4 . Our previous study revealed that 

the high-density amorphous (HDA) ice induced 

by high-pressure cryocooling is responsible for 

the high quality diffraction that is frequently 

obtainable from high-pressure cryocooled 

crystals 5 . 

Figure 2 shows the diffraction images of 

a high-pressure cryocooled crystal of the 

globular protein thaumatin, as the crystal is 

warmed from 80 to 170 K. By filtering out the 

crystal Bragg diffraction from these images, 

the water diffuse diffraction (WDD) was 

isolated, allowing the phase behavior of water 

present in the internal solvent channels to be 

studied. At the same time, the crystal response 

(variation of unit-cell parameters and crystal 

mosaicity, etc) and the protein molecular 

response to the phase transition of the solvent 

channel water could be studied by analysis of 

the crystal Bragg diffraction. 

Fig. 1: Solvent channels of a thaumatin crystal oriented along the crystallographic 

a axis. The channel diameter is approximately 3 nm. The solvent inside the channels 

occupies ~ 60 % of the total crystal volume. 

Fig. 2: X-ray diffraction 

images of a thaumatin 

crystal, high-pressure 

cryocooled at 200 MPa. The 

crystal was warmed from 80 

to 170 K. The primary water 

diffuse diffraction (WDD) 

peak (second innermost 

ring) at Q = 2.03 Å -1 indicates 

HDA ice at 80 K, and shifts to 

2.00 Å -1 at 110 K, 1.92 Å -1 at 

140 K, and finally to 1.73 Å -1 , 

indicative of LDA ice at 170 

K. The inner diffuse ring (Q = 

1.2 Å -1 ) is from an oil coating 

applied to the crystal. 


The radially integrated WDD profiles from a high-pressure 

cryocooled thaumatin crystal are shown in Figure 3. 

Interestingly, the 31 superimposed WDD profiles from 80 

to 170 K show apparent isosbestic points at Q = 2.0 and 

2.5 Å -1 , which suggests a possible decomposition of the 

intermediate states into a simple mixture of the initial 

and the final states. Indeed, the intermediate states could 

be reconstructed as a linear combination of the highdensity 

amorphous (HDA) ice at 80 K and the low-density 

amorphous (LDA) ice at 170 K. This observation provides 

strong evidence that the HDA ice formed inside the protein 

crystal undergoes a first order phase transition to LDA ice. 

The responses of the crystal unit cell volume and mosaicity 

during the phase transition are shown in Figure 4. The 

primary WDD peak position is superimposed as an indicator 

of the phase transition. A thaumatin crystal contains ~ 60 

% internal water and it is estimated that the crystal unitcell 

should expand ~ 14 % to hold all the expanded water 

during the phase transition based on the density of HDA 

ice (1.17 g/cm 3 ) and LDA ice (0.94 g/cm 3 ). Interestingly we 

found that the unit-cell volume expansion during the phase 

transition was only ~ 5 %, which is too small to hold all of 

the expanded water. More surprisingly, it was observed 

that the crystal mosaicity began to improve by ~ 25 % 

upon ice expansion. This indicates rearrangement of the 

protein molecules into better molecular packing during 

the ice phase transition. These observations (small unitcell 

expansion and unexpected mosaicity improvement) 

suggest that the HDA ice, which was originally in a solid 

state, converted to a liquid during the phase transition 

to LDA ice. As a control the crystal cryocooled at ambient 

pressure did not show the mosaicity improvement, 

confirming that the molecular rearrangement is not the 

consequence of temperature increase itself. 

The liquid state of water during the ice phase transition was 

supported by the atomic temperature factors (B-factors) 

shown in Figure 5. In macromolecular crystallography, 

the B-factors represent the effects of conformational 

fluctuations. The rising B-factor plots of the high-pressure 

cryocooled thaumatin molecule indicate that the reduced 

thermal motion during high-pressure cryocooling could be 

released during the ice phase transition, as if the molecules 

were exposed to a flexible environment. As a control, 

the B-factor of an ambient-pressure cryocooled protein 

molecule was monitored from 80 to 165 K and showed no 

significant rise. 

These observations have significant implications for the 

understanding of the anomalous properties of supercooled 

water, liquid water cooled below its freezing temperature. 

For example, the isothermal compressibility, isobaric heat 

capacity, and thermal expansion coefficient of supercooled 

water all display counterintuitive trends with decreasing 

temperature 6 . One promising theory that accounts for the 

anomalous behaviors of supercooled water is liquid-liquid 

(LL) critical point theory 7 . The LL critical point theory locates 

a second critical point of water in the supercooled region 

and predicts a first order phase transition between highdensity 

liquid (HDL) and low-density liquid (LDL) water. 

Fig. 3: Radially integrated WDD profiles from thaumatin crystal diffraction 

images. The 31 experimental WDD profiles from 80 to 170 K show apparent 

isosbestic points at Q = 2.0 and 2.5 Å -1 (left). WDD profiles reconstructed from 

2 states via singular value decomposition (SVD) analysis show a significant 

similarity to the experimental profiles (right). Residuals were calculated by 

subtracting the reconstructed profile from the experimental WDD profile at 

each temperature. 

Fig. 4: Crystal parameters from thaumatin crystals warmed from 80 to 170 K. 

Relative changes of the primary WDD peak position (blue circle) in d-spacing 

(d=2π/Q), crystal unit-cell volume (green square) and crystal mosaicity (red 

diamond) are shown. The values for WDD peak position and unit-cell volume 

are multiplied by 10. Note that the crystal high-pressure cryocooled at 

200 MPa shows less-than-expected unit-cell volume expansion (~5 %) and 

unexpected mosaicity improvement around 140 K. The crystal cryocooled 

at ambient pressure does not show the mosaicity improvement in the same 

temperature range. 

Fig. 5: B-factor profiles of thaumatin along its main chain. Each profile is 

one of 13 profiles from 80 to 165 K (blue = low temperatures and red = high 

temperatures). The B-factor profile from thaumatin at ambient conditions 

(0.1 MPa and 293 K) is superimposed as a reference (dotted black line). Note 

that the B-factors of the high-pressure cryocooled crystal rise dramatically 

during the HDA-LDA ice transition whereas the B-factors of the ambientpressure 

cryocooled crystal do not show significant rise in the same 

temperature range. 


However, experimental verification of the LL critical point theory is challenging due to spontaneous nucleation of water in 

the thermodynamic region in which supercooled water exists. Therefore, as an analogue to the HDL-LDL transition, the phase 

transition between HDA and LDA ice has been extensively studied under the assumption that HDA ice is the glassy form of HDL 

and LDA ice is the glassy form of LDL. However, no clear experimental evidence of the glass transition of HDA ice has thus far been 

presented. Furthermore, the phase transition between HDA and LDA ice has not been clearly demonstrated to be of first-order, as 

the intermediate states observed in this process could not be decomposed into the mixtures of HDA and LDA ice. 

Our experimental data from water confined in the solvent channels of protein crystals, based upon WDD profiles and Bragg 

diffraction analysis, suggest that HDA ice undergoes a clear first-order phase transition to LDA ice. The evidence for liquid water 

observed in between suggests a possible glass transition of HDA ice to HDL. Drawing upon the LL critical point theory, it is 

proposed that the HDA ice induced inside protein crystals by high-pressure cryocooling first transforms smoothly to HDL water 

(glass transition), then undergoes a first order transition to LDL water, and finally continuously converts to LDA ice through a glass 

transition. Further work is needed to provide more direct evidence on the existence of liquid water and to resolve subtleties in 

the liquid states (i.e., HDL and LDL). It also remains to be seen whether a liquid state of water exists during the HDA to LDA ice 

transition in the high-pressure cryocooled bulk water. These experiments may provide more insight into the phase behavior of 

supercooled water. 

References: 

1. C.U. Kim, B. Barstow, M.W. Tate, and S.M. Gruner; “Evidence for Liquid Water during the High-density to Low-density Amorphous Ice 

Transition”, Proc. Natl. Acad. Sci. USA 106, 4596-4600 (2009) 

2. C.U. Kim, R. Kapfer, and S.M. Gruner ; “High Pressure Cooling of Protein Crystals without Cryoprotectants”, Acta Cryst. D61, 

881-890 (2005) 

3. C.U. Kim, Q. Hao, and S.M. Gruner; “Solution of Protein Crystallographic Structures by High Pressure Cryocooling and Noble Gas 

Phasing”, Acta Cryst. D62, 687-694 (2006) 

4. C.U. Kim, Q. Hao, and S.M. Gruner; “High Pressure Cryocooling for Capillary Sample Cryoprotection and Diffraction Phasing at Long 

Wavelengths”, Acta Cryst. D63, 653-659 (2007) 

5. C.U. Kim, Y.-F. Chen, M.W. Tate, and S.M. Gruner; “Pressure Induced High-density Amorphous Ice in Protein Crystals”, J. Appl. Cryst. 

41, 1-7 (2008) 

6. P.G. Debenedetti, and H.E. Stanley; “Supercooled and Glassy Water”, Physics Today 56, 40-46 (2003) 

7. O. Mishima, and H.E. Stanley; “The Relationship Between Liquid, Supercooled and Glassy Water”, Nature 396, 329-335 (1998) 

CHESS News Magazine 2009

Cornell High Energy Synchrotron Source 

200L Wilson Laboratory 

Rte 366 & Pine Tree Road 

Ithaca, NY 14853-8001 

Web: www.chess.cornell.edu

Pdf - Cornell High Energy Synchrotron Source - Cornell University

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