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SSRL Headlines Vol. 12, No. 2  -  August 2011


Contents of this Issue:

  1. From the Director of SSRL: Continuous Improvement
  2. Science Highlight — Controlling Protein Aggregation: Lessons from Fungi
  3. Science Highlight — Exploiting Instability for Tomorrow’s Electronics
  4. Science Highlight — New Techniques for Identifying Iron Species in Geologic Samples
  5. Annual Users' Conference, October 22-26
  6. Awards: Stefan Mannsfeld, Jonathan Rivnay, Johanna Nelson
  7. User Administration Update
  8. How to Wow! "Secrets" for a Successful Proposal
  9. In the News: Graphene Electronics, Vemurafenib

1.   From the Director of SSRL: Continuous Improvement

Chi-Chang Kao
"Materials by Design" is the ultimate goal for materials science. The advances in theory, computation power, materials synthesis, and characterization tools over the past decade have brought this goal within reach. Synchrotron light sources, with their exceptional properties, now play a critical role in providing the characterization tools required by the materials research community. More importantly, synchrotrons need to provide the research community with access to these tools in a timely fashion so that the unique information the tools generate can effectively guide the theory and synthesis of new materials—which can again be studied at synchrotrons, leading to further improvements.

SSRL is working to make this feedback loop a smooth process. In the development of high-performance organic photovoltaic and electronic materials, for example, a close collaboration of SSRL staff and leaders in the research community has led to an improved understanding of the structure–function relationship and accelerated the development of new materials. At SSRL, we are constantly trying to improve all aspects of our operation, including outreach, training, instrument development, user support, automation, and data analysis, to optimize the process for the user community. Please let us know about the bottlenecks in your research that SSRL could help relieve, and your expertise that might be useful to others in your research community. You can either share this information with the beam line scientist you work with most closely or you can send me an e-mail directly.

Along these same lines, a meeting to coordinate industrial research conducted at Department of Energy Basic Energy Sciences-funded synchrotron and neutron facilities was held at SSRL on July 25-26. Attended by representatives from all the BES synchrotron facilities and the Spallation Neutron Source, the meeting launched an effort to begin addressing one of the key recommendations from the recent Basic Energy Sciences Advisory Committee report, Science for Energy Technology – Strengthening the Link between Basic Research and Industry, which states: BES-supported user facilities should seek to increase the level of industrial participation and use by considering refinements to its access policies, proposal selection criteria, and time allocations to more fully engage industry-based clean energy research; investigating how its existing and proposed beamlines and instrumentation could be adapted to the priority research directions and needs of industry outlined here; and engaging its beamline scientists and support staff to provide greater assistance to industrial users solving critical challenges in development and deployment of clean energy technologies.

The group reviewed the current industrial research at each facility, including industrial user statistics, instruments and facilities that are used most by industrial users, industrial research highlights, user portals, and Department of Energy and facility-specific policies affecting industrial users. In addition, the group shared their experiences on automation, data analysis, rapid access, remote-access, and standardization, and agreed to coordinate an initial set of instruments for industrial research and to organize targeted workshops for industrial applications. These workshops will engage facility staff, researchers from BES research programs within laboratories, as well as industrial researchers, research managers, and academic researchers.

These initiatives will benefit not only industrial researchers, but also the SSRL user community as a whole. In addition, we are working to keep SPEAR3 performance at the highest and most reliable levels possible. In the user run that ended July 25, SSRL's storage ring delivered photons to users for 4,786 hours with only 72 hours of unscheduled downtime, making for an availability of 98.5%. As I mentioned in my June column, the storage ring has also begun operating at 350 mA. Top-off injections now occur every 5 minutes, maintaining the stored current constant to better than 1%. This was the first full run with frequent top-off injection and the injector performed better than expected. SPEAR3 performance metrics for both the storage ring and the injector are summarized in the table below.

Accelerator Unscheduled Downtimes Availability Mean Time
Between Failures
Mean Time To Repair
SPEAR3 Storage Ring 173 events 98.5% 28 hours 25 minutes
SPEAR3 Injector 163 events 97.5% 29 hours 28 minutes

—Chi-Chang Kao

2.  Science Highlight — Controlling Protein Aggregation: Lessons from Fungi
       (contact: Roland Riek,

Prion figure
Unlike all other fatal infectious agents, which contain DNA and/or RNA, prions—the perpetrators behind Creutzfeldt-Jakob and mad cow diseases—are composed only of a protein in a misfolded form. This makes them extraordinarily hard to combat; in mammals, all known prion diseases are currently untreatable and fatal.

One fungus, Podospora anserina, naturally contains one of two nearly identical prion proteins, HET-s and HET-S. If one fungal colony begins to merge with a genetically distinct "invader" fungal species, HET-s and HET-S interact in such a way that they stop cell growth and lead to cell death, preserving the distinct genetic attributes of the two species.

In a recent study published in the journal Molecular Cell, a team led by Prof. S. Choe and R. Riek at the Salk Institute for Biological Studies sought to better understand which section of the proteins is involved in prion formation and propagation. Through x-ray structural analysis conducted at Stanford Synchrotron Radiation Lightsource Beam Line 7-1 and the Advanced Light Source as well as nuclear magnetic resonance studies, the team discovered that prion regulation is coded in the stability of the beginning of the protein (its "N-terminal domain") rather than in its structure, as was previously thought. The work also suggests that the generation of cell toxicity may be based on an activation of the N-terminal domain triggered by a mis-folding of the "prion forming domain" located at the end of the protein ("C-terminal"). This work offers one of the first in-depth models of the mechanism for prion-inhibition and activation of toxicity.

To learn more about this research see the full scientific highlight.

3.  Science Highlight — Exploiting Instability for Tomorrow’s Electronics
       (contact: Jun-Sik Lee,

Electronic instability figure
New, designer materials—the ones that can carry a charge without depleting it or offer dramatically faster, more efficient computer memory—take advantage of the interplay between the materials' degrees of freedom (in other words, the parameters that contribute to the materials' state). One such promising material, made of the elements lanthanum, strontium, and manganese, has previously demonstrated unusual magnetic properties depending on the particular mixture of lanthanum and strontium.

In a recent study undertaken at Brookhaven National Laboratory's National Synchrotron Light Source and published in Physical Review Letters, Stanford Synchrotron Radiation Lightsource scientists Jun-Sik Lee and Chi-Chang Kao, working with colleagues at NSLS, University of Illinois, University of Rutgers, and Pohang University of Science and Technology, took a closer look at this thin film.

The study revealed the spin and orbital orders of electrons in the sample as well as information about their ground states. These showed why the material's magnetic ground state sometimes follows one pattern (designated "A-type") and sometimes follows another (designated "CE-type"). What's more, the study revealied that these two patterns can co-exist within a single sample, or the entire sample can switch between the two patterns depending on the temperature and the sample’s exact chemical composition. This ability to very easily switch between the two patterns may be quite useful for the design of future spintronic devices like next-generation solid state computer hard drives and memory, offering a rich opportunity for future investigations.

To learn more about this research see the full scientific highlight.

4.  Science Highlight — New Techniques for Identifying Iron Species in Geologic Samples
       (contact: Lisa Mayhew,

Bassalt and iron figure
Iron, one of the most abundant metals on Earth's surface, often dominates the reactivity of rocks, soils, and sediments, and is important in many biogeochemical processes. A great challenge for biogeochemists is to identify the iron species in these natural materials at very small scales and to track changes in the iron species as these materials react with water.

To address this challenge, a team of researchers from University of ColoradoBoulder's Department of Geological Sciences and the Stanford Synchrotron Radiation Lightsource recently used SSRL Beam Line 2-3 to investigate the iron species in a water-rock reaction system at different time points. The team developed an integrated approach to data collection and processing that allowed them to identify and map unique iron-bearing components within a sample system, revealing the types of iron as well as their locations and distribution. Techniques commonly applied to soft x-ray analyses were used and processing the data immediately after collection enabled the researchers to specifically target subsequent analyses used to specifically identify the iron species. The combination of these techniques resulted in a novel method that identifies and distinguishes the unique species of any redox active element that can be investigated using hard x-rays.

In their study, the team investigated the behavior of iron in two common geological and aquifer materials—basalt and Fe(III) oxides—during reaction with anoxic seawater for both short (48 hours) and long (~1 year) reaction times. At both time points they were able to identify and map the starting materials. They found that the Fe(III) oxides did not react, which was contrary to what was expected in reducing conditions. After ~1 year, they detected and identified a new iron species that was not present in the starting materials and that indicated that basalt dissolution had occurred. The widespread distribution of these secondary phases throughout the sample area was also discovered. This work provides new insights into iron reactivity in reducing conditions, and offers a new technique for investigating the species and distribution of any element that can cycle dynamically in the natural environment.

This work was published in Environmental Science & Technology.

To learn more about this research see the full scientific highlight.

5.   Annual Users' Conference, October 22-26

Plan to participate in the annual SSRL/LCLS Users' Meeting and Workshops, October 22-26, to learn about and share groundbreaking research results as well as new opportunities that push our understanding and promote key innovations in energy and materials, biology, chemistry, catalysis, and environmental science. 

Keynote and award talks include:

  • The role of the U.S. Department of Energy Office of Science in the national research strategy - Patricia Dehmer (DOE);
  • X-ray laser interactions with biological systems: opportunities and limitations in determining atomic structure - Robin Santra (DESY);
  • X-ray laser interactions with materials: opportunities and limitations in determining electronic structure – Jo Stohr (LCLS);
  • Understanding nature's assembly of molecules to improve tomorrow's electronics – Stefan Mannsfeld (SLAC: William E. and Diane M. Spicer Young Investigator Award Presentation);
  • Implications of lattice disorder on charge transport in high-performance organic semiconductors – Jonathan Rivnay (Stanford: Melvin P. Klein Scientific Development Award Presentation).

TIME RESOLVED X-RAY SCIENCE AT HIGH REPETITION RATE WORKSHOP. In conjunction with the 2011 SSRL/LCLS Users' Meeting, SSRL and the Advanced Photon Source (APS) will jointly host a two-day workshop, October 22-23, focused on opportunities with short-pulse, high-repetition rate x-ray beams. The workshop will feature international speakers and panel experts presenting the scientific basis, preliminary results, and future potential of high rep-rate picosecond x-ray beams at the APS and SPEAR3 storage rings. The workshop will broadly focus on topics in materials science, chemistry, and atomic physics. The workshop agenda will also include presentations on accelerator operational modes, precision timing issues, detector challenges, and the relation of storage ring experiments with pump-probe experiments at the Linac Coherent Light Source. Dedicated time will be available for open discussions, a panel review section, and breakout sessions for report preparation. A primary goal of the workshop is to expand the user community for short-pulse, high repetition rate science at SPEAR3 and APS. For more information, contact the organizers: Aaron Lindenberg, Apurva Mehta, and Jeff Corbett from SLAC and Eric Dufresne, David Keavney, and Linda Young from ANL.

DE-MYSTIFYING THE LIGHT SOURCE EXPERIENCE WORKSHOP. A special workshop, De-Mystifying the Lightsource Experience, will be held on Sunday, October 23 to engage new scientists or provide a foundation for existing users to consider adding new techniques to their research toolkit. This workshop will discuss several techniques (EXAFS; scattering; protein crystallography; imaging; lenseless coherent imaging; RIXS, XES, PES; time resolution/low alpha mode; ultrafast and ultrashort capabilities); how experiments are performed; applications and examples of research experiments; why one might use the technique and what makes it novel and exciting. Contact Sarah Hayes or Sam Webb to learn more about reduced student registration for this special workshop.

CONCURRENT WORKSHOPS. Several concurrent workshops are planned for Tuesday, October 25:

  • Synchrotron Applications in Catalysis Chemistry;
  • Non-Linear X-ray Sciences and Optics;
  • Advanced Crystallography;
  • Future X-ray Sources: LCLS-II Challenges and Opportunities.

POSTER SESSION.. Students are encouraged to present posters at the poster session on Monday, October 24. We will hold a "Poster Slam" at the conclusion of the plenary session, just before the poster session begins, so that students can make a quick (1 minute) pitch for their poster. In addition to the opportunity to discuss their research projects, reduced registration fees, and poster prizes, students presenting posters get for free dinner on October 24 (indicate poster competition when completing the online registration). Winners of the Outstanding Student Poster Competition will also be asked to give a 5-minute presentation at the conclusion of the Users' Meeting on October 26. Send poster abstracts to Cathy Knotts, Natalya Brown, or Jackie Kerlegan before October 8.

HELP US PUBLICIZE. We would appreciate your help in advertising the SSRL/LCLS Users' Meeting and Workshops by alerting your colleagues and adding this meeting to any calendar of upcoming events within your office. We look forward to an interesting meeting, and we hope that you will be able to participate!

RESERVE LODGING AT STANFORD GUEST HOUSE. Users who need local accommodations are encouraged to make reservations at the Stanford Guest House, which features cable TV and DVD; high-speed, in-room internet access; complimentary coffee/tea; free parking; free fitness center; laundry facilities; and a 24-hour gift shop. Specify SSRL/LCLS/SLAC to take advantage of discounted rates.

6.   Awards

S. Mannsfeld
STEFAN MANNSFELD TO RECEIVE SPICER AWARD. Stefan Mannsfeld, staff scientist at SLAC, has been announced as the winner of the 2011 William E. and Diane M. Spicer Young Investigator Award. The award honors a young researcher whose work has benefitted from—or is beneficial to—either the Stanford Synchrotron Radiation Lightsource or the worldwide synchrotron community. It is open to senior graduate students and those who are seven or fewer years into their professional scientific careers. Mannsfeld will receive the award and give a presentation on his research on October 24 at the annual Users' Meeting. "I am very surprised and deeply honored to receive this award," Mannsfeld said. "I had such a big smile on my face when I came home that my wife knew right away that something good had happened." Read more in the SLAC News Center...

J. Rivnay
JONATHAN RIVNAY TO RECEIVE KLEIN AWARD. Jonathan Rivnay, a Stanford graduate student in materials science who has conducted significant research at the Stanford Synchrotron Radiation Lightsource on the relationships between the structure and electrical properties of organic semiconductors, has been selected to receive the 2011 Melvin P. Klein Scientific Development Award. Rivnay will receive the award and give a presentation on his research on October 24 at the annual Users' Meeting. "It's fantastic to have my work recognized in this way," Rivnay said. Read more in the SLAC News Center...

J. Nelson
JOHANNA NELSON WINS DENVER X-RAY CONFERENCE BEST X-RAY DIFFRACTION POSTER AWARD. SSRL Postdoc Johanna Nelson won the Best X-ray Diffraction Poster Award at the 2011 Denver X-ray Conference, held August 1-5 in Colorado Springs, Colorado. Johanna's work, which is part of a SLAC Laboratory Directed Research and Development project led by Yi Cui (Materials Science and Engineering, Stanford University), Mike Toney (SSRL), and Joy Andrews Hayter (SSRL), focuses on the performance of battery electrodes as they are charged and discharged. Johanna has used x-ray diffraction and transmission x-ray microscopy at SSRL to look at morphological and chemical changes in the batteries during operation. Knowledge gained from this project may contribute to development of batteries that can retain capacity over many cycles. Congratulations, Johanna!

7.   User Administration Update
       (contacts: Cathy Knotts,; Lisa Dunn,

CALL FOR SSRL X-RAY/VUV BEAM TIME REQUESTS - DUE SEPTEMBER 1. Proposal spokespersons or their authorized lead contacts on active proposals can submit new X-ray/VUV beam time requests by September 1 for the first SSRL scheduling period (mid November 2011 through mid February 2012). New proposals submitted June 1 are also eligible to submit requests by this date. Request beam time via the user portal. (Request a password if you have not already requested one or cannot remember your URA password; note this is different from your SSRL or SLAC password.)

CALL FOR NEW SSRL X-RAY/VUV PROPOSALS: DUE SEPTEMBER 1, DECEMBER 1, OR JUNE 1. New X-ray/VUV proposals can be submitted 3 times a year: September 1, December 1, June 1. Proposals submitted by September 1 will be peer reviewed, rated and eligible for beam time beginning in February 2012.

Follow these and other upcoming deadlines on the SSRL website.

SPEAR UPDATE AND SCHEDULE. 2010-11 SPEAR user operations ended on July 25, and several maintenance, upgrade, and construction projects are underway over the summer shutdown. Operations will resume again in mid November 2011; see the 2011-2012 SPEAR schedule.

NOMINATE REPRESENTATIVES TO THE UEC. We welcome your help to identify candidates for the SSRL Users' Executive Committee (UEC). Ballots will be compiled in September for the election to be held at the annual Users' Meeting October 22-26, 2011. Appointments to the SSRL UEC generally involve a 3-year commitment. Learn more on the Users' Meeting website.

8.   How to Wow! "Secrets" for a Successful Proposal
       (contact: C. Knotts,; Lisa Dunn,

What makes certain proposals stand out from the crowd in the review process? The Stanford Synchrotron Radiation Lightsource Proposal Review Panel says "A good proposal answers all the 'W'-questions: WHO is going to do WHAT, WHERE (beam line), WHEN (preferred time period), WHY, and HOW."

Beam time at SSRL is made available to users from around the world through proposals submitted via the online user portal three times annually, prior to each SSRL run cycle. Find this year's deadlines on the SSRL webpage.

User proposals are handled in a two-step process: The Proposal Review Panel (PRP) peer reviews and scores each proposal using a five-point scale. Proposal spokespersons are eligible to request beam time in each of the next six scheduling periods (2 years). Beam time requests are reviewed, a schedule for each beam line is centrally prepared by User Research Administration, and beam time is allocated in collaboration with the beam line scientists.

Here are some tips to answer the "W" questions and get your proposal off to a great start in the review process:

  • Start by reviewing the proposal instructions on the user portal (How to Submit an SSRL Proposal).
  • Plan a competitive proposal: Start with a clear, to-the-point title (better than flashy and/or vague). Invest the time to prepare a thorough proposal, and do not assume that the reviewers will be familiar with your work. Base your work on interesting science backed by a good, strong experimental plan. Spell out the importance and relevance of your proposed work (including background and specific aims). Plan experiments that are focused and avoid trying to do too much in one proposal. Submit a single proposal requesting time on multiple beam lines when the work is conceptually related, but submit separate proposals when your research covers a large range of materials or measurements.
  • Do your homework: Clearly define your experimental method, analytical and data interpretation methods, and the need for synchrotron radiation at SSRL. Choose the instrument/beam line best suited for your work. Request a reasonable number of shifts for your experiment—be sure the complexity of your work matches the time you are seeking. If your experiment requires a lot of advance set up and this preparation could be done during a shutdown day, include this in your proposal and beam time request.
  • Identify a good team of collaborators: Include experimenters who bring relevant experience to your experiment and list all experimenters who will play a role in your work, both those who will come to SSRL and those who won't. Beam line scientists are a great resource. Talk to them before submitting your proposal and include beam line scientists on your team if you are collaborating with them.
  • Back up your proposal with demonstrated performance: Include previous data and any preliminary results in your proposal. Cite relevant publications and be sure to inform us so that your papers and theses are on our publications list
  • Have your proposal reviewed by a colleague to ensure that your writing is clear, concise, and on topic—avoid information that is not directly relevant to your specific aims.
Many thanks to Connie Vanni and Pete R. Jemian at the APS for sharing their contributions to this article.

9.   In the News: Graphene Electronics, Vemurafenib

Nitrogen Charges Up Graphene
R&D Magazine
Researchers at SSRL, in collaboration with Columbia University’s Energy Frontier Research Center and scientists from Brookhaven National Laboratory, have demonstrated that it is possible to alter the electronic structure of graphene, a one-atom-thick sheet of carbon, through the direct substitution of individual nitrogen atoms for carbon atoms.

SLAC Beam Used to Develop New Melanoma Drug
Palo Alto Weekly
SSRL's role in the development of the melanoma drug Zelboraf, approved last week by the U.S. Food and Drug Administration, was the focus of an article in the Palo Alto Weekly.


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated for the U.S. Department of Energy Office of Basic Energy Sciences by Stanford University. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH National Institute of General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL website.

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Last Updated: 30 AUGUST 2011
Headlines Editor: Kelen Tuttle