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SSRL Headlines Vol. 11, No. 7  January, 2011


Contents of this Issue:

  1. From the Director of SSRL: Strategic Plan Development
  2. Science Highlight — Metal Templated Protein Interface Design
  3. Science Highlight — Effects of Thermal Annealing on Organic Solar Cells
  4. Science Highlight — Potential Anti-cancer Drug has Novel Mechanism of Action
  5. New SSRL Instruments Zoom in on Surfaces
  6. Call for Industry Representation on UEC
  7. SLAC Energy Task Force Town Hall Meeting February 4
  8. App for Synchrotron Users
  9. Youth Science Institute Gets into SLAC Science
  10. In Memoriam: Bob Batterman

1.   From the Director of SSRL: Strategic Plan Development

Chi-Chang Kao
Chi-Chang Kao
In January, SSRL's Scientific Advisory Committee (SAC), Machine Advisory Committee (MAC), and User Executive Committee (UEC) met at SLAC. All three groups will be critically important as we develop SSRL's strategic plan and vision for the future.

We recently expanded the SAC membership to provide better coverage in priority scientific areas and facility management. We are also looking to the SAC for help facilitating the formation of strategic alliances. In the SAC meeting, SSRL management presented an overview of the light source for the benefit of the new SAC members, and updated the SAC of the recent progress and changes at SSRL. And, most importantly, we presented the SAC with our vision and the current status of SSRL strategic plan development. In the coming months, we will work with the SAC to complete the plan.

As part of the SSRL strategy, it is critically important that SPEAR3 is operated reliably for the user program and that there is a clearly defined improvement plan to keep SPEAR3 competitive for the next decade and beyond. The MAC was charged to review the accelerator improvement plan developed by the accelerator staff and provide feedback. The MAC report will be discussed at the next SAC meeting to get input from the SAC on the prioritization of accelerator upgrades, in particular their relevance to the scientific programs.

At the UEC meeting, we discussed at length the ways in which we can communicate with the user community, in particular in the next few months as we develop the strategic plan. It was a very productive discussion and generated many great ideas. We will start by using this monthly column to provide everyone an update of the new directions being explored by SSRL and to solicit input and participation. In addition, we are looking at setting up a space on the SSRL website to allow more timely feedback than the monthly newsletter. The goal is for SSRL to engage in a timely fashion the user community as widely as possible-not only in the development of the strategic plan right now, but also in our future planning. In the meantime, please send your ideas on how to improve the communication between SSRL and user community to SSRL's new science information specialist, Kelen Tuttle, at

I look forward to planning SSRL's future together.

—Chi-Chang Kao

2.  Science Highlight — Metal Templated Protein Interface Design
       (contact: A. Tezcan,

MeTIR image
Metal Templated Interface Design (MeTIR)
It took nature billions of years to evolve proteins that can selectively bind to certain metals. Researchers are now seeking to create such proteins synthetically in the lab, with the end-goal of creating new metal-based functions.

A group of University of California-San Diego and University of North Carolina researchers recently used protein binding groups as building blocks, forming them around a metal before rigidifying the structure by engineering covalent and non-covalent bonds. By characterizing the structures-and the metal centers formed in the protein complexes-using SSRL's macromolecular crystallography Beam Lines 9-2 and 7-1, the research team was able to show that this templating approach successfully altered the protein's surface, yielding a unique protein architecture that self-assembled in the presence (or absence) of metals. This approach provides a new method for engineering protein interfacial interactions.

This work was published in the February 2, 2010 edition of the Proceedings of the National Academy of Sciences.

To learn more about this research see the full scientific highlight

3.  Science Highlight — Effects of Thermal Annealing on Organic Solar Cells
       (contacts: E. Verploegen,; M.F. Toney,

highlight figure
Architecture of an organic photovoltaic device.
Organic solar cells, which use organic polymers or small organic molecules to convert sunlight into a useable form of energy, are a promising new tool for providing inexpensive, environmentally friendly energy. To date organic solar cells have demonstrated comparatively low rates of efficiency, stability and strength. However, there is much room for improvement before the theoretical efficiency limits are reached.

In a recent x-ray scattering study undertaken at SSRL Beam Line 11-3, a team of Stanford and SLAC researchers studied how the molecular arrangement of the two components that often make up the active layer of an organic solar cell-the polymer that absorbs photons and converts them into an electric charge and the fullerene that accepts this charge and transports it out of the solar cell-is affected by the heating process, which in turn affects the cell's efficiency.

The study reveals that, in one of the most popular blends, the heating process can cause significant rearrangements of the active layers' structure, including the formation and rearrangement of crystals. By manipulating the layers' structures, the authors conclude, it may be possible to develop improve the performance of organic solar cell devices.

This work was published in the October 22, 2010 edition of Advanced Functional Materials.

To learn more about this research see the full scientific highlight

4.  Science Highlight — Potential Anti-cancer Drug has Novel Mechanism of Action
       (contacts: D. Wang,; S. Lippard,

Cisplatin, a platinum-based anti-cancer drug, is a widely-used and effective cancer chemotherapy drug. It slows the growth of cancer cells by inhibiting transcription through DNA modification, creating chemical links that serve as a roadblock as the polymerase attempts to transcribe the DNA into RNA. Since cancer cells can develop resistance to cisplatin and related drugs, researchers are interested in finding alternative treatments with different targets or mechanisms of action. Pyriplatin shows promise because, as one member of a potentially larger class of such candidates, it remains active in cisplatin-resistant cells and has different chemical and biological properties. Whereas most chemically modified DNAs affect transcription at the site of alteration, DNA modified by pyriplatin can be transcribed through the altered base but cannot continue further.

A team of researchers led by Profs. Stephen J. Lippard of MIT and Dong Wang of UCSD used SSRL macromolecular crystallography Beam Line 11-1 to solve crystal structures of the RNA pol II transcription complexes stalled by a pyriplatin-modification in a DNA template. They found that polymerase-induced structural perturbations of the DNA allow the pyriplatin-modified nucleotide to be transcribed but prevent the next DNA base from swinging into the active site of polymerase. Pyriplatin thus stops pol II from moving down the DNA template in a transcription-stalling mechanism that is significantly different from that achieved by cisplatin-modified DNA.

The mechanism revealed by this study will allow further development of different and more potent anti-cancer drugs. This work was published in the May 25, 2010 issue of the Proceedings of the National Academy of Sciences.

Highlights figure
RNA Pol II stalled by a monofunctional pyriplatin-DNA adduct.

To learn more about this research see the full scientific highlight

5.   New SSRL Instruments Zoom in on Surfaces

S. Kaya and H. Ogasawara
Sarp Kaya (left) and Hirohito Ogasawara at BL13-2. (Photo by Lori Ann White.)
Two new, state-of-the-art spectroscopy instruments at the Stanford Synchrotron Radiation Lightsource promise to give researchers both a broader and a deeper understanding of what happens during chemical reactions at the surfaces of materials. The first new endstation will enable experiments to take place in conditions that more closely mimic real-world conditions; the second will provide a closer look at the chemical bonds that form. The instruments-the Ambient Pressure Photoemission Spectroscopy Endstation, or APPES, and the Surface Science Endstation, or SSE-are being commissioned on SSRL Beam Line 13-2.

"Ambient pressure" is the key to the APPES's capabilities. The instrument uses x-rays to knock electrons off the surface of a material in a process called photoemission spectroscopy, a fairly common technique in surface characterization. Where the APPES differs is its ability to reliably capture data from a material under a few tenths of an atmosphere of pressure. Previously, photoemission spectroscopy required ultra-high vacuum conditions so that the liberated electrons would not be scattered away by atoms in the surrounding atmosphere. Read more at:

6.   Call for Industry Representation on UEC

The SSRL Users' Executive Committee (UEC) meets periodically with management as a forum to communicate the needs and desires of users regarding planning, operations and other issues of concern to those engaged in research at this facility. The UEC would like to add a representative from industry to the committee in order to better consider the perspectives of industry users, particularly to understand what may be helpful to industry users as well as any perceived barriers. User representatives are nominated and then elected by the general user community to serve three-year terms. The UEC meets every few months with the main meeting held in October in conjunction with the Annual Users' Conference and workshops. Please consider whether you or a colleague would be interested in standing for election to represent industry users. Submit nominations by February 15th to Additional information on the users' committee can be found on the Users' Organization website.

We encourage your feedback and suggestions.

7.   SLAC Energy Task Force Town Hall Meeting February 4

SLAC is working to develop a plan for the expansion of the laboratory's research program by establishing new strategic directions in energy-related research. This may include the integration of separate projects into a larger coordinated effort with defined goals and stronger and sustained support, a major expansion of existing research, creation of entirely new research in areas of strategic importance, and/or partnerships with other national labs and industry, as well as for research infrastructure development.

To accomplish this task, SLAC Chief Scientist Z.-X. Shen set up a task force that started its work in November 2010 and has already evaluated many potential topics. On February 4 from 10 a.m. to noon, the task force will hold a town hall meeting in SLAC's Kavli Auditorium to report preliminary findings and seek input from the broader SLAC/Stanford research community. Based on the findings and recommendations of the task force, SLAC Director Persis Drell intends to present SLAC's energy strategy to the Department of Energy Office of Science in spring 2011 as part of the laboratory business plan presentation. The results of this task force will also likely guide future Laboratory Directed Research and Development investments and lead to the development of specific funding proposals in the future.

8.   App for Synchrotron Users
       (contact: S. Webb,

Sam Webb's X-rayUtils app is a reference utility application for the iPhone, iTouch, and iPad that provides synchrotron scientists and users with all the information you wish you had easy access to at a beam line: status, lines, absorption, and ion chambers. The X-rayUtils app includes status updates for storage rings; general atomic properties, absorption edges, and fluorescence lines (with yields) for elements hydrogen through californium (a must for the x-ray absorption experimenter or microprobe user); an x-ray absorption calculator for absorption length and total absorption of any compound, given the x-ray energy, chemical formula, density and thickness of the compound of interest); by entering the basic properties of the ion chamber in your experiment (gas composition, pressure, energy, chamber length, measured voltage and amplifier gain) you will get the x-ray flux in photons per second.

For more info, see

9.   Youth Science Institute Gets into SLAC Science       

On January 19, SLAC welcomed 25 instructors and staff of the Youth Science Institute-a local non-profit which provides hands-on science education to over 35,000 children in the Bay Area-for a day of tours and presentations. The group visited SLAC's visualization laboratory, the Stanford Synchrotron Radiation Lightsource and the Linac Coherent Light Source and learned about topics ranging from how the first massive stars formed in the universe to studies of lead deposits found in 19th century silk clothing on display in American museums. YSI and SLAC will be looking for ways to foster new educational partnerships in the near future.

10.   In Memoriam: Bob Batterman       

Boris (Bob) Batterman, 80, a frequent SSRL user, died peacefully last month in his sleep. Bob was one of the founding fathers of synchrotron radiation research, the first director of the Cornell High Energy Synchrotron Source (CHESS), and one of the pioneers of dynamical diffraction theory and its application in materials science. A memorial service is planned for the spring.


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 by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. 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 Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 31 January 2011
Headlines Editor: K. Tuttle