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SSRL Headlines Vol. 11, No. 10  April, 2011


Contents of this Issue:

  1. From the Director of SSRL: Planning for this Fiscal Year and Many More to Come
  2. Science Highlight — Understanding the Innate Immune System
  3. Science Highlight — High-temperature Superconductor Spills Secret: A New Phase of Matter
  4. Stanford-Berkeley Group Awarded $25 Million for Advanced Solar Research
  5. Axel Brunger Receives DeLano Award
  6. Stern, Lytle, Sayers, and Rehr Win 2011 APS Arthur H. Compton Award
  7. Seen at SSRL: Leland Cogliani
  8. User Science Exhibition on Capitol Hill
  9. Science & Engineering Nifty Fifty
  10. Upcoming Events: New Scientific Computing Series; Annual Users' Conference
  11. User Administration Update
  12. In the News: A New Type of Battery, Reptile Skin, and Magnet Design

1.   From the Director of SSRL: Planning for this Fiscal Year and Many More to Come

Chi-Chang Kao
Chi-Chang Kao
We were recently informed about the FY11 budget for SSRL, which is on par with the budget we received in FY10. This is much better than what we had anticipated and we are grateful for the efforts made by everyone in the complex budget process. The new budget, although still very tight, will allow SSRL to complete the scheduled 2011 run and begin to invest in new capabilities, in particular undulator beam lines.

The experience of this year's budget process highlights the importance of the sustained effort made by the user community, through organizations such as the National User Facility Organization (NUFO) and Synchrotron Neutron User Group (SNUG), in communicating the impact of science and technology on the nation's economy and, in particular, the essential role the DOE Office of Science plays in supporting the nation's research infrastructure.

With that in mind, I encourage you to participate in this year's NUFO annual meeting, which will be held here at SLAC on June 27-29. The theme of this year's meeting is "NUFO Encourages Access & Awareness." The meeting will focus on outreach, access, science vision and funding, diversity, technology transfer, and working with industry. The meeting will also offer user representatives the chance to practice translating their science for the public, and user administrators the chance to hone their skills at delivering key messages about the science we do and why it is important.

Finally, SSRL together with DESY, KEK and CHESS is organizing a series of six workshops dedicated to scientific opportunities enabled by diffraction-limited, high repetition rate, hard x-ray sources-such as energy recovery linacs and ultimate storage rings-and high repetition rate FELs. These workshops, which will be held at Cornell University's Robert Purcell Conference Center throughout June, will help us formulate the long term strategy for SSRL. I encourage you to participate as much as possible. Detailed information about the workshops can be found on the CHESS website.

—Chi-Chang Kao

2.  Science Highlight — Understanding the Innate Immune System
       (contact: Tina Iverson,

While much is known about how the acquired immune system recognizes and responds to pathogens, the innate immune system, which also fights off infections and disease, is much less well understood. The inflammatory responses of the innate immune system can be activated by toll-like receptors (TLRs), which often bind to elements from pathogens that have a regular repeat, such as double-stranded RNA. Researchers theorize that TLRs may also bind to stable parts of outer membrane proteins or covalent modifications of these proteins. Either way, even if the pathogen mutates to try to escape host defense mechanisms, the TLRs will still recognize them.

In a recent study, researchers from Vanderbilt University Medical Center and Weill Cornell Medical College studied the outer membrane protein PorB from Neisseria meningitides, a causative agent of bacterial meningitis. By determining the outer membrane protein's crystal structure at SSRL's Beam Lines 9-2 and 11-1, and combining this with additional data collected at the Advanced Light Source and the Cornell High Energy Synchrotron Source, the research team was able to deduce that stationary electric charges on the N. meningitidis PorB structure may be important for the interaction. The TLRs' ability to bind to the outer membrane protein despite mutations can be explained by the fact that small changes in the electric charges have very little effect on the TLRs' overall attraction to N. meningitidis PorB.

This work was recently published in the Proceedings of the National Academy of Sciences.

Structure of N. meningitidis PorB
Structure of N. meningitidis PorB
To learn more about this research see the full scientific highlight

3.  Science Highlight — High-temperature Superconductor Spills Secret: A New Phase of Matter
       (contact: Donghui Lu,

Particle-hole symmetry breaking in the antinodal dispersion of pseudogapped Pb-Bi2201
Scientists have found the strongest evidence yet that a puzzling gap in the electronic structures of some high-temperature superconductors could indicate a new phase of matter. Understanding this "pseudogap" has been a 20-year quest for researchers who are trying to control and improve these breakthrough materials, with the ultimate goal of finding superconductors that operate at room temperature.

"Our findings point to management and control of this other phase as the correct path toward optimizing these novel superconductors for energy applications, as well as searching for new superconductors," said Zhi-Xun Shen of the Stanford Institute for Materials and Energy Science (SIMES), a joint institute of the Department of Energy's SLAC National Accelerator Laboratory and Stanford University. Shen led the team of researchers that made the discovery; their findings appear in the March 25 issue of Science.

The team found that electrons in the pseudogap phase, do not pair up as was previously understood. Instead, they reorganize into a distinct yet elusive order of their own. The knowledge that the pseudogap indicates a new phase of matter provides a clear signpost for follow-up research, according to Ruihua He, a post-doctoral researcher at the Advanced Light Source and first author of the paper. He outlined the next steps: "First to-do: uncover the nature of the pseudogap order. Second to-do: determine whether the pseudogap order is friend or foe to superconductivity. Third to-do: find a way to promote the pseudogap order if it's a friend and suppress it if it's a foe." Read the full SLAC press release.

To learn more about this research see the full scientific highlight

4.   Stanford-Berkeley Group Awarded $25 Million for Advanced Solar Research

A joint solar research effort managed by Stanford and the University of California-Berkeley has won $25 million in funding from the U.S. Department of Energy's SunShot Initiative, which seeks to aggressively drive solar energy innovations. Portions of the work will be conducted at the Stanford Synchrotron Radiation Lightsource, Lawrence Berkeley National Laboratory and the National Renewable Energy Laboratory.

The Stanford-Berkeley group, dubbed the Bay Area Photovoltaics Consortium, or BAPVC, will develop and test the innovative new materials, device structures and fabrication processes needed to produce inexpensive, efficient photovoltaic modules in high volume. The SunShot Initiative's ultimate goal is to reduce the cost of installed solar energy systems to one dollar a watt, an accomplishment that would enable solar energy systems to be broadly deployed across the country.

"It's a simple goal that will make solar competitive with the more conventional types of power," said BAPVC co-PI and SSRL Senior Scientist Mike Toney. To reach this goal, the consortium estimates they will need to bring down manufacturing costs and improve device performance to the point that manufacturing solar cell modules costs about 50 cents a watt. The other 50 cents a watt will go toward installation, power management, permitting and other costs needed to bring the collected energy to the electrical grid.

As the most widespread solar systems are based on just a few well-understood materials, BAPVC will search for and characterize new materials and processing that outperform the standard ones. The consortium will also conduct in situ analyses during processing to find the best fabrication processes to control material structure and defects.

To assure close alignment with industry and manufacturing needs, the consortium also includes industry participants: initial industry members include GE, Applied Materials, Corning, Boeing-Spectrolab, CaliSolar, Alta Devices, Intermolecular, Applied Materials, Bosch, NuvoSun, Solexant, Alion, Crystal Solar, Solar Junction, Encore Solar and Stion.

The BAPVC project is co-directed by Yi Cui, associate professor of materials science and engineering at Stanford, and Ali Javey, associate professor of electrical engineering and computer sciences at Berkeley.

In addition to the $25 million awarded to the BAPVC project, Secretary of Energy Steven Chu awarded $25 million to SVTC Technologies (San Jose, California) and $62.5 million to the U.S. Photovoltaic Manufacturing Consortium (Albany, New York, and Palm Bay, Florida). The SVTC Technologies work seeks to accelerate the development, manufacturing and commercialization of next-generation copper indium gallium selenide (CIGS) thin film photovoltaic manufacturing technologies. The U.S. Photovoltaic Manufacturing Consortium will create a fee-for-service manufacturing development facility that will enable start-ups, materials suppliers and other photovoltaic innovators to greatly reduce up-front capital and operating costs during product development and pilot production.

For more information, see the Department of Energy press release.

5.   Axel Brunger Receives DeLano Award

Axel T. Brunger
Axel Brunger, professor of Molecular and Cellular Physiology, of Neurology and Neurological Sciences, Photon Science and, by courtesy, of Structural Biology, has been named the winner of the American Society of Biochemistry and Molecular Biology's inaugural DeLano Award for Computational Biosciences.

The award, given for the first time this year, honors those who "create accessible and innovative development or applications of computer technology to enhance research in the life sciences at the molecular level," according to a press release issued by the society.

See the American Society of Biochemistry and Molecular Biology's press release for more information.

6.   Stern, Lytle, Sayers, and Rehr Win 2011 APS Arthur H. Compton Award

Congratulations to Ed Stern, Farrel Lytle, the late Dale Sayers and John Rehr, winners of the 2011 Advanced Photon Source's Arthur H. Compton award. Nominated for their pioneering development of the theory and use of x-ray absorption fine structure spectroscopy (XAFS), these individuals and their early work transformed how x-ray researchers around the world study local structure around x-ray absorbing atoms in gases, liquids, and amorphous and crystalline solids. Classic papers by these pioneers have been sited thousands of times and have influenced countless researchers.

7.   Seen at SSRL: Leland Cogliani

On Friday, April 22, SLAC hosted Senate Energy and Water Appropriations Subcommittee Staff Member Leland Cogliani. Cogliani's visit to SLAC included an overview of laboratory science and a tour of both SSRL and the Linac Coherent Light Source. Cogliani's time at SSRL focused in particular on partnerships with industry and included a meeting with Cocrystal Discovery, Inc., Scientist David Bushnell.

8.   User Science Exhibition on Capitol Hill

SSRL, the Linac Coherent Light Source and SLAC's particle physics and astrophysics user facilities were represented at the National User Facility Organization (NUFO) exhibit on Capitol Hill earlier this month. SSRL representatives Michael Toney and Cathy Knotts highlighted research underway at the facilities and addressed how the science underpins U.S. competitiveness and innovation. Learn more on the NUFO website.

9.   Science & Engineering Nifty Fifty

The second USA Science & Engineering Festival will be held in Washington D.C. April 27-29, 2012, and the expo will once again highlight the Nifty Fifty Program. "Nifty Fifty" refers to a group of high-profile researchers and professionals in science and engineering who will speak about their work and careers at middle and high schools in the Washington, DC area during the 2011/2012 school year. This year the program is being doubled: instead of 50, 100 researchers and professionals will take part.

To help inspire the next generation of scientists and engineers, please nominate scientists, engineers or related professionals who have had a major impact on their field to be considered for this elite cadre of professionals. Other fields such as law, business, government, and public service are also considered. The nomination form and more information can be found here on the festival website.

10.   Upcoming Events: New Scientific Computing Series; Annual Users' Conference

Seminars to Share Scientific Computing Knowledge, Experience - This month marks the beginning of a new scientific computing seminar series, which showcases scientific computing techniques from across the lab and beyond. Lectures by SLAC researchers will discuss the science made possible by the vast amounts of data produced by the LCLS, images of the universe in three dimensions and more. Scientists from other institutions will also share new methods for using computing to advance science. The first lecture, given by LCLS Instrument Scientist Garth Williams earlier this week, discussed new methods in coherent imaging and nano crystallography. Williams demonstrated how the raw data taken by the Coherent X-ray Imaging instrument-which can already exceed 700 megabytes per second and total more than 100 terabytes for some experiments-is converted into molecular and atomic structures. The lectures are currently scheduled for one Tuesday a month in SLAC's Kavli Auditorium. The next will take place on May 17.

Annual Users' Conference, October 24-26 - Plan to participate in the Annual SSRL/LCLS Users' Meeting and Workshops, October 24-26, 2011 to learn about new developments and share exciting user research at both LCLS and SSRL. The draft program and registration details will be posted shortly. In the meantime, please take a few moments to consider nominating your colleagues or students for the William E. and Diane M. Spicer Young Investigator Award, the Melvin P. Klein Professional Development Award, and the Farrel W. Lytle Award. Submit your nominations to Cathy Knotts ( These awards will be presented at the Users' Meeting. You can also reserve lodging for the meeting by contacting the Stanford Guest House. Specify SSRL/LCLS/SLAC to take advantage of discounted rates.

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

X-ray/VUV May-July Schedule Posted - Many beam lines were significantly oversubscribed, but we tried to accommodate as many user experiments as possible; view the SPEAR X-ray/VUV schedule from the SSRL website or view your specific beam time through the portal.

Call for New SSRL X-ray/VUV Proposals: Due June 1, September 1 or December 1 - New X-ray/VUV proposals can be submitted three times a year: June 1, September 1 and December 1. Proposals submitted by June 1 will be peer reviewed, rated and eligible for beam time beginning in November 2011.

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 for the first scheduling period (late November 2011 through February 2012) by September 1. (New proposals submitted June 1 are also eligible to submit requests by this date; ratings for new proposals will be provided in August). 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).

12.   In the News: A New Type of Battery, Reptile Skin, and Magnet Design

A New Type of Battery
Researchers at SLAC and Stanford have developed a new method of extracting energy using electrodes and a combination of freshwater and saltwater. Their methods of extraction offer 74% efficiency.
Salt Water Shows Promise as Battery Juice Wired Science
Stanford Researchers Use River Water and Salty Ocean Water to Generate Electricity Stanford Report

infra-red mapping image
First Image of Protein Residue in 50 Million Year-old Reptile Skin
The organic compounds surviving in fifty-million year-old fossilized reptile skin have been seen for the first time, thanks to a stunning infrared image produced by University of Manchester palaeontologists and geochemists. These infrared maps are backed up by the first ever element-specific maps of organic material in fossil skin generated using X-ray methods at SSRL.
Prehistoric Reptile Skin Secrets Revealed in New Image BBC News
Prehistoric Skin Holds Building Blocks of Life Discovery News

Redesigning the Magnet
SLAC researcher Sumohan Misra, collaborating with an Ames Laboratory team, recently reported altering the properties of a magnet by replacing key atoms in its structure.


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: 27 April 2011
Headlines Editor: K. Tuttle