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SSRL Headlines Vol. 11, No. 6  December, 2010


Contents of this Issue:

  1. Holiday Greetings from the Director of SSRL
  2. Science Highlight — SSRL's Hard X-rays Probe Model Fuel-Cell Catalyst
  3. Science Highlight — MRI Contrast Agent Chemically Linked to NSF Disease
  4. Science Highlight — Strange Discovery: Bacteria Built with Arsenic
  5. Carbon's Magnetic Personality: Persistent, but Only Skin-deep
  6. SSRL Looks to Future, Modifies Organizational Structure
  7. Astronaut John Grunsfeld Visits SSRL
  8. LCLS Call for Proposals — Due January 11, 2011

1.   Holiday Greetings from the Director of SSRL

Dear users, colleagues and friends of SSRL,

Chi-Chang Kao
Chi-Chang Kao
I can't believe how quickly four months can pass. Since I arrived at SSRL in late August, I've learned much and am becoming even more excited about the future of SSRL.

In FY2010, SSRL delivered 4,870 hours out of the 5,101 hours scheduled, for an average uptime of 95.5%, allowing approximately 1,400 scientists to conduct experiments. The new user run began in mid-November, and we look forward to ramping up to our goal of 500 mA beam current by the end of FY11. I offer my sincere gratitude to SSRL's outstanding staff members for keeping SSRL extremely competitive among the best synchrotron sources in the world. As I look forward to 2011, I'm very excited about where we're headed. Last week we announced a modified organizational structure (described in more detail below), which reflects our plans to expand the materials and chemical sciences programs and capitalize on our structural molecular biology programs. In the coming months, the new management team and I will engage the SSRL staff and user community in developing a strategic plan for SSRL. I invite you to join us in developing this plan.

But, before all that, I encourage you all to enjoy the upcoming winter shutdown, taking the time to relax and rejuvenate. Best wishes to you and your family for the holiday season.

—Chi-Chang Kao

2.  Science Highlight — SSRL's Hard X-rays Probe Model Fuel-Cell Catalyst
       (contacts: D. Freibel,; A. Nilsson,

PEMFC image
A beam of specially-tuned x-rays scatters off a platinum atom and into a detector, unaffected by the surrounding perchloric acid solution. (Image by Daniel Friebel.)
Researchers at SSRL have developed a new, more powerful way to probe the behavior of a key component in hydrogen fuel cells. The group, led by Daniel Friebel of SSRL and Anders Nilsson of SSRL and SIMES, coated a single crystal of rhodium with one layer of platinum atoms, creating a platinum catalyst that was in essence "all surface." The unique sample design allowed them to observe how the catalyst surface interacted with the type of acid-water environment typical of fuel cells. Using a relatively new type of spectroscopy called high-energy resolution fluorescence detection, the team identified how oxygen is bound to the platinum surface under different conditions. These oxygen-platinum interactions ranged from merely placing oxygen atoms onto an intact metallic surface to forming a surface oxide, which was very difficult to remove. Such interactions could play an important role in degrading the performance of fuel cells, and could be one reason why the reaction on the oxygen side of the fuel cell is inefficient, but it could also be involved in the degradation of the catalyst. All in situ x-ray absorption spectra were measured at SSRL on Beam Lines 6-2 and 11-2.

The new experimental approach appeared online recently in Physical Chemistry Chemical Physics.

To learn more about this research see the full scientific highlight

See also: SLAC Today article by Lori Ann White

3.  Science Highlight — MRI Contrast Agent Chemically Linked to NSF Disease
       (contacts: S. George,; S. Webb,

highlight figure
Light and synchrotron x-ray fluorescence (SXRF) microscopy images of the skin tissue showing element distribution.
Nephrogenic systemic fibrosis, or NSF, is a relatively new disease in which the skin becomes hardened, joint movement becomes difficult and, in extreme cases, an excessive and sometimes fatal fibrosis tissue forms around organs. So far, NSF has only been observed in patients with kidney dysfunction who have undergone an MRI that required the injection of gadolinium-based contrast agents (GBCAs). Researchers speculate that the patient's kidneys cannot break down the gadolinium, causing NSF, but until now there has been no direct evidence for such a link.

To determine whether a causal relationship exists between contrast agents and NSF, a team of researchers recently studied the gadolinium deposits in a skin sample from a patient with NSF using SSRL's microXAS imaging facility on Beam Line 2-3. The researchers were able to see not only that the sample contained small gadolinium deposits-as previous studies had also shown-but also that the gadolinium ion deposits were chemically different from those originally injected as contrast agents. This first direct evidence for the chemical release of gadolinium from GBCA in human tissue suggests that the ions were released from the original, biologically inaccessible form included in the contrast agent, which in turn suggests that the original contrast agent is breaking down in unintended ways. This implies a causal link between the contrast agents and NSF, knowledge that may help chemists and physicians better treat patients with NSF.

This work was published in the November 2010 edition of the British Journal of Dermatology.

To learn more about this research see the full scientific highlight

4.  Science Highlight — Strange Discovery: Bacteria Built with Arsenic
       (contacts: F. Wolfe-Simon,; S. Webb,

In a study that could rewrite biology textbooks, scientists have found the first known living organism that incorporates arsenic into the working parts of its cells. What's more, the arsenic replaces phosphorus, an element long thought essential for life. The results, based on experiments SSRL, were published on December 2 in Science Express.

"It seems that this particular strain of bacteria has actually evolved in a way that it can use arsenic instead of phosphorus to grow and produce life," said SSRL Staff Scientist Sam Webb, who led the research at SLAC. "Given that arsenic is usually toxic, this finding is particularly surprising."

Phosphorus forms part of the chemical backbone of DNA and RNA, the spiraling structures that carry genetic instructions for life. It is also a central component of ATP, which transports the chemical energy needed for metabolism within cells. Scientists have for decades thought that life could not survive without it.

But this was not the case for a strain of Halomonadaceae bacteria called GFAJ-1, found in an eastern California lake. Colonies of these bacteria flourished, as expected, when given a steady supply of phosphorus along with other necessities; yet when researchers replaced the phosphorus with arsenic, the colony continued to grow.

This suggested to Felisa Wolfe-Simon, a NASA research fellow and geobiologist in residence with the U.S. Geological Survey, that the bacteria were using the arsenic in place of phosphorus.

"We already knew that other microbes can 'breathe' arsenic, but it seemed these bacteria could be doing something new: building parts of themselves out of arsenic," said Wolfe-Simon, the paper's lead author. "To see if that was the case, we brought samples to SSRL. I came armed with the knowledge that the bacteria were doing something really weird, and I knew that SSRL Beam Line 2-3, in Sam's hands, could tell us more." Read the full SLAC Press Release.

Mono Lake
A panoramic view of Mono Lake. Located in eastern California, this ancient alkaline lake is known for its hypersalinity and high concentrations of arsenic. (Photo courtesy Henry Bortman.)

To learn more about this research see the full scientific highlight

5.   Carbon's Magnetic Personality: Persistent, but Only Skin-deep
       SLAC Today Article by Lori Ann White

It's a mainstay in biological molecules, but carbon isn't the kind of element you'd expect to find in a permanent magnet. Until now. Not only does carbon become magnetized with a little doctoring, as discovered in 2007, but new findings show this behavior comes naturally-no special treatment required-at the surface of a carbon-based material called graphite.

Researchers used both the Stanford Synchrotron Radiation Lightsource at SLAC and the Advanced Light Source at Lawrence Berkeley National Laboratory to discover not only carbon's innate magnetization, but also that only the surface becomes magnetized, a discovery that may bode well for future applications in electronics and computing. SSRL Staff Scientist Hendrik Ohldag and colleagues from the University of Leipzig and LBNL detailed their research in last week's New Journal of Physics. Their goal was to determine how carbon can be permanently magnetized-a property until recently thought to be confined to iron, nickel, cobalt and a handful of rare alloys. After confirming that their samples contained negligible amounts of magnetic impurities, the researchers got to work. Read more at:

6.   SSRL Looks to Future, Modifies Organizational Structure

On December 8, SSRL Director Chi-Chang Kao announced a slightly modified organizational structure for the SSRL Directorate at SLAC. The changes include removing the X-ray Research and Facilities Division and bringing the areas of research that were previously overseen by this division higher in the organization to become their own divisions. These new divisions are: Materials Sciences, Chemistry and Catalysis, Structural Molecular Biology, Structural Genomics, and the Beam Line Systems divisions. The changes, Kao said, will increase the visibility of these research programs, bring up new leaders within the organization, and position SSRL to achieve the growth outlined in the SLAC agenda.

"SPEAR3 is truly a world-class machine. With continued improvements and upgrades, SPEAR3 will be very competitive in comparison with third generation storage rings worldwide in the coming decade," Kao said. "Over the last few years, SSRL has successfully upgraded the optics and instruments of existing beam lines and has begun to construct completely new undulator beam lines to fully capitalize on the SPEAR3 upgrade. Now it is time to focus our attention on developing scientific programs in targeted areas where we think we can make the greatest impact. The strategy is to build on the existing strength of SSRL in structural molecular biology, exploit the synergy with LCLS and the growth areas in Photon Sciences Directorate, and develop stronger ties with research and talent on Stanford campus."

The new organizational structure, Kao added, provides focus to targeted scientific opportunities and promotes cross-fertilization among research programs. In addition, the structure adds a significant number of leadership positions to allow an aggressive approach in the development of new scientific programs, and it offers new opportunities for scientific staff to grow within SSRL. In the new organizational structure, the Materials Sciences division is headed by Mike Toney and Donghui Lu; Chemistry and Catalysis, by Britt Hedman; Structural Molecular Biology, by Mike Soltis and Hirotsugu Tsuruta; Structural Genomics, by Ashley Deacon; and Beam Line Systems, by Tom Rabedeau.

Kao said he considers SSRL an incubator of new research programs. With SSRL staff members' expertise in broad areas of science and technology and an even larger and more diverse user community, if there's a new area of science to explore, SSRL can probably find someone with the needed knowledge and experience. "The change is not big. In fact, it's pretty subtle. But it gives us a new layer of people who can help develop new science programs and become future leaders in synchrotron research and for SLAC," he said.

In addition to the reorganized divisions, Piero Pianetta and Britt Hedman will shift their roles slightly as well, with Pianetta leading the operations side of SSRL, working closely with the rest of SLAC and, in particular, the Accelerator Directorate. He will also have the responsibility to build a stronger in-house R&D into new x-ray techniques, optics, and instrumentation. Hedman, with her extensive experience and success in managing the structural biology program at SSRL, will lead the development of the new chemistry and catalysis division, the evolution of the structural molecular biology program, and mentoring of other division heads in program development.

"Britt and Piero have been absolutely critical to the success of SSRL, and in these new roles they will be able to contribute even more to the future success of SSRL," Kao said. "I look forward to working closely with them and the whole new management team."

In the next five to ten years, Kao says he seeks to transform SSRL into a world leading photon science facility that provides forefront experimental capabilities, attracts the best scientists in the world, and produces major discoveries and research with significant societal impact.

Grunsfeld Tour Photo
John Grunsfeld (center right) was joined on his tour of SSRL by Staff Scientist Joy Hayter (right), SLAC tour guide and researcher Keith Bechtol (left), and Stanford/SLAC astrophysicists Aurora Simionescu, Norbert Werner and Neelima Sehgal. [larger image]
7.   Astronaut John Grunsfeld Visits SSRL

On Thursday, December 9, astronaut John Grunsfeld toured SLAC, visiting the linac, LCLS and SSRL to see first-hand how x-rays can be used to investigate matter. Grunsfeld, who presented a special colloquium discussing his adventures in orbit and early results from NASA's recently upgraded Hubble Space Telescope, serves as Deputy Director of the Space Telescope Science Institute, the science operations center for Hubble and the James Webb Space Telescope.

"It's really a pleasure to be here," Grunsfeld said as he began his lecture. "I got to see some amazing things. People seem encoded at birth to be excited by two things: space and dinosaurs. We need to make sure we continue to encourage that."

8.   LCLS Call for Proposals — Due January 11, 2011       

Researchers are invited to submit scientific proposals for soft and hard x-rays at the LCLS AMO, SXR, XPP, CXI, XCS, and MEC (with limited capability) instruments. Proposals submitted by January 11 will be eligible for beam time ~October 2011-February 2012. Learn more about the latest developments by contacting LCLS staff scientists and reviewing detailed instrument descriptions available on the LCLS web site.

New capabilities available to users for this call include a ~100 nm focus in CXI and the first time availability of the XCS and MEC instruments. LCLS has demonstrated FEL operations over the energy range 480 eV to 10 keV using the fundamental with pulse energies of 1-3 mJ depending on the pulse duration. Further, LCLS will deliver photons up to 20 keV from a second harmonic afterburner with a flux reduced by roughly an order of magnitude. The pulse length can be varied over 70-300 fs for hard x-rays, while for soft x-rays, the range is extended to 70-500 fs. Shorter pulses (<10 fs) with reduced pulse energy (number of photons per pulse) can also be provided by returning the injector to run at lower charge. The maximum repetition rate of the LCLS is expected to be 120 Hz during this run.

Submit proposals at: (note: spokespersons must be registered and approved as users to submit a proposal)


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: 17 December 2010
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