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SSRL Headlines Vol. 9, No. 8  February, 2009


Contents of this Issue:

  1. Science Highlight — X-rays Focusing on Mercury
  2. Water: The Strangest Liquid
  3. White Paper on Science and Technology of Future Light Sources
  4. Dehmer Announces DOE Accelerator Workshop
  5. From the Directors of Photon Science and SIMES: An Energy Facet of the SLAC-Stanford Partnership
  6. Uwe Bergmann to Head Chemical and Materials Science and User Support Group
  7. Upcoming Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology
  8. User Experiments Resume on Upgraded BL4-1 and BL4-3 in March
  9. Rapid Access Program Expanded to Include BL7-2 XRD Experiments
  10. Purdue Scientist on Sabbatical at SLAC to Develop Ideas for Faster Synchrotron Imaging Methods
  11. User Research Administration Update

1.  Science Highlight — X-rays Focusing on Mercury
       (contact: G. George,

highlight figure
X-ray fluorescence images of anaesthetized zebrafish larvae.
Organomercury is a well-known poison, and the potential for exposure worries many communities worldwide. Developing embryos are especially susceptible to mercury poisoning, which can result in serious birth defects. Despite the awareness of mercury's adverse health affects, little is known about the mechanisms for mercury toxicity.

A research group led by Graham N. George and Ingrid J. Pickering from the University of Saskatchewan, Canada, used SSRL's beam lines 9-3 and 2-3 to develop a novel approach to identify which cells types attract mercury. They scanned mercury-exposed zebrafish larvae using synchrotron X-ray fluorescence imaging, which gave a direct image of where in the fish the mercury was collecting.

Zebrafish are often used as a model for human development. Cell types that absorb mercury in zebrafish larvae may also collect mercury in human embryos, and knowing which cells absorb mercury is critical to finding the mechanisms of its toxicity. In this study, zebrafish larvae were exposed to varying concentrations of methyl-mercury compounds. The images clearly showed hot-spot areas of high mercury concentrations in the bodies and tissues of the larval zebrafish. The researchers were surprised to discover that mercury strongly collected in the outer layer of the eye lens of the zebrafish larvae, even more than in known target organs such as the brain and liver. This layer is composed of rapidly dividing epithelial cells, since the larvae emerge before their eyes are fully developed. The mechanism for absorption of mercury by these fish eye lens cells may be similar to the mechanism by which rapidly dividing human fetus cells absorb mercury. If mercury similarly concentrates in the eyes of humans, this may help explain how mercury exposure can cause blindness, in addition to damaging the nervous system.

The method that the researchers used also simultaneously locates other elements, including calcium and zinc, in the zebrafish larvae. The technique can also be applied to locating other biologically toxic and important heavy metals such as arsenic and lead, to tracking minerals like zinc, iron and calcium during development, and in understanding the effectiveness of drugs which are supposed to remove toxic metals, such as chelating agents.

To learn more about this research see the full scientific highlight at:

2.  Water: The Strangest Liquid

Public Lecture Poster TN
Over 300 people attended this February 24 Public Lecture presented by Anders Nilsson, Photon Science Professor and Deputy Director of the Stanford Institute for Materials and Energy Sciences (SIMES). Nilsson discussed the many mysteries of water as well as current studies that are revolutionizing the way we see and understand one of the most fundamental substances of life. Water, H2O, is familiar to everyone-it shapes our bodies and our planet. But despite its abundance, water has remained a mystery, exhibiting many strange properties that are still not fully understood. Nilsson raised many questions in his talk such as why does liquid water have an unusually large capacity to store heat? And why is it denser than ice? Nilsson also summarized his investigations into water which are leading to fundamental discoveries about the structure and arrangement of water molecules. Participants in the lecture were buzzing with excitement afterwards, including Nilsson who commented, "It was a lot of work but I loved it. Such an inspiration to speak to such an interesting crowd. It was a kick for me."

Learn more about research activities on x-ray and electron spectroscopies applied to surfaces and interfaces, chemical bonding and reactions on surfaces, hydrogen bonding in water and organic systems, aqueous solutions and interfaces, heterogenous- and biomimetic enzyme catalysis at:

3.   White Paper on Science and Technology of Future Light Sources
       (contact: J. Stöhr,

White Paper Cover Image
In this short note, I would like to bring to your attention a joint paper written by scientists from the four DOE labs with synchtrotron radiation facilities: Argonne, Brookhaven, Berkeley and SLAC. The so-called White Paper was sent to DOE in December 2008 and makes the case for the continued investment in x-ray science in the US. In writing the document, the four labs worked together in an unprecedented way to create a compelling vision for the entire field of x-ray science. The paper was timed to be useful in briefing the incoming Obama administration.

The paper leads out with a general introduction of the important role of x-rays in science - past, present and future. In line with the goals of the new administration it then outlines how x-rays may be used to tackle important challenges facing humanity, including developing alternative sources of energy and improving health. It also links x-rays to the Grand Challenges recently formulated by the Basic Energy Sciences Advisory Committee of DOE. It outlines how meeting these challenges will require new x-ray tools that extend our reach into regions of higher spatial, temporal, and energy resolution.

I encourage you to read more about the identified scientific opportunities, the x-ray capabilities needed to address them, and the R&D required to create suitable sources at:

4.   Dehmer Announces DOE Accelerator Workshop
       February 20, 2009 SLAC Today Article by Calla Cofield

The Department of Energy is planning to host an accelerator science workshop in late 2009 to gather input toward "developing a national accelerator research and development stewardship effort," according to Office of Science Deputy Director for Science Programs Patricia Dehmer. Dehmer announced plans for the workshop at the 2009 AAAS meeting in a session on the future of accelerator science in the U.S. In her presentation, Dehmer said that the workshop would focus on "uses of accelerators throughout society, the desired performance characteristics of these and future accelerators, and the R&D efforts in the private and government sectors." The workshop is intended to host scientists as well as representatives from industry. Dehmer said it will be organized by Dennis Kovar, the associate director of High Energy Physics. The DOE has no announced other details about the workshop at this time.

5.   From the Directors of Photon Science and SIMES: An Energy Facet of the SLAC-Stanford Partnership
       February 13, 2009 SLAC Today article by Keith Hodgson and Z.-X. Shen

K. Hodgson
Z.-X. Shen
We are all acutely aware of the importance of energy-the criticality of reliable and sustainable supplies, the role of its cost on our economy, and the impact of energy production and use on the environment. The challenges facing us in the energy arena are not simple and solutions will come only through sustained investment in basic research and development utilizing multidisciplinary strategies that can be translated into practical applications.

Read more at:

6.   Uwe Bergmann to Head Chemical and Materials Science and User Support Group

U. Bergmann
SSRL is pleased to announce that Uwe Bergmann will take over as manager of Chemical and Materials Science and User Support within the Experimental Systems and Research Division at SSRL. The promotion recognizes Uwe's expertise and leadership in x-ray science. In his new role Uwe will assist the SSRL Directorate in the planning of instrumentation and beam lines to capture new research opportunities and with SSRL's evolution toward PEP-X.

The SSRL organization chart has been updated to reflect this change.

7.   Upcoming Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology
       (contact: H. Tsuruta,

A workshop on small-angle x-ray scattering and diffraction studies in Structural Biology will be held April 9-12, 2009 at SSRL. Online Registration is available at:

The workshop consists of two days of lectures, and two days of practical sessions on experimental and computational aspects of small-angle x-ray scattering studies in biology, particularly solution x-ray scattering. It will cover the following scientific and technological topics:

Lecturers include Dmitri Svergun (EMBL-Hamburg), Brian Shilton (Univ. Western Ontario), Osman Bilsel (Univ. Massachusetts), Vadim Cherezov (Scripps), Pehr Harbury (Stanford), Andrej Sali (UCSF), Daniel Kirschner (Boston College) and SSRL SMB staff members.

workshop artwork

The workshop dates immediately follow the West Coast Protein Crystallography Workshop in Asilomar, CA.

8.   User Experiments Resume on Upgraded BL4-1 and BL4-3 in March
       (contacts: J. Rogers,; M. Latimer,

The last of the SPEAR3-related beam line upgrades are complete, and users are eagerly planning their x-ray absorption spectroscopy (XAS) experiments on the newly upgraded BL4-1 and BL4-3. Resuming operations in early March, BL4-1 will be dedicated for XAS experiments in the 5.5-38 keV energy range, and BL4-3 will be dedicated to both XAS hard x-ray experiments and XAS measurements with special capabilities for soft x-ray measurements (from S K-edge and up, 2.4-6 keV). Applications include mainly molecular environmental and interface science, biology, chemistry and materials science.

Users interested in beam time on these beam lines must submit a beam time request for May-August scheduling period by the March 13 deadline.

9.   Rapid Access Program Expanded to Include BL7-2 XRD Experiments

A block of approximately 6 shifts of beam time will be set aside about every 6 weeks for rapid access x-ray diffraction (XRD) experiments on BL7-2. Allocation of beam time will be based on a brief proposal to be reviewed and rated by the SSRL Proposal Review Panel. Both new and current users are eligible to compete for this rapid access time. Rapid access proposals can be submitted at any time, and users will be notified ~2-4 weeks prior to allocated beam time.

New users scheduled for beam time under a rapid access proposal will be trained by SSRL staff on all aspects of the experimental setup (beam line optics, use of detectors and data collection software). Staff will also advise users on sample preparation and data analysis to help new users efficiently utilize their beam time and prepare them for successful future experiments.
  See BL7-2 XRD rapid access application

Users can also submit a brief scientific proposal to compete for a block of 3-6 shifts of beam time set aside for rapid access to several other techniques and beam lines, including:

10.   Purdue Scientist on Sabbatical at SLAC to Develop Ideas for Faster Synchrotron Imaging Methods
       February 25, 2009 SLAC Today Article by Lauren Schenkman

Synchrotron physicists are missing important scenes from their favorite film-the lives of atoms. "In every physicist's imagination you have this mental picture of how things move, like you're watching a movie," said Purdue University x-ray scientist Steve Durbin. Durbin is spending a six-month sabbatical at SLAC and Stanford's PULSE Institute for Ultrafast Energy Science. He's developing ideas for detectors that could make imaging methods at synchrotron sources a hundred times faster.

To make an atomic movie, you'd need to snap each frame with a shutter speed of at least a trillionth of a second, or picosecond. With that time resolution it would be possible to watch the energy of an incoming photon excite the electrons and then transfer to the atoms of a system, for example, causing movement that leads to a molecule breaking up or forming. But so far, such movies have existed only in physicists' imaginations.

"That timeframe has been totally inaccessible to the vast majority of x-ray synchrotron experiments in the past," Durbin said. "Most x-ray beams come out of a synchrotron in pulses of 100 picoseconds, which to a layman sounds incredibly fast, but this is still 100 times too slow to get to these fundamental atomic lifetimes." Even in the seemingly lightning-fast pulse from a synchrotron, the fine details of these electronic dynamics are blurred. Read more at:

11.   User Research Administration Update
       (contact: C. Knotts,

—Submit X-RAY/VUV Beam Time Requests before March 13
Users interested in requesting beam time for the third scheduling period for the 2009 run (~mid May through August 10, 2009) must submit requests before March 13 by logging into the User Research Administration web interface. Enter your email address and your password. If this is your first time using this system or if you don't remember your password, click on the blue text 'request a password' and follow the instructions to request/reset your password. Click on 'Beam Time Requests', and submit a separate request for each proposal, beam line, equipment configuration and/or each individual beam time period requested. With this system, you can clone a previous request or save a draft so that you can edit and complete it at a later date. You can also view your active proposals, accept your scheduled beam time, and submit your user support requests to inform us of who from your group plans to collect data at SSRL.

If the availability you indicate on your beam time request form changes prior to issuance of the schedule, please let us know immediately. The 2009 SPEAR operating schedule, which includes information on scheduled maintenance and accelerator physics studies, is available on the SSRL website at:

—Macromolecular Crystallography Proposals due April 1
Macromolecular Crystallography Proposals due April 1: If you are interested in submitting a standard program proposal for continuing 2-year access to SSRL's macromolecular crystallography beam lines, please submit a proposal by April 1.

As mentioned above, the Rapid Access Application is available for a set of shifts in a single 2-3 month scheduling period.

For more information regarding macromolecular crystallography beam time, contact L. Dunn (

—Ask for SSRL/SLAC Rooms at Guest House
We try to block rooms specifically for SSRL/SLAC use when we are aware of major Stanford events that may otherwise fill the Guest House (including graduation in June). These rooms can be accessed for any SLAC visitors just by asking. So if you run into problems getting a room at the Guest House, ask if there are any rooms set aside for SSRL or SLAC. Even if there are no rooms available when you call, ask the Guest House to add your name to their waitlist. As they get close to the sold out dates, especially four weeks in advance when most unreserved group block reservations start dropping off, rooms may become available.


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: 06 MAR 2009
Content Owner: L. Dunn
Page Editor: L. Dunn