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SSRL Headlines Vol. 7, No. 8  February, 2007


Contents of this Issue:

  1. Science Highlight — Five Images for the Price of One: Using X-ray Holography for Simultaneous Imaging
  2. Science Highlight — Using Microorganisms to Understand Hydrogen Catalysis
  3. Science Highlight — Ultrafast Bond Softening in Bismuth - a Femto-second Pump-probe SPPS Study
  4. XAS Course for Structural Molecular Biology Applications — March 13-16
  5. SSRL Advisory Committees Convene in February
  6. John Zachara among Eight DOE Lawrence Award Winners
  7. SSRL Macromolecular Crystallography Remote Data Collection
  8. X-ray/VUV Beam Time Requests due by March 5
  9. Photon Science Job Opportunities

1.  Science Highlight — Five Images for the Price of One: Using X-ray Holography for Simultaneous Imaging
       (contact: W.F. Schlotter,

The detected hologram is shown in false color with the number of photons detected denoted by the scale bar. [larger view]
Scientists at SSRL have demonstrated a novel approach for improving the efficiency of an x-ray microscopy technique that may in particular prove beneficial for imaging radiation-sensitive objects such as biological samples. The findings, published in the October 2006 issue of Applied Physics Letters, should enhance imaging of sensitive samples and improve imaging with future ultra-short pulsed light sources, such as the Linac Coherent Light Source.

Using Fourier Transform Holography (FTH) with 1.58 nm wavelength "soft x-rays," the team of scientists extended the detection limit of high-resolution lensless imaging without increasing radiation exposure. FTH reconstructs a sample's microscopic image from its soft x-ray scattering pattern alone. With this lensless technique, coherent light scattered by a sample interferes with light scattered from a reference aperture to form a hologram. An image of the sample is analytically reconstructed from the hologram using a simple, direct process called a Fourier transformation. By illuminating several references with coherent x-rays, multiple holographic images of the specimen are reconstructed simultaneously.

Holographic references were defined by five nanoscale holes, and the test sample was a 1-micron tall block letter F. Its diffraction pattern was recorded as a hologram on an x-ray sensitive digital camera. The researchers produced a recognizable composite image of the sample after detecting only 2500 x-ray photons. The group found that compiling holographic images from multiple reference sources improves image quality by minimizing noise from imaging systems.

The team of Stanford researchers and their collaborators conducted the proof-of-principle experiment at SSRL beam line 5-2.

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

2.  Science Highlight — Using Microorganisms to Understand Hydrogen Catalysis
      (contact: R.K. Szilagyi,

Molecular structure of FeFe-hydrogenase from Chlostridium pasteurianum I with H-cluster (catalytically active site) and accessory clusters.
The FeFe-hydrogenases are of great interest because they can catalyze both the forward and reversed dihydrogen uptake/evolution reactions. Under optimal conditions a single molecule of FeFe-hydrogenase can produce approximately 9000 molecules of hydrogen per second. This translates into a theoretical capacity for refueling the hydrogen tank of the Space Shuttle within 30 minutes. Thus, hydrogenases are considered as desirable biological targets for hydrogen-based energy production and utilization technologies.

Organisms that possess FeFe-hydrogenases are widely distributed among different microorganisms, including hyperthermophiles and algae. But understanding the chemistry driving the efficient hydrogen conversion has been difficult, due to in part because the molecules themselves are so large and complex. Now, researchers at Montana State University and collaborators have solved part of the puzzle by looking at a synthetic biomimetic molecule that structurally models the active site of these metalloenzymes.

Using sulfur K-edge x-ray absorption spectroscopy data from SSRL's beam line 6-2, the researchers probed the nature and the strength of the chemical interaction between the 4Fe- and the 2Fe-containing subclusters of the active site H-cluster. By comparing the spectra of each subcluster and the biomimetic H-cluster framework, the team found evidence for considerable electron delocalization between the subclusters, suggesting that the H-cluster is an electronically inseparable [6Fe-6S] cluster. Computer modeling on the separate and combined subclusters also show this delocalization by the presence of molecular orbitals that span the entire 6Fe-framework. Thus, the catalytic activity is determined by both subclusters together, not just the [2Fe-2S] subcluster that has been the focus of much past research.

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

3.  Science Highlight — Ultrafast Bond Softening in Bismuth - a Femto-second Pump-probe SPPS Study
      (contact: D.M. Fritz,

One hundred consecutive electro-optic signals.
In a recent experiment performed at SLAC and reported in the February 2 issue of Science, David Fritz and his SPPS colleagues have obtained our first direct view of the motion of atoms inside a crystal. This feat requires simultaneous Angstrom spatial and femtosecond temporal resolution. Synchrotrons have been providing subatomic resolution for decades, and ultrafast lasers have been capable of sub-picosecond timing for more than twenty years; but SPPS was the first instrument to combine both.

The Science report showed how the atoms in a Bi crystal move following excitation with an ultrafast laser. The Bismuth crystal structure is almost perfectly cubic, but has a slightly elongation along the diagonal of the cube, called a Peierls distortion. Calculating how this distortion arises from the electronic binding forces is something of a benchmark challenge for Density Functional Theories. In the work reported in Science, an extremely short laser pulse excites conduction electrons in the crystal, which suddenly releases the distortion partially, driving the crystal lattice to oscillate around a new less distorted position. This kind of rapid excitation leading to oscillations is much like the motion of a guitar string when plucked. The change in the crystal distortion with the density of conduction electrons is an important test of our understanding of nature of solid matter.

The crystal distortion oscillates for a brief time after the laser excites it - only a few picoseconds, but long enough to be easily resolved by the 160 femtosecond x-rays from SPPS. Fritz and his colleagues used this motion to measure not only the distortion, but the size and character of the binding force itself, over a range of distortions. They conclude that the presence of conduction electrons weakens the crystal bonds in a way that had been predicted but never before measured directly.

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

4.  XAS Course for Structural Molecular Biology Applications — March 13-16
      (contact: S. DeBeer George,

XAS Short Course Icon
The Structural Molecular Biology BioXAS group will host an X-ray Absorption Spectroscopy (XAS) Short Course at SSRL on March 13-16, 2007. The training will include two days of lectures which will cover basic theory, experimental considerations, and applications. The lectures will be followed by two days of rotating practical sessions, which will include hands-on data collection at the beam line and data analysis. Participants are encouraged to bring their own samples to test feasibility for future data collection. Space will be limited to 16 participants. For more information, please contact Serena DeBeer George ( or apply via the website at:

5.  SSRL Advisory Committees Convene in February
      (contact: J. Stöhr,

The SSRL Scientific Advisory Committee (SAC) convened on February 15-16 to review and advise management on current and proposed programs at SSRL. The meeting began with an update by SSRL Director Jo Stöhr on projects reviewed at the July 2006 SAC meeting, plans for staffing, and a discussion on SSRL's strategic planning process. Several representatives from the SSRL Users' Organization participated in a discussion aimed at finding ways to solicit scientific ideas from users and further engaging them in the process of prioritizing initiatives. Updates were provided on the Structural Molecular Biology Program, including presentations on RNA polymerase (Roger Kornberg), Macromolecular crystallography developments (Mike Soltis), Non-crystalline scattering studies in structural biology at SSRL - Instrument developments and scientific applications (Hirotsugu Tsuruta), and Biological XAS processes and scientific highlights (Britt Hedman). Uwe Bergmann and other members of the SSRL Recruitment and Retention Task Force also met with the SAC to discuss staff scientist advancement.

Following the SAC on February 16, meetings were held by the SSRL Structural Molecular Biology Advisory Committee and the SSRL Proposal Review Panel. In their executive session, the PRP determined ratings based on the peer reviews received for new proposals and program proposal extensions submitted during this last call for proposals.

6.  John Zachara among Eight DOE Lawrence Award Winners

John Zachara
In February, Secretary of Energy Samuel W. Bodman named the winners in the seven categories of the Ernest Orlando Lawrence Award: Environmental Science and Technology-John Zachara (PNNL); Materials Research-Paul Alivisatos (UC Berkeley, LBNL) and Moungi Bawendi (MIT); National Security-Malcolm J. Andrews (LANL); Life Sciences-Arup K. Chakraborty (MIT); Chemistry-My Hang V. Huynh (LANL); Physics-Marc Kamionkowski (Caltech); and Nuclear Technology-Steven Zinkle (ORNL). The Lawrence Award honors scientists and engineers for exceptional contributions in research and development that support the DOE and its mission to advance the national, economic and energy security of the United States. The award consists of a gold medal, a citation and an honorarium of $50,000. "These brilliant scientists and their varied and important research inspire us," Secretary Bodman said. "Their work reminds us of the importance of continued investment in science and the need for increased emphasis on basic research and math and science education programs."

John Zachara, who serves on the SSRL Proposal Review Panel and SSRL Scientific Advisory Committee, is an environmental geochemist from the Pacific Northwest National Laboratory in Richland, Washington. Zachara has made seminal scientific contributions to understanding geochemical and microbiologic factors that are critical to the fate and transport of metals and radionuclides in the environment. His studies of how toxic metals travel in the subsurface environment of the Department of Energy Hanford site are helping provide science-based environmental cleanup solutions with broad applications. Congratulations to John and the other Lawrence Award recipients.

7.   SSRL Macromolecular Crystallography Remote Data Collection Workshop Held in Australia

      (contact: A. Cohen,

SSRL has developed and supports remote access experiments for the macromolecular crystallography user community (see SSRL Headlines, August 2006 issue, for details). Using advanced software tools that enable network based control of highly automated beam lines, users are able to securely screen samples and collect crystallographic data from remote locations. The system makes use of high capacity sample storage cassettes and the Stanford Auto-Mounting (SAM) robotic system that is implemented on the macromolecular crystallography beam lines.

Workshop participants [larger view]
A Remote Access Data Collection workshop to train scientists in this mode of data collection was conducted on February 9, 2007 at the University of Melbourne. The workshop, organized by Peter Turner (University of Sydney) and Aina Cohen (SSRL), was attended by 29 participants representing 12 universities and research institutions within Australia and New Zealand. The workshop began with a presentation by Julian Adams describing the protein crystallography facilities at the newly constructed Australian Synchrotron (AS). In particular, beam line 3BM1, which will be commissioned over the next few months, will be used for high-throughput structural biology and will support remote access experimentation in a manner similar to SSRL. The 3BM1 beam line will incorporate the SSRL SAM system and Blu-Ice/DCS instrument control software package. Workshop lectures covered a variety of topics including a

8.   X-ray/VUV Beam Time Requests due by March 5

      (contact: C. Knotts,

X-ray/VUV Beam time requests for the final scheduling period in our FY2007 (May-August 6) are due by Monday, March 5.

9.   Photon Science Job Opportunities

A number of positions are currently available at SSRL, LUSI and LCLS. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


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: 02 MAR 2007
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