Previous Editions


SSRL Headlines Vol. 5, No. 10  April, 2005


Contents of this Issue:

  1. Science Highlight — First SPPS Results: Electro-optic Sampling and Ultra-fast Melting
  2. Science Highlight — Chemically Treated Wood Less Toxic than Feared
  3. SSRL/SLAC Hosts International FEL Conference, August 21-26, 2005
  4. The 2005 SMB Summer School September 12-15, 2005
  5. SSRL Users Visit Washington, DC
  6. New Developments in Macromolecular Crystallography
  7. Protein Model Building Research Program Funded by Joint NSF/NIGMS Initiative
  8. Controls Engineers Attend 2005 EPICS Meeting and Tour SPEAR3
  9. User Administration Update

1.  Science Highlight — First SPPS Results: Electro-optic Sampling and Ultra-fast Melting
      (contact: Jerry Hastings,

The Sub-Picosecond Pulse Source (SPPS) collaboration has published data from the first experiments ever using a linear accelerator-based femtosecond x-ray source. SPPS makes the world's shortest bunches of electrons in the SLAC linear accelerator and turns them into very bright pulses of x-ray light 1,000 times shorter than those made in synchrotron rings like SPEAR3. SPPS has many similarities to future free electron lasers like the Linac Coherent Light Source (LCLS) currently being built at SLAC.

Researchers used SPPS to develop and test a new timing technique, electro-optic sampling, which will be essential for many SPPS and LCLS experiments. To put data in order chronologically - important for seeing chemical or other reactions over time - researchers need to time-stamp the arrival of the laser pulse that starts a reaction, and the arrival of the x-ray pulse that observes the system. The strong electric field generated by each electron bunch alters the properties of an electro-optic crystal placed next to the beam, but only at the instant the electrons pass by. The characteristics of the laser light exiting the crystal reveal the electron bunch length and arrival time, and thus the x-ray pulse arrival time. In the other experiment, researchers shone laser light to melt a room-temperature crystal of semiconductor material, and sent x-ray pulses to probe the material. The scattered x-rays provided the first look at the first few femtoseconds in the transition from solid to liquid. In that time, the atom positions had on average the initial crystalline (regular, repeated) structure of the solid, yet the atoms had moved far from their starting positions, with the disordered structure of a liquid. The result is a very unusual, intermediate state of matter.

spps thumbnail To learn more about this research see: or

Note: Many authors contributed to this research. Full author lists can be found on the science highlight pages listed above.

2.  Science Highlight — Chemically Treated Wood Less Toxic than Feared
      (contact: Peter Nico,

The chemically treated wood used for playgrounds, fences and decks appears to be less toxic than feared. The chromated copper arsenate (CCA) mix protects commercial outdoor grade lumber from weathering, but in recent years the public and the government realized the chemicals could be potentially risky to the many people exposed to the ubiquitous wood. Recent analyses done at SSRL show that the arsenic and chromium is in a relatively stable chemical state and is bound to the wood fibers. Contrary to previous estimates of arsenic exposure, the research by Peter Nico of California State University, Stanislaus, and his colleagues supports the conclusion found that arsenic appears to be more stable than previously believed against leaching and subsequent absorption into the skin of those who come in contact with CCA-treated lumber.

The Environmental Protection Agency is preparing a human health risk assessment. The agency had initially estimated that the major routes of CCA-related arsenic exposure to younger children would be half from dermal absorption (through the skin), nearly half from ingestion, and 4% from exposure to arsenic-containing soils. The SSRL research resolved for the first time the chemical and structural states of the chemicals coating the wood, to better determine the actual risks of coming in contact with CCA-treated lumber. An x-ray technique called XANES yielded crucial information on the oxidation states of arsenic and chromium, showing the two chemicals to be in their less toxic forms. Their molecular structures, obtained through extended x-ray absorption fine structure (EXAFS) spectroscopy, show that the chemicals are in a fairly stable state and that they remain tightly bound to the wood despite weathering.

cca thumbnail To learn more about this research see: or

3.   SSRL/SLAC Hosts International FEL Conference, August 21-26, 2005
      (conference chairs: John Galayda,; Ingolf Lindau,

The 2005 International Free-Electron Laser (FEL) Conference will be held at Stanford University on August 21-26, 2005. The number of funded FEL projects is growing with over 12 FEL projects currently in various stages of planning and construction worldwide, including the Linac Coherent Light Source (LCLS) here at SLAC, SPARC at INFN Frascati, FERMI@Elletra, the Pohang Light Source FEL initiative in Korea, SCSS at SPring-8 in Japan, the European XFEL Laboratory in Hamburg and the Jefferson Lab FEL in Virginia. Approximately 300 scientists, engineers and project managers from these facilities will be participating in this meeting, reporting on their latest efforts. Prospective x-ray laser experimenters are also encouraged to participate in FEL2005. Registration and abstracts for this conference are now being accepted at the meeting website (abstracts due by May 31).

FEL2005 logo

4.   The 2005 SMB Summer School September 12-15, 2005
      (contact: Frances Liu,

SSRL will hold its 2005 Structural Molecular Biology Summer School during the period of September 12-15, 2005. This year the School will highlight the use and applications of two synchrotron x-ray techniques in the study of biological systems: X-ray Absorption Spectroscopy (XAS) and Macromolecular Crystallography (MC). Presentations from experts in the fields will be aimed at the graduate student level, but will also be appropriate for more experienced researchers entering the field. Lectures will be followed by interactive practical sessions giving participants the opportunity to learn data collection and analysis techniques first hand. The Summer School will be held at SSRL and facilities on the SLAC site. Enrollment will be limited so prospective participants should apply soon, and well before the August 1, 2005 deadline. Co-chairs are Serena DeBeer George and Clyde Smith. Details describing the Summer School, preliminary program, housing, costs and how to apply will be posted at

5.   SSRL Users Visit Washington, DC
      (contacts: Joy Andrews,; Glenn Waychunas,

Along with user community representatives from the three other DOE light sources, the Chair (Glenn Waychunas) and Vice Chair (Joy Andrews) of the SSRL Users' Organization Executive Committee visited Washington, DC on April 8. The purpose of this trip was to meet with representatives from Congress, the Office of Science Technology and Policy, and the Department of Energy to support funding for basic sciences. The overall feeling from the users who participated in these meetings is that user contact through letters and visits does make a difference in raising awareness and support for basic science programs within the DOE, especially when users communicate directly with their own local representatives. The light source representatives prepared a briefing package summarizing why synchrotrons are important and the impact of reduced budgets on users. This material is available on the user organization website:

If you have questions or if you would like to discuss how you can help, please contact us directly. We will be glad to assist you. Users interested in discussing this or other user-related issues are encouraged to participate in the next SSRL Users' Organization Meeting on Monday, July 11.

6.   New Developments in Macromolecular Crystallography
      (contact: Mike Soltis,

The Stanford Auto-Mounting (SAM) system is a fully automated crystal screening and data collection system developed with the goal of increasing efficiency, data quality and throughput on the Macromolecular Crystallography (MC) beam lines. A typical screening sequence currently takes ~3 minutes per crystal (robotic crystal mounting, auto sample centering, video and diffraction image acquisition at 0 and 90 degrees, and dismounting). Up to 288 samples can be screened in less than 17 hours without opening the experimental hutch door. This project was developed initially with funding from NIH NCRR and later with funding from NIH NIGMS to procure additional systems and to further develop the robotics automation and screening software as part of the Joint Center for Structural Genomics (JCSG) initiative. The SAM system is now fully integrated on all MC beam lines and has been used by more than a third of the SSRL MC user community.

A new MAR325 CCD detector was recently installed on BL9-2. The installation was completed within a week and test data were collected from crystals of myoglobin. The resulting statistics were excellent and the detector proved to excel in measuring weak diffraction data. Within a week, the JCSG group had screened over 300 samples and had solved 5 new MAD structures using the SAM system and the new detector on BL9-2. Several user groups have also reported that the detector has produced excellent anomalous diffraction data.

In addition, remote access tools have been developed that allow users to control experiments from remote locations anywhere in the world. In this mode, samples are mounted at users' home laboratories and are then shipped at cryogenic temperature to SSRL in SAM cassettes. A Remote Desktop application allows users to control experiments, process data and solve structures using home lab computers. During the commissioning phase, NIH NIAID members on a site visit at The Scripps Research Center in La Jolla, California, observed the remote screening of ~150 SARS-related protein crystals on BL11-1 (Peter Kuhn's group). More recently, a group in Australia screened crystals and collected several MAD data sets using BL9-2. The remote access mode of data collection will be available to the entire user community during the next scheduling period.

7.   Protein Model Building Research Program Funded by Joint NSF/NIGMS Initiative
      (contacts: Ashley Deacon,; Henry van den Bedem,

X-ray crystallography is the most widely used experimental technique to obtain a protein's three-dimensional structure. Flexible fragments in a protein, which are often vital for its biological function, are often poorly resolved in the data, and may lead to incomplete structural models.

A new collaborative project between researchers Henry van den Bedem and Ashley Deacon of the Joint Center for Structural Genomics at SSRL, Jim Milgram of the Department of Mathematics and Jean-Claude Latombe (PI) of the Department of Computer Science on Stanford campus has received 4 years of funding from a joint NSF/NIGMS program to develop a new mathematical model for a redundant, closed, protein-like kinematic chain. Techniques from algebraic geometry and differential topology, in particular Morse Theory, and probabilistic roadmap techniques from robotics will be used to investigate the mathematical structure of the set of configurations of missing fragments. These insights will be used together with experimental data and energy models to associate a likelihood with each configuration.

The project aims to develop novel algorithms to aid protein structure determination from experimental data, and to study important, dynamic properties of proteins. The research and developments described in this proposal will lead to improved 3-D models, which in turn will lead to a better understanding of a protein's function and will have a direct impact on medical research. A prototype algorithm to fit missing fragments into protein models, Xpleo, is available at

8.   Controls Engineers Attend 2005 EPICS Meeting and Tour SPEAR3

Controls engineers from around the world converged on SLAC this week for the 2005 Experimental Physics and Industrial Control System (EPICS) Meeting hosted by the LCLS and ESD Controls groups. A number of controls engineers from the Diamond Light Source and the Australian Synchrotron Project took the opportunity to tour the SPEAR3 control system hardware and user interfaces while they were here. They were also given a robotics demonstration by Mike Soltis and Scott McPhillips at Beam Line 11-1. For more information on the EPICS meeting see:

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

The deadline for submitting new X-ray and VUV proposals is May 1, and the next deadline for Macromolecular Crystallography proposals is July 1. Proposals submitted by these dates will be eligible for beam time during the 2006 user run. For more information on the proposal submittal, review and scheduling process, visit:


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.


To leave the SSRL-HEADLINES distribution, send email as shown below:

To: LISTSERV@SSRL.SLAC.STANFORD.EDU Subject: (blank, or anything you like)

The message body should read


That's all it takes. (If we have an old email address for you that is forwarded to your current address, the system may not recognize who should be unsubscribed. In that case please write to and we'll try to figure out who you are so that you can be unsubscribed.)

If a colleague would like to subscribe to the list, he or she should send To: LISTSERV@SSRL.SLAC.STANFORD.EDU and use the message body


SSRL Welcome Page | Research Highlights | Beam Lines | Accel Physics
User Admin | News & Events | Safety Office


Last Updated: 29 APR 2005
Content Owner: L. Dunn
Page Editor: L. Dunn