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SSRL Headlines Vol. 6, No. 10  April, 2006


Contents of this Issue:

  1. Science Highlight — SSRL Aids Development of Plastic Electronics
  2. Science Highlight — Developing Ways to Treat Arthritis
  3. SPEAR3 Accelerator Safety Envelope
  4. Streak Camera Measurements of the SPEAR3 Beam
  5. JCSG 5th Annual Meeting
  6. User Advocacy Update
  7. Apply for Berkeley-Stanford Summer School
  8. User Administration Update
  9. Photon Science Job Opportunities

1.  Science Highlight — SSRL Aids Development of Plastic Electronics
      (contact: M.F. Toney,

Schematic of orientation of crystals within the film.
For close to a decade, researchers have been trying to improve the performance of plastic semiconductors to the level of amorphous silicon - the semiconductor used in low-cost electronics such as photovoltaic cells for solar power and thin-film transistors used in flat screen laptops and TVs.

Stanford Synchrotron Radiation Laboratory (SSRL) and Stanford researchers have now shown that the electrical performance of plastic semiconductors can be controlled and improved with surface treatments. In their research, published in Nature Materials, they showed they could align the small crystals within the polymer by applying a thin layer of another kind of organic molecule on to the surface. The highly-oriented crystals give the material better performance in conducting electricity. Researchers used x-ray scattering facilities at SSRL to determine the orientation of the crystals.

In a related paper, also published in Nature Materials, Merck Chemicals in the United Kingdom developed a new polymer whose electrical mobility, related to conductivity, is the highest so far in a polymer, endowing the new polymer with performance comparable to amorphous silicon. SSRL, Stanford and the Palo Alto Research Center (PARC) scientists also characterized this new material, and found that it has very highly-oriented crystals. "The structural properties of this new material are unprecedented for a polymer" said former Stanford graduate student Joe Kline, now a postdoctoral researcher at the National Institute of Standards and Technology.

Semiconducting polymers have many advantages over amorphous silicon: they are cheaper, faster and less energy-intensive to make; they can be dissolved in a solution and sprayed on, like ink from an inkjet printer; and are flexible, an important trait for applications such as electronic paper.

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

2.  Science Highlight — Developing Ways to Treat Arthritis
       (contact: M. He,

 tnf-alpha figure
Unusual inhibition mechanism of a small-molecule antagonist of the trimeric cytokine TNF-a.
In rheumatoid arthritis and Crohn's disease, the immune system overreacts, provoking too much inflammation. One method of treatment is to inhibit the immune protein that incites inflammation, called tumor necrosis factor (TNF). Currently available anti-TNF therapeutics have made a significant difference to patients, but are costly to manufacture and require an I.V. or injection. Sunesis Pharmaceuticals of South San Francisco, in collaboration with Biogen Idec, is researching small molecules that will inhibit TNF. The advantage of using small molecules is that they can be administered orally, and be produced much less expensively.

A team of scientists from Sunesis used macromolecular crystallography beam lines facilities at Stanford Synchrotron Radiation Laboratory to determine the structure of a potential TNF small-molecule inhibitor. X-ray diffraction studies showed that the small molecule had migrated into the center of TNF, where TNF's three subunits normally join. The small molecule then dislodged one of the three subunits, completely disrupting TNF. Turning a protein from a trimer (three parts) into a dimer (two parts) is an unusual, but clearly effective, method of inhibiting the action of a molecule.

This research enables pharmaceutical companies to identify properties of small molecules in a systematic path towards the identification of the substances that have the most potent inhibitory effects.

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

3.   SPEAR3 Accelerator Safety Envelope
       (contact: R. Hettel,

It has been two years since photon beams were first delivered to users from the newly commissioned SPEAR3 light source. Routine SPEAR3 operation has been limited to 100-mA stored beam current at 3 GeV since that time by the DOE-issued Accelerator Safety Envelope (ASE) even though the machine was designed to operate at 500 mA. A milestone for SPEAR3 operation was reached recently when the DOE raised the ASE current limit to the design value.

The 100-mA ASE was formulated based on the outcome of the original Accelerator Readiness Review (ARR) that took place in 2003, a few months before SPEAR3 commissioning, when the full complement of radiation shielding and beam containment systems needed for higher current operation had not yet been designed and implemented. Since then, with the benefit of several special DOE-authorized accelerator physics test shifts at 500 mA, these components were developed and completed. In the fall of 2005 the "Phase II ARR" for high-current operation was held, which addressed operational and machine protection issues as well as the radiation safety systems, and the DOE confirmed that SSRL had successfully responded to the few findings from the review in early 2006. The only remaining impediment to raising the ASE to 500 mA was to make a final revision to the SPEAR3 Safety Analysis Document (SAD) to incorporate all the recent system modifications. This was accomplished by March and the final SAD was officially delivered to the DOE Site Office by the head of the SLAC ES&H Division, Sayed Rokni. On March 30, SLAC Director Jonathan Dorfan received a memorandum from Nancy Sanchez, the DOE Site Office Manager, raising the SPEAR3 ASE for beam current to 525 mA (to permit testing of interlocks designed to limit the operating current to 500 mA).

SSRL is planning to operate at 500 mA during special limited runs over the next year that will serve only the photon beam lines that have been fully converted for high-current operation. All beam lines presently undergoing upgrade will be ready for routine 500-mA operation following the summer 2007 shutdown.

4.   Streak Camera Measurements of the SPEAR3 Beam
      (contact: J. Corbett,

The electron beam in SPEAR3 is in fact a discrete series of 'bunches' separated in time by 2.1 ns. Each bunch radiates electro-magnetic energy extending from the infrared (<1 eV) to the hard x-ray (>10 keV) regime. For time-resolved applications, it is important to verify the bunch length and reduce the pulse duration to the minimum possible value. Following the recent opening of the SPEAR3 diagnostic beam line, scientists at SSRL performed streak camera measurements on individual bunches at visible light wavelengths (550 nm). The measurements confirm that the bunch structure matches the theoretical Gaussian distribution with 40 ps FWHM. Work is ongoing to characterize bunch length as a function of accelerator operating parameters (current, RF voltage, optics). Electron beam stability will be explored under a variety of conditions. The measurements were made possible by use of a steak camera on loan from Fernando Sannibale at the ALS and a 'synchroscan' unit on loan from APS. This work was performed in conjunction with Alan Fisher (PEP-II), Alex Lumpkin (APS), Walter Mok, Jim Sebek and Jeff Corbett (SSRL).

5.   JCSG 5th Annual Meeting
      (contact: A. Deacon,

The Joint Center for Structural Genomics (JCSG, held its 5th annual meeting on April 6-7, at The Scripps Research Institute (TSRI) in La Jolla, California. The JCSG is one of four large-scale structural genomics centers funded through the Protein Structure Initiative (PSI) of the National Institutes of General Medical Sciences (NIGMS).

This was the first annual meeting since the July 2005 start of the production phase of the PSI. A lot of exciting progress was reported. On the first day, the four core operational groups of the JCSG (Bioinformatics, Crystallomics, NMR and Structure Determination) each held sessions describing their core activities. The session for the SSRL-based Structure Determination Core highlighted the latest remote operation capabilities available at SSRL macromolecular crystallography beam lines through a real-time session, and the efforts that have been made to automate the structure determination process, as well as the streamlining of structure refinement. On the second day presentations focused on new technology and functional collaborations that are being pursued to strengthen the overall JCSG pipeline. A final session highlighted many of the interesting structures that have been solved by the JCSG and deposited in the Protein Data Bank, pointing to the need for follow-up studies to provide more detailed functional annotation for many of the proteins that are being studied.

6.  User Advocacy Update
      (contacts: J. Andrews,; C. Kim,; L. Downward,

NUFO: User representatives and administrators from user facilities are part of a group called NUFO (National User Facility Organization) which meets periodically to discuss issues of common interest, to share best practices, and to brainstorm opportunities for closer interactions Sacha Kopp (University of Texas at Austin), Chair of the Fermilab Users' Executive Committee, organized the last meeting held in Illinois at the end of March. This very constructive meeting included discussions about user advocacy as well as safety and security at user facilities (see The meeting featured an impressive panel of speakers who gave tips on communicating the need for basic sciences and user facilities to a broader audience as well as a summary of the President's American Competitiveness Initiative. NUFO representatives are exploring the possibility of a combined trip for synchrotron, neutron and high energy physics users to visit Washington, DC in October to further communicate the importance of basic science and scientific user facilities. In preparation for these types of activities, SLAC Users' Organization Chair Abner Soffer is arranging a brief workshop to encourage and enable users to communicate the excitement and importance of their research to a non-scientific audience (session tentatively scheduled for May 26 in the SLAC auditorium). The next NUFO meeting is tentatively scheduled for April 2007 in Berkeley.

Synchrotron and Neutron User's Group (SNUG) visit to Washington DC, April 10 2006. Rear: Pat Fulton, Clemens Heske (ALS; UNLV), James Kaduk (APS; Innovene), Gene Ice (APS; ORNL). Front: Peter Stephens (NSLS; StonyBrookU), Joy Andrews (SSRL; CSUEB), Corie Ralston (ALS; LBNL), Despina Louca (SNS/HFIR; UVa), Yan Gao (NSLS; GE), Christopher Kim (SSRL; Chapman U). Not Pictured: Tom Koetzle (IPNS; ANL)
SNUG: Last year, synchrotron and neutron users formed a new group, SNUG (Synchrotron and Neutron Users Group), to increase awareness and coordination of activities. At a SNUG meeting in Menlo Park last October, an advocacy committee of SNUG was created to organize events such as a trip to Washington, DC on April 9-11 (see briefing documents at During this visit, synchrotron and neutron users met with representatives from industry as well as representatives from Congress and their legislative assistants to communicate "Who They Are, Why They Matter". If you are interested in being part of future SNUG advocacy activities, please contact Joy Andrews, Chris Kim, or Lisa Downward.

SSRLUOEC: In addition to the above issues of user advocacy, several other issues were discussed at the April 17 meeting of the SSRL Users' Organization Executive Committee (SSRLUOEC). Topics included planning for SSRL's Annual Users' Meeting and Workshops (October 11-13, 2006), discussion of two versus three fills per day (currently shutters are closed for 2-5 minutes three times daily for SPEAR3 injection), future developments related to new imaging capabilities and continuous scans, preparations for 500 mA operations, and plans for timing mode studies. The SSRLUOEC represents the entire SSRL user community, and we would appreciate user feedback on these or any other issues of interest to users. The SSRLUOEC would also appreciate input from users on whether they would be interested in a proposal writing workshop to be held in conjunction with the October 12-13 Users' Meeting; if yes, what elements would you like to see included in such a workshop? Contact information for your user representatives is posted via the web:

7.   Apply for Berkeley-Stanford Summer School
       (contacts: D. Attwood,; A. Nilsson,

The fifth Berkeley-Stanford summer school will provide basic lectures on the synchrotron radiation process, requisite technologies, and a broad range of scientific applications. Visits to SSRL and the ALS will be included, with opportunities to interact with the professional staff and graduate students at both facilities. The summer school will be limited to approximately forty graduate students, with a preference for those pursuing doctoral research in the physical sciences in which synchrotron radiation is expected to play a significant role. The summer school is jointly sponsored by UC Berkeley; Stanford University; LBNL; and SSRL. Lectures will be presented by professors and scientists from these four organizations and their user communities. The summer school will be housed on the UC Berkeley campus. Co-chairs of the summer school are David Attwood ( and Anders Nilsson ( Details describing the summer school, planned lectures, housing, costs and how to apply are posted at

Applications should include a brief academic record, a statement describing the intended research area and how a knowledge of synchrotron radiation would enhance those studies, a list of publications (if any), and information on how to reach the applicant by email and phone through the period extending to the time of the summer school. Applications are now being accepted. Early decisions will be made beginning May 10 and final decisions by June 1.

8.  User Administration Update
      (contacts: C. Knotts,; L. Dunn,

Please submit new X-ray and VUV proposals by May 1; submit new Macromolecular Crystallography proposals by July 1. Proposals received by these dates will be reviewed in July and will be eligible for beam time beginning in November 2006.

If you are interested in help in preparing proposals, please let us know. We are exploring user interest in a proposal writing workshop later this year. For more information on the proposal submittal, review and scheduling process, visit:

9.   Photon Science Job Opportunities

A number of positions are currently available at the LCLS, LUSI and SSRL. 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: 28 APR 2006
Content Owner: L. Dunn
Page Editor: L. Dunn