Previous Editions


SSRL Headlines Vol. 7, No. 2  August, 2006


Contents of this Issue:

  1. Science Highlight — The Elusive Active Fold of a Catalytic RNA
  2. Call for Abstracts for SSRL33, October 12-13
  3. Calling Interested Users to Serve on the SSRLUO Executive Committee
  4. Several Workshops Offered on October 11
  5. Staff Director for the House Subcommittee on Energy Visits SLAC
  6. Ancient Science Revealed through X-ray Fluorescence Imaging
  7. Small-Angle X-ray Scattering and Diffraction Studies Workshop Wrap-up
  8. Remote Macromolecular Crystallography Data Collection
  9. SLAC Kids Day 2006 - the Biggest and Best Yet!
  10. Even Electrons Need a Vacation
  11. Hydrogen: Key to a Sustainable Future - Excerpts from SLAC Today
  12. Photon Science Job Opportunities

1.  Science Highlight — The Elusive Active Fold of a Catalytic RNA
      (contact: W.G. Scott, wgscott at

Ribbon Diagram
Genes, which are made of nucleic acids (DNA or RNA) contain the instructions for how to make proteins, but still enzymes made of proteins are needed to replicate the genes. This paradox was addressed ~20 years ago with the realization that some kinds of RNA can act as enzymes. These RNA enzymes, or ribozymes, are accordingly made of the genetic RNA material, but they act as chemical catalysts. This means that ribozymes would have enabled the first self-replicating molecules, also made of RNA, to copy themselves.

Scientists at the University of California-Santa Cruz came to Stanford Synchrotron Radiation Laboratory and the Advanced Light Source to use macromolecular crystallography beam line facilities to determine the three-dimensional structure of a full-length hammerhead ribozyme. The structure shows how the specific spatial arrangement of functional groups of the RNA allows them to mediate acid-base chemical catalysis. The researchers conclude that it appears these aspects of acid-base catalysis are so fundamental that they might be considered universal principles of macromolecular enzymology (both for proteins and RNAs).

The new findings are described by graduate student Monika Martick and her advisor, Professor William Scott, in the July 27 issue of the journal Cell.

Many academic and industrial laboratories are engineering ribozymes for potential use in fighting infectious and chronic diseases.

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

2.  Call for Abstracts for SSRL33, October 12-13
      (contact: C. Knotts,

Users are encouraged to share their research through poster presentations at the 33rd Annual SSRL Users' Meeting, October 12-13, 2006. This annual conference provides a forum for the presentation and discussion of new data and developments as well as plans for the future at SSRL. Abstracts received by September 20 will be included in the program materials. Register at

3.  Calling Interested Users to Serve on the SSRLUO Executive Committee
      (contact: J. Andrews, CSU East Bay, SSRLUOEC Chair,

Your help is needed to identify users who may be interested in serving on the SSRL Users' Organization Executive Committee (SSRLUOEC) — and you can nominate yourself! We are currently soliciting nominations for five positions on the SSRLUOEC in the following disciplines: materials/chemistry (2); biospectroscopy (1), macromolecular crystallography (1), and a graduate student in any discipline. This is a particularly exciting time in the life of the lab. Additional funding for the sciences is anticipated, thanks in large part to increased interest (and action) by users advocating the importance of basic science and facilities which support user science. Users have increased opportunities to more actively participate in the visioning and strategic planning process at SSRL (planning for operations and future developments such as new imaging capabilities, continuous scans, preparations for 500 mA operations, top-off injection and pulsed beam for timing mode studies). The SSRLUOEC serves in many other important functions: representing user interests to SLAC/SSRL management and advisory committees; promoting user science; coordinating advocacy activities with representatives from other DOE user facilities; organizing and hosting the annual SSRL Users' Meeting; and presenting awards to recognize scientific or technical accomplishments (Lytle Award, Klein Professional Development Award, Spicer Young Investigator Award, Outstanding Graduate Student Poster Awards). Take a few minutes to think about forward-thinking individuals who might be available to meet a few times a year to participate in these important activities, and forward your nominations to Cathy Knotts by September 15.

4.  Several Workshops Offered on October 11
      (contact: C. Knotts,

Ultrafast Dynamics on Surfaces and in Liquids - Anders Nilsson and Aaron Lindenberg, Organizers: This workshop is aimed at bringing together researchers interested in the ultrafast dynamics that occur on surfaces and in the liquid state of matter, as well as the development of techniques for probing such diverse phenomena. These include optical spectroscopy, x-ray spectroscopy, x-ray scattering, high harmonic generation, THz spectroscopy, photoemission, free electron lasers, as well as theoretical techniques. It will consist of a series of invited talks with time allotted for contributed or walk-in talks.

Electron Dynamics in Spin Systems - Yves Acremann, Peter Fischer, and Andreas Scholl, Organizers: The spin relaxation time of electrons controls the spin accumulation in ferromagnetic/nonmagnetic junctions, the current driven motion of domain walls in nanowires, the demagnetization time in laser-driven demagnetization experiments, and the life time of a spin population after optical pumping. Time-resolved X-ray dichroism techniques offer new ways of detecting spin dynamics and understanding the underlying physics. Because of their element specificity, the sensitivity to spin and orbital magnetization, and the possibility to reach nanometer spatial resolution, they are particularly suited for complex materials, multilayers, nanostructures, junctions, and multicritical systems with coupled spin, orbital, electric, and charge orders. This workshop aims at identifying the new science that can be addressed with next-generation ultrafast x-ray source applying bunch compression, laser slicing, and free electron lasers.

Register today to participate in these workshops or any of the other joint SSRL and ALS workshops including: Doing Research at Synchrotrons-An Introduction; Using the Uni-Puck and Web-Ice at ALS and SSRL (Joint Macromolecular Crystallography Workshop); Ultrafast Dynamics on Surfaces and in Liquids by Soft X-rays; Advanced Magnetic Spectroscopy; Opportunities and Challenges with Momentum-Resolved Inelastic X-ray Scattering; and Soft X-Ray Resonant Scattering and Reflectivity/Structure from Coherent Scattering: Dynamics and Static Imaging. Workshops will be held in conjunction with the ALS Users' Meeting on October 9-11 and the 33rd Annual Users' Meeting on October 11-13.

We look forward to an interesting and informative meeting, and we encourage you to join us!

5.   Staff Director for the House Subcommittee on Energy Visits SLAC

looking at structure with 3d glasses
Visitors Wearing 3d Glasses to View Structure
Kevin Carroll, Staff Director for the House Subcommittee on Energy, visited SLAC on August 3, 2006. After Persis Drell gave an initial introduction to the lab and its research, Carroll enjoyed a full tour of the facility. As luck would have it, he arrived at SSRL Beam Line 6-2 at exactly the same moment as a new geometric figure emerged from the ancient Archimedes text. He also visited Beam Line 9-2 for a brief demonstration of high-throughput macromolecular crystallography, and Beam Line 5-1 for information on research aimed at moving towards a hydrogen economy. The tour then continued on to BaBar, the linac and the Kavli Institute.

6.   Ancient Science Revealed through X-ray Fluorescence Imaging
      (contact: U. Bergmann,

Bergmann holding up image from Archimedes palimpsest
U. Bergmann holds up image of Archimedes palimpsest.
The most recent round of Archimedes palimpsest experiments on BL6-2 at SSRL in late July and early August received a flurry of media attention including a live webcast by the Exploratorium in San Francisco, an NPR interview, spots on the ABC, BBC, Fox and NBC News as well as widespread local and international press. See

The Archimedes palimpsest research at SSRL is a story about attempting to read hidden ancient scientific writings with modern high-tech tools and perhaps that's why the work has garnered so much media attention. Moreover, this research crosses fields of study to appeal to scientists, historians, mathematicians and the general public alike. Synchrotron-related science is well-suited for a growing trend towards interdisciplinary research and the Archimedes research has shown a bright spotlight on its unique possibilities.

For more on the history of the Archimedes palimpsest and an image bank of the pages of this historical document including those "seen" for the first time during the recent experiment, see:

7.   Small-Angle X-ray Scattering and Diffraction Studies Workshop Wrap-up
      (contact: H. Tsuruta,

The SSRL SMB Bio-SAXS/D team hosted a practical workshop July 28-30, 2006 to complement the bio-SAXS/D workshop held in October, 2005 with additional hands-on experimental tutorial sessions. The first half of the workshop was focused on oral presentations by invited expert speakers on mostly non-crystalline x-ray diffraction studies in structural biology, ranging from fundamentals of bio-SAXS/D techniques to cutting-edge advanced applications conducted at SSRL and elsewhere. These talks covered a comprehensive review of the structural biology research by SAXS/D techniques, interplay between small angle scattering and macromolecular crystallography, nucleic acid structures, virus maturation kinetics, a modeling approach based on atomic structures, membrane systems, the use of neutron scattering to complement x-ray studies, as well as a review of the SSRL SMB program and the prospect of SMB research using LCLS. Bio-SAXS/D staff discussed BL4-2 developments, practical issues in bio-SAXS/D experiments and software developments for data collection and processing.

The second half of the workshop was devoted to two half-day computational sessions and a series of experimental tutorial sessions. The computational practical sessions were given by Dmitri Svergun (EMBL-Hamburg), whose group has developed a number of powerful computational tools for solution scattering. A number of participants were given the opportunity to measure their own samples during a couple of hours of individually allocated beam time on BL4-2, and many managed to obtain encouraging results. These practical sessions were enthusiastically received by the participants, who engaged in active discussion with speakers and staff on scientific and practical issues in bio-SAXS/D studies.

workshop participants
Workshop participants

8.   Remote Macromolecular Crystallography Data Collection
      (contacts: A. Cohen,; S.M. Soltis,

Workshop participant pours liquid nitrogen into dewars as part of hands-on session.
Over the last year SSRL has begun supporting remote access experiments for the macromolecular crystallography community. Using advanced software tools that enable network based control of highly automated beam lines, users are able to screen samples and collect crystallographic data from remote locations, securely from anywhere in the world. 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. Currently about 75% of the SSRL macromolecular crystallography community uses the SAM systems routinely and about 50% of the community uses the remote access tools. General users screened over 20,000 crystals in 2005 using SAM. During the last year, members of the newly formed Center for High Throughput Structural Biology at the Hauptman-Woodward Medical Research Institute (HWI) used the SAM system remotely to screen over 1,300 crystals, collecting more than 30 data sets and solving 21 new structures including a novel membrane protein. Members of the Joint Center for Structural Genomics have used SAM to screen over 15,000 crystals over the last 4 years and have solved over 300 structures to date.

Recently, a remote data collection workshop was conducted on August 4, 2006 at HWI in Buffalo New York. The remotely held workshop, organized and run by Aina Cohen and SSRL coworkers and Edward Snell and HWI coworkers, was attended by 34 US and Canadian investigators predominantly from the East Coast. The workshop provided seminars and practical sessions covering the details of the remote access experiment including proper sample preparation and shipment for use with the SAM system, and remote operation of the Blu-Ice beam line control system.

Remote Access Workshop Participants
Workshop participants at HWI
A significant portion of the workshop was dedicated to introducing the remote desktop software that is used to remotely connect to Blu-Ice and subsequent installation and configuration of the software on the participants' personal laptop computers (PC, MAC and Linux are currently supported). The workshop was extremely successful as all participants were able to configure their laptops and operate the crystallography beam lines remotely. They were able to conduct remote screening experiments and also use newly developed web-based tools to score and index images for subsequent data collection (Web-Ice) and for drag-and-drop DVD backup of crystallographic data files. A dedicated robot at SSRL writes the DVDs which are subsequently mailed to the user's laboratory.

9.   SLAC Kids Day 2006 - the Biggest and Best Yet!

Over the past 5 years a volunteer committee of SLAC staff members, including SSRL's Teresa Troxel and Michelle Steger, has devoted a great deal of energy towards putting together a top-notch annual Kids Day event - building upon lessons learned and past successes each year. Their hard work paid off with a record high number of 254 kids attending this year's much anticipated event on Wednesday, August 16. The children were ushered into the SLAC Panofsky Auditorium to begin their day by listening to Chloe Zubieta, Joint Center for Structural Genomics at SSRL, give a talk on how she became a scientist. Following the talk children took part in workshop activities covering a wide variety of topics including cryogenics, biology, radiation, magnetics, metrology, vacuum, welding, waves and astrophysics. 18 workshops were offered in all, depending on the participant's age group. To cap off the day the children were treated to an ice cream social and a science talk with KIPAC's Phil Marshall.

All-in-all the event was a great success. SLAC Director Jonathan Dorfan commented in the August 21 edition of SLAC Today that, "Kids Day 2006 was the biggest and best yet." He went on to say, "Kids Day owes its success to the untiring volunteers who clearly made extra effort to create a memorable day for all. A day like this can change a child's life and trigger a permanent interest in science, and I believe this year's event did just that." Read more at:

10.   Even Electrons Need a Vacation
     —Brad Plummer, SLAC Today, August 7, 2006

On August 7, SPEAR3 shut down for annual maintenance and upgrades. The shutdown, which will last until October, gives engineers an opportunity to perform maintenance and equipment upgrades. This year many of the accelerator upgrades are geared toward implementing top-off injection in SPEAR3. Among these upgrades is a new ejection septum chamber, a device located at the point where electrons leave the booster ring to be injected into the SPEAR3 main storage ring. With the present chamber, the beam spreads out slightly as it passes through a special vacuum-tight window, reducing the efficiency of injecting electrons into SPEAR3. The new septum chamber will eliminate that problem and give operators a tighter beam out of the booster.

Also slated for upgrade is the 9-meter-long linear accelerator that creates the initial pulses that are boosted and injected into SPEAR3. The SPEAR3 linac, which is a miniature version of the 2-mile linac at SLAC, is receiving a second klystron that will roughly double the energy of electrons entering the booster. This extra energy should improve the capture of electrons into the booster and make top-off injection into SPEAR3 more efficient.

Preparations for the new BL12-2 will also continue during the shutdown with the installation of a new in-vacuum undulator, the first of its kind at SSRL. This undulator will give users a much higher degree of control over the x-rays produced. BL12-2 experimental hardware will also be installed in the new hutches that are being built this summer. The new beam line, which is for macromolecular crystallography and funded by the Gordon and Betty Moore foundation in a collaboration with Caltech, is scheduled to be commissioned in 2007.

11.   Hydrogen: Key to a Sustainable Future - Excerpts from SLAC Today

hydrogen bottle
Experts expect worldwide energy demand to double in the next 50 years. Many of those same experts also agree that cutting back on greenhouse emissions, particularly carbon dioxide, is the only way to avoid irreversible climate change. Considering the limited supply of fossil fuels, the trick for satisfying both realities lies not only in keeping up with today's energy needs, but to meet increasing future demand in ways that do not pollute the atmosphere with greenhouse gases. "Even maintaining current fossil fuel consumption, CO2 in the atmosphere would double to Industrial Revolution levels," says SSRL postdoctoral researcher Jennifer Leisch. "The goal is carbon-free energy." Read more at

A Microscopic Solution to an Enormous Problem: Hydrogen, the most plentiful element in the Universe, could potentially meet much of the world's demand for energy while reducing or eliminating our dependence on carbon-based fuels. The promise of carbon-free energy has researchers hunting for better ways of isolating this plentiful element, but for all its abundance, hydrogen has proved prohibitively tricky to produce. One answer may lie in sunlight. By directly applying the sun's energy to water within a special solar cell, scientists are inching closer to making usable hydrogen. "It's a materials issue," said SSRL researcher Theanne Schiros. "Hydrogen doesn't exist freely in nature, but with the right materials we can isolate it from other compounds." Read more at

Billions of Fuel Tanks May be Better than One: Meeting the world's future energy demands will be an enormous challenge on many fronts. While hydrogen gas has piqued the interest of researchers as a clean, renewable energy resource, a number of major obstacles remain before an integrated system of producing, storing, and using hydrogen can supplant fossil fuel usage in a meaningful way. Perhaps the biggest of these problems is how to store this plentiful gas. Viable techniques for producing and using hydrogen, while still years away, have been proven, at least in principle. But a workable option for containing-and therefore, distributing-hydrogen gas remains elusive. "The problem now is that at the most basic level, the technology simply doesn't exist," said Anton Nikitin, a PhD student conducting research at SSRL. "And if you don't have all the pieces of the puzzle, you can't build the system." Read more at

12.   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.


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: 31 AUG 2006
Content Owner: L. Dunn
Page Editor: L. Dunn