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SSRL Headlines Vol. 11, No. 1  July, 2010


Contents of this Issue:

  1. Science Highlight — Scientists Probe the Mechanism for Microbial Carbon Fixation
  2. Science Highlight — Chemical Analysis Shows an Ancient Ceramic Vessel was Broken and Burned in Cremation Burial
  3. First Results from the LCLS: Unpeeling Atoms and Molecules from the Inside Out
  4. From the Acting Director of SSRL: A Successful 2010 User Run
  5. 350 mA and Beyond...
  6. SLAC to Join New DOE Research Hub for Artificial Photosynthesis
  7. Annual SSRL/LCLS Users' Conference - Oct 17-21, 2010
  8. Call for Nominations for Spicer, Klein and Lytle Awards
  9. User Administration Update
  10. New AT&T Cell Tower Online
  11. Peninsula Bridge Summer Program Student Tour

1.  Science Highlight — Scientists Probe the Mechanism for Microbial Carbon Fixation
       (contacts: Y. Kung,; C. Drennan,

The (a) native and (b) cyanide-bound C-clusters from MtCODH/ACS.
The smallest organisms should not be overlooked when finding solutions to the problem of increasing pollutants and greenhouse gases in our atmosphere. Each year, some microorganisms using the enzyme carbon monoxide dehydrogenase (CODH) take an estimated 100 million tons of carbon monoxide (CO) from our air, while others use CODH to produce 10 billion tons of acetate from carbon dioxide (CO2). CODH catalyzes the reversible reaction of CO to CO2, which different types of bacteria use in different chemical synthetic pathways. The enzyme has a complicated metal cluster, the C-cluster, which includes nickel, iron, and sulfur ions in its active site that performs this unusual chemistry. Understanding how this catalysis works may provide insights to chemical engineers wanting to duplicate this chemical process as a solution to the build-up of greenhouse gases.

A team of scientists led by Catherine Drennan of MIT used SSRL Beam Line 11-1 and a beam line at ALS to decipher the mechanism of CODH's reaction. They solved crystal structures which depict the C-cluster bound to a substrate and an inhibitor. Analyzing the structures, they were able to deduce the roles of the bound metals and the mechanism of the reaction.

This clearer understanding of how this microbial enzyme performs this difficult chemistry may lead to methods to control pollutants and greenhouse gases in our atmosphere. This work was published in Biochemistry.

To learn more about this research see the full scientific highlight

2.  Science Highlight — Chemical Analysis Shows an Ancient Ceramic Vessel was Broken and Burned in Cremation Burial
       (contact: A. Mehta,

lekythoi image
(A) Greek white-ground lekythos from the Antikensammlung Staatliche Museen zu Berlin (F 2683) showing purplish-red discolouration. (B) Detail showing purplish-red
Anthropologists learn about ancient cultures through the objects left behind. Ritualistic artifacts give glimpses into the religious and belief systems of nonextant societies. Application of new techniques of chemical and structural analysis to the study of ancient objects can give more insight into how they were made and used.

A team led by Karen Trentelman of the Getty Conservation Institute in Los Angeles used SSRL Beam Line 2-3 to analyze the chemical composition of layers of glaze and aging on a funeral lekythoi, a Greek vessel for storing oil, from 5th century BCE Attica. They were particularly interested in a purplish discoloration on the surface layer of the lekythoi, and on many others like it. Using a variety of techniques, including electron probe microanalysis (EPMA), scanning electron microscopy (SEM), Micro x-ray absorption near edge structure (XANES), and extended x-ray absorption fine structure (EXAFS), the researchers found chemical evidence that the lekythoi was broken then burned with the body of the deceased as part of the funeral ceremony.

The analysis of this vessel deepens our understanding of Athenian customs. Using this technique, other museum artifacts might also share more of their ancient secrets. This work was published in the May 2010 issue of the Journal of Archeological Science.

To learn more about this research see the full scientific highlight

3.   First Results from the LCLS: Unpeeling Atoms and Molecules from the Inside Out
       Excerpted from June 30, 2010 SLAC Press Release

LCLS First Results
(Artwork by Gregory Stewart)
The first published scientific results from the LCLS, the world's most powerful hard x-ray laser, show its unique ability to control the behaviors of individual electrons within simple atoms and molecules by stripping them away, one by one —in some cases creating hollow atoms.

In a report published in the July 1 issue of Nature, a team led by Argonne National Laboratory physicist Linda Young describes how they were able to tune LCLS pulses to selectively strip electrons, one by one, from atoms of neon gas. By varying the photon energies of the pulses, they could do it from the outside in or—a more difficult task—from the inside out, creating so-called "hollow atoms."

In another report, published June 22 in Physical Review Letters, a team led by physicist Nora Berrah of Western Michigan University—the third group to conduct experiments at the LCLS—describes the first experiments on molecules. Her group also created hollow atoms, in this case within molecules of nitrogen gas, and found surprising differences in the way short and long laser pulses of exactly the same energies stripped and damaged the nitrogen molecules.

SLAC's Joachim Stöhr, director of the LCLS, said, "When we thought of the first experiments with LCLS ten years ago, we envisioned that the LCLS beam may actually be powerful enough to create hollow atoms, but at that time it was only a dream. The dream has now become reality." Read the full press release.

4.   From the Acting Director of SSRL: A Successful 2010 User Run
       July 30, 2010 SLAC Today article by Piero Pianetta

Piero Pianetta
Piero Pianetta
It is that time of year again at the Stanford Synchrotron Radiation Lightsource when the SPEAR3 storage ring shuts down, the users pack up and go home to analyze their data, and the support staff gear up for a busy period of upgrades and much needed maintenance activities as well as some well-deserved rest.

At the risk of repeating my column from last year, 2010 has been a great year for SSRL operations. We ran for the first time in true top-off mode, in which the current was kept constant in SPEAR3 by frequent (every 10 minute) injections. This mode of operation was approved for routine use only in June. The users have been extremely pleased with this operating mode-no more interruption of scans to wait for the injection to take place, and a 20 percent higher intensity since the beam is no longer allowed to decay for eight hours before filling. This mode of operation puts severe constraints on the reliability of all the SPEAR3 systems since the injector system must run continuously-any errors show up as a missed fill, which is evident on the beam current display. The occasional missed fill does not adversely affect the users. The goal of zero missed fills comes from a sense of pride from the operations staff and probably a few side-bets. Read more at:

5.   350 mA and Beyond...
       (contact: T. Rabedeau,

SSRL passed several more milestones on the road to realizing the full potential of the SPEAR3 upgrade in the past several weeks.

On June 28, just as SSRL staff were celebrating the start of frequent fill operations for users, the DOE approved the SSRL beam line safety envelope for 500 mA operations. Shortly thereafter, on July 13, all SSRL insertion device beam lines were operated successfully at 350 mA for radiological surveys and performance characterization. The results from this test were sufficiently encouraging that SSRL will start up in the fall with beam lines tuned and operating for users at 350 mA rather than the present 200 mA default current. After gaining further experience in the fall with 350 mA operation of beam line optics, detectors, etc. subsequent current increases towards the 500 mA SPEAR3 design current are envisioned for the 2011 run.

Higher current operations result in faster beam decay, so another welcome development was the July 9 approval of increased SPEAR3 injection power to 5 W. Increased injected beam power translates to faster fills as witnessed by peak injection rates in excess of 60 mA/minute with 5 W injection and routine top off injections which now require 3 seconds rather than the 5-6 seconds prior to the 5 W authorization. The increased authorized power is the culmination of several years of effort to improve the SPEAR3 injection efficiency thus resulting in lower injected beam loss and associated injected beam dose rates. Planned further improvements in the booster and the injection beam transport system promise enhanced injection reliability and reduced stored beam motion on injection. In fact, SSRL staff who participated in the 350 mA beam line test program were treated to a sneak peek into this future as the SPEAR3 fill frequency was doubled during this test to maintain approximately 0.5% current stability. During the 2011 run users will make their own acquaintance with such improvements.

6.   SLAC to Join New DOE Research Hub for Artificial Photosynthesis
       July 22, 2010 SLAC Today article by Glennda Chui

The Department of Energy has announced the creation of a new Energy Innovation Hub aimed at finding a practical way of making fuels with an artificial version of photosynthesis. Led by the California Institute of Technology and Lawrence Berkeley National Laboratory, the new Joint Center for Artificial Photosynthesis will include work at SLAC, Stanford, and University of California campuses in Berkeley, Santa Barbara, Irvine and San Diego.

Scientists have been looking for years for a way to mimic the way plants generate energy from the sun, a process that is the basis for nearly all life on Earth.

"This is something you can't do today," said SLAC's Anders Nilsson. "You can demonstrate it in principle, but it doesn't really work for practical use. The idea is that the hub will conduct research to see if this can be developed. If this could work, it would have a huge impact that will change our society."

Read more at:

7.   Annual SSRL/LCLS Users' Conference - Oct 17-21, 2010
       (contact: C. Knotts,

Plan to participate in the Annual SSRL/LCLS Users' Meeting and Workshops, October 17-21, 2010 to learn about new developments and share exciting user research at LCLS and SSRL.

8.   Call for Nominations for Spicer, Klein and Lytle Awards
       (contact: C. Knotts,

Please take a few moments to consider nominating your colleagues or students for one or more of the following awards which will be presented at the Joint SSRL and LCLS Users' Meeting, October 17-21, 2010:

9.   User Administration Update
       (contact: C. Knotts,

Our 2010 experimental run ended on July 26, and operations will resume in November; see our 2011 operating schedule.

SSRL BEAM TIME REQUEST DEADLINES. Proposal spokespersons or their authorized lead contacts can submit new beam time requests for the first scheduling period in our 2011 experimental run (late November 2010 - February 2011) by September 1. Requests for time on Macromolecular Crystallography (PX) time are due September 15. Proposals submitted June 1 (X-ray/VUV) and July 1 (PX) are currently under review and will be eligible for beam time during this first period. Ratings for these proposals should be distributed within the next few weeks. Request beam time via the user portal.

SUBMIT NEW SSRL PROPOSALS BY SEPTEMBER 1 OR DECEMBER 1. New proposals can be submitted 3 times a year: June 1, September 1, and December 1 for X-ray/VUV and April 1, July 1, and December 1 for Macromolecular Crystallography (PX). X-ray/VUV proposals submitted by September 1 will be peer reviewed, rated and eligible for beam time beginning in February 2011. Both X-ray/VUV and PX proposals should be submitted via the user portal.

COMPLETE END OF RUN SURVEY. Comments about your experience at SSRL are extremely important to us, and we need your feedback to meet our mission requirements, including assessment and reporting. If you haven't already done so, please submit an End of Run Summary Form through the user portal.

INFORM US OF PUBLICATIONS. After data have been collected, analyzed and prepared for publication, please inform us and acknowledge the user facility and funding agencies in your publications using the formats posted on the website: We strongly encourage you to contact us when exciting results are about to be published. We can work with users and the SLAC Office of Communication to develop the story and to communicate user research findings to a broader audience.

10.   New AT&T Cell Tower Online
cell phone tower
New AT&T cell phone tower (Photo by Lauren Rugani)

       Excerpted from July 26, 2010 SLAC Today article by Lauren Rugani

AT&T customers should notice an improvement in their cell phone signal at SLAC. A temporary cell tower, which went up behind Building 50 now provides service to the SLAC campus and immediate surrounding areas. A permanent tower will be installed on the roof of Building 50 after a seismic retrofit of the building is completed, within the next year. Read more at:

11.   Peninsula Bridge Summer Program Student Tour
       Excerpted from July 20, 2010 SLAC Today article by Lori White

tour grp
Tour group with J. Stubbs (Photo by Lori White)
Thirty-one bright, energetic fifth-grade girls from Peninsula Bridge Summer Program at Castilleja School in Palo Alto invaded SLAC on Tuesday, July 13, for a tour of the campus and a glimpse of the exciting possibilities science could offer in their own lives.

The girls began their adventure at the Visitors' Center, where SLACers Zoe Van Hoover and Kelen Tuttle introduced them to the lab's history and science. Apurva Mehta and Deborah Bard then explained x-rays and astrophysics. The afternoon offered opportunities for hands-on activities at SSRL.

"A major aim of our summer program is giving academically-motivated fifth-grade girls from low-income backgrounds access to and knowledge about exciting scientific exploration," said Mary Hurlbut, the girls' teacher. She said she was thrilled by their enthusiasm.


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: 30 July 2010
Content Owner: L. Dunn
Page Editor: L. Dunn