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SSRL Headlines Vol. 10, No. 3  September, 2009


Contents of this Issue:

  1. Science Highlight — Crystal Structure of an Intermediate State of a Mechanosensitive Membrane Channel
  2. Science Highlight — No Jahn-Teller Distortion of the Lattice Structure Found in the Cobalt Oxide La1-xSrxCoO3
  3. Science Highlight — New Research Puts Theory of Water Structure on Thin Ice
  4. Register to Participate in the SSRL/LCLS Users' Conference
  5. Vote for Users' Organization Executive Committee Membership
  6. Yulin Chen to Receive Spicer Young Investigator Award
  7. Leslie Jimison to Receive Klein Award
  8. Recovery Act Funding at Work in SSRL Upgrades
  9. Structural Molecular Biology Summer School Provides Hands-on Experience
  10. Please Report SSRL-Related Papers, Invited Talks, and Awards
  11. X-ray/VUV Beam Time Schedules Posted
  12. New Schedule for Shuttle Transport between SLAC and CalTrain

1.  Science Highlight — Crystal Structure of an Intermediate State of a Mechanosensitive Membrane Channel
       (contact: D.C. Rees,

highlight figure
Structures of SaMscL-Cdelta26 tetramer and TbMscL pentamer.
You have probably never seen a bacteria pop. Yet, as solution-filled balloons, bacterial cells are susceptible to changes in pressure. For example, microbes entering a fresh water solution from a salt solution would quickly succumb to death by swelling due to water rushing into the cells due to osmotic pressure differences. Bacteria do not pop because they are able to sense and respond to changes in pressure through mechanosensitive channels that transverse their membranes. These gates are like pressure relief valves, opening to ease pressure and closing when balance is restored.

A group of researchers led by Prof. Douglas C. Rees from Caltech have solved the crystal structure of one such transmembrane gate, the mechanosensitive channel of large conductance (MscL) from Staphylococcus aureus using SSRL Beam Line 12-2. Their 3.8 Å structure shows an intermediate state of the channel, between open and closed. It can be compared to a previous crystal structure of a homologous channel that was found in the closed state. The S. aureus channel is made of four subunits, while the previous structure had five. Despite that difference, the researchers found that the architecture of the two channels is similar, including similar transmembrane helices and conserved hydrophobic residues at the point of channel constriction.

Comparisons between the geometries of the channel components of the two structures have led the researchers to propose a two-step helix pivoting model of channel gating. This work was published in the September 3 issue of the journal Nature.

To learn more about this research see the full scientific highlight.

2.  Science Highlight — No Jahn-Teller Distortion of the Lattice Structure Found in the Cobalt Oxide La1-xSrxCoO3
       (contact: F. Bridges,

highlight figure
Sigma2(T) for LaCoO3 and the correlated Debye fit.
The arrangement of atoms in molecules and complexes that include atoms with many interacting electrons can be hard to predict. The Jahn-Teller (JT) effect sometimes predicts a geometric distortion of the oxygen octahedra surrounding transition metals such as Mn, Co, and Cu. In this model, for certain ground state configurations of the electrons on the metal atom, the total electronic energy can be reduced if the surrounding oxygen octahedra adopt a distorted structure that might seem unstable. The JT distortion is seen in many copper complexes, produces a metal-insulator transition in many manganites, and was predicted to affect the shape of the oxygen octahedra about Co (CoO6) in La1-xSrxCoO3.

A research group led by Frank (Bud) Bridges from UC Santa Cruz used SSRL Beam Line 10-2 to test this prediction. The group is interested in the cobalt oxide La1-xSrxCoO3 (LSCO) because it has unusual magnetic properties that are not well understood. They used extended x-ray absorption fine structure (EXAFS) spectroscopy and neutron pair distribution function (PDF) techniques to determine variations in the Co-O bond lengths in powdered samples as a function of temperature. Their data can be fit very well to the classic correlated Debye model without invoking any JT distortions in contrast to the manganites which show a large JT distortion. They therefore conclude that significant JT distortions are not present in the cobalt oxide LSCO.

The lack of a significant JT distortion of the oxygen octahedral about Co provides evidence against a proposed intermediate spin state for Co. Consequently, the observed unusual magnetism must arise from a mixture of strongly magnetic, high spin states and non-magnetic low spin states. This work was published in the January 16 issue (2009) of the journal Physical Review Letters.

To learn more about this research see the full scientific highlight.

3.  Science Highlight — New Research Puts Theory of Water Structure on Thin Ice
       (contacts: C. Huang,; A. Nilsson,

highlight figure
Water has unusual and complex properties that make it especially well suited to support life. Its macroscopic properties, like surface tension, solubility, and high melting and boiling temperatures, must come from its molecular properties. Although water is all around us, is essential for life, and is a small, simple molecule, we still do not understand how it behaves on a molecular level. We think of water as a fairly regular array of hydrogen-bonded molecules, where each oxygen bonds with a hydrogen on two other molecules. Since each water molecule can bond to four other water molecules, an ordered, tetrahedral symmetry can arise. This hydrogen bonding pattern has been assumed to account for water's special properties.

Using data obtained at SSRL Beam Lines 4-2 and 6-2 and at SPring-8 in Japan a research group led by Anders Nilsson from SLAC has made discoveries that challenge the current models of water behavior. The team used small angle x-ray scattering (SAXS; BL4-2), which can give structural information about non-crystalline materials, to measure inhomogeneities in the density of water at various temperatures. They saw fluctuations in terms of low density regions on a 1-nm scale that correspond to the ordered, tetrahedral model described above, but the majority of molecules were found in higher density regions. The structure and states of the molecules in these areas was found through x-ray emission spectroscopy (XES) and x-ray Raman spectroscopy (XRS; BL6-2),

techniques that analyze the electronic states of molecules. The researchers found that the molecules in the high density areas were forming asymmetrical, disordered structures, a sort of chaos in which floated some islands of tetrahedral order. Since the ratio of low to high density areas slightly decreased as the temperature increased from 4°C to 90°C, the researchers hypothesize that the water structure was finding a balance between minimizing enthalpy (through extensive hydrogen bonding in the low density structure) and maximizing entropy (the disorder of the high density structure).

This field has been hotly debated in the last few years. If accepted, the new model is a revolution in our perception of water structure. Time - and more experiments - will tell. This research was published in August by the journal Proceedings of the National Academy of Science.

To learn more about this research see the full scientific highlight.

4.   Register to Participate in the SSRL/LCLS Users' Conference
       (contact: C. Knotts,

Plan to attend and share your research results during the user poster session of the Annual SSRL/LCLS Users' Meeting and Workshops which will be held October 18-21 (SSRL/LCLS 2009). Students, in particular, are encouraged to present posters and compete for prizes, which include a certificate and a $100 award. Representatives of the SSRL Users' Organization will judge student posters, and prizes for outstanding posters will be presented during the meeting dinner. In addition to the reduced student registration fee, students presenting posters receive a free dinner (indicate student presenting poster during on-line registration). Submit abstracts for the user poster session by October 9 at:

The annual event kicks off on October 18 with a special symposium celebrating 35 years of outstanding science at the Stanford Synchrotron Radiation Lightsource, including honoring its founding Director Sebastian Doniach on the occasion of his 75th birthday. Thirty-five years ago, the Stanford Synchrotron Radiation Project (SSRP) - the precursor to today's SPEAR3 ring and the Stanford Synchrotron Radiation Laboratory (SSRL), recently renamed Stanford Synchrotron Radiation Lightsource - began operations. SSRL science launched with five experimental stations sharing the first x-ray beam line. The SSRP was the world's first synchrotron radiation hard x-ray lightsource based on an electron storage ring. In addition to reviewing technical accomplishments and research highlights, future scientific and technical opportunities for SSRL will be discussed at this special symposium.

LCLS/SSRL 2009 officially begins on October 19 with a joint plenary session featuring updates from SLAC and DOE, a preview of the workshops, the user science poster session, and a keynote presentation from Bill St. Arnaud on Green IT Developments. Also during the plenary session, Jo Stöhr will give a talk 'In Memory of H. C. Siegmann, the Father of Modern Spin Physics.' Yulin Chen will receive the Spicer Young Investigator Award and Leslie Jimison will receive the Klein Professional Development Award. Both will present their research (see details below). The Farrel Lytle Award will and the Outstanding Student Poster Session Awards will be presented at dinner on October 19.

On October 20, concurrent sessions will focus on SSRL and LCLS facility development, instrumentation, techniques and user science, followed by meetings of the respective SSRL and LCLS Users' Organizations.

On October 21, several concurrent workshops will be held including:
  • Imaging at SSRL with breakout sessions for Hard X-ray Micro- and Nano-Imaging as well as Nanoscale Imaging with the SSRL STXM
  • Macromolecular Crystallography - Sample Preparation and Synchrotron Data Collection
  • Soft X-ray Beam Line Experiment Preparation
  • X-ray Pump Probe Experiment Preparation
Register before October 9 to take advantage of the early registration discount.

5.   Vote for Users' Organization Executive Committee Membership
       (contact: C. Knotts,

Having full and engaged Users' Organization committees is essential, particularly during times of growth and change. Please take a few minutes to cast your ballots between October 2-19, 2009 to fill open positions on both the SSRL and LCLS Users' Organization Executive Committees. The results will be announced during the Users' Meeting.


6.   Yulin Chen to Receive Spicer Young Investigator Award
       SLAC Today Article by Lauren Knoche

highlight figure
Yulin Chen
Physicist Yulin Chen of the Stanford Institute for Materials and Energy Science has been awarded the 2009 William and Diane Spicer Young Investigator Award. The award, named for Stanford professor and SLAC researcher William Spicer (1929-2004), and his wife Diane, who passed away in 2009, is given to an early career researcher whose work has benefited from or is beneficial to the Stanford Synchrotron Radiation Lightsource or the overall lightsource community.

"I am very glad that our work was acknowledged," Chen said of the award. "I feel very excited not only because of the prize itself, but also because we could demonstrate the great opportunity SSRL provides for science. I hope the lab will keep developing its remarkable capabilities for experiments and become an even better platform for more exciting science to be carried out."

The award will be presented at the October 19 SSRL/LCLS Annual Users' Meeting at SLAC. The award includes a certificate and monetary gift of $1,000. In turn, Chen will give a short presentation describing his work.

Together with other theoretical and experimental physicists at SIMES, a joint collaboration between SLAC and Stanford University, Chen helped find bismuth telluride-an example of a new class of materials called topological insulators-which was originally predicted by theory in 2007. The experimental discovery has potential impact for future research in not only fundamental physics, but also semiconductor and energy science.

Topological insulators create a unique atmosphere for electrons, in which the electron spin and momentum are "locked" to each other on the surface of the material. This enables electrons to flow around non-magnetic impurities, instead of being scattered backward. This allows current to flow without loss of energy. Also, because electron spin and momentum are coupled, electron spin could be manipulated by an electric current applied across the surface of the topological insulator.

Physicists may use bismuth telluride to study the physics of relativity in a condensed matter system or to realize elusive particles such as magnetic monopoles or majorana fermions.

Chen's research indicated that bismuth telluride could be used at much higher temperatures than theory predicted, bringing this substance much closer to real applications. A topological insulator such as bismuth telluride could one day be used to make smaller transistors for use in more compact electronics that consume less energy. The material could also be used in novel spintronic devices without bulky magnets such as the read/write head in current hard drives. Being great thermoelectric material, bismuth telluride could even convert temperature gradients across itself to electricity or vice versa, for possible use in recycling waste heat into clean electricity or refrigeration without greenhouse coolant or cryogens.

"We study fundamental physics, but we also want to contribute to people's lives," Chen said.


7.   Leslie Jimison to Receive Klein Award
       SLAC Today Article by Nicholas Bock

highlight figure
Leslie Jimison
Stanford materials science graduate student Leslie Jimison has been chosen as the recipient of the 2009 Melvin P. Klein Scientific Development Award for her work at the Stanford Synchrotron Radiation Lightsource at SLAC National Accelerator Laboratory. Jimison will accept the award October 19 at the joint SSRL/LCLS Users' Meeting.

The recognition, which has been awarded annually since 2006, is given to undergraduates, graduate students and postdocs for outstanding research conducted at SSRL. The award comes with a $1,000 prize to help recipients disseminate their scientific results.

"The award is a kind recognition for my work at SSRL," Jimison said, adding that she will use the award funds to offset travel expenses. "It will allow me to attend a conference not otherwise possible, where I will share my ideas, learn new ideas from others and meet other people in my field."

Using the SSRL beam line, Jimison studied the conductive properties of semiconducting polymers-organic materials that could see use in technologies ranging from solar cells to flexible displays. The materials are characterized by amorphous regions punctuated by crystallites-tiny structures made of ordered patterns of atoms. Previous studies have shown that the arrangement of the crystallites within the non-crystalline regions has a large effect on the materials' electrical properties. Jimison's goal was to improve the overall understanding of the relationship.

"Because these organic films are relatively new materials, we don't know how the microstructure details affect charge transport," Jimison said. "We're trying to fill in the story."

Using the SSRL beam lines, Jimison and her colleagues developed a technique that combined x-ray diffraction data from several different analysis methods. The end result was a diffraction pattern that allowed the researchers to quantify aspects of the material structure not previously possible, including the ratio of crystalline to non-crystalline material present in the sample.

Jimison then applied the new technique to study the crystal structure in several lab-prepared samples. Jimison also made transistors out of the materials to study their electrical properties, looking for a correlation between the arrangement of crystallized regions and the materials' conductivity.

Working with her colleagues, Jimison is currently writing a paper to describe the new technique. Over the next few months, she hopes to refine the analysis method in order to extract more information and to study other materials systems.

"This was designed to be the first of a more general approach to study the microstructure of semiconducting thin films," she said. "There is lots of room for improvement."

Jimison is a fifth year doctoral student at Stanford. She was a National Science Foundation Graduate Research Fellow from 2005 to 2007, and received a bachelor's degree in materials science and engineering from North Carolina State University in 2004. She has co-authored journal articles in Advanced Materials, Physical Review and the Journal of Vacuum Science


8.   Recovery Act Funding at Work in SSRL Upgrades
       SLAC Today Article by Nicholas Bock

The Stanford Synchrotron Radiation Lightsource at the Department of Energy's SLAC National Accelerator Laboratory received an important boost this year, with $4.8 million in funding from the American Reinvestment and Recovery Act for repairs and upgrades during SSRL's annual three-month shutdown, and new scientific instruments in the year to come.

"The ARRA funding was a really big help; I don't know when we could have ever gotten these things done without it," said SSRL Acting Director Piero Pianetta. The funding will go toward seismic retrofits and key upgrades to SSRL's x-ray beam lines, which are used by scientists from around the world to conduct experiments in energy, materials, environmental and life sciences, accelerator physics and more.

Part of the Recovery Act funding will help SSRL develop an advanced spectroscopy facility that will allow researchers to study systems ranging from fuel cells to photosynthesis. This facility will rely critically on SSRL's plan to bring its SPEAR3 storage ring to its maximum operating capacity of 500 milliamperes. The ring has operated at 100 mA since its commissioning in 2004, although it recently received a boost to 200 mA. Running at full capacity will increase the brightness of the facility's x-ray beam lines, making SSRL an even more valuable tool for SSRL's scientific users.

"The results of an experiment depend on how many photons you can put on a sample," said Bob Hettel, deputy director for SLAC's Accelerator Directorate. "If you can put five times as many photons on a sample, some experiments can be done five times faster."

In other experiments, where the intense beam could be harmful to experimental samples, new schemes such as rapid sample scanning and fast shutters to remove the beam from the sample between measurements will be employed.

One of the biggest challenges in reaching full operating capacity, though, is making sure that the SSRL optical devices have a reliable cooling supply. Toward this end, $800,000 in Recovery Act funds will be used to help upgrade the cooling systems on SSRL's 11 monochromators-devices that filter incoming light to a single specified wavelength. Read more at:

9.   Structural Molecular Biology Summer School Provides Hands-on Experience
       SLAC Today Article by Lauren Knoche

The Structural Molecular Biology Summer School wrapped up Friday, September 11 after a full four days of lectures and hands-on training in data analysis. Participants ranged from graduate students and postdocs to early-career scientists interested in learning about x-ray light experiments that help identify the form and function of biological molecules.

"The Summer School showcases three different biology experiments that you can do with a synchrotron," said SSRL staff scientist Ritimukta Sarangi, who along with scientists Clyde Smith and Thomas Weiss organized the SMB Summer School. "We want students to know the skills and techniques that are available," Sarangi said. The Summer School takes place every two years.

This summer's program brought together 25 participants from the U.S. and Europe to explore the three experimental techniques macromolecular crystallography, small angle x-ray scattering and x-ray absorption spectroscopy. All three approaches allow scientists to study the structure of biological molecules using x-rays from a synchrotron. Students indicated on their Summer School applications which techniques interested them the most. Participants received hands-on training sessions for basic data analysis using their chosen technique. "Students go away with a basic knowledge of analyzing data and can interpret papers that they read which involve these analyses," Sarangi said.

The program highlights capabilities of the Stanford Synchrotron Radiation Lightsource user facilities, and informs potential future users. "We encourage the students to apply for beam time," Sarangi said. "We can help students design an experiment or assist those who may have an experiment in mind."

The SSRL SMB Summer School is supported by NIH NCRR, DOE BER and NIH NIGMS.

Read more at:

10.   Please Report SSRL-Related Papers, Invited Talks, and Awards
       (contacts: C. Knotts,; L. Dunn,

It is extremely important that users not only inform us whenever work conducted at SSRL results in a publication, but also acknowledge SSRL and our funding agencies in each publication. User help is needed to keep current records on publications including refereed journal papers, conference proceedings, book chapters and theses, invited lectures and major awards and patents based at least in part on work conducted at SSRL. This information allows SSRL to demonstrate scientific achievements and productivity when responding to requests sent out by the Department of Energy and the National Institutes of Health.

This information can be submitted anytime via email message to Lisa Dunn or Cathy Knotts or via the reference submission form at:

For recent publications lists and the proper acknowledgement statements see:

11.   X-ray/VUV Beam Time Schedules Posted
       (contact: C. Knotts,

Beam time schedules for experiments on X-ray and VUV lines during the first scheduling period in our FY2010 run have been posted to the web at:

12.   New Schedule for Shuttle Transport between SLAC and CalTrain

The Stanford Marguerite Line S shuttle connecting SLAC and CalTrain, as well as the new Rosewood Hotel, started running on a new schedule beginning Monday, September 14. Increasing alternative transportation ridership and reducing carbon emissions were the ultimate goals in upgrading the schedule. The new timetable focuses on only peak ridership periods.

Developed in a collaborative effort between SLAC and Stanford University's transportation and real estate departments, the new schedule will help to increase efficiencies, reduce operational costs and will ultimately contribute to both communities' sustainability goals in terms of carbon reductions. Approximately 19 pounds of carbon dioxide emissions are removed from the atmosphere for every gallon of gasoline saved through alternative transportation; the new schedule compliments these reductions and more

See the new Line S and also the schedule for connecting CalTrain service schedules at:


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 September 2009
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