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Vol. 13, No. 8 - February 2013
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From Director

PieroPianettaI’m writing this column as acting Associate Lab Director for SLAC’s Stanford Synchrotron Radiation Lightsource Directorate, a role I stepped into in November, when then-ALD Chi-Chang Kao became director of the laboratory. As many of you know, this isn't a new role for me, since I had served as acting ALD for SSRL before Chi-Chang joined the lab in 2010.

When I turned the keys to SSRL over to Chi-Chang at that time, the team made a great poster depicting me as the fictional space ranger Buzz Lightyear, appropriately titled “To 500 mA and Beyond.” This poster now hangs in my office and continues to remind me of the accomplishments we have made and are continuing to make with SPEAR3, the storage ring that accelerates electrons to produce x-ray beams for SSRL.

I relate this story because just two weeks ago we reached the first part of the goal listed on the poster:  SSRL is now routinely delivering its full current of 500 mA, providing faster and higher-resolution data collection to the researchers who come from all over the world to use our facility.

Although SPEAR3 first operated at 500 mA in 2005, we had to upgrade all the beam lines before we could consistently deliver this level of current to users. Upgrades included adding new photon beam containment systems and experimentally verifying that the higher level of current would not increase radiation levels on the experimental floor.

Around the time SPEAR3 was commissioned, we also realized that we needed to deliver top-off injection, a feature that was not part of the original upgrade project. This required substantial injector upgrades and a grueling review and approval process before we could deliver 500 mA with the expected beam stability and reliability. All this could not be done overnight, but as of February 13, 2013, we made it! SSRL now provides 500 mA of current to users with the high reliability they have come to expect. This is an outstanding accomplishment, made possible by the hard work and dedication of SLAC staff throughout the laboratory.

Now, the goal has shifted from the “To 500 mA” part of the poster title to the “and Beyond” part. I’m glad to say we have a lot of “and Beyond” programs in the works. These range from continued accelerator improvements in emittance and stability that will keep SPEAR3’s performance at state-of-the-art levels for years to come to new beam lines that will contribute to the understanding and development of materials for the next generation of energy technology. In all of this, by keeping our focus on the science, we can continue to drive new developments that benefit the nation.

Science Highlights

Systematic Expansion of Porous Crystals to Include Large MoleculesContacts: Hexiang Deng, Omar M. Yaghi, UC Berkeley

Recently, scientists at the University of California, Berkeley and Lawrence Berkeley National Laboratory and their collaborators synthesized a series of metal-organic frameworks (MOFs) with pores up to 98 Å in diameter—large enough to house protein molecules. For the first time the researchers were able to design strategies to overcome three major obstacles to increasing pore capacity: (a) limited solubility of large organic links; (b) structure interpenetration; and (c) collapse of pores after guest molecule removal. They targeted MOF-74, a well-studied MOF with a honeycomb-like pore structure built from linkers with one phenylene ring. Using powder diffraction data from SSRL BL2-1 and structural refinements, they demonstrated structures of remarkable stability, ultrahigh porosity and extremely large pore aperture, leading to a new size regime accessible for the inclusion of large organic, inorganic and biological molecules inside the pores of crystalline materials. Read more...

Tracing Nanoparticle Transformations in Soybean PlantsContacts: Contacts: Jorge L. Gardea-Torresdey (University of Texas at El Paso), Joy C. Andrews (Stanford Synchrotron Radiation Lightsource), Jose A. Hernandez-Viezcas (University of Texas at El Paso)

The global production of engineered nanoparticles (ENPs) is currently a trillion-dollar industry, with nanoparticles now found in products ranging from sunscreen, gas sensors and pigments (ZnO ENPs), to catalysts for internal combustion and oil cracking processes (cerium-based ENPs). While their benefits in such products are known, much is yet to be determined regarding their fate, transport, and toxicity in the environment, including the implications of the potential storage of these ENPs or their biotransformed products in the edible and reproductive organs of crop plants. A team of scientists have studied ENP uptake in soybean using micro-XRF and micro-XANES, to investigate the chemical forms of Ce and Zn within various parts of the soybean and possible transfer of the ENPs into the food chain. Read more...

X-rays Illuminate a Microscopic Picture of the Correlation between Nitrogen-dopant Bond Type and Electronic Effects in Single-layer GrapheneContacts: Theanne Schiros,Energy Frontier Research Center, Columbia University

Doping graphene with small amounts of another element such as nitrogen or boron enables scientists to "tune" its properties to make it more suitable for a variety of applications, such as contact material in solar cells.  Using soft x-ray spectroscopic techniques at SSRL Beam Lines 10-1 and 13-2, scientists from Columbia University in collaboration with SSRL staff have determined the chemically distinct species and different bond types that result from doping single-layers of graphene at sub-percent-level nitrogen doping.  As reported in the June 29, 2012, online edition of Nano Letters, the work produced a clear, microscopic picture of the different bond types and their diverse effects on the work function, carrier concentration, and the local electronic structure, results that may impact the future development of graphene-based devices.  Read more...


X-ray Laser Sees Photosynthesis in Action

A collaborative effort involving scientists from LBNL, SLAC and Stanford University, Technical University Berlin in Germany, Umeå and Stockholm Universities in Sweden, and the European Synchrotron Radiation Facility opened up new experimental capabilities to study catalysts, which efficiently speed up reactions in photosynthesis and other biological and industrial processes. Published in the February 14, 2013 issue of Science Express, the data were collected at the LCLS using two x-ray techniques simultaneously: crystallography to study the overall atomic structure of Photosystem II, and x-ray emission spectroscopy to document the electronic processes in the active-site cluster of the biological catalyst.

The collaboration was also one amongst light sources. Researchers noted the important complimentary work carried out at SSRL, ALS, and APS, which helped them to hone their techniques and test the instruments and crystals that were ultimately used in the LCLS experiment. Central to the work was the use of a new advanced spectrometer that records a full x-ray emission spectrum per x-ray pulse, and the testing of crystals and injection approaches. The emission instrument was initially tested and refined on SSRL Beam Lines 6-2 and 9-1, and ALS 5.0.2, the crystals and injector on SSRL BL12-2, and the crystals at ALS 5.0.2, and APS ID23 prior to use in the LCLS experiment.

The synchrotrons “are essential facilities to complement our LCLS research, and guide us to improving crystal quality,” said Junko Yano, the principal investigator for the LCLS experiment.

Read the SLAC Press Release


  • Biological Small Angle X-ray Scattering Workshop – March 18-20, 2013 

    The SSRL Structural Molecular Biology group will be hosting a comprehensive three-day workshop on the application and use of small angle x-ray scattering techniques in structural biology research. This workshop will include lectures on theoretical and experimental aspects of biological small angle scattering, hands-on experimental tutorials at the BioSAXS Beam Line 4-2, as well as software tutorial sessions on data analysis and modeling.  The workshop is planned for Monday-Wednesday, March 18-20, 2013. Registration is still open at the workshop website.

  • Synchrotron X-ray Absorption Spectroscopy Summer School – June 10-14, 2013

    SSRL will conduct the 2013 SSRL Summer School on Synchrotron X-Ray Absorption Spectroscopy between June 10 and June 14. The school will consist of two sets of parallel sessions, one covering basics of XANES and EXAFS data collection, FEFF based analysis and interpretation and the other covering advanced topics in data analysis, FEFF based near-edge analysis and DFT approaches to XANES data.

    The first curriculum will be suitable for beginner-level participants, who have little or no practical experience with EXAFS data collection and analysis. The second curriculum is designed around the needs of participants who already have some experience with data collection and FEFF-based data analysis and wish to learn more about approaches to data analysis for more challenging problems.

    Space is limited and interested participants are requested to submit an application early. The deadline to submit an application is April 15, 2013. (website forthcoming)

    Co-chairs for the Summer School are SSRL Staff Scientists John Bargar and Ritimukta Sarangi. The Summer School will be held at SSRL with additional facilities used at the SLAC National Acceleratory Laboratory site. Funding for the SMB Summer School program is provided by NIH-NIGMS, DOE-BES, and DOE-BER.

  • SSRL/LCLS Annual Users' Meeting & Workshops

    Meeting co-organizers Colleen Hansel (Woods Hole Oceanographic Institution), Christian Bressler (European XFEL), Jun-Sik Lee (SSRL) and Hae Ja Lee (LCLS), together with Cathy Knotts, have begun planning for our Annual Meeting. Your ideas for speakers, research and development to focus on and workshop topics are welcome. Please contact Cathy Knotts and/or the other co-organizers. Contact information can be found at the SSRL and LCLS UOEC websites.   Though tentatively set for October 2-4, 2013, we are also seeking input about date preferences for our Users' Meeting at:


  • Safety Training for SSRL User Badges – If you have beam time at SSRL coming up soon and do not know the status of your safety training, you can look it up in our User Portal. Once you have logged in,  click on the "User Information" link on the blue navigation bar under the image and then select "My Account".   Your current status for meeting the Safety Orientation (SON), GERT and CyberSecurity course requirements will be listed along with instructions and a link to the training site. 

  • Macromolecular Crystallography Proposal – The next deadline for new Macromolecular Crystallography proposals is April 1, 2013. Please submit proposals through our User Portal.


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 for the U.S. Department of Energy Office of Basic Energy Sciences by Stanford University. Additional support for the SSRL Structural Molecular Biology Program is provided by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences and the National Center for Research Resources. Additional information about SSRL and its operation and schedules is available from the SSRL web site.

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Questions? Comments? Contact Lisa Dunn