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Vol. 13, No. 9 - March 2013
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Science Highlights

Biotic-Abiotic Pathways: A New Paradigm for Uranium Reduction in SedimentsContact: John Bargar (SSRL)

As part of a larger, DOE-funded investigation into bioremediation of uranium in contaminated aquifers, a group of SSRL scientists made a surprising discovery about how uranium ions behave in the environment. In addition to overturning current scientific models, this research will lead to more efficient, less costly methods for uranium cleanup and mining. Their research hinged on the fundamental subject of electron transfer-redox reactions - in this case, what atoms gave up electrons to uranium. Prior to this study it was generally thought that enzymes on bacterial cells could donate electrons to highly soluble, highly mobile, and thus highly undesirable U6+ (uranyl), reducing it to the more stable U4+ oxidation state in the form of the mineral uraninite (UO2). Another possible path: iron sulfide (FeS) is also capable of donating electrons to uranyl, reducing it to UO2.

In the field, the SSRL team led by Senior Staff Scientist John Bargar placed fresh sediments into wells in a uranium contaminated aquifer in Rifle, CO during a bioremediation experiment conducted by researchers from Lawrence Berkeley National Laboratory.

At the end of the experiment, the sediments were harvested and brought back to SSRL. The research team used x-ray imaging at SSRL Beam Lines 10-2 and 2-3 to measure the micron-scale distribution of uranium in the aquifer sediments and to determine if it was closely associated with iron oxides or iron sulfides. Read more...

Watching Ions Hop in Superionic NanomaterialsContact: Aaron Lindenberg (PULSE/SSRL/Stanford University)

For the first time, ultrafast x-ray scattering and spectroscopic measurements carried out at SSRL, the Advanced Light Source and the Advanced Photon Source captured the atomic-level dynamics of a superionic nanocrystal as it transformed.

Superionic materials are multi-component solids which can simultaneously display characteristics of both a solid and a liquid: Above a critical temperature associated with a structural phase transition, one atomic species in the material exhibits liquid-like ionic conductivities and dynamic disorder within the rigid crystalline structure of the other. Applications such as electrochemical storage materials and resistive switching devices follow from this abrupt change in ionic mobility, but the atomistic pathways associated with this phase transition and the related functional properties that emerge at the nanoscale have been largely unknown and unexplored. Read more...

Element-Specific and Real-Time Observation of CO-Ru Chemisorption Bond Breaking with Soft X-ray SpectroscopyContacts: Hirohito Ogasawara (SSRL), Dennis Nordlund (SSRL) and Anders Nilsson (SUNCAT/SSRL)

An international collaboration of scientists, including several from SSRL, has taken advantage of the broad range of photon science capabilities available at the lab to investigate a proposal that adsorption and desorption of a molecule to a surface - both fundamental processes of interfacial chemistry - proceed through a transient "precursor" state in which the molecule is weakly bound to the surface. Their research focused on carbon monoxide adsorption/desorption on metal surfaces; although a large number of spectroscopic studies have been devoted to this reaction, the precursor state had never before been seen.

The researchers used a next-generation experimental setup developed at SSRL for both x-ray emission spectroscopy and x-ray absorption spectroscopy. The setup was equipped with a high-throughput compact grazing incidence grating spectrometer developed by Dennis Nordlund, Hirohito Ogasawara and Anders Nilsson. They started at SSRL Beam Line 13-2, first commissioning the setup and taking a static preparatory measurement of the CO-Ru chemisorption bond for the study. Read more...

Workshop Summary

Biological Small Angle X-ray Scattering Workshop

The SSRL Structural Molecular Biology Group hosted a workshop on the use of non-crystalline small-angle x-ray scattering and diffraction studies in structural biology research from March 18-20. This three-day comprehensive workshop included invited lectures by experts in the field during the first half followed by hands-on data acquisition sessions at the BioSAXS Beam Line 4-2 at SSRL in parallel with data analysis tutorials. Although the lectures were aimed at the graduate student/beginners level and did not assume any pre-knowledge of the SAXS techniques, they were also appropriate for experienced researchers. Thirty-five participants from all over the US and Europe with varying degrees of experience in the application of small angle scattering techniques to structural biology research attended the workshop. The organizers thank all the tutors for providing a valuable learning experience for everyone involved.

workshop image

Co-Chairs for this 2013 BioSAXS workshop were the entire SSRL SMB SAXS group - Thomas Weiss, Tsutomu Matsui, Lester Carter and Ping Liu. The hands-on data collection and analysis sessions were facilitated by Weiss, Matsui and Carter as well as by UCSF postdoctoral scholars Patrick Weinkam and Seung Joong Kim.

Funding for the SSRL Structural Molecular Biology Program and this workshop was provided by the National Institutes of Health, National Institute of General Medical Sciences Division of Biomedical Technology, Bioinformatics and Computational Biology and the Department of Energy, Office of Biological and Environmental Research.

Beam Line and Operations Updates

Beam Line 9-3 Mirror Replacement and Commissioning
Good progress is being made toward getting the user program restarted on Beam Line 9-3 after installation of its new M0 mirror. The beam line was opened at minimal current the afternoon of Monday, February 25 and was ready for 500 mA by Wednesday morning in preparation for optics re-commissioning to commence. Light was brought into the BL9-3 experimental hutch for the first time with the new mirror system on March 5 and the re-commissioning effort is well underway.

Update to Hutch Key Protocol
The hutch search/reset key (S/R) protocol for SSRL's hard x-ray beam has been updated. The S/R key is now being issued only once per valid Safety Checklist (SCL). Once issued, the S/R key remains under User control for the duration of the beam time covered by the checklist.

A combination-code key lock box has been installed adjacent to the S/R key drop box at each beam line. Experimenters will be given the combination so that they can put the key in the box when they leave the experimental area during their scheduled experiment for meals or to sleep, etc. The S/R key for each beam line is always to remain in the possession of an authorized staff or user, or locked in either the combination-code lock box or the S/R key lock box. The S/R key is NOT to be removed from the SSRL experimental area.

At the end of the beam time covered by the SCL the user puts the S/R key in the drop box rather than the combination-code lockbox at which time they record the date/time and their name in the beam line logbook.


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 analysis.

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 via the website is April 15, 2013.

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.  Application

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.  

User Research Administration

X-ray/VUV Proposal Submission
The next deadline for X-ray/VUV proposals is June 1, 2013. Please submit proposals through our User Portal.

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 Cyber Security course requirements will be listed along with instructions and a link to the training site. 


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