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Vol. 13, No. 12 - June 2013
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Science Highlights


Water-Rock Reactions Produce Hydrogen Gas at Temperatures within the Limits of LifeContacts: Lisa Mayhew & Alexis Templeton, University of Colorado - Boulder

Hydrogen gas is produced in chemical reactions between anoxic water and iron-rich rocks at temperatures above 200°C – conditions too hot to support life. However, at hydrothermal vents or hot springs, where hydrogen-rich fluids mix with cooler waters and temperatures have dropped sufficiently, hydrogen-consuming organisms can survive. Less is known about the amount and mechanism of hydrogen production from water-rock reactions occurring at temperatures within the temperature limits of life (≤122°C) and the potential for these reactions to support in situ microbial life. Given the large expanse of the Earth’s crust that likely interacts with water under these cooler conditions, it is possible that these low-temperature reactions could sustain extensive subsurface microbial communities away from Earth’s hot spots.

Researchers have used SSRL’s BL2-3 microXAS imaging instrument to study what happens in detail as hydrogen is produced at low temperatures when powdered rocks and minerals are submerged in anoxic water at 55°C and 100°C for a period of 100 days.  They found that spinels are key in hydrogen production, acting as mediators in the electron transfer between Fe2+ and water and thus play an important role in hydrogen production during low-temperature reactions. Read more...


The Long-Sought Structure of a-Catenin Defines Its Functions for Cell-Cell InteractionContact: The Scripps Research Institute Florida

Cells bind each other using specialized cell surface adhesion complexes called adherens junctions. These complexes direct the formation of tight, Velcro-like contacts that are essential for the development, architecture, maintenance, and function of tissues in all higher organisms. Exactly how this cell to cell binding is accomplished has not been fully understood.  Researchers from the Florida campus of The Scripps Research Institute (TSRI) have now solved a piece of this puzzle by determining the structure of α-catenin using SSRL’s Beam Line 11-1. Read more...

Meeting Summary

2013 SSRL Summer School on Synchrotron X-ray Absorption Spectroscopy

The 2013 Summer School on Synchrotron X-ray Absorption Spectroscopy was held at SSRL June 10-14. Two sets of parallel, overlapping Schools were organized; 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. This year’s intense Summer School was attended by 43 participants and was led by a team of 15 tutors.


The beginner session (10-13 June) consisted of one day of introductory and theoretical lectures on synchrotron based x-ray spectroscopy followed by lectures demonstrating scientific examples in biology, chemical catalysis, material science and environmental science. The lectures were followed by one full day of hands-on data collection at three beam lines; 11-2, 7-3 and 4-1. The participants were divided into small groups, providing individual attention for each participant. The participants learned the basics of beam line instrumentation, data collection techniques and proper sample preparation protocol. The hands-on data collection session was followed by a two-day classroom style data workup and analysis session. The participants learned various analysis techniques to obtain geometric and electronic information and speciation information from the x-ray absorption spectra they collected.

The advanced session (12-14 June), which was attended by participants already familiar with synchrotron-based spectroscopy, focused on advanced FEFF and DFT based geometric and electronic structure analysis methods. The School included a lecture series on the detailed principles behind EXAFS and XANES and on application of synchrotron spectroscopy to complicated systems, which posed challenges both in data collection and analysis. Advanced level EXAFS analysis focused on error reporting, correlation between fit parameters, treatment of multiple-scattering and other statistical parameters. It also included dedicated sessions on FEFF 9.0 based XANES analysis, which was followed by lectures on electronic structure information content of XANES and using DFT methods.

The School was supported by NIH-NIGMS, DOE-BER and DOE-BES.

More News

Research Paints New Picture of 'Dinobird' Feathers
Excerpted from June 11, 2013 SLAC Press Release

The first complete chemical analysis of feathers from Archaeopteryx, a famous fossil linking dinosaurs and birds, reveals that the feathers were patterned—light in color, with a dark edge and tip—rather than all black, as previously thought.

Scientists used x-ray fluorescence mapping on SSRL Beam Line 6-2 to find chemical traces of the original dinobird and its pigments in the rock that entombed it 150 million years ago.

"This is a big leap forward in our understanding of the evolution of plumage," said Phillip Manning, a paleontologist at the University of Manchester and lead author of the report which received advanced online publication May 31 and appears in print in the June issue of the Journal of Analytical Atomic Spectrometry. Read the full SLAC Press Release.

SSRL's X-rays Bring a 200-Year-Old Opera Back to Life

When, 216 years ago, someone mysteriously blacked out pages from the French opera Médée with charcoal, the music was lost to history. Now, scientists at Stanford’s National Accelerator Laboratory have brought those long-lost notes back to life. Read more in KQED Science News Blog.

Upcoming Events

SSRL/LCLS Annual Users' Conference and Workshops – October 1-4, 2013

Our Annual Users’ Conference is approaching fast. Please mark October 1-4 down on your calendars to join us for a line-up of workshops, science talks and a poster session geared for exploring new opportunities at SSRL and LCLS and highlighting the excellent science that is already being done at both.  The agenda includes:

KEYNOTE SPEAKERS for the October 3 Plenary Session

  • Science Case for Diffraction Limited Storage Ring, Oleg Shpyrko (University of California San Diego)
  • Science Case for Short Pulses Time Resolved Studies, Aaron Lindenberg (Stanford Institute for Materials & Energy Sciences - SIMES)
  • Exploring Matter in Extreme Conditions, Siegfried Glenzer (Stanford Institute for Materials & Energy Sciences - SIMES)
  • Novel Short Pulses at LCLS, Ryan Coffee (LCLS)

SATELLITE EVENTS                                          

  • Oct 1-2:  Using X-rays to Study Cultural Heritage. Organizers: Marc Walton (The Getty Conservation Institute), Apurva Mehta (SSRL)
  • Oct 1-2:  High-Intensity Laser-Plasma Interactions with a Free Electron Laser. Organizers: Siegfried Glenzer (SIMES), Roger Falcone (LBNL), Stefan Hau-Riege (LLNL)
  • Oct 4:      Early Career Scientist Associate Forum. Organizers: Hae Ja Lee (LCLS), Andre Schleife (LLNL)

USER CONFERENCE WORKSHOPS                                            

  • Oct 1:  Exploring an Inverse Compton Source (ICS) at SLAC. Organizers: Yijin Liu, Mike Toney
  • Oct 1:  Integrating Synchrotron Techniques into Environmental Carbon Science. Organizers: John Bargar, Colleen Hansel
  • Oct 1:  X-ray Spectroscopy for Chemical Catalysis. Organizers:  Mali Balasubramanian (APS/ANL), Tsu-Chien Weng, Jun-Sik Lee
  • Oct 1:  MicroXAS Imaging with SSRL's New 2-5 keV Beam Line 14-3. Organizer:  Sam Webb
  • Oct 1:  New Directions for High-Energy Density (HED) Physics at the Matter in Extreme Conditions Instrument. Organizers: Siegfried Glenzer, Phil Heimann
  • Oct 1:  Toward a Modular Framework for Lightsource Experiment Simulation. Organizer: Garth Williams
  • Oct 2:  AMO Science. Organizer:  Christoph Bostedt
  • Oct 2:  LCLS Data Analysis. Organizer:  Amedeo Perazzo
  • Oct 2:  LCLS Detectors. Organizers:  Gabriella Carini, Chris Kenney
  • Oct 2:  Synchrotron Techniques in Metal Biogeochemistry:  Across Time and Spatial Scales. Organizers: John Bargar, Colleen Hansel
  • Oct 4:  Soft X-ray (SXR) Science. Organizers: Bill Schlotter, Josh Turner
  • Oct 4:  Software for Serial Crystallography Data Analysis. Organizers: Anton Barty, Thomas White, Marc Messerschmidt
  • Oct 4:  Time Resolved Experiments at SSRL using Low Alpha Mode. Organizers:  Hendrik Ohldag, Apurva Mehta

Stay tuned for registration details!

User Administration Update

Upcoming Proposal Deadlines

  • September 1, 2013 for beam time on SSRL X-ray/VUV lines beginning in February 2014
  • July 1, 2013 for beam time on SSRL Macromolecular Crystallography lines beginning fall 2013
  • July 9, 2013 for beam time on LCLS instruments/beam lines for Run 9 beginning spring 2014
Please submit proposals through our User Portal.

User Badging and Site Access 

Please complete training and contact URA in advance of your beam time to help facilitate access and badging.  SLAC's ongoing site access upgrades include proximity card readers at the main entrance off Sand Hill Road as well as at Security Gates 17 and 30. You will obtain a SLAC User ID badge with proximity access when you complete training and check-in at the URA office in Building 120. Plan to arrive during URA office hours which are Monday-Friday 7 am-12 noon and 1-4 pm (except weekends and holidays). Upon your first visit to SLAC, provide photo ID and identify yourself as a user to SLAC Security. Turn right at the main SLAC entrance and visit the Security Office to obtain a temporary proximity card to allow you to pass through Gate 17 in order to get to the URA office for check-in. 

Users without valid training and SLAC ID badges will not be permitted through Gate 17 outside of the URA office hours unless they have arranged for and are accompanied by an escort (temporary badges can be obtained from SLAC Security located next to the main gate).  

Reminder:  SSRL's experimental run ends the morning of August 5.  SSRL users are not expected to need access to facilities within SLAC's research yard until we resume user operations in early November.   Please contact URA ahead of time if you do have a business reason to access facilities beyond Gate 17 during our shutdown.

The Stanford Synchrotron Radiation Lightsource (SSRL) is a third-generation light source producing extremely bright x-rays for basic and applied research.  SSRL attracts and supports scientists from around the world who use its state-of-the-art capabilities to make discoveries that benefit society. SSRL, a U.S. DOE Office of Science national user facility, is a Directorate of SLAC National Accelerator Laboratory, operated by Stanford University for the U.S. Department of Energy Office of Science.  The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences. For more information about SSRL science, operations and schedules, visit

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Questions? Comments? Contact Lisa Dunn