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Vol. 14, No. 10 - May 2014

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From the Director: Looking Forward to New Technologies and Partnerships


SSRL has seen a lot of activity over the past year with no sign of slowing down. In addition to the ongoing user program – with about 1,675 on-site and remote access users in 2013, over 520 journal papers and 91 theses completed by students using SSRL – we have a number of exciting upgrade projects and new beam lines in the works. We are currently planning for the DOE triennial review of SSRL in June, where we will be describing these past accomplishments and our future plans in great detail.

Over the next several years, SSRL will be executing on the SPEAR3 accelerator upgrade program with the goal of maintaining the high level of reliability of over 97 percent that our users have grown to expect, as well as further reducing emittance, which will enable research on smaller and more dilute samples.

On the beam line side, we have taken advantage of new partnerships to begin the development of three brand new beam lines and the upgrade of two others. The partnerships include a collaboration with Stanford University and The Scripps Research Institute to build and operate a new microbeam macromolecular crystallography beam line and joint programs with the DOE Energy Innovation Hubs and Energy Frontier Research Centers, whose goals range from achieving revolutionary advances in battery performance to developing a solar energy generation system based on artificial photosynthesis. SSRL is also partnering with the National Synchrotron Light Source (NSLS) with DOE support to add capacity at SSRL for existing NSLS users during the transition from NSLS shutting down in September 2014 and NSLS-II becoming fully operational. This collaboration offers critical help to the displaced NSLS users, while providing new capabilities to the overall user community.

Within SLAC, SSRL has been partnering with Photon Science and LCLS on energy and correlated materials research and macromolecular crystallography.

Besides keeping the staff very busy, all of this activity provides for a vibrant and ever-improving environment for our user community, adding state-of-the-art capabilities that draw in even more users.

Science Highlights


Deconstructing the Peptide-MHC Specificity of T Cell RecognitionContacts: Michael E. Birnbaum and K. Christopher Garcia, Stanford University

As a crucial part of an organism’s immune system, T cells detect and fight infection and cellular dysfunction. Each T cell has a unique T-cell receptor (TCR) on its surface that recognizes and binds peptide antigens, triggering an immune response. The peptide antigens themselves, often stemming from intruding organisms such as bacteria, are bound to molecules known as major histocompatibility complexes, or MHCs. TCRs show a great deal of diversity in order to ensure that the large number of potential antigens can be detected. Although of great medical interest, predicting what peptides a given TCR recognizes has been challenging. A team led by researchers has now found a way to increase the success of such predictions from 30 to up to 90 percent.  Read more...

See also: SLAC Press Release: Stanford Researchers Discover Immune System’s Rules of Engagement


Measurement of Transient Atomic-scale Displacements in Thin Films with Picosecond and Femtometer ResolutionContacts: Aaron Lindenberg and Michael Kozina, Stanford University/SLAC, and Apurva Mehta, SSRL

Optical pump/x-ray probe experiments are key for studies of ultrafast processes in a wide range of materials. In these experiments, an optical pump laser pulse excites a sample and is followed by an x-ray probe pulse that determines the sample’s response. Such studies have been primarily focused on non-equilibrium situations, in which the pump pulse causes strong perturbations, and typically probe pulses with rather low repetition rates. A team of researchers has recently put a complementary approach to the test, exploring weak perturbations and high repetition rates.  Read more...


Iron(IV)hydroxide pKa and the Role of Thiolate Ligation in CH Bond Activation by Cytochrome P450Contacts: Courtney M. Roach (Krest), SSRL and Michael T. Green, Pennsylvania State University

Cytochrome P450s make up a large family of iron-containing enzymes that catalyze the oxidation of organic substances. As nature’s detoxifiers, they are responsible for 75 percent of the phase one metabolism of pharmaceuticals. A long-standing mystery of P450s is how they can perform these rather aggressive reactions without damaging their own protein structures in auto-oxidation reactions. With a recent study researchers have made a large step forward in understanding this enigmatic chemistry, opening up new possibilities for biological, medical and synthetic P450 research. Read more...


The Ductility of Human Jaw Bone Attached to a ToothContacts: Sunita P. Ho, University of California San Francisco, Joy C. Andrews and Piero Pianetta, SSRL

Local changes of the periodontal ligament (PDL), i.e. the connective tissue fibers attaching teeth to the jaw bone, can cause abnormal dental conditions such as ankylosis, which affects growth and development of the jaw and potentially leads to jaw distortions. In a recent study researchers conducted an in-depth study of bony protrusions within the PDL space – changes that occur due to age and other factors.  Read more...

Upcoming Onsite Events

SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences, June 3-5, 2014

workshop image

The 7th SSRL SRXRS (Synchrotron Radiation-based X-ray Scattering techniques) School will provide a practical users' guide to planning and conducting scattering measurements at SSRL beam lines, and will cover important techniques including small angle scattering, thin-film scattering, powder diffraction, structure refinement and surface x-ray scattering. The school will address topics that are not commonly included in text books or class lectures, and typically obtained only through on-the-experiment training. There will be hands-on sessions at SSRL beam lines and session of diffraction theory and on data analysis. The school will also cover new instrumentation at SSRL scattering beam lines. This year's school, which will take place June 3-5, is organized by: Apurva Mehta, Stefan Mannsfeld, Chris Tassone, and Mike Toney.   See website

uxss poster

PULSE Institute - Ultrafast X-ray Summer Seminar, June 15-19, 2014

Hosted by the Stanford PULSE Institute, the UXSS is organized in collaboration with the Center for Free-Electron Laser Science at DESY in Hamburg, Germany, and the Helmholtz Virtual Institute for Dynamic Pathways in Multidimensional Landscapes, Germany.

The goal of UXSS 2014 is to disseminate information and train students and post-docs on new opportunities in ultrafast science, particularly using x-ray free electron lasers.  See website

SSRL School on Synchrotron X-ray Microscale Imaging Techniques, July 11-15, 2014 - Save the Date

The 1st SSRL SXRMI (Synchrotron X-ray MicroXAS Imaging) School will provide a practical users' guide to planning and conducting microXAS imaging experiments at SSRL beam lines. Students will participate in hands-on sessions at the beam lines, including on the following facilities: hard x-ray microXAS imaging (BL2-3), hard x-ray mesoprobe XAS imaging (BL10-2), and the newest microXAS imaging “tender” energy beam line (BL14-3).  The hands-on sessions will be paired with several sessions of data analysis and data mining of imaging data. The School will also cover new instrumentation and techniques at SSRL microXAS imaging beam lines and will include topics that can only be learned by direct access and experience at the facility through on-the-experiment training. This initial school, which will take place July 11-15, is organized by Sam Webb and Courtney Roach.  See website

High Power Laser Workshop, October 7-8, 2014 - Save the Date

SSRL/LCLS Annual Users' Conference and Workshops, October 7-10, 2014 - Save the Date

Macromolecular Crystallography: Stanford AutoMounter (SAM) Developers' Forum Workshop, October 10, 2014 - Save the Date

NUFO Event

User Science Exhibition in DC, June 10

A National User Facility Organization (NUFO) User Science Exhibition will be held on Tuesday, June 10, 2014 in the foyer of the U.S. House of Representatives Rayburn Office Building. Discovery and energy are the themes for the NUFO exhibition. Users are encouraged to participate in this event, which will feature hands-on demonstrations, videos, and examples of user and industry research. Contact NUFO Vice Chair Stephen Wasserman (  The Future of America is the Research of Today

User Research Administration Announcements

  • Proposal Deadlines

    – SSRL X-ray/VUV proposals can be submitted three times a year: June 1, and September 1 and December 1

    – SSRL Macromolecular Crystallography proposals can be submitted April 1 and July 1 and December 1.

    – LCLS proposals for experiments on AMO, SXR, XPP, CXI, XCS, MEC are due by 4 pm (PST) on July 29, 2014

    Submit proposals and beam time requests through the user portal.

  • Food Service Available during Construction of New Cafeteria in Science and User Support Building

    The SLAC Cafe, auditorium and visitor center are closed and will be replaced by a new Science and User Support Building (SUSB). During this construction (2013-2015), temporary food service will be provided by the Cardinal Chef Mobile Gourmet food trucks, 11am - 2pm in front of SLAC Building 27. Lunch menus are posted online.  See map

    In an effort to expand the food service available onsite SLAC offers a "Virtual Cafeteria" using services provided by the "Eat Club".  Eat Club is a local lunch delivery service. They collaborate with local restaurants to provide quality food fitting a variety of tastes at an affordable price. Orders are placed and paid for through their online service. The SLAC community can review the daily selections and place an online order in the morning using a personal credit card. Drop-off deliveries are made around noon each day to several locations around the site, inlcuding a drop-off location in the SSRL Building 120 Experimental Hall.  Individual on-line registration takes just a few minutes. The url for sign-up for a free account and for pre-order is

    A Starbucks kiosk near the Guest House parking lot is now open.   Starbucks offers daily walk-up coffee, takeout pastries and cold sandwiches. The kiosk is open from 6am to 6pm Monday through Friday.

SLAC Security Update

The Panofsky gate behind the guest house will no longer be available for pedestrian access to Sand Hill Road.  Please use the Main Gate instead.


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