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SSRL Headlines Vol. 12, No. 6 - December 2011


Contents of this Issue:

  1. From the Director — Outreach and Support Efforts
  2. Science Highlight — Manganese-II Oxidation: A Biotic and Abiotic Process
  3. Science Highlight — Characterization of Iron Diazene Complexes in Two Oxidation States
  4. Biological SAXS Symposium — A Tribute to Dr. Hiro Tsuruta
  5. Awards — Prof. Harold Hwang Named American Physical Society Fellow
  6. Announcements — Shipping, Survey, SSRL at the Exploratorium, NUFO
  7. Profile — Postdoc Eric Verploegen Energized by Experiences, Mentoring
  8. In the News — Metallurgy, Earth's Core, Nitrogenase

1.   From the Director: Outreach and Support Efforts  

Chi-Chang Kao
It's that time of year again and SSRL will soon shut down for the holidays. We have a lot to celebrate, as 2011 was once again a successful year full of innovative science. We ended the 2010-2011 user run year with an average uptime of 98.4%, delivering 4,775 hours out of the 4,851 hours scheduled, allowing approximately 1,515 scientists to conduct experiments. I offer my sincere gratitude to SSRL's outstanding staff members for keeping SSRL extremely competitive among the best synchrotron sources in the world.

As SSRL looks to 2012 and beyond, we plan to make a great synchrotron even better. As we continue to refine our strategic plan, the path forward for outreach and support efforts is becoming clear. Building on SSRL's well-established reputation for user support within the synchrotron research community, a strong connection to Stanford University, and close connections to technological developments in Silicon Valley, SSRL is working to identify the steps a new user or user community follows to take an idea through to the successful conclusion of an experiment, and make each step of the user experiment cycle even better. In this column, I would like to say just a few words about how we are doing and how we are planning to expand each step of this cycle. We look forward to your input and engagement in these activities.

(URA cycle)Reaching Out to New and Diverse Scientific Communities - New applications of synchrotron radiation continue to be discovered, even as synchrotron research has become more mature. A systematic outreach program will allow us to better capture these new opportunities. In the coming years, SSRL will continue to educate future generations of scientists and will increase the number of SSRL facility tours for local and visiting scientists who have an interest in conducting synchrotron research. In addition, SSRL will expand its outreach toward both local academic research groups and new industrial users, networking and collaborating with local start-ups and large multi-national companies to pursue opportunities in energy research, biotechnology, and information technology. SSRL also plans to increase its representation at conferences related to key scientific opportunities, including materials by design and emerging phenomena from complexity. 

Providing Introductory Workshops to Potential New Facility Users - After reaching out to new user communities, SSRL staff members follow up with introductory workshops that explain the ins and outs of synchrotron research, and brainstorm with the new user community ways to optimize the synchrotron techniques and instrumentation for that community's specific applications. In the next few years, SSRL will increase the number of such introductory workshops, including "Demystifying the Synchrotron Experience," an introduction to synchrotron science first held at SLAC in autumn 2011 and planned to continue on a regular basis, and will work to optimize tools for our new user communities.

Providing Tools for Experiment Design - A properly designed experiment is the key for a successful experiment. In addition, as demand of synchrotron beamtime continues to rise, better designed experiments will help to make the most efficient use of beamtime. SSRL will work with other synchrotron facilities to develop and disseminate tools, in particular experimental simulation tools. The Structural Molecular Biology (SMB) Division at SSRL has received glowing feedback from users for this kind of effort. SSRL will use lessons learned from SMB to develop and implement these tools for all facility beam lines.

Running Hands-on Tutorials - Hands-on tutorials are the best way for new users to get familiar with the facility and the staff members who operate the beamlines and instruments. They are also very useful for existing users who want to learn more advanced synchrotron tools. SSRL currently runs more than six types of hands-on tutorials that focus on synchrotron techniques and capabilities, including scattering, spectroscopy, imaging, structural molecular biology and remote access. Staff members regularly evaluate these tutorials to ensure they are meeting user needs.

Reviewing Proposals and Allocating Beam Time - In addition to the preexisting regular and rapid-access proposal processes and the letter-of-intent mechanism, SSRL recently designed a new proposal mechanism, the Collaborative Access Proposal, to foster collaborations between user groups and SSRL to enhance or develop a new capability or beam line or to engage in outreach activities to build up a new research area, technique or community. In the coming years, we will continue to evaluate our proposal mechanisms to make sure they suit our user community’s needs.

Assisting with Experimental Set Up and Data Collection - SSRL has nurtured a culture of pride among its staff in providing expert service and support—including technical support, access to machine shops and wet labs, assistance with sample preparation, remote access capabilities and reference databases. In the coming years, SSRL will seek to increase online visualization and data analysis capabilities so that users can optimize their use of beam time and subsequent analysis. We will also increase the support in instrument design to facilitate more sophisticated experiments.

Providing Tools and Support for Data Analysis - To optimize the productivity of users, the SSRL scientific staff has developed several data analysis software programs and graphical user interfaces, including SIX Pack, SMAK, TXM-Wizard, ADM, WXDiff, BLU-ICE, Web-Ice, and EXAFSPAK. These software packages (and in many case the source code) are available for free download. SSRL staff members continue to look for ways to improve existing data analysis tools and design new ones for the user community at large.

Communicating Results and Impact - SSRL staff members make a concerted effort to communicate science results with the general public, the media, the local community, and other scientists through public lectures, press releases, brochures, scientific conferences around the world, and even this monthly newsletter. Publicizing the scientific results of all we do is important for accountability, continued funding, and ensuring the highest impact of SSRL research. Here we need your help: After data have been collected, analyzed and prepared for publication, please acknowledge the user facility and funding agencies in your publications using the formats posted on the SSRL website. We also strongly encourage you to inform us via phone or e-mail when especially exciting results are about to be published so we can develop a press release and communicate user research findings to a broader audience.

If you have suggestions for how we can improve SSRL’s outreach and support efforts, we would very much like to hear them. Please feel free to e-mail me or User Research Administration Manager Cathy Knotts with your ideas.

In the meantime, I encourage you all to enjoy the upcoming winter shutdown, taking the time to relax and rejuvenate. Best wishes to you and your family for the holiday season.

2.  Science Highlight — Manganese-II Oxidation: A Biotic and Abiotic Process
       (contact: Colleen Hansel,

(Nitrogenase Progress)
Manganese, one of the most abundant metals in soils and rocks, is important to the health of the environment: As it cycles between manganese-II and nanocrystalline manganese-III/IV oxides, it plays an important role in controlling the cycle and transport of soil nutrients and contaminants. Yet because the process is kinetically hindered, manganese will not oxidize rapidly in air; manganese needs a catalyst, often bacteria, to spur the process into action. Through a better understanding of this process, it may become possible to more efficiently remove dangerous contaminants from soil and further understand the complex redox chemistry of this element.

In a recent study undertaken at SSRL Beam Line 11-2, a team of researchers led by Colleen Hansel of Harvard University sought to unravel one method by which manganese-II oxidizes. Previous work had revealed a novel bacterial pathway, which involves an extracellular chemical compound called a superoxide. Furthermore, if the bacterial catalysts were made ineffective within the first 12 hours of reaction, no oxidation occurred. But if the catalysts were made ineffective after 12 hours, the process continued uninhibited, likely due to the manganese oxide products themselves contributing to further oxidation.

The SSRL study revealed that this oxidation of manganese-II involves a combination of biotic and abiotic processes, and involves enzymatically produced superoxide and mineral catalysts. To maintain the oxidation rate, the team concluded, both biotic and abiotic processes are required throughout the cycle.

This research offers a step toward understanding the link between microbial metabolism and metal reduction-oxidation chemistry, and may help researchers design ways to manipulate the redox cycles of manganese to undertake successful environmental remediation.

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

3.   Science HighlightCharacterization of Iron Diazene Complexes in Two Oxidation States
       (contact: Caroline Saouma,, and Jonas Peters,

(Iron Diazene Complex)
The enzyme nitrogenase plays a critical role in converting nitrogen in the air into ammonia, a form that living organisms can use. Scientists have long sought to understand where at the active site of this enzyme, and how, this reaction takes place; among other things, they hope to eventually reverse-engineer it and replace the resource-intensive method widely used in industry with one that mimics nature's gentle version of the reaction.

Several mechanisms have been proposed to describe nitrogenase's reduction of N2 to NH3, in which   the active site works its way through a series of intermediate states as it reduces from N2 to NH3. Recent spectroscopic and reactivity >studies on the enzyme suggest that a mechanism that proceeds via diazene (N2H2) and hydrazine (N2H4) intermediates may be plausible. To facilitate identification of these intermediates, comparisons can be made to model iron complexes that feature these nitrogenase ligands. Recently, a team from the California Institute of Technology and Northwestern University sought to determine the geometric and electronic structures of two inorganic complexes that can mimic components of such states, [Fe2(μ-N2H2)]2+ and [Fe2(μ-N2H2)]1+, the latter of which is the first example of a paramagnetic diazene-ligated metal complex. Due to the small size of [Fe2(μ-N2H2)]1+ crystals and their extreme sensitivity to oxygen, the team was unable to determine their atomic structure by conventional x-ray diffraction means. By bringing their crystals to SSRL's micro-focus Beam Line 12-2, the team was able to determine the structure of [Fe2(μ-N2H2)]1+ and compare it to the structure of [Fe2(μ-N2H2)]2+.

The team found that the two states have similar geometry in their iron centers, although upon reduction the average distance between the iron and nitrogen atoms increases while the average distance between the two nitrogen atoms decreases slightly. This suggests that compared to previously characterized diazene-ligated iron complexes, [Fe2(μ-N2H2)]2+ features a distinct electronic structure, which is due to a different geometry about the iron centers. The complexes were also characterized by Digital Functional Theory calculations and several spectroscopic methods, which corroborate the electronic structure.

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

4.   Biological SAXS Symposium A Tribute to Dr. Hiro Tsuruta
       (contacts: Britt Hedman,, and Keith Hodgson,

(Hiro Tsuruta)
A symposium on biological small angle x-ray scattering will be held at SLAC on February 9, 2012 as a tribute to Dr. Hiro Tsuruta, who for almost 20 years led the development and operation of SSRL's structural biology SAXS (bioSAXS) Beam Line 4-2 facility. BL 4-2 is one of the most highly performing and productive experimental facilities of its kind in the world today, and has become a beam line of choice for weakly scattering and challenging biological systems.

Invited speakers will honor Hiro's keen scientific interests and intellectual curiosity while offering insights into past, present and future applications of bioSAXS. The symposium will encompass many aspects of the research field of biophysics, where Hiro pursued his strong interest in structure–function relationships in biological macromolecular assemblies at the molecular structure level. These research interests included macromolecular assemblies such as virus particles, molecular chaperon proteins, kinases, heatshock proteins and transcription regulators. Hiro often worked with collaborators to gain new understanding of these systems, including studies of dynamical structural changes using time-resolved techniques.

The symposium will be the full day of Thursday, February 9, beginning at 8:30 a.m. and concluding around 5:00 p.m. Light refreshments and lunch will be served. The symposium is open to all interested in attending; registration is required but there is no fee for attending.

Please join us in celebrating Hiro's international legacy in the growing area of bioSAXS science, for which he pursued new developments and science applications until the very end of his life in August of 2011.

5.   Awards: Prof. Harold Hwang Named American Physical Society Fellow

Harold Hwang, professor of Applied Physics and Photon Science at Stanford and SLAC, has been elected a fellow of the American Physical Society, a distinction conferred on just one-half of one percent of the Society’s membership. Read more in SLAC Today... 

6.   Announcements: Shipping, Survey, SSRL at the Exploratorium, NUFO

Shipping Changes. Users who ship items to and from SSRL should be aware that SLAC has a new approved customs broker and freight forwarder: Kamino International Transport, Inc. Learn more… Survey. is a resource for the global light source community. Supported by more than 20 synchrotrons and free electron lasers from around the world, it provides news, information, and educational materials about photon science facilities. We are currently reviewing the content of this website, with the aim of improving it for synchrotron users. As such, we invite you to take 10 minutes to complete this short survey on the kinds of information you would like to see on We would appreciate your response by Sunday, January 15.

SSRL at the Exploratorium. At 7:00 p.m. on Thursday, January 5, SSRL Staff Scientist Sam Webb will present a talk as part of the San Francisco Exploratorium's After Dark series. The talk, part of the "Rock, Paper, Scissors" event, will discuss a series of SSRL imaging experiments that seek to reveal pigments hidden within fossils. Learn more about the After Dark series on the Exploratorium website.

NUFO Seeks Participation in Working Groups. The National User Facility Organization (NUFO) is seeking participants in new working groups to assist in developing and implementing activities benefiting users. For more information about this project, and NUFO in general, visit their redesigned website. NUFO represents the interests of all users who conduct research at U.S. national scientific facilities and scientists from U.S. institutions who use facilities outside the United States. NUFO provides a unified voice to emphasize the critical role that user facilities like SSRL play in economic competitiveness and the education of the next generation of scientists.

7.   Profile: Postdoc Eric Verploegen Energized by Experiences, Mentoring

Eric Verploegen
If the excitement and enthusiasm of young scientists like Eric Verploegen could be pumped directly into the power grid, the world's energy problems could be solved tomorrow. It can't, though. So Verploegen has made it his goal to channel his energy into looking for solutions the old-fashioned way—hard work, and lots of it.

After three years studying organic photovoltaics as a postdoc with SSRL Material Sciences Division Leader Michael Toney and Stanford Chemistry Professor Zhenan Bao, Verploegen will now join Soane Energy, a small startup in Boston founded by ex-UC Berkeley faculty member David Soane, to develop methods to help clean up the processes used to extract oil from tar sands and natural gas from shale. Verploegen is not sure if there will be many synchrotrons in his future, but he deemed his time at SSRL invaluable. "My experience using synchrotrons has given me an intuition about self-assembly"—the manner in which polymers put themselves together.

Read the full profile of Eric Verploegen, written by Lori Ann White, in SLAC Today.

8. In the News — Metallurgy, Earth's Core, Nitrogenase

New Magnetic-Field-Sensitive Alloy Could Find Use in Novel Micromechanical Devices
A multi-institution team of researchers has combined modern materials research and an age-old metallurgy technique to produce an alloy that could be the basis for a new class of sensors and micromechanical devices controlled by magnetism. See full story in NIST Tech Beat...

Mineral Physicist to Use NSF Grant to Fuel Earthy Research, Educational Outreach
Wendy Li-Wen Mao, Stanford professor of Photon Science, SLAC and the Department of Geological & Environmental Sciences, will use a newly awarded NSF grant for mineral research and educational outreach. See full story in SLAC Today...

In an Enzyme Critical for Life, X-ray Emission Cracks Mystery Atom
An international team of scientists has used powerful synchrotron spectroscopy and computational modeling to reveal a mystery atom in the middle of a complex enzyme called nitrogenase, which had long hindered scientists' ability to study the enzyme fully. See full story in Space Daily...


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 structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH National Institute of General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL website.


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Last Updated: 16 DECEMBER 2011
Headlines Editor: Kelen Tuttle