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SSRL Headlines Vol. 6, No. 2  August, 2005


Contents of this Issue:

  1. Science Highlight — The Mighty Manganese Oxides
  2. Secretary of Energy Visits SLAC
  3. DOE BES Director of Materials Science Meets with SSRL and GLAM Scientists
  4. SSRL's Scientific Advisory Committee and Proposal Review Panel Convenes
  5. User Operations Update
  6. Update on SSRL Beam Lines and Techniques
  7. Nominations for SSRLUOEC and Registration for the Annual SSRL Users' Meeting & Workshops, October 15-19
  8. Students and Teachers Visit SLAC August 10
  9. 4th Stanford-Berkeley Summer School for Physical Science Held June 2005
  10. Got News?
  11. User Administration Update

1.  Science Highlight — The Mighty Manganese Oxides
      (contact: John Bargar,

Mn figure
Manganese oxides form in the oceanic water column as a result of the bacterially catalyzed oxidation of a relatively abundant form of dissolved manganese. As they settle through the water column, manganese oxides participate in myriad chemical reactions important to sea life and to maintaining the trace-metal composition of sea water. These reactions profoundly impact the geochemical cycling of carbon, nitrogen, sulfur, nutrients and containments.

Before, scientists did not know the identities of the bacteria-derived manganese oxides. A collaborative group of scientists from SSRL and the Oregon Health and Science University have used two synchrotron-based techniques to determine the identities of manganese oxides formed in sea water by a marine bacterium. The conclusion from both sets of measurements is that the manganese oxide produced in sea water is a poorly crystalline layered manganese oxide called birnessite. Identifying marine manganese oxides will substantially enhance scientists' ability to model and understand their roles in maintaining the chemistry of the oceans. This information will also directly contribute to a greater understanding of the properties of bacteriogenic manganese oxides, which are of great interest for their potential technological applications.

To learn more about this research see:

2.   Secretary of Energy Visits SLAC

Secretary Bodman and SLAC Director
SLAC was very honored to host a visit by Secretary of Energy Samuel Bodman on Thursday, August 4. Secretary Bodman spoke to an audience of ~1,000 SLAC staff and visitors gathered on the SLAC green about the important role of the Department of Energy and its facilities in our Nation's scientific research. He noted that "The Department's research facilities have special meaning for me. It is important in my view that if our economy is to be as productive and effective in the future as it is today - and as it has been for the last five decades - that we will have to maintain our leadership in science." During his tour, Secretary Bodman had an opportunity to visit SSRL and see examples of the beam lines and science being done with SPEAR3. More on Secretary Bodman's visit can be found at:

3.   DOE BES Director of Materials Science Meets with SSRL and GLAM Scientists

SSRL was also fortunate to be able to host a visit on Thursday, August 18 by Dr. Harriet Kung, Director of Materials Science at the DOE Office of Basic Energy Sciences. Dr. Kung gave a well-received presentation titled "BES/DMS&E Program Overview and Future Outlook". Students, staff scientists and faculty alike were impressed with the time she took to outline the present programs and future directions of the DOE-BES Division that she heads, which has a budget of $271M. Dr. Kung described how the Office of Basic Energy Sciences plans to insure SLAC's stability and longevity as it assumes an increased stewardship role for SLAC as the Photon Science program, anchored by SPEAR3 and LCLS, grows significantly in future years. For example, BES plans to strengthen research done by laboratory scientists who can take advantage of the unique capabilities offered by the light sources and instruments associated with them. Among the areas that will receive particular attention are ultrafast science and research related to the nation's energy supply. In the question period after her talk there was some lively discussion about the best way to improve the nation's energy supply.

Dr. Kung's talk was followed meetings with several staff scientists and a tour of SSRL's experimental floor where she was shown the area (currently under construction) in Bldg. 130 which will house the laboratory space for XLAM and for the Ultrafast Center (until the LCLS central laboratory office building is completed). The next stop was at BL11-2 where the actinide and environmental science is done, then on to BL5 to look at the surface research chamber, the speckle chamber and the high Tc chamber, and finally to BL6 to look at the microprobe and discuss where the new x-ray microscope will go. Dr. Kung met with students from the Stöhr, Nilsson and Pianetta research groups over lunch before meeting with several more members of the scientific staff and SLAC Director, Jonathan Dorfan. Dr. Kung spent the latter part of the day on the Stanford main campus visiting with a number of faculty at the Geballe Laboratory for Advanced Materials (GLAM). These meetings resumed the following day. The visit ended with late afternoon meetings with Dr. Arthur Bienenstock (Stanford Vice-Provost, Research) and Dr. Franklin Orr at GCEP.

4.   SSRL's Scientific Advisory Committee and Proposal Review Panel Convenes
      (contact: Keith Hodsgon,

Members of the SSRL Scientific Advisory and Proposal Review Panel (SAPRP) met at SLAC on August 11-12, to discuss a wide array of issues concerning SSRL. The committee provides strategic advice on a wide range of critical issues, including new program initiatives and management as well as detailed peer review of proposals. SLAC Director Jonathan Dorfan and SLAC Deputy Director/Photon Sciences Directorate Keith Hodgson were on hand to welcome the attendees. Keith brought the committee up to date on recent developments including the SLAC reorganization and the BES review that took place in February. James Safranek updated the panel on SPEAR3 and the progress being made toward the transition to top-off operation. Jo Stöhr discussed a vision for the future of SPEAR3 including several new initiatives. John Arthur gave a presentation on recent SPPS experiments and the plans for instrument development for the LCLS. Richard Lee (LLNL) gave a presentation on one of the scientific areas to be studied using the LCLS, plasma high energy density science, and John Galayda gave an update on the LCLS construction project. SSRLUOEC Vice Chair Joy Andrews (CSUEB) discussed recent activities by the SSRL Users' Organization Executive Committee. Cathy Knotts wrapped up the open-session agenda with an update on user research administration. In executive session, the panel also provided strategic advice to the SSRL directorate and determined ratings based on the peer reviews received for the 45 new proposals submitted during this last call for proposals. Members of this advisory panel are listed online at:

5.   User Operations Update

The 2005 user experimental run ended on August 1. In spite of the 4-day power outage in May (caused by a downed tree several miles away from SLAC), the average uptime for users was 95%. Additionally, our preliminary analysis indicates that over 900 users were on-site to participate in more than 750 experiments on 19 beam lines during this 6-month run (shortened due to electrical accident last October). During the current shutdown, a significant amount of beam line upgrades and construction activities are underway, including construction for the new BL12 alcove and associated chicane lattice installation, upgrades to BL10, BL9 and BL7. Everyone is reminded to exercise caution around these work zones and observe all posted safety precautions. A preliminary copy of 2006 user operations schedule, expected to resume on November 28, can be found at: preliminary.pdf

(See User Administration Update below (Item #11) for information on Beam Time Requests and TIP article at: for more information on beam line upgrades.))

6.   Update on SSRL Beam Lines and Techniques

BL11-3 - Materials Science Scattering, Reflectivity and Single Crystal Diffraction Experiments: This new beam line, utilizing a milli-radian of fan on the BL11 26-pole, 2.0-T wiggler insertion device, is a fixed energy beam line designed for shared use by the macromolecular crystallography and materials scattering communities. The beam line employs an off-cut, side scattering, focusing Si(311) crystal monochromator optimized at approximately 12,700 eV. Vertical focusing is provided by a 1 m long Rh-coated Si mirror located downstream of the monochromator. The vertical focused beam size at the sample position is less than 0.1 mm, while the horizontal focused beam size is 2.5 mm due to the effective source size. The flux in this spot (full beam) is approximately 2x1011 photons/sec at 100 mA. Both horizontal and vertical beam sizes can be set with slits. The beam line has a kappa diffractometer, and can have either a point detector or an area detector (but NOT simultaneously). Based on the detector, the beam line works in two modes.

In the point detector mode the beam line is controlled with SUPER, and the diffracted beam is analyzed with either Soller slits or two adjustable Huber slits. We are presently using a Bicron detector, but plan to implement a fast Rontec Si-drift detector, which provides approximately 200 eV energy resolution. The beam line is optimized for thin film scattering, specular and off-specular reflectivity, and other general single crystal diffraction. A vacuum chuck and He environment are available for samples, but at present only room-temperature experiments are possible. To date, this has been used to study structure in organic, metal, and semiconductor thin films and multilayers and charge-density waves in rare earth tri-tellurides.

In the area detector mode the beam line is controlled with Blu-Ice. We have two types of area detectors available; 2k x 2k ADSC Quantum4 CCD or an auto-readout MAR345 image plate system. The image plate has larger area and larger dynamic range, but it reads out more slowly and creates an artificial spot in the center of the plate. The image plate is, therefore, ideal for transmission measurements, either in a capillary or custom transmission cell. The area detector setup sacrifices Q space resolution, but collects a diffraction pattern from Q of 0.15 to 6 (1/A) in a few seconds. (We were able to collect a high quality diffraction pattern from water in less than a minute.) This configuration has been used for a wide range of experiments from a study of in-situ growth of biogenic minerals, to partial determination of texture in recrystallized pumice, to quick determination of single crystal orientation. (Contact Mike Toney, or Apurva Mehta, for more information on materials scattering capabilities and Mike Soltis, for macromolecular crystallography.)

BL5-1/2 - Commissioning SSRL's Newest Beam Line for Spectroscopy and Speckle: Commissioning of BL5-1/2 approached its final phase in July. Remarkable progress has been made in the 2005 run. Very bright monochromatic beam has been brought to both experimental end stations (BL5-1 and BL5-2), and the beam line optics, including the M0, monochromator, and refocusing mirrors, have been well aligned. All three gratings have been carefully optimized and characterized. Gas cell tests demonstrated that the monochromator achieves the expected theoretical resolution. For example, a resolving power close to 9000 has been obtained at the N2 K-edge for the 600 l/mm grating. In addition, very narrow beam with FWHM of 10 micron or less has been routinely obtained at the entrance slit, indicating excellent performance of the M0 mirror. Detailed focus tests at BL5-2 also achieved decent beam size that is close to theoretical value, at the experimental end station. Commissioning for these new end stations will continue when the SSRL run resumes operations in November, and results from these early commissioning experiments will be shared when they become available in 2006. (Contact Donghui Lu,, for more information)

Figure 1: The flux after refocusing mirror of beamline 5-1 as a function of energy resolution (exit slit). The inset shows a sample gas cell spectrum at N2 K-edge. Figure 2: A sample M0PITCH scan showing very narrow vertical beam profile at entrance slit, with a FWHM of ~9.2 micron.

BL1-4 SAXS Upgrade at SSRL: The materials science small angle x-ray scattering beam line at SSRL has been comprehensively rebuilt. The new maximum sample-to-detector distance of 2.5 m (from a previous maximum of 1.1 m), when coupled with the smaller divergence of the SPEAR3 beam (18 nm rad-1 from 130 nm rad-1) allows significantly larger correlation lengths to be probed: to a maximum ~400 nm, compared to a previous maximum ~90 nm. This new capacity has already enabled new scientific studies, including the characterization of pore sizes and distributions within nanoporous dealloyed metal films. The new experimental hutch also has sufficient space to install SAXS and WAXS detectors for simultaneous SAXS/WAXS experiments. (For more information, contact John Pople,


7.   Nominations for SSRLUOEC and Registration for the Annual SSRL Users' Meeting & Workshops, October 15-19
      (contact: Cathy Knotts,

Users Mtg Announcement
Call for SSRLUOEC Nominations: Users are encouraged to nominate colleagues interested in serving on the SSRLUOEC by the September 30 deadline. Ballots to be issued ~October 3, then ballots need to be returned by October 17 when the votes will be tallied and the new SSRLUOEC representatives will be announced. Users are also encouraged to attend the next meeting of the newly elected SSRLUOEC when they meet immediately following the annual conference - October 17 at ~3:30 pm. Minutes of SSRLUOEC meetings are posted on the Users Organization website:

Register to Participate: The 32nd Annual SSRL Users' Meeting & Workshops will be held at SLAC on October 15-19, 2005. The meeting will feature sessions on x-ray absorption spectroscopy, structural genomics, ultrafast science and a sampling of materials research from other DOE labs. There will also be a young investigators session and a poster session, with awards for outstanding graduate student posters (the cost of the awards dinner will be waived for graduate students participating in the poster competition). Several workshops will be offered before and after the Users' Meeting, including biological and materials small angle x-ray scattering, and soft x-ray science at LCLS.

8.   Students and Teachers Visit SLAC August 10

Kids@SLAC Day held Wednesday, August 10, attracted 222 children aged 9-16 years old. This fun and informative event provided an opportunity for kids to learn about what we do here at SSRL and SLAC, and to spark interest for potential science-related careers. The event kicked off with a talk by Juana Rudati, a scientist working on the SPPS experiment. Kids then had the option of choosing several workshops to attend including Optics, Mechanics, Astrophysics, Waves, Electronics, Catapults, Monster Muscles, Paleontology, GLAST, Radiation, Magnetics, Biology, Electric Motors, and Welding. The event included a BBQ lunch and an ice cream social with a Nitrogen ice cream demonstration. Activities concluded with a chance to 'Talk Science' with Graham George, former SSRL scientist and now at the University of Saskatchewan in Canada. Kids Day participants received a commemorative shirt which was designed by Jenine Fernandez, a 14-year old participant at the 2004 Kids Day at SLAC.

Also on August 10, a group of 16 high school science teachers from the Bay area were given a tour of SSRL. The tour, coordinated by SSRL Faculty Chair Gordon Brown, was held in conjunction with the Stanford EMSI Science Teachers' Workshop and included numerous stops at various SSRL experimental end stations to explain the type of experiments that can be done and to help provide a framework for the teachers to convey the breadth of user science to their students.

9.   4th Stanford-Berkeley Summer School for Physical Science Held June 2005
       (contact: Anders Nilsson,

The 4th joint Stanford-Berkeley summer school on synchrotron radiation and its applications in physical science was held June 12-17 at SLAC. The Stanford-Berkeley summer school, which attracted 47 students from various parts of the world, was jointly organized by Stanford University, UC Berkeley, LBNL, and the SSRL. The students came from diverse fields representing the full community of synchrotron radiation users including atomic and molecular physics, condensed matter physics, surface science, chemistry, material science, environmental science and biophysics. Altogether, there were seven countries represented by the participants with most of them enrolled for graduate studies in US. The program was designed to introduce students and postdocs to the fundamental properties of synchrotron radiation and how to understand and use spectroscopic, scattering and microscopy techniques in various scientific applications, with particular emphasis given to examples from physics, chemistry, and material science. Each student was also asked to give a presentation of their interest in synchrotron radiation and their present research project. Funding for the 2005 Stanford-Berkeley Summer School was provided by the student registration fees, with additional funding from SSRL, LBNL, and NSF. This summer school was part of the outreach activities within the NSF funded Stanford Environmental Science Institute and the ERC for EUV Science and Technology.
lightsources logo

10.   Got News?
      (contact: Cathy Knotts,

SSRL relies on you to inform us whenever you have exciting news and research results about to be published. Please take a few minutes to review our publication list to ensure that we have included any publications which resulted from use of the SSRL facilities in recent years ( And, whenever you are about to publish a new scientific paper or issue a press release, please contact Cathy Knotts (, 650-926-3191). We look forward to working with users and their home institutions to promote user research to a broader audience. Thank you.

Keep up to date with news from the world's light-source community by signing up for News Flash at, the Web site about and for the international light-source community. News Flash subscribers receive the latest light-source related news as soon as it is released. Subscribing is as easy as filling in a few fields at

11.   User Administration Update
        (contact: Cathy Knotts,

For this next 8-month 2006 user run, well over 1,000 users are expected on-site to conduct experiments. Information on becoming an SSRL user, submitting a proposal, or requesting beam time can be found at:

Spokespersons with active X-ray/VUV proposals who are interested in requesting beam time for the next scheduling period are reminded to submit beam time request by the September 19 deadline.

A message will be sent out to Macromolecular crystallography spokespersons in September regarding Beam Time Requests for the first scheduling period in the FY06 experimental run.

As spokespersons submit their requests, please note the following availability estimates for beam lines currently undergoing upgrades: BL10-1, BL10-2 and BL9-3 are expected to be ready for users by mid December 2005; BL9-1 and BL9-2 by January 2006. BL7-3 is expected to be available for users by February 2006, with BL7-1 and 7-2 a bit later in early 2006.

(See TIP article at: for more information on beam line upgrades.)


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 by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. 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 Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 31 JUL 2005
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