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SSRL Headlines Vol. 2, No. 5  November, 2001


Contents of This Issue:

  1.   Science Highlight - Complex Environmental Systems: Heavy Metals,    Mineral Surfaces, and Biofilms
  2.   DOE Under Secretary Visits SLAC
  3.   High Magnetic Field Facility Now Fully Functional
  4.   FY2002 Experimental Run Off to a Good Start
  5.   Crystallography Beam Lines Up and Running with New Developments
  6.   Janos Hajdu Discusses Interest in FEL Project at SLAC
  7.   User Research Administration Announcements
  8.   Job Opportunities at SSRL

1. Science Highlight - Complex Environmental Systems: Heavy Metals, Mineral Surfaces, and Biofilms
     (contact: Alexis Templeton, alexis@pangea.stanford.edu)

Microbial biofilms are widespread in soils and form microenvironments in which aqueous chemical conditions differ from that of the host ground water. Reactive functional groups on bacterial surfaces and in extracellular ligands provide a large array of binding sites for metals, posing the question of whether or not bacterial biomass plays a dominant role in controlling metal ion migration in soils and aquifers. Such processes could have major implications for ground water quality, as the migration and toxicity of heavy metal contaminants in the environment are controlled by interactions between the metal solutes, aqueous solutions, and soil materials. Recently, Templeton et al. (PNAS 98, 11897 (2001)) have used SSRL-based x-ray standing wave measurements coupled with XAS to probe the distributions of Pb(II), a common toxic soil contaminant, within mineral-biofilm-water systems. In-situ measurements were performed on biofilms grown on single-crystal a-Al2O3 surfaces, subsequently reacted with dilute Pb(II) solutions. Long-period x-ray standing wave results show that the biofilms do not passivate the underlying oxide surface and that the same high-energy sites which uptake Pb(II) on the biofilm-free oxide surface also play the dominant role in the mixed biofilm-mineral system. These results emphasize the importance of mineral surfaces as sinks for heavy metals in natural environments and raise questions about conventional assumptions that biofilm and organic coatings on mineral surfaces can change the way in which aqueous heavy metals interact with these surfaces.

More information regarding this research, including the reference to the recent publication in Science, can be found at:

2.  DOE Under Secretary Visits SLAC
     (contact: Jo Stöhr, stohr@ssrl.slac.stanford.edu)

As one stop on a tour of DOE laboratories in the Bay Area, Robert Card, DOE Under Secretary for Energy, Science and Environment, visited SLAC on October 30. This was his first visit to the various DOE laboratories since taking office and his intent was to gain a firsthand insight into the research conducted at these facilities. At SLAC, after being given an overview by Director Jonathan Dorfan, he was given a tour of the High Energy Physics facilities and SSRL. The SSRL tour was led by Gordon Brown, Keith Hodgson and Jo Stöhr and included three stops after a brief general overview of SSRL's facilities and operation. His first stop was at the Total Reflection X-Ray Fluorescence (TXRF) facility on Beam Line 6-2 where Katharina Baur, Sean Brennan and Piero Pianetta discussed the research program that is conducted in close collaboration with a number of industrial companies. Mr. Card then visited Beam Line 11-2, where he spent time with John Bargar and Gordon Brown discussing current molecular environmental science research. The emphasis was on the national importance of the work, in particular the work that is done at SSRL in collaboration with Los Alamos on environmental clean-up. The last stop was Beam Line 11-1 where Ana Gonzalez, Michael Soltis and Ashley Deacon explained the structural molecular biology program on BL11-1 and gave a demonstration of the sample transfer robot.

3.  High Magnetic Field Facility Now Fully Functional
     (contacts: John Arthur, arthur@ssrl.slac.stanford.edu, Lei Zhou, b_lzhou@slac.stanford.edu, Martin Greven, greven@loki.stanford.edu)

With the completion of its custom x-ray diffractometer, the High Magnetic Field facility at Beam Line 7-2 is now fully functional. This facility allows experiments to be carried out on samples subjected to steady-state magnetic fields of up to 12.85 T, at temperatures between 1.5 K and 400 K. Though optimized for x-ray scattering experiments, the facility at BL7-2 also has a limited ability to carry out x-ray absorption studies.

So far, four experiments have made use of the high-field facility. These experiments have studied phase transitions in magnets and other systems with strong electron correlations, using XAS, powder diffraction, and single crystal x-ray diffraction. Dr. Lei Zhou manages the facility.

4. FY2002 Experimental Run Off to a Good Start
    (contact: Piero Pianetta, pianetta@ssrl.slac.stanford.edu)

The shutdown activities, which included a significant amount of shielding work for SPEAR3 and the reinstallation of the repaired BL10 wiggler, came to a successful end in October. This was followed by a smooth start up of SPEAR in which the Beam Line 10 wiggler came back on-line without any problems. In addition, the lifetimes improved very quickly to the point where we could go to one injection per day only after three weeks of running and achieve an up time in these first few weeks of the run greater than 98%. During the course of the upcoming run, several liquid nitrogen cooled monochromators will be installed as will Beam Line 11-3, which will be used for materials diffraction and macromolecular crystallography.

5.  Crystallography Beam Lines Up and Running with New Developments
     (contacts: Peter Kuhn, pkuhn@slac.stanford.edu, Mike Soltis, soltis@ssrl.slac.stanford.edu)

The SSRL structural biology staff has been working extremely hard over the past many weeks to reassemble and troubleshoot a vast array of beam line hardware, electronics, computer systems and software for the start of the FY2002 experimental user run. The complex task of making all subsystems work in sync and bring the synchrotron beam through the optical elements onto the sample position is always a challenge, but was again completed successfully and on time for the wiggler crystallography beam lines. The SMB staff of engineers, scientists, technicians, software and systems developers, and others are looking forward to working with the users over the next eight months. In particular, during this startup phase the standardization and development strategy of 'plug and play' detector implementation proved to be critical. The advantage gained by having on-site replacement detectors and standard interfaces for different detectors across all beam lines was apparent when a CCD detector recently failed at the end of one user group's set of shifts. It was swapped for a replacement detector, and the station made operational, with the next user group losing only 3 hours of experimental beam time.

A significant number of advanced developments came on-line including live video feeds of the crystal position allowing a click-to-center routine via Blu-Ice, live video feeds of the experimental instrumentation, a remote controlled and beam sensing beamstop, fully automated and self-optimizing XAS scan for MAD data collection on BL9-2, and user controllable change of wavelengths on BLs 11-1 and 9-1. An improved web-site was also launched at http://smb.slac.stanford.edu providing contact information, operational details, and documentation about secure access to the beam lines for data analysis and backup.

6.  Janos Hajdu Discusses Interest in FEL Project at SLAC
     (contact: Ingolf Lindau, lindau@ssrl.slac.stanford.edu)

Professor Janos Hajdu from the Department of Biochemistry, Uppsala University, visited Stanford October 8 to November 4, 2001. Prof. Hajdu has an interest in using the proposed x-ray free-electron laser at Stanford for structural studies and imaging of biomolecules. Prof. Hajdu cites his interest in the following way:

"Today a detailed structural analysis is limited to macromolecules and macromolecular assemblies which can be crystallised. Many biologically important target complexes are difficult or impossible to crystallise. As a consequence, there are large, and systematically blank areas in structural biology today. Only a handful of membrane protein structures are known, structural studies on large assemblies are problematic, and there is no hope of reaching high resolution with currently available methods on non-repetitive and non-reproducible structures (e.g. cells). X-ray free-electron lasers have the potential of changing this picture. My group has done calculations, which explore the parameter space within which biomolecular imaging may be possible with an X-ray laser, like LCLS at Stanford, before damage-induced movements destroy the sample. The results show a substantially extended limit in radiation tolerance with intense x-ray pulses in the femtosecond time domain. The predicted radiation tolerance to hard x-rays in this regime is several orders of magnitude higher than theoretical limits in conventional x-ray experiments. At the outer extremes of these limits, scattering to high resolution may be recorded from large single macromolecules, viruses, nanocrystals and nanoclusters of proteins without the need to amplify scattered radiation through Bragg reflections. Averaging procedures can be applied to extend resolution when a reproducible sample scatters a sufficiently large number of photons for its orientation to be determined. Holographic imaging, the utilization of increased radiation tolerance, numerical alignment and averaging of many images, and the ease with which the phase problem can be solved from continuous diffraction images through over-sampling offers access to a whole new range of experiments in structural biology. Work on the development of an integrated experimental approach also includes studies on novel container-free sample handling methods to select and rapidly inject single hydrated molecules, nanoclusters of molecules and larger particles (e.g. viruses, ribosomes, and small living cells) into an intense x-ray beam, like the LCLS".

7.  User Research Administration Announcements
     (contacts: Cathy Knotts, knotts@ssrl.slac.stanford.edu, Lisa Dunn, lisa@ssrl.slac.stanford.edu)

  • Macromolecular Crystallography Proposals are Due December 1, 2001:
    Proposals submitted for this deadline will be rated in February and eligible for beam time starting in March 2002.

    More information regarding proposal submittal can be found at:

  • Rapid Access to Macromolecular Crystallography Beam Lines:
    A program to get a limited amount of Macromolecular Crystallography experiments on-line within a month of proposal submission has been put in place. As mentioned in the September Headlines, this program is not intended to replace SSRL's regular proposal review process for Macromolecular Crystallography research, but rather to provide a mechanism for rapid turnaround of new projects on a first-come, first-served basis. The proposals will be reviewed for scientific merit and feasibility.

    Five shifts have been set aside on Beam Line 9-1 from Jan. 28-30 for a tunable or fixed, single wavelength Rapid Access experiment. Applications for this beam time in January will be accepted between Dec. 1, 2001 and Jan. 2, 2002. The Rapid Access Application Form and more information on the process and the schedule for the remainder of the FY2002 experimental run is available at:

  • Scheduled Down Times:
    Please note the following beam line down times that have been scheduled for equipment installation and commissioning:

    • BL9-3 will be down from November 1 through January 24.

    • BL10-2 and BL10-1 will be down from January 22-February 7.

    • BL6-2 will be down from April 29-May 14.

  • New Beam Lines:
    As mentioned above, Beam Line 11-3 is being added at SSRL to better serve the materials diffraction and macromolecular crystallography communities. After commissioning this coming spring, the beam line is projected to be available for general user scheduling in the next run (starting Nov. 2002).

  • End-of-Run Surveys:
    A representative from each user group must complete an End-of-Run Summary after each beam time assignment. User feedback following beam time is extremely important to us. Your comments alert us to potential problems; provide valuable suggestions to better serve you; and give us information that we need to respond to various DOE reports throughout the year. Results of these surveys and user comments are shared with the SSRL Users' Organization, through the SSRLUO-EC Chair, as well as SSRL management. Forms are available at several locations throughout SSRL and via our website at:
    http://www-ssrl.slac.stanford.edu/users/ user_admin/form_ers.html

  • New Photo ID Requirements:
    A reminder that everyone must be prepared to present some form of photo identification to gain access to SLAC. Please have your ID out as you approach the main gate to facilitate more rapid entry for yourself and those behind you. As part of the check-in process at User Research Administration, SSRL is now issuing new user photo ID badges to expedite access to SLAC and SSRL facilities. These photo ID badges will be valid through the remainder of the FY2002 experimental run and should be kept for subsequent visits to SSRL during the year.

    New users are reminded to arrive between 8:00 a.m. and 2:00 p.m. to complete the new user documentation and safety orientation training required to issue an ID badge. For more information, contact Daphne Mitchell at 650-926-2079 (dmitchell@slac.stanford.edu)

8.  SSRL Job Opportunities
     (contact: Rochelle Roberts, rroberts@slac.stanford.edu)

SSRL currently has positions available for mechanical, electronic and beam line engineers and technicians. More information is available at the following web site: http://www-ssrl.slac.stanford.edu/jobs.html

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: http://www-ssrl.slac.stanford.edu/

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Last Updated: 19 DEC 2001
Content Owner: L. Dunn
Page Editor: L. Dunn