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SSRL Headlines Vol. 4, No. 9  March, 2004


Contents of this Issue:

  1. Science Highlight — Chromate Contamination at DOE Hanford Site Partly Contained by Natural Reactions with Sediments
  2. First SPEAR3 Light Seen at BL9-3 and Progress on Other Beam Lines and Commissioning
  3. Instrument Development Workshop held on LCLS Biological Imaging Experiments
  4. Pre-registration Required for On-site Users
  5. Stanford-Berkeley Physical Sciences Summer School Postponed until 2005
  6. Convenient On-site Lodging and Local Shuttle Service
  7. Upcoming Public Lecture on Synchrotron Radiation: The Light Fantastic
  8. User Administration Update

1.  Science Highlight - Chromate Contamination at DOE Hanford Site Partly Contained by Natural Reactions with Sediments
      (contact: John Zachara,

Toxic and carcinogenic chromate (hexavalent chromium as CrO42-) has contaminated the groundwater in Hanford, Washington. At Hanford, hexavalent chromium was used in the industrial process to recover plutonium from irradiated nuclear fuels. The resulting high-level waste corroded its storage tanks and leaked into the desert subsoils. Plumes of contaminated groundwater reaching the Columbia River pose a risk to spawning salmon. Because of the depth and large volume (millions of gallons) of the contaminant plumes, existing abatement technologies are largely ineffective for mitigating the contaminated groundwater at this location. However, recent research indicates that the naturally occurring sediments at the Hanford site can immobilize chromate.

John Zachara (PNNL), Gordon Brown, Jeffrey Catalano (Stanford University) and their colleagues used x-ray absorption spectroscopy at SSRL to safely test contaminated (and highly radioactive) soil samples to determine the relative amounts and chemical forms of the chromate (carcinogenic hexavalent chromium or less toxic trivalent chromium). They found that about 42% of the chromate in the contaminant plumes had become an immobile solid of trivalent chromium due to reacting with ferrous iron-bearing sediments in the aquifer. Unfortunately, more than half of the chromium in the plumes remains as the dangerous hexavalent form (chromate), which moves readily through the subsurface sediments. However, the discovery by Zachara's research group (which is one of many ongoing studies at SSRL looking at contaminated sediments from Hanford) is an important step toward mitigating the problem. Developing technical solutions to such large-scale contaminant problems requires key insights into the form of the contaminant, which is intimately linked to its reactivity. This information allows engineers to assess the hazards posed by such extreme chemical and radioactive materials, as well as to design the most effective, long-term strategies to deal with them.

For more information on this work see: or

2.  First SPEAR3 Light Seen at BL9-3 and Progress on Other Beam Lines and Commissioning
       (contact: Tom Rabedeau,

Another major milestone for the SPEAR3 commissioning and resumption of SSRL user operations occurred when first light was brought into Beam Line 9-3 on March 8. The light observed on the monitor inside BL9-3's hutch showed banding which is consistent with the effect of the separated pole pairs in the wiggler viewed at the 5-mrad off-axis observation angle of BL9-3. This effect could not be seen with the old SPEAR2 ring as its source size was so big that the radiation from each pole pair could not be resolved, so the effect of the reduced source size on SPEAR3 was immediately seen. Light has subsequently been brought into BLs 9-1, 9-2, 6-2, 10-1, 10-2, and 5-4. Commissioning efforts on these beam lines are already showing the improved performance under SPEAR3:

  • The performance of the BL6-2 Pt-coated fused silica M0 mirror, although not upgraded for SPEAR3, reflects the much smaller source size of SPEAR3. The horizontal width measures 860 microns (FWHM), a much smaller value than the SPEAR2 value of 2.3 mm.

  • A standard myoglobin data set was taken March 16, on BL9-1. The resulting anomalous difference map produced a superb Fe peak of 17 sigma at 12 KeV. This compares to an iron anomalous peak of 13 sigma in similar myoglobin tests in previous years on BL9-1.

  • The focused beam size on BL9-2 is ~1/3 the area compared to the size of the beam operating under SPEAR2 and there is a commensurate increase of ~3X in intensity. Diffraction images of small 65 micron crystal of Mb only required a short 5 second exposure time and produced an anomalous Fe peak of 20 Sigma at 12 KeV.
Despite several orbit interlock faults and a fill schedule requiring top offs four times per day at 6 am, 12 pm, 6 pm and 12 am (to further increase lifetimes by continuously scrubbing the vacuum chamber), SPEAR3 delivered a highly respectable 92.3% of the beam time scheduled during March 15-21, the first week of user operations. A 10-minute average fill time with SPEAR3 compared to the 20-minute SPEAR2 fill contributed to this delivery rate.

The first SPEAR3 data set was measured on BL9-3 on March 15, for biological x-ray absorption spectroscopy, and throughout this first scheduled block of user beam time, a number of data sets at excellent quality were obtained.

Beam line operations will continue to resume in stages, paced by completion of electrical work, hutch upgrades, PPS checkouts and certification, shielding, Radiation Physics approval and commissioning. Special SPEAR operation conditions will be required when beam lines are opened over the next several weeks, mainly in the form of brief access periods to remove the locks from the injection stoppers and lower currents (25-50 mA) for the first few hours. PA system announcements will be made before these periods and before fills. Users may request a brief delay on the fill time to coordinate their scans and maximize their data taking. SPEAR status updates are available on the website:

SPEAR3 will operate at 100 mA for this first user run while beam line optical components are upgraded and radiation shielding is added for higher current operation. During this first run year, the accelerator physics and engineering groups will characterize and optimize ring lattice and beam parameters, develop the fast orbit feedback system and ascertain beam stability issues that could be encountered at the higher currents being planned for operation following the initial commissioning run.

Operating and beam time schedules are available on the web at:

3.  Instrument Development Workshop held on LCLS Biological Imaging Experiments
       (contacts: Henry Chapman,; Keith Hodgson,

Over 60 participants attended the "Instrument Development Workshop for LCLS Biological Imaging Experiments." held at SLAC on March 15-16, 2004. The workshop consisted of a day and a half of presentations and discussion to determine the research needs for single-particle diffraction imaging, and other atomic-resolution imaging methods, to be carried out on the LCLS. The meeting consisted of briefings on critical aspects of the source, detectors, x-ray optics, effects of rapid photoionization on image degradation, data processing (classification of diffraction patterns, registration, and image reconstruction), and sample handling, among many other issues. Breakout sessions were also held to develop a thorough understanding of project risks, mitigation strategies as well as milestones, deliverables and costs. The overwhelming feeling at the workshop was that while much challenging research needs to take place to develop the required techniques, the community will be able to field imaging experiments at the LCLS at the 2009 operations date.

For more details regarding this workshop and the LCLS project see:

4.  Pre-registration Required for On-site Users
       (contact: Cathy Knotts,

U.S. Government regulations related to facility access require that facilities collect biographical information from users in advance of their scheduled visit and before ID badges can be issued. For users who are not U.S. citizens but were born in, are citizens of, or represent organizations from certain foreign countries that the government has identified as either sensitive or state sponsors of terrorism (SST), additional information must be collected and forwarded to the DOE for approval of the visit. Spokespersons are required to provide contact information for all collaborators who plan to be on-site to work under their proposals, and those collaborators must pre-register by completing the SSRL User Information Form at least 1 month before their anticipated visit. We recognize the time and effort needed to comply with this new requirement, and appreciate your full cooperation with this effort.

5.  Stanford-Berkeley Physical Sciences Summer Postponed until 2005

The 2004 Summer School Program has been postponed until summer 2005. Additional information on the 2005 Summer School will be forthcoming at a later date.

6.  Convenient On-site Lodging and Local Shuttle Service
       (contact: Cathy Knotts,

The SLAC Guest House provides comfortable and convenient accommodations for SSRL users and visitors at unbeatable rates including standard rooms with full size bed ($50), larger rooms with queen size bed ($65), and shared rooms with bunk beds ($32.50); all rooms have a private bathroom. Be sure to mention that you are an SSRL user when booking a reservation.

The Stanford Marguerite provides free shuttle service to several locations in the Palo Alto area. The SLAC line operates Monday-Friday (except holidays) between SLAC, SU Science & Engineering Quad, West Campus Residences, and Hoover Tower every 40 minutes from 7:30 am-6:00 pm. A SLAC shuttle operates Monday-Friday (except holidays) between the Palo Alto train station and SLAC from 6:41 am-8:15 am and again from 3:20 pm-5:00 pm.

7.  Upcoming Public Lecture on Synchrotron Radiation: The Light Fantastic
       (contact: Uwe Bergmann,

SLAC if offering a series of public lectures geared towards the nonscientific community. The next in the series, a synchrotron-related lecture given by Herman Winick, will be held on April 27, 2004 from 7:30-8:30 pm at the SLAC Panofsky Auditorium. See the SLAC Public Lecture Series web site for more information:

8.  User Administration Update
       (contacts: Cathy Knotts,; Lisa Dunn,

New Macromolecular Crystallography (MC) proposals are due April 1, and MC beam time requests for the next scheduling period are due on April 17.

New X-Ray/VUV proposals are due May 1 or November 1. Proposals instructions and forms can be found on the web at:


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: 30 MAR 2004
Content Owner: L. Dunn
Page Editor: L. Dunn