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SSRL Headlines Vol. 9, No. 7  January, 2009


Contents of this Issue:

  1. Science Highlight — The Competition for Iron Impacts the Global Carbon Cycle
  2. Science Highlight — Ions in the Clutches of Carbon Nanotubes
  3. New Hours for Security Gates
  4. Safety Update
  5. Energy Secretary Looks to National Laboratories for the Future
  6. SSRL Users' Organization Needs Your Feedback
  7. Accelerating SSRL: Working toward Top Off and Higher Current
  8. Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology April 9-12, 2009
  9. User Research Administration Update

1.  Science Highlight — The Competition for Iron Impacts the Global Carbon Cycle
       (contacts: O.W. Duckworth,; J.R. Bargar,; G. Sposito,

highlight figure
Top: Iron is thought to limit phytoplankton in much of the world's oceans. Bottom: Structure of the iron-siderophore complex ferrioxamine B
Phytoplankton are microorganisms that live in the ocean surface waters and are important because they act as lungs for the planet, consuming carbon dioxide and producing oxygen. Phytoplankton account for an astounding 50% of the total biological uptake (or sequestration) of carbon dioxide annually. Understanding the factors that affect the growth of phytoplankton, is therefore of particular importance for this carbon sequestration, since the amount of released carbon dioxide continues to increase world-wide. Phytoplankton need iron as a key nutrient, and being able to accumulate a sufficient amount is a much greater challenge than previously believed, according to a recent study by a team of researchers working in part at SSRL Beam Lines 11-2 and 2-3. The findings revealed that siderophores—special chelating molecules released by marine microorganisms to convert and gather iron in seawater, thereby making it available for plankton to absorb—have a harder time keeping the iron bound than was previously assumed. The results were published in the July 15, 2008 edition of Geochimica et Cosmochimica Acta.

Iron is a crucial element for living organisms, playing an important role, for example, in oxygen transport and the formation of enzymes. But because it is so reactive with oxygen, despite its being plentiful in the environment, most iron is locked up in compounds. Living organisms, however, have developed strategies for stripping, or chelating, iron out of other compounds. Siderophores—the chelating compounds released by marine microorganisms—strip bound iron atoms and store them in a form that can be absorbed by plankton. Until now, scientists considered iron sequestered within siderophores to be highly stable and relatively safe from outside scavengers.

Using a technique called Extended X-ray Absorption Fine Structure (EXAFS), the team discovered that iron captured by siderophores is in fact susceptible to recapture by manganese (Mn) oxides, another plentiful component present as minerals in seawater. Although the specific role of Mn oxides in seawater remains unclear, it is now apparent that its presence could have a disruptive impact on the growth of plankton. A better understanding of the factors associated with plankton growth may one day lead to important environmental remediation strategies, including reducing atmospheric carbon dioxide.

To learn more about this research see the full scientific highlight at:

2.  Science Highlight — Ions in the Clutches of Carbon Nanotubes
       (contacts: A. Mehta,; J.K Holt,

highlight figure
Illustration of the structural model for Br coordination to graphene materials, derived from a model fit of the activated carbon EXAFS data.
Currently, more than 1/6th of the people in the world lack safe and clean water. Population shifts, global warming and many other global changes will make this shortage even more critical in the coming years. Solutions to this problem lie in the development of new, energy-efficient means of purifying water. One of the traditional purification technologies—called membrane-based reverse osmosis—is very energy intensive, and this is spurring a flurry of activities into creating new, energy-efficient materials. Among the most promising of these materials are carbon nanotubes. A related material, activated carbon-basically carbon treated at extreme temperatures to achieve a high degree of microporosity and functionality—has been used for a century or more to filter water, and soak up unwanted compounds. However, the precise arrangements of the atoms that give rise to these purifying properties have mostly remained a mystery.

The most detailed picture yet of how specially arranged carbon atoms interact with and adsorb ions has emerged from new research conducted in part at SSRL Beam Lines 10-2 and 7-3. Using Extended X-ray Absorption Fine Structure (EXAFS) researchers looked at the arrangement of bromine ions near the surfaces of carbon nanotubes and activated carbon. The results were published in the October 30, 2008 online edition of Advanced Materials.

Carbon nanotubes are created when extremely thin sheets of graphite are rolled into tubes with walls one atom thick, and a diameter as small as a nanometer. Although they do possess many subtle and important differences, nanotubes appear to share many of activated carbon's unique properties in the presence of ions. The recent study sheds light on what researchers term "zigzag" sites present on the nanotube's surface, made up of carbon atoms configured in such a way as to attract and hold on to ions. These results help researchers better understand the surface chemistry of carbon nanotubes and potentially tailor it for a range of applications, from electronics to environmental science.

To learn more about this research see the full scientific highlight at:

3.  New Hours for Security Gates

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Click on image for larger version
It's important for onsite users to be aware that as of January 5, the Sector 30 gate is the only gate that remains open 24/7. Gate 17 is now open Monday through Friday from 6 a.m.-10 p.m. Outside of these hours pedestrians can enter through the turnstiles located at Gate 17 and behind Building 137. Vehicles can enter through the Sector 30 Gate and follow the PEP Ring Road to reach SSRL.

The Alpine Gate, which had been closed to regular traffic since the beginning of the LCLS construction project in June 2006, is now open during weekday commute hours: 6-10 a.m. and 3-6 p.m. A current SLAC ID badge is required to enter this gate. Users, visitors and anyone else without a SLAC ID badge will still need to check in at the main gate on Sand Hill Road.

4.   Safety Update
       (contact: M. Padilla,

A series of safety questions has been incorporated into our proposal, beam time request and support request processes, eliminating the requirement for submitting a separate hazard form. However, if a specific experimental hazard is identified as part of these processes, a Safety Review Summary must be signed off on by the spokesperson before the start of beam time.

Effective February 2009, Radiation Worker Training (RWT) will be required to conduct any work/experiments involving radioactive materials, including handling activated beam lines or components. Shortly, SLAC will launch RWT and GERT training modules via the web; however, the practical portion of the RWT training must be completed in person. Please contact Matt Padilla ( if you have questions.

Other safety information and requirements should be reviewed well in advance of scheduled beam time —specifically new training requirements for handling Radioactive Materials, see the following links:

5.   Energy Secretary Looks to National Laboratories for the Future
       January 23, 2009 Fermilab Today Article by Rhianna Wisniewski

Steven Chu
The Department of Energy's new leader, Energy Secretary Steven Chu, quite literally wants the organization to help save the world.

"The DOE will have to be the go-to organization for what we face in this country," Chu said in a satellite broadcast Thursday. "This agency, in my mind, is the key agency for the future of the U.S."

Chu's address to the national laboratories came a day after he was confirmed as the new administration's energy secretary. In his remarks, Chu focused on the need for new solutions to the problems facing the U.S. and the world, namely the economic crisis, combating climate change and finding alternative energy sources. To do this, he said, the country will need to rely on the national laboratories to develop a sound energy policy and to invent and transform new science and technologies that can be brought to the marketplace. Read more at:

6.   SSRL Users' Organization Needs Your Feedback
       (contact: W.W. Lukens,, SSRL UOEC Chair)

Please take a few minutes to complete the 2009 SSRL user survey which is an important tool to help us continue to provide excellent service to the SSRL User Community. The information you provide here will be used to organize the next Users' Meeting (tentatively scheduled October 19-21, 2009) and to report on user interests/issues to SSRL management and scientific advisory committees.

As an added incentive to provide your input, a random drawing of survey participants will be held for several SSRL prizes including gift certificates for the Guest House, SSRL/LCLS shirts, coffee mugs and SSRL baseball caps. If you want to be part of the drawing for prizes, just enter your email address at the end of the survey.

7.   Accelerating SSRL: Working toward Top Off and Higher Current
       (excerpted from January 22, 2009 SLAC Today Article by Calla Cofield

Accel Group
from left: SSRL Technology Development group's Steve Gierman, John Schmerge and Jeff Corbett with Accelerator Physics team members Xiobiao Huang and James Safranek
Most SSRL users are focused on the facility's x-rays, which they use to illuminate samples ranging from fossils to proteins. But it is the SPEAR3 storage ring that accelerates electrons to produce those x-rays, and it is the SSRL Accelerator Systems Department, or ASD, that oversees the function and maintenance of the ring.

These days, the ASD is working toward a major upgrade to SPEAR3 known as "top-off" mode, which will step up the electron beam's current, proportional to the number of photons in the x-ray beam, from 100 to 500 milliamperes. The Accelerator Physics group, a subgroup of ASD led by James Safranek, is responsible for simulating how the beam will behave in top-off mode, in order to identify safety hazards before they arise.

As the SPEAR3 beam circulates, it loses electrons. In top-off mode, 500-milliampere beam will decay even faster. The SPEAR3 injector will "top off" the beam current every few minutes, refilling it with electrons. When top off begins, the shutters separating the electron beam from the user x-ray beam lines will remain open (during the current fill procedure, they close). That open pathway between the shielded electron beam and the open x-ray beam line means Safranek and his group must anticipate any means by which the beam could veer off track or shower radioactive particles down to the user beam lines. Based on the group's simulations, the ASD is installing interlocks that will shut off the electron beam automatically if it ever shows signs of getting out of line. Read more at:

8.   Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology April 9-12, 2009
       (contact: H. Tsuruta,

The SSRL Structural Molecular Biology Group will host a comprehensive workshop on the use of primarily non-crystalline small-angle x-ray diffraction techniques in structural biology research. The main focus of the workshop is solution x-ray scattering studies on biological macromolecules. The first half of the workshop will have lectures on theoretical and experimental aspects of solution scattering as well as recent applications in biology. Computational approaches to data interpretation and structural modeling will also be covered. The workshop will also include related topics such as lipid and fiber diffraction studies. The second half of the workshop is devoted to experimental tutorials on solution x-ray scattering at Beam Line 4-2 and software demonstration/tutorial sessions. Participants are encouraged to bring their own samples for the experimental tutorials. A website with additional program and registration information will be linked from SSRL's home page soon at:
see also:

9.   User Research Administration Update
       (contact: C. Knotts,

—X-ray/VUV February-May Schedule Posted
The SSRL X-ray/VUV schedule for the next scheduling period (February through May 24) has been posted to the web, see

Please refer to the SPEAR operating schedule for dates when we will be DOWN for Maintenance or Accelerator Physics so that you can plan your visits accordingly

—Macromolecular Crystallography Beam Time Requests due January 30
Please submit a request for March through May 2009 beam time by Friday, January 30, at: If you are interested in beam time on SSRL's macromolecular crystallography beam lines, but do not currently have an established proposal, please submit a Rapid Access Application at:

More information regarding beam line capabilities and remote access, etc., can be found at:

—X-ray/VUV Beam Time Requests due March 13
If you are interested in requesting beam time for the third scheduling period for the 2009 run (~mid May through August 10, 2009), please submit your request before March 13 by logging into the User Research Administration web interface at:

If you run into any problems with the new URA web interface, or if you have suggestions to improve this process, please let us know. We welcome your feedback, and we look forward to your next visit to SSRL.


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 JAN 2009
Content Owner: L. Dunn
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