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SSRL Headlines Vol. 9, No. 12  June, 2009


Contents of this Issue:

  1. SSRL Achieves Major Top-off Injection Milestone
  2. Science Highlight — The Source of Airborne Lead: Recycling Pb-Contaminated Soils
  3. Science Highlight — Importance of Iron Speciation to Aerosol Solubility: Potential Effects of Aerosol Source on Ocean Photosynthesis
  4. Science Highlight — Marine Diatoms Survive Iron Droughts in the Ocean by Storing Iron in Ferritin
  5. Exotic Material Could Revolutionize Electronics
  6. Researchers Reveal Structure of Key Genetic Proofreading Protein
  7. Secretary of Energy Visits SLAC
  8. From the Director of SSRL: A Glimpse of SSRL's Future
  9. SSRL to Aid New Energy-Research Center
  10. July 29-31 LCLS Workshop: Science Drivers for Hard X-ray Upgrades
  11. SSRL Structural Molecular Biology Summer School - Sep 8-11, 2009
  12. Save the Date for the Annual SSRL/LCLS Users' Conference - Oct 18-21, 2009
  13. Call for Nominations for Spicer, Klein and Lytle Awards

1.   SSRL Achieves Major Top-off Injection Milestone
       (contact: J. Schmerge,

On June 25, after having received the required approvals, SSRL for the first time performed top-off injection of the SPEAR3 storage ring (that is injection with the beam line injection stoppers open). This represented a major milestone and came as a result of an approximately three-year effort led by the SSRL Accelerator Systems Division. Top-off injection approval required an extensive SPEAR3 Accelerator Physics study and injector optimization in collaboration with the SLAC Radiation Protection Department to prove that no injected electrons could escape the SPEAR3 accelerator and travel down beam lines into an x-ray hutch. A new electron beam containment system was designed based on the study results and was recently installed and commissioned.

Initially BLs 4, 5, 10 and 11 will remain open during injection and all other BLs will close. It is expected that BLs 6, 7 and 9 will be approved for top-off injection soon. BLs 12 and 13 may be approved for top-off before the end of the current run cycle, while bending magnet BLs 1, 2, 8 and 14 will not be approved until after the 2009 summer shutdown since they require new equipment installation. Thus it is anticipated that all BLs will be approved for top-off injection during the FY2010 run.

Implementing top-off injection is a significant milestone and an important step towards operations at higher current. SSRL is working to obtain approval to increase the stored current in SPEAR3 up to 200 mA this run, which ends August 10.

See also June 25, 2009 SLAC Today Article by Brad Plummer

2.  Science Highlight — The Source of Airborne Lead: Recycling Pb-Contaminated Soils
       (contact: N. Pingitore,

highlight figure
The amount of lead particulates in air has decreased significantly as the U.S. began adopting the use of unleaded gasoline and lead limits in the 1970s. Yet, because of the serious health hazards even very small amounts of lead pose to children, some experts believe no amount of lead in our environment is safe. Last year the EPA lowered the allowable lead level in the air by a factor of ten and some have called for an even lower limit. A recent study suggests that to do this one must not overlook the source of lead contamination beneath our feet. The soil serves as a reservoir for lead from the days of leaded gasoline and unregulated manufacturing and may determine a lower limit on the amount of airborne lead.

A research group led by Nicholas E. Pingitore Jr. of the University of Texas at El Paso analyzed soil and air samples from El Paso using SSRL Beam Lines 7-3 and 11-2. To identify the major chemical forms of lead in the air, they subjected 20 samples collected at three sites in 1999 and 2005 to x-ray absorption fine structure experiments. The advantage of using XAFS rather than other techniques is its sensitivity to very small amounts of an element and its ability to identify or characterize different forms or compounds of an element, in this case, lead. They found that the major component of lead in air was in the form of lead humate. Since lead humate forms exclusively in soil, the researchers conclude that the most of the lead in air came from the soil.

The U.S. has seen great reductions in lead contamination - both in the environment and its people's bodies - since it began efforts to reduce lead, but further lowering the levels of lead may be difficult. Greater reduction of the amount of lead in the air cannot be accomplished by solely reducing the current release of lead into the environment by industrial activities, since so much lead already exists in soil and is leaking into the air. But soil remediation is difficult and costly. The researchers suggest that investigation of the bioavailability lead humate, which relates to its health risk potential, will help inform public policy decisions. This work was published by the Public Library of Science ONE.

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

3.  Science Highlight — Importance of Iron Speciation to Aerosol Solubility: Potential Effects of Aerosol Source on Ocean Photosynthesis
       (contact: B.

highlight figure
The world's animals depend on plants, plants depend on photosynthesis, and photosynthesis depends on iron. Despite a relative abundance of this element, iron in a form useable by plants can be rare. Living organisms require soluble iron, which generally comes from environments in flux since iron settles into stable minerals unavailable to life. Since around 30-40% of oceans are iron-limited, understanding the sources of soluble iron is critical to understanding oceanic ecosystems, which are responsible for taking significant amounts of carbon out of the air.

Soluble iron can reach oceans by water currents carrying dusts or by air currents carrying aerosols. For example, glaciers in Alaska can produce iron-rich dust and aerosols as they grind rocks. Carried by air and water, the nutrients find their way to the North Pacific Ocean, supporting its ecosystems. Iron-rich aerosols do not only come from natural sources but are also made by burning fossil fuels. Not all aerosols are created equally; some contain iron that is thousands of times more soluble, and thus more life-supporting, than others. The solubility depends on the chemical form of the iron they carry.

A research team led by Benjamin C. Bostick from Dartmouth College and Andrew Schroth of the United States Geological Survey used SSRL Beam Lines 2-3 and 11-2 to measure the solubility of iron from various aerosol sources, both natural and man-made. Through x-ray absorption spectroscopy, they determined the iron's chemical forms in the samples. The sample with the highest iron solubility came from fossil fuel combustion, and that with the lowest iron solubility came from aerosols originating in the Saharan desert. The aerosols created when glaciers grind rocks beneath them had intermediate solubility.

This research suggests a complex relationship between iron cycles and climate change. While the burning of fossil fuels adds to carbon in the atmosphere, it also adds iron to the oceans that, through aquatic organisms, takes carbon out of the atmosphere. Additionally, receding glaciers caused by climate change will increase the amount and type of rock dust making its way to the oceans, which can also increase biological activity and carbon capture. This work was published in the April 26 issue of the journal Nature Geoscience.

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

4.  Science Highlight — Marine Diatoms Survive Iron Droughts in the Ocean by Storing Iron in Ferritin
       (contacts: A. Marchetti,; M.E.P. Murphy,

highlight figure
Diatoms, unicellular algae that exist almost anywhere there is water, have recently attracted attention as potential thwarters of climate change. Diatoms go through cycles of blooms, where they grow and multiply rapidly near the ocean's surface. Scarcity of a nutrient will trigger the end of a bloom and the algae sink, taking with them large amounts of sequestered carbon from the air to the bottom of the ocean. Because iron is a limiting nutrient in about 30-40% of the world's oceans, some researchers propose that artificially enriching iron in oceans would promote diatom growth and carbon dioxide capture similar to the hypothesized scenario that occurs during glacial periods when iron input into the ocean is higher. At least two types of diatoms that grow well in iron enrichment experiments use a protein called ferritin to grab and store iron. By stockpiling iron when it is plentiful, they can release it when the cell needs it. One of these species is the pennate diatom, Pseudo-nitzschia multiseries, a thin eukaryotic cell about a tenth of a millimeter long that most likely acquired ferritin through lateral gene transfer.

A team of researchers from the University of Washington and the University of British Columbia used SSRL Beam Lines 9-2 and 7-1, as well as the Canadian Light Source, to determine the macromolecular crystal structure of the pennate diatom's ferritin. They found that the ferritin forms a hollow ball made from 24 monomer subunits. Minimizing the potential for cell damage from storing such a reactive metal, the ferritin first oxidizes the iron atoms into a less reactive form then stores thousands of them in the hollow center of the complex. The ferritin storage subunits are localized to the chloroplasts, which require iron for capturing solar energy through photosynthesis.

The researchers found that diatoms containing iron-storing ferritin performed more cell divisions when grown in iron-free seawater than their counterparts that lack ferritin, suggesting that ferritin gives the cells an advantage in iron-limited ocean environments that receive intermittent iron fertilization. This work was published in the January 22 issue of the journal Nature.

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

5.   Exotic Material Could Revolutionize Electronics
       From June 15, 2009 SLAC National Accelerator Laboratory News Release

bismuth telluride
Surface electron band structure of bismuth telluride. (Image courtesy of Yulin Chen and Z. X. Shen.)
Physicists at the Department of Energy's SLAC National Accelerator Laboratory and Stanford University have confirmed the existence of a type of material that could one day provide dramatically faster, more efficient computer chips.

Recently-predicted and much-sought, the material allows electrons on its surface to travel with no loss of energy at room temperatures and can be fabricated using existing semiconductor technologies. Such material could provide a leap in microchip speeds, and even become the bedrock of an entirely new kind of computing industry based on spintronics, the next evolution of electronics.

Physicists Yulin Chen, Zhi-Xun Shen and their colleagues tested the behavior of electrons in the compound bismuth telluride. The results, published online June 11 in Science Express, show a clear signature of what is called a topological insulator, a material that enables the free flow of electrons across its surface with no loss of energy.

The discovery was the result of teamwork between theoretical and experimental physicists at the Stanford Institute for Materials & Energy Science (SIMES), a joint SLAC-Stanford institute. In recent months, SIMES theorist Shoucheng Zhang and colleagues predicted that several bismuth and antimony compounds would act as topological insulators at room-temperature. The new paper confirms that prediction in bismuth telluride. "The working style of SIMES is perfect," Chen said. "Theorists, experimentalists, and sample growers can collaborate in a broad sense."

The experimenters examined bismuth telluride samples using x-rays from BL5-4 at SSRL and BL10.0.1 at the ALS. When Chen and his colleagues investigated the electrons' behavior, they saw the clear signature of a topological insulator. Not only that, the group discovered that the reality of bismuth telluride was even better than theory.   Read the full SLAC news release.

6.   Researchers Reveal Structure of Key Genetic Proofreading Protein
       June 4, 2009 SLAC Today Article by Nicholas Bock

Dong Wang
Stanford structural biologist Dong Wang at an SSRL experiment hutch. (Photo by Nicholas Bock.)
Nature might abhor a vacuum, but it loves a backup plan. In living organisms, physiological systems are kept under tight control by hierarchies of organic safety catches and emergency releases, helping to make sure that things run as smoothly as possible.

A team of Stanford University researchers working in the lab of Nobel laureate Roger Kornberg recently used the high energy x-rays at the Stanford Synchrotron Radiation Lightsource to examine one such mechanism, the proofreading function of a vital protein called RNA polymerase. According to Dong Wang, a post-doctoral fellow with Kornberg's lab and the principal investigator in the study, the findings will not only provide scientists with a better idea of how protein production works, but could also give fresh insight into the design of cancer-fighting drugs. The results were published in the May 28 issue of Science.

Protein synthesis occurs in two main stages-first, DNA inside the nucleus is transcribed to RNA. During this step, called transcription, RNA polymerase skims along the DNA template, producing a complementary strand of RNA as it goes. In the second step, called translation, the cell's machinery reads the RNA and constructs the corresponding proteins. Read the full story.

7.   Secretary of Energy Visits SLAC

Secretary Chu
Secretary of Energy Steven Chu spoke at SLAC on Friday morning. (Photo by Brad Plummer.)
Secretary of Energy Steven Chu visited SLAC on June 27. Speaking to more than 700 SLAC staff, Secretary Chu in a wide-ranging speech that touched on worldwide emissions, climbing global temperatures, changing precipitation patterns, increasing atmospheric carbon dioxide concentrations and the rising sea level, and demonstrated how the energy challenge cuts across many areas and is intensely tied to our economic prosperity. He urged researchers to confront "the energy challenge."   See June 29, 2009 SLAC Today Article by Kelen Tuttle

8.   From the Director of SSRL: A Glimpse of SSRL's Future
       June 19, 2009 SLAC Today Article by Joachim Stöhr

Jo Stohr
Jo Stöhr
In my last column, I talked about the Stanford Synchrotron Radiation Lightsource's enduring status as a "top notch" x-ray user facility and promised to tell you how it plans to rejuvenate itself in the future. In the meantime, I have accepted the position of Linac Coherent Light Source Director. You may ask where this leaves my promised story. Not to worry, in this, my last column as SSRL Director, I will give you my vision of SSRL's future. If we fast-forward a decade, you should not be surprised to find SSRL in the limelight!

Clearly the eyes of the x-ray world are presently on LCLS due to its spectacular early success of producing a lasing x-ray beam and the upcoming first x-ray experiments in September. I expect LCLS to remain in the spotlight for well over a decade, with additional expansions of its early capabilities, facilities and revolutionary discoveries. But extending the horizon, say to ten to fifteen years, I see major opportunities for growth at SSRL. There are several reasons for this likely development.

In a December 2008 briefing paper of the incoming Obama administration, the four Department of Energy-funded x-ray facilities in the US-the Advanced Light Source, Advanced Photon Source, National Synchrotron Light Source and SSRL-produced a joint vision paper entitled "Science and Technology of Future Light Sources." This paper discusses the broader scientific challenges before us, including those in the major areas of energy, environment, health and technology, and focuses on the role x-rays can play in addressing them. It specifically looks at the types of future x-ray sources needed and comes to the conclusion that the nation's scientific needs will not be entirely met by the current ALS, APS, NSLS and SSRL facilities or even the LCLS and NSLS-II facilities under construction. It also emphasizes the need for two generic types of complementary x-ray sources based on linear accelerators and rings, respectively. The report therefore opens the door for a new x-ray facility at SLAC, which will be built after LCLS and its envisioned upgrades. This complementary ring-based light source, PEP-X, takes advantage of the existing PEP tunnel, accelerator components and infrastructure and will replace SPEAR3. It will provide the SSRL user program with one of the world's leading ring-based x-ray sources.

Operated either as a very low emittance storage ring or in conjunction with an energy recovery linac, PEP-X has already been incorporated as a key component into SLAC's long-term strategic plan. The combination of LCLS and PEP-X, in conjunction with SLAC/Stanford science programs that utilize these facilities, promises to make SLAC the world's leading photon science laboratory. Since both facilities are based on large accelerators, they are not only enabled by SLAC's strength in accelerator science and technology but more broadly help maintain accelerator science as a key core competency and capability of the lab, in good accord with the continued use of the word "accelerator" in the lab's new name. Toward the PEP-X goal, the SSRL Scientific Advisory Committee has recently recommended that future instrumentation and science programs be established in preparation for the greatly enhanced PEP-X brightness, and that new beam lines, if possible, be planned to be transferable to PEP-X. While the 10-15 year period toward the new source may appear daunting, experience with the planning and construction of new light sources has shown this to be quite a normal timeframe. After all, LCLS was first proposed seventeen years ago. Great things take time.

9.   SSRL to Aid New Energy-Research Center
       From June 8, 2009 SLAC Today Article by Michael Wall

The Center for Inverse Design will use quantum theory to identify and design materials.
As mentioned very briefly in the last edition of Headlines SSRL will play a key role in a new effort to make solar power more efficient and inexpensive.

SSRL will contribute to the Center for Inverse Design, or CID, a project headed by the Department of Energy's National Renewable Energy Laboratory in Golden, Colorado. CID is one of 46 DOE-funded Energy Frontier Research Centers. The EFRCs, announced by the White House April 27, will investigate ways to wean the U.S. energy economy off fossil fuels.

As its name suggests, CID will take an unconventional approach to materials design. Traditionally, scientists looking for materials or structures with certain properties, such as highly efficient solar cells, empirically test many possibilities before finding something suitable. Instead of relying on such trial-and-error methods, CID will use quantum theory and powerful computers to identify and design materials with the desired properties and, in favorable cases, synthesize them in the lab.

"The goal is to fundamentally change the way we make materials," said SSRL staff scientist Michael Toney, one of CID's 12 principal investigators and supervisor of its work at SSRL. Read the full story.

10.   July 29-31 LCLS Workshop: Science Drivers for Hard X-ray Upgrades

The LCLS had a dramatic start up at its shortest wavelength (1.5 Å) reaching saturation in April with 1.1 mJ per pulse energy (see press release) and P. Emma's paper at PAC 2009. This is the baseline performance, but there is room for more.

A workshop will be held at SLAC July 29-31, 2009, to discuss the scientific opportunities that near-term options for enhanced performance (wavelength reach, polarization, pulse duration, etc.) will enable as well as the science drivers for the long-term development of LCLS. This will be an opportunity for the broad scientific community to interact with the LCLS team and the FEL physicists to investigate what is wanted and where the science of LCLS might go. The format will allow for significant discussion amongst participants and will be an opportunity for community input as we look out over the next several years and beyond. User input into these discussions could expand our present scientific reach and take the LCLS in new scientific directions. For additional information, contact: Jerry Hastings (, Sebastien Boutet (, David Reis (, or Aymeric Robert (

Register at:

11.   SSRL Structural Molecular Biology Summer School - Sep 8-11, 2009
       (contact: R. Sarangi,

Download Poster
The biennial SSRL Structural Molecular Biology (SMB) Summer School provides a lecture series and practical application workshops on biological scientific applications of synchrotron radiation. The goal of the school is to disseminate information about the scientific opportunities in synchrotron radiation applications and train participants on the theoretical aspects, data acquisition and practical data analysis of different experimental techniques.

The 2009 SMB Summer School will focus on the use and application of X-ray Absorption Spectroscopy, Macromolecular Crystallography and Small Angle X-ray Scattering. Invited lectures from experts in these fields will be at the graduate student/post-doctoral level, but will also be appropriate for experienced researchers with expertise in one technique and an interest in learning other techniques to further the scope of their research. The four-day summer school will feature two days of lectures covering theoretical and experimental aspects, and two days of hands on training in data analysis. The afternoon of the last day will be reserved for question-and-answer sessions hosted by the co-chairs, which will be aimed at addressing specific queries from the participants.

Co-chairs for the 2009 SMB Summer School are SSRL Staff Scientists Ritimukta Sarangi (, Clyde Smith ( and Thomas Weiss ( Funding for the SMB Summer School program is provided by NIH-NCRR and DOE-BER.

Apply at:

12.   Save the Date for the Annual SSRL/LCLS Users' Conference - Oct 18-21, 2009
       (contact: C. Knotts,
User Mtg banner

Plan to participate in the Annual LCLS/SSRL Users' Meeting and Workshops, October 18-21, 2009 to learn about the latest plans, new developments and exciting user research at LCLS and SSRL. It is also a great time to interact with other scientists, potential colleagues, and vendors of light source related products and services.

The event kicks off on October 18 with a special symposium celebrating 35 years of outstanding science at the Stanford Synchrotron Radiation Lightsource. In addition to reviewing technical accomplishments and research highlights, future scientific and technical opportunities for SSRL will be discussed.

LCLS/SSRL 2009 officially begins on October 19 with a joint plenary session featuring updates from SLAC and DOE, a preview of the workshops, a user science poster session, and a keynote presentation. The Spicer Young Investigator Award, Klein Professional Development Award, Lytle Award, and the Outstanding Student Poster Session Awards will be presented on this day.

Separate sessions focusing on SSRL and LCLS facility development, instrumentation, and user science will be held concurrently on October 20, followed by meetings of the respective SSRL and LCLS Users' Organizations.

On October 21, several concurrent workshops will be held including Microimaging; Nanoscale Imaging with the SSRL STXM; Macromolecular Crystallography; Soft X-ray Beam Line Experiment Preparation; and X-ray Pump Probe Experiment Preparation.

Conference Website:

13.   Call for Nominations for Spicer, Klein and Lytle Awards
       (contact: C. Knotts,

Please take a few moments to consider nominating your colleagues or students for one or more of the following awards which will be presented at the Joint SSRL and LCLS Users' Meeting, October 18-21, 2009:

William E. Spicer Young Investigator Award —due August 1

Melvin P. Klein Professional Development Award —due August 1

Farrel W. Lytle Award —due August 15


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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