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SSRL Headlines Vol. 7, No. 3  September, 2006


Contents of this Issue:

  1. Science Highlight — Imaging of Biochemical Transformation of Arsenic in Plants
  2. Science Highlight — Shedding Light on Cheaper Communication
  3. Vote for the 2007 SSRLUO Executive Committee, Participate in SSRL33, and Attend the Next SSRLUOEC Meeting on October 13
  4. Adrian Cavalieri and David Fritz Share 2006 W.E. Spicer Young Investigator Award
  5. SSRL and Rocky Flats Plutonium Remediation
  6. JCSG Deposits 300th Protein Structure
  7. BL 5-1/2: SSRL's Newest Soft X-ray Beam Line Now Open for Users
  8. BL 2-3 Hard X-ray Microprobe Ready for Users
  9. New Text Book on Magnetism by SSRL Authors Highlights the Use of X-rays
  10. SSRL Footage Included in History Channel Special on Ink
  11. Important Upcoming Deadlines
  12. Photon Science Job Opportunities

1.  Science Highlight — Imaging of Biochemical Transformation of Arsenic in Plants
      (contacts: I.J. Pickering,; G.N. George,

The toxicity of arsenic is widely known, but perhaps less widely appreciated is that its level of toxicity critically depends on the chemical form. The fern Pteris vittata is one of a small group of plants that actively accumulates arsenic to a startling degree - an arsenic hyperaccumulator. P. vittata absorbs arsenic from soil, typically present as the relatively benign arsenate, and changes its chemical form to arsenite, which is one of the more toxic kinds of arsenic. The plant thrives on this toxic regimen, and it most likely does this to defend itself from hungry herbivores. The ability of P. vittata to take up arsenic has generated much excitement because of potential applications for environmental cleanup of drinking water and of contaminated sites.

P. vittata gametophyte, optical micrograph (A) and XAS images of arsenite (B) and arsenate (C), showing localization of arsenite in the large central cell vacuole, and discrete speckles of arsenate are localized in unknown sub-cellular compartments (possibly plant Golgi bodies).
Using x-ray absorption spectroscopy (XAS) imaging at the Stanford Synchrotron Radiation Laboratory's Beam Line 9-3, researchers from the University of Saskatchewan studied live specimens of the fern to learn what forms or arsenic are stored where in the plant and how it is converted. The (XAS) images show that the fern transports arsenate, common in the environment, from the roots to the fronds (leaves) through its vascular tissue. Once in the fronds, the plant chemically alters it to arsenite (the hydrated form of arsenic trioxide). This dangerous compound is stored in sealed compartments within the plant's cells, and is sent to tiny hairs that guard its reproductive cells (spores) near the edge of the fronds.

The researchers also studied the second part of the fern life cycle: a tiny plant called a gametophyte that mates pollen and ovule to recombine genetic information. Gametophytes are mostly only one-cell thick. The arsenite is kept in the cell's large central storage compartment. The plant keeps itself healthy by excluding arsenic from its cell walls, reproductive areas and nutrient-absorbing roots.

The study has clearly provided interesting and important insights that contribute to knowledge that will eventually enable environmental cleanup process to be implemented.

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

2.  Science Highlight — Shedding Light on Cheaper Communication
      (contact: J.P. Chang,

Proposed structures of Y2O3 films doped with low and high concentrations of Er3+
Fiber optic communication relies on the strength of a signal of light to deliver information, but over long distances that signal becomes dim and can lose its integrity. Amplifying the signal along the way can decrease signal loss, and scientists have been searching for new materials to build photonic signal amplifiers that are inexpensive and easily mass produced. Now, researchers from UCLA, working in part at the Stanford Synchrotron Radiation Laboratory Beam Line 11-2, have demonstrated how to deposit a special thin film with photoluminescent erbium (Er) onto silicon wafers. This technique could lead to the development of miniaturized optical amplifiers integrated with microchips for their incorporation into communications hardware.

Positively charged Er3+ is known for its ability to photoluminesce, which is a similar phenomenon at work in glow-in-the-dark paint. Previous research has shown that ionic Er incorporated in silica loses its reactivity to light, and until now researchers had no way to prevent this. Using Extended X-ray Absorption Fine Structure (EXAFS), the UCLA team showed that ions of Er must be deposited at a very specific concentration and in a certain arrangement, or the ions begin to interact with each other and cancel out the photoluminescent effect.

By doping 8 atom% ionic Er into yttrium oxide (Y2O3) thin films by atomic layer deposition, the Er ions remain sufficiently distant from each other to retain their photoluminescent properties. This percentage also assures that enough Er is incorporated into the thin film to have a strong amplifying effect.

The results of this study are published in Journal of Applied Physics. (T.T. Van, Bargar, J.R., and Chang, J.P. (2006) Structural investigation of Er coordination in Y2O3. J. Applied Physics 100, 023115). To learn more about this research see the full technical highlight at:

3.  Vote for the 2007 SSRLUO Executive Committee, Participate in SSRL33, and Attend the Next SSRLUOEC Meeting on October 13
      (contacts: J. Andrews, SSRLUOEC Chair,; C. Kim, SSRLUOEC Vice-Chair,

Voting to fill five open positions on the SSRL Users' Organization Executive Committee (SSRLUOEC) is now underway. Having a full and engaged committee is essential in a time of considerable change, continued funding concerns, and an increased desire on the part of SSRL for user feedback in defining its future vision and direction. So, please take a few minutes before noon on October 12 to cast your ballot. SSRLUOEC representatives will be elected by the SSRL user community by majority vote, and the results will be announced during the SSRL Users' Meeting Awards Dinner on October 12. Vote at:

There is still time to register for the 33rd Annual SSRL Users' Meeting and Workshops on October 11-13 (SSRL33). As an incentive to register early, everyone who pre-registers by October 5 will receive a free SSRL33 shirt. This annual meeting provides a forum for the presentation and discussion of new user research and technical developments as well as future plans for SSRL facilities. SSRL33 will feature a keynote presentation on the legacy and vision of Bill Oosterhuis, sessions on new opportunities for microfocusing and high resolution imaging, structural biology, ultrafast science and new scientific opportunities for SPEAR3. SSRL science highlights, a young investigators session and a poster session will be included. Although the deadline for printed material has passed, additional scientific posters will be accommodated as space allows.

Several joint SSRL-ALS workshops are being held on October 11 in conjunction with the meeting, including:
  • Ultrafast Dynamics on Surfaces and in Liquids (A. Nilsson, A. Lindenberg, Chairs)
  • Electron Dynamics in Spin Systems (Y. Acremann, P. Fischer, A. Scholl, Chairs)
  • Macromolecular Crystallography Workshop: Using the Uni-Puck and Web-Ice at ALS and SSRL (P. Adams, A. Cohen, N. Sauter, M. Soltis, C. Trame, Chairs)
    Workshop Agendas:
Additionally, we hope to have a healthy attendance at the next SSRLUOEC meeting on Friday, October 13, at 2 p.m. SSRL Director Jo Stöhr will facilitate a discussion to solicit feedback from SSRL's user community on prioritizing current opportunities, scientific and technical support for beam lines, and ideas for future scientific facilities. This meeting is open to all users and a reception will be held at its conclusion.

4.  Adrian Cavalieri and David Fritz Share 2006 W.E. Spicer Young Investigator Award

The Stanford Synchrotron Radiation Laboratory (SSRL) and the SSRL Users' Organization are pleased to announce that Adrian L. Cavalieri and David M. Fritz have been chosen to receive the 2006 William E. Spicer Young Investigator Award. The joint award, which consists of a plaque plus the shared $1,000 prize, will be presented at the 33rd Annual SSRL Users' Meeting awards dinner on Thursday, October 12, 2006. The following day, during the Young Investigators' Session, Drs. Cavalieri and Fritz will deliver presentations about their work: Clocking Femtosecond X-rays (A. Cavalieri) and Mapping the Excited State Potential Energy Surface of Bismuth (D. Fritz).

Although they have just begun their professional careers, Adrian Cavalieri and David Fritz have contributed greatly to synchrotron research. They have worked on many revolutionary experiments and have authored or co-authored several peer-reviewed publications in prestigious journals.

A. Cavalieri
Adrian Cavalieri
Adrian Cavalieri receives this award for adapting the electro-optic sampling technique to the SLAC linear accelerator, sensing each high-energy ultrashort electron pulse and providing femtosecond-level information about the pulse shape and arrival time. This work takes a great step towards solving one of the most difficult technical issues associated with the use of linear accelerators as ultrafast x-ray sources, providing a basis for precise synchronization between the x-ray source and the experimental dynamics. Adrian is currently a post doctoral researcher at the Max-Planck-Institute of Quantum Optics in Garching, Germany. He received his Ph.D. from the University of Michigan in 2005 as part of the Sub-Picosecond Pulse Source (SPPS) experimental team.

D. Fritz
David Fritz
David Fritz receives this award for developing a data-collection method which uses the electro-optic sampling technique to time-stamp x-ray diffraction data taken with the Sub-Picosecond Pulse Source, and demonstrating the utility of this method in a seminal study of the laser-excited transient state in bismuth. This work greatly expands the scope and precision of time-resolved experiments using linac-based x-ray sources by exploiting their natural timing jitter to explore the full time range of interest, while maintaining a resolution commensurate with the femtosecond-level pulse length. David Fritz recently joined the SLAC scientific staff as an LCLS instrument scientist, after receiving his Ph.D. from the University of Michigan earlier in 2006.

The contributions of Drs. Cavalieri and Fritz to the development of new x-ray techniques is exactly the sort of achievement that the W.E. Spicer Young Investigator Award was intended to recognize, and we enthusiastically congratulate them on their accomplishments.

5.  SSRL and Rocky Flats Plutonium Remediation
      (contact: D.L. Clark, LANL)

The Rocky Flats Environmental Technology Site (RFETS) is an environmental cleanup site located about 16 miles northwest of downtown Denver. Soils at RFETS are contaminated with actinide elements (Uranium, Plutonium, Americium) from improper storage of contaminated solvents and site operations. Until December 1989, the Rocky Flats Plant made components for nuclear weapons using various radioactive and hazardous materials, including plutonium, uranium and beryllium. In 1995 the site was designated an EPA Superfund cleanup site.

The DOE originally estimated site clean-up would cost $37 billion and take nearly 70 years. Independent contractor Kaiser-Hill and the DOE, working in close coordination with Rocky Flats stakeholders, devised an aggressive plan to complete the cleanup and closure of Rocky Flats by 2006 at an estimated cost between $6 billion and $8 billion.

Rocky Flats
The key to the aggressive clean-up strategy was to first understand the chemical and physical mechanisms controlling the transport of plutonium in the RFETS environment. The probability of release of plutonium from RFETS soils to the surrounding environment is governed by the solubility of its compounds in groundwater and surface waters, the tendency of plutonium compounds to be adsorbed, or stick to, minerals and organic materials in the soils, or be dispersed by wind. This understanding was key to choosing proper remediation strategies, the correct model for assessing public health risks, and aiding decisions for future land configuration and management.

Steven Conradson and co-workers from Los Alamos National Laboratory (LANL) used SSRL to measure x-ray absorption spectra (XAS) of samples of contaminated RFETS soils and concrete collected from the site. The XAS data, combined with ultrafiltration studies, showed that Pu was present predominantly as insoluble PuO2 that adheres to soil particles in the contaminated samples. This information provided a framework for decision makers to guide remediation efforts. Remediation efforts subsequently focused on removal of the layer of contaminated soil.

As a result of these studies, the clean-up was completed a year ahead of schedule in December 2005, likely saving the DOE and taxpayers billions of dollars. The XAS study, conducted in 2002, played a crucial role because it was the first spectroscopic confirmation of the form of plutonium in soils at RFETS. XAS showed unambiguously that plutonium in RFETS soils is insoluble. This recognition not only helped the Site develop the proper model to describe the transport mechanism of Pu and design a clean-up strategy, but significantly helped in gaining public trust.

6.   JCSG Deposits 300th Protein Structure
      (contact: (contact: A. Deacon,

A graphical representation of a protein molecule from a common type of bacteria, posted to the Protein Data Bank by JCSG.
The Joint Center for Structural Genomics (JCSG) recently deposited its 300th unique protein structure in the Protein Data Bank ( The JCSG is targeting representative protein structures from novel protein families that have a broad phylogenetic distribution. An emphasis is placed on proteins that are conserved between prokaryotic and eukaryotic organisms. The production activity has recently been accelerating and 150 new, unique protein structures are projected over the next 12 months. This is a direct result of development in high-throughput technology in all areas, at SSRL that of robotics, automatic screening and data collection, and automation in structure determination and refinement.

The JCSG is one of four large-scale structural genomics centers that form the production core of the Protein Structure Initiative (PSI), a research program funded through the National Institute of General Medical Sciences. The long-range goal of the PSI is to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences.

The JCSG is a collaboration between researchers at the University of California San Diego, the Burnham Institute, The Scripps Research Institute, the Genomics Institute of the Novartis Research Foundation and Stanford Synchrotron Radiation Laboratory (see for more details).

7.   BL 5-1/2: SSRL's Newest Soft X-ray Beam Line Now Open for Users
      (contact for BL5-1: H. Ogasawara,;
       contact for BL5-2: J. Luning,

A new, state-of-the-art spherical grating monochromator, covering the photon energy range from 150 eV to 1,200 eV, is now operational at Beam Line 5 using the existing 26-period elliptically polarizing undulator as source. This monochromator serves two branch lines, which are equipped with dedicated end stations for soft x-ray spectroscopy (BL 5-1) and soft x-ray small angle scattering (BL 5-2).

The spectroscopy branch line (5-1) uses K-B mirrors to focus the beam to a vertical spot size of 10 microns rms and horizontally to 75 microns rms. The end station is designed for surface and solid state experiments with ultra-high vacuum compatible samples up to 10 mm in diameter. The main chamber has an electron spectrometer (SES-100, VG-Scienta) for photoemission spectroscopy and partial electron yield detector for X-ray absorption spectroscopy. A horizontally mounted manipulator is provided for experiments with a minimum sample temperature of about 40 K. The manipulator transfers samples between the preparation chamber and the main chamber. Sputtering facilities, mass spectrometer and LEED optics are available in the preparation chamber. Gas dosing facilities and ports for evaporation sources are also available. Evaporation sources can be replaced without venting the preparation chamber. A second manipulator is also mounted vertically on the main chamber for transferring samples from a second preparation chamber with more limited facilities.

The second branch line (5-2) is tailored for resonant scattering of soft x-rays to study order phenomena on the nanometer length scale and their dynamics like chemical segregation in polymer blends or spin dynamics in magnetic nanostructures. Possible experimental techniques include 'small' angle scattering in transmission (theta < 20°) or reflection geometry (2 theta < 20°), scattering of coherent x-rays for lensless microscopy, x-ray photon correlation spectroscopy, and time resolved scattering by synchronizing an external pump with SPEAR3's bunch structure. The main detector is an in-vacuum direct illumination CCD with 1300x1340 pixels from Princeton Instruments, which can be replaced with a position sensitive multi-channel plate detector from Quantar Technologies. The beam line optics demagnify the source by about 3:1, yielding a divergence of 400 µrad in both, the horizontal and vertical plane. The inherent transverse coherence length of the x-ray beam is a few micrometers, which can be increased to several tens of micrometers by reducing the source divergence with apertures.

Users interested in submitting proposals for experiments on the new beam lines are reminded that the deadline is November 1.

8.   BL 2-3 Hard X-ray Microprobe Ready for Users
      (contact: S. Webb,

We are pleased to announce the availability of a new microprobe system for SSRL users on BL2-3. Ongoing commissioning of the equipment progressed over the last year, with successful data collected by user commissioning runs at the end of July 2006. The facility produces a 2 micron spot having 5x107 to 108 photons/sec. Experimental capabilities include x-ray fluorescence mapping and micro x-ray absorption spectroscopy. This facility is optimized for the energy range 15 to 23 keV, but it can be used at lower energies as well. Additional equipment (new fluorescence detectors, CCD diffraction area detector, cryogenic sample stage) will be installed and commissioned during the 2007 run. User requests for beam time at the hard x-ray microprobe will be scheduled in consecutive blocks.

If you are interested in submitting new proposals for microprobe experiments at BL2-3, remember that new X-ray/VUV proposals are due by November 1. Users with active proposals can request microprobe beam time for the next scheduling period by submitting a beam time request by the December 1 deadline (be sure to denote the microprobe setup in your equipment request). Contact Sam Webb with questions about the microprobe equipment, sample preparation, or data analysis.

9.   New Text Book on Magnetism by SSRL Authors Highlights the Use of X-rays

The synchrotron radiation community is well familiar with the dramatic developments in x-ray sources and science over the last fifteen years or so. Similarly, one of the oldest fields of physics, magnetism, has seen a spectacular recent advance. The giant magnetoresistance effect, discovered in 1988, is now used in every computer hard drive and has ushered in the age of "spintronics"- the use of the electron spin to sense, carry or manipulate information. This revolution forms the backdrop for the newly published textbook by SSRL physicists J. Stöhr and H. C. Siegmann. The book, "Magnetism, from Fundamentals to Nanoscale Dynamics," published by Springer Verlag as Volume152 in its Series in Solid State Sciences, grew from a proposed 400-page manuscript to an 820-page textbook. Written over five years, "Magnetism" is intended for late undergraduate and graduate students, academics, and scientists in research laboratories.

H. Siegmann & J.
Hans Christoph Siegmann and Jo Stöhr hold their new textbook.
Because of the importance of x-rays in modern magnetism research, the book emphasizes "x-ray dichroism," a term used for polarization dependent x-ray spectroscopy, scattering and microscopy studies. While magnetism research in the past was largely the domain of neutrons, x-rays are better suited for the study of modern magnetic materials, which come in the form of atomically engineered thin films, multilayers and lithographically made nanostructures. The power of x-rays comes from several inherent qualities. Their elemental and chemical specificity help unravel magnetic properties layer by layer. Their relatively large interaction cross-section and large polarization-dependent magnetic effects provide the sensitivity to analyze even the smallest amounts of magnetic material. Lastly, the ability of x-rays to see down to atomic dimensions, combined with the pulsed nature of synchrotron radiation, make possible the world's first ultrafast movies of magnetic processes in nanostructures.

More generally, the book gives a comprehensive account of magnetism's historical development, its physical foundations and the continuing research in the field. It covers both the classical and quantum mechanical aspects of magnetism as well as novel experimental techniques. It also highlights the scientific paradigm shift and technological revolution based on "spintronics" and ultrafast magnetization dynamics and how these developments are applied to magnetic storage and memory.

The authors would like to acknowledge weekly meetings and brainstorming sessions with SSRL and ALS scientists, input from industrial colleagues and support from the Office of Basic Energy Sciences of DOE.

Magnetism: From Fundamentals to Nanoscale Dynamics
Springer Series in Solid-State Sciences 152
Joachim Stöhr and Hans Christoph Siegmann
820 pages, 325 illustrations, hardcover
ISBN: 3-540-30282-4

10.   SSRL Footage Included in History Channel Special on Ink

"Invented by the Chinese in about 3000 BC, it spread the word of God and war. It set us free and spelled out our rights. It tells stories, sells products and solves crimes. It's ink and it's everywhere! From squid to soybeans, from ancient text to awesome tattoos, join us as we dip into the well for the scoop on ink." - History Channel

This upcoming feature, airing on Wednesday, October 4 (6 pm/10 pm) includes footage of work on the Archimedes Palimpsest experiment in late July on BL6-2. ( Check your local listings for the exact time in your area for this Modern Marvels documentary on ink.

11.   Important Upcoming Deadlines
      (contacts: C. Knotts,; L. Dunn,

12.   Photon Science Job Opportunities

A number of positions are currently available at the LCLS, LUSI and SSRL. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


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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