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SSRL Headlines Vol. 11, No. 3  September, 2010


Contents of this Issue:

  1. Message from SSRL's New Director Chi-Chang Kao
  2. Science Highlight — Obtaining Higher Resolution X-ray Microscopy Images Depends on Reference Shape
  3. Science Highlight — Structural Basis for Recognition of a Receptor to Its Signal Protein and to a Viral Homologue
  4. Register Now for the LCLS/SSRL Users' Meeting & Workshops, Oct 17-21, 2010
  5. Suncat: Working to Catalyze Energy Advances
  6. Diling Zhu to Receive Klein Award
  7. Vote for Users' Organization Executive Committee Membership
  8. Scientists from NREL Visit SLAC
  9. Automated Beam Line Messages Give SSRL Users a Break
  10. Input on SSRL-Related Publications Needed

1.   Message from SSRL's New Director Chi-Chang Kao
Chi-Chang Kao
Chi-Chang Kao
FY2010 was another very productive year for SSRL. SSRL delivered 4,870 hours out of the 5,101 hours scheduled, for an average uptime of 95.5%. Approximately 1,400 scientists conducted experiments, either on-site or remote, at SSRL's 31 experimental stations. In the next run cycle, starting in mid November, we expect to operate the storage ring at 350 mA in top-off mode for users and begin to prepare for 500 mA operation.

With the SPEAR3 upgrade near its full completion, we are reviewing the strategic plan SSRL developed a few years ago to take into account new scientific opportunities created by the energy challenge facing the Nation, the success of LCLS, and the need to bridge the gap between basic science and industrial research. In the coming months, we will work with staff and users to engage the scientific community at large to update SSRL's strategic plan in time for a DOE BES program review that will take place in February 2011.

Finally, we have an exciting program planned for the Annual Users' Conference which will be held here October 17-21, and we encourage everyone to participate to hear an update on recent SSRL activities, scientific highlights and our thinking so far about the future. I am looking forward to meeting all of you at the conference.

—Chi-Chang Kao, SSRL Director

2.  Science Highlight — Obtaining Higher Resolution X-ray Microscopy Images Depends on Reference Shape
       (contacts: D. Zhu,; A. Scherz,

Lensless holography experiment
Experiment performed at SSRL BL13-3.
X-ray microscopy is a useful tool for visualizing functional materials on the nanoscale. X-ray holography replaces the lens with a computer and obtains an image by Fourier inversion of the interference pattern. While, in principle, the resolution limit is given by the x-ray wavelength, in practice, the resolution is limited by the size of the reference being used.

A team of scientists led by Diling Zhu and Andreas Scherz of SIMES at SLAC used SSRL Beam Line 13-3 (at 650 eV) to test the use of a reference with sharp corners, instead of a round pinhole shape. The corners allow for a higher resolution reconstruction. Using a triangular reference, the researchers reconstructed an image of an iron/iron-oxide nanocube sample to 16 nm resolution, significantly better than the 30 nm resolution obtained by using a round pinhole reference made on the same reference fabrication machine.

The researchers' method obtains a sharper image of the iron/iron-oxide nanocube sample than alternative x-ray imaging methods, including iterative phase retrieval methods, scanning transmission x-ray microscopy (STXM), and transmission x-ray microscopy (TXM). This work was published in the 23 July issue of Physical Review Letters.

To learn more about this research see the full scientific highlight

See also: Klein Award below

3.  Science Highlight — Structural Basis for Recognition of a Receptor to Its Signal Protein and to a Viral Homologue
       (contacts: X.L. He,; K.C. Garcia,

semaphorin plexin complex image
Structures of the Sema7A/PlexinC1 complex, the free viral Semaphorin A39R, and the A39R/PlexinC1 complex.
Semaphorins are a group of proteins known for their critical role in nerve and vascular development and are bound by signaling receptors called Plexins. Some Semaphorins, including Sema7A, are involved in a variety of immune responses. Vaccinia virus, which is used in the smallpox vaccine, has a Sema7A homologue called A39R, which binds PlexinC1, Sema7A's receptor.

The research groups of Professors Xiao-Lin He of Northwestern University Feinberg School of Medicine, and Chris Garcia at Stanford/HHMI collaborated, using resources at SSRL and APS, to solve crystal structures of free viral Semaphorin A39R, Sema7A/PlexinC1 complex, and the A39R/PlexinC1 complex. They found that in both complexes, the Semaphorin and Plexin dock head-to-head. The 7-blade propeller-shaped Sema domains of both the Semaphorin and Plexin fit together edge-on. The viral Semaphorin A39R uses a reduced number of strong connections to accomplish binding despite being smaller.

Because of extensive structural conservation, the authors conclude that the viral Semaphorin A39R gene is an evolved form of the Sema7A gene, which was hijacked long ago, and did not come about by convergent evolution. The availability of these structures will inform future studies of Plexin and Semaphorin interactions, of the downstream biochemistry of this system, and of potential therapies for anti-tumor-progression and directional nerve regeneration. This work was published in the September 3 issue of Cell.

To learn more about this research see the full scientific highlight

4.   Register Now for the SSRL/LCLS Users' Meeting & Workshops, Oct 17-21, 2010
       (contact: C. Knotts,

Register for our Annual SSRL/LCLS Users' Meeting and Workshops by October 8 to take advantage of early registration fees.

Students, in particular, are encouraged to present posters and compete for prizes, which include a certificate and a $100 award. Representatives of the Users' Organization will judge student posters, and prizes for outstanding posters will be presented during the meeting dinner. In addition to the reduced student registration fee, students presenting posters receive a free dinner (indicate student presenting poster during on-line registration). Submit abstracts for the user poster session by October 8 at:

The event kicks off on October 17 with workshops focused on LCLS Data Analysis and LCLS II. LCLS/SSRL 2010 officially begins on October 18 with a joint plenary session featuring updates from SLAC and DOE, a keynote talk by Jens Norskov on "Converting Sunlight into Fuels - the Role of Interface Catalysis," science highlights from SSRL and LCLS, and a user science poster session. 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 19, followed by meetings of the respective SSRL and LCLS Users' Organizations.

A number of concurrent workshops will be held on Wednesday, October 20, including Frontiers in Biology with XFELs; Challenges in Imaging Processing in Tomographic Data Sets; High Energy Density Science; AMO Instrumentation and Science Opportunities; SXR Instrumentation and Science Opportunities; and Developing Strategies, Preparing and Getting the Most from Macromolecular Crystallography Experiments.

5.   Suncat: Working to Catalyze Energy Advances
       SLAC Today article by Lori Ann White

Suncat Group
The SUNCAT team. (Photo by Lori Ann White)
SUNCAT - the Center for Sustainable Energy through Catalysis - is a new initiative in the SLAC Photon Science Directorate that will focus on creating better catalysts for use in alternative energy industries. The Center is led by Professor Jens Norskov, who arrived at the beginning of June from his previous appointment as Director of the Center for Atomic-scale Materials Design at the Technical University of Denmark.

Norskov and his team want to gain such a clear and comprehensive understanding of catalytic processes that they can actually develop a theoretical basis for the design of new and better catalysts - "basically going from quantum mechanics to designing a new material," Norskov said. Catalysts are materials that can affect chemical reactions without themselves being changed. They are already widely exploited in industrial chemistry, but most catalysts now in use are far from perfect. Some are not efficient, while others include rare elements, and are thus expensive. Some, such as platinum (used to split water into hydrogen and oxygen), are both.

One new class of materials Norskov and his crew want to design would help capture the energy of the sun and store it in a form usable as fuel. In fact, SUNCAT is part of the Joint Center for Artificial Photosynthesis, a new Energy Innovation Hub created by the Department of Energy to do just that. The key to artificial photosynthesis is an energy-efficient way to "reduce" carbon dioxide-in other words, strip the oxygen off the molecule-in order to combine the carbon with hydrogen to make the fuels we burn.

"It hasn't yet been proven that this is possible," said SUNCAT staff scientist Frank Abild-Pedersen. "People have just discovered this field again." But if SUNCAT scientists can pull it off, that could, indeed, reduce the amount of carbon dioxide contributing to global warming. Read more at:

6.   Diling Zhu to Receive Klein Award
       SLAC Today article by Kelen Tuttle

Diling Zhu
Diling Zhu (Photo courtesy Diling Zhu)
Stanford applied physics graduate student Diling Zhu has been chosen as the recipient of the 2010 Melvin P. Klein Scientific Development Award for his work at SSRL. Zhu, who completed his Ph.D. research in the Stohr group, will accept the award October 18 at the joint SSRL-LCLS Users' Meeting.

The Klein award has been given annually since 2006 to undergraduates, graduate students and postdocs for outstanding research conducted at SSRL. The award comes with a $1,000 prize to help the recipient disseminate his or her scientific results.

"This was actually quite a surprise - a very good surprise," Zhu said. "I will do my best to give a good talk at the Users' Meeting."

Using SSRL Beam Lines 5-2 and 13-3, Zhu worked to develop a new experimental technique to carry out a process called x-ray holography. Whereas regular cameras record photons as they travel like particles, holography makes use of the wave-like properties of light. To do this, researchers illuminate a sample with a beam of coherent x-rays. Some of these x-rays are scattered by the object to be studied, while another portion are scattered by a reference structure. Much as the collision of two small water waves creates new ripple patterns, these two beams of light interact, forming interference patterns. Researchers then collect the scattered x-rays in a detector and typically employ computer algorithms to reconstruct the sample's two-dimensional image. Yet these algorithms require significant computing power and it is difficult to know whether something went wrong. Read more at:

See also: Science Highlight above

7.   Vote for Users' Organization Executive Committee Membership

Having full and engaged Users' Organization committees is essential, particularly during times of growth and change. Please take a few minutes to cast your ballots between September 30 - October 18, 2010 to fill open positions on both the SSRL and LCLS Users' Organization Executive Committees. The results will be announced during the Users' Meeting.

8.   Scientists from NREL Visit SLAC
       (contact: B. Hedman,

A group of senior scientists from the National Renewable Energy Laboratory (NREL) in Golden, Colorado, visited SLAC on September 20. The goal of the visit was to explore potential areas of mutual scientific interest and collaborative efforts in energy-related research broadly defined, and create ties between existing and future programs at both national laboratories. Presentations were given by NREL and SLAC Photon Science, SSRL and LCLS staff, followed by lengthy discussions. The visit was co-hosted by Z.-X. Shen (SLAC Chief Scientist) and Stuart Macmillan (NREL Chief Scientist), and the NREL delegation was headed by Associate Laboratory Director Ray Stults.

9.   Automated Beam Line Messages Give SSRL Users a Break
       SLAC Today Article by Lori Ann White

Sam Webb
Sam Webb at Beam Line 2-3. (Photo by Lori Ann White.)
Some SSRL users enjoyed a little extra peace of mind, as well as more regular meals and sleep, starting in early spring of 2010. That's when Sam Webb gave them a software tool that kept an eye on their experiments for them.

"Users would joke that it'd be nice if the beam line could call them," said Webb, an SSRL staff scientist and beam line support scientist. "I said, 'Well, technically that's not that hard to do.'"

Webb's tool tracks data collection, as well as the status of the SPEAR synchrotron accelerator, and notifies both users and Webb himself via text message or e-mail if something out of the ordinary occurs. Webb installed it on Beam Line 2-3, the dedicated microfocus imaging beam line, as well as Beam Line 10-2, which is run half-time in imaging mode. During this past run the messaging tool was offered as an option for users on Webb's beam lines. Read more at:

10.   Input on SSRL-Related Publications Needed
       (contacts: C. Knotts,; L. Dunn,

As always, we rely on you to provide information on your SSRL-related publications. Please send us an update on your journal articles, refereed conference proceedings, books, theses, invited talks, patents and awards if you haven't already done so recently. We would like your input as soon as possible, but it is never too late to report a publication that isn't currently on our list.

This information can be submitted anytime via email message to Lisa Dunn ( or Cathy Knotts ( or via the reference submission form at:

For recent publications lists and the proper acknowledgement statements see:


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 September 2010
Content Owner: L. Dunn
Page Editor: L. Dunn