Previous Editions____________________________________________________________________________SSRL Headlines Vol. 11, No. 3 September, 2010____________________________________________________________________________
Contents of this Issue:
1.
Message from SSRL's New Director Chi-Chang Kao
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
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
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
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.
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: http://today.slac.stanford.edu/feature/2010/suncat.asp
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
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.
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.
"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: http://today.slac.stanford.edu/feature/2010/ssrl-text.asp
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
(lisa@slac.stanford.edu) or Cathy Knotts (knotts@slac.stanford.edu) or via the
reference submission form at: http://smb.slac.stanford.edu/forms/reporting/form_publication.shtml
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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