Previous Editions__________________________________________________________________________SSRL Headlines Vol. 10, No. 3 September, 2009__________________________________________________________________________
Contents of this Issue:
A group of researchers led by Prof. Douglas C. Rees from Caltech have solved
the crystal structure of one such transmembrane gate, the mechanosensitive
channel of large conductance (MscL) from Staphylococcus aureus using
SSRL Beam Line 12-2. Their 3.8 Å structure shows an intermediate state of
the channel, between open and closed. It can be compared to a previous crystal
structure of a homologous channel that was found in the closed state. The S.
aureus channel is made of four subunits, while the previous structure had
five. Despite that difference, the researchers found that the architecture of
the two channels is similar, including similar transmembrane helices and
conserved hydrophobic residues at the point of channel constriction.
Comparisons between the geometries of the channel components of the two
structures have led the researchers to propose a two-step helix pivoting model
of channel gating. This work was published in the September 3 issue of the
journal Nature.
A research group led by Frank (Bud) Bridges from UC Santa Cruz used SSRL Beam
Line 10-2 to test this prediction. The group is interested in the cobalt oxide
La1-xSrxCoO3 (LSCO) because it has unusual
magnetic properties that are not well understood. They used extended x-ray
absorption fine structure (EXAFS) spectroscopy and neutron pair distribution
function (PDF) techniques to determine variations in the Co-O bond lengths in
powdered samples as a function of temperature. Their data can be fit very well
to the classic correlated Debye model without invoking any JT distortions in
contrast to the manganites which show a large JT distortion. They therefore
conclude that significant JT distortions are not present in the cobalt oxide
LSCO.
The lack of a significant JT distortion of the oxygen octahedral about Co
provides evidence against a proposed intermediate spin state for Co.
Consequently, the observed unusual magnetism must arise from a mixture of
strongly magnetic, high spin states and non-magnetic low spin states. This work
was published in the January 16 issue (2009) of the journal Physical Review
Letters.
Using data obtained at SSRL Beam Lines 4-2 and 6-2 and at SPring-8 in Japan a
research group led by Anders Nilsson from SLAC has made discoveries that
challenge the current models of water behavior. The team used small angle x-ray
scattering (SAXS; BL4-2), which can give structural information about
non-crystalline materials, to measure inhomogeneities in the density of water
at various temperatures. They saw fluctuations in terms of low density regions
on a 1-nm scale that correspond to the ordered, tetrahedral model described
above, but the majority of molecules were found in higher density regions. The
structure and states of the molecules in these areas was found through x-ray
emission spectroscopy (XES) and x-ray Raman spectroscopy (XRS; BL6-2),
techniques that analyze the electronic states of molecules. The researchers
found that the molecules in the high density areas were forming asymmetrical,
disordered structures, a sort of chaos in which floated some islands of
tetrahedral order. Since the ratio of low to high density areas slightly
decreased as the temperature increased from 4°C to 90°C, the
researchers hypothesize that the water structure was finding a balance between
minimizing enthalpy (through extensive hydrogen bonding in the low density
structure) and maximizing entropy (the disorder of the high density structure).
This field has been hotly debated in the last few years. If accepted, the new
model is a revolution in our perception of water structure. Time - and more
experiments - will tell. This research was published in August by the journal
Proceedings of the National Academy of Science.
Plan to attend and share your research results during the user poster session
of the Annual SSRL/LCLS Users' Meeting and Workshops which will be held October
18-21 (SSRL/LCLS 2009). Students, in particular, are encouraged to present
posters and compete for prizes, which include a certificate and a $100 award.
Representatives of the SSRL 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 9 at:
The annual event kicks off on October 18 with a special symposium celebrating
35 years of outstanding science at the Stanford Synchrotron Radiation
Lightsource, including honoring its founding Director Sebastian Doniach on the
occasion of his 75th birthday. Thirty-five years ago, the Stanford Synchrotron
Radiation Project (SSRP) - the precursor to today's SPEAR3 ring and the
Stanford Synchrotron Radiation Laboratory (SSRL), recently renamed Stanford
Synchrotron Radiation Lightsource - began operations. SSRL science launched
with five experimental stations sharing the first x-ray beam line. The SSRP was
the world's first synchrotron radiation hard x-ray lightsource based on an
electron storage ring. In addition to reviewing technical accomplishments and
research highlights, future scientific and technical opportunities for SSRL
will be discussed at this special symposium.
LCLS/SSRL 2009 officially begins on October 19 with a joint plenary session
featuring updates from SLAC and DOE, a preview of the workshops, the user
science poster session, and a keynote presentation from Bill St. Arnaud on
Green IT Developments. Also during the plenary session, Jo Stöhr will give
a talk 'In Memory of H. C. Siegmann, the Father of Modern Spin Physics.' Yulin
Chen will receive the Spicer Young Investigator Award and Leslie Jimison will
receive the Klein Professional Development Award. Both will present their
research (see details below). The Farrel Lytle Award will and the Outstanding
Student Poster Session Awards will be presented at dinner on October 19.
On October 20, concurrent sessions will focus on SSRL and LCLS facility
development, instrumentation, techniques and user science, followed by meetings
of the respective SSRL and LCLS Users' Organizations.
On October 21, several concurrent workshops will be held including:
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 October 2-19, 2009 to fill open positions on both the
SSRL and LCLS Users' Organization Executive Committees. The results will be
announced during the Users' Meeting.
SSRL UOEC: http://www-conf.slac.stanford.edu/ssrl-lcls/2009/SSRLvoteForm.asp
"I am very glad that our work was acknowledged," Chen said of the award. "I
feel very excited not only because of the prize itself, but also because we
could demonstrate the great opportunity SSRL provides for science. I hope the
lab will keep developing its remarkable capabilities for experiments and become
an even better platform for more exciting science to be carried out."
The award will be presented at the October 19 SSRL/LCLS Annual Users' Meeting
at SLAC. The award includes a certificate and monetary gift of $1,000. In turn,
Chen will give a short presentation describing his work.
Together with other theoretical and experimental physicists at SIMES, a joint
collaboration between SLAC and Stanford University, Chen helped find bismuth
telluride-an example of a new class of materials called topological
insulators-which was originally predicted by theory in 2007. The experimental
discovery has potential impact for future research in not only fundamental
physics, but also semiconductor and energy science.
Topological insulators create a unique atmosphere for electrons, in which the
electron spin and momentum are "locked" to each other on the surface of the
material. This enables electrons to flow around non-magnetic impurities,
instead of being scattered backward. This allows current to flow without loss
of energy. Also, because electron spin and momentum are coupled, electron spin
could be manipulated by an electric current applied across the surface of the
topological insulator.
Physicists may use bismuth telluride to study the physics of relativity in a
condensed matter system or to realize elusive particles such as magnetic
monopoles or majorana fermions.
Chen's research indicated that bismuth telluride could be used at much higher
temperatures than theory predicted, bringing this substance much closer to real
applications. A topological insulator such as bismuth telluride could one day
be used to make smaller transistors for use in more compact electronics that
consume less energy. The material could also be used in novel spintronic
devices without bulky magnets such as the read/write head in current hard
drives. Being great thermoelectric material, bismuth telluride could even
convert temperature gradients across itself to electricity or vice versa, for
possible use in recycling waste heat into clean electricity or refrigeration
without greenhouse coolant or cryogens.
"We study fundamental physics, but we also want to contribute to people's
lives," Chen said.
see: http://today.slac.stanford.edu/feature/2009/spicer-award-2009.asp
The recognition, which has been awarded annually since 2006, is given to
undergraduates, graduate students and postdocs for outstanding research
conducted at SSRL. The award comes with a $1,000 prize to help recipients
disseminate their scientific results.
"The award is a kind recognition for my work at SSRL," Jimison said, adding
that she will use the award funds to offset travel expenses. "It will allow me
to attend a conference not otherwise possible, where I will share my ideas,
learn new ideas from others and meet other people in my field."
Using the SSRL beam line, Jimison studied the conductive properties of
semiconducting polymers-organic materials that could see use in technologies
ranging from solar cells to flexible displays. The materials are characterized
by amorphous regions punctuated by crystallites-tiny structures made of ordered
patterns of atoms. Previous studies have shown that the arrangement of the
crystallites within the non-crystalline regions has a large effect on the
materials' electrical properties. Jimison's goal was to improve the overall
understanding of the relationship.
"Because these organic films are relatively new materials, we don't know how
the microstructure details affect charge transport," Jimison said. "We're
trying to fill in the story."
Using the SSRL beam lines, Jimison and her colleagues developed a technique
that combined x-ray diffraction data from several different analysis methods.
The end result was a diffraction pattern that allowed the researchers to
quantify aspects of the material structure not previously possible, including
the ratio of crystalline to non-crystalline material present in the sample.
Jimison then applied the new technique to study the crystal structure in
several lab-prepared samples. Jimison also made transistors out of the
materials to study their electrical properties, looking for a correlation
between the arrangement of crystallized regions and the materials'
conductivity.
Working with her colleagues, Jimison is currently writing a paper to describe
the new technique. Over the next few months, she hopes to refine the analysis
method in order to extract more information and to study other materials
systems.
"This was designed to be the first of a more general approach to study the
microstructure of semiconducting thin films," she said. "There is lots of room
for improvement."
Jimison is a fifth year doctoral student at Stanford. She was a National
Science Foundation Graduate Research Fellow from 2005 to 2007, and received a
bachelor's degree in materials science and engineering from North Carolina
State University in 2004. She has co-authored journal articles in Advanced
Materials, Physical Review and the Journal of Vacuum Science
see: http://today.slac.stanford.edu/feature/2009/klein-award.asp
The Stanford Synchrotron Radiation Lightsource at the Department of Energy's
SLAC National Accelerator Laboratory received an important boost this year,
with $4.8 million in funding from the American Reinvestment and Recovery Act
for repairs and upgrades during SSRL's annual three-month shutdown, and new
scientific instruments in the year to come.
"The ARRA funding was a really big help; I don't know when we could have ever
gotten these things done without it," said SSRL Acting Director Piero Pianetta.
The funding will go toward seismic retrofits and key upgrades to SSRL's x-ray
beam lines, which are used by scientists from around the world to conduct
experiments in energy, materials, environmental and life sciences, accelerator
physics and more.
Part of the Recovery Act funding will help SSRL develop an advanced
spectroscopy facility that will allow researchers to study systems ranging from
fuel cells to photosynthesis. This facility will rely critically on SSRL's plan
to bring its SPEAR3 storage ring to its maximum operating capacity of 500
milliamperes. The ring has operated at 100 mA since its commissioning in 2004,
although it recently received a boost to 200 mA. Running at full capacity will
increase the brightness of the facility's x-ray beam lines, making SSRL an even
more valuable tool for SSRL's scientific users.
"The results of an experiment depend on how many photons you can put on a
sample," said Bob Hettel, deputy director for SLAC's Accelerator Directorate.
"If you can put five times as many photons on a sample, some experiments can be
done five times faster."
In other experiments, where the intense beam could be harmful to experimental
samples, new schemes such as rapid sample scanning and fast shutters to remove
the beam from the sample between measurements will be employed.
One of the biggest challenges in reaching full operating capacity, though, is
making sure that the SSRL optical devices have a reliable cooling supply.
Toward this end, $800,000 in Recovery Act funds will be used to help upgrade
the cooling systems on SSRL's 11 monochromators-devices that filter incoming
light to a single specified wavelength. Read more at:
The Structural Molecular Biology Summer School wrapped up Friday, September 11
after a full four days of lectures and hands-on training in data analysis.
Participants ranged from graduate students and postdocs to early-career
scientists interested in learning about x-ray light experiments that help
identify the form and function of biological molecules.
"The Summer School showcases three different biology experiments that you can
do with a synchrotron," said SSRL staff scientist Ritimukta Sarangi, who along
with scientists Clyde Smith and Thomas Weiss organized the SMB Summer School.
"We want students to know the skills and techniques that are available,"
Sarangi said. The Summer School takes place every two years.
This summer's program brought together 25 participants from the U.S. and Europe
to explore the three experimental techniques macromolecular crystallography,
small angle x-ray scattering and x-ray absorption spectroscopy. All three
approaches allow scientists to study the structure of biological molecules
using x-rays from a synchrotron. Students indicated on their Summer School
applications which techniques interested them the most. Participants received
hands-on training sessions for basic data analysis using their chosen
technique. "Students go away with a basic knowledge of analyzing data and can
interpret papers that they read which involve these analyses," Sarangi said.
The program highlights capabilities of the Stanford Synchrotron Radiation
Lightsource user facilities, and informs potential future users. "We encourage
the students to apply for beam time," Sarangi said. "We can help students
design an experiment or assist those who may have an experiment in mind."
The SSRL SMB Summer School is supported by NIH NCRR, DOE BER and NIH NIGMS.
Read more at: http://today.slac.stanford.edu/a/2009/09-14.htm
It is extremely important that users not only inform us whenever work conducted
at SSRL results in a publication, but also acknowledge SSRL and our funding
agencies in each publication. User help is needed to keep current records on
publications including refereed journal papers, conference proceedings, book
chapters and theses, invited lectures and major awards and patents based at
least in part on work conducted at SSRL. This information allows SSRL to
demonstrate scientific achievements and productivity when responding to
requests sent out by the Department of Energy and the National Institutes of
Health.
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:
Beam time schedules for experiments on X-ray and VUV lines during the first
scheduling period in our FY2010 run have been posted to the web at:
The Stanford Marguerite Line S shuttle connecting SLAC and CalTrain, as well as
the new Rosewood Hotel, started running on a new schedule beginning Monday,
September 14. Increasing alternative transportation ridership and reducing
carbon emissions were the ultimate goals in upgrading the schedule. The new
timetable focuses on only peak ridership periods.
Developed in a collaborative effort between SLAC and Stanford University's
transportation and real estate departments, the new schedule will help to
increase efficiencies, reduce operational costs and will ultimately contribute
to both communities' sustainability goals in terms of carbon reductions.
Approximately 19 pounds of carbon dioxide emissions are removed from the
atmosphere for every gallon of gasoline saved through alternative
transportation; the new schedule compliments these reductions and more
See the new Line S and also the schedule for connecting CalTrain service
schedules at:
__________________________________________________________________________
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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