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SSRL Headlines Vol. 7, No. 11  May, 2007


Contents of this Issue:

  1. Science Highlight — Mapping Cellular Nutrient Highways
  2. Science Highlight — How to Turn Carbon into a Magnet? X-rays and Protons Give the Answer!
  3. Atoms Fly Apart in Direct Crystal Melting
  4. New X-ray Photon Correlation Spectroscopy and Lensless Imaging Capabilities
  5. June 9 Memorial Service for Jim Patel
  6. Wrap-up on Second Annual SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences
  7. Upcoming Schools, Users' Meetings and Workshops
  8. User Award Nominations Due in August
  9. User Administration Update
  10. Photon Science Job Opportunities

1.  Science Highlight — Mapping Cellular Nutrient Highways
       (contacts: H.W. Pinkett,; D.C. Rees,

ABC Transporter figure
Structure of ABC transporter HI1470/1: HI1471.
Scientists from Caltech have solved the crystal structure of an ATP-binding Cassette (ABC) transporter called HI1470/1 from the bacteria Haemophilus influenzae. This particular transporter, which is a member of a large family of related proteins prevalent in most organisms including humans, is responsible for moving nutrients across cell membranes. The structure of HI1470/1 exhibits an alternate conformation to that previously observed for the related transporter BtuCD, such that their pathways for moving nutrients open to opposite sides of the membrane. These results give scientists a look at both the beginning and ending stages of how proteins transport nutrients across the membrane bilayers that surround all cells.

Using x-ray diffraction data from SSRL beam line 9-2, subtle distinctions were found in the HI1470/1 transporter that could be relevant to the function of the protein. Namely, a twist of about 9 degrees was found about an axis perpendicular to the translocation pathway when central internal structures are aligned. These differences may shed light on how the protein changes from inward to outward shapes during the process of transporting nutrients.

Though the findings are not immediately applicable, they may prove important in future medicinal uses. For instance, some members of the ABC transporter family are involved in multi-drug resistance. Understanding the mechanism through which substances are transported across cell membranes may be the first step in developing inhibitors to keep medicines inside cells, which would increase a drug's effectiveness. Also, antibiotics could be developed that inhibit the transporters in infectious bacteria, starving them of essential nutrients.

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

2.  Science Highlight — How to Turn Carbon into a Magnet? X-rays and Protons Give the Answer!
      (contact: H. Ohldag,

The exclusive club of magnetic elements officially has a new member - carbon. Using a proton beam and advanced x-ray techniques, SLAC researchers in collaboration with colleagues from LBNL and the University of Leipzig in Germany have finally put to rest doubts about carbon's ability to be made magnetic.

Magnetic Carbon figure
A carbon film is hit by a high-energy proton beam, causing the magnetic moments of the atoms to align around the beam impact area and creating a ring-shaped magnetic pattern that can be imaged with a magnetic-force microscope (left). The x-ray microscope can then be used to "scan" the sample for magnetism associated with other elements. The absence of a ring pattern in scans for cobalt, nickel and iron prove that the sample contains only carbon (right)
"In the past, some groups thought they had discovered magnetic carbon," said Hendrik Ohldag, the paper's lead author and SSRL staff scientist. "Unfortunately, they realized later that they were misled by small amounts of iron, cobalt or nickel in their samples." In Leipzig, Ohldag's team applied a beam of protons to disrupt and align a portion of the electrons in samples of pure carbon, magnetizing tiny, measurable spots within the carbon. The team then used the x-ray microscope at ALS to obtain images of the magnetized portions - a measurement only possible with a state-of-the-art microscope that uses the brilliant x-ray beams generated when electrons accelerate around the ring of a synchrotron. The x-ray beam also enabled the team to verify beyond doubt that the sample remained free of impurities during the experiments, unlike the case in previous studies.

Harnessing the magnetic properties of carbon could one day revolutionize a range of fields from nanotechnology to electronics. Magnetism, which forms the basis of information storage and processing in computer hard drives, could be employed in novel ways in tomorrow's electronic devices.

The results appeared in the May 4 edition of Physical Review Letters.

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

3.   Atoms Fly Apart in Direct Crystal Melting
      (contacts: K. Gaffney,; P. Hillyard,

Using an intense laser and ultra-fast x-rays, SSRL researchers have observed the atomic events involved in rapid crystal melting. Ordinary thermal melting determines the fate of an ice cube in a cup of tea or an icicle out in the blazing sun. The slow-acting heat causes atomic nuclei within the ice to vibrate destructively, disrupting the chemical interactions between the atoms. This allows the ice to relax its shape from an ordered crystal to a disordered liquid.

At the Sub-Picosecond Pulse Source (SPPS), scientists used an alternative route to crystal melting that enabled them to make a "movie" of the atomic motions that lead to crystal disordering. The international collaboration used an ultra-fast, high-energy laser to rapidly "heat" the electrons in a crystal without "heating" the atomic nuclei; the laser "warmed" the outer electrons while leaving the heavy core of the atom "cold". In this "electronically driven melting," the electrons gained energy and exited their regular orbit around the core, instantly breaking the chemical bonds they had shared with electrons from neighboring atoms.

Short bursts of x-rays provided by the SPPS measured the atomic positions of the atoms in a semiconductor material. The data, published recently in Physical Review Letters, revealed that when their bonds destabilized, the atoms moved apart from each other quickly, as if repelling each other. The semiconductor material had visible melting damage after being struck by the laser. "This research provides verification that intense ultra-fast x-ray sources like the upcoming Linac Coherent Light Source (LCLS) will make possible the study of previously inaccessible material properties," said SSRL researcher Patrick Hillyard.
    SLAC Today article by Heather Rock Woods

4.   New X-ray Photon Correlation Spectroscopy and Lensless Imaging Capabilities

      (contact: S. Roy,

In April scientists began utilizing BL5-2, one of SSRL's newest experimental stations. This unique facility offers users a range of experimental capabilities for probing the structure and dynamics of materials at the nanoscale. Two principal techniques available at this new beam line that take advantage of SPEAR3's exceptional brightness are x-ray photon correlation spectroscopy and "lensless imaging." Neither would have been possible with the earlier generation SPEAR2. BL5-2 uses a special magnet - an elliptically polarizing undulator - to convert the stored electrons to soft x-rays. Special properties of the magnetic optics downstream of the undulator cause these soft x-rays to become "coherent." Coherence is a property of electromagnetic radiation (of which light or soft x-rays are two examples) which implies an orderliness of the parameters of the soft x-rays, rather than a randomness. This orderliness, much like that exhibited by laser light, distinguishes the soft x-rays produced at this new experimental station from other experimental stations at SPEAR3 in powerful ways. This opens up investigations into fluctuating, dynamic states of matter such as magnetism and electrical properties that are otherwise not possible at SPEAR3.

In many instances, the samples placed in the x-ray beams at SPEAR3 are crystallized. This has the advantage of presenting a regular, periodic pattern of molecules to the incoming beam, but the disadvantage that motion of the molecules is frozen in place. Coherent x-rays, however, enable researchers to probe samples that do not have regularly arranged, periodic structures-such as molecules that resist crystallization-and can identify individual elements and their dynamic states within a single sample.

During the upcoming annual shutdown later this summer (August-October), the experimental stations at BL5-2 as well as BL5-1 will be relocated to a permanent home on the new beam line 13. A new undulator on BL13 will offer an even brighter source of coherent x-rays, and new control systems will provide an operational platform especially optimized to take full advantage of the potential of SPEAR3. And once SPEAR3 begins operating at the design current of 500 mA (as is planned to begin partially during the next year's run), experiments at this station will take one-fifth the time as with the 100 mA in use today.

This new suite of tools also shares many similarities with the LCLS. The overlap is such that much work has been accomplished toward understanding how to best capitalize on the unique imaging capabilities of the LCLS. SPEAR3's continuing evolution is opening new doors at SSRL in the type of science available to our users now and in the future.

5.   June 9 Memorial Service for Jim Patel

J. Patel
Jim Patel
On March 3, SSRL lost an esteemed colleague with the death of Jamshed (Jim) R. Patel at the age of 81. Born and educated in India, Jim spent most of his career at Bell Laboratories, during that institution's years as a dominant scientific force. After retiring from Bell Labs, Jim moved to California in 1994, consulted at Intel Corporation, and took a joint position at SSRL and at the Advanced Light Source in Berkeley.

Jim's scientific interest throughout his career focused on defects in crystals. X-ray diffraction was the primary tool that he used. Starting with laboratory x-ray sources, Jim progressed to using 2nd and eventually 3rd generation synchrotron sources. Most recently, Jim was closely involved with creating and using the x-ray microdiffraction beam line 7.3.3 at ALS, studying electromigration-induced plasticity in interconnects on microchips, and strain associated with grain and domain boundaries in superconductors.

At SSRL, Jim was most often found at the x-ray scattering beam lines 2-1, 7-2, and 11-3. He used these beam lines to look at the damage induced in silicon crystals during ion-implantation doping. This doping technology is a critical component of modern semiconductor manufacturing, but the electrical properties of the doped material, and the diffusion of the dopants within the silicon, depend sensitively on the nature of the damaged lattice. Jim used his connections at Intel to obtain a variety of excellent samples, and used grazing-incidence diffuse x-ray scattering, along with high-resolution x-ray diffraction, Hall-effect measurements, and transmission electron microscopy to gain insight into the damage caused by implantation, its response to laser annealing, and the final distribution of dopants in the silicon lattice. According to SSRL colleague Apurva Mehta, "When we had beam time Jim would be at the beam line every morning until early evening and then often come back for a couple of hours after dinner to pour over data and guide the next set of experiments. And often he would take some of the data "home" - i.e., get it transferred to his home directories and often come next morning with some preliminary analysis". Not surprisingly, this work led to nearly a dozen scientific papers.

In addition to being a tireless and creative scientist, Jim was an exceptionally warm and friendly colleague. He served as mentor to a number of postdocs and graduate students during his time at SSRL, and collaborated with several other SSRL staff members. In 2005, his colleagues from around the world gathered to celebrate his 80th birthday with a workshop on x-ray microdiffraction. He leaves behind a formidable scientific legacy, a wide circle of friends, and an extensive family.

A memorial service will be held for Jim on Saturday, June 9, at 3:00 p.m., at Saint Raymond's Catholic Church, located at 1100 Santa Cruz Avenue, Menlo Park, CA. All who wish to remember Jim are welcome to attend.

6.   Wrap-up on Second Annual SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences
      (contacts: S. Webb,; C. Condron,; M. Toney,; J. Bargar,

Workshop participants
Workshop participants
The second annual SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences was held at SSRL on May 15-17, 2007. The aim of this workshop was for students, postdocs and researchers to gain practical knowledge in x-ray scattering methods with an emphasis on information that cannot be found in text books. More than 45 researchers, mostly graduate students and postdocs, attended the workshop. The first day consisted of introductory lectures on x-ray diffraction, how to get the most data out of your beam time, and how to apply various techniques. The second and third days involved "on-the-experiment" training at four of SSRL's beam lines (1-4, 2-1, 11-3, and 7-2), followed by data analysis demonstrations and Q&A sessions. The practical sessions were well attended, and all those that attended benefited greatly from these demonstrations.

Based on the comments received, the workshop was a big success. All the attendees came away with new knowledge about how to efficiently collect data at SSRL's scattering beam lines. Copies of all the talks have been posted at:

7.   Upcoming Schools, Users' Meetings and Workshops

At Other DOE Light Sources

8.   User Award Nominations due in August

9.   User Administration Update

      (contact: C. Knotts,

Submit new macromolecular crystallography proposals by July 1, 2007. For beam time before fall 2007, users can submit a Rapid Access proposal or contact L. Dunn ( for more information.

Rapid access proposals for structural molecular biology x-ray absorption spectroscopy experiments on BL7-3 can be submitted at any time. Periodic blocks are 6 shifts of beam time are set aside to allow new and current biological XAS users to perform feasibility tests. For questions, please contact Serena DeBeer George (

Rapid access proposals for structural molecular biology small angle x-ray scattering experiments on BL4-2 can also be submitted at any time.

10.   Photon Science Job Opportunities

A number of positions are currently available at SSRL and LUSI. 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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Last Updated: 31 MAY 2007
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