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SSRL Headlines Vol. 2, No. 2  Aug, 2001


Contents of This Issue:

  1. Science Highlight — A New Approach to 3D Structures of Macromolecules Utilizing Single Molecule Diffraction Images
  2. SSRL Proposal Review Panel Holds 51st Meeting
  3. Agreement between SASE-FEL Experimental Results and Photoinjector-to-FEL Simulation Codes Confirmed
  4. Marking the One-Year Anniversary of Headlines
  5. Highlights of the Recent Gordon Conference on X-ray Physics
  6. ERULF Program Facilitates Learning and Real Contributions
  7. New and Improved Capabilities on BLs 1-4, 9-3 and 11-2
  8. Upcoming Workshops and Users' Meeting Deadlines
  9. User Research Administration Announcements
  10. Job Opportunities at SSRL

1.  Science Highlights — A New Approach to 3D Structures of Macromolecules Utilizing Single Molecule Diffraction Images
     (contact: John Miao, miao@ssrl.slac.stanford.edu)

X-ray crystallography is currently the primary methodology to determine the 3D structure of macromolecules at or near atomic resolution. However, somewhere around 20-40% of protein molecules, including most of the important membrane proteins, are difficult or impossible to crystallize (and this can also be the case with other nanostructured materials). With the prospects of the LCLS X-ray free electron laser (X-FEL) becoming a reality in the next 5 years, a completely new approach to molecular imaging will become feasible. In a recent publication in Proc. Natl. Acad. Sci. USA, John Miao (SSRL), David Sayre (SUNY, Stony Brook) and Keith Hodgson (SSRL/Stanford) showed through simulations that a high resolution structure can be obtained from multiple single molecule diffraction images each generated by a femtosecond LCLS X-ray pulse. The phase problem can be solved by using an approach known as oversampling due to the continuous nature of the diffraction image (as distinct from a Bragg diffraction pattern which samples the molecular transform at a discrete frequency). This approach and phasing method does not require any ab initio information about the molecule, does not require an extended, ordered lattice array and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. The approach could provide a major new opportunity for the high resolution 3D structure determination of single biomolecules and other non-crystalline materials.

Follow-up commentaries on this article (PNAS 98, 6641 (2001)) have appeared in PNAS (June 5, 2001, Vol. 98, Issue 12, p. 6535), Nature Biotechnology (August 21, 2001, Vol. 19 Number 8, p. 739) and BioCentury, The Bernstein Report on Biobusiness (June 11, 2001, p. A6).

More information regarding this research can be found at:

2.  SSRL Proposal Review Panel Holds 51st Meeting
    (contact: Cathy Knotts, knotts@ssrl.slac.stanford.edu)

The SSRL Proposal Review Panel (PRP) held its 51st meeting on August 10-11, 2001. The PRP plays a key role in the peer-reviewed proposal process as ratings assigned by the PRP are used to determine beam time allocations. It also provides strategic advice and guidance on SSRL's programs and longer range planning. During this meeting, Keith Hodgson gave an overview of the SSRL scientific program and strategic issues for consideration by the PRP. Cathy Knotts gave a presentation on user operations. The PRP subpanels reviewed 57 new proposals and considered a number of proposal extension requests. An NIH NCRR SMB Advisory Committee Meeting was also held on Friday afternoon. On Saturday, the PRP conducted their annual review of participating research teams. In his closing remarks, PRP Chair Russ Chianelli (UTEP) recognized the good work being conducted at SSRL, particularly the timely response to the wiggler failure in February and keeping the SPEAR3 project on time and on budget.

3.  Agreement between SASE-FEL Experimental Results and Photoinjector-to-FEL Simulation Codes Confirmed
    (contact: Max Cornacchia, cornacchia@ssrl.slac.stanford.edu)

A meeting to review and discuss the experimental results and the physics of the VISA Free-Electron Laser experiment (reported in a previous Headline News) was held at SSRL on Thursday, August 9, 2001. The measurements of saturation, gain above 107 and gain length of the order of 19 cm were repeated and experimentally confirmed. A study was made of the computer simulation of the electron beam generation and transport, as well as of the SASE process, in the VISA experiment. Using the particle distribution created by the PARMELA and ELEGANT codes the team has been able to reproduce the measured FEL radiation intensity accurately and without any free parameters. This is the first time that such remarkable agreement between SASE-FEL experimental results and photoinjector-to-FEL simulation codes has been obtained.

These results are important because they increase confidence in the SASE-FEL theoretical description and to the validity of the predictions of the computer codes used to simulate the LCLS performance. More studies are required with regard to the understanding of the measured spectrum of the radiation, where some difference between the measurements and the simulations have been observed. A large number of spectra have been taken at different positions along the undulator and at different gain levels and these will be analyzed in the near future.

More information on the VISA experiment can be found at: http://www-ssrl.slac.stanford.edu/VISA/

4.  Marking the One-Year Anniversary of Headlines

Some of you may have noticed that we quietly marked the one-year anniversary of the SSRL Headlines with a change in the volume number last month. Our hope is that we are providing information that is both interesting and useful from a practical standpoint. In response to your suggestions, we have added several standing agenda items including the scientific highlight, User Research Administration Announcements and a link to job opportunities at SSRL. Previous editions have included information about beam line capabilities and development, meeting announcements and summaries, SPEAR3 updates and new scientific program initiatives and collaborations, etc. We welcome further suggestions about topics that you would like to see covered in the Headlines and want to highlight the exciting science you have published based on work done at SSRL.

The End of Run Summary is another forum we use for collecting input about your scientific results and how well we are meeting expectations for successful data collection at a synchrotron radiation source. We strongly encourage you to complete an End of Run Summary after each data collection trip to SSRL. We do read them and either try to keep up the good work or fix what's broken.

5.  Highlights of the Recent Gordon Conference on X-ray Physics
     (contacts: Sean Brennan, bren@ssrl.slac.stanford.edu, Jo Stöhr, Stohr@ssrl.slac.stanford.edu)

Several members of the SSRL scientific staff attended the Gordon Research Conference on X-ray Physics held at Connecticut College in New London CT during the last week of July. Many of the talks centered on science which takes advantage of coherent x-rays or ultra-short x-ray pulses. Gerd Materlik presented the TESLA x-ray free-electron laser (XFEL) project proposed at DESY in Germany and Jo Stöhr presented the history of the XFEL projects in the U.S. leading to LCLS at SLAC. Other sessions included talks by Janos Hajdu on single molecule diffraction using single FEL x-ray pulses. There was also a session on ultra-fast x-ray diffraction, followed by an informal afternoon meeting where the Sub-Picosecond Photon Source (SPPS) at SLAC was described. SPPS uses an undulator at the end of the SLAC linac and can serve as a test bed for LCLS through studies of electron beam compression, synchronization of electron and x-ray pulses, and ultra-fast pump-probe x-ray experiments. The response of the participants to SPPS was very positive and several scientists from Europe and the US expressed their interest to participate. The focus of the research presented at the conference made it clear that many of the participants are eager to take advantage of both the SPPS and LCLS sources.

6.  ERULF Program Facilitates Learning and Real Contributions

Previously known as the SISE program, the summer undergraduate internships are now called Energy Research Undergraduate Laboratory Fellowships (ERULF). Much of the mission and values of the 30-year old SISE program have been incorporated into the new program. ERULF remains a lecture and research participation program for undergraduate students who are traditionally underrepresented in science, such as women, and some minority and low income groups.

This summer SSRL hosted a great group of young people who accomplished a lot during their eight-week internships here. SSRL's macromolecular crystallography group took on three ERULF students. Tim McPhillips and Ana Gonzalez worked with Preeti Shanbhag to develop a "crystallographic calculator" application in tcl/tk that will significantly simplify several important data collection decisions. With mentoring from Aina Cohen and Paul Ellis, Nancy Fathali and Rajnesh Narayan worked on the sequencing, model building and refinement of an enzyme critical for valine catabolism - 3-hydroxyisobutyrate dehydrogenase (HIBADH). Lindsay Hopkins was assigned to the Beam Line Development group to help John Bagnasco and Doug Van Campen design, build and test several circuits for eventual use in a constant temperature water feedback equipment. Under the mentorship of Katharina Baur, a member of the Experimental Systems and Research Department (ESRD), Pablo Goldenzweig contributed in exploring the feasibility of total external x-ray fluorescence spectroscopy (TXRF) on silicon wafers directly beneath an ultra pure water layer. Working with Matthew Latimer, Dan Durkin and Allyson Soo Hoo, Tim Cheers created a java-script web page of XAS utilities including an energy-to-k-space calculator with an interactive periodic table and a monochromator angle/energy/wavelength calculator. Under the tutorship of staff accelerator physicist, Jeff Corbett, Sabrina Turner worked on the development of a user interface for the SPEAR orbit control system. Finally, John Castro worked with staff scientist Roman Tatchyn on a project to develop practical techniques for generating electron pulses in the atto-second range.

We wish these students the best of luck and hope that their experience at SSRL this summer proves to be a positive influence as they pursue their varied career goals.

7.  New and Improved Capabilities on BLs 1-4, 9-3 and 11-2
    (contacts: John Pople, pople@ssrl.slac.stanford.edu for 1-4, Matthew Latimer, latimer@ssrl.slac.stanford.edu for 9-3, John Barger, bargar@ssrl.slac.stanford.edu for 11-2)

A recently recommissioned small angle x-ray scattering (SAXS) facility on Beam Line 1-4 is available for general user operations. BL1-4 provides ~1010 photons/sec flux at a fixed wavelength of 0.1488 nm, and is intended for SAXS (or WAXS) materials science studies. The beam is independently focused in vertical and horizontal planes to provide a small spot size (500 x 300 microns h:v) and allows superstructures to be probed to a minimum q of 0.055 nm-1. A variety of sample environments allow solid or liquid samples to be studied at temperatures from ambient to 450 °C in an inert atmosphere, including a tensile testing device in which solid samples can be subjected in situ to uniaxial deformations from 0.05-1000 mm min-1 at temperatures from ambient to 120 °C. A CCD-based area detector provides rapid (25 ms) 2-dimensional 12-bit diffraction data - ideal for time resolved studies.

The biological XAS station on BL9-3 is undergoing some upgrades during the current summer shutdown. Specifically, the M0 mirror will be polished and receive a new coating. The monochromator will also be replaced by a liquid nitrogen-cooled one that will allow the beam line to run at higher energies and at full flux. Due to commissioning of these new optics, BL9-3 will likely not be available for general user scheduling until late January/early February 2002.

SSRL's newest high-flux XAS beam line to support molecular environmental science (MES) research (BL11-2) will be in user commissioning mode for much of November and December, with a transition to general user operations in January. BL11-2 currently provides approximately 10 times more flux (at ca. 10 keV) than SSRL beam lines commonly used for MES research and accesses the energy range 5-38 keV. In addition, BL11-2 has been optimized for experiments on radiological samples. The hutch contains a permanent secondary lining and ventilation control system and continuous air monitors. A radiological sample storage and inventory room is connected directly to the experimental hutch. The beam line has a high throughput, 30-element Ge detector equipped with digital signal processors for use on compositionally heterogeneous and dilute natural samples (see also www-ssrl.slac.stanford.edu/mes/BL_11_update.htm).

8.  Upcoming Workshops and Users' Meeting Deadlines
     (contact: Cathy Knotts, knotts@ssrl.slac.stanford.edu)

Three workshops have been planned in conjunction with the upcoming SSRL Users' Meeting. These workshops will be held concurrently on Wednesday, October 17.

1. Thin Film Scattering

2. Metrology with Sub-Picosecond X-ray Pulses

3. On the Roles of XAS and SAXS in Structural Genomics/Proteomics

Several important deadlines for SSRL's annual Users' Meeting on October 18-19 are fast approaching:

FYI - Other program information for the users' meeting can be found at the SSRL website: http://www-ssrl.slac. stanford.edu/conferences/ssrl28/ Dinner on October 18th will be a western-theme barbecue, so don't forget to wear your cowboy hats and boots!

9.  User Research Administration Announcements
     (contacts: Cathy Knotts, knotts@slac.stanford.edu, Lisa Dunn, lisa@ssrl.slac.stanford.edu)

The deadline for Macromolecular Crystallography Beam Time Requests covering November 2001-February 28, 2002 is Friday, August 31. Spokespersons with proposals eligible to receive beam time should have received an email message last week inviting them to submit their requests via the web at: http://smb.slac. stanford.edu/admin/form_bio_btrf.html

10.  SSRL Job Opportunities
    (contact: Rochelle Roberts, rroberts@slac.stanford.edu)

SSRL currently has positions available for mechanical, electronic and beam line engineers, technicians and administrative staff. More information is available at the following web site: http://www-ssrl.slac.stanford.edu/jobs.html

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: http://www-ssrl.slac.stanford.edu/

You can subscribe or remove your name from the distribution list by sending a brief email with your request to Lisa Dunn, editor, at lisa@ssrl.slac.stanford.edu.


Last Updated: 16 AUG 2001
Content Owner: L. Dunn
Page Editor: L. Dunn