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ALSNews Vol. 277 Print
Wednesday, 27 June 2007 00:00


First direct evidence of Dirac fermions in graphite

Structure of the complete 70S ribosome at 3.7 Å resolution

SAXS/WAXS beamline looks up close and far away

Peter Denes joins ALS as Engineering Deputy

The ALS experiences another safe and successful shutdown

ALS user Byron Freelon first recipient of the Morehouse Prize

The ALS Communications Group gets the word out

2007 ALS Users' Meeting

July 15 deadline for general user proposal submissions

General user proposal scores posted online

User Services Group Leader sought

News Links

Bay Area partnership to host DOE Bioscience Center

Future light: A look ahead with Roger Falcone

X-ray transparency

Demolition makes way for new ALS building

In nature, proteins sweep up nanoparticles

House Appropriations Committee backs full FY 2008 DOE science request




The ALS shut down on Monday, May 14, 2007, for planned installations and maintenance. User operations resumed on June 20, 2007.

For the user runs from
June 20–25:

Beam reliability*: 88.7%

Completion**: 88.7%

*Time delivered/time scheduled
**Percent of scheduled beam delivered without interruption

NOTE: Owing to a multiday data-archiver outage, these data are based on careful approximation—not on the usual (relatively precise)
directly logged data. This approximation should be reliable within ±1%.

Scheduled interruptions for the completion of Building 10 deconstruction were observed. All lost time resulted from problems with the injection system (mostly inefficient injection).

Questions about beam reliability should be sent to Dave Richardson ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

Requests for special operations use of the "scrubbing" shift should be sent to Rick Bloemhard ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it , x4738) by 1:00 p.m. Friday.

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Julie McCullough
Lori Tamura
Liz Moxon

Greg Vierra

LBNL/PUB-948 (2007)

This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Disclaimer.

First direct evidence of Dirac fermions in graphite

Contact: Alessandra Lanzara, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

The recent surge of interest in the electronic properties of graphene—that is, isolated layers of graphite just one atomic layer thick—has largely been driven by the discovery that electron mobility in graphene is ten times higher than in commercial-grade silicon, raising the possibility of high-efficiency, low-power, carbon-based electronics. Scientists attribute graphene's surprising current capacity (as well as a number of even stranger phenomena) to the presence of charge carriers that behave as if they are massless, "relativistic" quasiparticles called Dirac fermions. Harnessing these quasiparticles in real-world carbon-based devices, however, requires a deeper knowledge of their behavior under less-than-ideal circumstances, such as around defects, at edges, or in three dimensions—in other words, in graphite. At the ALS, a team of researchers using angle-resolved photoemission spectroscopy (ARPES) has now produced the first direct evidence of massless Dirac fermions in graphite coexisting with quasiparticles of finite effective mass and defect-induced localized states. Read more...

Dirac Fermions in Graphite

Publication about this research: S.Y. Zhou, G.-H. Gweon, J. Graf, A.V. Federov, C.D. Spataru, R.D. Diehl, Y. Kopelevich, D.-H. Lee, S.G. Louie, and A. Lanzara, "First direct observation of Dirac fermions in graphite," Nature Physics 2, 595 (2006).

Structure of the Complete 70S Ribosome at 3.7 Å Resolution

Contact: Harry Noller, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Ribosomes are RNA-based protein factories found in all living cells, responsible for translating the genetic information encoded in messenger RNA (mRNA) into proteins. The first x-ray structures of the complete 70S ribosome were determined in 1999 at 7.8 Å and in 2001 at 5.5 Å, using diffraction data collected at ALS Beamline 5.0.2. These structures showed how the ribosomal RNA and the more than 50 ribosomal proteins are organized to form the structure of the complete ribosome and the positions of the mRNA and transfer RNAs (tRNAs) in the ribosome. Now, using data collected at ALS Beamline 12.3.1, researchers from the University of California, Santa Cruz, have solved the structure of a Thermus thermophilus 70S ribosome functional complex at 3.7 Å resolution. Because of the large cell dimensions of ribosome crystals, they diffract weakly, and spots are crowded close together in the diffraction patterns. Consequently, the high-flux beams, sensitive large-area detectors, and well-focused, compact beam cross sections available at the ALS all played a crucial role in this work. Research in this area may lead to novel antibiotics targeting bacterial ribosomes that have developed resistance to current drugs. Read more...

Protein Machines

Publication about this research: A. Korostelev, S. Trakhanov, M. Laurberg, and H. Noller, "Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements," Cell 126, 1065 (2006).

SAXS/WAXS beamline looks up close and far away

Contacts: This e-mail address is being protected from spambots. You need JavaScript enabled to view it and This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Beamline 7.3.3 has been transformed from an x-ray microdiffraction facility into a simultaneous small-angle and wide-angle x-ray scattering (SAXS/WAXS) beamline, the only one of its kind at the ALS. The q-range for the SAXS/WAXS setup is from 0.004 Å–1 to 8.7 Å–1. The x-ray energy in regular operation mode is fixed at 10 keV and yields an x-ray flux of 1.7 x 1012 photons/s at the sample position. The beamline can accommodate a wide variety of samples, stages, and environments. This dual-detector endstation allows researchers to nondestructively examine proteins, protein complexes, and other large molecules in solution. These molecules can exist in a variety of states, and SAXS can follow the changes in shape from one state to another, impossible with traditional crystallography. The beamline can also accommodate research on polymer systems and liquid crystals, including determining nanophase structure and subtle structural changes, detectable as a function of temperature. As the SAXS/WAXS detectors probe the samples, they work in concert with other measuring devices. For example, a tensile stage stretches polymer materials, and multiple images report the changes in the structure. The beamline also provides a differential scanning calorimeter (DSC) stage for users, which can change sample temperature from about –200°C to +600°C, allowing precise monitoring of the morphology of the sample by taking images close to phase transitions.

SAXS WAXS Beamline and staff

SAXS/WAXS staff at beamline. Stage for placement of samples, far left; SAXS detector left, WAXS detector, far right. Staff, TOP, left to right: Howard Padmore, Wit Bras, Richard Celestre, Matthew Church, Alexander Hexemer; BOTTOM: Eliot Gann, Richard Kirian, Bruce Rude. (Not pictured: James Glossinger.)

The SAXS section of the beamline achieved first light last February, and WAXS achieved first light this month. The beamline's first experiment, in collaboration with Robert Birgeneau, UC Berkeley Chancellor and Professor of Physics, is already yielding results. The sample was a thermotropic liquid crystal that changed phases from isotropic to nematic to smectic as a function of temperature. The SAXS data were taken in situ while the sample was cooled from 80°C to 45°C. In addition to proteins and polymer systems, a third SAXS/WAXS research focus will be earth sciences, which, for example, will be concerned with the shape and growth process of nanoparticles in solution.

Peter Denes joins ALS as Engineering Deputy

Peter Denes, ALS Engineering DeputyPeter Denes, Berkeley Lab Engineering Division Deputy, is in the process of making the move over to the ALS as our Deputy for Engineering. "Peter has been a leader within Engineering and in detector development at the Lab, and we're now looking forward to his playing a larger role in these efforts for the ALS," said Roger Falcone, ALS Division Director.

In the Engineering Division, Denes was responsible for electronics, software, and instrumentation engineering and brings this expertise to his new position. Peter's dedicated and on-site presence will provide tighter coupling between the Engineering Division and the ALS, more integrated management of engineering resources within the ALS, and a long-range focus as the ALS looks to its future as well as to the next generation light source. A primary component of his job will be the ALS Detector Program. "This program is a virtual umbrella that brings together talent from the ALS, Engineering, and Physics to focus on the detector needs of the ALS," stated Peter. "Detectors can be purchased from manufacturers, but the unique requirements of the ALS beamlines often require unique detectors which are not available commercially." This new program aims to help users with existing detectors as well as to develop novel detectors that will improve ALS science. As the detector program gets off the ground, Peter also anticipates incorporating a postdoc program where new engineers can be mentored and trained. This detector program anticipates the Department of Energy's Office of Basic Energy Sciences (BES) detector and accelerator R&D initiative that is slated for FY 2008 and will enhance Berkeley Lab's ability to do research in this area.

Look for the detector workshop at the ALS Users' Meeting in October—"New Opportunities for Science with Advanced Detectors"—where Peter and Howard Padmore will provide an overview of the new program and user input will be sought on improvements and developments.

The ALS experiences another safe and successful shutdown

Contact: Steve Rossi, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Thanks to our dedicated and hard-working staff, we have another safe and successful shutdown behind us (the ALS resumed operation on June 20). Accelerator and beamline work accomplished during that time included front-end modifications at Beamline 4.0 to accommodate the new MERLIN beamline, installation of errant-photon-beam interlock features in Sector 4, a swap-out of the ailing superbend magnet in Sector 4, a full survey and alignment of the storage ring, continued commissioning of our new booster power supply system, and a myriad of other work. While our staff worked on technical projects, we also had major construction going on in the building. We accomplished phase one of a four-year effort to seismically retrofit the historic ALS dome. Coordination of this work with our own shutdown efforts proved challenging as it restricted access and was very noisy.

Before seismic retrofit

After seismic retrofit

Top: Before retrofit. Bottom: After retrofit. View additional images of the spring 2007 shutdown here.

The shutdown was also scheduled to coincide with the demolition of Building 10 because ofvibration concerns from the heavy work. The contractor quickly demolished the WWII-era building once the abatement of hazardous materials was completed. The site will remain a dirt pad until the beginning of construction on the User Support Building, scheduled for March 2008. Berkeley Lab has finalized a contract with Overaa Construction to complete the design work and construct this new user facility, and occupancy is anticipated for fall 2009.

ALS User Byron Freelon first recipient of the Morehouse Prize

Byron FreelonByron Freelon has been awarded the first Morehouse Prize by the National Society of Black Physicists (NSBP), which recognizes graduates of historically black colleges and universities who have shown considerable promise as physics researchers and teachers. The prize, awarded for his work in x-ray Raman scattering on artificial superconducting materials, and his strong support of NSBP student programs, includes a cash award and a travel grant to give a colloquium at Morehouse College. Freelon accepted the award at Morehouse College on April 5 and gave a talk entitled "Probing High-Temperature Superconductors with Layers and Light." Freelon attended Prairie View A&M University and received a Ph.D. in physics from the University of Minnesota in 2001. As a Berkeley Lab postdoc, he performed studies on high-temperature superconductors and developed a molecular beam epitaxy chamber at ALS Beamline 7.0.1. He is presently a research scientist in the UC Berkeley group led by Chancellor Robert Birgeneau exploring the behavior of high-temperature superconductors and liquid crystal systems using x-ray scattering. The Morehouse Physics Prize was established through a financial gift by Dr. and Mrs. Walter Massey. Dr. Massey is the current President of Morehouse College and a former Director of the National Science Foundation.

The ALS Communications Group gets the word out

Contact: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

For the last several months, ALSNews has been featuring user support groups, putting the names to the faces, and giving you an idea of what they do and who to call when you need assistance. Now we turn the spotlight on ourselves, the Communications Group. Our jobs are challenging and fun. We communicate about the science, people, and events of the ALS user community to scientists of all disciplines, students, teachers, the local community, Berkeley Lab staff, members of Congress, Department of Energy program managers, and people who just love science. So if you have recently published in a high-profile journal, need a cover, have a newsworthy item for ALSNews,, or a Lab press release, contact us at This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

Communications Group

Clockwise from top: Lori Tamura (writer/editor), Art Robinson (writer/editor), Greg Vierra (illustrator/designer), Julie McCullough (writer/editor), and Liz Moxon (writer/editor, team leader).

Here's how we get the word out:

  • ALS science highlights. We work with the users to create profiles of research conducted at the ALS. These highlights are presented in several ways: through the Activity Report, ALSNews, the ALS Web site, posters, and the ALS Science Bulletin, which is emailed to the stakeholders at the Department of Energy and other government agencies.
  • ALSNews. This web-based monthly e-newsletter turns the spotlight on what's going on around the facility (beamline upgrades, user services, safety updates), in the news (budget updates), and within the user community (awards and recognition).
  • ALS Web site. We provide the latest information for users and staff on ALS scientific meetings, conferences, and events.
  • Annual Activity Report. This tangible record is where we formally document our high-profile research, equipment and facility developments, and special events. Go here for a copy of the latest report.
  • Posters, displays, technical illustrations, and graphic design. A picture can be worth a thousand words. We work with the researchers to create original illustrations and revise and enhance existing ones. We provide art for print and web media, user events, conferences, and open houses.
  • Educational outreach. We provide tours and hands-on demonstrations for students and the general public.

2007 ALS Users’ Meeting

Contact: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

2007 ALS Users' MeetingGeneral information, meeting deadlines, online registration, and accommodations information for this year's ALS Users' Meeting, to be held at Berkeley Lab October 4-6, is now aviable on the Users' Meeting Web site. The early registration deadline is Saturday, September 15.

Abstract submission. The deadline for abstract submissions for oral presentations during the ALS Scientific Highlights session is Wednesday, August 15. The online submission Web page will be posted shortly.

Workshops. This year, 12 workshops, including several joint ALS-Molecular Foundry workshops (indicated with an *), will follow the end of the formal Users' Meeting program, beginning Friday afternoon (October 5) and continuing through Saturday (October 6). Workshop topics and respective organizers are as follows:

  • Ambient Pressure Photoelectron Spectroscopy (Hendrik Bluhm, Simon Mun, and Miquel Salmeron)
  • Advanced X-Ray Optics Metrology for Nanofocusing and Coherence Preservation (Valeriy Yashchuk and Kenneth Goldberg)
  • Atmospheric Aerosols (Mary Gilles)
  • Beyond Top-Off: Opportunities for Improved ALS Performance (David Robin and Christoph Steier)
  • Design and Function of Protein Nanostructures* (Ronald Zuckermann and Petrus Zwart)
  • Nanomagnetism* (Peter Fischer, Jeffrey Neaton, Holger Schmidt, and Tolek Tyliszczak)
  • New Infrared Science Opportunities at the ALS (Michael Martin, Peter Nico, and Fernando Sannibale)
  • New Opportunities for Science with Advanced Detectors (Peter Denes and Howard Padmore)
  • Photon-In/Photon-Out Inelastic X-Ray Scattering in Renewable Energy Science (Jinghua Guo and Franz Himpsel)
  • Polymer Science* (Harald Ade, Alexander Hexemer, and Bumjoon Kim)
  • Soft and Hard X-Ray Tomography (Gerry McDermott, Alastair MacDowell, and Dula Parkinson)
  • Theory at the ALS (Arun Bansil, Dung Hai Lee, and Zahid Hussain)

July 15 deadline for general user proposal submissions

Contact: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

The User Services Office is accepting general user proposals from scientists who wish to conduct research in the general sciences at the ALS during the running period from January through June 2008. The deadline is July 15, 2007. (This deadline does not apply to protein crystallography proposals, which have a separate process and schedule.) To submit a new proposal, fill out the ALS General User Proposal and Request for Beam Time form. For further information on proposals, go to the General User Proposals Web page.

General user proposal scores posted online

Contact: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

The general user beam time allocation process for the running period from July through December 2007 is complete for the general sciences. The number of eight-hour shifts requested was 5389, of which 3130 shifts (58%) were allocated. For more detailed results, including beamline score distributions and cutoff scores, go to General User Proposal Scores: General Sciences. Beam-time requests for general user experiments are reviewed twice each year. A Proposal Study Panel (PSP) evaluates each proposal, providing the basis for granting beam time. The PSP is made up of ten scientists from a variety of synchrotron scientific disciplines. There is a separate PSP that reviews the crystallography proposals six times each year. More information on the PSP and the general user proposal review process is available on the General User Proposals Web page.

User Services Group Leader sought

The ALS is looking for a User Services Group Leader. This individual is responsible for user services, experiment setup coordination, and communications. As a Group Leader, this person will be a member of the Strategic Management Team (which directs the strategic scientific course of the ALS) and helps determine the ALS long-range running schedule. Because commitment to safe and reliable operation at the facility is critical, the incumbent will assist in formulating and implementing key ALS user safety policies. To be successful, the Group Leader will have a Ph.D. degree or equivalent in the physical or biosciences with extensive experience in applications of synchrotron radiation science. This person must also have substantial leadership experience in planning, development, and management of a scientific user program. Job details and application instructions are at Click "Search" and enter 20716 in the search field.