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Berkeley Lab Currents

February 26, 1999


Computer Models Reveal New Clues To Protein Folding Patterns

By Paul Preuss

In a few seconds an origami artist can fold a sheet of paper into a bird, flower, pagoda or other intricate shape. In much less time a string of amino acids can fold itself into a protein, the kind of molecule that comes in many thousands of complex shapes and does most of the work of life. Origami can be taught, but no one knows how proteins fold themselves so quickly into the same shapes virtually every time.

Now, computer models devised by Daniel Rokhsar and his colleague Vijay Pande of the Physical Biosciences Division, applying the parallel-processing capabilities of the Cray T3E supercomputer at NERSC, have revealed unexpected regularities in the pathways of protein-like structures.

"Protein chains all fold differently -- even proteins of the same kind fold into their final state by sampling many different conformations -- because they start from different initial states," says Rokhsar. "Somehow they start from an unfolded state and achieve the folded structure quickly, reliably and reversibly."

For any protein there is a "native state conformation," a thermodynamically most-stable structure. These structures determine everything from the texture of hair to the catalytic coupling and uncoupling of innumerable enzymes essential to keep life's processes humming. Misfolded proteins can cause disease; in humans, for example, sickle-cell disease is caused by the misfolding of hemoglobin.

Proteins are assembled one amino-acid residue at a time, in the order specified by the gene for that protein (a length of DNA). Although experimenters have begun to relate specific sequences to protein families that share folding patterns, how the order of amino acids directs pathways to a protein's distinctively folded structure is not yet understood.

To demonstrate the magnitude of the challenge, Rokhsar suggests contemplating a ball on the end of a stick, a stand-in for a single amino acid residue. "Let's limit to five the directions the next stick-and-ball can extend -- right, left, up, down, or straight ahead," says Rokhsar. "If there are five links in the chain, that's five to the fifth ways the chain could fold -- 3,125 possibilities. If there are a hundred links in the chain (not unusual for a protein) there would be something like 10 to the 30th possibilities. If you tried them randomly, even a trillion times a second, it would take longer than the age of the universe to get the right structure."

Rokhsar, who is head of the Computational and Theoretical Biology Department in the Physical Biosciences Division and a professor of physics at UC Berkeley, and Pande, a Miller Postdoctoral Fellow in the Physics Department, approached the protein-folding problem by designing a model heteropolymer of 48 units whose properties define a stable "native structure" -- a compact lattice in three dimensions with each bend at a right angle, resembling a jungle gym made of Tinker Toys.

Using NERSC's Cray T3E, Rokhsar and Pande repeatedly unfolded the model by raising the simulated temperature, then lowered the temperature and watched it refold itself. For each folding sequence they separately tracked the position of each of the 48 "mers," the units equivalent to a protein's amino acid residues.

Even with a model far less complex than most real proteins, the number of possible initial conformations is astronomically large, and each path to stability is virtually unique. Typically some three-quarters of a million iterations were required before the model polymer stabilized.

Remarkably, Rokhsar and Pande discovered common features among the numerous folding pathways. At first the unfolded polymers fluctuated wildly through several hundred thousand configurations; then they suddenly settled into a partially folded intermediate state, in which a stable core structure was accompanied by flailing loops and dangling ends. After another couple of hundred thousand iterations, the polymer abruptly locked into its native state.

These sudden transitions are evocative of phase changes, like the changes from a gas to a liquid to a solid. There are distinct classes of intermediate states for the model polymer, however, which correspond to different groups of units that temporarily achieve stability during the intermediate phase. Each class of intermediate states represents a set of related pathways from the unfolded to the native state.

Separate classes of intermediate states were also seen when Rokhsar and Pande repeated their simulations with model polymers of 64 and 80 mers. These are closely analogous to partially unfolded states (PUFs) which have been observed in real proteins, as well as to intermediate states inferred to exist in other real proteins. It is likely that knowledge of PUFs, plus inferences about similar phases from other protein studies, can predict transition states of some kinds of proteins in the real world.

The discovery of well-defined transition states in model-polymer folding has important implications for the development of a general theory of protein folding. Verifying these results using models with atomistic detail is the next important step.

Rokhsar and Pande report their findings in the Feb. 16, 1999 Proceedings of the National Academy of Sciences.

A spectacular movie illustrating their lattice model of protein folding can be seen on the web at http://

Photo: Daniel Rokhsar (left) and and Vijay Pande of Physical Biosciences have created animated models of protein folding patterns. (XBD9902-00331)


Drell Praises National Labs In Report to UC Regents

By Don Johnston

Science and technology programs at the three national laboratories managed by the University of California continue to produce work of "very high quality" that ranges from "excellent to outstanding," according to the annual report by the UC President's Council on the National Laboratories. Sid Drell, chairman of the Council, presented the report to UC Regents at their meeting in San Francisco on February 18.

Each year the 20-member Council, made up of representatives from academia, government and private industry, reviews science and technology efforts as well as management and operations at Berkeley Lab, Los Alamos and Lawrence Livermore National Laboratories.

Drell noted that many of the greatest challenges faced by the laboratories are not so much solving scientific problems as bringing "strong and consistent management" to large, complex and costly projects.

"The labs realize that quality science must be tightly coupled to sound business and management skills in order to succeed in the current budget situation," he said. "The council is committed to reviewing and advising the labs as they strive for a superior project management that matches their technical expertise."

Projects Drell mentioned included the tri-lab Joint Genome Institute (JGI), Berkeley Lab's Advanced Light Source (ALS), the Accelerated Strategic Computing Initiative at Los Alamos and Livermore, the National Ignition Facility at Livermore, and the Los Alamos Dual-Axis Radiographic Hydrodynamic Test Facility.

Referring to the Joint Genome Institute, Drell noted that the "continuing attention of management" at the three labs has paid off for the genome project, with each of the three labs exceeding their sequencing goals for the year. "These were ambitious goals that required a rapid build-up in throughput, and they were accomplished with an accuracy well above defined genome community standards," Drell said. "It's exciting to report that, as of October 1998, the Joint Genome Institute ranks third in the world in sequencing output.

"But, even with this admirable progress, the Joint Genome Institute will have to continue a steep ramp-up of its sequencing production in order to meet accelerated national goals, which call for completion of the entire human sequence by the end of 2003," he said, adding that the Council will monitor JGI's efforts to have a leadership team "on board and running soon."

The ALS was cited as an example of a project that has "reaped significant rewards" from "leadership and organizational change" and closer collaboration with UC Berkeley. The Berkeley Lab facility now boasts a "burgeoning user base that is producing promising scientific advancements," Drell said. "The Advanced Light Source is now healthy."

Issues of sound management "are nowhere more critical" than in the national security programs at Livermore and Los Alamos laboratories, especially the Stockpile Stewardship and Management Program, he said, briefly describing the Accelerated Strategic Computing Initiative, the National Ignition Facility and the Dual-Axis Radiographic Hydrodynamic Test Facility.

"Each of these is a critical link in the stewardship program, and thus our future confidence in the remaining stockpile under a comprehensive test ban," Drell said.

Drell discussed other programs involved in the surveillance and diagnosis of the nuclear stockpile, emphasizing their importance to the laboratory directors' ability to certify the safety and reliability of the stockpile to President Clinton in an era of no nuclear testing. "This is a major responsibility and one that strongly relies on the success of the University of California, its reputation and its personnel policies in attracting and retaining top quality scientists and engineers."

Addressing environmental, safety and health issues, Drell said all three laboratories continue to strive "to implement integrated safety management throughout their institutions and to drive accountable performance from the lab director down through the line to each and every employee."

Drell expressed the council's concern that additional restriction might be placed on Laboratory Directed Research and Development (LDRD) funds used to finance competitively awarded research and development projects. Money is currently allocated at the lab directors' discretion, with some DOE restrictions, he explained. "It's important that these funds remain at the laboratories and be used to stimulate their long-term health and growth. The council will advise against removal of these funds from the control and use by the lab directors."

Examples Drell cited of research projects that had benefited from LDRD funding include adaptive optics, the search for dark matter, sensors for detecting chemical weapons agents, supernova cosmology and universe expansion, and proton radiography. "Some funds go to basic science projects, some to high-risk efforts with the potential of high payoff," he said. "All are awarded to stimulate innovative and productive science."

Drell updated regents on Livermore's PEREGRINE project. "This computer modeling technique once used to develop nuclear weapons and now used to vastly improve the efficacy of cancer radiation therapies is progressing toward commercialization."

Noting there were some new faces on the board of regents, Drell encouraged the regents to "take the opportunity to visit the labs and hear first-hand of the great science that is being done under the banner of the University of California."

At the conclusion of his report, Drell announced his intention to step down as chairman of the UC President's Council on the National Laboratories after six years, saying it was time for someone new to take leadership. "I agreed to stay for five years," he said. "I stayed on one more year. It's time for a change."

Drell strongly emphasized the importance of the University of California's management of the labs. "I hope the Regents will not forget how important it is that an institution of your reputation, traditions and values run these laboratories," he said. "The success of these laboratories in carrying out stockpile stewardship is the key to our being able to accomplish ratification of a comprehensive test ban," Drell said, adding, "What is more, the overall quality of the scientific work in non-national security areas also reflects the high standards of the University of California. I don't believe these laboratories would be anywhere as great as they are without your running them."

Don Johnston is a staff writer for Newsline, published by the Lawrence Livermore National Laboratory.

Photo: Sid Drell, chairman of the UC President's Council on the National Laboratories. (sid_drell.tiff)


Berkeley and Livermore to Collaborate on Fusion Research

By Lynn Yarris

Berkeley Lab has signed a five-year memorandum of agreement with Lawrence Livermore National Laboratory to collaborate as a Heavy-Ion Fusion Virtual National Laboratory (HIF-VNL). Under this agreement, the two labs are proposing an initiative to design and construct a unique particle accelerator that could address many of the critical technological issues concerning the use of heavy ion beams to drive an inertial fusion energy (IFE) reactor. This initiative is called the "Integrated Research Experiment."

While scientists at both laboratories have been working for years on inertial fusion energy, this agreement marks the first time scientists from one laboratory will relocate to another. Initially, six LLNL scientists will be coming to Berkeley Lab. The agreement calls for the HIF-VNL to be directed by the fusion program head within Berkeley Lab's Accelerator and Fusion Research Division (AFRD). Currently, that responsibility belongs to Roger Bangerter, a physicist who has headed inertial fusion research here since 1990, but whose 25 years in the field have included extended stints at Livermore and Los Alamos National Laboratories as well.

"The ultimate goal of the HIF-VNL agreement is to someday build an accelerator for inertial fusion research and development," Bangerter says. "Research from such a facility could one day lead to a reactor capable of producing sufficient energy for commercial purposes."

Fossil fuels are headed for extinction. Projected timetables for when this will happen vary, but the ultimate exhaustion of fossil fuel supplies is a certainty. Alternative energy sources must be found. Arguably, the most promising alternative is fusion, the energy source that lights up the Sun.

Fusion, which takes place when lighter atomic nuclei are combined to form heavier nuclei, releases roughly one million times the energy released by the burning of oil. A fusion power plant would use the nuclei of the two isotopes of hydrogen, deuterium and tritium, both of which are readily obtained and so plentiful as to be virtually inexhaustible. Unlike the burning of oil or other fossil fuels, a fusion reaction does not contribute to global warming. And unlike nuclear fission, fusion cannot sustain an uncontrolled chain reaction, and -- if done right -- does not produce high-level radioactive by-products that must be carefully stored for thousands of years.

In an IFE reactor, beams of energy would set-off or "drive" implosions within pea-sized capsules of fusion fuel that would cause the fuel to be ignited. The fuel burns so quickly it is confined by its own inertia long enough for the reaction to produce energy. It has been the consensus of fusion energy experts, including panelists from the National Academy of Sciences and the 1996 Fusion Energy Sciences Advisory Committee, that the most likely driver in a commercial power plant will be an accelerator of high-powered beams of heavy ions, such as xenon, mercury or cesium.

The use of heavy ion beams to drive inertial fusion reactions poses significant technical challenges. High beam power is traditionally achieved with high currents. Induction linacs, linear accelerators that induce an electromotive force on ions through rapid changes in magnetic field strengths, have proven capable of handling electrons at the required currents (10,000 amperes or more). However, transporting and focusing heavy ions at these currents may be another story, because of "space-charge" forces -- the mutually repulsive forces between so many positively charged ions.

The Integrated Research Experiment (IRE) being proposed under the HIF-VNL agreement is an induction linac that will answer questions abut beam injection, acceleration, pulse compression, final focus and chamber transport, and engineering design for an IFE heavy ion driver. The IRE might also be used to conduct high-density plasma interaction experiments and to address some of the target issues specific to heavy-ion drivers. No facility in the world today offers such capabilities.

Perhaps the most important question of all to be answered is whether or not the use of heavy ion beams to heat fusion targets in a commercial power plant could be done cost-effectively. The HIF-VNL collaborators do not ignore this vital issue. As Bangerter told a reporter for the publication Inside Energy in a recent interview:

"Sometimes when we look at fusion, we focus too much on one-of-a-kind facilities," Bangerter said. "But one of our long-term goals with the HIF-VNL collaboration is to find a way to build IFE reactors that can be mass-produced."


News Digest


Washington Report

DOE News

Eighty-five percent of the Department of Energy's 420 mission-critical computer systems are Y2K compliant, and that figure will rise to 98 percent by the end of March, according to John Gilligan, DOE's chief information officer.

DOE's chief financial officer, Michael Telson, has called a recent General Accounting Office review of the Department's high-risk management system "inaccurate, misleading and unbalanced." Telson says the GAO report's authors "selectively" picked and then presented "out of context" situations at DOE. Furthermore, he says, the GAO report failed to acknowledge management improvements at DOE, leaving readers with the erroneous impression that the Department still has not addressed problems that arose in the 1980s.

Linda Lingle has been named the new principal Deputy Assistant Secretary for Congressional and Intergovernmental Affairs. The appointment was announced by Energy Secretary Bill Richardson who said Lingle will help John Angell, the assistant secretary for congressional and intergovernmental affairs, maintain DOE's relations with Capitol Hill, state and local governments, Indian tribes, and other groups.

COSEPUP Supports Federal Efforts to Evaluate R&D

The Committee on Science, Engineering, and Public Policy (COSEPUP) -- a joint panel of the National Academy of Science (NAS), the National Academy of Engineering, and the Institute of Medicine - has challenged those who argue that the value of federally-funded R&D efforts cannot be evaluated as required by the terms called for in the Government Performance and Results Act (GPRA).

"Both applied and basic research programs can be evaluated meaningfully and on a regular basis," the COSEPUP panel concluded in a report issued on Feb. 17. The trick is to devise the right yardsticks, said the panel chair, Phillip Griffiths, director of the Institute for Advanced Study in Princeton.

In its report, the COSEPUP panel endorsed the use of outside experts as an expanded form of the peer review process that judges individual proposals. These outside experts would look at the quality and relevance of an agency's entire research portfolio. The report also called for a single agency to serve as a focus for research supported by multiple agencies, such as global climate change or information technology. This would help ensure that national goals are being addressed. The report also encouraged agencies to include their role as training centers when presenting their institutional plans.

The COSEPUP report is available online at

Lynn Yarris


Briefing on New Science Education Standards

The State of California's efforts to develop and implement new science education standards for K-12 schools will be discussed by two Berkeley Lab representatives on the standards commission at a "brown bag" briefing on Wednesday, March 3.

All employees are invited to bring their lunch and learn more about "Raising the Bar for Science Education in California" at noon in the Bldg. 50 auditorium.

Rollie Otto, head of the Laboratory's Center for Science and Engineering Education, is consultant and coordinator for building the science education framework under the auspices of the State Department of Education. Eric Norman, a senior scientist in the Nuclear Science Division, is a member of the Science Curriculum Framework and Criteria Committee.

Both will address the policies and issues that surround the exhaustive effort to get a new student curriculum approved by the year 2000 and implemented within five years.

For science standards, the debate over subject matter and teaching approaches has been lively and intense. Otto and Norman will describe those discussions and summarize the current status of the draft standards.

They will also recommend ways in which Berkeley Lab employees can get involved in improving science education in the schools.


AAAS Urges Scientific Community to Fight Data Access Policy Change

By Lynn Yarris

At a press briefing in Washington today the American Association for the Advancement of Science (AAAS), the world's largest interdisciplinary federation of scientists, urged the scientific community to "voice its concerns to Congress and the Administration about potential unintended consequences" of legislation that was inserted into a 4,000 page appropriations bill without debate or public hearings. The Association also recommended that the scientific community ask Congress to hold hearings on H.R. 88, a bill introduced by Rep. George Brown (D-CA) to repeal the legislation.

The legislation came in the form of a mandate that gives unprecedented public access to research data from federally funded projects. Specifically, the mandate is a proposed revision to Circular A-110 from the Office of Management and Budget (OMB). It would require federal agencies to respond to Freedom of Information Act (FOIA) requests for data from federally funded projects at universities, hospitals and other research institutions. Currently, research data that is not already in federal agency files is not subject to FOIA requests.

Despite the good intentions of the legislation, "the devil is in the details" of its scope, timing, and costs, according to Mark Frankel, director of the AAAS Program on Scientific Freedom, Responsibility and Law. In an editorial he wrote for the Feb. 19 issue of the journal Science (which is published by AAAS), Frankel argued that the mandate could threaten human health research and compromise scientists' intellectual property rights. It might also have a dampening effect on industry-university partnerships.

The mandate defines data as "information used by the federal government in developing policy or rules." What does this really mean? Frankel questioned. Will scientists be required to hand over their lab notebooks, tissue cultures, and field notes as data? How long will scientists have to sufficiently analyze their data before being required to make it public? What will be the costs to research institutions and scientists to fulfill these FOIA requests?

Under U.S. law, researchers have a year from the date that results are published to file a patent application. What happens if data are made publicly available through FOIA? AAAS has also raised a concern that the mandate's requirements could be exploited by organizations or businesses that feel threatened by particular research or the policies based on it.

OMB has acknowledged the complexity of the concerns raised and is encouraging the scientific community to respond during a public comment period that ends on April 5. In his editorial for Science, Frankel said the goal for the scientific community for this public comment period should be to help guide the OMB in "developing new rules that won't impede important research." Frankel also said it is important to negotiate the definition of "data" as well as the cost recovery process for institutions covered by the mandate.

Frankel's editorial and the AAAS briefing follow a call for action in a resolution issued by the AAAS Council, the 83-member elected body responsible for establishing the Association's general policies.

--Lynn Yarris


Science News


Looking at the Microworld with X-Ray Eyes

By Paul Preuss

In 1905, one of the papers that brought Albert Einstein international recognition was his explanation of the puzzling photoelectric effect: depending on its frequency, light falling on metal can stimulate the emission of electrons and a flow of electricity. How does it do that?

Light is quantized, Einstein proposed; the energy of the quantum (later named a photon) depends on the frequency of the light, and a quantum of the right energy boosts an electron out of its orbit.

The same phenomenon makes PEEM2, a new photoemission electron microscope recently commissioned at the Advanced Light Source (ALS), a powerful tool for studying materials: their structures, elemental make-up, chemical bonds, the orientation of their molecules, and their magnetic properties.

Focusing light-emitted electrons

X-rays or extreme ultraviolet light produced by the ALS can be tuned to knock copious amounts of electrons out of a sample. PEEM2 focuses those emitted electrons on a phosphor screen, and the visible-light image produced this way is acquired by a charge-coupled-device camera (CCD) with a resolution of 50 to 35 nanometers (billionths of a meter) or better -- ten times better than the resolution of the best optical microscopes.

PEEM2 accepts samples up to 15 millimeters wide and can be fitted with any one of four changeable apertures, from as wide as two millimeters to as narrow as 12 microns. "The narrowest aperture gives the highest resolution," explains Simone Anders, leader of the team in the ALS Experimental Systems Group, headed by Howard Padmore, which designed the microscope. "But there's a trade-off between resolution and electron transmission."

In a photoemission electron microscope, the x-ray spot illuminating the sample is wider than the microscope's field of view, and the resolution is limited only by the focusing system. PEEM2's four electrostatic lenses focus the image at variable magnification. A typical exposure time is several seconds, although the CCD can capture up to four images a second.

Electrons near the edge

PEEM2 combines the traditional strengths of photoemission electron microscopy, including the ability to determine surface topography, with such spectrographic techniques as Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy, which is practical only with synchrotron radiation.

In NEXAFS, an x-ray photon excites an electron orbiting the core of an atom or molecule, causing it to leave its orbit and jump to a higher energy level. The step-like vertical rise in a graph showing the absorption intensity as a function of the energy of the x-ray is called an "edge;" for each electron orbital, the position of the edge differs according to the individual element, chemical bond, or molecular orientation. By tuning radiation to different frequencies, spectrographic information can be derived, which then becomes part of the visual image, revealing just where in the sample certain elements or certain kinds of chemical bonds occur.

Electrons from spinning light

Mounted on beamline, PEEM2 uses light from a bending magnet, which can be masked to emit either linearly polarized light or circularly polarized light (either right or left). Linearly polarized light is useful to determine the orientation of bonds in thin films, for example.

Magnetic regions of a sample exhibit a phenomenon known as circular dichroism, the difference in their absorption of right and left circularly polarized light; a magnetic contrast is visible because of the different interaction of the spin of the radiation with magnetic domains of opposite orientation. With a beam tuned to a characteristic absorption edge of a magnetic material such as cobalt, PEEM2 can look at the surface of a computer disk and distinguish the orientation of its innumerable magnetic bits with high resolution.

"PEEM2 can even distinguish the magnetic properties of individual layers in multilayer structures," says Anders. "Magnetic multilayers may soon be used in magnetic memories, replacing electronic memory chips for various applications."

Electrons can do more

Anders lists other examples of the kind of research pertinent to the future of the electronics industry. "Because it can distinguish between chemical bonds, PEEM2 can map areas of predominately diamond-like bonds versus areas of graphite-like bonds in thin films of amorphous carbon, which are of potential use in flat-panel displays. And because PEEM2 can distinguish molecular orientations, it can be used to examine the mechanisms of polymer alignment." Aligned polymer thin films are important components of liquid crystal displays.

"The strength of PEEM2 is that no other microscope can do all this," Anders says. "That's one of the reasons why the Department of Energy entered into a CRADA [ a Cooperative Research and Development Agreement] with IBM to build and use it at the Advanced Light Source."

Anders and her coworkers, including Joachim Stöhr of IBM, Michael Scheinfein of Arizona State University, and a team of ALS engineers led by Ron Duarte, constructed PEEM2 over a three-year period and have been its principal users. But beginning this month, half the beam-time of the microscope and its beamline will be available to qualified outside users.

Meanwhile, Anders and her colleagues are advancing further toward the high-resolution frontier with a design for an even higher resolution instrument - the PEEM3.

Photo: Simone Anders of the ALS uses the PEEM2 microscope to study the orientation of magnetic domains in a storage device. (sanders.tif)


Be Part of Currents!

Do you have an interesting story or anecdote to tell? Did you or one of your colleagues accomplish something that you think others would like to hear about? Are you working on some interesting research? Do you have a picture you would like published in Currents? If so, please send your suggestions to msfriedlander@ We cannot publish every item submitted, but we will consider all your suggestions.


Around the Lab


DOE to Broaden Peer Review for Use of NERSC Supercomputers

By Jon Bashor

The Department of Energy this week announced a new policy of broader scientific peer review for the use of its largest unclassified scientific computing facility: the National Energy Research Scientific Computing Center (NERSC).

To advance the role of computing in DOE's scientific research programs, the department will also establish a new policy board to help chart the future of the facility.

NERSC, which moved to Berkeley Lab in 1996, is currently home to seven SGI/Cray supercomputers and serves about 2,500 researchers at national laboratories, universities and in industry.

"With the recent announcement of the President's proposed $366 million initiative to boost long-term computational science and information technology, it's important to begin laying a strong foundation for those programs," said Under Secretary of Energy Ernest Moniz. "This new policy for allocating time on our supercomputers will help do just that by using the computers most effectively, as well as making computing a more integral part of how we solve the nation's important scientific problems."

NERSC as national leader in high performance computing

The new policy will help ensure that NERSC becomes a national leader in using high performance computing as a tool for scientific discovery, just as DOE's light sources and particle accelerators are national and international leaders in their respective areas. As proposals are submitted, they will be subjected to peer review to evaluate the quality of science, how well the proposed research is aligned with the mission of DOE's Office of Science, and the readiness of the specific application and applicant to fully utilize the computing resources being requested.

The new policy is also expected to foster "start-up" or special projects that show promise. These are one-time allocations aimed at helping new projects get started, with a goal of applying for more time on NERSC's computers the following fiscal year.

Changing role of supercomputing

"Computing is becoming a new kind of tool for scientific discovery, and is no longer just a simple utility-like service, and it should be managed accordingly," said Berkeley Lab Director Charles V. Shank. "We want to ensure that we're getting the best science out of the facility, so we benchmarked how NERSC is managed vis-à-vis other national user facilities operated by DOE. This change is really part of our efforts to reinvent NERSC to better meet the nation's scientific computing needs."

The new approach combines guidelines from DOE, guidance from a policy board, and peer review by scientists. The change reflects the ever-broadening role of NERSC since it was founded in 1974 to provide computing resources for magnetic fusion research. Since then, the facility has expanded its scope to include high-energy physics, materials science, combustion, computational biology, astrophysics, energy research, chemistry and climate modeling.

In 1995, DOE began a process to change the supercomputing center from one which merely provided computing time to researchers to a center with intellectual resources to help scientists find newer and better ways to integrate scientific computing into their research efforts. Part of that process was a decision to relocate the center to Berkeley Lab.

Because DOE is a mission agency, charged with carrying out specific programs related to national needs, the majority of NERSC's resources will be focused on large-scale computational science programs. This research includes DOE's Grand Challenge projects in areas such as understanding magnetic materials, with applications in computer data storage and power generation (this project won the 1998 Gordon Bell Prize); designing advanced particle accelerators; and understanding the chemistry of elements such as uranium to enable more effective cleanup of contaminated DOE sites.

New committees established

The NERSC Program Advisory Committee will be responsible for the new scientific peer review process, which will be used to allocate 40 percent of NERSC's computing resources. The peer review and resource allocation process for the remaining 60 percent of NERSC's computing resources will be managed directly by the programs in the Department's Office of Science, reflecting their mission priorities.

To provide overall policy direction to the center and to help chart its future, Berkeley Lab will establish a NERSC Policy Board. The board will report directly to Lab Director Shank. This approach follows that of other major DOE facilities. Similarly, a national user group will advise NERSC on the current and future delivery of center resources and services.

More information on NERSC's new allocations policy can be found on the web at accounts/allocations/alloc2000/.

Photo: NERSC, which moved to Berkeley Lab in 1996, is currently home to Seven SGI/Cray supercomputers and serves about 2,500 researchers. Photo by Roy Kaltschmidt (XBD9901-00173)


FY 2000 LDRD Call for Proposals

Berkeley Lab Director Charles Shank has issued the call for proposals for the FY 2000 Laboratory Directed Research and Development (LDRD) program, which provides support for projects in forefront areas of science and can enrich Berkeley Lab's R&D capabilities and achievements.

Proposals are encouraged that fit in with the Laboratory's strategic directions. Two areas of special emphasis will be strategic projects in computational science and projects which continue to build the scientific productivity at the Advanced Light Source.

Multi-investigator and multi-divisional initiatives which attack problems of scale are also encouraged.

All projects should have a clearly stated problem that addresses a national need or DOE mission, coherent objectives, and a well-considered plan for leadership, organization and budget.

A call for proposals has been distributed to division directors and administrators. Principal investigators must submit proposals to division directors by Friday, April 2.

After conducting an internal review and evaluation, division directors will forward the proposals to the director's office. Division directors will then present the proposals from their divisions to review committees comprised of the director, deputy directors, associate laboratory director, and other division directors. Director Shank will make the final decisions.

The complete call for proposal, schedule, guidance, and forms are available online on Berkeley Lab's website at


Alan J. Bearden


Alan J. Bearden, professor emeritus of neurobiology and biophysics at UC Berkeley and a former senior staff scientist with Berkeley Lab's Biology and Medicine Division (a forerunner to today's Life Sciences Division) has died. He was 67.

Bearden succumbed to a heart attack on February 17. Although he retired in 1992, Bearden was recalled by the University in 1993 and has been conducting research with UCB's Department of Molecular and Cell Biology. An expert in auditory transduction and laser-interactive optics for cell biology, Bearden is perhaps best known for his invention of laser feedback microscopy (LFM). This technology made possible high-resolution scanning confocal light microscopes with a resolution approaching that of electron microscopes without requiring elaborate sample preparation.

Bearden is survived by his sons Colin and Roger Bearden.


Bulletin Board

Photo: Lab employees may purchase AC Transit and BART tickets from the Tripmobile -- a "store on wheels" operated by the Berkeley TRIP commuter store. The Tripmobile drives to Berkeley Lab during lunch time the first Thursday of every month. By buying tickets from the Tripmobile, employees may deduct up to $65 of their public transit costs from their pre-tax paychecks every month through a new program of commuter tax incentives. (See Currents, Feb. 12). Photo by Roy Kaltschmidt (XBD9902-00232-02)


Offsite Training on Radiation Detection

A special all-day training session on "The Principles and Limitations of Radiation Detection" will be held at the Airlie House Center in Arlington, Virginia on March 8-10.

The event is sponsored by the U.S. Department of Energy, Berkeley Lab, the Office of Industrial Technology, and the Idaho National Engineering and Environmental Laboratory

For more information contact Karen Paris at X5115 or KMParis@

Online information is available at Workshops/Radiationlimitations/ Titlepage.htm.


Camp Administrator Needed for Science Exploration Camp

The board of directors of the Science Exploration Camp (SEC) has decided to hire a camp administrator to help plan and organize this summer's science camp at Berkeley Lab. Laboratory employees who know someone who may be interested in this position may contact SEC at sciencecamp@ or call X6566.

The camp operates six-week summer sessions for children of Lab employees and guests. Until now the camp has been administered by its board of directors, but recent difficulties in recruiting new members led to the decision to hire an outside administrator.

A description of the camp administrator position can be found on SEC's website at secindex.htm.


Community College Initiative Planning Session

A two-day planning session will be held at Berkeley Lab on March 1 and March 2 to discuss the Lab's participation in the community college initiative announced by the Department of Energy earlier this month. (See story in the Feb. 12, 1999 issue of Currents.) Twenty to 30 faculty members from participating community colleges - selected by DOE in partnership with the American Association of Community Colleges - will take part.

The event will be held over the course of the two days at various locations on the Hill and will include tours of Lab facilities.

A special reception is planned for Monday, March 1 (4:30 p.m. at the cafeteria) for community college representatives, Lab mentors, students, and former students.

For more information contact Laurel Egenberger at X5190 or LLEgenberger@


13th National Conference of Black Physics Students UC Berkeley and Berkeley Lab, March 11-14

On March 11-14 UC Berkeley and Berkeley Lab will co-host the Thirteenth Annual Conference of Black Physics Students. Entitled "Physics at the Frontier: From Nanostructures to the Cosmos," the event is designed to assist and encourage black students who have shown interest and ability in physics and astronomy to enter and complete Ph.D. programs and to encourage them to pursue research, teaching, or technical careers in these fields.

This meeting will enable participants to interact with each other and with successful scientists. Approximately 165 to 190 students are expected to attend, both in undergraduate and graduate programs.

Events will include lectures and panel discussions (including a roundtable discussion with industry and university experts), meetings with recruiters, student presentations, poster sessions, a banquet, and tours of the campus and Berkeley Lab. Former Lab Director Andrew Sessler will be the keynote speaker at the March 12 dinner.

UC Berkeley will also bring in more than 100 minority public school students and their teachers on one of the conference days to heighten minority students' awareness of the opportunities open to them in science, with particular emphasis on physics and astronomy.

For more information contact Harry Reed of the Office of Workforce Diversity, X4232, or Bob Cahn, deputy director of the Physics Division, X4481.


Courier Services

The Facilities Department is providing the Lab with rush courier service with pick-up and delivery both on- and off-site. Transportation can deliver up to 2,000 pounds anywhere in the Bay Area or in central or northern California. On-site materials will be delivered within one hour. For off-site service, a driver is available during normal business hours for same-day pick up and delivery, with rush service depending on destination. To request a pick up, call Peggy Patterson at X5404.

Rush service is also available from IDS Courier, which operates 24 hours a day and provides pick-up and delivery service anywhere in the Bay Area and in portions of northern and central California. For information call Linda Wright at 548-3263.


LabVIEW User Group Meeting

A meeting will be held on March 23 to discuss "LabVIEW RT for Embedded Real-Time Applications." The free seminar will be held from 10 a.m. to noon in the Bldg. 50 auditorium. To register contact National Instruments at (800) 433-3488 or send e-mail to ni.register@


NERSC User Training Classes Next Month

NERSC User Services will present onsite classes for new and intermediate users of the Cray J90 and T3E computers and auxiliary systems on Tuesday and Wednesday, March 16-17. These classes will be from 30 to 60 minutes in length and will cover introduction to the J-90 and T3E, batch computing, NERSC file systems, debugging, performance tuning and monitoring, the ACTS Toolkit, and managing secure connections with SSH.

For more details see the NERSC website,, or contact Thomas M. DeBoni at TMDeBoni@ or X8617.


Currents Online

The full text and photographs of each edition of Currents are published online at You may find a link to Currents on the Lab's home page under the heading "Publications." The site allows users to do searches of past articles going back to 1994.

To set up your computer to access the web, call the Mac and PC Support Group at X4357.


Calendar of Events at Berkeley Lab


The Berkeley Lab Calendar is published biweekly here on the World Wide Web and in Currents by the Public Information Department. Employees can list a meeting, class, or event in the Calendar by using this submission form. The deadline for submissions is 5 p.m. on Monday in the week that Currents is published.

In addition to the events listed below, Berkeley Lab's Washington, D.C. Projects office is hosting a Science and Technology Seminars series. 

Scientific Conferences


March 1 - 14, 1999

General Interest


Community College Initiative Planning Session
March 1-2, various locations, contact Laurel Egenberger, X5190 Reception at 4:30, cafeteria


Community College Initiative Planning Session
March 1-2, various locations, contact Laurel Egenberger, X5190

Weight Watchers
Noon, Bldg. 26-109


LBNL Macintosh Users Group
Inaugural meeting 11 a.m., Bldg. 70A-3377

Brown Bag Briefing on Science Education Standards
Noon, Bldg. 50 auditorium


7:30-3:30, cafeteria parking lot

11:30-12:40, cafeteria parking lot


New Employee Orientation
9 a.m.-1 p.m., Bldg. 50 auditorium

Weight Watchers
Noon, Bldg. 26-109


Music Club
Noon, lower cafeteria


National Conference of Black Physics Students
UC Berkeley & Berkeley Lab

Items for the calendars may be sent via e-mail to currents_calendar@, faxed to X6641 or mailed to Bldg. 65B. The deadline for the March 12 issue is 5 p.m. Monday, March 8.

Seminars & Lectures

MARCH 1, Monday

Physics Department Colloquia, UC Berkeley
"How Hearing Happens: Physical Principles of Auditory Transduction and Frequency Tuning" will be presented by James Hudspeth of Howard Hughes Medical Institute, the Rockefeller University.
4:30 p.m., 1 LeConte Hall, UC Berkeley

MARCH 2, Tuesday

Department of Molecular and Cell Biology, UCB
"Oxidative Damage in Singapore and London: How Is My DNA Coping and Will the Food Help?" will be presented by Barry Halliwell from the National University of Singapore.
4 p.m., 177 Life Sciences Addition, UC Berkeley

MARCH 3, Wednesday

Science and Technology Seminars, Washington DC
"Dendrimers and Other Functional Polymers" will be presented by Jean Frechet of Material Sciences and UC Berkeley
1:30 p.m., LBNL Office, Washington, DC

MARCH 4, Thursday

Surface Science and Catalysis Science Seminar
"Exploring and Controlling the Atomic-Scale World" will be presented by Paul Weiss of Pennsylvania State University.
1:30 p.m., Bldg. 66 auditorium

MARCH 5, Friday

Surface Science and Catalysis Science Seminar
"Biomolecules on Surfaces: Anchoring and Properties" will be presented by Nicholas Spencer of ETH-Zurich, Switzerland.
1:30 p.m., Bldg. 66 auditorium

MARCH 8, Monday

Physics Department Colloquia, UC Berkeley
"Bose-Einstein Condensation of Atomic Hydrogen" will be presented by Daniel Kleppner of MIT.
4:30 p.m., 1 LeConte Hall, UC Berkeley

MARCH 10, Wednesday

Surface Science and Catalysis Science Seminar
"Growth and Structure of Thin Films and Superlattices" will be presented by Ivan Schuller of UC San Diego.
1:30 p.m., Bldg. 66 auditorium

MARCH 11, Thursday

Surface Science and Catalysis Science Seminar
"Surface Structure and Catalytic Activity of W(Mo)-Based Catalysts" will be presented by Marwan Houalla of Vanderbilt University.
1:30 p.m., Bldg. 66 auditorium

MARCH 12, Friday

Earth Sciences Division Seminar
"CO2 and He Emissions from a Magmatic Reservoir of Volcanic Gases at Mammoth Mountain, Long Valley Caldera, California" will be presented by Mack Kennedy of Earth Sciences.
11:00 a.m. Bldg. 90-2063

Center for Beam Physics Seminar
"Model-Independent Analysis and its Applications to Linacs and Rings" will be presented by John Irwin of SLAC.
10:30 a.m., Bldg. 71 conf. rm.


EH&S Class Schedule: March 1999

To enroll contact Susan Aberg at X7366 or enroll via the web ( Pre-registration is required for all courses.


Golf Club Scores

Results from the LBNL Golf Club tournament held last Saturday at Delta View in Pittsburg.

The next tournament will be held at Poppy Hills Golf Course in Pebble Beach on March 6. For information about the Golf Club call Mark Cusey at X2378.


Flea Market

Autos / Supplies

`82 TOYOTA Cressida, 4 dr luxury sedan, 136K mi, well maintained, good tires, new battery, good looking car, $1,950/b.o., Marie or Ray, 845-2445

`83 HONDA Civic 1500DX hatchback, exc cond, recond eng, runs perfectly, reliable, hassle-free, $2,100, Rob, X5798, Hai Ying, 524-3182 (eve)

`86 TOYOTA Tercel Deluxe, 4-dr hatchback auto, 86K mi, navy blue, am/fm, new timing belt, spark plugs, ignition rotor, fuel & air filters, tires, inner & outer bearings, well maintained, clean, ac needs recharging, $2,800/b.o., Ashok, X4651, 237-8806

`90 KAWASAKI EX500, 12K mi, blk, exc cond, new tires & brakes, $1,990, Markus, X7312, 524-1869

`93 MAZDA B2200 pickup, 5-spd, short-bed, 73K highway mi, extended warranty up to 100K mi, camper shell, bed liner, carpet kit, flip-up sun roof, am/fm/CD (Sony), ac, runs great, $5,800/b.o., Winnie, X7393

`93 TOYOTA Camry, V6LE wagon, 60K mi, silver, at, ac, ps, pw, am/fm/cass, 3rd seat, air bag, exc cond, $12,000, Yuki, X5090, 528-8059

`93 SUNFISH sailboat w/ trailer & some accessories, exc cond, white & aqua, has never sailed in salt water, $1,800/b.o., John, X5672


EL CERRITO HILLS, furn rm, bay view, household privileges incl util, use of washer/dryer, kitchen, 15 min from Lab, $600/mo, Larry, X5406, 237-3321

NORTH BERKELEY, 1 furn rm in 2-story house, 1 bth, washer/dryer, parking, Marzio, X7441, 559 7760

NORTH BERKELEY furn rm, quiet, large, comfortable, in Berkeley brown-shingle (Julia Morgan 1909), limited kitchen privileges, walk to campus, Lab, shuttle, BART, ideal for visiting scholar (1 person only), non-smoking, avail April 1, $450/mo, Rob, 843-5987.

OAKLAND, Crocker Highlands, 3 bdrm furn home, 2 cats, avail, April-June `99, $1,200/mo + cat care, negotiable, Kathy, X4385

ROCKRIDGE, rm in spacious 2 bdrm condominium, pool, sauna, gym, nr shopping center, bus stop, LBNL shuttle and BART, $450/mo, Lili, 655-6855


BIKE, Mtn, blue Schwinn, man's, 21 gears, essentially brand new, $150/b.o., Sokhieng, 644-2754

BIKE, Mtn, `95 Mongoose Rockadile, 17.5" frame, polished silver, barely used, great cond, plus set of road tires, $400/b.o., Rebecca, X4329, 547-7586

BOOTS, Snowboard, Burton freestyle, size 12, exc cond, $70, Rich, X6295, 526-7447

CARPORT in Moraga, space avail on Ascot Dr, $20/mo, Bob, (925) 376-2211

CLOCK, School, Seth Thomas octagon dial, 8 day, ca. 1880, $300; "Ionic", wall clock by New Haven, 8 day w/ time & strike, ca. 1860, $400, both in perfect orig cond, Gary Koehler, X7931, (925) 229-1241

CRIB w/ mattress, wooden, light finish, $110, Marion, X2915, 527-2524

DISCOVERY TOYS, educational books, software, from birth to adult, have a party and earn valuable points towards free product, Tracy, X7990, (925) 313-8920

DRYER, Whirlpool supreme, heavy duty, extra lg capacity, electric, 220v pwr supply, great cond, $250/b.o., X5607

MOVING SALE: dinette set, small round wooden table w/ two matching chairs, purchased from Cost Plus, very good cond, $70; computer desk, very good cond, $50; Brother brand very basic sewing machine, hardly used, $40; Krupps personal espresso maker + accessories, b.o., Melissa, X5790, 841-7528

POLES, ski, 1 set 42", the other 44", can be used by a skier around 5 ft tall, $2 ea, H. Matis, X5031, 540-6718

RECEIVER, Optimus, digital synthesized stereo, $40; Emerson, 5 pc. home theater speaker system, new in box, $35, Jim, X4855, (925) 609-8434

RUG, lg beige area rug, (11'x 18'), nylon, short nap, $50/b.o., Janet, X4450

SKIS, snow, Olin Extreme, 195cm w/ marker bindings, good cond, incl poles, $50, Paul, X2315, 655-6616

SKIS, snow, Volkel P10 Pro SL 205 cm, ESS bindings, $175/ b.o.; Head Cr X-10 205 cm w/ Tyrolia bindings, $100/b.o.; Rossignol 185cm, Tyrolia bindings, used once, $150/b.o.; Dynamic Slalom DP 200 cm, Tyrolia bindings, $100/b.o., Steve, X6598, (925) 689-7213

SOFABED, $150, 2 matching chairs, $70; antique mahogany drop leaf dining table, $175; mahogany parlor organ, pump style, very pretty and works, $175; Turkoman Takke rug, $1,000, Peter, 525-1917

WASHING MACHINE & DRYER, Whirlpool, extra lg capacity, washer, full range of features, dryer incl sensor that shuts off machine when clothes are dry, about 4 yrs old, used only by one person, $250/pr or b.o., Sherrill, X5984, 663-6242


COMPUTER (PC) for a continuation school in the East Bay, needs at least a 486, CD-ROM & Windows 95, it is a tax deductible donation, Mike, X4780

BICYCLE, mtn bike, for underprivileged boy 13 yrs old, will purchase, Bob, X6557, 527-6937

CAMP ADMINISTRATOR (part time, approx 10 hrs/wk) for Summer Exploration Camp at LBNL, March 1-Sept 3, 1999, e-mail

CARPOOL, looking to form carpool w/ rider & driver from Rodeo/Hercules area, beginning mid-March, hours flexible, Diana, X4070

HOUSING, 3 bdrm house or townhouse for visiting scholar and family from Pennsylvania, approx 8/26/99 - 6/10/2000, 2 adults, 2 children, non-smokers, no pets, Pat, X6845 or

HOUSING, Tunisian professor seeks 1 bdrm apt, May 1 to end of August, close to campus preferred, Alyssa, X5958

SUMMER HOME EXCHANGE, LBNL family of 5 seeks exchange w/ family in UK, Berkeley Victorian 5 bdrm home avail June15 to July 14, need home in London or Oxford from June 23 to July 8, our home is 3 blks from UCB & LBNL shuttle, car exchange avail, Mike, X4669

ROOMMATE, in 2 bdrm townhouse in Hayward, 2 windows in bdrm, 2 huge closets, own private bthrm, washer/dryer, nr Hayward & Castro Valley BART, non-smoker, no drugs, Leslie, X5541, 886-4851

SLIDE PROJECTOR, any model; bicycle home trainer, any model, Jan, X6676

HOST FAMILY needed by high school student from Belarus in international exchange program, 1 year starting winter `99; 16 years old, speaks English, friendly, willing to contribute to household chores; to find out more about program look up, Lana, X7668


TAHOE KEYS at South Lake Tahoe, 3 bdrm, 2-1/2 bath house, fenced yard, quiet area, close to skiing, other attractions, great views of water/mtns, $150/night, 2 night min, Bob, (925) 376-2211


COUCH, leather, Doug, X4567, 568-6386

PLANTS, green & yellow agave, currently 8", will grow to 3' to 4', have sharp spines, not appropriate for yards w/ toddlers, will do well on sunny hillsides, drought tolerant; fan-tailed guppies, free to established community aquariums, both adult & baby guppies, Janet, X4450

Lost & Found

FOUND: Set of keys on Feb. 24 near the Bldg. 50B loading dock area, contact William, X5785, or Martin, X4371

FOUND: silver earring, dangly cat & fish, nr Bldg 50A on Feb. 9, Jon, X5849

Flea Market Policy

Flea Market items may be e-mailed to fleamarket@, faxed to X6641, or mailed/delivered to Bldg. 65B. No ads will be taken by phone.

The deadline for the March 12 issue is 5 p.m. Friday, March 5.


Flea Market ad policy

Due to the large volume of ads received each week, ads are accepted only from LBNL employees, retirees, and on-site DOE personnel. No other ads will be accepted. We encourage past contributors to the Flea Market to use other local services, such as LBNL's online housing listing (call X6198 for information), and the UC Housing Office.

Please note also:


Currents/The View and the Communications Department Staff

Published once a month by the Communications Department for the employees and retirees of Berkeley Lab.

Reid Edwards, Public Affairs Department head
Ron Kolb, Communications Department head

Pamela Patterson, 486-4045,
Associate editor
Lyn Hunter, 486-4698,

Dan Krotz, 486-4019
Paul Preuss, 486-6249
Lynn Yarris, 486-5375

Ucilia Wang, 495-2402
Allan Chen, 486-4210
David Gilbert, (925) 296-5643

Caitlin Youngquist, 486-4020
Creative Services Office

Berkeley Lab
Communications Department
MS 65, One Cyclotron Road, Berkeley CA 94720
(510) 486-5771
Fax: (510) 486-6641

Berkeley Lab is managed by the University of California for the U.S. Department of Energy.

Flea Market is now online at


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