December 15, 2000 Search the Currents Archive

Extreme Low-Fat Diets Can Pose Heart Disease Risk to Some

The Transuranium People

Extreme Low-Fat Diets Can Pose Heart
Disease Risk to Some

By Lynn Yarris

Ronald Krauss

Because of certain inherited genetic traits, an extreme low-fat/ high-carbohydrate diet can, for some individuals, actually increase the risk of heart disease, says a Berkeley Lab scientist who is a leading authority on the subject.

Speaking at an international workshop on diet and gene interactions sponsored by the U.S. Department of Agriculture (USDA), Dr. Ronald Krauss, head of the Department of Molecular Medicine in Berkeley Lab’s Life Sciences Division, reported on the recent findings of his research group, which showed that in genetically susceptible individuals, an extreme low-fat/high-carbohydrate diet can produce metabolic reactions that cause a change in the cholesterol profile of their blood. An extreme low fat diet was defined as one in which fat comprised less than 25 percent of the total daily calorie intake.

In a patten A profile, low-density lipoproteins (LDLs or the "bad" cholesterol) in the blood are predominantly made up of relatively large and buoyant particles. In a pattern B profile, the LDL are smaller and more densely packed. Earlier studies by Krauss and others have already established that the pattern B profile poses a much greater risk of heart disease than the pattern A.

"Tests for these genetically susceptible traits are not widely available," says Krauss. "There are, however, clues, such as elevated levels of triglycerides (another type of blood fat linked to heart disease) and lowered levels of high-density lipoproteins (HDLs or the "good" cholesterol) when a patient goes on a very low-fat/ high-carbohydrate diet."

Heart disease remains the number one cause of death and disability in the United States, and increasing numbers of Americans, especially those over 50, have turned to diets aimed at lowering LDL cholesterol levels as a means of reducing the risk. While the effects of such dietary changes are beneficial to the population at large, these effects can vary widely among individuals, according to Krauss.

"Studies of dietary effects on LDL cholesterol must take into consideration that LDL is comprised of distinct subclasses that differ in particle size and density, and that there is variation in the distribution of these subclasses among individuals," he says. "Small LDL particles appear to have a greater atherogenic potential than large LDL particles by virtue of reduced receptor-mediated clearance, and higher arterial transport, proteoglycan binding, and oxidative susceptibility."

The interaction between diet and genes and how this interaction affects the two LDL subclass patterns may help explain why there can be so much variability in the effects of low-fat diets on the risk of heart disease. For patients who started out with the pattern B cholesterol profile, the study by Krauss and his research group showed that an extreme low-fat/high-carbohydrate diet can reduce the number of circulating small LDL particles, which in turn reduces the risk of heart disease. LDL particles carry cholesterol through the bloodstream and deposit it along arterial walls, creating a waxy buildup that can eventually restrict the flow of blood to the heart.

For patients who started out with the pattern A cholesterol profile, however, Krauss and his research group found that an extreme-low fat/ high-carbohydrate diet worked to reduce the cholesterol content of the LDL particles circulating in the blood. This depletion in the composition of the LDL particles resulted in a downsizing that in turn led to a conversion from the pattern A to the pattern B profile.

"Studies in families have indicated that LDL subclass patterns are influenced by major genes, and linkage of LDL particle size phenotypes to several candidate genes have been reported," says Krauss.

"However, overall heritability of LDL particle sizes is less than 50 percent, consistent with the strong influence of modifying factors on the expression of LDL subclass patterns."

Previously, these modifying factors were listed as age and gender, plus certain metabolic conditions that affect triglyceride levels such as abdominal adiposity and resistance to insulin. To these factors can now be added diet, says Krauss.

Results of the study by Krauss and his collaborators were originally reported in the June 2000 edition of the American Journal of Clinical Nutrition. Krauss’ coauthors on that paper were Darlene Dreon, Harriet Fernstrom, and Paul Williams.

The Transuranium People

By Paul Preuss

The Transuranium People: The Inside Story; by Darleane C. Hoffman, Albert Ghiorso, and Glenn T. Seaborg; Imperial College Press, 467 pages hc, $75.00

Berkeley Lab has been home to the discovery of more elements with atomic number greater than 92 than anyplace else in the world, beginning in 1940 with the discovery of element 93, neptunium, by Edwin McMillan and Philip Abelson at the University of California’s Radiation Laboratory.

Not all the Lab’s achievements have gone undisputed. Although these are not matters a nonspecialist can judge, a lively sense of history-still-unfolding is one of the fascinations of The Transuranium People.

Liveliness extends to the editing, which is sometimes antic. For example, a book’s page count is taken from its last numbered page (here 467), but this one comes with front matter running to Roman numeral xciii, an extra 93 pages — most in a long preface titled "Intimate glimpses of the authors’ early lives," an intriguing minivolume in itself.

Of Darleane Hoffman, we learn that in 1952 the personnel department at Los Alamos ruined her chance to participate in the discovery of elements 99 and 100 (einsteinium and fermium). Arriving from Oak Ridge to take up a job in the short-handed radiochemistry group there, Hoffman was told that "we don’t hire women in that division." What’s more, her security clearance had somehow been "lost." Meanwhile, in November, new elements had been produced in the world’s first thermonuclear explosion, and in December and January they were separated from coral debris from the test site. The personnel-department snafu wasn’t cleared up until March.

In 1941 Albert Ghiorso, then working for a supplier of ham radio equipment, was sent to the UC Rad Lab to hook up an intercom for the secretaries and to build some Geiger counters. "I was not told that it would be necessary to build hundreds of these devices for Prof. Glenn T. Seaborg’s group." By way of consolation, he married one of the secretaries, Wilma Belt.

When Seaborg went to Chicago to join the Manhattan Project’s Metallurgical Laboratory, he asked Ghiorso to come along. Although Ghiorso barely knew Seaborg, he agreed on condition "that I not be asked to build any more G-M [Geiger-Mueller] circuits." Later he learned that Wilma and Helen Griggs, Ernest Lawrence’s secretary (soon to be Mrs. Seaborg), had decided between them that Ghiorso belonged in Chicago. There he was to play a crucial role in developing new instruments.

Much of The Transuranium People is grouped into chapters describing the quest for new elements that often came in pairs — neptunium and plutonium, americium and curium, berkelium and californium, and so on — for reasons having to do with particular experimental methods or available energies.

Competition, controversy, and compromise were part of the quest from the beginning. In an intriguing chapter called "Naming controversies and the Transfermium Working Group," the authors recount a quarter-century of unsuccessful attempts to end the "dissent and confusion" surrounding credit for discoveries of elements 101 through 109.

Element 105 occasioned the worst clash. The authors contend that researchers at the Joint Institute for Nuclear Research at Dubna in Russia could not, as they claimed, have isolated element 105 in 1967 by the means described; a different isotope of 105 was made in 1970 at Berkeley Lab’s HILAC by Ghiorso and four colleagues, who named it hahnium.

Not until 1997 was a compromise reached by the International Union of Pure and Applied Chemistry, naming 105 dubnium and at the same time accepting the name seaborgium for element 106 — "in the interest of international harmony," as the American Chemical Society’s Committee on Nomenclature put it.

In this book 105 is called hahnium — the name by which it was best known for a quarter century.

The Transuranium People also includes an illuminating discussion of the excitement behind the search for "superheavy elements," those whose stability should increase with increasing atomic weight, notably the possibility that elements in "a ‘Magic Island’ or ‘Island of Stability’ with half-lives as long as a billion years might exist."

If so, they might be found in nature. But looking for an element "whose atomic number and chemistry I could only guess at seemed nearly impossible," remarked Hoffman, although in 1971 she had succeeded in separating minute amounts of plutonium from natural ores. Indeed all such searches have failed.

Instead, superheavies have been produced in accelerators. In 1999 Victor Ninov, Kenneth Gregorich, and their colleagues working at Berkeley Lab’s 88-Inch Cyclotron, created elements 118 and 116. A few months earlier, researchers working at Dubna had reported finding element 114; no one has yet laid claim to 113, 115, or 117. The quest continues — especially for those with the right number of neutrons and protons to form "magically" stable atoms.

Despite the often heavy technical going, there are enough personal revelations, anecdotes, opinions, gripes, brokered deals, and generous sharings of credit in The Transuranium People to entertain anyone with an interest in the history and promise of the "artificial" elements heavier than uranium.

The Chemistry of Heavy Elements

The chemistry of the heavy elements is as intriguing as their discovery. In recent studies of element 107, bohrium, the first challenge was to create a "long-lived" isotope. This was done at the 88-Inch Cyclotron by bombarding a target of berkelium 249 with a beam of neon 22 to produce bohrium 267, whose half-life is about 17 seconds.

The Berkeley team included Darleane Hoffman, Ken Gregorich, Heino Nitsche, postdoctoral fellows Uwe Kirbach and Carola Laue, and graduate students Joshua Patin, Dan Strellis, and Philip Wilk. Wilk, who notes Berkeley Lab’s "strong commitment to involving graduate students in hands-on research," had the opportunity to design and set up the experiment using what he calls "old Berkeley techniques;" these include the "Merry Go Around" wheel detector built in the 1970s, not unlike the vertical wheel first used in the 1960s to capture element 104, rutherfordium.

In the fall of 1999 these techniques were employed for over a month at the Paul Scherrer Institute (PSI) in Switzerland to capture just six atoms of bohrium. Bohrium compounds were injected into an apparatus that allowed measurements of their volatility.

Many of the individuals and institutions involved in studying the chemistry of bohrium play prominent roles The Transuranium People. In addition to PSI, the University of Bern, Berkeley Lab, and UC Berkeley, the participants included the Flerov Laboratory in Russia (Dubna), the Forschungzentrum Rossendorf, Gesellschaft für Schwerionenforschung (GSI), and Technical University of Dresden in Germany, and the Japan Atomic Energy Research Institute in Japan.

Making a Difference in the Science Classroom

By Lisa Gonzales

Rick Norman of Nuclear Science teaches astronomy to teachers in Vallejo. Photo by Roy Kaltschmidt

Thea Holladay’s ninth grade science students at Vallejo High School have a problem. A hypothetical international airport is going to be built on the Vallejo wetlands just north of Highway 37. It is up to them to study the related ecosystems and the environmental impact of such a construction on the wetlands and the neighboring areas. They will do that through readings, activities, lab work, and worksheets in order to prepare an environmental impact report at the end of the unit.

Most of the assignments for this project came out of Holladay’s participation in the Integrated Science Partnership Project (ISPP), a four-week summer program for Vallejo science teachers held at Berkeley Lab over the past three years. Funded by the California Postsecondary Education Commission, the ISPP brought 40 Vallejo science teachers to the Lab to work with researchers and compile curriculum materials in keeping with the district science standards. The materials were then distributed to all the science teachers in the district in order to supplement textbooks, develop classroom activities and experiments, and provide information on the latest research frontiers.

"Because I don’t have textbooks for my students, I have had to rely heavily on the materials compiled with the ISSP," says Holladay. Taking a concept developed during the summer program, Vallejo High School has rearranged the Lab materials into integrated themes, such as the H. G. Wells Mining Company (earth science, chemistry, and physics), Inner Journey (human body, chemistry, physics), and Outer Journey (energy, astronomy, physics).

The assistance the Lab provided to the Vallejo schools is greatly needed. According to statistics compiled by the California Department of Education, of the 3,500 ninth, tenth, and eleventh grade students who took the California high school science exam, 30 percent scored below the 25th percentile. Only 14 percent scored above the 75th percentile.

"There is a strong need for scientific literacy in the community, especially in our schools," says Rick Norman of the Nuclear Science Division, one of the Berkeley Lab scientists who give of their own time to various educational program. Norman, who also volunteers in his children’s public school classrooms, has served on the Curriculum Framework and Criteria Committee that developed the science content standards from kindergarten to 12th grade in California public schools. Last month, he gave two presentations to the ISPP teachers on astronomy, a subject unfamiliar to most of them.

"Rick made a broad presentation to the teachers in which he laid out important concepts in support of our teaching standards," says Don Hubbard, co-director of ISPP and a retired science teacher from Berkeley High School .

Norman’s presentation is part of the professional development that continues for the ISPP teachers throughout the school year. The teachers then assist the rest of the science teachers in the district with implementing the new curriculum, thereby allowing the work done at the Lab to benefit as many students as possible in the three high schools and four middle schools of the Vallejo School District.

"Most of what I have learned from the Lab scientists has involved research that didn’t even exist when I completed my undergraduate training," says Holladay. "Even though I’ve made an effort to keep up, nothing can replace the first-hand exposure to the real research." Furthermore, because her field of expertise is biology, Holladay needed the presentation on astronomy to fill in some of the gaps in her own education.

"A lot of kids say to their teachers, ‘Why should I believe this stuff?’" says Norman, who realized that many of the teachers do not feel confident enough with astronomy. At his presentations the teachers mostly wanted practical information that would allow them to answer students’ questions. "They wanted to be able to explain to their students why we believe certain concepts — such as the Big Bang and the origin of chemical elements — and how we know them to be true."

Concurs Holladay, "Rick’s explanation of the expansion of the universe was new to me. Without this lecture we would have continued to present outdated information to our students."

Working with the Lab has also helped Vallejo teachers established a network of educators.

"These people are recharged," says Hubbard. "Their experience with the Lab’s scientists has had both a personal and a professional impact. They realize that they are not alone but part of a community, that what they are doing will impact students after the kids have left the classroom. Now they have a sense that others will follow-up on what they have taught."

The impact of the ISPP’s work at the Lab has yet to be gauged by student achievement on standardized tests. "We are currently waiting on tracking data from achievement tests taken at the end of the academic year," says Hubbard. However, anecdotal evidence points to a marked improvement.

"So many teachers have told me that they are experiencing more success in the classroom due to the work they’ve done at the Lab through the ISPP," adds Hubbard. He believes this comes from a combination of increased classroom activities and experiments, a more coherent presentation of scientific ideas, and teachers who feel comfortable with the material they are teaching.

"The biggest challenge for our teachers is their own level of scientific literacy," says Norman. "We provide educational outreach to them in order to elevate these levels, and as we build connections, we can become an even greater resource to help our teachers. Then we will have an impact in the schools."

Holladay echoes these sentiments as she considers the effects of the teachers collaboration with Berkeley Lab. "We were given ‘real science’ to supplement and replace ‘textbook science’ and that has made a real difference."

Washington Report

DOE Casts Transition Reports Seeking to Avoid Confusion

DOE is preparing a series of documents for the next administration that identify major issues, including those that concern the national labs, which will require attention in the early part of 2001. These documents are intended to help ensure a smooth transition from the Clinton administration, Deputy Energy Secretary T.J. Glauthier told members of the Laboratory Operations Board (LOB).

"We are dedicated to making a smooth transition for whomever comes in to run the White House," Glauthier told LOB members at a meeting last week. Glauthier sits on a presidential committee consisting of deputy secretaries of all cabinet-level agencies that have been focusing on transition issues. The documents being prepared by DOE are relatively small in size (about five pages) and explain what issues are likely to come up in the first 90 days of the new administration. They also provide a budget summary.

"We’re making sure the materials can be quickly understood since we don’t know a person’s initial familiarity or unfamiliarity with DOE," Glauthier said.

Glauthier said the papers will not advocate specific solutions to issues but rather serve as a primer on DOE responsibilities. Among the key developments expected in January are a preliminary report on Nevada’s Yucca Mountain, a potential site for a nuclear-waste repository. DOE is scheduled to make a final recommendation on Yucca Mountain’s suitability for nuclear waste by July.

Glauthier said DOE hopes the reports will be good enough to avoid a repeat of the confusion he said occurred in 1993, when the outgoing Bush administration disconnected many of the phones in federal offices and even removed some computer hard drives, he said.

Performance-Based Management Wins Support of LOB

The performance-based management system implemented by DOE at its national laboratories has been considered successful, but its continued success will require "a concerted effort" by the new DOE leadership which takes office in January. So says the Laboratory Operations Board in a new draft report which calls for an "integrated" approach to performance-based management.

In performance-based management, top levels of DOE and laboratory management cooperate to define a set of requirements and desired results that are periodically measured to chart progress.

To fully implement performance management throughout DOE’s headquarters and field facilities, the LOB recommends a "corporate" approach, including appointment of a high-level manager as a "champion" for the effort.

The report lauds DOE efforts to implement performance-based management since 1992. "These plans have driven numerous agency-wide initiatives that are redefining and re-engineering agency and contractor managerial and operational systems and establishing more effective management oversight and accountability," the report says. — Lynn Yarris

Sharing in the SHARES Success

Contributions to Berkeley Lab’s SHARES campaign exceeded last year’s totals, with donations surpassing the six-figure mark, thanks to the generous contributions of the Lab community. A total of $100,650 was donated by 286 employees to assist various nonprofit agencies and organizations.

"The generosity of our employees demonstrates a real commitment to our neighbors and friends," says Ron Kolb, head for Public Communications, who coordinated the campaign. "The broad range of charitable organizations that were part of the SHARES campaign ensures that our giving will be felt throughout our community."

Volunteers in the SHARES campaign joined with members of the Directorate to celebrate the Lab’s successful fundraising efforts. Left to right are Sonia Mueller, Jennifer Rosado, Pier Oddone, Pat Butler, Director Charles Shank, Jane Tanamachi, Annette Fisher, Teresa Lynem, Reid Edwards, Sheril Miura, Sally Nasman, Ron Kolb, and Sherry Reineman.

Kolb also reminded those who may still want to donate that they may do so at any time, and especially before the Lab shutdown if they wish to gain the benefits of tax deduction during the current year. SHARES forms may be requested via e-mail from

Several community businesses and organizations contributed prizes to weekly donor drawings. Employees are encouraged to patronize the following in gratitude for their participation: Webvan, Cal Performances, Bison Brewery, Black Oak Books, the Radisson Hotel, the Berkeley Rep, Triple Rock Brewery, Juice Appeal, Berkeley Ironworks, Berkeley Art Museum, Lawrence Hall of Science, Chabot Space Observatory, Albany Bowl, Scandinavian Designs, and Pyramid Brewery.

Martha Krebs to Head One of Three New Science Institutes

Last week Governor Gray Davis announced the selection of the University of California at Los Angeles, San Diego, and San Francisco as the sites for three new California Institutes for Science and Innovation. These state-of-the-art research centers will focus on complex scientific challenges that require multidisciplinary strategies.

Martha Krebs, the former head of DOE’s Office of Science, will run the California Nanosystems Institute, a research project based at UCLA and UC Santa Barbara, she told Inside EnergyEXTRA.

"The challenge for our institute is to create and sustain the many partnerships needed to carry out nanosystems research among disciplines, between our campuses and with our industry and national laboratory colleagues," she said in a statement released by UCLA. The project has already attracted more than 30 corporate partners.

The other two institutes about to be launched are the California Institute for Telecommunications and Information Technology at UC San Diego, a collaboration with UC Irvine; and the California Institute for Bioengineering, Biotechnology and Quantitative Biomedicine at UC San Francisco, in collaboration with UC Berkeley and UC Santa Cruz.

Standing next to UC President Richard Atkinson in Sacramento last week, Governor Davis said,"Back in January, in my State of the State address, I proposed one of the most ambitious scientific research initiatives ever undertaken by the State of California. I wanted to create not one, but three world class research and innovation centers with a single mission: to invent the future. Now, thanks to the support of the Legislature and the hard work of so many from both the private sector and the UC community, that future is here."

When he first announced the proposal, the governor also pledged to request additional funding for a fourth institute — a Center for Information Technology at UC Berkeley.

Davis committed $75 million annually for four years to establish the centers, with each center receiving $25 million in state funds each year. In turn, the Institutes must obtain a two-to-one match of non-state funds for every dollar of state money they receive.

The three California Institutes for Science and Innovation will be launched immediately. — Monica Friedlander

DOE Fellowship Honors Seaborg

A new Energy Department fellowship named after the Nobel-winning pioneer of the atomic age will help the DOE document more than five decades of nuclear history while providing quality scholarship to doctoral students.

The Glenn T. Seaborg Fellowship will allow students to spend an academic year in Washington, D.C. working at the Energy Department to write what Richardson referred to as "the definitive history of this era,"

"This will be a story written for people, not historians," he said, "and it will help remind everyone of the sacrifices and strides made during this era."

The fellowship is open to all recent American history majors enrolled in a doctorate program in the United States. For more information contact Skip Gosling at

Berkeley Lab Scientists Solve Electron Gun Problem

By Paul Preuss

Ion Beam Rotisserie a cure for Flashover

To inject energetic electrons into the Thomas Jefferson National Accelerator Facility’s free electron laser, scientists at the facility in Newport News, Virginia, built a Photo-Emission Electron Gun designed to operate in vacuum at half a million volts. The gun’s "barrel" is a pair of cylindrical ceramic insulators, known as accelerator columns, made of pure alumina and capable of withstanding the high voltage.

No matter how good an insulator may be in bulk, its surface is vulnerable to failure. In a strong electric field, free electrons can be accelerated onto its surface. A single impact may scatter additional electrons, which impact the surface in turn. In an instant, an avalanche of electrons is rolling over the surface in a catastrophic flashover.

"Flashovers not only bring operations to a halt, they can do expensive damage," says physicist Larry Phillips of Jefferson Lab. "When we built the electron gun we knew it would be a challenge to operate it at high electric field strength without breakdown."

One way to prevent flashover is to add some conductivity to the surface of the insulator, so charge can bleed away before it builds up, but the metal coatings Phillips and his colleagues first tried behaved erratically.

Tim Siggins and Larry Phillips of the Thomas Jefferson National Facility with Berkeley Lab’s Ian Brown at AFRD’s vacuum-arc ion source.

At an accelerator conference Phillips heard a talk by Berkeley Lab’s Simone Anders on controlling the surface resistivity of ceramics using metal ion implantation. Anders, then with the Plasma Applications Group in Berkeley Lab’s Accelerator and Fusion Research Division (AFRD) headed by Ian Brown, described a vacuum-arc ion source originally built to produce beams of uranium ions for the Bevalac.

After the Bevalac was decommissioned, says Brown, "our research evolved toward ion implantation." The source had shown "nice characteristics for certain kinds of implants. It is very good at putting metal into alumina, for example."

Phillips says, "It sounded like it might be the answer to my problem." He, Brown, and their colleagues at Berkeley Lab and Jefferson Lab joined forces to lick the flashover problem.

"Ideally you want a good insulator with a surface that’s just slightly resistive, so charge can drain off," Brown explains, "and you want the resistivity even over the length of the ceramic."

Tests implanting titanium, gold, and platinum ions a few billionths of a meter into the surface of small ceramic coupons established that indeed surface resistivity could be controlled; the collaborators settled on platinum, which does not oxidize and makes a good cathode material.

The remaining challenge was to scale up the process from samples the size of postage stamps to cylinders as big as cooking pots. The Jefferson Lab team built a special cradle to fit on the target end of the implanter, tilted to hold the cylinder at a 55-degree angle to the ion beam and fitted to slowly rotate it as the broad beam played over the entire inner surface. The device was immediately nicknamed the "rotisserie."

"We are used to dealing with targets a hundred times smaller and implantation times of a few minutes to a few hours," Brown says, "It takes several days to process a single accelerator column, running the ion source at maximum beam."

Brown credits physicist Efim Oks of the High-Current Electronics Institute in Tomsk, Russia, working with AFRD’s Plasma Applications Group in a collaboration funded by the Department of Energy, for "getting the ion source operating at twice its former efficiency."

Of six implanted columns, two have already been assembled in the electron gun at Jefferson Lab. "We’ve had no problems whatsoever," says Phillips; indeed the gun quickly began operating at far higher efficiency than before. A second electron gun is planned.

Jefferson Lab’s free-electron laser, which has already achieved energies of 1.7 kilowatts, is being upgraded to far higher 10-kilowatt energies. A dependable high-voltage electron gun is essential to the effort. By tailoring the surface resistivity of its accelerator columns through metal ion implantation, the collaborators have met a major challenge to operating the gun at high field strengths without breakdown.

In Memoriam: James A. Harris

James Harris, the first black scientist to participate in major programs to identify new elements, died on Tuesday, Dec. 12 of a sudden illness. He was 68.

Harris was part of the Lab team that identified elements 104 and 105. As a member of the Nuclear Chemistry Division, he worked at Berkeley Lab starting in 1960 and until his retirement in 1988.

Born in Waco, Texas in 1932, Harris moved to the Bay Area in his teens and returned to Texas to earn his degree in chemistry from Huston-Tillotson College in Austin.

He is survived by his wife of 43 years, Helen, his five children — Cedric, Keith, Hilda, Kimberly, and James — and two grandchildren.

The next issue of Currents will present a closer look at Harris’ life and contributions to science and the Lab.


A member of the newly established Joint Genome Institute Policy Board was misidentified in the Dec. 1 issue of Currents. His correct name is James D. Watson, Nobel Laureate for the discovery of the double-helix structure of DNA, who is now President of the Cold Spring Harbor Laboratory in New York.

Lab Buys Cluster Computer to Advance Scientific Computing and Research

By Ion Bashor

In what could be a glimpse into the future of high-performance computing, Computing Sciences will buy and operate a 160-processor cluster computer from IBM to assess whether such a system can meet the day-to-day production demands of a scientific computing center.

Clusters are assemblies of commodity computers designed and networked to operate as a single system. By using off-the-shelf components, clusters can provide a cost-effective balance between price and computer performance. To date, most large scientific commodity clusters are used more for specific research applications than general-purpose production resources for computational science.

"There’s been a lot of hype about clusters over the past few years in the world of high-performance computing, but clusters are just now coming into their own," said NERSC Division Director Horst Simon. "Our goal with this new system is to see how well a commercially built cluster can perform in a demanding scientific environment. The cluster architecture could well be the supercomputer of the future and it behooves us to carefully and thoroughly test such a system."

The cluster is expected to be delivered by March 2001. It will be named "alvarez" after LBNL Nobel Laureate Luis Alvarez.

Its primary goal is to provide a testbed for NERSC and other staff to explore the applicability of such a system to support a highly parallel, numerically intensive workload. NERSC is interested in evaluating cluster architectures as an option for procuring large production computing systems in the future.

The second objective is to provide a computational resource to strategic Berkeley Lab projects and campus collaborations which require significant computational resources while requiring only limited technical support.

The system is being purchased using University of California-Directed Research and Development (UCDRD) funds, which are provided to the Laboratory by the University of California for research activities or research-related activities at the Laboratory.

One of the stated reasons for moving NERSC to Berkeley Lab was to better integrate computational science into LBNL research programs. Lab management will develop a procedure for allocating time on the cluster.

Once the system passes its acceptance tests and is running, NERSC will have priority access to the cluster. About half of resource hours will be provided to Lab and campus collaborations under the program. NERSC will provide archival storage to users of the Lab cluster and staff to configure and administer the system.

The cluster will consist of 160 Intel Pentium III processors, with a total of 500 gigabytes of shared disk space.

Said Tammy Welcome, head of the NERSC cluster computer project, "Buying a cluster now allows us to study a possible technology path of the future as well as provide limited computational support to several research efforts here at the Lab."

R&D Awards Nominations Now Accepted

Nominations for the prestigious R&D 100 Awards are due soon, with the Technology Transfer Department coordinating the submissions from Berkeley Lab. TTD would like to receive the titles of the technologies to be nominated by Jan. 16, 2001. In order to review and fine tune nominations, completed nominations should be submitted to TTD no later than Feb. 16, 2001.

The high-profile R&D 100 Awards recognize the 100 most technologically significant new products and pro-cesses of the year. Past recepients have included Polacolor film (1963), the flashcube (1965), the automated teller machine (1973), the halogen lamp (1974), the fax machine (1975), the liquid crystal display (1980), the printer (1986), Taxol anticancer drug (1993), and and HDTV (1998).

Berkeley Lab had two winners in 2000: Lara Gundel for Fine XAD Sorbent Coating and Xiaodong Xiang for Combinatorial synthesis (co-entry with Symyx Technologies, Inc.).

Products or technology must have been available for sale or licensing during the calendar year about to end (Jan.1 – Dec. 31, 2000). Judging is completed by late May and winners are notified in June.

Information and entry forms are available at http://www. Please make sure to read the section on "How To Win an R&D 100 Award."

Questions about submission dates and logistics may be submitted to Shanshan Taylor at X5366, For information on selection of technologies to nominate or other content, contact Cheryl Fragiadakis, X7020, cafragiadakis@

A video presentation by an editor of R&D Magazines on how to win an R&D 100 Award is available from Tech Transfer.

Brown-Bags for Calendar Upgrades

A series of brown-bag talks to showcase new features of the Lab’s central calendaring system will be held at noon on four consecutive Thursdays, beginning Jan. 11 in the Bldg. 50 auditorium.

Although the calendar application has a new name – Steltor CorporateTime — it is actually an upgrade of the Lab’s current Netscape Calendar. The new version will be rolled out in January. Watch Computing News, Headlines and e-mail for more information.

Scientist for the 21st Century Addresses Historic Institution

Trevor Hawkins

Trevor Hawkins made history in his native England last month, and that’s saying something in a country whose traditions run deep.

The director of Berkeley Lab’s Genomics Division and of the Department of Energy’s Joint Genome Institute (JGI), Hawkins gave a talk on Nov. 23 in London. The audience included members of the House of Lords and other Parliamentary offices, plus representatives from academia, industry and the media.

Hawkins addressed the prestigious Royal Institution of Great Britain as part of its successful Scientists for the New Century lecture series — a feat significant on its own, but made even more so by the fact that Hawkins, at 32 years old, is the youngest in the 200-year history of the Institution to deliver a formal public lecture. Michael Faraday, discoverer of electromagnetic induction and field theory, launched the tradition in the 19th century by appearing in the Christmas Lectures for Children and the Friday Evening Discourses programs.

Under the title "Genes, Society and Medicine," Hawkins covered a broad range of topics related to the Human Genome Project — the international public-private consortium whose goal is to determine the sequences of 3 billion chemical base pairs and to identify all 100,000 genes in human DNA. The JGI in Walnut Creek — a DOE collaboration of researchers primarily from Berkeley, Livermore and Los Alamos national labs — is a major player in the public effort.

After tracing the steps that led to the announcement last June of the completed draft sequence of the human genome, Hawkins explained JGI’s sequencing program, including its custom automation, computational genomics, and the terascale computing capabilities of the National Energy Research Scientific Computing Center (NERSC). He also described the related sequencing of the mouse and fugu fish genomes, the latter which is predominantly being pursued at JGI.

Hawkins concluded by projecting the potential long-term benefits of the project: earlier and more refined disease diagnoses, more personalized protocols, more sophisticated medical testing methods, and much more patient information. — Ron Kolb

Bulletin Board

Holiday Spirit Galore at Annual Reception

Santa, Fire Department staff and hundreds of other Lab employees kicked off holiday celebrations with the Director’s annual Holiday Reception on Wednesday afternoon. Happy Holidays to all!

Toy, Food and Coat Drive Continue

Berkeley Lab’s annual drive to collect toys, food and now coats to be donated to local charities continues through Dec. 19. Donation areas are located in the lobbies of the cafeteria, Bldg. 90, Bldg. 937, and Bldg. 62.

  • Food donations: nonperishable items (canned and dry goods)
  • Toys: new and gently used items for all ages (books, games, stuffed animals, etc.)
  • Coats: adult and children (all sizes), gently used

Contact Shelley Worsham at X6123 for more information.

New Financial Planning Series

The Lab’s Benefits Department has scheduled an array of financial consultations and presentations to help employees weigh their many investing options in the new year. Fidelity Investments will continue its retirement strategies consultations, with the schedule to be announced early in January.

Meanwhile, a series of financial presentations with a consultant from Merryll Lynch will kick off on Jan. 23. Because people have different styles of investing, Benefits will offer employees a chance to hear what other financial experts are saying. A certified financial manager from Merrill Lynch will cover a wide range of topics, from educational and estate planning to portfolio management. The Jan 23 presentation will be held from 12 to 1 p.m. in the Bldg. 66 auditorium.

Tips for a Safe Holiday

Fire Safety

Christmas trees can be a significant fire hazard. A freshly cut or potted tree is less of a fire hazard than a pre-cut tree due to the higher moisture content. Make sure artificial trees are made of flame retardant or noncombustible material. Secure any tree to a sturdy base to prevent it from tipping over and avoid placing it next to a fireplace, wood stove, heater or heat vent. Ornaments of plastic material should be kept from coming into contact with light bulbs; try to avoid ornaments made of styrofoam.

A video showing how severely and rapidly a Christmas tree fire develops can be seen at

Electrical Safety

• Use of festive lighting indoors, on the tree and outdoors: All outdoor lighting must be rated for outdoor use. Do not staple or nail the lights or risk damaging the insulation; use speciallly-designed plastic hooks and hangers instead. Do not use electric lights on metal artificial tree. And do not connect more than two or three light stringers together. All holiday lighting should be turned off or unplugged overnight or when leaving the home.

• Portable heaters: Make sure not to aim the heat at combustibles such as wrapped presents or trees. Electrical heaters also consume large amounts of power and can cause circuit breakers to trip, or fuses to blow when used with other electrical devices. Additional information on the use of electric portable heaters can be found at

Finally, since the holidays pose an increased fire risk, this is an ideal time to test your smoke detectors and install new batteries as needed.

For additional information contact fire protection engineers Tony Yuen at X6095, Rob Campbell at X6370, or electrical safety engineer Tom Caronna at X4314.

Update your Name, Address for W2s

Employees who have moved during the last year and did not inform Human Resources about the change will need to update the information before the holiday shutdown in order to receive the W2 form. Please refer to your most recent paycheck for the address on file and send updates to your HR Center (by e-mail or hard copy) by Thursday, Dec. 21.

Contacts for HR centers include: Computing Sciences, Kim Andrews, 50B-4230; General Sciences, Marcus Davis, 50-4037K; Energy Sciences, Teresa Hardy, 90-1121B; Biosciences, Cheryl Belton, Donner; ASD/CFO, Tina Aitkens, 937-0508; Engineering, Pamala Williams-Perkins; 46A-1132, Facilities, Deborah Martin, 69-0227.

Holiday Shutdown Information

Berkeley Lab will shut down for the holidays starting Friday, Dec. 22 and will reopen on Tuesday, Jan. 2.

For Wednesday and Thursday, Dec. 27 and 27, employees may use either vacation or leave without pay. New employees who have not accrued enough vacation may receive an advance against future accrual for these days. Should you choose to take leave without pay, make sure to request that option.

Friday, Dec. 22, Christmas Eve Holiday
Monday, Dec. 25, Christmas Holiday
Tuesday, Dec. 26, Administrative Holiday
Wednesday, Dec. 27, Employee Vacation/LWOP
Thursday, Dec. 28, Employee Vacation/LWOP
Friday, Dec. 29, New Year’s Eve Holiday
Monday, Jan. 1, New Year’s Day Holiday

The complete text of the Laboratory’s policy on holidays may be found in Regulations and Procedures Manual §2.10, located on the web at

The holiday shutdown also offers a significant opportunity for energy cost savings, which are realized provided employees shut down equipment and utilities.

A minimum work forces will continue the following functions during the shutdown, including plant maintenance technicians, the Fire Department, and staff responsible for environmental protection, radiation assessment, animal care, and mail. Special programmatic needs may require additional employees to work during the shutdown.

All employees who work during the shutdown period must have advance approval by their division director.

Those who do work during the shutdown period can contribute to the energy savings by setting back thermostats in their workspace; shutting off nonessential lights and equipment; using small portable heaters and work station lighting; and keeping outside windows and doors closed. Have a happy and safe holiday!


General Interest

DECEMBER 22, Friday


Currents Holiday
Publication Schedule

Because of the holiday break, Currents will skip one issue and not publish on Dec. 29. The first issue of 2001 will be Jan. 12.

Please make a note for all submission deadlines, calendar items and Flea Market ads. Thank you.

Send us your announcements

Announcements for the General Calendar and Bulletin Board page may be sent to Seminar & Lectures items may be mailed to currents_ calendar@ You may also fax items to X6641 or mail them to Bldg. 65B.

The deadline for the Jan. 12 issue is 5 p.m. Monday, Jan. 8.

Seminars & Lectures

JANUARY 4, Thursday


Overcharge Protection for the New Generation of Lithium Batteries
Speaker: Thomas Richardson, EET Division

Noon, Bldg. 90-3148

JANUARY 9, Tuesday


Regulation of Cell Morphology and Ashesion by Ras and its Effectors Speaker: Martin McMahon, Cancer Research Institute, University of California, San Francisco
4:00 p.m., Bldg. 84, Rm. 318

JANUARY 11, Thursday,

Rechargeable Batteries, Photochromics, Electrochemical Lithography. From Interfacial Studies to Practical Applications
Speaker: Robert Kostecki, EET Division
Noon, Bldg. 90-3148

New EH&S Course Offered

A new one-hour training class, EHS0277: Confined Space Permit Writer training, will be offered by EH&S. The course is required for employees who write procedural Confined Space Permits and will be offered according to the following schedule:

Wednesday, Jan. 10, 9-10 a.m., Bldg. 75-124
Friday, Jan. 12, 1-2 p.m., Bldg. 75-124

Wednesday, Jan. 17, 9-10 a.m., Bldg. 75-124
Friday, Jan. 19, 1-2 p.m., Bldg. 75-124

Wednesday, Jan. 24, 9-10 a.m., Bldg. 75-124
Friday, Jan. 26, 1-2 p.m., Bldg. 75-124

Wednesday, Jan. 31, 9-10 a.m., Bldg. 75-124
Friday, Feb. 2, 1-2 p.m., Bldg. 75-124

Pre-enrollment is required and space is limited to eight persons per session. To enroll, send name, employee id number, and session preferred to Questions may be directed to Susan Aberg at X2228.

EH&S Classes – January 2001







EHS 116

First Aid

8:30 – 12:30



EHS 10

Introduction to EH&S at LBNL

8:30 – 10:15

50 aud


EHS 275

Confined Space Hazards

9:00 – 11:00



EHS 330

Lead Hazard Awareness

11:00 – 12:00



EHS 123

Adult CPR

8:30 – 12:00



EHS 400

Radiation Protection-Fundamentals

1:00 – 4:00



EHS 348

Chemical Hygiene/Safety

9:30 – 12:00



EHS 231

Compressed Gas Safety

1:00 – 3:00



EHS 530

Fire Extinguisher Safety

10:00 – 11:30



EHS 260

Basic Electrical Hazard Awareness

1:00 – 2:30



EHS 432

Radiation Protection-Lab Safety

9:00 – 12:00



EHS 604

Hazardous Waste Generators

9:30 – 11:00



EHS 622

Radioactive/Mixed Waste Generators

11:00 – 12:00



EHS 280

Laser Safety

1:00 – 4:00



EHS 256

Lockout/Tagout (LO/TO)

10:00 – 11:30


* Includes EHS 392/405, followed by the orientation. Please arrive at 8:15 for sign-in.

For more information or to enroll, contact Susan Aberg at or enroll via the web at Preregistration is required for all courses except EHS 10 (Introduction to EH&S). Times and locations are subject to change. For a full, updated schedule of EH&S training sessions see

AIM Computer Classes: Jan. 2000

AIM, a Walnut Creek-based computer software training firm, provides onsite PC computer courses to Lab employees.





Window 98 Fundamentals



PowerPoint 97 Fundamentals



FrontPage 98 Fundamentals



Access 97 Fundamentals



Excel 97 Fundamentals



Illustrator 8.0 Fundamentals


Classes are held in Bldg. 51L from 9 a.m. to 4 p.m. Class descriptions and registration procedure are available online at For more information or to provide feedback about the program, contact Heather Pinto at

All in-house courses at this time are taught on PCs with Windows 98®. The 97 series programs are used by the newest version of Microsoft Office for Windows 98®. Series 6.x programs for the Mac are nearly identical to the Windows 98® versions. For users of a Mac 6.x series or an older Mac or PC version, the material covered in these courses will be applicable.

Flea Market

Autos / Supplies

‘95 BUICK REGAL GS, blk w/ tan leather int, 3.8 V6 engine, all pwr, moonrf, ac, sport susp, new tires, 124K all-highway mi, exc cond, factory maint schedule, $9,500/bo, (925) 735 6526

‘93 SATURN Sedan SL2, white w/ tan int, at, all pwr, pwr moonrf, good cond, $5,500/bo, Norm, X6724, 533-8765

‘94 SUBARU Wagon L, green w/ tan int, at, all pwr, good cond, $6,000/bo, Norm, X6724, 533-8765

‘92 DODGE GRAND CARAVAN LE, awd, anti-lock brakes, quad seating, ac, radio/tape/cd stacker, looks good, runs well, $5,000, Tracy, X5215, 727-0135

‘90 PORSCHE CARRERA 4 Cabriolet, white, 95K mi, exc cond, clean, just serviced by Kahler, $29,900/bo, John, X5901, 465-4090

‘88 CHEVY NOVA, 5 dr hatch, at, 116K mi, runs well; or '86 MAZDA 626 4 dr sedan, 5 sp man trans, 114K mi, good cond; either for $1,800, will sell car that gets highest offer, Ron, 530-1289

‘85 HONDA CIVIC, pwr steer, auto, radio/cass, 140K mi, good cond, $1,300/bo, Jens X6174, 524-7216 betw 6-7 pm.

‘85 CX2500 GTi, 4 dr sedan, sunrf, exc cond, good tires, new clutch, original owner, serviced at Citroen & European Car Service in So SF, 86K mi, Xavier, X4041, 848-4487

8’ CABOVER CAMPER, 2 side jack, $500; 7’ cabover camper, 4 corner jacks, $500; 6’ camper shell, fiberglass, $100; 2 horse circle J trailer, gold/tan, ramp, $1,400, Charlotte, 232-4506

SEAT COVERS for car, 2 for front bucket seats, blue & gray woven tweed upholstery, barely used, $10/bo; Melissa, 665-5572, lv msg

SNOW TIRE CABLE CHAINS, 2 sets, radial tire fits 14" & 15" rims, $20/ea, Maureen, X4595


BERKELEY room for short term sublet, 1 blk from UCB & LBNL shuttles, furn, new carpet, $500/ mo, avail through spring ‘01, Lisa, X4800, 665-9683

BERKELEY, short-term, elegant 1 bdrm/1 bth, lower Victorian flat, completely furn, hardwd floors, persian carpets, antiques, lush gardens, cable for tv, dsl, laundry room, quiet residential neighborhood, walking dist to BART, UC & LBNL shuttle, close to bus, avail Dec to end of Mar, $1,500/ mo+util+$35 cleaning fee every 2 weeks, $20/person/mo laundry use, Alexandra, 843-5224

KENSINGTON house, furn, 3 bdrm, view, garden patio, quiet, 2 cats, prefer visiting LBNL staff, avail 2/1/01 for spring term, flex, $1,300-1,400 depending on family size, Ruth, 526-2007

NORTH BERKELEY, sm garden cottage, 1 person only, walk to shuttle, bike provided, near Walnut Sq, breakfast daily, $28/day, $875/month, avail 12/22, Helen, 527-3252

NORTH BERKELEY, studio cottage in exchange for 10 hrs weekly of gardening, some household chores & assisting in puppy care, util + laundry facilities incl, great & congenial setting, knowledge of gardening & gen maint work req’d, avail Jan 1, Mike, X4669, 526-4238 fax,

NORTH OAKLAND condo in duplex, 3 bdrm, 2 w/ loft beds, 1.5 bth, indoor hot tub, furn, fireplace, 2 cats, no smoking, green yard, walk to shopping, BART, bus or LBNL shuttle, avail 1/20 tp 5/20/01; $2,000/mo incl hot tub, util & 1 local phone line; $1,900/mo without tub, $4,000 sec dep, Jim, 654-1900

OAKLAND, Lake Merritt, studio, close to BART, $695/mo, gas/water/trash paid, Jin, 531-6379

ROCKRIDGE, room in house, very nice neighborhood, 10 min walk to Rockridge BART and LBNL shuttle, priv bath, wonderful bay view, avail starting Jan 15, $730/mo, Helene, 655-2534.

Housing Wanted

HOUSING NEEDED, 2-3 bdrm apt for roughly 2 weeks around Christmas/New Year period, Xin, X7845, 540-6713

GRAD STUDENT & wife seek housing beg July/Aug 2001, prefer quiet neighborhood, in-law/cottage ideal, Marc, X7940

VISITING RESEARCHER from Finland arriving in Jan ‘01 would like to rent a furn/partly furn studio or 1 bdrm close to Lab transp for 3-6 mos to start, Sami Hahto,, dlhawkins@

VISITING RESEARCHER from Japan w/ family seeks 2-bdrm house/apt, 3/1 – 9/30, Yoshiyuki Shimoda,, phone: ++81-727-82-3223, or Mary Ann, X7437

VISITING RESEARCHER from Spain seeks shared living quarters or studio w/in biking or walking dist from LBNL, up to $800/mo, single, non-smoker, arrive Jan. 8 for 24 months, Igor Villareal,, or Steve Visco,


ALUMINUM BOAT, 12’ w/ motor, $800/bo; roofing repair, licensed, large or small jobs, quick response, free estimates, refs, Bob, (925) 283-3932, 947-1964

CHIHUAHUAS, 2 males, 6 mo, had puppy shots, white w/brn & blk, 1 long hair, 1 short hair, $200; pygmy goat, female, $35, Charlotte, 232-4506

DINING TABLE, rectangular, cherry stained oak, w/ 4 chairs on casters, $300; Italian glass/marble coffee & end table set, $250; solid pine rectangular coffee table, $100; Danish white queen bed w/ Serta matt & matching night stands, $200/bo, Dave, X4506

ESPRESSO MAKER, mass coffee, almost new, has milk steamer, makes great latte and espresso, $60/bo, Jon, X2794

KITCHEN WORK TABLE w/ 2 stools, $20; 17’’ computer monitor, $150, medicine cabinet, $10; German stroller, full suspension, removable board for 2nd child, $125; sideboard w/ drawers, $15; rug, $12; 2 tents for 2 persons, $15/ea; doll cradle, $10; doll highchair, $5; Fisherprice playkitchen, $10; bike lock, $10; Italian stroller, blue, $30; coffeemaker, $10; Jens, X6174, 524-7216 betw 6-7 p.m.

MINI BLINDS, lt blue, 70"Wx 45"H, $25; mini blinds, dark brown, 69 3/4"Wx41 1/2"H, $25, Maureen, X4595

MOVING SALE, dining table + 4 chairs, $40; lge comp desk w/ printer stand, storage, $50; end table, $15; full size futon, futon cover, frame (couch or bed), $80; storage cart, $5; dresser, $25; mirrored vanity w/bench, $30; office chair, $10; microwave, $40; Dawn, X7303, 649-8290

PACIFIC BELL PARK COLOR PHOTO PANORAMA, 9" x 30", shot Sept 7 at the San Diego vs. Giants night game by Lab photographer Roy Kaltschmidt, makes great Christmas gift, $65, Roy, X5731

ROLLTOP DESK, solid oak, 12 small drawers, 2 file drawers, 4 large drawers, 1 secret compartment, exc cond, opp $2,200, asking $950/bo, you transport, Barbara, X7840, (925)939-7754


TELESCOPE, amateur; chess table; buying stamps & covers, also trade, Ruth, 526-2007


GE REFRIGERATOR, old & worn yet fully operational, haul it and it's yours, Doug, X7141, 559-7850


SOUTH LAKE TAHOE, spacious chalet in Tyrol area, close to Heavenly, fully furn, peek of the lake from the front porch, sleeps 8+, sunny deck, pool & spa in club house, close to casinos & other attractions, Angela, X7712, Pat/Maria, 724-9450

TAHOE KEYS at S. Lake Tahoe, 3 bdrm house, 2-1/2 bth, fenced yard, quiet, sunny, close to attractions, prvt dock, great view, $150/night, 2 night min, Bob, (925)376-2211 (REPEAT)


RIDER/ DRIVER WANTED in Van pool for 1 person leaving 6 a.m. from Antioch to Berkeley campus Mon-Fri, Tere,, 642-9322

Flea Market Policy

Ads are accepted only from LBNL employees, retirees, and onsite DOE personnel. Only items of your own personal property may be offered for sale.

Submissions must include name, affiliation, extension, and home phone number. Ads must be submitted in writing via e-mail (, fax (X6641), or delivered/mailed to Bldg. 65B.

Ads run one week only unless resubmitted, and are repeated only as space permits. They may not be retracted once submitted for publication.

The deadline for the Jan. 12 issue Thursday, Jan. 4.