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News from the San Diego Supercomputer Center

May 2008

Friends and Colleagues,

Prepare for a number of exciting announcements this summer, starting with the following request to mark your calendar and save the date: On October 14, 2008, SDSC will dedicate its new building addition at UC San Diego, kicking off the official start of a new era for SDSC. The new building addition is an 80,000 "green" square foot expansion which was awarded LEED (Leadership in Energy and Environmental Design) Silver equivalent status, meaning it met certain optimal standards for energy efficiency across a variety of sustainability categories. SDSC's new building addition will operate 53% more efficiently than California standards and earned a California Public Utilities Commission "Best Practices Award" at the annual UC/CSU/CCC Sustainability Conference.

As UCSD's largest data center, the new SDSC building addition was designed as a "living laboratory" for efficiency initiatives. These include the use of a hybrid displacement ventilation system instead of conventional air conditioning (allowing the building to thermodynamically "breathe"), the integration of building orientation, sun shades, low-E window glazing, exposed concrete interiors, balloon-framed walls and a reflecting roof (to further reduce energy consumption), and the positioning of building sensors (to measure energy consumption and thermal effectiveness), providing references for future building designs. The new 5,000 square-foot data center also features large high-efficiency air handling units that blow from below, rather than on-floor computer room air handling units. This maximizes space, uses medium-temperature rather than chilled water, and integrates sensors to match cooling with real-time loads. SDSC's existing 13,000 square-foot data center also has been retrofitted with other energy-saving innovations, with more to come.

The "greening" of SDSC doesn't stop with the building itself. SDSCer Allan Snavely and UCSD CSE Professor Tajana Simunic Rosing are instrumenting SDSC machines to investigate "green applications" which maintain low power throughout execution, SDSCer Phil Papadapolous and others have been working with colleagues at UCSD to use SDSC space for a centrally administered campus condo facility to save remodeling and energy costs for research clusters on campus, and we are already working with colleagues at Calit2, across UCSD, and within the UC system on green projects to be demonstrated at the new building dedication.

We hope you will be able to join us for this great upcoming event, so please mark your calendars for the October 14 dedication and stay tuned for an exciting summer at SDSC.

Fran Berman

First 3-D Image of a Genome
Using a multidisciplinary mix of geometry, biological research and techniques developed to solve problems on supercomputers, scientists at the University of California, San Diego have shown for the first time how a genome is organized in three-dimensional space. Researchers led by Cornelis Murre, a professor of biology at UC San Diego, and Steve Cutchin, senior scientist for visualization services at SDSC, used the gene encoding the immunoglobulin heavy chain locus - responsible for generating diverse kinds of antibodies - to demonstrate the structure of the genome. The observations, as reported by researchers in the April 18 issue of the journal Cell, permit an insight into the structure of the human genome, which until now has remained elusive. Said Murre, "it has remained unclear as to how the genome is organized in three-dimensional space. This is an important issue since the regulation of gene expression is controlled by interactions of genomic elements that are separated by large genomic distances. Thus, our team wanted to determine how the genome is structured within the nucleus."
Chronopolis Launched to Preserve Digital Data
The Chronopolis Digital Preservation Demonstration Project, one of the Library of Congress' latest efforts to collect and preserve at-risk digital information, has been officially launched as a multi-member partnership to meet the archival needs of a wide range of cultural and social domains. Chronopolis is a digital preservation data grid framework being developed by SDSC, the UC San Diego Libraries, and their partners at the National Center for Atmospheric Research (NCAR) in Colorado and the University of Maryland's Institute for Advanced Computer Studies (UMIACS). A key goal of the project is to provide cross-domain collection sharing for long-term preservation, using existing high-speed educational and research networks and mass-scale storage infrastructure investments.
Protein Data Bank Archives 50,000th Molecular Structure
The Protein Data Bank, the single worldwide repository for the three-dimensional structures of large molecules and nucleic acids, reached a significant milestone in April by releasing into its archive the 50,000th molecular structure. The PDB allows biological researchers and students to study, store, and share molecular information on a global scale. Officially founded in 1971, the archive receives about 25 new structures from scientists daily - and more than 5 million files are downloaded from the PDB archive every month. Notable examples include recent structures of the adrenergic receptor, which will revolutionize the discovery of drugs to fight heart disease, allergies, and numerous other diseases, and the many structures of enzymes from HIV, which have been pivotal in the design of new therapies to fight AIDS. The RCSB PDB is based at Rutgers University in New Jersey, under the direction of Helen M. Berman; and SDSC and the Skaggs School of Pharmacy at UC San Diego, under the leadership of Philip E. Bourne, associate director of the RCSB PDB, professor of pharmacology at the Skaggs School, and a distinguished scientist at SDSC.
A Tangled Web: MIT Researchers Unravel Secrets of Spider Silk's Strength
The strength of a biological material such as spider silk lies in the specific geometric configuration of structural proteins, which have small clusters of weak hydrogen bonds that work cooperatively to resist force and dissipate energy, according to researchers from the Massachusetts Institute of Technology (MIT). Working in collaboration with applications scientist Ross Walker at SDSC, MIT scientists found that this structure makes the lightweight natural material as strong as steel, even though the "glue" of hydrogen bonds that hold spider silk together at the molecular level is 100 to 1,000 times weaker than the powerful glue of steel's metallic bonds, or even Kevlar's covalent bonds. Based on theoretical modeling and large-scale atomistic simulations conducted on SDSC's IBM Blue Gene/L supercomputer, scientists harnessed the power of 4,096 processors working in parallel to simulate how spider silk compounds react at the atomic level to structural stresses. This new understanding of exactly how a protein's configuration enhances strength could help engineers create new materials that mimic spider silk's lightweight robustness. It could also benefit research on muscle tissue and amyloid fibers found in brain tissue.
J. Andrew McCammon Receives ACS 2008 National Award for Computational Chemistry
J. Andrew McCammon, the Joseph E. Mayer Chair of Theoretical Chemistry at UC San Diego, is the recipient of the American Chemical Society's 2008 National Award for Computers in Chemical and Pharmaceutical Research. He received the prestigious ACS award at the society's annual meeting on April 8 in New Orleans. McCammon, a chemistry and biochemistry professor in UCSD's Division of Physical Sciences, also is a Distinguished Professor of Pharmacology at UC San Diego, an Investigator of the Howard Hughes Medical Institute, and a Fellow of SDSC since 1995. As a leader in computer-aided drug discovery programs, McCammon has been using SDSC's extensive data-oriented computer resources to further his research on molecular interactions. He is credited with inventing theoretical methods for accurately predicting and interpreting molecular recognition, the rates of reactions, and other properties of chemical systems. These methods are playing an ever-increasing role in the design of new drugs, including the latest anti-HIV agent Raltegravir from Merck, developed using McCammon's methods.

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