SCIENCE & ENGINEERING NEWS

Pittsburgh, P.A. — The Pittsburgh Supercomputing Center (PSC) has received $8.6 million from the National Institutes of Health to renew the PSC program in biomedical supercomputing. The grant, which became effective August 1, covers five years and supports work by PSC scientists applying high-performance computing and communications to research in biomedicine. It also funds PSC to provide computational resources, consulting and training to biomedical researchers around the country.

“For over 12 years, the Pittsburgh Supercomputing Center has provided national leadership in applying advanced computational resources to biomedical research,” said Michael Marron, associate director for biomedical technology at NIH’s National Center for Research Resources. “This grant is part of NCRR’s ongoing commitment to bring together leading-edge computational resources and experts in computing with experts in biology and medicine to solve some of the important problems in biomedicine facing the nation.”

“Our training activities reach hundreds of biomedical researchers each year,” said biochemist David Deerfield, who directs the PSC biomedical program. “Techniques we’ve developed are helping scientists nationwide cope with the explosion of genome data. The bottom line is that a great deal of important biomedical work over the last decade wouldn’t have been done without NIH support for this program.”

Recent biomedical research at PSC includes notable results for the protein-folding problem, a major challenge of molecular biology. Scientists seek to uncover the rules governing relationships between a protein’s sequence of amino-acids and its folded shape, information that would permit drugs to be custom-engineered for particular purposes.

Simulations at PSC in 1998 by Peter Kollman and colleagues at the University of California, San Francisco tracked the folding process of a small protein in water for a full microsecond, an enormous length of time for this kind of study, 100 times longer than similar work – providing new insights into protein folding.

A series of studies in 1999-2000, by Klaus Schulten and colleagues at the University of Illinois, Urbana-Champaign, helped open a little-understood class of proteins, called mechanical proteins, to detailed study. With computer simulations, this group uncovered atomic-level details of how these proteins unfold when stretched. “During an important period of time,” noted Schulten, “PSC support has been a key to the success of computational biology.”

Other notable biomedical research at PSC includes the following:

— Computer simulations by PSC physicist Marcela Madrid and colleagues provide detailed new understanding of an HIV enzyme, reverse transcriptase, that is an important target for AIDS drugs.

— Combining high-speed networking with powerful computing, a team of researchers at PSC, Carnegie Mellon and the University of Pittsburgh Medical Center showed that functional MRI brain-imaging can be a real-time clinical tool in diagnosis of brain pathology.

— Using computationally intensive informatics techniques they developed, PSC scientist Hugh Nicholas and University of Pittsburgh biologist John Hempel revealed previously unknown relationships between sequence and folded structure in the aldehyde dehydrogenase family of enzymes, work that offers promise for reducing side-effects from chemotherapy.

— Working with the Center for Biomedical Informatics at the University of Pittsburgh, PSC scientists are assessing a range of technologies that can improve the ability of researchers at separate locations to collaborate.

Projects supported by the new NIH grant include: (1) developing improved methods to determine structure and thermodynamic properties of proteins, with Charles Brooks, Scripps Research Institute; (2) applying statistical and signal processing methods to elucidate the cooperative behavior of neurons, with Tai Sing Lee and Rob Kass, Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon; and (3) developing a database of pathology images and automated techniques for database searching, with Dr. Michael Becich, University of Pittsburgh Medical School.

Since its inception in 1987, PSC’s biomedical program has provided access to computing resources for more than 800 biomedical research projects involving nearly 1,800 researchers in 43 states and the District of Columbia. The center’s workshops on computational biology have trained more than 2,000 researchers in the use of high-performance computing for biomedical research, in such areas as sequence analysis in genome research, the structure of proteins and DNA, and biological fluid dynamics.

For more information see: http://www.psc.edu/biomed/biomed.html

The Pittsburgh Supercomputing Center is a joint effort of Carnegie Mellon University and the University of Pittsburgh together with the Westinghouse Electric Company. It was established in 1986 and is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry.

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