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Computer Science Colloquium Toward Millisecond-Scale Molecular Dynamics Simulations of ProteinsDavid E. Shaw Friday, November 2, 2007, 11:30 A.M.
Directions: http://cs.nyu.edu/csweb/Location/directions.html Host
Zvi Kedem, kedem@cs.nyu.edu, (212) 998-3101 SynopsisThe ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful new tool for drug discovery. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond-about three orders of magnitude beyond the duration of the longest current MD simulations. Our research group is currently building a specialized, massively parallel machine called Anton which, when completed in late 2008, should be capable of executing millisecond-scale classical MD simulations of proteins surrounded by explicitly represented water. We have also recently completed a parallel MD package called Desmond, which uses novel algorithms and numerical techniques to achieve unprecedented simulation speed on an ordinary computational cluster. This talk will provide an overview of our work on parallel algorithms and machine architectures for high-speed MD simulation, and will describe research conducted recently within our lab in which lengthy Desmond simulations helped elucidate the dynamics and functional mechanisms of two biologically important proteins. These computational studies yielded testable predictions which have subsequently been validated through laboratory experiments. BioDavid E. Shaw received his Ph.D. from Stanford University in 1980 and served on the faculty of the Computer Science Department at Columbia University until 1986, when he turned his attention to the emerging field of computational finance. In 1988, he founded the D. E. Shaw group, an investment and technology development firm that now has approximately 1,200 employees and more than $30 billion in aggregate investment capital. In 2001, Dr. Shaw returned to full-time, hands-on scientific research, and now leads a research group in the field of computational biochemistry. His lab is currently involved in the design of novel algorithms and machine architectures for high-speed molecular dynamics simulations of proteins and other biological macromolecules, and in the application of such simulations to basic scientific research in structural biology and biochemistry and to the process of computational drug design.In 1994, President Clinton appointed Dr. Shaw to the President's Council of Advisors on Science and Technology, in which capacity he served as chairman of the Panel on Educational Technology. He has since testified before the National Science Board and several Congressional committees on various topics related to science and technology policy. Dr. Shaw is a fellow of the American Academy of Arts and Sciences, and was elected to the board of directors of the American Association for the Advancement of Science in 2000. Refreshments will be served
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