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SCS DISTINGUISHED LECTURE SERIES
4:00 PM - Wean Hall 7500
3:30 PM Distinguished Donuts - Outside the Hall
The Bruce Nelson Memorial Lecture
David E. Shaw, Ph.D.
Founder and Chief Scientist
D.E. Shaw Research and
Senior Research Fellow
Center for Computational Biology and Bioinformatics
Columbia University
Toward Millisecond-Scale Molecular Dynamics Simulations of Proteins:
Algorithms, Architectures, and ApplicationsThe 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. My 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 one or more proteins at an atomic level of detail. 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.Speaker Bio: David E. Shaw serves as chief scientist of D. E. Shaw Research and as a senior research fellow at the Center for Computational Biology and Bioinformatics at Columbia University. He received his Ph.D. from Stanford University in 1980, served on the faculty of the Computer Science Department at Columbia until 1986, and founded the D. E. Shaw group in 1988. Since 2001, Dr. Shaw has been involved in full-time, hands-on research in the field of computational biochemistry. His lab is currently involved in the development of new algorithms and machine architectures for high-speed molecular dynamics simulations of biological macromolecules, and in the application of such simulations to basic scientific research and computer-assisted drug design. In 1994, President Clinton appointed Dr. Shaw to the President’s Council of Advisors on Science and Technology. He is a fellow of the American Association for the Advancement of Science, and was elected to its board of directors in 1998. Dr. Shaw is also a fellow of the American Academy of Arts and Sciences and a member of the Computer Science and Telecommunications Board of the National Academies.
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