Speaker: David E. Shaw, Chief Scientist, D. E. Shaw Research
Title: Anton: A Special Purpose Machine That Achieves a 100-Fold Speedup in Biomolecular Simulations
3:30 p.m. reception will be followed by a lecture at 4 p.m.
Abstract:
Molecular dynamics (MD) simulation has long been recognized as a potentially transformative tool for understanding the behavior of proteins and other biological macromolecules, and for developing a new generation of precisely targeted drugs. Many biologically important phenomena, however, occur over timescales that have previously fallen far outside the reach of MD technology. We have constructed a specialized, massively parallel machine, called Anton, that is capable of performing atomic-level simulations of proteins at a speed roughly two orders of magnitude beyond that of the previous state of the art. The machine has now simulated the behavior of a number of proteins for periods as long as two milliseconds — approximately 200 times the length of the longest such simulation previously published — revealing aspects of protein dynamics that were previously inaccessible to both computational and experimental study. The speed at which Anton performs these simulations is in large part the result of a tightly coupled codesign process in which the machine architecture was developed in concert with novel algorithms, including an asymptotically optimal parallel algorithm (with highly attractive constant factors) for the range-limited N-body problem.
Biography:
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 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 biomolecular simulations, and in the application of such simulations to basic scientific research and computer-assisted drug design. The special-purpose supercomputer he designed, along with its use to answer longstanding open questions about the process of protein folding, were selected by the journal Science as one of the ten most important scientific breakthroughs of the year 2010.
Dr. Shaw was appointed to the President’s Council of Advisors on Science and Technology by President Clinton in 1994, and again by President Obama in 2009. He is a fellow of the American Academy of Arts and Sciences and of the American Association for the Advancement of Science, a member of the Computer Science and Telecommunications Board of the National Academies, and a winner of the ACM Gordon Bell Prize.
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