———- Forwarded message ———-
From: Ed Lazowska <lazowska@cs.washington.edu>
Date: Thu, Apr 7, 2011 at 5:20 PM
Subject: [cs-ugrads] Talk by David E. Shaw, April 28
David Shaw has done some amazing things. Please be sure to attend
this talk on April 28.
https://www.cs.washington.edu/htbin-post/mvis/mvis?ID=1015
Joint Computer Science & Engineering / Biochemistry Colloquium
Thursday April 28, 3:30 p.m., EEB 105
Anton: A Special-Purpose Machine That
Achieves a Hundred-Fold Speedup in
Biomolecular Simulations
David E. Shaw
D. E. Shaw Research and
Center for Computational Biology and Bioinformatics, Columbia University
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 a millisecond — approximately 100 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.
The Speaker: David E. Shaw serves as chief scientist of D. E. Shaw
Research, where he leads an interdisciplinary research group in the
field of computational biochemistry, and is a Senior Research Fellow
at Columbia University. Earlier, he founded D. E. Shaw & Co., an
investment and technology development firm. Dr. Shaw serves on the
President’s Council of Advisors on Science and Technology, and
recently co-chaired the PCAST working group for assessing the Federal
Networking and Information Technology Research and Development
program. He is a fellow of the American Academy of Arts & Sciences,
and serves on the Computer Science and Telecommunications Board of the
National Academies.
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