The 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. We are 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 such biomolecular systems. Achieving this performance
has required the development of both a novel hardware architecture and
novel algorithms, with the combination of the two selected to maximize
efficiency of execution while preserving sufficient flexibility to
accommodate anticipated advances in simulation methodology. This talk
will focus on the interplay between architectural and algorithmic
choices in the design of Anton.
Biography
Ron Dror joined D. E. Shaw Research in 2002 as its first hire and now
serves as deputy to Chief Scientist David E. Shaw. Ron's
responsibilities include group-wide coordination of interdisciplinary
research in computational structural biology, algorithms, and computer
achitecture, unified by the theme of biomolecular simulation.
Previously, he conducted both computational and experimental research in
genomics, vision, and neurophysiology. He completed a Ph.D. in
Electrical Engineering and Computer Science at MIT and an M.Phil. in
Biological Sciences as a Churchill Scholar at the University of
Cambridge, after graduating summa cum laude with a B.S. in Electrical
Engineering and a B.A. in Mathematics from Rice University.
