Emerging Computational Architectures
Fall 2007 Lecture Series

Presented by...
The Architecture and Compilers Group
Computer and Information Sciences Department
University of Pennsylvania

"A Computational Microscope for Molecular Biology: Coupling Algorithms and Architecture to Simulate Proteins on Millisecond Time Scales"
Ron Dror
Senior Research Scientist, D. E. Shaw Research
Wu & Chen Auditorium, 3-4pm
Tuesday, November 13th


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.


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.

Organized by Milo Martin and Amir Roth

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