Organick Lecture Series
David E. Shaw
Chief Scientist
D.E. Shaw Research
Center for Computational Biology and Bioinformatics, Columbia University
Tuesday, April 3, 2012
104 Lower Warnock Engineering Bldg.
Reception 11:50 a.m.
Lecture 12:15 p.m.
Title: Anton: A Special-Purpose Machine That Achieves a Hundred-Fold Speedup in Biomolecular Simulations
David E. Shaw
Chief Scientist
D.E. Shaw Research
Center for Computational Biology and Bioinformatics, Columbia University
Tuesday, April 3, 2012
104 Lower Warnock Engineering Bldg.
Reception 11:50 a.m.
Lecture 12:15 p.m.
Title: Anton: A Special-Purpose Machine That Achieves a Hundred-Fold Speedup in Biomolecular Simulations
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.
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.