Architectures and Algorithms for
Millisecond-Scale Molecular Dynamics Simulations of Proteins

David E. Shaw

Chief Scientist at D. E. Shaw Research
Senior Research Fellow at Columbia's Center for Computational Biology and Bioinformatics
and
Adjunct Professor of Biomedical Informatics in Columbia's medical school

Abstract: 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 -- several orders of magnitude beyond the duration of the longest current MD simulations.  Our research group is currently building a specialized, massively parallel machine, called Anton, which should soon be capable of executing millisecond-scale MD simulations of proteins at an atomic level of detail.  Anton’s highly accelerated execution of such simulations is attributable in large part to specialized logic for the high-speed calculation of pairwise interactions between particles and/or gridpoints separated by no more than some specified cutoff radius.

In particular, each of Anton’s 512 ASICs, which are implemented using 90-nm technology, includes a “high-throughput interaction subsystem” incorporating 32 highly specialized pipelines running at 800 MHz.  During every cycle, each of these pipelines produces a pairwise-interaction result that would require approximately 50 arithmetic operations to calculate on a general-purpose processor.  Novel algorithms and architectural features are used to greatly reduce the requirements for inter- and intra-chip communication, allowing Anton to feed these pipelines and collect their results at a speed sufficient to take advantage of the machine’s computational power.  The ASIC also includes a “flexible subsystem” based on eight programmable “geometry cores,” each containing eight arithmetic pipelines.

This talk will provide an overview of our work on parallel algorithms and machine architectures for high-speed MD simulation, with special attention to the respective roles of specialized vs. general-purpose hardware, and to the techniques used to minimize communication at various levels within the system.

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 full time, 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 molecular dynamics simulations of biological macromolecules, and in the application of such simulations to basic scientific research and computer-assisted drug design.  In 1994, President Clinton appointed Dr. Shaw to the President’s Council of Advisors on Science and Technology.  He is a fellow of the American Association for the Advancement of Science, and was elected to its board of directors in 1998.  Dr. Shaw is also a fellow of the American Academy of Arts and Sciences and a member of the Computer Science and Telecommunications Board of the National Academies.