CARNEGIE MELLON UNIVERSITY

INNOVATIVE SUPERCOMPUTING FOR BREAKTHROUGH MOLECULAR DYNAMICS ABSTRACT A partnership between D.E. Shaw Research (DESRES) and the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center (PSC) will enable breakthrough advances in Molecular Dynamics (MD) research. DESRES has recently developed new supercomputing technology that can accelerate MD simulations by about 100-fold. For this project, DESRES has offered a gift of community access to one of their supercomputers (Anton) hosted at the NRBSC/PSC. This gift is truly unprecedented, and would allow the MD research community to investigate important outstanding questions on scales of biological time that up until now have been completely inaccessible. Many important biomolecular processes occur over times on the order of milliseconds. MD simulations provide insights into the behavior of proteins, cell membranes, RNA, and DNA at an atomic level of detail, but with discrete time steps on the order of femtoseconds (10–15 seconds), current simulations typically can reach no more than about 100 nanoseconds of biological time per day of wall-clock time for medium-size molecular systems. Thus, most existing MD simulations remain in the nanosecond range of simulated time, with only a few runs extending to a microsecond. In contrast, an Anton prototype is now able to run simulations of comparable molecular systems at rates about two orders of magnitude faster. Such dramatic acceleration could literally transform the way that molecular structure and function are studied. For the first time, scientists might visualize and predict critically important biochemical phenomena, including the structural changes that underlie protein function, and the interactions between two proteins or between a protein and a candidate drug molecule. At that level, MD simulations could begin to answer important open biomedical questions, contribute substantially to drug development, and provide direct inputs to simulations of cells and tissues run with Brownian Dynamics and related stochastic diffusion-reaction algorithms at even longer time-scales. In this highly innovative project, DESRES and the NRBSC will partner to make an Anton supercomputer available to the national research community. A national allocation mechanism will be implemented, and powerful new open-source data analysis methods will be developed as well. This project will enable breakthrough science, and may also usher in a new era of specialized computers developed for biomedical modeling and simulation, spanning molecular to cellular and tissue scales of space and time.

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