Grand Challenge: Millisecond-scale Molecular Dynamics Simulations

David E. Shaw, chief scientist of D.E. Shaw Research and a senior research fellow at the Center for Computational Biology and Bioinformatics, Columbia University, opened the SIAM Conference on Parallel Processing for Scientific Computing with a plenary talk on his group’s exciting new research: designing massively parallel machine architectures and algorithms for the grand challenge of millisecond-scale molecular dynamics simulations of biological macromolecules.
D.E. Shaw Research (DESRES) conducts research in computational biochemistry to elucidate structures and dynamic behaviors of proteins. Molecular dynamics simulation is an important tool for the modeling of protein-size systems (25,000–50,000 atoms in water); applications include the development of new drugs. The grand challenge is to simulate such systems as long trajectories, in the millisecond time scale, where biologically interesting phenomena occur. Among these phenomena are the folding of proteins, the binding of drugs to molecular targets, interactions between proteins, and the dynamics of conformational changes in macromolecules. To put this molecular dynamics challenge into perspective, a single processor can simulate about one nanosecond in a day, and a massively parallel code might be able to simulate about one hundred nanoseconds per day. Meeting this grand challenge will thus require close to a hundred-fold speedup, which in turn will require new massively parallel architectures and innovative algorithms. Full Story

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About Rich
FlexRex began his life as a cartoon character I created a Sun Microsystems. As the world's first "fictional blogger," he appeared in numerous parody films that made fun of the whole work-from-home thing. Somewhere along the line, the Sun IT department adopted FlexRex as their spokesman in a half-dozen security awareness films for employees. So when I left Sun recently, I started FlexRex Communications, a Marketing company in Portland, Oregon.

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