Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone
Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign
Commun. ACM, Vol. 52 (October 2009), pp. 34-41


   title={Probing biomolecular machines with graphics processors},

   author={Phillips, J.C. and Stone, J.E.},

   journal={Communications of the ACM},








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GPU acceleration and other computer performance increases will offer critical benefits to biomedical science. Computer simulation has become an integral part of the study of the structure and function of biological molecules. For years, parallel computers have been used to conduct these computationally demanding simulations and to analyze their results. These simulations function as a “computational microscope,” allowing the scientist to observe details of molecular processes too small, fast, or delicate to capture with traditional instruments. Over time, commodity GPUs (graphics processing units) have evolved into massively parallel computing devices, and more recently it has become possible to program them in dialects of the popular C/C++ programming languages.
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