Video: DE Shaw – Toward Millisecond-Scale Molecular Dynamics Simulations of Proteins

In this video, Dr. John Salmon, D. E. Shaw Research, presents at the International Supercomputing Conference in Dresden, Germany. Recorded June 20, 2008.
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 — about three 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, when completed in late 2008, should be capable of executing millisecond-scale classical MD simulations of one or more proteins at an atomic level of detail. We have also recently completed a parallel MD package called Desmond, which uses novel algorithms and numerical techniques to achieve unprecedented simulation speed on an ordinary computational cluster. This talk will provide an overview of our work on parallel algorithms and machine architectures for high-speed MD simulation, and will touch on selected biological research conducted recently within our lab.


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.

One Response to Video: DE Shaw – Toward Millisecond-Scale Molecular Dynamics Simulations of Proteins

  1. talking_head says:

    This video might as well just be .mp3 audio, since
    the camera just pans the talking head and not the
    slides, so important to the presentation. Thumbs down.

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