Large-scale computing in protein folding, molecular recognition, and self-assembly on Blue Gene

Jed Pitera, IBM Almaden Research Center

In late 1999, the IBM Corporation announced a five-year research program to develop a massively parallel computer architecture, Blue Gene, which would be used to simulate biomolecular processes such as protein folding. Over a decade later, Blue Gene has gone from a research vision to a real product, with Blue Gene/L and Blue Gene/P systems deployed in supercomputer centers around the world and work continuing on next generation systems. On October 7, 2009, the Blue Gene Project was awarded the U.S. National Medal of Technology and Innovation. The Blue Gene project was not just a hardware design effort, but also included a science program focused on using Blue Gene systems to study protein folding and membrane protein dynamics.

In this talk, I will describe some of those protein folding simulations as well as our ongoing research program where we use Blue Gene systems to study problems in the life sciences, chemistry, and materials science.

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