TCB Publications - Abstract

Kirby Vandivort, James C. Phillips, Elizabeth Villa, Peter L. Freddolino, James Gumbart, Leonardo G. Trabuco, Danielle E. Chandler, Jen Hsin, Christopher B. Harrison, Laxmikant Kale, and Klaus Schulten. Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software. Proceedings of the 2008 TeraGrid Conference, 2008.

VAND2008 Atomic-level views of biomolecules, like DNA or protein, furnished foremost experimentally, have revolutionized modern science and technology, leading from DNA structure to genomics and from protein structure to modern pharmacology. In order to learn how life “works” and to turn living cells into factories for clean energy and affordable drugs, our century needs to know the entire cell,atom-by-atom. The required resolution can be furnished through advances in crystallography and electron microscopy; the former routinely providing atomic-level views of most biomolecules and the latter moving rapidly towards whole cell views. The data from these experiments are synthesized into atomic-level movies of the cells through the “computational microscope” of molecular dynamics simulations on massively parallel computers. We present a brief introduction to molecular dynamics simulation, followed by three current projects demonstrating the capabilities of the method running on TeraGrid hardware. The projects span a wide range of structural systems biology research, focusing on (i) the folding dynamics and mechanisms of small proteins; (ii) the ribosome, a large molecular machine responsible for protein synthesis; and (iii) the chromatophore, an entire organelle in photosynthetic bacteria. All three studies proceed in close collaboration with experimental researchers.


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