Greg Voth, Gary Ayton, and Thomas Cheatham of the University of Utah are supported by the Division of Chemistry through the Information Technology Research program in a collaborative effort between theoretical chemistry and computational biology. They will develop and implement a novel multi-scale computational grid simulation method designed to examine spatially and temporally coupled phenomena in large biomolecular assemblies. Applications include DNA, actin filaments, microtubes, and amyloid plaques.
Currently, it is computationally intractable to perform atomistic simulations on macro-scale dimensional problems. Moreover, traditional continuum simulation methods break down as the meso-scale regime is reached. This research is expected to result in the construction of a viable micro-to-macro simulation methodology which, in the context of large biological systems, will address long-range electrostatics, water vibrations, solvent interactions, conformational sampling, and external fields.