THEORETICAL SIMULATION OF BIOLOGICAL SYSTEMS

This proposal describes an NIH Research Resource devoted to the development of novel algorithms and software for theoretical simulations of biological systems. The core research team has expertise in quantum chemistry, statistical mechanics, molecular modeling, and biophysical theory; advances in all of these areas will be pursued and synthesized into integrated, user friendly simulation codes that will be distributed to the biophysical research community. Methodological improvements will arise both from new mathematical technology and from efficient exploitation of rapidly evolving computer architectures, including massively parallel machines. Resource participants have already developed four major simulation codes, which will form a base on which to build the new Resource software. Initial collaborative efforts will involve experimentalists whose work will benefit from the state of the art theoretical calculations on complex biological systems allowed by the Resource technology. Projects include modeling of enzymatic reactions, studies of the thermodynamics and photophysical properties of metal complexes bound to DNA, and X-ray crystallographic and NMR structural studies of proteins and nucleic acids. In subsequent years, the Resource software will be widely disseminated, with a national conference on biomolecular simulation serving as a forum for presenting advances achieved by the Resource and other research groups.