Charles L. Brooks III is the Warner-Lambert/Parke-Davis Professor of Chemistry and a Professor of Biophysics. He is affiliated with the department of Chemistry, Biophysics Program, program in Applied Physics, Molecular Biophysics Training Program (Director), program in Chemical Biology, Bioinformatics Graduate Program, Center for Computational Medicine and Bioinformatics and the Medicinal Chemistry Interdepartmental Graduate Program. The research in the group of Charles L. Brooks III is focused on the application of statistical mechanics, quantum chemistry and computational methods to chemically and physically oriented problems in biology. The group develops and applies computational models to studies of the dynamics of proteins, nucleic acids and their complexes, including virus structure and assembly. They specifically develop novel computational methods for the inclusion of pH effects in modeling biological systems. Significant focus is in the development of a large, world-wide distributed software package for molecular simulations, CHARMM. Efforts are ongoing to explore new means of parallel and accelerated computation utilizing scalable parallel algorithms for molecular dynamics and integrated CPU/GPU computational models.
- Vibrational end electronic relaxation. The pathways of intramolecular energy redistribution within molecules and intermolecular energy transfer between molecules, which dictate chemical reactivity, are governed by the rates of these processes. The pronounced quantum nature of these processes is attributed to the large gap between vibrational and electronic energy levels.
- Proton and electron transfer reactions. The elementary steps of many complex chemical processes are based on such reactions. Their pronounced quantum nature is attributed to the light mass of protons and electrons, which often give rise to quantum tunneling and zero-point energy effects.
- Nonadiabatic dynamics. Such dynamics underlie photochemistry and nonlinear spectroscopy is quantum in nature since it involves simultaneous motion on several potential surfaces that correspond to different electronic or vibrational states.
The challenge involved in simulating the quantum molecular dynamics of such systems has to do with the fact that the computational effort involved in solving the time-dependent Schrodinger equation is exponentially larger than that involved in Newton’s equations. As a result, a numerically exact solution of the Schrondinger equation is not feasible for a system that consists of more than a few atoms. The main research thrust of the Geva group is aimed at developing rigorous and accurate mixed quantum-classical, quasi-classical and semiclassical methods that would make it possible to simulate equilibrium and nonequilibrium quantum dynamics of systems that consist of hundreds of atoms and molecules. We put emphasis on applications to experimentally-relevant disordered complex condensed phase systems such as molecular liquids, which serve as hosts for many important chemical processes. We also specialize in modeling and analyzing different types of time resolved electronic and vibrational spectra that are used to probe molecular dynamics in those systems, often in collaboration with experimental groups.
In order to understand the relationship between molecular structure and dynamics and biological function, the Frank research group seeks to develop and deploy integrative modeling tools to elucidate the structure and dynamics of biologically relevant molecules. Our methods will utilize readily accessible experimental observables from a variety of sources to first guide structure prediction efforts and then guide atomistic simulations to map the entire conformational landscape of these molecules. We are primarily interested in using our methods to understand how functional ribonucleic acids, either by themselves or in concert with other molecules, achieve specific cellular functions. Our research makes heavy use of advanced machine learning and optimization techniques.