CRC: Connecting Biology with Chemistry through Multiscale Theory and Computer Simulation

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Gregory A. Voth, David P. Goldenberg, Valeria P. Molinero (University of Utah) and Hans C. Anderson (Stanford University) are jointly supported to develop new theoretical and computational capabilities for biomolecular assemblies. Their approach begins at the molecular scale and extends to much larger length and time scales relevant to biological systems (peptides, proteins, RNA). Key project goals include: 1) Development of a theoretical and computer simulation capability to describe biomolecular systems at multiple scales, including a systematic approach for coarse-graining biomolecular systems starting with atomistic-scale molecular dynamics data; 2) development of new approaches to modeling real dynamical behavior in multiscale coarse-grained models; and 3) application of these new tools to end point applications including the variable resolution coarse-grained modeling of the ribosome and the HIV viral capsid. The coarse-graining method development will also involve an international collaboration with computational biophysicist V. Tozzini (Scuola Normale Superiore, Pisa Italy) and theoretical chemist Arthur F. Voter (Los Alamos National Laboratory). Collaborations on the ribosome will be with experimentalist Jody Puglisi (Stanford) and computational biologist Kevin Sanbonmatsu (Los Alamos National Laboratory), while collaborations on the HIV capsid will be with Wesley Sunquist (Utah).The 21st Century is witnessing an emerging scientific revolution at the interface between the biological and physical sciences. Computational modeling of biological systems using physical concepts and methods is a key aspect of this revolution. The specific end point applications of this project will help provide new insight into key biological processes and improve our understanding of disease mechanisms and treatments. The concepts and computer simulation methods from this project will be broadly disseminated through published literature, cyberinfrastructure, a workshop, and direct and indirect collaborations. The educational impacts will also be significant, as the multiscale biophysical modeling results and concepts will implemented into the undergraduate chemistry curriculum. Outreach to high school science teachers will also be an important component of the project. This project is funded by the Collaborative Research in Chemistry Program and is, in part, a successful continuation of a past project (Voth, PI) funded by the NSF Information Technology Research Program.