Theory of Biomolecular Structure and Dynamics

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This project will develop and apply methods for using computers to understand the activity of biological molecules. In particular, the molecular dynamics method (which uses computers to trace out the atomic motion within such molecules) will be further developed. Computational tools that will emerge during the next period will include more accurate models for the watery solvent around the simulated biological molecules, and more powerful methods for sampling the shapes and energetic properties of the biological molecules. Challenging new applications include exploration of the biophysics of protein kinases and Ras proteins, and new studies of cytochrome P450s and protein-assisted membrane fusion. The training of young scientists will continue to be a central focus of the project. More than a dozen group members moved on to tenure-track faculty positions in the preceding project period. A similar number of undergraduates participated in research prior to going on to graduate school; many of these students are first authors of journal articles based on their work, and several are from underrepresented groups in science. All of these recruitment activities will continue. Group members will also continue to have the opportunity to teach in regular courses at UCSD and in summer schools offered by the NSF Center for Theoretical Biological Physics. This contributes to the success of the group in training young scientists for academic and research careers, and also represents a valuable outreach activity to the scientific community. Additional societal benefits expected to emerge from the research include practical new methods for the study of molecular recognition, which will be helpful in the design of useful molecules and devices. All the computational tools developed in this project will be distributed as freely as possible.