Theory of Biomolecular Structure and Dynamics

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Molecular dynamics simulation studies play an ever-increasing role in molecular biophysics. They provide unique insights into the mechanisms of biomolecular activity, aid in the interpretation and integration of experimental information, and - increasingly - contribute to the design of novel biomolecular and supramolecular systems. The work that will be conducted during the next project period will add to the theoretical foundations for such studies, contribute a variety of new simulation tools, and apply simulations to probe the activity of important biological systems. In the theory area, ongoing efforts to improve the rigor of free energy calculations will be extended with the goal of forging practical new methods for the study of molecular recognition. In the area of simulation tools, algorithms and codes will be created to allow faster exploration of the conformations of biopolymers and to enable molecular dynamics simulations at constant pH. Challenging new applications are planned to explore the biophysics of protein kinase regulation and the action of nicotinic acetylcholine receptors.This project will develop and apply methods for using computers to understand the activity of biological molecules. Computational tools that will emerge during the next period will include enhancements to several widely used software packages to allow molecular dynamics simulations at constant pH, enhanced sampling via accelerated molecular dynamics, and more accurate calculations of free energy. The PI will continue to distribute all codes developed in the next project period as freely as possible. The training of young scientists will continue to be a central focus of the PI's group. More than a dozen group members moved on to tenure-track faculty positions in the current 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. During the next project period, 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 PI's group in training young scientists for academic and research careers, and also represents a valuable outreach activity to the scientific community.