Multi-resolution framework for the characterization of protein mechanisms

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Prof. Cecilia Clementi of Rice University is supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry to develop multiscale protein models and new strategies to explore complex free energy landscapes. This project uses coarse graining as the starting point to develop multi-resolution protein models, which are combined with a theoretically robust framework involving a supersymmetric generalization of the Fokker-Planck diffusion equation, and a mathematically rigorous definition of collective variables. These methods are applied to rapidly locate rare event regions in molecular dynamics landscapes, and give a robust foundation for benchmarking and creating new models of complex systems. The developed methodology is used to characterize the functional aspects of protein dynamics on timescales out of reach to conventional approaches.The broader impacts of this research are in the biological sciences. Prof. Clementi is involved with the development of courses in computational molecular biology and an outreach program involving presentations to local schools.This project is co-funded by the Molecular Biophysics program in Division of Molecular and Cellular Biology.