Recent advances in theoretical and computational methodology will be presented that are designed to simulate biomolecular and other soft matter systems across multiple length and time scales. The approach provides a systematic connection between all-atom molecular dynamics, coarse-grained modeling, and mesoscopic phenomena. At the heart of the approach are methods for deriving coarse-grained models from molecular structures and their underlying atomic-scale interactions. This particular aspect of the work has strong connections to the theory of renormalization, but it is developed and implemented for heterogeneous biomolecular. An important component of the methodology has become the concept of the “ultra-” coarse-grained (UCG) model and its associated computational implementation. The latter aspect of this research concerns the unique numerical algorithms for these highly coarse-grained molecular dynamics simulations, leading to fast execution speeds that can be scaled over hundreds of thousands of computational cores. An important application of the UCG multiscale approach to study key features of large multi-protein complexes such as the long time kinetics of HIV-1 virus capsid assembly will be presented.

Ultra-coarse-graining and its application to biomolecular complexes

251st National Meeting (2016)

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