Download Quantum Dynamics in the Condensed Phase

Theory and Simulation of Biomolecular Systems: Surmounting the Challenge
of Bridging the Scales
Gregory A. Voth
Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics,
The University of Chicago, Chicago, IL, USA
A multiscale and theoretical and computational methodology will be discussed for studying
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 is a method for deriving
coarse-grained models from molecular structures and their underlying atomistic-scale
interactions. This particular aspect of the work has strong connections to the theory of
renormalization, but it is more broadly developed and implemented for heterogeneous systems.
Another important component of the methodology has become the new concept of the “ultra-”
coarse-grained (UCG) model and its associated computational implementation. In the UCG
regime, e.g., at a resolution level coarser or much coarser than one amino acid residue per
effective CG particle in proteins, there exists the possibility of multiple metastable states
“within” the CG sites for a given UCG configuration. This methodology is accomplished by
augmenting existing effective particle CG schemes to allow for discrete state transitions and
configuration-dependent resolution. The UCG aspect of this research also involves 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.
Illustrations of the approach will first be provided for UCG models of liquids, while more
complex UCG applications will then be presented for large multi-protein complexes such as the
HIV-1 virus capsid assembly, actin filaments, and protein-mediated membrane remodeling as
time allows.
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