Seminar 16th March 2012 2 p.m. Building 27, Lecture room 2001
Theory and Simulation of Biomolecular Systems: Surmounting the Challenge of Bridging the Scales
Professor Gregory A. Voth
Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, University of Chicago
- AMBER, Artificial Neural Networks, Bioinformatics, Biomathematics, Biomechanics, Biomedical, Biomolecular Organisation, Biomolecular simulations, C, CASTEP, Complex Systems, Computer Science, Elasticity, Electromagnetism, FFT, Finite differences, Finite elements, Flight simulation, Fortran, Heat transfer, HECToR, HPC, HPCx, Human environment interaction, Iridis, Jaguar, Landscape evolution, Molecular Dynamics, Monte Carlo, Multi-physics, Multigrid solvers, Multipole methods, NWCHEM, Onetep, Pervasive computing, Quantum Chemistry, Structural biology, Systems biology, Vim, Xmgrace
- Chris-Kriton Skylaris
A multiscale theoretical and computational methodology will be presented for studying biomolecular 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 protein structures and their underlying molecular-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. A critical component of the methodology is also its connection to experimental structural data such as cryo-EM or x-ray, thus making it “hybrid” in its character. Applications this overall multiscale approach to study key features of large multi-protein complexes such the HIV-1 virus capsid, the entire HIV-1 immature virion, actin filaments, and protein-mediated membrane remodeling will be presented as time allows.