Pruning degrees of freedom in biomolecular dynamics simulations through coarse-graining and continuum approaches

Klaus Schulten, Computational Biophysics, UIUC

Biomolecular dynamics simulations applied to relevant biological systems confront often length scales and time scales beyond their reach. The reason is that the systems to be simulated are too large and processes to be monitored are too slow. Through reduction in the spatial resolution of simulations one can actually extend simulations to relevant length and time scales. The lecture introduces three promising approaches to achieve such reduction in a controlled manner (amino acid-based and shape based coarse graining, multiscale molecular dynamics) and illustrates their application to self-organized assembly of lipids and proteins, to the stability of virus capsids, and to DNA loops induced by proteins. The issue of full reconstruction of degrees of freedom after pruning is addressed, too.