Methods for the Enhanced Sampling of (i) Long-time Kinetics and (ii) Large-scale Dynamics of Biomolecules

Ioan Andricioaei, University of California, Irvine

Abstract: I will present methods that allow for the enhanced calculation of long-time kinetics of complex classical systems based on the Wiener stochastic path integral formalism. Assigning weights to Langevin trajectories of artificially biased dynamics allows for the calculation of time correlation functions for the unbiased system of interest via re-weighting. In the context of fluctuation theorems, a similar strategy allows for the analytical derivation of new, exact formulas for the entropy-enthalpy components of the free energy directly from non-equilibrium dynamics. Secondly, I will present a methodology that uses molecular-dynamics derived parameters to scale up the dynamics of DNA molecules on the micrometer-microsecond scale via Kirchhoff elasticity theory for elastic rods.

Lastly I will discuss dynamical arrest transitions in proteins with the language of jamming theory, and present universality curves for protein folding, granular jamming, and the glass transition in glass forming liquids.