Stochastic Process Approximations Of Steered Molecular Dynamics Simulations
Christopher P. Calderon, Computational and Applied Mathematics, Rice University, 6100 Main St, Houston, TX 77251-1892

Methods for computing equilibrium properties from nonequilibrium simulations/data have received a lot of attention in chemical physics due to their potential relevance to a wide variety of systems. I briefly discuss an established result (the Jarzynski Equality) which can be used to develop sampling schemes that utilize nonequilibrium control strategies to force (and determine equilibrium energy changes associated with) rapid state changes in molecular systems in a prescribed amount of simulation time. Obtaining high accuracy within this type of framework often requires a large number of independent nonequilibrium trajectories. The number of realizations needed for acceptable accuracy is typically too large for practical computations; this has motivated the development of several sampling and approximation schemes.

In this talk, surrogate process approximations (SPAs) are introduced and their relevance to free energy calculations is discussed. This type of modeling is complicated by the fact that the signals coming from the atomistic process have contributions coming from many different time and length scales; numerical procedures for treating these types of issues will also be discussed. The SPA methodology is demonstrated by using it to approximate both the dynamics and free energy changes associated with (single molecule) polymer stretching and ion transport through a membrane channel.

Extended Abstract Status: Not Uploaded

Numerical Methods and Simulation of Multiscale Systems I

The Preliminary Program for 2007 Annual Meeting