Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.

ABSTRACT: We demonstrate how the surrogate process approximation (SPA) method can be used to compute both the potential of mean force along a reaction coordinate and the associated diffusion coefficient using a relatively small number (10-20) of bidirectional nonequilibrium trajectories coming from a complex system. Our method provides confidence bands which take the variability of the initial configuration of the high-dimensional system, continuous nature of the work paths, and thermal fluctuations into account. Maximum-likelihood-type methods are used to estimate a stochastic differential equation (SDE) approximating the dynamics. For each observed time series, we estimate a new SDE resulting in a collection of SPA models. The physical significance of the collection of SPA models is discussed and

SUBMITTER: Calderon CP 

PROVIDER: S-EPMC2832035 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature