Wednesday, July 4, 2012

1207.0225 (Jan-Hendrik Prinz et al.)

Spectral rate theory    [PDF]

Jan-Hendrik Prinz, John D. Chodera, Frank Noe
Classical rate theories fail in cases where the observable(s) or order parameter(s) used are poor reaction coordinates and no clear separation between reactants and products is possible. Here, we present a general rate theory for ergodic dynamical systems in thermal equilibrium which allows the systematic estimation errors made by standard rate theories to be understood and quantified. We also elucidate the connection of spectral rate theory with the popular Markov state model- ing (MSM) approach for molecular simulation studies. An optimal rate estimator is formulated that gives robust and unbiased results even for poor reaction coordinates and can be applied to both computer simulations and single-molecule experiments. No definition of a dividing surface is required, and a measure of the reaction coordinate quality (RCQ) becomes readily available. Additionally, the respective projected probability distributions can be obtained for the reactant and product states along the observed order parameter, even when these strongly overlap. The approach is demonstrated on numerical examples and experimental single-molecule force probe data.
View original:

No comments:

Post a Comment