Transition Path Sampling Simulations of Biological Systems

Abstract

Transition path sampling is a computational method for the simulation of rare but important events occurring in complex systems. Based on a statistical mechanics in trajectory space, transition path sampling can be applied to identify mechanisms and de- termine rate constants. Here we review the basic ideas and algorithms of transition path sampling and discuss some recent applications of this methodology to problems in mo- lecular biology including protein folding, enzyme catalysis, and processes occurring in lipid bilayers.