Download or read book Master Equation Models of Macromolecular Dynamics from Atomistic Simulation written by John D. Chodera and published by . This book was released on 2006 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation is concerned with the construction, validation, and use of master equation models for the study of macromolecular conformational dynamics. The master equation formalism is a powerful tool for describing the dynamics of a system that can be characterized by a discrete-state, continuous-time Markov process. Once constructed from a large quantities of short trajectories, the evolution of experimentally measurable dynamical observables can be computed and compared with experiment. Additionally, information not yet directly accessible to experiment but which may be useful in aiding understanding or the generation of novel hypotheses, such as folding pathways, transiently populated conformations, and mean first passage times, can also be easily obtained. We demonstrate that a master equation model constructed from short trajectories can describe slow conformational dynamics for a solvated alanine peptide over long times, propose a number of tests to tell whether a model constructed from short trajectories will adequately describe dynamics over long times, and describe an algorithm for the automatic construction of these models from simulation data. While the focus here is on protein folding and dynamics, these techniques are very general, and can be broadly applied to problems in biomolecular dynamics.