Macroscopic dynamics of complex metastable systems: Theory, algorithms, and application to B-DNA
This article is a survey of the present state of the transfer operator approach to the effective dynamics of metastable complex systems, and the variety of algorithms associated with it. We introduce new methods, and we emphasize both the conceptional foundations and the concrete application to the conformation dynamics of a biomolecular system. The algorithmic aspects are illustrated by means of several examples of various degrees of complexity, culminating in their application to a full-scale molecular dynamics simulation of a B-DNA oligomer.
Keywords: metastable states ; biomolecular conformations ; hidden Markov model ; maximum likelihood principle ; free energy ; stochastic differential equations ; molecular dynamics ; B-Dna ; inter base pair parameters ; Hybrid Monte-Carlo ; Hidden Markov-Models ; Molecular-Dynamics ; Free-Energy ; Identification ; Temperature ; Simulations ; Semigroups ; Reduction
Record created on 2010-11-30, modified on 2016-08-09