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.


Published in:
Siam Journal On Applied Dynamical Systems, 7, 532-560
Year:
2008
Keywords:
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 Record created 2010-11-30, last modified 2018-03-17


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