Journal
LINEAR ALGEBRA AND ITS APPLICATIONS
Volume 398, Issue -, Pages 161-184Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.laa.2004.10.026
Keywords
Markov chains; cluster algorithms; Perron cluster analysis; conformation dynamics
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The key to molecular conformation dynamics is the direct identification of metastable conformations, which are almost invariant sets of molecular dynamical systems. Once some reversible Markov operator has been discretized, a generalized symmetric stochastic matrix arises. This matrix can be treated by Perron cluster analysis, a rather recent method involving a Perron cluster eigenproblem. The paper presents an improved Perron cluster analysis algorithm, which is more robust than earlier suggestions. Numerical examples are included. (C) 2004 Elsevier Inc. All rights reserved.
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