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Robust Perron Cluster Analysis in Conformation Dynamics

Please always quote using this URN: urn:nbn:de:0297-zib-7415
  • 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.

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Author:Peter Deuflhard, Marcus Weber
Document Type:ZIB-Report
Tag:Markov chains; Perron cluster analysis; cluster algorithms; conformation dynamics
MSC-Classification:62-XX STATISTICS / 62Hxx Multivariate analysis [See also 60Exx] / 62H30 Classification and discrimination; cluster analysis [See also 68T10]
65-XX NUMERICAL ANALYSIS / 65Fxx Numerical linear algebra / 65F15 Eigenvalues, eigenvectors
91-XX GAME THEORY, ECONOMICS, SOCIAL AND BEHAVIORAL SCIENCES / 91Cxx Social and behavioral sciences: general topics (For statistics, see 62- XXg 91C05 Measurement theory / 91C20 Clustering [See also 62D05]
Date of first Publication:2003/07/01
Series (Serial Number):ZIB-Report (03-19)
Published in:Appeared in : Linear Algebra and Its Applications, Special Issue on Matrices and Mathematical Biology, Vol. 398c, 161-184 (2005)
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