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Conformation Kinetics as a Reduced Model for Transition Pathways

Please always quote using this URN: urn:nbn:de:0297-zib-8763
  • The complexity of molecular kinetics can be reduced significantly by a restriction to metastable conformations which are almost invariant sets of molecular dynamical systems. With the Robust Perron Cl uster Analysis PCCA+, developed by Weber and Deuflhard, we have a tool available which can be used to identify these conformations from a transition probability matrix. This method can also be applied to the corresponding transition rate matrix which provides important information concerning transition pathways of single molecules. In the present paper, we explain the relationship between these tw o concepts and the extraction of conformation kinetics from transition rates. Moreover, we show how transition rates can be approximated and conclude with numerical examples.

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Author:Susanna Kube, Marcus Weber
Document Type:ZIB-Report
Tag:Robust Perron Cluster Analysis; conformation kinetics; transition rates
MSC-Classification:60-XX PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX) / 60Jxx Markov processes / 60J75 Jump processes
62-XX STATISTICS / 62Hxx Multivariate analysis [See also 60Exx] / 62H30 Classification and discrimination; cluster analysis [See also 68T10]
Date of first Publication:2005/09/28
Series (Serial Number):ZIB-Report (05-43)
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