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Conformation Kinetics as a Reduced Model for Transition Pathways

Please always quote using this URN:urn:nbn:de:0296-matheon-4838
  • 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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Metadaten
Author:Susanna Röblitz, Marcus Weber
URN:urn:nbn:de:0296-matheon-4838
Referee:Peter Deuflhard
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2008/03/26
Release Date:2008/12/03
Institute:Freie Universität Berlin
Zuse Institute Berlin (ZIB)
Preprint Number:496
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