Coarse Grained Molecular Kinetics

Please always quote using this URN: urn:nbn:de:0297-zib-9299
  • The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by clustering methods like the Robust Perron Cluster Analysis (PCCA+). Up to now it is an open question how this coarse graining in space can be transformed to a coarse graining of the Markov chain while preserving the essential dynamic information. In the following article we aim at a consistent coarse graining of transition probabilities or rates on the basis of metastable conformations such that important physical and mathematical relations are preserved. This approach is new because PCCA+ computes molecular conformations as linear combinations of the dominant eigenvectors of the transition matrix which does not hold for other clustering methods.

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Metadaten
Author:Susanna Kube, Marcus Weber
Document Type:ZIB-Report
MSC-Classification:65-XX NUMERICAL ANALYSIS / 65Cxx Probabilistic methods, simulation and stochastic differential equations (For theoretical aspects, see 68U20 and 60H35) / 65C40 Computational Markov chains
65-XX NUMERICAL ANALYSIS / 65Fxx Numerical linear algebra / 65F15 Eigenvalues, eigenvectors
65-XX NUMERICAL ANALYSIS / 65Pxx Numerical problems in dynamical systems [See also 37Mxx] / 65P99 None of the above, but in this section
80-XX CLASSICAL THERMODYNAMICS, HEAT TRANSFER (For thermodynamics of solids, see 74A15) / 80Axx Thermodynamics and heat transfer / 80A30 Chemical kinetics [See also 76V05, 92C45, 92E20]
Date of first Publication:2006/06/27
Series (Serial Number):ZIB-Report (06-35)
Published in:Appeared as : "A coarse grained method for the identification of transition rates between molecular conformations" in Journal of Chemical Physics, 126(2) 2007