Journal
MULTISCALE MODELING & SIMULATION
Volume 6, Issue 2, Pages 396-416Publisher
SIAM PUBLICATIONS
DOI: 10.1137/060675423
Keywords
dynamical systems; metastability; molecular conformations; cluster analysis; sampling; aggregation/disaggregation; domain decomposition
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Whenever the invariant stationary density of metastable dynamical systems decomposes into almost invariant partial densities, its computation as eigenvector of some transition probability matrix is an ill-conditioned problem. In order to avoid this computational difficulty, we suggest applying an aggregation/disaggregation method which addresses only well-conditioned subproblems and thus results in a stable algorithm. In contrast to existing methods, the aggregation step is done via a sampling algorithm which covers only small patches of the sampling space. Finally, the theoretical analysis is illustrated by two biomolecular examples.
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