Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems

By Christof Schutte, Wilhelm Huisinga, Peter Deuflhard. 2001

132 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f46b31ef85b961b2514c494c54908d119fbaea8a

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In Molecular Biology

Citations in the corpus

Almost-invariant sets and invariant manifolds — Connecting probabilistic and geometric descriptions of coherent structures in flows (2009, methodology): “Two different families of approaches have been developed in the past for the analysis of transport and mixing processes in dynamical systems: (i) geometric methods which make use of invariant ∗ Corresponding author.”
An analytic framework for identifying finite-time coherent sets in time-dependent dynamical systems (2012, background): “Transfer operator-based methods have been very successful in resolving almost-invariant objects in a variety of applied settings, including molecular dynamics (to identify molecular conformations) [43], ocean dynamics (to map oceanic gyres) [20, 8], steady or periodically forced fluid flow (to ident”
Metastability and Dominant Eigenvalues of Transfer Operators (2006, methodology): “In the first step, the canonical ensemble has been sampled by means of the Hamiltonian system with randomized momenta [18, 36 ].”
ON ULAM APPROXIMATION OF THE ISOLATED SPECTRUM AND EIGENFUNCTIONS OF HYPERBOLIC MAPS (2006, methodology): “Perron-Frobenius operators and their spectra have been very successful in the identification of molecular conformations [24]; transfer operators have enabled the detection of strange eigenmodes in fluid flow [21]; and Perron-Frobenius methods are being used to study the designs of office plans to en”
A semi-invertible Oseledets Theorem with applications to transfer operator cocycles (2010, methodology): “The eigenfunctions associated with these isolated eigenvalues have been used to detect slowly mixing structures in a variety of physical systems, see, for example, [26, 8, 12, 7].”
Transition Path Theory for Markov Jump Processes (2009, background): “the fastest molecular motions) such that the associated subset of configurations is metastable [29].”