Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems

Ch. Schütte, W. Huisinga and P. Deuflhard
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Ch. Schütte: Freie Universität Berlin, Mathematisches Institut I
W. Huisinga: Freie Universität Berlin, Mathematisches Institut I
P. Deuflhard: Konrad-Zuse-Zentrum Berlin (ZIB)

A chapter in Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems, 2001, pp 191-223 from Springer

Abstract: Abstract The article surveys the development of novel mathematical concepts and algorithmic approaches based thereon in view of their possible applicability to biomolecular design. Both a first deterministic approach, based on the Frobenius-Perron operator corresponding to the flow of the Hamiltonian dynamics, and later stochastic approaches, based on a spatial Markov operator or on Langevin dynamics, can be subsumed under the unified mathematical roof of the transfer operator approach to effective dynamics of molecular systems. The key idea of constructing specific transfer operators especially taylored for the purpose of conformational dynamics appears as the red line throughout the paper. Different steps of the algorithm are exemplified by a trinucleotide molecular system as a small representative of possible RNA drug molecules.

Keywords: Transfer operator; Markov process; Markov chain; molecular; dynamics; biomolecular conformations; canonical ensemble; transition probability; Hamiltonian dynamics; Langevin dynamics; nearly degenerate eigenvalues; Perron cluster (search for similar items in EconPapers)
Date: 2001
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-642-56589-2_9

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DOI: 10.1007/978-3-642-56589-2_9

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