Computing the minimal rebinding effect for nonreversible processes

DOI10.1137/20M1334966zbMATH Open1465.60067arXiv2007.08403OpenAlexW3138566856MaRDI QIDQ5857930FDOQ5857930

Susanne Röhl, Marcus Weber, Konstantin Fackeldey

Publication date: 8 April 2021

Published in: Multiscale Modeling & Simulation (Search for Journal in Brave)

Abstract: The aim of this paper is to investigate the rebinding effect, a phenomenon describing a "short-time memory" which can occur when projecting a Markov process onto a smaller state space. For guaranteeing a correct mapping by the Markov State Model, we assume a fuzzy clustering in terms of membership functions, assigning degrees of membership to each state. The macro states are represented by the membership functions and may be overlapping. The magnitude of this overlap is a measure for the strength of the rebinding effect, caused by the projection and stabilizing the system. A minimal bound for the rebinding effect included in a given system is computed as the solution of an optimization problem. Based on membership functions chosen as a linear combination of Schur vectors, this generalized approach includes reversible as well as non-reversible processes.

Full work available at URL: https://arxiv.org/abs/2007.08403

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zbMATH Keywords

Markov state modelSchur decompositionmolecular kineticsrebinding

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Stochastic matrices (15B51) Dynamic continuum models (systems of particles, etc.) in time-dependent statistical mechanics (82C21)

Cites Work

• Robust Perron cluster analysis in conformation dynamics
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• An introduction to Markov state models and their application to long timescale molecular simulation
• Matlab code for sorting real Schur forms
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• A square root approximation of transition rates for a Markov state model
• Finding metastabilities in reversible Markov chains based on incomplete sampling
• Computing the Minimal Rebinding Effect Included in a Given Kinetics

Cited In (2)

• Computing the Minimal Rebinding Effect Included in a Given Kinetics
• Discrete minification processes and reversibility

Uses Software

• Matlab

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