Computing the minimal rebinding effect for nonreversible processes

DOI10.1137/20M1334966MaRDI QIDQ5857930zbMATH OpenOpenAlexFDO

Authors Susanne Röhl, Marcus Weber, Konstantin Fackeldey

Publication date 8 April 2021

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

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

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)

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.

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Cites work

• scientific article; zbMATH DE number 1779195 (Why is no real title available?)
• A square root approximation of transition rates for a Markov state model
• An introduction to Markov state models and their application to long timescale molecular simulation
• Computing the Minimal Rebinding Effect Included in a Given Kinetics
• Finding metastabilities in reversible Markov chains based on incomplete sampling
• Matlab code for sorting real Schur forms
• Meshless methods in conformation dynamics
• Robust Perron cluster analysis in conformation dynamics

Cited in

(2)

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

Describes a project that uses

Uses Software

• Matlab

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