A square root approximation of transition rates for a Markov state model

DOI10.1137/120899959MaRDI QIDQ2848633zbMATH OpenOpenAlexFDO

Authors Han Cheng Lie, Konstantin Fackeldey, Marcus Weber

Publication date 26 September 2013

Published in SIAM Journal on Matrix Analysis and Applications (Search for Journal in Brave)

Full work available at URL https://semanticscholar.org/paper/11b61aa05a6743e211e5d140139b15a4bcd6993f

zbMATH Keywords

linear programmingMarkov chainsmetastabilitymeshfree methodsVoronoiMarkov state models

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10)

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Cited in

(13)

• A meshless discretization method for Markov state models applied to explicit water peptide folding simulations
• A convergent discretization method for transition path theory for diffusion processes
• Finite Volumes for a Generalized Poisson-Nernst-Planck System with Cross-Diffusion and Size Exclusion
• Revisiting the state transition frequency formula
• A review of Girsanov reweighting and of square root approximation for building molecular Markov state models
• Finite Volumes for Simulation of Large Molecules
• Consistency and convergence for a family of finite volume discretizations of the Fokker-Planck operator
• Computing the minimal rebinding effect for nonreversible processes
• An overview and practical guide to building Markov state models
• Finding metastabilities in reversible Markov chains based on incomplete sampling
• Extending transition path theory: periodically driven and finite-time dynamics
• On the square-root approximation finite volume scheme for nonlinear drift-diffusion equations
• Convergences of the squareroot approximation scheme to the Fokker–Planck operator

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