Transition Path Theory for Markov Jump Processes

DOI10.1137/070699500zbMath1185.60086OpenAlexW2055484248MaRDI QIDQ3182789

Christof Schütte, Philipp Metzner, Eric Vanden-Eijnden

Publication date: 16 October 2009

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

Full work available at URL: https://doi.org/10.1137/070699500

zbMATH Keywords

directed graphinfinitesimal generatorMarkov jump processreactive trajectoriestransition path theoryprobability currenttransition rate

Mathematics Subject Classification ID

Numerical analysis or methods applied to Markov chains (65C40) Continuous-time Markov processes on discrete state spaces (60J27)

Related Items (46)

On the optimal importance process for piecewise deterministic Markov process ⋮ A graph-algorithmic approach for the study of metastability in Markov chains ⋮ Explore stochastic instabilities of periodic points by transition path theory ⋮ Computational Identification of Irreducible State-Spaces for Stochastic Reaction Networks ⋮ Finding Dominant Structures of Nonreversible Markov Processes ⋮ Metastability of the two-dimensional Blume-Capel model with zero chemical potential and small magnetic field ⋮ An efficient jet marcher for computing the quasipotential for 2D SDEs. Enhancing accuracy and efficiency of quasipotential solvers ⋮ Estimation of reactive fluxes in gradient stochastic systems using an analogy with electric circuits ⋮ Computing Freidlin's cycles for the overdamped Langevin dynamics. Application to the Lennard-Jones-38 cluster ⋮ A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations ⋮ Metastable Markov chains ⋮ Revisit of macroscopic dynamics for some non-equilibrium chemical reactions from a Hamiltonian viewpoint ⋮ Coupling rare event algorithms with data-based learned committor functions using the analogue Markov chain ⋮ Overcoming the timescale barrier in molecular dynamics: Transfer operators, variational principles and machine learning ⋮ Hamilton Dynamics in Chemical Reactions: the Maupertuis Principle, Transition Paths and Energy Landscape ⋮ Transition Path Theory for Langevin Dynamics on Manifolds: Optimal Control and Data-Driven Solver ⋮ Optimal Reaction Coordinates: Variational Characterization and Sparse Computation ⋮ Generative methods for sampling transition paths in molecular dynamics ⋮ Adaptive Importance Sampling Based on Fault Tree Analysis for Piecewise Deterministic Markov Process ⋮ Computing committors in collective variables via Mahalanobis diffusion maps ⋮ Macrophage phenotype transitions in a stochastic gene-regulatory network model ⋮ Analysis and optimization of weighted ensemble sampling ⋮ Metastable behavior in Markov processes with internal states ⋮ Continuous-time Random Walks for the Numerical Solution of Stochastic Differential Equations ⋮ Modularity revisited: a novel dynamics-based concept for decomposing complex networks ⋮ Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations ⋮ Modularity of directed networks: cycle decomposition approach ⋮ Identifying transition states of chemical kinetic systems using network embedding techniques ⋮ SPECTRWM: Spectral Random Walk Method for the Numerical Solution of Stochastic Partial Differential Equations ⋮ Transition manifolds of complex metastable systems. Theory and data-driven computation of effective dynamics ⋮ Point Cloud Discretization of Fokker--Planck Operators for Committor Functions ⋮ Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading ⋮ Local and global perspectives on diffusion maps in the analysis of molecular systems ⋮ Statistical analysis of the first passage path ensemble of jump processes ⋮ Transitions States of Stochastic Chemical Kinetic Systems ⋮ Reactive trajectories and the transition path process ⋮ Extending transition path theory: periodically driven and finite-time dynamics ⋮ A probabilistic decomposition-synthesis method for the quantification of rare events due to internal instabilities ⋮ A Mathematical Framework for Exact Milestoning ⋮ Flows in complex networks: theory, algorithms, and application to lennard-Jones cluster rearrangement ⋮ Sticky Brownian Motion and Its Numerical Solution ⋮ Metastability of reversible random walks in potential fields ⋮ A Convergent Discretization Method for Transition Path Theory for Diffusion Processes ⋮ Collapse of transitional wall turbulence captured using a rare events algorithm ⋮ Data-driven efficient solvers for Langevin dynamics on manifold in high dimensions ⋮ Markov Model Theory

This page was built for publication: Transition Path Theory for Markov Jump Processes