Special Topic: Markov Models of Molecular Kinetics

Abstract

The Journal of Chemical Physics (JCP) article collection on Markov Models of Molecular Kinetics (MMMK) features recent advances developing and using Markov State Models (MSMs) in atomistic molecular simulations and related applications. This editorial provides a brief overview of the state of the art in the field and relates it to the articles in this JCP collection.

References in corpus (30)

• Escaping free-energy minima
• A nonequilibrium equality for free energy differences
• Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
• A Data-Driven Approximation of the Koopman Operator: Extending Dynamic Mode Decomposition
• On Dynamic Mode Decomposition: Theory and Applications
• Identification of slow molecular order parameters for Markov model construction
• VAMPnets: Deep learning of molecular kinetics
• Simulating rare events in equilibrium or non-equilibrium stochastic systems
• Caliber based spectral gap optimization of order parameters (SGOOP) for sampling complex molecular systems
• Variational cross-validation of slow dynamical modes in molecular kinetics
• Variational Encoding of Complex Dynamics
• Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules
• Galerkin Approximation of Dynamical Quantities using Trajectory Data
• Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
• Hierarchical Nystrom Methods for Constructing Markov State Models for Conformational Dynamics
• Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias
• Variational Selection of Features for Molecular Kinetics
• Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics
• Artificial Intelligence Assists Discovery of Reaction Coordinates and Mechanisms from Molecular Dynamics Simulations
• Identification and Analysis of Transition and Metastable Markov States
• Identification of kinetic order parameters for non-equilibrium dynamics
• The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models
• Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics
• xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
• Cycle representatives for the coarse-graining of systems driven into a non-equilibrium steady state
• A kernel-based approach to molecular conformation analysis
• Dimensional Reduction of Markov State Models from Renormalization Group Theory
• Molecular search with conformational change: One-dimensional discrete-state stochastic model
• Non-equilibrium Markov state modeling of periodically driven biomolecules
• Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Cited by in corpus (10)

• Perspective on integrating machine learning into computational chemistry and materials science
• Thirty years of molecular dynamics simulations on posttranslational modifications of proteins
• Correlation Functions, Mean First Passage Times and the Kemeny Constant
• Towards a Benchmark for Markov State Models: The Folding of HP35
• Coupling rare event algorithms with data-based learned committor functions using the analogue Markov chain
• Perspective: Time irreversibility in systems observed at coarse resolution
• Data-driven methods to estimate the committor function in conceptual ocean models
• Sampling a rare protein transition with a hybrid classical-quantum computing algorithm
• Reweighting non-equilibrium steady-state dynamics along collective variables
• Force probe simulations using an adaptive resolution scheme