ArticleThe Journal of chemical physics2022
Transition rate theory, spectral analysis, and reactive paths.
Article in The Journal of chemical physics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Deep learning of position-dependent diffusivity from umbrella sampling molecular dynamics simulations.The Journal of chemical physics · 2026Article
- Article
- A continuous-space analytical framework for committor functions from molecular dynamics.The Journal of chemical physics · 2026Article
- Following the Committor Flow: A Data-Driven Discovery of Transition Pathways.Journal of chemical theory and computation · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- An Exact Multiple-Time-Step Variational Formulation for the Committor and the Transition Rate.The journal of physical chemistry. B · 2026Article
- Membrane Permeability of Sucrose Calculated from Equilibrium Time-Correlation Functions Using Molecular Dynamics Simulations with Enhanced Sampling.The journal of physical chemistry. B · 2025Article
- Iterative variational learning of committor-consistent transition pathways using artificial neural networks.Nature computational science · 2025Article
- Reaction Coordinates Are Optimal Channels of Energy Flow.Annual review of physical chemistry · 2025Review
- Mechanism of Fe(II) Chemisorption on Hematite(001) Revealed by Reactive Neural Network Potential Molecular Dynamics.The journal of physical chemistry letters · 2025Article
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.Journal of chemical theory and computation · 2024Article
- Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP.Nature communications · 2024Article
- How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?The journal of physical chemistry. B · 2024Article
- Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations.Journal of chemical theory and computation · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Predicting rare events using neural networks and short-trajectory data.Journal of computational physics · 2023Article
- Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning.Journal of chemical theory and computation · 2023Article
- Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction.The Journal of chemical physics · 2023Article
- Density functional theory and ab initio molecular dynamics reveal atomistic mechanisms for carbonate clumped isotope reordering.Science advances · 2023Article
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Abstract
The kinetics of a dynamical system dominated by two metastable states is examined from the perspective of the activated-dynamics reactive flux formalism, Markov state eigenvalue spectral decomposition, and committor-based transition path theory. Analysis shows that the different theoretical formulations are consistent, clarifying the significance of the inherent microscopic lag-times that are implicated, and that the most meaningful one-dimensional reaction coordinate in the region of the transition state is along the gradient of the committor in the multidimensional subspace of collective variables. It is shown that the familiar reactive flux activated dynamics formalism provides an effective route to calculate the transition rate in the case of a narrow sharp barrier but much less so in the case of a broad flat barrier. In this case, the standard reactive flux correlation function decays very slowly to the plateau value that corresponds to the transmission coefficient. Treating the committor function as a reaction coordinate does not alleviate all issues caused by the slow relaxation of the reactive flux correlation function. A more efficient activated dynamics simulation algorithm may be achieved from a modified reactive flux weighted by the committor. Simulation results on simple systems are used to illustrate the various conceptual points.
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