ArticleThe journal of physical chemistry. A2021
String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor.
Article in The journal of physical chemistry. A, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A continuous-space analytical framework for committor functions from molecular dynamics.The Journal of chemical physics · 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
- Advanced Computational Methods in Protein Simulations: A Case Study of Enhanced Sampling Applied to Membrane Transporters.Advances in experimental medicine and biology · 2026Review
- Nonparametric Determination of the Committor in Multimolecular Systems.Journal of chemical theory and computation · 2025Article
- Iterative variational learning of committor-consistent transition pathways using artificial neural networks.Nature computational science · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal.Journal of computational chemistry · 2025Article
- Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space.Nature communications · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE.Journal of chemical information and modeling · 2024Article
- How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?The journal of physical chemistry. B · 2024Article
- Article
- 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
- AlphaFold2-RAVE: From Sequence to Boltzmann Ranking.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
- Chasing collective variables using temporal data-driven strategies.QRB discovery · 2023Article
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Abstract
The kinetics of a dynamical system comprising two metastable states is formulated in terms of a finite-time propagator in phase space (position and velocity) adapted to the underdamped Langevin equation. Dimensionality reduction to a subspace of collective variables yields familiar expressions for the propagator, committor, and steady-state flux. A quadratic expression for the steady-state flux between the two metastable states can serve as a robust variational principle to determine an optimal approximate committor expressed in terms of a set of collective variables. The theoretical formulation is exploited to clarify the foundation of the string method with swarms-of-trajectories, which relies on the mean drift of short trajectories to determine the optimal transition pathway. It is argued that the conditions for Markovity within a subspace of collective variables may not be satisfied with an arbitrary short time-step and that proper kinetic behaviors appear only when considering the effective propagator for longer lag times. The effective propagator with finite lag time is amenable to an eigenvalue-eigenvector spectral analysis, as elaborated previously in the context of position-based Markov models. The time-correlation functions calculated by swarms-of-trajectories along the string pathway constitutes a natural extension of these developments. The present formulation provides a powerful theoretical framework to characterize the optimal pathway between two metastable states of a system.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.