ArticleThe journal of physical chemistry letters2022
Committor-Consistent Variational String Method.
Article in The journal of physical chemistry letters, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Learning the reaction coordinate: collective variables from physical intuition to generative models.Digital discovery · 2026Review
- Following the Committor Flow: A Data-Driven Discovery of Transition Pathways.Journal of chemical theory and computation · 2026Article
- The role of fluctuations in the nucleation process.Proceedings of the National Academy of Sciences of the United States of America · 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
- Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space.Nature communications · 2025Article
- Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.Journal of chemical theory and computation · 2024Article
- Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib.Journal of chemical information and modeling · 2024Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning.Journal of chemical theory and computation · 2023Article
- Chasing collective variables using temporal data-driven strategies.QRB discovery · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
The treatment of slow and rare transitions in the simulation of complex systems poses a great computational challenge. A powerful approach to tackle this challenge is the string method, which represents the transition path as a one-dimensional curve in a multidimensional space of collective variables. Commonly used strategies for pathway optimization include aligning the tangent of the string to the local mean force or to the mean drift determined from swarms of short trajectories. Here, a novel strategy is proposed, allowing the string to be optimized based on a variational principle involving the unidirectional reactive flux expressed in terms of the time-correlation function of the committor. The method is illustrated with model systems and then probed with the alanine dipeptide and a coarse-grained model of the barstar-barnase protein complex. Successive iterations variationally refine the string toward an optimal transition pathway following the gradient of the committor between two metastable states.
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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.