ArticleMolecular simulation2014
Recent developments in methods for identifying reaction coordinates.
Article in Molecular simulation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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Who cites it
16 citing papers in PubMed.
- The role of fluctuations in the nucleation process.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Reaction Coordinates Are Optimal Channels of Energy Flow.Annual review of physical chemistry · 2025Review
- Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation.Nature communications · 2025Article
- Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.Journal of chemical theory and computation · 2024Article
- Exact reaction coordinates for flap opening in HIV-1 protease.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Committor-Consistent Variational String Method.The journal of physical chemistry letters · 2022Article
- Transition rate theory, spectral analysis, and reactive paths.The Journal of chemical physics · 2022Article
- Article
- Mechanism for the rare fluctuation that powers protein conformational change.The Journal of chemical physics · 2022Article
- Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology.The journal of physical chemistry. B · 2021Article
- Sequential Water and Headgroup Merger: Membrane Poration Paths and Energetics from MD Simulations.Biophysical journal · 2020Article
- Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.Journal of chemical theory and computation · 2018Article
- Transition Manifolds of Complex Metastable Systems: Theory and Data-Driven Computation of Effective Dynamics.Journal of nonlinear science · 2018Article
- A benchmark for reaction coordinates in the transition path ensemble.The Journal of chemical physics · 2016Article
- Reaction mechanism and reaction coordinates from the viewpoint of energy flow.The Journal of chemical physics · 2016Article
- Reducing the cost of evaluating the committor by a fitting procedure.The Journal of chemical physics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.
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Registered trials
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.