ArticleJournal of chemical theory and computation2020
Value of Temporal Information When Analyzing Reaction Coordinates.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation.The journal of physical chemistry. B · 2022Article
- On distributions of barrier crossing times as observed in single-molecule studies of biomolecules.Biophysical reports · 2021Article
- Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.The journal of physical chemistry. B · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Reaction coordinates chart pathways from reactants to products of chemical reactions. Determination of reaction coordinates from ensembles of molecular trajectories has thus been the focus of many studies. A widely used and insightful choice of a reaction coordinate is the committor function, defined as the probability that a trajectory will reach the product before the reactant. Here, we consider alternatives to the committor function that add useful mechanistic information, the mean first passage time, and the exit time to the product. We further derive a simple relationship between the functions of the committor, the mean first passage time, and the exit time. We illustrate the diversity of mechanisms predicted by alternative reaction coordinates with several toy problems and with a simple model of protein searching for a specific DNA motif.
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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.