ArticleThe Journal of chemical physics2019
Identification of kinetic order parameters for non-equilibrium dynamics.
Article in The Journal of chemical physics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- An Expanded Markov State Model-Transition Path Theory Framework for Ion Conduction Reactive Pathways through Membrane Channels.The journal of physical chemistry letters · 2026Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles.Journal of chemical theory and computation · 2023Article
- Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel.Journal of chemical information and modeling · 2023Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Reconciling conformational heterogeneity and substrate recognition in cytochrome P450.Biophysical journal · 2021Article
- Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions.The journal of physical chemistry. B · 2021Article
- Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.Journal of chemical theory and computation · 2020Article
- Identification of Druggable Kinase Target Conformations Using Markov Model Metastable States Analysis of apo-Abl.Journal of chemical theory and computation · 2020Article
- IR Spectroscopy Can Reveal the Mechanism of KBiophysical journal · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly varying collective variables, where subsequent analyses are made, such as clustering or estimation of free energy profiles or Markov state models. However, existing "dynamical" dimension reduction methods, such as the time-lagged independent component analysis (TICA), are only valid if the dynamics obeys detailed balance (microscopic reversibility) and typically require long, equilibrated simulation trajectories. Here, we develop a dimension reduction method for non-equilibrium dynamics based on the recently developed Variational Approach for Markov Processes (VAMP) by Wu and Noé. VAMP is illustrated by obtaining a low-dimensional description of a single file ion diffusion model and by identifying long-lived states from molecular dynamics simulations of the KcsA channel protein in an external electrochemical potential. This analysis provides detailed insights into the coupling of conformational dynamics, the configuration of the selectivity filter, and the conductance of the channel. We recommend VAMP as a replacement for the less general TICA method.
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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.