Identification of kinetic order parameters for non-equilibrium dynamics

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 m...

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Veröffentlicht in:The Journal of chemical physics 2019-04, Vol.150 (16), p.164120
Hauptverfasser: Paul, Fabian, Wu, Hao, Vossel, Maximilian, de Groot, Bert L., Noé, Frank
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container_issue 16
container_start_page 164120
container_title The Journal of chemical physics
container_volume 150
creator Paul, Fabian
Wu, Hao
Vossel, Maximilian
de Groot, Bert L.
Noé, Frank
description 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.
doi_str_mv 10.1063/1.5083627
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source AIP Journals Complete; Alma/SFX Local Collection
subjects Balancing
Clustering
Computer simulation
Coupling (molecular)
Electrochemical potential
Free energy
Independent component analysis
Ion diffusion
Macromolecules
Markov chains
Molecular dynamics
Order parameters
Parameter identification
Physics
Proteins
Reduction
Resistance
Selectivity
Trajectories
title Identification of kinetic order parameters for non-equilibrium dynamics
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