ArticleBiophysical journal2023
Inferring equilibrium transition rates from nonequilibrium protocols.
Article in Biophysical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics.The journal of physical chemistry. B · 2025Article
- Adaptive resetting for informed search strategies and the design of non-equilibrium steady-states.Nature communications · 2025Article
- Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.Journal of chemical theory and computation · 2024Article
- Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules.Biophysical reviews · 2022Review
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Authors and funding
2 authors.
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Abstract
We develop a theory for inferring equilibrium transition rates from trajectories driven by a time-dependent force using results from stochastic thermodynamics. Applying the Kawasaki relation to approximate the nonequilibrium distribution function in terms of the equilibrium distribution function and the excess dissipation, we formulate a nonequilibrium transition state theory to estimate the rate enhancement over the equilibrium rate due to the nonequilibrium protocol. We demonstrate the utility of our theory in examples of pulling of harmonically trapped particles in one and two dimensions, as well as a semiflexible polymer with a reactive linker in three dimensions. We expect our purely thermodynamic approach will find use in both molecular simulation and force spectroscopy experiments.
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