Inferring equilibrium transition rates from nonequilibrium protocols
arXiv:2208.05585 · doi:10.1016/j.bpj.2023.03.031
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 1 and 2 dimensions, as well as a semi-flexible polymer with a reactive linker in 3 dimensions. In all cases we find that we are able to infer the transition rates more effectively than phenomenological approaches based on Bell's law. We expect our thermodynamic approach will find use in both molecular simulation and force spectroscopy experiments.
arXiv comment4 pages, 3 figures, comments welcome
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