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Inferring equilibrium transition rates from nonequilibrium protocols.

Benjamin Kuznets-Speck1, David T Limmer2

  • 1Biophysics Graduate Group, University of California, Berkeley, Berkeley, California.

Biophysical Journal
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Summary
This summary is machine-generated.

This study introduces a new thermodynamic theory to calculate how time-dependent forces change transition rates. The method estimates rate enhancement in nonequilibrium systems, applicable to molecular simulations and experiments.

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Area of Science:

  • Statistical mechanics
  • Physical chemistry
  • Biophysics

Background:

  • Inferring transition rates is crucial for understanding chemical reactions and molecular processes.
  • Nonequilibrium processes are common in biological systems and experimental techniques.
  • Existing methods often struggle to accurately capture dynamics under time-dependent driving forces.

Purpose of the Study:

  • To develop a theoretical framework for calculating equilibrium transition rates from time-dependent trajectories.
  • To quantify the rate enhancement caused by nonequilibrium protocols using stochastic thermodynamics.
  • To provide a general method applicable to various systems and dimensions.

Main Methods:

  • Utilizing results from stochastic thermodynamics.
  • Applying the Kawasaki relation to approximate nonequilibrium distribution functions.
  • Formulating a nonequilibrium transition state theory based on excess dissipation.

Main Results:

  • Developed a theory to estimate rate enhancement over equilibrium rates.
  • Demonstrated the theory's utility in one and two-dimensional systems (e.g., pulling trapped particles).
  • Validated the approach for a three-dimensional semiflexible polymer with a reactive linker.

Conclusions:

  • The developed thermodynamic approach accurately estimates rate enhancement in driven systems.
  • This method offers a powerful tool for analyzing molecular dynamics under external forces.
  • The theory is expected to be valuable for molecular simulation and force spectroscopy experiments.