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Separating forward and backward pathways in nonequilibrium umbrella sampling.

Alex Dickson1, Aryeh Warmflash, Aaron R Dinner

  • 1James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

The Journal of Chemical Physics
|June 24, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces nonequilibrium umbrella sampling to accurately calculate reaction rates by treating forward and backward pathways distinctly. The method efficiently determines rates and describes complex systems like circadian oscillations.

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Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Biophysics

Background:

  • Umbrella sampling is used for steady-state distributions.
  • Nonequilibrium processes require flux accumulation.
  • Reversible and irreversible systems differ in trajectory ensembles.

Purpose of the Study:

  • To develop a method for treating forward and backward pathways in nonequilibrium umbrella sampling.
  • To enable free calculation of exact rates as phase space flux.
  • To apply the method to systems with intermediates and steady-state limit cycles.

Main Methods:

  • Working in an extended space to separate forward and backward pathways.
  • Calculating exact rates as phase space flux.
  • Simulating a two-dimensional potential and circadian oscillations.

Main Results:

  • Nonequilibrium umbrella sampling is more efficient than forward flux sampling for systems with intermediates.
  • The method successfully describes steady-state limit cycles, including circadian oscillations.
  • The path of a limit cycle in 22 order parameters and its oscillation period were obtained.

Conclusions:

  • The developed nonequilibrium umbrella sampling method provides an efficient way to calculate rates for complex systems.
  • This technique offers a unified approach for both equilibrium and nonequilibrium processes.
  • The method is versatile, applicable to various dynamic processes including oscillations.