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Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?

Divesh Bhatt1, Daniel M Zuckerman

  • 1Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Biomedical Sciences Tower 3, Pittsburgh, PA 15260.

Journal of Chemical Theory and Computation
|August 27, 2011
PubMed
Summary
This summary is machine-generated.

Microscopic reversibility in non-equilibrium systems is not always symmetrical. This study shows exact symmetry occurs only in special conditions, with approximate symmetry in others, impacting chemistry, physics, and biology.

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Area of Science:

  • Physical Chemistry
  • Biophysics
  • Chemical Physics

Background:

  • The principle of microscopic reversibility is fundamental but has ambiguities in non-equilibrium processes.
  • Applications in protein folding/unfolding and binding/unbinding dynamics are unclear.
  • Existing kinetic analyses require extension for non-equilibrium scenarios.

Purpose of the Study:

  • To formally demonstrate conditions for precise and approximate symmetry in forward and reverse non-equilibrium processes.
  • To analyze the symmetry of protein unfolding/folding and binding/unbinding.
  • To clarify ambiguities in applying microscopic reversibility to complex systems.

Main Methods:

  • Utilizing continuum-space calculations to extend previous kinetic analyses.
  • Performing numerical calculations on toy and molecular systems.
  • Conducting exact calculations on kinetic models of induced fit in protein-ligand binding.

Main Results:

  • Demonstrated that precise symmetry of forward and reverse processes is rare, occurring only under specific conditions.
  • Identified separate conditions under which approximate symmetry is exhibited.
  • Verified exact, approximate, and broken symmetry scenarios through diverse computational and experimental data.

Conclusions:

  • The symmetry of non-equilibrium processes is conditional, not universal.
  • Challenges and ambiguities exist in designing and analyzing experiments and simulations of these processes.
  • This work provides a formal framework for understanding reversibility in complex biological and chemical systems.