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A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts

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Published on: December 1, 2018

Extending the fluctuation theorem to describe reaction coordinates.

Sterling Paramore¹, Gary S Ayton, Gregory A Voth

¹Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.

The Journal of Chemical Physics

|February 17, 2007

Summary

The fluctuation theorem now extends to reaction coordinates, not just work done. This advance simplifies reconstructing potential of mean force from nonequilibrium simulations.

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An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

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Published on: December 4, 2017

Area of Science:

Statistical Mechanics
Physical Chemistry
Computational Biophysics

Background:

The fluctuation theorem analyzes work distribution in small, non-equilibrium systems subjected to external fields.
It is increasingly relevant for single-molecule experiments and simulations.
Current applications primarily focus on work done on the system.

Purpose of the Study:

To extend the fluctuation theorem to encompass fluctuations in a system's reaction coordinate.
To provide a generalized derivation of Hummer and Szabo's method for potential of mean force reconstruction.
To demonstrate simplified implementation of this method.

Main Methods:

Theoretical extension of the fluctuation theorem.
Generalized derivation of the potential of mean force reconstruction expression.
Atomistic simulations of a biomolecular system.

Main Results:

The fluctuation theorem can be successfully extended to include reaction coordinate fluctuations.
This extension yields a generalized derivation of the Hummer and Szabo expression.
Atomistic simulations validate the theoretical findings.

Conclusions:

The generalized fluctuation theorem offers a more accessible approach to analyzing nonequilibrium processes.
This framework facilitates the reconstruction of potential of mean force from simulation data.
The study provides a robust theoretical and computational basis for future research in molecular dynamics.