title: Extending the fluctuation theorem to describe reaction coordinates.
abstract: The fluctuation theorem describes the distribution of work done on small systems which have been pushed out of equilibrium in response to an external field. The theorem has recently been a subject of much interest for describing single-molecule experiments and simulations. In this communication, it is shown how the fluctuation theorem can be extended to describe fluctuations not only in the work done on a system, but also in a reaction coordinate. The extension explored in this work allows for a generalized derivation of Hummer and Szabo's expression (G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. 98, 3658 (2001)) for reconstructing the potential of mean force from nonequilibrium trajectories. The derivation demonstrates how implementation of this expression can be more easily facilitated. Atomistic simulations of a biomolecular system are presented which support these results.
authors.affiliation: Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.
authors.forename: Sterling
authors.initials: S
authors.lastname: Paramore
authors.forename: Gary S
authors.initials: GS
authors.lastname: Ayton
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D004058:Diffusion; D004735:Energy Transfer; D008958:Models, Molecular; D016008:Statistical Distributions; D013816:Thermodynamics