Entropy production for mechanically or chemically driven biomolecules

TL;DR

This paper analyzes entropy production in biomolecules under mechanical or chemical driving, deriving theoretical relations and clarifying the roles of different entropy sources in non-equilibrium processes.

Contribution

It provides a unified theoretical framework for entropy production in biomolecules driven mechanically or chemically, including new exact relations and clarification of degenerate states.

Findings

Total entropy change obeys an integral fluctuation theorem.

Exact relations are derived for coupled slow degrees of freedom.

Theoretical framework applies to colloidal systems and biomolecular conformational transitions.

Abstract

Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or annihilation) occurs in the molecular conformation proper or in the surrounding medium. Within a Langevin dynamics, a unique identification of these two contributions is possible. The total entropy change obeys an integral fluctuation theorem and a class of further exact relations, which we prove for arbitrarily coupled slow degrees of freedom including hydrodynamic interactions. These theoretical results can therefore also be applied to driven colloidal systems. For transitions between different internal conformations of a biomolecule involving unbalanced chemical reactions, we provide a thermodynamically consistent formulation and identify again the two sources of entropy production, which obey similar exact relations. We clarify the particular role degenerate states have in such a description.