Non-linear irreversible thermodynamics of single-molecule experiments

TL;DR

This paper extends irreversible thermodynamics to non-linear regimes in single-molecule experiments, analyzing RNA stretching, entropy production, and resonant phenomena with theoretical and experimental agreement.

Contribution

It develops a non-linear thermodynamic framework for single-molecule experiments, including entropy production and kinetic equations under external constraints.

Findings

Critical oscillations in RNA under external forces

Entropy produced during configurational hopping

Good agreement of hopping rates with experiments

Abstract

Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external constraints, we are able to calculate the entropy production and the general non-linear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events, and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.