Extremely rare ultra-fast non-equilibrium processes can be close to equilibrium: RNA unfolding and refolding

TL;DR

This study numerically investigates RNA unfolding and refolding under varying forces, demonstrating that rare non-equilibrium processes can closely resemble equilibrium behavior, verified through high-precision work distribution measurements and fluctuation theorems.

Contribution

It introduces a sophisticated large-deviation algorithm to measure work distributions with unprecedented precision, confirming Crooks and Jarzynski theorems for RNA processes.

Findings

Rare non-equilibrium processes can be similar to equilibrium ones.

High-precision work measurements verify fluctuation theorems.

Configurations during near-equilibrium non-equilibrium processes resemble equilibrium states.

Abstract

We study numerically the behavior of RNA secondary structures under influence of a varying external force. This allows to measure the work $W$ during the resulting fast unfolding and refolding processes. Here, we investigate a medium-size hairpin structure. Using a sophisticated large-deviation algorithm, we are able to measure work distributions with high precision down to probabilities as small as $10^{-46}$. Due to this precision and by comparison with exact free-energy calculations we are able to verify the theorems of Crooks and Jarzynski. Furthermore, we analyze force-extension curves and the configurations of the secondary structures during unfolding and refolding for typical equilibrium processes and non-equilibrium processes, conditioned to selected values of the measured work $W$, typical and rare ones. We find that the non-equilibrium processes where the work values are close to those which are most relevant for applying Crooks and Jarzynski theorems, respectively, are most and quite similar to the equilibrium processes. Thus, a similarity of equilibrium and non-equilibrium behavior with respect to a mere scalar variable, which occurs with a very small probability but can be generated in a controlled but non-targeted way, is related to a high similarity for the set of configurations sampled along the full dynamical trajectory.