Thermodynamic geometry of minimum-dissipation driven barrier crossing

TL;DR

This paper analyzes the thermodynamic geometry of a model for bistable nucleic acid hairpins, revealing how optimal driving protocols minimize dissipation by focusing on the barrier interface, with implications for molecular motors and free energy estimation.

Contribution

It introduces a thermodynamic geometric framework for understanding minimum-dissipation protocols in bistable systems, highlighting the role of the friction coefficient at metastable interfaces.

Findings

Friction coefficient peaks sharply at metastable interfaces.

Optimal protocols linger at interfaces to maximize barrier crossing.

Principles apply to biomolecular motor design and free energy estimation.

Abstract

We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are governed by a generalized linear response friction coefficient. Our analysis and simulations demonstrate that the friction coefficient of the driving protocols is sharply peaked at the interface between metastable regions, which leads to minimum-dissipation protocols that drive rapidly within a metastable basin, but then linger longest at the interface, giving thermal fluctuations maximal time to kick the system over the barrier. Intuitively, the same principle applies generically in free energy estimation (both in steered molecular dynamics simulations and in single-molecule experiments), provides a design principle for the construction of thermodynamically efficient coupling between stochastic objects, and makes a prediction regarding the construction of evolved biomolecular motors.