Thermodynamic geometry of minimum-dissipation driven barrier crossing

Area of Science:

• Thermodynamics
• Biophysics
• Statistical Mechanics

Background:

• Bistable dynamics are crucial in biological systems, such as nucleic acid hairpin folding.
• Single-molecule force-extension experiments provide insights into these dynamics near equilibrium.
• Understanding optimal driving protocols is key for efficient manipulation of such systems.

Purpose of the Study:

• To explore the thermodynamic geometry of systems exhibiting bistable dynamics.
• To identify optimal (minimum-dissipation) driving protocols for these systems.
• To connect findings to free energy estimation and biomolecular motor design.

Main Methods:

• Analysis of a simple system modeling nucleic acid hairpin bistable dynamics.
• Investigation of generalized linear response friction coefficients near equilibrium.
• Characterization of friction coefficient behavior at the interface between metastable regions.

Main Results:

• Optimal driving protocols are governed by a generalized linear response friction coefficient.
• The friction coefficient exhibits sharp peaks at the interface between metastable regions.
• Minimum-dissipation protocols involve rapid driving within basins and prolonged pauses at interfaces.

Conclusions:

• Optimal protocols leverage thermal fluctuations by pausing at interfaces to facilitate transitions.
• The findings offer a design principle for efficient coupling of stochastic objects.
• The study predicts strategies for constructing evolved biomolecular motors and improving free energy estimation techniques.