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Optimal driving protocols for bistable systems, like nucleic acid hairpins, minimize energy dissipation. These protocols accelerate through stable states and pause at interfaces, leveraging thermal fluctuations for efficient transitions.

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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.