Optimized free energies from bidirectional single-molecule force spectroscopy

Abstract

An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy - valid for biasing potentials of arbitrary stiffness - are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

4 pages, 2 figures

References in corpus (12)

• A nonequilibrium equality for free energy differences
• The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences
• Equilibrium free energy differences from nonequilibrium measurements: a master equation approach
• Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
• Path ensembles averages in systems driven far-from-equilibrium
• Rare events and the convergence of exponentially averaged work values
• Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality
• Single-ensemble nonequilibrium path-sampling estimates of free energy differences
• Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise
• Optimal estimates of free energies from multi-state nonequilibrium work data
• Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators
• Multiple Potentials of Mean Force from Biased Experiments Along a Single Coordinate

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