Roles of Local Non-equilibrium Free Energy in the Description of Biomolecules

Abstract

When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and Tanaka (L. Jinwoo and H. Tanaka, Sci. Rep. 2015, 5, 7832) have provided mathematical proof that such a process's non-equilibrium free energy profile over a system's substates has Jarzynski's work as content, which spontaneously dissipates while molecules perform their tasks. Here we numerically verify this fact and give a practical example where we analyze a computer simulation of RNA translocation by a ring-shaped ATPase motor. By interpreting the cyclic process of substrate translocation as a series of quenching, relaxation, and second quenching, the theory gives how much individual sub-states of the ATPase motor have been energized until the end of the process. It turns out that the efficiency of RNA translocation is $48\sim 60\%$ for most molecules, but $12\%$ of molecules achieve $80\sim 100\%$ efficiency, which is consistent with the literature. This theory would be a valuable tool for extracting quantitative information about molecular non-equilibrium behavior from experimental observations.

References in corpus (17)

• A nonequilibrium equality for free energy differences
• Stochastic thermodynamics, fluctuation theorems, and molecular machines
• The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences
• Entropy production along a stochastic trajectory and an integral fluctuation theorem
• Fluctuation theorem for stochastic dynamics
• Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
• Information heat engine: converting information to energy by feedback control
• Path ensembles averages in systems driven far-from-equilibrium
• The Fluctuation Theorem as a Gibbs Property
• Fluctuation Theorems
• Comparison of far-from-equilibrium work relations
• Dissipation and lag in irreversible processes
• Experimental free energy measurements of kinetic molecular states using fluctuation theorems
• Experimental test of the differential fluctuation theorem and a generalized Jarzynski equality for arbitrary initial states
• Recovery of free energy branches in single molecule experiments
• Local non-equilibrium thermodynamics
• Fluctuation relations: a pedagogical overview