The Crooks relationship in single molecule pulling simulations of coupled harmonic oscillators (2509.01801v1)

Abstract: In this work, we propose two models of coupled harmonic oscillators under Brownian motion to computationally study the applications of fluctuation theorems. This paper also illustrates how to analytically calculate free energy differences for these systems. The computational results clearly show that Crooks relation is able to predict free energy differences between initial and final canonical ensembles with around $1\%$ accuracy by using probability distributions of cumulative work done during nonequilibrium protocols carried out with velocities up to three orders of magnitude larger than the quasi-stationary evolution velocity. The curves of instantaneous force and cumulative work for the second model resemble those obtained experimentally on the unfolding of ARN molecules. Hence, the proposed systems are not just useful to illustrate the performance and conceptual significance of the fluctuation theorems, but also they could be studied as simplified models for biophysical systems.