Potential Fluctuation Equality for Free Energy Evaluation

TL;DR

This paper introduces a novel method to evaluate free energy landscapes by measuring fluctuations in external potentials, eliminating the need for traditional extension-versus-force measurements, and successfully applies it to DNA base pair breaking in simulations.

Contribution

The authors propose a new approach to reconstruct free energy landscapes without EVF curves, based on potential fluctuation measurements and a theoretical proof extending Jarzynski's equality.

Findings

Accurately computed free energy barrier for DNA base pair breaking (1.7 kcal/mol)

Method aligns well with experimental free energy values (1.9-2.1 kcal/mol)

Approach reveals possible transition pathways in molecular dynamics simulations

Abstract

Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by extension-versus-force (EVF) curves. We proposed a new approach that enables us to reconstruct such FELs without necessity of measuring EVF curves. We proved that any free energy changes could be computed by measuring the fluctuations of a harmonic external potential in final states. The main assumption of our proof is that one should probably treat a potential's minimum {\lambda} (thought to be control parameter) and time in separate and independent manners. We recovered Jarzynski's equality from the introduction of a double Heaviside function. We then applied the approach in molecular dynamics (MD) simulations to compute the free energy barrier of breaking DNA base pairs (bps). The free energy barrier for breaking a CG bp in our simulations is identified as 1.7 +/- 0.2 kcal/mol that is in a very beautiful agreement with experimental values [2-4] of about 1.9 to 2.1 kcal/mol. Interestingly, the history of our computed free energies probably represents a favorable transition pathway.