Free Energy Evaluation in Polymer Translocation via Jarzynski Equality
Abstract
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide free energy estimates for unbiased three dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite size scaling properties.
Keywords
Cite
@article{arxiv.1401.8040,
title = {Free Energy Evaluation in Polymer Translocation via Jarzynski Equality},
author = {Felipe Mondaini and Luca Moriconi},
journal= {arXiv preprint arXiv:1401.8040},
year = {2015}
}
Comments
14 pages, 5 figures, Accepted for publication in Physics Letters A