Free energy of a folded polymer under cylindrical confinement

Abstract

Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a function of $\lambda$, the end-to-end distance of the polymer. In the case of a flexible linear polymer, $F(\lambda )$ is a linear function in the folded regime with a gradient that scales as $f\equiv |dF/d\lambda |\sim N^0{D}^{-1.20\pm 0.01}$ for a tube of diameter $D$ and a polymer of length $N$. This is close to the prediction $f\sim N^0{D}^{-1}$ obtained from simple scaling arguments. The discrepancy is due in part to finite-size effects associated with the de-Gennes blob model. A similar discrepancy was observed for the folding of a single arm of a three-arm star polymer. We also examine backfolding of a semiflexible polymer of persistence length $P$ in the classic Odijk regime. In the overlap regime, the derivative scales $f\sim N^0{D}^{-1.72\pm 0.02}{P}^{-0.35\pm 0.01}$, which is close to the prediction $f\sim N^0{D}^{-5/3}{P}^{-1/3}$ obtained from a scaling argument that treats interactions between deflection segments at the second virial level. In addition, the measured free energy cost of forming a hairpin turn is quantitatively consistent with a recent theoretical calculation. Finally, we examine the scaling of $F(\lambda )$ for a confined semiflexible chain in the presence of an S-loop composed of two hairpins. While the predicted scaling of the free energy gradient is the same as that for a single hairpin, we observe a scaling of $f\sim D^{-1.91\pm 0.03}{P}^{-0.36\pm 0.01}$. Thus, the quantitative discrepancy between this measurement and the predicted scaling is somewhat greater for S-loops than for single hairpins.

17 papes, 12 figures