Entropic unfolding of flexible polymers in nanotubes: a Langevin dynamics study

Abstract

Langevin dynamics simulations of the bead–spring model are employed to study the unfolding dynamics of a flexible hairpin polymer which has been inserted in a cylindrical nanochannel. Because the hairpin polymer is not in an equilibrium configuration the molecule starts unfolding until reaching a stretched configuration inside the tube. We study the effect of the channel diameter D on the unfolding relaxation time. The effect of the number of monomers N in the folded arm on the relaxation time is also investigated. We show the unfolding time τ_R ∼ DN² for small channel diameters. These results can be explained and understood using scaling arguments of the polymer segregation theory. Our simulations are in agreement with experimental observations of DNA unfolding in solid-state nanochannels.