• computational simulations;
  • computer modeling;
  • macroporous polymers;
  • molecular dynamics;
  • nanotechnology;
  • simulations


The unfolding dynamics of a flexible hairpin polymer inserted in a square nanochannel is studied using Brownian dynamics simulations of the bead-spring model. Because the hairpin polymer is not an equilibrium configuration, the molecule starts unfolding until it reaches a stretched configuration inside the tube. We study the effect of varying the channel height and width D, and the number of monomers N in the folded arm on the unfolding times. We show that for square nanochannels, the unfolding time scales as DN2, for small values of D. The unfolding relaxation dynamics obeys similar mechanisms described in the escaping dynamics of partially inserted polymers in cylindrical nanotubes. We also show that the velocity of the polymer center of mass scales as D−1, in agreement with DNA unfolding experiments in solid-state nanochannels and recent computational simulations. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2013, 51, 1411–1418