Effect of Cylindrical Confinement on the Collapse Dynamics of a Polymer

Structure and dynamics of a polymer gets significantly altered under confinement. By means of molecular dynamics simulations using the deterministic Nosé-Hoover thermostat (NHT) and stochastic Langevin thermostat (LT), we explore the effect of cylindrical confinement on the collapse kinetics of a homopolymer following an abrupt quench from good- to poor-solvent conditions. Irrespective of the thermostat, the observed collapse phenomenology consists of two distinct stages. The first stage involves the formation and growth of local connected clusters resembling pearl-necklace intermediates, ultimately culminating in a single sausage-like cluster. In the second stage, the sausage-like intermediate evolves into a spherical globule via surface-energy minimization. These two stages are disentangled using a shape parameter characterizing the individual pearls or clusters, allowing us to extract the respective relaxation times and their power-law scaling with the polymer chain length. For both NHT and LT, the pearl-necklace relaxation time τp is independent of R. On the other hand, the sausage-relaxation time τs decreases monotonically up to a certain value of R, beyond which it saturates. While under NHT the relaxation in both stages is temperature dependent, under LT the pearl-necklace stage is almost insensitive to temperature. Quantitative analysis using Arrhenius plots of the relaxation times enables us to extract the corresponding activation energies Ea. For NHT, the estimated Ea for the pearl-necklace stage is independent of R. In contrast, for both NHT and LT, Ea for the sausage-relaxation stage is significantly higher under strong confinement than under weak confinement. At a fixed temperature, the cluster growth during the pearl-necklace stage obeys a universal power law irrespective of R for both thermostats. However, for a fixed R, the behavior is nonuniversal with respect to temperature for NHT, while it is largely temperature independent for LT. These differences in the dynamics of the pearl-necklace stage are attributed to the distinct underlying transport mechanisms associated with the two thermostats. Finally, we propose viable scenarios for the experimental realization of polymer collapse inside cylindrical nanochannels.