Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulation


The Journal of Chemical Physics, 86:1567–1585, 1987


In order to examine the validity of the reptation model of motion in a dense collection of polymers, dynamic Monte Carlo (MC) simulations of polymer chains composed of n beads confined to a diamond lattice were undertaken as a function of polymer concentration ϕ and degree of polymerization n. We demonstrate that over a wide density range these systems exhibit the experimentally required molecular weight dependence of the center‐of‐mass self‐diffusion coefficient D∼n−2.1 and the terminal relaxation time of the end‐to‐end vector τR∼n3.4. Thus, these systems should represent a highly entangled collection of polymers appropriate to look for the existence of reptation. The time dependence of the average single bead mean‐square displacement, as well as the dependence of the single bead displacement on position in the chain were examined, along with the time dependence of the center‐of‐mass displacement. Furthermore, to determine where in fact a well‐defined tube exists, the mean‐square displacements of a polymer chain down and perpendicular to its primitive path defined at zero time were calculated, and snapshots of the primitive path as a function of time are presented. For an environment where all the chains move, no evidence of a tube, whose existence is central to the validity of the reptation model, was found. However, if a single chain is allowed to move in a partially frozen matrix of chains (where all chains but one are pinned every ne beads, and where between pin points the other chains are free to move), reptation with tube leakage is recovered for the single mobile chain. The dynamics of these chains possesses aspects of Rouse‐like motion; however, unlike a Rouse chain, these chains undergo highly cooperative motion that appears to involve a backflow between chains to conserve constant average density. While these simulations cannot preclude the onset of reptation at higher molecular weight, they strongly argue at a minimum for the existence with increasing n of a crossover regime from simple Rouse dynamics in which reptation plays a minor role at best.