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Updated: Oct 9, 2025

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Computer simulations of melts of ring polymers with nonconserved topology: A dynamic Monte Carlo lattice model
Mattia Alberto Ubertini1, Angelo Rosa1
1Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
Abstract:
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on a fcc lattice which explicitly takes into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer strands may cross through each other. By applying the method to systems of interacting ring polymers at melt conditions, we characterize their structure and dynamics by measuring, in particular, the amounts of knots and links which are formed during the relaxation process. In comparison with standard melts of unknotted and unconcatenated rings, our simulations demonstrate that the mechanism of strand crossing makes polymer dynamics faster provided the characteristic timescale of the process is smaller than the typical timescale for chain relaxation in the unperturbed state, in agreement with recent experiments employing solutions of DNA rings in the presence of the type II topoisomerase enzyme. In the opposite case of slow rates the melt is shown to become slower, and this prediction may be easily validated experimentally.
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