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arXiv · 2606.02063

SPOCK*: A simple program for simulating knotted and concatenated polymer rings off-lattice

Franco Ferrari·Marcin R. Piątek
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Abstract

The purpose of this work is to present SPOCK*, a Monte Carlo code specifically written to investigate the thermodynamic and mechanical properties of polymers in the presence of topological constraints. The interactions between the monomers are described by a Lennard-Jones potential. Pulling forces can be applied to one or more monomers. Simple and fast algorithms have been implemented to preserve the topology and to compute the energy of the sampled conformations. After a new conformation is accepted, only the difference of energy between the new and the old conformations needs to be evaluated. In this way the simulation time grows linearly with the polymer size. A strategy based on the fluctuations of the specific heat capacity has been developed in order to avoid bottlenecks like the trapping of the system in a deep local minima at low temperature. Currently, the averages of the following observables are computed: specific heat capacity, elongation and gyration radius.

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Franco Ferrari, Marcin R. Piątek. 2026-06-01. SPOCK*: A simple program for simulating knotted and concatenated polymer rings off-lattice. https://arxiv.org/abs/2606.02063

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