Simulation of ring polymer melts with GPU acceleration

Publication date

2018

Authors

Schram, RaoulORCID 0000-0001-6616-230XISNI 0000000443855770
Barkema, GerardORCID 0000-0001-5289-4147ISNI 0000000117189768

Editors

Advisors

Supervisors

Document Type

Article
Open Access logo

License

taverne

Abstract

We implemented the elastic lattice polymer model on the GPU (Graphics Processing Unit), and show that the GPU is very efficient for polymer simulations of dense polymer melts. The implementation is able to perform up to 4.1⋅109 Monte Carlo moves per second. Compared to our standard CPU implementation, we find an effective speed-up of a factor 92. Using this GPU implementation we studied the equilibrium properties and the dynamics of non-concatenated ring polymers in a melt of such polymers, using Rouse modes. With increasing polymer length, we found a very slow transition to compactness with a growth exponent ν≈1/3 . Numerically we find that the longest internal time scale of the polymer scales as N3.1 , with N the molecular weight of the ring polymer.

Keywords

GPU, Ring polymers, Monte, Carlo simulations, Chromatin organization, Taverne

Citation

Schram, R D & Barkema, G T 2018, 'Simulation of ring polymer melts with GPU acceleration', Journal of Computational Physics, vol. 363, pp. 128-139. https://doi.org/10.1016/j.jcp.2018.02.027