Simulation of ring polymer melts with GPU acceleration

R.D. Schram; G.T. Barkema

doi:10.1016/j.jcp.2018.02.027

Simulation of ring polymer melts with GPU acceleration

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	128-139
Journal	Journal of Computational Physics
Volume	363
DOIs	https://doi.org/10.1016/j.jcp.2018.02.027
Publication status	Published - 2018

Keywords

GPU
Ring polymers
Monte
Carlo simulations
Chromatin organization

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10.1016/j.jcp.2018.02.027

1-s2.0-S0021999118301098-mainFinal published version, 557 KBLicence: Taverne

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title = "Simulation of ring polymer melts with GPU acceleration",

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",

author = "R.D. Schram and G.T. Barkema",

year = "2018",

doi = "10.1016/j.jcp.2018.02.027",

language = "English",

volume = "363",

pages = "128--139",

journal = "Journal of Computational Physics",

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T1 - Simulation of ring polymer melts with GPU acceleration

AU - Schram, R.D.

AU - Barkema, G.T.

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - GPU

KW - Ring polymers

KW - Monte

KW - Carlo simulations

KW - Chromatin organization

U2 - 10.1016/j.jcp.2018.02.027

DO - 10.1016/j.jcp.2018.02.027

M3 - Article

SN - 0021-9991

VL - 363

SP - 128

EP - 139

JO - Journal of Computational Physics

JF - Journal of Computational Physics

ER -

Simulation of ring polymer melts with GPU acceleration

Abstract

Keywords

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