Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.
An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.
SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom.
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Brackley
SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom.
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Morozov
SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom.
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Marenduzzo
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004548:Elasticity; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011108:Polymers / Q000737:chemistry*; D012984:Software
D011108:Polymers; D004247:DNA