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Literature DB >> 24712817

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

C A Brackley¹, A N Morozov¹, D Marenduzzo¹.

Abstract

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.

Entities: Chemical

Mesh：

Substances：
Polymers
DNA

Year: 2014 PMID： 24712817 DOI： 10.1063/1.4870088

Source DB: PubMed Journal: J Chem Phys ISSN： 0021-9606 Impact factor: 3.488

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Cited

11 in total

1. DNA elasticity from coarse-grained simulations: The effect of groove asymmetry.

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2. Self-assembling DNA nanotubes to connect molecular landmarks.

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3. Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

Authors: Oliver Henrich; Yair Augusto Gutiérrez Fosado; Tine Curk; Thomas E Ouldridge
Journal: Eur Phys J E Soft Matter Date: 2018-05-10 Impact factor: 1.890

Review 4. Mechanistic modeling of chromatin folding to understand function.

Authors: Chris A Brackey; Davide Marenduzzo; Nick Gilbert
Journal: Nat Methods Date: 2020-06-08 Impact factor: 28.547

5. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.

Authors: Fabrizio Benedetti; Aleksandre Japaridze; Julien Dorier; Dusan Racko; Robert Kwapich; Yannis Burnier; Giovanni Dietler; Andrzej Stasiak
Journal: Nucleic Acids Res Date: 2015-02-04 Impact factor: 16.971

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

1. DNA elasticity from coarse-grained simulations: The effect of groove asymmetry.

2. Self-assembling DNA nanotubes to connect molecular landmarks.

3. Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

Review 4. Mechanistic modeling of chromatin folding to understand function.

5. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.

6. Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids.

7. Effects of supercoiling on enhancer-promoter contacts.

8. Nucleosome positions alone can be used to predict domains in yeast chromosomes.

9. Flagellar arrangements in elongated peritrichous bacteria: bundle formation and swimming properties.

10. Topological digestion drives time-varying rheology of entangled DNA fluids.