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0.InitialConfigurations
1.Static
2.RandomJump
3.JumpToMaxDens
README.md
README.md

LAMMPS implementation of TopoII using and external code

We model a torsionally relaxed (nicked) DNA plasmid 7.2 kbp-long as a bead-spring polymer made of 1000 beads with bead-size σ=2.5 nm=7.3 bp and connected by finitely extensible springs. The persistence length of the polymer is set to lp=5σ. Beads interact via a purely steric Lennard-Jones repulsion while the TopoII-bound segment is modelled as a 50 beads (L=360 bp)-long segment displaying soft interactions with the other beads thereby allowing the TopoII-bound segment to undergo strand-crossing with a small energy penalty (2 kBT). For details in the model and the system used we refer the reader to our paper: D. Michieletto, et al. "Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation".

All the simulation scripts in this repository are set to start from a N=1000 beads thermally equilibrated polymer tied in a 51 torus knot. This and other initial configurations are provided inside the folder 0.InitialConfigurations. The files are written in the correct format to be read by LAMMPS.

The position of the TopoII-bound segment can be either:

  • 1.Static: Meaning that at the begining of the simulation (t=0), the position of the topoII is chosen randomly and then it stays in the same position during the course of the simulation.
  • 2.Random Jump: The positions of the topoII is updated with a certain frequency and it is placed randomly along the contour length of the polymer.
  • 3. Jump to maximum density: The positions of the topoII is updated with a certain frequency and it is placed in the site of maximum density of beads along the contour length of the polymer.

A brief explanation of the implementation in each of these cases and the scripts to run these simulations are provided inside the corresponding folders in this repository.

All the LAMMPS scripts have been tested using the current stable-version of LAMMPS (29-October-2020). To built the LAMMPS executables please make sure that the MOLECULE package is installed. This is a standard package that come with LAMMPS, and can be enabled before compiling, e.g. with the command: make yes-molecule.