# 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 = 50 nm. Beads interact via a purely
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 k<sub>B</sub>T). 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 5<sub>1</sub> 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.
