Topo2 implementation into LAMMPS with 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 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 configurations (31 and unknot) 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:
- Static:
- Random:
- Jump to maximum density: