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README.md 1.08 KiB

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)

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

  • Static:
  • Random:
  • Jump to maximum density: