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Here you will find the c++ codes and LAMMPS scripts to run simulations of the topological relaxation of bead-spring polymers (which are initially knotted) by the action of a simulated TopoII protein.

MD simulations of reconnecting polymer rings

Design Informatics PCB Arduino Library

lab for anlp

2D and 3D Monte Carlo seismic tomography

MD simulations in LAMMPS based on AFM data

Geometric descriptors of knotted and linked arcs

Codes to simulate recoloring of a polymer based on competing epigenetic marks.

This is a repo for codes to simulate trans-grabbing loop extrusion factors (developed by Andrea Bonato)

Codes to simulate condensins and loop extruders that can grab polymer segments in 3D. Developed by Andrea Bonato