TAPLab

Codes to reconstruct the topology after a polymer condensation process

Geometric descriptors of knotted and linked arcs

Codes to simulate DNA integration in DNA braids.

MD simulations in LAMMPS based on AFM data

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

Codes to model melts of supercoiled DNA plasmids

Codes to run "superstructure" a modified version of DBSCAN. See https://rupress.org/jcb/article/220/5/e202010003/211893/Parameter-free-molecular-super-structures

MD simulations of reconnecting polymer rings

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