Scripts and molecular dynamics simulation code from the Aiden Lab. Developed by Adrian Sanborn.

The molecular dynamics code here will reproduce the simulations presented in various publications. The HOOMD-Blue package is required. Note that HOOMD was rewritten in version 2.x and the code here is not compatible with these newer versions. This code is compatible with v1.3.3, which can be compiled from source.

Simulations can be run via the command

hoomd hoomd_sim.py

hoomd_sim.py executes the main simulation commands. hoomd_utils.py contains some helper code. get_extrusion_bonds.py pre-computes the positions of each CTCF-cohesin-mediated extrusion bond at each time point in the simulation.

in.probs contains the forward and reverse probability, for each monomer, that the extrusion complex will slide past it (i.e. 1 - halting probability). It should always have the same number of lines as the polymer length N.

parameters.txt contains the major parameters, including:

• N - number of monomers, each monomer usually represents 1kb of chromatin
• steps - number of simulation steps to run during the initial collapse
• print_every - number of time steps between saving simulation snapshots
• nextrude - number of extrusion steps to run
• steps_per_extrude - number of simulation time steps for each extrusion step
• nbonds - number of extrusion bonds, randomly initialized
• T - temperature
• gamma - solvent viscosity
• epsilon, sigma, and lj_cut - describe the strength and range of the Lennard-Jones forces between polymer beads.
• k_bb and r0_bb - the strength and length of the polymer backbone bonds
• k_loop and r0_loop - the strength and length of the extrusion loop bonds
• dt - size of each time step Many parameters above are described in more detail in the HOOMD documentation.

For simulations with compartmentalization, compartments.txt contains the compartment designations as a list of the number of consecutive monomers (first column) of a designed type (second column). parameters.txt then includes the following:

• comp_spread - the variability of compartment boundary in different replicates, measured in the number of beads
• epsilon_intra - strength of LJ forces between beads of the same type
• epsilon-inter - strength of LJ forces between beads of different types

Contacts are counted as any pair of beads within a distance of 1.5. VMD can be used to visualize simulations by first importing sim_topology.xml and then sim_trajectory.dcd.