The supplied code runs the A-GRMC calculation on MATLAB. There are two main programs. The LoopExtrusionBothCondensins.m and MakeStructures.m.

The LoopExtrusionBothCondensins.m runs an A-GRMC calculation when supplied with the number of condensins, number of bound condensins, extrusion rate etc. The code

delete('LoopListsCond1/*')
delete('LoopListsCond2/*')

deletes the old files containing the loop locations. The file pofL_cdf_inv.mat contains a numerical the step-size distribution function for loop extrusion. The SamplePofL.m helper function samples this distribution function. The parameters controlling the calculation are written at the beginning of the file, as follows:

monomerSize = 100; %bps
delT = 1; %seconds
pauseTime = 7; %seconds
residenceTimeRealCond1 = 2*60; %seconds
residenceTimeRealCond2 = 6*60; %seconds
nSites = 1000000; %Each monomer is 100 bp

nCond1Total = 2550;
nCond1Bound = 1210;

nCond2Total = 343;
nCond2Bound = 211;

extrusionRateReal = 1500; %bp/s

Additional parameters controlling the simulation print frequency and maximum simulation time respectively are set as follows:

freq = 360;
tMaxSim = 60*60/delT;

To perform the calculation setup a directory as shown as below.

Then one can run the code LoopExtrusionBothCondensins.m to generate the loop locations.

The MakeStructures.m code is responsible for accepting loop location output from the previous code and generating structures. The parameters are as follows

len = 10000; %1 bead = 1 kbp;
b = 1;
rc = 1;
kBT=1;
sqrtkBT = sqrt(kBT);
relLoopStrength = 1;
k = 3/b^2*kBT;
nSamples = 100;

nLoopsCond1 = 2550;
nLoopsCond2 = 343;
nTimes = 9;
runMax = 1;
fileID = fopen('structureTest.xyz','w');

These two codes can be used to generate any of the results in our paper. Additional codes are placed in the folder named Additional Codes