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Happy to finally see our work on coexistence of loop-extrusion and polymer phase-separation in chromatin folding at the single-molecule level, published in Nature Communications:
https://www.nature.com/articles/s41467-022-31856-6
Recently, I started using Julia and Molly.jl for modeling loop-extrusion and in general active polymers. That's why scripts on those repos are kind of abandoned and are only for hoomd v2.9.x. However if someone wants to use hoomd for such modeling, they can be useful.
Running intensive simulations, we benchmark active loop-extrusion, SBS polymer model and a hybrid model made of those, in reproducing exp. contact and distance data measured in IMR90 and HCT116 cells.
Scripts for running simulations (using HOOMD 2.9.x) can be found here:
https://github.com/ehsanirani/PhaseSeparation-LoopExtrusion-MD
Also, the loop-extrusion script can be used independently, available on @codeberg@mastodon.technology :
https://codeberg.org/ehsan/LE4hoomd