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.