Fig. 1
From: Theoretical principles of transcription factor traffic on folded chromatin
Description of the simulation setup. a The polymer is made of p (polymer) and a (anchor) particles, connected by harmonic springs. Binders (b particles) are introduced to bridge a particles. Tracers (t particles) interact non-specifically with both p and a particles. Binders and tracers interact only by hard-core repulsion, i.e., by volume exclusion. b Snapshot of a simulation together with the simulation box. c Zoom-in of a loop formed by the binders and their binding sites, along with the tracers bound nearby (yellow)
