Spatial organization of a heterogeneous polymer in a crowded medium

In a crowded medium, a chain molecule can be entropically phase-separated into a condensed state. Here, we study the spatial organization of a heterogeneous polymer (with ring topology) by crowding effects, using molecular dynamics simulations. Our parameter choices are inspired by the Escherichia coli chromosome: the polymer consists of small and big monomers; the big monomers dispersed along the backbone mimic the binding of RNA polymerases. Our results clarify the conditions under which big monomers can be entropically clustered in a crowded medium. These results support the view that crowding can promote clustering of transcription-active units into the so-called transcription foci in a crowded cellular space.