A de-localised knotted state is stabilised by the action of multiple (here 2) SMC proteins. Note that the essential crossings are instead localised. Dark-grey = polymer backbone. Light-grey = extruded segments. Cyan = shortest knotted arc.
A trefoil knot is simplified through the synergistic action of SMC and Topo2
A delocalised trefoil knot on a polymer is localised by the slip-link-like protein SMC cohesin/condensin
Simulated HIV integration in a nucleosome
HIV integration in a condensed (poly-nucleosome) fibre
4D Epigenome: Transition from Swollen-Disordered to Compact-Ordered phases of chromatin.

Transition from Stretched-Disordered to Compact-Ordered phase of a "recolourable polymer" model for a chromatin fibre with dynamic epigenome

A knotted soliton

Configuration of a ring within a dense solution. The left configuration highlights the bases of (hierarchical) loops, which are marked by coloured beads. The right configuration shows the presence of "branches" (or double-folded structures), which are marked by red beads.

Plasmids undergoing gel extrophoresis through a network of solid nanowires (Rahong et al, Sci Rep 2014). Notice the non-monotonic change in average speed for increasing values of the external electric field. Courtesy of T. Yasui.