Fig. 1
a Coarse graining of microscopic details of double stranded DNA into a bead-spring polymer. b A polymer model for the nucleosome: highlighted are the features of DNA stiffness (set by penalising large angles θ between consecutive pairs of monomers) and connectivity (set by penalising large extensions x between consecutive beads). We also account for excluded volume interactions and pair-attraction represented by the wrapping of the orange segment around the histone octamer (here a blue spherical bead). c Schematics showing that integration events on DNA deform the substrate. d Snapshots from molecular dynamics simulations showing an integration event within a nucleosome. Color scheme: orange = wrapped host DNA, green= viral DNA, grey = non-wrapped host DNA. Adapted from Ref. [54]