Figure 1
From: Mapping the spectrum of 3D communities in human chromosome conformation capture data
3D communities in simulated fractal globules. (a, left) The 3D representation of fractal globule from the CDP algorithm. The colors highlight communities that we detect using Eq. (2), γ = 0.6. (a, right) The communities are not contiguous: the small globule is a subsection of the lower left part of polymer, and the stretched version shows the alternating communities (ABCAB). (b–d) The contact maps of simulated fractal globules after KR-normalization, with various resolution parameters: (b) γ = 0.4, (c) γ = 0.6, and (d) γ = 0.8. To show non-contiguous communities, we superimpose them as the squares; the same color indicates that they belong to the same 3D community. (e) The end-to-end distance for the fractal (FG, blue) and the equilibrium globules (EG, red) averaged over 200 polymer realizations. The triangles denote the end-to-end distance for community boundaries, and dashed lines represent the chain as a whole. To find the communities, we use γ = 0.4. The data are obtained from the simulation of 200 sample globules for each polymer model. The error bars show the standard error of the mean, and the two guided slopes (1/2 and 1/3) show the known scaling of equilibrium and fractal globules at intermediate length scales. (f) The same data as in the panel (e), where we scale the vertical axis with the radius of gyration \({R}_{g}(\,\,=\,\sqrt{\frac{1}{2{N}^{2}}{\sum }_{i,j}\,{\Vert {{\bf{r}}}_{i}-{{\bf{r}}}_{j}\Vert }^{2}})\) where N is the total number of polymer segments and ri is the coordinate of the ith segment.
