Fig 1.
A. Scheme of local chromatin reconstruction based on a cross-linked polymer model (red bead of diameter σ) connected by springs (blue) with random connectors (green dots). The ball B(Rg) (orange domain) defines the radius gyration. B. Mean gyration radius vs number of random cross-linkers Nc, for various densities ρ: a smooth transition occurs from a swollen chain to a compact state (Nmon = 2000). C-E. Linear chain (red monomers) without random connectors embedded in Nmol Brownian molecules (blue). Random connectors drive the free particles outside B(Rg). When there are Nbs binding sites, the concentration of molecules cmol(r) at distance r from the center, is depleted in B(Rg) (lower panels).
Fig 2.
A. Molecular radial distribution function gmol(r) for various Nc ∈ {50, 100, 200, 500} at density ρ = 0.05σ−3, compared to the refence constant dashed line. Full (resp. empty) symbols indicate cases with Nbs = 0 (Nbs = 10). B. Polymer radial distribution function gmon(r). C. Molecules-monomers pair correlation function gmol(r). D. Pore size distribution. Inset: average mesh size ζ vs. Nc.
Fig 3.
A. Schematic representation of molecular trajectories penetrating the phase separeted region Ω over a characteristic length Lin with and without binding sites (green). B. Mean time 〈τin〉 spent by a molecule inside the PSD versus number of connectors Nc for various densities ρ. Full (resp. empty) symbols indicate cases with Nbs = 0 (Nbs = 10). C. Ratio of the penetration length 〈Lin〉 to the gyration radius 〈Rg〉 versus Nc. D. Mean binding time 〈τb〉 vs Nc. E. Ratio of the local density ρb estimated around the binding sites to the overall density ρ (no binding sites).
Fig 4.
A. Schematic representation of a trajectory (yellow) inside the PSD, with the polymer center of mass CM (color shadows). A molecule spends a random time τe before crossing the boundary. B. Average escaping time 〈τe〉 from the PSD versus Nc with and without binding sites. C-H. MSD of molecules escaping from the PSD for different values Nc = 200, 400, 600, with Nbs = 0 (left column) and Nbs = 10 (right). Curves are colored according the range of the initial position (white inside, dark outside the PSD). Gray regions indicate the mean escape time 〈τe〉 timescale. The binning length is . I. Anomalous α-exponent computed from the MSD of escaping particles in the time interval τ ∈ [1, 10−1τe] with respect to the initial radial position r. Full (reps. empty) points correspond to Nbs = 0 (resp. Nbs = 10). J. Anomalous α-exponent computed from the MSD of monomers in the polymer center of mass reference, in the time interval τ ∈ [1, 10−1τe] with respect to the initial radial position r.
Fig 5.
Few examples of trajectories of escaping particles for systems with Nc = 200, 400, 600 (columns) and Nbs = 0, 10 (rows) highlighted with different colors.
On each surface the projected trajectories are shown in gray, orange circles represent the projections of the Ω regions defined by the gyration radius.
Fig 6.
Vector fields on the plane x−y, z = 0, computed from escaping particle trajectories with Nc = 200, 400, 600 connectors (columns) and Nbs = 0, 10 (rows).
Circles represent the projections of the Ω regions defined by the gyration radius.
Table 1.
A values computed from the simulated trajectories described in Fig 6.
Fig 7.
Summary of a Phase Separated Domain, described by a RCL-volume extrusion model, revealing a transition from anomalous diffusion to normal diffusion near the boundary.