Figure 4.

Microscopic mechanisms of PS induction. (A) Possible mechanisms leading to PS and driving contact formation between regulatory elements. (B) The number of binders N_b composing the three main clusters (green curves). Note the linear increase during time. Below is shown the distance of the main clusters from the bs (d_bs-clust, brown curves). Here, binding affinity E_b-bs = 3.1 K_BT and concentration c is ∼1.5%. (C) shows the same as in (B), with E_b-bs = 5.1 K_BT. (D) The average distance <d_bs-clust> at early stage of the dynamics (see Methods) for different concentrations c and binding affinities E_b-bs. (E) The number of binders N_b of the first four largest clusters monitored over a highly time-resolved simulation. In dynamics 1, the gradual and continuous decrease of the top second cluster (green curve) and the gradual increase of the top first cluster (red curve) indicate an evaporation process. Conversely, in dynamics 2, the top second cluster drops and the top first cluster increases, respectively, in a discontinuous way, indicating the coalescence between the two (green plus red). Simulations were performed with E_b-b = 3.0 K_BT, E_b-bs = 3.1 K_BT, and c being ∼1.9%. (F) Schematic representation of evaporation and coalescence, the microscopic mechanisms that regulate PS dynamics. To see this figure in color, go online.