TF formation kinetics and effects of target promoter clustering and mesh size. (A) Typical time evolution of the number of all Swi4-containing transcription factor complexes in small (10 fl) cells, showing DNA-free Swi4 (dimer; blue), DNA-free SBF (gray), DNA-bound Swi4d (dimer; orange), and DNA-bound SBF (yellow). (B) Typical time evolution of the number of all Mbp1-containing transcription factor complexes: DNA-free Mbp1d (dimer; blue), DNA-free MBF (gray), DNA-bound Mbp1d (dimer; orange), and DNA-bound MBF (yellow). Plots are for averages over 10 independent simulations. Gray-shaded regions indicate the standard error of the mean at each time point for each species. (C and E) Effect of promoter clustering on G1/S TF clustering in simulations. 2D projections of the 3D output of a typical simulation in the absence of G1/S promoters clustering, showing Swi4 dimers (green dots), Mbp1 dimers (red), Swi6 dimers (blue), and G1/S DNA promoters (black dots) in a small (10 fl, panel C) and a large (31.5 fl, panel E) cell. (D and F) Simulation mesh size does not affect G1/S TF clustering. (D) Mesh size, 10 nm. (F) Mesh size, 60 nm. Both graphs show Swi4 dimers (green dots), Mbp1 dimers (red), Swi6 dimers (blue), and G1/S DNA promoters (black dots) in a typical small cell (10 fl). In C–F, not all molecules/sites are shown at some pixels where Swi4, Mbp1, Swi6, and G1/S promoters dots overlap.