Fig. 4: Holimaps for three-node gene networks.
From: Holimap: an accurate and efficient method for solving stochastic gene network dynamics
a Illustration of the 2-HM and 4-HM for a three-node gene network, where three genes regulate each other along the counterclockwise direction. Feedback is mediated by cooperative binding of hi copies of protein Pi to gene Gi+1, where G4 is understood to be G1. b A repressilator with cooperative binding. Here the cooperativities are chosen as hi = 3 for i = 1, 2, 3 such that the deterministic system of rate equations produces sustained oscillations. c Time evolution of the mean and Fano factor of fluctuations in the number of molecules of protein P1 computed using the SSA (with 105 trajectories), LMA, and 2-HM. d Comparison of the time-dependent distributions of protein P1 at 15time points computed using the SSA (with 105 trajectories), LMA, 2-HM, and hybrid SSA+2-HM (with 2000 trajectories). See Supplementary Note 1 for the technical details of this figure. Source data are provided as a Source Data file.
