Fig. 3. Improving the repressilator’s oscillatory strength.

A Depiction of the repressilator network with three gene expression systems whose output proteins cyclically repress each other. When present, the sponge plasmid can bind TetR proteins, thereby raising the derepression threshold of the cI gene. B Shows the effect of the sponge on the PSD. It can be seen that the sponge sharpens the PSD peak for promoter cooperativity H = 1.5 but this effect is lost for H = 2. C Plots the single-cell trajectories with and without the sponge for promoter cooperativity H = 1.5, and they show that the oscillations are more regular in the latter case. Comparison of the PSD estimated with our Padé PSD method with the PSDs estimated with DFT is provided. For these estimations, Q = 10 simulated trajectories were used. D Repeats the computational analysis in panel (C) for promoter cooperativity H = 2.