Fig. 3.

(a) Deterministic calculation of oscillatory features in a system with mRNA, cooperative binding of proteins to each other, and a separate step binding to the gene; region I is oscillatory, region II has decaying oscillations, and region III is non-oscillatory. Due to the fact that the distinction betweeen II and III is somewhat dependent on initial conditions, there may be some overlap between those two regions as discussed in the Methods section. (b) Stochastic calculation of coherence, given by $2\frac{\sum \mathrm{\Theta }(d\varphi )}{\sum |d\varphi |}-1$ where $d\varphi$ is the difference in angle in mRNA–protein space. (c) Stochastic calculation of the standard deviation of the period distribution divided by its mean.