Figure 5.

The results of exploring the logic configurations (LCs) belonging to the abstract topologies of the (a) 2-loop and (b) 3-loop Arabidopsis models. Cost scores are shown for the optimal fit of each LC to synthetic data. As in figure 4, each LC is indexed by its decimal expansion. Scores of 0 and 1 indicate the best and worst fits, respectively. Triangles denote LCs for which the Boolean model yields a viable clock. LCs mirroring the activation and inhibition pattern of the corresponding DE models in figure 1c,d are plotted in red. In (a), only LCs yielding scores less than 0.75 are shown. Of these, there are three LCs consistent with the activation and inhibition pattern of the equivalent DE model from a possible total of four. From this subset, G = (10011011) emerges as the optimal configuration yielding a viable clock. For this circuit, both LHY and TOC1 can independently inhibit Y, while TOC1 is repressed unless LHY is repressed while Y is activated (the corresponding gates are both of the AND type). In (b), only the eight LCs obtained by varying the gates of the PRR–LHY loop were considered: all other gates were fixed to those of the optimal 2-loop configuration. Of these eight possible circuits, two LCs were consistent with the equivalent DE model, from which G = (10011011011) is identified as the optimal configuration giving a viable clock. This LC corresponds to a clock network in which LHY is repressed unless PRR is inactive and X is active (the corresponding gate is of the AND type).