Figure 2.
The abstract topologies for the logic representations of the clock circuits shown in figure 1. Genes are boxed and arrows denote regulatory interactions. (a) The single-loop Neurospora model. (b) The 2-loop Neurospora model. (c) The 2-loop Arabidopsis model. (d) The 3-loop Arabidopsis model. Numerals l index logic gates gl ∈ {0,1} that can be varied to generate different regulatory structures. Numerals at the end of an arrow index the single-input gate defining that interaction. Numerals within boxes index logic gates governing double-input interactions. Diamonds represent light inputs, with the corresponding fixed gates in ovals indicating how these affect the target species (e.g. in (c), L2 and L3 are combined with an OR gate after which the resulting bitstring is combined with the output of Y through an AND gate; see §4 for full details). τjs represent the circuit delays and Tis the discretization thresholds used to fit continuous data.