A Generic Mechanism for Adaptive Growth Rate Regulation
Figure 1
Schematic Representation of Our Cell Model
The model consists of two networks, i.e., a gene regulatory network and a metabolic network. As a schematic example, simple networks consisted of n = 7 genes and m = 6 metabolic substrates are shown. The red arrows in the regulatory network represent activation of expressions, while green lines with blunt ends represent inhibition. The arrows from a gene to itself mean autoregulation of expressions. As a result of these regulatory interactions, the dynamics of expression levels of proteins have multiple attractors. The metabolic reactions, represented by blue arrows, are controlled by expression levels of corresponding proteins. The correspondence between metabolic reactions and gene products (proteins) are shown by the thin black arrows. The regulatory matrix Wij of the presented network takes W21 = W32 = W33 = W45 = W56 = W67 = W77 = 1, W24 = W53 = W57 = −1, and 0 otherwise. The reaction matrix Con(i,j,k) metabolic network takes a value 1 for the elements (1,3,1)(2,3,2)(3,4,3)(6,3,4)(4,5,5)(6,4,6)(5,6,7), and 0 otherwise. The choice of n = 7 in the figure is only for schematic illustration, and in the actual simulation we used much larger networks with n = 20 ∼ 100. In the present paper, we adopt a much larger network with n = 96 genes and m = 32 substrates.