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Table 2 The list of symbols employed in the ordinary differential equations associated to the designs from Figure 2.

From: Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation

Symbol Definition & Comments
A concentration of the activator (nM)
R concentration of the repressor (nM)
t model time (hours)
DNA-binding constant of the activator A
DNA-binding constant of the repressor R
dimerization constant of the activator A to A2
dimerization constant of the repressor R to R2
multimerization constant of the activator A to A n
dimerization constant of the repressor R to R m
δ A degradation rate of the activator A
δ R degradation rate of the repressor R
Δ δ A /δR,non-dimensional parameter of the model
x , the nondimensional variable associated to the activator, when the activator is a dimer
y , the nondimensional variable associated to the repressor, when the repressor is a dimer
τ tδ R , the nondimensional time variable of the model
α the transcriptional synergy conferred by the activator bound to DNA
β , the nondimensional parameter of the transcriptional response from the activator promoter, with γ A , the translation rate of the activator A; β A , the transcription rate of the mRNA of the activator; α A , activator mRNA degradation; , total activator promoter number. The root order n denotes the multimerization degree of the TF binding to DNA (i.e. n = 2, dimer; n = 4, tetramer). The subscript from , the equilibrium constant for multimer formation, also denotes its dependence on the multimerization of the binding factor.
γ , the nondimensional parameter of the transcriptional response from the repressor promoter, similar to β. See also [18]. Notice also the multimerization degree appears here as m with similar consequences as for the β parameter.
σ , the binding ratio of the repressor compared to the activator.