Mathematical modeling assists the design of synthetic regulatory networks, and models that can predict the performance of a design are fundamental for synthetic biology. The predictability depends crucially on what assumptions the model considers. For example, a common assumption is to consider negligible the effects of intracellular physical space. The mathematical model described in this paper accounts for molecular diffusion and shows how simulations of network performance are decisively affected by the distance between its components, suggesting that the spatial specification of the circuit alone can be exploited as a design parameter in synthetic biology to select programmable output levels.

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