This chapter describes some of the design tradeoffs arising from the interaction between synthetic circuits and the host organism. It first considers the effects of competition for shared cellular resources on circuits' behavior. In particular, circuits (endogenous and exogenous) share a number of cellular resources. The insertion or induction of synthetic circuits in the cellular environment changes for these resources, with possibly undesired repercussions on the functioning of the circuits. Independent circuits may become coupled when they share common resources that are not in overabundance. This fact leads to constraints among the concentrations of proteins in synthetic circuits, which should be accounted for in the design phase. Next, the chapter looks at the effect of biological noise on the design of devices requiring high gains. Specifically, the chapter illustrates possible design tradeoffs between retroactivity attenuation and noise amplification that emerge due to the intrinsic noise of biomolecular reactions.
Keywords: design tradeoffs, synthetic circuits, host organism, circuit behavior, independent circuits, cellular resources, biological noise, retroactivity attenuation, noise amplification, biomolecular reactions
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