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We develop an approach aimed at optimizing the parameters of a network ofbiochemical logic gates for reduction of the "analog" noise buildup.Experiments for three coupled enzymatic AND gates are reported, illustratingour procedure. Specifically, starch - one of the controlled network inputs - isconverted to maltose by beta-amylase. With the use of phosphate (anothercontrolled input), maltose phosphorylase then produces glucose. Finally,nicotinamide adenine dinucleotide (NAD+) - the third controlled input - isreduced under the action of glucose dehydrogenase to yield the opticallydetected signal. Network functioning is analyzed by varying selective inputsand fitting standardized few-parameters "response-surface" functions assumedfor each gate. This allows a certain probe of the individual gate quality, butprimarily yields information on the relative contribution of the gates to noiseamplification. The derived information is then used to modify our experimentalsystem to put it in a regime of a less noisy operation.

Network Analysis of Biochemical Logic for Noise Reduction and Stability: A System of Three Coupled Enzymatic AND Gates