Two-Input Enzymatic Logic Gates Made Sigmoid by Modifications of the Biocatalytic Reaction Cascades

Oleksandr Zavalov; Vera Bocharova; Jan Halamek; Lenka Halamkova; Sevim Korkmaz; Mary A. Arugula; Soujanya Chinnapareddy; Evgeny Katz; Vladimir Privman

arXiv · 1305.5929

Two-Input Enzymatic Logic Gates Made Sigmoid by Modifications of the Biocatalytic Reaction Cascades

Oleksandr Zavalov·Vera Bocharova·Jan Halamek·Lenka Halamkova·Sevim Korkmaz·Mary A. Arugula·Soujanya Chinnapareddy·Evgeny Katz·Vladimir Privman

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Abstract

Computing based on biochemical processes is a newest rapidly developing field of unconventional information and signal processing. In this paper we present results of our research in the field of biochemical computing and summarize the obtained numerical and experimental data for implementations of the standard two-input OR and AND gates with double-sigmoid shape of the output signal. This form of response was obtained as a function of the two inputs in each of the realized biochemical systems. The enzymatic gate processes in the first system were activated with two chemical inputs and resulted in optically detected chromogen oxidation, which happens when either one or both of the inputs are present. In this case, the biochemical system is functioning as the OR gate. We demonstrate that the addition of a "filtering" biocatalytic process leads to a considerable reduction of the noise transmission factor and the resulting gate response has sigmoid shape in both inputs. The second system was developed for functioning as an AND gate, where the output signal was activated only by a simultaneous action of two enzymatic biomarkers. This response can be used as an indicator of liver damage, but only if both of these of the inputs are present at their elevated, pathophysiological values of concentrations. A kinetic numerical model was developed and used to estimate the range of parameters for which the experimentally realized logic gate is close to optimal. We also analyzed the system to evaluate its noise-handling properties.

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Oleksandr Zavalov, Vera Bocharova, Jan Halamek, Lenka Halamkova, Sevim Korkmaz, Mary A. Arugula, Soujanya Chinnapareddy, Evgeny Katz, Vladimir Privman. 2013-05-25. Two-Input Enzymatic Logic Gates Made Sigmoid by Modifications of the Biocatalytic Reaction Cascades. https://arxiv.org/abs/1305.5929

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