Enzymatic AND Logic Gate with Sigmoid Response Induced by Photochemically Controlled Oxidation of the Output

Abstract

We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output, allowing the gate's response to be made sigmoid in both inputs. New functional forms are developed for quantifying the kinetics of such systems, specifically designed to model their response in terms of signal and information processing. These theoretical expressions are tested for the studied system, which also allows us to consider aspects of biochemical information processing such as noise transmission properties and control of timing of the chemical and physical steps.

Control of Noise in Chemical and Biochemical Information Processing

“…Our presentation has been limited to AND gates and related systems. Indeed, all the recent studies, with one exception: an XOR gate, [214] of noise control in (bio)chemical computing have thus far been for AND gates and, furthermore, again with just one recent exception, [215] only for those with the binary 0 set at the physical zeros of chemical concentrations. While these limitations are natural for chemical kinetics, they are definitely not typical for applications envisaged, notably, multi-input biomedical sensing.…”

Majority and Minority Gates Realized in Enzyme-Biocatalyzed Systems Integrated with Logic Networks and Interfaced with Bioelectronic Systems

“…While computational applications of biomolecular systems 14−16 competing with modern electronics are rather futuristic, their use in low scale information processing for biosensing 17−19 and bioactuating, 20−22 particularly aiming at medical use 23−26 and operation in a biological environment, 27,28 is already feasible at the present level of technology. Rapid progress in enzyme-based information processing systems resulted in the design of biocatalytic cascades mimicking various Boolean logic gates, 1 including AND, [29][30][31][32][33][34][35][36]34,36,37 NAND,38,39 NOR,36,39 CNOT, 40 XOR,34,36,41,42 INHIBIT,34,36 Identity, 36 and Inverter 36 gates. Assembling enzyme logic gates in complex networks composed of several concatenated gates resulted in an increased complexity of the information processing systems.…”

Biocomputing — tools, aims, perspectives

“…Rapid progress in enzyme-based information processing systems has resulted in the design of biocatalytic cascades mimicking various Boolean logic gates [19 ], including AND [30][31][32][33][34], OR [33,35], NAND [36], NOR [34,36], CNOT [37], XOR [33,34,38,39], INHIBIT [33,34], Identity [34] and Inverter [34] gates. In order to digitalize chemical processes the reacting species considered as logic input signals were applied at two levels of their concentrations: their physical absence (zero concentration) was defined as logic 0 input, while logic 1 input was defined as experimentally optimized and conveniently high concentration, thus allowing significant separation in the produced output signals when inputs 0 or 1 were applied in different combinations.…”

“…The enabled AND function with the recycling step, Figure 4d, bars 'b', allowed good separation between the output signals produced in the presence of low and high concentration of the input signals, thus allowing conclusion on the LI only when both biomarkers appeared at their pathophysiological elevated concentrations (1,1 input signals). This approach with a recycling step (called a 'filter' by analogy with its electronic counterpart) was successfully applied to improve logic performance of other gates by converting convex response function to sigmoidal dependence, thus allowing sharp transition from 0 to 1 logic output [30][31][32].…”