Optimization of Enzymatic Logic Gates and Networks for Noise Reduction and Stability

Biochemical computing attempts to process information with biomolecules and biological objects. In this work we review our results on analysis and optimization of single biochemical logic gates based on enzymatic reactions, and a network of three gates, for reduction of the "analog" noise buildup. For a single gate, optimization is achieved by analyzing the enzymatic reactions within a framework of kinetic equations. We demonstrate that using co-substrates with much smaller affinities than the primary substrate, a negligible increase in the noise output from the logic gate is obtained as compared to the input noise. A network of enzymatic gates is analyzed by varying selective inputs and fitting standardized few-parameters response functions assumed for each gate. This allows probing of the individual gate quality but primarily yields information on the relative contribution of the gates to noise amplification. The derived information is then used to modify experimental single gate and network systems to operate them in a regime of reduced analog noise amplification.Comment: 7 pages in PD

Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change

We consider a realization of the XOR logic gate in a system involving two competing biocatalytic reactions, for which the logic-1 output is defined by these two processes causing a change in the optically detected signal. A model is developed for describing such systems in an approach suitable for evaluation of the analog noise amplification properties of the gate and optimization of its functioning. The initial data are fitted for gate quality evaluation within the developed model, and then modifications are proposed and experimentally realized for improving the gate functioning

Enzymatic Logic Gates with Noise-Reducing Sigmoid Response

Biochemical computing is an emerging field of unconventional computing that attempts to process information with biomolecules and biological objects using digital logic. In this work we survey filtering in general, in biochemical computing, and summarize the experimental realization of an AND logic gate with sigmoid response in one of the inputs. The logic gate is realized with electrode-immobilized glucose-6-phosphate dehydrogenase enzyme that catalyzes a reaction corresponding to the Boolean AND functions. A kinetic model is also developed and used to evaluate the extent to which the performance of the experimentally realized logic gate is close to optimal.Comment: 14 pages, 2 figures, PD