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

Abstract

We develop an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. Experiments for three coupled enzymatic AND gates are reported, illustrating our procedure. Specifically, starch - one of the controlled network inputs - is converted to maltose by beta-amylase. With the use of phosphate (another controlled input), maltose phosphorylase then produces glucose. Finally, nicotinamide adenine dinucleotide (NAD+) - the third controlled input - is reduced under the action of glucose dehydrogenase to yield the optically detected signal. Network functioning is analyzed by varying selective inputs and fitting standardized few-parameters "response-surface" functions assumed for each gate. This allows a certain probe 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 our experimental system to put it in a regime of a less noisy operation.

31 pages, PDF

References in corpus (1)

• Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit?

Cited by in corpus (23)

• Enzyme-Based Logic Systems for Information Processing
• Enzymatic AND-Gate Based on Electrode-Immobilized Glucose-6-Phosphate Dehydrogenase: Towards Digital Biosensors and Biochemical Logic Systems with Low Noise
• Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications
• Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid "Filter" Response
• Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change
• Networked Enzymatic Logic Gates with Filtering: New Theoretical Modeling Expressions and Their Experimental Application
• Analog Noise Reduction in Enzymatic Logic Gates
• Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic
• Modeling somatic computation with non-neural bioelectric networks
• Enzymatic AND Logic Gate with Sigmoid Response Induced by Photochemically Controlled Oxidation of the Output
• Control of Noise in Chemical and Biochemical Information Processing
• Modularity of Biochemical Filtering for Inducing Sigmoid Response in Both Inputs in an Enzymatic AND Gate
• Towards Biochemical Filter with Sigmoidal Response to pH Changes: Buffered Biocatalytic Signal Transduction
• Bioinspired Associative Memory System Based on Enzymatic Cascades
• Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications
• Design of Digital Response in Enzyme-Based Bioanalytical Systems for Information Processing Applications
• Realization of Associative Memory in an Enzymatic Process: Towards Biomolecular Networks with Learning and Unlearning Functionalities
• Can bio-inspired information processing steps be realized as synthetic biochemical processes?
• Towards Biosensing Strategies Based on Biochemical Logic Systems
• Promises and Challenges in Continuous Tracking Utilizing Amino Acids in Skin Secretions for Active Multi-Factor Biometric Authentication for Cybersecurity
• Optimization of Enzymatic Logic Gates and Networks for Noise Reduction and Stability
• Modeling and Modifying Response of Biochemical Processes for Biocomputing and Biosensing Signal Processing
• Theoretical Modeling Expressions for Networked Enzymatic Signal Processing Steps as Logic Gates Optimized by Filtering