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

Towards Biochemical Filter with Sigmoidal Response to pH Changes: Buffered Biocatalytic Signal Transduction

We realize a biochemical filtering process by introducing a buffer in a biocatalytic signal-transduction logic system based on the function of an enzyme, esterase. The input, ethyl butyrate, is converted into butyric acid-the output signal, which in turn is measured by the drop in the pH value. The developed approach offers a versatile "network element" for increasing the complexity of biochemical information processing systems. Evaluation of an optimal regime for quality filtering is accomplished in the framework of a kinetic rate-equation model.Comment: PDF, 23 page

Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate

We consider a realization of the XOR logic gate in a process biocatalyzed by an enzyme (here horseradish peroxidase: HRP), the function of which can be inhibited by a substrate (hydrogen peroxide for HRP), when the latter is inputted at large enough concentrations. A model is developed for describing such systems in an approach suitable for evaluation of the analog noise amplification properties of the gate. The obtained data are fitted for gate quality evaluation within the developed model, and we discuss aspects of devising XOR gates for functioning in "biocomputing" systems utilizing biomolecules for information processing

Artificial Muscle Reversibly Controlled by Enzyme Reactions

Chemically induced actuation of a polypyrrole (Ppy) artificial muscle was controlled by biocatalytic reactions, resulting in changes in the redox state of the polymer film mediated by soluble redox species. The biocatalytic process triggered by diaphorase in the presence of NADH resulting in the reduction of the Ppy film was reflected by the potential shift in the negative direction generated in the film. Conversely, the biocatalytic process driven by laccase in the presence of O₂ resulted in the oxidation of the Ppy film, thus yielding the positive potential shift. Both reactions produced opposite bending of the Ppy flexible strip, allowing reversible actuation controlled by the biocatalytic processes. The biocatalytic reactions governing the chemical actuator can be extended to multistep cascades processing various patterns of biochemical signals and mimicking logic networks. The present chemical actuator exemplifies the first mechanochemical device controlled by biochemical means with the possibility to scale up the complexity of the biochemical signal-processing system

Bioelectrocatalytic Oxidation of Alkanes in a JP‑8 Enzymatic Biofuel Cell

Alkanes are attractive fuels for fuel cells due to their high energy density, but their use has not transitioned to biofuel cells. This paper discusses the development of a novel enzyme cascade utilizing alkane monooxygenase (AMO) and alcohol oxidase (AOx) to perform mediated bioelectrocatalytic oxidation of hexane and octane. This was then applied for the bioelectrocatalysis of the jet fuel JP-8, which was tested directly in an enzymatic biofuel cell to evaluate performance. The enzymatic catalysts were shown to be sulfur tolerant and produced power densities up to 3 mW/cm² from native JP-8 without desulfurization as opposed to traditional metal catalysts, which require fuel preprocessing

Layer-by-Layer Assembled Carbon Nanotube-Acetylcholinesterase/Biopolymer Renewable Interfaces: SPR and Electrochemical Characterization

Developing simple, reliable, and cost-effective methods of renewing an inhibited biocatalyst (e.g., enzymatic interfaces) on biosensors is needed to advance multiuse, reusable sensor applications. We report a method for the renewal of layer-by-layer (LbL) self-assembled inhibition-based enzymatic interfaces in multiwalled carbon nanotube (MWCNT) armored acetylcholinesterase (AChE) biosensors. The self-assembly process of MWCNT dispersed enzymes/biopolymers was investigated using surface plasmon resonance (SPR). The LbL fabrication consisted of alternating cushion layers of positively charged CNT-polyethylenimine (CNT-PEI) and negatively charged CNT-deoxyribonucleic acid (CNT-DNA) and a functional interface consisting of alternating layers of CNT-PEI and negatively charged CNT-acetylcholine esterase (CNT-AChE, pH 7.4). The observed SPR response signal increased while assembling the different layers, indicating the buildup of multiple layers on the Au surface. A partial desorption of the top enzymatic layer in the LbL structure was observed with a desorption strategy employing alkaline treatment. This indicates that the strong interaction of CNT-biopolymer conjugates with the Au surface was a result of both electrostatic interactions between biopolymers and the surface binding energy from CNTs: the closer the layers are to the Au surface, the stronger the interactions. In contrast, a similar LbL assembly of soluble enzyme/polyelectrolytes resulted in stronger desorption on the surface after the alkaline treatment; this led to the investigation of AChE layer removal, permanently inhibited after pesticide exposure on glassy carbon (GC) electrodes, while keeping the cushion layers intact. The desorption strategy permitted the SPR and electrochemical electrode surfaces to be regenerated multiple times by the subsequent self-assembly of fresh PEI/AChE layers. Flow-mode electrochemical amperometric analysis demonstrated good stability toward the determination of acetylcholine with 97.1 ± 2.7% renewability. Our simple, inexpensive approach shows the potential of renewable LbL self-assembled functional interfaces for multiple uses in a wide field of applications such as biosensing, various biotechnological processes, and the food and health industries