Brian E. Fratto

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

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 gates 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.

Reversible Logic Gates Based on Enzyme‐Biocatalyzed Reactions and Realized in Flow Cells: A Modular Approach

Reversible logic gates, such as the double Feynman gate, Toffoli gate and Peres gate, with 3-input/3-output channels are realized using reactions biocatalyzed with enzymes and performed in flow systems. The flow devices are constructed using a modular approach, where each flow cell is modified with one enzyme that biocatalyzes one chemical reaction. The multi-step processes mimicking the reversible logic gates are organized by combining the biocatalytic cells in different networks. This work emphasizes logical but not physical reversibility of the constructed systems. Their advantages and disadvantages are discussed and potential use in biosensing systems, rather than in computing devices, is suggested.

Controlled Logic Gates-Switch Gate and Fredkin Gate Based on Enzyme-Biocatalyzed Reactions Realized in Flow Cells.

Controlled logic gates, where the logic operations on the Data inputs are performed in the way determined by the Control signal, were designed in a chemical fashion. Specifically, the systems where the Data output signals directed to various output channels depending on the logic value of the Control input signal have been designed based on enzyme biocatalyzed reactions performed in a multi-cell flow system. In the Switch gate one Data signal was directed to one of two possible output channels depending on the logic value of the Control input signal. In the reversible Fredkin gate the routing of two Data signals between two output channels is controlled by the third Control signal. The flow devices were created using a network of flow cells, each modified with one enzyme that biocatalyzed one chemical reaction. The enzymatic cascade was realized by moving the solution from one reacting cell to another which were organized in a specific network. The modular design of the enzyme-based systems realized in the flow device allowed easy reconfiguration of the logic system, thus allowing simple extension of the logic operation from the 2-input/3-output channels in the Switch gate to the 3-input/3-output channels in the Fredkin gate. Further increase of the system complexity for realization of various logic processes is feasible with the use of the flow cell modular design.

Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions

It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule-modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA-based logic gates. The enzyme-based Fredkin gate with three input and three output signals was connected to the DNA-based Feynman gate with two input and two output signals-both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input-controlled signal-routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing.

An Enzyme‐Based Half‐Adder and Half‐Subtractor with a Modular Design

A half-adder and a half-subtractor have been realized using enzymatic reaction cascades performed in a flow cell device. The individual cells were modified with different enzymes and assembled in complex networks to perform logic operations and arithmetic functions. The modular design of the logic devices allowed for easy re-configuration, enabling them to perform various functions. The final output signals, represented by redox species [Fe(CN)6 ](3-/4-) or NADH/NAD(+) , were analyzed optically to derive the calculation results. These output signals might be applicable in the future for actuation processes, for example, substance release activated by logically processed signals.

Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications

We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

Biomolecular Computing Realized in Parallel Flow Systems: Enzyme-Based Double Feynman Logic Gate

An enzyme system organized in a flow device with three parallel channels was used to mimic a reversible Double Feynman Gate (DFG) with three input and three output signals. Reversible conversion of NAD+ and NADH cofactors was used to perform XOR logic operations, while biocatalytic oxidation of NADH resulted in Identity operation working in parallel. The first biomolecular realization of a DFG gate is promising for integrating into complex biomolecular networks operating in future unconventional biocomputing systems, as well as for novel biosensor applications.

Utilization of a fluidic infrastructure for the realization of enzyme-based Boolean logic operations

Abstract The paper overviews the origin and motivation of the unconventional molecular computing, specially emphasizing the advantages of biomolecular systems for designing highly sophisticated logic circuits. Technological solutions based on flow design of enzyme-based logic gates are discussed and illustrated with examples. Integration of the enzyme-based logic gates and their concatenated assemblies with signal-responsive materials and electronic interfaces is suggested as a platform for biomedical sensors/actuators digitally responding in the Yes/No format to various combinations of biomolecular signals, particularly represented by biomarkers important in biomedical applications. The complexity of the designed enzyme-based logic systems allowed for logically reversible computing, thus being a step forward in the development of biomolecular computing devices. The features of reversible biocomputing systems are discussed, particularly emphasizing their logic reversibility, but not physical reversibility. Perspectives and novel advances are discussed in the conclusion section, giving a futuristic vision for the possible applications of biomolecular computing systems in various biomedical and specifically in theranostic applications. Fluidic enzyme-based logic systems for biosensor applications

Enzyme-Based Reversible Logic Gates Operated in Flow Cells

Reversible logic gates, such as Feynman gate (Controlled NOT), Double Feynman gate, Toffoli gate and Peres gate, with 2-input/2-output and 3-input/3-output channels, were realized using reactions biocatalyzed by enzymes and performed in flow systems. The flow devices were constructed using a modular approach, where each flow cell was modified with one enzyme that biocatalyzed one chemical reaction. Assembling the biocatalytic flow cells in different networks, with different pathways for transporting the reacting species, allowed the multi-step processes mimicking various reversible logic gates. The chapter emphasizes “logic” reversibility but not the “physical” reversibility of the constructed systems. Their advantages and disadvantages are discussed and potential use in biosensing systems, rather than in computing devices, is suggested.

An Enzyme‐based 1:2 Demultiplexer Interfaced with an Electrochemical Actuator

An enzyme-based 1:2 demultiplexer is designed in a flow system composed of three cells where each one is modified with a different enzyme: hexokinase, glucose dehydrogenase and glucose-6-phosphate dehydrogenase. The Input signal activating the biocatalytic cascade is represented by glucose, while the Address signal represented by ATP is responsible for directing the Input signal to one of the output channels, depending on the logic value of the Address. The biomolecular 1:2 demultiplexer is extended to include two electrochemical actuators releasing entrapped DNA molecules in the active output channel. The modular design of the system allows for easy exchange and extension of the functional elements. The present demultiplexer can be easily integrated in various biomolecular logic systems, including different logic gates based on the enzyme- or DNA-based reactions, as well as containing different chemical actuators, for example, with a biomolecular release function.