Network analysis of biochemical logic for noise reduction and stability: a system of three coupled enzymatic and gates.
TLDR
In this paper, the authors developed an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. But their work was limited to 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.read more
Citations
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Enzyme-based logic systems for information processing
Evgeny Katz,Vladimir Privman +1 more
TL;DR: This critical review of enzymatic systems which involve biocatalytic reactions utilized for information processing (biocomputing) highlights design and uses of non-Boolean network elements, e.g., filters, as well as developments motivated by potential novel sensor and biotechnology applications.
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Digital biosensors with built-in logic for biomedical applications—biosensors based on a biocomputing concept
Joseph Wang,Evgeny Katz +1 more
TL;DR: By processing complex patterns of multiple physiological markers, such multisignal digital biosensors should have a profound impact upon the rapid diagnosis and treatment of diseases, and particularly upon the timely detection and alert of medical emergencies.
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Synthesizing biomolecule-based Boolean logic gates.
TL;DR: Various types of biomolecular logic gates that have been synthesized are discussed, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.
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Multiplexing of injury codes for the parallel operation of enzyme logic gates
Jan Halámek,Joshua Ray Windmiller,Jian Zhou,Min-Chieh Chuang,Padmanabhan Santhosh,Guinevere Strack,Mary A. Arugula,Soujanya Chinnapareddy,Vera Bocharova,Joseph Wang,Evgeny Katz +10 more
TL;DR: The development of a highly parallel enzyme logic sensing concept employing a novel encoding scheme for the determination of multiple pathophysiological conditions is reported, which enabled the effective discrimination of 64 unique pathological conditions to offer a comprehensive high-fidelity diagnosis of multiple injury conditions.
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Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems
TL;DR: An interface that enables communication of otherwise incompatible nucleic-acid and enzyme-computational systems is developed that is universal because the enzymatic and DNA computing systems are independent of each other in composition and complexity.
References
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Journal ArticleDOI
A molecular photoionic AND gate based on fluorescent signalling
TL;DR: A receptor is described that operates as a logic device with two input channels: the fluorescence signal depends on whether the molecule binds hydrogen ions, sodium ions or both and the input/output characteristics of this molecular device correspond to those of an AND gate.
Journal ArticleDOI
Molecular logic and computing.
TL;DR: Molecular substrates can be viewed as computational devices that process physical or chemical 'inputs' to generate 'outputs' based on a set of logical operators, which aid chemical (especially intracellular) sensing, small object recognition and intelligent diagnostics.
Journal ArticleDOI
Chemical approaches to molecular logic elements for addition and subtraction.
TL;DR: Recent developments to attain molecular systems with increased logic capabilities is described, including bioinspired systems based on DNA and enzymes, as well as chemical molecular logic gates.
Journal ArticleDOI
DNA-based photonic logic gates: AND, NAND, and INHIBIT.
TL;DR: By employing the universal recognition properties of DNA simple photonic logic gates can be created that are capable of AND, NAND, and INHIBIT logic operations.