Experimental Realization of a High-Quality Biochemical XOR Gate.

We report an experimental realization of a biochemical XOR gate function that avoids many of the pitfalls of earlier realizations based on biocatalytic cascades. Inputs-represented by pairs of chemicals-cross-react to largely cancel out when both are nearly equal. The cross-reaction can be designed to also optimize gate functioning for noise handling. When not equal, the residual inputs are further processed to result in the output of the XOR type, by biocatalytic steps that allow for further gate-function optimization. The quality of the realized XOR gate is theoretically analyzed.

[1]  Vladimir Privman,et al.  Enzyme-based logic analysis of biomarkers at physiological concentrations: and gate with double-sigmoid "filter" response. , 2012, The journal of physical chemistry. B.

[2]  Vladimir Privman,et al.  Design of High Quality Chemical XOR Gates with Noise Reduction. , 2017, Chemphyschem : a European journal of chemical physics and physical chemistry.

[3]  Andrew Adamatzky,et al.  Physarum Machines: Computers from Slime Mould , 2010 .

[4]  Vladimir Privman,et al.  Enzyme-based logic: OR gate with double-sigmoid filter response. , 2012, The journal of physical chemistry. B.

[5]  Lei Wang,et al.  Logic gate system with three outputs and three inputs based on switchable electrocatalysis of glucose by glucose oxidase entrapped in chitosan films. , 2015, Chemistry, an Asian journal.

[6]  Evgeny Katz,et al.  Controlled Logic Gates-Switch Gate and Fredkin Gate Based on Enzyme-Biocatalyzed Reactions Realized in Flow Cells. , 2016, Chemphyschem : a European journal of chemical physics and physical chemistry.

[7]  Vladimir Privman,et al.  Enzymatic AND logic gate with sigmoid response induced by photochemically controlled oxidation of the output. , 2013, The journal of physical chemistry. B.

[8]  Vladimir Privman,et al.  Networked enzymatic logic gates with filtering: new theoretical modeling expressions and their experimental application. , 2013, The journal of physical chemistry. B.

[9]  G. A. Truesdale,et al.  Solubility of Oxygen in Water , 1954, Nature.

[10]  Evgeny Katz,et al.  Digital Biosensors with Built‐in Logic for Biomedical Applications , 2011 .

[11]  Vladimir Privman,et al.  Realization and properties of biochemical-computing biocatalytic XOR gate based on signal change. , 2010, The journal of physical chemistry. B.

[12]  Wojciech Macyk,et al.  Light-driven OR and XOR programmable chemical logic gates. , 2006, Journal of the American Chemical Society.

[13]  Evgeny Katz,et al.  Reversible logic gates based on enzyme-biocatalyzed reactions and realized in flow cells: a modular approach. , 2015, Chemphyschem : a European journal of chemical physics and physical chemistry.

[14]  Evgeny Katz,et al.  Digital biosensors with built-in logic for biomedical applications—biosensors based on a biocomputing concept , 2010, Analytical and bioanalytical chemistry.

[15]  Mary A. Arugula,et al.  Molecular AND logic gate based on bacterial anaerobic respiration. , 2012, Chemical communications.

[16]  Z. Ezziane DNA computing: applications and challenges , 2006 .

[17]  Byung Chan Kim,et al.  Enzyme logic gates based on enzyme-coated carbon nanotubes , 2011 .

[18]  Y. Benenson Biomolecular computing systems: principles, progress and potential , 2012, Nature Reviews Genetics.

[19]  Vladimir Privman Biomolecular computing: learning through play. , 2010, Nature nanotechnology.

[20]  Erik E. Josberger,et al.  An enzyme logic bioprotonic transducer , 2015 .

[21]  A. P. de Silva,et al.  Molecular logic and computing. , 2007, Nature nanotechnology.

[22]  Shaojun Dong,et al.  Label-free and enzyme-free platform for the construction of advanced DNA logic devices based on the assembly of graphene oxide and DNA-templated AgNCs. , 2016, Nanoscale.

[23]  E. Katz,et al.  DNA Release from Fe3+ -Cross-Linked Alginate Films Triggered by Logically Processed Biomolecular Signals: Integration of Biomolecular Computing and Actuation. , 2017, Chemphyschem : a European journal of chemical physics and physical chemistry.

[24]  Sai Bi,et al.  Hyperbranched Hybridization Chain Reaction for Triggered Signal Amplification and Concatenated Logic Circuits. , 2015, Angewandte Chemie.

[25]  A. P. D. S. and,et al.  Proof-of-Principle of Molecular-Scale Arithmetic , 2000 .

[26]  P. Kofinas,et al.  Enzyme Induced Stiffening of Nanoparticle-Hydrogel Composites with Structural Color. , 2015, ACS nano.

[27]  Jan Halámek,et al.  An enzyme-based reversible CNOT logic gate realized in a flow system. , 2014, The Analyst.

[28]  Mary A. Arugula,et al.  Network analysis of biochemical logic for noise reduction and stability: a system of three coupled enzymatic and gates. , 2008, The journal of physical chemistry. B.

[29]  Jan Halámek,et al.  Analysis of biomarkers characteristic of porcine liver injury--from biomolecular logic gates to an animal model. , 2012, The Analyst.

[30]  E. Katz,et al.  A biocatalytic cascade with several output signals—towards biosensors with different levels of confidence , 2014, Analytical and Bioanalytical Chemistry.

[31]  Yi Xiao,et al.  Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. , 2010, Journal of the American Chemical Society.

[32]  Vladimir Privman,et al.  Control of Noise in Chemical and Biochemical Information Processing , 2010, ArXiv.

[33]  I. Willner,et al.  Logic gates and elementary computing by enzymes. , 2006, The journal of physical chemistry. A.

[34]  Itamar Willner,et al.  Concatenated logic gates using four coupled biocatalysts operating in series , 2006, Proceedings of the National Academy of Sciences.

[35]  Mary A. Arugula,et al.  Enzyme-based NAND and NOR logic gates with modular design. , 2009, The journal of physical chemistry. B.

[36]  I. Willner,et al.  Elementary arithmetic operations by enzymes: a model for metabolic pathway based computing. , 2006, Angewandte Chemie.

[37]  Evgeny Katz,et al.  Biocatalytic Enzyme Networks Designed for Binary-Logic Control of Smart Electroactive Nanobiointerfaces , 2012, Topics in Catalysis.

[38]  Vladimir Privman,et al.  Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate , 2011, The journal of physical chemistry. B.

[39]  Evgeny Katz,et al.  Switchable electrode controlled by enzyme logic network system: approaching physiologically regulated bioelectronics. , 2009, Journal of the American Chemical Society.

[40]  D. Stefanovic,et al.  Exercises in Molecular Computing , 2014, Accounts of chemical research.

[41]  A. Prasanna de Silva,et al.  Molecular computing: A layer of logic , 2008, Nature.

[42]  Uwe Pischel,et al.  Molekulare Logik mit Speicherfunktion , 2010 .

[43]  J. Fraser Stoddart,et al.  Logic Operations at the Molecular Level. An XOR Gate Based on a Molecular Machine , 1997 .

[44]  Jing Yang,et al.  Aptamer-Binding Directed DNA Origami Pattern for Logic Gates. , 2016, ACS applied materials & interfaces.

[45]  Jian Zhou,et al.  Multiplexing of injury codes for the parallel operation of enzyme logic gates. , 2010, The Analyst.

[46]  Alberto Credi,et al.  Moleküle, die Entscheidungen treffen , 2007 .

[47]  A. Prasanna de Silva,et al.  Molecular Logic-based Computation , 2012 .

[48]  R. Weiss,et al.  A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.

[49]  Matthew R. Lakin,et al.  Catalytic Molecular Logic Devices by DNAzyme Displacement , 2014, Chembiochem : a European journal of chemical biology.

[50]  Vânia F. Pais,et al.  Information processing with molecules--Quo vadis? , 2013, Chemphyschem : a European journal of chemical physics and physical chemistry.

[51]  K. Szaciłowski Digital information processing in molecular systems. , 2008, Chemical reviews.

[52]  Shaojun Dong,et al.  Molecular aptamer beacon tuned DNA strand displacement to transform small molecules into DNA logic outputs. , 2014, Chemical communications.

[53]  R. Weiss,et al.  Multi-input Rnai-based Logic Circuit for Identification of Specific , 2022 .

[54]  A. P. Silva,et al.  A supramolecular chemistry basis for molecular logic and computation , 2007 .

[55]  K. Szaciłowski Infochemistry: Information Processing at the Nanoscale , 2012 .

[56]  Vladimir Privman,et al.  Enzyme-based logic systems for information processing. , 2009, Chemical Society reviews.

[57]  A. Raichur,et al.  Dual enzyme responsive microcapsules simulating an "OR" logic gate for biologically triggered drug delivery applications. , 2013, Chemical communications.

[58]  John Moult,et al.  Towards computing with proteins , 2006, Proteins.

[59]  Uwe Pischel,et al.  Molecules with a sense of logic: a progress report. , 2015, Chemical Society reviews.

[60]  Zehavit Dadon,et al.  Building Logic into Peptide Networks: Bottom‐Up and Top‐Down , 2011 .

[61]  E. Katz,et al.  Boolean Logic Gates that Use Enzymes as Input Signals , 2008, Chembiochem : a European journal of chemical biology.

[62]  Xiaogang Qu,et al.  Enzyme-regulated the changes of pH values for assembling a colorimetric and multistage interconnection logic network with multiple readouts. , 2015, Analytica chimica acta.

[63]  E. Katz Biocomputing - tools, aims, perspectives. , 2015, Current opinion in biotechnology.

[64]  Lei Wang,et al.  Multiple-stimuli responsive bioelectrocatalysis based on reduced graphene oxide/poly(N-isopropylacrylamide) composite films and its application in the fabrication of logic gates. , 2015, ACS applied materials & interfaces.

[65]  Darko Stefanovic,et al.  Chemistry at a Higher Level of Abstraction , 2011 .

[66]  Uwe Pischel,et al.  Advanced molecular logic with memory function. , 2010, Angewandte Chemie.

[67]  Noah Lotan,et al.  A biochemical logic gate using an enzyme and its inhibitor. Part II: The logic gate. , 2003, Bio Systems.

[68]  Shlomo Magdassi,et al.  Multienzyme Inkjet Printed 2D Arrays. , 2015, ACS applied materials & interfaces.

[69]  Vladimir Privman,et al.  Modularity of biochemical filtering for inducing sigmoid response in both inputs in an enzymatic AND gate. , 2013, The journal of physical chemistry. B.

[70]  Evgeny Katz,et al.  Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems. , 2015, Angewandte Chemie.

[71]  A. Credi Molecules that make decisions. , 2007, Angewandte Chemie.

[72]  E. Katz Enzyme-Based Logic Gates and Networks with Output Signals Analyzed by Various Methods. , 2017, ChemPhysChem.