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Martynov AI, Belov AS, Nevolin VK. Using non-adiabatic excitation transfer for signal transmission between molecular logic gates. NANOSCALE 2024; 16:14879-14898. [PMID: 39037702 DOI: 10.1039/d4nr01206b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Molecular logic gates (MLGs) are molecules which perform logic operations. They can potentially be used as building blocks for nano-sized computational devices. However, their physical and functional integration is a difficult task which remains to be solved. The problem lies in the field of signal exchange between the gates within the system. We propose using non-adiabatic excitation transfer between the gates to address this problem while absorption and fluorescence are left to communicate with external devices. Excitation transfer was studied using the modified Bixon-Jortner-Plotnikov theory with the example of the 3H-thioxanthene-TTF-dibenzo-BODIPY covalently linked triad. Several designs of the molecule were studied in a vacuum and cyclohexane. It was found that the molecular logic system has to be planar and rigid to isolate radiative interfaces from other gates. Functioning of these gates is based on dark πσ*-states in contrast to bright ππ*-states of radiative interfaces. There are no fundamental differences between ππ* → πσ* and ππ* → ππ* transitions for cases when an exciton hops from one gate to another. The rates of such transitions depend only on an energy gap between states and the distance between gates. The circuit is highly sensitive to the choice of solvent which could rearrange its state structure thereby altering its behavior. According to the obtained results, non-adiabatic transfer can be considered as one of the possible ways for transmitting a signal between MLGs.
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Affiliation(s)
- A I Martynov
- National Research University of Electronic Technology, 1 Shokin Square, Zelenograd, Moscow, Russia.
| | - A S Belov
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie gory, Moscow, Russia
| | - V K Nevolin
- National Research University of Electronic Technology, 1 Shokin Square, Zelenograd, Moscow, Russia.
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Fratto BE, Lewer JM, Katz E. An Enzyme-Based Half-Adder and Half-Subtractor with a Modular Design. Chemphyschem 2016; 17:2210-7. [PMID: 27037520 DOI: 10.1002/cphc.201600173] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 01/01/2023]
Abstract
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.
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Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Jessica M Lewer
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA.
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Shritz R, Shapira R, Borzin E, Tumanskii B, Reichstein W, Meichner C, Schwaiger F, Reichstein PM, Kreyenschmidt J, Haarer D, Kador L, Eichen Y. Measuring Cumulative Exposure to Oxygen with a Diphenylphosphine–Alkyl Naphthaleneimide Luminescence Turn‐On Dyad. Chemistry 2015; 21:11531-7. [DOI: 10.1002/chem.201500479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/14/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Rozalia Shritz
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Technion City 3200008 Haifa (Israel)
| | - Reut Shapira
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Technion City 3200008 Haifa (Israel)
| | - Elena Borzin
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Technion City 3200008 Haifa (Israel)
| | - Boris Tumanskii
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Technion City 3200008 Haifa (Israel)
| | - Werner Reichstein
- Institute of Physics and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth (Germany)
| | - Christoph Meichner
- Institute of Physics and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth (Germany)
| | - Florian Schwaiger
- Institute of Physics and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth (Germany)
| | - Paul M. Reichstein
- Institute of Physics and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth (Germany)
| | - Judith Kreyenschmidt
- Institute of Animal Science, University of Bonn, Katzenburgweg 7‐9, 53115 Bonn (Germany)
| | - Dietrich Haarer
- Institute of Physics and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth (Germany)
| | - Lothar Kador
- Institute of Physics and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth (Germany)
| | - Yoav Eichen
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Technion City 3200008 Haifa (Israel)
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Gentili PL. Small steps towards the development of chemical artificial intelligent systems. RSC Adv 2013. [DOI: 10.1039/c3ra44657c] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Halámek J, Bocharova V, Arugula MA, Strack G, Privman V, Katz E. Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate. J Phys Chem B 2011; 115:9838-45. [DOI: 10.1021/jp2041372] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Vera Bocharova
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Mary A. Arugula
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Guinevere Strack
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Vladimir Privman
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
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8
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Baroncini M, Semeraro M, Credi A. Processing Chemical and Photonic Signals by Artificial Multicomponent Molecular Systems. Isr J Chem 2011. [DOI: 10.1002/ijch.201000065] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Amelia M, Zou L, Credi A. Signal processing with multicomponent systems based on metal complexes. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.01.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Privman V, Zhou J, Halámek J, Katz E. Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change. J Phys Chem B 2010; 114:13601-8. [DOI: 10.1021/jp107562p] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Privman
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Jian Zhou
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Jan Halámek
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
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Melnikov D, Strack G, Zhou J, Windmiller JR, Halámek J, Bocharova V, Chuang MC, Santhosh P, Privman V, Wang J, Katz E. Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications. J Phys Chem B 2010; 114:12166-74. [DOI: 10.1021/jp105912e] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitriy Melnikov
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Guinevere Strack
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Jian Zhou
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Joshua Ray Windmiller
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Jan Halámek
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Vera Bocharova
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Min-Chieh Chuang
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Padmanabhan Santhosh
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Joseph Wang
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
| | - Evgeny Katz
- Department of Physics, Clarkson University, Potsdam, New York 13676, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13676, and Department of NanoEngineering, University of California−San Diego, La Jolla, California 92093
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Arugula MA, Bocharova V, Halámek J, Pita M, Katz E. Enzyme-based multiplexer and demultiplexer. J Phys Chem B 2010; 114:5222-6. [PMID: 20350002 DOI: 10.1021/jp101101b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A digital 2-to-1 multiplexer and a 1-to-2 demultiplexer were mimicked by biocatalytic reactions involving concerted operation of several enzymes. Using glucose oxidase (GOx) and laccase (Lac) as the data input signals and variable pH as the addressing signal, ferrocyanide oxidation in the output channel was selectively activated by one from two inputs, thus mimicking the multiplexer operation. A demultiplexer based on the enzyme system composed of GOx, glucose dehydrogenase (GDH) and horseradish peroxidase (HRP) allowed selective activation of different output channels (oxidation of ferrocyanide or reduction of NAD(+)) by the glucose input. The selection of the output channel was controlled by the addressing input of NAD(+). The designed systems represent important novel components of future branched enzyme networks processing biochemical signals for biosensing and bioactuating.
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Affiliation(s)
- Mary A Arugula
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam New York 13699-5810, USA
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Digital biosensors with built-in logic for biomedical applications—biosensors based on a biocomputing concept. Anal Bioanal Chem 2010; 398:1591-603. [DOI: 10.1007/s00216-010-3746-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/11/2010] [Accepted: 04/12/2010] [Indexed: 11/29/2022]
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Silvi S, Constable EC, Housecroft CE, Beves JE, Dunphy EL, Tomasulo M, Raymo FM, Credi A. All-optical integrated logic operations based on chemical communication between molecular switches. Chemistry 2009; 15:178-85. [PMID: 19021180 DOI: 10.1002/chem.200801645] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Molecular logic gates process physical or chemical "inputs" to generate "outputs" based on a set of logical operators. We report the design and operation of a chemical ensemble in solution that behaves as integrated AND, OR, and XNOR gates with optical input and output signals. The ensemble is composed of a reversible merocyanine-type photoacid and a ruthenium polypyridine complex that functions as a pH-controlled three-state luminescent switch. The light-triggered release of protons from the photoacid is used to control the state of the transition-metal complex. Therefore, the two molecular switching devices communicate with one another through the exchange of ionic signals. By means of such a double (optical-chemical-optical) signal-transduction mechanism, inputs of violet light modulate a luminescence output in the red/far-red region of the visible spectrum. Nondestructive reading is guaranteed because the green light used for excitation in the photoluminescence experiments does not affect the state of the gate. The reset is thermally driven and, thus, does not involve the addition of chemicals and accumulation of byproducts. Owing to its reversibility and stability, this molecular device can afford many cycles of digital operation.
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Affiliation(s)
- Serena Silvi
- Dipartimento di Chimica G. Ciamician, Università di Bologna via Selmi 2, 40126 Bologna, Italy
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Kumar S, Luxami V, Saini R, Kaur D. Superimposed molecular keypad lock and half-subtractor implications in a single fluorophore. Chem Commun (Camb) 2009:3044-6. [DOI: 10.1039/b900131j] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Privman V, Strack G, Solenov D, Pita M, Katz E. Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit? J Phys Chem B 2008; 112:11777-84. [DOI: 10.1021/jp802673q] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Privman
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Guinevere Strack
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Dmitry Solenov
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Marcos Pita
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
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Affiliation(s)
- Konrad Szaciłowski
- Uniwersytet Jagielloński, Wydział Chemii, ul. Romana Ingardena 3, 30-060 Kraków, Poland
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Luxami V, Kumar S. Molecular half-subtractor based on 3,3′-bis(1H-benzimidazolyl-2-yl)[1,1′]binaphthalenyl-2,2′-diol. NEW J CHEM 2008. [DOI: 10.1039/b805558k] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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