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Kubodera Y, Horisaka M, Kuze M, Suematsu NJ, Amemiya T, Steinbock O, Nakata S. Coexistence of oscillatory and reduced states on a spherical field controlled by electrical potential. CHAOS (WOODBURY, N.Y.) 2022; 32:073103. [PMID: 35907716 DOI: 10.1063/5.0097010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
The Belousov-Zhabotinsky (BZ) reaction was investigated to elucidate features of oscillations depending on the applied electrical potential, E. A cation-exchange resin bead loaded with the catalyst of the BZ reaction was placed on a platinum plate as a working electrode and then E was applied. We found that global oscillations (GO) and a reduced state coexisted on the bead at a negative value of E and that the source point of GO changed depending on E. The thickness of the reduced state was determined by a yellow colored region which corresponded to the distribution of Br2. The present studies suggest that the distribution of the inhibitor, Br-, which is produced from Br2, plays an important role in the existence of the reduced state and GO, and the source point of GO.
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Affiliation(s)
- Yujin Kubodera
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Mari Horisaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Masakazu Kuze
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, 4-21-1 Nakano, Nakano-ku, Tokyo 164-8525, Japan
| | - Nobuhiko J Suematsu
- Meiji Institute for Advanced Study of Mathematical Sciences (MIMS) and Graduate School of Advanced Mathematical Sciences, Meiji University, 4-21-1 Nakano, Nakano-ku, Tokyo 164-8525, Japan
| | - Takashi Amemiya
- Graduate School of Environment and Information Sciences, Yokohama National University (YNU), 79-7 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan
| | - Oliver Steinbock
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA
| | - Satoshi Nakata
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
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2
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Abstract
Unconventional and, specifically, wave computing has been repeatedly studied in laboratory based experiments by utilizing chemical systems like a thin film of Belousov–Zhabotinsky (BZ) reactions. Nonetheless, the principles demonstrated by this chemical computer were mimicked by mathematical models to enhance the understanding of these systems and enable a more detailed investigation of their capacity. As expected, the computerized counterparts of the laboratory based experiments are faster and less expensive. A further step of acceleration in wave-based computing is the development of electrical circuits that imitate the dynamics of chemical computers. A key component of the electrical circuits is the memristor which facilitates the non-linear behavior of the chemical systems. As part of this concept, the road-map of the inspiration from wave-based computing on chemical media towards the implementation of equivalent systems on oscillating memristive circuits was studied here. For illustration reasons, the most straightforward example was demonstrated, namely the approximation of Boolean gates.
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3
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Draper T, Poros-Tarcali E, Pérez-Mercader J. pH Oscillating System for Molecular Computation as a Chemical Turing Machine. ACS OMEGA 2022; 7:6099-6103. [PMID: 35224372 PMCID: PMC8867811 DOI: 10.1021/acsomega.1c06505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
It has previously been demonstrated that native chemical Turing machines can be constructed by exploiting the nonlinear dynamics of the homogeneous oscillating Belousov-Zhabotinsky reaction. These Turing machines can perform word recognition of a Chomsky type 1 context sensitive language (CSL), demonstrating their high computing power. Here, we report on a chemical Turing machine that has been developed using the H2O2-H2SO4-SO3 2--CO3 2- pH oscillating system. pH oscillators are different to bromate oscillators in two key ways: the proton is the autocatalytic agent, and at least one of the reductants is always fully consumed in each turnover-meaning the system has to be operated as a flow reactor. Through careful design, we establish a system that can also perform Chomsky type 1 CSL word recognition and demonstrate its power through the testing of a series of in-language and out-of-language words.
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Affiliation(s)
- Thomas
C. Draper
- Department
of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, Massachusetts 02138-1204, United States
| | - Eszter Poros-Tarcali
- Department
of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, Massachusetts 02138-1204, United States
| | - Juan Pérez-Mercader
- Department
of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, Massachusetts 02138-1204, United States
- Santa
Fe Institute, Santa Fe, New Mexico 87501, United States
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4
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Mallphanov IL, Vanag VK. Chemical micro-oscillators based on the Belousov–Zhabotinsky reaction. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
The results of studies on the development of micro-oscillators (MOs) based on the Belousov –Zhabotinsky (BZ) oscillatory chemical reaction are integrated and systematized. The mechanisms of the BZ reaction and the methods of immobilization of the catalyst of the BZ reaction in micro-volumes are briefly discussed. Methods for creating BZ MOs based on water microdroplets in the oil phase and organic and inorganic polymer microspheres are considered. Methods of control and management of the dynamics of BZ MO networks are described, including methods of MO synchronization. The prospects for the design of neural networks of MOs with intelligent-like behaviour are outlined. Such networks present a new area of nonlinear chemistry, including, in particular, the creation of a chemical ‘computer’.
The bibliography includes 250 references.
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5
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Adamatzky A. Towards proteinoid computers. Hypothesis paper. Biosystems 2021; 208:104480. [PMID: 34265376 DOI: 10.1016/j.biosystems.2021.104480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Proteinoids - thermal proteins - are produced by heating amino acids to their melting point and initiation of polymerisation to produce polymeric chains. Proteinoids swell in aqueous solution into hollow microspheres. The proteinoid microspheres produce endogenous burst of electrical potential spikes and change patterns of their electrical activity in response to illumination. The microspheres can interconnect by pores and tubes and form networks with a programmable growth. We speculate on how ensembles of the proteinoid microspheres can be developed into unconventional computing devices.
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6
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Draper TC, Dueñas-Díez M, Pérez-Mercader J. Exploring the symbol processing 'time interval' parametric constraint in a Belousov-Zhabotinsky operated chemical Turing machine. RSC Adv 2021; 11:23151-23160. [PMID: 35480432 PMCID: PMC9036302 DOI: 10.1039/d1ra03856g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Chemical reactions are powerful molecular recognition machines. This power has been recently harnessed to build actual instances of each class of experimentally realizable computing automata, using exclusively small-molecule chemistry (i.e. without requiring biomolecules). The most powerful of them, a programmable Turing machine, uses the Belousov–Zhabotinsky oscillatory chemistry, and accepts/rejects input sequences through a dual oscillatory and thermodynamic output signature. The time interval between the aliquots representing each letter of the input is the parameter that determines the time it takes to run the computation. Here, we investigate this critical performance parameter, and its effect not only on the computation speed, but also on the robustness of the accept/reject oscillatory and thermodynamic criteria. Our work demonstrates that the time interval is a non-trivial design parameter, whose choice should be made with great care. The guidelines we provide can be used in the optimization of the speed, robustness, and energy efficiency of chemical automata computations. Chemical reactions are powerful molecular recognition machines.![]()
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Affiliation(s)
- Thomas C Draper
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA
| | - Marta Dueñas-Díez
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA.,Repsol Technology Lab c/Agustín de Betancourt, s/n., 28935, Móstoles Madrid Spain
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA.,Santa Fe Institute Santa Fe New Mexico 87501 USA
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7
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Dueñas-Díez M, Pérez-Mercader J. Native Chemical Computation. A Generic Application of Oscillating Chemistry Illustrated With the Belousov-Zhabotinsky Reaction. A Review. Front Chem 2021; 9:611120. [PMID: 34046394 PMCID: PMC8144498 DOI: 10.3389/fchem.2021.611120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/17/2021] [Indexed: 11/18/2022] Open
Abstract
Computing with molecules is at the center of complex natural phenomena, where the information contained in ordered sequences of molecules is used to implement functionalities of synthesized materials or to interpret the environment, as in Biology. This uses large macromolecules and the hindsight of billions of years of natural evolution. But, can one implement computation with small molecules? If so, at what levels in the hierarchy of computing complexity? We review here recent work in this area establishing that all physically realizable computing automata, from Finite Automata (FA) (such as logic gates) to the Linearly Bound Automaton (LBA, a Turing Machine with a finite tape) can be represented/assembled/built in the laboratory using oscillatory chemical reactions. We examine and discuss in depth the fundamental issues involved in this form of computation exclusively done by molecules. We illustrate their implementation with the example of a programmable finite tape Turing machine which using the Belousov-Zhabotinsky oscillatory chemistry is capable of recognizing words in a Context Sensitive Language and rejecting words outside the language. We offer a new interpretation of the recognition of a sequence of chemicals representing words in the machine's language as an illustration of the “Maximum Entropy Production Principle” and concluding that word recognition by the Belousov-Zhabotinsky Turing machine is equivalent to extremal entropy production by the automaton. We end by offering some suggestions to apply the above to problems in computing, polymerization chemistry, and other fields of science.
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Affiliation(s)
- Marta Dueñas-Díez
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, MA, United States.,Repsol Technology Lab, Madrid, Spain
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University, Cambridge, MA, United States.,Santa Fe Institute, Santa Fe, NM, United States
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8
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Muzika F, Schreiberová L, Schreiber I. Advanced Chemical Computing Using Discrete Turing Patterns in Arrays of Coupled Cells. Front Chem 2020; 8:559650. [PMID: 33195048 PMCID: PMC7658265 DOI: 10.3389/fchem.2020.559650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/30/2020] [Indexed: 11/13/2022] Open
Abstract
We examine dynamical switching among discrete Turing patterns that enable chemical computing performed by mass-coupled reaction cells arranged as arrays with various topological configurations: three coupled cells in a cyclic array, four coupled cells in a linear array, four coupled cells in a cyclic array, and four coupled cells in a branched array. Each cell is operating as a continuous stirred tank reactor, within which the glycolytic reaction takes place, represented by a skeleton inhibitor-activator model where ADP plays the role of activator and ATP is the inhibitor. The mass coupling between cells is assumed to be operating in three possible transport regimes: (i) equal transport coefficients of the inhibitor and activator (ii) slightly faster transport of the activator, and (iii) strongly faster transport of the inhibitor. Each cellular array is characterized by two pairs of tunable parameters, the rate coefficients of the autocatalytic and inhibitory steps, and the transport coefficients of the coupling. Using stability and bifurcation analysis we identified conditions for occurrence of discrete Turing patterns associated with non-uniform stationary states. We found stable symmetric and/or asymmetric discrete Turing patterns coexisting with stable uniform periodic oscillations. To switch from one of the coexisting stable regimes to another we use carefully targeted perturbations, which allows us to build systems of logic gates specific to each topological type of the array, which in turn enables to perform advanced modes of chemical computing. By combining chemical computing techniques in the arrays with glycolytic excitable channels, we propose a cellular assemblage design for advanced chemical computing.
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Affiliation(s)
- František Muzika
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Czechia
| | - Lenka Schreiberová
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Czechia
| | - Igor Schreiber
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Czechia
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9
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Proskurkin IS, Smelov PS, Vanag VK. Experimental verification of an opto-chemical "neurocomputer". Phys Chem Chem Phys 2020; 22:19359-19367. [PMID: 32822448 DOI: 10.1039/d0cp01858a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A theoretically predicted hierarchical network of pulse coupled chemical micro-oscillators and excitable micro-cells that we call a chemical "neurocomputer" (CN) or even a chemical "brain" is tested experimentally using the Belousov-Zhabotinsky reaction. The CN consists of five functional units: (1) a central pattern generator (CPG), (2) an antenna, (3) a reader for the CPG, (4) a reader for the antenna unit, and (5) a decision making (DM) unit. A hybrid CN, in which such chemical units as readers and DM units are replaced by electronic units, is tested as well. All these variations of the CN respond intelligently to external signals, since they perform an automatic transition from a current to a new dynamic mode of the CPG, which is similar to the antenna dynamic mode that in turn is induced by external signals. In other words, we show for the first time that a network of pulse coupled chemical micro-oscillators is capable of intelligent adaptive behavior.
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Affiliation(s)
- Ivan S Proskurkin
- Centre for Nonlinear Chemistry, Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russia.
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10
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Abstract
A substrate does not have to be solid to compute. It is possible to make a computer purely from a liquid. I demonstrate this using a variety of experimental prototypes where a liquid carries signals, actuates mechanical computing devices and hosts chemical reactions. We show hydraulic mathematical machines that compute functions based on mass transfer analogies. I discuss several prototypes of computing devices that employ fluid flows and jets. They are fluid mappers, where the fluid flow explores a geometrically constrained space to find an optimal way around, e.g. the shortest path in a maze, and fluid logic devices where fluid jet streams interact at the junctions of inlets and results of the computation are represented by fluid jets at selected outlets. Fluid mappers and fluidic logic devices compute continuously valued functions albeit discretized. There is also an opportunity to do discrete operation directly by representing information by droplets and liquid marbles (droplets coated by hydrophobic powder). There, computation is implemented at the sites, in time and space, where droplets collide one with another. The liquid computers mentioned above use liquid as signal carrier or actuator: the exact nature of the liquid is not that important. What is inside the liquid becomes crucial when reaction-diffusion liquid-phase computing devices come into play: there, the liquid hosts families of chemical species that interact with each other in a massive-parallel fashion. I shall illustrate a range of computational tasks, including computational geometry, implementable by excitation wave fronts in nonlinear active chemical medium. The overview will enable scientists and engineers to understand how vast is the variety of liquid computers and will inspire them to design their own experimental laboratory prototypes. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
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Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Lab, Department of Computer Science and Creative Technologies, University of the West of England , Bristol , UK
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11
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Gorecki J. Applications of Information Theory Methods for Evolutionary Optimization of Chemical Computers. ENTROPY 2020; 22:e22030313. [PMID: 33286087 PMCID: PMC7516772 DOI: 10.3390/e22030313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 12/29/2022]
Abstract
It is commonly believed that information processing in living organisms is based on chemical reactions. However, the human achievements in constructing chemical information processing devices demonstrate that it is difficult to design such devices using the bottom-up strategy. Here I discuss the alternative top-down design of a network of chemical oscillators that performs a selected computing task. As an example, I consider a simple network of interacting chemical oscillators that operates as a comparator of two real numbers. The information on which of the two numbers is larger is coded in the number of excitations observed on oscillators forming the network. The parameters of the network are optimized to perform this function with the maximum accuracy. I discuss how information theory methods can be applied to obtain the optimum computing structure.
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Affiliation(s)
- Jerzy Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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12
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Adamatzky A, Tsompanas M, Draper TC, Fullarton C, Mayne R. Liquid Marble Photosensor. Chemphyschem 2019; 21:90-98. [PMID: 31696651 DOI: 10.1002/cphc.201900949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/30/2019] [Indexed: 01/31/2023]
Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing LaboratoryUniversity of the West of England, Coldharbour Lane Bristol BS16 1QY UK
| | | | - Thomas C. Draper
- Unconventional Computing LaboratoryUniversity of the West of England, Coldharbour Lane Bristol BS16 1QY UK
| | - Claire Fullarton
- Unconventional Computing LaboratoryUniversity of the West of England, Coldharbour Lane Bristol BS16 1QY UK
| | - Richard Mayne
- Unconventional Computing LaboratoryUniversity of the West of England, Coldharbour Lane Bristol BS16 1QY UK
- Department of Applied SciencesUniversity of the West of England, Coldharbour Lane Bristol BS16 1QY UK
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13
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Dueñas-Díez M, Pérez-Mercader J. How Chemistry Computes: Language Recognition by Non-Biochemical Chemical Automata. From Finite Automata to Turing Machines. iScience 2019; 19:514-526. [PMID: 31442667 PMCID: PMC6710637 DOI: 10.1016/j.isci.2019.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/08/2019] [Accepted: 08/02/2019] [Indexed: 11/28/2022] Open
Abstract
Every problem in computing can be cast as decision problems of whether strings are in a language or not. Computations and language recognition are carried out by three classes of automata, the most complex of which is the Turing machine. Living systems compute using biochemistry; in the artificial, computation today is mostly electronic. Thinking of chemical reactions as molecular recognition machines, and without using biochemistry, we realize one automaton in each class by means of one-pot, table top chemical reactors: from the simplest, Finite automata, to the most complex, Turing machines. Language acceptance/rejection criteria by automata can be formulated using energy considerations. Our Turing machine uses the Belousov-Zhabotinsky chemical reaction and checks the same symbol in an Avogadro′s number of processors. Our findings have implications for chemical and general computing, artificial intelligence, bioengineering, the study of the origin and presence of life on other planets, and for artificial biology. Computations are language recognition events carried out by “computing automata” Chemical reactions are molecular recognition events equivalent to automata Words in a language can be represented by sequences of chemical reactants Inorganic reactions like automata, including Turing machines, recognize languages
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Affiliation(s)
- Marta Dueñas-Díez
- Repsol Technology Lab, c/ Agustín de Betancourt s/n, Móstoles, Madrid 28935, Spain; Department of Earth and Planetary Sciences, Harvard Origins of Life Initiative, Harvard University, 20 Oxford Street, Cambridge, MA 02138, USA
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences, Harvard Origins of Life Initiative, Harvard University, 20 Oxford Street, Cambridge, MA 02138, USA; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
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14
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Adamatzky A, Fullarton C, Phillips N, De Lacy Costello B, Draper TC. Thermal switch of oscillation frequency in Belousov-Zhabotinsky liquid marbles. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190078. [PMID: 31183147 PMCID: PMC6502391 DOI: 10.1098/rsos.190078] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
External control of oscillation dynamics in the Belousov-Zhabotinsky (BZ) reaction is important for many applications including encoding computing schemes. When considering the BZ reaction, there are limited studies dealing with thermal cycling, particularly cooling, for external control. Recently, liquid marbles (LMs) have been demonstrated as a means of confining the BZ reaction in a system containing a solid-liquid interface. BZ LMs were prepared by rolling 50 μl droplets in polyethylene (PE) powder. Oscillations of electrical potential differences within the marble were recorded by inserting a pair of electrodes through the LM powder coating into the BZ solution core. Electrical potential differences of up to 100 mV were observed with an average period of oscillation ca 44 s. BZ LMs were subsequently frozen to -1°C to observe changes in the frequency of electrical potential oscillations. The frequency of oscillations reduced upon freezing to 11 mHz cf. 23 mHz at ambient temperature. The oscillation frequency of the frozen BZ LM returned to 23 mHz upon warming to ambient temperature. Several cycles of frequency fluctuations were able to be achieved.
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Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Laboratory, Department of Computer Science and Creative Technologies, Centre for Research in Biosciences, University of the West of England, Bristol BS16 1QY, UK
| | - Claire Fullarton
- Unconventional Computing Laboratory, Department of Computer Science and Creative Technologies, Centre for Research in Biosciences, University of the West of England, Bristol BS16 1QY, UK
| | - Neil Phillips
- Unconventional Computing Laboratory, Department of Computer Science and Creative Technologies, Centre for Research in Biosciences, University of the West of England, Bristol BS16 1QY, UK
| | - Ben De Lacy Costello
- Unconventional Computing Laboratory, Department of Computer Science and Creative Technologies, Centre for Research in Biosciences, University of the West of England, Bristol BS16 1QY, UK
- Institute of Biosensing Technology, Centre for Research in Biosciences, University of the West of England, Bristol BS16 1QY, UK
| | - Thomas C. Draper
- Unconventional Computing Laboratory, Department of Computer Science and Creative Technologies, Centre for Research in Biosciences, University of the West of England, Bristol BS16 1QY, UK
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15
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Toth R, Taylor AF. The Tris(2,2'-Bipyridyl)Ruthenium-Catalysed Belousov–Zhabotinsky Reaction. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967406779946928] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Belousov – Zhabotinsky (BZ) reaction is the prototypical oscillating chemical reaction. The tris(2,2'-bipyridine)ruthenium-catalysed BZ reaction (often simply referred to as the ruthenium-catalysed BZ reaction) displays photosensitivity and has been widely exploited for examination of the effects of illumination on nonlinear reaction kinetics. In this review, we investigate the behaviour of the ruthenium-catalysed BZ reaction. The mechanism of the reaction is analysed and we examine how light sensitivity is incorporated into kinetic models of the reaction. The temporal dynamics of the photosensitive reaction is presented and, finally, we discuss the extraordinary wealth of behaviour that has been observed in the spatially-distributed system when perturbed by visible light.
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Affiliation(s)
- Rita Toth
- University of the West of England, Bristol, UK
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16
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Abstract
We propose that fungi Basidiomycetes can be used as computing devices: information is represented by spikes of electrical activity, a computation is implemented in a mycelium network and an interface is realized via fruit bodies. In a series of scoping experiments, we demonstrate that electrical activity recorded on fruits might act as a reliable indicator of the fungi's response to thermal and chemical stimulation. A stimulation of a fruit is reflected in changes of electrical activity of other fruits of a cluster, i.e. there is distant information transfer between fungal fruit bodies. In an automaton model of a fungal computer, we show how to implement computation with fungi and demonstrate that a structure of logical functions computed is determined by mycelium geometry.
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17
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Adamatzky A, Phillips N, Weerasekera R, Tsompanas MA, Sirakoulis GC. Street map analysis with excitable chemical medium. Phys Rev E 2018; 98:012306. [PMID: 30110822 DOI: 10.1103/physreve.98.012306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 06/08/2023]
Abstract
Belousov-Zhabotinsky (BZ) thin layer solution is a fruitful substrate for designing unconventional computing devices. A range of logical circuits, wet electronic devices, and neuromorphic prototypes have been constructed. Information processing in BZ computing devices is based on interaction of oxidation (excitation) wave fronts. Dynamics of the wave fronts propagation is programed by geometrical constraints and interaction of colliding wave fronts is tuned by illumination. We apply the principles of BZ computing to explore a geometry of street networks. We use two-variable Oregonator equations, the most widely accepted and verified in laboratory experiments BZ models, to study propagation of excitation wave fronts for a range of excitability parameters, with gradual transition from excitable to subexcitable to nonexcitable. We demonstrate a pruning strategy adopted by the medium with decreasing excitability when wider and ballistically appropriate streets are selected. We explain mechanics of streets selection and pruning. The results of the paper will be used in future studies of studying dynamics of cities and characterizing geometry of street networks.
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Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Laboratory, University of the West of England, Bristol, United Kingdom
| | - Neil Phillips
- Unconventional Computing Laboratory, University of the West of England, Bristol, United Kingdom
| | - Roshan Weerasekera
- Unconventional Computing Laboratory, University of the West of England, Bristol, United Kingdom
| | | | - Georgios Ch Sirakoulis
- Department of Electrical and Computer Engineering, Democritus University of Thrace, Xanthi, Greece
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18
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Gorecki J, Kitahata H, Suematsu NJ, Koyano Y, Skrobanska P, Gryciuk M, Malecki M, Tanabe T, Yamamoto H, Nakata S. Unidirectional motion of a camphor disk on water forced by interactions between surface camphor concentration and dynamically changing boundaries. Phys Chem Chem Phys 2017; 19:18767-18772. [DOI: 10.1039/c7cp03252h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Dynamically changing boundaries induce unidirectional motion of a camphor disk on water, which is regarded as a signal diode.
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Affiliation(s)
- Jerzy Gorecki
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | | | - Nobuhiko J. Suematsu
- Graduate School of Advanced Mathematical Sciences and Meiji Institute of Advanced Study of Mathematical Sciences
- Meiji University
- Tokyo 164-8525
- Japan
| | - Yuki Koyano
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
| | - Paulina Skrobanska
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | - Marian Gryciuk
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | - Maciej Malecki
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | - Takahiro Tanabe
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
| | - Hiroya Yamamoto
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
| | - Satoshi Nakata
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
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19
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Stovold J, O’Keefe S. Associative Memory in Reaction-Diffusion Chemistry. EMERGENCE, COMPLEXITY AND COMPUTATION 2017. [DOI: 10.1007/978-3-319-33921-4_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Gizynski K, Gorecki J. Cancer classification with a network of chemical oscillators. Phys Chem Chem Phys 2017; 19:28808-28819. [DOI: 10.1039/c7cp05655a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We discuss chemical information processing considering dataset classifiers formed with a network of interacting droplets.
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Affiliation(s)
- Konrad Gizynski
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | - Jerzy Gorecki
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
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21
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Adamatzky A. On Emulation of Flueric Devices in Excitable Chemical Medium. PLoS One 2016; 11:e0168267. [PMID: 27997561 PMCID: PMC5173363 DOI: 10.1371/journal.pone.0168267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/29/2016] [Indexed: 11/18/2022] Open
Abstract
Flueric devices are fluidic devices without moving parts. Fluidic devices use fluid as a medium for information transfer and computation. A Belousov-Zhabotinsky (BZ) medium is a thin-layer spatially extended excitable chemical medium which exhibits travelling excitation wave-fronts. The excitation wave-fronts transfer information. Flueric devices compute via jets interaction. BZ devices compute via excitation wave-fronts interaction. In numerical model of BZ medium we show that functions of key flueric devices are implemented in the excitable chemical system: signal generator, and, xor, not and nor Boolean gates, delay elements, diodes and sensors. Flueric devices have been widely used in industry since late 1960s and are still employed in automotive and aircraft technologies. Implementation of analog of the flueric devices in the excitable chemical systems opens doors to further applications of excitation wave-based unconventional computing in soft robotics, embedded organic electronics and living technologies.
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Affiliation(s)
- Andrew Adamatzky
- University of the West of England, Bristol, United Kingdom
- * E-mail:
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22
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Gizynski K, Gruenert G, Dittrich P, Gorecki J. Evolutionary Design of Classifiers Made of Droplets Containing a Nonlinear Chemical Medium. EVOLUTIONARY COMPUTATION 2016; 25:643-671. [PMID: 27728772 DOI: 10.1162/evco_a_00197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Unconventional computing devices operating on nonlinear chemical media offer an interesting alternative to standard, semiconductor-based computers. In this work we study in-silico a chemical medium composed of communicating droplets that functions as a database classifier. The droplet network can be "programmed" by an externally provided illumination pattern. The complex relationship between the illumination pattern and the droplet behavior makes manual programming hard. We introduce an evolutionary algorithm that automatically finds the optimal illumination pattern for a given classification problem. Notably, our approach does not require us to prespecify the signals that represent the output classes of the classification problem, which is achieved by using a fitness function that measures the mutual information between chemical oscillation patterns and desired output classes. We illustrate the feasibility of our approach in computer simulations by evolving droplet classifiers for three machine learning datasets. We demonstrate that the same medium composed of 25 droplets located on a square lattice can be successfully used for different classification tasks by applying different illumination patterns as its externally supplied program.
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Affiliation(s)
- Konrad Gizynski
- Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Gerd Gruenert
- Bio Systems Analysis Group, Institute of Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Peter Dittrich
- Bio Systems Analysis Group, Institute of Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jerzy Gorecki
- Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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23
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Adamatzky A. Binary full adder, made of fusion gates, in a subexcitable Belousov-Zhabotinsky system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032811. [PMID: 26465532 DOI: 10.1103/physreve.92.032811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Indexed: 06/05/2023]
Abstract
In an excitable thin-layer Belousov-Zhabotinsky (BZ) medium a localized perturbation leads to the formation of omnidirectional target or spiral waves of excitation. A subexcitable BZ medium responds to asymmetric local perturbation by producing traveling localized excitation wave-fragments, distant relatives of dissipative solitons. The size and life span of an excitation wave-fragment depend on the illumination level of the medium. Under the right conditions the wave-fragments conserve their shape and velocity vectors for extended time periods. I interpret the wave-fragments as values of Boolean variables. When two or more wave-fragments collide they annihilate or merge into a new wave-fragment. States of the logic variables, represented by the wave-fragments, are changed in the result of the collision between the wave-fragments. Thus, a logical gate is implemented. Several theoretical designs and experimental laboratory implementations of Boolean logic gates have been proposed in the past but little has been done cascading the gates into binary arithmetical circuits. I propose a unique design of a binary one-bit full adder based on a fusion gate. A fusion gate is a two-input three-output logical device which calculates the conjunction of the input variables and the conjunction of one input variable with the negation of another input variable. The gate is made of three channels: two channels cross each other at an angle, a third channel starts at the junction. The channels contain a BZ medium. When two excitation wave-fragments, traveling towards each other along input channels, collide at the junction they merge into a single wave-front traveling along the third channel. If there is just one wave-front in the input channel, the front continues its propagation undisturbed. I make a one-bit full adder by cascading two fusion gates. I show how to cascade the adder blocks into a many-bit full adder. I evaluate the feasibility of my designs by simulating the evolution of excitation in the gates and adders using the numerical integration of Oregonator equations.
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Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Centre, University of the West of England, Bristol, United Kingdom
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24
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Gorecki J, Gizynski K, Guzowski J, Gorecka JN, Garstecki P, Gruenert G, Dittrich P. Chemical computing with reaction-diffusion processes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015; 373:rsta.2014.0219. [PMID: 26078345 DOI: 10.1098/rsta.2014.0219] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/29/2015] [Indexed: 06/04/2023]
Abstract
Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction-diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed.
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Affiliation(s)
- J Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - K Gizynski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - J Guzowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - J N Gorecka
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 36/42, 02-668 Warsaw, Poland
| | - P Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - G Gruenert
- Department of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - P Dittrich
- Department of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
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25
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Urban PL. Compartmentalised chemistry: from studies on the origin of life to engineered biochemical systems. NEW J CHEM 2014. [DOI: 10.1039/c4nj00894d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Gorecki J, Gorecka JN, Adamatzky A. Information coding with frequency of oscillations in Belousov-Zhabotinsky encapsulated disks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:042910. [PMID: 24827316 DOI: 10.1103/physreve.89.042910] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Indexed: 05/20/2023]
Abstract
Information processing with an excitable chemical medium, like the Belousov-Zhabotinsky (BZ) reaction, is typically based on information coding in the presence or absence of excitation pulses. Here we present a new concept of Boolean coding that can be applied to an oscillatory medium. A medium represents the logical TRUE state if a selected region oscillates with a high frequency. If the frequency fails below a specified value, it represents the logical FALSE state. We consider a medium composed of disks encapsulating an oscillatory mixture of reagents, as related to our recent experiments with lipid-coated BZ droplets. We demonstrate that by using specific geometrical arrangements of disks containing the oscillatory medium one can perform logical operations on variables coded in oscillation frequency. Realizations of a chemical signal diode and of a single-bit memory with oscillatory disks are also discussed.
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Affiliation(s)
- J Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland and Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszynski University, Dewajtis 5, 01-815 Warsaw, Poland
| | - J N Gorecka
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 36/42, 02-668 Warsaw, Poland
| | - Andrew Adamatzky
- Unconventional Computing Centre and Department of Computer Science, University of the West of England, Bristol BS16 1QY, England
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27
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Sun MZ, Zhao X. Multi-bit binary decoder based on Belousov-Zhabotinsky reaction. J Chem Phys 2013; 138:114106. [DOI: 10.1063/1.4794995] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ming-Zhu Sun
- Institute of Robotics and Automatic Information System, Nankai University, Tianjin, China
| | - Xin Zhao
- Institute of Robotics and Automatic Information System, Nankai University, Tianjin, China
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28
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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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29
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Stevens WM, Adamatzky A, Jahan I, Costello BDL. Time-dependent wave selection for information processing in excitable media. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:066129. [PMID: 23005184 DOI: 10.1103/physreve.85.066129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/24/2012] [Indexed: 06/01/2023]
Abstract
We demonstrate an improved technique for implementing logic circuits in light-sensitive chemical excitable media. The technique makes use of the constant-speed propagation of waves along defined channels in an excitable medium based on the Belousov-Zhabotinsky reaction, along with the mutual annihilation of colliding waves. What distinguishes this work from previous work in this area is that regions where channels meet at a junction can periodically alternate between permitting the propagation of waves and blocking them. These valvelike areas are used to select waves based on the length of time that it takes waves to propagate from one valve to another. In an experimental implementation, the channels that make up the circuit layout are projected by a digital projector connected to a computer. Excitable channels are projected as dark areas and unexcitable regions as light areas. Valves alternate between dark and light: Every valve has the same period and phase, with a 50% duty cycle. This scheme can be used to make logic gates based on combinations of or and and-not operations, with few geometrical constraints. Because there are few geometrical constraints, compact circuits can be implemented. Experimental results from an implementation of a four-bit input, two-bit output integer square root circuit are given.
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Affiliation(s)
- William M Stevens
- Faculty of Environment and Technology, University of the West of England, Bristol BS16 1QY, United Kingdom.
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30
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Zhang GM, Wong I, Chou MT, Zhao X. Towards constructing multi-bit binary adder based on Belousov-Zhabotinsky reaction. J Chem Phys 2012; 136:164108. [DOI: 10.1063/1.3702846] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Guo-Mao Zhang
- Institute of Robotics and Automatic Information System, Nankai University, Tianjin, China
| | - Ieong Wong
- Mechanical and Aerospace Engineering Department, University of California Los Angeles, Los Angeles, California 90095-1597, USA
| | - Meng-Ta Chou
- Electrical Engineering Department, University of California Los Angeles, Los Angeles, California 90095-1594, USA
| | - Xin Zhao
- Institute of Robotics and Automatic Information System, Nankai University, Tianjin, China
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31
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32
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Lacy Costello BD, Adamatzky A, Jahan I, Zhang L. Towards constructing one-bit binary adder in excitable chemical medium. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Adamatzky A, De Lacy Costello B, Bull L, Holley J. Towards Arithmetic Circuits in Sub-Excitable Chemical Media. Isr J Chem 2011. [DOI: 10.1002/ijch.201000046] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Nakata S, Kashima K, Kitahata H, Mori Y. Phase Wave between Two Oscillators in the Photosensitive Belousov−Zhabotinsky Reaction Depending on the Difference in the Illumination Time. J Phys Chem A 2010; 114:9124-9. [DOI: 10.1021/jp105204n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Satoshi Nakata
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Department of Physics, Graduate School of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan, PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Humanities and Sciences, Ochanomizu University, 2-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Kenji Kashima
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Department of Physics, Graduate School of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan, PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Humanities and Sciences, Ochanomizu University, 2-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hiroyuki Kitahata
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Department of Physics, Graduate School of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan, PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Humanities and Sciences, Ochanomizu University, 2-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yoshihito Mori
- Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Department of Physics, Graduate School of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan, PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Humanities and Sciences, Ochanomizu University, 2-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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35
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Nakabayashi S. ELECTROCHEMISTRY 2010; 78:773-778. [DOI: 10.5796/electrochemistry.78.773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem. Comput Biol Chem 2009; 33:253-60. [PMID: 19577519 DOI: 10.1016/j.compbiolchem.2009.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 04/25/2009] [Accepted: 05/29/2009] [Indexed: 11/23/2022]
Abstract
In the arsenal of tools that a computational modeller can bring to bare on the study of cardiac arrhythmias, the most widely used and arguably the most successful is that of an excitable medium, a special case of a reaction-diffusion model. These are used to simulate the internal chemical reactions of a cardiac cell and the diffusion of their membrane voltages. Via a number of different methodologies it has previously been shown that reaction-diffusion systems are at multiple levels Turing complete. That is, they are capable of computation in the same manner as a universal Turing machine. However, all such computational systems are subject to a limitation known as the Halting problem. By constructing a universal logic gate using a cardiac cell model, we highlight how the Halting problem therefore could limit what it is possible to predict about cardiac tissue, arrhythmias and re-entry. All simulations for this work were carried out on the GPU of an XBox 360 development console, and we also highlight the great gains in computational power and efficiency produced by such general purpose processing on a GPU for cardiac simulations.
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37
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Ichino T, Fujio K, Matsushita M, Nakata S. Wave Propagation in the Photosensitive Belousov−Zhabotinsky Reaction Across an Asymmetric Gap. J Phys Chem A 2009; 113:2304-8. [DOI: 10.1021/jp809955z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takatoshi Ichino
- Department of Intelligent Systems, School of Biology-Oriented Science and Technology, Kinki University, Wakayama 649-6493, Japan, Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan, and Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Kenji Fujio
- Department of Intelligent Systems, School of Biology-Oriented Science and Technology, Kinki University, Wakayama 649-6493, Japan, Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan, and Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Mariko Matsushita
- Department of Intelligent Systems, School of Biology-Oriented Science and Technology, Kinki University, Wakayama 649-6493, Japan, Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan, and Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Satoshi Nakata
- Department of Intelligent Systems, School of Biology-Oriented Science and Technology, Kinki University, Wakayama 649-6493, Japan, Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan, and Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan
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38
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de Lacy Costello B, Toth R, Stone C, Adamatzky A, Bull L. Implementation of glider guns in the light-sensitive Belousov-Zhabotinsky medium. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:026114. [PMID: 19391813 DOI: 10.1103/physreve.79.026114] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 11/20/2008] [Indexed: 05/27/2023]
Abstract
In cellular automata models a glider gun is an oscillating pattern of nonquiescent states that periodically emits traveling localizations (gliders). The glider streams can be combined to construct functionally complete systems of logical gates and thus realize universal computation. The glider gun is the only means of ensuring the negation operation without additional external input and therefore is an essential component of a collision-based computing circuit. We demonstrate the existence of glider-gun-like structures in both experimental and numerical studies of an excitable chemical system-the light-sensitive Belousov-Zhabotinsky reaction. These discoveries could provide the basis for future designs of collision-based reaction-diffusion computers.
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Affiliation(s)
- Ben de Lacy Costello
- Centre for Research in Analytical, Material and Sensor Sciences, University of the West of England, Bristol, BS16 1QY, United Kingdom.
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39
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Toth R, Stone C, Adamatzky A, de Lacy Costello B, Bull L. Dynamic control and information processing in the Belousov–Zhabotinsky reaction using a coevolutionary algorithm. J Chem Phys 2008; 129:184708. [DOI: 10.1063/1.2932252] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Affiliation(s)
- Konrad Szaciłowski
- Uniwersytet Jagielloński, Wydział Chemii, ul. Romana Ingardena 3, 30-060 Kraków, Poland
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41
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Epstein IR, Berenstein IB, Dolnik M, Vanag VK, Yang L, Zhabotinsky AM. Coupled and forced patterns in reaction-diffusion systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2008; 366:397-408. [PMID: 17673412 DOI: 10.1098/rsta.2007.2097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Several reaction-diffusion systems that exhibit temporal periodicity when well mixed also display spatio-temporal pattern formation in a spatially distributed, unstirred configuration. These patterns can be travelling (e.g. spirals, concentric circles, plane waves) or stationary in space (Turing structures, standing waves). The behaviour of coupled and forced temporal oscillators has been well studied, but much less is known about the phenomenology of forced and coupled patterns. We present experimental results focusing primarily on coupled patterns in two chemical systems, the chlorine dioxide-iodine-malonic acid reaction and the Belousov-Zhabotinsky reaction. The observed behaviour can be simulated with simple chemically plausible models.
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Affiliation(s)
- Irving R Epstein
- Department of Chemistry and Volen Center for Complex Systems, Brandeis University, MS 015, Waltham, MA 02454, USA.
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42
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Bull L, Budd A, Stone C, Uroukov I, de Lacy Costello B, Adamatzky A. Towards unconventional computing through simulated evolution: control of nonlinear media by a learning classifier system. ARTIFICIAL LIFE 2008; 14:203-22. [PMID: 18331191 DOI: 10.1162/artl.2008.14.2.203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We propose that the behavior of nonlinear media can be controlled automatically through evolutionary learning. By extension, forms of unconventional computing (viz., massively parallel nonlinear computers) can be realized by such an approach. In this initial study a light-sensitive subexcitable Belousov-Zhabotinsky reaction in which a checkerboard image, composed of cells of varying light intensity projected onto the surface of a thin silica gel impregnated with a catalyst and indicator, is controlled using a learning classifier system. Pulses of wave fragments are injected into the checkerboard grid, resulting in rich spatiotemporal behavior, and a learning classifier system is shown to be able to direct the fragments to an arbitrary position through dynamic control of the light intensity within each cell in both simulated and real chemical systems. Similarly, a learning classifier system is shown to be able to control the electrical stimulation of cultured neuronal networks so that they display elementary learning. Results indicate that the learned stimulation protocols identify seemingly fundamental properties of in vitro neuronal networks. Use of another learning scheme presented in the literature confirms that such fundamental behavioral characteristics of a given network must be considered in training experiments.
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Affiliation(s)
- Larry Bull
- Faculty of Computing, Engineering & Mathematics, University of the West of England, Coldharbour Lane, Frenchay, Bristol BS16 1QY, UK.
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43
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Matsushita M, Nakata S, Kitahata H. Characteristic Features in the Collision of Chemical Waves Depending on the Aspect Ratio of a Rectangular Field. J Phys Chem A 2007; 111:5833-8. [PMID: 17555302 DOI: 10.1021/jp068207n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photosensitive Belousov-Zhabotinsky (BZ) reaction was investigated on a double rectangular field composed of two rectangular routes, which was drawn using computer software and then projected using a liquid-crystal projector on a filter paper soaked with BZ solution. When two chemical waves were generated on the rectangular routes as the initial condition, the nature of the collision of the waves could be theoretically classified into four categories depending on the initial phase difference between the two waves and the aspect ratio of the rectangular routes. The experimental results were consistent with the features of the theoretical prediction. These results suggest that the feature of wave propagation characteristically develops depending on the geometry of the excitable fields.
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Affiliation(s)
- Mariko Matsushita
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan
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Affiliation(s)
- Irving R Epstein
- Department of Chemistry and the Volen Center for Complex Systems, Brandeis University, Waltham, MA 02454-9110, USA.
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Gorecka JN, Gorecki J, Igarashi Y. One Dimensional Chemical Signal Diode Constructed with Two Nonexcitable Barriers. J Phys Chem A 2007; 111:885-9. [PMID: 17266229 DOI: 10.1021/jp0662404] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Excitable chemical systems can process information coded in excitation pulses. Here we demonstrate the simplest realization of a chemical signal diode that transmits pulses in one direction only. It is constructed with only two different nonexcitable barriers. The proposed diode has been tested in numerical simulations and in experiments with Ru-catalyzed Belousov-Zhabotinsky reaction.
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Affiliation(s)
- Joanna N Gorecka
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 36/42, 02-668 Warsaw, Poland.
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Nakata S, Morishima S, Ichino T, Kitahata H. Coexistence of Wave Propagation and Oscillation in the Photosensitive Belousov−Zhabotinsky Reaction on a Circular Route. J Phys Chem A 2006; 110:13475-8. [PMID: 17165872 DOI: 10.1021/jp0636221] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photosensitive Belousov-Zhabotinsky (BZ) reaction was investigated on a circular ring, which was drawn using computer software and then projected on a film soaked with BZ solution using a liquid-crystal projector. Under the initial conditions, a chemical wave propagated with a constant velocity on the black ring under a bright background. When the background was rapidly changed to dark, coexistence of the oscillation on part of the ring and propagation of the chemical wave on the other part was observed. These experimental results are discussed in relation to the nature of the photosensitive BZ reaction and theoretically reproduced based on a reaction-diffusion system using the modified Oregonator model.
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Affiliation(s)
- Satoshi Nakata
- Department of Chemistry, Nara University of Education, Nara 630-8528, Japan.
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Affiliation(s)
- Irving R Epstein
- Department of Chemistry and Volen Center for Complex Systems, MS 015, Brandeis University, Waltham, MA 02454-9110, USA.
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Epstein IR, Pojman JA, Steinbock O. Introduction: Self-organization in nonequilibrium chemical systems. CHAOS (WOODBURY, N.Y.) 2006; 16:037101. [PMID: 17014235 DOI: 10.1063/1.2354477] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and current state of the field.
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Affiliation(s)
- Irving R Epstein
- Department of Chemistry, MS 015, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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Bishop KJM, Gray TP, Fialkowski M, Grzybowski BA. Microchameleons: nonlinear chemical microsystems for amplification and sensing. CHAOS (WOODBURY, N.Y.) 2006; 16:037102. [PMID: 17014236 DOI: 10.1063/1.2240142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In biological systems, the coupling of nonlinear biochemical kinetics and molecular transport enables functional sensing and "signal" amplification across many length scales. Drawing on biological inspiration, we describe how artificial reaction-diffusion (RD) microsystems can provide a basis for sensing applications, capable of amplifying micro- and nanoscopic events into macroscopic visual readouts. The RD applications reviewed here are based on a novel experimental technique, WETS for Wet Stamping, which offers unprecedented control over RD processes in microscopic and complex geometries. It is discussed how RD can be used to sense subtle differences in the thickness and/or absorptivity of thin absorptive films, amplify macromolecular phase transitions, detect the presence and quality of self-assembled monolayers, and provide dynamic spatiotemporal readouts of chemical "metabolites."
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Affiliation(s)
- K J M Bishop
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Affiliation(s)
- Akiko Kaminaga
- Department of Chemistry and Volen Center for Complex Systems, MS 015, Brandeis University, Waltham, MA 02454, USA
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