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Gorecki J, Muzika F. Chemical Memory with Discrete Turing Patterns Appearing in the Glycolytic Reaction. Biomimetics (Basel) 2023; 8:biomimetics8020154. [PMID: 37092406 PMCID: PMC10123649 DOI: 10.3390/biomimetics8020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023] Open
Abstract
Memory is an essential element in information processing devices. We investigated a network formed by just three interacting nodes representing continuously stirred tank reactors (CSTRs) in which the glycolytic reaction proceeds as a potential realization of a chemical memory unit. Our study is based on the 2-variable computational model of the reaction. The model parameters were selected such that the system has a stable limit cycle and several distinct, discrete Turing patterns characterized by stationary concentrations at the nodes. In our interpretation, oscillations represent a blank memory unit, and Turing patterns code information. The considered memory can preserve information on one of six different symbols. The time evolution of the nodes was individually controlled by the inflow of ATP. We demonstrate that information can be written with a simple and short perturbation of the inflow. The perturbation applies to only one or two nodes, and it is symbol specific. The memory can be erased with identical inflow perturbation applied to all nodes. The presented idea of pattern-coded memory applies to other reaction networks that allow for discrete Turing patterns. Moreover, it hints at the experimental realization of memory in a simple system with the glycolytic reaction.
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Affiliation(s)
- Jerzy Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Frantisek Muzika
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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2
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Bartlett S, Louapre D. Provenance of life: Chemical autonomous agents surviving through associative learning. Phys Rev E 2022; 106:034401. [PMID: 36266823 DOI: 10.1103/physreve.106.034401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/21/2022] [Indexed: 06/16/2023]
Abstract
We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning systems have been widely studied in cognitive science and artificial intelligence but are most commonly implemented in highly complex or carefully engineered systems, such as animal brains, artificial neural networks, DNA computing systems, and gene regulatory networks, among others. The ability to encode environmental information and use it to make simple predictions is a benchmark of biological resilience and underpins a plethora of adaptive responses in the living hierarchy, spanning prey animal species anticipating the arrival of predators to epigenetic systems in microorganisms learning environmental correlations. Given the ubiquitous and essential presence of learning behaviors in the biosphere, we aimed to explore whether simple, nonliving dissipative structures could also exhibit associative learning. Inspired by previous modeling of associative learning in chemical networks, we simulated simple systems composed of long- and short-term memory chemical species that could encode the presence or absence of temporal correlations between two external species. The ability to learn this association was implemented in Gray-Scott reaction-diffusion spots, emergent chemical patterns that exhibit self-replication and homeostasis. With the novel ability of associative learning, we demonstrate that simple chemical patterns can exhibit a broad repertoire of lifelike behavior, paving the way for in vitro studies of autonomous chemical learning systems, with potential relevance to artificial life, origins of life, and systems chemistry. The experimental realization of these learning behaviors in protocell or coacervate systems could advance a new research direction in astrobiology, since our system significantly reduces the lower bound on the required complexity for autonomous chemical learning.
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Affiliation(s)
- Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA and Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - David Louapre
- Ubisoft Entertainment, 94160 Saint-Mandé, France and Science Étonnante, 75014 Paris, France†
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From classical metal-catalyzed homogeneous oscillators to an uncatalyzed version of the Belousov–Zhabotinsky reaction: a review. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-021-02151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Identification of the best medium for experiments on chemical computation with Belousov–Zhabotinsky reaction and ferroin-loaded Dowex beads. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-022-02171-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractOur study is focused on identification of the best medium for future experiments on information processing with Belousov–Zhabotinsky reaction proceeding in Dowex beads with immobilized catalyst inside. The optimum medium should be characterized by long and stable nonlinear behavior, mechanical stability and should allow for control with electric potential. We considered different types of Dowex ion-exchange resins, bead distributions and various initial concentrations of substrates: malonic acid and 1,4-cyclohexanedione. The electric potential on platinum electrodes, stabilized by a potentiostat is used to control medium evolution. A negative electric potential generates activator species HBrO2 on the working electrode according to the reaction: BrO3− + 2e− + 3H+ → HBrO2 + H2O, while positive electric potential attracts inhibitor species Br− to the proximity of it. We study oscillation amplitude and period stability in systems with ferroin loaded Dowex 50W-X2 and Dowex 50W-X8 beads during experiments exceeding 16 h. It has been observed, that the above mentioned resins generate a smaller number of CO2 bubbles close to the beads than Dowex 50W-X4, which makes Dowex 50W-X2 and Dowex 50W-X8 more suitable for applications in chemical computing. We report amplitude stability, oscillation frequency, merging and annihilation of travelling waves in a lattice of Dowex 50W-X8 beads (mesh size 50–100) in over 19 h long experiments with equimolar solution of malonic acid and 1,4-cyclohexanedione. This system looks as a promising candidate for chemical computing devices that can operate for a day.
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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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Gyevi-Nagy L, Lantos E, Gehér-Herczegh T, Tóth Á, Bagyinka C, Horváth D. Reaction fronts of the autocatalytic hydrogenase reaction. J Chem Phys 2018; 148:165103. [PMID: 29716212 DOI: 10.1063/1.5022359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have built a model to describe the hydrogenase catalyzed, autocatalytic, reversible hydrogen oxidation reaction where one of the enzyme forms is the autocatalyst. The model not only reproduces the experimentally observed front properties, but also explains the found hydrogen ion dependence. Furthermore, by linear stability analysis, two different front types are found in good agreement with the experiments.
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Affiliation(s)
- László Gyevi-Nagy
- Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vértanúk tere 1, Szeged H-6720, Hungary
| | - Emese Lantos
- Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vértanúk tere 1, Szeged H-6720, Hungary
| | - Tünde Gehér-Herczegh
- Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vértanúk tere 1, Szeged H-6720, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Aradi vértanúk tere 1, Szeged H-6720, Hungary
| | - Csaba Bagyinka
- Institute of Biophysics, Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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Gizynski K, Gorecki J. Chemical memory with states coded in light controlled oscillations of interacting Belousov–Zhabotinsky droplets. Phys Chem Chem Phys 2017; 19:6519-6531. [DOI: 10.1039/c6cp07492h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The information storing potential of droplets, in which an oscillatory, photosensitive Belousov–Zhabotinsky (BZ) reaction proceeds, is investigated experimentally.
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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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Gorecki J, Gorecka JN, Nowakowski B, Ueno H, Yoshikawa K. How many enzyme molecules are needed for discrimination oriented applications? Phys Chem Chem Phys 2016; 18:20518-27. [PMID: 27405538 DOI: 10.1039/c6cp03860c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical reactions establish a molecular mechanism for information processing in living organisms. Here we consider a simple enzymatic reaction model that can be used to discriminate parameters characterizing periodic reagent inflow. Numerical simulations based on the kinetic equations show that there exist a range of inflow frequencies and amplitudes in which the time evolution of the system is very sensitive to small changes in the values of these parameters. However, the kinetic equations are derived for the thermodynamic limit, whereas in a real biological medium, like a cell, the number of enzyme molecules is an integer and finite. We use stochastic simulations to estimate discriminator reliability as a function of the number of enzyme molecules involved. For systems with 10 000 molecules the functionality predicted by kinetic equations is confirmed. If the number of molecules is decreased to 100, discrimination becomes unreliable.
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Affiliation(s)
- Jerzy Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Joanna N Gorecka
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Bogdan Nowakowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. and SGGW, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Hiroshi Ueno
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
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Muzika F, Schreiberová L, Schreiber I. Discrete Turing patterns in coupled reaction cells in a cyclic array. REACTION KINETICS MECHANISMS AND CATALYSIS 2016. [DOI: 10.1007/s11144-016-1004-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Muzika F, Bánsági T, Schreiber I, Schreiberová L, Taylor AF. A bistable switch in pH in urease-loaded alginate beads. Chem Commun (Camb) 2015; 50:11107-9. [PMID: 25111059 DOI: 10.1039/c4cc03936j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bistable switch from a low pH (unreacted "off") state to a high pH (reacted "on") state was obtained in enzyme-loaded gel beads in response to supra-threshold substrate concentrations.
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Affiliation(s)
- F Muzika
- Department of Chemical Engineering, Institute of Chemical Technology, Prague, 16628 Prague 6, Czech Republic
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Muzika F, Schreiberová L, Schreiber I. Chemical computing based on Turing patterns in two coupled cells with equal transport coefficients. RSC Adv 2014. [DOI: 10.1039/c4ra08859j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Two diffusively coupled reaction cells with a nonlinear reaction are used to perform chemical computing based on targeted perturbations switching between two Turing patterns defining two states of a logical device.
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