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Gentili PL, Stano P. Living cells and biological mechanisms as prototypes for developing chemical artificial intelligence. Biochem Biophys Res Commun 2024; 720:150060. [PMID: 38754164 DOI: 10.1016/j.bbrc.2024.150060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Artificial Intelligence (AI) is having a revolutionary impact on our societies. It is helping humans in facing the global challenges of this century. Traditionally, AI is developed in software or through neuromorphic engineering in hardware. More recently, a brand-new strategy has been proposed. It is the so-called Chemical AI (CAI), which exploits molecular, supramolecular, and systems chemistry in wetware to mimic human intelligence. In this work, two promising approaches for boosting CAI are described. One regards designing and implementing neural surrogates that can communicate through optical or chemical signals and give rise to networks for computational purposes and to develop micro/nanorobotics. The other approach concerns "bottom-up synthetic cells" that can be exploited for applications in various scenarios, including future nano-medicine. Both topics are presented at a basic level, mainly to inform the broader audience of non-specialists, and so favour the rise of interest in these frontier subjects.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.
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2
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Lee WS, Enomoto T, Akimoto AM, Yoshida R. Emergent Synchronous Volumetric Oscillation in Hierarchically Structured Self-Oscillating Gel Clusters. J Phys Chem B 2024; 128:5268-5279. [PMID: 38759232 DOI: 10.1021/acs.jpcb.4c01821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Emergent properties accompanying synchronization among oscillators are vital characteristics in biological systems. Belousov-Zhabotinsky (BZ) oscillators are an artificial model to study the emergence and synchronization in life. This research represents a self-oscillating gel system with clusterable properties to experimentally examine synchronous and emergent properties at a fundamental hierarchical level. Incorporating acrylic acid (AAc) moieties within the gel network facilitates cluster formation through hydrogen bonding in an acidic BZ substrate solution. Upon clustering, both homogeneous and heterogeneous gel assemblies─ranging from double to quadruple clusters─exhibit increased and synchronized periods and amplitudes during the BZ reaction. Notably, in heterogeneous clusters, gel units with initially short periods and small volumetric amplitudes display a significant increase, aligning with the lonfger periods and larger amplitudes of other elements within the cluster, an emergent property. This research can pave the way for a better understanding of synchronous and emergent properties in biological oscillators such as cardiomyocytes.
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Affiliation(s)
- Won Seok Lee
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takafumi Enomoto
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Aya Mizutani Akimoto
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryo Yoshida
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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3
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Onishi Y, Kitahata H, Suematsu NJ. Periodical alternation between precipitation and dissolution of camphor solid film on an ethanol solution. Phys Rev E 2024; 109:044801. [PMID: 38755815 DOI: 10.1103/physreve.109.044801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/02/2024] [Indexed: 05/18/2024]
Abstract
Rhythmic behaviors are generally observed in nonlinear chemical reactions such as the Belousov-Zhabotinsky reaction and enzymatic reactions. Similarly, a simple phase change can also lead to rhythmic behavior. It has been reported previously that camphor solid films alternate between generation and disappearance on ethanol (EtOH) solution, and a phenomenological mechanism has been suggested for this. The evaporation of EtOH decreases the temperature on the surface of the solution via vaporization heat and induces precipitation in the camphor solid film. At this time, the film prevents evaporation, and thus, the surface temperature increases due to thermal diffusion from the atmosphere, resulting in dissolution of the solid film. To verify the previously suggested phenomenological mechanism, we controlled the evaporation rate of EtOH using a porous plastic cover. As a result, the period of oscillation increased with decreasing pore diameter, and finally, the oscillation did not occur without pore in the cover, where the camphor solid film was not observed. Additionally, a new mathematical model was proposed, and the numerical calculations agreed well with experimental observations. Linear stability and bifurcation analyses revealed the detailed mechanism of this phenomenon, which agreed well with the phenomenological explanation mentioned above.
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Affiliation(s)
- Yuhei Onishi
- Graduate School of Advanced Mathematical Sciences, Meiji University, 4-21-1 Nakano, Tokyo 164-8525, Japan
| | - Hiroyuki Kitahata
- Graduate School of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
| | - Nobuhiko J Suematsu
- Meiji Institute for Advanced Study of Mathematical Sciences (MIMS), Meiji University, 4-21-1 Nakano, Tokyo 164-8525, Japan and School of Interdisciplinary Mathematical Sciences, Meiji University, 4-21-1 Nakano, Tokyo 164-8525, Japan
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4
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Stano P, Gentili PL, Damiano L, Magarini M. A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things? Molecules 2023; 28:5564. [PMID: 37513436 PMCID: PMC10385758 DOI: 10.3390/molecules28145564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
| | - Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Luisa Damiano
- Department of Communication, Arts and Media, IULM University, 20143 Milan, Italy
| | - Maurizio Magarini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
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5
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Provata A. From Turing patterns to chimera states in the 2D Brusselator model. CHAOS (WOODBURY, N.Y.) 2023; 33:033133. [PMID: 37003796 DOI: 10.1063/5.0130539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
The Brusselator has been used as a prototype model for autocatalytic reactions and, in particular, for the Belousov-Zhabotinsky reaction. When coupled at the diffusive limit, the Brusselator undergoes a Turing bifurcation resulting in the formation of classical Turing patterns, such as spots, stripes, and spirals in two spatial dimensions. In the present study, we use generic nonlocally coupled Brusselators and show that in the limit of the coupling range R→1 (diffusive limit), the classical Turing patterns are recovered, while for intermediate coupling ranges and appropriate parameter values, chimera states are produced. This study demonstrates how the parameters of a typical nonlinear oscillator can be tuned so that the coupled system passes from spatially stable Turing structures to dynamical spatiotemporal chimera states.
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Affiliation(s)
- A Provata
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos," 15341 Athens, Greece
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Liu Y, Pérez-Mercader J, Kiss IZ. Synchronization of Belousov-Zhabotinsky oscillators with electrochemical coupling in a spontaneous process. CHAOS (WOODBURY, N.Y.) 2022; 32:093128. [PMID: 36182363 DOI: 10.1063/5.0096689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
A passive electrochemical coupling approach is proposed to induce spontaneous synchronization between chemical oscillators. The coupling exploits the potential difference between a catalyst redox couple in the Belousov-Zhabotinsky (BZ) reaction, without external feedback, to induce surface reactions that impact the kinetics of the bulk system. The effect of coupling in BZ oscillators under batch condition is characterized using phase synchronization measures. Although the frequency of the oscillators decreases nonlinearly over time, by a factor of 2 or more within 100 cycles, the coupling is strong enough to maintain synchronization. In such a highly drifting system, the Gibbs-Shannon entropy of the cyclic phase difference distribution can be used to quantify the coupling effect. We extend the Oregonator BZ model to account for the drifting natural frequencies in batch condition and for electrochemical coupling, and numerical simulations of the effect of acid concentration on synchronization patterns are in agreement with the experiments. Because of the passive nature of coupling, the proposed coupling scheme can open avenues for designing pattern recognition and neuromorphic computation systems using chemical reactions in a spontaneous process.
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Affiliation(s)
- Yifan Liu
- Department of Earth and Planetary Sciences, Harvard Origins of Life Initiative, Harvard University, 20 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences, Harvard Origins of Life Initiative, Harvard University, 20 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - István Z Kiss
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, Missouri 63103, USA
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Melcher L, Rennert E, Ross J, Rust M, Robertson-Anderson R, Das M. Sustained order-disorder transitions in a model colloidal system driven by rhythmic crosslinking. SOFT MATTER 2022; 18:2920-2927. [PMID: 35343534 DOI: 10.1039/d1sm01583d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biological systems have the unique ability to self-organize and generate autonomous motion and work. Motivated by this, we investigate a 2D model colloidal network that can repeatedly transition between disordered states of low connectivity and ordered states of high connectivity via rhythmic binding and unbinding of biomimetic crosslinkers. We use Langevin dynamics to investigate the time-dependent changes in structure and collective properties of this system as a function of colloidal packing fractions and crosslinker oscillation periods and characterize the degree of order in the system by using network connectivity, bond length distributions, and collective motion. Our simulations suggest that we can achieve distinct states of this colloidal system with pronounced differences in microstructural order and large residence times in the ordered state when crosslinker kinetics and lifetimes depend directly on the oscillation period and this oscillation period is much larger than the colloidal diffusion time. Our results will provide insights into the rational design of smart active materials that can independently cycle between ordered and disordered states with desired material properties on a programmed schedule.
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Affiliation(s)
- Lauren Melcher
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, NY, USA.
| | - Elisabeth Rennert
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, USA
- Physical Sciences Division and Biological Sciences Division, University of Chicago, Chicago, NY, USA
| | - Jennifer Ross
- Department of Physics, Syracuse University, Syracuse, NY, USA
| | - Michael Rust
- Department of Biology, University of Chicago, Chicago, IL, USA
| | | | - Moumita Das
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, NY, USA.
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, USA
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8
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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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Prathom K, Young TR. Universality of stable multi-cluster periodic solutions in a population model of the cell cycle with negative feedback. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:455-522. [PMID: 34490835 DOI: 10.1080/17513758.2021.1971781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
We study a population model where cells in one part of the cell cycle may affect the progress of cells in another part. If the influence, or feedback, from one part to another is negative, simulations of the model almost always result in multiple temporal clusters formed by groups of cells. We study regions in parameter space where periodic 'k-cyclic' solutions are stable. The regions of stability coincide with sub-triangles on which certain events occur in a fixed order. For boundary sub-triangles with order 'rs1', we prove that the k-cyclic periodic solution is asymptotically stable if the index of the sub-triangle is relatively prime with respect to the number of clusters k and neutrally stable otherwise. For negative linear feedback, we prove that the interior of the parameter set is covered by stable sub-triangles, i.e. a stable k-cyclic solution always exists for some k. We observe numerically that the result also holds for many forms of nonlinear feedback, but may break down in extreme cases.
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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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Mallphanov IL, Vanag VK. Distance dependent types of coupling of chemical micro-oscillators immersed in a water-in-oil microemulsion. Phys Chem Chem Phys 2021; 23:9130-9138. [DOI: 10.1039/d1cp00758k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A system of micro-spheres immersed in a water-in-oil microemulsion (ME) is studied both theoretically and experimentally.
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Affiliation(s)
- Ilya L. Mallphanov
- Centre for Nonlinear Chemistry
- Immanuel Kant Baltic Federal University
- Kaliningrad 236016
- Russia
| | - Vladimir K. Vanag
- Centre for Nonlinear Chemistry
- Immanuel Kant Baltic Federal University
- Kaliningrad 236016
- Russia
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12
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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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13
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Light and chemical oscillations: Review and perspectives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2019.100321] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Mallphanov IL, Vanag VK. Fabrication of New Belousov–Zhabotinsky Micro-Oscillators on the Basis of Silica Gel Beads. J Phys Chem A 2020; 124:272-282. [PMID: 31899640 DOI: 10.1021/acs.jpca.9b09127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ilya L. Mallphanov
- Center for Nonlinear Chemistry, Immanuel Kant Baltic Federal University, 14 A. Nevskogo str., Kaliningrad 236016, Russia
| | - Vladimir K. Vanag
- Center for Nonlinear Chemistry, Immanuel Kant Baltic Federal University, 14 A. Nevskogo str., Kaliningrad 236016, Russia
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Vanag VK. Size- and position-dependent bifurcations of chemical microoscillators in confined geometries. CHAOS (WOODBURY, N.Y.) 2020; 30:013112. [PMID: 32013504 DOI: 10.1063/1.5126404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
The present theoretical study deals with microparticles (beads) that contain an immobilized Belousov-Zhabotinsky (BZ) reaction catalyst. In the theoretical experiment, a BZ bead is immersed in a small water droplet that contains all of the BZ reaction reagents but no catalyst. Such heterogeneous reaction-diffusion BZ systems with the same BZ reactant concentrations demonstrate various dynamic modes, including steady state and low-amplitude, high-amplitude, and mixed-mode oscillations (MMOs). The emergence of such dynamics depends on the sizes of the bead and water droplet, as well as on the location of the bead inside the droplet. MMO emergence is explained by time-delayed positive feedback in combination with a canard phenomenon. If two identical BZ beads are immersed in the same droplet, many different dynamic modes including chaos are observed.
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Affiliation(s)
- Vladimir K Vanag
- Center for Nonlinear Chemistry, Immanuel Kant Baltic Federal University, 14 A. Nevskogo St., Kaliningrad 236041, Russia
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16
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Couture J, Lena A, Maselko J, Pantaleone J. Growth and form of a self-constructing tube network. CHAOS (WOODBURY, N.Y.) 2019; 29:123103. [PMID: 31893671 DOI: 10.1063/1.5125688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
When a small amount of liquid is quickly injected into another liquid with similar density, the fluid jet usually does not propagate very far. However, when the two solutions chemically react to form a flexible membrane at their interface, then structures that are long and branching can form. Here, we describe the tube networks produced when a small amount of AlCl3 solution is quickly injected into a NaOH solution. Single straight tubes do not occur, but straight tubular "stems" with 2-5 "branches" are observed. The branches emerge relatively symmetrically from the stem at a common branching junction. These structures can have a ratio of propagation distance to stem width as large as 50. The stem and branches grow by the stretching of the membrane sheathing the closed tube system. These tube networks occasionally exhibit the spontaneous creation of new branches at a junction and also the splitting of a branching junction. A model explains why the branches occur, why they are symmetric around the central stem, and why the initial growth speed is insensitive to the flow rate.
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Affiliation(s)
- J Couture
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska 99508, USA
| | - A Lena
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska 99508, USA
| | - J Maselko
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska 99508, USA
| | - J Pantaleone
- Department of Physics, University of Alaska Anchorage, Anchorage, Alaska 99508, USA
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17
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Fengler E, Totz JF, Kaluza P, Engel H. Directed adaptation of synchronization levels in oscillator communities. CHAOS (WOODBURY, N.Y.) 2019; 29:063101. [PMID: 31266320 DOI: 10.1063/1.5094490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
We present an adaptive control scheme that realizes desired dynamics of an oscillator network with a given number of communities by adjusting the coupling weights between oscillators accordingly. The scheme allows, for example, to simultaneously establish different pregiven synchronization levels in the particular communities as well as phase relationships between them. We apply the method in numerical simulations with all-to-all and randomly coupled networks. Moreover, we provide an experimental proof of concept validating our numerical findings in a network of optically coupled photosensitive chemical micro-oscillators.
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Affiliation(s)
- Enrico Fengler
- Technische Universität Berlin, Institut für Theoretische Physik, Hardenbergstraße 36, EW 7-1, 10623 Berlin, Germany
| | - Jan Frederik Totz
- Technische Universität Berlin, Institut für Theoretische Physik, Hardenbergstraße 36, EW 7-1, 10623 Berlin, Germany
| | - Pablo Kaluza
- National Scientific and Technical Research Council & Faculty of Exact and Natural Sciences, National University of Cuyo, Padre Contreras 1300, 5500 Mendoza, Argentina
| | - Harald Engel
- Technische Universität Berlin, Institut für Theoretische Physik, Hardenbergstraße 36, EW 7-1, 10623 Berlin, Germany
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18
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Hankins MJ, Gáspár V, Kiss IZ. Abrupt and gradual onset of synchronized oscillations due to dynamical quorum sensing in the single-cathode multi-anode nickel electrodissolution system. CHAOS (WOODBURY, N.Y.) 2019; 29:033114. [PMID: 30927839 DOI: 10.1063/1.5087405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
The nonlinear dynamics of an oscillatory Ni electrodissolution-hydrogen ion reduction system are explored in a multi-electrode anode-single cathode system. A mathematical analysis of the charge balance equations reveals that the coupling scheme is similar to dynamical quorum sensing, where the number of anode wires affects a parameter related to the population density. In a parameter region where the large population exhibits stationary behavior, with sufficiently strong coupling (with small individual resistances attached to the anode wires), synchronized oscillations emerge abruptly with decreasing the number of anodes. Therefore, an "inverse" dynamical quorum sensing takes place. With weak coupling the transition is gradual. The experiments are supported by numerical simulation of a kinetic model of the process. The results thus show that the description of nontrivial cathode-anode interactions in the form of dynamical quorum sensing provides an efficient way of analyzing the dynamical response of complex, interacting electrochemical reactions.
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Affiliation(s)
- Michael J Hankins
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, USA
| | - Vilmos Gáspár
- Laboratory of Nonlinear Chemical Dynamics, Institute of Chemistry, Eötvös Loránd University, Pázmány P. sétány 1/A, Budapest 1117, Hungary
| | - István Z Kiss
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63103, USA
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19
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Bullara D, De Decker Y, Epstein IR. On the possibility of spontaneous chemomechanical oscillations in adsorptive porous media. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2018; 376:rsta.2017.0374. [PMID: 30420542 PMCID: PMC6232597 DOI: 10.1098/rsta.2017.0374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/15/2018] [Indexed: 06/09/2023]
Abstract
We derive general conditions for the emergence of sustained chemomechanical oscillations from a non-oscillatory adsorption/desorption reaction in a gas/solid porous medium. The oscillations arise from the nonlinear response of the solid matrix to the loading of the adsorbed species. More particularly, we prove that, in order for oscillations to occur, adsorption of the gas must in general cause a swelling of the solid matrix. We also investigate the prototypical case of Langmuir kinetics both numerically and analytically.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)'.
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Affiliation(s)
- D Bullara
- Department of Chemistry, Brandeis University, Waltham, MA 02454-9110, USA
| | - Y De Decker
- Interdisciplinary Center for Nonlinear Phenomena and Complex Systems (CENOLI), Nonlinear Physical Chemistry Unit, Université Libre de Bruxelles (ULB), Campus Plaine, C.P. 231, Brussels, Belgium
| | - I R Epstein
- Department of Chemistry, Brandeis University, Waltham, MA 02454-9110, USA
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Affiliation(s)
- Támás Bánsági
- Department of Chemistry; University of Birmingham; Edgbaston, Birmingham B15 2TT UK
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield S1 3JD UK
| | - Annette F. Taylor
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield S1 3JD UK
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22
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Horvath V, Epstein IR. Pulse-coupled Belousov-Zhabotinsky oscillators with frequency modulation. CHAOS (WOODBURY, N.Y.) 2018; 28:045108. [PMID: 31906644 DOI: 10.1063/1.5021585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inhibitory perturbations to the ferroin-catalyzed Belousov-Zhabotinsky (BZ) chemical oscillator operated in a continuously fed stirred tank reactor cause long term changes to the limit cycle: the lengths of the cycles subsequent to the perturbation are longer than that of the unperturbed cycle, and the unperturbed limit cycle is recovered only after several cycles. The frequency of the BZ reaction strongly depends on the acid concentration of the medium. By adding strong acid or base to the perturbing solutions, the magnitude and the direction of the frequency changes concomitant to excitatory or inhibitory perturbations can be controlled independently of the coupling strength. The dynamics of two BZ oscillators coupled through perturbations carrying a coupling agent (activator or inhibitor) and a frequency modulator (strong acid or base) was explored using a numerical model of the system. Here, we report new complex temporal patterns: higher order, partially synchronized modes that develop when inhibitory coupling is combined with positive frequency modulation (FM), and complex bursting patterns when excitatory coupling is combined with negative FM. The role of time delay between the peak and perturbation (the analog of synaptic delays in networks of neurons) has also been studied. The complex patterns found under inhibitory coupling and positive FM vanish when the delay is significant, whereas a sufficiently long time delay is required for the complex temporal dynamics to occur when coupling is excitatory and FM is negative.
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Affiliation(s)
- Viktor Horvath
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Irving R Epstein
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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Liu Y, Yuan L, Pan C, Gao J, Zhou W, Gao Q. Photoinduced Oscillations and Pulse Waves in the Hydrogen Peroxide–Sulfite–Ferrocyanide Reaction. J Phys Chem A 2018; 122:1175-1184. [DOI: 10.1021/acs.jpca.7b10025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Liu
- College
of Chemical Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Ling Yuan
- College
of Chemical Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Changwei Pan
- College
of Chemical Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Jianmin Gao
- Department
of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Wenxiu Zhou
- College
of Chemical Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Qingyu Gao
- College
of Chemical Engineering, China University of Mining and Technology, Xuzhou 221116, China
- Department
of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, United States
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24
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Gentili PL, Giubila MS, Germani R, Romani A, Nicoziani A, Spalletti A, Heron BM. Optical Communication among Oscillatory Reactions and Photo-Excitable Systems: UV and Visible Radiation Can Synchronize Artificial Neuron Models. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Maria Sole Giubila
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Raimondo Germani
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Aldo Romani
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Andrea Nicoziani
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - B. Mark Heron
- Department of Chemical Sciences; School of Applied Science; University of Huddersfield, Queensgate; Huddersfield HD1 3DH UK
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25
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Gentili PL, Giubila MS, Germani R, Romani A, Nicoziani A, Spalletti A, Heron BM. Optical Communication among Oscillatory Reactions and Photo-Excitable Systems: UV and Visible Radiation Can Synchronize Artificial Neuron Models. Angew Chem Int Ed Engl 2017; 56:7535-7540. [PMID: 28560808 DOI: 10.1002/anie.201702289] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/27/2017] [Indexed: 11/08/2022]
Abstract
Neuromorphic engineering promises to have a revolutionary impact in our societies. A strategy to develop artificial neurons (ANs) is to use oscillatory and excitable chemical systems. Herein, we use UV and visible radiation as both excitatory and inhibitory signals for the communication among oscillatory reactions, such as the Belousov-Zhabotinsky and the chemiluminescent Orban transformations, and photo-excitable photochromic and fluorescent species. We present the experimental results and the simulations regarding pairs of ANs communicating by either one or two optical signals, and triads of ANs arranged in both feed-forward and recurrent networks. We find that the ANs, powered chemically and/or by the energy of electromagnetic radiation, can give rise to the emergent properties of in-phase, out-of-phase, anti-phase synchronizations and phase-locking, dynamically mimicking the communication among real neurons.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Maria Sole Giubila
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Raimondo Germani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Aldo Romani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Andrea Nicoziani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - B Mark Heron
- Department of Chemical Sciences, School of Applied Science, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
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26
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Gines G, Zadorin AS, Galas JC, Fujii T, Estevez-Torres A, Rondelez Y. Microscopic agents programmed by DNA circuits. NATURE NANOTECHNOLOGY 2017; 12:351-359. [PMID: 28135261 DOI: 10.1038/nnano.2016.299] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 12/14/2016] [Indexed: 05/03/2023]
Abstract
Information stored in synthetic nucleic acids sequences can be used in vitro to create complex reaction networks with precisely programmed chemical dynamics. Here, we scale up this approach to program networks of microscopic particles (agents) dispersed in an enzymatic solution. Agents may possess multiple stable states, thus maintaining a memory and communicate by emitting various orthogonal chemical signals, while also sensing the behaviour of neighbouring agents. Using this approach, we can produce collective behaviours involving thousands of agents, for example retrieving information over long distances or creating spatial patterns. Our systems recapitulate some fundamental mechanisms of distributed decision making and morphogenesis among living organisms and could find applications in cases where many individual clues need to be combined to reach a decision, for example in molecular diagnostics.
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Affiliation(s)
- G Gines
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - A S Zadorin
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - J-C Galas
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - T Fujii
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - A Estevez-Torres
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - Y Rondelez
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
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27
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Jiang X, Abrams DM. Symmetry-broken states on networks of coupled oscillators. Phys Rev E 2016; 93:052202. [PMID: 27300875 DOI: 10.1103/physreve.93.052202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Indexed: 06/06/2023]
Abstract
When identical oscillators are coupled together in a network, dynamical steady states are often assumed to reflect network symmetries. Here, we show that alternative persistent states may also exist that break the symmetries of the underlying coupling network. We further show that these symmetry-broken coexistent states are analogous to those dubbed "chimera states," which can occur when identical oscillators are coupled to one another in identical ways.
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Affiliation(s)
- Xin Jiang
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
- LMIB and School of Mathematics and Systems Science, Beihang University, Beijing 100191, China
| | - Daniel M Abrams
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
- Northwestern Institute for Complex Systems, Northwestern University, Evanston, Illinois 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
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28
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Snari R, Tinsley MR, Wilson D, Faramarzi S, Netoff TI, Moehlis J, Showalter K. Desynchronization of stochastically synchronized chemical oscillators. CHAOS (WOODBURY, N.Y.) 2015; 25:123116. [PMID: 26723155 DOI: 10.1063/1.4937724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Experimental and theoretical studies are presented on the design of perturbations that enhance desynchronization in populations of oscillators that are synchronized by periodic entrainment. A phase reduction approach is used to determine optimal perturbation timing based upon experimentally measured phase response curves. The effectiveness of the perturbation waveforms is tested experimentally in populations of periodically and stochastically synchronized chemical oscillators. The relevance of the approach to therapeutic methods for disrupting phase coherence in groups of stochastically synchronized neuronal oscillators is discussed.
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Affiliation(s)
- Razan Snari
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6045, USA
| | - Mark R Tinsley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6045, USA
| | - Dan Wilson
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Sadegh Faramarzi
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6045, USA
| | - Theoden Ivan Netoff
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Jeff Moehlis
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Kenneth Showalter
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506-6045, USA
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