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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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2
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Kumar P, Gangopadhyay G. Glycolytic Wave Patterns in a Simple Reaction-diffusion System with Inhomogeneous Influx: Dynamic Transitions. Chemphyschem 2023; 24:e202200643. [PMID: 36478341 DOI: 10.1002/cphc.202200643] [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: 08/26/2022] [Revised: 11/21/2022] [Indexed: 12/12/2022]
Abstract
An inhomogeneous profile of chemostatted species generates a rich variety of patterns in glycolytic waves depicted in a Selkov reaction-diffusion framework here. A key role played by diffusion amplitude and symmetry in the chemostatted species profile in dictating the fate of local spatial dynamics involving periodic, quasiperiodic, and chaotic patterns and transitions among them are investigated systematically. More importantly, various dynamic transitions, including wave propagation direction changes, are illustrated in interesting situations. Besides numerical results, our analytical formulation of the amplitude equation connecting complex Ginzburg-Landau and Lambda-omega representation shed light on the phase dynamics of the system. This systematic study of the glycolytic reaction-diffusion wave is in line with previous experimental results in open spatial reactor and will provide a knowledge about the dynamics that shape and control biological information processing and related phenomena.
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Affiliation(s)
- Premashis Kumar
- S. N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106, India
| | - Gautam Gangopadhyay
- S. N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106, India
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3
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Miele Y, Jones SJ, Rossi F, Beales PA, Taylor AF. Collective Behavior of Urease pH Clocks in Nano- and Microvesicles Controlled by Fast Ammonia Transport. J Phys Chem Lett 2022; 13:1979-1984. [PMID: 35188399 PMCID: PMC9007528 DOI: 10.1021/acs.jpclett.2c00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The transmission of chemical signals via an extracellular solution plays a vital role in collective behavior in cellular biological systems and may be exploited in applications of lipid vesicles such as drug delivery. Here, we investigated chemical communication in synthetic micro- and nanovesicles containing urease in a solution of urea and acid. We combined experiments with simulations to demonstrate that the fast transport of ammonia to the external solution governs the pH-time profile and synchronizes the timing of the pH clock reaction in a heterogeneous population of vesicles. This study shows how the rate of production and emission of a small basic product controls pH changes in active vesicles with a distribution of sizes and enzyme amounts, which may be useful in bioreactor or healthcare applications.
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Affiliation(s)
- Ylenia Miele
- Department
of Chemistry and Biology, University of
Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Stephen J. Jones
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Federico Rossi
- Department
of Earth, Environmental and Physical Sciences, University of Siena, Pian dei Mantellini 44, 53100 Siena, Italy
| | - Paul A. Beales
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Annette F. Taylor
- Chemical
and Biological Engineering, University of
Sheffield, Sheffield S1 3JD, U.K.
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4
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Kumar P, Gangopadhyay G. Nonequilibrium thermodynamic characterization of chimeras in a continuum chemical oscillator system. Phys Rev E 2022; 105:034208. [PMID: 35428096 DOI: 10.1103/physreve.105.034208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
The emergence of the chimera state as the counterintuitive spatial coexistence of synchronous and asynchronous regimes is addressed here in a continuum chemical oscillator system by implementing a relevant complex Ginzburg-Landau equation with global coupling. This study systematically acquires and characterizes the evolution of nonequilibrium thermodynamic entities corresponding to the chimera state. The temporal evolution of the entropy production rate exhibits a beat pattern with a series of equidistant spectral lines in the frequency domain. Symmetric profiles associated with the incoherent regime appear in descriptions of the dynamics and thermodynamics of the chimera. It is shown that identifying the semigrand Gibbs free energy of the state as the Gabor elementary function can reveal the guiding role of the information uncertainty principle in shaping the chimera energetics.
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Affiliation(s)
- Premashis Kumar
- S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700 106, India
| | - Gautam Gangopadhyay
- S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700 106, India
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5
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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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Dúzs B, Molnár I, Lagzi I, Szalai I. Reaction-Diffusion Dynamics of pH Oscillators in Oscillatory Forced Open Spatial Reactors. ACS OMEGA 2021; 6:34367-34374. [PMID: 34963922 PMCID: PMC8697004 DOI: 10.1021/acsomega.1c04269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Studying the effect of coupling and forcing of oscillators is a significant area of interest within nonlinear dynamics and has provided evidence of many interesting phenomena, such as synchronization, beating, oscillatory death, and phase resetting. Many studies have also reported along this line in reaction-diffusion systems, which are preferably explored experimentally by using open reactors. These reactors consist of one or two homogeneous (well-stirred) tanks, which provide the boundary conditions for a spatially distributed part. The spatiotemporal dynamics of this configuration in the presence of temporal oscillations in the homogeneous part has not been systematically investigated. This paper aims to explore numerically the effect of time-periodic boundary conditions on the dynamics of open reactors provided by autonomous and forced oscillations in the well-stirred part. A simple model of pH oscillators can produce various phenomena under these conditions, for example, superposition and modulation of spatiotemporal oscillations and forced bursting. The autonomous oscillatory boundary conditions can be generated by the same kinetic instabilities that result in spatiotemporal oscillations in the spatially distributed part. The forced oscillations are induced by sinusoidal modulation on the inflow concentration of the activator in the tank. The simulations confirmed that this type of forcing is more effective when the modulation period is longer than the residence time of the well-stirred part. The use of time-periodic boundary conditions may open a new perspective in the control and design of spatiotemporal phenomena in open one-side-fed and two-side-fed reactors.
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Affiliation(s)
- Brigitta Dúzs
- Institute
of Chemistry, Eötvös L. University, 1117 Pázmány P. S.
1/A, Budapest 1117, Hungary
| | - István Molnár
- Institute
of Chemistry, Eötvös L. University, 1117 Pázmány P. S.
1/A, Budapest 1117, Hungary
| | - István Lagzi
- Department
of Physics and MTA-BME Condensed Matter Physics Research Group, Budapest University of Technology and Economics, 1111 Budafoki út 8, Budapest 1111, Hungary
| | - István Szalai
- Institute
of Chemistry, Eötvös L. University, 1117 Pázmány P. S.
1/A, Budapest 1117, Hungary
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Lawson HS, Holló G, Német N, Teraji S, Nakanishi H, Horvath R, Lagzi I. Design of non-autonomous pH oscillators and the existence of chemical beat phenomenon in a neutralization reaction. Sci Rep 2021; 11:11011. [PMID: 34040025 PMCID: PMC8155044 DOI: 10.1038/s41598-021-90301-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
Abstract
The beat in physical systems is a transparent and well-understood phenomenon. It may occur in forced oscillatory systems and as a result of the interference of two waves of slightly different frequencies. However, in chemical systems, the realization of the latter type of the beat phenomenon has been lacking. Here we show that a periodic titration of acid and alkaline solutions with each other using programmable syringe pumps in a continuous stirred-tank reactor exhibits the beat phenomenon in the temporal pH oscillation pattern if the time periods of sinusoidal inflow rates of the reagents are slightly different. Interestingly, the frequency of the chemical beat pattern follows the well-known relationship from physics, namely the frequency of the beat is equal to the absolute value of the difference of the two wave frequencies. Based on our strategy, we can design and engineer non-autonomous pH oscillatory systems, in which the characteristics of the temporal oscillations (amplitude, time period) can easily and precisely be controlled by the experimental conditions such as the inflow rates and feed concentrations. The demonstrated phenomena can be exploited in practical applications, we use the non-autonomous pH oscillators to drive the reversible assembly and disassembly of pH-sensitive building blocks (oleic acid and gold nanoparticles), both highly relevant in nanotechnology and biomedical applications.
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Affiliation(s)
- Hugh Shearer Lawson
- Department of Physics, Budapest University of Technology and Economics, Budafoki út 8, Budapest, 1111, Hungary
| | - Gábor Holló
- MTA-BME Condensed Matter Physics Research Group, Budapest University of Technology and Economics, Budafoki út 8, Budapest, 1111, Hungary
| | - Norbert Német
- Department of Physics, Budapest University of Technology and Economics, Budafoki út 8, Budapest, 1111, Hungary
| | - Satoshi Teraji
- Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Hideyuki Nakanishi
- Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Robert Horvath
- Nanobiosensorics Group, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly Thege M. u. 29-33, Budapest, 1121, Hungary
| | - István Lagzi
- Department of Physics, Budapest University of Technology and Economics, Budafoki út 8, Budapest, 1111, Hungary.
- MTA-BME Condensed Matter Physics Research Group, Budapest University of Technology and Economics, Budafoki út 8, Budapest, 1111, Hungary.
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