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Noguchi H, van Wijland F, Fournier JB. Cycling and spiral-wave modes in an active cyclic Potts model. J Chem Phys 2024; 161:025101. [PMID: 38973763 DOI: 10.1063/5.0221050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024] Open
Abstract
We studied the nonequilibrium dynamics of a cycling three-state Potts model using simulations and theory. This model can be tuned from thermal-equilibrium to far-from-equilibrium conditions. At low cycling energy, the homogeneous dominant state cycles via nucleation and growth, while spiral waves are formed at high energy. For large systems, a discontinuous transition occurs from these cyclic homogeneous phases to spiral waves, while the opposite transition is absent. Conversely, these two modes can coexist for small systems. The waves can be reproduced by a continuum theory, and the transition can be understood from the competition between nucleation and growth.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Frédéric van Wijland
- Laboratoire Matière et Systèmes Complexes (MSC), Université Paris Cité & CNRS, 75013 Paris, France
| | - Jean-Baptiste Fournier
- Laboratoire Matière et Systèmes Complexes (MSC), Université Paris Cité & CNRS, 75013 Paris, France
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2
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Fraggedakis D, Bazant MZ. Tuning the stability of electrochemical interfaces by electron transfer reactions. J Chem Phys 2020; 152:184703. [DOI: 10.1063/5.0006833] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dimitrios Fraggedakis
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Martin Z. Bazant
- Departments of Chemical Engineering and Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Kim IP, Benderskii VA. Kinetics of Radical Chain Polymerization: 2. Linear Waves of Macroradical Growth. HIGH ENERGY CHEMISTRY 2019. [DOI: 10.1134/s0018143919050072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Kim IP, Kats EI, Benderskii V. Kinetics of Radical Chain Polymerization: 1. Time-Dependent Distributions of Macroradicals and Oligomers. HIGH ENERGY CHEMISTRY 2019. [DOI: 10.1134/s0018143919040076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Bazant MZ. Thermodynamic stability of driven open systems and control of phase separation by electro-autocatalysis. Faraday Discuss 2017; 199:423-463. [DOI: 10.1039/c7fd00037e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Motivated by the possibility of electrochemical control of phase separation, a variational theory of thermodynamic stability is developed for driven reactive mixtures, based on a nonlinear generalization of the Cahn–Hilliard and Allen–Cahn equations. The Glansdorff–Prigogine stability criterion is extended for driving chemical work, based on variations of nonequilibrium Gibbs free energy. Linear stability is generally determined by the competition of chemical diffusion and driven autocatalysis. Novel features arise for electrochemical systems, related to controlled total current (galvanostatic operation), concentration-dependent exchange current (Butler–Volmer kinetics), and negative differential reaction resistance (Marcus kinetics). The theory shows how spinodal decomposition can be controlled by solo-autocatalytic charge transfer, with only a single faradaic reaction. Experimental evidence is presented for intercalation and electrodeposition in rechargeable batteries, and further applications are discussed in solid state ionics, electrovariable optics, electrochemical precipitation, and biological pattern formation.
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Affiliation(s)
- Martin Z. Bazant
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Mathematics
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6
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Reigada R, Mikhailov AS. Equilibrium microphase separation in the two-leaflet model of lipid membranes. Phys Rev E 2016; 93:010401. [PMID: 26871009 DOI: 10.1103/physreve.93.010401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 06/05/2023]
Abstract
Because of the coupling between local lipid composition and the thickness of the membrane, microphase separation in two-component lipid membranes can take place; such effects may underlie the formation of equilibrium nanoscale rafts. Using a kinetic description, this phenomenon is analytically and numerically investigated. The phase diagram is constructed through the stability analysis for linearized kinetic equations, and conditions for microphase separation are discussed. Simulations of the full kinetic model reveal the development of equilibrium membrane nanostructures with various morphologies from the initial uniform state.
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Affiliation(s)
- Ramon Reigada
- Departament de Química Física i Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Avinguda Diagonal 647, 08028 Barcelona, Spain
| | - Alexander S Mikhailov
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Department of Mathematics and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan
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John K, Alonso S, Bär M. Traveling waves and global oscillations triggered by attractive molecular interactions in an excitable system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:052913. [PMID: 25493864 DOI: 10.1103/physreve.90.052913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 06/04/2023]
Abstract
During pattern formation in spatially extended systems, different mechanisms with different characteristic length scales, e.g., reaction-diffusion processes or molecular interactions, can be active. Such multiscale effects may generate new phenomena, which are not observed in systems where pattern formation occurs on a single scale. Here, we derive and analyze a reaction-diffusion model of the FitzHugh-Nagumo type with short-range attractive molecular interactions of the activator species. The model exhibits a wave instability. Simulations in one and two dimensions show traveling waves with a wavelength set by the parameters of the molecular interaction in the model. In two dimensions, simulations reveal a labyrinthine arrangement of the waves in systems with isotropic diffusion, whereas parallel bands of counterpropagating waves are formed in simulations of a model with anisotropic diffusion. The latter findings are in good qualitative agreement with experimental observation in the catalytic NO+H_{2} reaction on an anisotropic Rh(110) surface. In addition we have identified a transition regime in the simulations, where a short scale instability triggers global oscillations in an excitable regime.
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Affiliation(s)
- Karin John
- Université Grenoble Alpes, LIPhy, F-38000 Grenoble, France and Centre National de la Recherche Scientifique, LIPhy, F-38000 Grenoble, France
| | - Sergio Alonso
- Physikalisch-Technische Bundesanstalt, Abbestrasse 2-12, D-10587 Berlin, Germany
| | - Markus Bär
- Physikalisch-Technische Bundesanstalt, Abbestrasse 2-12, D-10587 Berlin, Germany
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8
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Berenstein I, Bullara D, De Decker Y. Stationary spots and stationary arcs induced by advection in a one-activator, two-inhibitor reactive system. CHAOS (WOODBURY, N.Y.) 2014; 24:033129. [PMID: 25273209 DOI: 10.1063/1.4894826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper studies the spatiotemporal dynamics of a reaction-diffusion-advection system corresponding to an extension of the Oregonator model, which includes two inhibitors instead of one. We show that when the reaction-diffusion, two-dimensional problem displays stationary patterns the addition of a plug flow can induce the emergence of new types of stationary structures. These patterns take the form of spots or arcs, the size and the spacing of which can be controlled by the flow.
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Affiliation(s)
- Igal Berenstein
- Center for Nonlinear Phenomena and Complex Systems (CENOLI), NonLinear Physical Chemistry Unit, Université libre de Bruxelles (ULB), Campus Plaine, C.P. 231, Brussels B-1050, Belgium
| | - Domenico Bullara
- Center for Nonlinear Phenomena and Complex Systems (CENOLI), NonLinear Physical Chemistry Unit, Université libre de Bruxelles (ULB), Campus Plaine, C.P. 231, Brussels B-1050, Belgium
| | - Yannick De Decker
- Center for Nonlinear Phenomena and Complex Systems (CENOLI), NonLinear Physical Chemistry Unit, Université libre de Bruxelles (ULB), Campus Plaine, C.P. 231, Brussels B-1050, Belgium
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Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles. Proc Natl Acad Sci U S A 2014; 111:E2636-45. [PMID: 24979791 DOI: 10.1073/pnas.1404855111] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Centrosomes are highly dynamic, spherical organelles without a membrane. Their physical nature and their assembly are not understood. Using the concept of phase separation, we propose a theoretical description of centrosomes as liquid droplets. In our model, centrosome material occurs in a form soluble in the cytosol and a form that tends to undergo phase separation from the cytosol. We show that an autocatalytic chemical transition between these forms accounts for the temporal evolution observed in experiments. Interestingly, the nucleation of centrosomes can be controlled by an enzymatic activity of the centrioles, which are present at the core of all centrosomes. This nonequilibrium feature also allows for multiple stable centrosomes, a situation that is unstable in equilibrium phase separation. Our theory explains the growth dynamics of centrosomes for all cell sizes down to the eight-cell stage of the Caenorhabditis elegans embryo, and it also accounts for data acquired in experiments with aberrant numbers of centrosomes and altered cell volumes. Furthermore, the model can describe unequal centrosome sizes observed in cells with perturbed centrioles. We also propose an interpretation of the molecular details of the involved proteins in the case of C. elegans. Our example suggests a general picture of the organization of membraneless organelles.
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Tinsley MR, Collison D, Showalter K. Propagating precipitation waves: experiments and modeling. J Phys Chem A 2013; 117:12719-25. [PMID: 24191642 DOI: 10.1021/jp4095479] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traveling precipitation waves, including counterrotating spiral waves, are observed in the precipitation reaction of AlCl3 with NaOH [Volford, A.; et al. Langmuir 2007, 23, 961 - 964]. Experimental and computational studies are carried out to characterize the wave behavior in cross-section configurations. A modified sol-coagulation model is developed that is based on models of Liesegang band and redissolution systems. The dynamics of the propagating waves is characterized in terms of growth and redissolution of a precipitation feature that travels through a migrating band of colloidal precipitate.
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Affiliation(s)
- Mark R Tinsley
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506-6045, United States
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11
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Rao T, Xiao T, Hou Z. Entropy production in a mesoscopic chemical reaction system with oscillatory and excitable dynamics. J Chem Phys 2012; 134:214112. [PMID: 21663349 DOI: 10.1063/1.3598111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Stochastic thermodynamics of chemical reaction systems has recently gained much attention. In the present paper, we consider such an issue for a system with both oscillatory and excitable dynamics, using catalytic oxidation of carbon monoxide on the surface of platinum crystal as an example. Starting from the chemical Langevin equations, we are able to calculate the stochastic entropy production P along a random trajectory in the concentration state space. Particular attention is paid to the dependence of the time-averaged entropy production P on the system size N in a parameter region close to the deterministic Hopf bifurcation (HB). In the large system size (weak noise) limit, we find that P ∼ N(β) with β = 0 or 1, when the system is below or above the HB, respectively. In the small system size (strong noise) limit, P always increases linearly with N regardless of the bifurcation parameter. More interestingly, P could even reach a maximum for some intermediate system size in a parameter region where the corresponding deterministic system shows steady state or small amplitude oscillation. The maximum value of P decreases as the system parameter approaches the so-called CANARD point where the maximum disappears. This phenomenon could be qualitatively understood by partitioning the total entropy production into the contributions of spikes and of small amplitude oscillations.
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Affiliation(s)
- Ting Rao
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
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Rao T, Zhang Z, Hou ZH, Xin HW. Coarse-grained Simulations of Chemical Oscillation in Lattice Brusselator System. CHINESE J CHEM PHYS 2011. [DOI: 10.1088/1674-0068/24/04/425-433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Dobrovolska T, Krastev I, Jović B, Jović V, Beck G, Lačnjevac U, Zielonka A. Phase identification in electrodeposited Ag–Cd alloys by anodic linear sweep voltammetry and X-ray diffraction techniques. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.01.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Vanag VK. Dissipative structures in systems of diffusion-bonded chemical nano- and micro oscillators. RUSS J GEN CHEM+ 2011. [DOI: 10.1134/s107036321101035x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Yoneya M, Tabe Y, Yokoyama H. Molecular dynamics simulation of condensed-phase chiral molecular propellers. J Phys Chem B 2010; 114:8320-6. [PMID: 20536201 DOI: 10.1021/jp101066t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations were performed for an axial-chiral liquid crystalline (LC) monolayer under trans-monolayer gas flow. The rotational dynamics of the monolayer chiral LC molecule along its long-molecular axis were analyzed at the molecular level. We found a precise correspondence between the flow-driven molecular rotation direction and molecular chirality as well as between the rotation direction and the trans-monolayer flow direction. The rotational direction exactly corresponded to what was expected in the proposed chiral molecular propeller model (Tabe, Y.; Yokoyama, H. Nat. Mater. 2003, 2, 806). Among the four trans-monolayer gas species we investigated, we found argon to be the most efficient at driving the chiral molecular propeller and helium the least efficient.
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Affiliation(s)
- M Yoneya
- Nanotechnology Research Institute, Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba 305-8568, Japan
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16
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski BA. Reaction-diffusion systems in intracellular molecular transport and control. Angew Chem Int Ed Engl 2010; 49:4170-98. [PMID: 20518023 PMCID: PMC3697936 DOI: 10.1002/anie.200905513] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
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Affiliation(s)
- Siowling Soh
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Marta Byrska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Kristiana Kandere-Grzybowska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Bartosz A. Grzybowski
- Department of Chemistry, Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, Homepage: http://www.dysa.northwestern.edu
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski B. Reaktions-Diffusions-Systeme für intrazellulären Transport und Kontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905513] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Abstract
Cellular membrane systems delimit and organize the intracellular space. Most of the morphological rearrangements in cells involve the coordinated remodeling of the lipid bilayer, the core of the membranes. This process is generally thought to be initiated and coordinated by specialized protein machineries. Nevertheless, it has become increasingly evident that the most essential part of the geometric information and energy required for membrane remodeling is supplied via the cooperative and synergistic action of proteins and lipids, as cellular shapes are constructed using the intrinsic dynamics, plasticity and self-organizing capabilities provided by the lipid bilayer. Here, we analyze the essential role of proteo-lipid membrane domains in conducting and coordinating morphological remodeling in cells.
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Affiliation(s)
- Anna V Shnyrova
- Laboratory of Cellular and Molecular Biology, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1855, USA
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Sciascia L, Rossi F, Sbriziolo C, Liveri MLT, Varsalona R. Oscillatory dynamics of the Belousov–Zhabotinsky system in the presence of a self-assembling nonionic polymer. Role of the reactants concentration. Phys Chem Chem Phys 2010; 12:11674-82. [DOI: 10.1039/c003033c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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