1
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Gentili PL, Capaccioni A, Germani R, Fantacci S. The Versatile Photo-Thermal Behaviour of a 2-Hydroxyazobenzene. Molecules 2023; 28:molecules28031183. [PMID: 36770849 PMCID: PMC9920310 DOI: 10.3390/molecules28031183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Photochromic compounds are employed in implementing neuron surrogates. They will boost the development of neuromorphic engineering in wetware. In this work, the photochromic behaviours of (E)-3,4,6-trichloro-2-(p-diazenil)-phenol (t-DZH) and its conjugated phenoxide base (t-DZ) have been investigated experimentally in three different media: (1) pure acetonitrile, (2) in water and acetonitrile mixed in a 1/1 volume ratio, and (3) in an aqueous micellar solution of 3-(N,N-Dimethylmyristylammonio)propanesulfonate (SB3-14). The analysis of the spectral and kinetic features of t-DZH and t-DZ has been supported by quantum-mechanical DFT calculations, the maximum entropy method, and the determination of their colourability (C). The versatility of t-DZH and t-DZ makes them promising molecular probes of micro-environments and potential ingredients of photochemical oscillators required for implementing pacemaker neurons capable of communicating through optical signals in wetware.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: ; Tel.: +39-0755855573
| | - Antonio Capaccioni
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Raimondo Germani
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Simona Fantacci
- Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta” (CNR-SCITEC), 06123 Perugia, Italy
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2
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Nguindjel ADC, de Visser PJ, Winkens M, Korevaar PA. Spatial programming of self-organizing chemical systems using sustained physicochemical gradients from reaction, diffusion and hydrodynamics. Phys Chem Chem Phys 2022; 24:23980-24001. [PMID: 36172850 DOI: 10.1039/d2cp02542f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Living organisms employ chemical self-organization to build structures, and inspire new strategies to design synthetic systems that spontaneously take a particular form, via a combination of integrated chemical reactions, assembly pathways and physicochemical processes. However, spatial programmability that is required to direct such self-organization is a challenge to control. Thermodynamic equilibrium typically brings about a homogeneous solution, or equilibrium structures such as supramolecular complexes and crystals. This perspective addresses out-of-equilibrium gradients that can be driven by coupling chemical reaction, diffusion and hydrodynamics, and provide spatial differentiation in the self-organization of molecular, ionic or colloidal building blocks in solution. These physicochemical gradients are required to (1) direct the organization from the starting conditions (e.g. a homogeneous solution), and (2) sustain the organization, to prevent it from decaying towards thermodynamic equilibrium. We highlight four different concepts that can be used as a design principle to establish such self-organization, using chemical reactions as a driving force to sustain the gradient and, ultimately, program the characteristics of the gradient: (1) reaction-diffusion coupling; (2) reaction-convection; (3) the Marangoni effect and (4) diffusiophoresis. Furthermore, we outline their potential as attractive pathways to translate chemical reactions and molecular/colloidal assembly into organization of patterns in solution, (dynamic) self-assembled architectures and collectively moving swarms at the micro-, meso- and macroscale, exemplified by recent demonstrations in the literature.
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Affiliation(s)
| | - Pieter J de Visser
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Mitch Winkens
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Peter A Korevaar
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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3
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Hunter I, Norton MM, Chen B, Simonetti C, Moustaka ME, Touboul J, Fraden S. Pattern formation in a four-ring reaction-diffusion network with heterogeneity. Phys Rev E 2022; 105:024310. [PMID: 35291089 DOI: 10.1103/physreve.105.024310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/28/2022] [Indexed: 11/07/2022]
Abstract
In networks of nonlinear oscillators, symmetries place hard constraints on the system that can be exploited to predict universal dynamical features and steady states, providing a rare generic organizing principle for far-from-equilibrium systems. However, the robustness of this class of theories to symmetry-disrupting imperfections is untested in free-running (i.e., non-computer-controlled) systems. Here, we develop a model experimental reaction-diffusion network of chemical oscillators to test applications of the theory of dynamical systems with symmeries in the context of self-organizing systems relevant to biology and soft robotics. The network is a ring of four microreactors containing the oscillatory Belousov-Zhabotinsky reaction coupled to nearest neighbors via diffusion. Assuming homogeneity across the oscillators, theory predicts four categories of stable spatiotemporal phase-locked periodic states and four categories of invariant manifolds that guide and structure transitions between phase-locked states. In our experiments, we observed that three of the four phase-locked states were displaced from their idealized positions and, in the ensemble of measurements, appeared as clusters of different shapes and sizes, and that one of the predicted states was absent. We also observed the predicted symmetry-derived synchronous clustered transients that occur when the dynamical trajectories coincide with invariant manifolds. Quantitative agreement between experiment and numerical simulations is found by accounting for the small amount of experimentally determined heterogeneity in intrinsic frequency. We further elucidate how different patterns of heterogeneity impact each attractor differently through a bifurcation analysis. We show that examining bifurcations along invariant manifolds provides a general framework for developing intuition about how chemical-specific dynamics interact with topology in the presence of heterogeneity that can be applied to other oscillators in other topologies.
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Affiliation(s)
- Ian Hunter
- Brandeis University Physics, Waltham, Massachusetts 02453, USA
| | - Michael M Norton
- Center for Neural Engineering, Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Bolun Chen
- Volen National Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02453, USA.,Department of Physics, Boston University, Boston Massachusetts 02215, USA
| | - Chris Simonetti
- Brandeis University Physics, Waltham, Massachusetts 02453, USA
| | | | - Jonathan Touboul
- Volen National Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02453, USA.,Brandeis University Mathematics Department, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- Brandeis University Physics, Waltham, Massachusetts 02453, USA
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4
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Design of a new photochromic oscillator: towards dynamical models of pacemaker neurons. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-021-02122-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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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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6
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Budroni MA, Pagano G, Conte D, Paternoster B, D'ambrosio R, Ristori S, Abou-Hassan A, Rossi F. Synchronization scenarios induced by delayed communication in arrays of diffusively coupled autonomous chemical oscillators. Phys Chem Chem Phys 2021; 23:17606-17615. [PMID: 34369507 DOI: 10.1039/d1cp02221k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We study the impact of delayed feedbacks in the collective synchronization of ensembles of identical and autonomous micro-oscillators. To this aim, we consider linear arrays of Belousov-Zhabotinsky (BZ) oscillators confined in micro-compartmentalised systems, where the delayed feedback mimics natural lags that can arise due to the confinement properties and mechanisms driving the inter-oscillator communication. The micro-oscillator array is modeled as a set of Oregonator-like kinetics coupled via mass exchange of the chemical messengers. Changes in the synchronization patterns are explored by varying the delayed feedback introduced in the messenger species Br2. A direct transition from anti-phase to in-phase synchronization and back to the initial anti-phase scheme is observed by progressively increasing the time delay from zero to the value T0, which is the oscillation period characterising the system without any delayed coupling. The route from anti- to in-phase oscillations (and back) consists of regimes where windows of in-phase oscillations are periodically broken by anti-phase beats. Similarities between these phase transition dynamics and synchronization scenarios characterising the coordination of oscillatory limb movements are finally discussed.
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Affiliation(s)
- Marcello A Budroni
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100 Sassari, Italy.
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7
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Moustaka ME, Norton MM, Blanc B, Horvath V, Aghvami SA, Fraden S. Partition, Reaction, and Diffusion Coefficients of Bromine in Elastomeric Polydimethylsiloxane. J Phys Chem B 2021; 125:5937-5951. [PMID: 34044537 DOI: 10.1021/acs.jpcb.1c01552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experiments and models were used to determine the extent to which aqueous bromine permeated into, and reacted with, the elastomer polydimethylsiloxane (PDMS). Thin films of PDMS were immersed in bromine water, and the absorbance of bromine in the aqueous phase was measured as a function of time. Kinetics were studied as a function of mass and thickness of the immersed PDMS films. We attribute the decrease of bromine in solution to permeation into PDMS, followed by a combination of diffusion, reversible binding, and an irreversible reaction with PDMS. In order to decouple the irreversible reaction from the reversible processes, kinetics were also studied for bromine-passivated PDMS films. Fits of the models to a variety of experiments yielded the partition coefficient of bromine between the water and PDMS phases, the diffusion constant of bromine in PDMS, the irreversible reaction constant between bromine and PDMS, the molar concentration of the reactive sites within PDMS, and the on and off rates of reversible binding of bromine to PDMS. Developing a quantitative reaction-diffusion model accounting for the transport of bromine through PDMS is necessary for the design of microfluidic devices fabricated using PDMS, which are used in experimental studies of the nonlinear dynamics of reaction-diffusion networks containing Belousov-Zhabotinsky chemical oscillators.
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Affiliation(s)
- Maria Eleni Moustaka
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael M Norton
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Baptiste Blanc
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Viktor Horvath
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - S Ali Aghvami
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
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8
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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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9
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Sheehy J, Hunter I, Moustaka ME, Aghvami SA, Fahmy Y, Fraden S. Impact of PDMS-Based Microfluidics on Belousov-Zhabotinsky Chemical Oscillators. J Phys Chem B 2020; 124:11690-11698. [PMID: 33315410 DOI: 10.1021/acs.jpcb.0c08422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sub-nanoliter volumes of the Belousov-Zhabotinsky (BZ) reaction are sealed in microfluidic devices made from polydimethylsiloxane (PDMS). Bromine, which is a BZ reaction intermediate that participates in the inhibitory pathway of the reaction, is known to permeate into PDMS, and it has been suggested that PDMS and bromine can react ( J. Phys. Chem. A. 108, 2004, 1325-1332). We characterize the extent to which PDMS affects BZ oscillations by varying the volume of the PDMS surrounding the BZ reactors. We measure how the oscillation period varies with PDMS volume and compare with a theoretical reaction-diffusion model, concluding that bromine reacts with PDMS. We demonstrate that minimizing the amount of PDMS by making the samples as thin as possible maximizes the number of oscillations before the BZ reaction reaches equilibrium and ceases to oscillate. We also demonstrate that the deleterious effects of the PDMS-BZ interactions are somewhat mitigated by imposing constant chemical boundary conditions through using a light-sensitive catalyst, ruthenium, in combination with patterned illumination. Furthermore, we show that light can modulate the frequency and phase of the BZ oscillators contained in a PDMS matrix by 20-30%.
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Affiliation(s)
- James Sheehy
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Ian Hunter
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria Eleni Moustaka
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - S Ali Aghvami
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Youssef Fahmy
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
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10
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Abstract
A substrate does not have to be solid to compute. It is possible to make a computer purely from a liquid. I demonstrate this using a variety of experimental prototypes where a liquid carries signals, actuates mechanical computing devices and hosts chemical reactions. We show hydraulic mathematical machines that compute functions based on mass transfer analogies. I discuss several prototypes of computing devices that employ fluid flows and jets. They are fluid mappers, where the fluid flow explores a geometrically constrained space to find an optimal way around, e.g. the shortest path in a maze, and fluid logic devices where fluid jet streams interact at the junctions of inlets and results of the computation are represented by fluid jets at selected outlets. Fluid mappers and fluidic logic devices compute continuously valued functions albeit discretized. There is also an opportunity to do discrete operation directly by representing information by droplets and liquid marbles (droplets coated by hydrophobic powder). There, computation is implemented at the sites, in time and space, where droplets collide one with another. The liquid computers mentioned above use liquid as signal carrier or actuator: the exact nature of the liquid is not that important. What is inside the liquid becomes crucial when reaction-diffusion liquid-phase computing devices come into play: there, the liquid hosts families of chemical species that interact with each other in a massive-parallel fashion. I shall illustrate a range of computational tasks, including computational geometry, implementable by excitation wave fronts in nonlinear active chemical medium. The overview will enable scientists and engineers to understand how vast is the variety of liquid computers and will inspire them to design their own experimental laboratory prototypes. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
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Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Lab, Department of Computer Science and Creative Technologies, University of the West of England , Bristol , UK
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11
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Budroni MA, Torbensen K, Ristori S, Abou-Hassan A, Rossi F. Membrane Structure Drives Synchronization Patterns in Arrays of Diffusively Coupled Self-Oscillating Droplets. J Phys Chem Lett 2020; 11:2014-2020. [PMID: 32078774 DOI: 10.1021/acs.jpclett.0c00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Networks of diffusively coupled inorganic oscillators, confined in nano- and microcompartments, are effective for predicting and understanding the global dynamics of those systems where the diffusion of activatory or inhibitory signals regulates the communication among different individuals. By taking advantage of a microfluidic device, we study the dynamics of arrays of diffusively coupled Belousov-Zhabotinsky (BZ) oscillators encapsulated in water-in-oil single emulsions. New synchronization patterns are induced and controlled by modulating the structural and chemical properties of the phospholipid-based biomimetic membranes via the introduction of specific dopants. Doping molecules do not alter the membrane basic backbone, but modify the lamellarity (and, in turn, the permeability) or interact chemically with the reaction intermediates. A transition from two-period clusters showing 1:2 period-locking to one-period antiphase synchronization is observed by decreasing the membrane lamellarity. An unsynchronized scenario is found when the dopant is able to interfere with chemical communication by reacting with the chemical messengers.
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Affiliation(s)
- Marcello A Budroni
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), CP231, 1050 Brussels, Belgium
| | - Kristian Torbensen
- Sorbonne Université, CNRS, PHysico-chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), F-75005 Paris, France
| | - Sandra Ristori
- Department of Chemistry & CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Ali Abou-Hassan
- Sorbonne Université, CNRS, PHysico-chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), F-75005 Paris, France
| | - Federico Rossi
- Department of Physical Science, Earth and Environment, University of Siena, Pian dei Mantellini, 44 53100 Siena (SI), Italy
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12
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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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13
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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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14
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Budroni MA, Torbensen K, Pantani OL, Ristori S, Rossi F, Abou-Hassan A. Microfluidic compartmentalization of diffusively coupled oscillators in multisomes induces a novel synchronization scenario. Chem Commun (Camb) 2020; 56:11771-11774. [DOI: 10.1039/d0cc05046f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multisome compartments encapsulating the Belousov–Zhabotinsky reaction produced by microfluidics arranged in 1D arrays showed a novel type of global synchronization.
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Affiliation(s)
| | - Kristian Torbensen
- Sorbonne Université
- CNRS UMR 8234
- PHysico-chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX)
- Paris F-75005
- France
| | - Ottorino L. Pantani
- Department of Agrifood Production and Environmental Sciences
- University of Florence P.le delle Cascine 28
- Firenze 50144
- Italy
| | - Sandra Ristori
- Department of Chemistry & CSGI
- University of Florence
- Sesto Fiorentino 50019
- Italy
| | - Federico Rossi
- Department of Earth
- Environmental and Physical Sciences – DEEP Sciences – University of Siena
- Siena 53100
- Italy
| | - Ali Abou-Hassan
- Sorbonne Université
- CNRS UMR 8234
- PHysico-chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX)
- Paris F-75005
- France
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15
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Norton MM, Tompkins N, Blanc B, Cambria MC, Held J, Fraden S. Dynamics of Reaction-Diffusion Oscillators in Star and other Networks with Cyclic Symmetries Exhibiting Multiple Clusters. PHYSICAL REVIEW LETTERS 2019; 123:148301. [PMID: 31702219 DOI: 10.1103/physrevlett.123.148301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/09/2019] [Indexed: 06/10/2023]
Abstract
We experimentally and theoretically investigate the dynamics of inhibitory coupled self-driven oscillators on a star network in which a single central hub node is connected to k peripheral arm nodes. The system consists of water-in-oil Belousov-Zhabotinsky ∼100 μm emulsion drops contained in storage wells etched in silicon wafers. We observed three dynamical attractors by varying the number of arms in the star graph and the coupling strength: (i) unlocked, uncorrelated phase shifts between all oscillators; (ii) locked, arm hubs synchronized in phase with a k-dependent phase shift between the arm and central hub; and (iii) center silent, a central hub stopped oscillating and the arm hubs oscillated without synchrony. We compare experiment to theory. For case (ii), we identified a logarithmic dependence of the phase shift on star degree, and were able to discriminate between contributions to the phase shift arising from star topology and oscillator chemistry.
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Affiliation(s)
- Michael M Norton
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Nathan Tompkins
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
- Physics Department, Wabash College, Crawfordsville, Indiana 47933, USA
| | - Baptiste Blanc
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | | | - Jesse Held
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
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16
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Tian L, Li M, Patil AJ, Drinkwater BW, Mann S. Artificial morphogen-mediated differentiation in synthetic protocells. Nat Commun 2019; 10:3321. [PMID: 31346180 PMCID: PMC6658542 DOI: 10.1038/s41467-019-11316-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/02/2019] [Indexed: 11/09/2022] Open
Abstract
The design and assembly of artificial protocell consortia displaying dynamical behaviours and systems-based properties are emerging challenges in bottom-up synthetic biology. Cellular processes such as morphogenesis and differentiation rely in part on reaction-diffusion gradients, and the ability to mimic rudimentary aspects of these non-equilibrium processes in communities of artificial cells could provide a step to life-like systems capable of complex spatiotemporal transformations. Here we expose acoustically formed arrays of initially identical coacervate micro-droplets to uni-directional or counter-directional reaction-diffusion gradients of artificial morphogens to induce morphological differentiation and spatial patterning in single populations of model protocells. Dynamic reconfiguration of the droplets in the morphogen gradients produces a diversity of membrane-bounded vesicles that are spontaneously segregated into multimodal populations with differentiated enzyme activities. Our results highlight the opportunities for constructing protocell arrays with graded structure and functionality and provide a step towards the development of artificial cell platforms capable of multiple operations. The ability to mimic aspects of cellular process that rely on reaction-diffusion gradients could provide a step to building life-like systems capable of complex behaviour. Here the authors demonstrate morphological differentiation in coacervate micro-droplets.
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Affiliation(s)
- Liangfei Tian
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Mei Li
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Avinash J Patil
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Bruce W Drinkwater
- Faculty of Engineering, Queens Building, University of Bristol, Bristol, BS8 1TR, UK
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
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17
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Tian L, Li M, Liu J, Patil AJ, Drinkwater BW, Mann S. Nonequilibrium Spatiotemporal Sensing within Acoustically Patterned Two-Dimensional Protocell Arrays. ACS CENTRAL SCIENCE 2018; 4:1551-1558. [PMID: 30555908 PMCID: PMC6276052 DOI: 10.1021/acscentsci.8b00555] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Indexed: 05/03/2023]
Abstract
Acoustically trapped periodic arrays of horseradish peroxidase (HRP)-loaded poly(diallydimethylammonium chloride) / adenosine 5'-triphosphate coacervate microdroplet-based protocells exhibit a spatiotemporal biochemical response when exposed to a codiffusing mixture of substrate molecules (o-phenylenediamine (o-PD) and hydrogen peroxide (H2O2)) under nonequilibrium conditions. Unidirectional propagation of the chemical concentration gradients gives rise to time- and position-dependent fluorescence signal outputs from individual coacervate microdroplets, indicating that the organized protocell assembly can dynamically sense encoded information in the advancing reaction-diffusion front. The methodology is extended to arrays comprising spatially separated binary populations of HRP- or glucose oxidase-containing coacervate microdroplets to internally generate a H2O2 signal that chemically connects the two protocell communities via a concerted biochemical cascade reaction. Our results provide a step toward establishing a systematic approach to study dynamic interactions between organized protocell consortia and propagating reaction-diffusion gradients, and offer a new methodology for exploring the complexity of protocellular communication networks operating under nonequilibrium conditions.
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Affiliation(s)
- Liangfei Tian
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Mei Li
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Juntai Liu
- School
of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K.
| | - Avinash J. Patil
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Bruce W. Drinkwater
- Faculty
of Engineering, Queens Building, University
of Bristol, Bristol BS8 1TR, U.K.
| | - Stephen Mann
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
- E-mail:
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