1
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Leathard AS, Beales PA, Taylor AF. Design of oscillatory dynamics in numerical simulations of compartment-based enzyme systems. CHAOS (WOODBURY, N.Y.) 2023; 33:123128. [PMID: 38149992 DOI: 10.1063/5.0180256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023]
Abstract
Enzymatic reactions that yield non-neutral products are known to involve feedback due to the bell-shaped pH-rate curve of the enzyme. Compartmentalizing the reaction has been shown to lead to transport-driven oscillations in theory; however, there have been few reproducible experimental examples. Our objective was to determine how the conditions could be optimized to achieve pH oscillations. We employed numerical simulations to investigate the hydrolysis of ethyl acetate in a confined esterase enzyme system, examining the influence of key factors on its behavior. Specific parameter ranges that lead to bistability and self-sustained pH oscillations and the importance of fast base transport for oscillations in this acid-producing system are highlighted. Suggestions are made to expand the parameter space for the occurrence of oscillations, including modifying the maximum of the enzyme pH-rate curve and increasing the negative feedback rate. This research not only sheds light on the programmable nature of enzyme-driven pH regulation but also furthers knowledge on the optimal design of such feedback systems for experimentalists.
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Affiliation(s)
- Anna S Leathard
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annette F Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
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2
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From classical metal-catalyzed homogeneous oscillators to an uncatalyzed version of the Belousov–Zhabotinsky reaction: a review. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-021-02151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Bohner B, Bánsági T, Tóth Á, Horváth D, Taylor AF. Periodic Nucleation of Calcium Phosphate in a Stirred Biocatalytic Reaction. Angew Chem Int Ed Engl 2020; 59:2823-2828. [PMID: 31833161 PMCID: PMC7027757 DOI: 10.1002/anie.201911213] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/24/2022]
Abstract
Highly ordered superstructures composed of inorganic nanoparticles appear in natural and synthetic systems, however the mechanisms of non-equilibrium self-organization that may be involved are still poorly understood. Herein, we performed a kinetic investigation of the precipitation of calcium phosphate using a process widely found in microorganisms: the hydrolysis of urea by enzyme urease. With high initial ratio of calcium ion to phosphate, periodic precipitation was obtained accompanied by pH oscillations in a well-stirred, closed reactor. We propose that an internal pH-regulated change in the concentration of phosphate ion is the driving force for periodicity. A simple model involving the biocatalytic reaction network coupled with burst nucleation of nanoparticles above a critical supersaturation reproduced key features of the experiments. These findings may provide insight to the self-organization of nanoparticles in biomineralization and improve design strategies of biomaterials for medical applications.
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Affiliation(s)
- Bíborka Bohner
- Department of Physical Chemistry and Materials ScienceUniversity of SzegedRerrich Béla tér 1.6720SzegedHungary
| | - Tamás Bánsági
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Ágota Tóth
- Department of Physical Chemistry and Materials ScienceUniversity of SzegedRerrich Béla tér 1.6720SzegedHungary
| | - Dezső Horváth
- Department of Applied and Environmental ChemistryUniversity of SzegedRerrich Béla tér 1.6720SzegedHungary
| | - Annette F. Taylor
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
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4
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Bohner B, Bánsági T, Tóth Á, Horváth D, Taylor AF. Periodic Nucleation of Calcium Phosphate in a Stirred Biocatalytic Reaction. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bíborka Bohner
- Department of Physical Chemistry and Materials ScienceUniversity of Szeged Rerrich Béla tér 1. 6720 Szeged Hungary
| | - Tamás Bánsági
- School of ChemistryUniversity of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Ágota Tóth
- Department of Physical Chemistry and Materials ScienceUniversity of Szeged Rerrich Béla tér 1. 6720 Szeged Hungary
| | - Dezső Horváth
- Department of Applied and Environmental ChemistryUniversity of Szeged Rerrich Béla tér 1. 6720 Szeged Hungary
| | - Annette F. Taylor
- Department of Chemical and Biological EngineeringUniversity of Sheffield Mappin Street Sheffield S1 3JD UK
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5
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Modelling Bacteria-Inspired Dynamics with Networks of Interacting Chemicals. Life (Basel) 2019; 9:life9030063. [PMID: 31362385 PMCID: PMC6789575 DOI: 10.3390/life9030063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
One approach to understanding how life-like properties emerge involves building synthetic cellular systems that mimic certain dynamical features of living cells such as bacteria. Here, we developed a model of a reaction network in a cellular system inspired by the ability of bacteria to form a biofilm in response to increasing cell density. Our aim was to determine the role of chemical feedback in the dynamics. The feedback was applied through the enzymatic rate dependence on pH, as pH is an important parameter that controls the rates of processes in cells. We found that a switch in pH can be used to drive base-catalyzed gelation or precipitation of a substance in the external solution. A critical density of cells was required for gelation that was essentially independent of the pH-driven feedback. However, the cell pH reached a higher maximum as a result of the appearance of pH oscillations with feedback. Thus, we conclude that while feedback may not play a vital role in some density-dependent behavior in cellular systems, it nevertheless can be exploited to activate internally regulated cell processes at low cell densities.
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6
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Markovic VM, Bánsági T, McKenzie D, Mai A, Pojman JA, Taylor AF. Influence of reaction-induced convection on quorum sensing in enzyme-loaded agarose beads. CHAOS (WOODBURY, N.Y.) 2019; 29:033130. [PMID: 30927847 DOI: 10.1063/1.5089295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
In theory, groups of enzyme-loaded particles producing an acid or base may show complex behavior including dynamical quorum sensing, the appearance of synchronized oscillations above a critical number or density of particles. Here, experiments were performed with the enzyme urease loaded into mm-sized agarose beads and placed in a solution of urea, resulting in an increase in pH. This behavior was found to be dependent upon the number of beads present in the array; however, reaction-induced convection occurred and plumes of high pH developed that extended to the walls of the reactor. The convection resulted in the motion of the mm-sized particles and conversion of the solution to high pH. Simulations in a simple model of the beads demonstrated the suppression of dynamical quorum sensing in the presence of flow.
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Affiliation(s)
- Vladimir M Markovic
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Tamás Bánsági
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
| | - Dennel McKenzie
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA
| | - Anthony Mai
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA
| | - John A Pojman
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA
| | - Annette F Taylor
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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7
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Jones SJ, Taylor AF, Beales PA. Towards feedback-controlled nanomedicines for smart, adaptive delivery. Exp Biol Med (Maywood) 2019; 244:283-293. [PMID: 30205721 PMCID: PMC6435888 DOI: 10.1177/1535370218800456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
IMPACT STATEMENT The timing and rate of release of pharmaceuticals from advanced drug delivery systems is an important property that has received considerable attention in the scientific literature. Broadly, these mostly fall into two classes: controlled release with a prolonged release rate or triggered release where the drug is rapidly released in response to an environmental stimulus. This review aims to highlight the potential for developing adaptive release systems that more subtlety modulate the drug release profile through continuous communication with its environment facilitated through feedback control. By reviewing the key elements of this approach in one place (fundamental principles of nanomedicine, enzymatic nanoreactors for medical therapies and feedback-controlled chemical systems) and providing additional motivating case studies in the context of chronobiology, we hope to inspire innovative development of novel "chrononanomedicines."
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Affiliation(s)
- Stephen J. Jones
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Annette F. Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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8
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Muzika F, Růžička M, Schreiberová L, Schreiber I. Oscillations of pH in the urea–urease system in a membrane reactor. Phys Chem Chem Phys 2019; 21:8619-8622. [DOI: 10.1039/c9cp00630c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Urea–urease reaction in an open reservoir–membrane–reactor system displays regular spontaneous oscillations of pH.
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Affiliation(s)
- František Muzika
- Department of Chemical Engineering, University of Chemistry and Technology, Prague
- 166 28 Praha 6
- Czech Republic
| | - Matěj Růžička
- Department of Chemical Engineering, University of Chemistry and Technology, Prague
- 166 28 Praha 6
- Czech Republic
| | - Lenka Schreiberová
- Department of Chemical Engineering, University of Chemistry and Technology, Prague
- 166 28 Praha 6
- Czech Republic
| | - Igor Schreiber
- Department of Chemical Engineering, University of Chemistry and Technology, Prague
- 166 28 Praha 6
- Czech Republic
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9
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Doldán-Martelli V, Míguez DG. Drug treatment efficiency depends on the initial state of activation in nonlinear pathways. Sci Rep 2018; 8:12495. [PMID: 30131510 PMCID: PMC6104077 DOI: 10.1038/s41598-018-30913-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/03/2018] [Indexed: 11/28/2022] Open
Abstract
An accurate prediction of the outcome of a given drug treatment requires quantitative values for all parameters and concentrations involved as well as a detailed characterization of the network of interactions where the target molecule is embedded. Here, we present a high-throughput in silico screening of all potential networks of three interacting nodes to study the effect of the initial conditions of the network in the efficiency of drug inhibition. Our study shows that most network topologies can induce multiple dose-response curves, where the treatment has an enhanced, reduced or even no effect depending on the initial conditions. The type of dual response observed depends on how the potential bistable regimes interplay with the inhibition of one of the nodes inside a nonlinear pathway architecture. We propose that this dependence of the strength of the drug on the initial state of activation of the pathway may be affecting the outcome and the reproducibility of drug studies and clinical trials.
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Affiliation(s)
| | - David G Míguez
- Centro de Biología Molecular Severo Ochoa, Depto. de Física de la Materia Condensada, Instituto Nicolás Cabrera and IFIMAC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28046, Madrid, Spain.
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10
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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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11
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Li C, Lin J, Gao L, Lin H, Lin J. Modeling and simulation of enzymatic gluconic acid production using immobilized enzyme and CSTR-PFTR circulation reaction system. Biotechnol Lett 2018; 40:649-657. [PMID: 29349627 DOI: 10.1007/s10529-018-2509-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/08/2018] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Production of gluconic acid by using immobilized enzyme and continuous stirred tank reactor-plug flow tubular reactor (CSTR-PFTR) circulation reaction system. RESULTS A production system is constructed for gluconic acid production, which consists of a continuous stirred tank reactor (CSTR) for pH control and liquid storage and a plug flow tubular reactor (PFTR) filled with immobilized glucose oxidase (GOD) for gluconic acid production. Mathematical model is developed for this production system and simulation is made for the enzymatic reaction process. The pH inhibition effect on GOD is modeled by using a bell-type curve. CONCLUSIONS Gluconic acid can be efficiently produced by using the reaction system and the mathematical model developed for this system can simulate and predict the process well.
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Affiliation(s)
- Can Li
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Jinan, 250100, China
| | - Jianqun Lin
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Jinan, 250100, China
| | - Ling Gao
- Institute of Information Science and Engineering, School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Huibin Lin
- Shandong Academy of Chinese Medicine, Jinan, China
| | - Jianqiang Lin
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Jinan, 250100, China.
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12
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Influence of Oscillatory Enzyme Activity on the Reaction Kinetics: Mathematical Model. J Comput Biol 2017; 24:1065-1070. [DOI: 10.1089/cmb.2017.0001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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13
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Merindol R, Walther A. Materials learning from life: concepts for active, adaptive and autonomous molecular systems. Chem Soc Rev 2017; 46:5588-5619. [DOI: 10.1039/c6cs00738d] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A broad overview of functional aspects in biological and synthetic out-of-equilibrium systems.
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Affiliation(s)
- Rémi Merindol
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
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14
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Gallas MR, Gallas JAC. Nested arithmetic progressions of oscillatory phases in Olsen's enzyme reaction model. CHAOS (WOODBURY, N.Y.) 2015; 25:064603. [PMID: 26117128 DOI: 10.1063/1.4921178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report some regular organizations of stability phases discovered among self-sustained oscillations of a biochemical oscillator. The signature of such organizations is a nested arithmetic progression in the number of spikes of consecutive windows of periodic oscillations. In one of them, there is a main progression of windows whose consecutive number of spikes differs by one unit. Such windows are separated by a secondary progression of smaller windows whose number of spikes differs by two units. Another more complex progression involves a fan-like nested alternation of stability phases whose number of spikes seems to grow indefinitely and to accumulate methodically in cycles. Arithmetic progressions exist abundantly in several control parameter planes and can be observed by tuning just one among several possible rate constants governing the enzyme reaction.
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Affiliation(s)
- Marcia R Gallas
- Instituto de Altos Estudos da Paraíba, Rua Infante Dom Henrique 100-1801, 58039-150 João Pessoa, Brazil and Departamento de Física, Universidade Federal da Paraíba, 58051-970 João Pessoa, Brazil
| | - Jason A C Gallas
- Instituto de Altos Estudos da Paraíba, Rua Infante Dom Henrique 100-1801, 58039-150 João Pessoa, Brazil and Departamento de Física, Universidade Federal da Paraíba, 58051-970 João Pessoa, Brazil
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15
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Bánsági T, Taylor AF. Role of Differential Transport in an Oscillatory Enzyme Reaction. J Phys Chem B 2014; 118:6092-7. [DOI: 10.1021/jp5019795] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tamás Bánsági
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
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16
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McDonald AG, Tipton KF. Effects of tyramine and 4-aminophenol on the oscillating peroxidase-oxidase reaction. J Phys Chem B 2014; 118:18-25. [PMID: 24351130 DOI: 10.1021/jp406707s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxidase-oxidase oscillator, a model of biological oscillations, is usually studied in conjunction with the effector molecule, 2,4-dichlorophenol. In this account, we present evidence of the effects of a naturally occurring phenol, tyramine, on the reaction, and also those of the structurally similar 4-aminophenol. Whereas 2,4-dichlorophenol gives rise to sustained oscillations at 40 μM, it was discovered that tyramine promotes damped oscillations at a concentration of 120 μM. Oxidation of NADH was completely inhibited by 4-aminophenol and ascorbate. In separate experiments, the peroxidase-catalyzed ring coupling of tyramine and 4-aminophenol was observed, which in the case of tyramine, may provide an explanation for the damping of oscillations.
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Affiliation(s)
- Andrew G McDonald
- School of Biochemistry and Immunology, Trinity College , Dublin 2, Ireland
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17
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Network nonlinearities in drug treatment. Interdiscip Sci 2013; 5:85-94. [PMID: 23740389 DOI: 10.1007/s12539-013-0165-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/25/2012] [Accepted: 03/22/2013] [Indexed: 10/26/2022]
Abstract
Despite major achievements in the understanding of human disease, there is a general perception that the drug development industry has failed to meet the expectations that recent advances in biotechnology should drive. One of the potential sources of failure of many next generation drugs is that their targets are embedded in highly nonlinear signaling pathways and gene networks with multiple negative and positive feedback loops of regulation. There is increasing evidence that this complex network shapes the response to external perturbations in the form of drug treatment, originating bistability, hypersensitivity, robustness, complex dose-response curves or schedule dependent activity. This review focuses on the effect of nonlinearities on signaling and gene networks involved in human disease, using tools from Nonlinear Dynamics to discuss the implications and to overcome the effects of the nonlinearities on regulatory networks.
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18
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Galas JC, Haghiri-Gosnet AM, Estévez-Torres A. A nanoliter-scale open chemical reactor. LAB ON A CHIP 2013; 13:415-423. [PMID: 23223849 DOI: 10.1039/c2lc40649g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
An open chemical reactor is a container that exchanges matter with the exterior. Well-mixed open chemical reactors, called continuous stirred tank reactors (CSTR), have been instrumental for investigating the dynamics of out-of-equilibrium chemical processes, such as oscillations, bistability, and chaos. Here, we introduce a microfluidic CSTR, called μCSTR, that reduces reagent consumption by six orders of magnitude. It consists of an annular reactor with four inlets and one outlet fabricated in PDMS using multi-layer soft lithography. A monolithic peristaltic pump feeds fresh reagents into the reactor through the inlets. After each injection the content of the reactor is continuously mixed with a second peristaltic pump. The efficiency of the μCSTR is experimentally characterized using a bromate, sulfite, ferrocyanide pH oscillator. Simulations accounting for the digital injection process are in agreement with experimental results. The low consumption of the μCSTR will be advantageous for investigating out-of-equilibrium dynamics of chemical processes involving biomolecules. These studies have been scarce so far because a miniaturized version of a CSTR was not available.
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19
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Wrobel MM, Bánsági T, Scott SK, Taylor AF, Bounds CO, Carranza A, Pojman JA. pH wave-front propagation in the urea-urease reaction. Biophys J 2013; 103:610-615. [PMID: 22947878 DOI: 10.1016/j.bpj.2012.06.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/06/2012] [Accepted: 06/14/2012] [Indexed: 11/27/2022] Open
Abstract
The urease-catalyzed hydrolysis of urea displays feedback that results in a switch from acid (pH ~3) to base (pH ~9) after a controllable period of time (from 10 to >5000 s). Here we show that the spatially distributed reaction can support pH wave fronts propagating with a speed of the order of 0.1-1 mm min(-1). The experimental results were reproduced qualitatively in reaction-diffusion simulations including a Michaelis-Menten expression for the urease reaction with a bell-shaped rate-pH dependence. However, this model fails to predict that at lower enzyme concentrations, the unstirred reaction does not always support fronts when the well-stirred reaction still rapidly switches to high pH.
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Affiliation(s)
| | - Tamás Bánsági
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Stephen K Scott
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Annette F Taylor
- School of Chemistry, University of Leeds, Leeds, United Kingdom.
| | - Chris O Bounds
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana
| | - Arturo Carranza
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana
| | - John A Pojman
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana
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20
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Nováková A, Schreiberová L, Schreiber I. Study of dynamics of glucose-glucose oxidase-ferricyanide reaction. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2011. [DOI: 10.1134/s003602441113019x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Das D, Ghosh P, Ray DS. Marginal states in a cubic autocatalytic reaction. J Chem Phys 2011; 135:124104. [DOI: 10.1063/1.3640012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Roy T, Bhattacharjee JK, Mallik AK. Periodic orbits in glycolytic oscillators: from elliptic orbits to relaxation oscillations. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:19. [PMID: 21359930 DOI: 10.1140/epje/i2011-11019-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 01/19/2011] [Indexed: 05/30/2023]
Abstract
We consider the Sel'kov model of glycolytic oscillator for a quantitative study of the limit cycle oscillations in the system. We identify a region of parameter space where perturbation theory holds and use both Linstedt Poincaré technique and harmonic balance to obtain the shape and frequency of the limit cycle. The agreement with the numerically obtained result is excellent. We also find a different extreme, where the limit cycle is of the relaxation oscillator variety, has a large time period and it is seen that, as a particular parameter in the model is varied, the time period increases indefinitely. We characterize this divergence numerically. A calculational method is devised to capture the divergence approximately.
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Affiliation(s)
- T Roy
- Department of Physics, Jadavpur University, 700032, Kolkata, India.
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23
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Hu G, Pojman JA, Scott SK, Wrobel MM, Taylor AF. Base-Catalyzed Feedback in the Urea−Urease Reaction. J Phys Chem B 2010; 114:14059-63. [DOI: 10.1021/jp106532d] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gang Hu
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States, and School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - John A. Pojman
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States, and School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stephen K. Scott
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States, and School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Magdalena M. Wrobel
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States, and School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annette F. Taylor
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States, and School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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24
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Wilson BP, Yliniemi K, Murtomäki L, Kontturi K. Sympathetic current oscillations at an enzyme electrode induced by potential oscillations at a Pt surface. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2009.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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25
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Abstract
Abstract
Spontaneous chemical oscillations are uncovered in the uncatalyzed bromate–pyrocatechol reaction conducted in a stirred batch reactor. Phase diagrams show that the oscillatory behavior is more sensitive to the ratio of [bromate]/[pyrocatechol] than their actual concentrations. The long induction time observed in the system is insensitive to the initial presence of brominated pyrocatechol species. Quenching experiments illustrate that the studied chemical oscillator is both bromide and radical controlled. In addition, this new uncatalyzed bromate oscillator exhibits both light-induced and light-quenched oscillatory behaviors. Preliminary mechanistic characterization with UV/vis absorption method and mass spectrometry suggests the formation of bromo-1,2-benzoquinone through the reaction between pyrocatechol and bromine.
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Bakeš D, Schreiberová L, Schreiber I, Hauser MJB. Analysis of complex oscillatory dynamics of a pH oscillator. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407090117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Harati M, Amiralaei S, Green J, Wang J. Chemical oscillations in the 4-aminophenol–bromate photoreaction. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.03.099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Míguez DG, Vanag VK, Epstein IR. Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase. Proc Natl Acad Sci U S A 2007; 104:6992-7. [PMID: 17420460 PMCID: PMC1855356 DOI: 10.1073/pnas.0611438104] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Indexed: 11/18/2022] Open
Abstract
Waves and patterns in living systems are often driven by biochemical reactions with enzymes as catalysts and regulators. We present a reaction-diffusion system catalyzed by the enzyme glucose oxidase that exhibits traveling wave patterns in a spatially extended medium. Fronts and pulses propagate as a result of the coupling between the enzyme-catalyzed autocatalytic production and diffusion of hydrogen ions. A mathematical model qualitatively explains the experimental observations.
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Affiliation(s)
- David G. Míguez
- Department of Chemistry and Volen Center for Complex Systems, MS 015, Brandeis University, Waltham, MA 02454
| | - Vladimir K. Vanag
- Department of Chemistry and Volen Center for Complex Systems, MS 015, Brandeis University, Waltham, MA 02454
| | - Irving R. Epstein
- Department of Chemistry and Volen Center for Complex Systems, MS 015, Brandeis University, Waltham, MA 02454
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