Formulation of Oscillatory Reaction Mechanisms by Deduction from Experiments

Stemwedel, Janet D.; Ross, John; Schreiber, Igor

doi:10.1002/9780470141489.ch5

Cited by 10 publications

(7 citation statements)

References 41 publications

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“…A study of the oscillatory peroxidase-oxidase reaction, including experiments and the formation of a reaction mechanism, by the methods described in this section is given in ref .…”

Section: Oscillatory Reactionsmentioning

confidence: 99%

“…The more then 10 experiments discussed in ref 18 are sufficient to determine the reaction mechanism of a given oscillatory reaction. An analysis of the Belusov-Zhabotinsky reaction (ref 17 p 154 ff) identifies the essential and nonessential species, their connectivities, and the classification 1B; see Figure 14. A study of the oscillatory peroxidase-oxidase reaction, including experiments and the formation of a reaction mechanism, by the methods described in this section is given in ref 18.…”

Section: Oscillatory Reactionsmentioning

confidence: 99%

“…In 1991 we published studies of oscillatory reactions − that produced a mechanistic classification of such systems on the basis, in part, of stoichiometric net work analysis and a series of more than 10 experiments done on the whole system. (An extensive introduction to this subject is given in chapter XI of ref .)…”

Section: Oscillatory Reactionsmentioning

confidence: 99%

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Determination of Complex Reaction Mechanisms. Analysis of Chemical, Biological and Genetic Networks

Ross

2008

J. Phys. Chem. A

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We present several methods of determining, not guessing, complex chemical reaction mechanisms and their functions. One method is based on the theory of correlation functions of measured time series of concentrations of chemical species; another is on measurements of temporal responses of concentrations to various perturbations of arbitrary magnitude; a third deals with the analysis of oscillatory systems; a fourth is on the use of genetic algorithms to determine functions of chemical reaction networks. All methods are applicable to chemical, biochemical, and biological reaction systems and to genetic networks and systems biology. The methods depend on the design of appropriate experiments on the whole system and corresponding theories for interpretation that lead to information on the causal chemical connectivity of species, on reaction pathways, on reaction mechanisms, on control centers in the system, and on functions of the system. The first three methods require no assumption of a model or hypothesis, nor extensive calculations, unlike the interpretation of measurements made on a gene network at only one time.

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“…A study of the oscillatory peroxidase-oxidase reaction, including experiments and the formation of a reaction mechanism, by the methods described in this section is given in ref .…”

Section: Oscillatory Reactionsmentioning

confidence: 99%

Section: Oscillatory Reactionsmentioning

confidence: 99%

See 1 more Smart Citation

Determination of Complex Reaction Mechanisms. Analysis of Chemical, Biological and Genetic Networks

Ross

2008

J. Phys. Chem. A

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“…Each of the two main categories is divided into subcategories B and C, which differ in the topological arrangement of type Z species (negative feedback via exit reaction or an input reaction to the autocatalytic cycle). The division of oscillators into individual subcategories (1B, 1C, 2B, 2C) is indicated by several methods; 26 here we use mutual phase shifts of oscillating species computed from the eigenvector associated with pure imaginary eigenvalues.…”

Section: Resultsmentioning

confidence: 99%

“…23,24 At the Hopf bifurcation (specified by pure imaginary eigenvalues of J), classification and determination of the role of species in oscillations 23,24 can be done, for example, by calculating mutual phase shifts of oscillating species, 25 or by other methods. 26,27 The software used for network analysis and classification of oscillators is home-made (written in Fortran and Matlab), additional dynamic and bifurcation analysis was done by using CONT. 28…”

Section: Stochiometric Network Analysismentioning

confidence: 99%

Stoichiometric network analysis of the photochemical processes in the mesopause region

Hadač

Schreiber

2011

Phys. Chem. Chem. Phys.

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The mechanism of photochemistry in the mesopause region entails a chemical oscillator forced by solar short-wave radiation. A model with periodic forcing between day and night conditions produces nonlinear dynamics including period-doubling bifurcations and chaos. The photochemical mechanism represents a network involving positive and negative feedbacks that can be examined by methods of stoichiometric network analysis. We use these methods to decompose the network into irreducible subnetworks and then apply linear stability analysis to find all possible sources of oscillatory instabilities in the mesopause chemistry. These oscillators are classified according to topological features in their reaction networks and phase shifts of oscillating species. We subsequently compare phase shifts indicated by the network analysis with those from direct simulations to identify a specific subnetwork in the mechanism underlying the complex oscillatory dynamics observed in earlier simulations.

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Mechanistic classification of electrochemical oscillators — an operational experimental strategy

Strasser

Eiswirth

Koper

1999

Journal of Electroanalytical Chemistry

196

234

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Formulation of Oscillatory Reaction Mechanisms by Deduction from Experiments

Cited by 10 publications

References 41 publications

Determination of Complex Reaction Mechanisms. Analysis of Chemical, Biological and Genetic Networks

Determination of Complex Reaction Mechanisms. Analysis of Chemical, Biological and Genetic Networks

Stoichiometric network analysis of the photochemical processes in the mesopause region

Mechanistic classification of electrochemical oscillators — an operational experimental strategy

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