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9780195178685

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

by ; ; ; ; ;
  • ISBN13:

    9780195178685

  • ISBN10:

    0195178688

  • Format: Hardcover
  • Copyright: 2005-11-24
  • Publisher: Oxford University Press

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Summary

In a chemical system with many chemical species several questions can be asked: what species react with other species: in what temporal order: and with what results? These questions have been asked for over one hundred years about simple and complex chemical systems, and the answers constitutethe macroscopic reaction mechanism. In Determination of Complex Reaction Mechanisms authors John Ross, Igor Schreiber, and Marcel Vlad present several systematic approaches for obtaining information on the causal connectivity of chemical species, on correlations of chemical species, on the reactionpathway, and on the reaction mechanism. Basic pulse theory is demonstrated and tested in an experiment on glycolysis. In a second approach, measurements on time series of concentrations are used to construct correlation functions and a theory is developed which shows that from these functions information may be inferred on the reactionpathway, the reaction mechanism, and the centers of control in that mechanism. A third approach is based on application of genetic algorithm methods to the study of the evolutionary development of a reaction mechanism, to the attainment given goals in a mechanism, and to the determination of areaction mechanism and rate coefficients by comparison with experiment. Responses of non-linear systems to pulses or other perturbations are analyzed, and mechanisms of oscillatory reactions are presented in detail. The concluding chapters give an introduction to bioinformatics and statisticalmethods for determining reaction mechanisms.

Table of Contents

1 Introduction,
1(6)
1.1 Some Basic Definitions,
3(1)
1.2 Introduction to Classical Identification,
4(3)
2 Introduction to Chemical Kinetic Processes,
7(4)
2.1 Macroscopic, Deterministic Chemical Kinetics,
7(2)
2.2 Disordered Kinetics,
9(1)
2.3 Fluctuations,
9(2)
3 A Brief Review of Methodology for the Analysis of Biochemical Reactions and Cells,
11(23)
3.1 Introduction,
11(1)
3.2 Measurement of Metabolite Concentrations,
11(4)
3.3 Principles and Applications of Mass Spectrometry,
15(3)
3.4 Genome-Wide Analyses of mRNA and Proteins,
18(5)
3.5 Fluorescent Imaging,
23(4)
3.6 Conclusions,
27(7)
4 Computations by Means of Macroscopic Chemical Kinetics,
34(12)
4.1 Chemical Neurons and Logic Gates,
35(2)
4.2 Implementation of Computers by Macroscopic Chemical Kinetics,
37(3)
4.3 Computational Functions in Biochemical Reaction Systems,
40(6)
5 Response of Systems to Pulse Perturbations,
46(12)
5.1 Theory,
46(7)
5.2 An Example: The Glycolytic Pathway,
53(5)
6 Experimental Test of the Pulse Perturbation Method for Determining Causal Connectivities of Chemical Species in a Reaction Network,
58(7)
7 Correlation Metric Construction: Theory of Statistical Construction of Reaction Mechanisms,
65(22)
8 Experimental Test and Applications of Correlation Metric Construction,
87(10)
9 Density Estimation,
97(7)
9.1 Entropy Metric Construction (EMC),
97(5)
9.2 Entropy Reduction Method (ERM),
102(2)
10 Applications of Genetic Algorithms to the Determination of Reaction Mechanisms, 104(21)
10.1 A Short Primer on Genetic Algorithms,
104(2)
10.2 Selection of Regulation of Flux in a Metabolic Model,
106(6)
10.3 Evolutionary Development of Biochemical Oscillatory Reaction Mechanisms,
112(7)
10.4 Systematic Determination of Reaction Mechanism and Rate Coefficients,
119(3)
10.5 Summary,
122(3)
11 Oscillatory Reactions, 125(45)
11.1 Introduction,
125(2)
11.2 Concepts and Theoretical Constructs,
127(11)
11.3 Experiments Leading to Information about the Oscillatory Reaction Mechanism,
138(13)
11.4 Examples of Deduction of Reaction Mechanism from Experiments,
151(15)
11.5 Limits of Stoichiometric Network Analysis,
166(4)
12 Lifetime and Transit Time Distributions and Response Experiments in Chemical Kinetics, 170(37)
12.1 Lifetime Distributions of Chemical Species,
171(2)
12.2 Response Experiments and Lifetime Distributions,
173(9)
12.3 Transit Time Distributions in Complex Chemical Systems,
182(6)
12.4 Transit Time Distributions, Linear Response, and Extracting Kinetic Information from Experimental Data,
188(4)
12.5 Errors in Response Experiments,
192(5)
12.6 Response Experiments for Reaction–Diffusion Systems,
197(8)
12.7 Conclusions,
205(2)
13 Mini-Introduction to Bioinformatics, 207(16)
13.1 Clustering,
209(1)
13.2 Linearization in Various Forms,
209(1)
13.3 Modeling of Reaction Mechanisms,
210(1)
13.4 Boolean Networks,
211(2)
13.5 Correlation Metric Construction for Genetic Networks,
213(2)
13.6 Bayesian Networks,
215(5)
13.7 Some Other Illustrative Approaches,
220(3)
Index, 223

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