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

Hardcover | October 17, 2006

byJohn Ross, Igor Schreiber, Marcel O. Vlad

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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.

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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 Dete...

John Ross is at Stanford University (Emeritus). Igor Schreiber is at Prague Institute of Chemical Technology. Peter J. Oefner is at Stanford University.

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Format:HardcoverDimensions:242 pages, 6.42 × 9.29 × 0.91 inPublished:October 17, 2006Publisher:Oxford University PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:0195178688

ISBN - 13:9780195178685

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Table of Contents

1. Introduction1.1. Some Basic Definitions1.2. Introduction to Classical Identification2. Introduction to Chemical Kinetic Processes2.1. Macroscopic, Deterministic Chemical Kinetics2.2. Disordered Kinetics2.3. Fluctuations3. A Brief Review of Methodology for the Analysis of Biochemical Reactions and Cells3.1. Introduction3.2. Measurement of Metabolite Concentrations3.3. Principles and Applications of Mass Spectrometry3.4. Genome-Wide Analyses of mRNA and Proteins3.5. Fluorescent Imaging3.6. Conclusions4. Computations by Means of Macroscopic Chemical Kinetics4.1. Chemical Neurons and Logic Gates4.2. Implementation of Computers by Macroscopic Chemical Kinetics4.3. Computational Functions in Biochemical Reaction Systems5. Response of Systems to Pulse Perturbations5.1. Theory5.2. An Example: The Glycolytic Pathway6. Experimental Test of the Pulse Pertubation Method for Determining Casual Connectivities of Chemical Species in a Reaction Network7. Correlation Metric Construction: Theory of Statistical Construction of Reaction Mechanisms8. Experimental Test and Applications of Correlation Metric Construction9. Destiny Estimation9.1. Entropy Metric Construction (EMC)9.2. Entropy Reduction Method (ERM)10. Applications of Genetic Algorithms to the Determination of Reaction Mechanisms10.1. A Shory Primer on Genetic Algorithms10.2. Selection Regulation of Flux in a Metabolic Model10.3. Evolutionary Development of Biochemical Oscillatory Reaction Mechanisms10.4. Systematic Determination of Reaction Mechanism and Rate Coefficients10.5. Summary11. Oscillatory Reactions11.1. Introduction11.2. Concepts and Theoretical Constructs11.3. Experiments Leading to Information about the Oscillatory Reaction Mechanism11.4. Examples of Deduction of Reaction Mechanism from Experiments11.5. Limits of Stoichiometric Network Analysis12. Lifetime and Transit Time Distributions and Response Experiments in Chemical Kinetics12.1. Lifetime Distributions of Chemical Species12.2. Response Experiments and Lifetime Distributions12.3. Transit Time Distributions, in Complex Chemical Systems12.4. Transit Time Distributions, Linear Response, and Extracting Kinetic Information from Experimental Data12.5. Errors in Response Experiments12.6. Response Experiments for Reaction-Diffusion Systems12.7. Conclusions13. Mini-Introduction to Bioinformatics13.1. Clustering13.2. Linearization in Various Forms13.3. Modeling of Reaction Mechanisms13.4. Boolean Networks13.5. Correlation Metric Construction for Genetic Networks13.6. Bayesian Networks13.7. Some Other Illustrative ApproachesIndex

Editorial Reviews

"For readers who want a fresh view of one of the central challenges in reaction kinetics, this is the book for you. There's no other book like it on the market. It should be useful to a wide audience in many fields including chemistry, biochemistry, biotechnology, engineering, and genomics."-- Chemical and Engineering News