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

Intro -- Contents -- 1 Introduction -- 1.1 Some Basic Definitions -- 1.2 Introduction to Classical Identification -- 2 Introduction to Chemical Kinetic Processes -- 2.1 Macroscopic, Deterministic Chemical Kinetics -- 2.2 Disordered Kinetics -- 2.3 Fluctuations -- 3 A Brief Review of Methodology for the Analysis of Biochemical Reactions and Cells -- 3.1 Introduction -- 3.2 Measurement of Metabolite Concentrations -- 3.3 Principles and Applications of Mass Spectrometry -- 3.4 Genome-Wide Analyses of mRNA and Proteins -- 3.5 Fluorescent Imaging -- 3.6 Conclusions -- 4 Computations by Means of Macroscopic Chemical Kinetics -- 4.1 Chemical Neurons and Logic Gates -- 4.2 Implementation of Computers by Macroscopic Chemical Kinetics -- 4.3 Computational Functions in Biochemical Reaction Systems -- 5 Response of Systems to Pulse Perturbations -- 5.1 Theory -- 5.2 An Example: The Glycolytic Pathway -- 6 Experimental Test of the Pulse Perturbation Method for Determining Causal Connectivities of Chemical Species in a Reaction Network -- 7 Correlation Metric Construction: Theory of Statistical Construction of Reaction Mechanisms -- 8 Experimental Test and Applications of Correlation Metric Construction -- 9 Density Estimation -- 9.1 Entropy Metric Construction (EMC) -- 9.2 Entropy Reduction Method (ERM) -- 10 Applications of Genetic Algorithms to the Determination of Reaction Mechanisms -- 10.1 A Short Primer on Genetic Algorithms -- 10.2 Selection of Regulation of Flux in a Metabolic Model -- 10.3 Evolutionary Development of Biochemical Oscillatory Reaction Mechanisms -- 10.4 Systematic Determination of Reaction Mechanism and Rate Coefficients -- 10.5 Summary -- 11 Oscillatory Reactions -- 11.1 Introduction -- 11.2 Concepts and Theoretical Constructs -- 11.3 Experiments Leading to Information about the Oscillatory Reaction Mechanism.

11.4 Examples of Deduction of Reaction Mechanism from Experiments -- 11.5 Limits of Stoichiometric Network Analysis -- 12 Lifetime and Transit Time Distributions and Response Experiments in Chemical Kinetics -- 12.1 Lifetime Distributions of Chemical Species -- 12.2 Response Experiments and Lifetime Distributions -- 12.3 Transit Time Distributions in Complex Chemical Systems -- 12.4 Transit Time Distributions, Linear Response, and Extracting Kinetic Information from Experimental Data -- 12.5 Errors in Response Experiments -- 12.6 Response Experiments for Reaction-Diffusion Systems -- 12.7 Conclusions -- 13 Mini-Introduction to Bioinformatics -- 13.1 Clustering -- 13.2 Linearization in Various Forms -- 13.3 Modeling of Reaction Mechanisms -- 13.4 Boolean Networks -- 13.5 Correlation Metric Construction for Genetic Networks -- 13.6 Bayesian Networks -- 13.7 Some Other Illustrative Approaches -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- Y -- Z.

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.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.