Determination of Complex Reaction Mechanisms

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 Pertubation Method for Determining Casual 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.: Destiny 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 Shory Primer on Genetic Algorithms
10.2: Selection 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