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

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

Avainsanat: SCIENCE / Chemistry / Physical & Theoretical SCI013050