- •Copyright © 2006 by Oxford University Press, Inc.
- •Contents
- •1 Introduction
- •References
- •2.1 Macroscopic, Deterministic Chemical Kinetics
- •2.2 Disordered Kinetics
- •2.3 Fluctuations
- •References
- •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
- •3.5 Fluorescent Imaging
- •3.6 Conclusions
- •References
- •4.1 Chemical Neurons and Logic Gates
- •4.2 Implementation of Computers by Macroscopic Chemical Kinetics
- •4.3 Computational Functions in Biochemical Reaction Systems
- •References
- •5.1 Theory
- •5.2 An Example: The Glycolytic Pathway
- •References
- •6 Experimental Test of the Pulse Perturbation Method for Determining Causal Connectivities of Chemical Species in a Reaction Network
- •Reference
- •Discussion
- •References
- •References
- •9 Density Estimation
- •9.1 Entropy Metric Construction (EMC)
- •9.2 Entropy Reduction Method (ERM)
- •References
- •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
- •10.5 Summary
- •References
- •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
- •References
- •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
- •12.7 Conclusions
- •References
- •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
- •References
- •Index
10 DETERMINATION OF COMPLEX REACTION MECHANISMS
References
[1]Berry, R. S.; Rice, S. A.; Ross, J. Physical Chemistry, 2nd ed.; Oxford University Press: Oxford, 2000.
[2]Shlesinger, M. Fractal time in condensed matter. Annu. Rev. Phys. Chem. 1988, 39, 269–290.
[3]Plonka, A. Time-Dependent Reactivity of Species in Condensed Media; Springer: Berlin, 1986.
[4]Zwanzig, R. Rate processes with dynamic disorder. Acc. Chem. Res. 1990, 23, 148–152.
[5]Ross, J.; Vlad, M. O. Nonlinear kinetics and new approaches to complex reaction mechanisms. Annu. Rev. Phys. Chem. 1999, 50, 51–78. See the section on “Rate processes in disordered systems” and references therein.
[6]Gardiner, C. W. Handbook of Stochastic Methods, 2nd ed.; Springer: New York, 1990.
[7]Van Kampen, N. G. Stochastic Processes in Physics and Chemistry, 2nd ed.; Elsevier: Amsterdam, 1992.