Deterministic Kinetics in Chemistry and Systems Biology, 2015
The Dynamics of Complex Reaction Networks
SpringerBriefs in Molecular Science Series

This book gives a concise overview of the mathematical foundations of kinetics used in chemistry and systems biology. The analytical and numerical methods used to solve complex rate equations with the widely used deterministic approach will be described, with primary focus on practical aspects important in designing experimental studies and the evaluation of data. The introduction of personal computers transformed scientific attitudes in the last two decades considerably as computational power ceased to be a limiting factor. Despite this improvement, certain time-honored approximations in solving rate equations such as the pre-equilibrium or the steady-state approach are still valid and necessary as they concern the information content of measured kinetic traces. The book shows the role of these approximations in modern kinetics and will also describe some common misconceptions in this field.

Rates and Rate Equations.- Concentration and its Change in Time.- Reactions and the Reducibility of Chemical Systems.- Intermediates and Catalysts.- Open Systems: Flow of Reactants and Photons.- Experimental Design and its Limitations.- Systems Biology: Chemical Kinetics for Biologists.- Solving Rate Equations.- Analytical Possibilities.- Single-Concentration Rate Equations.- Multiple-Concentration Rate Equations.- Numerical Methods.- Fitting to Measured Data.- Inevitable Approximations.- The Method of Flooding.- Kinetically Separate Phases.- Rate Determining Steps.- Steady State Approximation.- Pre-Equilibrium Approach.- Relaxation Kinetics.- Chain Reactions.- Clock Reactions.- Competition Kinetics and Chemical Clocks.- Parameter Insensitivity and Indistinguishable Schemes.- Statistical Kinetics.- A Qualitative Approach to Chemical Kinetics.- Information from Parameter Values.- Diffusion Controlled Processes.- Activation and Transition States.- Electrostatic Effects.- Isotope Effects.- Structure-Reactivity Relationships.- Common Pitfalls.- The Fallacy of Reaction Rates.- The Fallacy of Rate Constants.- The Fallacy of Rate Coefficients.- The Fallacy of Consecutive Processes.- The Fallacy of Parallel Processes.- The Fallacy of the Rate Determining Step.- The Fallacy of Exchange Reactions.- Misconceptions About Activation Parameters.- The Fallacy of the Activation Energy.- The Fallacy of the Activation Free Energy.- The Fallacy of the Activation Entropy.- The Fallacy of the Activation Volume.- The Fallacy of the Isokinetic Temperature.- The Fallacy of the Diffusion Limited Rate Constant.- The Fallacy of Unimolecular Reactions.- The Fallacy of Radical Scavengers.- The Fallacy of Linearization.- The Fallacy of the Coefficient of Determination.- The Fallacy of Curve Fitting.