Table of Contents
Chapter 2: Reaction Kinetics and Biological Dynamics
Supplementary Material
Electronic Notebooks
Exercises
Figures - electronic sources
Bibliography - electronic access - chapter 2
Text Outline
Missing Topics
Chapter 2: Reaction Kinetics and Biological Dynamics
Supplementary Material
Electronic Notebooks
These all depend on Mathematica(R) and xCellerator. See
Software availability
Introductory example: {A->B, B->C
}
Mass action kinetics
Stochastic simulation algorithm (SSA) example
PIP3 metabolism
Analytic solution of 2×2 master equation for binding/unbinding
Analytic solution of trivalent reaction A+B <–> C
MAPK cascade model
of Huang and Ferrell 1996
Exercises
Hill functions
Master equation
Trivalent mass action
Figures - electronic sources
Hill functions, n=1 and n=2
Convergence of bound/unbound probability
S-E-P deterministic simulation
S-E-P stochastic simulation
Bibliography - electronic access - chapter 2
Here
Text Outline
2.1 Example: Growth factor response
2.2 Elementary dynamical models
2.3 Mapping biology to mathematics and computation
2.4 Causal network dynamics
2.5 Summary
Missing Topics