Systems Biology: Computational and Mathematical Methods

by E. Mjolsness, P. Baldi, and B. Shapiro

Table of Contents

Chapter 2: Reaction Kinetics and Biological Dynamics

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

Trace: • biological_dynamics_and_reaction_kinetics

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