Modeling Dynamic Biological Systems

1 Introduction.- 1 Modeling Dynamic Biological Systems.- 2 Exploring Dynamic Biological Systems.- 3 Risky Population.- 4 Steady State, Oscillation, and Chaos in Population Dynamics.- 5 Spatial Dynamics.- 2 Physical and Biochemical Models.- 6 Law of Mass Action.- 7 Catalyzed Product.- 8 Two-Stage Nutrient Uptake Model.- 9 Iodine Compartment Model.- 10 The Brusselator.- 11 Fitzhugh-Nagumo Neuron Model.- 12 Solar Radiation to Nonobstructed Inclined Surfaces.- 3 Genetics Models.- 13 Mating and Mutation of Alleles.- 14 Natural Selection, Mutation, and Fitness.- 4 Models of Organisms.- 15 Odor-Sensing Model.- 16 Stochastic Resonance.- 17 Heartbeat Model.- 18 Bat Thermoregulation.- 19 The Optimum Plant.- 20 Infectious Diseases.- 5 Single Population Models.- 21 Adaptive Population Control.- 22 Roan Herds.- 23 Population Dynamics of Voles.- 24 Lemming Model.- 25 Multistage Insect Models.- 26 Two Age-Class Parasite Model.- 27 Monkey Travels.- 28 Biosynchronicity.- 6 Multiple Population Models.- 29 Wildebeest Model.- 30 Nicholson-Bailey Host-Parasitoid Model.- 31 Diseased and Healthy Immigrating Insects.- 32 Two-Species Colonization Model.- 33 Herbivore-Algae Predator-Prey Model.- 34 The Grass Carp.- 35 Recruitment and Trophic Dynamics of Gizzard Shad.- 36 Modeling Spatial Dynamics of Predator-Prey Interactions in a Changing Environment.- 7 Catastrophe and Self-Organization.- 37 Catastrophe.- 38 Spruce Budworm Dynamics.- 39 Sandpile.- 40 Earthquake.- 41 Game of Life.- 42 Daisyworld.- 8 Conclusion.- 43 Building a Modeling Community.- A1 Installation Instructions for Macintosh Version.- A2 Installation Instructions for Windows Version.- A3 Quick Help Guide.- A3.1 Overview of STELLA Operating Environment.- A3.2 Drawing an Inflow to a Stock.- A3.3 Drawing an Outflow from a Stock.- A3.4 Replacing a Cloud with a Stock.- A3.5 Bending Flow Pipes.- A3.6 Repositioning Flow Pipes.- A3.7 Reversing Direction of a Flow.- A3.8 Flow Define Dialog—Builtins.- A3.9 Moving Variable Names.- A3.10 Drawing Connectors.- A3.11 Defining Graphs and Tables.- A3-12 Dynamite Operations on Graphs and Tables.- MADONNA Quick Start.- B1 Installation of MADONNA.- B2 Example: Harmonic Oscillator.- B2.1 Writing the Model Equations.- B2.2 Compiling the Model.- B2.3 Running the Model.- B2.4 The Graph Window.- B2.5 Multiple Runs.- References.