Introduction to Computational Science
Angela B. Shiflet and George W. Shiflet

CONTENTS FOR SECOND EDITION

Preface

1 OVERVIEW

Module 1.1    Overview of Computational Science
Module 1.2    The Modeling Process

2 SYSTEM DYNAMICS PROBLEMS WITH RATE PROPORTIONAL TO AMOUNT

Module 2.1    System Dynamics Tool—Tutorial 1
Module 2.2    Unconstrained Growth and Decay
Module 2.3    Constrained Growth
Module 2.4    System Dynamics Tool: —Tutorial 2
Module 2.5    Drug Dosage

3 FORCE AND MOTION

Module 3.1    Modeling Falling and Skydiving
Module 3.2    Modeling Bungee Jumping
Module 3.3    Tick Tock—The Pendulum Clock
Module 3.4    Up, Up, and Away—Rocket Motion

4 SYSTEM DYNAMICS MODELS WITH INTERACTIONS

Module 4.1    Competition
Module 4.2    Predator-Prey Models
Module 4.3    Modeling the Spread of SARS—Containing Emerging Disease
Module 4.4    Modeling a Persistent Plague—Malaria
Module 4.5    Enzyme Kinetics—A Model of Control

5 COMPUTATIONAL ERROR

Module 5.1    Computational Toolbox—Tools of the Trade: Tutorial 1
Module 5.2    Errors

6 SIMULATION TECHNIQUES

Module 6.1    Computational Toolbox—Tools of the Trade: Tutorial 2
Module 6.2    Euler's Method
Module 6.3    Runge-Kutta 2 Method
Module 6.4    Runge-Kutta 4 Method

7 ADDITIONAL SYSTEM DYNAMICS PROJECTS

Module 7.1    Radioactive Chains—Never the Same Again
Module 7.2    Turnover and Turmoil—Blood Cell Populations
Module 7.3    Deep Trouble—Ideal Gas Laws and Scuba Diving
Module 7.4    What Goes Around Comes Around—The Carbon Cycle
Module 7.5    A Heated Debate—Global Warming
Module 7.6    Plotting the Future—How Will the Garden Grow?
Module 7.7    Cardiovascular System—A Pressure Pressure-Filled Model
Module 7.8    Electrical Circuits—A Complete Story
Module 7.10    Feeding the Problem—Antibiotic Resistance
Module 7.11    Fueling Our Cells—Carbohydrate Metabolism
Module 7.12    Mercury Pollution—Getting on Our Nerves
Module 7.13    Managing to Eat—What’s the Catch?
Module 7.14    Control Issues—The Operon Model
Module 7.15    Troubling Signals—Colon Cancer

8 DATA-DRIVEN MODELS

Module 8.1    Computational Toolbox—Tools of the Trade: Tutorial 3
Module 8.2    Function Tutorial
Module 8.3    Empirical Models

9 SIMULATING WITH RANDOMNESS

Module 9.1    Computational Toolbox—Tools of the Trade: Tutorial 4
Module 9.2    Simulations
Module 9.3    Random Numbers from Various Distributions
Module 9.4    Computational Toolbox—Tools of the Trade: Tutorial 5
Module 9.5    Random Walk

10 CELLULAR AUTOMATON DIFFUSION SIMULATIONS

Module 10.1    Computational Toolbox—Tools of the Trade: Tutorial 6
Module 10.2    Diffusion: Overcoming Differences
Module 10.3    Spreading of Fire
Module 10.4    Movement of Ants—Taking the Right Steps
Module 10.5    Biofilms—United They Stand, Divided They Colonize

11 AGENT-BASED MODELS

Module 11.1    Agent-Based Tool: Tutorial 1
Module 11.2    Agents of Interaction: Steering a Dangerous Course
Module 11.3    Agent-Based Tool: Tutorial 2
Module 11.4    Introducing the Cane Toad – Able Invader

12 HIGH-PERFORMANCE COMPUTING

Module 12.1    Concurrent Processing
Module 12.2    Parallel Algorithms

13 MATRIX MODELS

Module 13.1    Computational Toolbox—Tools of the Trade: Tutorial 7
Module 13.2    Matrices for Population Studies—Linked for Life
Module 13.3    Time after Time—Age- and Stageuctured Models
Module 13.5    The Next Flu Pandemic: Old Enemy—New Identity

14 ADDITIONAL CELLULAR AUTOMATA, AGENT-BASED AND MATRIX PROJECTS

Module 14.1    Polymers—Strings of Pearls
Module 14.2    Solidification—Let’s Make It Crystal Clear!
Module 14.3    Foraging—Finding a Way to Eat
Module 14.4    Pit Vipers—Hot Bodies, Dead Meat
Module 14.5    Mushroom Fairy Rings—Growing in Circles
Module 14.6    Spread of Disease—Sharing Bad News
Module 14.7    HIV—The Enemy Within
Module 14.8    Predator-Prey—"Catch Me If You Can"
Module 14.9    Clouds—Bringing It All Together
Module 14.10    Fish Schooling—Hanging Together, Not Separately
Module 14.11    Spaced Out—Native Plants Lose to Exotic Invasives
Module 14.12     Re-Solving the Problems with Cellular Automaton Simulations
Module 14.13    Re-Solving the Problems with Agent-Based Simulations
Module 14.14    Computational Code-Breaking—Deciphering Our Own Mysteries
Module 14.15    Social Networks—Value in Being Well- Connected

Glossary
Answers to Selected Exercises
Index