| B.1 |
Basics of Solving Ordinary Differential Equations |
| B.1.1 |
Creating the ODE File |
| B.1.2 |
Running the Program |
| B.1.3 |
The Main Window |
| B.1.4 |
Solving the Equations, Graphing and Plotting |
| B.1.5 |
Saving and Printing Plots |
| B.1.6 |
Changing Parameters and Initial Data |
| B.1.7 |
Looking at the Numbers: The Data Viewer |
| B.1.8 |
Saving and Restoring the State of Simulations |
| B.1.9 |
Important Numerical Parameters |
| B.1.10 |
Command Summary: The Basics |
| B.2 |
Phase Planes and Nonlinear Equations |
| B.2.1 |
Direction Fields |
| B.2.2 |
Nullclines and Fixed Points |
| B.2.3 |
Command Summary: Phase Planes and Fixed Points |
| B.3 |
Bifurcation and Continuation |
| B.3.1 |
General Steps for Bifurcation Analysis |
| B.3.2 |
Hopf Bifurcation in the FitzHugh-Nagumo Equations |
| B.3.3 |
Hints for Computing Complete Bifurcation Diagrams |
| B.4 |
Partial Differential Equations: The Method of Lines |
| B.5 |
Stochastic Equations |
| B.5.1 |
A Simple Brownian Ratchet |
| B.5.2 |
A Sodium Channel Model |
| B.5.3 |
A Flashing Ratchet |
