Simulator
We have developed a simple AC simulator designed for the problem set.
You don't have to use this code. It is simply a framework to get you started. This simulator contains 3 source files:
This code should work on Windows, Linux, and Unix. We have successfully compiled it on Windows. We haven't yet compiled it on other platforms, but it should work with little alteration. If you use MS Visual Studio on Windows, then use the following project: . The following source compiles on Red Hat Linux 7.2: linuxACSim.tar.gz. A gui written in Gtk is available as well. If you find any bugs or have a OS port that would be of use to the class in general, please let us know and we can share the information with the class.
The AC simulation is written in generic C and is independent of the visualization package. The GUI uses OpenGL libraries and the platform-independent Glut windowing environment. You may already have these libraries on your machine, but it is up to you to figure out your own compilation environment. Here is a good reference for setting up OpenGL on Windows, MacOS, and Sun/Solaris.
Yet another disclaimer: This problem set is on the long side and we recommend that you start early. We have provided the simulator so that you can focus on the actual AC and not on mundane coding aspects. It should, once compiled, demonstrate a single bacterium following a chemical gradient. However, to get to this point we have built in some of our own assumptions about the world/chemistry that you may not want to keep. For example, the chemical reactor we use is a variant of the stochastic molecular collision method described on p228 of the Dittrich paper. You may, however, want to try out a spatial reaction grid such as the one used in Ziegler paper.
Good luck!