My colleague Dan Damelin just created an amazing model of the electron transport chain, which can be found here. This simulation shows an extremely complicated process in molecular biology, which involves many interdependent processes happening simultaneously. While it is debatable how such a complex simulation can deliver anything instructive (perhaps a fairer question to ask is: is the topic itself apprehensible to kids?), the simulation demonstrates the level of complexity of the Molecular Workbench modeling system. The scripts that are driving this simulation probably have thousands of lines of code.
