Mathematica code (CRN-to-DNA-Examples.nb) for enumerating the strand displacement reactions in the DNA implementation of any given target chemical reaction network, scaling the system into an experimentally realistic regime, and simulating the ideal target system together with the DNA implementation. Contains the five examples from the text.
Required package for entering CRNs in Mathematica: CRNSimulator.m.
Note: A more recent version of the package is on David Soloveichik's website.
Save CRN-to-DNA-Examples.nb and CRNSimulator.m in the same directory, and open CRN-to-DNA-Examples.nb.
The code was tested on Mathematica 7.0.1.
Note that the pulse counter example can take a while to evaluate.