You can turn Petri nets into stochastic nets using some formal procedures. Stochastic nets have a "master equation" which spits out a system of PDEs representing reactions where many many things happen at the same time, and so it makes more sense to think in terms of concentrations etc.

We are working to capture this categorically as well. We are perfectly conscious of how a discrete system won't help you if you have an Avogadro number of things going around. Just give us time. :)