Of course there are many systems for modelling processes. These fall under the category of process algebras. The key examples are $\pi$-calculus, CCS, ACP and CSP.
Process calculi have basic mechanisms for specifying process behaviour including: sending and receiving of messages (synchronously or asynchronously), creating parallel processes, nondeterministic choice between behaviours, and the replication of processes. Although the calculi are small in terms of the number of constructs, they are very expressive and a vast amount of research has gone into studying their properties.
The $\pi$-calculus differs from the others in that it allows, in essence, processes to be passed as first class values. It actually allows channel names to be passed around as first class values, enabling changes in the dynamic topology. This is probably the calculus you want because it offers the greatest dynamicity.
CSP (communicating sequential processes) is a little odd, when seen from a perspective of modelling molecules. It does have plenty of backing theory and tool support. (Invented by C. A. R. Hoare.)
CCS and ACP have less dynamicity than the $\pi$-calculus, but they are much easier to analyse and simulate. A solid toolset called $\mu$CRL (and $\mu$CRL2) are available for ACP. Similar tools are sure to exist for CCS.
I'd start examining the related work (see below) and then find which of the modelling formalisms suit what you are looking for.
There has in fact been quite a lot of work modelling chemical reactions and biological processes using process algebra.
Probably the best place to look is Luca Cardelli's publication list. His whole line of research on BioComputing has probably 30 papers on the topic. This talk gives an overview of much of his work. This one is slightly more formal, though reading the papers is really the only way to see the details.
One approach that directly models chemical processes is CHAM (the chemical abstract machine). The key ingredient here is a solution of molecules and membranes. There are heating and cooling rules for rearranging the molecules and for removing junk. These rules are reversible. Finally there reaction rules which model reactions. In contrast to process algebras, CHAM models are not so worried about the syntax of processes, so you can invent your own representation of the molecules.
Rewrite logic as realised in the toolset Maude offers another more or less direct approach to specifying such reactions. One need only specify the rewrite rules, the handing of the "soup" is automatic. The toolset would enable the simulation and analysis of (smallish) chemical reactions. A probabilistic variant of Maude also exists.