At the beginning of **Communicating and Mobile Systems: the Pi-Calculus** by Robin Milner, there is a introduction on automata and how they can simulate each other so that they cannot be distinguished : **Bisimulation**.  (cf [Bisimulation][1] on wikipedia)

I don't remember well, I should re-read the chapter, but there was a trouble with simulation and bisimulation that made them not sufficient for computational equivalences.

Thus Robin Milner introduces his Pi-Calculus and exposes it for the rest of the book.

Ultimately, in his last book **The Space and Motion of Communicating Agents**, you could have a look at Robin Milner's Bigraphs. They can model Automata, Petri nets, Pi-Calculus and other computational methodologies.




  [1]: http://en.wikipedia.org/wiki/Bisimulation