Matt’s reference is probably the best place to start since it crops up several times in a search of “cyberspace thom morphogenesis”. Rene Thom is the mathematician whose topological investigations have been taken up by such theorists as Jean Petitot and applied to semiotic processes. It is the mathematical construct of “phase space” that I had in mind when I suggested that one way of approaching and representing the dynamic nature of networks.
I tend not to draw a sharp dichotomy between the virtual and the physical. In part, this is due to adopting a general systems framework. I like to think of the Internet as a subset of Cyberspace (and the WWW as a subset of the Internet.) Cyberspace would include Interactive Voice Response system, cell phone systems, automated video monitoring. Within such a framework the question of synchronization becomes crucial. What happens if the spatial representation of network activity is refocussed as a representation of the “state of the system” — I think what emerges is a representation of a holding pattern (and the potential for it not to hold). Thom’s work in catastrophe theory and his exploration of strange attractors are to me the place to look for representations of dynamical systems — especially networks where relays, nodes and traffic patterns can shift [neat to be able to map meterological data with network traffic data :)]
Not sure if the above helps. However you may be interested in a thread on the Poetics of Cyberspace pursued on Humanist in 2000