The present invention provides a model that can be use to describe biological processes having a complex spatial geometry, for example, cell signaling processes. The models can also be used to model the pathology underlying diseases characterized by disrupted signaling pathways, and to identify target proteins at an appropriate site in a signal transduction network such that modulation of the target proteins elicits therapeutic effects. Methods of modeling diffusion processes, as well as machine-readable products embodying the methods are also disclosed.