Self-adaptation of communication protocols is a major issue in the conception of future services for the ambient Internet. These protocols will have to provide adequate services to complex, mobile, cooperative application with dynamic requirements distributed in highly heterogeneous environments, partially wireless and ad hoc with variable and evolutive constraints. In this highly dynamic context, providing efficient solutions requires handling adaptability not only at the behavioral level, but also at the architectural level. End-to-end modular architecture protocols are a promising solution to support architectural self-adaptation to the context. Following this approach, the contributions presented in this paper address the automated choice of internal architecture for configurable Transport level protocols. Tackling this need by means of informal models may lead to non generic and suboptimal solutions due to the complexity of the problem. We propose to guide adaptation by an analytical model which is then evaluated against simulation results.