In this thesis we investigate the vulnerabilities present in protocols and the damage that can arise if these vulnerabilities are exploited by a malicious node. In particular, we model protocols using Petri nets. Petri nets allow us to simulate the protocols and reason about them. Attacks are also modeled using Petri nets. We develop a tool to correlate the protocol Petri net and the attack Petri net to identify the worst vulnerability in the protocol and a payoff function is applied to measure the potential damage. Once the weak link in the protocol is identified, we propose approaches to reduce or eliminate the identified vulnerability. The modified protocol is also modeled as a Petri net.Computer Science Departmen