Advances in computing and communication technologies are blurring the distinction between today's PCs and mobile phones. With expected smart phones sales to skyrocket, lack of awareness regarding securing them, and access to personal and proprietary information, has resulted in the recent surge of mobile malware. In addition to using traditional social-engineering techniques such as email and file-sharing, malware unique to Bluetooth, Short Messaging Service (SMS) and Multimedia Messaging Service (MMS) messages are being used. Large scale simulations of malware on wireless networks have becomes important and studying them under realistic device deployments is important to obtain deep insights into their dynamics and devise ways to control them. In this dissertation, we present EpiNet: an individual-based scalable high-performance oriented modeling environment for simulating the spread of mobile malware over large, dynamic networks. EpiNet can be used to undertake comprehensive studies during both planning and response phase of a malware epidemic in present and future generation wireless networks. Scalability is an important design consideration and the current EpiNet implementation can scale to 3-5 million device networks and case studies show that large factorial designs on million device networks can be executed within a day on 100 node clusters. Beyond compute time, EpiNet has been designed for analysts to easily represent a range of interventions and evaluating their efficacy. The results indicate that Bluetooth malware with very low initial infection size will not result in a major wireless epidemic. The dynamics are dependent on the network structure and, activity-based mobility models or their variations can yield realistic spread dynamics. Early detection of the malware is extremely important in controlling the spread. Non-adaptive response strategies using static graph measures such as degree and betweenness are not effective. Device-based detection mechanisms provide a much better means to control the spread and only effective when detection occurs early on. Automatic signature generation can help in detecting newer strains of the malware and signature distributions through a central server results in better control of the spread. Centralized dissemination of patches are required to reach a large proportion of devices to be effective in slowing the spread. Non-adaptive dynamic graph measures such as vulnerability are found to be more effective. Our studies of SMS and hybrid malware show that SMS-only malware spread slightly faster than Bluetooth-only malware and do not spread to all devices. Hybrid malware spread orders of magnitude faster than either SMS-only or Bluetooth-only malware and can cause significant damage. Bluetooth-only malware spread faster than SMS-only malware in cases where density of devices in the proximity of an infected device is higher. Hybrid malware can be much more damaging than Bluetooth-only or SMS-only malware and we need mechanisms that can prevent such an outbreak. EpiNet provide a means to propose, implement and evaluate the response mechanisms in realistic and safe settings.Ph. D.