Nowadays, autonomous vehicles are no longer stranger to robotic applications and military settings. However, the idea of “self-driving cars” regularly cruising through highways and urban streets was a futuristic concept just a few years ago; yet recently it has become accepted as a technological development whose time has come. Generally, the following arguments can justify the use of automated vehicles, namely, a computer-controlled vehicle can drive better than a human and it can keep steady cruising speeds which enhances fuel efficiency, it can easily process huge available online data (GPS data, IMU data, weather and traffic condition data, etc.) which is an overwhelming task for human drivers, it can promptly and accurately adjust its driving without being distracted like humans, it does not blink and it does not sleep (unless there is a crash...). However, besides the existing counter-arguments regarding moral and legal issues, there exist significant technical and research questions and challenges, and the ultimate goal of this proposal is to address some of these open research problems. The key element that enables “self-driving cars” is their connectivity to other cars and to the infrastructure (e.g., traffic lights). Thus, the term Connected Automated Vehicle (CAV) has emerged. A system of CAVs moving through a transportation network is a prototypical Cyber-Physical System (CPS) as it combines the physical dynamics dictated by each vehicle’s engine and motion control with the cyber components provided by the wireless communication networking that enables CAVs to exchange state information. Moreover, if CAVs are to function as a cooperative multi-agent system, there is a need for a control and coordination layer in this CPS, as well as controllers associated with each CAV to regulate its individual acceleration and speed and to make higher-level decisions such as routing or parking. CAVs provide an appealing opportunity for enabling users to better monitor transportation network conditions and to improve traffic flow. The key challenges to be considered in this proposal emerge from requirements to enhance the safety, cyber security, energy consumption efficiency, and to lower the congestion both in highway and urban traffic. A key feature of the proposed research is that it is addressing practical challenging engineering problems that CAV-based cyber-physical systems are faced with in ensuring their performance objectives under different real traffic scenarios. As identified by the Qatar Ministry of Transport and Communications (MoTC), an intelligent transportation system is an emerging field where Qatar should have a key part and this proposal aims at achieving different technological advances toward achieving this goal. There is a significant interest for development of rigorous design and analysis methods for coordination, communicating, and cyber security of CAV-based cyber-physical systems and it is expected that the methodologies and tools that are developed and implemented by researchers in this project will make a significant contribution towards safe, secure, reliable, resilient, and scalable management of these systems. Qatar has already started a journey to foster smart cities such as Lusail City and Musheireb downtown and the innovative work conducted by the researchers will have a significant impact and contribution to the advancement of knowledge and to the enhancement of Qatar’s expertise in the highly advanced domain of intelligent transportation systems for future smart cities.