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Cyber-Physical Systems (CPSs) integrate physical processes, computational resources, and communication capabilities. This enables the use of digital information and control technologies to improve the monitoring, operation, and planning of the systems. Among the fields of application of CPSs, we can find medicine, automotive systems, process control, energy, avionics, robotics, or defense, to cite a few. Some CPSs are formed by identifiable entities or agents, sometimes heterogeneous, that isolated already represent a complete control system with its own computation and sensing (though limited) capacities, but when considered as a whole are able to perform complex tasks not achievable by their own. Despite their potential and advantages, security is a primary concern and challenge in a CPS, since the tight coupling between the cyber and the physical parts broadens the number and nature of potential threats, making the system vulnerable to intentional and unforeseen attacks that can damage the physical system and have disastrous consequences. Thus, the main goal of this project is the design of resilient and secure control architectures, strategies and algorithms which help to face threats and attacks at the different levels of a cooperative CPS and respond to them so that the system maintains an acceptable level of operational normality. The challenge is to integrate safety and robustness in systems with components that have constraints on computation, cost, power availability, and communication capabilities, as well as partial knowledge of the overall system and their environment.