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The paper suggests a new methodology for secure cyber–physical systems design. The proposed methodology consists of two main cycles. The main goal of the first cycle is in design of the system model, while the second one is about development of the system prototype. The key idea of the methodology is in providing of the most rational solutions that are improving the security of cyber–physical systems. Such solutions are called alternatives and built according to functional requirements and non-functional limitations to the system. Each cycle of the methodology consists of the verification process and seven stages that are associated with the used cyber–physical system model. The objective of the verification process is in checking of constructed models and prototypes in terms of their correctness and compatibility. The model represents cyber–physical systems as sets of building blocks with network between …