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The paper is devoted to issues of creation of cross-functional analytical complex for simulation of the process of operation of the security system elements. Basic objectives, a design concept and an interrelation of main elements of the complex are described. The proposed conception of the analytical complex provides an opportunity to simulate processes for evaluating the effectiveness of physical protection system of a nuclear facility. The complex uses models, that take into account features of the object, parameters of technical means and tactics of adversaries. Recommendations were made for applying of this conception for training specialists in the field of physical protection of nuclear materials.