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When the Faculty was founded in 1955, the predecessor of the present-day Department of Nuclear Reactors was the Department of Nuclear Engineering headed by Bohumil Kvasil. Although there were changes in its title during the years, the main objective of the Department has been preserved, i.e., to prepare high quality specialists for Czech nuclear power engineering.

In the 1960s the existing structures were redistributed and the department was renamed. From 1970 the Department existed under the name of the Department of Applied Nuclear Physics and was headed first by Čestmír Šimáně and then by Petr Otčenášek. In 1979 the Department moved to its present premises within the campus of the Faculty of Mathematics and Physics of Charles University at the address Prague 8, V Holešovičkách 2. However, following a decision by the Rector, in 1981 the Department was abolished and the specialization in Nuclear Reactors became a part of the Department of Physics headed by Ivan Štoll.

In June 1990 an independent structure of the training nuclear reactor VR-1 was detached from the Department of Physics with Karel Matějka as a Head. In relation with the reactor VR-1 start-up in 1991 the Department of Nuclear Reactors (DNR) was established, headed by Karel Matějka, and the Reactor VR-1 workplace became its part. Later, after Karel Matějka, the new Head of the Department became L´ubomír Sklenka in 2008.
The Department of Nuclear Reactors ensures courses in the branch of nuclear engineering. Courses are focused on theoretical and experimental reactor physics, neutron applications, study of the nuclear fuel cycle and safe operation of nuclear power plants and research reactors. They also concentrate on thermodynamics, reactor dynamics and principles of heat transfer. An important part represents radiation protection and the study of biological effects of ionizing radiation.

Since the establishment of the Department in 1955 emphasis has been placed on combination of teaching/learning with science and research. New findings and project results are integrated into courses in order to offer a high standard of instruction. Students have the opportunity to take part in running projects in the form of students´ year projects in which they learn to do systematic scientific work and to solve tasks. During their study they have the chance to work in research institutions or nuclear power companies and gain practical knowledge. Academic instruction is developed by students‘ participation in experiments at the VR-1 reactor and in laboratories. Students are encouraged to use the tools of information technology and some up-to-date calculation computing codes in their work (neutron characteristics calculations, thermodynamic properties of systems).

Graduates from the Department join projects of fuel cycle modification, nuclear power plant operation support, projects for construction of new power engineering sources and development and testing of new control and safety systems. They find placements as operators or reactor physicists in nuclear power plants and research institutes operating their own reactor, or they may find an academic position.