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This volume is the collected and extended notes from the lectures on Hamiltonian dynamical systems and their applications that were given at the NATO Advanced Study Institute in Montreal in 2007. Many aspects of the modern theory of the subject were covered at this event, including low dimensional problems as well as the theory of Hamiltonian systems in infinite dimensional phase space; these are described in depth in this volume. Applications are also presented to several important areas of research, including problems in classical mechanics, continuum mechanics, and partial differential equations. These lecture notes cover many areas of recent mathematical progress in this field, including the new choreographies of many body orbits, the development of rigorous averaging methods which give hope for realistic long time stability results, the development of KAM theory for partial differential equations in one and in higher dimensions, and the new developments in the long outstanding problem of Arnold diffusion.