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We introduce GBDT version of Darboux transformation for symplectic and Hamiltonian systems as well as for Shin-Zettl systems and Sturm-Liouville equations. These are the first results on Darboux transformation for general-type Hamiltonian and for Shin-Zettl systems. The obtained results are applied to the corresponding transformations of the Weyl-Titchmarsh functions and to the construction of explicit solutions of dynamical symplectic systems, of two-way diffusion equations and of indefinite Sturm-Liouville equations. The energy of the explicit solutions of dynamical systems is expressed (in a quite simple form) in terms of the parameter matrices of GBDT.

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