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A theory of rank perturbation of symplectic matrices and Hamiltonian systems with periodic coefficients using a base of isotropic subspaces, is presented. After showing that the fundamental matrix of the rank perturbation of Hamiltonian system with periodic coefficients and the rank perturbation of the fundamental matrix of the unperturbed system are the same, the Jordan canonical form of is given. Two numerical examples illustrating this theory and the consequences of rank perturbations on the strong stability of Hamiltonian systems were also given.

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