We study a simple model consisting of an atomic ion and a polar molecule trapped in a single setup, taking into consideration their electrostatic interaction. We determine analytically their collective modes of excitation as a function of their masses, trapping frequencies, distance, and the molecules electric dipole moment. We then discuss the application of these collective excitations to cool molecules, to entangle molecules and ions, and to realize two-qubit gates between them. We finally present a numerical analysis of the possibility of applying these tools to study magnetically ordered phases of two-dimensional arrays of polar molecules, a setup proposed to quantum-simulate some strongly-correlated models of condensed matter.
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