By means of optimal control techniques we model and optimize the manipulation of the external quantum state (center-of-mass motion) of atoms trapped in adjustable optical potentials. We consider in detail the cases of both non interacting and interacting atoms moving between neighboring sites in a lattice of a double-well optical potentials. Such a lattice can perform interaction-mediated entanglement of atom pairs and can realize two-qubit quantum gates. The optimized control sequences for the optical potential allow transport faster and with significantly larger fidelity than is possible with processes based on adiabatic transport.
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