Transport of Bose-Einstein condensates in magnetic microtraps, controllable by external parameters such as wire currents or radio-frequency fields, is studied within the framework of optimal control theory (OCT). We derive from the Gross-Pitaevskii equation the optimality system for the OCT fields that allow to efficiently channel the condensate between given initial and desired states. For a variety of magnetic confinement potentials we study transport and wavefunction splitting of the condensate, and demonstrate that OCT allows to drastically outperfrom more simple schemes for the time variation of the microtrap control parameters.
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