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We experimentally demonstrate quantum process tomography of controlled-Z and controlled-NOT gates using capacitively-coupled superconducting phase qubits. These gates are realized by using the state of the phase qubit. We obtain a process fidelity of 0.70 for the controlled-phase and 0.56 for the controlled-NOT gate, with the loss of fidelity mostly due to single-qubit decoherence. The controlled-Z gate is also used to demonstrate a two-qubit Deutsch-Jozsa algorithm with a single function query.

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