Abstract
A controlled-NOT logic gate based on conditional spectroscopy has been demonstrated recently for a pair of superconducting flux qubits [Plantenberg et al., Nature 447, 836 (2007)]. Here we study the fidelity of this type of gate applied to a phase qubit coupled to a resonator (or a pair of capacitively coupled phase qubits). Our results show that an intrinsic fidelity of more than 99% is achievable in 45ns.