  In this paper we present an experimentally realizable microwave pulse
sequence that effects a Controlled NOT (C-NOT) gate operation on a Josephson
junction-based flux-qubit/resonator system with high fidelity in the end state.
We obtained a C-NOT gate process fidelity of 0.988 (0.980) for a two (three)
qubit/resonator system under ideal conditions, and a fidelity of 0.903 for a
two qubit/resonator system under the best, currently achieved, experimental
conditions. In both cases, we found that "qubit leakage" to higher levels of
the resonator causes a majority of the loss of fidelity, and that such leakage
becomes more pronounced as decoherence effects increase.
