Abstract
Based on a cavity QED framework, we theoretically describe a universal set of logic gates which are implemented by passing a multi-level atom initially in its ground state through a multi-mode cavity. The qubits are encoded on the cavity modes and the atom plays the role of an ancilla which will not be entangled with the final result of a gate operation. We apply the multiphoton resonance theory of Shore to develop effective two- and three-level Hamiltonians, so that the proper values for detunings, coupling coefficients, and interaction times for gate operations can be determined. This enables us to examine a faster iSWAP gate than our previous study and to examine numerically the effects of decoherence on both the iSWAP gate and our previously presented Fredkin gate which used the same multi-mode approach. We also present results that show how conditional measurements of the ancilla atom can improve gate fidelities in these cases.