Based on a multimode multilevel Jaynes-Cummings model and multiphoton resonance theory, a set of universal two- and three-qubit gates, namely the iSWAP and the Fredkin gates, has been realized where dual-rail qubits are encoded in cavities. In this way the information has been stored in cavities and the off-resonant atomic levels have been eliminated by the semi-classical theory of an effective two-level Hamiltonian. A further semi-classical model, namely the spin-$J$ model, has been introduced so that a complete population inversion for levels of interest has been achieved and periodic multilevel multiphoton models have been performed. The combination of the two semi-classical models has been employed to address two-level, three-level, four-level, and even five-level configurations. The impact of decoherence processes on the fidelity of the iSWAP and the Fredkin gates has been studied.
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