Abstract
We propose a scheme for implementing single-qubit and nontrivial two-qubit gate operations in a system with superconducting quantum interference devices (SQUIDs) via Raman transitions in circuit QED. The gate operations only involve the two lower flux states of the SQUID, and hence the effect of the excited state can be neglected. By encoding quantum information into the decoherence free subspace of the SQUID system, the evolution of the system results in fault-tolerant quantum gates. The effect of decoherence caused by the decay of the transmission line resonator is investigated.