Solid state devices for quantum bit computation (qubits) are not perfect isolated two-level systems, since additional higher energy levels always exist. One example is the Josephson flux qubit, which consists on a mesoscopic SQUID loop with three Josephson junctions operated at or near a magnetic flux of half quantum. We study intrinsic leakage effects, i.e., direct transitions from the allowed qubit states to higher excited states of the system during the application of pulses for quantum computation operations. The system is started in the ground state and rf- magnetic field pulses are applied at the qubit resonant frequency with pulse intensity $f_p$. A perturbative calculation of the average leakage for small $f_p$ is performed for this case, obtaining that the leakage is quadratic in $f_p$, and that it depends mainly on the matrix elements of the supercurrent. Numerical simulations of the time dependent Schrodinger equation corresponding to the full Hamiltonian of this device were also performed. From the simulations we obtain the value of $f_p$ above which the two-level approximation breaks down, and we estimate the maximum Rabi frequency that can be achieved. We study the leakage as a function of the ratio $alpha$ among the Josephson energies of the junctions of the device, obtaining the best value for minimum leakage ($alphaapprox0.85$). The effects of flux noise on the leakage are also discussed.
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