We analyze the requirements for fault-tolerant quantum computation with atom-atom gates based on cavity quantum electrodynamics (cQED) mediated by a photon with a finite pulse length. For short photon pulses, the distorted shape of the reflected pulses from the cQED system is a serious error source. We optimize the cQED system parameters to minimize the infidelity due to the shape distortion and the photon losses in a well-balanced manner for the fault-tolerant scheme using probabilistic gates [H. Goto and K. Ichimura, Phys. Rev. A 80, 040303(R) (2009)]. Our optimization greatly relaxes the requirements for fault-tolerant quantum computation in some parameter regions, compared with the conventional optimization method where only the photon loss is minimized without considering the shape distortion [H. Goto and K. Ichimura, Phys. Rev. A 82, 032311 (2010)]. Finally, we show that reducing the cavity length is an effective way to reduce the errors of this type of gate in the case of short photon pulses.
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