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We describe an entanglement purification protocol (EPP) for atomic entangled pair using photonic Faraday rotation. It is shown that after the two single photons input-output process in cavity QED, the high quality entangled atomic state can be obtained from the low quality mixed entangled atomic states. Different from other EPPs, the two pairs of mixed states do not need to intact directly. As the photonic Faraday rotation works on the low-Q cavities, this EPP is useful in both quantum communication and computation.

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