Creation of quantum computer is outstanding fundamental and practical problem. The quantum computer could be used for execution of very complicated tasks which are not solvable with the classical computers. The first prototype of solid state quantum computer was created in 2009 with superconducting qubits. However, it suffers from the decoherent processes and it is desirable to find more practical encoding of qubits with long-lived coherence. It could be single impurity or vacancy centers in solids, but their interaction with electromagnetic radiation is rather weak. So, here, ensembles of atoms were proposed for the qubit encoding by using the dipole blockade mechanism in order to turn multilevel systems in two level ones. But dipole-dipole based blockade introduces an additional decoherence that limits its practical significance. Recently, the collective blockade mechanism has been proposed for the system of three-level atoms by using the different frequency shifts for the Raman transitions between the collective atomic states characterized by a different number of the excited atoms. Here, we propose two qubit gate by using another collective blockade mechanism in the system of two level atoms based on exchange interaction via the virtual photons between the multi-atomic ensembles in the resonator. Also we demonstrate the possibility of three qubit gate (Controlled SWAP gate) using a suppression of the swap-process between two multi-atomic ensembles due to dynamical shift of the atomic levels controlled by the states of photon encoded qubit
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