In this work, we present an integrated waveguide-resonator scheme of an atomic quantum transistor with a multi-qubit memory. The quantum transistor is realized in an atomic-photon molecule formed of a linear chain of three interconnected resonators, each of which contains one resonant three-level atom. The resonators are connected through the waveguides to the quantum memory containing long-lived multi-atomic ensembles capable of storage of photonic qubits with an arbitrary temporal mode. We consider the protocols for implementation of one- and two-qubit operations in the proposed scheme over a system of qubits stored in quantum memory. The advantages and experimental implementation of the proposed scheme are also discussed.
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