We analyse the problem of a single mode field interacting with a pair of two level atoms. The atoms enter and exit the cavity at different times. Instead of using constant coupling, we use time dependent couplings which represent the spatial dependence of the mode. Although the system evolution is adiabatic for most of the time, a previously unstudied energy crossing plays a key role in the system dynamics when the atoms have a time delay. We show that conditional atom-cavity entanglement can be generated, while for large photon numbers the entangled system has a behaviour which can be mapped onto the single atom Jaynes-Cummings model. Exploring the main features of this system we propose simple and fairly robust methods for entangling atoms independently of the cavity, for quantum state mapping, and for implementing SWAP and C-NOT gates with atomic qubits.
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