We analyze the coupling of atoms or atom-like emitters to nanophotonic waveguides in the presence of propagating acoustic waves. Specifically, we show that strong index modulations induced by such waves can drastically modify the effective photonic density of states and thereby influence the strength, the directionality, as well as the overall characteristics of photon emission and absorption processes. These effects enable a complete dynamical control of light-matter interactions in waveguide structures, which even in a two dimensional system can be used to efficiently exchange individual photons along selected directions and with a very high fidelity. Such a quantum acousto-optical control provides a versatile tool for various quantum networking applications ranging from the distribution of entanglement via directional emitter-emitter interactions to the routing of individual photonic quantum states via acoustic conveyor belts.
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