We theoretically investigate the properties of a double-well bosonic Josephson junction coupled to a single trapped ion. We find that the coupling between the wells can be controlled by the internal state of the ion, which can be used for studying mesoscopic entanglement between the two systems and to measure their interaction with high precision. As a particular example we consider a single $^{87}$Rb atom and a small Bose-Einstein condensate controlled by a single $^{171}$Yb$^+$ ion. We calculate inter-well coupling rates reaching hundreds of Hz, while the state dependence amounts to tens of Hz for plausible values of the currently unknown s-wave scattering length between the atom and the ion. The analysis shows that it is possible to induce either the self-trapping or the tunneling regime, depending on the internal state of the ion. This enables the generation of large scale ion-atomic wavepacket entanglement within current technology.
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