The use of an electron beam to remove ultracold atoms from selected sites in an optical lattice has opened up new opportunities to study transport in quantum systems [R. Labouvie {it et al. }, Phys. Rev. Lett. {bf 115}, 050601 (2015)]. Inspired by this experimental result, we examine the effects of number difference, dephasing, and initial quantum statistics on the filling of an initially depleted middle well in the three-well inline Bose-Hubbard model. We find that the well-known phenomenon of macroscopic self-trapping is the main contributor to oscillatory negative differential conductivity in our model, with phase diffusion being a secondary effect. However, we find that phase diffusion is required for the production of direct atomic current, with the coherent process showing damped oscillatory currents. We also find that our results are highly dependent on the initial quantum states of the atoms in the system.
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