  Experimental realizations of charged ions and neutral atoms in overlapping
traps are gaining increasing interest due to their wide research application
ranging from chemistry at the quantum level to quantum simulations of
solid-state systems. Here, we describe a system in which we overlap a single
ground-state cooled ion trapped in a linear Paul trap with a cloud of ultracold
atoms such that both constituents are in the $\mu$K regime. Excess micromotion
(EMM) currently limits atom-ion interaction energy to the mK energy scale and
above. We demonstrate spectroscopy methods and compensation techniques which
characterize and reduce the ion's parasitic EMM energy to the $\mu$K regime
even for ion crystals of several ions. We give a substantial review on the
non-equilibrium dynamics which governs atom-ion systems. The non-equilibrium
dynamics is manifested by a power-law distribution of the ion's energy. We
overview the coherent and non-coherent thermometry tools which we used to
characterize the ion's energy distribution after single to many atom-ion
collisions.
