Full molecular dynamics simulations of a single trapped ion in a neutral bath
We present full molecular dynamics simulations that explicitly incorporate the simultaneous interactions between a trapped ion and a bath of neutral atoms. In contrast to conventional molecular dynamics treatments, this framework enables a systematic assessment of how the atomic-gas density influences both the ion's cooling dynamics and its steady-state mean kinetic energy. Our results show that the gas density measurably modifies the ion's average kinetic energy, albeit only weakly, in qualitative disagreement with predictions obtained from standard molecular dynamics simulations. In addition, the calculations indicate that short-range features of the atom-ion interaction potential become increasingly consequential as the atomic density increases. Simulations including many atoms yield higher mean kinetic energies than standard molecular dynamics, a trend we attribute to the transient formation of molecular-ion complexes. Finally, we observe that for a fixed ion, lighter atomic baths lead to a smaller final ion average kinetic energy than heavier atomic baths.