Alkaline-earth (AE) atoms have metastable clock states with minute-long optical lifetimes, high-spin nuclei, and SU($N$)-symmetric interactions that uniquely position them for advancing atomic clocks, quantum information processing, and quantum simulation. The interplay of precision measurement and quantum many-body physics is beginning to foster an exciting scientific frontier with many opportunities. Few particle systems provide a window to view the emergence of complex many-body phenomena arising from pairwise interactions. Here, we create arrays of isolated few-body systems in a fermionic ${}^{87}$Sr three-dimensional (3D) optical lattice clock and use high resolution clock spectroscopy to directly observe the onset of both elastic and inelastic multi-body interactions. These interactions cannot be broken down into sums over the underlying pairwise interactions. We measure particle-number-dependent frequency shifts of the clock transition for atom numbers $n$ ranging from 1 to 5, and observe nonlinear interaction shifts, which are characteristic of SU($N$)-symmetric elastic multi-body effects. To study inelastic multi-body effects, we use these frequency shifts to isolate $n$-occupied sites and measure the corresponding lifetimes. This allows us to access the short-range few-body physics free from systematic effects encountered in a bulk gas. These measurements, combined with theory, elucidate an emergence of multi-body effects in few-body systems of sites populated with ground-state atoms and those with single electronic excitations. By connecting these few-body systems through tunneling, the favorable energy and timescales of the interactions will allow our system to be utilized for studies of high-spin quantum magnetism and the Kondo effect.
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