We observed a strong modulation in the current-voltage characteristics of SrRuO$_3$/Nb:SrTiO$_3$ Schottky junctions by Mn substitution in SrRuO$_3$, which induces a metal-insulator transition in bulk. The temperature dependence of the junction ideality factor indicates an increased spatial inhomogeneity of the interface potential with substitution. Furthermore, negative differential resistance was observed at low temperatures, indicating the formation of a resonant state by Mn substitution. By spatially varying the position of the Mn dopants across the interface with single unit cell control, we can isolate the origin of this resonant state to the interface SrRuO$_3$ layer. These results demonstrate a conceptually different approach to controlling interface states by utilizing the highly sensitive response of conducting perovskites to impurities.
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