Superconductor-topological insulator (SC-TI) heterostructures were proposed to be a possible platform to realize and control Majorana zero-modes. Despite experimental signatures indicating their existence, univocal interpretation of the observed features demands theories including realistic electronic structures. To achieve this, we solve the Kohn-Sham-Dirac-Bogoliubov-de Gennes equations for ultrathin Bi$_2$Se$_3$ films on superconductor PdTe, within the fully relativistic Korringa-Kohn-Rostoker method, and investigate quasiparticle spectra as a function of chemical potential and film thickness. We find a strongly momentum-dependent proximity-induced gap feature where the gap sizes highly depend on characteristics of the TI states. The interface TI Dirac state is relevant to the induced gap only when the chemical potential is close to the Dirac-point energy. Otherwise, at a given chemical potential, the largest induced gap arises from the highest-energy quantum-well states, whereas the smallest gap arises from the TI topological surface state with its gap size depending on the TI pairing potential.
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