In this work, we use a combination of first-principles calculations under the density functional theory framework and heat transport simulations using the atomistic Greens function (AGF) method to quantitatively predict the contribution of the different scattering mechanisms to the thermal interface conductance of epitaxial CoSi$_2$-Si interfaces. An important development in the present work is the direct computation of interfacial bonding from density functional perturbation theory (DFPT) and hence the avoidance of commonly used `mixing rules to obtain the cross-interface force constants from bulk material force constants. Another important algorithmic development is the integration of the recursive Greens function (RGF) method with B{u}ttiker probe scattering that enables computationally efficient simulations of inelastic phonon scattering and its contribution to the thermal interface conductance. First-principles calculations of electron-phonon coupling reveal that cross-interface energy transfer between metal electrons and atomic vibrations in the semiconductor is mediated by delocalized acoustic phonon modes that extend on both sides of the interface, and phonon modes that are localized inside the semiconductor region of the interface exhibit negligible coupling with electrons in the metal. We also provide a direct comparison between simulation predictions and experimental measurements of thermal interface conductance of epitaxial CoSi$_2$-Si interfaces using the time-domain thermoreflectance technique. Importantly, the experimental results, performed across a wide temperature range, only agree well with predictions that include all transport processes: elastic and inelastic phonon scattering, electron-phonon coupling in the metal, and electron-phonon coupling across the interface.
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