The structure and dynamical properties of the Fe$_3$Si/GaAs(001) interface are investigated by density functional theory and nuclear inelastic scattering measurements. The stability of four different atomic configurations of the Fe$_3$Si/GaAs multilayers is analyzed by calculating the formation energies and phonon dispersion curves. The differences in charge density, magnetization, and electronic density of states between the configurations are examined. Our calculations unveil that magnetic moments of the Fe atoms tend to align in a plane parallel to the interface, along the [110] direction of the Fe$_3$Si crystallographic unit cell. In some configurations, the spin polarization of interface layers is larger than that of bulk Fe$_3$Si. The effect of the interface on element-specific and layer-resolved phonon density of states is discussed. The Fe-partial phonon density of states measured for the Fe$_3$Si layer thickness of three monolayers is compared with theoretical results obtained for each interface atomic configuration. The best agreement is found for one of the configurations with a mixed Fe-Si interface layer, which reproduces the anomalous enhancement of the phonon density of states below 10 meV
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