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Due to their large surface to volume ratio, the performance of nanoscale or nanostructured materials and devices is often dominated by processes at free surfaces or interfaces. Understanding and quantifying these phenomena and harnessing them for improved performance are key challenges in nanoscience and nanotechnology. Molecular dynamics modeling is playing an increasingly important role in this field due to its ability to provide a connection between a material’s atomic structure and its thermo-mechanical response. In this paper we describe the use of molecular dynamics to predict the structure of nanoscale heterostructures of interest in nanoelectronics applications and phonon thermal transport in Si nanowires where sub-continuum effects play a dominant role.