Classical trajectory molecular dynamics methods are used to investigate the critical strain of single-walled carbon nanotubes ("SWT") and the strength and extent of the interactions between 3D Ge structures on the surface of Si(001). The discrete model is capable of giving some insight into the critical strain of the SWT's beyond the limits of the continuous model and allow us to investigate the effects of lattice distortion due to the placement of Ge structures on the surface of a Si substrate. Total energy calculations performed using classical three-body interatomic potentials with appropriate boundary conditions for each case are used to investigate the two systems. We discuss the development of a parallel code to simulate short-ranged empirical potentials such as those of Stillinger and Weber, Tersoff, and Tersoff-Brenner. We then use the Tersoff potential to model C and Si/Ge system. Data collected are used to examine the behavior of the two systems.