This dissertation undertakes theoretical and computational research to characterize and understand in detail atomic configurations and electronic structural properties of surfaces and interfaces at the nano-scale, with particular emphasis on identifying the factors that control atomic-scale diffusion and transport properties. The overarching goal is to outline, with examples, a predictive modeling procedure of stable structures of novel materials that, on the one hand, facilitates a better understanding of experimental results, and on the other hand, provide guidelines for future experimental work. The results of this dissertation are useful in future miniaturization of electronic devices, predicting and engineering functional novel nanostructures. A variety of theoretical and computational tools with different degrees of accuracy is used to study problems in different time and length scales. Interactions between the atoms are derived using both ab-initio methods based on Density Functional Theory (DFT), as well as semiempirical approaches such as those embodied in the Embedded Atom Method (EAM), depending on the scale of the problem at hand. The energetics for a variety of surface phenomena (adsorption, desorption, diffusion, and reactions) are calculated using either DFT or EAM, as feasible. For simulating dynamic processes such as diffusion of adatoms on surfaces with dislocations the Molecular Dynamics (MD) method is applied. To calculate vibrational mode frequencies, the infinitesimal displacement method is employed. The combination of non-equilibrium Green’s function (NEGF) and DFT is used to calculate electronic transport properties of molecular devices as well as interfaces and junctions.