There has been a remarkable growth rate in computing performance for many years, however, the technology roadmap has indicated that current scaling trends cannot continue forever. Research in the fields of physics, chemistry, and electronics has demonstrated that Quantum-dot Cellular Automata (QCA) is a viable nanotechnology in the area of computing. Experimental success has led to the evolution of a research track that looks at QCA-based circuit design that may help scaling trends continue. The research contained in this thesis includes an investigation into the physical spacings of QCA devices and the harmful effects of defects and faults on basic QCA circuit elements. Various simulation tools are utilized to explore these issues. A statistical mechanical simulation tool in particular is extended specifically for a molecular implementation of QCA. Because of the higher defect rates expected at the nanoscale, steps have been taken to design reprogrammable logic from QCA devices. Specifically, a novel QCA-based Programmable Logic Array (PLA) structure is considered.