Selective yet efficient transport between the cell nucleus and cytoplasm is critical to cellular function as the nuclear pore complex is a major point of regulation for gene expression, signal transduction, immune response, oncogenesis and viral propagation. The combined physical structure of the pore, biochemical interaction of transport factors with pore components and the presence of the cellular milieu create conditions under which selective and efficient nucleocytoplasmic transport can occur. In this dissertation, I explore the significance of structure and interaction on transport of globular proteins and polymeric mRNA cargo through the crowded pore. In the first part of this work, an agent based modeling software framework is developed and validated for accurately simulating discrete and stochastic reaction-diffusion systems. A simulation environment representing the structure of the nuclear pore complex along with rules for the dynamics of protein movement and interaction was created using in vivo and in vitro reported parameters. This setup was then used to perform in silico experiments on the role of pore-cargo affinity in optimizing transport efficiency. These experiments demonstrate the pore's sensitivity to cargo affinity in maintaining efficient transport and suggest that a higher affinity binding site at the side of the pore where transport is terminated increases efficiency by reducing futile shuttling of cargo complexes. In the final part of this dissertation, I extend my agent based modeling framework to look at aspects of mRNA export that have remained unaddressed in experimental works. Variations in the number and spacing of transport receptors bound to the mRNA are shown to play a critical role in transport efficiency. In these experiments, a single transport receptor at the 5' end appeared insufficient for facilitating export. Increasing transport receptor coverage along the length of the mRNA improved the chances of successful export. Additionally, it was observed that the presence of a transport receptor near either the 5' or 3' terminus is required for successful export as it likely promotes the emergence of a favorable threading conformation. Finally, it was observed that the use of a single fluorescent tag to track and report mRNA export time, as is standard in current experimental work, is likely to underestimate true transport times. These findings have implications in the design of targeted delivery and export of polymeric molecules into and out the nucleus.