Polymer nanoparticle composites (PNCs) have become an important topic of research due to their highly tunable macroscopic properties. Compared to pure polymers, PNCs can exhibit increases in mechanical strength, altered thermodynamic properties, and simultaneous improvement in permeability and selectivity in small molecule transport. Understanding the fundamental physics that control the behavior of both components in PNCs can provide insight to material design. In PNCs, the microscopic variations often dominate the behavior at the macroscopic level. Previous research has shown significant deviations in both polymer conformation and dynamics near the nanoparticle (NP) surfaces from bulk polymers. However, the heterogeneous nature of the PNCs makes understanding microscopic details using macroscopic experiments a difficult task. Therefore, computational methods have been employed to investigate the polymer conformation, mechanics, and dynamics at the molecular level. In this dissertation, I use model PNCs with two levels of NP loading to investigate the origins of the various changes in properties. First, I use molecular dynamics (MD) simulations to examine a class of PNCs with ultra-high NP loading, in which the volume fraction of NPs is near the random-close-pack limit ( > 50% ). This class of PNCs can be produced with either partial or complete filling of polymers, allowing for easy control of void volume within the packings. In these PNCs, the polymer chains are highly confined due to the large number of NP surfaces, thus are drastically altered in their conformation and dynamics. The second PNC system studied in this dissertation has a dilute amount of well-dispersed NPs to avoid NP-NP interaction and polymer confinement. In this case, I use both MD simulations and classical density functional theory (cDFT) to understand the effect of NP-polymer interactions, solid curvature, and polymer molecular weight on polymer dynamics and mechanics near the surface. In the Appendices of this dissertation, I briefly discuss my work on understanding mechanical failure modes in glassy material, and an attempt to experimentally measure the polymer infiltration mechanism in fabricating the PNCs with ultra-high NP loading using neutron reflectometry.