The complexity of intermolecular interactions and confinement in polymer - nanoparticle systems leads to spatial variations in structure and dynamics at both the meso and nanoscale. Molecular simulation holds great promise as a means of predicting these effects and understanding their microscopic origin. In order to shed some light onto local structure and segmental dynamics of atactic polystyrene/silica (PS/SiO2) and atactic polystyrene/fullerene (PS/C60) melt systems, molecular simulations have been conducted using two interconnected levels of representation: 1) A coarse-grained representation. Equilibration of coarse-grained polymer-nanoparticle systems at all length scales is achieved via connectivity-altering Monte Carlo simulations. 2) An atomistic representation. Initial configurations for atomistic molecular dynamics (MD) simulations are obtained by reverse mapping well-equilibrated coarse-grained configurations. The local structure around a silica nanoparticle immersed in the PS matrix, PS segmental, and local dynamics in both composites and mechanical properties and entanglements in PS/SiO2 are studied.