A combination of computational chemistry and molecular dynamics (MD) approaches was used to study two polymer-nanoparticle composite (PNPC) systems, first a model bead spring polymer with spherical nanoparticles and generalized interactions, and second, a Poly(dimethylsiloxane) (PDMS)-silica system with accurate quantum chemistry (QC) based force fields. The following molecular processes, which are fundamental to the reinforcement of polymer-nanoparticle composites (PNPC), were studied: (1) the effect of nanoparticle-polymer interactions and polymer molecular weight on nanoparticle dispersion and distribution, (2) the free energy and conformational changes when stretching individual PDMS chains in a melt, and (3) the effect of silica fillers with different surface modifications on the properties of PDMS chains at the interface. In the model PNPC consisting of spherical nanoparticles in a bead-spring polymer melt, it was found that when the polymer-nanoparticle interactions were relatively weak the polymer matrix promoted nanoparticle aggregation. Increasingly attractive nanoparticle-polymer interactions led to strong adsorption of the polymer chains on the surface of the nanoparticles and promoted dispersion of the nanoparticles and were independent of polymer molecular weight. A classical force field for PDMS and its oligomers has been derived on the basis of intermolecular binding energies, molecular geometries, molecular electrostatic potentials, and conformational energies obtained from quantum chemistry calculations and in MD simulations and it accurately reproduces the properties of PDMS melts of various molecular weights. MD simulations using umbrella sampling methods to sample the free energy of stretching a PDMS oligomer in a melt of PDMS oligomers found that the restoring forces were mainly a result of the changes in entropy of the chain as the chain was contracted or stretched, and only at severe extensions did energetic contributions due to deformation of internal bends make a significant contribution to the free energy. Finally, MD simulations of PDMS with silica and modified silica surfaces that accurately predicted the changes in PDMS dynamics with the addition of SiO2 observed in quasielastic neutron scattering experiments. Surface modifications of the silica particles affected the PDMS chain dynamics but no significant hydrogen bonding was observed in the MD simulations of PDMS near silica surfaces.