DNA linker mediated self-assembly of nanoparticles- grafting complementary sequences of single stranded DNA to nanoparticles to program their self-assembly, is a flexible strategy for designing novel polymer nanocomposites. In this dissertation, a scale-accurate coarse grained model of nanoparticles grafted with DNA is developed. Using Molecular Dynamics simulations, the dynamics of self-assembly and equilibrium phases are investigated for systems where nanoparticles are spherical or anisotropic.