Polymer nanocomposites (PNCs) are hybrid materials incorporating organic or inorganic nanoparticles (NPs) with at least one dimension in the submicron scale. Over the last two decades, these materials have drawn a remarkable attention due to their central role in industrial formulations and technological applications, extending from food packaging to smart coatings. Incorporating nanoparticles (NPs) to a polymer matrix can significantly alter the conformation and the mobility of the polymer chains in their proximity. Moreover, understanding the delicate balance between the enthalpic and entropic interactions is crucial to control and predict the ability of NPs to diffuse and disperse in the polymer matrix. The impact of these interactions on the structure and the dynamics of polymer chains and NPs is fully revealed in how a number of macroscopic properties changes, justifying the high interest on these materials for industrial applications. In this thesis, the impact on the structure, dynamics, viscosity and thermal conductivity of a number of microscopic properties is investigated by performing Molecular Dynamics (MD) simulations. Specifically, the PNC is represented by a coarse-grained model of a melt of linear homopolymer chains containing spherical NPs. Throughout this work, a number of parameters are modified in order to unveil possible patterns in the PNCâs performance. To this end, this work focuses on the consequences of modifying the NP size dispersity, NP-polymer chain relative size, and chainsâ degree of stiffness. Four theoretical models describing the diffusivity of NPs, three of which include nano-scale corrections, have been averaged to study the dependence of dilute NPsâ diffusivity on the NP polydispersity index. By comparing these models to the simulation results at different degrees of polydispersity, it is possible to obtain a more complete picture of their validity as compared to the monodisperse case. Regarding the diffusion of polymer chains, simulation results were in good agreement with the experimental results previously obtained by Composto and coworkers (Soft Matter 2012, 8, 6512), which relate the chainsâ diffusivity to the average interparticle distance. As far as the transport properties are concerned, they show a weaker dependence on the polydispersity index. By contrast, results on viscosity and thermal conducitivity show that they are conditioned by the polymer-NP specific interfacial area and the inverse average mass, respectively. These results are in good agreement with previous experimental results. A deeper examination of this intriguing deviation from viscosity predictions in traditional composites, reveals a non-trivial combination of thickening and thinning effects contributing to the final viscosity of the PNC. This thesis also address the influence of the chainsâ stiffness on the dynamical and viscous behaviour. An isotropic-to-nematic phase transition is observed, regardless of the NP-monomer interactions, below which a monotonic increase of both properties is observed, whereas orientationally ordered systems dramatically modify them, resulting into a steep increase or a smooth decrease depending on the direction in which they are measured.