Theory, modeling and simulation (TMS) tools constitute key enabling technologies for making fundamental advances in nanoscience and for making nanotechnology a practical reality. Many of the problems encountered in this field are inherently multiscale modeling. In this talk, we provide an overview of the role of TMS in nanoscience, as well as an overview of our multiscale TMS research in nanotribology, molecular electronics, and hybrid organic-inorganic nanocomposites.