In this work, our goal is to understand the major factors in self-assembly of nanostructures, and then to predict new techniques for efficiently bringing nanscale objects together in an ordered, controlled manner. We employ a combination of ab initio and classical molecular dynamics to investigate the possible self assembly of inorganic nanoparticles, including silicon nanowires and carbon nanotubes. The critical steps involve intelligent, selective chemical functionalization and the ability to calculate accurately the subtle interplay of energetic contributions, including competition with solvation effects. In some cases, high-accuracy quantum Monte Carlo simulations are performed to gauge the accuracy of the DFT energetics, and to fit classical potentials more accurately for the larger molecular dynamics runs.