We present theoretical study of carbon nanotubes as novel transport channels for electrons and molecules using atomistic simulation. For electronic transport, we present self-consistent tight-binding study of the electronic and transport properties of semiconducting carbon nanotubes in contact with metal electrodes at different contact geometries. We analyze the Schottky barrier effect at the metal-nanotube interface by examining the electrostatics, the band line up and the conductance of the metal-nanotube wire-metal junction as a function of the nanotube channel length. For molecular transport, we analyze the dynamics of rigid and semi-flexible molecules spontaneously inserted into the nanotubes as engineered flow channels in aqueous environment. We show that in the absence of water solvation, the van der Waals interaction between the molecule and the nanotube wall can induce a rapid spontaneous encapsulation of the molecule inside the nanotube channel. The encapsulation process is strongly impeded for nanotube dissolved in water due to the competition between the van der Waals, hydrophobic and hydrogen bonding interactions in the nanotube/water/molecule complex.