A detailed characterization of the physics of novel nanopore systems has the potential to revolutionize water filtration, nanofluidics, and biomolecule detection technologies. I give my characterizations of five nanopore systems as my dissertation. First, I present my study of nanopores in polyethylene terephthalate (PET), revealing the mechanism for variance in current rectification based on cation species. Second, I demonstrate the mechanism of selective probe capture in bacterial toxin protein α-hemolysin (aHL) using dielectrophoresis. Third, I introduce the first simulation of molecular artificial water channel pillar[5]arene (PAP) and uncover the mechanics of its water transport and self-aggregation properties. Fourth, I characterize the water permeability and ion rejection of truncated human membrane protein aquaporin-1 (AQP) in simulation. Finally, I present MD simulation of truncated AQP as a voltage-gated ionic diode and as the functional element of a double-membrane ionic pump.