| In this thesis, we design novel types of molecular nanosystems, and use non-equilibrium molecular dynamics simulations to study their properties. The nanosystems are mostly based on carbon structures, such as carbon nanotubes, nanocones, graphene and fullerenes. They are also doped by various atoms and chemically modified. Once the structures are designed, we calculate their electronic parameters (geometries, charges, etc.) ab initio by Gaussian03, and use them as input data in our molecular dynamics simulations realized with the NAMD code. We model these systems in gas and liquid phases, at different conditions (ensembles, boundaries and damping), and drive them out of equilibrium by external forces, electrical fields, pressure gradients, etc. We investigate the ability of these nanosystems to recognize and selectively bind molecules, control activities of catalysts attached to them, selectively pass ions and control their flow, pump molecules by mechanical means, drag molecules and ions adsorbed on their surfaces, rotate when driven by electron tunneling, etc. The model systems allow us also to test new physical and chemical phenomena and laws at the nanoscale. The characteristics and principles of these models can be applied in experimental construction of real future nanosystems. |
