Molecular motors are nature’s nanomachines, and are the essential agents of movement that are an integral part of many living organisms. The supramolecular machine, called the nuclear pore complex (NPC), controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in all biological cells. In the presence of appropriate chemical stimuli, the NPC opens or closes, like a gating mechanism, and permits the flow of material into and out of the nucleus. As a first step in understanding the design characteristics of the NPC, nanoscale studies were conducted to understand the transport characteristics of an idealized NPC model using CFD analysis, discrete element transport and coupled fluid-solid analysis. Results of pressure and velocity profiles obtained from the models indicate that the fluid density, flexibility of walls and the geometry of the flow passage are important in the design of NPC based nano- and micro-motors.