With ongoing progress in nanofabrication techniques, the technology for isolating, studying, and manipulating single biological molecules is developing at a prodigious rate. Correspondingly, new opportunities to study the behavior of individual biological molecules within a well defined system are emerging. Further, through a combination of applying external forces and harnessing the entropic forces intrinsic to these systems, methods for manipulating the molecules into specific confirmations or behavior lead to a host of applications involving identification, separation, and imaging. In this talk, I will discuss the research directions that I propose to establish at Oregon State University to explore both the fundamentals underlying the dynamics in these systems and the use of this knowledge for applications such as improved device design. In discussing specific projects, the research is roughly broken into two aspects: nanofluidic devices and nanoparticles. Nanofluidic systems of key interest such as nanopores, nanopits, and nanowells will be discussed by outlining the motivation for study and the road-map to achieve results. Following this, the evolution of an ongoing research project studying applications of nanoparticles will also be presented.