The fusion of biology and nanotechnology holds amazing promise for revolutionizing medicine and personal technology. In order to take advantage of the great feats of engineering coming out of these fields, there needs to be theories and computational tools capable of describing the interface between the pristine and ordered world of precision electronics and the hot, wet, and stochastic world of biology. The success of these technologies will depend on our abilities to design and optimize interactions of biomolecules and solid-state materials down to the atomic scale. In my research at the University of Illinois, I have used molecular dynamics (MD) as a tool to describe the atomic-scale interactions driving the function of biomolecules and their interface with solid-state devices, and I have sought to use it as a starting point to create new methods for modeling, designing, and optimizing these interactions. In my dissertation, I show the methodologies that I use in my work and the range of possibilities that they present for researchers in the field, and I present my research on the modeling of the interface between biological and synthetic materials in (1) immunosurfaces used for detection of live bacteria; (2) protein transport through a nanochannel; (3) deriving the Langmuir constant for adsorption for small, organic molecules on synthetic surfaces; (4) creating a multiscale model for transport in micro- and nanofluidic devices; (5) synthetic analogs of biological ion channels. It is my hope that the research that I have performed in my doctoral studies here at the University of Illinois at Urbana-Champaign will be a template for future research and interdisciplinary science. The work I have done here has shown the possibilities of the MD method for studying the physical interface of biological and synthetic components, and I have developed new techniques that can be used by researchers in field to further the science and engineering of bionanotechnology and nanobiotechnology.