In our research in the area of molecular biophysics we use the methods of modern continuum mechanics and numerical analysis to develop the elastic rod model of DNA and to apply that model in the study of DNA-protein interactions. We employ exact solutions in the Kirchhoff-Clebsch theory of elastic rods to calculate the influence that small changes in geometric end conditions can have on the tertiary structure of DNA segments. One of the goals of this research is the development of an understanding the influence of bound proteins on equilibrium distributions of topoisomers.