Selected topics on the dynamics of DNA

Several related and unrelated topics concerning the dynamics of DNA (deoxyribonucleic acid) are explored. Chapters 1 and 2 present, respectively, a qualitative and quantitative over-view of the techniques used in constructing the dynamical force constant matrix and for solving for its normal modes of vibration. Chapter 3 presents the formalism for modification of the above technique for non-equilibrium configurations when the harmonic approximation is no longer valid. The methods of the dynamical matrix formalism are then applied to a new set of neutron scattering data of DNA and the phonon spectrum and speed of sound are predicted. Chapter 5 presents a model, referred to as the subunit model which shows that in the frequency regime of about 10$\sp{10}-$10$\sp{13}$Hz a DNA base pair may be modeled as a system of 6 rigidly bound sub-structures. In chapter 6 we apply the techniques presented in chapter 3 and model the phase change of GC DNA as it passes from A conformation to B conformation. The remaining three chapters are devoted to modifications to and extensions of the Lippincott-Schroeder model of the hydrogen bond. We first extend the calculation of the associated force constant to cover non-equilibrium extensions by evaluating the full functional form of the second derivative of the potential. We then model a bent bond in three dimensions and show how to describe off-axis hydrogen configurations. Finally, a multiple hydrogen or three-center bond is modeled and predictions are made in accordance with recent experimental evidence of such a bond