Dynamics of A-GC homopolymer crystal with sodium ions: Green function approach
Abstract
Lattice dynamics theory has been applied to determine the vibrational modes for a single DNA molecule (deoxyribonucleic acid) with and without the counterions and the surrounding water molecules. The need to study the dynamics of DNA crystals come from several reasons. Firstly, the understanding of the dynamics of DNA molecules through experiment are mostly based upon the infra-red or Raman scattering spectrum. The spectra for the DNA molecules in solution are broadened due to the interactions between the DNA molecules with the molecules in the solution. The best experimental lines which reflect the characteristics of the DNA molecules are those for DNA crystals. This fact prompted us to study the dynamics of the DNA crystals. Secondly, the interactions between the double helices (interhelical interactions) are important in some areas of DNA dynamics. These interactions have been shown to play a major role in stabilizing the crystalline A or B conformation (1) and they are suspected to be a crucial element in conformation change of DNA molecules (2). In this thesis we use lattice dynamics to calculate the vibrational modes of a DNA crystal through use of the Green function method. It is hoped that the result of this study of the influence of the interhelical interactions on the dynamics of DNA will help us to understand more about the mechanism of the function of the DNA molecules. As a result, we concentrate on the biologically significant crystal modes with frequencies less than 100 wave numbers. The background and information is given in Chapters 1 and 2. The dynamics of an isolated DNA molecule is summarized to help to understand the dynamics of the DNA crystal that follows. In Chapter 3, the lattice dynamics of a perfect DNA molecule is studied in detail. Chapter 4 shows how the Green function method is applied to the study of a DNA crystal to reduce the dimension of the matrix to be normalized. Chapters 5 and 6 list the results and the conclusions. The DNA crystal modes are roughly sorted into two categories; i.e. interhelical and intrahelical, according to the influence of the interhelical interactions. The characteristics of the crystal modes are analyzed according to the patterns of the displacement vectors and the frequency shifts from the segment modes. Comparisons with the experimental observations are made and predictions are drawn.
Degree
Ph.D.
Advisors
Prohofsky, Purdue University.
Subject Area
Physics|Molecules|Condensation
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