Abstract
This project has investigated the major forces responsible for the folding of DNA or RNA polypeptide chains, in order to form the stable geometrical structure of the double helix and to find out the potential curvature in the 3-Dimensional (3D) structure of DNA, where the sequence is poly-A, poly-C, i.e. poly-single or double nucleotide. Two different algorithms have been developed. Each algorithm implements the Monte Carlo annealing method and has been used to model and minimize linear, single and double stranded B-DNA sequences. The force field used is composed of a limited number of bonded and non-bonded interactions. A variety of DNA sequences and sizes was investigated containing coding and non-coding, random and real, homogeneous or heterogeneous sequences in the range 2 to 40 base pairs. During the work different graphical display methods and algorithms for large macromolecules were investigated by using in most cases the OpenGL graphics library. The advantages and disadvantages of different programming language and graphical systems for molecular visualization have been studied. Software has been developed using OpenGL, VCL and Win32 programming interfaces to allow visualization of macromolecules such as DNA in mono and stereo using both Red/Green and VR glasses.