Ab Initio Simulation of Double Strand b-DNA Molecules

Deoxyribonucleic acid or DNA is a nucleic acid molecule that is pivotal to all living organisms and biomedical science as well as nanotechnology. The properties of DNA are ultimately based on the fundamental electronic structure under interatomic interactions. However, there are still relatively few ab initio calculations of the electronic properties of DNA molecules. This talk presents some results on the electronic structure and optical properties of two models of double strand b-DNA molecules, AT10 and GC10. They were constructed using a combination of modeling tools. These models are periodic in the axial (z) direction with 10 base pairs (AT or GC) and 20 Na ions acting as counter ions to neutralize the PO4 groups in the backbone. The calculations were performed using the first-principles density functional theory based OLCAO method. The calculated optical dielectric functions show high anisotropy in the energy range above the HOMO-LUMO gap. Also to be discussed are the results of over-stretching the DNA model (AT10 model) under tensile strain. The overall goal is to apply methods in condensed matter theory to complex bimolecular systems for greater insights. The importance of interdisciplinary collaborations along this line computational research will be discussed.