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NERSC Initiative for Scientific Exploration (NISE) 2009 Awards

Elasticity of Two b-DNA Models

Wai-Yim Ching, University of Missouri, Kansas City

Sonsoring NERSC Project: Theoretical Studies of the Electronic Structures and Properties of Complex Ceramic Crystals and Novel Materials (mp250), Principal Investigator: Wai-Yim Ching, University of Missouri, Kansas City

NISE Award: 900,000 Hours
Award Date: October 2009

We propose to study the elasticity of two b-DNA models. In the last year, we have constructed two b-DNA models each with periodicity in the axial direction (z-direction) of the double helix. The first model has 10 AT base pairs (A=Adenine, T= Thymine). The second one has 10 CG base pairs (C=Cytosine, G=Guanine). The periodicity in the z direction renders the model to have a twist angle of approximately 36, which is consistent with experimental observation. Each of these two b-DNA models has 20 charged PO4 groups. 20 Na ions near the PO4 groups are added to the model as counterions. The first model has a total of 660 atoms and the second one has 650 atoms. The structures of these two models were fully relaxed using VASP and their electronic structures were calculated using the first principles OLCAO method. Both of these two codes have been used on Franklin.

We intend to study the elastic properties of these two DNA models by systematically extending the models in the z direction and obtaining their total energies for each extension. It is known that the DNA can be stretched up to 90% (strain > 0.9). The bonding between the double-stranded DNA is due to the hydrogen (H) bonding between respective base pairs. Stretching the DNA in the axial direction strand breaks the H-bonds. We plan to create 10 stretched models for each of the 10-base pair models by incrementally extending them by 2% to 5% each. From the energy vs. strain relation, the elastic moduli of the two DNA models can be obtained. Results from such accurate ab initio simulations can be compared with available experimental data thereby gain valuable insights on the mechanical properties of DNA.