A Hybrid Atomistic Approach for the Mechanics of Deoxyribonucleic Acid Molecules

S Adhikari (Swansea University), EI Saavedra Flores (Universidad de Santiago de Chile, Chile), F Scarpa (University of Bristol), R Chowdhury (Indian Institute of Technology Roorkee, India) & MI Friswell (Swansea University)

Journal of Nanotechnology in Engineering and Medicine, Vol. 4, No. 4, November 2013, paper 041006

Abstract

The paper proposes a new modeling approach for the prediction and analysis of the mechanical properties in deoxyribonucleic acid (DNA) molecules based on a hybrid atomistic-finite element continuum representation. The model takes into account of the complex geometry of the DNA strands, a structural mechanics representation of the atomic bonds existing in the molecules and the mass distribution of the atoms by using a lumped parameter model. A thirteen-base-pair DNA model is used to illustrate the proposed approach. The properties of the equivalent bond elements used to represent the DNA model have been derived. The natural frequencies, vibration mode shapes and equivalent continuum mechanical properties of the DNA strand are obtained. The results from our model compare well with a high-fidelity Molecular Mechanics simulation and existing MD and experimental data from open literature.

Paper Availability

This material has been published in the Journal of Nanotechnology in Engineering and Medicine, Vol. 4, No. 4, November 2013, paper 041006, the only definitive repository of the content that has been certified and accepted after peer review. Copyright and all rights therein are retained by ASME.


Link to paper using doi: 10.1115/1.4027690

Journal of Nanotechnology in Engineering and Medicine