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Research Papers

A Hybrid Atomistic Approach for the Mechanics of Deoxyribonucleic Acid Molecules

[+] Author and Article Information
S. Adhikari, M. I. Friswell

College of Engineering,
Swansea University,
Singleton Park,
Swansea SA2 8PP, UK

E. I. Saavedra Flores

Departamento de Ingeniería en Obras Civiles,
Universidad de Santiago de Chile,
Avenue Ecuador 3659,
Santiago, Chile

F. Scarpa

Bristol Centre for Nanoscience and
Quantum Information (NSQI),
Tyndall Avenue,
Bristol BS8 1FD, UK

R. Chowdhury

Department of Civil Engineering,
Indian Institute of Technology Roorkee,
Roorkee 247 667, India

Manuscript received April 10, 2014; final manuscript received May 9, 2014; published online June 10, 2014. Assoc. Editor: Abraham Wang.

J. Nanotechnol. Eng. Med 4(4), 041003 (Jun 10, 2014) (7 pages) Paper No: NANO-14-1033; doi: 10.1115/1.4027690 History: Received April 10, 2014; Revised May 09, 2014

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 13-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.

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Figures

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Fig. 2

The three primary deformations mechanisms of the atomic bonds

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Fig. 1

The original DNA molecule from the pdb file and the converted finite element model. The nodes on the left with darker marks represent the atoms of the DNA strand which are fixed.

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Fig. 3

The distribution of thickness versus length of equivalent beams representing different chemical groups within the DNA molecule

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Fig. 4

The variation of Young's modulus versus thickness of equivalent beams representing different chemical groups within the DNA molecule

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Fig. 5

Comparison between the first 15 natural frequencies obtained from the MM model and the present FE approach

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Fig. 6

The first four mode shapes for the DNA obtained from our FE model, with their corresponding natural frequencies. One side of the molecule is clamped and another side is free.

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