A Hybrid Atomistic Approach for the Mechanics of Deoxyribonucleic Acid Molecules

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 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.

Boundary condition-selective length dependence of the flexural rigidity of microtubules

“…[49]. This UFF has been used for various nanoscale materials including deoxyribonucleic acid [51], ( ) tubulin monomer [52], carbon nanotube [53] and graphene sheet [54].…”

Buckling of hybrid nanocomposites with embedded graphene and carbon nanotubes

“…Similar to that of C-C bonds, the mechanical properties of other bonds in the inter-linker can also be obtained by universal force field (UFF) [2,39]. These mechanical properties are presented in Table 3.…”

Piezoelectric effects in boron nitride nanotubes predicted by the atomistic finite element method and molecular mechanics

“…authors [9][10][11][12]. The method has even been applied to deoxyribonucleic acid as a way to study the mechanics of DNA [13]. The method is based on the concept of taking energy equivalence between the strain energy of deformed beams and the deformation energy of molecular bonds as given by MM potential models.…”