Johannes Kalliauer et al 2021 A new approach to the mechanics of DNA

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Title: A new approach to the mechanics of DNA

Abstract: Traditionally, DNA sequences are considered as cylindrical straight isotropic beams , but this lead to unrealistic ratios between torsional and bending stiffnesses . The deformation characteristics of long biological macromolecules, such as DNA or collagen, can be lucidly described by the terms “bending”, “stretching”, “torsion” and “shearing”. These terms appear in a subset of continuum mechanics, called beam theory, while the standard numerical modelling procedure for macromolecules, which is molecular dynamics, does not allow for a direct introduction of these deformation characteristics . This deficit has motivated the theoretical development of a transition or upscaling procedure from molecular dynamics to beam theory . It consists of two steps: (i) translation of potential energies into systems of equilibrated forces and moments; (ii) upscaling, through the principle of virtual power, the forces and moments arising from (i), to the scale where the macromolecule itself is considered as a beam structure. As a first application, the above-described novel strategy is realised for a sequence of DNA base pairs, elucidating the source of the somehow paradox stretching-torsion coupling these molecules are known for.

More Details can be found in: Johannes Kalliauer, Gerhard Kahl, Stefan Scheiner, Christian Hellmich, A new approach to the mechanics of DNA: Atoms-to-beam homogenization, Journal of the Mechanics and Physics of Solids, Volume 143, 2020, 104040, ISSN 0022-5096, https://doi.org/10.1016/j.jmps.2020.1.... (https://www.sciencedirect.com/science...)

Keywords: Linear elasticity; Beam; Energy methods; Finite differences; Flexibility; Young’s modulus; Stretching stiffness; Free energy

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