Discrete-to-continuum models for biomedical applications of RNA nanotubes

Abstract

RNA macromolecular structures are very important in the currently boosting field of bionanotechnology, including a range of biomedical applications. In order to expand the applications of these RNA nanoclusters obtained from the self assembly of the ribonucleic acid (RNA) building blocks, it is critical to be able to better understand and predict their properties. Therefore, we model the RNA nanotubes of different sizes using molecular dynamics simulations and then study the mechanical properties of such nanotubes with continuum models implemented with the finite element methodology. We present details of our novel discrete-to-continuum models, and explain how the atomistic models in this field can be used to develop the continuum macroscopic models which would allow to calculate elastic properties of RNA nanotubes using the finite element method. By using the elastic constants available for nucleic acids, we demonstrate how to obtain the distribution of the displacement field due to stress along different directions of the RNA nanotube. These new results pave the road to our better understanding of RNA nanotube stability in biomedical applications.