Coarse-Grained Models of RNA Nanotubes for Large Time Scale Studies in Biomedical Applications.

In order to describe the physical properties of large time scale biological systems, coarse-grained models play an increasingly important role. In this paper we develop Coarse-Grained (CG) models for RNA nanotubes and then, by using Molecular Dynamics (MD) simulation, we study their physical properties. Our exemplifications include RNA nanotubes of 40 nm long, equivalent to 10 RNA nanorings connected in series. The developed methodology is based on a coarse-grained representation of RNA nanotubes, where each coarse bead represents a group of atoms. By decreasing computation cost, this allows us to make computations feasible for realistic structures of interest. In particular, for the developed coarse-grained models with three bead approximations, we calculate the histograms for the bond angles and the dihedral angles. From the dihedral angle histograms, we analyze the characteristics of the links used to build the nanotubes. Furthermore, we also calculate the bead distances along the chains of RNA strands in the nanoclusters. The variations in these features with the size of the nanotube are discussed in detail. Finally, we present the results on the calculation of the root mean square deviations for a developed RNA nanotube to demonstrate the equilibration of the systems for drug delivery and other biomedical applications such as medical imaging and tissue engineering.

Atomistic to continuum model for studying mechanical properties of RNA nanotubes.

With rapid advancements in the emerging field of RNA nanotechnology, its current and potential applications, new important problems arise in our quest to better understand properties of RNA nanocomplexes. In this paper, our focus is on the modeling of RNA nanotubes which are important for many biological processes. These RNA complexes are also important for human beings, with their theurapeutical and biomedical applications discussed vigorously in the literature over the recent years. Here, we develop a continuum model of RNA nanotubes, originally obtained from self assembly of RNA building blocks in the molecular dynamics simulation. Based on the finite element method, we calculate the elastic properties of these nanostructures and provide a relationship between stress and strain induced in the RNA nanotube. We also analyze the variations in the displacement vector along the assembly axis for RNA nanotubes of different sizes. In particular, we show that oscillations in the amplitudes of strains and displacements significantly differ for such RNA nanotubes. These findings are discussed in the context of atomistic simulations and experimental results in this field.

Wettability alteration of calcite oil wells: Influence of smart water ions.

Further enhancement of crude oil recovery in the enhanced recovery stage from calcite oil wells is a major global challenge for oil industry. Experimental results suggest that ions present in sea water, also called smart water, have a significant influence on the wettability alteration (less oil wet) of calcite surface. In this paper, by utilizing Density Functional Theory (DFT) and Quantum Molecular Dynamics (QMD) simulations, we investigate the effect of additive ions of sea water in oil recovery by using acetic acid as a model compound of crude oil molecules. We find that Na+ ions precipitate to the calcite surface and form Na acetate. The binding energy of Na acetate is larger than original oil molecule (acetic acid), which reduces oil recovery. On the other hand, Mg2+ and [Formula: see text] ions can also reach to the calcite surface in proximity and modify the calcite surface. The binding energy of oil molecule on modified calcite surface is smaller than on pure calcite surface, which enhances oil recovery. Our results might help in understanding interaction among oil, water and additives ions of smart water for further experimental investigations.

Relaxation of electron-hole spins in strained graphene nanoribbons.

We investigate the influence of magnetic field originating from the electromechanical effect on the spin-flip behaviors caused by electromagnetic field radiation in the strained graphene nanoribbons (GNRs). We show that the spin splitting energy difference (≈10 meV) due to pseudospin is much larger than the spin-orbit coupling effect (Balakrishnan et al 2013 Nat. Phys. 9 284) that might provide an evidence of broken symmetry of degeneracy. The induced spin splitting energy due to ripple waves can be further enhanced with increasing values of applied tensile edge stress for potential applications in straintronic devices. In particular, we show that the enhancement in the magnitude of the ripple waves due to externally applied tensile edge stress extends the tuning of spin-flip behaviors to larger widths of GNRs.