Transport properties of RNA nanotubes using molecular dynamics simulation

Abstract

We present novel molecular dynamics studies of transport properties of RNA nanotubes. Specifically, we determine the velocity trajectories for the phosphorous atom at the phosphate backbone of the RNA nanotube, the oxygen atom at sugar ring, and the23Na+and35Cl−ions in physiological solutions. At the constant temperature simulation it has been found that the fluctuation of the velocities is small and consistent with simulation time. We have also presented the velocity autocorrelation function for the phosphorous atom in RNA nanotubes that provides better insight into the diffusion direction of the system in physiological solution. We compare our results calculated computationally with the available experimental results.