Modeling of RNA nanotubes using molecular dynamics simulation.

In this study, we construct novel RNA nanoclusters, RNA nanotubes made of several nanorings up to the size of 20 nm, utilizing the molecular dynamics simulation, and study their structural properties [i.e., the root mean square deviation, the radius of gyration and the radial distribution function (RDF)] in physiological solutions that can be used for drug delivery into the human body. The patterns of energy and temperature variations of the systems are also discussed. Furthermore, we study the concentration of ions around the tube as a function of time at a particular temperature. We have found that when the temperature increases, the number of ions increases within a certain distance of the tube. We report that the number of ions within this distance around the tubes decreases in quenched runs. This indicates that some ions evaporate with decrease in temperature, as has been observed in the case of the nanoring. RDF plots also demonstrate a similar trend with temperature, as was found in the case of RNA nanorings.

Ordering of a thin lubricant film due to sliding.

A thin lubricant film confined between two substrates in moving contact is studied using Langevin molecular dynamics with the coordinate- and velocity-dependent damping coefficient. It is shown that an optimal choice of the interaction within the lubricant can lead to minimal kinetic friction as well as to low critical velocity of the stick-slip to smooth-sliding transition. The strength of this interaction should be high enough (relative to the strength of the interaction of lubricant atoms with the substrates) so that the lubricant remains in a solid state during sliding. At the same time, the strength of the interaction should not be too high, in order to allow annealing of defects in the lubricant at slips.

Locked-to-running transition in the two-dimensional underdamped driven Frenkel-Kontorova model.

We study the nonlinear dc response of a two-dimensional underdamped system of interacting atoms subject to an isotropic periodic external potential with triangular symmetry. We consider various values of the effective elastic constant of the system, two different atomic interaction potentials, and different concentrations of atoms. In the case of a closely packed layer, when its structure is commensurate with the substrate, there is a locked-to-running transition as a function of the driving force, whose mechanism depends on the effective elastic constant. For a low elastic constant, where the layer is weakly coupled, the transition is achieved via the creation of an avalanche of moving particles that leaves a depleted region in its wake. On increasing the effective elastic constant the depleted region becomes less marked and there is a crossover to a scenario in which an island of moving particles nucleates the transition. In the case of a partially filled atomic layer, several dynamical phase transitions between states with different atomic mobility are observed. The mobility of atoms as a function of the external force can vary nonmonotonically with increasing force. For the case of a small external damping, the system can be trapped at a large force in an immobile metastable state, thus demonstrating a "fuse-safety device" on an atomic scale.