Nanocars assembly on a surface: coarse-grained molecular dynamics study

Abstract

Using coarse-grained molecular dynamics (CGMD), the simulations of the nanostructures are performed considerably faster and with low computational costs. In the present study, a coarse-grained model is proposed for describing the surface assembly of a molecular machine called a nanotruck. In this model, we assumed that the interactions of fullerene wheels have the main role in the nanocars interactions. The analysis of the potential energy reveals three stable configurations in the interaction of two nanocars. The stable configuration of nanocars obtained from the coarse-grained model is in agreement with the results of the all-atom molecular dynamics simulations. Simulating the stable configurations at temperatures of , and, K, we examined the thermal stability and separation of nanocars. Since each stable configuration shows a specific radius of gyration, we employed this parameter to study the thermal stability of configurations at different temperatures. At K, the nanocars maintain their stable configurations, and at the temperature of K, the nanocars are able to change their relative orientations. The thermal energy supplied at K and higher temperatures is sufficient to break the cluster of two nanocars, and the molecules are separated at this temperature range. The potential energy of the interaction of two molecules finds zero value during the simulation time, which refers to the separation of nanotrucks at this temperature. In the next step, we evaluate the surface arrangement of larger clusters, including four and eight nanocars. Considering the relative orientations of each pair of neighboring nanocars, it is concluded that the stable orientations of nanocars are similar to those observed in the cluster of two nanocars. The results of the coarse-grained model on the assembly of nanocars are consistent with the conclusions of the all-atom simulations of nanocars. The proposed coarse-grained model can be employed to study the assembly of other fullerene-based nanocars.

Keywords

• molecular dynamics simulations
• coarse-graining
• nanocars
• molecular machines
• self-assembly