Simulation of a flat folding nano-swimmer confined in a nanopore

Abstract

We use molecular dynamics simulations to investigate the displacement of a simple butterfly-like molecular motor inside nanopores of various radii filled with a viscous medium. The medium is modeled with a versatile potential that may be adjusted to represent a large number of materials. It was found previously that the motor folding not only increases its displacement but also creates elementary diffusion processes inside the medium, related to the opening angle of the motor folding. The presence of these processes changes the medium dynamics and in turn affects the motor displacement. Therefore we test the motor displacement with different activations of the medium inside the pore by varying the motor opening angles. We find that the optima of the motor displacement oscillate with pore sizes and that the optimal radii depend on the activation of the medium. These results imply that it is possible to choose the activation or opening angle that optimizes the motor displacement for a given pore size. Results also show that the activation decreases strongly the confinement hindering of the motor motion, in particular for small pores. Finally, analyzing the distribution probability of the motor position and the density of elementary motions we find that the motor is mainly located in the center of the pore. We find spikes in the density of elementary motions when the motor goes away from the center, suggesting important contributions of the motor bouncing motions on the pore walls.

arXiv admin note: text overlap with arXiv:2109.02260

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