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 commentarXiv admin note: text overlap with arXiv:2109.02260

References in corpus (46)

• Novel type of phase transition in a system of self-driven particles
• Self-motile colloidal particles: from directed propulsion to random walk
• Testing Mode-Coupling Theory for a Supercooled Binary Lennard-Jones Mixture I: The van Hove Correlation Function
• Glassy dynamics of kinetically constrained models
• Scaling behavior in the $\beta$-relaxation regime of a supercooled Lennard-Jones mixture
• Testing Mode-Coupling Theory for a Supercooled Binary Lennard-Jones Mixture II: Intermediate Scattering Function and Dynamic Susceptibility
• The 2019 Motile Active Matter Roadmap
• Computational models for active matter
• Pressure and Phase Equilibria in Interacting Active Brownian Spheres
• Life around the scallop theorem
• How does the relaxation of a supercooled liquid depend on its microscopic dynamics?
• Generalized Thermodynamics of Phase Equilibria in Scalar Active Matter
• Excitations are localized and relaxation is hierarchical in glass-forming liquids
• Fundamental differences between glassy dynamics in two and three dimensions
• Tuning the random walk of active colloids
• No many-scallop theorem: Collective locomotion of reciprocal swimmers
• Autonomous engines driven by active matter: Energetics and design principles
• Active glasses
• Swimming at Low Reynolds Number in Fluids with Odd (Hall) Viscosity
• Enhanced diffusion by reciprocal swimming
• A direct link between active matter and sheared granular systems
• Anomalous diffusion of driven particles in supercooled liquids
• Anomalous Topological Active Matter
• Collective forces in scalar active matter
• Atomic Mechanism of Flow in Simple Liquids under Shear
• Continuous breakdown of Purcell's scallop theorem with inertia
• Pattern-induced local symmetry breaking in active matter systems
• Dynamics of Water Confined in Mesopores with Variable Surface Interaction
• Manifestations of Dynamical Facilitation in Glassy Materials
• Light mediated emergence of surface patterns in azopolymers at low temperatures
• Negative Differential Mobility and Trapping in Active Matter Systems
• Cooperative motions in a finite size model of liquid silica: an anomalous behavior
• A simple diatomic potential that prevents crystallization in supercooled liquids simulations
• How does the motion of the surrounding molecules depend on the shape of a folding molecular motor ?
• Induced cooperative motions in a medium driven at the nanoscale: Searching for an optimum excitation period
• Folding time dependence of the motions of a molecular motor diluted inside an amorphous medium
• Kinetic Monte-Carlo Algorithms for Active-Matter systems
• Passive swimming in low Reynolds number flows
• Pros and cons of swimming in a noisy environment
• Self-organization of supercooled liquids confined inside nano-porous materials
• Simulations of supercooled water under passive or active stimuli
• Enhanced diffusion in finite-size simulations of a fragile diatomic glass former
• A toy model mimicking cage effect, structural fluctuations and kinetic constraints in supercooled liquids
• Effective swimming strategies in low Reynolds number flows
• Comparison of time reversal symmetric and asymmetric nano-swimmers oriented with an electric field in soft matter
• Activation of a supercooled liquid confined in a nanopore