Numerical Modeling of Anisotropic Particle Diffusion through a Cylindrical Channel

Abstract

The transport of molecules and particles through single pores is the basis of biological processes, including DNA and protein sequencing. As individual objects pass through a pore, they cause a transient change in the current that can be correlated with the object size, surface charge, and even chemical properties. The majority of experiments and modeling have been performed with spherical objects, while much less is known about the transport characteristics of aspherical particles, which would act as a model system, for example, for proteins and bacteria. The transport kinetics of aspherical objects is an especially important, yet understudied, problem in nanopore analytics. Here, using the Wiener process, we present a simplified model of the diffusion of rod-shaped particles through a cylindrical pore, and apply it to understand the translation and rotation of the particles as they pass through the pore. Specifically, we analyze the influence of the particles’ geometrical characteristics on the effective diffusion type, the first passage time distribution, and the particles’ orientation in the pore. Our model shows that thicker particles pass through the channel slower than thinner ones, while their lengths do not affect the passage time. We also demonstrate that both spherical and rod-shaped particles undergo normal diffusion, and the first passage time distribution follows an exponential asymptotics. The model provides guidance on how the shape of the particle can be modified to achieve an optimal passage time.

Keywords

• overdamped diffusion
• channels and pores
• first passage time
• artificial pore
• numerical modeling
• stochastic dynamics