Boundary accumulation of active rods in microchannels with elliptical cross-section

Many motile microorganisms and biomimetic microparticles have been successfully modeled as active rods-elongated bodies capable of self-propulsion. A hallmark of active rod dynamics under confinement is their tendency to accumulate at the walls. Unlike passive particles, which typically sediment and cease their motion at the wall, accumulated active rods continue to move along the wall, reorient, and may even escape from it. In addition to boundary accumulation, active rods also exhibit upstream swimming and a tendency to concentrate in regions of high boundary curvature. The dynamics of active rods at the wall and those away from it result in complex and nontrivial distributions. In this work, we examine how wall curvature and extruding fluid flow affect the distribution of active rods by studying elliptical perturbations of tubelike three-dimensional microchannels, that is, cylindrical confinements with circular cross-sections that are common in both natural systems and practical applications. We develop a computational model for individual active rods and, through both analytical methods and Monte Carlo simulations, investigate how their accumulation distribution depends on the background flow, rotational diffusion, and the cross-sectional aspect ratio. Additionally, we examined the role of wall torque on accumulated active rods. While it promotes escape by aligning rods tangentially along flat walls, we showed, both theoretically and numerically, that stable entrapment can occur at regions of high curvature despite this torque.