SI Video 1: Monte Carlo simulations for individual active rods swimming in the cylindrical channels with an elliptic cross-section. The video demonstrates that active rods tend to swim upstream and concentrate at locations of high curvature.

SI Video 2: Monte Carlo simulations for individual active rods and three different flow rates. The video illustrates how the spreading of active rod density profiles depends on the background flow rates. Namely, the upstream front is flat and moves with the speed independent of the background flow rate. The downstream front is parabolic and its speed grows with the background flow rate.       

SI Video 3: Monte Carlo simulations of individual active rods accounting for wall torque are presented. In the upper half of the video, the 3D dynamics of the active rods is shown. The micro-channel is oriented horizontally, with active rods represented as red segments with a green front. In the lower half of the video, projections of the active rods onto the xy-plane are displayed. When an active rod swims along the micro-channel, it appears as a green point in the lower part of the video. Conversely, when an active rod swims across the micro-channel, it appears as a long rod segment. The video illustrates that active rods concentrate at the locations of highest curvature and then reorient to swim along the micro-channel. It also demonstrates that active rods are transported along the wall more quickly and detach from the wall more often compared to simulations that do not account for wall torque.

SI Video 4: Monte Carlo simulations of individual active rods in the 2D lake problem, without wall torque. There is no background flow or rotational diffusion. In this scenario, an active rod does not reorient, so it collides with the wall and swims along it until it reaches a point where the rod is exactly perpendicular to the wall’s curvature. An active rod is depicted as a red segment with the green front and black center.  

SI Video 5: Monte Carlo simulations of individual active rods in the 2D lake problem, with wall torque. There is a trapping region at high curvature points where all active rods eventually accumulate. This video illustrates the bifurcation phenomenon, that is, there is a threshold curvature so that the perpendicular-to-wall orientation is unstable for sub-critical curvatures and is stable for super-critical curvatures. Instability of the perpendicular-to-wall orientation implies that the active rod will swim away from the current wall location. Note the difference between this video and SI Video 4: in both videos, active rods accumulate at high curvature locations. However, in SI Video 4, active rods can, though with a small probability, end up at a low curvature location, whereas in the current video, no active rods are found away from high curvature locations.     

SI Video 6: Monte Carlo simulations of individual active rods in the 2D circular lake, with sub-critical and super-critical wall torque coefficients. An active rod is depicted as a red segment with the green front and black center. In the sub-critical case (left), active rods eventually slow down in a position perpendicular to the wall curve. In the super-critical case (right), there is a limiting angle such that the angle between an active rod and the wall converges to it, and all active rods swim along the wall, either clockwise or counter-clockwise, at the same speed.    

SI Video 7: Monte Carlo simulations for individual active rods in a rectangular micro-channel. Active rods are initiated at z=0 (note the axis z is oriented horizontally in the video) with random orientation and (x,y)-location. The video illustrates the four-lane structure of the active rod transport, that is, the active rods accumulate at corners.