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Systems of active particles are often affected by confinement due to nearby boundaries. Recently, there has been interest in the effect of confinement by complex three dimensional geometries, as might occur in structured environments such as porous media, foams, gels, or biological tissues and ducts. The effects of confinement for particles moving along boundaries has been extensively studied, but in three dimensions active particles move not only parallel to boundaries, but also towards or away from boundaries. The consequences of this fore-aft clearance is less well understood. Swimmers that actively remodel their environment create an ideal situation to study the effect of clearance, since they maintain a steady clearance while translating. By numerically studying the locomotion of the bacterium Helicobacter pylori, which de-gels surrounding gastric mucus to make a co-moving pocket of fluid around itself, we show that the effect of three-dimensional confinement is controlled by clearance, rather than distance from a parallel boundary. Analytical calculations show that the effect of clearance can be understood in terms of flow structures, such as the generic pusher and puller flows of active particles, indicating that our results should apply to a wide range of confined active particles. |
