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Systems of active particles are often affected by confinement due to nearbyboundaries. Recently, there has been interest in the effect of confinement bycomplex three dimensional geometries, as might occur in structured environmentssuch as porous media, foams, gels, or biological tissues and ducts. The effectsof confinement for particles moving along boundaries has been extensivelystudied, but in three dimensions active particles move not only parallel toboundaries, but also towards or away from boundaries. The consequences of thisfore-aft clearance is less well understood. Swimmers that actively remodeltheir environment create an ideal situation to study the effect of clearance,since they maintain a steady clearance while translating. By numericallystudying the locomotion of the bacterium Helicobacter pylori, which de-gelssurrounding gastric mucus to make a co-moving pocket of fluid around itself, weshow that the effect of three-dimensional confinement is controlled byclearance, rather than distance from a parallel boundary. Analyticalcalculations show that the effect of clearance can be understood in terms offlow structures, such as the generic pusher and puller flows of activeparticles, indicating that our results should apply to a wide range of confinedactive particles.

Fore-aft clearance controls how three-dimensional confinement affects micropropulsion