  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.
