  Geometric confinement plays an important role in the dynamics of natural and
synthetic microswimmers from bacterial cells to self-propelled particles in
high-throughput microfluidic devices. However, little is known about the
effects of geometric confinement on the emergent global patterns in such
self-propelled systems. Recent experiments on bacterial cells give conflicting
reports of cells spontaneously organizing into a spiral vortex in a thin
cylindrical droplet and cells aggregating at the inner boundary in a spherical
droplet. We investigate here, in an idealized physical model, the interplay
between geometric confinement and level of flagellar activity on the emergent
collective patterns. We show that decreasing flagellar activity induces a
hydrodynamically-triggered transition in confined microswimmers from swirling
to global circulation (vortex) to boundary aggregation and clustering. These
results highlight that the complex interplay between confinement, flagellar
activity and hydrodynamic flows in concentrated suspensions of microswimmers
could lead to a plethora of global patterns that are difficult to predict from
geometric consideration alone.
