Title: Micro-swimmer collective dynamics in Brinkman flows

Abstract: Suspensions of swimming micro-organisms are known to undergo intricate collective dynamics as a result of hydrodynamic and collision interactions. Micro-swimmers, such as bacteria and micro-algae, naturally live and have evolved in complex habitats that include impurities, obstacles and interfaces. To elucidate their dynamics in a heterogeneous environment, we consider a continuum theory where the the micro-swimmers are embedded in a Brinkman wet porous medium, which models viscous flow with an additional resistance or friction due to the presence of smaller stationary obstacles. The conservation equation for the swimmer configurations includes advection and rotation by the immersing fluid, and is coupled to the viscous Brinkman fluid flow with an active stress due to the swimmers' motion in it. Resistance alters individual swimmer locomotion and the way it disturbs the surrounding fluid, and thus it alters its hydrodynamic interactions with others and and such affects collective dynamics.The entropy analysis and the linear stability analysis of the system of equations both reveal that resistance delays and hinders the onset and development of the collective swimming instabilities, and can completely suppress it if sufficiently large. Simulations of the full nonlinear system confirm these. We contrast the results with previous theoretical studies on micro-swimmers in homogeneous viscous flow, and discuss relevant experimental realizations.