Self-organisation of confined active matter
Active matter theory studies the collective behaviour of self-propelled organisms or objects. Although the field has made great progress in the past decade, little is known of the role played by confinement and surfaces. This thesis analyses the self-organisation of dense bacterial suspensions in three different microchambers: flattened drops, racetracks and lattices of cavities. Suspensions of swimming bacteria are well-known to spontaneously form macroscopic quasi-turbulent patterns such as jets and swirls. Confinement inside flattened drops and racetracks stabilises their motion into a spiral vortex and wavy streams, respectively. We have quantitatively measured and analysed bacterial circulation and discovered cells at the interfaces to move against the bulk. To understand this phenomenon, we developed a method able to measure simultaneously the directions of swimming and of motion. Experiments in drops reveal that cells align in a helical pattern, facing outward and against the main bulk circulation. Likewise, bacteria in racetracks share a biased orientation against the overall stream. Particle-based simulations confirm these results and identify hydrodynamic interactions as the main driving force: bacteria generate long-range fluid flows which advect the suspension in the bulk against its swimming direction, resulting in the double-circulation pattern. We have finally injected dense suspensions of bacteria into lattices of cavities. They form a single vortex in each cavity, initially spinning clockwise or counterclockwise with equal probabilities. Changing the topology of the lattice and the geometry of connections between cavities allows us to control the lattice state (random, ferromagnetic, antiferromagnetic, or unstable). Edge currents along interfaces and connections appear to determine the lattice organisation. We finally propose an Ising model to understand experimental results and estimate Hamiltonian and interactions parameters. This work opens new perspectives for the study of active matter and, we hope, will have a great impact on the field.
Active Matter, Bacillus Subtilis, Swimming Bacteria, Self-organisation, Confinement, Fluid Flows
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