The spontaneous collective motion of self-propelled agents is ubiquitous in the natural world, and it often occurs in complex environments, be it bacteria and cells migrating through polymeric extracellular matrix or animal herds and human crowds navigating structured terrains. Much is known about flocking dynamics in pristine backgrounds, but how do spatio-temporal heterogeneities in the environment impact such collective self-organization? I will present two model systems, a colloidal active fluid negotiating disordered obstacles and a confined dense bacterial suspension in a viscoelastic medium, as controllable platforms to explore this question and highlight general mechanisms for active self-organization in complex environments. By combining theory and experiment, I will show how flocks on disordered substrates organize into a novel dynamic vortex glass phase, akin to vortex glasses in dirty superconductors, while the presence of viscoelasticity can calm the otherwise turbulent swarming of bacteria, allowing the emergence of a large scale coherent and even oscillatory vortex when confined on the millimetre scale.

Active matter systems are composed of constituents, each one in nonequilibrium, that consume energy in order to move [1]. A characteristic feature of active matter is collective motion leading to nonequilibrium phase transitions or large scale directed motion [2]. A number of recent works have featured active particles interacting with obstacles, either moving or fixed [3,4,5]. When an active particle encounters an asymmetric obstacle, different behaviours are detected depending on the nature of its active motion. On the one side, rectification effects arise in a suspension of run-and-tumble particles interacting with a wall of funnelled-shaped openings, caused by particles persistence length [6]. The same trapping mechanism could be responsible for the intake of microorganisms in the underground leaves [7] of Carnivorous plants [8]. On the other side, for aligning particles [9] interacting with a wall of funnelled-shaped openings, trapping happens on the (opposite) wider opening side of the funnels [10,11]. Interestingly, when funnels are located on a circular array, trapping is more localised and depends on the nature of the Vicsek model. Active particles can be synthetic (such as synthetic active colloids) or alive (such as living bacteria). A prototypical model to study living microswimmers is P. fluorescens, a rod shaped and biofilm forming bacterium. Biofilms are microbial communities self-assembled onto external interfaces. Biofilms can be described within the Soft Matter physics framework [12] as a viscoelastic material consisting of colloids (bacterial cells) embedded in a cross-linked polymer gel (polysaccharides cross-linked via proteins/multivalent cations), whose water content vary depending on the environmental conditions. Bacteria embedded in the polymeric matrix control biofilm structure and mechanical properties by regulating its matrix composition. We have recently monitored structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress [13,14]. We have demonstrated that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions. REFERENCES [1] C. Bechinger et al. Rev. Mod. Phys. 88, 045006 (2016); [2] T. Vicsek, A. Zafeiris Phys. Rep. 517, 71 (2012); [3] C. Bechinger, R. Di Leonardo, H. Lowen, C. Reichhardt, G. Volpe, and G. Volpe, Reviews of Modern Physics 88, 045006 (2016); [4] R Martinez, F Alarcon, DR Rodriguez, JL Aragones, C Valeriani The European Physical Journal E 41, 1 (2018); [5] DR Rodriguez, F Alarcon, R Martinez, J Ramírez, C Valeriani, Soft matter 16 (5), 1162 (2020); [6] C. O. Reichhardt and C. Reichhardt, Annual Review of Condensed Matter
Physics 8, 51 (2017); [7] W Barthlott, S Porembski, E Fischer, B Gemmel Nature 392, 447 (1998); [8] C B. Giuliano, R Zhang, R.Martinez Fernandez, C.Valeriani and L.Wilson (in preparation, 2021); [9] R Martinez, F Alarcon, JL Aragones, C Valeriani Soft matter 16 (20), 4739 (2020); [10] P. Galajada, J. Keymer, P. Chaikin and R.Austin, Journal of bacteriology, 189, 8704 (2007); [11] M. Wan, C.O. Reichhardt, Z. Nussinov, and C. Reichhardt, Physical Review Letters 101, 018102 (2008); [12] J N. Wilking , T E. Angelini , A Seminara , M P. Brenner , and D A. Weitz MRS Bulletin 36, 385 (2011); [13]J Jara, F Alarcón, A K Monnappa, J Ignacio Santos, V Bianco, P Nie, M Pica Ciamarra, A Canales, L Dinis, I López-Montero, C Valeriani, B Orgaz, Frontiers in microbiology 11, 3460 (2021); [14] P Nie, F Alarcon, I López-Montero, B Orgaz, C Valeriani, M Pica Ciamarra

Many microorganisms and cells function in complex (non-Newtonian) fluids, which are mixtures of different materials and exhibit both viscous and elastic stresses. For example, mammalian sperm swim through cervical mucus on their journey through the female reproductive tract, and they must penetrate the viscoelastic gel outside the ovum to fertilize. In micro-scale swimming the dynamics emerge from the coupled interactions between the complex rheology of the surrounding media and the passive and active body dynamics of the swimmer. We use computational models of swimmers in viscoelastic fluids to investigate and provide mechanistic explanations for emergent swimming behaviors. I will discuss how flexible filaments (such as flagella) can store energy from a viscoelastic fluid to gain stroke boosts due to fluid elasticity. I will also describe 3D simulations of model organisms such as C. Reinhardtii and mammalian sperm, where we use experimentally measured stroke data to separate naturally coupled stroke and fluid effects. We explore why strokes that are adapted to Newtonian fluid environments might not do well in viscoelastic environments.