We study the collective dynamics of elongated swimmers in a very thin fluid layer by devising long, filamentous, non-tumbling bacteria. The strong confinement induces weak nematic alignment upon collision, which, for large enough density of cells, gives rise to global nematic order. This homogeneous but fluctuating phase, observed on the largest experimentally-accessible scale of millimeters, exhibits the properties predicted by standard models for flocking such as the Vicsek-style model of polar particles with nematic alignment: true long-range nematic order and non-trivial giant number fluctuations.PACS numbers: 47.63. Gd, 05.65.+b 87.18.Gh 87.18.Hf Collective motion of self-propelled elements, as seen in bird flocks, fish schools, bacterial swarms, etc., is so ubiquitous that it has driven physicists to search for its possibly universal properties [1][2][3]. If generic and robust features of such active matter systems exist, they should also be present in the emergent phenomena observed in simple models. Evidence for such universality has been provided by many theoretical and numerical studies of dry active matter systems where local alignment competes with noise, following the seminal works by Vicsek et al.[4], Toner, Tu , and Ramaswamy et al. [5][6][7][8][9]. It was notably understood that the transition to orientational order/collective motion, in this context, is best described as a phase-separation between a disordered gas and an ordered 'liquid' separated by a coexistence phase whose nature depends on the symmetries of the system [3,[10][11][12][13][14][15][16]. The homogeneous but highly fluctuating liquid phase is characterized by unique properties often different from those of equilibrium orientationally-ordered phases. In particular, the crucial coupling between the order and the density fields generates anomalously-large number fluctuations from the algebraic correlations of orientation and density [5][6][7][8][9].Such 'giant' number fluctuations (GNF), being relatively easy to measure experimentally, have become the landmark signature of orientationally-ordered active matter. Several experimental studies have indeed searched for GNF using controllable systems simpler than bird flocks and fish schools such as biofilaments driven by molecular motors [17], colloids consuming electric energy [18], shaken granular materials [19][20][21], monolayers of fibroblast cells [22], and common bacteria [23,24]. However, none of these experiments has been fully convincing in demonstrating the presence of bona fide GNF * nishiguchi@daisy.phys.s.u-tokyo.ac.jp as predicted from the works of Toner, Tu, Ramaswamy et al. [3, 7, 8], and observed in Vicsek-style models [10, 11, 13, 14]. These GNF have to be discussed in a fluctuating phase with global long-range orientational order and are distinct from the trivial, non-asymptotic ones present in the case of phase-separation into dense clusters sitting in a disordered sparse gas. In some experiments, only normal number fluctuations were found [17,18]. In others, GNF ...

To elucidate mechanisms of mesoscopic turbulence exhibited by active particles, we experimentally study turbulent states of nonliving self-propelled particles. We realize an experimental system with dense suspensions of asymmetrical colloidal particles (Janus particles) self-propelling on a two-dimensional surface under an ac electric field. Velocity fields of the Janus particles in the crowded situation can be regarded as a sort of turbulence because it contains many vortices and their velocities change abruptly. Correlation functions of their velocity field reveal the coexistence of polar alignment and antiparallel alignment interactions, which is considered to trigger mesoscopic turbulence. Probability distributions of local order parameters for polar and nematic orders indicate the formation of local clusters with particles moving in the same direction. A broad peak in the energy spectrum of the velocity field appears at the spatial scales where the polar alignment and the cluster formation are observed. Energy is injected at the particle scale and conserved quantities such as energy could be cascading toward the larger clusters.

A suspension of swimming bacteria is possibly the simplest realization of active matter, i.e. a class of systems transducing stored energy into mechanical motion. Collective swimming of hydrodynamically interacting bacteria resembles turbulent flow. This seemingly chaotic motion can be rectified by a geometrical confinement. Here we report on self-organization of a concentrated suspension of motile bacteria Bacillus subtilis constrained by two-dimensional (2D) periodic arrays of microscopic vertical pillars. We show that bacteria self-organize into a lattice of hydrodynamically bound vortices with a long-range antiferromagnetic order controlled by the pillars’ spacing. The patterns attain their highest stability and nearly perfect order for the pillar spacing comparable with an intrinsic vortex size of an unconstrained bacterial turbulence. We demonstrate that the emergent antiferromagnetic order can be further manipulated and turned into a ferromagnetic state by introducing chiral pillars. This strategy can be used to control a wide class of active 2D systems.

We study the active dynamics of self-propelled asymmetrical colloidal particles (Janus particles) fueled by an AC electric field. Both the speed and direction of the self-propulsion, and the strength of the attractive interaction between particles can be controlled by tuning the frequency of the applied electric field and the ion concentration of the solution. The strong attractive force at high ion concentration gives rise to chain formation of the Janus particles, which can be explained by the quadrupolar charge distribution on the particles. Chain formation is observed irrespective of the direction of the self-propulsion of the particles. When both the position and the orientation of the heads of the chains are fixed, they exhibit beating behavior reminiscent of eukaryotic flagella. The beating frequency of the chains of Janus particles depends on the applied voltage and thus on the selfpropulsive force. The scaling relation between the beating frequency and the self-propulsive force deviates from theoretical predictions made previously on active filaments. However, this discrepancy is resolved by assuming that the attractive interaction between the particles is mediated by the quadrupolar distribution of the induced charges, which gives indirect but convincing evidence on the mechanisms of the Janus particles. This signifies that the dependence between the propulsion mechanism and the interaction mechanism, which had been dismissed previously, can modify the dispersion relations of beating behaviors. In addition, hydrodynamic interaction within the chain, and its effect on propulsion speed, are discussed. These provide new insights into active filaments, such as optimal flagellar design for biological functions.

Recent experiments have shown that the complex spatio-temporal vortex structures emerging in active fluids are susceptible to weak geometrical constraints. This observation poses the fundamental question of how boundary effects stabilize a highly ordered pattern from seemingly turbulent motion. Here we show, by a combination of continuum theory and experiments on a bacterial suspension, how artificial obstacles guide the flow profile and reorganize topological defects, which enables the design of bacterial vortex lattices with tunable properties. To this end, the continuum model is extended by appropriate boundary conditions. Beyond the stabilization of square and hexagonal lattices, we also provide a striking example of a chiral, antiferromagnetic lattice exhibiting a net rotational flow, which is induced by arranging the obstacles in a Kagome-like array.

Type IV pili (TFP) are multifunctional micrometer-long filaments expressed at the surface of many prokaryotes. In Neisseria meningitidis, TFP are crucial for virulence. Indeed, these homopolymers of the major pilin PilE mediate interbacterial aggregation and adhesion to host cells. However, the mechanisms behind these functions remain unclear. Here, we simultaneously determined regions of PilE involved in pilus display, auto-aggregation, and adhesion by using deep mutational scanning and started mining this extensive functional map. For auto-aggregation, pili must reach a minimum length to allow pilus-pilus interactions through an electropositive cluster of residues centered around Lys140. For adhesion, results point to a key role for the tip of the pilus. Accordingly, purified pili interacting with host cells initially bind via their tip-located major pilin and then along their length. Overall, these results identify functional domains of PilE and support a direct role of the major pilin in TFP-dependent aggregation and adhesion.

Microswimmers exhibit more diverse behavior in quasi-two dimensions than in three dimensions. Such behavior remains elusive due to the analytical difficulty of dealing with two parallel solid boundaries. The existence of additional obstacles in quasi-two-dimensional systems further complicates the analysis. We fabricated microscopic pillars in quasi-two dimensions by etching glass coverslips and observed the interactions between swimming bacteria and the pillars. Bacteria got trapped around the circular pillars and the trapping efficiency increased as the quasi-two-dimensionality was increased or as the curvature of the pillars was decreased. Experiments with elliptic pillars demonstrated the possibility that the local curvature of the obstacle controls the trapping efficiency.

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