Recovering the activity parameters of an active fluid confined in a sphere.

The properties of an active fluid, for example, a bacterial bath or a collection of microtubules and molecular motors, can be accessed through the dynamics of passive particle probes. Here, in the perspective of analyzing experimental situations of confinement in droplets, we consider the kinematics of a negatively buoyant probe particle in an active fluid, both confined within a spherical domain. The active bath generates a fluctuating flow that pushes the particle with a velocity that is modeled as a colored stochastic noise, characterized by two parameters, the intensity and memory time of the active flow.

Frustrated 'run and tumble' of swimming bacteria in nematic liquid crystals.

In many situations, bacteria move in complex environments, as soils, oceans or the human gut-track, where carrier fluids show complex structures associated with non-Newtonian rheology. Many fundamental questions concerning the ability to navigate in such environments remain unsolved. Recently, it has been shown that the kinetics of bacterial motion in structured fluids as liquid crystals (LCs) is constrained by the orientational molecular order (or director field) and that novel spatio-temporal patterns arise.

Run-to-Tumble Variability Controls the Surface Residence Times of E. coli Bacteria.

Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and biofilm formation. We use a novel two-color, three-dimensional Lagrangian tracking technique to follow simultaneously the body and the flagella of a wild-type Escherichia coli. We observe long surface residence times and surface escape corresponding mostly to immediately antecedent tumbling.

Single-trajectory characterization of active swimmers in a flow.

We develop a maximum likelihood method to infer relevant physical properties of elongated active particles. Using individual trajectories of advected swimmers as input, we are able to accurately determine their rotational diffusion coefficients and an effective measure of their aspect ratio, also providing reliable estimators for the uncertainties of such quantities. We validate our theoretical construction using numerically generated active trajectories upon no flow, simple shear, and Poiseuille flow, with excellent results.

Chirality-induced bacterial rheotaxis in bulk shear flows.

Interaction of swimming bacteria with flows controls their ability to explore complex environments, crucial to many societal and environmental challenges and relevant for microfluidic applications such as cell sorting. Combining experimental, numerical, and theoretical analysis, we present a comprehensive study of the transport of motile bacteria in shear flows. Experimentally, we obtain with high accuracy and, for a large range of flow rates, the spatially resolved velocity and orientation distributions.

"super-contaminates" narrow ducts fostered by broad run-time distribution.

One notable feature of bacterial motion is their ability to swim upstream along corners and crevices, by leveraging hydrodynamic interactions. This motion through anatomic ducts or medical devices might be at the origin of serious infections. However, it remains unclear how bacteria can maintain persistent upstream motion while exhibiting run-and-tumble dynamics.

A combined rheometry and imaging study of viscosity reduction in bacterial suspensions.

Suspending self-propelled "pushers" in a liquid lowers its viscosity. We study how this phenomenon depends on system size in bacterial suspensions using bulk rheometry and particle-tracking rheoimaging. Above the critical bacterial volume fraction needed to decrease the viscosity to zero, [Formula: see text], large-scale collective motion emerges in the quiescent state, and the flow becomes nonlinear.

Magnetotactic bacteria in a droplet self-assemble into a rotary motor.

From intracellular protein trafficking to large-scale motion of animal groups, the physical concepts driving the self-organization of living systems are still largely unraveled. Self-organization of active entities, leading to novel phases and emergent macroscopic properties, recently shed new light on these complex dynamical processes. Here we show that under the application of a constant magnetic field, motile magnetotactic bacteria confined in water-in-oil droplets self-assemble into a rotary motor exerting a torque on the external oil phase.

Oscillatory surface rheotaxis of swimming E. coli bacteria.

Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E.

Non-local rheology in dense granular flows: Revisiting the concept of fluidity.

The aim of this article is to discuss the concepts of non-local rheology and fluidity, recently introduced to describe dense granular flows. We review and compare various approaches based on different constitutive relations and choices for the fluidity parameter, focusing on the kinetic elasto-plastic model introduced by Bocquet et al. (Phys.

Mechanical fluctuations suppress the threshold of soft-glassy solids: The secular drift scenario.

We propose a dynamical mechanism leading to the fluidization by external mechanical fluctuations of soft-glassy amorphous material driven below the yield stress. The model is based on the combination of memory effect and nonlinearity, leading to an accumulation of tiny effects over a long term. We test this scenario on a granular packing driven mechanically below the Coulomb threshold.

Turning Bacteria Suspensions into Superfluids.

The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidence for a low-shear Newtonian plateau characterized by a shear viscosity decreasing with concentration.

Living on the edge: transfer and traffic of E. coli in a confined flow.

We quantitatively study the transport of E. coli near the walls of confined microfluidic channels, and in more detail along the edges formed by the interception of two perpendicular walls. Our experiments establish the connection between bacterial motion at the flat surface and at the edges and demonstrate the robustness of the upstream motion at the edges.

Clogging transition of many-particle systems flowing through bottlenecks.

When a large set of discrete bodies passes through a bottleneck, the flow may become intermittent due to the development of clogs that obstruct the constriction. Clogging is observed, for instance, in colloidal suspensions, granular materials and crowd swarming, where consequences may be dramatic. Despite its ubiquity, a general framework embracing research in such a wide variety of scenarios is still lacking.

Nonlocal rheology of granular flows across yield conditions.

The rheology of dense granular flows is studied numerically in a shear cell controlled at constant pressure and shear stress, confined between two granular shear flows. We show that a liquid state can be achieved even far below the yield stress, whose flow can be described with the same rheology as above the yield stress. A nonlocal constitutive relation is derived from dimensional analysis through a gradient expansion and calibrated using the spatial relaxation of velocity profiles observed under homogeneous stresses.

Non-Newtonian viscosity of Escherichia coli suspensions.

The viscosity of an active suspension of E. coli bacteria is determined experimentally as a function of the shear rate using a Y-shaped microfluidic channel. From the relative suspension viscosity, we identify rheological thickening and thinning regimes as well as situations at low shear rate where the viscosity of the bacteria suspension can be lower than the viscosity of the suspending fluid.

Hot spots in an athermal system.

We study experimentally the dynamical heterogeneities occurring at slow shear, in a model amorphous glassy material, i.e., a 3D granular packing.

Creep and fluidity of a real granular packing near jamming.

We study the internal dynamical processes taking place in a granular packing below yield stress. At all packing fractions and down to vanishingly low applied shear, a logarithmic creep is observed. The experiments are analyzed using a viscoelastic model which introduces an internal, time-dependent, fluidity variable.

Enhanced diffusion due to active swimmers at a solid surface.

We consider two systems of active swimmers moving close to a solid surface, one being a living population of wild-type E. coli and the other being an assembly of self-propelled Au-Pt rods. In both situations, we have identified two different types of motion at the surface and evaluated the fraction of the population that displayed ballistic trajectories (active swimmers) with respect to those showing randomlike behavior.

Mesoscopic length scale controls the rheology of dense suspensions.

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height.

Nonlocal rheological properties of granular flows near a jamming limit.

We study the rheology of sheared granular flows close to a jamming transition. We use the approach of partially fluidized theory (PFT) with a full set of equations extending the thin layer approximation derived previously for the description of the granular avalanches phenomenology. This theory provides a picture compatible with a local rheology at large shear rates [G.

Spreading of a granular droplet.

The influence of controlled vibrations on the granular rheology is investigated in a specifically designed experiment in which a granular film spreads under the action of horizontal vibrations. A nonlinear diffusion equation is derived theoretically that describes the evolution of the deposit shape. A self-similar parabolic shape (the "granular droplet") and a spreading dynamics are predicted that both agree quantitatively with the experimental results.

Transverse instability of avalanches in granular flows down an incline.

Avalanche experiments on an erodible substrate are analyzed using the "partial fluidization" model of dense granular flows. The model identifies a family of propagating solitonlike avalanches with shape and velocity controlled by the inclination angle and the depth of the substrate. At high inclination angles, the solitons display a transverse instability, followed by coarsening and fingering similar to recent experimental observation.

Erosion patterns in a sediment layer.

We report here on a laboratory-scale experiment which reproduces a rich variety of natural patterns with few control parameters. In particular, we focus on intriguing rhomboid structures often found on sandy shores and flats. We show that the standard views based on water surface waves do not explain the phenomenon, and we evidence a different mechanism based on mud avalanche instability.

Reorganization of a dense granular assembly: the unjamming response function.

We investigate the mechanical properties of a static dense granular assembly in response to a local forcing. To this end, a small cyclic displacement is applied on a grain in the bulk of a two-dimensional disordered packing under gravity and the displacement fields are monitored. We evidence a dominant long range radial response in the upper half part above the solicitation and after a large number of cycles the response is "quasireversible" with a remanent dissipation field exhibiting long range streams and vortexlike symmetry.