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. A motility model accounting for a large behavioral variability in run-time duration reproduces all experimental findings and gives new insights into surface trapping efficiency.

Rheology of bacterial superfluids in viscous environments.

Viscous environments are ubiquitous in nature and in engineering applications, from mucus in lungs to oil recovery strategies in the earth's subsurface - and in all these environments, bacteria also thrive. The behavior of bacteria in viscous environments has been investigated for a single bacterium, but not for active suspensions. Dense populations of pusher-type bacteria are known to create superfluidic regimes where the effective viscosity of the entire suspension is reduced through collective motion, and the main purpose of this study is to investigate how a viscous environment will affect this behavior. Using a Couette rheometer, we measure shear stress as a function of the applied shear rate to define the effective viscosity of suspensions of Escherichia coli (E. coli), while varying both the bacterial density within the suspension and the viscosity of the suspending fluid. We document the remarkable observation that E. coli decreases the effective suspension viscosity to near-zero (superfluidic regime) for all solvent viscosities tested (1-17 mPa s). Specifically, we observe that the bacterial density needed to trigger this superfluidic regime and the maximum shear rate under which this regime can be sustained both decrease with increasing solvent viscosity. We find that the resulting rheograms can be well approximated by the Carreau-Yasuda law. Using this, we propose a constitutive model as a function of the solvent viscosity and the bacterial concentration only. This model captures the onset of the superfluidic regime and offers promising avenues for the modelling of flow of bacterial suspensions in viscous environments.

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. Being designed to rely on single-particle data, our method eases applications in experimental conditions where swimmers exhibit a strong morphological diversity. We briefly discuss some of such ongoing experimental applications, specifically, in the characterization of swimming E. coli in a flow.

The influence of motility on bacterial accumulation in a microporous channel.

We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body which is propelled by a force-free mechanism. To account for the behavior of living bacteria, the model also incorporates a run-and-tumble process. The model bacteria are capable of hydrodynamically interacting with both of the channel walls and the obstacle. This enables the bacteria to get reoriented when experiencing a shear-flow. We demonstrate that this model is capable of reproducing the bacterial accumulation on the rear side of an obstacle, as has recently been experimentally observed by [G. L. Miño, et al., Adv. Microbiol., 2018, 8, 451] using E. coli bacteria. By systematically varying the external flow strength and the motility of the bacteria, we resolve the interplay between the local flow strength and the swimming characteristics that lead to the accumulation. Moreover, by changing the geometry of the channel, we also reveal the important role of the interactions between the bacteria and the confining walls for the accumulation process.

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. We confirm a theoretical prediction that such instability should be suppressed by confinement. Our results also show that a recent application of active liquid-crystal theory to such systems is untenable.

Large scale flow visualization and anemometry applied to lab-on-a-chip models of porous media.

The following is a report on an experimental technique that allows one to quantify and map the velocity field with very high resolution and simple equipment in large 2D devices. Illumination through a grid is proposed to reinforce the contrast in the images and allow one to detect seeded particles that are pixel-sized or even smaller. The velocimetry technique that we have reported is based on the auto-correlation functions of the pixel intensity, which we have shown are directly related to the magnitude of the local average velocity. The characteristic time involved in the decorrelation of the signal is proportional to the tracer size and inversely proportional to the average velocity. We have reported on a detailed discussion about the optimization of relevant involved parameters, the spatial resolution and the accuracy of the method. The technique is then applied to a model porous medium made of a random channel network. We show that it is highly efficient to determine the magnitude of the flow in each of the channels of the network, opening the door to the fundamental study of the flows of complex fluids. The latter is illustrated with a yield stress fluid, in which the flow becomes highly heterogeneous at small flow rates.

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. In the semidilute regime, for particularly active bacteria, the suspension displays a "superfluidlike" transition where the viscous resistance to shear vanishes, thus showing that, macroscopically, the activity of pusher swimmers organized by shear is able to fully overcome the dissipative effects due to viscous loss.

Autocatalytic reaction fronts inside a porous medium of glass spheres.

We analyze experimentally chemical wave propagation in the disordered flow field of a porous medium. The reaction fronts travel at a constant velocity that drastically depends on the mean flow direction and rate. The fronts may propagate either downstream and upstream but, surprisingly, they remain static over a range of flow rate values. Resulting from the competition between the chemical reaction and the disordered flow field, these frozen fronts display a particular sawtooth shape. The frozen regime is likely to be associated with front pinning in low velocity zones, the number of which varies with the ratio of the mean flow and the chemical front velocities.

Experimental study of ERT monitoring ability to measure solute dispersion.

This paper reports experimental measurements performed to test the ability of electrical resistivity tomography (ERT) imaging to provide quantitative information about transport parameters in porous media such as the dispersivity α, the mixing front velocity u, and the retardation factor R(f) associated with the sorption or trapping of the tracers in the pore structure. The flow experiments are performed in a homogeneous porous column placed between two vertical set of electrodes. Ionic and dyed tracers are injected from the bottom of the porous media over its full width. Under such condition, the mixing front is homogeneous in the transverse direction and shows an S-shape variation in the flow direction. The transport parameters are inferred from the variation of the concentration curves and are compared with data obtained from video analysis of the dyed tracer front. The variations of the transport parameters obtained from an inversion performed by the Gauss-Newton method applied on smoothness-constrained least-squares are studied in detail. While u and R(f) show a relatively small dependence on the inversion procedure, α is strongly dependent on the choice of the inversion parameters. Comparison with the video observations allows for the optimization of the parameters; these parameters are found to be robust with respect to changes in the flow condition and conductivity contrast.

Permeability of self-affine aperture fields.

We introduce a model that allows for the prediction of the permeability of self-affine rough channels (one-dimensional fracture) and two-dimensional fractures over a wide range of apertures. In the lubrication approximation, the permeability shows three different scaling regimes. For fractures with a large mean aperture or an aperture small enough to the permeability being close to disappearing, the permeability scales as the cube of the aperture when the zero level of the aperture is set to coincide with the disappearance of the permeability. Between these two regimes, there is a third regime where the scaling is due to the self-affine roughness. For rough channels, the exponent is found to be 3-1/H, where H is the Hurst exponent. For two-dimensional fractures, it is necessary to introduce an equivalent aperture b(c) to make the scaling regime apparent. b(c) is defined as the hydraulic aperture of the most restrictive barrier crossing the fracture normal to the flow direction. This regime is characterized by an exponent higher than that for the one-dimensional case: it is 2.25 for H=0.8 and 2.16 for H=0.3.

Low self-affine exponents of fractured glass ceramics surfaces.

The geometry of postmortem rough fracture surfaces of porous glass ceramics made of sintered glass beads is shown experimentally to be self-affine with an exponent zeta=0.40+/-0.04, remarkably lower than the "universal" value zeta=0.8 frequently measured for many materials. This low value of zeta is similar to that found for sandstone samples of similar microstructure and is also practically independent on the porosity phi in the range investigated (3%< or =phi< or =26%) as well as on the bead diameter d and of the crack growth velocity. In contrast, the roughness amplitude normalized by d increases linearly with phi while it is still independent, within experimental error, of d and of the crack propagation velocity. An interpretation of this variation is suggested in terms of a transition from transgranular to intergranular fracture propagation with no influence, however, on the exponent zeta.