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. In addition, bacteria concentration and velocity profiles in the bulk are directly measured in the microchannel.

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. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments.

We study pattern formation during tensile deformation of confined viscoelastic layers. The use of a model system [poly(dimethylsiloxane) with different degrees of cross-linking] allows us to go continuously from a viscous liquid to an elastic solid. We observe two distinct regimes of fingering instabilities: a regime called “elastic” with interfacial crack propagation, where the fingering wavelength scales only with the film thickness, and a bulk regime called “viscoelastic,” where the fingering instability shows a Saffman-Taylor-like behavior. We find good quantitative agreement with theory in both cases and present a reduced parameter describing the transition between the two regimes and allowing us to predict the observed patterns over the whole range of viscoelastic properties.

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. Upstream migration of E. coli at the edges is possible at much larger flow rates compared to motion at the flat surfaces. Interestingly, the speed of bacteria at the edges mainly results from collisions between bacteria moving along this single line. We show that upstream motion not only takes place at the edge but also in an “edge boundary layer” whose size varies with the applied flow rate. We quantify the bacterial fluxes along the bottom walls and the edges and show that they result from both the transport velocity of bacteria and the decrease of surface concentration with increasing flow rate due to erosion processes. We rationalize our findings as a function of local variations in the shear rate in the rectangular channels and hydrodynamic attractive forces between bacteria and walls.

Significance: Elastic filaments and semiflexible polymers occur ubiquitously in biophysical systems and are key components of many complex fluids, yet our understanding of their conformational dynamics under flow is incomplete. Here, we report on experimental observations of actin filaments in simple shear and characterize their various dynamical regimes from tumbling to buckling and snaking. Numerical simulations accounting for elastohydrodynamics as well as Brownian fluctuations show perfect agreement with measurements. Using a reduced-order theoretical model, we elucidate the unexplained mechanism for the transition to snaking. Our results pave the way for a better understanding of biophysical processes, as well as the rheology of sheared soft materials, and provide a theoretical framework for the exploration of the dynamics of dilute and semidilute suspensions.

A combined experimental, numerical and theoretical investigation of the geometric scaling of the onset of a purely elastic flow instability in serpentine channels is presented. Good qualitative agreement is obtained between experiments, using dilute solutions of flexible polymers in microfluidic devices, and three-dimensional numerical simulations using the upper-convected Maxwell model. The results are confirmed by a simple theoretical analysis, based on the dimensionless criterion proposed by Pakdel & McKinley (Phys. Rev. Lett., vol. 77, 1996, pp. 2459–2462) for onset of a purely elastic flow instability. Three-dimensional simulations show that the instability is primarily driven by the curvature of the streamlines induced by the flow geometry and not due to the weak secondary flow in the azimuthal direction. In addition, the simulations also reveal that the instability is time-dependent and that the flow oscillates with a well-defined period and amplitude close to the onset of the supercritical instability.