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Many bacteria live in natural and clinical environments with abundant macromolecular polymers. Macromolecular fluids commonly display viscoelasticity and non-Newtonian rheological behavior; it is unclear how these complex-fluid properties affect bacterial transport in flows. Here we combine high-resolution microscopy and numerical simulations to study bacterial response to shear flows of various macromolecular fluids. In stark contrast to the case in Newtonian shear flows, we found that flagellated bacteria in macromolecular flows display a giant capacity of upstream swimming (a behavior resembling fish swimming against current) near solid surfaces: The cells can counteract flow washing at shear rates up to ~65 $s^{-1}$, one order of magnitude higher than the limit for cells swimming in Newtonian flows. The significant enhancement of upstream swimming depends on two characteristic complex-fluid properties, namely viscoelasticity and shear-thinning viscosity; meanwhile, increasing the viscosity with a Newtonian polymer can prevent upstream motion. By visualizing flagellar bundles and modeling bacterial swimming in complex fluids, we explain the phenomenon as primarily arising from the augmentation of a "weathervane effect" in macromolecular flows due to the presence of a viscoelastic lift force and a shear-thinning induced azimuthal torque promoting the alignment of bacteria against the flow direction. Our findings shed light on bacterial transport and surface colonization in macromolecular environments, and may inform the design of artificial helical microswimmers for biomedical applications in physiological conditions.

Bacteria often exhibit upstream swimming, which can cause the contamination of biomedical devices and the infection of organs including the urethra or lungs. This process, called rheotaxis, has been studied extensively in Newtonian fluids. However, most microorganisms thrive in non-Newtonian fluids that contain suspended polymers such as mucus and biofilms. Here, we investigate the rheotatic behavior of E. coli near walls in non-Newtonian fluids. Our experiments demonstrate that bacterial upstream swimming is enhanced by an order of magnitude in shear-thinning polymeric fluids relative to Newtonian fluids. This result is explained by direct numerical simulations, revealing a torque that promotes the alignment of bacteria against the flow. From this analysis, we develop a theoretical model that accurately describes experimental rheotatic data in both Newtonian and shear-thinning fluids.

Earth's aquatic environments are inherently stratified layered systems where interfaces between layers serve as ecological niches for microbial swimmers, forming colonies known as Active Carpet (AC). Previous theoretical studies have explored the hydrodynamic fluctuations exerted by ACs in semi-infinite fluid media, demonstrating their capability to enhance thermal diffusion and mass transport in aquatic systems. Yet, little is understood about the fluid dynamics and impact of ACs residing in confined layered environments, like slicks floating on water bodies. In this study, we report novel solutions for the hydrodynamic fluctuations induced by ACs geometrically confined between a free surface and a fluid-fluid interface characterized by a jump in fluid viscosity. Combining theory and numerical experiments, we investigate the topology of the biogenic hydrodynamic fluctuations in a confined, thin fluid environment. We reveal that within this thin layer, ACs gives shape to three characteristic regions: Region I is the closest zone to the AC and the fluid-fluid interface, where hydrodynamic fluctuations are dominantly vertical; Region II is further up from the AC and is characterized by isotropic hydrodynamic fluctuations; Region III is the furthest region, near the free surface and is dominated by horizontal flow fluctuations. We demonstrate that the extent of these regions depends strongly on the degree of confinement, i.e. the layer thickness and the strength of the viscosity jump. Lastly, we show that confinement fosters the emergence of large-scale flow structures within the layer housing the ACs--not previously reported. Our findings shed light on the complex interplay between confinement and hydrodynamics in floating viscous film biological systems, providing valuable insights with implications spanning from ecological conservation to bio-inspired engineering.

Communities of swimming microorganisms often thrive near liquid-air interfaces. We study how such `active carpets' shape their aquatic environment by driving biogenic transport in the water column beneath them. The hydrodynamic stirring that active carpets generate leads to diffusive upward fluxes of nutrients from deeper water layers, and downward fluxes of oxygen and carbon. Combining analytical theory and simulations, we examine the biogenic transport by studying fundamental metrics, including the single and pair diffusivity, the first passage time for particle pair encounters, and the rate of particle aggregation. Our findings reveal that the hydrodynamic fluctuations driven by active carpets have a region of influence that reaches orders of magnitude further in distance than the size of the organisms. These nonequilibrium fluctuations lead to a strongly enhanced diffusion of particles, which is anisotropic and space-dependent. Fluctuations also facilitate encounters of particle pairs, which we quantify by analysing their velocity pair correlation functions as a function of distance between the particles. We found that the size of the particles plays a crucial role in their encounter rates, with larger particles situated near the active carpet being more favourable for aggregation. Overall, this research broadens our comprehension of aquatic systems out of equilibrium and how biologically driven fluctuations contribute to the transport of fundamental elements in biogeochemical cycles.

Active emulsions can spontaneously form self-propelled droplets or phoretic micropumps. It has been predicted that the interaction with their self-generated chemical fields can lead to multistable higher-order flows and chemodynamic phenomena. However, it remains unclear how such reaction-advection-diffusion instabilities can emerge from the interplay between chemical reactions and interfacial hydrodynamics. Here, we simultaneously measure the flow fields and the chemical concentration fields using dual-channel microscopy for oil droplets that dynamically solubilize in a supramicellar aqueous surfactant solution. We developed an experimentally tractable setup with micropumps, droplets that are pinned between the top and bottom surfaces of a microfluidic reservoir, which we compare directly to predictions from a Brinkman squirmer model to account for the confinement. With increasing droplet radius, we observe (i) a migration of vortex flows from the posterior to the anterior of the droplet, analogous to a transition from pusher- to puller-type swimmers, (ii) a bistability between dipolar and quadrupolar flow modes, and, eventually, (iii) a transition to multipolar modes. We also investigate how the dynamics evolve over long time periods. Together, our observations suggest that a local build-up of chemical products leads to a saturation of the surface, which controls the propulsion mechanism. These multistable dynamics can be explained by the competing time scales of slow micellar diffusion governing the chemical buildup and faster molecular diffusion powering the underlying transport mechanism. Our results are directly relevant to phoretic micropumps, but also shed light on the interfacial activity dynamics of self-propelled droplets and other active emulsion systems

Innovations in fluid mechanics are leading to better food since ancient history, while creativity in cooking inspires applied and fundamental science. Here, we review how recent advances in hydrodynamics are changing food science, and we highlight how the surprising phenomena that arise in the kitchen lead to discoveries and technologies across the disciplines, including rheology, soft matter, biophysics and molecular gastronomy. This review is structured like a menu, where each course highlights different aspects of culinary fluid mechanics. Our main themes include multiphase flows, complex fluids, thermal convection, hydrodynamic instabilities, viscous flows, granular matter, porous media, percolation, chaotic advection, interfacial phenomena, and turbulence. For every topic, we first provide an introduction accessible to food professionals and scientists in neighbouring fields. We then assess the state-of-the-art knowledge, the open problems, and likely directions for future research. New gastronomic ideas grow rapidly as the scientific recipes keep improving too., Comment: Review paper, 80 pages, 30 figures, 1050 references. Comments/suggestions to improve this arXiv submission are most welcome. Please contact us, and we will try to incorporate them

One of the major challenges in modern robotics is controlling micromanipulation by active and adaptive materials. In the respiratory system, such actuation enables pathogen clearance by means of motile cilia. While various types of artificial cilia have been engineered recently, they often involve complex manufacturing protocols and focus on transporting liquids only. Here, we create soft magnetic carpets via an easy self-assembly route based on the Rosensweig instability. These carpets can transport liquids but also solid objects that are larger and heavier than the artificial cilia, using a crowd-surfing effect. This amphibious transportation is locally and reconfigurably tuneable by simple micromagnets or advanced programmable magnetic fields with a high degree of spatial resolution. We identify and model two surprising cargo reversal effects due to collective ciliary motion and non-trivial elastohydrodynamics. While our active carpets are generally applicable to integrated control systems for transport, mixing and sorting, these effects could also be exploited for microfluidic viscosimetry and elastometry.

Micro-swimmers can serve as cargo carriers that move deep inside complex flow networks. When a school collectively entrains the surrounding fluid, their transport capacity can be enhanced. This effect is quantified with good agreement between experiments with self-propelled droplets and a confined Brinkman squirmer model. The volume of liquid entrained can be much larger than the droplet itself, amplifying the effective cargo capacity over an order of magnitude, even for dilute schools. Hence, biological and engineered swimmers can efficiently transport materials into confined environments., Comment: 15 pages, 3 videos. PRL, in press. https://journals.aps.org/prl/accepted/92073Y5eQ3214f79977928f65ce99424e72a173bb

Geometric confinements are frequently encountered in the biological world and strongly affect the stability, topology, and transport properties of active suspensions in viscous flow. Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmer moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. The interfacial viscous stresses induced by the surfactant are described by the well-established Boussinesq-Scriven constitutive rheological model. Moreover, the active agent is represented by a force dipole and the resulting fluid-mediated hydrodynamic couplings between the swimmer and the confining drop are investigated. We find that the presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation. Exact solutions for the velocity images for the Stokeslet and dipolar flow singularities inside the drop are introduced and expressed in terms of infinite series of harmonic components. Our results offer useful insights into guiding principles for the control of confined active matter systems and support the objective of utilizing synthetic microswimmers to drive drops for targeted drug delivery applications., Comment: 19 pages, 7 figures. Regular article contributed to the Topical Issue of the European Physical Journal E entitled "Physics of Motile Active Matter" edited by Gerhard Gompper, Clemens Bechinger, Holger Stark, and Roland G. Winkler

The navigation of micro-robots in complex flow environments is controlled by rheotaxis, the reorientation with respect to flow gradients. Here we demonstrate how payloads can be exploited to enhance the motion against flows. Using fully resolved hydrodynamic simulations, the mechanisms are described that allow micro-robots of different shapes to reorient upstream. We find that cargo pullers are the fastest at most flow strengths, but pushers feature a non-trivial optimum as a function of the counter flow strength. Moreover, the rheotactic performance can be maximised by tuning the micro-robot shape or cargo size. These results may be used to control micro-swimmer navigation, but they also apply to rheotaxis in microbial ecology and the prevention of bacterial contamination dynamics., Comment: 10 pages, 4 figures

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrates through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing to accurately predict most of our results analytically. This analytical theory helps identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict mechanical properties of synthetic minimal membranes., Comment: 16 pages, 6 figures. Revised manuscript resubmitted to J. Chem. Phys

We demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full theory is developed in terms of gradients in the active matter density and velocity, and applied to bacterial turbulence, topological defects and clustering. Currents with complex spatiotemporal patterns are obtained, which are tuneable through confinement. Our findings show that diversity in carpet architecture is essential to maintain biofunctionality., Comment: 5 pages, 4 figures, and Supplementary Information

Geometric confinements are frequently encountered in soft matter systems and in particular significantly alter the dynamics of swimming microorganisms in viscous media. Surface-related effects on the motility of microswimmers can lead to important consequences in a large number of biological systems, such as biofilm formation, bacterial adhesion and microbial activity. On the basis of low-Reynolds-number hydrodynamics, we explore the state diagram of a three-sphere microswimmer under channel confinement in a slit geometry and fully characterize the swimming behavior and trajectories for neutral swimmers, puller- and pusher-type swimmers. While pushers always end up trapped at the channel walls, neutral swimmers and pullers may further perform a gliding motion and maintain a stable navigation along the channel. We find that the resulting dynamical system exhibits a supercritical pitchfork bifurcation in which swimming in the mid-plane becomes unstable beyond a transition channel height while two new stable limit cycles or fixed points that are symmetrically disposed with respect to the channel mid-height emerge. Additionally, we show that an accurate description of the averaged swimming velocity and rotation rate in a channel can be captured analytically using the method of hydrodynamic images, provided that the swimmer size is much smaller than the channel height., Comment: 19 pages, 9 figures. Article contributed to the Topical Issue of the Journal of Physics: Condensed Matter, entitled "Transport in Narrow Channels" edited by Paolo Malgaretti, Gleb Oshanin, and Julian Talbot

Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer's hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers' hydrodynamic properties., Comment: 12 pages, 9 figures, 2 tables

A plethora of active matter models exist that describe the behavior of self-propelled particles (or swimmers), both with and without hydrodynamics. However, there are few studies that consider shape-anisotropic swimmers and include hydrodynamic interactions. Here, we introduce a simple method to simulate self-propelled colloids interacting hydrodynamically in a viscous medium using the lattice-Boltzmann technique. Our model is based on raspberry-type viscous coupling and a force/counter-force formalism which ensures that the system is force free. We consider several anisotropic shapes and characterize their hydrodynamic multipolar flow field. We demonstrate that shape-anisotropy can lead to the presence of a strong quadrupole and octupole moments, in addition to the principle dipole moment. The ability to simulate and characterize these higher-order moments will prove crucial for understanding the behavior of model swimmers in confining geometries., Comment: 11 pages, 3 figures, 3 tables

One of the principal mechanisms by which surfaces and interfaces affect microbial life is by perturbing the hydrodynamic flows generated by swimming. By summing a recursive series of image systems we derive a numerically tractable approximation to the three-dimensional flow fields of a Stokeslet (point force) within a viscous film between a parallel no-slip surface and no-shear interface and, from this Green's function, we compute the flows produced by a force- and torque-free micro-swimmer. We also extend the exact solution of Liron & Mochon (1976) to the film geometry, which demonstrates that the image series gives a satisfactory approximation to the swimmer flow fields if the film is sufficiently thick compared to the swimmer size, and we derive the swimmer flows in the thin-film limit. Concentrating on the thick film case, we find that the dipole moment induces a bias towards swimmer accumulation at the no-slip wall rather than the water-air interface, but that higher-order multipole moments can oppose this. Based on the analytic predictions we propose an experimental method to find the multipole coefficient that induces circular swimming trajectories, allowing one to analytically determine the swimmer's three-dimensional position under a microscope., Comment: 35 pages, 11 figures, 5 tables

Interactions between microorganisms and their complex flowing environments are essential in many biological systems. We develop a model for microswimmer dynamics in non-Newtonian Poiseuille flows. We predict that swimmers in shear-thickening (-thinning) fluids migrate upstream more (less) quickly than in Newtonian fluids and demonstrate that viscoelastic normal stress differences reorient swimmers causing them to migrate upstream at the centreline, in contrast to well-known boundary accumulation in quiescent Newtonian fluids. Based on these observations, we suggest a sorting mechanism to select microbes by swimming speed., Comment: Four figures and 56 references