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The mobility of particles in fluid membranes is a fundamental aspect of many biological processes. In a 1975 paper [1], Saffman and Delbr\"uck demonstrated how the presence of external Stokesian solvents is crucial in regularising the apparently singular flow within an infinite flat membrane. In the present paper, we extend this classical work and compute the rotational mobility of a rigid finite-sized particle located inside a spherical membrane embedded in Stokesian solvents. Treating the particle as a spherical cap, we solve for the flow semi-analytically as a function of the Saffman-Delbr\"uck (SD) length (ratio of membrane to solvent viscosity) and the solid angle formed by the particle. We study the dependence of the mobility and flow on inclusion size and SD length, recovering the flat-space mobility as a special case. Our results will be applicable to a range of biological problems including rotational Brownian motion, the dynamics of lipid rafts, and the motion of aquaporin channels in response to water flow. Our method will provide a novel way of measuring a membrane's viscosity from the rotational diffusion of large inclusions, for which the commonly used planar Saffman-Delbr\"uck theory does not apply.

Motivated by the aim of understanding the effect of media heterogeneity on the swimming dynamics of flagellated bacteria, we study the rotation and swimming of rigid helices in dilute suspensions experimentally and theoretically. We first measure the torque experienced by, and thrust force generated by, helices rotating without translating in suspensions of neutrally buoyant particles with varying concentrations and sizes. Using the ratio of thrust to drag forces $\xi$ as an empirical proxy for propulsion efficiency, our experiments indicate that $\xi$ increases with the concentration of particles in the fluid, with the enhancement depending strongly on the geometric parameters of the helix. To rationalize these experimental results, we then develop a dilute theoretical approach that accounts for the additional hydrodynamic stress generated by freely suspended spheres around the helical tail. We predict similar enhancements in the drag coefficient ratio and propulsion at a given angular speed in a suspension and study its dependence on the helix geometry and the spatial distribution of the suspended spheres. These results are further reinforced by experiments on freely swimming artificial swimmers, which propel faster in dilute suspensions, with speed increases over $60 \%$ for optimal geometries. Our findings quantify how biological swimmers might benefit from the presence of suspended particles, and could inform the design of artificial self-propelled devices for biomedical applications.

Flagellated bacteria are hydrodynamically attracted to rigid walls, yet past work shows a 'hovering' state where they swim stably at a finite height above surfaces. We use numerics and theory to reveal the physical origin of hovering. Simulations first show that hovering requires an elongated cell body and results from a tilt away from the wall. Theoretical models then identify two essential asymmetries: the response of width-asymmetric cells to active flows created by length-asymmetric cells. A minimal model reconciles near and far-field hydrodynamics, capturing all key features of hovering., Comment: 6 pages, 3 figures. To appear in Physical Review Research (2024)

Cytoplasmic streaming, the persistent flow of fluid inside a cell, induces intracellular transport, which plays a key role in fundamental biological processes. In meiosis II mouse oocytes (developing egg cells) awaiting fertilisation, the spindle, which is the protein structure responsible for dividing genetic material in a cell, must maintain its position near the cell cortex (the thin actin network bound to the cell membrane) for many hours. However, the cytoplasmic streaming that accompanies this stable positioning would intuitively appear to destabilise the spindle position. Here, through a combination of numerical and analytical modelling, we reveal a new, hydrodynamic mechanism for stable spindle positioning beneath the cortical cap. We show that this stability depends critically on the spindle size and the active driving from the cortex, and demonstrate that stable spindle positioning can result purely from a hydrodynamic suction force exerted on the spindle by the cytoplasmic flow. Our findings show that local fluid dynamic forces can be sufficient to stabilise the spindle, explaining robustness against perturbations not only perpendicular but also parallel to the cortex. Our results shed light on the importance of cytoplasmic streaming in mammalian meiosis., Comment: 23 pages, 9 figures

Numerous studies have explored the link between bacterial swimming and the number of flagella, a distinguishing feature of motile multiflagellated bacteria. We revisit this open question using augmented slender-body theory simulations, in which we resolve the full hydrodynamic interactions within a bundle of helical filaments rotating and translating in synchrony. Unlike previous studies, our model considers the full torque-speed relationship of the bacterial flagellar motor, revealing its significant impact on multiflagellated swimming. Because the viscous load per motor decreases with flagellar number, the bacterial flagellar motor (BFM) transitions from the high-load to the low-load regime at a critical number of filaments, leading to bacterial slowdown as further flagella are added to the bundle. We explain the physical mechanism behind the observed slowdown as an interplay between the load-dependent generation of torque by the motor, and the load-reducing cooperativity between flagella, which consists of both hydrodynamic and non-hydrodynamic components. The theoretically predicted critical number of flagella is remarkably close to the values reported for the model organism \textit{Escherichia coli}. Our model further predicts that the critical number of flagella increases with viscosity, suggesting that bacteria can enhance their swimming capacity by growing more flagella in more viscous environments, consistent with empirical observations., Comment: 24 pages, 6 figures, 1 table

The existence of temperature gradients within eukaryotic cells has been postulated as a source of natural convection in the cytoplasm, i.e. bulk fluid motion as a result of temperature-difference-induced density gradients. Recent computations have predicted that a temperature differential of $\Delta T \approx 1$ K between the cell nucleus and the cell membrane could be strong enough to drive significant intracellular material transport. We use numerical computations and theoretical calculations to revisit this problem in order to further understand the impact of temperature gradients on flow generation and advective transport within cells. Surprisingly, our computations yield flows that are an order of magnitude weaker than those obtained previously for the same relative size and position of the nucleus with respect to the cell membrane. To understand this discrepancy, we develop a semi-analytical solution of the convective flow inside a model cell using a bi-spherical coordinate framework, for the case of an axisymmetric cell geometry (i.e. when the displacement of the nucleus from the cell centre is aligned with gravity). We also calculate exact solutions for the flow when the nucleus is located concentrically inside the cell. The results from both theoretical analyses agree with our numerical results, thus providing a robust estimate of the strength of cytoplasmic natural convection and demonstrating that these are much weaker than previously predicted. Finally, we investigate the ability of the aforementioned flows to redistribute solute within a cell. Our calculations reveal that, in all but unrealistic cases, cytoplasmic convection has a negligible contribution toward enhancing the diffusion-dominated mass transfer of cellular material.

Bubble-propelled catalytic colloids stand out as a uniquely efficient design for artificial controllable micromachines, but so far lack a general theoretical framework that explains the physics of their propulsion. Here we develop a combined diffusive and hydrodynamic theory of bubble growth near a spherical catalytic colloid, that allows us to explain the underlying mechanism and the influence of environmental and material parameters. We identify two dimensionless groups, related to colloidal activity and the background fluid, that govern a saddle-node bifurcation of the bubble growth dynamics, and calculate the generated flows analytically for both slip and no slip boundary conditions on the bubble. We finish with a discussion of the assumptions and predictions of our model in the context of existing experimental results, and conclude that some of the observed behaviour, notably the ratchet-like gait, stems from peculiarities of the experimental setup rather than fundamental physics of the propulsive mechanism., Comment: Main text 20 pages, appendix 23 pages. 8 figures

This paper presents a multilevel algorithm specifically designed for radio-interferometric imaging in astronomy. The proposed algorithm is used to solve the uSARA (unconstrained Sparsity Averaging Reweighting Analysis) formulation of this image restoration problem. Multilevel algorithms rely on a hierarchy of approximations of the objective function to accelerate its optimization. In contrast to the usual multilevel approaches where this hierarchy is derived in the parameter space, here we construct the hierarchy of approximations in the observation space. The proposed approach is compared to a reweighted forward-backward procedure, which is the backbone iteration scheme for solving the uSARA problem.

We study slender, helical elastic rods subject to distributed forces and moments. Focussing on the case when the helix axis remains straight, we employ the method of multiple scales to systematically derive an 'equivalent-rod' theory from the Kirchhoff rod equations: the helical filament is described as a naturally-straight rod (aligned with the helix axis) for which the extensional and torsional deformations are coupled. Importantly, our analysis is asymptotically exact in the limit of a 'highly-coiled' filament (when the helical wavelength is much smaller than the characteristic lengthscale over which the filament bends due to external loading) and is able to account for large, unsteady displacements. In addition, our analysis yields explicit conditions on the external loading that must be satisfied for a straight helix axis. In the small-deformation limit, we exactly recover the coupled wave equations used to describe the free vibrations of helical coil springs, thereby justifying previous equivalent-rod approximations in which linearised stiffness coefficients are assumed to apply locally and dynamically. We then illustrate our theory with two loading scenarios: (I) a heavy helical rod deforming under its own weight; and (II) the dynamics of axial rotation (twirling) in viscous fluid, which may be considered as a simple model for a bacteria flagellar filament. In both scenarios, we demonstrate excellent agreement with solutions of the full Kirchhoff rod equations, even beyond the formal limit of validity of the highly-coiled assumption. More broadly, our analysis provides a framework to develop reduced models of helical rods in a wide variety of physical and biological settings, and yields analytical insight into their elastic instabilities. In particular, our analysis indicates that tensile instabilities are a generic phenomenon when both distributed forces and moments are present., Comment: 46 pages, 11 figures

The humble Petri dish is perhaps the simplest setting in which to examine the locomotion of swimming organisms, particularly those whose body size is tens of microns to millimetres. The fluid layer in such a container has a bottom no-slip surface and a stress-free upper boundary. It is of fundamental interest to understand the flow fields produced by the elementary and composite singularities of Stokes flow in this geometry. Building on the few particular cases that have previously been considered in the literature, we study here the image systems for the primary singularities of Stokes flow subject to such boundary conditions - the stokeslet, rotlet, source, rotlet dipole, source dipole and stresslet - paying particular attention to the far-field behavior. In several key situations, the depth-averaged fluid flow is accurately captured by the solution of an associated Brinkman equation whose screening length is proportional to the depth of the fluid layer. The case of hydrodynamic bound states formed by spinning microswimmers near a no-slip surface, discovered first using the alga $Volvox$, is reconsidered in the geometry of a Petri dish, where the power-law attractive interaction between microswimmers acquires unusual exponentially screened oscillations., Comment: 27 pages, 7 figures

Biased locomotion is a common feature of microorganisms, but little is known about its impact on self-organisation. Inspired by recent experiments showing a transition to large-scale flows, we study theoretically the dynamics of magnetotactic bacteria confined to a drop. We reveal two symmetry-breaking mechanisms (one local chiral and one global achiral) leading to self-organisation into global vortices and a net torque exerted on the drop. The collective behaviour is ultimately controlled by the swimmers' microscopic chirality and, strikingly, the system can exhibit oscillations and memory-like features.

The Drosophila melanogaster embryo, an elongated multi-nucleated cell, is a classical model system for eukaryotic development and morphogenesis. Recent work has shown that bulk cytoplasmic flows, driven by cortical contractions along the walls of the embryo, enable the uniform spreading of nuclei along the anterior-posterior (AP) axis necessary for proper embryonic development. Here we propose two mathematical models to characterise cytoplasmic flows driven by tangential cortical contractions in elongated cells. Assuming Newtonian fluid flow at low Reynolds number in a spheroidal cell, we first compute the flow field exactly, thereby bypassing the need for numerical computations. We then apply our results to recent experiments on nuclear transport in cell cycles 4-6 of Drosophila embryo development. By fitting the cortical contractions in our model to measurements, we reveal that experimental cortical flows enable near-optimal axial spreading of nuclei. A second mathematical approach, applicable to general elongated cell geometries, exploits a long-wavelength approximation to produce an even simpler solution, with errors below 5% compared to the full model. An application of this long-wavelength result to transport leads to fully analytical solutions for the nuclear concentration that capture the essential physics of the system, including optimal axial spreading of nuclei., Comment: 19 pages, 9 figures

Eukaryotic swimming cells such as spermatozoa, algae or protozoa use flagella or cilia to move in viscous fluids. The motion of their flexible appendages in the surrounding fluid induces propulsive forces that balance with the viscous drag on the cells and lead to a directed swimming motion. Here, we use our recently built database of cell motility (BOSO-Micro) to investigate the extent to which the shapes of eukaryotic swimming cells may be optimal from a hydrodynamic standpoint. We first examine the morphology of flexible flagella undergoing waving deformation and show that their amplitude-to-wavelength ratio is near the one predicted theoretically to optimise the propulsive efficiency of active filaments. Next, we consider ciliates, for which locomotion is induced by the collective beating of short cilia covering their surface. We show that the aspect ratio of ciliates are close to the one predicted to minimise the viscous drag of the cell body. Both results strongly suggest a key role played by hydrodynamic constraints, in particular viscous drag, in shaping eukaryotic swimming cells., Comment: to be published in J. Fluid Mech

This paper presents a multilevel framework for inertial and inexact proximal algorithms, that encompasses multilevel versions of classical algorithms such as forward-backward and FISTA. The methods are supported by strong theoretical guarantees: we prove both the rate of convergence and the convergence of the iterates to a minimum in the convex case, an important result for ill-posed problems. We propose a particular instance of IML (Inexact MultiLevel) FISTA, based on the use of the Moreau envelope to build efficient and useful coarse corrections, fully adapted to solve problems in image restoration. Such a construction is derived for a broad class of composite optimization problems with proximable functions. We evaluate our approach on several image reconstruction problems and we show that it considerably accelerates the convergence of the corresponding one-level (i.e. standard) version of the methods, for large-scale images.

This article measures how sparsity can make neural networks more robust to membership inference attacks. The obtained empirical results show that sparsity improves the privacy of the network, while preserving comparable performances on the task at hand. This empirical study completes and extends existing literature., Comment: arXiv admin note: duplicate of arXiv:2304.07234

Sparse neural networks are mainly motivated by ressource efficiency since they use fewer parameters than their dense counterparts but still reach comparable accuracies. This article empirically investigates whether sparsity could also improve the privacy of the data used to train the networks. The experiments show positive correlations between the sparsity of the model, its privacy, and its classification error. Simply comparing the privacy of two models with different sparsity levels can yield misleading conclusions on the role of sparsity, because of the additional correlation with the classification error. From this perspective, some caveats are raised about previous works that investigate sparsity and privacy.

Recent experiments in cell biology have probed the impact of artificially-induced intracellular flows in the spatiotemporal organisation of cells and organisms. In these experiments, mild dynamical heating via focused infrared light from a laser leads to long-range, thermoviscous flows of the cytoplasm inside a cell, a method popularised in cell biology as FLUCS (focused-light-induced cytoplasmic streaming). Here, we present a fully analytical, theoretical model describing the fluid flow and transport of tracers induced by the laser at all length scales in two-dimensional confinement. The focused light causes a small, local temperature change, which in turn results in a small change in the density and viscosity of the fluid locally. We analytically solve for the instantaneous flow field due to the translation of a heat spot of arbitrary time-dependent amplitude along a scan path. We show that the leading-order instantaneous flow results purely from thermal expansion. It is proportional to the magnitude of the temperature perturbation, with far-field behaviour typically dominated by a source or sink flow and proportional to the rate of change of the heat-spot amplitude. In contrast, and in agreement with experimental measurements, the net displacement of a tracer due to a full scan of the heat spot is quadratic in the heat-spot amplitude, as it results from the interplay of thermal expansion and thermal viscosity changes. The corresponding average velocity of tracers over a scan is a hydrodynamic source dipole in the far field, with direction dependent on the relative importance of thermal expansion and thermal viscosity changes. Our quantitative findings show excellent agreement with recent experimental results and will enable the design of new controlled experiments to establish the physiological role of physical transport processes inside cells., Comment: 57 pages, 43 figures

To swim through a viscous fluid, a flagellated bacterium must overcome the fluid drag on its body by rotating a flagellum or a bundle of multiple flagella. Because the drag increases with the size of bacteria, it is expected theoretically that the swimming speed of a bacterium inversely correlates with its body length. Nevertheless, despite extensive research, the fundamental size-speed relation of flagellated bacteria remains unclear with different experiments reporting conflicting results. Here, by critically reviewing the existing evidence and synergizing our own experiments of large sample sizes, hydrodynamic modeling and simulations, we demonstrate that the average swimming speed of \textit{Escherichia coli}, a premier model of peritrichous bacteria, is independent of their body length. Our quantitative analysis shows that such a counterintuitive relation is the consequence of the collective flagellar dynamics dictated by the linear correlation between the body length and the number of flagella of bacteria. Notably, our study reveals how bacteria utilize the increasing number of flagella to regulate the flagellar motor load. The collective load sharing among multiple flagella results in a lower load on each flagellar motor and therefore faster flagellar rotation, which compensates for the higher fluid drag on the longer bodies of bacteria. Without this balancing mechanism, the swimming speed of monotrichous bacteria generically decreases with increasing body length, a feature limiting the size variation of the bacteria. Altogether, our study resolves a long-standing controversy over the size-speed relation of flagellated bacteria and provides new insights into the functional benefit of multiflagellarity in bacteria., Comment: 10 pages, 6 figures (accepted by PNAS)

Biological and artificial microswimmers often self-propel in external flows of vortical nature; relevant examples include algae in small-scale ocean eddies, spermatozoa in uterine peristaltic flows and bacteria in microfluidic devices. A recent experiment has shown that swimming bacteria in model vortices are expelled from the vortex all the way to a well-defined depletion zone (Sokolov and Aranson (2016) "Rapid expulsion of microswimmers by a vortical flow." Nature Comm. 7, 11114). In this paper, we propose a theoretical model to investigate the dynamics of elongated microswimmers in elementary vortices, namely active particles in two- and three-dimensional rotlets. A deterministic model first reveals the existence of bounded orbits near the centre of the vortex and unbounded orbits elsewhere. We further discover a conserved quantity of motion that allows us to map the phase space according to the type of the orbit (bounded vs unbounded). We next introduce translational and rotational noise into the system. Using a Fokker--Planck formalism, we quantify the quality of trapping near the centre of the vortex by examining the probability of escape and the mean time of escape from the region of deterministically bounded orbits. We finally show how to use these findings to formulate a prediction for the radius of the depletion zone, which compares favourably with the experiments of Sokolov and Aranson (2016).

This paper presents a multilevel FISTA algorithm, based on the use of the Moreau envelope to build the correction brought by the coarse models, which is easy to compute when the explicit form of the proximal operator of the considered functions is known. This approach is supported by strong theoretical guarantees: we prove both the rate of convergence and the convergence of the iterates to a minimum in the convex case, an important result for ill-posed problems. We evaluate our approach on image restoration problems and we show that it outperforms classical FISTA for large-scale images.

The breakup of a fluid jet into droplets has long fascinated natural scientists, with early research dating back to the 19th century. Infinitesimal perturbations to a jet grow because of surface tension, which eventually leads to breakup of the jet into droplets (Rayleigh-Plateau instability). Although this classical phenomenon has long been studied, it is not clear how it is modified when the fluid is replaced by an active fluid. In this study, we investigate instabilities of a jet of an active fluid. The active fluid is modelled by a suspension of microswimmers that propel themselves by generating surface tangential velocities, i.e. squirmers. The squirmers are assumed to be bottom-heavy and heavier than the surrounding fluid, so that a downward jet of the active fluid self-assembles under gravity. Hydrodynamic interactions between squirmers are computed using the Stokesian dynamics method, in which near-field hydrodynamics are accurately calculated. We find that jets of active fluids are unstable, with different unstable modes between pullers and pushers. For an active fluid of pullers, the jet breaks up into droplets in a varicose manner reminiscent of a Newtonian fluid. For pushers, on the other hand, the jet buckles and undergoes a waving (sinuous) instability. The physical mechanisms for these two instabilities can be understood by an inspection of the stress fields in the jets and parametric study reveals the importance of hydrodynamic interactions in the instabilities. Although both gravity and bottom-heaviness play an essential role in realizing the downward jet, their influence on the instability is found to be limited. Our findings help reveal new features of the collective properties of active fluids., Comment: Physical Review Fluids (2022), to appear

To rotate continuously without jamming, the flagellar filaments of bacteria need to be locked in phase. While several models have been proposed for eukaryotic flagella, the synchronization of bacterial flagella is less well understood. Starting from a reduced model of flexible and hydrodynamically-coupled bacterial flagella, we rigorously coarse-grain the equations of motion using the method of multiple scales, and hence show that bacterial flagella generically synchronize to zero phase difference via an elastohydrodynamic mechanism. Remarkably, the far-field rate of synchronization is maximized at an intermediate value of elastic compliance, with surprising implications for bacteria., Comment: 18 pages, 6 figures, 2 tables. Accepted for publication in Physical Review Letters: https://journals.aps.org/prl/accepted/f3071Yc1T031a78775a87695a0e87c6e9330aa8c8

We consider the dynamics of micro-sized, asymmetrically-coated thermoresponsive hydrogel ribbons (microgels) under periodic heating and cooling in the confined space between two planar surfaces. As the result of the temperature changes, the volume and thus the shape of the slender microgel change, which lead to repeated cycles of bending and elastic relaxation, and to net locomotion. Small devices designed for biomimetic locomotion need to exploit flows that are not symmetric in time (non-reciprocal) to escape the constraints of the scallop theorem and undergo net motion. Unlike other biological slender swimmers, the non-reciprocal bending of the gel centreline is not sufficient here to explain for the overall swimming motion. We show instead that the swimming of the gel results from the flux of water periodically emanating from (or entering) the gel itself due to its shrinking (or swelling). The associated flows induce viscous stresses that lead to a net propulsive force on the gel. We derive a theoretical model for this hypothesis of jet-driven propulsion, which leads to excellent agreement with our experiments.

The Green's function of the incompressible Stokes equations, the stokeslet, represents the singular flow due to a point force. Its classical value in an unbounded fluid has been extended near surfaces of various shapes, including flat walls and spheres, and in most cases the presence of a surface leads to an advection flow induced at the location of the point force. In this paper, motivated by the biological transport of cargo along polymeric filaments inside eukaryotic cells, we investigate the reaction flow at the location of the point force due to a rigid slender filament located at a separation distance intermediate between the filament radius and its length (i.e. we compute the advection of the point force induced by the presence of the filament). An asymptotic analysis of the problem reveals that the leading-order approximation for the force distribution along the axis of the filament takes a form analogous to resistive-force theory but with drag coefficients that depend logarithmically on the distance between the point force and the filament. A comparison of our theoretical prediction with boundary element computations show good agreement. We finally briefly extend the model to the case of curved filaments.

The four-roll mill, wherein four identical cylinders undergo rotation of identical magnitude but alternate signs, was originally proposed by GI Taylor to create local extensional flows and study their ability to deform small liquid drops. Since an extensional flow has an unstable eigendirection, a drop located at the flow stagnation point will have a tendency to escape. This unstable dynamics can however be stabilised using, e.g., a modulation of the rotation rates of the cylinders. Here we use Reinforcement Learning, a branch of Machine Learning devoted to the optimal selection of actions based on cumulative rewards, in order to devise a stabilisation algorithm for the four-roll mill flow. The flow is modelled as the linear superposition of four two-dimensional rotlets and the drop is treated as a rigid spherical particle smaller than all other length scales in the problem. Unlike previous attempts to devise control, we take a probabilistic approach whereby speed adjustments are drawn from a probability density function whose shape is improved over time via a form of gradient ascent know as Actor-Critic method. With enough training, our algorithm is able to precisely control the drop and keep it close to the stagnation point for as long as needed. We explore the impact of the physical and learning parameters on the effectiveness of the control and demonstrate the robustness of the algorithm against thermal noise. We finally show that Reinforcement Learning can provide a control algorithm effective for all initial positions and that can be adapted to limit the magnitude of the flow extension near the position of the drop.

Synthetic microswimmers offer models for cell motility and their tunability makes them promising candidates for biomedical applications. Here we measure the acoustic propulsion of bimetallic micro-rods that, when trapped at the nodal plane of a MHz acoustic resonator, swim with speeds of up to 300 microns per second. While past acoustic streaming models predict speeds that are more than one order of magnitude smaller than our measurements, we demonstrate that the acoustic locomotion of the rods is driven by a viscous, non-reciprocal mechanism relying on shape anisotropy akin to that used by swimming cells and that reproduces our data with no adjustable parameters.

The locomotion of microorganisms and spermatozoa in complex viscoelastic fluids is of critical importance in many biological processes such as fertilization, infection, and biofilm formation. Depending on their propulsion mechanisms, microswimmers display various responses to a complex fluid environment: increasing or decreasing their swimming speed and efficiency, modifying their propulsion kinematics and swimming gaits, and experiencing different hydrodynamic interactions with their surroundings. In this article, we review the fundamental physics of locomotion of biological and synthetic microswimmers in complex viscoelastic fluids. Starting from a continuum framework, we describe the main theoretical approaches developed to model microswimming in viscoelastic fluids, which typically rely on asymptotically small dimensionless parameters. We then summarise recent progress on the mobility of single cells propelled by cilia, waving flagella and rotating helical flagella in unbounded viscoelastic fluids. We next briefly discuss the impact of other physical factors, including the micro-scale heterogeneity of complex biological fluids, the role of Brownian fluctuations of the microswimmers, the effect of polymer entanglement and the influence of shear-thinning viscosity. In particular, for solutions of long polymer chains whose sizes are comparable to the radius of flagella, continuum models cannot be used and instead Brownian Dynamics for the polymers can predict the swimming dynamics. Finally, we discuss the effect of viscoelasticity on the dynamics of microswimmers in the presence of surfaces or external flows and its impact on collective cellular behavior.

The design of artificial microswimmers is often inspired by the strategies of natural microorganisms. Many of these creatures exploit the fact that elasticity breaks the time-reversal symmetry of motion at low Reynolds numbers, but this principle has been notably absent from model systems of active, self-propelled microswimmers. Here we introduce a class of microswimmer that spontaneously self-assembles and swims without using external forces, driven instead by surface phase transitions induced by temperature variations. The swimmers are made from alkane droplets dispersed in aqueous surfactant solution, which start to self-propel upon cooling, pushed by rapidly growing thin elastic tails. When heated, the same droplets recharge by retracting their tails, swimming for up to tens of minutes in each cycle. Thermal oscillations of approximately 5 degrees Celsius induce the swimmers to harness heat from the environment and recharge multiple times. We develop a detailed elastohydrodynamic model of these processes and highlight the molecular mechanisms involved. The system offers a convenient platform for examining symmetry breaking in the motion of swimmers exploiting flagellar elasticity. The mild conditions and biocompatible media render these microswimmers potential probes for studying biological propulsion and interactions between artificial and biological swimmers., Comment: Supplementary information available

Hydrodynamic interactions (HIs) are important in biophysics research because they influence both the collective and the individual behaviour of microorganisms and self-propelled particles. For instance, HIs at the micro-swimmer level determine the attraction or repulsion between individuals, and hence their collective behaviour. Meanwhile, HIs between swimming appendages (e.g. cilia and flagella) influence the emergence of swimming gaits, synchronised bundles and metachronal waves. In this study, we address the issue of HIs between slender filaments separated by a distance larger than their contour length (d>L) by means of asymptotic calculations and numerical simulations. We first derive analytical expressions for the extended resistance matrix of two arbitrarily-shaped rigid filaments as a series expansion in inverse powers of d/L>1. The coefficients in our asymptotic series expansion are then evaluated using two well-established methods for slender filaments, resistive-force theory (RFT) and slender-body theory (SBT), and our asymptotic theory is verified using numerical simulations based on SBT for the case of two parallel helices. The theory captures the qualitative features of the interactions in the regime d/L>1, which opens the path to a deeper physical understanding of hydrodynamically governed phenomena such as inter-filament synchronisation and multiflagellar propulsion. To demonstrate the usefulness of our results, we next apply our theory to the case of two helices rotating side-by-side, where we quantify the dependence of all forces and torques on the distance and phase difference between them. Using our understanding of pairwise HIs, we then provide physical intuition for the case of a circular array of rotating helices. Our theoretical results will be useful for the study of HIs between bacterial flagella, nodal cilia, and slender microswimmers.

A highly organized and densely packed lattice of molecular machinery within the sarcomeres of muscle cells powers contraction. Although many of the proteins that drive contraction have been studied extensively, the mechanical impact of fluid shearing within the lattice of molecular machinery has received minimal attention. It was recently proposed that fluid flow augments substrate transport in the sarcomere, however, this analysis used analytical models of fluid flow in the molecular machinery that could not capture its full complexity. By building a finite element model of the sarcomere, we estimate the explicit flow field, and contrast it with analytical models. Our results demonstrate that viscous drag forces on sliding filaments are surprisingly small in contrast to the forces generated by single myosin molecular motors. This model also indicates that the energetic cost of fluid flow through viscous shearing with lattice proteins is likely minimal. The model also highlights a steep velocity gradient between sliding filaments and demonstrates that the maximal radial fluid velocity occurs near the tips of the filaments. To our knowledge, this is the first computational analysis of fluid flow within the highly structured sarcomere.

Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies., Comment: Database available in the Center for Open Science (OSF) repository (https://osf.io/4tyx6/). Open source version of the database available on GitHub (https://github.com/marcos-fvr/BOSO-micro)

Cellular appendages conferring motility, such as flagella or cilia, are known to synchronise their periodic beats. The origin of synchronisation is a combination of long-range hydrodynamic interactions with physical mechanisms allowing the phases of these biological oscillators to evolve. Two of such mechanisms have been identified by previous work, the elastic compliance of the periodic orbit or oscillations driven by phase-dependent biological forcing. To help uncover the physical mechanism for hydrodynamic synchronisation most essential overall in biology, we theoretically investigate the effect of strong confinement on the effectiveness of hydrodynamic synchronisation. We use minimal models where appendages are modelled as rigid spheres forced to move along circular trajectories near a rigid surface. Strong confinement is modelled by adding a second nearby surface, parallel to the first one, where the distance between the surfaces is much smaller than the typical distance between the cilia. We calculate separately the impact of confinement on the synchronisation dynamics of the elastic compliance and the force modulation mechanisms and compare our results to the case with no confinement. Applying our results to the biologically-relevant situation of nodal cilia, we show that force modulation is a mechanism that leads to phase-locked states under strong confinement that are very similar to those without confinement as a difference with the elastic compliance mechanism. Our results point therefore to the robustness of force modulation for synchronisation, an important feature for biological dynamics that suggests it could be the most essential physical mechanism overall in arrays of nodal cilia. We further examine the distinct situation of primary cilia and show in that case that the difference in robustness of the mechanisms is not as pronounced but still favours the force modulation.

Motivated by recent experiments demonstrating that motile algae get trapped in draining foams, we study the trajectories of microorganisms confined in model foam channels (section of a Plateau border). We track single Chlamydomonas reinhardtii cells confined in a thin three-circle microfluidic chamber and show that their spatial distribution exhibits strong corner accumulation. Using empirical scattering laws observed in previous experiments (scattering with a constant scattering angle), we next develop a two-dimension geometrical model and compute the phase space of trapped and periodic trajectories of swimmers inside a three-circles billiard. We find that the majority of cell trajectories end up in a corner, providing a geometrical mechanism for corner accumulation. Incorporating the distribution of scattering angles observed in our experiments and including hydrodynamic interactions between the cells and the surfaces into the geometrical model enables us to reproduce the experimental probability density function of micro-swimmers in microfluidic chambers. Both our experiments and models demonstrate therefore that motility leads generically to trapping in complex geometries.

The geometric phase techniques for swimming in viscous flows express the net displacement of a swimmer as a path integral of a field in configuration space. This representation can be transformed into an area integral for simple swimmers using Stokes theorem. Since this transformation applies for any loop, the integrand of this area integral can be used to help design these swimmers. However, the extension of this Stokes theorem technique to more complicated swimmers is hampered by problems with variables that do not commute and by how to visualise and understand the higher dimensional spaces. In this paper, we develop a treatment for each of these problems, thereby allowing the displacement of general swimmers in any environment to be designed and understood similarly to simple swimmers. The net displacement arising from non-commuting variables is tackled by embedding the integral into a higher dimensional space, which can then be visualised through a suitability constructed surface. These methods are developed for general swimmers and demonstrated on {three} benchmark examples: Purcell's two-hinged swimmer, an axisymmetric squirmer in free space {and an axisymmetric squirmer approaching a free interface}. We show in particular that for swimmers with more than two modes of deformation, there exists an infinite set of strokes that generate each net displacement. Hence, in the absence of additional restrictions, general microscopic swimmers do not have a single stroke that maximises their displacement., Comment: 42 pages, 11 figures

In tissues as diverse as amphibian skin and the human airway, the cilia that propel fluid are grouped in sparsely distributed multiciliated cells (MCCs). We investigate fluid transport in this "mosaic" architecture, with emphasis on the trade-offs that may have been responsible for its evolutionary selection. Live imaging of MCCs in embryos of the frog $Xenopus~laevis$ shows that cilia bundles behave as active vortices that produce a flow field accurately represented by a local force applied to the fluid. A coarse-grained model that self-consistently couples bundles to the ambient flow reveals that hydrodynamic interactions between MCCs limit their rate of work so that when the system size is large compared to a single MCC, they best shear the tissue at low area coverage, a result that mirrors findings for other sparse distributions such as cell receptors and leaf stomata., Comment: 5 pages, 4 figures; Supplemental Material (4 pages, 4 figures) included

Synchronisation is often observed in the swimming of flagellated cells, either for multiple appendages on the same organism or between the flagella of nearby cells. Beating cilia are also seen to synchronise their dynamics. In 1951, Taylor showed that the observed in-phase beating of the flagella of co-swimming spermatozoa was consistent with minimisation of the energy dissipated in the surrounding fluid. Here we revisit Taylor's hypothesis for three models of flagella and cilia: (1) Taylor's waving sheets with both longitudinal and transverse modes, as relevant for flexible flagella; (2) spheres orbiting above a no-slip surface to model interacting flexible cilia; and (3) whirling rods above a no-slip surface to address the interaction of nodal cilia. By calculating the flow fields explicitly, we show that the rate of working of the model flagella or cilia is minimised in our three models for (1) a phase difference depending on the separation of the sheets and precise waving kinematics; (2) in-phase or opposite-phase motion depending on the relative position and orientation of the spheres; and (3) in-phase whirling of the rods. These results will be useful in future models probing the dynamics of synchronisation in these setups.

We experimentally and theoretically study the dynamics of a low-Reynolds number helical swimmer moving across viscosity gradients. Experimentally, a double-layer viscosity is generated by superposing two miscible fluids with similar densities but different dynamic viscosities. A synthetic helical magnetically-driven swimmer is then made to move across the viscosity gradients along four different configurations: either head-first (pusher swimmer) or tail-first (puller), and through either positive (i.e. going from low to high viscosity) or negative viscosity gradients. We observe qualitative differences in the penetration dynamics for each case. We find that the swimming speed can either increase or decrease while swimming across the viscosity interface, which results from the fact that the head and the tail of the swimmer can be in environments in which the local viscosity leads to different relative amounts of drag and thrust. In order to rationalize the experimental measurements, we next develop a theoretical hydrodynamic model. We assume that the classical resistive-force theory of slender filaments is locally valid along the helical propeller and use it to calculate the swimming speed as a function of the position of the swimmer relative to the fluid-fluid interface. The predictions of the model agree well with experiments for the case of positive viscosity gradients. When crossing across a negative gradient, gravitational forces in the experiment become important, and we modify the model to include buoyancy, which agrees with experiments. In general our results show that it is harder for a pusher swimmer to cross from low to high viscosity, whereas for a puller swimmer it is the opposite. Our model is also extended to the case of a swimmer crossing a continuous viscosity gradient.

We conduct experiments with force-free magnetically-driven rigid helical swimmers in Newtonian and viscoelastic (Boger) fluids. By varying the sizes of the swimmer body and its helical tail, we show that the impact of viscoelasticity strongly depends on the swimmer geometry: it can lead to a significant increase of the swimming speed (up to a factor of five), a similar decrease (also up to a factor of five) or it can have approximately no impact. Analysis of our data along with theoretical modeling shows that the influence of viscoelasticity on helical propulsion is controlled by a snowman-like effect, previously reported for dumbbell swimmers, wherein the front-back asymmetry of the swimmer leads to a non-Newtonian elastic force that can either favor or hinder locomotion.

Active systems such as microorganisms and self-propelled particles show a plethora of collective phenomena, including swarming, clustering, and phase separation. Control over the propulsion direction and switchability of the interactions between the individual self-propelled units may open new avenues in designing of materials from within. Here, we present a self-propelled particle system, consisting of half-gold coated titania ($\mathrm{TiO}_2$) particles, in which we can fast and on-demand reverse the propulsion direction, by exploiting the different photocatalytic activities on both sides. We demonstrate that the reversal in propulsion direction changes the nature of the hydrodynamic interaction from attractive to repulsive and can drive the particle assemblies to undergo both fusion and fission transitions. Moreover, we show these active colloids can act as nucleation sites, and switch rapidly the interactions between active and passive particles, leading to reconfigurable assembly and disassembly. Our experiments are qualitatively described by a minimal hydrodynamic model., Comment: 28 pages, 4 figures

Swimming eukaryotic microorganisms such as spermatozoa, algae and ciliates self-propel in viscous fluids using travelling wave-like deformations of slender appendages called flagella. Waves are predominant because Purcell's scallop theorem precludes time-reversible kinematics for locomotion. Using the calculus of variations on a periodic long-wavelength model of flagellar swimming, we show that the planar flagellar kinematics maximising the time-averaged propulsive force for a fixed amount of energy dissipated in the surrounding fluid correspond for all times to waves travelling with constant speed, potentially on a curved centreline, with propulsion always in the direction opposite to the wave.

Most motile bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. These semi-rigid filaments repeatedly join ('bundle') and separate ('unbundle'), resulting in a two-gait random walk-like motion of the cell. In this process, hydrodynamic interactions between the filaments are known to play an important role and can be categorised into two distinct types: direct interactions mediated through flows that are generated through the actuation of the filaments themselves, and indirect interactions mediated through the motion of the cell body (i.e. flows induced in the swimming frame that result from propulsion). To understand the relative importance of these two types of interactions, we study a minimal singularity model of flagellar bundling. Using hydrodynamic images, we solve for the flow analytically and compute both direct and indirect interactions exactly as a function of the length of the flagellar filaments and their angular separation. We show (i) that the generation of thrust by flagella alone is sufficient to drive the system towards a bundled state through both types of interaction; (ii) that indirect advection dominates for long filaments and at wide separation, i.e. primarily during the early stages of the bundling process; and (iii) that, in contrast, direct interactions dominate when flagellar filaments are in each other's wake, which we characterise mathematically. We further introduce a numerical elastohydrodynamic model that allows us to compute the dynamics of the helical axes of each flagellar filament while analysing direct and indirect interactions separately. With this we show (iv) that the shift in balance between direct and indirect interactions is non-monotonic during the bundling process, with a peak in direct dominance, and that different sections of the flagella are affected by these changes to different extents., Comment: 34 pages, 9 figures

Circular milling, a stunning manifestation of collective motion, is found across the natural world, from fish shoals to army ants. It has been observed recently that the plant-animal worm $Symsagittifera~roscoffensis$ exhibits circular milling behaviour, both in shallow pools at the beach and in Petri dishes in the laboratory. Here we investigate this phenomenon, through experiment and theory, from a fluid dynamical viewpoint, focusing on the effect that an established circular mill has on the surrounding fluid. Unlike systems such as confined bacterial suspensions and collections of molecular motors and filaments that exhibit spontaneous circulatory behaviour, and which are modelled as force dipoles, the front-back symmetry of individual worms precludes a stresslet contribution. Instead, singularities such as source dipoles and Stokes quadrupoles are expected to dominate. A series of models is analyzed to understand the contributions of these singularities to the azimuthal flow fields generated by a mill, in light of the particular boundary conditions that hold for flow in a Petri dish. A model that treats a circular mill as a rigid rotating disc that generates a Stokes flow is shown to capture basic experimental results well, and gives insights into the emergence and stability of multiple mill systems., Comment: 28 pages, 9 figures; Supplementary Videos available at website of REG

A growing body of work on the dynamics of eukaryotic flagella has noted that their oscillation frequencies are sufficiently high that the viscous penetration depth of unsteady Stokes flow is comparable to the scales over which flagella synchronize. Incorporating these effects into theories of synchronization requires an understanding of the global unsteady flows around oscillating bodies. Yet, there has been no precise experimental test on the microscale of the most basic aspects of such unsteady Stokes flow: the orbits of passive tracers and the position-dependent phase lag between the oscillating response of the fluid at a distant point and that of the driving particle. Here, we report the first such direct Lagrangian measurement of this unsteady flow. The method uses an array of $30$ submicron tracer particles positioned by a time-shared optical trap at a range of distances and angular positions with respect to a larger, central particle, which is then driven by an oscillating optical trap at frequencies up to $400$ Hz. In this microscale regime, the tracer dynamics is considerably simplified by the smallness of both inertial effects on particle motion and finite-frequency corrections to the Stokes drag law. The tracers are found to display elliptical Lissajous figures whose orientation and geometry are in agreement with a low-frequency expansion of the underlying dynamics, and the experimental phase shift between motion parallel and orthogonal to the oscillation axis exhibits a predicted scaling form in distance and angle. Possible implications of these results for synchronization dynamics are discussed., Comment: 13 pages, 7 figures

We derive a general formula for the inertialess dynamics of active particles in linear viscoelastic fluids by means of a modified reciprocal theorem. We then demonstrate that force-free active particles in Maxwell-like linear viscoelastic fluids with no retardation have exactly the same dynamics as in Newtonian fluids. In contrast, active particles in Jeffreys-like fluids with retardation can display markedly different dynamics, including net motion under reciprocal actuation thereby breaking the scallop theorem., Comment: Error in equation (17). Missing term in time derivative

In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are sufficient to deform long microtubules, as are the collective fluid flows generated by many moving motors. Studies of streaming during oocyte development in the fruit fly $D.~melanogaster$ have shown a transition from a spatially-disordered cytoskeleton, supporting flows with only short-ranged correlations, to an ordered state with a cell-spanning vortical flow. To test the hypothesis that this transition is driven by fluid-structure interactions we study a discrete-filament model and a coarse-grained continuum theory for motors moving on a deformable cytoskeleton, both of which are shown to exhibit a $swirling~instability$ to spontaneous large-scale rotational motion, as observed., Comment: 6 pages, 5 figures and Supplementay Material (5 pages, 5 figures); SM video at website of REG

Solutions to the Stokes equations written in terms of a small number of hydrodynamic image singularities have been a useful tool in theoretical and numerical computations for nearly fifty years. In this article, we extend the catalogue of known solutions by deriving the flow expressions due to a general point torque and point source in the presence of a stationary sphere with either a no-slip or a stress-free (no shear) boundary condition. For an axisymmetric point torque and a no-slip sphere the image system simplifies to a single image point torque, reminiscent of the solution for a point charge outside an equipotential sphere in electrostatics. By symmetry, this also gives a simple representation of the solution due to an axisymmetric point torque inside a rigid spherical shell. In all remaining cases, the solution can be described by a collection of physically intuitive point and line singularities. Our results will be useful for the theoretical modelling of the propulsion of microswimmers and efficient numerical implementation of far-field hydrodynamic interactions in this geometry., Comment: 30 pages, 8 figures

Many species of bacteria swim through viscous environments by rotating multiple helical flagella. The filaments gather behind the cell body and form a close helical bundle, which propels the cell forward during a "run". The filaments inside the bundle cannot be continuously actuated, nor can they easily unbundle, if they are tangled around one another. The fact that bacteria can passively form coherent bundles, i.e. bundles which do not contain tangled pairs of filaments, may appear surprising given that flagella are actuated by uncoordinated motors. In this article, we establish the theoretical conditions under which a pair of rigid helical filaments can form a tangled bundle, and we compare these constraints with experimental data collected from the literature. Our results suggest that bacterial flagella are too straight and too far apart to form tangled bundles based on their intrinsic, undeformed geometry alone. This makes the formation of coherent bundles more robust against the passive nature of the bundling process, where the position of individual filaments cannot be controlled., Comment: Supplementary information available at https://doi.org/10.1038/s41598-020-64974-6

Magnetic microrobots that swim through liquid media are of interest for minimally invasive medical procedures, bioengineering, and manufacturing. Many of the envisaged applications, such as micromanipulation and targeted cargo delivery, necessitate the use and adequate control of multiple microrobots, which will increase the velocity, robustness, and efficacy of a procedure. While various methods involving heterogeneous geometries, magnetic properties, and surface chemistries have been proposed to enhance independent control, the main challenge has been that the motion between all microwsimmers remains coupled through the global control signal of the magnetic field. Katsamba and Lauga proposed transchiral microrobots, a theoretical design with magnetized spirals of opposite handedness. The competition between the spirals can be tuned to give an intrinsic nonlinearity that each device can function only within a given band of frequencies. This allows individual microrobots to be selectively controlled by varying the frequency of the rotating magnetic field. Here we present the experimental realization and characterization of transchiral micromotors composed of independently driven magnetic helices. We show a swimming micromotor that yields negligible net motion until a critical frequency is reached and a micromotor that changes its translation direction as a function of the frequency of the rotating magnetic field. This work demonstrates a crucial step towards completely decoupled and addressable swimming magnetic microrobots.

Through billions of years of evolution, microorganisms mastered unique swimming behaviors to thrive in complex fluid environments. Limitations in nanofabrication have thus far hindered the ability to design and program synthetic swimmers with the same abilities. Here we encode multi-behavioral responses in artificial swimmers such as microscopic, self-propelled tori using nanoscale 3D printing. We show experimentally and theoretically that the tori continuously transition between two primary swimming modes in response to a magnetic field. The tori also manipulate and transport other artificial swimmers, bimetallic nanorods, as well as passive colloidal particles. In the first behavioral mode, the tori accumulate and transport nanorods; in the second mode, nanorods align along the tori's self-generated streamlines. Our results indicate that such shape-programmed microswimmers have the potential to manipulate biological active matter, e.g. bacteria or cells.

The design of artificial microswimmers has generated significant research interest in recent years, for promise in applications such as nanomotors and targeted drug-delivery. However, many current designs suffer from a common problem, namely the swimmers remain in the fluid indefinitely, posing risks of clogging and damage. Inspired by recently proposed experimental designs, we investigate mathematically the dynamics of degradable active particles. We develop and compare two distinct chemical models for the decay of a swimmer, taking into account the material composition and nature of the chemical or enzymatic reaction at its surface. These include a model for dissolution without a reaction, as well as models for a reacting swimmer studied in the limit of large and small Damk\"ohler number. A new dimensionless parameter emerges that allows the classification of colloids into ballistic and diffusive type. Using this parameter, we perform an asymptotic analysis to derive expressions for colloid lifetimes and their total mean-squared displacement from release and validate these by numerical Monte Carlo simulations of the associated Langevin dynamics. Supported by general scaling relationships, our theoretical results provide new insight into the experimental applicability of a wide range of designs for degradable active colloids.