Fluid Physics of Life

Insect-pathogenic fungi such as Entomopthora muscae rely for their transmission on the ejection of conidial spores. The shower of spores needs to reach sufficiently far to land on a new susceptible host – in this case a house fly. Here we investigate the mechanism of forcible ejection of fungal spores from the tip of micrometric stalks which penetrate outward from an infected fly cadaver. Each stalk act as a soft water cannon, using a liquid pressure buildup to eject a jet of protoplasm and the spore initially attached to the stalk. To study its physics, we design a millimetric model “soft cannon”: an elastomeric fluid-filled barrel plugged with a projectile. This allows precise control of the stored elastic energy via the break-through pressure required for projectile ejection, which is set by the known and adjustable geometry and elasticity of the cannon. We study the resulting ejection velocity of the projectile and identify the energy conversion efficiency as function of cannon properties. We extend our force-balance model to the ejection of fungal conidia and predict that ejection velocity decreases with spore size. Our ballistic model – taking into account the estimated ejection velocity of primary E. muscae conidia from high-speed visualization – predicts that a conidium of ≳10 µm is able to traverse a quiescent boundary layer of a few millimeters under aerodynamic drag conditions. This corroborates with the naturally observed two-step ‘cascade’ of E. muscae spores, where a (smaller) secondary conidium can be ejected from a secondary conidiophore formed by a primary conidium.

Active fluids like suspensions of bacteria, microtubule bundles and artificial microswimmers consist of individuals that are able to transform internal energy into a directed motion. Many efforts have been made to understand the influence of individual’s properties onto the emergence of pattern on the meso- or macroscale. In the talk, we first formulate “microscopic” equations of motion for a collection of active particles that interact through short-range alignment and long-range hydrodynamic interactions and are subject to rotational and translational noise. A derivation of “mesoscale” continuum equations from the equations of motion of this collection of interacting model swimmers will thnen be sketched. Depending on the symmetry of the interaction between swimmers the continuum equations obtained lead to polar or nematic order parameter equations coupled to the hydrodynamic equation of the surrounding fluid. As a result, the different symmetries lead to the emergence of different topological defect as well as different forms of collective motion and patterns. Here, the phenomenon of mesoscale turbulence is discusssed in detail and compared to recent experiments. Finally, the topic of control of emerging patterns in swimmer suspensions by means of external fields and periodic arrays of obstacles is addressed.

The slime mould \textit{Physarum polycephalum} is a very simple unicellular but seemingly intelligent organism with a network-like body. Its complex behaviour requires the ability to propagate, store and process information. Recently, it has been shown that \textit{Physarum} propagates information about stimuli with the fluid flows throughout its network. And most inspiringly, \textit{Physarum} was observed to adapt its networks tube radii network-wide in response to stimuli, reaching a steady-state as a long term response to the applied stimuli, keeping a memory of the stimuli in its network morphology. Inspired by this observation we here investigate the capacity to store information about previous stimuli in the morphology of an adaptive flow network. We model the organism as a flow network whose radii can change when optimising the network to have least energy dissipation. We observe how the system reacts to localised changes and the timescale of its responses to applied stimuli by numerical simulation. Through theoretical understanding we aim to pin-point to the information storing and processing capabilities of adaptive flow networks in general and \textit{Physarum} networks specifically.

The hydraulic system of trees allows long-distance water transport under negative pressure from the soil to the leaves. Although plant water transport has utmost importance for the functioning of our biosphere, its mechanisms are not yet fully understood. As a result, we have not been able yet to develop artificial transport systems under negative pressure, unless under very controlled, unnatural conditions. Available evidence suggests that porous cell walls between water conducting cells play a crucial role in water transport of plants by determining both hydraulic efficiency and safety. The nanoporous walls provide considerable hydraulic resistance, contribute to transport redundancy, and prevent to some extent spreading of air from embolised water conducting cells to water-filled ones. My PhD thesis focuses on the chemical and mechanical properties of porous cell walls in water conducting cells of the xylem tissue in order to better understand the functional mechanisms of water transport through these very thin, mesoporous media. For this purpose, the stiffness of wet (i.e., never-dried) and dehydrated porous cell walls is studied using atomic force microscopy, which offers a sensitive approach to measure detailed surface properties in situ. These data enable us to increase a better understanding of hydraulic failure by potential pressure differences across neighbouring cells. Besides this experimental work, I am reviewing the concept of "negative pressure", which is typically poorly described in the field of plant sciences, leading to considerable confusion and misunderstanding. Therefore, it is important to find a common, interdisciplinary language between biologists, physicists and chemists to define negative pressure and its related phenomena in an accessible and comprehensive way.

Soft plates immersed in fluids appear in many biological processes, including swimming, flying, and breathing. These plates deform in response to fluid flows, yet fluid stresses are in turn influenced by the plate deformation. We present a mathematical model examining the flow of a viscous fluid in a narrow slit formed by two elastic plates, and demonstrate a strongly nonlinear flow response. The volumetric flow rate first increases linearly with pressure; however, the bending of the plates reduces the gap size and the flow rate is reduced. Finally, the slit closes and no longer permits flow. Our model, which is based on low-Reynolds-number hydrodynamics and linear plate theory, yields insights into two competing effects: While the plate bending generally reduces the slit aperture, it also causes the two plates to move apart thus increasing the gap. Implications to biomedical flows are discussed and potential applications to flow control in man-made systems are considered.

Ischemic brain strokes are a major concern for public health. Major strokes obstructing main arteries cause reorganization of flows throughout the microvasculatuare, likely with a long lasting influence on brain microvasculature behaviour and topology. Strikingly flow reorganization is different in different parts of the brain vasculature. While the loopy surface arteriole network undergoes stops and reversals during a stroke, the penetrating arterioles exhibit steady flow direction. One hypothesis is that the flow reorganisation at the surface prevents changes in the penetrating arterioles. We here investigate if network topology and hierarchy of the system drives penetrating arterioles to be robust asking: Is the network designed to be resilient to such changes? To test this hypothesis, we analytically solved the flows in a toy model of an H porous system, showing that flow reversal in the penetrating arterioles can happen only for great pressure instabilities, due to the hierarchy and topology of the network. Currently, we are testing the same hypothesis in two dimensional irregular networks optimised for transport and in a real dataset of murine microvasculature.

It is well known that flagellated bacteria swim in circles near surfaces. However, recent experiments have shown that a sulfide-oxidizing bacterium named \textit{Thiovulum majus} can transition from swimming in circles to a surface bound state where it stops swimming while remaining free to move laterally along the surface. In this bound state, the cell rotates perpendicular to the surface with its flagella pointing away from it. Using numerical simulations and a simplified theoretical analysis, we demonstrate the existence of a fluid-structure interaction instability that causes cells with relatively short flagella to become surface bound.

Red blood cells (RBCs) show a complex behaviour in flow due to the intricate interplay between their membrane elasticity and hydrodynamic stresses [1]. During malaria infection, adhesion of infected red blood cells (iRBCs) to endothelial cells lining microvasculature is a key step for the parasite survival and its further multiplication. During the parasite development inside RBCs, iRBC morphology, stiffness, and adhesiveness change drastically, leading to a complex adhesion behaviour of iRBCs (e.g., crawling, flipping, rolling) under flow. Using a particle-based mesoscale hydrodynamics approach and a coarse-grained model of iRBC, we show that adhesion dynamic states not only depend on the stage of infection or membrane elasticity, but also on flow shear stresses. We show that a mid-stage iRBC flips at lower shear stresses in flow, which is replaced by crawling motion beyond critical shear stress. The critical shear stress increases with both membrane stiffness and viscosity contrast between the cytosol and suspending medium [2]. The transition from flipping to crawling resembles tumbling to the tank-treading transition of RBCs in free shear flow. Such a change in adhesion dynamics directly affects the interaction of iRBCs with vascular endothelium [3].

We discuss the physical mechanisms that promote or suppress the nucleation of a fluid-filled lumen inside a cell assembly or a tissue. We discuss lumen formation in a continuum theory of tissue material properties in which the tissue is described as a two-fluid system to account for its permeation by the interstitial fluid, and we include fluid pumping as well as active electric effects. Considering a spherical geometry and a polarized tissue, our work shows that fluid pumping and tissue flexoelectricity play a crucial role in lumen formation. We furthermore explore the large variety of long-time states that are accessible for the cell aggregate and its lumen. Our work reveals a role of the coupling of mechanical, electrical and hydraulic phenomena in tissue lumen formation.

Compartmentalisation is essential for eukaryotic cell function, allowing the division of metabolic and regulatory processes into membrane-bound, specialised compartments, such as organelles. In recent years, intracellular phase separation has garnered much attention as a non-membrane means of organising components through the formation of droplet-like compartments, which are functionally implicated in both health and disease. Evidence suggests that droplet clearance involves autophagy, a highly-conserved degradation system in which membrane sheets expand and bend to isolate portions of the cell interior inside autophagosomes. Interestingly, the wrapping of elastic polymer sheets around water droplets or ‘capillary origami’ resembles the bending of autophagic membrane sheets around droplets. In my talk, I will summarise our recent results on phase separation, the droplet-membrane interaction and sequestration of droplets by autophagic membranes.

Recent work on self-organized remodelling of vasculature in slime-mold, leaves venation systems or vessel systems in vertebrates has provided a plethora of potential adaptation mechanisms. All these have in common the underlying hypothesis of a flow driven machinery, meant to prune primary plexi in order to optimize the system's dissipation, flow uniformity or more, with different versions of constraints. Nevertheless, the long-term dynamics of adapting networks whose architecture and function is particularly dependent of their respective environment have not been properly understood. Therefore, interwoven capillary systems such as found in the liver, kidney and pancreas, present a novel challenge regarding the field of coupled distribution networks. We here present an advanced version of the discrete Hu-Cai model, coupling two spatial networks in 3D. We show that spatial coupling of two flow adapting networks can control the onset of topological complexity given the system is exposed to short-term flow fluctuations. Further, our approach results in an alternative form of Murray's law, which incorporates the local vessel interactions and flow fluctuations.

We present a theoretical treatment of elastic deformation caused by living cells embedded in a gel-like elastic medium. We are interested in the elastic response to the external force at a distance somewhere inside the elastic body. We utilize Boussinesq’s solution to derive the relevant equations that related the elastic parameters and cell deformation. The theory includes the forces that arise from the deformation of the elastic matrix.

Chemotaxis - the navigation of biological cells guided by chemical gradients - is crucial for bacterial foraging, immune responses, and guidance of sperm cells to the egg during fertilization. Previous work on chemotaxis focused predominantly on idealized conditions of perfect chemical gradients. However, natural gradients are affected by distortions, e.g. by turbulent flows in the ocean. Recent experiments with bacteria[1] and sperm cells from marine invertebrates[2] have surprisingly revealed the existence of an optimal turbulence strength at which the chemotaxis is more effective than for still water conditions with perfect gradients. Using sperm chemotaxis in steady and unsteady shear flows as a prototypical example, we reproduce an optimal turbulence strength in numerical simulations. We can understand the origin of this optimum and quantify it. For this we apply linear response theory to the concentration filaments, which are typical for scalar turbulence: We explain how external flows distort sperm swimming paths and concentration gradients, but at the same time extend the spatial range of these gradients. The combination of these two competing effects accounts for the optimal turbulence strength. We compare our theoretical results to previous experiments. [1] Taylor, Stocker; Science 2012 [2] Zimmer, Riffell; PNAS 2011

During mouse preimplantation development, the formation of the blastocoel, a fluid-filled lumen, breaks the radial symmetry of the blastocyst. What controls the formation and positioning of this basolateral lumen remains obscure. We find that accumulation of pressurized fluid fractures cell-cell contacts into hundreds of micron-size lumens. Microlumens eventually discharge their volumes into a single dominant lumen, which we model as a process akin to Ostwald ripening, underlying the coarsening of foams. Using chimeric mutant embryos, we tune the hydraulic fracturing of cell-cell contacts and steer the coarsening of microlumens, allowing us to successfully manipulate the final position of the lumen. We conclude that hydraulic fracturing of cell-cell contacts followed by contractility-directed coarsening of microlumens sets the first axis of symmetry of the mouse embryo.

Immunoglobulin A (IgA) is a class of antibodies produced by the adaptive immune system and secreted into the gut lumen to fight pathogenic bacteria. We demonstrated that the main physical effect of these antibodies is to enchain daughter bacteria, i.e. to cross-link bacteria into clusters as they divide, preventing them from interacting with epithelial cells, thus protecting the host. These antibody-mediated links between bacteria may break over time. To investigate the interaction between the time scales of bacterial replication and of link breaking, we study several models using analytical and numerical calculations. We obtain the resulting distribution of chain sizes, that we fit to experimental data. Our models show robustly that at higher replication rates, bacteria replicate before the link between daughter bacteria breaks, leading to growing cluster sizes. On the contrary at low growth rates two daughter bacteria have a high probability to break apart. Thus the gut could produce IgA against all the bacteria it has encountered, but the most affected bacteria would be the fast replicating ones, that are more likely to destabilize the microbiota. The next step is to integrate this into a spatial model of the bacterial dynamics along the digestive tract.

Neuronal activity induces changes in blood flow by locally dilating vessels in the brain microvasculature. How can the local dilation of a single vessel increase flow-based metabolite supply, given that flows are globally coupled within microvasculature? Solving the supply dynamics for rat brain microvasculature, we find one parameter regime to dominate physiologically. This regime allows for robust increase in supply independent of the position in the network, which we explain analytically. We show that local coupling of vessels promotes spatial clustering in increased supply by dilation.

Magnetic microswimmers can behave differently in a microfluidic channel, which can be tuned by controlling the external magnetic field, e.g., magnetotactic bacteria can either be distributed uniformly or form clusters along the microchannel depending on the strength of the magnetic field. We develop a theoretical framework to deal with the collective motion of the magnetic swimmers in a fluidic environment, where the swimmers can interact with each other by magnetic dipole-dipole interaction and/or hydrodynamic interaction. With the theory, we disclose the mechanism underlying different behaviours of the magnetic swimmers (radial focusing, longitudinal clustering and radial condensation) in the microfluidic channel.

Wall entrapment of swimming bacteria such as E. coli has been studied both experimentally and theoretically. However, the underlying mechanisms of the cell-wall interaction is only partially resolved and contradicting experimental and theoretical results have to be addressed. Here, we study the near-wall behaviour of E. coli by applying mesoscale hydrodynamic simulations. The bacterium cell is composed of spherocylindrical body and several helical flagella constructed of point particles and the fluid is described by the multiparticle collision dynamics approach. we identify three main stages of wall-entrapment: approach, alignment, and surface swimming, as was resolved experimentally. While the cell swims close to a surface, a fast oscillation around the swimming direction is observed. Moreover, absorbed cells swim with a preferred orientation pointing toward the wall. we see increasing the initial angle of swimming does not change the collision angle, indicating that steric interactions are primary driving force for cell reorientation. However, hydrodynamic effects are visible in the velocity of the cell which slows down as the cell approached the wall.

The process of making an oocyte starting from a germline tissue is a fundamental cellular process. Oogenesis demonstrates remarkable mechanical as well as hydrodynamic phenomena across organisms. Dynamic size regulation and mechanical symmetry breaking in germ cell population (within a syncytia) leads to heterogeneous growth leading to cell fate decisions. The roundworm C. elegans has a tubular syncytial (tissue architecture with connected cytoplasm) germline, which achieves germ-cell growth by hydrodynamic flows that range across 400 microns. By quantitative analysis and theoretical modeling, we discover that germ cells actively generate long-range hydrodynamic flows along the germline, while also locally maintaining their homogenous size. The coupling of cell mechanics and hydrodynamic fields lead to active pressure-tuning, which yields a hydraulic instability setting a critical size for the germ-cells in the absence of active sources. This mechanism ensures selection and growth of germ cells beyond a critical size at the expense of smaller cells and is independent of the apoptotic machinery. We unravel the physical basis of oogenesis and cell elimination by combining cellular mechanics and active hydrodynamics. Our findings elucidate a novel connection of cell fate and mechanics of volume regulation, and proposes a cell death mechanism that is emergent out of cellular competition rather than programmed.

A state of low oxygen occurs frequently in soil, water and multicellular tissues and has played a pivotal evolutionary role in shaping multicellularity. While the social amoeba Dictyostelium discoideum is an obligatory aerobic organism, its ecological niche in the soil and around large amount of bacteria will expose the amoeba to reduced oxygen availability. We have recently observed that vertically confining a micro-colony of Dictyostelium cells in a growth medium triggers cells to move quickly outward of the self-generated central hypoxia area and thus form an expending ring. The analysis of the cells behavior within the micro-colony reveals a complex response to hypoxia depending upon their position: - Cells at the very hypoxic center are immobile but remains viable even after three days. - Cells closer to the ring present a clear outward directionality. - Cells at intermediate positions are very polarized and motile but with limited outward directionality - Cells within the outer part of the ring are poorly polarized as typical vegetative cells Using a fluorescent oxygen sensor included in a thin PDMS film, we can show that the ring of cells occurs at the level of a sharp oxygen gradient. The various cell behaviors in the micro-colony was mimicked using an in silico cellular Potts model that includes both a positive aerotaxis upon an oxygen gradient but also a differential response to the absolute oxygen concentration. While the signaling pathway behind aerotaxis remains unclear, preliminary data suggest that PhyA and Skp1 influence oxygen sensing of the vegetative cells.

Sperm cells swim through the fluid by a periodic wave-like beating of their flagellum [1-3]. At low Reynolds numbers and in confinement, the directed motion of sperm is strongly influenced by steric and hydrodynamic wall interactions. We model sperm motility in mesoscale hydrodynamics simulations by imposing a planar traveling bending wave along the flagellum [2]. Sperm are simulated swimming in curved, straight, shallow and zigzag-shaped microchannels [4]. Our simulation results reveal a consistent picture of passive sperm guidance that is dominated by the steric interactions of the beat pattern with the nearby surfaces. In particular, we identified the beat-shape envelope to critically determine surface attraction strength. For swimming in zigzag microchannels, the deflection-angle distribution at sharp corners is calculated and found to be in good agreement with recent microfluidic experiments [5]. The simulations reveal a strong dependence of the deflection angle on the orientation of the beat plane with respect to the channel sidewall, and thus deepen the understanding of sperm navigation under strong confinement. Detachment of sperm, while swimming along curved walls, is dominated by the change of beat-plane orientation. We show how a buckling instability of the flagellar beat with increasing wavelength yields a three-dimensional beat pattern. Therefore, either a three-dimensional beat pattern or strong confinement in shallow channels drastically increases surface attraction. [1] J. Elgeti et al., Rep. Prog. Phys. 78, 056601 (2015) [2] J. Elgeti et al., Biophys. J. 99, 1018 (2010) [3] G. Saggiorato et al., Nat. Commun. 8, 1415 (2017) [4] S. Rode, J. Elgeti, Gompper, NJP 21, 013016 (2019) [5] V. Kantsler et al., PNAS, 110, 1187–92 (2013)

The collective dynamics of cell plays the key role in many fundamental biological processes like morphogenesis, tissue repair and tumour metastasis etc. Madin-Darby canine kidney (MDCK) cells have been established as one model system to study collective cell migration. On adhesive substrates, cells grow in roughly circular colonies, expanding with time and displaying fascinating motile behavior. Two aspects of their motion lie at the heart of this study: (a) Cells move throughout the colony, forming large scale patterns like swirls or fingers at the edge; reflecting a fluid like behaviour of the cell colony. At the same time, (b) the colonies are extremely cohesive. The colony is not maintained by a constant flux of cells leaving and entering from the surrounding. Instead, the surrounding is devoid of cells, one might say these colonies display liquid-vacuum coexistence. The active Brownian particle (ABP) model has been used intensively to model such motile cell colonies. However, ”normal” ABP’s show either liquid-gas coexistence - with a finite density of cells away from the colony, or crystallize, if the adhesion is strong enough to prevent particles from escaping. We propose a novel particle-particle interaction potential that allows for cells to move, despite strong adhesion. We show that this model results in colonies with fluid like properties while remaining cohesive in nature at the same time. Furthermore, these colonies can be under tensile stress, as reported for growing MDCK colonies.

Cell motility is often biased by biochemical and biophysical directional cues such as chemotaxis or durotaxis. Recently, a spatial gradient in the density of cell-sized obstacles was used to direct migration of persistently moving cells towards regions of low obstacle densities: a process called topotaxis. Using numerical simulations we study topotaxis of persistently moving active Brownian particles (ABPs). We demonstrate that ABPs perform topotaxis and that topotaxis is stronger for larger obstacle density gradients and for ABPs with larger persistence lengths. By numerically and analytically studying ABPs in square lattices of constant obstacle density we demonstrate that topotaxis of ABPs is a result of a density-dependent eective persistence length which is smaller for larger obstacle densities. Our results demonstrate that persistent motion on itself is sucient to obtain topotaxis and could be a starting point for exploring topotaxis of active particles and cells in much greater detail.

V. Satarifard and R. Lipowsky The interactions of membranes and vesicles with liquid droplets represent a new and relatively unexplored research field. One example is provided by aqueous phase separation of polymer solutions within lipid vesicles.[Dimova, RL, Advanced Materials Interfaces, 2017; RL, J. Phys. Chem. B, 2018] Such aqueous two-phase systems lead to wetting transitions at membranes, vesicle budding, and membrane tubulation. Analogous wetting phenomena are also relevant in the context of cell biology, where phase separation within the cytosol leads to biomolecular condensates (also known as membrane-less organelles), which behave like liquid droplets. Wetting of membranes starts with the nucleation and growth of nanodroplets, a process that is not accessible to optical microscopy but can be elucidated by molecular dynamics (MD) simulations. Recent MD simulations revealed that the contact line tension between nanodroplets and membranes is often negative and leads to nonaxisymmetric contact lines, which eventually form tight-lipped membrane necks. [VS et al., ACS Nano, 2018] MD simulations become, however, unfeasible when the interfacial tension becomes too low. Indeed, as we decrease this tension, the interface becomes more and more fuzzy, and we would need to simulate larger and larger droplets to obtain reliable results. Therefore, to explore the low tension regime, we have started to use an alternative approach based on energy minimization, which is computationally less expensive. This approach allows us to a wide range of parameters and to systematically determine the dependence of membrane wetting phenomena on interfacial tension, bending rigidity, line tension, and spontaneous curvature. We observe the new morphological transformation that involves both vesicles and droplets, including another regime with broken rotational symmetry. Finally, we determine the boundary between symmetric and asymmetric contact line geometries within the three-dimensional parameter space. Our results can be used to estimate line tensions from experimental observations.

Foraging behaviour of animals is generally described as optimized for maximal energy uptake per time spend foraging within optimal foraging theory. Food sources often occur as food patches, so that foraging becomes a balance between time spent for exploration and time spent for patch exploitation leading to the question at which point a patch should be abandoned. Foraging behaviour in a patchy habitat can also be observed in unicellular but spatially extended organisms like Physarum polycephalum. However, it is unclear which foraging strategy the large and adaptive network-like morphology allows for. The plasmodial network of P. polycephalum adapts its morphology in the process of foraging by mass transport. Recent observations show that on encounter of a food patch, depending on body size, the whole body is relocated for exploitation. We here study the morphological changes as a function of network size and nutritional state by introducing a model for the exploration and exploitation phases in P. polycephalum. We estimate the energy uptake from our foraging observations in order to obtain rules for the foraging behaviour.

Memory and anticipation are complex phenomena that have developed in higher species to predict and adapt to changing conditions. Even the unicellular slime mold Physarum polycephalum has been reported to anticipate periodic events. As a plasmodial tubular network, P. polycephalum changes its morphology in order to forage, and pumps cytoplasm throughout its body using oscillatory contractions of tubes organised in a peristaltic wave. Here, we show that P. polycephalum reacts towards periodic blue light stimulation by a reoccurring pattern of temporal cytoplasm pumping modulations. Quantifying tube contractions during both periodic stimulation and anticipation testing we uncover that anticipation behaviour reflects the organism’s internal time-scales likely associated with the rhythmically contracting actin cortex lining the tubes. Comparison with theoretical models suggests that anticipation behaviour is a result of non-linear mechanical properties of the contracting actin cortex.

Active matter systems are driven out-of-equilibrium due to injection of energy at the microscopic scale. We consider a scalar concentration field to describe a continuum theory of active colloidal suspensions, which account for the exchange of locally conserved momentum between the colloids and the solvent. We study the role of active hydrodynamic interactions in determining nucleation and growth in such a field theory and find novel dynamic phases.

Bacteria in the environment often interact with particulate matter, from the marine snow responsible for carbon export from the upper ocean in the biological pump, to carrier particles in wastewater treatment plants. A key determinant of the ecological interaction between bacteria and particles is their encounter rate. Approaches to date have focused on the diffusive regime, with sinking particles larger than the typical run length of a bacterium, and have shown that bacterial motility can greatly enhance encounter rate. These formulations neglect the effect of the shear generated by the particle's motion on the motility of the bacteria, yet shear is the major component of the encounter process in the ballistic regime, relevant for (the most abundant) small sinking particles. Here, we combine analytical and numerical calculations to quantify the encounter rates between sinking particles and non-motile or motile microorganisms in the ballistic regime, by explicitly accounting for the shape of the microorganisms and the role of the hydrodynamic shear created by the particle on rotational dynamics. We complement results with selected experiments on non-motile diatoms. We find that the shape-shear coupling significantly affects the encounter rate and the typical attachment location on the particle. A non-motile elongated microorganism avoids sinking particles because shear aligns it tangentially to the particle surface. As a result, the encounter rate is reduced by a factor proportional to the square of the bacterial aspect ratio as compared to a spherical cell. Conversely, a non-motile flat microorganisms utilizes its full size for the interception, because it tumbles under shear. For motile elongated microorganisms, the elongation-shear coupling increases the encounter rate approximately twofold compared to ballistic motility without shear for particles sinking at a similar speed to the bacterial swimming speed. Surprisingly, the same coupling dramatically reduces the encounter rate with faster sinking particles, compared to ballistic motility without shear, until the non-motile limit is recovered at sinking speeds 100-fold larger than the swimming speed. Both effects are a consequence of hydrodynamic focusing and screening upstream and downstream of the sinking particle. In contrast, motile flat microorganisms, such as artificial Janus-type microswimmers, experience upstream focusing, leading to high encounter rate. Elongated microorganisms typically attach to the leeward side of the particle, creating a physical source of heterogeneity in particle colonization, whereas flat motile microorganisms colonize it more uniformly. Applying these findings to realistic ocean conditions, we find that the flow created by a sinking particle leads to a ten-fold decrease in the encounter rate with motile bacteria when particles sink fast, compared to the ballistic motility without shear, indicating that flow can have important consequences in the colonization and ultimately degradation of particles, which drive one of the most important carbon fluxes in the ocean.

Motile cilia on ciliated epithelia in airways, brain and oviduct display coordinated beating in the form of metachronal waves, presumably due to mutual hydrodynamic coupling, which is important for efficient fluid transport. How the shape of the cilia beat determines the direction and wavelength of metachronal waves is not fully understood, nor is robustness with respect to noise in the presence of multiple synchronized states. We perform hydrodynamic simulations of cilia carpets, using experimental beat patterns, using a computationally efficient framework of Lagrangian Mechanics of Active Systems (LAMAS). Thereby, we determine all metastable synchronized states and their fundamental perturbation modes, which characterize the dispersion relation of metachronal waves.

How organisms acquire their shape is a central question in biology. Although morphogenesis is studied across different scales, ranging from the single cell level to the level of a whole organism, it remains challenging to investigate how distinct tissues establish coordinated morphogenesis at the organismal scale. Here, we take advantage of the relatively simple bilayered body plan of the sea anemone Nematostella vectensis to study organismal morphogenesis in the context of axial elongation. During development, Nematostella undergoes a transition from an almost spherical larva to a tubular-shaped polyp. Concomitantly with this dramatic shape change, developing Nematostella exhibit dynamic life history behaviors, such as cilia-based swimming, settlement, cavity expansion, and muscle-driven contractions. Physically constrained larvae fail to elongate properly, suggesting the importance of these emerging behaviors for normal development. To build an integrated framework for axial elongation that incorporates the emerging behaviors of multicellular systems, we combine a high-throughput live imaging approach with computational image analysis to monitor freely developing animals. We image isolated larvae in a 384 well plate for several days using a screening microscope, and establish automated measurement of multiple features, including body length and width, circularity, motility and body contractions. Interestingly, we identify strong correlations between axial elongation dynamics and specific organismal behaviors. Using genetic, pharmacological, and mechanical perturbations, we are testing the link between axial elongation and the mechanics of select organismal behaviors, and how such global forces acting across entire tissues impact cellular dynamics. Together, these experiments will establish a novel paradigm to interrogate the relationship between morphogenesis and the emerging behaviors of multicellular systems.

Many cells in the human body have to move through dense complex fluids such as various cells in the extracellular matrix or bacteria in mucus. While the motion of swimming bacteria in simple Newtonian fluids can be well quantified using continuum low Reynolds number hydrodynamics, the presence of supramolecular elements such as biopolymers leads to a much more complex behavior. Although the presence of polymers generally lowers particle mobility, surprisingly, several experiments have shown that bacterial speeds increase in polymeric fluids, but there is no clear understanding why. We perform extensive coarse-grained MPCD simulations of a bacterium swimming in explicitly modeled solutions of supramolecular model polymers of different lengths, stiffness and densities. We observe an increase of up to 60% in swimming speed with polymer density and show that this is a consequence of a non-uniform distribution of polymers in the vicinity of the bacterium leading to an effective slip. However, this alone cannot explain the large speed-up, but coupling to the chirality of the bacterial flagellum is essential. Finally we present results for swimming in crosslinked polymer networks where hydrodynamics is screened and speed enhancement is also observed. A. Zöttl, J. M. Yeomans, J. Phys.: Condens. Matter 31, 234001 (2019) A. Zöttl, J. M. Yeomans, Nat. Phys., doi.org/10.1038/s41567-019-0454-3, (2019)