Numerical simulations of microorganisms in homogeneous turbulence: chemical response and sedimentation.

Participant name Bearon, Rachel Bees, Martin Benzi, Roberto Brandt, Luca Calzavarini, Enrico Title and abstract The transport of active swimmers in shear flows. Many micro-organisms such as bacteria and
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Participant name Bearon, Rachel Bees, Martin Benzi, Roberto Brandt, Luca Calzavarini, Enrico Title and abstract The transport of active swimmers in shear flows. Many micro-organisms such as bacteria and algae swim in fluid environments. This swimming behaviour can interact with fluid motions to generate transport which differs both from that experienced by passive tracers in flow and micro-swimmers in the absence of flow. Examples will include a mechanistic model for helical gravitactic phytoplankton and a model for slender bacteria which undergo runand-tumble chemotaxis in a channel. Orientation and dispersion of swimming microorganisms in laminar and turbulent flows. To understand large-scale behavioural dynamics of plankton in complex flows it is necessary to disentangle mechanisms for individual behaviour, and systematically scale-up to a continuum or population-level description of a suspension. Here, I shall describe how the coupling of external torques and stimuli with micro- and macro-scale fluid dynamics can result in effective biased motion, not necessarily in the intended direction, leading to dispersion phenomena in laminar and turbulent flows that are qualitatively distinct from tracer particles. New results will be presented for a population-level description of the relative drift and diffusion of non-biased swimming cells in flows in constrained environments. Competition between fast and slow diffusing species. We study an individual based model in which two spatially-distributed species, characterized by different diffusivities, compete for resources. We consider several examples with homogeneous and distributed resource and subject to compressible and incompressible advection. In all cases, at varying the parameters, we observe a transition from a regime in which diffusing faster confers an effective selective advantage to one in which it constitutes a disadvantage. We analytically estimate the magnitude of this advantage (or disadvantage) and test it by measuring fixation probabilities in simulations of the individual-based model. Our results provide a framework to quantify evolutionary pressure for increased or decreased dispersal in a given environment. Numerical simulations of microorganisms in homogeneous turbulence: chemical response and sedimentation. A Lagrangian model of Copepod dynamics: clustering by escape jumps in turbulence. Planktonic copepods are small crustaceans that have the ability to swim by quick powerful jumps. Such an aptness is used to escape from high shear regions, which may be caused either by flow perturbations, produced by a large predator (i.e. fish larave), or by the inherent highly turbulent dynamics of the ocean. Through a combined experimental and numerical study, we investigate the impact of jumping behaviour on the small-scale patchiness of copepods in a turbulent environment. Crimaldi, John De Lillo, Filippo De Monte, Silvia Dynamics of Motile Phytoplankton in Turbulence: Experimental and Numerical Investigations of Microscale Patchiness. The collective impact of phytoplankton in biogeochemical cycles stems from interactions at the microscale, and the nature of these interactions depends on the spatial distribution of individual phytoplankton cells. Numerical simulations from the Stocker lab (e.g., Durham et al., 2011) demonstrate that turbulence biases the swimming direction of motile phytoplankton, resulting in the generation of microscale patchiness. This unmixing process is driven by gyrotactic coupling between Kolmogorov-scale velocity gradients and the phytoplankton motility; the degree of generated patchiness depends both on features of the flow and the organism. In this talk, I will discuss results and challenges from preliminary experiments to directly visualize and measure microscale phytoplankton distributions in realistic turbulent flows. Live populations of motile phytoplankton were introduced into a purpose-built grid-turbulence facility that generates approximately homogeneous, isotropic turbulence. Planar laser-induced fluorescence (PLIF) was then used to image 2D distributions of individual cells, enabling direct calculations of patchiness for two species and several flow cases. Future work will extend these measurements to 3D for a wider range of species and flows. I will also discuss numerical simulations of gyrotactic aggregation to demonstrate the role of Lagrangian Coherent Structures (LCS) on patch formation. Neutrally Buoyant Organisms in Stratified Turbulence. Numerical simulations of a density-stratified, turbulent flow are employed to investigate the formation of thin layers of non-swimming organisms around an equilibrium depth, where their density equals that of the fluid. We find that the resulting distribution has non-trivial properties beyond the simple vertical localization. The consequences for the formation of thin phytoplankton layers are discussed. On the distribution of rare marine microbial genetic sequences. Rare species are an notable feature of communities, and their assessment influences both the understanding of the ecological dynamics, and conservation policies. Quantification of biodiversity strongly depends on the capacity of resolving rare organisms, and hypothesis about the distribution of their abundance is often used as a means of estimating biodiversity in cases of under-sampling. Mathematical models on community composition generically predict that the abundance of rare species decreases exponentially with their rank. This behaviour is supported by observations of animal populations, in spite of the relatively small number of different coexisting species. Molecular methods, providing many hundreds of different genetic sequences per sample, open the door to a more precise analysis of the tail of species of low abundance. Even if the rare biosphere is often associated to the existence of a long tail of rare sequences, few studies have addressed the shape of such a tail, and provided different results depending on the class of organism and environment under study. In this talk, I will present evidence that the tail of rare sequences in marine planktonic communities appear to follow a power law with a highly consistent exponent in more than 50 locations of the global ocean, sampled during the Tara oceans expedition. I will discuss different hypothesis on the mechanisms that may shape planktonic communities across ecological and evolutionary time scales. Durham, M. William Karp-Boss, Lee Kiørboe, Thomas Lauga, Eric Turbulent unmixing: how flow drives patchiness in the distribution of phytoplankton. Phytoplankton are often heterogeneously distributed at the centimeter scale, corresponding to the size of the smallest turbulent fluctuations. We demonstrate that this patchiness can originate from a coupling between turbulent shear and gyrotactic motility, a defining feature of many phytoplankton species. By tracking individual cells within a direct numerical simulation (DNS) of turbulence, we observed gyrotactic phytoplankton aggregate in tightly packed clusters. The fate of a species is characterized by two dimensionless parameters, measuring cell stability and swimming speed. These models are confirmed with by measuring the distribution of Heterosigma akashiwo within a vortical flow. By reducing the mean distance between organisms, this previously unconsidered mechanism can markedly increase encounter rates, which control nearly all ecological interactions in the ocean. Phytoplankton sinking in turbulent flows. Turbulence is a ubiquitous and important feature of the upper mixed layer where phytoplankton reside. On scales relevant to individual cells and colonies, dissipating turbulence thins diffusive boundary layers around cells and affects probabilities of encounter critical for processes such as predator-prey interactions and aggregation. Superimposed on ambient fluid motion are local motions of cells due to swimming and gravitational settling. Phytoplankton cells, particularly the large and morphologically diverse, non-motile diatoms, are denser than their surrounding fluid and therefore sink. Sinking holds significant implications to the residence time of cells in the photic zone and ultimately to phytoplankton productivity and fluxes of carbon and other elements to the deeper ocean. How settling cells interact with ambient turbulence is not well understood. Results from experimental and numerical studies show that turbulence enhances sinking (or rising) velocities of a variety of particles including phytoplankton. In addition, interactions between settling particles and turbulence can lead to clustering. Proposed explanations to the observed behaviors have focus on inertial mechanisms of acceleration. However, in the parameter space defined by the characteristics of phytoplankton, shape and buoyancy control may be much more important than inertia in determining phytoplankton-turbulence interactions. Small-scale turbulence and organism-organism interaction in the ocean. Small-scale turbulence may enhance collision rates between microscopic particles and organisms in the plankton and, thus, have direct implications for fundamental ecological processes in the ocean, including formation of marine snow and predator-prey encounter rates. Because many plankton perceive their environment, including their prey and predators, through fluid signals, turbulence may also interfere indirectly with organism interactions. I will review and discuss experimental and theoretical evidence of such effects of small-scale turbulence. Fluid dynamics at the level of one cell Many small organisms possess flagella, slender whiplike appendages which are actuated in a periodic fashion in fluids and allow the cells to self-propel. In this talk we highlight some interesting fluid dynamics phenomena at the level of one cell and its flagella. We review the classical physics for flagellar propulsion, summarise some classical examples where flow physics has successfully shed light on biology, and focus on our recent work on the interactions between multiple deforming flagella. Mahadevan, Amala Mariani, Patrizio Nelson, David Plankton Patchiness. The availability of light and nutrients essential to the growth of phytoplankton are variable and modulated by the complex dynamics of the upper ocean. Dynamical instabilities and changing surface conditions lead to an evolving oceanic environment and turbulent flow field that support episodic growth, while stirring and transporting phytoplankton. This results in a patchy distribution of phytoplankton with a large fraction of the biological activity concentrated in hotspots. Here, I will examine the variability of phytoplankton concentrations on scales of km using satellite and in situ data. Using models for mixed layer dynamics and productivity, I will demonstrate physical processes that modulate the conditions for phytoplankton growth on time scales of order a day and solicit a strong biological response. I will argue that episodic phytoplankton productivity and patchy distributions are triggered by ocean dynamics and are critical to the ecosystem built on the success of organisms that rely on the aggregation of food. Swimming under the risk of predation: plankton encounter rates and selfoverlap in calm and turbulent conditions. Movement is a fundamental behavior of organisms that brings about beneficial encounters with resources but also exposes them to dangers of predation. Those constraints and the tradeoff between benefits and risks should shape the movement patterns adopted by organisms. This tradeoff can be hypothesized as being particularly apparent in the behavior of plankton, which inhabits a dilute 3D environment where there are few refuges or orienting landmarks. In this talk I will present an analysis of the swimming path geometries of plankton based on laboratory observations and numerical modeling. A volumetric Monte Carlo sampling approach is used to analyze 3D zooplankton tracks collected in calm water conditions and to derive a self-overlap function. The self-overlap function appears to reveal the tradeoffs between the efficient search for prey and minimization of predation risk. The results demonstrate that swimming patterns in plankton are highly correlated and display non-random properties that reduce predation risk in pelagic environments and are consistent with lifetime fitness optimization. Moreover, these behaviors differ between species and gender, and change with local environmental conditions, indicating state and stage dependent tradeoffs in movement behavior and suggesting efficient adaptive behavior in planktonic organisms. We expand the approach introducing turbulence in our analyses and describing the encounter dynamics of different behavioral patterns in both calm and turbulent conditions. This is done using a numerical agent-based model of the plankton encounter rate that is coupled to kinematic simulations of the turbulent flow. Competition and cooperation at high Reynolds number. Microorganisms living in the ocean can be subject to strong turbulence, with cell division times in the middle of a Kolmogorov-like cascade of eddy turnover times. We start with the dynamics of a diffusive Fisher equation describing cell proliferation in one and two dimensions, coupled to turbulent advection. Inertial effects and cell buoyancy lead us to study effectively compressible advecting velocity fields. For strong enough compressible turbulence, reproducing microorganisms such as bacteria and phytoplankton track, in a quasilocalized fashion, sinks in the turbulent field, with important consequences for the carrying capacity and for fixation times when two genetically different species compete. We describe a model, inspired by experiments on baker's yeast, which focuses on both competition and cooperation. Pagonabarraga, Ignacio Rafai, Salima Hydrodynamic cooperativity in active suspensions: self organization and cluster phase formation. Active systems generate motion due to energy consumption, usually associated to their internal metabolism or to appropriate, localized, interfacial chemical reactivity. As a result, these systems are intrinsically out of equilibrium and their collective properties result as a balance between their direct interactions and the indirect coupling to the medium in which they displace. In many circumstances self-propelled particle swim and move inside a fluid environment. The role of the medium in the collective behavior of such systems remains less well understood. In particular, the effect it may have modulating or modifying the understood mechanisms for selfassembly in their absence has not been properly addressed. A dynamical approach is required to analyze the evolution of such active suspensions and quantify their selfassembly and ability to generate intermediate and large scale stable structures. The use of computational models that couple individuallyresolved self-propelling particles and the continuum solvent in which they move provides a useful means to analyze and quantify the properties of spontaneous emerging structures. I will describe how to take advantage of coarse grained computational methods that capture the essence of activity generation and the appropriate hydrodynamic coupling when ensembles of active particles move together. I will analyze the relevant physical mechanisms underlying the specific properties of model active suspensions. By focusing on simplified models, it is possible to identify the relevant parameters which control such behavior. Understanding the mechanical principles which determine the emergence of cooperativity will provide a solid basis to clarify the role of hydrodynamics in active materials and understand how to combine them with biochemical interactions to control their properties and behavior. Flowing properties of a microswimmer suspension. Suspensions of motile living organisms represent a non equilibrium system of condensed matter of great interest on a fundamental point of view as well as for industrial applications. These are suspensions composed of self-driven units - active particles- able to convert stored energy into movement. Interactions between active particles and the liquid they are swimming in give rise to mechanical stresses and large scale collective motion that have recently attracted a lot of interest in physics and mechanics communities. From the industrial point of view, microalgae are used in many applications ranging from the food industry to the development of new generations of biofuels. The biggest challenges concerning all this applications are the separation, filtration and concentration processes of microalgae. There is thus a real need of a better understanding of the flow of active matter to achieve a optimal control of these systems. I ll present our recent work on microswimmer suspensions: rheological properties of active suspensions as well as the «microscopic» characteristics of the random walk of the green microalga Chlamydomonas Reinhardtii. We have recently shown that hydrodynamics of a microalgae suspension coupled with phototaxis* leads to a spontaneous concentration of the suspension toward the center of the channel. Experiments as well as simulations will be presented. *Biased movement that occurs when an organism moves in response to the stimulus of light. Schmitt, François Plankton in marine turbulence. Marine planktonic organisms live in turbulent flows and see the world in a Lagrangian way. They have developed, over many generations, a strong adaptation to the fluctuations of the fluid they live in. The results are complex behaviors and population dynamics. Here we propose an overview of our previous results in two topics related to plankton complex dynamics. First, we discuss phytoplankton concentration in relation with turbulence, from field measurements. Florescence is a proxy of phytoplankton concentration and can be recorded in situ, at high frequency (typically 1 Hz). Fixed point as well as Lagrangian measurements of fluorescence have been analyzed, and compared to temperature simultaneous measurements, which belong to turbulent passive scalars. Scaling laws for the characterization of intermittency are obtained, and depending on the scale, phytoplankton is seen as been close to a passive scalar, or to behave as a chemically or biologically active scalar. Such methodology is illustrated with several case studies, recorded in Eulerian or Lagrangian way in the eastern English Channel. We also discuss zooplankton behavior by considering copepods swimming statistics. Copepods have developed, over a very large number of generations, swimming abilities as trade-off between the energetic cost of swimming and the benefits of swimming behavior, for mating, for food intake and for avoiding predators. The swimming strategy is genetically programmed to adapt to the turbulent flow corresponding to their ecological niche. In the experiments considered here, copepods are taken from the field, placed in the laboratory in an aquarium, and filmed. Image analysis provides access to trajectories, velocities, and in some cases (when high speed cameras are used) acceleration. Copepod swimming behavior is statistically characterized in the framework of anomalous diffusion and multifractal random walks. Clustering is also performed to study the behavior using symbolic dynamics. With such tools, copepod s sex, development stage, species, and environmental conditions may be considered. Finally we also discuss the role of very large acceleration events as a predator avoidance strategy, and analyse high speed (1000 frames per second) records of jump events of the species Eurytemora affinis and Acartia tonsa: the statistics of the jump duration, time between jumps, velocity and acceleration dynamics during jump events, are considered for both species. Stocker, Roman How much fluid
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