We study the dynamics and the statistics of dilute suspensions of gyrotactic swimmers, a model for many aquatic motile microorganisms. By means of extensive numerical simulations of the Navier-Stokes equations at different Reynolds numbers, we investigate preferential sampling and small scale clustering as a function of the swimming (stability and speed) and shape parameters, considering in particular the limits of spherical and rod-like particles. While spherical swimmers preferentially sample local downwelling flow, for elongated swimmers we observe a transition from downwelling to upwelling regions at sufficiently high swimming speed. The spatial distribution of both spherical and elongated swimmers is found to be fractal at small scales in a wide range of swimming parameters. The direct comparison between the different shapes shows that spherical swimmers are more clusterized at small stability and speed numbers, while for large values of the parameters elongated cells concentrate more. The relevance of our results for phytoplankton swimming in the ocean is briefly discussed.
We study the small scale clustering of gyrotactic swimmers transported by a turbulent flow, when the intrinsic variability of the swimming parameters within the population is considered. By means of extensive numerical simulations, we find that the variety of the population introduces a characteristic scale $R^*$ in its spatial distribution. At scales smaller than $R^*$ the swimmers are homogeneously distributed, while at larger scales an inhomogeneous distribution is observed with a fractal dimension close to what observed for a monodisperse population characterized by mean parameters. The sc…
Marine plankton are usually modeled as settling elongated micro-swimmers. For the first time, we consider the torque induced by fluid inertia on such swimmers, and we discover that they spontaneously swim in the direction opposite to gravity. We analyze the equilibrium orientation of swimmers in quiescent fluid and the mean orientation in turbulent flows using direct numerical simulations. Similar to well-known gyrotaxis mechanisms, the effect of fluid inertial torque can be quantified by an effective reorientation time scale. We show that the orientation of swimmers strongly depends on the re…
Suspensions of microswimmers are a rich source of fascinating new fluid mechanics. Recently we predicted the active pipe flow dispersion of gyrotactic microalgae, whose orientation is biased by gravity and flow shear. Analytical theory predicts that these active swimmers disperse in a markedly distinct manner from passive tracers (Taylor dispersion). Dispersing swimmers display nonzero drift and effective diffusivity that is non-monotonic with P$é$clet number. Such predictions agree with numerical simulations, but hitherto have not been tested experimentally. Here, to facilitate comparison, we…
We study the dynamics of gyrotactic swimmers in turbulence, whose orientation is governed by gravitational torque and local fluid velocity gradient. The gyrotaxis strength is measured by the ratio of the Kolmogorov time scale to the reorientation time scale due to gravity, and a large value of this ratio means the gyrotaxis is strong. By means of direct numerical simulations, we investigate the effects of swimming velocity and gyrotactic stability on spatial accumulation and alignment. Three-dimensional Vorono{\"ı} analysis is used to study the spatial distribution and time evolution of the pa…
Phytoplankton patchiness, namely the heterogeneous distribution of microalgae over multiple spatial scales, dramatically impacts marine ecology. A spectacular example of such heterogeneity occurs in thin phytoplankton layers (TPLs), where large numbers of photosynthetic microorganisms are found within a small depth interval. Some species of motile phytoplankton can form TPLs by gyrotactic trapping due to the interplay of their particular swimming style (directed motion biased against gravity) and the transport by a flow with shear along the direction of gravity. Here we consider gyrotactic swi…
Many plankton species undergo daily vertical migration to large depths in the turbulent ocean. To do this efficiently, the plankton can use a gyrotactic mechanism, aligning them with gravity to swim downwards, or against gravity to swim upwards. Many species show passive mechanisms for gyrotactic stability. For example, bottom-heavy plankton tend to align upwards. This is efficient for upward migration in quiescent flows, but it is often sensitive to turbulence which upsets the alignment. Here we suggest a simple, robust active mechanism for gyrotactic stability, which is only lightly affected…
A suspension of gyrotactic microalgae Chlamydomonas augustae swimming in a cylindrical water vessel in solid-body rotation is studied. Our experiments show that swimming algae form an aggregate around the axis of rotation, whose intensity increases with the rotation speed. We explain this phenomenon by the centripetal orientation of the swimming direction towards the axis of rotation. This centripetal focusing is contrasted by diffusive fluxes due to stochastic reorientation of the cells. The competition of the two effects lead to a stationary distribution, which we analytically derive from a …
Recent studies show that spherical motile micro-organisms in turbulence subject to gravitational torques gather in down-welling regions of the turbulent flow. By analysing a statistical model we analytically compute how shape affects the dynamics, preferential sampling, and small-scale spatial clustering. We find that oblong organisms may spend more time in up-welling regions of the flow, and that all organisms are biased to regions of positive fluid-velocity gradients in the upward direction. We analyse small-scale spatial clustering and find that oblong particles may either cluster more or l…
Active matter, composed of self-propelled entities, forms a wide class of out-of-equilibrium systems that display striking collective behaviors among which the so-called active turbulence where spatially and time disordered flow patterns spontaneously arise in a variety of {active systems}. De facto, the active turbulence naming suggests a connection with a second seminal class of out-of-equilibrium systems, fluid turbulence, and yet of very different nature with energy injected at global system scale rather than at the elementary scale of single constituents. Indeed the existence of a possibl…
Particular types of plankton in aquatic ecosystems can coordinate their motion depending on the local flow environment to reach regions conducive to their growth or reproduction. Investigating their swimming strategies with regard to the local environment is important to obtain in-depth understanding of their behavior in the aquatic environment. In the present research, to examine an impact of the shape and gravity on a swimming strategy, plankton is considered as settling swimming particles of ellipsoidal shape. The Q-learning approach is adopted to obtain swimming strategies for smart partic…
Shear flow significantly affects the transport of swimming algae in suspension. For example, viscous and gravitational torques bias bottom-heavy cells to swim towards regions of downwelling fluid (gyrotaxis). It is necessary to understand how such biases affect algal dispersion in natural and industrial flows, especially in view of growing interest in algal photobioreactors. Motivated by this, we here study the dispersion of gyrotactic algae in laminar and turbulent channel flows using direct numerical simulation (DNS) and the analytical swimming dispersion theory of Bees and Croze (2010). Tim…
We study the effect of turbulence on marine life by performing numerical simulations of motile microorganisms, modelled as prolate spheroids, in isotropic homogeneous turbulence. We show that the clustering and patchiness observed in laminar flows, linear shear and vortex flows, are significantly reduced in a three-dimensional turbulent flow mainly because of the complex topology; elongated micro-orgamisms show some level of clustering in the case of swimmers without any preferential alignment whereas spherical swimmers remain uniformly distributed. Micro-organisms with one preferential swimmi…
Collective behaviour in suspensions of microswimmers is often dominated by the impact of long-ranged hydrodynamic interactions. These phenomena include active turbulence, where suspensions of pusher bacteria at sufficient densities exhibit large-scale, chaotic flows. To study this collective phenomenon, we use large-scale (up to $N=3\times 10^6$) particle-resolved lattice Boltzmann simulations of model microswimmers described by extended stresslets. Such system sizes enable us to obtain quantitative information about both the transition to active turbulence and characteristic features of the t…
Effect of swimming mode on shielding of odor traces in turbulence
Machine Learning Genoa Center (MaLGa) & Department of Civil, Chemical and Environmental Engineering, University of Genoa（热那亚大学机器学习和环境工程学院）；Gran Sasso Science Institute (GSSI)（格兰萨索科学研究所）；INFN–Laboratori Nazionali del Gran Sasso（意大利国家核物理研究所格兰萨索国家实验室）
In this communication we address some hydrodynamic aspects of recently revisited drift mechanism of biogenic mixing in the ocean (Katija and Dabiri, Nature vol. 460, pp. 624-626, 2009). The relevance of the locomotion gait at various spatial scales with respect to the drift is discussed. A hydrodynamic scenario of the drift based on unsteady inertial propulsion, typical for most small marine organisms, is proposed. We estimate its effectiveness by taking into account interaction of a swimmer with the turbulent marine environment. Simple scaling arguments are derived to estimate the comparative…
In this Letter, we study the collective behaviour of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedently large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial turbulence. We show that, even well below the transition, swimmers move in a correlated fashion that cannot be described by a mean-field approach. We develop a novel kinetic theory that captures these correlations and is non-perturbative in the swimmer density. To provide an experimentally accessible measure of correlations, we calculate the diffusivity of passive tracers …
Marine microorganisms must cope with complex flow patterns and even turbulence as they navigate the ocean. To survive they must avoid predation and find efficient energy sources. A major difficulty in analysing possible survival strategies is that the time series of environmental cues in non-linear flow is complex, and that it depends on the decisions taken by the organism. One way of determining and evaluating optimal strategies is reinforcement learning. In a proof-of-principle study, Colabrese et al. [Phys. Rev. Lett. (2017)] used this method to find out how a micro-swimmer in a vortex flow…
We consider arbitrary, possibly turbulent, Boussinesq flow which is smooth below a dissipative scale $l_d$. It is demonstrated that the stability of the flow with respect to growth of fluctuations with scale smaller than $l_d$ leads to a non-trivial constraint. That involves the dimensionless strength $Fl$ of fluctuations of the gradients of the scalar in the direction of gravity and the Rayleigh scale $L$ depending on the Rayleigh number $Ra$, the Nusselt number $Nu$ and $l_d$. The constraint implies that the stratified fluid at rest, which is linearly stable, develops instability in the limi…
There is much current interest in modelling suspensions of algae and other micro-organisms for biotechnological exploitation, and many bioreactors are of tubular design. Using generalized Taylor dispersion theory, we develop a population-level swimming-advection-diffusion model for suspensions of micro-organisms in a vertical pipe flow. In particular, a combination of gravitational and viscous torques acting on individual cells can affect their swimming behaviour, which is termed gyrotaxis. This typically leads to local cell drift and diffusion in a suspension of cells. In a flow in a pipe, sm…
