Swimming Orientation Research Articles

On The Preparation Of Training Data For 3D Tracking Of Position And Orientation Of Microswimmers Using Defocusing And Deep Learning

The use of image analysis algorithms based on deep convolutional neural networks (CNNs) is opening new possibilities in experimental techniques for fluid dynamics. In the field of microscopic 3D particle tracking based on defocusing, it has been shown on synthetic images that CNNs can be used to determine not only the depth position but also the orientation of non-spherical microscopic particles or specimens. However, the translation of such approaches to experimental setups is challenging, especially due to the difficulty of obtaining reliable labeled images to train the neural networks. In this work, we propose a method to obtain labeled images of microswimmers from conventional microscopy images, exploiting the properties of the swimming motion at low Reynolds numbers, where inertial effects are negligible. This method allows us to obtain ground truth values of orientation and depth position of a microorganism swimming at a regular pace that can be used as training data for CNNs. The proposed methodology was used to obtain labeled images from experimental videos of the micro-organism Euplotes Vannus. The labeled images were used to train a VGG16 network, providing an estimated uncertainty in the determination of the orientation angles psi, theta, phi, and the depth position Z of 2.4%, 1.4%, 2.3%, and 3.5%, respectively.

Effect of scattered/diffuse flux on the phototactic bioconvection in the absence of collimated flux

The main objective of this paper is to investigate the impact of diffuse/scattered flux in the absence of collimated flux on the stability of an isotropic scattering algal suspension. The linear stability analysis predicts an unstable mode of disturbance shifts from a non-oscillatory (an overstable) to an overstable (a non-oscillatory) state at the variation of diffuse flux for fixed parameters at the bioconvective instability. However, overstable solutions are observed only at the higher cell swimming speed and a higher extinction coefficient. The critical Rayleigh number increases as the magnitude of diffuse flux intensifies. This indicates that a suspension illuminated by higher levels of diffuse flux is more stable. Furthermore, the lower (higher) swimming speed enhances (diminishes) the suspension's stability, especially in low (high) light conditions. Also, the horizontal component of swimming orientation becomes more influential with a higher level of diffuse flux, particularly at smaller pattern wavelengths, resulting in behavior akin to gyrotaxis in certain instances.

Acoustic Target Strength of Jellyfish, Nemopilema nomurai, Measured at Multi-Frequency and Multi-Orientation

The jellyfish Nemopilema nomurai occupies an important position in the Northwest Pacific ecosystem, and monitoring its biomass is necessary to ensure the protection of fishery resources and the safety of offshore industrial production. The acoustic method has been proposed for jellyfish flux estimation and bloom warning, in which the target strength (TS) of the jellyfish is a crucial parameter. However, varied swimming orientations of jellyfish aggregation result in different backscatter strengths. The acoustic echo characteristics in horizontal swimming orientations and multi-frequency broadband signals are yet to be revealed. This study aims to obtain the TS of jellyfish in various orientations and to comprehensively investigate the jellyfish acoustic echo features at various frequency broadband sounds. In an anechoic tank, we used wide-band echosounder and 70 kHz, 120 kHz, and 200 kHz split-beam transducers to measure the TS of jellyfish swimming omnidirectionally. The results show a difference of approximately 4 dB in the jellyfish’s normalized TS at 70 kHz (frequency range: 45 kHz to 95 kHz) and 200 kHz (frequency range: 160 kHz to 260 kHz) center frequency. The normalized TS of jellyfish varies by around 8 dB between horizontal and vertical swimming orientations. For jellyfish swimming horizontally, the TS and bell diameter have the following least squares fits: T S D 70 k H z = 20 log D − 89.36 r 2 = 0.83 ; T S D 200 k H z = 20 log D − 93.85 r 2 = 0.83 . The swimming orientation has significant effects on TS estimation and model construction.

Sharp turns and gyrotaxis modulate surface accumulation of microorganisms

The accumulation of swimming microorganisms at surfaces is an essential feature of various physical, chemical, and biological processes in confined spaces. To date, this accumulation is mainly assumed to depend on the change of swimming speed and angular velocity caused by cell-wall contact and hydrodynamic interaction. Here, we measured the swimming trajectories of Heterosigma akashiwo (a biflagellate marine alga) near vertical and horizontal rigid boundaries. We observed that the probability of sharp turns is greatly increased near a vertical wall, resulting in significant changes in the distributions of average swimming speed, angular velocity, and rotational diffusivity near the wall (a quantity that has not previously been investigated) as functions of both distance from the wall and swimming orientation. These cannot be satisfactorily explained by standard hydrodynamic models. Detailed examination of an individual cell trajectory shows that wall contact by the leading flagellum triggers complex changes in the behavior of both flagella that cannot be incorporated in a mechanistic model. Our individual-based model for predicting cell concentration using the measured distributions of swimming speed, angular velocity, and rotational diffusivity agrees well with the experiment. The experiments and model are repeated for a cell suspension in a vertical plane, bounded above by a horizontal wall. The cell accumulation beneath the wall, expected from gyrotaxis, is considerably amplified by cell-wall interaction. These findings may shed light on the prediction and control of cell distribution mediated by gyrotaxis and cell-wall contact.

Point-to-Point Navigation of a Fish-Like Swimmer in a Vortical Flow With Deep Reinforcement Learning

Efficient navigation in complex flows is of crucial importance for robotic applications. This work presents a numerical study of the point-to-point navigation of a fish-like swimmer in a time-varying vortical flow with a hybrid method of deep reinforcement learning (DRL) and immersed boundary–lattice Boltzmann method (IB-LBM). The vortical flow is generated by placing four stationary cylinders in a uniform flow. The swimmer is trained to discover effective navigation strategies that could help itself to reach a given destination point in the flow field, utilizing only the time-sequential information of position, orientation, velocity and angular velocity. After training, the fish can reach its destination from random positions and orientations, demonstrating the effectiveness and robustness of the method. A detailed analysis shows that the fish utilizes highly subtle tail flapping to control its swimming orientation and take advantage of the reduced streamwise flow area to reach it destination, and in the same time avoiding entering the high flow velocity area.

Barriers Impeding Active Mixing of Swimming Microbes in a Hyperbolic Flow

We present experiments on the motion of swimming microbes in a laminar, hyperbolic flow. We test a theory that predicts the existence of swimming invariant manifolds (SwIMs) that act as invisible, one-way barriers that block the motion of the microbes. The flow is generated in a cross-channel in a PDMS cell, driven by syringe pumps. The swimming microbes are euglena and tetraselmis, both single-celled, eukaryotic algae. The algae are not ideal smooth-swimmers: there is significant rocking in their motion with occasional tumbles and a swimming speed that can vary. The experiments show that the swimming algae are bound very effectively by the predicted SwIMs. The different shapes and swimming behavior of the euglena and tetraselmis affect the distribution of swimming angles, with the elongated euglena having a larger probability of swimming in a direction parallel to the outflow directions. The differences in swimming orientation affect the ability of the microbes to penetrate the manifolds that act as barriers to passive tracers. The differing shapes of the euglena and tetraselmis also affect probabilities for the microbes to escape in one direction or the other along the outflow.

Gyrotactic trapping of micro-swimmers in simple shear flows: a study directly from the fundamental Smoluchowski equation

Thin phytoplankton layers with vertically compressed structures found in stratified lakes and coastal water bodies have been a hot-spot in marine science and fluid mechanics. Although extensive efforts have been made to explore gyrotactic trapping as a possible mechanism, obvious inconsistencies remain there between the generalised Taylor dispersion method and individual-based model. In this work, a study directly from the fundamental Smoluchowski equation is carried out on the gyrotactic trapping mechanism in representative simple shear flows. With no approximation made to the fundamental equation and applying a biorthogonal expansion to the local moments of the probability density function, the evolution and steady state of the transport process are in good agreement with results of individual-based model, thus removing the gap between the continuum approach and individual-based model. The influences of strongly varying shear rate and boundary effect are reasonably scrutinised. The average swimming orientation with fixed local shear is highlighted as time-dependent rather than steady as previously assumed. The variations of characteristic time of the transient thin layer as functions of the flow intensity, gyrotaxis intensity and swimming ability are characterised. Sedimentation of the micro-swimmers is considered in some cases to reflect that micro-organisms are possibly negatively buoyant, with corresponding boundary conditions devised. A steady thin layer can be realised in the solution by adding a small settling speed to counteract the gravitactic focusing at the upper surface.

Chemical design of self-propelled Janus droplets

Chemical design of self-propelled Janus droplets

Stable Schooling Formations Emerge from the Combined Effect of the Active Control and Passive Self-Organization

This work presents a numerical study of the collective motion of two freely-swimming swimmers by a hybrid method of the deep reinforcement learning method (DRL) and the immersed boundary-lattice Boltzmann method (IB-LBM). An active control policy is developed by training a fish-like swimmer to swim at an average speed of 0.4 L/T and an average orientation angle of 0∘. After training, the swimmer is able to restore the desired swimming speed and orientation from moderate external perturbation. Then the control policy is adopted by two identical swimmers in the collective swimming. Stable side-by-side, in-line and staggered formations are achieved according to the initial positions. The stable side-by-side swimming area of the follower is concentrated to a small area left or right to the leader with an average distance of 1.35 L. The stable in-line area is concentrated to a small area about 0.25 L behind the leader. A detailed analysis shows that both the active control and passive self-organization play an important role in the emergence of the stable schooling formations, while the active control works for maintaining the speed and orientation in case the swimmers collide or depart from each other and the passive self-organization works for emerging a stable schooling configuration. The result supports the Lighthill conjecture and also highlights the importance of the active control.

Coupling 3D hydraulic simulation and fish telemetry data to characterize the behaviour of migrating smolts approaching a bypass

Human-induced river fragmentation is a major threat to migratory fish species. Restoring river connectivity requires the construction of fish passage solutions, such as fishways for upstream and downstream migration. While many studies focussed on the upstream migration of diadromous fishes, and especially of adult Atlantic salmons (Salmo salar), we analyze juvenile behaviour under different hydraulic conditions at reservoir to improve the development of effective bypass systems for downstream passage of salmon smolt. Based on coupling three-dimensional (3D) computational fluid dynamics (CFD) simulations to smolt positions tracked by two-dimensional (2D) telemetry, the present study aimed to explore smolt behaviour in relation to hydraulic cues. More specifically, we explored how hydraulic conditions influence fish behaviour and how fish navigate depending on this behaviour. In 2017, 23 smolts were tracked in the reservoir of Poutès (Allier River, France), associated with different turbine discharge rates. 3D CFD simulations were performed and validated against field measurements in the reservoir upstream of the hydropower plant. The study of fish displacements in relation to flow conditions provided new insights with the use of thrust force, swimming orientation and direction as means to precisely characterize smolt behaviour, which can help in the design of downstream migration passage facilities. At Poutès dam, flow velocity, flow acceleration and turbulent kinetic energy are very low and therefore can lead to fish disorientation. However, results underlined that having a minimum flow velocity of 20 cm/s in reservoirs is sufficient to prevent delay and allow fish navigation.

Model-Aided Real-Time Localization and Parameter Identification of a Magnetic Endoscopic Capsule Using Extended Kalman Filter

Capsule endoscopy is a minimally invasive diagnostic technology for gastrointestinal diseases providing images from the human's digestion system. Developing a robust and real-time localization algorithm to determine the orientation and position of the endoscopic capsule is a crucial step toward medical diagnostics. In this paper, we propose a novel model-aided real-time localization approach to estimate the position and orientation of a magnetic endoscopic capsule swimming inside the stomach. In the proposed method, the governing equations of the motion of an ellipsoidal capsule inside the fluid, considering different hydrodynamics interactions, are derived. Then, based on the dynamic model, an Extended Kalman Filter (EKF) driven by the noisy measurements of the multiple magnetic sensors is developed. According to the simulations, the proposed method not only can accurately localize the endoscopic capsule but also can identify the unknown parameters of the dynamic model. The results confirm the superiority of our proposed method compared to the conventional localization technique in the presence of dynamic model uncertainties and corrupted sensor data. Experimental realization of the proposed technique proves the achievement of high accuracy in the trajectory estimation of the magnetic endoscopic capsule.

Motion of an active particle in a linear concentration gradient

Janus particles self-propel by generating local tangential concentration gradients along their surface. These gradients are present in a layer whose thickness is small compared to the particle size. Chemical asymmetry along the surface is a prerequisite to generate tangential chemical gradients, which gives rise to diffusio-osmotic flows in a thin region around the particle. This results in an effective slip on the particle surface. This slip results in the observed “swimming” motion of a freely suspended particle even in the absence of externally imposed concentration gradients. Motivated by the chemotactic behavior of their biological counterparts (such as sperm cells, neutrophils, macrophages, bacteria, etc.), which sense and respond to external chemical gradients, the current work aims at developing a theoretical framework to study the motion of a Janus particle in an externally imposed linear concentration gradient. The external gradient along with the self-generated concentration gradient determines the swimming velocity and orientation of the particle. The dominance of each of these effects is characterized by a non-dimensional activity number A (ratio of applied gradient to self-generated gradient). The surface of Janus particle is modeled as having a different activity and mobility coefficient on the two halves. Using the Lorentz reciprocal theorem, an analytical expression for the rotational and translational velocity is obtained. The analytical framework helps us divide the parameter space of surface activity and mobility into four regions where the particle exhibits different trajectories.

Nearshore wave characteristics as cues for swimming orientation in flatback turtle hatchlings

Waves are thought to provide an important directional cue for hatchlings of marine turtles to navigate through the nearshore zone and to facilitate dispersal to oceanic waters. As the flatback turtle (Natator depressus) is the only species of marine turtle that lacks an oceanic juvenile stage and remains on the continental shelf throughout the entire life cycle, it is possible that hatchlings of this species do not use wave cues for early dispersal. Here, we used a wave flume to examine the response of flatback turtle hatchlings to waves as a cue for nearshore dispersal. We exposed hatchlings to two types of waves (sea and swell waves) differing in height and period commonly experienced at nesting locations and monitored swimming direction (orientation). Hatchlings oriented towards shorter period (3 s) sea waves with both small (6 cm peak to trough) and large (12 cm peak to trough) wave heights. Orientation of hatchlings to longer period (8 s) swell waves only occurred with large (16 cm peak to trough) and not with small (7 cm peak to trough) wave heights. Acceleration generated by waves was the strongest predictor of directional preference in hatchling bearings. There was a positive relationship between maximum acceleration and directional preference, with hatchling bearings more concentrated (r-value 0.98) towards the oncoming wave direction with waves that produced the highest acceleration (sea waves with largest wave heights). These waves were similar to sea waves generated from onshore winds, which was the most common type of wave we measured at a flatback turtle nesting beach. Our study has confirmed that despite lacking an oceanic development stage, flatback hatchlings, like other species of sea turtles, can detect and respond to wave cues, and that the accelerations generated by waves may be a key characteristic of waves that drives orientation.

Verification of the Backscattering Strength Based on the Swimming Behavior of Antarctic Krill

This study provides an estimate of the SDWBA-modelled mean target strength for given sets of krill length and swimming orientation. The range of the dB identification window for krill length was between 28 mm and 67 mm and the distribution of swimming orientation N[11.0°, 4.0°] was estimated to be between 0.06–10.97 dB, while the range estimated using N[53.1°, 21.4°], i.e., the distribution of orientation obtained under the brightest illuminance level, was 5.21–9.82 dB. The range of the dB window calculated using N[45.2°, 23.0°], obtained under the second brightest illuminance level, was 3.83–11.76 dB, and the range calculated with N[48.1°, 23.0°], obtained under the third illuminance level, was 3.83–11.76 dB. The range of the dB window calculated by N[45.9°, 23.0°] was 3.41–11.75 dB, and the range of the dB window for krill length ranging from 28 mm to 67 mm was 4.05–11.34 dB. In all the swimming orientations, the smaller the krill size was the lower the averaged target strength value was; likewise, the larger the krill size was the higher the averaged target strength value was. The result indicated that swimming orientation impacted greatly on the range of frequency differences of Antarctic krill.

Active control of bacteria swimming orientation in a liquid crystal matrix by using UV light

Bacteria are omnipresent in nature. They also play a key role in biomedical industry and new technologies. A capability to control their movement may be very useful both for their study and applications. Here we explore the possibility of such active control of the movement of flagellated bacteria (a bacterium that can swim thanks to the rotation of its long screw-like helix). We demonstrate that we can dynamically change the swimming direction of bacteria by incorporating them into a liquid crystal media where the phase transition is locally controlled by UV illumination. This work opens new avenues to develop lab-on-a-chip devices that could be used as a micro-farm to “harvest” and study bacteria.

Microscale topographic surfaces modulate three-dimensional migration of human spermatozoa

Sperm migration in the female reproductive tract is vital for reproduction. Surface topography is expected to be a vital determinant on this process. Using digital holographic microscopy (DHM), we investigated three-dimensional (3D) motion dynamics of human spermatozoa near a flat glass surface and microscale topographic surfaces with tunable roughness fabricated by a monolayer of closely packed silica colloidal particles. Generally, the rougher surfaces show negative impacts on the sperm migration through the hydrodynamic interactions modulated by surface topography, reflected as oscillating trajectories with wider swimming orientation distribution, reduced 3D velocity and less helical/hyperactivated/hyerhelical motions. Nevertheless, slight difference is observed for the sperm motion near the flat glass surface and the surface with a feature dimension similar to the sperm tail. Our study provides new insights in understanding and manipulating sperm motions.

The swimming orientation of multicellular magnetotactic prokaryotes and uncultured magnetotactic cocci in magnetic fields similar to the geomagnetic field reveals differences in magnetotaxis between them.

Magnetotactic bacteria have intracellular chains of magnetic nanoparticles, conferring to their cellular body a magnetic moment that permits the alignment of their swimming trajectories to the geomagnetic field lines. That property is known as magnetotaxis and makes them suitable for the study of bacterial motion. The present paper studies the swimming trajectories of uncultured magnetotactic cocci and of the multicellular magnetotactic prokaryote 'Candidatus Magnetoglobus multicellularis' exposed to magnetic fields lower than 80μT. It was assumed that the trajectories are cylindrical helixes and the axial velocity, the helix radius, the frequency and the orientation of the trajectories relative to the applied magnetic field were determined from the experimental trajectories. The results show the paramagnetic model applies well to magnetotactic cocci but not to 'Ca. M. multicellularis' in the low magnetic field regime analyzed. Magnetotactic cocci orient their trajectories as predicted by classical magnetotaxis but in general 'Ca. M. multicellularis' does not swim following the magnetic field direction, meaning that for it the inversion in the magnetic field direction represents a stimulus but the selection of the swimming direction depends on other cues or even on other mechanisms for magnetic field detection.

Dispersion of active particles in confined unidirectional flows

Transport of micro-organisms in confined flows can be characterized by a one-dimensional overall dispersion mechanism, of importance to various biotechnological applications. Based on Brenner’s generalized Taylor dispersion theory, an overall dispersion model is analytically studied in the present work for a dilute suspension of active particles in confined unidirectional flows. With the confined section of the channel and the swimming orientation space taken together as the local space and the longitudinal coordinate standing for the one-dimensional global space, this model is analytically accurate and possessed of wide adaptability in terms of the swimming Péclet number. The Robin boundary condition is introduced to account for wall accumulation of active particles, and compared with a typical reflection boundary condition. Complications associated with the boundary conditions for analytical derivation are removed respectively by a decomposition of the distribution function and an extension of the flow field. Interesting solutions are concretely found and intensively illustrated. Detailed case studies on the transport of spherical and rod-like particles to illustrate the dispersion mechanism are presented with respect to a Couette flow and a plane Poiseuille flow. Associated with the local distribution of particles, extensive descriptions are given for the dynamical system behaviours such as accumulation near both stable points/lines and boundaries, symmetric polarization structure, closed orbits, trapping effect, nematic alignments and bimodalization of swimming direction. For spherical particles, the accumulation is shown leading to a reduction of the overall dispersivity in both of the flows, while for rod-like active particles in the Couette flow, the accumulation can result in an enhancement of dispersion, due to the nematic alignments of particles towards streamlines.

Swimming performance of a bio-inspired robotic vessel with undulating fin propulsion

Undulatory fin propulsion exhibits a high degree of maneuver control—an ideal feature for underwater vessels exploring complex environments. In this work, we developed and tested a self-contained, free-swimming robot with a single undulating fin running along the length of the robot, which controls both forward motion and directional maneuvers. We successfully replicated several maneuvers including forward swimming, reversed motion, diving, station-keeping and vertical swimming. For each maneuver, a series of experiments was performed as a function of fin frequency, wavelength and traveling wave direction to measure swimming velocities, orientation angles and mean power consumption. In addition, 3D flow fields were measured during forward swimming and station-keeping using volumetric particle image velocimetry (PIV). The efficiency for forward swimming was compared using three metrics: cost of transport, wave efficiency and Strouhal number (St). The results indicate that the cost of transport exhibits a V-shape trend with the minimum value at low swimming velocity. The robot reaches optimal wave efficiency and locomotor performance at a range of 0.2–0.4 St. Volumetric PIV data reveal the shed of vortex tubes generated by the fin during forward swimming and station keeping. For forward swimming, a series of vortex tubes are shed off the fin edge with a lateral and downward direction with respect to the longitudinal axis of the fin. For station keeping, flow measurements suggest that the vortex tubes are shed at the mid-section of the fin while the posterior and anterior segment of the vortex stay attached to the fin. These results agree with the previous vortex structures based on simulations and 2D PIV. The development of this vessel with high maneuverability and station keeping performance has applications for oceanography, coastal exploration, defense, the oil industry and other marine industries where operations are unsafe or impractical for divers or human-piloted vessels.

Coastal chemical cues for settlement of the southern rock lobster, Jasus edwardsii

Larval behavior plays an important role in dispersal and settlement of marine organisms with cues from the environment often providing crucial guidance for facilitating these processes. The post-larvae, or pueruli, of the southern rock lobster, Jasus edwardsii (Hutton, 1875), are known to migrate over long distances from oceanic water and settle on coastal reefs using a combination of onshore transport and active nocturnal swimming. In laboratory experiments, we examined environmental cues used for this migration, specifically whether chemical cues in coastal vs oceanic seawater influenced their swimming orientation and their rate of development to juveniles. In total, 66% of pueruli actively swam toward coastal water rather than oceanic water (n = 41), indicating that they may use chemical cues in their settlement processes. Holding pueruli in coastal water vs artificial seawater did not expedite the development of pueruli to benthic juvenile stage, indicating that other cues could be important to the final settlement process. The present study suggests that chemical cues are being used in settlement processes during the onshore migration to settlement sites in this ecologically and economically important species.