Three-dimensional Swimming Research Articles

Viscosity-dependent swimming patterns assist Aliivibrio fischeri for symbiont partner finding

Bacteria employ diverse swimming patterns for chemotaxis, influenced by factors including flagellar arrangements, motor rotation, flagellar filament configurations, and polymorphism. Understanding the chemotactic strategy of in locating a squid partner is paramount for comprehending this highly species-specific symbiosis. In this study, we applied three-dimensional swimming tracking and real-time visualization of lophotrichous flagellar configurations. These techniques unveiled viscosity-dependent transitions in swimming patterns, shifting from push-pull to push-wrap modes. Notably, our research also revealed coupled flagellar switching and polymorphic transformations during the wrap mode, significantly extending 's backward swimming duration and, consequently, its overall runtime. This strategic adaptation allows to broaden its effective search range, particularly within high-viscosity environments like the squid light organ. In response to attractants, the coupling rate is reduced to facilitate efficient short-range searching. These innovative chemotactic strategies ensure precise navigation for in locating and colonizing its symbiotic partner, the squid . Published by the American Physical Society 2024

Real-time 3D tracking of swimming microbes using digital holographic microscopy and deep learning.

The three-dimensional swimming tracks of motile microorganisms can be used to identify their species, which holds promise for the rapid identification of bacterial pathogens. The tracks also provide detailed information on the cells' responses to external stimuli such as chemical gradients and physical objects. Digital holographic microscopy (DHM) is a well-established, but computationally intensive method for obtaining three-dimensional cell tracks from video microscopy data. We demonstrate that a common neural network (NN) accelerates the analysis of holographic data by an order of magnitude, enabling its use on single-board computers and in real time. We establish a heuristic relationship between the distance of a cell from the focal plane and the size of the bounding box assigned to it by the NN, allowing us to rapidly localise cells in three dimensions as they swim. This technique opens the possibility of providing real-time feedback in experiments, for example by monitoring and adapting the supply of nutrients to a microbial bioreactor in response to changes in the swimming phenotype of microbes, or for rapid identification of bacterial pathogens in drinking water or clinical samples.

Mechanism Insights of Antibacterial Surfaces Coated with Dead Probiotics.

To understand the antimicrobial effect of surfaces fabricated with dead probiotics, we prepared surfaces decorated with dead probiotics Lactobacillus rhamnosus GG (LGG) with varied inactivation methods and explored their inhibitory interactions with Pseudomonas aeruginosa (PAO1). By combining several techniques, i.e., digital holographic microscopy (DHM), atomic force microscopy (AFM), RNA sequencing, and metabolomic analysis, we studied the three-dimensional (3D) swimming behaviors, surface adhesion, biofilm formation, and adaptive responses of PAO1 near such surfaces. The results show that planktonic PAO1 decreases their flick and reverse motions by downregulating the chemotaxis pathway and accelerates with less accumulation near dead LGG surfaces by upregulating the flagellar assembly pathway and decreasing cyclic adenosine monophosphate. Distinct from live siblings, the surfaces decorated with dead LGG show a significant reduction in adhesion strength with PAO1 and inhibit biofilm formation with more downregulated genes in the Pseudomonas quinolone signal and biofilm formation pathway. We demonstrate that the antibacterial ability of such surfaces stems from the gradually released lysate from the dead LGG that is unfavorable to PAO1 in close proximity. The releasing rate and order depend on the cell membrane integrity, which closely relates to the inactivation methods.

Robust acoustic trapping and perturbation of single-cell microswimmers illuminate three-dimensional swimming and ciliary coordination

We report a label-free acoustic microfluidic method to confine single, cilia-driven swimming cells in space without limiting their rotational degrees of freedom. Our platform integrates a surface acoustic wave (SAW) actuator and bulk acoustic wave (BAW) trapping array to enable multiplexed analysis with high spatial resolution and trapping forces that are strong enough to hold individual microswimmers. The hybrid BAW/SAW acoustic tweezers employ high-efficiency mode conversion to achieve submicron image resolution while compensating for parasitic system losses to immersion oil in contact with the microfluidic chip. We use the platform to quantify cilia and cell body motion for wildtype biciliate cells, investigating effects of environmental variables like temperature and viscosity on ciliary beating, synchronization, and three-dimensional helical swimming. We confirm and expand upon the existing understanding of these phenomena, for example determining that increasing viscosity promotes asynchronous beating. Motile cilia are subcellular organelles that propel microorganisms or direct fluid and particulate flow. Thus, cilia are critical to cell survival and human health. The unicellular alga Chlamydomonas reinhardtii is widely used to investigate the mechanisms underlying ciliary beating and coordination. However, freely swimming cells are difficult to image with sufficient resolution to capture cilia motion, necessitating that the cell body be held during experiments. Acoustic confinement is a compelling alternative to use of a micropipette, or to magnetic, electrical, and optical trapping that may modify the cells and affect their behavior. Beyond establishing our approach to studying microswimmers, we demonstrate a unique ability to mechanically perturb cells via rapid acoustic positioning.

Design and Implementation of a Miniature Jellyfish-Inspired Robot

With the development of the global marine industry, the demand to investigate underwater environments using robots is increasing. Inspired by the unique structure and excellent swimming ability of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Aurelia aurita</i> , a miniature jellyfish-inspired robot is developed. The robot comprises a headshell, six tentacles, a primary drive component, two flywheel steering components, a lightweight foam block, a dsPIC control system, and an energy supply component. The tentacles are covered with a 0.1-mm-thick silicone membrane and modeled in the shape of an umbrella. The membrane is driven by a gear motor to mimic the contraction and expansion of the interior cavity of a jellyfish; it exhibits the swimming behavior via water jet propulsion. Three-dimensional swimming is achieved by the flywheel steering components following the conservation of angular momentum. A built-in LoRa communication module (433 MHz) enables a robust, real-time connection between the robot and a terrestrial console. The small-sized, lightweight jellyfish robot has a diameter of 110 mm and a height of 140 mm; it weighs 318 g and achieves autonomous swimming with low power consumption. The robot can be used for underwater signal relay, environmental monitoring, and geological investigations.

A subcycling/non-subcycling time advancement scheme-based DLM immersed boundary method framework for solving single and multiphase fluid–structure interaction problems on dynamically adaptive grids

In this paper, we present an adaptive implementation of the distributed Lagrange multiplier (DLM) immersed boundary (IB) method on multilevel collocated grids for solving single- and multiphase fluid–structure interaction (FSI) problems. Both a non-subcycling time advancement scheme and a subcycling time advancement scheme, which are applied to time-march the composite grid variables on a level-by-level basis, are presented; these schemes use the same time step size and a different time step size, respectively, on different levels. This is in contrast to the existing adaptive versions of the IB method in the literature, in which coarse- and fine-level variables are simultaneously solved and advanced in a coupled fashion. A force-averaging technique and a series of synchronization operations are constructed to achieve excellent momentum and mass conservation across multiple levels of grid hierarchy. We demonstrate the versatility of the present multilevel framework by simulating problems with various types of kinematic constraints imposed by structures on fluids, such as imposing a prescribed motion, free motion, and time-evolving shape of a solid body. The DLM method is also coupled to a robust level set method-based two-phase fluid solver to simulate challenging multiphase flow problems, including wave energy harvesting using a mechanical oscillator. The capabilities and robustness of the computational framework are validated against a variety of benchmarking single-phase and multiphase FSI problems from the literature, which include a three-dimensional swimming eel model to demonstrate the significant speedup and efficiency that result from employing the present multilevel subcycling FSI scheme.

Identifying three-dimensional swimming corridors for fish to match their swimming characteristics under different hydropower plant operations: Optimization of entrance location for fish-passing facilities

Fish that require migration are often diverse in the dam-built river, and some of them are benthic. For fish to pass efficiently across the dams, it is necessary to identify the swimming corridors and possible cluster areas of the target fish. However, previous studies have only predicted the two-dimensional swimming corridors of a single species. In this study, the relationships between the swimming behaviours of different species of fish and the three-dimensional (3D) hydrodynamic field were determined, and a model of the 3D swimming corridors corresponding to the fish swimming characteristics was constructed. The model was verified by a fish acoustic telemetry experiment. By simulating the river 3D hydrodynamic field in different scenarios, the possible swimming corridors and clustering areas of the target fish were further evaluated. We showed that the swimming corridors of the target fish were different among different scenarios, and the swimming corridors were mainly concentrated on both sides of the mainstream. With increased flow due to power station operation, the proportion of potential swimming corridors of target fish throughout the basin gradually decreased, and the proportion of velocity barrier zones of target fish gradually increased. By analyzing the possible swimming corridors of the target fish, the slow-flowing areas near the suddenly narrowed swimming corridors were considered to be the areas of target fish clustering. The cluster areas of the target fish weres also the optimal choice of the fish passing facility entrances, so as to ensure the best fish-crossing effect. The reliable and quantitative 3D fish swimming corridors model proposed in this study can provide a scientific basis for the layout of fish-crossing facilities and facilitate the scientific operation and management of the reservoir in the fish spawning season.

Design and analysis of a novel tendon-driven continuum robotic dolphin

In this paper, a novel continuum robotic dolphin termed ‘ConRoDolI’ is proposed and developed. The biomimetic robot features dual tendon driving continuum mechanisms that are utilized to replicate the twisting and bending motions of the dolphin’s caudal vertebrae and thoracic vertebrae. More importantly, a central pattern generator based kinematics is analyzed to yield stable dolphin-like swimming. In the meantime, the relationship between the backbone shape and both the tendon length as well as position and orientation are explored. Furthermore, multimodal swimming gaits are designed to pave the way for a three-dimensional (3D) swimming decoupling solution, involving forwarding swimming, multiple yaw patterns, and multiple pitch patterns. All of these endow the robotic dolphin with 3D maneuverability. Finally, extensive experiments demonstrate the feasibility of the proposed biomimetic mechatronic design and control approach. The forward swimming speed is 0.44 body lengths per second (BL/s). The steering radius of the robot is about 0.11 BL with an angular velocity of 10°/s and the diving speed is about 0.13 BL/s. The average propulsion efficiency is about 0.6 with the maximum is over 0.8. The obtained results shed light on the improvement of aquatic maneuverability associated with new-concept underwater vehicles.

Fish-like three-dimensional swimming with an autonomous, multi-fin, and biomimetic robot

Fish migrate across considerable distances and exhibit remarkable agility to avoid predators and feed. Fish swimming performance and maneuverability remain unparalleled when compared to robotic systems, partly because previous work has focused on robots and flapping foil systems that are either big and complex, or tethered to external actuators and power sources. By contrast, we present a robot—the Finbot—that combines high degrees of autonomy, maneuverability, and biomimicry with miniature size (160 cm3). Thus, it is well-suited for controlled three-dimensional experiments on fish swimming in confined laboratory test beds. Finbot uses four independently controllable fins and sensory feedback for precise closed-loop underwater locomotion. Different caudal fins can be attached magnetically to reconfigure Finbot for swimming at top speed (122 mm s−1 ≡ 1 BL s−1) or minimal cost of transport (CoT = 8.2) at Strouhal numbers as low as 0.53. We conducted more than 150 experiments with 12 different caudal fins to measure three key characteristics of swimming fish: (i) linear speed-frequency relationships, (ii) U-shaped CoT, and (iii) reverse Kármán wakes (visualized with particle image velocimetry). More fish-like wakes appeared where the CoT was low. By replicating autonomous multi-fin fish-like swimming, Finbot narrows the gap between fish and fish-like robots and can address open questions in aquatic locomotion, such as optimized propulsion for new fish robots, or the hydrodynamic principles governing the energy savings in fish schools.

Identifying Three-Dimensional Swimming Corridors for Fish to Match Their Swimming Characteristics Under Different Hydropower Plant Operations: Optimization of Entrance Location for Fish-Passing Facilities

Identifying Three-Dimensional Swimming Corridors for Fish to Match Their Swimming Characteristics Under Different Hydropower Plant Operations: Optimization of Entrance Location for Fish-Passing Facilities

Sharp interface immersed boundary method for simulating three-dimensional swimming fish

A second order finite-difference numerical method is used to solve the Navier–Stokes equations of incompressible flow, in which the solid body with complex geometry is immersed into the fluid domain with orthogonal Cartesian meshes. To account for influences of the solid body, interactive forces are applied as boundary conditions at Cartesian grid nodes located in the exterior but in the immediate vicinity of the solid body. Fluid flow velocities in these nodes are reconstructed to track and control the deformation of the solid body, in which the local direction normal to the body surface is employed using the level-set function. The capabilities of this method are demonstrated by the application to fish swimming, and the computed behaviors of swimming fish agree well with experimental ones. The results elucidate that the ability of swimming fish to produce more thrust and high efficiency is closely related to the Reynolds number. The single reverse Kármán street tends to appear when both the Strouhal number and tail-beating frequency are small, otherwise the double-row reverse Kármán street appears. The algorithm can capture the geometry of a deformable solid body accurately, and performs well in simulating interactions between fluid flow and the deforming and moving body.

Locomotion control of a biomimetic robotic fish based on closed loop sensory feedback CPG model

ABSTRACT This paper presents mechatronic design and hierarchical locomotion control of a biomimetic robotic fish for three-dimensional swimming modes. Inspired by biological features of Lamprey, a closed loop sensory feedback Central Pattern Generator (CPG) model is adapted to hierarchical control mechanism in order to provide robust and effective biomimetic control structure. A sensory feedback mechanism plays an important role to react external stimuli from environment. In addition, a closed loop fuzzy logic control structure is developed as a brain model to decide adaptive swimming modes according to sensory information. In order to provide three-dimensional motion abilities, the Centre of Gravity (CoG) control mechanism is designed and controlled by a back-forth proportional control structure. Experimental results are obtained to prove the CPG-based closed loop sensory feedback control structure with the developed robotic fish prototype.

Migration of Gyrotactic Micro-Organisms in Water

Understanding the swimming characteristics of micro-organisms is significant for modelling the migration of motile cells and corresponding ecological risk assessments associated with harmful algae in oceans and estuaries. Presented in this paper is an experimental and numerical investigation of swimming characteristics of a typical gyrotactic micro-organism, Heterosigma akashiwo (H. akashiwo) in water, based on the technology of planar laser-induced fluorescence and the finite volume method. Two-dimensional swimming velocity of algal cells are obtained by analyzing cells’ trajectories in the vertical plane, and three-dimensional swimming velocity is reconstructed based on the assumption that cells’ swimming is isotropic in the horizontal plane. Four important parameters are given to reflect the swimming characteristics of gyrotactic cells in still water, including the mean swimming speed (Vs = 146 μm/s), the relative strength of reorientation by gravitational torque to rotational diffusion (λ = 1.96), the time scale of reorientation (B = 5.6 s), and rotational diffusivity (Dr = 0.046 rad2/s). A database of the ambient vorticity, mean swimming velocity and diffusivity tensor is established, by solving Fokker-Planck equation for the probability density function of cells’ swimming under the combined action of gravity, rotational diffusion, and the ambient vorticity. The mean swimming velocity and translational diffusion tensor of H. akashiwo are found to change with the horizontal and vertical vorticity. It is also shown that gyrotactic cells swim in a given direction for a weak horizontal vorticity, in contrast to cells’ tumbling and being trapped for a strong horizontal vorticity.

Mechatronic Design and Manufacturing of the Intelligent Robotic Fish for Bio-Inspired Swimming Modes

This paper presents mechatronic design and manufacturing of a biomimetic Carangiform-type autonomous robotic fish prototype (i-RoF) with two-link propulsive tail mechanism. For the design procedure, a multi-link biomimetic approach, which uses the physical characteristics of a real carp fish as its size and structure, is adapted. Appropriate body rate is determined according to swimming modes and tail oscillations of the carp. The prototype is composed of three main parts: an anterior rigid body, two-link propulsive tail mechanism, and flexible caudal fin. Prototype parts are produced with 3D-printing technology. In order to mimic fish-like robust swimming gaits, a biomimetic locomotion control structure based on Central Pattern Generator (CPG) is proposed. The designed unidirectional chained CPG network is inspired by the neural spinal cord of Lamprey, and it generates stable rhythmic oscillatory patterns. Also, a Center of Gravity (CoG) control mechanism is designed and located in the anterior rigid body to ensure three-dimensional swimming ability. With the help of this design, the characteristics of the robotic fish are performed with forward, turning, up-down and autonomous swimming motions in the experimental pool. Maximum forward speed of the robotic fish can reach 0.8516 BLs-1 and excellent three-dimensional swimming performance is obtained.

A Simple Setup to Perform 3D Locomotion Tracking in Zebrafish by Using a Single Camera

Generally, the measurement of three-dimensional (3D) swimming behavior in zebrafish relies on commercial software or requires sophisticated scripts, and depends on more than two cameras to capture the video. Here, we establish a simple and economic apparatus to detect 3D locomotion in zebrafish, which involves a single camera capture system that records zebrafish movement in a specially designed water tank with a mirror tilted at 45 degrees. The recorded videos are analyzed using idTracker, while spatial positions are calibrated by ImageJ software and 3D trajectories are plotted by Origin 9.1 software. This easy setting allowed scientists to track 3D swimming behavior of multiple zebrafish with low cost and precise spatial position, showing great potential for fish behavioral research in the future.

Development of a swim-type ROV for narrow space inspection

ABSTRACTThe swim-type remotely operated vehicle (ROV) for inspection of narrow spaces in nuclear power plants has been developed. Many structures are crowded in a confined space at regular intervals in the bottom area of a reactor. So, the thickness of the ROV shape is an important design point to ensure that the ROV can move in the space. The developed ROV has a three-dimensional swimming mechanism using six thrusters, three cameras for observing the position while moving and for making inspections easily, and a localization system. The localization system combines two elements: a gyroscope to detect the progression direction; and a slit laser that detects the progression distance using the optical cutting method. The localization method is called the modified inertial navigation (MIN) method and it was evaluated in a mock-up examination. The ROV was able to move smoothly using the MIN method and its position could be detected without making a mistake in the route followed.

On a Miniature Free-Swimming Robotic Fish with Multiple Sensors

Bio-inspired robotic fish hold strong promise for underwater missions. This paper deals with the design and control issues of a miniature free-swimming robotic fish with multiple sensors. Specifically, a synthesized mechanical design scheme mainly relying on a two-link serial mechanism and a pair of mechanical pectoral fins is first presented. Next, a bio-inspired Central Pattern Generator (CPG) based control method aided by feedback information from multiple sensors of various types to achieve three-dimensional swimming is proposed. Finally, experimental results on the 35-centimetre-long robotic fish verify the efficacy of the proposed mechatronic design and control methods. It is found that the CPG control combined with sensory information greatly contributes to swimming ability and intelligence of the robotic fish.

Three-dimensional swimming motility of microorganism in the near-wall region

Microbial organisms are easily observed in geometrically confined environments. The swimming characteristics of these microorganisms are largely influenced by the presence of a solid surface. Their swimming behavior in the near-wall region shows different physical motilities. In this study, digital in-line holographic particle tracking velocimetry technique is used to investigate the three-dimensional (3D) motile characteristics of Prorocentrum minimum, especially in the near-wall region. The effects of the interaction between the microorganism and a solid wall on the 3D swimming characteristics, such as helix parameters, orientation, and attraction to the wall, are experimentally analyzed. As a result, swimming microorganisms are observed to have high motility and thrust generation near the wall, compared with the unrestrained free-swimming ones. In addition, the swimming direction tends to become parallel to the wall and they concentrate near the solid surface.

High-throughput analysis of horse sperms’ 3D swimming patterns using computational on-chip imaging

Using a high-throughput optical tracking technique that is based on partially-coherent digital in-line holography, here we report a detailed analysis of the statistical behavior of horse sperms’ three-dimensional (3D) swimming dynamics. This dual-color and dual-angle lensfree imaging platform enables us to track individual 3D trajectories of ∼1000 horse sperms at sub-micron level within a sample volume of ∼9μL at a frame rate of 143 frames per second (FPS) and collect thousands of sperm trajectories within a few hours for statistical analysis of their 3D dynamics. Using this high-throughput imaging platform, we recorded >17,000 horse sperm trajectories that can be grouped into six major categories: irregular, linear, planar, helical, ribbon, and hyperactivated, where the hyperactivated swimming patterns can be further divided into four sub-categories, namely hyper-progressive, hyper-planar, hyper-ribbon, and star-spin. The large spatio-temporal statistics that we collected with this 3D tracking platform revealed that irregular, planar, and ribbon trajectories are the dominant 3D swimming patterns observed in horse sperms, which altogether account for >97% of the trajectories that we imaged in plasma-free semen extender medium. Through our experiments we also found out that horse seminal plasma in general increases sperms’ straightness in their 3D trajectories, enhancing the relative percentage of linear swimming patterns and suppressing planar swimming patterns, while barely affecting the overall percentage of ribbon patterns.

Three-dimensional swimming tadpole mini-robot using three-axis Helmholtz coils

Electromagnetic-actuated robotic systems have been studied recently for special purposes. Because these systems use external magnetic fields to control their robots, the robots can have simple structures and move with much freedom. In particular, these electromagnetic actuation (EMA) systems are being widely adopted for the actuation of biomedical mini-robots and microrobots for minimally invasive surgery (MIS) and diagnosis. We previously reported, as a feasible biomedical robot, the biomimetic swimming tadpole mini-robot, which can only swim above water. Indeed, the two-dimensional (D) plane swimming tadpole mini-robot is limited in its use because of its motility in the 2D plane. Therefore, this paper proposes a 3D swimming tadpole mini-robot that can move freely in water. First, in the proposed 3D swimming tadpole mini-robot, the buoyancy force was regulated for subaqueous swimming, and the permanent magnet was rearranged for precise movement. Second, to attain a 3D swimming motion, the actuation mechanism of the robot was developed using an EMA system. Finally, various experiments verified that the proposed 3D swimming tadpole mini-robot can swim freely in a 3D water environment.