Otar Akanyeti

A fish perspective: detecting flow features while moving using an artificial lateral line in steady and unsteady flow

For underwater vehicles to successfully detect and navigate turbulent flows, sensing the fluid interactions that occur is required. Fish possess a unique sensory organ called the lateral line. Sensory units called neuromasts are distributed over their body, and provide fish with flow-related information. In this study, a three-dimensional fish-shaped head, instrumented with pressure sensors, was used to investigate the pressure signals for relevant hydrodynamic stimuli to an artificial lateral line system. Unsteady wakes were sensed with the objective to detect the edges of the hydrodynamic trail and then explore and characterize the periodicity of the vorticity. The investigated wakes (Kármán vortex streets) were formed behind a range of cylinder diameter sizes (2.5, 4.5 and 10 cm) and flow velocities (9.9, 19.6 and 26.1 cm s−1). Results highlight that moving in the flow is advantageous to characterize the flow environment when compared with static analysis. The pressure difference from foremost to side sensors in the frontal plane provides us a useful measure of transition from steady to unsteady flow. The vortex shedding frequency (VSF) and its magnitude can be used to differentiate the source size and flow speed. Moreover, the distribution of the sensing array vertically as well as the laterally allows the Kármán vortex paired vortices to be detected in the pressure signal as twice the VSF.

FILOSE for Svenning: A Flow Sensing Bioinspired Robot

The trend of biomimetic underwater robots has emerged as a search for an alternative to traditional propeller-driven underwater vehicles. The drive of this trend, as in any other areas of bioinspired and biomimetic robotics, is the belief that exploiting solutions that evolution has already optimized leads to more advanced technologies and devices. In underwater robotics, bioinspired design is expected to offer more energy-efficient, highly maneuverable, agile, robust, and stable underwater robots. The 30,000 fish species have inspired roboticists to mimic tuna [1], rays [2], boxfish [3], eels [4], and others. The development of the first commercialized fish robot Ghostswimmer by Boston Engineering and the development of fish robots for field trials with specific applications in mind (http://www.roboshoal. com) mark a new degree of maturity of this engineering discipline after decades of laboratory trials.

Fish optimize sensing and respiration during undulatory swimming

Previous work in fishes considers undulation as a means of propulsion without addressing how it may affect other functions such as sensing and respiration. Here we show that undulation can optimize propulsion, flow sensing and respiration concurrently without any apparent tradeoffs when head movements are coupled correctly with the movements of the body. This finding challenges a long-held assumption that head movements are simply an unintended consequence of undulation, existing only because of the recoil of an oscillating tail. We use a combination of theoretical, biological and physical experiments to reveal the hydrodynamic mechanisms underlying this concerted optimization. Based on our results we develop a parsimonious control architecture that can be used by both undulatory animals and machines in dynamic environments.

Afferent and motoneuron activity in response to single neuromast stimulation in the posterior lateral line of larval zebrafish

The lateral line system of fishes contains mechanosensory receptors along the body surface called neuromasts, which can detect water motion relative to the body. The ability to sense flow informs many behaviors, such as schooling, predator avoidance, and rheotaxis. Here, we developed a new approach to stimulate individual neuromasts while either recording primary sensory afferent neuron activity or swimming motoneuron activity in larval zebrafish (Danio rerio). Our results allowed us to characterize the transfer functions between a controlled lateral line stimulus, its representation by primary sensory neurons, and its subsequent behavioral output. When we deflected the cupula of a neuromast with a ramp command, we found that the connected afferent neuron exhibited an adapting response which was proportional in strength to deflection velocity. The maximum spike rate of afferent neurons increased sigmoidally with deflection velocity, with a linear range between 0.1 and 1.0 μm/ms. However, spike rate did not change when the cupula was deflected below 8 μm, regardless of deflection velocity. Our findings also reveal an unexpected sensitivity in the larval lateral line system: stimulation of a single neuromast could elicit a swimming response which increased in reliability with increasing deflection velocities. At high deflection velocities, we observed that lateral line evoked swimming has intermediate values of burst frequency and duty cycle that fall between electrically evoked and spontaneous swimming. An understanding of the sensory capabilities of a single neuromast will help to build a better picture of how stimuli are encoded at the systems level and ultimately translated into behavior.

Refuging rainbow trout selectively exploit flows behind tandem cylinders.

ABSTRACT Fishes may exploit environmental vortices to save in the cost of locomotion. Previous work has investigated fish refuging behind a single cylinder in current, a behavior termed the Kármán gait. However, current-swept habitats often contain aggregations of physical objects, and it is unclear how the complex hydrodynamics shed from multiple structures affect refuging in fish. To begin to address this, we investigated how the flow fields produced by two D-shaped cylinders arranged in tandem affect the ability of rainbow trout (Oncorhynchus mykiss) to Kármán gait. We altered the spacing of the two cylinders from l/D of 0.7 to 2.7 (where l=downstream spacing of cylinders and D=cylinder diameter) and recorded the kinematics of trout swimming behind the cylinders with high-speed video at Re=10,000–55,000. Digital particle image velocimetry showed that increasing l/D decreased the strength of the vortex street by an average of 53% and decreased the frequency that vortices were shed by ∼20% for all speeds. Trout were able to Kármán gait behind all cylinder treatments despite these differences in the downstream wake; however, they Kármán gaited over twice as often behind closely spaced cylinders (l/D=0.7, 1.1, and 1.5). Computational fluid dynamics simulations show that when cylinders are widely spaced, the upstream cylinder generates a vortex street that interacts destructively with the downstream cylinder, producing weaker, more widely spaced and less-organized vortices that discourage Kármán gaiting. These findings are poised to help predict when fish may seek refuge in natural habitats based on the position and arrangement of stationary objects. Highlighted Article: Closely spaced structures submerged within a current produce organized flows that encourage refuging in fish.

Frequency response properties of primary afferent neurons in the posterior lateral line system of larval zebrafish.

The ability of fishes to detect water flow with the neuromasts of their lateral line system depends on the physiology of afferent neurons as well as the hydrodynamic environment. Using larval zebrafish (Danio rerio), we measured the basic response properties of primary afferent neurons to mechanical deflections of individual superficial neuromasts. We used two types of stimulation protocols. First, we used sine wave stimulation to characterize the response properties of the afferent neurons. The average frequency-response curve was flat across stimulation frequencies between 0 and 100 Hz, matching the filtering properties of a displacement detector. Spike rate increased asymptotically with frequency, and phase locking was maximal between 10 and 60 Hz. Second, we used pulse train stimulation to analyze the maximum spike rate capabilities. We found that afferent neurons could generate up to 80 spikes/s and could follow a pulse train stimulation rate of up to 40 pulses/s in a reliable and precise manner. Both sine wave and pulse stimulation protocols indicate that an afferent neuron can maintain their evoked activity for longer durations at low stimulation frequencies than at high frequencies. We found one type of afferent neuron based on spontaneous activity patterns and discovered a correlation between the level of spontaneous and evoked activity. Overall, our results establish the baseline response properties of lateral line primary afferent neurons in larval zebrafish, which is a crucial step in understanding how vertebrate mechanoreceptive systems sense and subsequently process information from the environment.

The effect of flow speed and body size on Karman gait kinematics in rainbow trout.

SUMMARY We have little understanding of how fish hold station in unsteady flows. Here, we investigated the effect of flow speed and body size on the kinematics of rainbow trout Kármán gaiting behind a 5 cm diameter cylinder. We established a set of criteria revealing that not all fish positioned in a vortex street are Kármán gaiting. By far the highest probability of Kármán gaiting occurred at intermediate flow speeds between 30 and 70 cm s−1. We show that trout Kármán gait in a region of the cylinder wake where the velocity deficit is about 40% of the nominal flow. We observed that the relationships between certain kinematic and flow variables are largely preserved across flow speeds. Tail-beat frequency matched the measured vortex shedding frequency, which increased linearly with flow speed. Body wave speed was about 25% faster than the nominal flow velocity. At speeds where fish have a high probability of Kármán gaiting, body wavelength was about 25% longer than the cylinder wake wavelength. Likewise, the lateral (i.e. cross-stream) amplitude of the tail tip was about 50% greater than the expected lateral spacing of the cylinder vortices, while the body center amplitude was about 70% less. Lateral body center acceleration increased quadratically with speed. Head angle decreased with flow speed. While these values are different from those found in fish swimming in uniform flow, the strategy for locomotion is the same; fish adjust to increasing flow by increasing their tail-beat frequency. Body size also played a role in Kármán gaiting kinematics. Tail-beat amplitudes of Kármán gaiting increased with body size, as in freestream swimming, but were almost three times larger in magnitude. Larger fish had a shorter body wavelength and slower body wave speed than smaller fish, which is a surprising result compared with freestream swimming, where body wavelength and wave speed increased with size. In contrast to freestream swimming, tail-beat frequency for Kármán gaiting fish did not depend on body size and was a function of the vortex shedding frequency.

A kinematic model of Kármán gaiting in rainbow trout

SUMMARY A mechanistic understanding of how fishes swim in unsteady flows is challenging despite its prevalence in nature. Previous kinematic studies of fish Kármán gaiting in a vortex street behind a cylinder only report time-averaged measurements, precluding our ability to formally describe motions on a cycle-by-cycle basis. Here we present the first analytical model that describes the swimming kinematics of Kármán gaiting trout with 70–90% accuracy. We found that body bending kinematics can be modelled with a travelling wave equation, which has also been shown to accurately model free-stream swimming kinematics. However, free-stream swimming and Kármán gaiting are separated in the parameter space; the amplitude, wavelength and frequency values of the traveling wave equation are substantially different for each behavior. During Kármán gaiting, the wave is initiated at the body center, which is 0.2L (where L is total body length) further down the body compared with the initiation point in free-stream swimming. The wave travels with a constant speed, which is higher than the nominal flow speed just as in free-stream swimming. In addition to undulation, we observed that Kármán gaiting fish also exhibit substantial lateral translations and body rotations, which can constitute up to 75% of the behavior. These motions are periodic and their frequencies also match the vortex shedding frequency. There is an inverse correlation between head angle and body angle: when the body rotates in one direction, the head of the fish turns into the opposite direction. Our kinematic model mathematically describes how fish swim in vortical flows in real time and provides a platform to better understand the effects of flow variations as well as the contribution of muscle activity during corrective motions.

V67L Mutation Fills an Internal Cavity To Stabilize RecA Mtu Intein

Inteins mediate protein splicing, which has found extensive applications in protein science and biotechnology. In the Mycobacterium tuberculosis RecA mini-mini intein (ΔΔIhh), a single valine to leucine substitution at position 67 (V67L) dramatically increases intein stability and activity. However, crystal structures show that the V67L mutation causes minimal structural rearrangements, with a root-mean-square deviation of 0.2 Å between ΔΔIhh-V67 and ΔΔIhh-L67. Thus, the structural mechanisms for V67L stabilization and activation remain poorly understood. In this study, we used intrinsic tryptophan fluorescence, high-pressure nuclear magnetic resonance (NMR), and molecular dynamics (MD) simulations to probe the structural basis of V67L stabilization of the intein fold. Guanidine hydrochloride denaturation monitored by fluorescence yielded free energy changes (ΔGf°) of -4.4 and -6.9 kcal mol-1 for ΔΔIhh-V67 and ΔΔIhh-L67, respectively. High-pressure NMR showed that ΔΔIhh-L67 is more resistant to pressure-induced unfolding than ΔΔIhh-V67 is. The change in the volume of folding (ΔVf) was significantly larger for V67 (71 ± 2 mL mol-1) than for L67 (58 ± 3 mL mol-1) inteins. The measured difference in ΔVf (13 ± 3 mL mol-1) roughly corresponds to the volume of the additional methylene group for Leu, supporting the notion that the V67L mutation fills a nearby cavity to enhance intein stability. In addition, we performed MD simulations to show that V67L decreases side chain dynamics and conformational entropy at the active site. It is plausible that changes in cavities in V67L can also mediate allosteric effects to change active site dynamics and enhance intein activity.

Accelerating fishes increase propulsive efficiency by modulating vortex ring geometry

Significance The ability to move is one of the key evolutionary events that led to the complexity of vertebrate life. The most speciose group of vertebrates, fishes, displays an enormous variation of movement patterns during steady swimming. We discovered that this behavioral diversity collapses into one movement pattern when fishes are challenged to increase their swimming speed, regardless of their body size, shape, and ecology. Using flow visualization and biomimetic models, we provide the first mechanistic understanding of how this conserved movement pattern allows fishes to accelerate quickly. Swimming animals need to generate propulsive force to overcome drag, regardless of whether they swim steadily or accelerate forward. While locomotion strategies for steady swimming are well characterized, far less is known about acceleration. Animals exhibit many different ways to swim steadily, but we show here that this behavioral diversity collapses into a single swimming pattern during acceleration regardless of the body size, morphology, and ecology of the animal. We draw on the fields of biomechanics, fluid dynamics, and robotics to demonstrate that there is a fundamental difference between steady swimming and forward acceleration. We provide empirical evidence that the tail of accelerating fishes can increase propulsive efficiency by enhancing thrust through the alteration of vortex ring geometry. Our study provides insight into how propulsion can be altered without increasing vortex ring size and represents a fundamental departure from our current understanding of the hydrodynamic mechanisms of acceleration. Our findings reveal a unifying hydrodynamic principle that is likely conserved in all aquatic, undulatory vertebrates.