John Dabiri is Professor of Civil & Environmental Engineering and of Mechanical Engineering at Stanford University. His research focuses on science and technology at the intersection of fluid mechanics, energy and environment, and biology. Honors for this work include a MacArthur Fellowship, an Office of Naval Research Young Investigator Award, and a Presidential Early Career Award for Scientists and Engineers (PECASE). Popular Science magazine named him one of its "Brilliant 10" scientists for his research in bio-inspired propulsion. For his research in bio-inspired wind energy, Bloomberg Businessweek magazine listed him among its Technology Innovators, and MIT Technology Review magazine named him one of its 35 innovators under 35. In 2014, he was elected a Fellow of the American Physical Society. He currently serves on the Editorial Boards of the Journal of Fluid Mechanics and the Journal of the Royal Society Interface, and he is a member of the U.S. National Committee for Theoretical and Applied Mechanics.
Professor, Civil and Environmental Engineering
Professor, Mechanical Engineering
Honors & Awards
Fellow, American Physical Society (2014)
MacArthur Fellow, John D. and Catherine T. MacArthur Foundation (2010)
Presidential Early Career Award for Scientists and Engineers (PECASE), Office of Science and Technology Policy (2009)
Ph.D., California Institute of Technology, Bioengineering with minor in Aeronautics (2005)
M.S., California Institute of Technology, Aeronautics (2003)
B.S.E. summa cum laude, Princeton University, Mechanical and Aerospace Engineering (2001)
Current Research and Scholarly Interests
The Dabiri Lab conducts research at the intersection of fluid mechanics, energy and environment, and biology.
- Fluid Mechanics
ME 351A (Aut)
Independent Studies (7)
- Advanced Engineering Problems
CEE 399 (Aut, Win, Spr, Sum)
- Directed Investigation
BIOE 392 (Aut, Win, Spr, Sum)
- Directed Reading in Biophysics
BIOPHYS 399 (Sum)
- Engineering Problems
ME 391 (Aut, Win, Spr, Sum)
- Engineering Problems and Experimental Investigation
ME 191 (Aut, Win, Spr)
- Graduate Research
BIOPHYS 300 (Sum)
- Independent Study in Civil Engineering for CEE-MS Students
CEE 299 (Aut, Win, Spr)
- Advanced Engineering Problems
- Prior Year Courses
- Coherent structure colouring: identification of coherent structures from sparse data using graph theory JOURNAL OF FLUID MECHANICS 2017; 811: 468-486
- Flow Kinematics in Variable-Height Rotating Cylinder Arrays JOURNAL OF FLUIDS ENGINEERING-TRANSACTIONS OF THE ASME 2016; 138 (11)
- Performance enhancement of downstream vertical-axis wind turbines JOURNAL OF RENEWABLE AND SUSTAINABLE ENERGY 2016; 8 (5)
- A Kinematic Description of the Key Flow Characteristics in an Array of Finite-Height Rotating Cylinders JOURNAL OF FLUIDS ENGINEERING-TRANSACTIONS OF THE ASME 2016; 138 (7)
- Pressure evolution in the shear layer of forming vortex rings PHYSICAL REVIEW FLUIDS 2016; 1 (1)
- Three-dimensional flow field around and downstream of a subscale model rotating vertical axis wind turbine EXPERIMENTS IN FLUIDS 2016; 57 (3)
- Turbulence in vertical axis wind turbine canopies PHYSICS OF FLUIDS 2015; 27 (11)
- A comparison of wake measurements in motor-driven and flow-driven turbine experiments EXPERIMENTS IN FLUIDS 2015; 56 (7)
- A New Approach To Wind Energy: Opportunities And Challenges 3rd Physics of Sustainable Energy (PSE) Conference AMER INST PHYSICS. 2015: 51–57
- Suction-based propulsion as a basis for efficient animal swimming. Nature communications 2015; 6: 8790-?
Multi-jet propulsion organized by clonal development in a colonial siphonophore.
2015; 6: 8158-?
Physonect siphonophores are colonial cnidarians that are pervasive predators in many neritic and oceanic ecosystems. Physonects employ multiple, clonal medusan individuals, termed nectophores, to propel an aggregate colony. Here we show that developmental differences between clonal nectophores of the physonect Nanomia bijuga produce a division of labour in thrust and torque production that controls direction and magnitude of whole-colony swimming. Although smaller and less powerful, the position of young nectophores near the apex of the nectosome allows them to dominate torque production for turning, whereas older, larger and more powerful individuals near the base of the nectosome contribute predominantly to forward thrust production. The patterns we describe offer insight into the biomechanical success of an ecologically important and widespread colonial animal group, but, more broadly, provide basic physical understanding of a natural solution to multi-engine organization that may contribute to the expanding field of underwater-distributed propulsion vehicle design.
View details for DOI 10.1038/ncomms9158
View details for PubMedID 26327286
- Low-order modeling of wind farm aerodynamics using leaky Rankine bodies JOURNAL OF RENEWABLE AND SUSTAINABLE ENERGY 2014; 6 (6)
- Observations of large-scale fluid transport by laser-guided plankton aggregations PHYSICS OF FLUIDS 2014; 26 (10)
Emergent aerodynamics in wind farms
2014; 67 (10): 66-67
View details for Web of Science ID 000346121600024
- Induced drift by a self-propelled swimmer at intermediate Reynolds numbers PHYSICS OF FLUIDS 2014; 26 (9)
- Ambient fluid motions influence swimming and feeding by the ctenophore Mnemiopsis leidyi JOURNAL OF PLANKTON RESEARCH 2014; 36 (5): 1310-1322
- Fluid-Structure Interaction Modeling of Vertical-Axis Wind Turbines JOURNAL OF APPLIED MECHANICS-TRANSACTIONS OF THE ASME 2014; 81 (8)
- Nested contour dynamics models for axisymmetric vortex rings and vortex wakes JOURNAL OF FLUID MECHANICS 2014; 748: 521-548
An algorithm to estimate unsteady and quasi-steady pressure fields from velocity field measurements
JOURNAL OF EXPERIMENTAL BIOLOGY
2014; 217 (3): 331-336
We describe and characterize a method for estimating the pressure field corresponding to velocity field measurements such as those obtained by using particle image velocimetry. The pressure gradient is estimated from a time series of velocity fields for unsteady calculations or from a single velocity field for quasi-steady calculations. The corresponding pressure field is determined based on median polling of several integration paths through the pressure gradient field in order to reduce the effect of measurement errors that accumulate along individual integration paths. Integration paths are restricted to the nodes of the measured velocity field, thereby eliminating the need for measurement interpolation during this step and significantly reducing the computational cost of the algorithm relative to previous approaches. The method is validated by using numerically simulated flow past a stationary, two-dimensional bluff body and a computational model of a three-dimensional, self-propelled anguilliform swimmer to study the effects of spatial and temporal resolution, domain size, signal-to-noise ratio and out-of-plane effects. Particle image velocimetry measurements of a freely swimming jellyfish medusa and a freely swimming lamprey are analyzed using the method to demonstrate the efficacy of the approach when applied to empirical data.
View details for DOI 10.1242/jeb.092767
View details for Web of Science ID 000331204100012
View details for PubMedID 24115059
- Pinch-off of non-axisymmetric vortex rings JOURNAL OF FLUID MECHANICS 2014; 740: 61-96
Bending rules for animal propulsion
Animal propulsors such as wings and fins bend during motion and these bending patterns are believed to contribute to the high efficiency of animal movements compared with those of man-made designs. However, efforts to implement flexible designs have been met with contradictory performance results. Consequently, there is no clear understanding of the role played by propulsor flexibility or, more fundamentally, how flexible propulsors should be designed for optimal performance. Here we demonstrate that during steady-state motion by a wide range of animals, from fruit flies to humpback whales, operating in either air or water, natural propulsors bend in similar ways within a highly predictable range of characteristic motions. By providing empirical design criteria derived from natural propulsors that have convergently arrived at a limited design space, these results provide a new framework from which to understand and design flexible propulsors.
View details for DOI 10.1038/ncomms4293
View details for Web of Science ID 000332667600040
View details for PubMedID 24548870
- Optimal vortex formation in a self-propelled vehicle JOURNAL OF FLUID MECHANICS 2013; 737: 78-104
Passive energy recapture in jellyfish contributes to propulsive advantage over other metazoans
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2013; 110 (44): 17904-17909
Gelatinous zooplankton populations are well known for their ability to take over perturbed ecosystems. The ability of these animals to outcompete and functionally replace fish that exhibit an effective visual predatory mode is counterintuitive because jellyfish are described as inefficient swimmers that must rely on direct contact with prey to feed. We show that jellyfish exhibit a unique mechanism of passive energy recapture, which is exploited to allow them to travel 30% further each swimming cycle, thereby reducing metabolic energy demand by swimming muscles. By accounting for large interspecific differences in net metabolic rates, we demonstrate, contrary to prevailing views, that the jellyfish (Aurelia aurita) is one of the most energetically efficient propulsors on the planet, exhibiting a cost of transport (joules per kilogram per meter) lower than other metazoans. We estimate that reduced metabolic demand by passive energy recapture improves the cost of transport by 48%, allowing jellyfish to achieve the large sizes required for sufficient prey encounters. Pressure calculations, using both computational fluid dynamics and a newly developed method from empirical velocity field measurements, demonstrate that this extra thrust results from positive pressure created by a vortex ring underneath the bell during the refilling phase of swimming. These results demonstrate a physical basis for the ecological success of medusan swimmers despite their simple body plan. Results from this study also have implications for bioinspired design, where low-energy propulsion is required.
View details for DOI 10.1073/pnas.1306983110
View details for Web of Science ID 000326243100066
View details for PubMedID 24101461
Biomimetic and Live Medusae Reveal the Mechanistic Advantages of a Flexible Bell Margin
2012; 7 (11)
Flexible bell margins are characteristic components of rowing medusan morphologies and are expected to contribute towards their high propulsive efficiency. However, the mechanistic basis of thrust augmentation by flexible propulsors remained unresolved, so the impact of bell margin flexibility on medusan swimming has also remained unresolved. We used biomimetic robotic jellyfish vehicles to elucidate that propulsive thrust enhancement by flexible medusan bell margins relies upon fluid dynamic interactions between entrained flows at the inflexion point of the exumbrella and flows expelled from under the bell. Coalescence of flows from these two regions resulted in enhanced fluid circulation and, therefore, thrust augmentation for flexible margins of both medusan vehicles and living medusae. Using particle image velocimetry (PIV) data we estimated pressure fields to demonstrate a mechanistic basis of enhanced flows associated with the flexible bell margin. Performance of vehicles with flexible margins was further enhanced by vortex interactions that occur during bell expansion. Hydrodynamic and performance similarities between robotic vehicles and live animals demonstrated that the propulsive advantages of flexible margins found in nature can be emulated by human-engineered propulsors. Although medusae are simple animal models for description of this process, these results may contribute towards understanding the performance of flexible margins among other animal lineages.
View details for DOI 10.1371/journal.pone.0048909
View details for Web of Science ID 000311935800167
View details for PubMedID 23145016
- Perturbation response and pinch-off of vortex rings and dipoles JOURNAL OF FLUID MECHANICS 2012; 704: 280-300
A tissue-engineered jellyfish with biomimetic propulsion
2012; 30 (8): 792-797
Reverse engineering of biological form and function requires hierarchical design over several orders of space and time. Recent advances in the mechanistic understanding of biosynthetic compound materials, computer-aided design approaches in molecular synthetic biology 4,5 and traditional soft robotics, and increasing aptitude in generating structural and chemical micro environments that promote cellular self-organization have enhanced the ability to recapitulate such hierarchical architecture in engineered biological systems. Here we combined these capabilities in a systematic design strategy to reverse engineer a muscular pump. We report the construction of a freely swimming jellyfish from chemically dissociated rat tissue and silicone polymer as a proof of concept. The constructs, termed 'medusoids', were designed with computer simulations and experiments to match key determinants of jellyfish propulsion and feeding performance by quantitatively mimicking structural design, stroke kinematics and animal-fluid interactions. The combination of the engineering design algorithm with quantitative benchmarks of physiological performance suggests that our strategy is broadly applicable to reverse engineering of muscular organs or simple life forms that pump to survive.
View details for DOI 10.1038/nbt.2269
View details for Web of Science ID 000307416900023
View details for PubMedID 22820316
- Energy exchange in an array of vertical-axis wind turbines JOURNAL OF TURBULENCE 2012; 13 (38): 1-13
- Quantitatively Measuring In situ Flows using a Self-Contained Underwater Velocimetry Apparatus (SCUVA) JOVE-JOURNAL OF VISUALIZED EXPERIMENTS 2011
- Potential order-of-magnitude enhancement of wind farm power density via counter-rotating vertical-axis wind turbine arrays JOURNAL OF RENEWABLE AND SUSTAINABLE ENERGY 2011; 3 (4)
- Vortex-enhanced propulsion JOURNAL OF FLUID MECHANICS 2011; 668: 5-32
- Quantification of flows generated by the hydromedusa Aequorea victoria: a Lagrangian coherent structure analysis MARINE ECOLOGY PROGRESS SERIES 2011; 435: 111-123
Simultaneous field measurements of ostracod swimming behavior and background flow
Limnology and Oceanography: Fluids and Environment
2011; 1: 135-146
View details for DOI 10.1215/21573698-1472410
Quantitatively measuring in situ flows using a self-contained underwater velocimetry apparatus (SCUVA).
Journal of visualized experiments : JoVE
The ability to directly measure velocity fields in a fluid environment is necessary to provide empirical data for studies in fields as diverse as oceanography, ecology, biology, and fluid mechanics. Field measurements introduce practical challenges such as environmental conditions, animal availability, and the need for field-compatible measurement techniques. To avoid these challenges, scientists typically use controlled laboratory environments to study animal-fluid interactions. However, it is reasonable to question whether one can extrapolate natural behavior (i.e., that which occurs in the field) from laboratory measurements. Therefore, in situ quantitative flow measurements are needed to accurately describe animal swimming in their natural environment. We designed a self-contained, portable device that operates independent of any connection to the surface, and can provide quantitative measurements of the flow field surrounding an animal. This apparatus, a self-contained underwater velocimetry apparatus (SCUVA), can be operated by a single scuba diver in depths up to 40 m. Due to the added complexity inherent of field conditions, additional considerations and preparation are required when compared to laboratory measurements. These considerations include, but are not limited to, operator motion, predicting position of swimming targets, available natural suspended particulate, and orientation of SCUVA relative to the flow of interest. The following protocol is intended to address these common field challenges and to maximize measurement success.
View details for DOI 10.3791/2615
View details for PubMedID 22064442
Stealth predation and the predatory success of the invasive ctenophore Mnemiopsis leidyi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2010; 107 (40): 17223-17227
In contrast to higher metazoans such as copepods and fish, ctenophores are a basal metazoan lineage possessing a relatively narrow set of sensory-motor capabilities. Yet lobate ctenophores can capture prey at rates comparable to sophisticated predatory copepods and fish, and they are capable of altering the composition of coastal planktonic communities. Here, we demonstrate that the predatory success of the lobate ctenophore Mnemiopsis leidyi lies in its use of cilia to generate a feeding current that continuously entrains large volumes of fluid, yet is virtually undetectable to its prey. This form of stealth predation enables M. leidyi to feed as a generalist predator capturing prey, including microplankton (approximately 50 μm), copepods (approximately 1 mm), and fish larvae (>3 mm). The efficacy and versatility of this stealth feeding mechanism has enabled M. leidyi to be notoriously destructive as a predator and successful as an invasive species.
View details for DOI 10.1073/pnas.1003170107
View details for Web of Science ID 000282512000033
View details for PubMedID 20855619
Fish schooling as a basis for vertical axis wind turbine farm design
BIOINSPIRATION & BIOMIMETICS
2010; 5 (3)
Most wind farms consist of horizontal axis wind turbines (HAWTs) due to the high power coefficient (mechanical power output divided by the power of the free-stream air through the turbine cross-sectional area) of an isolated turbine. However when in close proximity to neighboring turbines, HAWTs suffer from a reduced power coefficient. In contrast, previous research on vertical axis wind turbines (VAWTs) suggests that closely spaced VAWTs may experience only small decreases (or even increases) in an individual turbine's power coefficient when placed in close proximity to neighbors, thus yielding much higher power outputs for a given area of land. A potential flow model of inter-VAWT interactions is developed to investigate the effect of changes in VAWT spatial arrangement on the array performance coefficient, which compares the expected average power coefficient of turbines in an array to a spatially isolated turbine. A geometric arrangement based on the configuration of shed vortices in the wake of schooling fish is shown to significantly increase the array performance coefficient based upon an array of 16 x 16 wind turbines. The results suggest increases in power output of over one order of magnitude for a given area of land as compared to HAWTs.
View details for DOI 10.1088/1748-3182/5/3/035005
View details for Web of Science ID 000282152500006
View details for PubMedID 20729568
Ecosystem Engineers in the Pelagic Realm: Alteration of Habitat by Species Ranging from Microbes to Jellyfish
INTEGRATIVE AND COMPARATIVE BIOLOGY
2010; 50 (2): 188-200
Ecosystem engineers are species that alter the physical environment in ways that create new habitat or change the suitability of existing habitats for themselves or other organisms. In marine systems, much of the focus has been on species such as corals, oysters, and macrophytes that add physical structure to the environment, but organisms ranging from microbes to jellyfish and finfish that reside in the water column of oceans, estuaries, and coastal seas alter the chemical and physical environment both within the water column and on the benthos. By causing hypoxia, changing light regimes, and influencing physical mixing, these organisms may have as strong an effect as species that fall more clearly within the classical category of ecosystem engineer. In addition, planktonic species, such as jellyfish, may indirectly alter the physical environment through predator-mediated landscape structure. By creating spatial patterns of habitats that vary in their rates of mortality due to predation, planktonic predators may control spatial patterns and abundances of species that are the direct creators or modifiers of physical habitat.
View details for DOI 10.1093/icb/icq051
View details for Web of Science ID 000280279800004
View details for PubMedID 21558198
Phenotypic plasticity in juvenile jellyfish medusae facilitates effective animal-fluid interaction
2010; 6 (3): 389-393
Locomotion and feeding in marine animals are intimately linked to the flow dynamics created by specialized body parts. This interaction is of particular importance during ontogeny, when changes in behaviour and scale challenge the organism with shifts in fluid regimes and altered functionality. Previous studies have indicated that Scyphozoan jellyfish ontogeny accommodates the changes in fluid dynamics associated with increasing body dimensions and velocities during development. However, in addition to scale and behaviour that-to a certain degree-underlie the control of the animal, flow dynamics are also dependent on external factors such as temperature. Here, we show phenotypic plasticity in juvenile Aurelia aurita medusae, where morphogenesis is adapted to altered fluid regimes imposed by changes in ambient temperature. In particular, differential proportional growth was found to compensate for temperature-dependent changes in viscous effects, enabling the animal to use adhering water boundary layers as 'paddles'-and thus economize tissue-at low temperatures, while switching to tissue-dominated propulsion at higher temperatures where the boundary layer thickness is insufficient to serve for paddling. This effect was predicted by a model of animal-fluid interaction and confirmed empirically by flow-field visualization and assays of propulsion efficiency.
View details for DOI 10.1098/rsbl.2010.0068
View details for Web of Science ID 000277559000030
View details for PubMedID 20335200
- Role of vertical migration in biogenic ocean mixing GEOPHYSICAL RESEARCH LETTERS 2010; 37
A wake-based correlate of swimming performance and foraging behavior in seven co-occurring jellyfish species
JOURNAL OF EXPERIMENTAL BIOLOGY
2010; 213 (8): 1217-1225
It is generally accepted that animal-fluid interactions have shaped the evolution of animals that swim and fly. However, the functional ecological advantages associated with those adaptations are currently difficult to predict on the basis of measurements of the animal-fluid interactions. We report the identification of a robust, fluid dynamic correlate of distinct ecological functions in seven jellyfish species that represent a broad range of morphologies and foraging modes. Since the comparative study is based on properties of the vortex wake--specifically, a fluid dynamical concept called optimal vortex formation--and not on details of animal morphology or phylogeny, we propose that higher organisms can also be understood in terms of these fluid dynamic organizing principles. This enables a quantitative, physically based understanding of how alterations in the fluid dynamics of aquatic and aerial animals throughout their evolution can result in distinct ecological functions.
View details for DOI 10.1242/jeb.034660
View details for Web of Science ID 000276031900005
View details for PubMedID 20348332
A Lagrangian approach to identifying vortex pinch-off
2010; 20 (1)
A criterion for identifying vortex ring pinch-off based on the Lagrangian coherent structures (LCSs) in the flow is proposed and demonstrated for a piston-cylinder arrangement with a piston stroke to diameter (L/D) ratio of approximately 12. It is found that the appearance of a new disconnected LCS and the termination of the original LCS are indicative of the initiation of vortex pinch-off. The subsequent growth of new LCSs, which tend to roll into spirals, indicates the formation of new vortex cores in the trailing shear layer. Using this criterion, the formation number is found to be 4.1+/-0.1, which is consistent with the predicted formation number of approximately 4 of Gharib et al. [Gharib et al. J. Fluid Mech. 360, 121 (1998)]. The results obtained using the proposed LCS criterion are compared with those obtained using the circulation criterion of Gharib et al. and are found to be in excellent agreement. The LCS approach is also compared against other metrics, both Lagrangian and Eulerian, and is found to yield insight into the pinch-off process that these do not. Furthermore, the LCS analysis reveals a consistent pattern of coalescing or "pairing" of adjacent vortices in the trailing shear layer, a process which has been extensively documented in circular jets. Given that LCSs are objective and insensitive to local errors in the velocity field, the proposed criterion has the potential to be a robust tool for pinch-off identification. In particular, it may prove useful in the study of unsteady and low Reynolds number flows, where conventional methods based on vorticity prove difficult to use.
View details for DOI 10.1063/1.3275499
View details for Web of Science ID 000276211400048
View details for PubMedID 20370303
Functional Morphology and Fluid Interactions During Early Development of the Scyphomedusa Aurelia aurita
2009; 217 (3): 283-291
Scyphomedusae undergo a predictable ontogenetic transition from a conserved, universal larval form to a diverse array of adult morphologies. This transition entails a change in bell morphology from a highly discontinuous ephyral form, with deep clefts separating eight discrete lappets, to a continuous solid umbrella-like adult form. We used a combination of kinematic, modeling, and flow visualization techniques to examine the function of the medusan bell throughout the developmental changes of the scyphomedusa Aurelia aurita. We found that flow around swimming ephyrae and their lappets was relatively viscous (1 < Re < 10) and, as a result, ephyral lappets were surrounded by thick, overlapping boundary layers that occluded flow through the gaps between lappets. As medusae grew, their fluid environment became increasingly influenced by inertial forces (10 < Re < 10,000) and, simultaneously, clefts between the lappets were replaced by organic tissue. Hence, although the bell undergoes a structural transition from discontinuous (lappets with gaps) to continuous (solid bell) surfaces during development, all developmental stages maintain functionally continuous paddling surfaces. This developmental pattern enables ephyrae to efficiently allocate tissue to bell diameter increase via lappet growth, while minimizing tissue allocation to inter-lappet spaces that maintain paddle function due to boundary layer overlap.
View details for Web of Science ID 000273409200008
View details for PubMedID 20040752
- Circulation Generation and Vortex Ring Formation by Conic Nozzles JOURNAL OF FLUIDS ENGINEERING-TRANSACTIONS OF THE ASME 2009; 131 (9)
A viscosity-enhanced mechanism for biogenic ocean mixing
2009; 460 (7255): 624-U87
Recent observations of biologically generated turbulence in the ocean have led to conflicting conclusions regarding the significance of the contribution of animal swimming to ocean mixing. Measurements indicate elevated turbulent dissipation--comparable with levels caused by winds and tides--in the vicinity of large populations of planktonic animals swimming together. However, it has also been noted that elevated turbulent dissipation is by itself insufficient proof of substantial biogenic mixing, because much of the turbulent kinetic energy of small animals is injected below the Ozmidov buoyancy length scale, where it is primarily dissipated as heat by the fluid viscosity before it can affect ocean mixing. Ongoing debate regarding biogenic mixing has focused on comparisons between animal wake turbulence and ocean turbulence. Here, we show that a second, previously neglected mechanism of fluid mixing--first described over 50 years ago by Charles Darwin--is the dominant mechanism of mixing by swimming animals. The efficiency of mixing by Darwin's mechanism is dependent on animal shape rather than fluid length scale and, unlike turbulent wake mixing, is enhanced by fluid viscosity. Therefore, it provides a means of biogenic mixing that can be equally effective in small zooplankton and large mammals. A theoretical model for the relative contributions of Darwinian mixing and turbulent wake mixing is created and validated by in situ field measurements of swimming jellyfish using a newly developed scuba-based laser velocimetry device. Extrapolation of these results to other animals is straightforward given knowledge of the animal shape and orientation during vertical migration. On the basis of calculations of a broad range of aquatic animal species, we conclude that biogenic mixing via Darwin's mechanism can be a significant contributor to ocean mixing and nutrient transport.
View details for DOI 10.1038/nature08207
View details for Web of Science ID 000268454300049
View details for PubMedID 19641595
Lagrangian coherent structures in low Reynolds number swimming
JOURNAL OF PHYSICS-CONDENSED MATTER
2009; 21 (20)
This work explores the utility of the finite-time Lyapunov exponent (FTLE) field for revealing flow structures in low Reynolds number biological locomotion. Previous studies of high Reynolds number unsteady flows have demonstrated that ridges of the FTLE field coincide with transport barriers within the flow, which are not shown by a more classical quantity such as vorticity. In low Reynolds number locomotion (O(1)-O(100)), in which viscous diffusion rapidly smears the vorticity in the wake, the FTLE field has the potential to add new insight to locomotion mechanics. The target of study is an articulated two-dimensional model for jellyfish-like locomotion, with swimming Reynolds number of order 1. The self-propulsion of the model is numerically simulated with a viscous vortex particle method, using kinematics adapted from previous experimental measurements on a live medusan swimmer. The roles of the ridges of the computed forward- and backward-time FTLE fields are clarified by tracking clusters of particles both backward and forward in time. It is shown that a series of ridges in front of the jellyfish in the forward-time FTLE field transport slender fingers of fluid toward the lip of the bell orifice, which are pulled once per contraction cycle into the wake of the jellyfish, where the fluid remains partitioned. A strong ridge in the backward-time FTLE field reveals a persistent barrier between fluid inside and outside the subumbrellar cavity. The system is also analyzed in a body-fixed frame subject to a steady free stream, and the FTLE field is used to highlight differences in these frames of reference.
View details for DOI 10.1088/0953-8984/21/20/204105
View details for Web of Science ID 000265418600010
View details for PubMedID 21825514
- Transport of inertial particles by Lagrangian coherent structures: application to predator-prey interaction in jellyfish feeding JOURNAL OF FLUID MECHANICS 2009; 623: 75-84
- Optimal Vortex Formation as a Unifying Principle in Biological Propulsion ANNUAL REVIEW OF FLUID MECHANICS 2009; 41: 17-33
The 'upstream wake' of swimming and flying animals and its correlation with propulsive efficiency
JOURNAL OF EXPERIMENTAL BIOLOGY
2008; 211 (16): 2669-2677
The interaction between swimming and flying animals and their fluid environments generates downstream wake structures such as vortices. In most studies, the upstream flow in front of the animal is neglected. In this study, we demonstrate the existence of upstream fluid structures even though the upstream flow is quiescent or possesses a uniform incoming velocity. Using a computational model, the flow generated by a swimmer (an oscillating flexible plate) is simulated and a new fluid mechanical analysis is applied to the flow to identify the upstream fluid structures. These upstream structures show the exact portion of fluid that is going to interact with the swimmer. A mass flow rate is then defined based on the upstream structures, and a metric for propulsive efficiency is established using the mass flow rate and the kinematics of the swimmer. We propose that the unsteady mass flow rate defined by the upstream fluid structures can be used as a metric to measure and objectively compare the efficiency of locomotion in water and air.
View details for DOI 10.1242/jeb.015883
View details for Web of Science ID 000258297000017
View details for PubMedID 18689420
In situ field measurements of aquatic animal-fluid interactions using a Self-Contained Underwater Velocimetry Apparatus (SCUVA)
LIMNOLOGY AND OCEANOGRAPHY-METHODS
2008; 6: 162-171
View details for Web of Science ID 000256497900001
An overview of a Lagrangian method for analysis of animal wake dynamics
JOURNAL OF EXPERIMENTAL BIOLOGY
2008; 211 (2): 280-287
The fluid dynamic analysis of animal wakes is becoming increasingly popular in studies of animal swimming and flying, due in part to the development of quantitative flow visualization techniques such as digital particle imaging velocimetry (DPIV). In most studies, quasi-steady flow is assumed and the flow analysis is based on velocity and/or vorticity fields measured at a single time instant during the stroke cycle. The assumption of quasi-steady flow leads to neglect of unsteady (time-dependent) wake vortex added-mass effects, which can contribute significantly to the instantaneous locomotive forces. In this paper we review a Lagrangian approach recently introduced to determine unsteady wake vortex structure by tracking the trajectories of individual fluid particles in the flow, rather than by analyzing the velocity/vorticity fields at fixed locations and single instants in time as in the Eulerian perspective. Once the momentum of the wake vortex and its added mass are determined, the corresponding unsteady locomotive forces can be quantified. Unlike previous studies that estimated the time-averaged forces over the stroke cycle, this approach enables study of how instantaneous locomotive forces evolve over time. The utility of this method for analyses of DPIV velocity measurements is explored, with the goal of demonstrating its applicability to data that are typically available to investigators studying animal swimming and flying. The methods are equally applicable to computational fluid dynamics studies where velocity field calculations are available.
View details for DOI 10.1242/jeb.007641
View details for Web of Science ID 000253196300016
View details for PubMedID 18165256
- Medusan morphospace: phylogenetic constraints, biomechanical solutions, and ecological consequences INVERTEBRATE BIOLOGY 2008; 127 (3): 265-290
- Transport and stirring induced by vortex formation JOURNAL OF FLUID MECHANICS 2007; 593: 315-331
- A potential-flow, deformable-body model for fluid-structure interactions with compact vorticity: application to animal swimming measurements EXPERIMENTS IN FLUIDS 2007; 43 (5): 655-664
- Geometry of unsteady fluid transport during fluid-structure interactions JOURNAL OF FLUID MECHANICS 2007; 589: 125-145
Renewable fluid dynamic energy derived from aquatic animal locomotion
BIOINSPIRATION & BIOMIMETICS
2007; 2 (3): L1-L3
Aquatic animals swimming in isolation and in groups are known to extract energy from the vortices in environmental flows, significantly reducing muscle activity required for locomotion. A model for the vortex dynamics associated with this phenomenon is developed, showing that the energy extraction mechanism can be described by simple criteria governing the kinematics of the vortices relative to the body in the flow. In this way, we need not make direct appeal to the fluid dynamics, which can be more difficult to evaluate than the kinematics. Examples of these principles as exhibited in swimming fish and existing energy conversion devices are described. A benefit of the developed framework is that the potentially infinite-dimensional parameter space of the fluid-structure interaction is reduced to a maximum of eight combinations of three parameters. The model may potentially aid in the design and evaluation of unsteady aero- and hydrodynamic energy conversion systems that surpass the Betz efficiency limit of steady fluid dynamic energy conversion systems.
View details for DOI 10.1088/1748-3182/2/3/L01
View details for Web of Science ID 000207170300005
View details for PubMedID 17848785
Morphological diversity of medusan lineages constrained by animal-fluid interactions
JOURNAL OF EXPERIMENTAL BIOLOGY
2007; 210 (11): 1868-1873
Cnidarian medusae, commonly known as jellyfish, represent the earliest known animal taxa to achieve locomotion using muscle power. Propulsion by medusae requires the force of bell contraction to generate forward thrust. However, thrust production is limited in medusae by the primitive structure of their epitheliomuscular cells. This paper demonstrates that constraints in available locomotor muscular force result in a trade-off between high-thrust swimming via jet propulsion and high-efficiency swimming via a combined jet-paddling propulsion. This trade-off is reflected in the morphological diversity of medusae, which exhibit a range of fineness ratios (i.e. the ratio between bell height and diameter) and small body size in the high-thrust regime, and low fineness ratios and large body size in the high-efficiency regime. A quantitative model of the animal-fluid interactions that dictate this trade-off is developed and validated by comparison with morphological data collected from 660 extant medusan species ranging in size from 300 microm to over 2 m. These results demonstrate a biomechanical basis linking fluid dynamics and the evolution of medusan bell morphology. We believe these to be the organising principles for muscle-driven motility in Cnidaria.
View details for DOI 10.1242/jeb.003772
View details for Web of Science ID 000246665600011
View details for PubMedID 17515413
Non-invasive measurement of instantaneous forces during aquatic locomotion: a case study of the bluegill sunfish pectoral fin
JOURNAL OF EXPERIMENTAL BIOLOGY
2007; 210 (4): 685-698
Swimming and flying animals generate unsteady locomotive forces by delivering net momentum into the fluid wake. Hence, swimming and flying forces can be quantified by measuring the momentum of animal wakes. A recently developed model provides an approach to empirically deduce swimming and flying forces based on the measurement of velocity and vortex added-mass in the animal wake. The model is contingent on the identification of the vortex boundary in the wake. This paper demonstrates the application of that method to a case study quantifying the instantaneous locomotive forces generated by the pectoral fins of the bluegill sunfish (Lepomis macrochirus Rafinesque), measured using digital particle image velocimetry (DPIV). The finite-time Lyapunov exponent (FTLE) field calculated from the DPIV data was used to determine the wake vortex boundary, according to recently developed fluid dynamics theory. Momentum of the vortex wake and its added-mass were determined and the corresponding instantaneous locomotive forces were quantified at discrete time points during the fin stroke. The instantaneous forces estimated in this study agree in magnitude with the time-averaged forces quantified for the pectoral fin of the same species swimming in similar conditions and are consistent with the observed global motion of the animals. A key result of this study is its suggestion that the dynamical effect of the vortex wake on locomotion is to replace the real animal fin with an ;effective appendage', whose geometry is dictated by the FTLE field and whose interaction with the surrounding fluid is wholly dictated by inviscid concepts from potential flow theory. Benefits and limitations of this new framework for non-invasive instantaneous force measurement are discussed, and its application to comparative biomechanics and engineering studies is suggested.
View details for DOI 10.1242/jeb.02692
View details for Web of Science ID 000244632700019
View details for PubMedID 17267654
- The formation number of vortex rings formed in uniform background co-flow JOURNAL OF FLUID MECHANICS 2006; 556: 147-166
Fast-swimming hydromedusae exploit velar kinematics to form an optimal vortex wake
JOURNAL OF EXPERIMENTAL BIOLOGY
2006; 209 (11): 2025-2033
Fast-swimming hydromedusan jellyfish possess a characteristic funnel-shaped velum at the exit of their oral cavity that interacts with the pulsed jets of water ejected during swimming motions. It has been previously assumed that the velum primarily serves to augment swimming thrust by constricting the ejected flow in order to produce higher jet velocities. This paper presents high-speed video and dye-flow visualizations of free-swimming Nemopsis bachei hydromedusae, which instead indicate that the time-dependent velar kinematics observed during the swimming cycle primarily serve to optimize vortices formed by the ejected water rather than to affect the speed of the ejected flow. Optimal vortex formation is favorable in fast-swimming jellyfish because, unlike the jet funnelling mechanism, it allows for the minimization of energy costs while maximizing thrust forces. However, the vortex ;formation number' corresponding to optimality in N. bachei is substantially greater than the value of 4 found in previous engineering studies of pulsed jets from rigid tubes. The increased optimal vortex formation number is attributable to the transient velar kinematics exhibited by the animals. A recently developed model for instantaneous forces generated during swimming motions is implemented to demonstrate that transient velar kinematics are required in order to achieve the measured swimming trajectories. The presence of velar structures in fast-swimming jellyfish and the occurrence of similar jet-regulating mechanisms in other jet-propelled swimmers (e.g. the funnel of squid) appear to be a primary factor contributing to success of fast-swimming jetters, despite their primitive body plans.
View details for DOI 10.1242/jeb.02242
View details for Web of Science ID 000237643700011
View details for PubMedID 16709905
Optimal vortex formation as an index of cardiac health
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2006; 103 (16): 6305-6308
Heart disease remains a leading cause of death worldwide. Previous research has indicated that the dynamics of the cardiac left ventricle (LV) during diastolic filling may play a critical role in dictating overall cardiac health. Hence, numerous studies have aimed to predict and evaluate global cardiac health based on quantitative parameters describing LV function. However, the inherent complexity of LV diastole, in its electrical, muscular, and hemodynamic processes, has prevented the development of tools to accurately predict and diagnose heart failure at early stages, when corrective measures are most effective. In this work, it is demonstrated that major aspects of cardiac function are reflected uniquely and sensitively in the optimization of vortex formation in the blood flow during early diastole, as measured by a dimensionless numerical index. This index of optimal vortex formation correlates well with existing measures of cardiac health such as the LV ejection fraction. However, unlike existing measures, this previously undescribed index does not require patient-specific information to determine numerical index values corresponding to normal function. A study of normal and pathological cardiac health in human subjects demonstrates the ability of this global index to distinguish disease states by a straightforward analysis of noninvasive LV measurements.
View details for DOI 10.1073/pnas.0600520103
View details for Web of Science ID 000236999000045
View details for PubMedID 16606852
- Lagrangian analysis of fluid transport in empirical vortex ring flows PHYSICS OF FLUIDS 2006; 18 (4)
- Effect of time-dependent piston velocity program on vortex ring formation in a piston/cylinder arrangement PHYSICS OF FLUIDS 2006; 18 (3)
- Note on the induced Lagrangian drift and added-mass of a vortex JOURNAL OF FLUID MECHANICS 2006; 547: 105-113
- Starting flow through nozzles with temporally variable exit diameter JOURNAL OF FLUID MECHANICS 2005; 538: 111-136
On the estimation of swimming and flying forces from wake measurements
JOURNAL OF EXPERIMENTAL BIOLOGY
2005; 208 (18): 3519-3532
The transfer of momentum from an animal to fluid in its wake is fundamental to many swimming and flying modes of locomotion. Hence, properties of the wake are commonly studied in experiments to infer the magnitude and direction of locomotive forces. The determination of which wake properties are necessary and sufficient to empirically deduce swimming and flying forces is currently made ad hoc. This paper systematically addresses the question of the minimum number of wake properties whose combination is sufficient to determine swimming and flying forces from wake measurements. In particular, it is confirmed that the spatial velocity distribution (i.e. the velocity field) in the wake is by itself insufficient to determine swimming and flying forces, and must be combined with the fluid pressure distribution. Importantly, it is also shown that the spatial distribution of rotation and shear (i.e. the vorticity field) in the wake is by itself insufficient to determine swimming and flying forces, and must be combined with a parameter that is analogous to the fluid pressure. The measurement of this parameter in the wake is shown to be identical to a calculation of the added-mass contribution from fluid surrounding vortices in the wake, and proceeds identically to a measurement of the added-mass traditionally associated with fluid surrounding solid bodies. It is demonstrated that the velocity/pressure perspective is equivalent to the vorticity/vortex-added-mass approach in the equations of motion. A model is developed to approximate the contribution of wake vortex added-mass to locomotive forces, given a combination of velocity and vorticity field measurements in the wake. A dimensionless parameter, the wake vortex ratio (denoted Wa), is introduced to predict the types of wake flows for which the contribution of forces due to wake vortex added-mass will become non-negligible. Previous wake analyses are re-examined in light of this parameter to infer the existence and importance of wake vortex added-mass in those cases. In the process, it is demonstrated that the commonly used time-averaged force estimates based on wake measurements are not sufficient to prove that an animal is generating the locomotive forces necessary to sustain flight or maintain neutral buoyancy.
View details for DOI 10.1242/jeb.01813
View details for Web of Science ID 000232546800014
View details for PubMedID 16155224
- Vortex motion in the ocean: In situ visualization of jellyfish swimming and feeding flows 22nd Annual Gallery of Fluid Motion Meeting AMER INST PHYSICS. 2005
The role of optimal vortex formation in biological fluid transport
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
2005; 272 (1572): 1557-1560
Animal phyla that require macro-scale fluid transport for functioning have repeatedly and often independently converged on the use of jet flows. During flow initiation these jets form fluid vortex rings, which facilitate mass transfer by stationary pumps (e.g. cardiac chambers) and momentum transfer by mobile systems (e.g. jet-propelled swimmers). Previous research has shown that vortex rings generated in the laboratory can be optimized for efficiency or thrust, based on the jet length-to-diameter ratio (L/D), with peak performance occurring at 3.5
View details for DOI 10.1098/rspb.2005.3109
View details for Web of Science ID 000231504300005
View details for PubMedID 16048770
Flow patterns generated by oblate medusan jellyfish: field measurements and laboratory analyses
JOURNAL OF EXPERIMENTAL BIOLOGY
2005; 208 (7): 1257-1265
Flow patterns generated by medusan swimmers such as jellyfish are known to differ according the morphology of the various animal species. Oblate medusae have been previously observed to generate vortex ring structures during the propulsive cycle. Owing to the inherent physical coupling between locomotor and feeding structures in these animals, the dynamics of vortex ring formation must be robustly tuned to facilitate effective functioning of both systems. To understand how this is achieved, we employed dye visualization techniques on scyphomedusae (Aurelia aurita) observed swimming in their natural marine habitat. The flow created during each propulsive cycle consists of a toroidal starting vortex formed during the power swimming stroke, followed by a stopping vortex of opposite rotational sense generated during the recovery stroke. These two vortices merge in a laterally oriented vortex superstructure that induces flow both toward the subumbrellar feeding surfaces and downstream. The lateral vortex motif discovered here appears to be critical to the dual function of the medusa bell as a flow source for feeding and propulsion. Furthermore, vortices in the animal wake have a greater volume and closer spacing than predicted by prevailing models of medusan swimming. These effects are shown to be advantageous for feeding and swimming performance, and are an important consequence of vortex interactions that have been previously neglected.
View details for DOI 10.1242/jeb.01519
View details for Web of Science ID 000228602400013
View details for PubMedID 15781886
- A revised slug model boundary layer correction for starting jet vorticity flux THEORETICAL AND COMPUTATIONAL FLUID DYNAMICS 2004; 17 (4): 293-295
- Fluid entrainment by isolated vortex rings JOURNAL OF FLUID MECHANICS 2004; 511: 311-331
- Delay of vortex ring pinchoff by an imposed bulk counterflow PHYSICS OF FLUIDS 2004; 16 (4): L28-L30
Sensitivity analysis of kinematic approximations in dynamic medusan swimming models
JOURNAL OF EXPERIMENTAL BIOLOGY
2003; 206 (20): 3675-3680
Models of medusan swimming typically rely on kinematic approximations to observed animal morphology to make such investigations tractable. The effect of these simplifications on the accuracy of predicted dynamics has not been examined in detail. We conduct a case study of the scyphozoan jellyfish Chrysaora fuscescens to isolate and quantify the sensitivity of dynamic models to common kinematic approximations. It is found that dynamic models exhibit strong dependence on the nature of some approximations and the context in which they are implemented. Therefore it is incorrect and potentially misleading to assume that achieving kinematic similarity in models of measured animal locomotion will necessarily provide dynamically correct models.
View details for DOI 10.1242/jeb.00597
View details for Web of Science ID 000187393500018
View details for PubMedID 12966059
- Vortex ring pinchoff in the presence of simultaneously initiated uniform background co-flow PHYSICS OF FLUIDS 2003; 15 (7): L49-L52
Toward empirical evaluation of left ventricle function: A novel mathematical mapping
24th Annual International Conference of the Engineering-in-Medicine-and-Biology-Society/Annual Fall Meeting of the Biomedical-Engineering-Society (EMBS 2002 BMES)
IEEE. 2002: 1270–1271
View details for Web of Science ID 000180194800616