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Kamran Mohseni - One of the best experts on this subject based on the ideXlab platform.

  • Identifying and modeling motion primitives for the hydromedusae Sarsia tubulosa and Aequorea victoria.
    Bioinspiration & biomimetics, 2015
    Co-Authors: Isaac J. Sledge, Michael Krieg, Doug Lipinski, Kamran Mohseni
    Abstract:

    The movements of organisms can be thought of as aggregations of motion primitives: motion segments containing one or more significant actions. Here, we present a means to identify and characterize motion primitives from recorded movement data. We address these problems by assuming that the motion sequences can be characterized as a series of dynamical-system-based pattern generators. By adopting a nonparametric, Bayesian formalism for learning and simplifying these pattern generators, we arrive at a purely data-driven model to automatically identify breakpoints in the movement sequences. We apply this model to swimming sequences from two hydromedusa. The first hydromedusa is the prolate Sarsia tubulosa, for which we obtain five motion primitives that correspond to bell cavity pressurization, jet formation, jetting, cavity fluid refill, and coasting. The second hydromedusa is the oblate Aequorea victoria, for which we obtain five motion primitives that correspond to bell compression, vortex separation, cavity fluid refill, vortex formation, and coasting. Our experimental results indicate that the breakpoints between primitives are correlated with transitions in the bell geometry, vortex formation and shedding, and changes in derived dynamical quantities. These dynamics quantities include terms like pressure, power, drag, and thrust. Such findings suggest that dynamics information is inherently present in the observed motions.

  • an arbitrary lagrangian eulerian formulation for the numerical simulation of flow patterns generated by the hydromedusa textit Aequorea victoria
    arXiv: Fluid Dynamics, 2010
    Co-Authors: Mehmet Sahin, Kamran Mohseni
    Abstract:

    A new geometrically conservative arbitrary Lagrangian-Eulerian (ALE) formulation is presented for the moving boundary problems in the swirl-free cylindrical coordinates. The governing equations are multiplied with the radial distance and integrated over arbitrary moving Lagrangian-Eulerian quadrilateral elements. Therefore, the continuity and the geometric conservation equations take very simple form similar to those of the Cartesian coordinates. The continuity equation is satisfied exactly within each element and a special attention is given to satisfy the geometric conservation law (GCL) at the discrete level. The equation of motion of a deforming body is solved in addition to the Navier-Stokes equations in a fully-coupled form. The mesh deformation is achieved by solving the linear elasticity equation at each time level while avoiding remeshing in order to enhance numerical robustness. The resulting algebraic linear systems are solved using an ILU(k) preconditioned GMRES method provided by the PETSc library. The present ALE method is validated for the steady and oscillatory flow around a sphere in a cylindrical tube and applied to the investigation of the flow patterns around a free-swimming hydromedusa \textit{Aequorea victoria} (crystal jellyfish). The calculations for the hydromedusa indicate the shed of the opposite signed vortex rings very close to each other and the formation of large induced velocities along the line of interaction while the ring vortices moving away from the hydromedusa. In addition, the propulsion efficiency of the free-swimming hydromedusa is computed and its value is compared with values from the literature for several other species. The fluid dynamics video presented here shows the time variation of the instantaneous three-dimensional vorticity isosurfaces around a free-swimming hydromedusa \textit{Aequorea victoria}.

  • The numerical comparison of flow patterns and propulsive performances for the hydromedusae Sarsia tubulosa and Aequorea victoria.
    Journal of Experimental Biology, 2009
    Co-Authors: Mehmet Sahin, Kamran Mohseni, Sean P. Colin
    Abstract:

    SUMMARY The thrust-generating mechanism of a prolate hydromedusa Sarsia tubulosa and an oblate hydromedusa Aequorea victoria was investigated by solving the incompressible Navier–Stokes equations in the swirl-free cylindrical coordinates. The calculations clearly show the vortex dynamics related to the thrust-generating mechanism, which is very important for understanding the underlying propulsion mechanism. The calculations for the prolate jetting hydromedusa S. tubulosa indicate the formation of a single starting vortex ring for each pulse cycle with a relatively high vortex formation number. However, the calculations for the oblate jet-paddling hydromedusa A. victoria indicate shedding of the opposite-signed vortex rings very close to each other and the formation of large induced velocities along the line of interaction as the vortices move away from the hydromedusa in the wake. In addition to this jet propulsion mechanism, the hydromedusa9s bell margin acts like a paddle and the highly flexible bell margin deforms in such a way that the low pressure leeward side of the bell margin has a projected area in the direction of motion. This thrust is particularly important during refilling of the subumbrella cavity where the stopping vortex causes significant pressure drag. The swimming performances based on our numerical simulations, such as swimming velocity, thrust, power requirement and efficiency, were computed and support the idea that jet propulsion is very effective for rapid body movement but is energetically costly and less efficient compared with the jet-paddling propulsion mechanism.

  • Flow structures and fluid transport for the hydromedusae Sarsia tubulosa and Aequorea victoria.
    Journal of Experimental Biology, 2009
    Co-Authors: Doug Lipinski, Kamran Mohseni
    Abstract:

    SUMMARY The flow structures produced by the hydromedusae Sarsia tubulosa and Aequorea victoria are examined using direct numerical simulation and Lagrangian coherent structures (LCS). Body motion of each hydromedusa is digitized and input to a CFD program. Sarsia tubulosa uses a jetting type of propulsion, emitting a single, strong, fast-moving vortex ring during each swimming cycle while a secondary vortex of opposite rotation remains trapped within the subumbrellar region. The ejected vortex is highly energetic and moves away from the hydromedusa very rapidly. Conversely, A. victoria , a paddling type hydromedusa, is found to draw fluid from the upper bell surface and eject this fluid in pairs of counter-rotating, slow-moving vortices near the bell margins. Unlike S. tubulosa , both vortices are ejected during the swimming cycle of A. victoria and linger in the tentacle region. In fact, we find that A. victoria and S. tubulosa swim with Strouhal numbers of 1.1 and 0.1, respectively. This means that vortices produced by A. victoria remain in the tentacle region roughly 10 times as long as those produced by S. tubulosa , which presents an excellent feeding opportunity during swimming for A. victoria . Finally, we examine the pressure on the interior bell surface of both hydromedusae and the velocity profile in the wake. We find that S. tubulosa produces very uniform pressure on the interior of the bell as well as a very uniform jet velocity across the velar opening. This type of swimming can be well approximated by a slug model, but A. victoria creates more complicated pressure and velocity profiles. We are also able to estimate the power output of S. tubulosa and find good agreement with other hydromedusan power outputs. All results are based on numerical simulations of the swimming jellyfish.

  • an arbitrary lagrangian eulerian formulation for the numerical simulation of flow patterns generated by the hydromedusa Aequorea victoria
    Journal of Computational Physics, 2009
    Co-Authors: Mehmet Sahin, Kamran Mohseni
    Abstract:

    A new geometrically conservative arbitrary Lagrangian-Eulerian (ALE) formulation is presented for the moving boundary problems in the swirl-free cylindrical coordinates. The governing equations are multiplied with the radial distance and integrated over arbitrary moving Lagrangian-Eulerian quadrilateral elements. Therefore, the continuity and the geometric conservation equations take very simple form similar to those of the Cartesian coordinates. The continuity equation is satisfied exactly within each element and a special attention is given to satisfy the geometric conservation law (GCL) at the discrete level. The equation of motion of a deforming body is solved in addition to the Navier-Stokes equations in a fully-coupled form. The mesh deformation is achieved by solving the linear elasticity equation at each time level while avoiding remeshing in order to enhance numerical robustness. The resulting algebraic linear systems are solved using an ILU(k) preconditioned GMRES method provided by the PETSc library. The present ALE method is validated for the steady and oscillatory flow around a sphere in a cylindrical tube and applied to the investigation of the flow patterns around a free-swimming hydromedusa Aequorea victoria (crystal jellyfish). The calculations for the hydromedusa indicate the shed of the opposite signed vortex rings very close to each other and the formation of large induced velocities along the line of interaction while the ring vortices moving away from the hydromedusa. In addition, the propulsion efficiency of the free-swimming hydromedusa is computed and its value is compared with values from the literature for several other species.

Donald J Leo - One of the best experts on this subject based on the ideXlab platform.

  • biomimetic jellyfish inspired underwater vehicle actuated by ionic polymer metal composite actuators
    Smart Materials and Structures, 2012
    Co-Authors: Joseph S Najem, Stephen A Sarles, Barbar J Akle, Donald J Leo
    Abstract:

    This paper presents the design, fabrication, and characterization of a biomimetic jellyfish robot that uses ionic polymer metal composites (IPMCs) as flexible actuators for propulsion. The shape and swimming style of this underwater vehicle are based on the Aequorea victoria jellyfish, which has an average swimming speed of 20 mm s 1 and which is known for its high swimming efficiency. The Aequorea victoria is chosen as a model system because both its bell morphology and kinematic properties match the mechanical properties of IPMC actuators. This medusa is characterized by its low swimming frequency, small bell deformation during the contraction phase, and high Froude efficiency. The critical components of the robot include the flexible bell that provides the overall shape and dimensions of the jellyfish, a central hub and a stage used to provide electrical connections and mechanical support to the actuators, eight distinct spars meant to keep the upper part of the bell stationary, and flexible IPMC actuators that extend radially from the central stage. The bell is fabricated from a commercially available heat-shrinkable polymer film to provide increased shape-holding ability and reduced weight. The IPMC actuators constructed for this study demonstrated peak-to-peak strains of 0.7% in water across a frequency range of 0.1‐1.0 Hz. By tailoring the applied voltage waveform and the flexibility of the bell, the completed robotic jellyfish with four actuators swam at an average speed 0.77 mm s 1 and consumed 0.7 W. When eight actuators were used the average speed increased to 1.5 mm s 1 with a power consumption of 1.14 W. (Some figures may appear in colour only in the online journal)

Fabio Beltram - One of the best experts on this subject based on the ideXlab platform.

  • Single amino acid replacement makes Aequorea victoria fluorescent proteins reversibly photoswitchable.
    Journal of the American Chemical Society, 2009
    Co-Authors: Ranieri Bizzarri, Michela Serresi, Francesco Cardarelli, Stefania Abbruzzetti, Barbara Campanini, Cristiano Viappiani, Fabio Beltram
    Abstract:

    Reversibly photoswitchable (i.e., photochromic) fluorescent proteins open the way to a number of advanced bioimaging techniques applicable to living-cell studies such as sequential photolabeling of distinct cellular regions, innovative FRET schemes, or nanoscopy. Owing to the relevance of fluorescent proteins from Aequorea victoria (AFPs) for cell biology, a photochromic "toolbox" constituted by several AFPs is highly desirable. Here we introduce four new photochromic AFPs whose reversible photoswitching occurs between the native bright and a dark state at low illumination power, on account of a very efficient cis-trans photoisomerization. Most remarkably, the optical bistability of these AFPs derives from the single E222Q mutation in the primary sequence. Apparently, the E222Q substitution can restore the intrinsic photochromic behavior of the isolated chromophore. The significance of these mutants for high-resolution in vivo cell imaging is shown by means of photochromic FRET experiments.

Joseph S Najem - One of the best experts on this subject based on the ideXlab platform.

  • biomimetic jellyfish inspired underwater vehicle actuated by ionic polymer metal composite actuators
    Smart Materials and Structures, 2012
    Co-Authors: Joseph S Najem, Stephen A Sarles, Barbar J Akle, Donald J Leo
    Abstract:

    This paper presents the design, fabrication, and characterization of a biomimetic jellyfish robot that uses ionic polymer metal composites (IPMCs) as flexible actuators for propulsion. The shape and swimming style of this underwater vehicle are based on the Aequorea victoria jellyfish, which has an average swimming speed of 20 mm s 1 and which is known for its high swimming efficiency. The Aequorea victoria is chosen as a model system because both its bell morphology and kinematic properties match the mechanical properties of IPMC actuators. This medusa is characterized by its low swimming frequency, small bell deformation during the contraction phase, and high Froude efficiency. The critical components of the robot include the flexible bell that provides the overall shape and dimensions of the jellyfish, a central hub and a stage used to provide electrical connections and mechanical support to the actuators, eight distinct spars meant to keep the upper part of the bell stationary, and flexible IPMC actuators that extend radially from the central stage. The bell is fabricated from a commercially available heat-shrinkable polymer film to provide increased shape-holding ability and reduced weight. The IPMC actuators constructed for this study demonstrated peak-to-peak strains of 0.7% in water across a frequency range of 0.1‐1.0 Hz. By tailoring the applied voltage waveform and the flexibility of the bell, the completed robotic jellyfish with four actuators swam at an average speed 0.77 mm s 1 and consumed 0.7 W. When eight actuators were used the average speed increased to 1.5 mm s 1 with a power consumption of 1.14 W. (Some figures may appear in colour only in the online journal)

Werner Funke - One of the best experts on this subject based on the ideXlab platform.

  • cracks in the β can fluorescent proteins from anemonia sulcata anthozoa actinaria
    Proceedings of the National Academy of Sciences of the United States of America, 2000
    Co-Authors: Ja Rg Wiedenmann, Carsten Elke, Klausdieter Spindler, Werner Funke
    Abstract:

    Abstract We characterize two green fluorescent proteins (GFPs), an orange fluorescent protein, and a nonfluorescent red protein isolated from the sea anemone Anemonia sulcata. The orange fluorescent protein and the red protein seem to represent two different states of the same protein. Furthermore, we describe the cloning of a GFP and a nonfluorescent red protein. Both proteins are homologous to the GFP from Aequorea victoria. The red protein is significantly smaller than other GFP homologues, and the formation of a closed GFP-like β-can is not possible. Nevertheless, the primary structure of the red protein carries all features necessary for orange fluorescence. We discuss a type of β-can that could be formed in a multimerization process.

  • cracks in the β can fluorescent proteins from anemonia sulcata anthozoa actinaria
    Proceedings of the National Academy of Sciences of the United States of America, 2000
    Co-Authors: Ja Rg Wiedenmann, Carsten Elke, Klausdieter Spindler, Werner Funke
    Abstract:

    We characterize two green fluorescent proteins (GFPs), an orange fluorescent protein, and a nonfluorescent red protein isolated from the sea anemone Anemonia sulcata. The orange fluorescent protein and the red protein seem to represent two different states of the same protein. Furthermore, we describe the cloning of a GFP and a nonfluorescent red protein. Both proteins are homologous to the GFP from Aequorea victoria. The red protein is significantly smaller than other GFP homologues, and the formation of a closed GFP-like beta-can is not possible. Nevertheless, the primary structure of the red protein carries all features necessary for orange fluorescence. We discuss a type of beta-can that could be formed in a multimerization process.