@article {62, title = {How Euglena gracilis swims: Flow field reconstruction and analysis.}, journal = {Physical Review E}, volume = {103}, year = {2021}, pages = {023102}, abstract = {

Euglena gracilis is a unicellular organism that swims by beating a single anterior flagellum. We study the nonplanar waveforms spanned by the flagellum during a swimming stroke and the three-dimensional flows that they generate in the surrounding fluid. Starting from a small set of time-indexed images obtained by optical microscopy on a swimming Euglena cell, we construct a numerical interpolation of the stroke. We define an optimal interpolation (which we call synthetic stroke) by minimizing the discrepancy between experimentally measured velocities (of the swimmer) and those computed by solving numerically the equations of motion of the swimmer driven by the trial interpolated stroke. The good match we obtain between experimentally measured and numerically computed trajectories provides a first validation of our synthetic stroke. We further validate the procedure by studying the flow velocities induced in the surrounding fluid. We compare the experimentally measured flow fields with the corresponding quantities computed by solving numerically the Stokes equations for the fluid flow, in which the forcing is provided by the synthetic stroke, and find good matching. Finally, we use the synthetic stroke to derive a coarse-grained model of the flow field resolved in terms of a few dominant singularities. The far field is well approximated by a time-varying Stresslet, and we show that the average behavior of Euglena during one stroke is that of an off-axis puller. The reconstruction of the flow field closer to the swimmer body requires a more complex system of singularities. A system of two Stokeslets and one Rotlet, that can be loosely associated with the force exerted by the flagellum, the drag of the body, and a torque to guarantee rotational equilibrium, provides a good approximation.\ 

}, keywords = {BEM, flow reconstruction, general defocusing particle tracking, Micro-swimmers, non-planar flagellar wave forms, particle tracking velocimetry, Stokes singularities}, doi = {10.1103/PhysRevE.103.023102}, author = {Nicola Giuliani and Massimiliano Rossi and Giovanni Noselli and Antonio DeSimone} } @article {63, title = {Rods coiling about a rigid constraint: Helices and perversions}, journal = {Proceedings of the Royal Society A}, volume = {477}, year = {2021}, pages = {20200817}, abstract = {

Mechanical instabilities can be exploited to design innovative structures, able to change their shape in the presence of external stimuli. In this work, we derive a mathematical model of an elastic beam subjected to an axial force and constrained to smoothly slide along a rigid support, where the distance between the rod midline and the constraint is fixed and finite. Using both theoretical and computational techniques, we characterize the bifurcations of such a mechanical system, in which the axial force and the natural curvature of the beam are used as control parameters. We show that, in the presence of a straight support, the rod can deform into shapes exhibiting helices and perversions, namely transition zones connecting together two helices with opposite chirality. The mathematical predictions of the proposed model are also compared with some experiments, showing a good quantitative agreement. In particular, we find that the buckled configurations may exhibit multiple perversions and we propose a possible explanation for this phenomenon based on the energy landscape of the mechanical system.

}, keywords = {bifurcation theory, elastic rods, finite-element simulations, helices, perversions, weakly nonlinear analysis}, doi = {/10.1098/rspa.2020.0817}, author = {Davide Riccobelli and Giovanni Noselli and Antonio DeSimone} } @article {59, title = {Mechanics of axisymmetric sheets of interlocking and slidable rods}, journal = {Journal of the Mechanics and Physics of Solids}, volume = {141}, year = {2020}, pages = {103969}, abstract = {

In this work, we study the mechanics of metamaterial sheets inspired by the pellicle of Euglenids. They are composed of interlocking elastic rods which can freely slide along their edges. We characterize the kinematics and the mechanics of these structures using the special Cosserat theory of rods and by assuming axisymmetric deformations of the tubular assembly. Through an asymptotic expansion, we investigate both structures that comprise a discrete number of rods and the limit case of a sheet composed by infinitely many rods. We apply our theoretical framework to investigate the stability of these structures in the presence of an axial load. Through a linear analysis, we compute the critical buckling force for both the discrete and the continuous case. For the latter, we also perform a numerical post-buckling analysis, studying the non-linear evolution of the bifurcation through finite elements simulations.\ 

}, keywords = {Biomimetic structures, Elastic structures, Helical rods, Mechanical instabilities, Metamaterials, Post-buckling analysis}, doi = {10.1016/j.jmps.2020.103969}, author = {Davide Riccobelli and Giovanni Noselli and Marino Arroyo and Antonio De Simone} } @article {53, title = {A fluorescent dye method suitable for visualization of one or more rat whiskers}, journal = {Bio-protocol}, volume = {8}, year = {2018}, chapter = {e2749}, abstract = {

Visualization and tracking of the facial whiskers is critical to many studies of rodent behavior. High-speed videography is the most robust methodology for characterizing whisker kinematics, but whisker visualization is challenging due to the low contrast of the whisker against its background. Recently, we showed that fluorescent dye(s) can be applied to enhance visualization and tracking of whisker(s) (Rigosa et al., 2017), and this protocol provides additional details on the technique.\ 

}, keywords = {barrel cortex, Dye, Fluorescence, Tactile perception, Tracking, Whisker}, doi = {10.21769/BioProtoc.2749}, author = {Jacopo Rigosa and Alessandro Lucantonio and Giovanni Noselli and Arash Fassihi and Fabrizio Manzino and Francesca Pulecchi and Mathew E Diamond} } @article {44, title = {Dye-enhanced visualization of rat whiskers for behavioral studies}, journal = {eLife}, volume = {6:e25290}, year = {2017}, abstract = {

Visualization and tracking of the facial whiskers is required in an increasing number of rodent studies. Though many approaches have been employed, only high-speed videography has proven adequate for measuring whisker motion and deformation during interaction with an object. However, whisker visualization and tracking is challenging for multiple reasons, primary among them the low contrast of the whisker against its background. Here we demonstrate a fluorescent dye method suitable for visualization of one or more rat whiskers. The process makes the dyed whisker(s) easily visible against a dark background. The coloring does not influence the behavioral performance of rats trained on a vibrissal vibrotactile discrimination task, nor does it affect the whiskers{\textquoteright} mechanical properties.

}, keywords = {behavioral studies, dye-enhanced visualization, rat whiskers}, doi = {10.7554/eLife.25290}, author = {Jacopo Rigosa and Alessandro Lucantonio and Giovanni Noselli and Arash Fassihi and Erik Zorzin and Fabrizio Manzino and Francesca Pulecchi and Mathew E Diamond} } @article {52, title = {Kinematics of flagellar swimming in Euglena gracilis: Helical trajectories and flagellar shapes}, journal = {Proceedings of the National Academy of Sciences of USA}, volume = {114}, year = {2017}, pages = {13085{\textendash}13090}, abstract = {

The flagellar swimming of euglenids, which are propelled by a single anterior flagellum, is characterized by a generalized helical motion. The 3D nature of this swimming motion, which lacks some of the symmetries enjoyed by more common model systems, and the complex flagellar beating shapes that power it make its quantitative description challenging. In this work, we provide a quantitative, 3D, highly resolved reconstruction of the swimming trajectories and flagellar shapes of specimens of Euglena gracilis. We achieved this task by using high-speed 2D image recordings taken with a conventional inverted microscope combined with a precise characterization of the helical motion of the cell body to lift the 2D data to 3D trajectories. The propulsion mechanism is discussed. Our results constitute a basis for future biophysical research on a relatively unexplored type of eukaryotic flagellar movement.\ 

}, keywords = {3D flagellum shapes, Euglena gracilis, helical trajectories, microscopy imaging, microswimmers}, doi = {10.1073/pnas.1708064114}, author = {Massimiliano Rossi and Giancarlo Cicconofri and Alfred Beran and Giovanni Noselli and Antonio DeSimone} }