Session R26: Biofluids: Locomotion XIII - Bacteria/Flapping

Turbulence-Copepod Interactions: Response of \textit{Acartia tonsa} to Burgers Vortex

Turbulence can affect the vertical position of copepods by altering their position, yet in situ studies suggest that, in many oceanic regimes, copepods alter their vertical position due to a behavioral response to turbulence. Numerous studies have examined copepod response to laminar flow fields, such as escaping from siphons and aggregating in thin layers. In contrast, little information exists on how they react to fine-scale turbulent fluid motions typically encountered in their natural marine environment. The hypothesis to be tested is that fine-scale turbulence alters copepod behavior, manifest as alterations in directed movement and changes in swimming kinematics. We present behavioral assays of the response of the coastal marine copepod, \textit{Acartia tonsa}, to Burgers vortices. The rotation rate and axial strain rate of the Burgers vortices are specified to correspond to the vortices with the median dissipation rate in turbulent conditions typically encountered in coastal and near surface regions. The target conditions are defined by mean turbulent dissipation rates of 0.009 and 0.096 cm$^{2}$/s$^{3}$, respectively. The three dimensional flow field of each vortex treatment is quantified via tomographic-PIV, allowing for the analysis of copepod response to specific hydrodynamic cues such as deformation rate and vorticity. Copepod trajectories are analyzed in order to correlate the behavior responses (quantified as swimming kinematics) to the hydrodynamic sensory cue.   

Visualizing viral transport and host infection

A virus is a non-motile infectious agent that can only replicate inside a living host. They consist of a \textless 100 nm diameter capsid which houses their DNA, and a \textless 20 nm diameter tail used to inject DNA to the host, which are classified into three different morphologies by the tail type: short tail ($\sim$ 10 nm, podovirus), rigid contractile tail ($\sim$ 100 nm, myovirus), or flexible noncontractile tail ($\sim$ 300 nm, siphovirus). Combining microfluidics with epifluorescent microscopy, we studied the simultaneous diffusive transport governing the initial encounter and ultimately the infection of a non-motile cyanobacteria host ($\sim$ 1 $\mu$m; prochlorococcus) and their viral (phage) counterparts in real time. This methodology allows us to quantify the virus-host encounter/adsorption dynamics and subsequently the effectiveness of various tail morphologies for viral infection. Viral transport and the role of viral morphology in host-virus interactions are critical to our understanding of both ecosystem dynamics and human health, as well as to the evolution of virus morphology.   

Bacterial locomotion, adsorption and growth over chemically patterned surfaces

Complex dynamic interactions between bacteria and chemically patched interface that mimics the heterogeneous energy landscape of a real-life interfacial environment are studied in the paper. We explore effects of these spatially varying chemical patches on bacterial locomotion, adsorption, biofilm formation and the film growth rate. Using micro-fabrication and soft-lithography, we have fabricated PDMS microfluidic channels with a solid substrate covered by micro-scale chemical patches. Arrays of 2D geometries of characteristic scales varying from 10 to 50 $\mu$m are transferred onto a glass substrate by soft-lithography. The substrate is functionalized to generate alternating hydrophobic and hydrophilic regions and bonded with the channel. The 3D swimming characteristics near these surfaces, such as swimming velocity, linear and angular dispersions, are measured \textit{in-situ} using 3D digital holographic microscopy. The observations are used to examine the mechanisms involved in adsorption and desorption of swimming bacteria onto the substrate. Long-term experiments are conducted to quantify the growth rate and structures of colony. A correlation between various length scales of the substrate and bacteria motility are observed.   

Shear alters motility of \textit{Escherichia coli}

Understanding of locomotion of microorganisms in shear flows drew a wide range of interests in microbial related topics such as biological process including pathogenic infection and biophysical interactions like biofilm formation on engineering surfaces. We employed microfluidics and digital holography microscopy to study motility of \textit{E. coli} in shear flows. We controlled the shear flow in three different shear rates: 0.28 s$^{-1}$, 2.8 s$^{-1}$, and 28 s$^{-1}$ in a straight channel with the depth of 200 $\mu $m. Magnified holograms, recorded at 15 fps with a CCD camera over more than 20 minutes, are analyzed to obtain 3D swimming trajectories and subsequently used to extract shear responses of \textit{E.coli}. Thousands of 3-D bacterial trajectories are tracked. The change of bacteria swimming characteristics including swimming velocity, reorientation, and dispersion coefficient are computed directly for individual trajectory and ensemble averaged over thousands of realizations. The results show that shear suppresses the bacterial dispersions in bulk but promote dispersions near the surface contrary to those in quiescent flow condition. Ongoing analyses are focusing to quantify effect of shear rates on tumbling frequency and reorientation of cell body, and its implication in locating the hydrodynamic mechanisms for shear enhanced angular scattering.   

Rheological behaviour of a suspension of microswimmers varying in motor characteristics

A suspension of motile cells exhibits complex rheological properties due to their collective motion. We measure the shear viscosity of suspensions of Escherichia coli strains varying in motor characteristics such as duration of run and tumble. At low cell densities, all strains irrespective of their motor characteristics exhibiting a linear increase in viscosity with cell density suggesting that the cells behave as a suspension of rods with an effective aspect ratio set by the motor characteristics of the bacteria. As the cell density is increased beyond a critical value, the viscosity drops sharply signaling the presence of strongly coordinated motion among bacteria. The critical density depends not only on the magnitude of shear but also the motor characteristics of individual cells. High shear rate disrupts the coordinated motion reducing its behavior, once again, to a suspension of inactive particles.   

Near wake features of a flying European Starling

A great deal of research focusing on flapping wings has been motivated by their high performance capabilities, especially in low Reynolds number configurations where static wing performance typically suffers. The approaches to studying flapping wings have taken different forms. One form has been the systematic investigation of the parameters that influence the relationship between flapping wings and their wake. The other form, and the approach used in the present work, is the investigation of flapping wings in nature. While the earliest work on the flapping wings of animals consists of observations of bird flight by Leonardo DaVinci, advances in technology have allowed for quantitative measurements of the wake. The near wake of a freely flying European starling has been measured using high speed, time-resolved, particle image velocimetry, simultaneously with high speed cameras which imaged the bird. These have been used to measure the near wake two-dimensional velocity field that can be associated with the bird's location and wing configuration in an avian wind tunnel. Time series of the velocities have been expressed as composite wake plots, which depict segments of the wing beat cycle for various spanwise locations in the wake. Measurements indicate that downwash is not produced during the upstroke, suggesting that the upstroke does not generate lift. As well, the wake velocities imply the presence of streamwise vortical structures, in addition to tip vortices. These two characteristics indicate similarities between the wake of a bird and the wake of a bat.   

Unsteady Propulsors in Ground Effect

Experimental and computational results are presented on an airfoil undergoing pitch oscillations in ground effect, that is, close to a solid boundary. The time-averaged thrust is found to increase monotonically as the mean position of the airfoil approaches the boundary while the propulsive efficiency stays relatively constant, showing that ground effect can enhance thrust at little extra cost for a pitching airfoil. Vortices shed into the wake form pairs rather than vortex streets, so that in the mean a momentum jet is formed that angles away from the boundary.   

Robotic penguin-like propulsor with novel spherical joint

We have designed and manufactured an innovative spherical joint mechanism with three actuated degrees of freedom, aimed at mimicking a penguin shoulder and enabling a potential propulsion technology with high efficiency and maneuverability. In addition, the mechanism might also lead to propellers with directional thrusting capability. A parallel architecture was chosen for this type of mechanism in order to ensure rigidity as well high actuation frequencies and amplitudes. Indeed, as the motors are fixed, inertial forces are lower than for a serial robot. The resulting spherical parallel mechanism (SPM) with coaxial shafts was designed and manufactured with the following specifications: fixed center of rotation (spherical joint); working frequency of 2.5 Hz under charge; unlimited rotation about main axis; and arbitrary motion within a cone of 60 degrees. The equations for the inverse kinematics of the mechanism have been established and can yield the trajectories of each actuator for any desired motion applied to the oar or blade. The technology will be illustrated with preliminary experiments in a hydrodynamic channel at the University of Applied Sciences - hepia - Switzerland.