Session M17: Biofluids: Microswimmers Experiments II

Swimming simply: Minimal models and stroke optimization for biological systems

In this talk, we examine how to represent the kinematics of swimming biological systems. We present a new method of extracting optimal curvature-space basis modes from high-speed video microscopy images of motile spermatozoa by tracking their flagellar kinematics. Using as few as two basis modes to characterize the swimmer's shape, we apply resistive force theory to build a model and predict the swimming speed and net translational and rotational displacement of a sperm cell over any given stroke. This low-order representation of motility yields a complete visualization of the system dynamics. The visualization tools provide refined initialization and intuition for global stroke optimization and improve motion planning by taking advantage of symmetries in the shape space to design a stroke that produces a desired net motion. Comparing the predicted optimal strokes to those observed experimentally enables us to rationalize biological motion by identifying possible optimization goals of the organism. This approach is applicable to a wide array of systems at both low and high Reynolds numbers.   

How synthetic microswimmers move, turn, flip, and spread

We study the dynamics of bimetallic rods that are propelled catalytically in a fluid of chemical fuel. Our experiments reveal that self-propelled rods near a surface undergo systematic turns, spontaneous flips, and dispersion at a rate that saturates with increasing speed. These phenomena can be explained quantitatively by our mathematical model only by incorporating a slight curvature in the rods. The model shows how minor variations in particle shape lead to major changes in trajectory patterns and diffusivity, and offers insight into dispersion of both synthetic and biological swimmers.   

Evolved to fail: Bacteria induce flagellar buckling to reorient

Many marine bacteria swim with a single helical flagellum connected to a rotary motor via a 100 nm long universal joint called the ``hook.'' While these bacteria have seemingly just one degree of freedom, allowing them to swim only back and forth, they in fact exhibit large angular reorientations mediated by off-axis ``flicks'' of their flagellum. High-speed video microscopy revealed the mechanism underpinning this turning behavior: the buckling of the hook during the exceedingly brief (10 ms) forward run that follows a reversal. Direct measurements of the hook's mechanical properties corroborated this result, as the hook's structural stability is governed by the Sperm number, which compares the compressive load from propulsion to the elastic restoring force of the hook. Upon decreasing the Sperm number below a critical value by reducing the swimming speed, the frequency of flicks diminishes sharply, consistent with the criticality of buckling. This elegant, under-actuated turning mechanism appears widespread among marine bacteria and may provide a novel design concept in micro-robotics.   

Aerotaxis in Bacterial Turbulence

Concentrated suspensions of motile bacteria exhibit correlated dynamics on spatial scales much larger than an individual bacterium. The resulting flows, visually similar to turbulence, can increase mixing and decrease viscosity. However, it remains unclear to what degree the collective dynamics depend on the motile behavior of bacteria at the individual level. Using a new microfluidic device to create controlled horizontal oxygen gradients, we studied the two dimensional behavior of dense suspensions of \textit{Bacillus subtilis}. This system makes it possible to assess the interplay between the coherent large-scale motions of the suspension, oxygen transport, and the directional response of cells to oxygen gradients (aerotaxis). At the same time, this device has enabled us to examine the onset of bacterial turbulence and its influence on the propagation of the diffusing oxygen front, as the bacteria begin in a dormant state and transition to swimming when exposed to oxygen.   

Undulatory Swimming in Shear-thinning Fluids

Many fluids in which microorganisms move, feed, and reproduce possess shear-rate dependent viscosity behavior (e.g. shear-thinning). Such fluids include wet soil, clay suspension, mucus, and gels. In this talk, we experimentally investigate the effects of shear-rate dependent viscosity on the swimming behavior of the nematode \emph{Caenorhabditis elegans} using velocimetry and tracking methods. Here, aqueous solutions of xanthan gum, which is a rod-like stiff polymer, are used with concentrations varying from the semi-dilute to the concentrated regime. The data is compared to swimming in simple, Newtonian fluids. We find that the nematode swims at an approximately constant speed in the semi-dilute regime. Surprisingly, the nematode exhibits 40\% increases in swimming speed once immersed in a concentrated solution. The enhancement in swimming speed seems to be related to the dynamics of rod-like polymer networks formed in concentrated solutions.   

Interaction of bacteria and a chemically patterned surface

We are investigating the mechanisms involved in the interactions between bacteria and chemically patched oil-water interface. Using micro-fabrication and soft-lithography, we have engineered a chemically patterned solid surface to mimic the real interfacial environment. Arrays of 2D geometries whose characteristic size ranges from 10$\mu $m to 100$\mu $m are patterned onto a glass substrate and subsequently functionalized using Octadecyltrichlorosilane (OTS). The photoresist covering geometries is further removed after functionalization. Consequently, a chemically patterned surface with alternating hydrophobic and hydrophilic regions is produced as the substrate for microfluidics. The effects of this surface on bacteria attachment and detachment are evaluated \textit{in-situ}. The growth rates of biofilm are quantified by measuring the morphology of bacterial colony. To elucidate hydrodynamic mechanism involved, bacteria swimming characteristics, such as swimming velocity, angle, tumbling frequency and dispersion, is measured within a microfluidics with a patterned substrate using 3D digital holographic microscopy. Comparative studies on smooth swimming and tumbling capable strains over such surfaces will also be presented.   

Hydrodynamic behavior of shaking flasks used for producing a recombinant protein by filamentous bacteria

Shake flasks are widely used for culture research. The agitation rate is one of the factors that determines the mass transfer. However, it has not been studied in detail. In this work, a comparison of the hydrodynamic performance for conventional, baffled and coiled spring Erlenmeyer flasks is presented. The velocity fields for a horizontal plane were measured by means of a Particle Image Velocimetry (PIV) technique and high speed videos were recorded to observe the behavior of the interface as a function of the agitation rate. It was observed not only that there is a strong dependence between the geometry and the hydrodynamics, but also there is a good agreement with the results obtained previously by Gamboa et al, in 2011, with the evaluation of the influence of culture conditions of \textit{S. lividans} on protein O-glycosylation. The turbulence intensity increases with shaken rate. However, for the baffled geometry, it was observed a decrease for a critical speed, which is related with the \textit{in}-phase and \textit{out-}phase regions. These results can be an explanation for the variations in protein productivity as a function of the flask geometry and the differences in aggregation morphology and the pattern of O-glycosylation of the recombinant protein.   

Scalar transport by planktonic swarms

Nutrient and energy transport in the ocean is primarily governed by the action of physical phenomena. In previous studies it has been suggested that aquatic fauna may significantly contribute to this process through the action of the induced drift mechanism. In this investigation, the role of planktonic swarms as ecosystem engineers is assessed through the analysis of scalar transport within a stratified water column. The vertical migration of Artemia salina is controlled via luminescent signals on the top and bottom of the column. The scalar transport of fluorescent dye is visualized and quantified through planar laser induced fluorescence (PLIF). Preliminary results show that the vertical movement of these organisms enhances scalar transport relative to control cases in which only buoyancy forces and diffusion are present.   

Myco-fluidics: The fluid dynamics of fungal chimerism

Chimeras--fantastical creatures formed as amalgams of many animals--have captured the human imagination since Ancient times. But they are also surprisingly common in Nature. The syncytial cells of filamentous fungi harbor large numbers of nuclei bathed in a single cytoplasm. As a fungus grows these nuclei become genetically diverse, either from mutation or from exchange of nuclei between different fungal individuals, a process that is known to increase the virulence of the fungus and its adaptability. By directly measuring nuclear movement in the model ascomycete fungus {\it Neurospora crassa}, we show that the fungus' tolerance for internal genetic diversity is enabled by hydrodynamic mixing of nuclei acting at all length scales within the fungal mycelium. Mathematical modeling and experiments in a mutant with altered mycelial morphology reveal some of the exquisite hydraulic engineering necessary to create these mixing flows from spatially coarse pressure gradients.   

Turbulence from a microorganism's perspective: Does the open ocean feel different than a coral reef?

Microorganisms in the ocean live in turbulent flows. Swimming microorganisms navigate through the water (e.g. larvae land on suitable substrata, predators find patches of prey), but the mechanisms by which they do so in turbulent flow are poorly understood as are the roles of passive transport versus active behaviors. Because microorganisms are smaller than the Kolmagorov length (the smallest scale of eddies in turbulent flow), they experience turbulence as a series of linear gradients in the velocity that vary in time. While the average strength of these gradients and a timescale can be computed from some typical characteristics of the flow, such as the turbulent kinetic energy or the dissipation rate, there are indications that organisms are disproportionally affected by rare, extreme events. Understanding the frequency of such events in different environments will be critical to understanding how microorganisms respond to and navigate in turbulence. To understand the hydrodynamic cues that microorganisms experience in the ocean we must measure velocity gradients in realistic turbulent flow on the spatial and temporal scales encountered by microorganisms. We have been exploring the effect of the spatial resolution of PIV and DNS of turbulent flow on the presence of velocity gradients of different magnitudes at the scale of microorganisms. Here we present some results of PIV taken at different resolutions in turbulent flow over rough biological substrata to illustrate the challenges of quantifying the fluctuations in velocity gradients encountered by aquatic microorganisms.