Bulletin of the American Physical Society
72nd Annual Meeting of the APS Division of Fluid Dynamics
Volume 64, Number 13
Saturday–Tuesday, November 23–26, 2019; Seattle, Washington
Session H32: Biological Fluid Dynamics: Single Cells and Bacteria II |
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Chair: Arezoo Motevalizadeh Ardekani, Purdue Room: 614 |
Monday, November 25, 2019 8:00AM - 8:13AM |
H32.00001: Approach to finite-size prey by the choanoflagellate Salpingoeca rosetta Kiarash Samsami, Henry Fu The choanoflagellate \textit{S. rosetta }is a unicellular eukaryote with a single flagellum and a collar of microvilli. It feeds on bacteria by utilizing the fluid currents generated by the beating of its flagellum that bring its prey to the surface of the collar and ingesting the bacterium. \textit{S. rosetta }is observed as a single thecate cell, a single swimming cell, a rosette shaped colony with flagella pointing outwards, and a chain shaped colony with each cell attached laterally to two neighboring cells. As a close relative of animals, this ability to form colonies and the possible resulting survival advantages could provide insight on origins of multicellularity. Prior works have studied fluid uptake and flow fields for \textit{S. rosetta} single cells and colonies as a measure of feeding performance. However the bacterial prey is comparable in size to the \textit{S. rosetta} cell and hence may have a considerable effect on the flow in near field. Here we study the hydrodynamics of a single cell or a colony approaching a finite size prey, simulating actual geometries of both. We study the approach time and velocities of single cells and colonies for different prey sizes and initial positions to compare their feeding performance. [Preview Abstract] |
Monday, November 25, 2019 8:13AM - 8:26AM |
H32.00002: Bacterial Motility Near a Surface Nicholas Coltharp Bacteria spend much of their time in complex environments: colonies of bacteria form biofilms on surfaces, and even free-swimming bacteria may find their range of motion limited by their environment. To understand how they navigate through such environments, our first step is to construct a physically-realistic model of an \textit{E. coli} bacterium. We then use the method of regularized Stokeslets and the method of images to compute its swimming speed, body rotation rate, and flagellar torque in a homogeneous viscous fluid. As we vary the distance of the model bacterium from a surface, our results agree well with those of other techniques, and with no experimental values. We also simulate a bacterium swimming in heterogeneous fluids with suspended microstructures such as elastic polymers and filamentous networks, similar to what real bacteria experience. [Preview Abstract] |
Monday, November 25, 2019 8:26AM - 8:39AM |
H32.00003: In silico micro-swimmers: runs and tumbles Sookkyung Lim We present a mathematical model of a micro-swimmer E. coli that can freely run by a flagellar bundle and tumble by motor reversals. The Kirchhoff rod theory is used to model the elastic helical flagella and the rod-shaped cell body is represented by a hollow ellipsoid that can translate and rotate as a neutrally buoyant rigid body. The hydrodynamic interaction between the fluid and the bacteria is described by the regularized version of Stokes flow. In this talk, we will focus on how bacteria can swim and reorient the course of swimming and how parts of bacteria play a role in swimming. [Preview Abstract] |
Monday, November 25, 2019 8:39AM - 8:52AM |
H32.00004: Swimming microalga as a micro-mixer in confined spaces. Mojtaba Jarrahi, Pedro Arana-Agudelo, Adama Creppy, Behnam Taidi, Harold Auradou The unicellular green alga Chlamydomonas uses two anterior flagella to swim in a breaststroke-like pulling motion, covering a distance of about seven to ten times its body size per second. This fast swimmer stirs the surrounding fluid like a mobile micro-mixer. How strong is this mixing? The few studies available on this subject, measured the diffusion of tracer particles around Chlamydomonas (a single cell or/and a suspension) to show mixing enhancement. However, we know that mixing process consists of folding and stretching of fluid elements. Diffusion of the tracer particles can not be enough appropriate to characterize mixing features. In this work, we follow the separation of the tracers, initially close together, when swimming of a Chlamydomonas cell influences them. In this way, we quantify the mixing in different zones around the microswimmer. Some other aspects of the motility of Chlamydomonas in a confined environment, like residence time and light effects, are also investigated. Microscopy of Chlamydomonas and the tracers (Carboxylated yellow-green polystyrene microspheres, diameter $=$ 0.5 $\mu $m) was carried out inside square bottom well arrays (125$\mu $m x 125$\mu $m x 60$\mu $m). [Preview Abstract] |
Monday, November 25, 2019 8:52AM - 9:05AM |
H32.00005: Squirmer in a density-stratified fluid Vaseem Shaik, Arezoo Ardekani In this work, we analyze the motion of a two-mode spherical squirmer in a linearly density stratified fluid using the method of matched asymptotic expansions. We assume that the quasi-steady conditions prevail, inertia is negligible, stratification and advective transport rate of density are small, and the swimmer is oriented either vertically upwards or downwards. We consider a swimmer that is either far away from its neutrally buoyant position (NBP) or close to its NBP. Using the Boussinesq approximation, we find that stratification reduces the speed of a swimmer that is far from its NBP irrespective of the swimming gait while the stratification reduces (resp. increases) the speed of a pusher (resp. puller) swimmer that is close to its NBP. We can understand the former observation by considering a settling rigid sphere in a stratified fluid whereas the latter observation is consistent with the reported direct numerical simulations. Close to the swimmer, the flow field is approximately the same in the homogeneous and the stratified fluid but far from the swimmer, the flow field in these two fluids is significantly different. We also comment on the power consumption and the swimming efficiency in a stratified fluid. [Preview Abstract] |
Monday, November 25, 2019 9:05AM - 9:18AM |
H32.00006: Fibrous flagellar hairs of Chlamydomonas reinhardtii do not enhance swimming Guillermo Amador, Da Wei, Marie-Eve Aubin-Tam, Daniel Tam The flagella of Chlamydomonas reinhardtii possess fibrous ultrastructures of nanometer-scale thickness known as mastigonemes. While these structures are hypothesized to enhance flagellar thrust, detailed hydrodynamic evidence supporting this claim is lacking. In this study, we present a comprehensive investigation into the hydrodynamic effects of mastigonemes using genetically modified mutants lacking the fibrous structures. Through high speed observations of freely swimming cells, we found the average and maximum swimming speeds to be unaffected by the presence of mastigonemes. In addition to swimming speeds, no significant difference was found for flagellar gait kinematics. Following our observations of swimming kinematics, we present direct measurements of the hydrodynamic forces generated by flagella with and without mastigonemes. These measurements were conducted using optical tweezers, which enabled high temporal and spatial resolution of hydrodynamic forces. Through our measurements, we found no significant difference in propulsive flows due to the presence of mastigonemes. Direct comparison between experimental measurements and numerical simulations revealed that swimming hydrodynamics were accurately captured without including mastigonemes on the modeled swimmer's flagella. Therefore, mastigonemes do not appear to increase the flagella's effective area while swimming, as previously thought. Our results refute the claim that mastigonemes enhance flagellar thrust in C. reinhardtii, and so their function still remains enigmatic. [Preview Abstract] |
Monday, November 25, 2019 9:18AM - 9:31AM |
H32.00007: Hydrodynamic and chemotactic influences in bacterial foraging Nikhil Desai, Vaseem Shaik, Arezoo Ardekani The discovery that marine bacteria can break down the hydrocarbons in oil for nutrition has motivated a fundamental understanding of the mechanisms underpinning oil-microbe interactions, e.g., the effect of oil-water interfaces on the hydrodynamics of swimming microbes. Hydrodynamic interactions enable the passive capture of microswimmers around rigid/fluid spherical obstacles, which has important consequences on a bacterium's ability to populate nutrient sources like marine snow, oil drops etc. In this talk, we first demonstrate theoretically, that surfactant-laden drops act as more effective hydrodynamic traps for bacteria than clean drops. Next, we explain the important differences between hydrodynamic trapping around stationary versus translating obstacles. Finally, we show how hydrodynamic interactions are complemented by chemotaxis to non-trivially alter the distribution of marine bacteria around both stationary oil drops and sinking marine snow particles effusing hydrocarbon/nutrient plumes. We thus delineate the effects of various physicochemical influences--like nutrient distribution, fluid-flow and proximity to interfaces--on microbial behavior in natural environments. [Preview Abstract] |
Monday, November 25, 2019 9:31AM - 9:44AM |
H32.00008: Hydrodynamic essentials of flagellar bundling Alexander Chamolly, Eric Lauga A lot of recent research activity has addressed the swimming dynamics of prokaryotic cells, in particular the formation of bundles of helical flagella in bacteria such as \emph{E. coli}. The exact dynamics of this process are complex, and most hitherto proposed computational models aiming for a detailed description have involved an interplay between a number of physical effects including long-range hydrodynamic interactions, elastic restoring forces and short-range steric interactions while respecting the overall force and torque balance between flagella and the cell body. In this study we aim to understand what fundamental physical mechanism triggers bundle formation in the first place. We distinguish between active bundling, induced by hydrodynamic interaction of the flexible flagella with each other, and passive bundling, triggered by advection of fluid around a moving cell body. We propose a minimal analytical model that involves only the essential hydrodynamics of flagellar propulsion and show that it is able to predict the dynamics of bundling, as well as the relative strength of both hydrodynamic effects. [Preview Abstract] |
Monday, November 25, 2019 9:44AM - 9:57AM |
H32.00009: A minimal model for Spiroplasma chemotaxis Christian Esparza Lopez, Eric Lauga \textit{Spiroplasma} is a small helical bacterium that swims and performs chemotaxis in a non conventional way. Instead of actuating flagella, it swims by progressively shifting the chirality of its body. The change in geometry gives rise to a wall domain - a kink - which propagates along the cell body. The chirality is then reverted in a similar fashion completing a swimming stroke. The whole deformation is non-reciprocal in time, therefore movement at low Reynolds number is achieved with the bacterium moving in the direction opposite to the kink pair propagation. Based on experimental observations, we develop a minimal model to describe \textit{Spiroplasma} chemotaxis. We start by a simple resistive force theory model of the bacterium swimming gait. Using symmetry arguments we show how to calculate the net rotation and translation of the bacterium during one full stroke. We obtain expressions for the linear displacement as a function of the time between kinks, $\tau_k$, that compare favourably with numerical computations. Using our theoretical results, we then construct a random walk model for \textit{Spiroplasma} and we obtain expressions for its diffusivity $D_e$ and chemotactic drift velocity $v_d$ as a function of $\tau_k$ and the kink angle $\theta$. [Preview Abstract] |
Monday, November 25, 2019 9:57AM - 10:10AM |
H32.00010: Hydrodynamics of bacterial spinning top Kenta Ishimoto We have theoretically and numerically investigated mono-flagellated bacterial swimming dynamics near a wall boundary with considering elastic hook flexibility to understand hydrodynamic interactions underlying the bacterial upright spinning motion, which has referred as ‘low-Reynolds-number spinning top’ in a recent experimental study. We establish an elastohydrodynamic stability theory and found that the vertical spinning motion is enabled by the mechanical competition between the destabilization by the flagellar propulsion and rotational stabilization by the elastic coupling of the hook. These results demonstrate the mechanical nature of the behaviours in rich diversity and could contribute to our deeper understandings of the bacterial surface motility and biofilm formation. [Preview Abstract] |
Monday, November 25, 2019 10:10AM - 10:23AM |
H32.00011: Hydrodynamics of prey capture in ciliated microorganisms Mads Rode, Thomas Kiorboe, Anders Andersen Unicellular microorganisms play a key role in the biological processes in the ocean. Here we focus on the marine ciliate \textit{Euplotes vannus}, which uses complex arrangements of cilia with periodic beat patterns to generate a feeding flow, retain prey particles, and transport the retained particles to the mouth region of the cell. We describe the hydrodynamics of prey capture to answer how the flow-rate of the feeding current and the prey size spectrum depend on motion and design of the organelles. We use particle image velocimetry to determine the feeding flow quantitatively, and particle tracking to identify retained and lost prey particles and to follow their transport to the mouth region. We have observed \textit{E. vannus} to both swim freely and crawl or sit on solid surfaces. When freely swimming, the ciliate generates a puller-like flow field seemingly without feeding, and when sitting it generates a strong feeding flow that resembles the flow due to a point force at the front of the cell. [Preview Abstract] |
Monday, November 25, 2019 10:23AM - 10:36AM |
H32.00012: Dynamics of growth and form in prebiotic vesicles Thomas Fai, Teresa Ruiz-Herrero, L. Mahadevan The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is controlled by physicochemical processes that include the intercalation of amphiphiles into the membrane, fluid flow across the membrane, and elastic deformations of the membrane. To understand prebiotic vesicular forms and their dynamics, we construct a minimal model that couples membrane growth, deformation, and fluid permeation, ultimately couched in terms of two dimensionless parameters that characterize the relative rate of membrane growth and the membrane permeability. Numerical simulations show that our model captures the morphological diversity seen in extant precursor mimics of cellular life, and might provide simple guidelines for the synthesis of these complex shapes from simple ingredients. [Preview Abstract] |
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