Bulletin of the American Physical Society
74th Annual Meeting of the APS Division of Fluid Dynamics
Volume 66, Number 17
Sunday–Tuesday, November 21–23, 2021; Phoenix Convention Center, Phoenix, Arizona
Session T06: Biological fluid dynamics: Single Cells and Bacteria |
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Chair: Alejandro Martinez-Calvo, Princeton Room: North 122 AB |
Tuesday, November 23, 2021 12:40PM - 12:53PM |
T06.00001: Bacterial reconcentration in microchannels of varying cross-section and flow Ameya Gajanan Prabhune, Max D Liljenstolpe, Andy S Garcia-Gordillo, Nuris Figueroa-Morales Upstream swimming bacteria in unidirectional flows have been associated with spreading infections in tubular organ systems such as human respiratory and urinary tracts. Persistent swimmers such as Escherichia coli can rapidly contaminate capillaries by swimming against the flow, irrespective of its speed. Here, we report on anomalous accumulation of swimming bacteria depending on the cross-section of the microfluidic conduits: narrower microchannels subjected to flow result in increased bacterial concentrations with respect to wider channels that are directly connected. Our experimental findings can be rationalized by means of stochastic simulations accounting for bacterial speed and interactions with flow and confining structures. This newly observed phenomenon can one day be utilized to predict or avoid the onset of bacterial settling in biological or soil networks. |
Tuesday, November 23, 2021 12:53PM - 1:06PM |
T06.00002: Time dependence of trajectories and motor torque in Vibrio anguillarum Kiarash Samsami, Mehdi Jabbarzadeh, Henry C Fu The flagellar motor is at the center of bacterial motility. In this work we study the motor torque of the monotrichous bacterium Vibrio Anguillarum through experimental observations and numerical simulations. We observe the bacterial cells and their flagella while freely swimming to obtain the cell and the flagellum geometry, the cell’s trajectory, and its kinematics. We use our experimental data to compute the motor torque using a numerical model based on the method of regularized Stokeslets and the assumption of a force-free swimmer. The variance in the size of the studied cells creates different motor loads and allows us to measure a torque versus motor speed curve for this species. We compare our torque-speed data with the data in the literature published for other species. Our method allows us to measure the time-dependent torque along a freely swimming cell’s trajectory, including variations in torque and speed as the cell swims forward and in reverse. |
Tuesday, November 23, 2021 1:06PM - 1:19PM |
T06.00003: Spiraling galaxies of microtubules Michael J Shelley, Gokberk Kabacaoglu, David Stein, Abdullah Sami, Jesse Gatlin Look inside a living cell as it prepares to divide and you will find in it arrays of stiff biopolymers -- microtubules --radiating outwards from mobile nucleating sites called centrosomes. By interacting with cell boundaries and motor-proteins, centrosomal arrays move and position genetic material in the cell. This motion takes place in the fluidic slurry -- cytoplasm -- that fills the cell. Given the complexity of real cells, understanding how centrosomes do their job is difficult. New experiments have created artificial cells enclosing artificial centrosomes that, like their wildtype counterparts, nucleate microtubule arrays and move. These experiments show microtubule arrays stably centered in its cell, arrays spinning like spiral galaxies, and rotating arrays switching back and forth like a washing machine. We recover and organize this complex dynamics in a fluid-structure model of growing microtubules pushing against the cell boundary, and against each other through the surrounding fluid. Analysis of a coarse-grained model shows that the system is controlled by a combination of microtubule density and cell size, and the collective organization of microtubule bending by hydrodynamics. Large-scale simulations show that rotation and oscillations arise from an intricate and surprising interplay between C-shaped and S-shaped microtubule bending modes. |
Tuesday, November 23, 2021 1:19PM - 1:32PM |
T06.00004: Rate invariance and scallop theorem in viscosity gradients Christian Esparza Lopez, Eric Lauga Self-propulsion at low-Reynolds numbers requires a swimmer to deform its body in a non-reciprocal manner in order to achieve locomotion (i.e. the sequence of shapes taken by the body must be different from the same sequence played in reverse). This is known as Purcell's scallop theorem, and it is fundamental for the study of both biological and artificial microorganisms. This theorem is only valid for an inertialess, force- and torque-free swimmer moving in an unbounded and otherwise quiescent Newtonian fluid. Mechanisms have been proposed to allow locomotion of reciprocal swimmers, including finite inertia, elasticity in the fluid, and hydrodynamic interactions. Recent studies have focused their attention on the dynamics of low-Reynolds number swimmers moving in fluids of variable viscosity. Since a non-homogeneous viscosity breaks the translational symmetry of the swimmer's environment, in this talk we ask the question: Are viscosity gradients sufficient to escape the constraints of the scallop theorem? |
Tuesday, November 23, 2021 1:32PM - 1:45PM |
T06.00005: Reconstructing large-scale intracellular flows Sayantan Dutta, Reza Farhadifar, GOKBERK KABACAOGLU, Wen Lu, Vladimir I Gelfand, Stanislav Y Shvartsman, Michael J. Shelley Cytoplasmic streaming is essential to intracellular transport and mixing in large plant and animal cells. Drosophila oogenesis is an extensively studied biological process where streaming can be studied quantitatively by focusing on the cytoplasmic flows in the growing oocyte. Due to limitations in imaging and analytical approaches, the three-dimensional structure of these flows has remained unknown. We present the first quantitative view of its structure, using particle image velocimetry, biophysical modelling, and computational analysis. Our results reveal a single vortex that spans the entire oocyte, has the maximal fluid speed of ~100 nm/s, and can be quantitatively explained with a model whereby a passive fluid is entrained by a self-organized cytoskeletal activity underneath the plasma membrane. The emerging picture sheds light on related biological contexts and highlights the wealth of open questions in the applied mathematics and computational physics of intracellular flows. |
Tuesday, November 23, 2021 1:45PM - 1:58PM |
T06.00006: Local intracellular flow fields driven by active stresses of molecular motors Mehdi Molaei, Wen-hung Chou, Steven A Redford, Margaret Gardel Cells actively render both fluid-like and solid-like behaviors. While cells need to be solid enough to maintain mechanical integrity and tissue shape, they also need to be fluid enough to allow necessary remodeling. The rheological properties can be controlled by both mechanical and biochemical processes in the cell. Hence, measuring intracellular flow is a crucial step in understanding subcellular mechanochemical feedback systems. Here, we study flow fields in transient actomyosin networks driven by polymerization and depolymerization of actin filaments, as well as contractile stresses of non-muscle myosin molecular motors. We first start by showing how active stresses propagate in 2d liquid crystalline structure and in disordered networks that are formed by actin filaments. In particular, the response functions of contractile and stable gels are characterized. We then measure the retrograde flow fields of stress fibers in single cells. To understand the convoluted feedback loops in the actomyosin cytoskeleton, we perturb multiple controlling pathways including those that alter viscoelasticity of the network, effective active stresses, and the dynamics of actin filaments. |
Tuesday, November 23, 2021 1:58PM - 2:11PM |
T06.00007: Bacterial swimmers with a polar flagellar bundle: pull, push, and wrapping Sookkyung Lim, Jeungeun Lim, Yongsam Kim, Wanho Lee Flagellated bacteria swim in a fluid environment by rotating motors embedded in the cell membrane and consequently rotating helical flagella. Swimming strategies of such bacteria vary depending on the number of flagella and their arrangement across the cell body. In this talk, we present a mathematical model of lophotrichous bacteria such as Pseudomonas putida that have multiple flagella at one polar end. P. putida undergo a classical event of pull-wrapping-push cycle. To investigate the fluid-cell interaction, we explicitly model the cell as a neutrally buoyant rigid body, treat the flagella as helical elastic rods modeled by a nonstandard Kirchhoff rod theory, and couple the bacterium to a viscous fluid with the regularized Stokes formulation. The simulation results may provide the insight into the underlying swimming mechanism of lophotrichous bacteria. |
Tuesday, November 23, 2021 2:11PM - 2:24PM |
T06.00008: A Geometric Criterion for the Optimal Spreading of Active Polymers in Porous Media Christina Kurzthaler, Suvendu Mandal, Tapomoy Bhattacharjee, Hartmut Löwen, Sujit S Datta, Howard A Stone We perform Brownian dynamics simulations of active stiff polymers undergoing run-reverse dynamics, and so mimic bacterial swimming, in porous media. In accord with recent experiments of \emph{Escherichia coli}, the polymer dynamics are characterized by trapping phases interrupted by directed hopping motion through the pores. We find that the effective translational diffusivities of reversing agents can be enhanced up to two orders in magnitude, compared to their non-reversing counterparts, and exhibit a non-monotonic behavior as a function of the reversal rate, which we rationalize using a coarse-grained model. Furthermore, we discover a geometric criterion for the optimal spreading, which emerges when their run lengths are comparable to the longest straight path available in the porous medium. More significantly, our criterion unifies results for porous media with disparate pore sizes and shapes and thus provides a fundamental principle for optimal transport of microorganisms and cargo-carriers in densely-packed biological and environmental settings. |
Tuesday, November 23, 2021 2:24PM - 2:37PM |
T06.00009: Bacterial Olympics: swimming speed is independent of body size Shashank Kamdar, Dipanjan Ghosh, Tejesh Cheepuru, Lorraine Francis, Xiang Cheng For human swimming at Re ~ 106, size typically matters: the winners' podium is typically occupied by taller athletes. Here, we image the motility of Escherichia coli, a flagellated bacterial strain swimming at Re ~ 10-6, using confocal microscopy. In particular, we explore the correlation between bacterial swimming speeds and their body sizes. Counterintuitively, we find that the speed of bacteria is constant, irrespective of their body size in the range of 1 μm up to 3 μm. To understand this surprising observation, we visualize E. coli flagella by fluorescent labeling. The results demonstrate the relation between the bacterial cell body and flagellar conformation, which is not accounted for in the existing theoretical framework of bacterial motility. Thus, our study provides new insights for bacterial motility relevant to a wide range of biological and biomedical processes. |
Tuesday, November 23, 2021 2:37PM - 2:50PM |
T06.00010: Active particles in external fields Vaseem A Shaik, Gwynn J Elfring In external fields such as heat, light or viscosity gradients, active particles perform taxis by aligning along or against the field and propelling along this steady state orientation with a speed that is different from that in the absence of the field. We discuss how the boundary conditions on the particle can crucially alter the dynamics of active particles in viscosity gradients and hence the viscotaxis phenomenon. More generally, the external fields can be used to control the speed and orientation of the active particles, ultimately allowing one to control the accumulation of active matter. In a field that weakly reorients the particles, the particles accumulate in the regions of low speed, but in a field that strongly reorients the particles, they align along or against the field and accumulate downstream or upstream relative to the field. In this talk we discuss these effects of external fields on particles, particularly in the presence of walls and on the wall-bound accumulation of active matter. |
Tuesday, November 23, 2021 2:50PM - 3:03PM |
T06.00011: Active flows in endoplasmic reticulum networks Pyae Hein Htet, Edward Avezov, Eric Lauga The endoplasmic reticulum (ER) is a network of fluid-filled tubules and sheets which performs essential cellular functions such as protein and lipid synthesis and processing. Single particle tracking in peripheral ER networks has revealed slow diffusive motion inside nodes (i.e. the junctions between tubules) and much faster transport across tubules. The uncoordinated stochastic pinching of tubules was proposed as a possible mechanism behind ER solute transport (Holcman et al. 2018 Nature Cell Biol. vol. 20). We study theoretically the fluid dynamics of such active networks using a viscous hydraulic model of realistic ER geometries forced stochastically by finite-size pinching. We find that our model predicts tubule traversal speeds an order of magnitude lower than those measured experimentally, suggesting that pinching tubules may not be able to account for ER solute transport. We next explore alternative mechanisms for flow generation within the network. |
Tuesday, November 23, 2021 3:03PM - 3:16PM |
T06.00012: Viscoelasticity of the Cell Membrane Dictates Cross Stream Migration of Red Blood Cells in Micro-Confined Shear Flow Devi P Panigrahi, Suman Chakraborty Red blood cells (RBCs) deform uniquely in human body microvasculature, enabling their dynamic evolution in complex physiological fluidic pathways. While these deformation characteristics are linked with certain diseased conditions, the explicit role of viscoelasticity of the RBC membrane remains unclear. Here, we employ a 3D lattice-Boltzmann model for elucidating the role of membrane rheology towards dictating its migration in a micro-confined shear flow, mediated by a balance between hydrodynamic forces due to tumbling and wall-induced lift forces. For a stiffer and less fluidic membrane, the RBC is observed to attain a centerline equilibrium position due to the dominance of tank-treading over tumbling kinematics, resulting in substantial wall-induced lift forces. We demarcate the parametric boundaries between centerline and off-center equilibrium configurations and highlight their implications in microvasculature flow dynamics. These results are expected to open up novel paradigms of exclusive mapping of the viscoelastic properties of RBC membrane with various physiological disorders using patient-specific data. |
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