Bulletin of the American Physical Society
73rd Annual Meeting of the APS Division of Fluid Dynamics
Volume 65, Number 13
Sunday–Tuesday, November 22–24, 2020; Virtual, CT (Chicago time)
Session K04: Biological Fluid Dynamics: Single Cells and Bacteria (8:45am - 9:30am CST)Interactive On Demand
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K04.00001: Hydrodynamics and direction change of tumbling bacteria Mariia Dvoriashyna, Eric Lauga The bacterium {\it Escherichia coli} swims by rotating several helical flagellar filaments, which are gathered in a bundle behind the cell during `runs' wherein the cell moves steadily forward. In between runs, the cell undergoes quick `tumble' events, during which at least one flagellum reverses its rotation direction and separates from the bundle, resulting in erratic motion in place. Alternating between runs and tumbles allows cells to sample space by stochastically changing their propulsion direction after each tumble. Statistically this change of direction is not uniform, with a distribution skewed towards smaller angles with an average of about 67$^\circ$, first measured by Berg and Brown in 1972. In the present work we develop a theoretical approach to model the angular distribution of swimming {\it E. coli} cells during tumbles. We first use past experimental imaging to construct a kinematic description of the dynamics of the flagellar filaments. We then use low-Reynolds number hydrodynamics to compute the consequences of the kinematic model on the force and torque balance of the cell, and deduce the change in orientation. Numerical simulations of our model are in good agreement with experimental observations. [Preview Abstract] |
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K04.00002: Numerical simulation of shear-induced drug encapsulation. Mehdi Nikfar, Meghdad Razizadeh, Yaling Liu Recent studies show that shear-induced drug loading methods in the microfluidic device is an efficient intracellular drug loading approach. In this study, a cellular-scale numerical model based on dissipative Lattice Boltzmann Method and spring connected network is utilized for modeling the drug encapsulation into a compound cell after rapid squeezing through microfluidic channels. The radius of the shear-induced pores is computed via a mathematical correlation derived from the results of coarse-grained molecular dynamics. We assume that the drug loading occurs after squeezing as a result of passive diffusion. To calculate the drug concentration inside the cell, a mathematical correlation is proposed for passive diffusion after squeezing. The numerical algorithm is validated by simulation a compound cell under simple shear flow. Upon the validation, the drug concentration inside the cell is quantified for different range of squeezing velocities, constriction lengths and constriction widths. The results show that the drug loading is enhanced by increasing the squeezing velocity, increasing the constriction length and decreasing constriction width. Our results are qualitatively in agreement with experimental observations. [Preview Abstract] |
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K04.00003: Helicoidal microswimmers in a flow: Generalized Jeffery orbits Kenta Ishimoto We theoretically study the dynamics of a helicoidal microswimmer with arbitrary shape in a linear background flow and derive a generalized version of the Jeffery equations for the angular dynamics of the object. A helicoidal object, which is defined by a rotational symmetry, is a larger symmetry class that includes a body of rotation. The helicoidal Jeffery equations include a new constant from the chirality of the object, derived from the inhomogeneous chirality distribution along the axis of the rotational symmetry, whereas the overall chirality of the object contributes to the drift velocity. Further investigations are made for an object in a simple shear flow, and the dynamics with different parameter values are clarified. A bacterial swimmer is considered as an example of a helicoidal object, and we calculate the values of the constants in the generalized Jeffery equations for a typical morphology of Escherichia coli, being consistent with recent experimental and theoretical results. [Ref] K. Ishimoto, J. Fluid Mech. 892 (2020) A11. [Preview Abstract] |
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K04.00004: The Role of Motor Reversal and Hook-Winding Timescales in Run-Reverse-Flick Motility. Mehdi Jabbarzadeh, Henry C. Fu Monotrichous bacteria reverse rotation direction of the motor to go forward (CCW) and reverse (CW). During reverse motility (CW) the hook, which is a short flexible joint between the motor and longer helical flagellar filament, unwinds and its flexibility decreases. Switching from reverse to forward swimming, bacteria reorient by a "flick" during which the unwound hook deforms under compressional loads. Previously, we developed an efficient and accurate numerical approach to simulate flexible filaments and described run-reverse-flick motility while prescribing motor torques and time-dependent hook stiffnesses. However, experimental torque-speed measurements of the flagellar motor suggest that immediately after the reversal, torque and rotation rates should be drastically limited. In addition, the stiffness should vary in time only through the winding state of the hook. Here, we study motor reversal and hook winding timescales during short pre-flick motility (\textasciitilde 10ms) to obtain more realistic winding-dependent hook stiffnesses for wound and unwound hooks, incorporating the torque-speed characteristics of the motor. We explain how fast winding of the hook leads to experimentally observed flick reorientation. [Preview Abstract] |
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K04.00005: The role of fluid transport in cancer metastasis to bone Trung Le, Lahcen Akerkouch, Haneesh Jasuja, Kalpana Katti, Dinesh Katti Prostate Cancer exhibits a susceptibility to metastasize to bone resulting in a significantly high morbidity and mortality rate. While mechanotransduction has been known to play an important role in normal cellular growth, it is unclear how it regulates cancer cells growth, especially inside bones. In this work, we investigate the influence of mechanical signals to prostate cancer cells progression to bone. Prostate cancer cells are seeded in a tissue engineered bone scaffold, which is under a steady flow mimicking blood transport. We perform Computational Fluid Dynamics (CFD) simulations based on micro-Computed Tomography scans of the scaffold, which is exposed to various flow conditions. The CFD simulations are performed with the immersed boundary method (Gilmanov, Le, Sotiropoulos, JCP 300, 1, 2015). Our simulation results show a uniform fluid dispersion outside the scaffold. However, the fluid transport inside the bone scaffold is complex and dependent on the porous topology arrangements. A critical threshold for the pore size is found at which maximum velocity within the scaffold is reached. From experimental observation, we observe the significant changes in the growth of cancer cells depending on shear forces condition. [Preview Abstract] |
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K04.00006: Analyzing Cytoplasmic Flow using Digital Inline Holography Zilong He, Jiarong Hong Macromolecules within cytoplasm undergo diffusive motion in different modes including sub-diffusion, hindered, and enhanced diffusive. In larger cells (D\textgreater 0.1 mm), different topologies of cytoplasmic streaming (rotational streaming, correlated random flow, circulation streaming, etc.) are observed, functioning to promote diffusion transport. These kinds of cytoplasmic flow provide valuable insights on the cell activities and transport phenomena within the cell. However, prior method of studying cytoplasmic flows, including fluorescence recovery after photobleaching and force spectrum microscopy, are indirect and time-consuming and requiring advanced instrumentation. In comparison, digital inline holography (DIH) is a non-invasive imaging technique that can directly probe into the diffusive phenomena in the cytoplasm with very low energy dose required for illumination. Here we employ DIH to probe into the cytoplasmic flows of budding yeast and investigate the change of diffusive motions within the cytoplasm at different stages of a cell division cycle. Our results show DIH can serve as a promising tool to probe different modes of cytoplasmic flows and characterize the change of cell activities. [Preview Abstract] |
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K04.00007: Cell-Surface Protein Dynamics Due to Exocytosis-Driven Membrane Flows Ben Gross, Otger Campas Living cells constantly regulate the protein composition of their surface (plasma membrane) by adding and removing proteins through exo- and endo-cytosis. The spatial localization of exocytosis on the cell surface reduces the local membrane tension and, together with tension-dependent endocytosis, generates plasma membrane flows that advect proteins. These emergent flows depend on the geometry of the cell and compete with protein diffusion to specify the steady-state protein distribution on the cell surface. Inspired by the case of walled cells, such as fungal, bacterial or plant cells, we study the protein dynamics and steady-state distributions generated by advection-diffusion in fixed, compact cell geometries. Given an exocytosis spatial distribution set by the cell, we determine the resulting membrane flows on the curved surface (plasma membrane) and solve for the dynamics of proteins that emerges from diffusion and advection. In addition, we study how cell size, cell geometry and the properties of the emergent flows affect the steady-state protein distribution on the cell surface. [Preview Abstract] |
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K04.00008: Incorporating recirculation effects into metrics of feeding performance for zooplankton Kiarash Samsami, Ludivine Sanchez Arias, Henry C Fu The feeding performance of zooplankton influences their evolution and can explain their behavior. A commonly-used metric for feeding performance is the volume of fluid that can be scanned for food, as measured by the fluid flow through a filtering or capturing surface. However, this measure does not take into account whether the flow contains fresh nutrient particles or already-filtered fluid. Here we show that such a metric may give incorrect results for organisms that produce recirculatory flows, and describe how to construct a metric which correctly accounts for recirculation based on the velocity field of the feeding current. We demonstrate our metric using two example zooplankton, Salpingoeca rosetta and Vorticella. We use the method of regularized Stokeslets to compute the velocity field around these two microorganisms, based upon organism kinematics obtained from the literature and our experimental observations. We determine the part of the flow that contains fresh nutrient particles by examining the pathlines of Lagrangian particles that pass through the defined surfaces that we are interested in, and compare with flow rates computed from the velocity fields. [Preview Abstract] |
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K04.00009: Active particles near surfaces Arman Abtahi, Gwynn Elfring Active particles (swimming microorganisms or synthetic active particles) are very often situated near no-slip surfaces. The presence of the interface modifies the flow field generated by active particles, leads to changes in the dynamics of individual active particles, but also affects the hydrodynamic interactions with nearby particles. We investigate the role of hydrodynamic interactions on the dynamics of swimmers near walls by means of a modified Stokesian Dynamics approach. We also discuss the tendency of flexible swimmers to deform due to hydrodynamic interactions with a no-slip interface thereby altering their near-wall dynamics. [Preview Abstract] |
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K04.00010: Teamwork in the viscous oceanic microscale Eva Kanso, Rubens M. Lopes, J. Rudi Strickler, John O. Dabiri, John H. Costello Nutrient acquisition is crucial for oceanic microbes and competitive solutions to solve this challenge have evolved among a range of unicellular protists.~ However, solitary solutions are not the only approach found in natural populations. A diverse array of oceanic protists form temporary or even long-lasting attachments to other protists and marine aggregates. Do these planktonic consortia provide benefits to their members? Here we use empirical and modeling approaches to evaluate whether the relationship between a large centric diatom,~\textit{Coscinodiscus wailesii,~}and a ciliate epibiont,\textit{~Pseudovorticella coscinodisci,~}provides~nutrient~flux benefits to its members. We find that fluid flows generated by ciliary beating can increase nutrient flux to a diatom cell surface by 500{\%} compared to a still cell without ciliate epibionts. This cosmopolitan species of diatom does not form consortia in all environments but frequently joins such consortia in nutrient depleted waters. Our results demonstrate that symbiotic consortia provide a cooperative alternative to unicellular solutions for nutrient acquisition in challenging environments. [Preview Abstract] |
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K04.00011: Liquid Jet Interaction with an Elastic Cell Wall Maziyar Jalaal, Michael Gomez, Raymond Goldstein Recent results (Jalaal et al. Phys. Rev. Lett. 125, 028102) have elucidated how marine dinoflagellates respond to fluid and mechanical stresses by emitting flashes of bioluminescence. Those stresses deform the cell wall on scales of 1-10 microns, with forces estimated in the nanonewton range. As a first step toward understanding the mechanics of these processes, we study here the elastohydrodynamic problem of a liquid jet interacting with a deformable cell wall; the latter described within thin-shell theory. Abstracting the jet as a point force, we solve for the flow and deformation of the shell, arising from a nearby stokeslet. The results are supplemented with finite-element calculations that begin to probe beyond the Stokes regime. [Preview Abstract] |
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K04.00012: The art of coarse Stokes: algorithmic developments for zero Reynolds number biological flow David Smith, Meurig Gallagher, Rudi Schuech The method of regularized stokeslets has provided an accessible approach for solving biological Stokes flow problems, in particular cell motility and cilia-driven flow for over a decade. In this talk we describe and benchmark some recent algorithmic developments in this method relating to `coarse force' discretization, Richardson extrapolation, higher order accurate `blobs', inclusion of the double layer potential, and GPU acceleration. Alone and in combination, these approaches are capable of significantly extending the scientific scope of the method. [Preview Abstract] |
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K04.00013: Active sinking particles: Sessile filter-feeders can fundamentally alter the fate of sinking aggregates. Deepak Krishnamurthy, Manu Prakash, Rachel Pepper Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in waste-water treatment plants using ``activated sludge'' processes. In both these contexts, the sinking aggregates are ``active'', since they are hot-spots of biological activity and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these aggregates has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. 2020) to follow model sinking aggregates (agar spheres) with attached \textit{Vorticella }over long distances while simultaneously measuring local flows. We find that attached \textit{Vorticella} cause substantial changes to sinking trajectories, rotation rates, and also re-shape boundary layers near the aggregate. We postulate that these hydrodynamic effects are likely to lead to very different mass transfer rates than for particles without attached organisms, and are also likely to change the sinking dynamics of these aggregates, both in marine and fresh-water contexts. [Preview Abstract] |
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K04.00014: A computational platform for biomechanics problems in the cell Gokberk Kabacaoglu, Michael Shelley Polymer filament and motor-protein assemblies are major structural components of biological cells. Filaments' nonlinear deformation and hydrodynamic interactions with the other immersed structures lead to complicated flows that have important mechanical and transport properties. I will review our computational platform for the large-scale three-dimensional simulations of flexible filaments, motor proteins and rigid bodies in a Stokesian fluid. We use non-local slender body theory for the fluid-structure interactions of the filaments and a second-kind boundary integral formulation for rigid bodies and the confining boundary. We also incorporate the key biophysical elements such as the filaments' (de)polymerization kinetics and motor proteins. I will discuss recent applications of this platform: the orientation and positioning of the mitotic spindle (the organelle that orchestrates the division of chromosomes); swirling flows induced by the interaction of motor proteins and thousands of microtubules attached to a cortex, as observed in early development of the Drosophila oocyte; and the dynamics of microtubule arrays in large cells driven by streaming flows created by moving motor-proteins, as has been proposed as the basis for centering of spindles in large embryos. [Preview Abstract] |
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K04.00015: Geometric effects induce anomalous size-dependent bacterial transport in structured environments Pooja Chopra, David A. Quint, Ajay Gopinathan, Bin Liu Variations of transport efficiency in structured environments between distinct individuals in a bacterial community is both hard to study and poorly understood. Here, we demonstrate the sensitive size-dependence of bacterial swimming in a micropillar array by using a tracking microscope to follow individual cells over extended durations. Using a non-tumbling E. coli strain, we show that long-term transport switches from a trapping dominated state for shorter cells to a much more dispersive state for longer cells above a critical bacterial size set by the pillar array geometry. Using a combination of experiments and modeling, we show that this anomalous size-dependence arises from an enhancement of the escape rate from trapping for longer cells caused by nearby pillars. Our results show that geometric effects can lead to bacterial size being a sensitive tuning knob for bacterial transport in structured environments. Our results therefore have implications for the morphological adaptation of bacteria to structured habitats and can provide insights into the design of metamaterials for controlling the transport of bacteria at the single-cell level. [Preview Abstract] |
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K04.00016: Modeling of Chemotaxis in Porous Media. Uttam Kumar, Subramaniam Pushpavanam Peritrichous bacterial motility is characterized by a sequence of run and tumble events. In the presence of chemical gradients, tumble frequency gets reduced, and the bacteria population experiences a drift towards higher concentration of chemoattractants (favourable chemicals). The understanding of the movement of bacteria in porous media like agar gel is important to develop a point of care devices. Here, how the microbe’s motility gets affected due to collision with solid walls is not clearly understood. How the microbe’s motility gets altered due to pore size distribution is unknown. In this work, we model the movement of bacteria in a porous medium based on the continuous-time random walk (CTRW) approach. This result in the system being described by a fractional differential equation. Here we present a mathematical model that incorporates changes of bacterial motility as exhibiting anomalous diffusive behaviour in porous media. We use a finite difference numerical method for solving the governing fractional differential equations. These model equations are relevant in the context of biological systems with crowding. We also design a diffusion-based microfluidic device for generating a steady and stable concentration gradient for studying chemotaxis in agar gel, which contains a fluid-filled porous medium. Results obtained from numerical simulation are compared with experimental data. textbf{Keywords:} Chemotaxis, Fractional calculus, Anomalous diffusion, Random walk. \newpage \textbf{\textit{References}} \begin{enumerate} \item Bhattacharjee, T. {\&} Datta, S. S. Bacterial hopping and trapping in porous media. \textit{Nat. Commun.} \textbf{10}, 2075 (2019). \end{enumerate} [Preview Abstract] |
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K04.00017: On the relation between red blood cell flexibility and the oxygenation-deoxygenation process Mehdi Niazi Ardekani, Amir Saadat, Jiandi Wan, Juan Santiago, Eric Shaqfeh A host of diseases directly influence the mechanical and chemical properties of the blood’s main cellular component, red blood cells (RBCs). Among these, Chronic Fatigue Syndrome, Sepsis, and COVID19 are examples. The symptoms including fatigue, orthostatic intolerance and cognitive disturbances suggest poor tissue oxygenation even with normal hemoglobin concentration. On the other hand, it has been shown very recently that local oxygen pressure can change and control RBC deformability and, in turn, capillary cell velocity. We recently developed a microfluidic device and analysis platform to accurately measure, for the first time, the intrinsic flexibility of many RBCs. We will present extensions of this platform toward the problem of studying the effects of oxygen concentration levels on RBC deformability. This will include a new numerical model for oxygen transport developed and added to our existing RBC simulation methods. This method is based on an immersed finite element method (for the cell mechanics) and a finite-volume incompressible flow solver, that allows for simulation of RBC flows where the membrane shear modulus varies with the oxygen concentration inside the cell. Our goal is to demonstrate the relation between poor tissue oxygenation and RBC cell elasticity. [Preview Abstract] |
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K04.00018: Red Blood Cell Deformation Index and Simulation Performance in Lattice-Boltzmann Method and Dissipative Particle Dynamics Kacper Ostalowski, Michael Hood, Jifu Tan Cardiovascular disease is the leading cause of death in the United States. Taking up roughly 40{\%} of blood volume, red blood cells (RBC) are the main cell component of blood. Thus, an accurate and efficient RBC model is needed to study complex biological flows. In this study, we present two different approaches to model blood flow with cells: a dissipative particle dynamics (DPD) model and a hybrid particle-continuum model. In DPD, all the particles interact through DPD interactions. The effects of high-viscosity cytoplasm inside the RBC is also studied by separating the internal and external fluids on each side of the membrane. In the particle-continuum model the fluid is solved by the lattice Boltzmann Method (LBM). The immersed boundary method is used to handle fluid-solid interactions. Viscosity of the RBC cytoplasm is maintained by tracking the RBC membrane and adjusting the viscosity of the LBM fluid inside the RBC. The deformation index is measured and compared between the two methods and experimental results. The effects of thermal fluctuations on the system is studied using DPD. The performance of DPD simulations is compared against the performance of LBM simulations, with advantages of either method also being explored. [Preview Abstract] |
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