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 P32: Biological Fluid Dynamics: General III |
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Chair: John Brady, Caltech Room: 614 |
Monday, November 25, 2019 5:16PM - 5:29PM |
P32.00001: Hydrodynamics of interphase chromatin Achal Mahajan, Wen Yan, Alexandra Zidovska, Michael J. Shelley, David Saintillan Recent spectroscopy experiments on interphase chromatin have uncovered the existence of long-ranged coherent sub-diffusive motions on the scale of microns and persisting for seconds. These motions were found to be ATP-dependent suggesting the involvement of molecular motors. Motivated by these observations, we use Brownian dynamics simulations to elucidate the effects of microscale activity on the behavior and spatiotemporal dynamics of long flexible polymer chains in viscous solvents. We develop a coarse-grained model where active events are modeled as stochastic force dipoles, which drive long-ranged fluid flows inside an ellipsoidal nucleus. Numerical simulations based on a boundary integral formulation along with a kernel-independent fast multipole method demonstrate the key role played by hydrodynamic interactions and topological constraints in driving large-scale motions and chromatin reconfigurations. [Preview Abstract] |
Monday, November 25, 2019 5:29PM - 5:42PM |
P32.00002: Application of a High-Speed Plenoptic Camera for 3D Measurements in Small-Scale Biological Flows Zu Puayen Tan, Richard Alarcon, Johannes Allen, Brian S. Thurow, Anthony Moss The application of conventional multi-camera tomographic-PIV and related 3D techniques to study biological flows remains limited due to their expense, complexity and bulk. This is particularly true for small experiments (e.g., heart-valve and micro-swimmer) or portable setups (e.g., carried by divers in open-water measurements) where equipment footprint is a critical constraint. In this presentation, we propose single-camera plenoptic-PIV as an attractive alternative to the standard multi-camera techniques. Specifically, a modular kHz-rate plenoptic camera newly developed at Auburn University will be introduced. The system, composed of a single main-lens, a microlens adaptor and an off-the-shelf high-speed camera, was used to characterize unsteady 3D flows around a 2cm ctenophore Mnemiopsis in a 71x40x34mm volume. Various 3D flow features such as the creature's downwash and intermittent vortex-ejections were successfully captured. These will be presented to showcase the plenoptic system's capabilities for measuring small-scale biological flows. [Preview Abstract] |
Monday, November 25, 2019 5:42PM - 5:55PM |
P32.00003: Visualizing flow inside a bone porous medium using an MRI machine. Suyue Han, Todd Currier, Mahdiar Edraki, Boyuan Liu, Maureen Lynch, Yahya Modarres-Sadeghi We have used Phase-Contrast Magnetic Resonance Imaging (PC-MRI) flow measurement to quantify flow inside a 3D-printed artificial scaffold model to understand the flow behavior inside the 3D model of bone metastasis due to an applied perfusion. In order to perform the test using an MRI machine, a nonmagnetic water tunnel was designed and built. A 3D surface model created from a micro-CT scan of an artificial scaffold model was used to make the 3D-printed scaffold model. The 3D-printed scaffold was placed in the test section of the water tunnel inside the MRI machine. The flow velocity was varied over a range and images were captured using the MRI machine. The phase and magnitude data from the MRI experiment were then processed using an in-house code to quantify the flow inside the scaffold. [Preview Abstract] |
Monday, November 25, 2019 5:55PM - 6:08PM |
P32.00004: A mathematical framework for developing freezing protocols in cryopreservation Mohit Dalwadi, Sarah Waters, Helen Byrne, Ian Hewitt Cryopreservation is the process of preserving biological constructs by cooling to temperatures low enough to halt biochemical processes, such as metabolism. This allows biomaterials to be kept in `suspended animation', with important applications in tissue engineering, fertility, and food security. However, many freezing protocols have low recovery rates. In general, cooling too quickly results in the formation of lethal intracellular ice, while cooling too slowly amplifies the toxic effects of the cryoprotective agents (CPA) added to limit ice formation. \\ In this talk, we present a mathematical model for cryopreservation to understand and quantify these observations. We consider a system consisting of three different regions: ice, extracellular liquid, and intracellular liquid. The two interfacial boundaries separating the three phases can move and must be determined as part of the solution. The presence of CPA lowers the freezing point of the system, and the cell membrane moves due to the osmotic pressure difference across the membrane. We introduce two metrics to characterize the cell damage caused by freezing, accounting for supercooling and CPA toxicity. Given cell properties, we show how these damage metrics can be used to predict an optimal cooling rate. [Preview Abstract] |
Monday, November 25, 2019 6:08PM - 6:21PM |
P32.00005: Characterization of mucus macro-rheology from the silver carp, \textit{Hypophthalmichthys molitrix} Kartik V Bulusu, Samantha Racan, L Patricia Hernandez, Michael W Plesniak The silver carp, \textit{Hypophthalmichthys molitrix} is a planktivorous filter feeder fish introduced to control algal blooms in natural waterways of the US. Since the early 1970s this invasive species has infested the Mississippi River basin. Its extraordinary feeding-efficiency is attributed to two unique organs viz., (i) the gill rakers (GR) and (ii) the palatal folds that enable capturing of food particles through the porous GR membranes. The GR mucus has the potential to enhance the filter feeding process by functioning as an adhesive and a transport vehicle for food particles. It is a gel-like, complex biological fluid that responds to external force and comprises a macromolecular network of glycoproteins (or mucins). Viscoelasticity and steady-state viscosity of the GR mucus of silver carps obtained from Hart Creek, Missouri River were investigated using a rheometer (DHR-2, TA Instruments) with cone geometry (1-deg., 40 mm dia.) and a Peltier plate. A digital camera attachment (546800.902, TA Instruments) was used to monitor microstructure changes. These experiments are aimed at understanding the role of mucus-laden fluid flow through porous GR channels and ultimately, the tremendous success of the silver carp in outcompeting native fish species. [Preview Abstract] |
Monday, November 25, 2019 6:21PM - 6:34PM |
P32.00006: Self-organization of microtubules in cell-sized droplets Ya Gai, Sagar Setru, Bernardo Gouveia, Howard Stone, Sabine Petry We combine droplet microfluidics and cell-free biological systems to examine the effect of confinement and nucleation on the assembly of microtubule (MT) networks. Central to the spindle assembly is the spatial organization of MTs, a long tubular structure formed through the polymerization of tubulin dimmers. Such organization is regulated by RanGTP, a GTPase associated with chromosomal activities and acting as part of a major nucleation pathway for MTs. RanGTP has been explored using Xenopus egg extracts, a model cell-free system for probing spindle assembly. Most extract-based assays were performed in a test tube where cell-sized confinement was missing. Therefore, we asked whether confinement can affect the MT networks. We used droplet microfluidics for encapsulating extract-based assays by generating monodisperse, extract-in-oil droplets. By varying droplet diameters and encapsulated Ran concentrations, we demonstrate that these two physical factors regulate the assembly of MT networks. Together, the two factors yield MT networks with various steady-state architectures. Our results highlight the prominent role of MT nucleation in the self-organization of MTs in cell confinement and might have direct implications in nucleation-controlled soft material processing. [Preview Abstract] |
Monday, November 25, 2019 6:34PM - 6:47PM |
P32.00007: Stokes' law in complex liquids and inside cell cytoplasm Karol Makuch, Robert Holyst, Tomasz Kalwarczyk, Piotr Garstecki, John F. Brady The `viscosity' experienced by a small tracer particle in complex liquids depends both on its size and on the structure of the liquid, which itself may contain different length scales. Thus, in a microrheological experiment the complex liquid may best be described by wave-vector-dependent viscosity $\eta $(k). Here we derive Stokes' law in complex liquids and formulate a method to determine the wave-vector-dependent viscosity from microrheological experimental data. We initiate our approach by determining the wave-vector-dependent viscosities $\eta $(k) of HeLa and Escherichia Coli cell cytoplasm from the experimental data on diffusion of macromolecules in these systems. Determination of this quantity opens an avenue for computer simulations of motion and biochemical reactions inside living cells. [Preview Abstract] |
Monday, November 25, 2019 6:47PM - 7:00PM |
P32.00008: Freshwater Copepod Behavior in Turbulent Eddies M. Ruszczyk, D.R. Webster, J. Yen Previous studies have shown that marine copepod behavior is modulated by turbulence. We seek to expand on this observation by investigating a freshwater species, \textit{Hesperodiaptomus shoshone}, and how it responds to small-scale turbulent vortices. The calanoid copepod \textit{H. shoshone }is a dominant predator in high-altitude alpine lakes, ranging from 2-4 mm in length. The Burgers vortex model was used to simulate dissipative eddies with four levels of turbulent dissipation rates ranging from 0.002-0.25 cm$^{\mathrm{2}}$/s$^{\mathrm{3}}$, mimicking turbulent conditions found in natural habitats. Tomographic PIV was used to quantify the vortex circulation and axial strain rate of the vortices. \textit{H. shoshone }males and females were separately exposed to the four Burgers vortex treatments in a horizontal axis orientation plus a stagnant fluid control treatment. In comparison to the morphologically-similar marine copepod \textit{Calanus finmarchicus, H. shoshone }appears minimally responsive to the Burgers vortex. \textit{H. shoshone }swimming speeds remained similar under different turbulence conditions, showed no circular trajectories, and made minimal attempts to escape the vortex. These results were consistent between males and females and suggest \textit{H. shoshone }are not responsive to hydrodynamic cues of the vortex structure. The contrasting behavior will be discussed in the context of the ecology and environmental conditions of the different habitats. [Preview Abstract] |
Monday, November 25, 2019 7:00PM - 7:13PM |
P32.00009: Computational Investigations on Flow-mediated Transport Processes at the Blood-thrombus Interface Debanjan Mukherjee Pathological clotting of blood, referred to as thrombosis, is the primary cause of diseases like stroke and heart-attack which are associated with significant morbidity and mortality. Thrombus (blood clot) formation, and its behavior, is governed by multiple underlying physiological processes which are intimately related to flow and transport. Of specific importance is the role of transport processes near the blood-thrombus interface, and permeation of biochemical species (drug or coagulation factors) into the thrombus. Here we present the latest developments in our investigations into creating a computational multi-physics modeling framework for thrombus biomechanics and bio-transport. Our framework is based on a combination of Galerkin stabilized finite element method, and Lagrangian particle based approach. We have employed our framework to conduct a range of computational experiments to illustrate flow mediated near thrombus transport using thrombus models reconstructed from microscopy image data. We will present results from our computational investigations into: (a) the role of blood-thrombus interface properties on transport; (b) biochemical species permeation across the thrombus interface; and (c) subsequent influence on intra-thrombus transport. [Preview Abstract] |
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