Bulletin of the American Physical Society
69th Annual Meeting of the APS Division of Fluid Dynamics
Volume 61, Number 20
Sunday–Tuesday, November 20–22, 2016; Portland, Oregon
Session M20: Bio: General Topics II |
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Chair: Aloke Kumar, University of Alberta Room: D137-138 |
Tuesday, November 22, 2016 8:00AM - 8:13AM |
M20.00001: Failure of bacterial streamers in creeping flows Ishita Biswas, Ranajay Ghosh, Mohtada Sadrzadeh, Aloke Kumar In the recent years, the dynamical response of filamentous bacterial aggregates called bacterial streamer in creeping flows has attracted attention. We report the observation of `necking-type' instability leading to failure in bacterial (\textit{Pseudomonas fluorescens}) streamers formed in creeping flows. Quantification of the failure process was made possible through the use of 200 nm red fluorescent polystyrene tracer particles embedded in the bacterial extracellular polymeric substances (EPS). The nonlinear failure behavior shows distinct phases of deformation with mutually different characteristic times, which end with a distinct localized failure of the streamer. We also develop a simplified analytical model to describe the experimental observations of the failure phenomena. The theoretical power law relationship between critical stretch ratio and the fluid velocity scale matches closely experimental observations. [Preview Abstract] |
Tuesday, November 22, 2016 8:13AM - 8:26AM |
M20.00002: Coupled gel spreading and diffusive transport models describing microbicidal drug delivery Claire Funke, Kelsey MacMillan, Anthony S. Ham, Andrew J. Szeri, David F. Katz Gels are a drug delivery platform being evaluated for application of active pharmaceutical ingredients, termed microbicides, that act topically against infection by sexually transmitted HIV. Despite success in one Phase IIb trial of a vaginal gel delivering tenofovir, problems of user adherence to designed gel application regimen compromised results in two other trials. The microbicide field is responding to this issue by simultaneously analyzing behavioral determinants of adherence and pharmacological determinants of drug delivery. Central to both user adherence and mucosal drug delivery are gel properties (e.g. rheology) and applied volume. The specific problem to be solved here is to develop a model for how gel rheology and volume, interacting with loaded drug concentration, govern the transport of the microbicide drug tenofovir into the vaginal mucosa to its stromal layer. The analysis here builds upon our current understanding of vaginal gel deployment and drug delivery, incorporating key features of the gel's environment, fluid production and subsequent gel dilution, and vaginal wall elasticity. We consider the microbicide drug tenofovir as it is the most completely studied drug, in both \textit{in vitro }and \textit{in vivo }studies, for use in vaginal gel application. Our goal is to contribute to improved pharmacological understanding of gel functionality, providing a computational tool that can be used in future vaginal microbicide gel design. [Preview Abstract] |
Tuesday, November 22, 2016 8:26AM - 8:39AM |
M20.00003: Biofluid dynamics of two phase stratified flow through flexible membranes. Dinesh Bhagavatula Nvssr, Pushpavanam S Two phase stratified flows between flexible membranes arise in biological flows like lung airway reopening, blood flow in arteries and movement of spinal cord. It is important to understand the physics behind the interaction of flexible membranes and the fluid flow. In this work, a theoretical model is developed and different types of instabilities that arise due to the fluid flow are understood. The solid membrane is modeled as an incompressible linear viscoelastic solid. To simplify the analysis, inertia in the solid is neglected. Linear stability analysis is carried around the base state velocity of the fluid and displacement field of the solid. The flow is perturbed by a small disturbance and a normal mode analysis is carried out to study the growth rate of the disturbance. An eigenvalue problem in formulated using Chebyshev spectral method and is solved to obtain the growth rate of the disturbance. The effect of different parameters such as thickness of the flexible membrane, Reynolds number, viscosity ratio, density ratio, Capillary number and Weissenberg number on the stability characteristics of the flow is studied in detail. Dispersion curves are obtained which explain the stability of the flow. A detail energy analysis is carried out to determine different ways through which energy transfers from the base flow to the disturbed flow. [Preview Abstract] |
Tuesday, November 22, 2016 8:39AM - 8:52AM |
M20.00004: Transition of torque pattern in undulatory locomotion due to wave number variation in resistive force dominated media Yang Ding, Tingyu Ming In undulatory locomotion, torque (bending moment) is required along the body to overcome the external forces from environments and bend the body. Previous observations on animals using less than two wavelengths on the body showed such torque has a single traveling wave pattern. Using resistive force theory model and considering the torque generated by external force in a resistive force dominated media, we found that as the wave number (number of wavelengths on the locomotor's body) increases from 0.5 to 1.8, the speed of the traveling wave of torque decreases. When the wave number increases to 2 and greater, the torque pattern transits from a single traveling wave to a two traveling waves and then a complex pattern that consists two wave-like patterns. By analyzing the force distribution and its contribution to the torque, we explain the speed decrease of the torque wave and the pattern transition. [Preview Abstract] |
Tuesday, November 22, 2016 8:52AM - 9:05AM |
M20.00005: Mechanics of kinetochore microtubules and their interactions with chromosomes during cell division Ehssan Nazockdast, Sebastian Fürthauer, Stephanie Redemann, Johannes Baumgart, Norbert Lindow, Andrea Kratz, Steffen Prohaska, Thomas Müller-Reichert, Michael Shelley The accurate segregation of chromosomes, and subsequent cell division, in Eukaryotic cells is achieved by the interactions of an assembly of microtubules (MTs) and motor-proteins, known as the mitotic spindle. We use a combination of our computational platform for simulating cytoskeletal assemblies and our structural data from high-resolution electron tomography of the mitotic spindle, to study the kinetics and mechanics of MTs in the spindle, and their interactions with chromosomes during chromosome segregation in the first cell division in C.elegans embryo. We focus on kinetochore MTs, or KMTs, which have one end attached to a chromosome. KMTs are thought to be a key mechanical component in chromosome segregation. Using exploratory simulations of MT growth, bending, hydrodynamic interactions, and attachment to chromosomes, we propose a mechanical model for KMT-chromosome interactions that reproduces observed KMT length and shape distributions from electron tomography. We find that including detailed hydrodynamic interactions between KMTs is essential for agreement with the experimental observations. [Preview Abstract] |
Tuesday, November 22, 2016 9:05AM - 9:18AM |
M20.00006: Coarse-grained Simulations of Conformational Changes in Multidrug Resistance Transporters S M Yead Jewel, Prashanta Dutta, Jin Liu The overexpression of multidrug resistance (MDR) systems on the gram negative bacteria causes serious problems for treatment of bacterial infectious diseases. The system effectively pumps the antibiotic drugs out of the bacterial cells. During the pumping process one of the MDR components, AcrB undergoes a series of large-scale conformational changes which are responsible for drug recognition, binding and expelling. All-atom simulations are unable to capture those conformational changes because of computational cost. Here, we implement a hybrid coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid, to investigate the proton-dependent conformational changes of AcrB. The simulation results in early stage (\textasciitilde 100 ns) of proton-dependent conformational changes agree with all-atom simulations, validating the coarse-grained model. The coarse-grained force field allows us to explore the process in microsecond simulations. Starting from the crystal structures of Access(A)/Binding(B)/Extrusion(E) monomers in AcrB, we find that deprotonation of Asp407 and Asp408 in monomer E causes a series of large-scale conformational changes from ABE to AAA in absence of drug molecules, which is consistent with experimental findings. [Preview Abstract] |
Tuesday, November 22, 2016 9:18AM - 9:31AM |
M20.00007: Investigation of polymeric scaffold degradation for drug delivery and neovascularization applications Kartik V. Bulusu, Mitra Alibouzar, Nathan J. Castro, Lijie G. Zhang, Kausik Sarkar, Michael W. Plesniak Degradable polymer-based prosthetics for the treatment of osseous tissue defects, maxillo-/cranio-facial trauma and brain injury face two common clinical obstacles impeding efficient tissue engraftment i.e., controlled material release and neovascularization. Ascertaining the time scales of polymer degradation for controlled delivery of drugs and nutrients is critical to treatment efficacy and strategy. We incorporated multiple experimental methodologies to understand the driving forces of transport mechanisms in polyvinyl alcohol-based (PVA) 3D-printed scaffolds of different porosity. Scaffold degradation was monitored various pulsatile flow conditions using MEMS-based pressure catheters and an ultrasonic flow rate sensor. Ultrasonic properties (bulk attenuation and sound velocity) were measured to monitor the degradation process in a static, alkaline medium. Viscosity and the absorption spectra variations with PVA-solute concentrations were measured using a rheometer and a spectrophotometer, respectively. A simple mathematical model based on Fick’s law of diffusion provides the fundamental description of solute transport from the scaffold matrices. However, macroscopic material release could become anomalous or non-Fickian in complex polymeric scaffold matrices. [Preview Abstract] |
Tuesday, November 22, 2016 9:31AM - 9:44AM |
M20.00008: Simulations of heart valves by thin shells with non-linear material properties. Iman Borazjani, Hafez Asgharzadeh, Mohammadali Hedayat The primary function of a heart valve is to allow~blood~to flow in only one direction through the~heart. Triangular thin-shell finite element formulation is implemented, which considers only translational degrees of freedom, in three-dimensional domain to simulate heart valves undergoing large deformations. The formulation is based on the nonlinear Kirchhoff thin-shell theory. The developed method is intensively validated against numerical and analytical benchmarks. This method is added to previously developed membrane method to obtain more realistic results since ignoring bending forces can results in unrealistic wrinkling of heart valves. A nonlinear Fung-type constitutive relation, based on experimentally measured biaxial loading tests, is used to model the material properties for response of the in-plane motion in heart valves. Furthermore, the experimentally measured liner constitutive relation is used to model the material properties to capture the flexural motion of heart valves. The Fluid structure interaction solver adopts a strongly coupled partitioned approach that is stabilized with under-relaxation and the Aitken acceleration technique. [Preview Abstract] |
Tuesday, November 22, 2016 9:44AM - 9:57AM |
M20.00009: Modes of thrust generation in flying animals Haoxiang Luo, Jialei Song, Bret Tobalske For flying animals in forward flight, thrust is usually much smaller as compared with weight support and has not been given the same amount of attention. Several modes of thrust generation are discussed in this presentation. For insects performing slow flight that is characterized by low advance ratios (i.e., the ratio between flight speed and wing speed), thrust is usually generated by a ``backward flick'' mode, in which the wings moves upward and backward at a faster speed than the flight speed. Paddling mode is another mode used by some insects like fruit flies who row their wings backward during upstroke like paddles (Ristroph et al, PRL, 2011). Birds wings have high advance ratios and produce thrust during downstroke by directing aerodynamic lift forward. At intermediate advance ratios around one (e.g., hummingbirds and bats), the animal wings generate thrust during both downstroke and upstroke, and thrust generation during upstroke may come at cost of negative weight support. These conclusions are supported by previous experiment studies of insects, birds, and bats, as well as our recent computational modeling of hummingbirds. [Preview Abstract] |
Tuesday, November 22, 2016 9:57AM - 10:10AM |
M20.00010: Non-invasive quantification of hemodynamics in human choriocapillaries. Huidan (Whitney) Yu, Rou Chen, Senyou An, James McDonough, Bradley Gelfand, Jun Yao The development of retinal disease is inextricably linked to defects in the choroidal blood supply. However, to date a description of the hemodynamics in the human choroidal circulation is lacking. Through high resolution choroidal vascular network mapped from immunofluorescent labeling and confocal microscopy of human cadaver donor eyes. We noninvasively quantify hemodynamics including velocity, pressure, and wall-shear stress (WSS) in choriocapillaries through mesoscale modeling and GPU-accelerated fast computation. This is the first-ever map of hemodynamic parameters (WSS, pressure, and velocity) in anatomically accurate human choroidal vasculature in health and disease. The pore scale simulation results are used to evaluate porous media models with the same porosity and boundary conditions. [Preview Abstract] |
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