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 H20: Bio:Biofilms and General Bioflows |
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Chair: Jeff Eldredge, University of California, Los Angeles Room: D137-138 |
Monday, November 21, 2016 10:40AM - 10:53AM |
H20.00001: Fluid dynamic effects on staphylococci bacteria biofilms Erica Sherman, Kenneth Bayles, Jennifer Endres, Timothy Wei \textit{Staphylococcus aureus} bacteria are able to form biofilms and distinctive tower structures that facilitate their ability to tolerate treatment and to spread within the human body. The formation of towers, which break off, get carried downstream and serve to initiate biofilms in other parts of the body are of particular interest here. It is known that flow conditions play a role in the development, dispersion and propagation of biofilms in general. The influence of flow on tower formation, however, is not at all understood. This work is focused on the effect of applied shear on tower development. The hypothesis being examined is that tower structures form within a specific range of shear stresses and that there is an as yet ill defined fluid dynamic phenomenon that occurs hours before a tower forms. In this study, a range of shear stresses is examined that brackets 0.6 dynes/cm$^{\mathrm{2}}$, the nominal shear stress where towers seem most likely to form. This talk will include \textmu PTV measurements and cell density data indicating variations in flow and biofilm evolution as a function of the applied shear. Causal relations between flow and biofilm development will be discussed. [Preview Abstract] |
Monday, November 21, 2016 10:53AM - 11:06AM |
H20.00002: Effects of biofilm on flow over and through a permeable bed Farzan Kazemifar, Gianluca Blois, Marcelo Aybar, Patricia Perez-Calleja, Robert Nerenberg, Sumit Sinha, Richard Hardy, James Best, Gregory Sambrook-Smith, Kenneth Christensen Biofilms constitute an important form of bacterial life in aquatic environments and are present at the interface of fluids and solids, such as riverbeds. Biofilms are permeable, heterogeneous, and deformable structures that can influence the flow and mass/momentum transport, yet their interaction with flow is not fully understood in part due to technical obstacles impeding quantitative experimental investigations. The porosity of river beds results in the generation of a diverse mosaic of `suction' and `ejection' events that are far removed from typical assumptions of turbulent flow structure over an impermeable bed. In this work, the effect of biofilm on bed permeability is studied. Experiments are conducted in a closed water channel equipped with 4-cm-deep permeable bed models consisting of horizontal cylinders normal to the bulk flow direction, forming an idealized two-dimensional permeable bed. Prior to conducting flow experiments, the models are placed within an independent biofilm reactor to initiate and control the biofilm growth. Once a targeted biofilm growth stage is achieved, the models are transferred to the water channel and subjected to transitional and turbulent flows. Long-distance microscopic particle image velocimetry measurements are performed to quantify the effect of biofilm on the turbulence structure of the free flow as well as the freestream-subsurface flow interaction. [Preview Abstract] |
Monday, November 21, 2016 11:06AM - 11:19AM |
H20.00003: High resolution PIV of flow over biofilm covered walls Joel Hartenberger, Marc Perlin, Steven Ceccio Microbial, `slime' biofilms detrimentally affect the performance of engineered systems used every day from heat exchangers to large ocean-going vessels. The presence of a slime layer on a pipe wall or external boundary often leads to a significant increase in drag and may alter the nature of the turbulence in the adjacent flow. Despite these consequences, relatively few efforts have been undertaken to understand the underlying physical processes which couple biofilm characteristics with increased drag and other alterations to the flow. Experiments performed in a 1:14 scale replica of the US Navy's Large Cavitation Channel (LCC) at the University of Michigan investigate the effect of biofilm composition, coverage and thickness on the development of an external turbulent boundary layer (TBL) through the use of conventional and micro PIV. A range of fields of view (FOVs) were used to capture both the inner and outer regions of the boundary layer. The fine resolution of micro PIV gives an in-depth look at the near-wall region of the flow and may provide evidence linking specific biofilm features with flow characteristics while the less resolved, larger FOVs capture flow behavior to the freestream. Measurement techniques used to characterize the biofilm will be presented along with a description of the mean flow and turbulent fluctuations in the TBL. [Preview Abstract] |
Monday, November 21, 2016 11:19AM - 11:32AM |
H20.00004: The effects of an algal biofilm on the turbulent boundary layer at high Reynolds number Elizabeth Murphy, Julio Barros, Michael Schultz, Karen Flack, Cecily Steppe, Matthew Reidenbach Algal biofilms are an important fouling community on ship hulls, with severe economic consequences due to increased drag. As with other types of roughness on aquatic surfaces, biofilms increase skin friction and thus induce severe drag penalties. In fact, slime layers appear to induce greater drag than would be predicted by the roughness height alone. Our work indicates that this is likely due to two characteristics of algal biofilms: i) flexible streamers that protrude into the flow, and ii) the compliant nature of a biofilm layer. High resolution PIV was used to measure the turbulent boundary layer flow over diatomaceous biofilm grown under dynamic conditions. Local mean streamwise velocity profiles were used to estimate the local wall shear stresses and to determine the similarity between the inner and outer layers of the boundary layer and those of a smooth wall. Spatially explicit turbulent kinetic energy (TKE), Reynolds shear stress (RSS), swirling strength and quadrant analyses over the biofilm were compared to those over a smooth wall and a rigid mesh roughness. We found that the combination of canopy flow due to streamers coupled with compliant wall-flow interactions result in large wall shear stresses and higher turbulence. [Preview Abstract] |
Monday, November 21, 2016 11:32AM - 11:45AM |
H20.00005: The impact of shearing flows on electroactive biofilm formation, structure, and current generation A-Andrew Jones, Cullen Buie A special class of bacteria exist that directly produce electricity. First explored in 1911, these electroactive bacteria catalyze hydrocarbons and transport electrons directly to a metallic electron acceptor forming thicker biofilms than other species. Electroactive bacteria biofilms are thicker because they are not limited by transport of oxygen or other terminal electron acceptors. Electroactive bacteria can produce power in fuel cells. Power production is limited in fuel cells by the bacteria's inability to eliminate protons near the insoluble electron acceptor not utilized in the wild. To date, they have not been successfully evolved or engineered to overcome this limit. This limitation may be overcome by enhancing convective mass transport while maintaining substantial biomass within the biofilm. Increasing convective mass transport increases shear stress. A biofilm may respond to increased shear by changing biomass, matrix, or current production. In this study, a rotating disk electrode is used to separate nutrient from physical stress. This phenomenon is investigated using the model electroactive bacterium \textit{Geobacter sulfurreducens} at nutrient loads comparable to flow-through microbial fuel cells. We determine biofilm structure experimentally by measuring the porosity and calculating the tortuosity from confocal microscope images. Biofilm adaptation for electron transport is quantified using electrical impedance spectroscopy. Our ultimate objective is a framework relating biofilm thickness, porosity, shear stress and current generation for the optimization of bioelectrochemical systems [Preview Abstract] |
Monday, November 21, 2016 11:45AM - 11:58AM |
H20.00006: LES of Laminar-to-Turbulent Particle-Fluid Dynamics in Human and Nonhuman Primate Airways: Applications to Aerosolized Drug Delivery Animal Testing Taylor Geisler, Sourav Padhy, Eric Shaqfeh, Gianluca Iaccarino Both the human health benefit and risk from the inhalation of aerosolized medications is often predicted by extrapolating experimental data taken using nonhuman primates to human inhalation. In this study, we employ Large Eddy Simulation to simulate particle-fluid dynamics in realistic upper airway models of both humans and rhesus monkeys. We report laminar-to-turbulent flow transitions triggered by constrictions in the upper trachea and the persistence of unsteadiness into the low Reynolds number bifurcating lower airway. Micro-particle deposition fraction and locations are shown to depend significantly on particle size. In particular, particle filtration in the nasal airways is shown to approach unity for large aerosols (~8 microns) or high-rate breathing. We validate the accuracy of LES mean flow predictions using MRV imaging results. Additionally, particle deposition fractions are validated against experiments in 3 model airways. [Preview Abstract] |
Monday, November 21, 2016 11:58AM - 12:11PM |
H20.00007: Using Computational Fluid Dynamics to examine airflow characteristics in Empty Nose Syndrome Tim Flint, Mahdi Esmaily-Moghadam, Andrew Thamboo, Nathalia Velasquez, Jayakar V. Nayak, Mathieu Sellier, Parviz Moin The enigmatic disorder, empty nose syndrome (ENS), presents with a complex subjective symptom profile despite objectively patent nasal airways, and recent reports suggest that surgical augmentation of the nasal airway can improve quality of life and ENS-related complaints. In this study, computational fluid dynamics (CFD) was performed both prior to, and following, inferior turbinate augmentation to model the resultant changes in airflow patterns and better understand the pathophysiology of ENS. An ENS patient with marked reduction in ENS symptoms following turbinate augmentation was identified, and pre- and post-operative CT imaging was collected. A Finite element framework with the variational multiscale method (Esmaily-Moghadam, Comput. Methods Appl. Mech. Engrg. 2015) was used to compute the airflow, temperature, and moisture transport through the nasal cavity. Comparison of the CFD results following corrective surgery showed higher levels of airflow turbulence. Augmentation produced 50{\%}, 25{\%}, and 25{\%} increases in root mean square pressure, wall shear stress, and heat flux respectively. These results provide insight into the changes in nasal airflow characteristics attainable through surgical augmentation, and by extension, how nasal airflow patterns may be distorted in the `overly patent' airway of ENS patients. [Preview Abstract] |
Monday, November 21, 2016 12:11PM - 12:24PM |
H20.00008: Numerical tool development of fluid-structure interactions for investigation of obstructive sleep apnea Chien-Jung Huang, Susan White, Shao-Ching Huang, Sanjay Mallya, Jeff Eldredge Obstructive sleep apnea (OSA) is a medical condition characterized by repetitive partial or complete occlusion of the airway during sleep. The soft tissues in the upper airway of OSA patients are prone to collapse under the low pressure loads incurred during breathing. The ultimate goal of this research is the development of a versatile numerical tool for simulation of air-tissue interactions in the patient specific upper airway geometry. This tool is expected to capture several phenomena, including flow-induced vibration (snoring) and large deformations during airway collapse of the complex airway geometry in respiratory flow conditions. Here, we present our ongoing progress toward this goal. To avoid mesh regeneration, for flow model, a sharp-interface embedded boundary method is used on Cartesian grids for resolving the fluid-structure interface, while for the structural model, a cut-cell finite element method is used. Also, to properly resolve large displacements, non-linear elasticity model is used. The fluid and structure solvers are connected with the strongly coupled iterative algorithm. The parallel computation is achieved with the numerical library PETSc. Some two- and three- dimensional preliminary results are shown to demonstrate the ability of this tool. [Preview Abstract] |
Monday, November 21, 2016 12:24PM - 12:37PM |
H20.00009: Clinical questions and the role CFD can play Saikat Basu, PhD, Julia S. Kimbell, PhD, Adam M. Zanation, MD, Charles S. Ebert, MD, Brent A. Senior, MD Use of computational fluid dynamics has revolutionized our perspectives on flow problems in engineering. These tools are however still underused in exploring clinical questions. Here we present some representative CFD-based findings that can improve current clinical practice. Chronic rhinosinusitis (CRS) is a complex inflammatory disease affecting over 11 million Americans yearly. It obstructs sinus pathways, thus hindering ventilation and clearance. Prescribed topical medications are often ineffective even after surgeries, partially owing to scanty drug delivery to the affected areas. We focus on improving the use of the most frequently used topical nasal sprays. From computed tomography (CT) scans, we develop 3D sinonasal airway models on the medical imaging software Mimics$^{\text{TM}}$, which are then meshed using ICEM-CFD$^{\text{TM}}$ followed by airflow and particle simulations on Fluent$^{\text{TM}}$ (v.14.5, ANSYS, Inc.). The results quantify aerosol particle delivery to target cavities before and after surgical alleviation. Various combinations of breathing techniques and head-nozzle orientations can increase target-site particle deposition over depositions using prevalent physician recommendations, and our findings facilitate identification of such optimal conditions. [Preview Abstract] |
Monday, November 21, 2016 12:37PM - 12:50PM |
H20.00010: Multi-scale analysis of active turbulence in living fluids Amin Doostmohammadi, Javier Urzay, Julia Yeomans Pattern formation in biological fluids manifests in the form of spatio-temporal chaos and is considered as a new class of turbulent flows. Here, we investigate the similarities and distinctions between turbulent-like flows in living fluids at low Reynolds numbers and classic high-Reynolds turbulence using multi-scale statistical tools. Turbulent characteristics of active flows are compared in two and three dimensions. In particular, we quantify the intermittency of meso-scale turbulence and explore energy cascades in two and three dimensions. Energy fluxes associated with viscous dissipation and local energy injection from active particles are quantified, shedding light on inter-scale phenomena in chaotic biological fluids. [Preview Abstract] |
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