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 S29: Biological Fluid Dynamics : Biofilms |
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Chair: Philip Pearce, Harvard Medical School Room: 611 |
Tuesday, November 26, 2019 10:31AM - 10:44AM |
S29.00001: Characterization of friction drag over biofilms and rigid analogs Elizabeth Callison, Joel Hartenberger, James Gose, Marc Perlin, Steven Ceccio Soft biofilms can form at flow boundaries, producing increased friction drag which can adversely affect the performance of hydrodynamic systems. The underlying mechanisms of drag production in soft biofilms are not well understood. Surface roughness, compliance, and the presence of streamers within the boundary layer flow can all contribute to the development of friction drag by turbulent boundary layers. To examine the drag producing flow, flat plates covered in biofilms were studied in the Skin-Friction Flow Facility at the University of Michigan. Experiments evaluating the drag produced by the live biofilm were then compared to those of solid, three-dimensional printed, rigid replicas to differentiate the measured drag forces and their components. These rigid replicas were generated via additive manufacturing using in situ measurements of the biofilm surface profile collected at several flow speeds and growth incubation times. The hydrodynamic performance of the biofilms was determined through pressure drop measurements as well as planar particle image velocimetry of the channel flow. Comparisons of the resistance curves for the rigid replicas and live biofilm will be discussed and flow measurements will be presented. [Preview Abstract] |
Tuesday, November 26, 2019 10:44AM - 10:57AM |
S29.00002: Flow-induced symmetry breaking in growing bacterial biofilms Philip Pearce, Boya Song, Dominic Skinner, Rachel Mok, Raimo Hartmann, Praveen Singh, Jeffrey Oishi, Knut Drescher, Jorn Dunkel Bacterial biofilms are matrix-bound multicellular communities. Biofilms represent a major form of microbial life on Earth and serve as a model active nematic system, in which activity results from growth of the rod-shaped bacterial cells. In their natural environments, from human organs to industrial pipelines, biofilms have evolved to grow robustly under significant fluid shear. Despite intense practical and theoretical interest, it is unclear how strong fluid flow alters the local and global architectures of biofilms. Here, we combine highly time-resolved single-cell live imaging with 3D multi-scale modeling to investigate the effects of flow on the dynamics of all individual cells in growing biofilms. Our experiments and cell-based simulations reveal that, in the initial stages of development, the flow induces a downstream gradient in cell orientation, causing asymmetrical droplet-like biofilm shapes. In the later stages, when the majority of cells are sheltered from the flow by the surrounding extracellular matrix, buckling-induced cell verticalization in the biofilm core restores radially symmetric biofilm growth, in agreement with predictions from a 3D continuum model. [Preview Abstract] |
Tuesday, November 26, 2019 10:57AM - 11:10AM |
S29.00003: Four-Phase Hybrid Model of Bacterial Biofilm Growth Xing Jin, Jeffrey Marshall, Matthew Wargo Bacterial biofilms play a critical role in environmental processes, water treatment, human health, and food processing. They exhibit highly complex dynamics due both to their physical structure and to the complex chemical interactions of the microorganisms that construct them. We present a new type of hybrid computational model that treats biofilms as an interaction between four component types -- bacteria, extracellular polymeric substance (EPS), water, and nutrients (substrates). The bacteria are modeled as discrete particles and the other three components are modeled as interacting continua. Bacterial cells consume water and nutrients in order to grow, divide and produce EPS. The model predicts bacterial colony formation as a tree-like structure, with a large part of the EPS production occurring near the colony border where nutrient concentration is highest. EPS flows outward from the bacterial colony, while water flows inward. The lubrication force, the ratio of bacteria and EPS growth rates, the yield coefficient, and osmotic pressure are all found to have important and complex influences on biofilm development. [Preview Abstract] |
Tuesday, November 26, 2019 11:10AM - 11:23AM |
S29.00004: Oscillating Diffusion - A New Diffusion Mechanism for Nanoparticles Exposed to Ultrasound in a Hydrogel Jeffrey Marshall, Dong Ma, Junru Wu Diffusion is the primary mechanism for transport of particles and chemicals in a biofilm, which is essential for many biofilm mitigation strategies. The current research reports on a recently discovered diffusion mechanism which we call oscillatory diffusion. In this mechanism, an oscillating flow (ultrasound) can be used to significantly enhance nanoparticle diffusion in a porous medium (a biofilm hydrogel). It is assumed here that the particle and pore sizes are such as to exhibit hindered diffusion, caused by intermittent capturing of particles by the porous medium for brief time periods. The research includes experimental studies with different particle sizes in which the enhancement of particle diffusion coefficient in a hydrogel by ultrasound exposure is confirmed and detailed measurements are reported. A simple stochastic model of the oscillatory diffusion process is presented. Preliminary results will also be presented for a larger-scale experiment in which the time-accurate particle path is measured in a porous bed in the presence of an oscillatory flow. This latter experiment seeks to examine the proposed oscillatory diffusion mechanism and validate mathematical models for this process. [Preview Abstract] |
Tuesday, November 26, 2019 11:23AM - 11:36AM |
S29.00005: Bioemulsification of hexadecane by Marinobacter sp17 George Kapellos, Nicolas Kalogerakis, Patrick S. Doyle The ability of the halotolerant microbes Marinobacter sp17 to emulsify hexadecane and form biofilms over the surface of dispersed hexadecane droplets is investigated in batch and microfluidic microcosms. In batch microcosms, these microbes transform a layer of hexadecane, initially floating over seawater, to a highly polydisperse oil-in-water emulsion. The evolution of the droplet size distribution is followed by microscopic image analysis and dynamic light scattering measurements and is found to be multimodal with peaks over a range spanning from hundreds of nanometers up to several millimeters. Over time, the average droplet diameter is reduced by the combined effects of biodegradation and accumulating emulsification capacity. The droplet shrinking that is caused by biodegradation alone, is also determined for individual hexadecane droplets using a custom-made microfluidic device and phase-contrast microscopy. Furthermore, the structure of the microbial biofilms that coat and degrade hexadecane droplets is visualized and quantified with confocal microscopic imaging. Experimental results are discussed in conjunction with a recently developed compound particle-in-cell model. [Preview Abstract] |
Tuesday, November 26, 2019 11:36AM - 11:49AM |
S29.00006: Ion-Mediated Swelling in a Model of Gastric Mucus Gel Owen Lewis, James Keener, Aaron Fogelson The gastric mucus layer serves a protective function in the human stomach, shielding the epithelium from the digestive machinery of the stomach, but It is not understood how this gel layer is maintained \emph{in vivo}. Mucus degradation via digestion of the gel network at the lumen must be balanced by secretion and swelling of new mucus at the stomach wall. These processes, are dependent on the local ionic composition of the gel solvent, which varies throughout the layer. Here, we present a comprehensive model of mucus-like polyelectrolyte gel based on a two-phase framework. This model extends classical theory to account for the dependence of the Flory interaction parameter and standard free energies on transient, ion-mediated crosslinks within the gel network. We present a computational investigation of the dynamic swelling behavior of the model. In particular, we quantify the rate at which a globule of crosslinked gel swells when exposed to an ionic bath as a function of bath concentration and network chemistry. We show that the swelling rate has a non-monotone dependence on the molarity of the bath solution, in part due to the existence of an additional chemical pressure not predicted by classical theory. [Preview Abstract] |
Tuesday, November 26, 2019 11:49AM - 12:02PM |
S29.00007: Active carpets, part 1: Transport driven by bacterial clusters and topological defects Francisca Guzmán-Lastra, Arnold Mathijssen, Andreas Kaiser, Hartmut Löwen Biological activity is highly concentrated on surfaces, from molecular motors and ciliary arrays to sessile suspension feeders and biofilms – together they form the class of `active carpets'. While the physics of active suspensions has raised considerable interest, it remains unclear how energy and momentum injection from active surfaces can drive living systems out of equilibrium. Here we demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and we propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full theory is developed in terms of gradients in the active matter density and velocity, and applied to bacterial turbulence, topological defects and clustering. Currents with complex spatiotemporal patterns are obtained, which are tunable through confinement. Our findings show that diversity in carpet architecture is essential to maintain biofunctionality. [Preview Abstract] |
Tuesday, November 26, 2019 12:02PM - 12:15PM |
S29.00008: Active carpets, part 2: Generalisation of Fick's laws for enhanced diffusion and particle capture by life at interfaces Arnold JTM Mathijssen, Francisca Guzman-Lastra, Manu Prakash, Hartmut Loewen Fluctuations lie at the core of biological processes, facilitating diffusive transport and driving the cell's molecular machinery. Fick's laws of diffusion are well established in classical thermodynamics, but living systems operate far from thermal equilibrium as energy is injected locally by activity, which can give rise to surprising effects not captured by passive diffusion. Especially on surfaces this metabolic activity is highly concentrated, from molecular motors through ciliary arrays to sessile suspension feeders and bacterial biofilms, together forming the class of `active carpets'. Here, we consider the flows generated by these different active surfaces and show how they can enhance diffusion, directed transport, and particle capture. We derive the diffusion coefficients as a function of distance from these active carpets and we formulate the corresponding generalised Fick's laws. These laws feature remarkable solutions, including non-Boltzmannian sedimentation profiles with particles hovering a finite distance above the active carpet, and enhanced particle capture by a raised diffusive flux. Our results shed new light on the non-equilibrium properties of materials with active boundary conditions and life at interfaces. [Preview Abstract] |
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