Virtual Workshop: Complex Flows in Biological Systems

Workshop to be held virtually on zoom, October 23, 2020 12pm-3pm ET

Please register at this link to attend and access zoom information:

Registered participants (using link above) will receive additional information about the workshop, including a link to a slack workspace to facilitate chat and communication during the workshop. Please email Paula Sanematsu or Bobby Carroll for additional information.

Schedule (all times Eastern):

12-12:55 pm: Dr. Mimi Koehl, Department of Integrative Biology, University of California, Berkeley, “Navigating in a turbulent environment”

Abstract: When organisms locomote and interact in nature, they must navigate through complex habitats that vary on many spatial scales, and they are buffeted by turbulent wind or water currents and waves that also vary on a range of spatial and temporal scales.  We have been using the microscopic larvae of bottom-dwelling marine animals to study how the interaction between the swimming by an organism and the turbulent water flow around them determines how they move through the environment.  Many bottom-dwelling marine animals produce microscopic larvae that are dispersed to new sites by ambient water currents, and then must land on surfaces in suitable habitats.  Field and laboratory measurements enabled us to quantify the fine-scale, rapidly-changing patterns of water velocity vectors and of chemical cue concentrations near coral reefs and along fouling communities (organisms growing on docks and ships). We also measured the swimming behavior of larvae of reef-dwelling and fouling community animals, and their responses to chemical and mechanical cues.  We used these data to design agent-based models of larval behavior.  By putting model larvae into our real-world flow and chemical data, which varied on spatial and temporal scales experienced by microscopic larvae, we could explore how different responses by larvae affected their transport and their recruitment into reefs or fouling communities.  The most effective strategy for recruitment depends on habitat.

12:55-1:40 pm: Dr. Gabriel Juarez, Mechanical Science and Engineering Department, University of Illinois at Urbana-Champaign, “Bacteria growth and self-organization at liquid interfaces can buckle and deform oil droplets”

Bacteria growth, colony formation, and the emergence of structure in biofilms at rigid interfaces is an ongoing area of research relevant to many natural and industrial processes. Cell growth and aggregation at liquid interfaces, however, are less understood and yet fundamental to chemical and environmental processes, such as fermentation and hydrocarbon biodegradation. In this presentation, I will discuss ongoing experimental work where we use microfluidics and time-lapse microscopy to examine the growth of rod-shaped bacteria on stationary oil droplets with maximum diameters ranging from 10 to 200 micrometers. After 72 hours, we observe that droplets above a critical diameter become living oil-water interfaces while droplets below a critical diameter do not change at all. The emergence of the rich behavior of living oil-water interfaces is a result of the coupling between the adsorption and growth of bacteria at finite-area liquid interfaces. The interplay between bacteria morphology and interfacial curvature results in the self-organization of a monolayer of cells with long-range orientational order at the droplet surface. As cell growth and division continue, the stress generated from cell-cell steric interactions gives rise to the emergence of mesoscale collective motion followed by the deformation of the droplet surface, including buckling and tubulation. This setup functions as a useful model system to gain insight into active stresses at deformable interfaces and improves our understanding of microbial oil biodegradation and its potential impact on the transport and dispersion of oil droplets in the ocean water column.

1:40-1:50 pm: break

1:50-2:30 pm: Short talks

Dr. Paula Sanematsu, Department of Physics and BioInspired Institute, Syracuse University, “Tissue flow during development and its role in symmetry breaking in the zebrafish embryo”

Left-right (LR) asymmetry present in internal organs of vertebrates initiates during embryonic development with observable changes to individual cell shapes which are vital to create functional organs. Kupffer’s vesicle (KV) in the zebrafish embryo is a transient organ that acts as the LR organizer. As the KV moves through the surrounding tailbud tissue during development, KV cells change shape along the anterior-posterior (AP) axis which results in an uneven distribution of cilia. While it is known that asymmetric distribution of cilia is necessary for establishing LR asymmetry, the preceding changes in cell shape remain poorly understood. Researchers have searched for biochemical signaling gradients that may regulate KV architecture, but so far none have been identified. In this work, we take a different approach by analyzing how mechanical forces applied by tailbud tissue flow around the KV can contribute to changes in cell shape. We develop a fully 3D vertex model of the tissue architecture, instead of the usual 2D models, to better quantify the 3D forces at play. We study how the KV’s motion through the tailbud, the corresponding drag force, and ultimately the change of cilia distribution as a function of model parameters. We use particle image velocimetry (PIV) analysis to characterize movement of tailbud cells. Velocity gradients from PIV analysis along with preliminary simulation results of shear stresses and pressure acting on KV indicate that drag forces are indeed present and play a role in cell shape changes.

Dr. Melissa Green Department of Mechanical and Aerospace Engineering and BioInspired Institute, Syracuse University,”The flow fields and forces generated by oscillatory swimmers”
Fish and aquatic mammals propel themselves using the hydrodynamic thrust generated by the oscillation of their fins, flukes, and flexible bodies. These fluid-structure interactions create complex three-dimensional vortex wakes that require intensive simulations or refined experiments to resolve. A continuing question in the field of bio-inspired fluid dynamics is whether and how the structure and evolution of the vortex wakes relate to the forces on the body surfaces. A comprehensive mapping of flow structure to surface pressure and forces would enable the design and actuation of efficient and effective propulsors and control surfaces. In our lab we use extensive experimental wake measurements in the flow around simple models of fish-like body motions, combined with fundamental but fast computational models of wake dynamics in order to untangle those connections. Volumetric three-component phase-averaged velocity fields are obtained from stacked stereoscopic PIV measurements in the flow around isolated caudal fin models and a two degree-of-freedom full fish model. The discrete vortex method generates parameter sweeps of 2D time-resolved simulations, and we can link regions of shed vorticity with specific force terms in the model equations. The combined study has shown how the timing of vorticity release does in fact correlate with forces generated, but the physical mechanism (added mass or circulatory) of that thrust production depends on the time-resolved kinematics of the fin motion.

2:30-3pm: Breakout discussion rooms