Bulletin of the American Physical Society
76th Annual Meeting of the Division of Fluid Dynamics
Sunday–Tuesday, November 19–21, 2023; Washington, DC
Session L07: Biofluids: Collective Behavior and Active Matter II |
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Chair: Brato Chakrabarti, Flatiron Institute Room: 103A |
Monday, November 20, 2023 8:00AM - 8:13AM |
L07.00001: A coarse-grained model for cytoplasmic streaming Brato Chakrabarti, Michael J Shelley Cytoplasmic streaming is a striking example of fluid-structure interactions within living cells. Egg cells are among the largest, and transporting by diffusion of the proteins necessary for their development is extremely slow. In the later stages of the developing fruit fly egg, a coherent circulatory flow emerges that spans the entire ~200 μm scale cell. This streaming flow is driven by the motion of nanometric motors transporting subcellular cargo along stiff biopolymers (microtubules) anchored at the cell wall. Streaming is crucial for the organism's development, but exactly what functions are fulfilled remains unclear. Here we theoretically investigate the transition to streaming and the consequent transport and mixing. For this, we use a coarse-grained continuum theory that captures the collective response of microtubules and motors that drive the internal flows. This model has the form of a boundary force field fully coupled to an internal Stokesian flow. In particular, we study how the flow line topology is influenced by microtubule density and the geometry of the egg cell, as well as first-passage times from sources to sinks. |
Monday, November 20, 2023 8:13AM - 8:26AM |
L07.00002: Interaction between swarming active matter and flow: the impact on Lagrangian coherent structures Xinyu Si, Lei Fang In recent years, research topics concerning active matter have drawn interest from diverse communities. It has been suggested that active matter-as represented by organisms such as zooplankton-has great potential in ocean mixing due to its intrinsic mobility and the sheer amount of biomass. However, prior investigations have predominantly overlooked the influence of external background flow, despite the ubiquity of flow driven by various sources in nature. The interaction between active matter and external flow structures has long been neglected. Here, we conducted experiments using a typical centimeter swimmer, A. salina, and an electromagnetically driven quasi-two-dimensional flow to study the interaction between active matter and flow. We focused on the impact of swarming active matter on hyperbolic Lagrangian coherent structures (LCSs) that mark the most straining regions in the flow. We illustrated that the impact of active matter on LCSs was much more significant compared to localized random noise with similar energy input. In addition, we revealed that the perturbation generated by active matter could couple with the background flow and further deform the LCSs. In addition to the impact on the most straining hyperbolic regions of flow, we also revealed that the rotational elliptical region of the flow was much more susceptible to active matter perturbation. We further described how the influence of active matter changed with their number densities and background flow intensities. We revealed that the LCSs could be decently altered even at a small number density of active matter. Through this work, we aim to provide valuable insights and draw attention to the problem regarding the interaction between active matter and external flow structures. |
Monday, November 20, 2023 8:26AM - 8:39AM |
L07.00003: Rectification of translational bacterial motors Maria Luisa L Cordero, Edgardo Rosas, Marjorie Etchevers A dense suspension of swimming bacteria encapsulated in an aqueous droplet immersed in oil can set the droplet in motion, thus turning the droplet into a “translational bacterial motor”. The droplet movement is caused by the bacterial collective motion, through the generation of viscous forces in the thin lubrication film between the drop and the substrate. Thus, at short time scales the drop motion is ballistic, driven by the coherent bacterial movement, but at long time scales it is random, due to the fluctuating nature of the bacterial turbulent motion. To rectify the movement of the translational bacterial motors, we break the spatial symmetry by an anisotropic substrate. We use standard and greyscale UV lithography to produce and explore different geometries and spatial patterning of the substrate. By using a substrate with an array of triangular pillars, the x-y symmetry is broken, which reflects on different diffusion rates in each direction. This is contrasted with round pillars, for which no asymmetry is observed. On the other hand, the use of ratchet-like substrates produces a net rectification of the translational bacterial motors. |
Monday, November 20, 2023 8:39AM - 8:52AM |
L07.00004: Building Cytoskeletal Circuits via Branched Microtubule Network: Experimental Realizations Meisam Zaferani, Ryungeun Song, Sabine Petry, Howard A Stone Cytoskeletal elements self-organize into intricate hierarchical structures and form the molecular basis for cellular functions. A remarkable example is the axonal microtubule (MT) architecture that facilitates controlled neuronal migration, axon extension, and molecular transport over long distances. Inspired by axons, we have developed cytoskeletal circuits: controllable platforms for engineering robust MT architectures, with potential for novel on-chip nanotechnologies. These circuits combine the branching MT nucleation pathway with microfabrication techniques, enabling the adaptive self-organization of uniformly polarized MT arrays within microfluidic confinements. The geometrical features of the microstructures allow for control over this self-organizing process. We have successfully constructed and characterized various elements, including turns, divisions, biased divisions, and MT diodes, to fabricate diverse MT architectures on a chip. In this presentation, we will focus on the experimental results of our study, where our aim was to elucidate the fundamental principles underlying the self-organization of branched MT networks in various geometries. |
Monday, November 20, 2023 8:52AM - 9:05AM |
L07.00005: Dynamics of a free bacterial vortex Hong Tan Micro-particles around a collapsing bubble are focused into a cluster of high concentration. Inspired by this phenomenon, we develop a new microfluidic device to study the phase behavior of micro-swimmers of high densities, without using any confinement or external field. After being radially aligned by a contracting gas bubble, bandings and a vortex are observed in a bacterial suspension. We study the periodic structure of the bandings during their formation and how they finally become bacterial turbulence. The result might help to enrich our understanding on active matter collective motion, which might enhance dispersion of microbes in a natural environment where bubble collapse regularly happens. |
Monday, November 20, 2023 9:05AM - 9:18AM |
L07.00006: Dynamic Flow Control Through Active Matter Programming Language Fan Yang, Shichen Liu, Heun Jin Lee, Rob Phillips, Matt Thomson Dynamic networks of cytoskeleton and motor proteins can generate force that is essential in many cellular functions. In this talk, we show how to use biological active matter, which consumes chemical energy and generates force at molecular scales, to drive microfluidics towards constructing a single programmable device that can solve various micron-scale transport problems. Here, using optically-controlled motor-microtubule systems, we introduce a programming strategy for microfluidic control where flow fields are assembled through linear superposition of a set of fundamental flows generated by predefined programming modules. In general, the active matter is highly non-linear and will break down the linearity of Stokes flows. Combining experiments and theories, we identify a critical length for the spacing among the composition of optical signals, over which the flows created by different signals can be linearly superposed, and below which the superposition fails due to transport of active networks. Based on superposition, we define a modular active matter programming language that can spatiotemporally sculpt and composite complex flow fields. We build a coarse-grained model that quantitatively predicts the active fluid dynamics under arbitrary optical input. Model-driven programming design and optimization are realized in experiments for particle transport, extensional rheology of polymers and micron-scale manipulation tasks of human cells. |
Monday, November 20, 2023 9:18AM - 9:31AM |
L07.00007: Hydrodynamic classification of fish-like undulating swimmers in high-density schools John M Kelly, Yu Pan, Alec Menzer, Haibo Dong Two-dimensional numerical simulations of carangiform fish swimming are used to investigate the mechanisms for hydrodynamic benefit via fluid interactions in large planar fish schools. It is observed that the average efficiency of the 10-fish school swimming is increased by 30% over a single swimmer, along with a thrust production improvement of 114%. The performance results and flow analyses uncover the associated hydrodynamic interaction mechanisms in large schools. First, anterior body suction arises from the proximity of the suction side of the tail to the head of the next fish. Next, the block effect is shown to occur as fish are added to the back of the school, and the partial block effect is demonstrated along the edges of the school. Finally, the wall effect is proven to enhance the flow of momentum downstream and thus increase the net forward force of the school. Because these primary body-body interactions are based on the arrangement of surrounding fish, a classification of individual fish within the school arises based on the interactions for each group and is reflected in the performance of the individuals. It is shown that the school can be separated as front fish, middle fish, edge fish, and back fish based not only on the geometric position but also performance and wake characteristics. Finally, the groupings and mechanisms observed are proven to be consistent over a range of Reynolds numbers and school arrangements. |
Monday, November 20, 2023 9:31AM - 9:44AM |
L07.00008: Fish school dynamics: characterizing transient formations Hungtang Ko, Abigail Girma, Yangfan Zhang, Radhika Nagpal, George V Lauder Fish schools have long been thought to favor a diamond formation during migration due to reduced fluid drag and hydrodynamic stability, as suggested by Lighthill and Weih. To test this conjecture, we monitored and tracked schools of giant danios (Devario aequipinnatus) for 10 hours under flow conditions. Surprisingly, our observations revealed that fish schools did not settle into any stable formation during the experiments; instead, they continuously rearranged their positions. This finding challenges the notion of self-stabilizing formations in fish schools. |
Monday, November 20, 2023 9:44AM - 9:57AM |
L07.00009: An analytical model of induced flow velocity by vertically migrating swarms informed by 3D organism tracking Nina Mohebbi, Joonha Hwang, Matthew K Fu, John O Dabiri The fluid transport associated with swarming vertical migrations of zooplankton in the ocean may have significant implications for climate modeling, solute mixing, and gas exchange. We utilize brine shrimp (Artemia salina) as a model organism to investigate the effects of collective movement on the fluid environment. Leveraging the positive phototaxis of brine shrimp, we induce synchronized vertical migration and capture three-dimensional trajectories of individual swimmers within the swarm with a single camera and scanning laser. An analytical model estimates the mean convection velocity induced by the animals’ combined wakes. Individual animal wake structures are derived semi-empirically and combined with captured animal trajectories to construct a theoretical fluid velocity field based on a momentum-conserving model of wake superposition. |
Monday, November 20, 2023 9:57AM - 10:10AM |
L07.00010: The Effects of Flow, Light, and Aggregation Density on Antarctic Krill School Behavior David W Murphy, Kuvvat Garayev, Carlyn Scott Antarctic krill (Euphausia superba) are a key species in the Southern Ocean food web. This species forms a variety of aggregation types (e.g. massive schools, diffuse swarms) which may enhance swimming efficiency or improve awareness of predators, prey, or mates. However, little is known about how krill aggregations respond to environmental variables. Here we describe a novel annular flume designed to test the response of Antarctic krill schools of different densities to various light and flow levels in the laboratory. We conducted experiments at Palmer Station, Antarctica, varying krill group density (1-19 krill L-1), flow speed (no flow, low flow, and high flow), and light level (bright light vs complete darkness). An overhead camera showed that krill schools were most organized at a density of around 9 krill L-1 and, in the absence of flow, were more organized in the light as compared to the dark at all school densities. Further, flow generally organized the krill schools via rheotaxis, especially when light was absent. A synchronized high magnification stereophotogrammetry system produced corresponding swimming speed and nearest neighbor distance distributions, revealing that the more organized krill swam faster. These results indicate the relative importance of group density, vision, and rheotaxis in the formation and maintenance of krill schools. The facility developed here also can be used to test other schooling organisms such as fish. |
Monday, November 20, 2023 10:10AM - 10:23AM |
L07.00011: Fingering instability of growing multi-species microbial communities Carolina Trenado Yuste, Alejandro Martinez-Calvo, Hyunseok Lee, Jeffrey C Gore, Ned S Wingreen, Sujit S Datta In nature, bacteria are frequently found in colonies, a communal lifestyle that is known to provide advantages to the group, such as resistance to stressors, adhesion to surfaces, and collective access and processing of resources. Bacterial colonies can consist of different species and cells with different heritable phenotypes sharing and competing for space and essential resources. However, the mechanisms that set the shape of a growing multi-species microbial community remain poorly understood. To address this gap of knowledge we perform experiments on growing 2D bacterial colonies comprised by two different species. In agreement with previous works, we find that cells often segregate into single-strain concentric domains as the colony expands. After segregation, the outer expanding front remains smooth but the inner expanding front can develop an instability in which the boundary separating the two species forms a wavy, rough shape. To understand the mechanisms underlying such instability, we consider a minimal continuum model that incorporates cell growth and cell-substrate friction, both of which can vary between single-strain domains. Stability analysis and numerical simulations suggest that a segregated multi-strain colony becomes morphologically unstable when domains grow at different rates and exhibit different cell-substrate friction forces. Our model recapitulates the experimental observations, suggesting that a minimal mechanistic description captures the morphodynamics of growing multi-strain bacterial colonies. Moreover, our theoretical framework is not restricted to bacterial colonies, and can be extended to other growth-driven processes in living matter and ecological systems, such as developmental processes, the expansion of heterogeneous tumors, or engineered living materials. |
Monday, November 20, 2023 10:23AM - 10:36AM |
L07.00012: How bacteria in evaporating drops escape the coffee-ring effect Twan Wilting, Hanneke Gelderblom, Myrthe Reijnier, Remy Colin When a droplet containing E. coli bacteria evaporates, the bacteria get transported to the contact line and form a deposit, similar to the classic coffee-ring effect. However, here we show that when the number density of the motile bacteria is large enough, entirely new types of structures may form: radially inward-pointing fingers that consist of bacteria that move collectively inward thereby escaping the deposit. At high number density these fingers destabilize and undergo a flapping motion. We investigate the physical mechanism behind the formation of these bacterial structures. By performing systematic experiments we quantify the effect of the evaporation rate, bacterial number density and motility on the formation, evolution and dimensions of the bacterial deposit. We show that the fingers are caused by an instability in number density; due to their collective motion the bacteria induce a flow that transports additional bacteria to regions that are already dense and allows them to escape from the contact line. |
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