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1. Hierarchical Transitions and Fractal Wrinkling Drive Bacterial Pellicle Morphogenesis

   Qin, B. ; Fei, C. ; Wang, B. ; Stone, H.A. ; Wingreen, N.S. ; Bassler, B.L. ( April 2021 , Proceedings of the National Academy of Sciences of the United States of America)

   Bacterial cells can self-organize into structured communities at fluid-fluid interfaces. These soft, living materials composed of cells and extracellular matrix are called pellicles. Cells residing in pellicles garner group-level survival advantages such as increased antibiotic resistance. The dynamics of pellicle formation and, more generally, how complex morphologies arise from active biomaterials confined at interfaces are not well understood. Here, using Vibrio cholerae as our model organism, a custom-built adaptive stereo microscope, fluorescence imaging, mechanical theory, and simulations, we report a fractal wrinkling morphogenesis program that differs radically from the well-known coalescence of wrinkles into folds that occurs in passive thinmore »films at fluid-fluid interfaces. Four stages occur: growth of founding colonies, onset of primary wrinkles, development of secondary curved ridge instabilities, and finally the emergence of a cascade of finer structures with fractal-like scaling in wavelength. The time evolution of pellicle formation depends on the initial heterogeneity of the film microstructure. Changing the starting bacterial seeding density produces three variations in the sequence of morphogenic stages, which we term the bypass, crystalline, and incomplete modes. Despite these global architectural transitions, individual microcolonies remain spatially segregated, and thus the community maintains spatial and genetic heterogeneity. Our results suggest that the memory of the original microstructure is critical in setting the morphogenic dynamics of a pellicle as an active biomaterial.« less
2. Bacterial scattering in microfluidic crystal flows reveals giant active Taylor–Aris dispersion

   https://doi.org/10.1073/pnas.1819613116  

   Dehkharghani, Amin ; Waisbord, Nicolas ; Dunkel, Jörn ; Guasto, Jeffrey S. ( June 2019 , Proceedings of the National Academy of Sciences)

   The natural habitats of planktonic and swimming microorganisms, from algae in the oceans to bacteria living in soil or intestines, are characterized by highly heterogeneous fluid flows. The complex interplay of flow-field topology, self-propulsion, and porous microstructure is essential to a wide range of biophysical and ecological processes, including marine oxygen production, remineralization of organic matter, and biofilm formation. Although much progress has been made in the understanding of microbial hydrodynamics and surface interactions over the last decade, the dispersion of active suspensions in complex flow environments still poses unsolved fundamental questions that preclude predictive models for microbial transport andmore »spreading under realistic conditions. Here, we combine experiments and simulations to identify the key physical mechanisms and scaling laws governing the dispersal of swimming bacteria in idealized porous media flows. By tracing the scattering dynamics of swimming bacteria in microfluidic crystal lattices, we show that hydrodynamic gradients hinder transverse bacterial dispersion, thereby enhancing stream-wise dispersion ∼ 100 -fold beyond canonical Taylor–Aris dispersion of passive Brownian particles. Our analysis further reveals that hydrodynamic cell reorientation and Lagrangian flow structure induce filamentous density patterns that depend upon the incident angle of the flow and disorder of the medium, in striking analogy to classical light-scattering experiments.« less
3. High-Reynolds-number fractal signature of nascent turbulence during transition

   https://doi.org/10.1073/pnas.1916636117  

   Wu, Zhao ; Zaki, Tamer A. ; Meneveau, Charles ( February 2020 , Proceedings of the National Academy of Sciences)

   Transition from laminar to turbulent flow occurring over a smooth surface is a particularly important route to chaos in fluid dynamics. It often occurs via sporadic inception of spatially localized patches (spots) of turbulence that grow and merge downstream to become the fully turbulent boundary layer. A long-standing question has been whether these incipient spots already contain properties of high-Reynolds-number, developed turbulence. In this study, the question is posed for geometric scaling properties of the interface separating turbulence within the spots from the outer flow. For high-Reynolds-number turbulence, such interfaces are known to display fractal scaling laws with a dimensionmore »overflow='scroll'>D≈7/3, where the 1/3 excess exponent above 2 (smooth surfaces) follows from Kolmogorov scaling of velocity fluctuations. The data used in this study are from a direct numerical simulation, and the spot boundaries (interfaces) are determined by using an unsupervised machine-learning method that can identify such interfaces without setting arbitrary thresholds. Wide separation between small and large scales during transition is provided by the large range of spot volumes, enabling accurate measurements of the volume–area fractal scaling exponent. Measurements show a dimension of$D=2.36\pm 0.03$over almost 5 decades of spot volume, i.e., trends fully consistent with high-Reynolds-number turbulence. Additional observations pertaining to the dependence on height above the surface are also presented. Results provide evidence that turbulent spots exhibit high-Reynolds-number fractal-scaling properties already during early transitional and nonisotropic stages of the flow evolution.

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4. Biofilms at interfaces: microbial distribution in floating films

   https://doi.org/10.1039/C9SM02038A  

   Desai, Nikhil ; Ardekani, Arezoo M. ( February 2020 , Soft Matter)

   Cellular motility is a key function guiding microbial adhesion to interfaces, which is the first step in the formation of biofilms. The close association of biofilms and bioremediation has prompted extensive research aimed at comprehending the physics of microbial locomotion near interfaces. We study the dynamics and statistics of microorganisms in a ‘floating biofilm’, i.e. , a confinement with an air–liquid interface on one side and a liquid–liquid interface on the other. We use a very general mathematical model, based on a multipole representation and probabilistic simulations, to ascertain the spatial distribution of microorganisms in films of different viscosities. Ourmore »results reveal that microorganisms can be distributed symmetrically or asymmetrically across the height of the film, depending on their morphology and the ratio of the film's viscosity to that of the fluid substrate. Long-flagellated, elongated bacteria exhibit stable swimming parallel to the liquid–liquid interface when the bacterial film is less viscous than the underlying fluid. Bacteria with shorter flagella on the other hand, swim away from the liquid–liquid interface and accumulate at the free surface. We also analyze microorganism dynamics in a flowing film and show how a microorganism's ability to resist ‘flow-induced-erosion’ from interfaces is affected by its elongation and mode of propulsion. Our study generalizes past efforts on understanding microorganism dynamics under confinement by interfaces and provides key insights on biofilm initiation at liquid–liquid interfaces.« less
5. Mesoscale structure of wrinkle patterns and defect-proliferated liquid crystalline phases

   https://doi.org/10.1073/pnas.1916221117  

   Tovkach, Oleh ; Chen, Junbo ; Ripp, Monica M. ; Zhang, Teng ; Paulsen, Joseph D. ; Davidovitch, Benny ( February 2020 , Proceedings of the National Academy of Sciences)

   Thin solids often develop elastic instabilities and subsequently complex, multiscale deformation patterns. Revealing the organizing principles of this spatial complexity has ramifications for our understanding of morphogenetic processes in plant leaves and animal epithelia and perhaps even the formation of human fingerprints. We elucidate a primary source of this morphological complexity—an incompatibility between an elastically favored “microstructure” of uniformly spaced wrinkles and a “macrostructure” imparted through the wrinkle director and dictated by confinement forces. Our theory is borne out of experiments and simulations of floating sheets subjected to radial stretching. By analyzing patterns of grossly radial wrinkles we find twomore »sharply distinct morphologies: defect-free patterns with a fixed number of wrinkles and nonuniform spacing and patterns of uniformly spaced wrinkles separated by defect-rich buffer zones. We show how these morphological types reflect distinct minima of a Ginzburg–Landau functional—a coarse-grained version of the elastic energy, which penalizes nonuniform wrinkle spacing and amplitude, as well as deviations of the actual director from the axis imposed by confinement. Our results extend the effective description of wrinkle patterns as liquid crystals [H. Aharoniet al.,Nat. Commun.8, 15809 (2017)], and we highlight a fascinating analogy between the geometry–energy interplay that underlies the proliferation of defects in the mechanical equilibrium of confined sheets and in thermodynamic phases of superconductors and chiral liquid crystals.

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