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We investigate the effects of bacterial activity on the mixing and transport properties of a passive scalar in time-periodic flows in experiments and in a simple model. We focus on the interactions between swimming Escherichia coli and the Lagrangian coherent structures (LCSs) of the flow, which are computed from experimentally measured velocity fields. Experiments show that such interactions are non-trivial and can lead to transport barriers through which the scalar flux is significantly reduced. Using the Poincaré map, we show that these transport barriers coincide with the outermost members of elliptic LCSs known as Lagrangian vortex boundaries. Numerical simulations further show that elliptic LCSs can repel elongated swimmers and lead to swimmer depletion within Lagrangian coherent vortices. A simple mechanism shows that such depletion is due to the preferential alignment of elongated swimmers with the tangents of elliptic LCSs. Our results provide insights into understanding the transport of micro-organisms in complex flows with dynamical topological features from a Lagrangian viewpoint.

To address the global water shortage crisis, one of the promising solutions is to collect freshwater from the environmental resources such as fog. However, the efficiency of conventional fog collectors remains low due to the viscous drag of fog-laden wind deflected around the collecting surface. Here, we show that the three-dimensional and centimetric kirigami structures can control the wind flow, forming quasi-stable counter-rotating vortices. The vortices regulate the trajectories of incoming fog clusters and eject extensive droplets to the substrate. As the characteristic structural length is increased to the size of vortices, we greatly reduce the dependence of fog collection on the structural delicacy. Together with gravity-directed gathering by the folds, the kirigami fog collector yields a collection efficiency of 16.1% at a low wind speed of 0.8 m/s and is robust against surface characteristics. The collection efficiency is maintained even on a 1 m 2 collector in an outdoor setting. Water shortage not only occurs in arid regions, but also in humid area with little precipitation, despite abundant fog. Authors develop robust and scalable 3D centimetric kirigami structures to control wind flow and regulate the trajectories of incoming fog, yielding high fog collection efficiency.

Microorganisms are ubiquitous in nature and technology. They inhabit diverse environments, ranging from small river tributaries and lakes, to oceans, as well as wastewater treatment plants and food manufacturing. In many of these environments, microorganisms coexist with settling particles. Here, we investigate the effects of microbial activity (swimming E. coli) on the settling dynamics of passive colloidal particles using particle tracking methods. Our results reveal the existence of two distinct regimes in the correlation length scale ($L_u$) and the effective diffusivity of the colloidal particles ($D_{eff}$), with increasing bacterial concentration ($\\phi _b$). At low $\\phi _b$, the parameters $L_u$ and $D_{eff}$ increase monotonically with increasing $\\phi _b$. Beyond critical $\\phi _b$, a second regime is found where both $D_{eff}$ and $L_u$ are independent of $\\phi _b$. We demonstrate that the transition between these regimes is characterized by the emergence of bioconvection. We use experimentally measured particle-scale quantities $L_u$ and $D_{eff}$ to predict the critical bacterial concentration for the diffusion–bioconvection transition.

Understanding mixing and transport of passive scalars in active fluids is important to many natural (e.g., algal blooms) and industrial (e.g., biofuel, vaccine production) processes. Here, we study the mixing of a passive scalar (dye) in dilute suspensions of swimming Escherichia coli in experiments using a two-dimensional (2D) time-periodic flow and in a simple simulation. Results show that the presence of bacteria hinders large-scale transport and reduces overall mixing rate. Stretching fields, calculated from experimentally measured velocity fields, show that bacterial activity attenuates fluid stretching and lowers flow chaoticity. Simulations suggest that this attenuation may be attributed to a transient accumulation of bacteria along regions of high stretching. Spatial power spectra and correlation functions of dye-concentration fields show that the transport of scalar variance across scales is also hindered by bacterial activity, resulting in an increase in average size and lifetime of structures. On the other hand, at small scales, activity seems to enhance local mixing. One piece of evidence is that the probability distribution of the spatial concentration gradients is nearly symmetric with a vanishing skewness. Overall, our results show that the coupling between activity and flow can lead to nontrivial effects on mixing and transport.

Microorganisms, primitive unicellular forms of life, form the basis of the food web and play crucial roles in the Earth’s biogeochemical cycles. Habitats of microorganisms, from oceans and lakes to soil and human intestines, are often characterized by constant fluid motion. Fluid flow exerts forces and torques on microorganisms that affect their movement and distribution, and transports essential chemicals on which they rely for sensing, foraging, and mating. As a result, flow has a broad range of effects on the behaviors of microorganisms, including their locomotion, reproduction, nutrient uptake, and communication. Despite many efforts to understand microbiology in aquatic environments, it remains a challenge to interpret the physical and biological behaviors of microorganisms in the presence of fluid flows, particularly unsteady and chaotic flows.In this thesis, I investigate the interaction between motile microorganisms and dynamical structures in chaotic flows, and the effects of such interaction on transport and mixing. The flow dynamical structures investigated here are known as the Lagrangian coherent structures (LCSs). First, I characterize the transport and mixing in a spatially periodic chaotic flow with swimming Escherichia coli. The microorganisms are found to align and accumulate near structures of strong stretching of fluid parcels, or namely, the hyperbolic LCSs. Such alignment and accumulation of microorganisms lead to reduction in large-scale transport but enhancement in small-scale mixing. Second, I examine the transport and mixing with E. coli in a more complex spatially aperiodic chaotic flow. The microorganisms are found to escape and deplete in vortex-like dynamical structures known as the elliptic LCSs. The depletion leads to enhanced transport barriers into which the transport of diffusive chemicals is much slower. Lastly, I investigate the mixing in the self-generated chaotic flows of swarming Serratia marcescens and show that dilute polymers can substantially enhance mixing induced by collective behaviors. Overall, this dissertation elucidates the nontrivial effects of the interaction between microorganisms and flow structures on transport and mixing.

Understanding mixing and transport of passive scalars in active fluids is important to many natural (e.g., algal blooms) and industrial (e.g., biofuel, vaccine production) processes. Here, we study the mixing of a passive scalar (dye) in dilute suspensions of swimming Escherichia coli in experiments using a two-dimensional (2D) time-periodic flow and in a simple simulation. Results show that the presence of bacteria hinders large-scale transport and reduces overall mixing rate. Stretching fields, calculated from experimentally measured velocity fields, show that bacterial activity attenuates fluid stretching and lowers flow chaoticity. Simulations suggest that this attenuation may be attributed to a transient accumulation of bacteria along regions of high stretching. Spatial power spectra and correlation functions of dye-concentration fields show that the transport of scalar variance across scales is also hindered by bacterial activity, resulting in an increase in average size and lifetime of structures. On the other hand, at small scales, activity seems to enhance local mixing. One piece of evidence is that the probability distribution of the spatial concentration gradients is nearly symmetric with a vanishing skewness. Overall, our results show that the coupling between activity and flow can lead to nontrivial effects on mixing and transport.

In the midst of the COVID-19 pandemic, many live musical activities had to be postponed and even canceled to protect musicians and audience. Orchestral ensembles face a particular challenge of contamination because they are personnel heavy and instrumentally diverse. A chief concern is whether wind instruments are vectors of contamination through aerosol dispersion. This study, made possible by the participation of members of the Philadelphia Orchestra, brings insight on the modes of production and early life of aerosols of human origin emitted by wind instruments. We find that these instruments produce aerosol levels that are comparable to normal speech in quantity and size distribution. However, the exit jet flow speeds are much lower than violent expiratory events (coughing, sneezing). For most wind instruments, the flow decays to background indoor-air levels at approximately 2 meters away from the instrument's opening. Long range aerosol dispersion is thus via ambient air currents.

Microorganisms are ubiquitous in nature and technology. They inhabit diverse environments ranging from small river tributaries and lakes to oceans, as well as wastewater treatment plants and food manufacturing. In many of these environments, microorganisms coexist with settling particles. Here, we investigate the effects of microbial activity (swimming \\textit{E. coli}) on the settling dynamics of passive colloidal particles using particle tracking methods. Our results reveal the existence of two distinct regimes in the correlation length scale (\\(L_u\\)) and the effective diffusivity of the colloidal particles (\\(D_{e\\!f\\!f}\\)), with increasing bacterial concentration (\\(\\phi_b\\)). At low \\(\\phi_b\\), the parameters \\(L_u\\) and \\(D_{e\\!f\\!f}\\) monotonically increases with increasing \\(\\phi_b\\). Beyond a critical \\(\\phi_b\\), second regime is found in which both \\(D_{e\\!f\\!f}\\) and \\(L_u\\) are independent of \\(\\phi_b\\). We demonstrate that the transition between these regimes is characterized by the emergence of bioconvection. We use experimentally-measured particle-scale quantities (\\(L_u\\), \\(D_{e\\!f\\!f}\\)) to predict the critical bacterial concentration for the diffusion-bioconvection transition.

This is a manuscript accepted for publication on Physical Review Fluids, Gallery of Fluid Motion special issue. The manuscript is associated with a poster winner of the 39th Annual Gallery of Fluid Motion Award, for work presented at the 74th Annual Meeting of the American Physical Society's Division of Fluid Dynamics (Phoenix, AZ, USA 2021).

Understanding mixing and transport of passive scalars in active fluids is important to many natural (e.g. algal blooms) and industrial (e.g. biofuel, vaccine production) processes. Here, we study the mixing of a passive scalar (dye) in dilute suspensions of swimming Escherichia coli in experiments using a two-dimensional (2D) time-periodic flow and in a simple simulation. Results show that the presence of bacteria hinders large scale transport and reduce overall mixing rate. Stretching fields, calculated from experimentally measured velocity fields, show that bacterial activity attenuates fluid stretching and lowers flow chaoticity. Simulations suggest that this attenuation may be attributed to a transient accumulation of bacteria along regions of high stretching. Spatial power spectra and correlation functions of dye concentration fields show that the transport of scalar variance across scales is also hindered by bacterial activity, resulting in an increase in average size and lifetime of structures. On the other hand, at small scales, activity seems to enhance local mixing. One piece of evidence is that the probability distribution of the spatial concentration gradients is nearly symmetric with a vanishing skewness. Overall, our results show that the coupling between activity and flow can lead to nontrivial effects on mixing and transport.