Paulo E. Arratia

Spatial manipulation of flow gradients and chemical microenvironments is essential for understanding fundamental biological mechanisms and investigating therapeutic responses in adherent cells. Convection-dominated gradient generators in microfluidic devices enable tunable chemical and shear stress gradients across large cell culture areas. However, most concentration generators are irreversibly sealed and operate in a narrow range of shear stresses, which restricts access to the cells after treatment and the physiological relevance of the flow conditions. Here, we present a reversibly sealable microfluidic platform that enables spatiotemporally controlled delivery of multiple small molecules to mammalian cells grown on large glass coverslips. Our device generates a relatively wide range of shear stresses and robust, spatially predictable chemical gradients across centimeter-scale areas and provides optical access compatible with live-cell imaging; it operates in the Stokes and laminar flow regimes. A mechanical sandwich clamp enables leak-free perfusion into the cell culture chamber and access to the cells after treatment. We experimentally and numerically demonstrate the ability to modulate the amount of mixing between co-flowing streams of small molecules. We verify the uptake of fluorophores across a monolayer of cells and assess their viability after perfusion and removal from the device. This platform provides a versatile and reusable approach for studying cellular responses to microenvironmental gradients in varied physiologically relevant shear stress conditions.

This repository contains the MATLAB simulation code accompanying the paper: "Native propulsion architecture enables bundle-preserving run-reverse-turn motility in the human pathobiont Selenomonas sputigena" by Zhi Ren*, Albane Théry*, Yee-Wai Cheung, Nigel Steager, Zixuan Wen, Michelle Crispin, Julia Radzio, Edward Steager, Li Shen, Yi-Wei Chang, Paulo E. Arratia, Kathleen J Stebe and Hyun Koo. The code simulates the swimming of a flagellated bacterium by coupling an elastic flagellum model (Kirchhoff rod theory) with a rigid cell body and low-Reynolds-number hydrodynamics (regularised Stokeslets and rotlets). It was used to investigate how cell body shape, flagellum implantation site, and motor torque together determine the run-reverse-turn motility characteristic of S. sputigena.

This repository contains the MATLAB simulation code accompanying the paper: "Native propulsion architecture enables bundle-preserving run-reverse-turn motility in the human pathobiont Selenomonas sputigena" by Zhi Ren*, Albane Théry*, Yee-Wai Cheung, Nigel Steager, Zixuan Wen, Michelle Crispin, Julia Radzio, Edward Steager, Li Shen, Yi-Wei Chang, Paulo E. Arratia, Kathleen J Stebe and Hyun Koo. The code simulates the swimming of a flagellated bacterium by coupling an elastic flagellum model (Kirchhoff rod theory) with a rigid cell body and low-Reynolds-number hydrodynamics (regularised Stokeslets and rotlets). It was used to investigate how cell body shape, flagellum implantation site, and motor torque together determine the run-reverse-turn motility characteristic of S. sputigena.

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing nonequilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: 1) coarse-graining star polymers at challenging levels of coarse-graining while preserving nonequilibrium statistics, and 2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

We observe the emergence of a distinct, elasticity-driven flow state in a yield-stress fluid in the absence of inertia. Numerical simulations show that this elasto-plastic turbulent state is characterized by a broad spectrum of fluctuations in velocity and stress. Results show a non-monotonic relationship between the volume fraction of the unyielded flow and plasticity. Surprisingly, we find that above a critical value of plasticity, the system can fluidize. Our results reveal the complex interplay between elasticity and plasticity in simple shear flows, indicating that plasticity can enhance rather than hinder momentum transport.

We observe the emergence of a distinct, elasticity-driven flow state in a yield-stress fluid in the absence of inertia. Numerical simulations show that this elasto-plastic turbulent state is characterized by a broad spectrum of fluctuations in velocity and stress. Results show a non-monotonic relationship between the volume fraction of the unyielded flow and plasticity. Surprisingly, we find that above a critical value of plasticity, the system can fluidize. Our results reveal the complex interplay between elasticity and plasticity in simple shear flows, indicating that plasticity can enhance rather than hinder momentum transport.

Soils and sediments are soft, amorphous materials with complex microstructures and mechanical properties, that are also building blocks for industrial materials such as concrete. These Earth-mediated materials evolve under prolonged environmental pressures like mechanical stress, chemical gradients, and biological activity. Here, we introduce geomimicry, a new paradigm for designing sustainable materials by learning from the emergent and adaptive dynamics of Earth-mediated matter. Drawing a parallel to biomimicry, we posit that these geomaterials follow evolutionary design rules, adapting their structure and function in response to persistent natural forces through locally evolved interactions and compositions. Our central argument is that by decoding these rules - primarily through understanding the emergence of novel exotic properties from multiscale interactions between heterogenous components - we can engineer a new class of adaptive, sustainable matter. We propose two complementary approaches here. The top-down approach looks to nature to identify building blocks and map them to functional groups defined by their mechanical behaviors, and then examine how environmental training tunes interactions among these groups. The bottom up approach seeks to leverage and test this framework, building earth materials one component at a time under fluctuating environmental stresses that guide assembly of complex and out-of-equilibrium materials. The goal is to create materials with programmed functionalities, such as erosion resistance or self-healing capabilities. Geomimicry offers a pathway to re-imagine climate-resilient soils and precision agriculture to new insights into planetary terraforming, fundamentally shifting the focus from static compositions to dynamic, evolving systems that are mediated via their environment.

Salps are underwater invertebrates considered to be among the world's most energy-efficient examples of jet propulsion. They can swim as solitary individuals or as physically connected colonies, coordinating their jets to produce collective movement. Inspired by salps, we developed the SALP (Salp-inspired Approach to Low-energy Propulsion) system, where individual SALP robots can be physically connected into a multi-SALP group, and we investigate the coupled effects of physical arrangement and jet coordination on the swimming performance and energy efficiency of a two-SALP system. We conduct free swimming tests to evaluate locomotion performance metrics and find that the two-SALP system, when properly coordinated, is able to swim with 15.7% higher speed and 11.3% lower cost of transport than the single SALP. Supporting flow characterization experiments using particle image velocimetry reveal vortex ring structures emanating from robot SALP nozzles. The data suggest that propulsion performance is affected by the spatial arrangement of the vortex ring structure. In particular, we find that SALP systems that produce a parallel vortex ring arrangement produce less vortex circulation and impulse than an in-series vortex ring arrangement. Overall, the SALP system is a useful platform for exploring salp-inspired multi-jet locomotion strategies, enabling decoupling of physical and control parameters to expose underlying locomotion physics in ways that are difficult with the biological salp. These insights advance our understanding of multi-jet locomotion and support the development of more energy-efficient jet-propelled underwater robots in the future.

Many different microswimmers propel themselves using flagella that beat periodically. The shape of the flagellar beat and swimming speed have been observed to change with fluid rheology. We quantify changes in the flagellar waveforms of Chlamydomonas reinhardtii in response to changes in fluid viscosity using (i) shape mode analysis and (ii) a full swimmer simulation to analyse how shape changes affect the swimming speed and to explore the dimensionality of the shape space. By decomposing the gait into the time-independent mean shape and the time-varying stroke, we find that the flagellar mean shape substantially changes in response to viscosity, while the changes in the time-varying stroke are more subtle. Using the swimmer simulation, we quantify how the swimming speed is affected by the dimensionality of the flagellar shape reconstruction, and we show that the observed change in swimming speed with viscosity is explained by the variations in mean flagellar shape and beat frequency, while the changes in swimming speed from the different time-varying strokes are on the scale of variation between cells. This article is part of the theme issue ‘Biological fluid dynamics: emerging directions’.

Many different microswimmers propel themselves using flagella that beat periodically. The shape of the flagellar beat and swimming speed have been observed to change with fluid rheology. We quantify changes in the flagellar waveforms of Chlamydomonas reinhardtii in response to changes in fluid viscosity using (1) shape mode analysis and (2) a full swimmer simulation to analyze how shape changes affect the swimming speed and to explore the dimensionality of the shape space. By decomposing the gait into the time-independent mean shape and the time-varying stroke, we find that the flagellar mean shape substantially changes in response to viscosity, while the changes in the time-varying stroke are more subtle. Using the swimmer simulation, we quantify how the swimming speed is affected by the dimensionality of the flagellar shape reconstruction, and we show that the observed change in swimming speed with viscosity is explained by the variations in mean flagellar shape and beat frequency, while the changes in swimming speed from the different time-varying strokes are on the scale of variation between cells.

Many microorganisms exhibit upstream swimming, which is important to many biological processes and can cause contamination of biomedical devices and the infection of organs. This process, called rheotaxis, has been studied extensively in Newtonian fluids. However, most microorganisms thrive in non-Newtonian fluids that contain suspended polymers such as mucus and biofilms. Here, we investigate the rheotactic behavior of Escherichia coli near walls in non-Newtonian fluids. Our experiments demonstrate that bacterial upstream swimming is enhanced by an order of magnitude in shear-thinning (ST) polymeric fluids relative to Newtonian fluids. This result is explained by direct numerical simulations, revealing a torque that promotes the alignment of bacteria against the flow. From this analysis, we develop a theoretical model that accurately describes experimental rheotactic data in both Newtonian and ST fluids.

When turbulent boundary layer flows encounter abrupt roughness changes, an Internal Boundary Layer (IBL) forms. Equilibrium theory breaks down in the nonequilibrium IBL, which may extend O(10) km for natural atmospheric flows. Here, we find that the IBL possesses a characteristic time-scale associated with the IBL height, $δ_i$. We show that $δ_i$ and the edge velocity set the scales of the mean and defect velocity profiles within the IBL, for simulation and experimental data covering a multitude of roughness transition types. We present a nontrivial extension of equilibrium theory to the dynamically adjusting IBL, which can be useful for modeling a range of environmental and industrial flows.

Researchers looking for sustainable materials with optimal mechanical properties may draw inspiration from a baseball tradition. For nearly 100 y, a mysterious mud harvested from an undisclosed river site in New Jersey (USA) has been the agent of choice in the USA's Major League Baseball for "de-glossing" new baseballs. It is unclear, however, what makes this "Rubbing Mud" work. Here, we perform a multiscale investigation of the rheology and tribology of this mud material under baseball-relevant conditions and identify three mechanisms by which the mud alters the surface properties of the baseball. First, the mud creates a more uniform baseball surface by filling in pores in the leather; this is possible because of its relatively high cohesion (clays and organics) making the material remarkably shear thinning. Second, the residue of cohesive particles coating the baseball effectively doubles contact adhesion. Third, a sparse population of angular sand grains are bonded to the baseball by clay-sized particles, leaving a studded surface that enhances friction. The proportions of cohesive, frictional, and viscous elements in Rubbing Mud conspire to create a soft material with an unusual mix of properties, that could find other applications in the development of sustainable geomaterials. Our improved understanding of the flow and friction of natural muds may also find use in modeling natural hazards such as mudslides and for locomotion in muddy environments.

The original version of this Article contained an error in Fig. 5b, in which the y -axis label displayed an ‘ α ‘ instead of an ‘ n ’.

While experiments and simulations have provided a rich picture of the dynamic heterogeneity in glasses at constant temperature or under steady shear, the dynamics of glasses under oscillatory shear remain comparatively less explored. Recent work has shown that oscillatory shear protocols can embed a ``memory'' into a glass's structure, whereby the material will exhibit dynamics that are encoded by the oscillatory shear protocol applied. However, most of the computational work studying the memory effect has been performed in the zero temperature limit, and the effects of thermalization are poorly characterized. In this work, we use nonequilibrium molecular dynamics simulations to study the dynamics of a model two-dimensional glass former at low, non-zero temperatures under oscillatory shear. While we show that the systems' dynamics are independent of sample preparation for either small or larger strain amplitudes, the dynamics become distinct near the yield point when the deformation is applied at finite temperature. We then characterize the dynamic heterogeneity using two metrics, one derived from the vibrational modes and one that exploits machine learning to identify regions prone to rearrangement. This analysis provides evidence that the dynamics below and above yield emerge from distinct structural origins that may be important for developing improved constitutive models that can predict memory in disordered solids.

When wet soil becomes fully saturated by intense rainfall, or is shaken by an earthquake, it may fluidize catastrophically. Sand-rich slurries are treated as granular suspensions, where the failure is related to an unjamming transition, and friction is controlled by particle concentration and pore pressure. Mud flows are modeled as gels, where yielding and shear-thinning behaviors arise from inter-particle attraction and clustering. Here we show that the full range of complex flow behaviors previously reported for natural debris flows can be reproduced with three ingredients: water, silica sand, and kaolin clay. Going from sand-rich to clay-rich suspensions, we observe continuous transition from brittle (Coulomb-like) to ductile (plastic) yielding. We propose a general constitutive relation for soil suspensions, with a particle rearrangement time that is controlled by yield stress and jamming distance. Our experimental results are supported by models for amorphous solids, suggesting that the paradigm of non-equilibrium phase transitions can help us understand and predict the complex behaviors of Soft Earth suspensions. Regarding the failure and flow of wet soil, a question that remains is how soil material composition influences rheology. Based on Soft Earth suspension flow experiments, the authors discover a continuous transition from frictional-to-cohesive rheology recreating all complex behaviors reported for natural soil slurries.

Bacteria often exhibit upstream swimming, which can cause the contamination of biomedical devices and the infection of organs including the urethra or lungs. This process, called rheotaxis, has been studied extensively in Newtonian fluids. However, most microorganisms thrive in non-Newtonian fluids that contain suspended polymers such as mucus and biofilms. Here, we investigate the rheotatic behavior of E. coli near walls in non-Newtonian fluids. Our experiments demonstrate that bacterial upstream swimming is enhanced by an order of magnitude in shear-thinning polymeric fluids relative to Newtonian fluids. This result is explained by direct numerical simulations, revealing a torque that promotes the alignment of bacteria against the flow. From this analysis, we develop a theoretical model that accurately describes experimental rheotatic data in both Newtonian and shear-thinning fluids.

Equations of motion are developed for the oscillatory rotation of a disk suspended between twisted strings kept under tension by a hanging mass, to which additional forces may be applied. In the absence of forcing, damped harmonic oscillations are observed to decay with an exponential time envelope for two different string types. This is consistent with damping caused by string viscosity, rather than air turbulence, and may be quantified in terms of a quality factor. To test the proposed equation of motion and model for viscous damping within the string, we measure both the natural oscillation frequency and the quality factor for widely varied values of string length, string radius, disk moment of inertia, and hanging mass. The data are found to scale in good accord with predictions. A variation where rotational kinetic energy is converted back and forth to spring potential energy is also discussed.

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.

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.

Many microorganisms propel themselves through complex media by deforming their flagella. The beat is thought to emerge from interactions between forces of the surrounding fluid, the passive elastic response from deformations of the flagellum and active forces from internal molecular motors. The beat varies in response to changes in the fluid rheology, including elasticity, but there are limited data on how systematic changes in elasticity alter the beat. This work analyses a related problem with fixed-strength driving force: the emergence of beating of an elastic planar filament driven by a follower force at the tip of a viscoelastic fluid. This analysis examines how the onset of oscillations depends on the strength of the force and viscoelastic parameters. Compared to a Newtonian fluid, it takes more force to induce the instability in viscoelastic fluids, and the frequency of the oscillation is higher. The linear analysis predicts that the frequency increases with the fluid relaxation time. Using numerical simulations, the model predictions are compared with experimental data on frequency changes in the bi-flagellated alga Chlamydomonas reinhardtii . The model shows the same trends in response to changes in both fluid viscosity and Deborah number and thus provides a possible mechanistic understanding of the experimental observations.

Multi-RNA co-transfection is starting to be employed to stimulate immune responses to SARS-CoV-2 viral infection. While there are good reasons to utilize such an approach, there is little background on whether there are synergistic RNA-dependent cellular effects. To address this issue, we use transcriptome-induced phenotype remodeling (TIPeR) via phototransfection to assess whether mRNAs encoding the Spike and Nucleocapsid proteins of SARS-CoV-2 virus into single human astrocytes (an endogenous human cell host for the virus) and mouse 3T3 cells (often used in high-throughput therapeutic screens) synergistically impact host cell biologies. An RNA concentration-dependent expression was observed where an increase of RNA by less than 2-fold results in reduced expression of each individual RNAs. Further, a dominant inhibitory effect of Nucleocapsid RNA upon Spike RNA translation was detected that is distinct from codon-mediated epistasis. Knowledge of the cellular consequences of multi-RNA transfection will aid in selecting RNA concentrations that will maximize antigen presentation on host cell surface with the goal of eliciting a robust immune response. Further, application of this single cell stoichiometrically tunable RNA functional genomics approach to the study of SARS-CoV-2 biology promises to provide details of the cellular sequalae that arise upon infection in anticipation of providing novel targets for inhibition of viral replication and propagation for therapeutic intervention.

Creep is a generic descriptor of slow motions -- in the context of materials, it describes quasi-static deformation of a solid when subjected to stresses below the global yield, at which all rigidity collapses and the material flows. Here, we experimentally investigate creep, flow, and the transition between the two states in a granular heap flow. Within the surface flowing layer the dimensionless strain rate diminishes with depth, there is an absence of spatial correlations, and there is no aging dynamics. Beneath this layer, the bulk creeps via localized avalanches of plasticity, and there is significant aging. The transition between fast surface flow and slow bulk creep and aging is observed to be in the vicinity of a critical inertial number of $I = 10^{-5}$. Surprisingly, at the cessation of surface flow and the `quenching' of the pile, creep persists in the absence of the flowing layer; albeit with significant differences for a pile that experiences a long duration of surface flow (strongly annealed) and one where flow during preparation does not last long (weakly annealed). Our results contribute to an emerging view of athermal granular creep, showing similarities across dry and submerged systems. Quenched quiescent heaps that creep indefinitely, however, present a challenge to granular rheology, and open new possibilities for interpreting and casting creep and deformation of soils in nature.

Red blood cells (RBC), the primary carriers of oxygen in the body, play a crucial role across several biomedical applications, while also being an essential model system of a deformable object in the microfluidics and soft matter fields. However, RBC behavior in viscoelastic liquids, which holds promise in enhancing microfluidic diagnostic applications, remains poorly studied. We here show that using viscoelastic polymer solutions as a suspending carrier causes changes in the clustering and shape of flowing RBC in microfluidic flows when compared to a standard Newtonian suspending liquid. Additionally, when the local RBC concentration increases to a point where hydrodynamic interactions take place, we observe the formation of equally-spaced RBC structures, resembling the viscoelasticity-driven ordered particles observed previously in the literature, thus providing the first experimental evidence of viscoelasticity-driven cell ordering. The observed RBC ordering, unaffected by polymer molecular architecture, persists as long as the surrounding medium exhibits shear-thinning, viscoelastic properties. Complementary numerical simulations reveal that viscoelasticity-induced repulsion between RBCs leads to equidistant structures, with shear-thinning modulating this effect. Our results open the way for the development of new biomedical technologies based on the use of viscoelastic liquids while also clarifying fundamental aspects related to multibody hydrodynamic interactions in viscoelastic microfluidic flows.

When wet soil becomes fully saturated by intense rainfall, or is shaken by an earthquake, it may fluidize catastrophically. Sand-rich slurries are treated as granular suspensions, where the failure is related to an unjamming transition. Mud flows are modeled as gels, where yielding and shear-thinning behaviors arise from inter-particle attraction and clustering. Here we show that the full range of complex flow behaviors previously reported for natural debris flows can be reproduced with three ingredients: water, silica sand, and kaolin clay. Going from sand-rich to clay-rich suspensions, we observe continuous transition from brittle to ductile yielding. We propose a general constitutive relation for soil suspensions, with a particle rearrangement time that is controlled by yield stress and jamming distance. Our experimental results are supported by models for amorphous solids, suggesting that the paradigm of non-equilibrium phase transitions can help us understand and predict the complex behaviors of Soft Earth suspensions.

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 E. 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 microorganisms in complex flows with dynamical topological features from a Lagrangian viewpoint.

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 ($ϕ_b$). At low $ϕ_b$, the parameters $L_u$ and $D_{e\!f\!f}$ monotonically increases with increasing $ϕ_b$. Beyond a critical $ϕ_b$, second regime is found in which both $D_{e\!f\!f}$ and $L_u$ are independent of $ϕ_b$. 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.

Abstract Soils around the planet creep, despite wide variations in particle properties and environments. This sub‐yield “flow” of soil interacts with a variety of boundaries, in terms of geometry and friction. Here we explore the veracity of recent observations of undisturbed, gravity‐driven creep, by testing a suite of materials and boundary configurations in an experimental hillslope. Using an optical interferometry technique, we demonstrate that creep is a generic relaxation process whose qualitative dynamics are insensitive to grain properties. Velocity profiles are exponential, albeit with a defect near the no‐slip boundary. Quantitative patterns such as spatial variability and magnitude of strain rates, however, are exquisitely sensitive to the details of the experiment. The emerging picture is that creep is accomplished by localized plastic failure, which induces an elastic redistribution. Similar patterns have been observed in model glasses and on earthquake faults, indicating that sub‐yield relaxation in disordered materials may share common physics.

Low Reynolds number swimmers frequently move near boundaries, such as spirochetes moving through porous tissues and sperm navigating the reproductive tract. Furthermore, these microorganisms must often navigate non-Newtonian fluids such as mucus, which are typically shear-thinning and viscoelastic. Here, we experimentally investigate such a system using the model biological organism \textit{C. elegans} swimming through microfluidic channels containing viscous Newtonian fluids and viscoelastic fluids. Swimmer kinematics and resulting flow fields are measured as a function of channel width and therefore the strength of confinement. Results show that, for viscoelastic fluids, weak or moderate confinement can lead to enhancement in propulsion speed but for strong confinement this enhancement is lost and the swimming speed is slower than for an unconfined nematode. We use theory developed for bending elastic filaments in viscoelastic fluids to show that while (weak) confinement leads to increases in swimming speed there is a, $De-$ dependent, $Wi$ (Weissenberg number) number transition from a linear stress response regime to a nonlinear (or exponential) stress response regime. The experimentally obtained velocity fields are used to calculate a Weissenberg number to show that the decrease in swimming speed with confinement is likely related to growth in elastic stresses around the swimmer.

We report a room temperature, environmentally benign, water-based, single-step direct nanoimprint process to pattern dielectric metasurfaces using aqueous titanium dioxide (TiO 2 ) nanocrystal (NC) inks, which are free of polymer additives or nonaqueous solvents typically used in nanofabrication. The metasurfaces are composed of TiO 2 NC structures with a high refractive index of 1.94 ± 0.02 at 543 nm. TiO 2 NC metasurfaces are designed to resonate at visible wavelengths and are fabricated as two-dimensional nanopillar gratings atop waveguides. Guided mode resonances within the waveguide couple to the overlaying gratings and scatter into free space, forming high quality ( Q ) factor quasi-guided mode (QGM) resonances. Electric and magnetic QGM resonances are observed, and their environmental refractive index sensitivities ( S ) are measured to be 69.1 and 70.4 nm/RIU, respectively, with a figure of merit (FOM) = Q × S > 3000. The use of water-based inks and the room temperature processing allow integration of TiO 2 NC metasurfaces on rigid and flexible, polymeric substrates.

Experimental data reported in the publication "The (in)sensitivity of granular creep to materials and boundaries". jupyter notebook codes are included for data analysis and generating figures in the paper. datasets for Kaolinite material and for smooth and rough boundaries

Experimental data reported in the publication "The (in)sensitivity of granular creep to materials and boundaries". jupyter notebook codes are included for data analysis and generating figures in the paper. datasets for Kaolinite material and for smooth and rough boundaries

Many microorganisms propel through complex media by deformations of their flagella. The beat is thought to emerge from interactions between forces of the surrounding fluid, passive elastic response from deformations of the flagellum, and active forces from internal molecular motors. The beat varies in response to changes in the fluid rheology, including elasticity, but there is limited data on how systematic changes in elasticity alters the beat. This work analyzes a related problem with fixed-strength driving force: the emergence of beating of an elastic planar filament driven by a follower force at the tip in a viscoelastic fluid. This analysis examines how the onset of oscillations depends on the strength of the force and viscoelastic parameters. Compared to a Newtonian fluid, it takes more force to induce the instability in viscoelastic fluids, and the frequency of the oscillation is higher. The linear analysis predicts that the frequency increases with the fluid relaxation time. Using numerical simulations, the model predictions are compared with experimental data on frequency changes in bi-flagellated alga Chlamydomonas reinhardtii. The model shows the same trends in response to changes in both fluid viscosity and Deborah number, and thus provides a mechanistic understanding of the experimental observations.

We explore the relationship between a machine-learned structural quantity (softness) and excess entropy in simulations of supercooled liquids. Excess entropy is known to scale well the dynamical properties of liquids, but this quasi-universal scaling is known to breakdown in supercooled and glassy regimes. Using numerical simulations, we test whether a local form of the excess entropy can lead to predictions similar to those made by softness, such as the strong correlation with particles' tendency to rearrange. In addition, we explore leveraging softness to compute excess entropy in the traditional fashion over softness groupings. Our results show that the excess entropy computed over softness-binned groupings is correlated with activation barriers to rearrangement.

We explore the relationship between a machine-learned structural quantity (softness) and excess entropy in simulations of supercooled liquids. Excess entropy is known to scale well the dynamical properties of liquids, but this quasi-universal scaling is known to breakdown in the supercooled and glassy regimes. Using numerical simulations, we test whether a local form of the excess entropy can lead to predictions that derive from softness, which has been shown to correlate well with the tendency for individual particles to rearrange. To that end, we explore leveraging softness to compute excess entropy in the traditional fashion over softness groupings. Our results show that by computing the excess entropy over softness-binned groupings, we can build a strong quantitative relationship between the rearrangement barriers across the explored systems.