Paulo E. Arratia

• University of Pennsylvania

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...

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 su...

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 timescale associated with the IBL height, δi. We show that δi and the...

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...

Blood is mainly comprised of red blood cells (RBCs) that determine the unique flow properties of blood in the circulatory system. RBCs, the primary carriers of oxygen in the body, also 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 fie...

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...

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 yiel...

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...

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...

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 applicati...

Supplementary Information for “Morphology, repulsion, and ordering of red blood cells in viscoelastic flows under confinement”

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 fi...

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 rheolo...

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 (sw...

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 p...

We investigate the effects of bacterial activity on the mixing and transport properties of two-dimensional, time-periodic flows in experiments and in a simple model. We focus on the interactions between swimming E. coli and the flow Lagrangian Coherent Structure (LCS), which are computed from experimentally measured velocity fields. Experiments sho...

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...

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, incl...

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 wheth...

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 w...

Mud is a suspension of fine-grained particles (sand, silt, and clay) in water. The interaction of clay minerals in mud gives rise to complex rheological behaviors, such as yield stress, thixotropy and viscoelasticity. Here, we experimentally examine the flow behaviors of kaolinite clay suspensions, a model mud, using steady shear rheometry. The flo...

Microorganisms encounter complex unsteady flows, including algal blooms in marine settings, microbial infections in airways, and bioreactors for vaccine and biofuel production. Here, we study the transport of active swimmers in two-dimensional time-periodic flows using Langevin simulations and experiments with swimming bacteria. We find that long-t...

Many microorganisms live and evolve in complex fluids. Examples include mammalian spermatozoa in cervical mucus, worms (e.g., C. elegans) in wet soil, and bacteria (e.g., H. pylori) in our stomach lining. Due to the presence of (bio)polymers and/or solids, such fluids often display nonlinear response to (shear) stresses including viscoelasticity an...

This paper is associated with a poster winner of a 2021 American Physical Society's Division of Fluid Dynamics (DFD) Gallery of Fluid Motion Award for work presented at the DFD Gallery of Fluid Motion. The original poster is available online at the Gallery of Fluid Motion, https://doi.org/10.1103/APS.DFD.2021.GFM.P0036.

Numerous natural systems depend on the sedimentation of passive particles in presence of swimming microorganisms. Here, we investigate the dynamics of the sedimentation of spherical colloids at various E. coli concentration within the dilute regime. Results show the appearance of two sedimentation fronts, a spherical particle front and the bacteria...

Debris flows are dense and fast-moving complex suspensions of soil and water that threaten lives and infrastructure. Assessing the hazard potential of debris flows requires predicting yield and flow behavior. Reported measurements of rheology for debris flow slurries are highly variable and sometimes contradictory due to heterogeneity in particle c...

Many microorganisms live and evolve in complex fluids. Examples include mammalian spermatozoa in cervical mucus, worms (e.g., \textit{C. elegans}) in wet soil, and bacteria (e.g., \textit{H. pylori}) in our stomach lining. Due to the presence of (bio)polymers and/or solids, such fluids often display nonlinear response to (shear) stresses including...

Viscoelastic fluids are a common subclass of rheologically complex materials that are encountered in diverse fields from biology to polymer processing. Often the flows of viscoelastic fluids are unstable in situations where ordinary Newtonian fluids are stable, owing to the nonlinear coupling of the elastic and viscous stresses. Perhaps more surpri...

Mud is a suspension of fine-grained particles (sand, silt, and clay) in water. The interaction of clay minerals in mud gives rise to complex rheological behaviors, such as yield stress, thixotropy and viscoelasticity. Here, we experimentally examine the flow behaviors of kaolinite clay suspensions, a model mud, using steady shear rheometry. The flo...

Numerous natural systems showcase the sedimentation of passive particles in presence of swimming microorganisms. Here, we investigate the dynamics of the sedimentation of spherical colloids at various E. coli concentration within the dilute regime. Results show the appearance of two sedimentation fronts, a spherical particle front and a bacteria fr...

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).

The vast majority of alluvial deposits have some degree of cohesion, typically due to the presence of clays and/or organic matter. Determining the threshold fluid shear stress, τc, necessary to entrain these sediments is essential for predicting erosion rates and morphodynamics of rivers, tidal channels, and coasts. Cohesive sediments present a gre...

In the midst of the COVID-19 pandemic, many live musical activities had to be postponed and even canceled to protect musicians and the audience. Orchestral ensembles face a particular challenge of contamination, because they are personally heavy and instrumentally diverse. A chief concern is whether wind instruments are vectors of contamination thr...

Supplemental Materials of the manuscript titled "Flow and aerosol dispersion from wind musical instruments", published on Physics of Fluids 34, 087115 (2022). https://doi.org/10.1063/5.0098273

We experimentally investigate the effects of polymer additives on the collective dynamics of swarming Serratia marcescens in quasi two-dimensional (2D) liquid films. We find that even minute amounts of polymers (< 20 ppm) can significantly enhance swimming speed and promote largescale coherent structures. Velocity statistics show that polymers supp...

Supplementary Materials of the manuscript titled "Polymers in Swarming Bacterial Turbulence".

A new model helps to predict under which conditions a species of bacteria will switch to a static lifestyle.

The critical fluid-shear stress for the onset of sediment transport, θ c , varies with the history of applied shear. This effect has been primarily attributed to compaction; the role of shear jamming is less explored. We examine the response of a granular bed to fluid-shear stress cycles of varying magnitude and direction, and determine isotropic a...

Debris flows are dense and fast-moving complex suspensions of soil and water that threaten lives and infrastructure. Assessing the hazard potential of debris flows requires predicting yield and flow behavior. Reported measurements of rheology for debris-flow slurries are highly variable and sometimes contradictory, due to heterogeneity in grain siz...

A fundamental challenge regarding disordered solids is predicting macroscopic yield—the point at which elastic behaviour changes to plastic behaviour—from the microscopic arrangements of constituent particles. Yield is accompanied by a sudden and large increase in energy dissipation due to the onset of plastic rearrangements. This suggests that one...

We investigate the rheological behavior of athermal particle suspensions using experiments and theory. A generalized version of the homogenization estimates of Ponte Castañeda and Willis [J. Mech. Phys. Solids, 43(12), 1919-1951 (1995)] is presented for the effective viscosity of athermal suspensions accounting for additional microstructural featur...

Granular hydrogels are an exciting class of microporous and injectable biomaterials that are being explored for many biomedical applications, including regenerative medicine, 3D printing, and drug delivery. Granular hydrogels often possess low mechanical moduli and lack structural integrity due to weak physical interactions between microgels. This...

Background: Saliva is a complex fluid that lubricates the oropharynx and facilitates chewing, swallowing, and vocalization. Viscoelasticity is critical for the ability of saliva to fulfill these functions. Xerostomia, or a sensation of dry mouth, occurs in 17-26% of the population. Although many equate xerostomia with hyposalivation, high-risk pat...

Can far-from-equilibrium material response under arbitrary loading be inferred from equilibrium data and vice versa? Can the effect of element transmutation on mechanical behavior be predicted? Remarkably, such extrapolations are possible in principle for systems governed by stochastic differential equations, thanks to a set of exact relations betw...

In the midst of the COVID-19 pandemic, many live musical activities had to be postponed and even cancelled 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...

In the midst of the SARS-COVID-19 pandemic, many live musical activities had to be postponed and even cancelled 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 thr...

We present a solvable model inspired by dimensional analysis for the time-dependent spreading of droplets that partially wet a substrate, where the spreading eventually stops and the contact angle reaches a nonzero equilibrium value. We separately consider small droplets driven by capillarity and large droplets driven by gravity. To explore both re...

The coupling between the swimming motion of microorganisms and chaotic flows can lead to intriguing physical phenomena. Pictured are beautiful dye mixing patterns from the concentration gradient field in chaotic mixing.

We present a solvable model inspired by dimensional analysis for the time-dependent spreading of droplets that partially wet a substrate, where the spreading eventually stops and the contact angle reaches a nonzero equilibrium value. We separately consider small droplets driven by capillarity and large droplets driven by gravity. To explore both re...

The critical fluid-shear stress for the onset of sediment transport, $\theta_c$, varies with the history of applied shear. This effect has been attributed to compaction, but the role of shear jamming is unexplored. We examine the response of a granular bed to fluid-shear stress cycles of varying magnitude and direction, and determine isotropic and...

Can far-from-equilibrium material response under arbitrary loading be inferred from equilibrium data and vice versa? Can the effect of element transmutation on mechanical behavior be predicted? Remarkably, such extrapolations are possible in principle for systems governed by stochastic differential equations, thanks to a set of exact relations betw...

Significance How does the swimming motion of bacteria affect the mixing of passive scalars in chaotic flows? Answers to this question can lead to a better understanding of the formation of algal blooms in oceans and lakes, as well as potentially useful applications in vaccine and biofuel production. Our experiments show that the presence of swimmin...

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 centimet...

Viscoelastic fluids are a common subclass of rheologically complex materials that are encountered in diverse fields from biology to polymer processing. Often the flows of viscoelastic fluids are unstable in situations where ordinary Newtonian fluids are stable, owing to the nonlinear coupling of the elastic and viscous stresses. Perhaps more surpri...

When stressed sufficiently, solid materials yield and deform plastically via reorganization of microscopic constituents. Indeed, it is possible to alter the micro-structure of materials by judicious application of stress, an empirical pro- cess utilized in practice to enhance the mechanical properties of metals. Un- derstanding the interdependence...

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...

Soil creeps imperceptibly but relentlessly downhill, shaping landscapes and the human and ecological communities that live within them. What causes this granular material to ‘flow’ at angles well below repose? The unchallenged dogma is churning of soil by (bio)physical disturbances. Here we experimentally render slow creep dynamics down to micron s...

A fundamental challenge for disordered solids is predicting macroscopic yield from the microscopic arrangements of constituent particles. Yield is accompanied by a sudden and large increase in energy dissipation due to the onset of plastic rearrangements. This suggests that one path to understanding bulk rheology is to map particle configurations t...

The nature of yield in amorphous materials under stress has yet to be fully elucidated. In particular, understanding how microscopic rearrangement gives rise to macroscopic structural and rheological signatures in disordered systems is vital for the prediction and characterization of yield and the study of how memory is stored in disordered materia...

Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of th...

Plain Language Summary When suspended sediment is transported from land to the ocean by river, the water surrounding the sediment particles changes from fresh to salty. This change creates increased interparticle attraction, leading sediment to aggregate and deposit. In contrast to ocean salinity, artificial fertilizers may contain different salts...

Purpose We present a novel perfusion phantom for validation of arterial spin labeled (ASL) perfusion MRI methods and protocols. Methods Impinging jets, driven by a peristaltic pump, were used to achieve perfusion‐like mixing of magnetically labeled inflowing fluid within a perfusion compartment. The phantom was validated by varying pump rates and...

Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of th...

Supplementary data for "Formation of stable aggregates by fluid-assembled solid bridges", PNAS February 18, 2020, 117 (7) 3375-3381

While the dynamics of initiation and cessation of debris flows are complex and transient, one may gain insight by simplifying the boundary conditions to probe the flow resistance of these suspensions to prescribed shear forces; the essence of rheology. For decades, researchers have measured and debated the meaning of rheology from suspensions of de...

Mud forms the foundation of many coastal and tidal environments. Clay suspensions carried downstream from rivers encounter saline waters, which encourages aggregation and sedimentation by reducing electrostatic repulsion among particles. We perform experiments to examine the effects of surface charge on both the rate and style of sedimentation, usi...

Using holographic particle tracking, we report the three-dimensional flow structure organizing the viscoelastic instability in cross-channel flow. Beyond a critical Wi, the advective core flow undergoes an out-of-plane instability marked by the emergence of tertiary flow, resembling that of the toroidal vortices in Taylor-Couette geometry. The out-...

Significance When stressed sufficiently, many solids plastically deform and flow. This plastic deformation induces irreversible structural changes, which are sometimes used in practice to manipulate microstructure of materials to achieve desired mechanical properties. Unfortunately, our limited fundamental understanding of the interdependence of pl...

Soil-mantled hillslopes owe their smooth, convex shape to creep; the slow and persistent, gravity-driven motion of grains on slopes below the angle of repose. Existing models presume that soil creep occurs via mechanical displacement of grains by (bio)physical disturbances. Recent simulations, however, suggest that soil can creep without these dist...

Failure of amorphous materials is characterized by the emergence of dissipation. The connection between particle dynamics, dissipation, and overall material rheology, however, has still not been elucidated. Here, we take a new approach relating trajectories to yielding, using a custom built interfacial stress rheometer, which allows for measurement...

The nature of yield in amorphous materials under stress is yet to be fully elucidated. In particular, understanding how microscopic rearrangement gives rise to macroscopic structural and rheological signatures in disordered systems is vital for the prediction and characterization of yield and the study of how memory is stored in disordered material...

The yield transition of amorphous materials is characterized by a swift increase of energy dissipation. The connection between particle dynamics, dissipation, and overall material rheology, however, has still not been elucidated. Here, we take a new approach relating trajectories to yielding, using a custom built interfacial stress rheometer, which...

An electronic tongue (e-tongue) is a multisensory system usually applied to complex liquid media that uses computational/statistical tools to group information generated by sensing units into recognition patterns, which allow the identification/distinction of samples. Different types of e-tongues have been previously reported, including microfluidi...

When a colloidal suspension is dried, capillary pressure may overwhelm repulsive electrostatic forces, assembling aggregates that are out of thermal equilibrium. This poorly understood process confers cohesive strength to many geological and industrial materials. Here we observe evaporation-driven aggregation of natural and synthesized particulates...

Miniaturized devices capable of active swimming at low Reynolds numbers are of fundamental importance and possess potential biomedical utility. The design of colloidal microswimmers requires not only miniaturizing reconfigurable structures, but also understanding their interactions with media at low Reynolds numbers. We investigate the dynamics of...

The flow of viscoelastic fluids in channels and pipes remains poorly understood, particularly at low Reynolds numbers. Here, we investigate the flow of polymeric solutions in straight channels using pressure measurements and particle tracking. The flow friction factor fη versus flow rate exhibits two regimes: a transitional regime marked by rapid i...

Swarming colonies of the light-responsive bacteria Serratia marcescens grown on agar exhibit robust fluctuating large-scale flows that include arrayed vortices, jets and sinuous streamers. We study the immobilization and quenching of these collective flows when the moving swarm is exposed to intense wide-spectrum light with a substantial ultraviole...

Particle aggregation builds soils, biological structures, and many industrial and pharmaceutical products. Existing theories can explain aggregation in colloidal suspensions that results from interfacial electrostatic forces. When a suspension is dried, however, capillary pressure may overwhelm these forces, creating aggregates that are out of ther...

The vast majority of alluvial deposits have some degree of cohesion, typically due to the presence of clays and/or organic matter. Determining the threshold fluid shear stress necessary to entrain these sediments is essential for predicting erosion rates and morphodynamics of rivers, tidal channels, and coasts. Cohesive sediments present a greater...

Viscoelastic flow past a cylinder is a classic benchmark problem that is not completely understood. Using novel three-dimensional (3D) holographic particle velocimetry, we report three main discoveries of the elastic instability upstream of a single cylinder in viscoelastic channel flow. First, we observe that upstream vortices initiate at the corn...

Propagating interfaces are ubiquitous in nature, underlying instabilities and pattern formation in biology and material science. Physical principles governing interface growth are well understood in passive settings; however, our understanding of interfaces in active systems is still in its infancy. Here, we study the evolution of an active-passive...

Spinal muscular atrophy (SMA) is a neuromuscular disease characterized by degeneration of spinal motor neurons resulting in variable degrees of muscular wasting and weakness. It is caused by a loss-of-function mutation in the survival motor neuron (SMN1) gene. Caenorhabditis elegans mutants lacking SMN recapitulate several aspects of the disease in...

The flow of viscoelastic fluids in channels and pipes remain poorly understood, particularly at low Reynolds numbers. Here, we investigate the flow of polymeric solutions in straight channels using pressure measurements and particle tracking. The law of flow resistance is established by measuring the flow friction factor $f_{\eta}$ versus flow rate...