arXiv subjects

Paulo E. Arratia

Publications and source records attributed to Paulo E. Arratia.

At least 19 recordsLinked to original sources

arXiv2026

Lagrangian dynamics unveil polymer conformation in viscoelastic flows

The complex flow behavior of viscoelastic fluids emerges from a feedback between fluid stress and the out-of-equilibrium conformational dynamics of their constituent polymer chains. While constitutive models can predict flow and stress fields in simple geometries, a fundamental understanding of the mechanisms regulating viscoelastic flows with mixed kinematics and non-trivial polymer dynamics remains elusive. Quantifying the history-dependent conformation of polymer chains in flow is essential to resolve these complex systems. To address this knowledge gap, we employ direct Lagrangian tracking of individual DNA molecules to reveal their conformational dynamics in microfluidic viscoelastic flows for different polymer contour lengths and concentrations. Comparing the measured molecular extension and orientation reveals discrepancies with canonical constitutive models, which do not fully capture the transient dynamics. Our measurements show a distinct anisotropy in polymer relaxation and shape, which couple the polymer's rotation and extension through hydrodynamic drag, regulating their Lagrangian mechanics. These findings emphasize the importance of Lagrangian polymer history and the need to account for non-trivial intra-molecular mechanics to improve constitutive descriptions of viscoelastic flows.

physics.flu-dyn↗

arXiv2026

Geomimicry: Emergent Dynamics in Earth-Mediated Complex Materials

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.

cond-mat.soft↗

arXiv2026

Emergence of Purely Elasto-Plastic Turbulence in Shear Flows

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.

physics.flu-dyn↗

arXiv2025

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

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 non-equilibrium 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 novel 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 non-equilibrium 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.

cs.LG↗

arXiv2025

An Alternative Scaling for Roughness Transitions in Turbulent Flows: The Role of the Internal Boundary Layer

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.

physics.flu-dyn↗

arXiv2025

Quantification of Flagellar Gait Changes with Combined Shape Mode Analysis and Swimming Simulations

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.

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arXiv2024

Enhancement of bacterial rheotaxis in non-Newtonian fluids

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.

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arXiv2024

Origins of complexity in the rheology of Soft Earth suspensions

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.

cond-mat.soft↗

arXiv2024

The Equation of Motion for Taut-Line Buzzers

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.

cond-mat.soft↗

arXiv2024

Enhancing Transport Barriers with Swimming Microorganisms in Chaotic Flows

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.

physics.flu-dyn↗

arXiv2024

Athermal granular creep in a quenched sandpile

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.

cond-mat.soft↗

arXiv2024

Effect of fluid elasticity on the emergence of oscillations in an active elastic filament

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.

physics.flu-dyn↗

arXiv2023

Sedimentation dynamics of passive particles in dilute bacterial suspensions: emergence of bioconvection

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.

physics.flu-dyn↗

arXiv2023

Exploring the Relationship Between Softness and Excess Entropy in Glass-forming Systems

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.

cond-mat.soft↗

arXiv2022

Understanding the rheology of kaolinite clay suspensions using Bayesian inference

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 flow curves exhibit both yield stress and rheological hysteresis behaviors for various kaolinite volume fractions ($ϕ_k$). Further understanding of these behaviors requires fitting to existing constitutive models, which is challenging due to numerous fitting parameters. To this end, we employ a Bayesian inference method, Markov chain Monte Carlo (MCMC), to fit the experimental flow curves to a microstructural viscoelastic model. The method allows us to estimate the rheological properties of the clay suspensions, such as viscosity, yield stress, and relaxation time scales. The comparison of the inherent relaxation time scales suggests that kaolinite clay suspensions are strongly viscoelastic and weakly thixotropic at relatively low $ϕ_k$, while being almost inelastic and purely thixotropic at high $ϕ_k$. Overall, our results provide a framework for predictive model fitting to elucidate the rheological behaviors of natural materials and other structured fluids.

cond-mat.soft↗

arXiv2022

Life in Complex Fluids: Swimming in Polymers

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 viscoelasticity and shear-rate dependent viscosity. The successful interaction between these microorganisms and their fluid environment is critical to the function of many biological processes including human reproduction, ecosystem dynamics, and the spread of disease \& infection. This interaction is often nonlinear and can lead to many unexpected behavior. Here, I will discuss developments in characterizing, modeling, and understanding the swimming behavior of model microorganism in viscoelastic and shear-thinning fluids. Three main microorganisms will be explored: (i) the nematode \textit{C. elegans}, an undulatory swimmer; (ii) the green algae \textit{C. reinhardtii}, a puller swimmer; and (iii) the bacterium \textit{E. coli}, a pusher swimmer. Investigation with artificial particles/swimmers will also be discussed; such studies are helpful in decoupling the biology from hydrodynamic effects. We will explore the interactions between these swimmers' gaits, geometry, and actuation and fluid rheological behavior using mostly experiments, and discuss these results relative to numerical and analytical predictions.

physics.flu-dyn↗

arXiv2022

Phase-separation during sedimentation of dilute bacterial suspensions

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 front. We find that the bacteria front behave diffusive at short times, whereas at long times decays linearly. The sedimentation speed of passive particles decays at a constant speed and decreases as bacteria concentration ($ϕ_b$) is increased. As $ϕ_b$ is increased further, the sedimentation speed becomes independent of $ϕ_b$. The timescales of the bacteria front is associated with the particle settling speeds. Remarkably, all experiments collapse onto a single master line by using the bacteria front timescale. A phenomenological model is proposed that captures the sedimentation of passive particles in active fluids.

cond-mat.soft↗

arXiv2022

Mixing in chaotic flows with swimming bacteria

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).

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