arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

At least 37 records · Page 2Linked to original sources

arXiv2025

Three-dimensional active turbulence in microswimmer suspensions: simulations and modelling

Active turbulence is a paradigmatic and fascinating example of self-organized motion at large scales occurring in active matter. We employ massive hydrodynamic simulations of suspensions of resolved model microswimmers to tackle the phenomenon in semi-dilute conditions at a mesoscopic level. We measure the kinetic energy spectrum and we detect a $k^{-3}$ power law regime. The velocity distributions are of Lévy type, a distinct difference with inertial turbulence. Furthermore, we propose a reduced order dynamical deterministic model for active turbulence, inspired to shell models for classical turbulence, whose numerical and analytical study confirms the spectrum powerlaw observed in the simulations and reveals hints of a non-Gaussian, intermittent, physics of active turbulence. Direct numerical simulations and modelling also agree in pointing to a phenomenological picture whereby, in the absence of an energy cascade à la Richardson forbidden by the low Reynolds number regime, it is the coupling between fluid velocity gradients and bacterial orientation that gives rise to a multiscale dynamics.

cond-mat.soft↗

arXiv2025

Non-Reciprocal Interactions Reshape Topological Defect Annihilation

We show how non-reciprocal ferromagnetic interactions between neighbouring planar spins in two dimensions, affect the behaviour of topological defects. Non-reciprocity is introduced by weighting the coupling strength of the two-dimensional XY model by an anisotropic kernel. As a consequence, in addition to the topological charge $q$, the actual shape of the defects becomes crucial to faithfully describe their dynamics. Non-reciprocal coupling twists the spin field, selecting specific defect shapes, dramatically altering the pair annihilation process. Defect annihilation can either be enhanced or hindered, depending on the shape of the defects concerned and the degree of non-reciprocity in the system. We introduce a continuous description -- for which the phenomenological coefficients can be explicitly written in terms of the microscopic ones -- that captures the behaviour of the lattice model.

cond-mat.stat-mech↗

arXiv2025

Colloidal Model for Investigating Optimal Efficiency in Weakly Coupled Ratchet Motors

We investigate the transport of superparamagnetic colloidal particles along self-assembled tracks using a periodically applied magnetic field as a model for ratchet-like mechanisms. Through video microscopy and simulations, we examine how factors such as particle size, track roughness, and the shape, intensity, and frequency of the applied potential influence transport efficiency. The findings reveal that processive motion can be achieved without residual attraction, with optimal transport efficiency governed by the combined effects of particle size ratios, actuation frequency, track roughness, and asymmetry in the applied potential. Additionally, we explore alternative strategies, including weak residual attraction and alternating magnetic fields, to further enhance efficiency. These findings provide valuable insights for the development of synthetic micro/nanomotors with potential applications in drug delivery and environmental remediation.

cond-mat.soft↗

arXiv2024

Sedimentation and structure of squirmer suspensions under gravity

The effect of gravity on the collective motion of living microswimmers, such as bacteria and micro-algae, is pivotal to unravel not only bio-convection patterns but also the settling of bacterial biofilms on solid surfaces. In this work, we investigate suspensions of microswimmers under the influence of a gravitational field and hydrodynamics, simulated via dissipative particle dynamics (DPD) coarse-grained model. We first study the collective sedimentation of passive colloids and microswimmers of the puller and pusher types upon increasing the imposed gravitational field and compare with previous results. Once sedimentation occurs, we observe that, as the gravitational field increases, the bottom layer undergoes a transition to an ordered state compatible with a hexagonal crystal. In comparison with passive colloids, both pullers and pushers easily rearrange at the bottom layer to anneal defects. Specifically, pullers are better than pushers in preserving the hexagonal order of the bottom mono-layer at high gravitational fields.

cond-mat.soft↗

arXiv2024

Active droplets controlled by enzymatic reactions

The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple generic model to study the interplay between two enzyme populations and a two-state protein. In one state, the protein forms condensed droplets through attractive interactions, while in the other state, the proteins remain dispersed. Each enzyme catalyzes the production of one of these two protein states only when reactants are in its vicinity. A key feature of our model is the explicit representation of enzyme trajectories, capturing the fluctuations in their local concentrations. The spatially dependent growth rate of droplets naturally arises from the stochastic motion of these explicitly modeled enzymes. Using two complementary numerical methods, (1) Brownian Dynamics simulations, and (2) a hybrid method combining Cahn-Hilliard-Cook diffusion equations with Brownian Dynamics for the enzymes, we investigate how enzyme concentration and dynamics influence the evolution with time, and the steady-state number and size of droplets. Our results show that the concentration and diffusion coefficient of enzymes govern the formation and size-selection of biocondensates.

cond-mat.soft↗

arXiv2024

Curvature induces and enhances transport of spinning colloids through narrow channels

The effect of curvature and how it induces and enhances the transport of colloidal particles driven through narrow channels represent an unexplored research avenue. Here we combine experiments and simulations to investigate the dynamics of magnetically driven colloidal particles confined through a narrow, circular channel. We use an external precessing magnetic field to induce a net torque and spin the particles at a defined angular velocity. Due to the spinning, the particle propulsion emerges from the different hydrodynamic coupling with the inner and outer walls and strongly depends on the curvature. The experimental findings are combined with finite element numerical simulations that predict a positive rotation translation coupling in the mobility matrix. Further, we explore the collective transport of many particles across the curved geometry, making an experimental realization of a driven single file system. With our finding, we elucidate the effect of curvature on the transport of microscopic particles which could be important to understand the complex, yet rich, dynamics of particle systems driven through curved microfluidic channels.

cond-mat.soft↗

arXiv2024

Noise-Induced Phase Separation and Time Reversal Symmetry Breaking in Active Field Theories driven by persistent noise

Within the Landau-Ginzburg picture of phase transitions, scalar field theories develop phase separation because of a spontaneous symmetry-breaking mechanism. This picture works in thermodynamics but also in the dynamics of phase separation. Here we show that scalar non-equilibrium field theories undergo phase separation just because of non-equilibrium fluctuations driven by a persistent noise. The mechanism is similar to what happens in Motility-Induced Phase Separation where persistent motion introduces an effective attractive force. We observe that Noise-Induced Phase Separation occurs in a region of the phase diagram where disordered field configurations would otherwise be stable at equilibrium. Measuring the local entropy production rate to quantify the time-reversal symmetry breaking, we find that such breaking is concentrated on the boundary between the two phases.

cond-mat.stat-mech↗

arXiv2024

Active particles confined in deformable droplets

Active particles under soft confinement such as droplets or vesicles present intriguing phenomena, as collective motion emerges alongside the deformation of the environment. A model is employed to systematically investigate droplet morphology and particle distribution in relation to activity and concentration,revealing that active particles have the capacity to induce enhanced shape fluctuations in the droplet interface with respect to the thermal fluctuations, aligning with recent experimental observations. A rich phase behaviour can be identified with two different mechanism of droplet breakage.

cond-mat.soft↗

arXiv2024

Lattice Boltzmann simulation of deformable fluid-filled bodies: progress and perspectives

With the rapid development of studies involving droplet microfluidics, drug delivery, cell detection, and microparticle synthesis, among others, many scientists have invested significant efforts to model the flow of these fluid-filled bodies. Motivated by the intricate coupling between hydrodynamics and the interactions of fluid-filled bodies, several methods have been developed. The objective of this review is to present a compact foundation of the methods used in the literature in the context of lattice Boltzmann methods. For hydrodynamics, we focus on the lattice-Boltzmann method due to its specific ability to treat time and spatial-dependent boundary conditions and to incorporate new physical models in a computationally efficient way. We split the existing methods into two groups with regard to the interfacial boundary: fluid-structure and fluid-fluid methods. The fluid-structure methods are characterised by the coupling between fluid dynamics and mechanics of the flowing body, often used in applications involving membranes and similar flexible solid boundaries. We further divide fluid-structure-based methods into two subcategories, those which treat the fluid-structure boundary as a continuum medium and those that treat it as a discrete collection of individual springs and particles. Next, we discuss the fluid-fluid methods, particularly useful for the simulations of fluid-fluid interfaces. We focus on models for immiscible droplets and their interaction in a suspending fluid and describe benchmark tests to validate the models for fluid-filled bodies.

cond-mat.soft↗

arXiv2024

Capillary imbibition in lubricant coated channels

Capillary imbibition underpins many processes of fundamental and applied relevance in fluid mechanics. A limitation to the flow is the coupling to the confining solid, which induces friction forces. Our work proposes a general theoretical framework for the modeling of the transport of liquids in lubricant impregnated surfaces. We show that for sufficiently small lubricant viscosity, dissipation entirely occurs in the lubricant layer, resulting in a linear growth of the advancing front. As a result, an external force gives rise to an exponential front growth. This new capacity to control multiphase flows sets new experimental challenges that can be determinant for micro and nanofluidic devices.

physics.flu-dyn↗

arXiv2024

Clogging transition and anomalous transport in driven suspensions in a disordered medium

We study computationally the dynamics of forced, Brownian particles through a disordered system. As the concentration of mobile particles and/or fixed obstacles increase, we characterize the different regimes of flow and address how clogging develops. We show that clogging is preceded by a wide region of anomalous transport, characterized by a power law decay of intermittent bursts. We analyze the velocity distribution of the moving particles and show that this abnormal flow region is characterized by a coexistence between mobile and arrested particles, and their relative populations change smoothly as clogging is approached. The comparison of the regimes of anomalous transport and clogging with the corresponding scenarios of particles pushed through a single bottleneck show qualitatively the same trends highlighting the generality of the transport regimes leading to clogging.

cond-mat.soft↗

arXiv2024

From flocking to glassiness in dense disordered polar Active Matter

Living materials such as biological tissues or bacterial colonies are collections of heterogeneous entities of different sizes, capable of autonomous motion, and often capable of cooperating. Such a degree of complexity brings to collective motion on large scales. However, how the competition between geometrical frustration, autonomous motion, and the tendency to move cooperatively impact large-scale behavior remains an open question. We implement those three ingredients in a model of active matter and show that the system, in forming migratory patterns, can arrange in bands or develop long-range order, depending on the density of the system. We also show that the active material undergoes a reentrant glass transition triggered by the alignment interaction that typically causes only collective migratory motion. Finally, we observe that polar order destroys active phase separation, producing homogeneous, disordered moving configurations.

cond-mat.soft↗

arXiv2024

Discontinuous transition in electrolyte flow through charge-patterned nanochannels

We investigate the flow of an electrolyte through a rigid nanochannel decorated with a surface charge pattern. Employing lattice Boltzmann and dissipative particle dynamics methods, as well as analytical theory, we show that the electro-hydrodynamic coupling leads to two distinct flow regimes. The accompanying discontinuous transition between slow, ionic, and fast, Poiseuille flows is observed at intermediate ion concentrations, channel widths, and electrostatic coupling strengths. These findings indicate routes to design nanochannels containing a typical aqueous electrolyte that exhibit a digital on/off flux response, which could be useful for nanofluidics and ionotronic applications.

cond-mat.soft↗

arXiv2023

Activity-driven emulsification of phase-separating binary mixtures

Systems containing active components are intrinsically out of equilibrium, while binary mixtures reach their equilibrium configuration when complete phase separation is achieved. Active particles are found to stabilise non-equilibrium morphologies in phase separating binary mixtures by arresting coarsening by exerting active pressure that competes with surface tension driving forces. For moderate activities, an emulsion morphology is stabilised, where the droplet size is well-defined and controlled by activity. Conversely, the ability of active particles to drive phase-separated mixtures away from their equilibrium configuration is shown. A rich co-assembly behaviour is shown due to the competing energy scales involved in the system.

cond-mat.soft↗

arXiv2023

Hydrodynamics is Needed to Explain Propulsion in Chemophoretic Colloidal Rafts

Active particles driven by a chemical reaction are the subject of intense research to date due to their rich physics, being intrinsically far from equilibrium, and their multiple technological applications. Recent attention in the field is now shifting towards exploring the fascinating dynamics of mixture of active and passive systems. Here we realize active colloidal rafts, composed of a single catalytic particle encircled by several shells of passive microspheres assembled via light activated, chemophoretic flow. We show that considering only diffusiophoresis can explain the cluster kinetics but not the cluster propulsion behavior. Thus, using the Lorenz reciprocal theorem, we show that propulsion emerges by considering hydrodynamics via the diffusioosmotic answer of the substrate to the generated chemophoretic flow. While diffusioosmotic flows are often relegate to a secondary role, our work demonstrates their importance to understand the rich physics of active catalytic systems.

cond-mat.soft↗

arXiv2023

Minimal numerical ingredients describe chemical microswimmers's 3D motion

The underlying mechanisms and physics of catalytic Janus microswimmers is highly complex, requiring details of the associated phoretic fields and the physiochemical properties of catalyst, particle, boundaries, and the fuel used. Therefore, developing a minimal (and more general) model capable of capturing the overall dynamics of these autonomous particles is highly desirable. In the presented work, we demonstrate that a coarse-grained dissipative particle-hydrodynamics model is capable of describing the behaviour of various chemical microswimmer systems. Specifically, we show how a competing balance between hydrodynamic interactions experienced by a squirmer in the presence of a substrate, gravity, and mass and shape asymmetries can reproduce a range of dynamics seen in different experimental systems. We hope that our general model will inspire further synthetic work where various modes of swimmer motion can be encoded via shape and mass during fabrication, helping to realise the still outstanding goal of microswimmers capable of complex 3-D behaviour

cond-mat.soft↗

arXiv2023

Coexistence of defect morphologies in three dimensional active nematics

We establish how active stress globally affects the morphology of disclination lines of a three dimensional active nematic liquid crystal under chaotic flow. Thanks to a defect detection algorithm based on the local nematic orientation, we show that activity selects a crossover length scale in between the size of small defect loops and the one of long and tangled defect lines of fractal dimension $2$. This length scale crossover is consistent with the scaling of the average separation between defects as a function of activity. Moreover, on the basis of numerical simulation in a 3D periodic geometry, we show the presence of a network of regular defect loops, contractible onto the $3$-torus, always coexisting with wrapping defect lines. While the length of regular defects scales linearly with the emerging active length scale, it verifies an inverse quadratic dependence for wrapping defects. The shorter the active length scale, the more the defect lines wrap around the periodic boundaries, resulting in extremely long and buckled structures.

cond-mat.soft↗

arXiv2023

Effect of Contact Inhibition Locomotion on confined cellular organization

Experiments performed using micro-patterned one dimensional collision assays have allowed a precise quantitative analysis of the collective manifestation of contact inhibition locomotion (CIL) wherein, individual migrating cells reorient their direction of motion when they come in contact with other cells. Inspired by these experiments, we present a discrete, minimal 1D Active spin model that mimics the CIL interaction between cells in one dimensional channels. We analyze the emergent collective behaviour of migrating cells in such confined geometries, as well as the sensitivity of the emergent patterns to driving forces that couple to cell motion. In the absence of vacancies, akin to dense cell packing, the translation dynamics is arrested and the model reduces to an equilibrium spin model which can be solved exactly. In the presence of vacancies, the interplay of activity-driven translation, cell polarity switching, and CIL results in an exponential steady cluster size distribution. We define a dimensionless Péclet number Q - the ratio of the translation rate and directional switching rate of particles in the absence of CIL. While the average cluster size increases monotonically as a function of Q, it exhibits a non-monotonic dependence on CIL strength, when the Q is sufficiently high. In the high Q limit, an analytical form of average cluster size can be obtained approximately by effectively mapping the system to an equivalent equilibrium process involving clusters of different sizes wherein the cluster size distribution is obtained by minimizing an effective Helmholtz free energy for the system. The resultant prediction of exponential dependence on CIL strength of the average cluster size and Q^{1/2} dependence of the average cluster size is borne out to reasonable accuracy as long as the CIL strength is not very large.

physics.bio-ph↗