arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

At least 19 recordsLinked to original sources

arXiv2026

Beyond the Markovian limit: Exact solutions for active motion in a power-law viscoelastic bath

Active particles from bacteria to synthetic microswimmers often navigate viscoelastic media with complex relaxation dynamics. The classical active Brownian model that assumes instantaneous friction is clearly not applicable to describe such motility, while the non-Markovian processes combined with viscoelasticity are relatively unexplored. Here, we develop an analytical theory for an active particle in a power-law viscoelastic medium by solving coupled non-Markovian generalized Langevin equations for translational and rotational degrees of freedom. The viscoelastic memory results in novel phenomena such as fractional short-time transport, enhanced long-time persistence, and de-correlation of the instantaneous force and the swimmer orientation. We demonstrate that the memory kernel controls the anomalous scaling exponents, while the activity determines the crossover between sub-diffusive, ballistic and diffusive regimes. Our work provides a framework for theoretical description of biological and synthetic micro swimmers in complex biological and polymeric environments.

cond-mat.soft↗

arXiv2026

Chiral Dynamics of an Intruder across Dilute and Hydrodynamic Regimes

We introduce and simulate an analytically tractable model for an intruder of arbitrary shape in a nonequilibrium bath, with chirality originating from the bath, the intruder, or their coupling. In the dilute regime, a Langevin description derived from a Boltzmann-Lorentz equation shows how intruder geometry governs ratchet effects and odd response. In the dense regime, the dynamics of the intruder are instead governed by the hydrodynamic modes of the bath and edge currents, which are described by a Stokes equation including a chiral torque density. Our results link shape to chiral transport and show that odd response arises from distinct mechanisms in the dilute and dense limits.

cond-mat.stat-mech↗

arXiv2026

Kinetic and Hydrodynamic Theories of Chiral Intruder Dynamics in Nonequilibrium Baths

We study the chiral dynamics of an intruder immersed in a nonequilibrium bath in two complementary limits: the dilute kinetic regime and the dense hydrodynamic regime. In the dilute limit, starting from a Boltzmann-Lorentz description, we derive an effective Langevin equation whose coefficients are given explicitly by geometry-dependent boundary integrals. This formulation separates the effects of intruder-shape chirality from those of chiral intruder-bath interactions. We find that the chiral interactions generate an odd response and a torque, whereas the chirality of the intruder leads to a ratchet effect. We also show that fluctuation-dissipation-like relations exist and that certain symmetry-allowed couplings vanish in the dilute regime. In the dense regime, we argue that intruder dynamics are governed primarily by bath hydrodynamics and torque-density-driven edge currents not captured by the previous framework. These currents can generate both an antisymmetric drag and a curvature-induced torque, leading to an antisymmetric response when inertia is accounted for. Taken together, these results provide a step toward understanding the mechanisms governing the chiral dynamics of an intruder in a nonequilibrium bath across different scales.

cond-mat.stat-mech↗

arXiv2026

Topological delocalisation of confined 3D active nematics

Defect lines in 3D active nematic systems are intriguing topological singularities whose out-of-equilibrium dynamics remain elusive in confined settings. Here, we numerically study 3D active nematics confined within closed cylinders to elucidate the roles of geometry and activity. We reveal a competition between passive elasticity, which causes localisation of defects near edges, and activity, which endows defects with motility and gives rise to disorderly, delocalised dynamics. Varying boundary curvature, activity strength, and cylinder radius reveals a state space of static and dynamic localisation states, including handle-like configurations and chaotic motion bounded within the cylinder endcap. As activity is tuned to induce delocalisation, we identify phase transition signatures, including pronounced fluctuations and an emergent power law scaling of defect number and average defect length. We find that these scaling properties are strongly altered by confinement: unlike in bulk systems where activity governs length distributions, confinement tunes an activity-independent characteristic length, with an exponent reminiscent of self-avoiding confined polymers. These results establish confinement of inhomogeneous curvature as a versatile mechanism for controlling active topological dynamics.

cond-mat.soft↗

arXiv2026

Universal transport of active colloids with sensory delay in motility landscapes

We experimentally, numerically and analytically explore the diffusive transport of active colloidal particles with sensory delay, navigating motility landscapes in which the self-propulsion speed depends on space. We show how the transport properties can be obtained by replacing the space dependence of the self-propulsion speed by a dynamical stochastic switching process in the absence of delay, and extend the theory for systems with finite delayed responses. We obtain analytical results for the mean square displacement and the effective diffusion coefficient which accurately predict experimental measurements and numerical simulations across multiple scales. We show how, within the regime of validity of the delay-extended theory, density patterns and effective diffusion obey universal scaling forms. Our work provides minimal framework describing the transport properties of active swimmers with internal adaptation dynamics in motility landscapes.

cond-mat.stat-mech↗

arXiv2026

Hierarchical Bayesian calibration of mesoscopic models for ultrasound contrast agents from force spectroscopy data

Ultrasound-guided drug and gene delivery (USDG) is a promising non-invasive approach for targeted therapeutic applications. Mechanical properties of encapsulated microbubbles (EMBs), which serve as contrast agents, strongly affect their specific interactions with ultrasound and are thus critical to the success and efficiency of USDG. Accurate calibration of high-fidelity particle-based models of EMB capsid mechanics is computationally challenging because direct Bayesian inference with dissipative particle dynamics (DPD) is prohibitively expensive. We employ a surrogate-accelerated Bayesian calibration workflow that combines deep neural network (DNN) surrogates, transitional Markov chain Monte Carlo sampling, and hierarchical regularization across EMB diameters. Using this framework, we develop two data-informed DPD models of commercial EMB agents, i.e., Definity and SonoVue, and perform inference of force field parameters based on published compression experiments for Definity and indentation experiments for SonoVue, each spanning three distinct diameters. The inferred posteriors show that key model parameters, such as the stretching stiffness and bending modulus, are consistently constrained by the available data. The presented methodology can be used to derive bespoke, data-informed models for a wide range of ultrasound contrast agents, including encapsulated gas vesicles, EMBs with diverse capsids consisting of lipids, proteins, or polymers, and functionalized with ligands.

cond-mat.soft↗

arXiv2026

Dynamics of O(2) excitations in a non-reciprocal medium

We investigate emergent dynamics due to non-reciprocity in the $\mathcal{O}(2)$ model. The lattice XY model, where non-reciprocity stems from vision cone like couplings, can be described by a continuum description in which non-reciprocity translates into a new term depending on the rotational of the orientation field. We argue that non-reciprocity is akin to activity and we highlight the connection between our hydrodynamic equation and the constant density Toner-Tu framework. The active force advects and reshapes patterns, a generic feature found in many non-reciprocal systems. We show how $1d$ excitations in the non-reciprocal $\mathcal{O}(2)$ model can be described by a generalized Burgers equation, derived from our continuum model. We then extend the results to $2d$ perturbations. As such, we establish the first principles of excitation trajectory control in a non-reciprocal $\mathcal{O}(2)$ medium. Concretely, we explain how tuning the degree of non-reciprocity and the orientation of the background medium impacts the time evolution of excitations. We also showcase how initially different excitations lead to very different dynamical behavior. Non-reciprocity also affects the stability of defect-free excitations with non-zero winding numbers and, unlike in its equilibrium $O(2)$ counterpart, enables the system, above a certain threshold, to relax to its ground state.

cond-mat.stat-mech↗

arXiv2025

Is the active suspension in a complex viscoelastic fluid more chaotic or more ordered?

The habitat of microorganisms is typically complex and viscoelastic. A natural question arises: Do polymers in a suspension of active swimmers enhance chaotic motion or promote orientational order? We address this issue by performing lattice Boltzmann simulations of squirmer suspensions in polymer solutions. At intermediate swimmer volume fractions, comparing to the Newtonian counterpart, polymers enhance polarization by up to a factor of 26 for neutral squirmers and 5 for pullers, thereby notably increasing orientational order. This effect arises from hydrodynamic feedback mechanism: squirmers stretch and align polymers, which in turn reinforce swimmer orientation and enhance polarization via hydrodynamic and steric interactions. The mechanism is validated by a positive correlation between polarization and a defined polymer-swimmer alignment parameter. Our findings establish a framework for understanding collective motion in complex fluids and suggest strategies for controlling active systems via polymer-mediated interactions.

cond-mat.soft↗

arXiv2025

Protocol to evaluate the viscoelastic response of a polymer suspension to an active agent via oscillatory shear rheometry

Microorganisms inhabit viscoelastic environments, where their locomotion can deform polymers and trigger local complex viscoelastic responses. However, a systematic approach to quantify such responses remains lacking. Here, we propose a protocol that maps the shear effect induced by an active agent to oscillatory shear rheometry. The central idea is to establish a correspondence between the mean shear rate generated by swimming and that produced by an oscillating plate. In this mapping, the swimming velocity and active stress are translated into an effective oscillation frequency and strain amplitude. The resulting viscoelastic response can then be evaluated by standard oscillatory rheometry. The protocol is validated using lattice Boltzmann simulations of a squirmer embedded in polymer solutions. Our framework is generic and can be naturally extended to active microrheology, providing a pathway to quantify swimmer-induced viscoelasticity.

cond-mat.soft↗

arXiv2025

Simulating active agents under confinement with Dissipative Particles (hydro)Dynamics

We study active agents embedded in bulk or in confinement explicitly considering hydrodynamics and simulating the swimmers via an implementation inspired by the squirmer model. We develop a Dissipative Particle Dynamics scheme for the solvent. This approach allows us to properly deal not only with hydrodynamics but also with thermal fluctuations. On the other side, this approach enables us to study active agents with complex shapes, ranging from spherical colloids to polymers. To start with, we study a simple spherical colloid. We analyze the features of the velocity fields of the surrounding solvent, when the colloid is a pusher, a puller or a neutral swimmer either in bulk or confined in a cylindrical channel. Next, we characterise its dynamical behaviour by computing the mean square displacement and the long time diffusion when the active colloid is in bulk or in a channel (varying its radius) and analyze the orientation autocorrelation function in the latter case. While the three studied squirmer types are characterised by the same bulk diffusion, the cylindrical confinement considerably modulates the diffusion and the orientation autocorrelation function. Finally, we focus our attention on a more complex shape: an active polymer. We first characterise the structural features computing its radius of gyration when in bulk or in cylindrical confinement, and compare to known results obtained without hydrodynamics. Next, we characterise the dynamical behaviour of the active polymer by computing its mean square displacement and the long time diffusion. On the one hand, both diffusion and radius of gyration decrease due to the hydrodynamic interaction when the system is in bulk. On the other hand, the effect of confinement is to decrease the radius of gyration, disturbing the motion of the polymer and thus reducing its diffusion.

cond-mat.soft↗

arXiv2025

Hydrodynamic Mechanism of Colloidal Propulsion through Momentum Exchange

Propulsion of colloidal particles due to momentum transfer from localized surface reactions is investigated by solving the exact unsteady Stokes equation. We model the effect of surface reactions as either a {\it force dipole} acting on the fluid or a {\it pair force} acting on both the colloid and the fluid. Our analysis reveals that after a single reaction event the colloid's velocity initially decays as $\sim t^{-1/2}$, followed by a long-time tail decay $\sim t^{-5/2}$. This behavior is distinct from the $\sim t^{-3/2}$ decay seen for simple impulsively forced particles, a result of the force-free nature of the reaction mechanism. The velocity and transient dynamics are strongly controlled by the distance of the reaction from the colloid surface. For a colloid subject to periodic reactions, the theory predicts a steady-state velocity that is comparable to experimental results and previous simulations, suggesting that direct momentum transfer is a relevant mechanism for self-propulsion in systems like Janus particles. Finally, our study shows that fluid compressibility is not required for momentum transfer to produce colloidal propulsion.

cond-mat.soft↗

arXiv2025

Sorting of binary active-passive mixtures in designed microchannels

Mixtures of active and passive particles are ubiquitous at the microscale. Many essential microbial processes involve interactions with dead or immotile cells or passive crowders. When passive objects are immersed in active baths, their transport properties are enhanced and can be tuned by controlling active agents' spatial and orientational distribution. Active-passive mixtures provide a platform to explore fundamental questions about the emergent behaviour of passive objects under simultaneous thermal and active noise and a foundation for technological applications in cargo delivery and bioremediation. In this work, we use computational simulations to study an active-passive mixture confined in microchannels designed with funnel-like obstacles that selectively allow the passage of passive particles. Active particles follow overdamped Langevin translational dynamics and run-and-tumble rotational dynamics. We find that adjusting the tumbling rate of active agents and the microchannel geometry leads to a maximum enhancement of the transport properties of the passive particles (diffusion coefficient and advective velocity) that correlates with the highest mixture sorting efficiency and the shortest response time.

cond-mat.soft↗

arXiv2025

Active spin model for cell assemblies on 1D substrates

The experimental use of micropatterned quasi-1D substrates has emerged as an useful experimental tool to study the nature of cell-cell interactions and gain insight on collective behaviour of cell colonies. Inspired by these experiments, we propose an active spin model to investigate the emergent properties of the cell assemblies. The lattice gas model incorporates the interplay of self-propulsion, polarity directional switching, intra-cellular attraction, and contact Inhibition Locomotion (CIL). In the absence of vacancies, which corresponds to a confluent cell packing on the substrate, the model reduces to an equilibrium spin model which can be solved exactly. In the presence of vacancies, the clustering is controlled by a dimensionless Peclet Number, Q - the ratio of magnitude of self-propulsion rate and directional switching rate of particles. In the absence of CIL interactions, we invoke a mapping to Katz-Lebowitz-Spohn(KLS) model to determine an exact analytical form of the cluster size distribution in the limit Q << 1. In the limit of Q >> 1, the cluster size distribution exhibits an universal scaling behaviour (in an approximate sense), such that the distribution function can be expressed as a scaled function of Q, particle density and CIL interaction strength. We characterize the phase behaviour of the system in terms of contour plots of average cluster size. The average cluster size exhibit a non-monotonic dependence on CIL interaction strength, attractive interaction strength, and self-propulsion.

cond-mat.soft↗

arXiv2025

Segregation and cooperation in active colloidal binary mixtures

The complex interactions underlying collective motion in biological systems give rise to emergent behaviours such as flocking, sorting, and cooperative transport. These dynamics often involve species with different motilities coordinating movement to optimize navigation and survival. Synthetic analogues based on active colloids offer a controlled platform to explore such behaviours, yet most experimental realizations remain limited to monodisperse systems or mixtures of passive and active particles. Here, we investigate dense binary mixtures of active Janus colloids with distinct motilities and independently tunable alignment, actuated by AC electric fields. We demonstrate experimentally and numerically that both species form highly dynamic polar clusters, with alignment emerging independently of propulsion speed. In mixed populations, interspecies interactions lead to effective segregation and cooperative motion, including transient enhancement of slower particle motility. Our results reveal how motility contrast and alignment combine to drive self-organization in active mixtures, offering strategies for designing reconfigurable materials with collective functionalities.

cond-mat.soft↗

arXiv2025

Phase separation in a chiral active fluid of inertial self-spinning disks

We show that systematic particle rotations in a fluid composed of disk-shaped spinners can spontaneously lead to phase separation. The phenomenon arises out of a homogeneous and hydrostatic stationary state, due to a pressure feedback mechanism that increases local density fluctuations. We show how this mechanism induces phase separation, coined as Rotation Induced Phase Separation (RIPS), when the active rotation is not properly counterbalanced by translational friction. A low density phase can coexist with a dense chiral liquid due to the imbalance between pressure and stress transmitted through chiral flows when a significant momentum transfer between rotational and translational motion can be sustained. As a consequence, RIPS is expected to appear generically in chiral fluids.

cond-mat.soft↗

arXiv2025

Unravel the rotational and translational behavior of a single squirmer in flexible polymer solutions at different Reynolds numbers

Microorganisms thrive in complex environments and their behavior in fluids holds significant importance for various medical and industrial applications. By conducting Lattice Boltzmann simulations, the transport and rotational properties of a generic squirmer are investigated in solutions embedded with flexible polymers at different Reynolds numbers. The interplay of activity and heterogeneously distributed polymers have profound influences on these properties. Remarkable enhancements of up to three orders of magnitude in the rotational motion, along with apparent decays in self-propelling velocities, are observed for squirmers with non-zero active stresses. These extraordinary phenomena stem from the squirmer-polymer mechanical and hydrodynamic interactions. Specifically, polymer wrapping occurs in front of a pusher, while numerous polymers are absorbed in the rear of a puller. Both mechanisms enhance the rotational motion and simultaneously impede translations through forces and torques arising from direct contacts or asymmetric local flows induced by polymers. The source dipole flow fields generated by a neutral swimmer rapidly advect polymers to the rear, leaving no apparent impacts on its rotational and transport properties. The influences of Reynolds number Re and squirmer-polymer boundary conditions (no-slip and repulsive) on the dynamics are addressed. In short, the no-slip boundary condition results in more profound effects on both rotational and translational properties at Re = 0.8. However, at Re = 0.04, the disparity between the two boundary conditions diminishes due to the heightened fluid viscous drag, which impedes direct contacts between squirmers and polymers. Our results reveal the relevance of system heterogeneity and highlight the essential role of squirmer-polymer mechanical and hydrodynamic interactions in shaping the behavior of swimmers in viscoelastic fluids.

cond-mat.soft↗

arXiv2025

Activity leads to topological phase transition in 2D populations of heterogeneous oscillators

Populations of heterogeneous, noisy oscillators on a two-dimensional lattice display short-range order. Here, we show that if the oscillators are allowed to actively move in space, the system undergoes instead a Berezenskii-Kosterlitz-Thouless transition and exhibits quasi-long-range order. This fundamental result connects two paradigmatic models -- XY and Kuramoto model -- and provides insight on the emergence of order in active systems.

cond-mat.stat-mech↗

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.

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