arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

At least 55 records · Page 3Linked to original sources

arXiv2023

Activity-induced asymmetric dispersion in confined channels with constriction

Microorganisms, such as E.Coli, are known to display upstream behavior and respond rheotactically to shear flows. In particular, E.Coli suspensions have been shown to display strong sensitivity to spatial constrictions, leading to an anomalous densification past the constriction for incoming fluid velocities comparable to the microoganism's self propulsion speed. We introduce a Brownian dynamics model for ellipsoidal self-propelling particles in a confined channel subject to a constriction. The model allows to identify the relevant parameters that characterize the relevant dynamical regimes of the accumulation of the active particles at the constriction, and clarify the mechanisms underlying the experimental observations. We find that particles are trapped in butterfly-like attractors in front of the constriction, which is the origin of the symmetry breaking in the emerging density profiles of active particles passing the constriction. In addition, the probability of trapping and thus the strength of asymmetry is affected by size of the particles and geometry of the channel, as well as the ratio of fluid velocity to propulsion speed.

cond-mat.soft↗

arXiv2022

Onsager reciprocal relations and chemo-mechanical coupling for chemically-active colloids

Similar to cells, bacteria, and other microorganisms, synthetic chemically-active colloids can harness the energy from their environment through a surface chemical reaction and use its energy to self-propel in fluidic environments. In this paper, we study the chemo-mechanical coupling that leads to the self-propulsion of chemically active colloids. The coupling between chemical reactions and momentum transport is a consequence of the Onsager reciprocal relations. They state that the velocity and the surface reaction rate are related to the mechanical and chemical affinities through a symmetric matrix. A consequence of the Onsager reciprocal relations is that, if a chemical reaction drives the motion of the colloid, then an external force generates a reaction rate. Here, we investigate the Onsager reciprocal relations for a spherical active colloid that catalyzes a reversible surface chemical reaction between two species. We solve the relevant transport equations using a perturbation expansion and numerical simulations to demonstrate the validity of the reciprocal relations around the equilibrium. Our results are consistent with previous studies and highlight the key role of solute advection in preserving the symmetry of the Onsager matrix. Finally, we show that the Onsager reciprocal relations break down around a nonequilibrium steady state, which has implications for the thermal fluctuations of the active colloids used in experiments.

cond-mat.soft↗

arXiv2022

Microscopic field theory for structure formation in systems of self-propelled particles with generic torques

We derive a dynamical field theory for self-propelled particles subjected to generic torques and forces by explicitly coarse-graining their microscopic dynamics, described by a many-body Fokker-Planck equation. The model includes both intrinsic torques inducing self-rotation, as well as interparticle torques leading to, for instance, the local alignment of particles' orientations. Within this approach, although the functional form of the pairwise interactions does not need to be specified, one can directly map the parameters of the field theory onto the parameters of particle-based models. We perform a linear stability analysis of the homogeneous solution of the field equations and find both long-wavelength and short-wavelength instabilities. The former signals the emergence of a macroscopic structure, which we associate with motility-induced phase separation, while the second one signals the growth of a finite structure with a characteristic size. Intrinsic torques hinder phase separation, pushing the onset of the long-wavelength instability to higher activities. Further, they generate finite-sized structures with a characteristic size proportional to both the self-propulsion velocity and the inverse of the self-rotation frequency. Our results show that a general mechanism might explain why chirality tends to suppress motility-induced phase separation but instead promotes the formation of non-equilibrium patterns.

cond-mat.soft↗

arXiv2022

From Motility-Induced Phase-Separation to Glassiness in Dense Active Matter

Dense active systems are widespread in nature, examples range from bacterial colonies to biological tissues. Dense clusters of active particles can be obtained by increasing the packing fraction of the system or taking advantage of a peculiar phenomenon named motility-induced phase separation (MIPS). In this work, we explore the phase diagram of a two-dimensional model of active glass and show that disordered active materials develop a rich collective behaviour encompassing both MIPS and glassiness. We find that, although the glassy state is almost indistinguishable from that of equilibrium glasses, the mechanisms leading to its fluidization do not have any equilibrium counterpart. Our results can be rationalized in terms of a crossover between a low-activity regime, where glassy dynamics is controlled by an effective temperature, and a high-activity regime, which drives the system towards MIPS.

cond-mat.soft↗

arXiv2022

Impact of dipole-dipole interactions on motility-induced phase separation

We present a hydrodynamic theory for systems of dipolar active Brownian particles which, in the regime of weak dipolar coupling, predicts the onset of motility-induced phase separation (MIPS), consistent with Brownian dynamics (BD) simulations. The hydrodynamic equations are derived by explicitly coarse-graining the microscopic Langevin dynamics, thus allowing for a quantitative comparison of parameters entering the coarse-grained model and particle-resolved simulations. Performing BD simulations at fixed density, we find that dipolar interactions tend to hinder MIPS, as first reported in [Liao et al., Soft Matter, 2020, 16, 2208]. Here we demonstrate that the theoretical approach indeed captures the suppression of MIPS. Moreover, the analysis of the numerically obtained, angle-dependent correlation functions sheds light into the underlying microscopic mechanisms leading to the destabilization of the homogeneous phase.

cond-mat.soft↗

arXiv2022

Phase behaviour of active particles in block copolymer melts

Block copolymer melts offer a unique template to control the position and alignment of nanoparticles due to their ability to self-assemble into periodic ordered structures. Active Brownian particles are shown to co-assemble with block copolymers leading to emergent organised structures. The block copolymer acts as a soft confinement that can control the self-propulsion of the active Brownian particles, both for interface-segregated and selective nanoparticles. At moderate activity regimes, active Brownian particles can form organised structures such as polarised trains or rotating vortexes. At high activity, the contrast in the polymeric and colloidal time scales can lead to particle swarms with distorted block copolymer morphology, due to the competition between the polymeric self-assembly and the active Brownian self-propulsion.

cond-mat.soft↗

arXiv2022

A lattice Boltzmann model for self-diffusiophoretic particles near and at liquid-liquid interfaces

We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved solvent hydrodynamics and, thanks to its versatility, it can handle important aspects of the multiphysics of the problem, including particle wettability and differential solubility of the product in the two liquid phases. The method is extensively validated in simple numerical experiments, whose outcome is theoretically predictable, and then applied to the study of the behaviour of active particles next to and trapped at interfaces. We show that their motion can be variously steered by tuning relevant control parameters, such as the phoretic mobilities, the contact angle and the product solubility.

cond-mat.soft↗

arXiv2021

Small Obstacle in a Large Polar Flock

We show that arbitrarily large polar flocks are susceptible to the presence of a single small obstacle. In a wide region of parameter space, the obstacle triggers counter-propagating dense bands leading to reversals of the flow. In very large systems, these bands interact yielding a never-ending chaotic dynamics that constitutes a new disordered phase of the system. While most of these results were obtained using simulations of aligning self-propelled particles, we find similar phenomena at the continuous level, not when considering the basic Toner-Tu hydrodynamic theory, but in simulations of truncations of the relevant Boltzmann equation.

cond-mat.soft↗

arXiv2021

Hydrodynamic and geometric effects in the sedimentation of model run-and-tumble bacteria

The sedimentation process in a suspension of bacteria is the result of the competition between gravity and the intrinsic motion of the microorganisms. We perform simulations of run-and-tumble "squirmers" that move in a fluid medium, focusing on the dependence of the non-equilibrium steady state on the bacterial swimming properties. We find that for high enough activity, the density profiles are no longer simple exponentials; we recover the numerical results via the introduction of a local effective temperature, suggesting that the breakdown of the Perrin-like exponential form is a collective effect due to the onset of fluid-mediated dynamic correlations among particles. We show that analogous concepts can fit also the case of shakers, for which we report the first study of this kind. Moreover we provide evidences of scenarios where the solvent hydrodynamics induces nonlocal effects which require the fully three-dimensional dynamics to be taken into account in order to understand sedimentation of active suspensions. Finally, analyzing the statistics of the bacterial swimming orientations, we discuss the emergence of polar order in the steady state sedimentation profiles.

cond-mat.soft↗

arXiv2021

Phase separation of self-propelled disks with ferromagnetic and nematic alignment

We present a comprehensive study of a model system of repulsive self-propelled disks in two dimensions with ferromagnetic and nematic velocity alignment interactions. We characterize the phase behavior of the system as a function of the alignment and self-propulsion strength, featuring orientational order for strong alignment and Motility-Induced Phase Separation (MIPS) at moderate alignment but high enough self-propulsion. We derive a microscopic theory for these systems yielding a close set of hydrodynamic equations from which we perform a linear stability analysis of the homogenous disordered state. This analysis predicts MIPS in the presence of aligning torques. The nature of the continuum theory allows for an explicit quantitative comparison with particle-based simulations, which consistently shows that ferromagnetic alignment fosters phase separation, while nematic alignment does not alter either the nature or the location of the instability responsible for it. In the ferromagnetic case, such behavior is due to an increase of the imbalance of the number of particle collisions along different orientations, giving rise to the self-trapping of particles along their self-propulsion direction. On the contrary, the anisotropy of the pair correlation function, which encodes this self-trapping effect, is not significantly affected by nematic torques. Our work shows the predictive power of such microscopic theories to describe complex active matter systems with different interaction symmetries and sheds light on the impact of velocity-alignment interactions in Motility-Induced Phase Separation.

cond-mat.soft↗

arXiv2021

Collective motion of run-and-tumble particles drives aggregation in one-dimensional systems

Active matter deals with systems whose particles consume energy at the individual level in order to move. To unravel features such as the emergence of collective structures several models have been suggested, such as the on-lattice model of run-and-tumble particles implemented via the Persistent Exclusion Process (PEP). In our work, we study a one dimensional system of run-and-tumble repulsive or attractive particles, both on and off lattice. Additionally, we implement a cluster motility dynamics in the on-lattice case (since in the off-lattice case cluster motility arises from the individual particle dynamics). While we observe important differences between discrete and continuous dynamics, few common features are of particular importance. Increasing particle density drives aggregation across all different systems explored. For non-attractive particles, the effects of particle activity on aggregation are largely independent of the details of the dynamics. On the contrary, once attractive interactions are introduced, the steady state, which is completely determined by the interplay between these and the particles' activity, becomes highly dependent on the details of the dynamics.

cond-mat.soft↗

arXiv2021

Alignment interactions drive structural transitions in biological tissues

Experimental evidence shows that there is a feedback between cell shape and cell motion. How this feedback impacts the collective behavior of dense cell monolayers remains an open question. We investigate the effect of a feedback that tends to align the cell crawling direction with cell elongation in a biological tissue model. We find that the alignment interaction promotes nematic patterns in the fluid phase that eventually undergo a non-equilibrium phase transition into a quasi-hexagonal solid. Meanwhile, highly asymmetric cells do not undergo the liquid-to-solid transition for any value of the alignment coupling. In this regime, the dynamics of cell centers and shape fluctuation show features typical of glassy systems.

cond-mat.soft↗

arXiv2021

Unified analysis of Topological Defects in 2D systems of Active and Passive disks

We provide a comprehensive quantitative analysis of localized and extended topological defects in the steady state of 2D passive and active repulsive Brownian disk systems. We show that, both in and out-of-equilibrium, the passage from the solid to the hexatic is driven by the unbinding of dislocations, in quantitative agreement with the KTHNY singularity. Instead, although disclinations dissociate as soon as the liquid phase appears, extended clusters of defects largely dominate below the solid-hexatic critical line. The latter percolate in the liquid phase very close to the hexatic-liquid transition, both for continuous and discontinuous transitions, in the homogeneous liquid regime. At critical percolation the clusters of defects are fractal with statistical and geometric properties that, within our numerical accuracy, are independent of the activity and compatible with the universality class of uncorrelated critical percolation. We also characterize the spatial organization of different kinds of point-like defects and we show that the disclinations are not free, but rather always very near more complex defect structures. At high activity, the bulk of the dense phase generated by Motility-Induced Phase Separation is characterized by a density of point-like defects, and statistics and morphology of defect clusters, set by the amount of activity and not the packing fraction. Hexatic domains within the dense phase are separated by grain-boundaries along which a finite network of topological defects resides, interrupted by gas bubbles in cavitation. The fractal dimension of this network diminishes for increasing activity. This structure is dynamic in the sense that the defect network allows for an unzipping mechanism that leaves free space for gas bubbles to appear, close, and even be released into the dilute phase.

cond-mat.stat-mech↗

arXiv2021

Clustering of topological defects in two-dimensional melting of active and passive disks

We provide a quantitative analysis of all kinds of topological defects present in 2D passive and active repulsive disk systems. We show that the passage from the solid to the hexatic is driven by the unbinding of dislocations. Instead, although we see dissociation of disclinations as soon as the liquid phase appears, extended clusters of defects largely dominate below the solid-hexatic critical line. The latter percolate at the hexatic-liquid transition in continuous cases or within the coexistence region in discontinuous ones, and their form gets more ramified for increasing activity.

cond-mat.soft↗

arXiv2021

Spontaneous chiralization of polar active colloids

Polar active particles constitute a wide class of synthetic colloids that are able to propel along a preferential direction, given by their polar axis. Here, we demonstrate a generic self-phoretic mechanism that leads to their spontaneous chiralization through a symmetry breaking instability. We find that the transition of an active particle from a polar to a chiral symmetry is characterized by the emergence of active rotation and of circular trajectories. We show that the instability is driven by the advection of a solute that interacts differently with the two portions of the particle surface and it occurs through a supercritical pitchfork bifurcation.

cond-mat.soft↗

arXiv2020

Spontaneous polarization and locomotion of an active particle with surface-mobile enzymes

We examine a mechanism of locomotion of active particles whose surface is uniformly coated with mobile enzymes. The enzymes catalyze a reaction that drives phoretic flows but their homogeneous distribution forbids locomotion by symmetry. We find that the ability of the enzymes to migrate over the surface combined with self-phoresis can lead to a spontaneous symmetry breaking instability whereby the homogeneous distribution of enzymes polarizes and the particle propels. The instability is driven by the advection of enzymes by the phoretic flows and occurs above a critical Péclet number. The transition to polarized motile states occurs via a supercritical or subcritical pitchfork bifurcations, the latter of which enables hysteresis and coexistence of uniform and polarized states.

cond-mat.soft↗

arXiv2020

Extraction of the propulsive speed of catalytic nano- and micro-motors under different motion dynamics

Motion of active particles, such as catalytic micro- and nano-motors, is usually characterized via either dynamic light scattering or optical microscopy. In both cases, speed of particles is obtained from the calculus of the mean square displacement (MSD) and typically, the theoretical formula of the MSD is derived from the motion equations of an active Brownian particle. One of the most commonly reported parameters is the speed of the particle, usually attributed to its propulsion, and is widely used to compare the motion efficiency of catalytic motors. However, it is common to find different methods to compute this parameter, which are not equivalent approximations and do not possess the same physical meaning. Here, we review the standard methods of speed analysis and focus on the errors that arise when analyzing the MSD of self-propelled particles. We analyze the errors from the computation of the instantaneous speed, as well as the propulsive speed and diffusion coefficient through fittings to parabolic equations, and we propose a revised formula for the motion analysis of catalytic particles moving with constant speed that can improve the accuracy and the amount of information obtained from the MSD. Moreover, we emphasize the importance of spotting the presence of different motion dynamics, such as particles with active angular speed or that move under the presence of drift, and how the breaking of ergodicity can completely change the analysis by considering particles with an exponentially decaying speed. In all cases, real data from enzymatically propelled micro-motors and simulations are used to back up the theories. Finally, we propose several analytical approaches and analyze limiting cases that will help to deal with these scenarios while still obtaining accurate results.

cond-mat.soft↗

arXiv2020

Fluctuation-Dissipation Relations in the absence of Detailed Balance: formalism and applications to Active Matter

We present a comprehensive study about the relationship between the way Detailed Balance is broken in non-equilibrium systems and the resulting violations of the Fluctuation-Dissipation Theorem. Starting from stochastic dynamics with both odd and even variables under Time-Reversal, we exploit the relation between entropy production and the breakdown of Detailed Balance to establish general constraints on the non-equilibrium steady-states (NESS), which relate the non-equilibrium character of the dynamics with symmetry properties of the NESS distribution. This provides a direct route to derive extended Fluctuation-Dissipation Relations, expressing the linear response function in terms of NESS correlations. Such framework provides a unified way to understand the departure from equilibrium of active systems and its linear response. We then consider two paradigmatic models of interacting self-propelled particles, namely Active Brownian Particles (ABP) and Active Ornstein-Uhlenbeck Particles (AOUP). We analyze the non-equilibrium character of these systems (also within a Markov and a Chapman-Enskog approximation) and derive extended Fluctuation-Dissipation Relations for them, clarifying which features of these active model systems are genuinely non-equilibrium.

cond-mat.stat-mech↗