arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

At least 91 records · Page 5Linked to original sources

arXiv2018

Full phase diagram of active Brownian disks: from melting to motility-induced phase separation

We establish the complete phase diagram of self-propelled hard disks in two spatial dimensions from the analysis of the equation of state and the statistics of local order parameters. The equilibrium melting scenario is maintained at small activities, with coexistence between active liquid and hexatic order, followed by a proper hexatic phase and a further transition to an active solid. As activity increases, the emergence of hexatic and solid order is shifted towards higher densities. Above a critical activity and for a certain range of packing fractions, the system undergoes MIPS and demixes into low and high density phases; the latter can be either disordered (liquid) or ordered (hexatic or solid) depending on activity.

cond-mat.stat-mech↗

arXiv2018

Stabilization of overlapping biofilaments by passive crosslinkers

The formation, maintenance and reorganization of the cytoskeletal filament network is essential for a number of cellular processes. While the crucial role played by active forces generated by motor proteins has been studied extensively, only recently the importance of passive forces exerted by non-enzymatic crosslinkers has been realized. The interplay between active and passive proteins manifests itself, e.g., during cell division, where the spindle structure formed by overlapping microtubules is subject to both active sliding forces generated by crosslinking motor proteins and passive forces exerted by passive crosslinkers, such as Ase1 and PRC1. We propose a minimal model to describe the stability behaviour of a pair of anti-parallel overlapping microtubules resulting from the competition between active motors and passive crosslinkers. We obtain the stability diagram which characterizes the formation of stable overlap of the MT pair, identify the controlling biological parameters which determine their stability, and study the impact of mutual interactions between motors and passive crosslinkers on the stability of these overlapping filaments.

physics.bio-ph↗

arXiv2018

Velocity alignment promotes motility-induced phase separation

We study the phase behavior of polar Active Brownian Particles moving in two-spatial dimensions and interacting through volume exclusion and velocity alignment. We combine particle-based simulations of the microscopic model with a simple mean-field kinetic model to understand the impact of velocity alignment on the motility-induced phase separation of self-propelled disks. We show that, as the alignment strength is increased, approaching the onset of collective motion from below, orientational correlations grow, rendering the diffusive reorientation dynamics slower. As a consequence, the tendency of particles to aggregate into isotropic clusters is enhanced, favoring the complete de-mixing of the system into a low and high-density phase.

cond-mat.soft↗

arXiv2018

Cell Dynamic Simulations of Diblock Copolymer/Colloid Systems

The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer composition but also on the size, shape, and surface properties of the colloids. The dynamics of this kind of systems using a hybrid mesoscopic approach has been studied in this work. A continuum description for the polymer is used, while colloids are individually resolved. The method allows for a variable preference of the colloids, which can have different sizes, to the different components the block copolymer is made of. The impact that the nanoparticle preference for either, both, or none of the blocks has on the collective properties of nanoparticle-block copolymer composites can be analyzed. Several experimental results are reproduced covering colloid-induced phase transition, particles' placement within the matrix, and the role of incompatibilities between colloids and monomers.

cond-mat.soft↗

arXiv2018

Mesoscopic electrohydrodynamic simulations of binary colloidal suspensions

A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a BGK collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solvent-solvent and solvent-solute interactions are implemented using a pseudopotential model. The Nernst-Planck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the link-flux method. The colloids are resolved on the lattice and coupled to the hydrodynamics and electrokinetics through appropriate boundary conditions. We present the first full integration of these three elements. The model is validated by comparing with known analytic solutions of ionic distributions at fluid interfaces, dielectric droplet deformations and the electrophoretic mobility of colloidal suspensions. Its possibilities are explored by considering various physical systems, such as breakup of charged and neutral droplets and colloidal dynamics at either planar or spherical fluid interfaces.

cond-mat.soft↗

arXiv2018

Collective motion of Active Brownian Particles with polar alignment

We present a comprehensive computational study of the collective behavior emerging from the competition between self-propulsion, excluded volume interactions and velocity-alignment in a two-dimensionnal model of active particles. We consider an extension of the Active Brownian Particles model where the self-propulsion direction of the particles aligns with the one of their neighbors. We analyze the onset of collective motion (flocking) in a low-density regime (10% surface area) and show that it is mainly controlled by the strength of velocity-alignment interactions: the competition between self-propulsion and crowding effects plays a minor role in the emergence of flocking. However, above the flocking threshold, the system presents a richer pattern formation scenario than analogous models without alignment interactions (Active Brownian Particles) or excluded volume effects (Vicsek-like models). Depending on the parameter regime, the structure of the system is characterized by either a broad distribution of finite-sized polar clusters or the presence of an amorphous, highly fluctuating, large-scale traveling structure which can take a lane-like or band-like form (and usually a hybrid structure which is halfway in between both). We establish a phase diagram that summarizes collective behavior of polar Active Brownian Particles and propose a generic mechanism to describe the complexity of the large-scale structures observed in systems of repulsive self-propelled particles.

cond-mat.soft↗

arXiv2017

A Unified Description of Colloidal Thermophoresis

We use the dynamic length and time scale separation in suspensions to formulate a general description of colloidal thermophoresis. Our approach allows an unambiguous definition of separate contributions to the colloidal flux and clarifies the physical mechanisms behind non-equilibrium motion of colloids. In particular, we derive an expression for the interfacial force density that drives single-particle thermophoresis in non-ideal fluids. The issuing relations for the transport coefficients explicitly show that interfacial thermophoresis has a hydrodynamic character that cannot be explained by a purely thermodynamic consideration. Our treatment generalises the results from other existing approaches, giving them a clear interpretation within the framework of non-equilibrium thermodynamics.

cond-mat.soft↗

arXiv2017

Emergent Hydrodynamic Bound States Between Magnetically Powered Micropropellers

Hydrodynamic interactions (HIs), namely solvent mediated long-range interactions between dispersed particles, play a crucial role in the assembly and dynamics of many active systems, from swimming bacteria to swarms of propelling microrobots. Here we experimentally demonstrate the emergence of long-living hydrodynamic bound states between model micro-swimmers at low Reynolds number. A rotating magnetic field forces colloidal hematite microparticles to translate at a constant and frequency-tunable speed close to a bounding plane in a viscous fluid. At high driving frequency, HIs dominate over magnetic dipolar ones, and close propelling particles couple into bound states by adjusting their translational speed in order to optimize the transport of the pair. The physical system is described by considering the HIs with the boundary surface and the effect of gravity, providing an excellent agreement with the experimental data for all the range of parameters explored. Moreover, we show that in dense suspensions, these bound states can be extended to onedimensional arrays of particles assembled by the sole HIs. Our results manifest the importance of the boundary surface in the interaction and dynamics of confined propelling microswimmers.

cond-mat.soft↗

arXiv2017

Bidirectional motion of filaments: Role of motor proteins and passive cross linkers

In eukaryotic cells, motor proteins (MP) bind to cytoskeletal filaments and move along them in a directed manner generating active stresses. During cell division a spindle structure of overlapping antiparallel microtubules (MT) form whose stability and dynamics under the influence of MPs has been studied extensively. Although passive cross linkers (PCL) were known to provide structural stability to filamentous network, consequences of the interplay between ATP dependent active forces of MPs and passive entropic forces of PCLs on MT overlap remains largely unexplored. Here, we formulate and characterize a model to study this, using linear stability analysis and numerical integration. In presence of PCLs, we find dynamic phase transitions with changing activity exhibiting regimes of stable partial overlap with or without oscillations, instability towards complete overlap, and stable limit cycle oscillations that emerge via a supercritical Hopf bifurcation characterized by an oscillation frequency determined by the MP and PCL parameters. We show that the overlap dynamics and stability depend crucially on whether both the MTs of overlapping pair are movable or one is immobilized, having potential implications for in vivo and in vitro studies.

physics.bio-ph↗

arXiv2017

Active Brownian Equation of State: Metastability and Phase Coexistence

As a result of the competition between self-propulsion and excluded volume interactions, purely repulsive self-propelled spherical particles undergo a motility-induced phase separation (MIPS). We carry out a systematic computational study, considering several interaction potentials, systems confined by hard walls or with periodic boundary conditions, and different initial protocols. This approach allows us to identify that, despite its non-equilibrium nature, the equations of state of Active Brownian Particles (ABP) across MIPS verify the characteristic properties of first-order liquid-gas phase transitions, meaning, equality of pressure of the coexisting phases once a nucleation barrier has been overcome and, in the opposite case, hysteresis around the transition as long as the system remains in the metastable region. Our results show that the equations of state of ABPs quantitatively account for their phase behaviour, providing a firm basis to describe MIPS as an equilibrium-like phase transition.

cond-mat.soft↗

arXiv2016

Programmable Active Janus Droplets Driven by Water/Alcohol Phase Separation

We report the existence of self-propelled Janus droplets driven by phase separation, which are able to deliver cargo in a programmable manner. The self-propelling droplets are initially formed by a water/ethanol mixture in a squalane/monoolein solution, and evolve in up to three stages depending on ethanol concentration. In the first stage, the droplet propulsion is generated by Marangoni flow originating from the solubilization of ethanol in the oily phase. During this process the droplets absorb surfactant molecules; in combination with the continuous loss of ethanol this leads to a phase separation of the water/ethanol/monoolein mixture and the formation of Janus droplets, i.e. a water-rich droplet connected to an ethanol-rich droplet that is able to deliver cargo. We characterize the different evolution stages of self-propulsion by the flow field around the droplet that evolves from a weak pusher, over a neutral swimmer, to a dimer of neutral swimmers. Finally, we utilize this active system to deliver DNA as a cargo. Tuning the delay time before phase separation, by varying the chemical composition of the droplets, several different cargo delivery processes can be programmed.

cond-mat.soft↗

arXiv2016

Emergent structures and dynamics of cell colonies by contact inhibition of locomotion

Cells in tissues can organize into a broad spectrum of structures according to their function. Drastic changes of organization, such as epithelial-mesenchymal transitions or the formation of spheroidal aggregates, are often associated either to tissue morphogenesis or to cancer progression. Here, we study the organization of cell colonies by means of simulations of self-propelled particles with generic cell-like interactions. The interplay between cell softness, cell-cell adhesion, and contact inhibition of locomotion (CIL) yields structures and collective dynamics observed in several existing tissue phenotypes. These include regular distributions of cells, dynamic cell clusters, gel-like networks, collectively migrating monolayers, and 3D aggregates. We give analytical predictions for transitions between noncohesive, cohesive, and 3D cell arrangements. We explicitly show how CIL yields an effective repulsion that promotes cell dispersal, thereby hindering the formation of cohesive tissues. Yet, in continuous monolayers, CIL leads to collective cell motion, ensures tensile intercellular stresses, and opposes cell extrusion. Thus, our work highlights the prominent role of CIL in determining the emergent structures and dynamics of cell colonies.

physics.bio-ph↗

arXiv2016

Morphology of clusters of attractive dry and wet self-propelled spherical particle suspensions

In order to asses the effect of hydrodynamics in the assembly of active attractive spheres, we simulate a semi-dilute suspension of attractive self-propelled spherical particles in a quasi two dimensional geometry comparing the case with and without hydrodynamics interactions. To start with, independently on the presence of hydrodynamics, we observe that depending on the ratio between attraction and propulsion, particles either coarsen or aggregate forming finite-size clusters. Focusing on the clustering regime, we characterize two different clusters parameters, i.e. their morphology and orientational order, and compare the case when active particles behave either as pushers or pullers (always in the regime where inter-particles attractions competes with self-propulsion). Studying cluster phases for squirmers with respect to those obtained for active Brownian disks (indicated as ABP), we have shown that hydrodynamics alone can sustain a cluster phase of active swimmers (pullers), while ABP form cluster phases due to the competition between attraction and self propulsion. The structural properties of the cluster phases of squirmers and ABP are similar, although squirmers show sensitivity to active stresses. Active Brownian disks resemble weakly pusher squirmer suspensions in terms of cluster size distribution, structure of the radius of gyration on cluster size and degree of cluster polarity.

cond-mat.soft↗

arXiv2016

Spontaneous aggregation and global polar ordering in squirmer suspensions

We have developed numerical simulations of three dimensional suspensions of active particles to characterize the capabilities of the hydrodynamic stresses induced by active swimmers to promote global order and emergent structures in active suspensions. We have considered squirmer suspensions embedded in a fluid modeled under a Lattice Boltzmann scheme. We have found that active stresses play a central role to decorrelate the collective motion of squirmers and that contractile squirmers develop significant aggregates.

cond-mat.soft↗

arXiv2016

Synchronization in dynamical networks of locally coupled self-propelled oscillators

Systems of mobile physical entities exchanging information with their neighborhood can be found in many different situations. The understanding of their emergent cooperative behaviour has become an important issue across disciplines, requiring a general conceptual framework in order to harvest the potential of these systems. We study the synchronization of coupled oscillators in time-evolving networks defined by the positions of self-propelled agents interacting in real space. In order to understand the impact of mobility in the synchronization process on general grounds, we introduce a simple model of self-propelled hard disks performing persistent random walks in 2$d$ space and carrying an internal Kuramoto phase oscillator. For non-interacting particles, self-propulsion accelerates synchronization. The competition between agent mobility and excluded volume interactions gives rise to a richer scenario, leading to an optimal self-propulsion speed. We identify two extreme dynamic regimes where synchronization can be understood from theoretical considerations. A systematic analysis of our model quantifies the departure from the latter ideal situations and characterizes the different mechanisms leading the evolution of the system. We show that the synchronization of locally coupled mobile oscillators generically proceeds through coarsening verifying dynamic scaling and sharing strong similarities with the phase ordering dynamics of the 2$d$ XY model following a quench. Our results shed light into the generic mechanisms leading the synchronization of mobile agents, providing a efficient way to understand more complex or specific situations involving time-dependent networks where synchronization, mobility and excluded volume are at play.

cond-mat.soft↗

arXiv2016

Entropically-induced asymmetric passage times of charged tracers across corrugated channels

We analyze the diffusion of charged and neutral tracers suspended in an electrolyte embedded in a channel of varying cross-section. Making use of systematic approximations, the diffusion equation governing the motion of tracers is mapped into an effective $1D$ equation describing the dynamics along the longitudinal axis of the channel where its varying-section is encoded as an effective entropic potential. This simplified approach allows us to characterize tracer diffusion under generic confinement by measuring their mean first passage time (MFPT). In particular, we show that the interplay between geometrical confinement and electrostatic interactions strongly affect the MFTP of tracers across corrugated channels hence leading to alternative means to control tracers translocation across charged pores. Finally, our results show that the MFPTs of a charged tracer in opposite directions along an asymmetric channel may differ. We expect our results to be relevant for biological as well synthetic devices whose dynamics is controlled by the detection of diluted tracers.

cond-mat.soft↗

arXiv2016

Colloidal Microworms Propelling via a Cooperative Hydrodynamic Conveyor Belt

We study propulsion arising from microscopic colloidal rotors dynamically assembled and driven in a viscous fluid upon application of an elliptically polarized rotating magnetic field. Close to a confining plate, the motion of this self-assembled microscopic worm results from the cooperative flow generated by the spinning particles which act as a hydrodynamic "conveyor belt." Chains of rotors propel faster than individual ones, until reaching a saturation speed at distances where induced-flow additivity vanishes. By combining experiments and theoretical arguments, we elucidate the mechanism of motion and fully characterize the propulsion speed in terms of the field parameters.

cond-mat.soft↗

arXiv2015

Clustering and pattern formation in chemorepulsive active colloids

We demonstrate that migration away from self-produced chemicals (chemorepulsion) generates a generic route to clustering and pattern formation among self-propelled colloids. The clustering instability can be caused either by anisotropic chemical production, or by a delayed orientational response to changes of the chemical environment. In each case, chemorepulsion creates clusters of a self-limiting area which grows linearly with self-propulsion speed. This agrees with recent observations of dynamic clusters in Janus colloids (albeit not yet known to be chemorepulsive). More generally, our results could inform design principles for the self-assembly of chemorepulsive synthetic swimmers and/or bacteria into nonequilibrium patterns.

cond-mat.soft↗