arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

At least 73 records · Page 4Linked to original sources

arXiv2020

Novel Catchbond mediated oscillations in motor-microtubule complexes

Generation of mechanical oscillation is ubiquitous to wide variety of intracellular processes. We show that catchbonding behaviour of motor proteins provides a generic mechanism of generating spontaneous oscillations in motor-cytoskeletal filament complexes. We obtain the phase diagram to characterize how this novel catch bond mediated mechanism can give rise to bistability and sustained limit cycle oscillations and results in very distinctive stability behaviour, including bistable and non-linearly stabilised in motor-microtubule complexes in biologically relevant regimes. Hitherto, it was thought that the primary functional role of the biological catchbond was to improve surface adhesion of bacteria and cell when subjected to external forces or flow field. Instead our theoretical study shows that the imprint of this catch bond mediated physical mechanism would have ramifications for whole gamut of intracellular processes ranging from oscillations in mitotic spindle oscillations to activity in muscle fibres.

q-bio.SC↗

arXiv2020

Dynamics and Clogging of colloidal monolayers magnetically driven through an heterogeneous landscape

We combine experiments and numerical simulations to investigate the emergence of clogging in a system of interacting paramagnetic colloidal particles driven against a disordered landscape of larger obstacles. We consider a single aperture in a landscape of immobile silica particles which are irreversibly attached to the substrate. We use an external rotating magnetic field to generate a traveling wave potential which drives the magnetic particles against these obstacles at a constant and frequency tunable speed. Experimentally we find that the particles display an intermittent dynamics with power law distributions at high frequencies. We reproduce these results by using numerical simulations and shows that clogging in our system arises at large frequency, when the particles desynchronize with the moving landscape. Further, we use the model to explore the hidden role of flexibility in the obstacle displacements and the effect of hydrodynamic interactions between the particles. We also consider numerically the situation of a straight wall and investigate the range of parameters where clogging emerges in such case. Our work provides a soft matter test-bed system to investigate the effect of clogging in driven microscale matter.

cond-mat.soft↗

arXiv2020

Propulsion and energetics of a minimal magnetic microswimmer

In this manuscript we describe the realization of a minimal hybrid microswimmer, composed of a ferromagnetic nanorod and a paramagnetic microsphere. The unbounded pair is propelled in water upon application of a swinging magnetic field that induces a periodic relative movement of the two composing elements, where the nanorod rotates and slides on the surface of the paramagnetic sphere. When taken together, the processes of rotation and sliding describe a finite area in the parameter space, which increases with the frequency of the applied field. We develop a theoretical approach and combine it with numerical simulations, which allow us to understand the dynamics of the propeller and explain the experimental observations. Furthermore, we demonstrate a reversal of the microswimmer velocity by varying the length of the nanorod, as predicted by the model. Finally, we determine theoretically and in experiments the Lighthill's energetic efficiency of this minimal magnetic microswimmer.

cond-mat.soft↗

arXiv2020

Block copolymer-nanorod co-assembly in thin films: effects of rod-rod interaction and confinement

Simulations and experiments of nanorods (NRs) show that co-assembly with block copolymer (BCP) melts leads to the formation of a superstructure of side-to-side NRs perpendicular to the lamellar axis. A mesoscopic model is validated against scanning electron microscopy (SEM) images of CdSe NRs mixed with polystyrene-block-poly(methyl methacrylate). It is then used to study the co-assembly of anisotropic nanoparticles (NPs) with a length in the same order of magnitude as the lamellar spacing. The phase diagram of BCP/NP is explored as well as the time evolution of the NR. NRs that are slightly larger than the lamellar spacing are found to rotate and organise side-to-side with a tilted orientation with respect to the interface. Strongly interacting NPs are found to dominate the co-assembly while weakly interacting nanoparticles are less prone to form aggregates and tend to form well-ordered configurations.

cond-mat.soft↗

arXiv2019

Phase Behavior of Block Copolymer Nanocomposite Systems

Nanocomposite materials made of block copolymer and nanoparticles display properties which can be different from the purely polymeric matrix. The resulting material is a crossover of the original properties of the block copolymer and the presence of the assembled nanoparticles. We propose a mesoscopic study via cell dynamic simulations to quantitatively assert the properties of such hybrid materials. The most relevant parameters are identified to be the fraction of nanoparticles in the system and its chemical affinity, while the nanoparticle size with respect to the block copolymer length scales plays a role in the assembly. The morphological phase diagram of the block copolymer is constructed for nanoparticles with chemical affinity ranging from A-compatible to B-compatible for a symmetric A-B diblock copolymer. Block-compatible nanoparticles is found to induce a phase transition due to changes in the effective concentration of the hosting phase, while interface-compatible particles induces the appearance of two new phases due to the saturation of the diblock copolymer interface.

cond-mat.soft↗

arXiv2019

Large scale three dimensional simulations of hybrid block copolymer/nanoparticle systems

Block copolymer melts self-assemble in the bulk into a variety of nanostructures, making them perfect candidates to template the position of nanoparticles. The morphological changes of block copolymers are studied in the presence of a considerable filling fraction of colloids. Furthermore, colloids can be found to assemble into ordered hexagonally close-packed structures in a defined number of layers when softly confined within the phase-separated block copolymer. A high concentration of interface-compatible nanoparticles leads to complex block copolymer morphologies depending on the polymeric composition. Macrophase separation between the colloids and the block copolymer can be induced if colloids are unsolvable within the matrix. This leads to the formation of ellipsoid-shaped polymer-rich domains elongated along the direction perpendicular to the interface between block copolymer domains.

cond-mat.soft↗

arXiv2019

Non-spherical nanoparticles in block copolymer composites: nanosquares, nanorods and diamonds

A hybrid block copolymer(BCP) nanocomposite computational model is proposed to study nanoparticles(NPs) with a generalised shape including squares, rectangles and rhombus. Simulations are used to study the role of anisotropy in the assembly of colloids within BCPs, ranging from NPs that are compatible with one phase, to neutral NPs. The ordering of square-like NPs into grid configurations within a minority BCP domain was investigated, as well as the alignment of nanorods in a lamellar-forming BCP, comparing the simulation results with experiments of mixtures of nanoplates and PS-\textit{b}-PMMA BCP. The assembly of rectangular NPs at the interface between domains resulted in alignment along the interface. The aspect ratio is found to play a key role on the aggregation of colloids at the interface, which leads to a distinct co-assembly behaviour for low and high aspect ratio NPs.

cond-mat.soft↗

arXiv2019

Direct Measurement of Lighthill's Energetic Efficiency of a Minimal Magnetic Microswimmer

The realization of artificial microscopic swimmers able to propel in viscous fluids is an emergent research field of fundamental interest and vast technological applications. For certain functionalities, the efficiency of the microswimmer in converting the input power provided through an external actuation into propulsive power output can be critical. Here we use a microswimmer composed by a self-assembled ferromagnetic rod and a paramagnetic sphere and directly determine its swimming efficiency when it is actuated by a swinging magnetic field. Using fast video recording and numerical simulations we fully characterize the dynamics of the propeller and identify the two independent degrees of freedom which allow its propulsion. We then obtain experimentally the Lighthill's energetic efficiency of the swimmer by measuring the power consumed during propulsion and the energy required to translate the propeller at the same speed. Finally, we discuss how the efficiency of our microswimmer could be increased upon suitable tuning of the different experimental parameters.

cond-mat.soft↗

arXiv2019

Co-assembly of Janus nanoparticles in block copolymer systems

Block copolymer are ideal matrices to control the localisation of colloids. Furthermore, anisotropic nanoparticles such as Janus nanoparticles possess an additional orientational degree of freedom that can play a crucial role in the formation of highly ordered materials made of block copolymers. This work presents a mesoscopic simulation method to assert the co-assembly of Janus nanoparticles in a block copolymer mixture, finding numerous instances of aggregation and formation of ordered configurations which can be related to dispersions of pure Janus colloids. Comparison with chemically homogeneous neutral nanoparticles determines that Janus nanoparticles are less prone to induce bridging along lamellar domains, thus being a less destructive way to segregate nanoparticles at interfaces. The combination of asymmetric block copolymer and asymmetric Janus nanoparticles can result in assembly of colloids in an even number of layers within one of the block domains.

cond-mat.soft↗

arXiv2019

Asymmetric and Long Range Interactions in Shaken Granular Media

We use a computational model to investigate the emergence of interaction forces between pairs of intruders in a horizontally vibrated granular fluid. The time evolution of a pair of particles shows a maximum of the likelihood to find the pair at contact in the direction of shaking. This relative interaction is further studied by fixing the intruders in the simulation box where we identify effective mechanical forces, and torques between particles and quantify an emergent long range attractive force as a function of the shaking relative angle, amplitude, and the packing density of grains. We determine the local density and kinetic energy profiles of granular particles along the axis of the dimer to find no gradients in the density fields and additive gradients in the kinetic energies.

cond-mat.soft↗

arXiv2019

Confinement-controlled rectification in a geometric nanofluidic diode

Recent experiments with electrolytes driven through conical nanopores give evidence of strong rectified current response. In such devices, the asymmetry in the confinement is responsible of the non-Ohmic response, suggesting that the interplay of entropic and enthalpic forces plays a major role. Here we propose a theoretical model to shed light on the physical mechanism underlying ionic current rectification (ICR). By use of an effective description of the ionic dynamics we explore the system's response in different electrostatic regimes. We show that the rectification efficiency, as well as the channel selectivity, is driven by the surface-to-bulk conductivity ratio Dukhin length rather than the electrical double layer overlap.

cond-mat.mes-hall↗

arXiv2019

Linear response theory and Green-Kubo relations for active matter

We address the question of how interacting active systems in a non-equilibrium steady-state respond to an external perturbation. We establish an extended fluctuation-dissipation theorem for Active Brownian Particles (ABP) which highlights the role played by the local violation of detailed balance due to activity. By making use of a Markovian approximation we derive closed Green-Kubo expressions for the diffusivity and mobility of ABP and quantify the deviations from the Stokes-Einstein relation. We compute the linear response function to an external force using unperturbed simulations of ABP and compare the results with the analytical predictions of the transport coefficients. Our results show the importance of the interplay between activity and interactions in the departure from equilibrium linear response.

cond-mat.stat-mech↗

arXiv2019

Unravelling the role of phoretic and hydrodynamic interactions in active colloidal suspensions

Active fluids comprise a variety of systems composed of elements immersed in a fluid environment which can convert some form of energy into directed motion; as such they are intrinsically out-of-equilibrium in the absence of any external forcing. A fundamental problem in the physics of active matter concerns the understanding of how the characteristics of the autonomous propulsion and agent-agent interactions determine the collective dynamics of the system. We study numerically suspensions of self-propelled diffusiophoretic colloids, in (quasi)-2d configurations, accounting for both dynamically resolved solute-mediated phoretic interactions and solvent-mediated hydrodynamic interactions. Our results show that the system displays different scenarios at changing the colloid-solute affinity and it develops a cluster phase in the chemoattractive case. We study the statistics of cluster sizes and cluster morphologies for different magnitudes of colloidal activity. Finally, we provide evidences that hydrodynamics plays a relevant role in the aggregation kinetics and cluster morphology, significantly hindering the cluster growth.

cond-mat.soft↗

arXiv2019

Orientational order and morphology of clusters of self-assembled Janus swimmers

Due to the combined effect of anisotropic interactions and activity, Janus swimmers are capable to self-assemble in a wide variety of structures, many more than their equilibrium counterpart. This might lead to the development of novel active materials capable of performing tasks without any central control. Their potential application in designing such materials endows trying to understand the fundamental mechanism in which these swimmers self-assemble. In the present work, we study a quasi-two dimensional semi-dilute suspensions of two classes of amphiphilic spherical swimmers whose direction of motion can be tuned: either swimmers propelling in the direction of the hydrophobic patch (WP), or swimmers propelling in the opposite direction (towards the hydrophilic side) (AP). In both systems we have systematically tuned swimmers' hydrophobic strength and signature, and observed that the anisotropic interactions, characterized by the angular attractive potential and its interaction range, in competition with the active stress, pointing towards or against the attractive patch gives rise to a rich aggregation phenomenology.

cond-mat.soft↗

arXiv2019

Driving an electrolyte through a corrugated nanopore

We characterize the dynamics of a $z-z$ electrolyte embedded in a varying-section channel. In the linear response regime, by means of suitable approximations, we derive the Onsager matrix associated to externally enforced gradients in electrostatic potential, chemical potential, and pressure, for both dielectric and conducting channel walls. We show here that the linear transport coefficients are particularly sensitive to the geometry and the conductive properties of the channel walls when the Debye length is comparable to the channel width. In this regime, we found that one pair of off-diagonal Onsager matrix elements increases with the corrugation of the channel transport, in contrast to all other elements which are either unaffected by or decrease with increasing corrugation. Our results have a possible impact on the design of blue-energy devices as well as on the understanding of biological ion channels through membranes

cond-mat.soft↗

arXiv2019

Flocking and spreading dynamics in populations of self-propelled agents

Populations of self-propelled mobile agents - animal groups, robot swarms or crowds of people - that exchange information with their surrounding, host fascinating cooperative behaviors. While in many situations of interest the agents motion is driven by the transmission of information (e.g. the presence of an approaching predator) from neighboring peers, previous modeling efforts have focused on situations where agents either sit on static networks, or move independently of the information spreading across the population. Here, we introduce a reference model to tackle this current lack of general framework. We consider mobile agents which align their direction of motion (based on the Kuramoto dynamics) and carry an internal state governed by the Susceptible-Infected-Susceptible (SIS) epidemic process, characterizing the spread of information in the population, and affecting the way agents move in space. We show that the feedback between the agents motion and information spreading is responsible for (i) the enhancement of both flocking and information spreading, (ii) the emergence of complex spatial structures, or swarms, which can be controlled by the velocity of the agents. The SIS dynamics is able to drive a flocking phase transition even in the absence of explicit velocity-alignment, recovering a behavior reminiscent of Vicsek-like systems but featuring macro-phase separation rather than micro-phase separation. We show that the formation of dense swarms at low velocities reduces the epidemic threshold of information spreading with respect to the mean field limit. By bridging together soft active matter physics and agent based modeling of complex systems, we shed light upon a general positive feedback mechanism that crucially affects the collective behavior of mobile agents, providing a reference framework to study realistic situations where this mechanism is at play.

physics.soc-ph↗

arXiv2019

Activity induced synchronization: From Mutual Flocking to Chiral Self-Sorting

Synchronization, the temporal coordination of coupled oscillators, allows fireflies to flash in unison, neurons to fire collectively and human crowds to fall in step on the London Millenium bridge. Here, we interpret active (or self-propelled) chiral microswimmers with a distribution of intrinsic frequencies as motile oscillators and show that they can synchronize over very large distances, even for local coupling in 2D. This opposes to canonical non-active oscillators on static or time-dependent networks, leading to synchronized domains only. A consequence of this activity-induced synchronization is the emergence of a `mutual flocking phase', where particles of opposite chirality cooperate to form superimposed flocks moving at a relative angle to each other, providing a chiral active matter analogue to the celebrated Toner-Tu phase. The underlying mechanism employs a positive feedback loop involving the two-way coupling between oscillators' phase and self-propulsion, and could be exploited as a design principle for synthetic active materials and chiral self-sorting techniques

cond-mat.stat-mech↗

arXiv2018

Active microrheology in corrugated channels

We analyze the dynamics of a tracer particle embedded in a bath of hard spheres confined in a channel of varying section. By means of Brownian dynamics simulations we apply a constant force on the tracer particle and discuss the dependence of its mobility on the relative magnitude of the external force with respect to the entropic force induced by the confinement. A simple theoretical one-dimensional model is also derived, where the contribution from particle-particle and particle-wall interactions is taken from simulations with no external force. Our results show that the mobility of the tracer is strongly affected by the confinement. The tracer velocity in the force direction has a maximum close to the neck of the channel, in agreement with the theory for small forces. Upon increasing the external force, the tracer is effectively confined to the central part of the channel and the velocity modulation decreases, what cannot be reproduced by the theory. This deviation marks the regime of validity of linear response. Surprisingly, when the channel section is not constant the effective friction coefficient is reduced as compared to the case of a plane channel. The transversal velocity, which cannot be studied with our model, follows the qualitatively the derivative of the channel section, in agreement previous theoretical calculations for the tracer diffusivity in equilibrium.

cond-mat.soft↗