arXiv subjects

Ignacio Pagonabarraga

Publications and source records attributed to Ignacio Pagonabarraga.

At least 109 records · Page 6Linked to original sources

arXiv2015

Tracer diffusion of hard-sphere binary mixtures under nano-confinement

The physics of diffusion phenomena in nano and micro channels has attracted a lot of attention in recent years, due to its close connection with many technological, medical and industrial applications. In the present paper we employ a kinetic approach to investigate how the confinement in nanostructured geometries affects the diffusive properties of fluid mixtures and leads to the appearance of properties different from those of bulk systems. In particular, we derive an expression for the friction tensor in the case of a bulk fluid mixture confined to a narrow slit having undulated walls. The boundary roughness leads to a new mechanism for transverse diffusion, and can even lead to an effective diffusion along the channel larger than the one corresponding to a planar channel of equivalent section. Finally we discuss a reduction of the previous equation to a one dimensional effective diffusion equation in which an entropic term encapsulates the geometrical information on the channel shape.

cond-mat.soft↗

arXiv2015

Driven Transport on open filaments with inter-filament switching processes

We study a two filament driven lattice gas model with oppositely directed species of particles moving on two parallel filaments with filament switching processes and particle inflow and outflow at filament ends. The filament switching process is {\it correlated} such that particles switch filaments with finite probability only when oppositely directed particles meet on the same filament. This model mimics some of the coarse grained features observed in context of microtubule (MT) based intracellular transport, wherein cellular cargo loaded and off-loaded at filament ends are transported on multiple parallel microtubule (MT) filaments and can switch between the parallel microtubule filaments. We focus on a regime where the filaments are weakly coupled, such that filament switching rates scale inversely as the length of the filament. We find that the interplay (off)loading processes at the boundaries and the filament switching process leads to some distinctive features of the system. These features includes occurrence of variety of phases in the system with inhomogeneous density profiles including localized density shocks, density difference across the filaments and bidirectional current flows in the system. We analyze the system by developing a mean field (MF) theory and comparing the results obtained from the MF theory with the Monte Carlo (MC) simulations of the dynamics of the system. We find that the steady state density and current profiles of particles and the phase diagram obtained within the MF picture matches quite well with MC simulation results. These findings maybe useful for studying multi-filament intracellular transport.

cond-mat.soft↗

arXiv2015

Geometrically-tuned channel permeability

We characterize the motion of charged as well as neutral tracers, in an electrolyte embedded in a varying section channel. We exploit a set of systematic approximations that allows us to simplify the problem, yet capturing the essential of the interplay between the geometrical confinement provided by the corrugated channel walls and the electrolyte properties. Our simplified approach allows us to characterize the transport properties of corrugated channels when a net flux of tracers is obtained by keeping the extrema of the channel at different chemical potentials. For highly diluted tracer suspensions, we have characterized tracers currents and we have estimated the net electric current which occurs when both positively and negatively charged tracers are considered.

cond-mat.soft↗

arXiv2014

Working under confinement

We analyze the performance of a Brownian ratchet in the presence of geometrical constraints. A two-state model that describes the kinetics of molecular motors is used to characterize the energetic cost when the motor proceeds under confinement, in the presence of an external force. We show that the presence of geometrical constraints has a strong effect on the performance of the motor. In particular, we show that it is possible to enhance the ratchet performance by a proper tuning of the parameters characterizing the environment. These results open the possibility of engineering entropically-optimized transport devices.

physics.bio-ph↗

arXiv2014

Entropic electrokinetics: recirculation, particle separation and negative mobility

We show that when particles are suspended in an electrolyte confined between corrugated charged surfaces, electrokinetic flows lead to a new set of phenomena such as particle separation, mixing for low-Reynolds micro- and nano-metric devices and negative mobility. Our analysis shows that such phenomena arise, for incompressible fluids, due to the interplay between the electrostatic double layer and the corrugated geometrical confinement and that they are magnified when the width of the channel is comparable to the Debye length. Our characterization allows us to understand the physical origin of such phenomena therefore shading light on their possible relevance in a wide variety of situations, ranging from nano- and micro-fluidic devices to biological systems.

cond-mat.soft↗

arXiv2014

On the role of composition entropies in the statistical mechanics of polydisperse systems

Polydisperse systems are commonly encountered when dealing with soft matter in general or any non simple fluid. Yet their treatment within the framework of statistical thermodynamics is a delicate task as the latter has been essentially devised for simple --- non fully polydisperse --- systems. In this paper, we address the issue of defining a non ambiguous combinatorial entropy for these systems. We do so by focusing on the general property of extensivity of the thermodynamic potentials and discussing a specific mixing experiment. This leads us to introduce the new concept of composition entropy for single phase systems that we do not assimilate to a mixing entropy. We then show that they do not contribute to the thermodynamics of the system at fixed composition and prescribe to substract $\ln N!$ from the free energy characterizing a system however polydisperse it can be. We then re-derive general expressions for the mixing entropy between any two polydisperse systems and interpret them in term of distances between probability distributions and show that one of these metrics relates naturally to a recent extension of Landauer's principle. We then propose limiting expressions for the mixing entropy in the case of mixing with equal proportion in the original compositions and finally address the challenging problem of chemical reactions.

cond-mat.stat-mech↗

arXiv2014

Accounting for adsorption and desorption in lattice Boltzmann simulations

We report a Lattice-Boltzmann scheme that accounts for adsorption and desorption in the calculation of mesoscale dynamical properties of tracers in media of arbitrary complexity. Lattice Boltzmann simulations made it possible to solve numerically the coupled Navier-Stokes equations of fluid dynamics and Nernst-Planck equations of electrokinetics in complex, heterogeneous media. Associated to the moment propagation scheme, it became possible to extract the effective diffusion and dispersion coefficients of tracers, or solutes, of any charge, e.g. in porous media. Nevertheless, the dynamical properties of tracers depend on the tracer-surface affinity, which is not purely electrostatic, but also includes a species-specific contribution. In order to capture this important feature, we introduce specific adsorption and desorption processes in a Lattice-Boltzmann scheme through a modified moment propagation algorithm, in which tracers may adsorb and desorb from surfaces through kinetic reaction rates. The method is validated on exact results for pure diffusion and diffusion-advection in Poiseuille flows in a simple geometry. We finally illustrate the importance of taking such processes into account on the time-dependent diffusion coefficient in a more complex porous medium.

physics.flu-dyn↗

arXiv2013

Theory of wetting-induced fluid entrainment by advancing contact lines on dry surfaces

We report on the onset of fluid entrainment when a contact line is forced to advance over a dry solid of arbitrary wettability. We show that entrainment occurs at a critical advancing speed beyond which the balance between capillary, viscous and contact line forces sustaining the shape of the interface is no longer satisfied. Wetting couples to the hydrodynamics by setting both the morphology of the interface at small scales and the viscous friction of the front. We find that the critical deformation that the interface can sustain is controlled by the friction at the contact line and the viscosity contrast between the displacing and displaced fluids, leading to a rich variety of wetting-entrainment regimes. We discuss the potential use of our theory to measure contact-line forces using atomic force microscopy, and to study entrainment under microfluidic conditions exploiting colloid-polymer fluids of ultra-low surface tension.

cond-mat.soft↗

arXiv2013

Confined Brownian ratchets

We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential. The cases of a flashing ratchet, a two-state model and a ratchet under the influence of a temperature gradient are analyzed in detail. We show the emergence of a strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may take place in situations where none of those mechanisms leads to rectification when acting individually. The combined rectification mechanisms may lead to bidirectional transport and to new routes to segregation phenomena. Confined Brownian ratchets (CBR) could be used to control transport in mesostructures and to engineer new and more efficient devices for transport at the nanoscale.

cond-mat.soft↗

arXiv2012

Running faster together: huge speed up of thermal ratchets due to hydrodynamic coupling

We present simulations that reveal a surprisingly large effect of hydrodynamic coupling on the speed of thermal ratchet motors. The model that we use considers particles performing thermal ratchet motion in a hydrodynamic solvent. Using particle-based, mesoscopic simulations that maintain local momentum conservation, we analyze quantitatively how the coupling to the surrounding fluid affects ratchet motion. We find that coupling can increase the mean velocity of the moving particles by almost two orders of magnitude, precisely because ratchet motion has both a diffusive and a deterministic component. The resulting coupling also leads to the formation of aggregates at longer times. The correlated motion that we describe increases the efficiency of motor-delivered cargo transport and we speculate that the mechanism that we have uncovered may play a key role in speeding up molecular motor-driven intracellular transport.

cond-mat.soft↗

arXiv2012

Cooperative rectification in confined Brownian ratchets

We analyze the rectified motion of a Brownian particle in a confined environment. We show the emergence of strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may develop even in situations where separately the ratchet and the geometric restrictions do not give rise to particle motion. The combined rectification effects can lead to bidirectional transport depending on particle size, resulting in a new route for segregation. The reported mechanism can be used to control transport in mesostructures and nanodevices in which particles move in a reduced space.

cond-mat.mes-hall↗

arXiv2011

Growth saturation of unstable thin films on transverse-striped hydrophilic-hydrophobic micropatterns

Using three-dimensional numerical simulations, we demonstrate the growth saturation of an unstable thin liquid film on micropatterned hydrophilic-hydrophobic substrates. We consider different transverse-striped micropatterns, characterized by the total fraction of hydrophilic coverage and the width of the hydrophilic stripes. We compare the growth of the film on the micropatterns to the steady states observed on homogeneous substrates, which correspond to a saturated sawtooth and growing finger configurations for hydrophilic and hydrophobic substrates, respectively. The proposed micropatterns trigger an alternating fingering-spreading dynamics of the film, which leads to a complete suppression of the contact line growth above a critical fraction of hydrophilic stripes. Furthermore, we find that increasing the width of the hydrophilic stripes slows down the advancing front, giving smaller critical fractions the wider the hydrophilic stripes are. Using analytical approximations, we quantitatively predict the growth rate of the contact line as a function of the covering fraction, and predict the threshold fraction for saturation as a function of the stripe width.

cond-mat.soft↗

arXiv2011

Instrinsic oscillations of treadmilling microtubules in a motor bath

We analyse the dynamics of overlapping antiparallel treadmilling microtubules in the presence of crosslinking processive motor proteins that counterbalance an external force. We show that coupling the force-dependent velocity of motors and the kinetics of motor exchange with a bath in the presence of treadmilling leads generically to oscillatory behavior. In addition we show that coupling the polymerization kinetics to the external force through the kinetics of the crosslinking motors can stabilize the oscillatory instability into finite-amplitude nonlinear oscillations and may lead to other scenarios, including bistability.

cond-mat.soft↗

arXiv2011

Lattice Boltzmann - Langevin simulations of binary mixtures

We report a hybrid numerical method for the solution of the model H fluctuating hydrodynamic equations for binary mixtures. The momentum conservation equations with Landau-Lifshitz stresses are solved using the fluctuating lattice Boltzmann equation while the order parameter conservation equation with Langevin fluxes are solved using the stochastic method of lines. Two methods, based on finite difference and finite volume, are proposed for spatial discretisation of the order parameter equation. Special care is taken to ensure that the fluctuation-dissipation theorem is maintained at the lattice level in both cases. The methods are benchmarked by comparing static and dynamic correlations and excellent agreement is found between analytical and numerical results. The Galilean invariance of the model is tested and found to be satisfactory. Thermally induced capillary fluctuations of the interface are captured accurately, indicating that the model can be used to study nonlinear fluctuations.

cond-mat.stat-mech↗

arXiv2011

Phase segregation and transport in a two species multi-lane system

We present a two channel driven lattice gas model with oppositely directed species moving on two parallel lanes with lane switching processes. We study correlated lane switching mechanism for particles so that switching may occur with finite probability only when oppositely directed species meet on the same channel. The system is analyzed for closed ring with conserved total particle number. For asymmetric particle exchange between the lanes, the system exhibits unique polarization phenomenon with segregation of oppositely directed species between the two lanes. The polarization phenomenon can be understood as a consequence of existence of an absorbing steady state. For symmetric exchange rate of particles between the lanes, the system remains unpolarized, with equal particle density on both the lanes in the thermodynamic limit of large system size. We study the system using a combination of a Mean Field(MF) analysis and Monte Carlo simulations. The nature of phase segregation that we see for this system, is distinct from driven particle systems which are in contact with particle reservoir. The features observed for this minimal model will have ramifications for biofilament based intracellular transport, wherein cellular cargo, e.g; organelles and vesicles are transported by oppositely directed particles on multiple filament tracks.

cond-mat.stat-mech↗

arXiv2011

Colloids electrophoresis for strong and weak ion diffusivity

We study the electrophoretic flow of suspensions of charged colloids with a mesoscopic method that allows to model generic experimental conditions. We show that for highly charged colloids their electrophoretic mobility increases significantly and displays a mobility maximum on increasing the colloidal charge for all salt concentrations. The electrophoretic mobility of highly charged colloids is also enhanced significantly when ion advection is dominant, leading to a strong heterogeneity in the local electrophoretic response especially at low salt concentration, when ion diffuse layers overlap.

cond-mat.soft↗

arXiv2011

Determination of the zeta potential for highly charged colloidal suspensions

We compute the electrostatic potential at the surface, or zeta potential $ζ$, of a charged particle embedded in a colloidal suspension using a hybrid mesoscopic model. We show that for weakly perturbing electric fields, the value of $ζ$ obtained at steady state during electrophoresis is statistically indistinguishable from $ζ$ in thermodynamic equilibrium. We quantify the effect of counterions concentration on $ζ$. We also evaluate the relevance of the lattice resolution for the calculation of $ζ$ and discuss how to identify the effective electrostatic radius.

cond-mat.soft↗

arXiv2010

Lattice-gas model for active vesicle transport by molecular motors with opposite polarities

We introduce a multi-species lattice gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargoes being carried by oppositely directed molecular motors, moving on a single biofilament. Building on a totally asymmetric exclusion process (TASEP) to characterize the motion of the interacting cargoes, we allow for mass exchange with the environment, input and output at filament boundaries and focus on the role of interconversion rates and how they affect the directionality of the net cargo transport. We quantify the effect of the various different competing processes in terms of non-equilibrium phase diagrams. The interplay of interconversion rates, which allow for flux reversal and evaporation/deposition processes introduce qualitatively new features in the phase diagrams. We observe regimes of three-phase coexistence, the possibility of phase re-entrance and a significant flexibility in how the different phase boundaries shift in response to changes in control parameters. The moving steady state solutions of this model allows for different possibilities for the spatial distribution of cargo vesicles, ranging from homogeneous distribution of vesicles to polarized distributions, characterized by inhomogeneities or {\it shocks}. Current reversals due to internal regulation emerge naturally within the framework of this model. We believe this minimal model will clarify the understanding of many features of collective vesicle transport, apart from serving as the basis for building more exact quantitative models for vesicle transport relevant to various {\it in-vivo} situations.

cond-mat.stat-mech↗