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Ali Naji

Publications and source records attributed to Ali Naji.

At least 19 recordsLinked to original sources

Smart navigation through a rotating barrier: Deep reinforcement learning with application to size-based separation of active microagents

We employ deep reinforcement learning methods to investigate shortest-time navigation strategies for smart active Brownian particles (microagents), which self-propel through a rotating potential barrier in a static, viscous, fluid background. The microagent's motion begins at a specified origin and terminates at a designated destination. The potential barrier is modeled as a localized, repulsive Gaussian potential with finite support, whose peak location rotates at a given angular velocity about a fixed center within the plane of motion. We use the Advantage Actor-Critic approach to train microagents for their origin-to-destination navigation through the barrier. By employing this approach, we demonstrate that the rotating potential (as opposed to a static one) enables size-based sorting and separation of the microagents. In other words, microagents of different radii arrive at the destination at sufficiently well-separated average times, facilitating their sorting. The efficiency of particle sorting is quantified by introducing specific separation measures. We also demonstrate how training the microagents in a noisy background, as opposed to a noise-free one, can improve the precision of their size-based sorting. Our findings suggest promising avenues for future research on smart active particles equipped with deep reinforcement learning to navigate complex environments, particularly in microscale applications.

cond-mat.soft

Active osmotic-like pressure on permeable inclusions

We use a standard minimal active Brownian model to investigate the osmotic-like effective pressure generated by active fluids on fixed hollow inclusions. These inclusions are enclosed by a permeable (albeit nonflexible) membrane, and the interior and exterior regions of the inclusions have different particle motility strengths. We consider both rectangular and disklike inclusions and analyze the effects of various system parameters, such as excluded volume interaction between active particles, hardness of membrane and active particle density, on the effective pressure produced on the enclosing membrane. We focus on the range of intermediate to high motility strengths and analyze the effective pressure in the steady state. Our findings for the active pressure produced in the interior and exterior regions of the inclusion indicate that the pressure is higher in the region with lower motility due to the relatively stronger accumulation of active particles.

cond-mat.soft

Bag boundaries for quasispinor confinement within nanolanes on a graphene sheet

We revisit the problem of bag boundary conditions within a field-theoretic approach to study confinement of massless Dirac quasispinors in monolayer graphene. While no-flux bag boundaries have previously been used to model lattice termination sites in graphene nanoribbons, we consider a generalized setting in which the confining boundaries are envisaged as arbitrary straight lines drawn across a graphene sheet and the quasispinor currents are allowed to partially permeate (leak) through such boundaries. We specifically focus on rectangular nanolanes defined as areas confined between a pair of parallel lines at arbitrary separation on an unbounded lattice. We show that such nanolanes exhibit a considerable range of bandgap tunability depending on their widths and armchair, zigzag or intermediate orientation. The case of nanoribbons can be derived as a special limit from the nanolane model. In this case, we clarify certain inconsistencies in previous implementations of no-flux bag boundaries and show that the continuum approach reproduces the tight-binding bandgaps accurately (within just a few percent in relative deviation) even as the nanoribbon width is decreased to just a couple of lattice spacings. This accentuates the proper use of boundary conditions when field-theoretic approaches are applied to graphene systems.

cond-mat.mes-hall

Shear-induced bimodality and stability analysis of chiral spheroidal swimmers

We study the shear-induced behavior of chiral (circle-swimming) and nonchiral swimmers in a planar channel subjected to Poiseuille (pressure-driven) flow. The swimmers are modeled as active Brownian spheroids, self-propelling with a fixed-magnitude velocity, pointing along their axis of symmetry. We consider both cases of prolate and oblate swimmers and focus primarily on swimmers that possess an intrinsic, or active, counterclockwise angular velocity, in addition to the shear-induced angular velocity they acquire within the channel flow (Jeffery orbits). The probabilistic results are established using a Smoluchowski equation within the position orientation phase space that is solved numerically. We show that the interplay between shear- and chirality-induced angular velocities, combined with the effects due to particle self-propulsion and steric particle-wall interactions, lead to an interesting range of effects, including pinning, off-centered and near-wall accumulation of swimmers within the channel. This is further accompanied by the linear stability analysis of swimmers, used to explain the probabilistic results. We discuss the qualitative differences of probabilistic results that emerge due to the different regimes of rotational dynamics of swimmers in channel flow, particularly the shear-trapping/-escaping of prolate/oblate swimmers and the difference in latitudes of fixed points associated with each swimmer shape. Our results point to possible mechanisms for flow-driven separation of active spheroidal particles based on their chirality strength.

cond-mat.soft

Brownian noise effects on magnetic focusing of prolate and oblate spheroids in channel flow

We investigate Brownian noise effects on magnetic focusing of prolate and oblate spheroids carrying permanent magnetic dipoles in channel (Poiseuille) flow subject to a uniform magnetic field. The focusing is effected by the low-Reynolds-number wall-induced hydrodynamic lift which can be tuned via tilt angle of the field relative to the flow direction. This mechanism is incorporated in a steady-state Smoluchowski equation that we solve numerically to analyze the noise effects through the joint position-orientation probability distribution function of spheroids within the channel. The results feature partial and complete pinning of spheroidal orientation as the field strength is increased and reveal remarkable and even counterintuitive noise-induced phenomena (specifically due to translational particle diffusivity) deep into the strong-field regime. These include field-induced defocusing, or lateral broadening of the focused spheroidal layer, upon strengthening the field. We map out focusing `phase' diagrams based on the field strength and tilt angle to illustrate different regimes of behavior including centered focusing and defocusing in transverse field, and off-centered focusing in tilted fields. The latter encompasses two subregimes of optimal and shouldered focusing where spheroidal density profiles across the channel width display either an isolated off-centered peak or a skewed peak with a pronounced shoulder stretching toward the channel center. We corroborate our results by analyzing stability of deterministic fixed points and a reduced one-dimensional probabilistic theory which we introduce to semiquantitatively explain noise-induced behavior of pinned spheroids under strong fields. We also elucidate the implications of our results for efficient shape-based sorting of magnetic spheroids.

cond-mat.soft

Drag force on cylindrical intruders in granular media: Experimental study of lateral vs axial intrusion and high grain-polydispersity effects

We report on experimentally measured drag force experienced by a solid cylinder penetrating a granular bed of glass beads including, specifically, a highly polydisperse sample with grain sizes in the range 1-100 μm. We consider both cases of lateral and axial intrusion in which the long axis of the cylinder is held horizontally and vertically, respectively. We explore different regimes of behavior for the drag force as a function of the penetration depth. In lateral intrusion, where the motion is effectively quasi-two-dimensional, we establish quantitative comparisons with existing theoretical predictions across the whole range of depths. In axial intrusion, we observe peculiar undulations in the force-depth profiles in a wide range of intrusion speeds and for different cylinder diameters. We argue that these undulations reflect general shear failure in the highly polydisperse sample and can be understood based on the ultimate bearing capacity theory on a semiquantitative level.

cond-mat.soft

Non-Markovian modeling of non-equilibrium fluctuations and dissipation in active viscoelastic biomatter

Based on a Hamiltonian that incorporates the elastic coupling between a tracer and active particles, we derive a generalized Langevin model for the non-equilibrium mechanical response of active viscoelastic biomatter. Our model accounts for the power-law viscoelastic response of the embedding polymeric network as well as for the non-equilibrium energy transfer between active and tracer particles. Our analytical expressions for the frequency-dependent response function and the positional autocorrelation function agree nicely with experimental data for red blood cells and actomyosin networks with and without ATP. The fitted effective active-particle temperature, elastic constants and effective friction coefficients of our model allow straightforward physical interpretation.

cond-mat.soft

Rectification of polymer translocation through nanopores by chiral and nonchiral active particles

We study unbiased translocation of a flexible polymer chain through a membrane pore under the influence of active noise and steric exclusion using Langevin dynamics simulations. The active noise is incorporated by introducing nonchiral and chiral active particles on one or both sides of the membrane. Translocation of the polymer into either side of the pore is assisted by an effective pulling due to particle activity and is hindered by an effective pushing due to steric repulsions between the polymer and active particles. As a result of the competition between these effective forces, we find a transition between two rectified ({\em cis}-to-{\em trans} and {\em trans}-to-{\em cis}) states. This transition is identified by a sharp increase of translocation time. It varies depending on the system parameters such as particle activity, area fraction and chirality whose effects are explored in this work.

cond-mat.soft

Active dipolar spheroids in shear flow and transverse field: Population splitting, cross-stream migration and orientational pinning

We study the steady-state behavior of active, dipolar, Brownian spheroids in a planar channel subjected to an imposed Couette flow and an external transverse field, applied in the 'downward' normal-to-flow direction. The field-induced torque on active spheroids (swimmers) is taken to be of magnetic form by assuming that they have a permanent magnetic dipole moment, pointing along their self-propulsion (swim) direction. Using a continuum approach, we show that a host of behaviors emerge over the parameter space spanned by the particle aspect ratio, self-propulsion and shear/field strengths, and the channel width. The cross-stream migration of the model swimmers is shown to involve a regime of linear response (quantified by a linear-response factor) in weak fields. For prolate swimmers, the weak-field behavior crosses over to a regime of full swimmer migration to the bottom half of the channel in strong fields. For oblate swimmers, a counterintuitive regime of reverse migration arises in intermediate fields, where a macroscopic fraction of swimmers reorient and swim to the top channel half at an acute `upward' angle relative to the field axis. The diverse behaviors reported here are analyzed based on the shear-induced population splitting (bimodality) of the swim orientation, giving two distinct, oppositely polarized, swimmer subpopulations (albeit very differently for prolate/oblate swimmers) in each channel half. In strong fields, swimmers of both types exhibit net upstream currents relative to the laboratory frame. The onsets of full migration and net upstream current depend on the aspect ratio, enabling efficient particle separation strategies in microfluidic setups.

cond-mat.soft

Effective interactions between inclusions in a chiral active bath inside a channel

Colloidal inclusions suspended in a bath of smaller particles experience an effective bath-mediated attraction at small intersurface separations, which is known as the depletion interaction. In an active bath of nonchiral self-propelled particles, the effective force changes from attraction to repulsion; an effect that is suppressed, when the active bath particles are chiral. Using Brownian Dynamics simulations, we study the effects of channel confinement and bath chirality on the effective forces and torques that are mediated between two inclusions that may be fixed within the channel or may be allowed to rotate freely as a rigid dimer around its center of mass. We show that the confinement has a strong effect on the effective interactions, depending on the orientation of the dimer relative to the channel walls. The active particle chirality leads to a force imbalance and, hence, a net torque on the inclusion dimer, which we investigate as a function of the bath chirality strength and the channel height.

cond-mat.soft

Effective interactions mediated between two permeable disks in an active fluid

We study steady-state properties of a bath of active Brownian particles (ABPs) in two dimensions in the presence of two fixed, permeable (hollow) disklike inclusions, whose interior and exterior regions can exhibit mismatching motility (self-propulsion) strengths for the ABPs. We show that such a discontinuous motility field strongly affects spatial distribution of ABPs and thus also the effective interaction mediated between the inclusions through the active bath. Such net interactions arise from soft interfacial repulsions between ABPs that sterically interact with and/or pass through permeable membranes assumed to enclose the inclusions. Both regimes of repulsion and attractive (albeit with different mechanisms) are reported and summarized in overall phase diagrams.

cond-mat.soft

Noncentral forces mediated between inclusions in a bath of active Brownian rods

Using Brownian Dynamics simulations, we study effective interactions mediated between two identical and impermeable disks (inclusions) immersed in a bath of identical, active (self-propelled), Brownian rods in two spatial dimensions, by assuming that the self-propulsion axis of the rods may generally deviate from their longitudinal axis. When the self-propulsion is transverse (perpendicular to the rod axis), the accumulation of active rods around the inclusions is significantly enhanced, causing a more expansive steric layering (ring formation) of the rods around the inclusions, as compared with the reference case of longitudinally self-propelling rods. As a result, the transversally self-propelling rods also mediate a significantly longer ranged effective interaction between the inclusions. The bath-mediated interaction arises due to the overlaps between the active-rod rings formed around the inclusions, as they are brought into small separations. When the self-propulsion axis is tilted relative to the rod axis, we find an asymmetric imbalance of active-rod accumulation around the inclusion dimer. This leads to a noncentral interaction, featuring an anti-parallel pair of transverse force components and, hence, a bath-mediated torque on the dimer.

physics.comp-ph

Electrostatic interaction between SARS-CoV-2 virus and charged electret fibre

While almost any kind of face mask offers some protection against particles and pathogens of different sizes, the most efficient ones make use of a layered structure where one or more layers are electrically charged. This electret layer is essential to efficient filtration of difficult-to-capture small particles, yet the exact nature of electrostatic capture with respect to both the charge on the particles and the electret fibres as well as the effect of immediate environment remains unclear. Here, we explore in detail the electrostatic interaction between the surface of a single charged electret fibre and a model of SARS-CoV-2 virus. Using Poisson-Boltzmann electrostatics coupled to a detailed spike protein charge regulation model, we show how pH and salt concentration drastically change both the scale and the sign of the interaction. Furthermore, the configuration of the few spike proteins closest to the electret fibre turns out to be as important for the strength of the interaction as their total number on the virus, a direct consequence of spike protein charge regulation. The results of our work elucidate the details of virus electrostatics and contribute to the general understanding of efficient virus filtration mechanisms.

physics.bio-ph

Active particles with polar alignment in ring-shaped confinement

We study steady-state properties of a suspension of active, nonchiral and chiral, Brownian particles with polar alignment and steric interactions confined within a ring-shaped (annulus) confinement in two dimensions. Exploring possible interplays between polar interparticle alignment, geometric confinement and the surface curvature, being incorporated here on minimal levels, we report a surface-population reversal effect, whereby active particles migrate from the outer concave boundary of the annulus to accumulate on its inner convex boundary. This contrasts the conventional picture, implying stronger accumulation of active particles on concave boundaries relative to the convex ones. The population reversal is caused by both particle alignment and surface curvature, disappearing when either of these factors is absent. We explore the ensuing consequences for the chirality-induced current and swim pressure of active particles and analyze possible roles of system parameters, such as the mean number density of particles and particle self-propulsion, chirality and alignment strengths.

cond-mat.soft

Confinement-induced alternating interactions between inclusions in an active fluid

In a system of colloidal inclusions suspended in a thermalized bath of smaller particles, the bath engenders an attractive force between the inclusions, arising mainly from entropic origins, known as the depletion force. In the case of active bath particles, the nature of the bath-mediated force changes dramatically from an attractive to a repulsive one, as the strength of particle activity is increased. We study such bath-mediated effective interactions between colloidal inclusions in a bath of self-propelled Brownian particles, being confined in a narrow planar channel. Confinement is found to have a strong effect on the interaction between colloidal particles, however, this mainly depends on the colloidal orientation inside the channel. Effect of the confinement on the interaction of colloidal disk is controlled by the layering of active particles on the surface boundaries. This can emerge as a competitive factor, involving the tendencies of the channel walls and the colloidal inclusions in accumulating the active particles in their own proximity.

cond-mat.soft

Surface alignment disorder and pseudo-Casimir forces in smectic-A liquid crystalline films

Random (disordered) components in the surface anchoring of the smectic-A liquid crystalline film in general modify the thermal pseudo-Casimir interaction. Anchoring disorder of the quenched type is in general decoupled from the thermal pseudo-Casimir force and gives rise to an additional disorder-generated interaction, in distinction to the annealed disorder, whose effect on the pseudo-Casimir force is non-additive. We consider the effects of the surface anchoring disorder by assuming that one of the substrates of the film is contaminated by a disorder source, resulting in a Gaussian-weighted distribution of the preferred molecular anchoring orientation (easy axes) on that substrate, having a finite mean and variance or, more generally, a homogeneous in-plane, two-point correlation function. We show that the presence of disorder, either of the quenched or annealed type, leads to a significant reduction in the magnitude of the net thermal fluctuation force between the confining substrates of the film. In the quenched case this is a direct consequence of an additive free energy dependent on the variance of the disorder, while in the annealed case, the suppression of the interaction force can be understood based on a disorder-renormalized, effective anchoring strength.

cond-mat.soft

Pseudo-Casimir interactions and surface anchoring duality in bookshelf geometry of smectic-A liquid crystals

We analyze the transverse intersubstrate pseudo-Casimir force, arising as a result of thermal fluctuations of the liquid crystalline layers of a smectic-A film confined between two planar substrates in a bookshelf geometry, in which the equidistant smectic layers are placed perpendicular to the bounding surfaces. We discuss the variation of the interaction force as a function of the intersubstrate separation in the presence of surface anchoring to the substrates, showing that the force induced by confined fluctuations is attractive and depends on the penetration length as well as the layer spacing. The strongest effect occurs for tightly confined fluctuations, in which the surface anchoring energy is set to infinity, where the force per area scales linearly with the thermal energy and inversely with the fourth power of the intersubstrate separation. By reducing the strength of the surface anchoring energy, the force first becomes weaker in magnitude but then increases in magnitude as the surface anchoring strength is further reduced down to zero, in which case the force tends to that obtained in the limit of strong anchoring.

cond-mat.soft

Rodlike counterions at heterogeneously charged surfaces

We study the spatial and orientational distribution of rodlike counterions (such as mobile nanorods) as well as the effective interaction mediated by them between two plane-parallel surfaces that carry fixed (quenched) heterogeneous charge distributions. The rodlike counterions are assumed to have an internal charge distribution, specified by a multivalent monopolar moment and a finite quadrupolar moment, and the quenched surface charge is assumed to be randomly distributed with equal mean and variance on the two surfaces. While equally charged surfaces are known to repel within the traditional mean-field theories, the presence of multivalent counterions has been shown to cause attractive interactions between uniformly charged surfaces due to the prevalence of strong electrostatic couplings that grow rapidly with the counterion valency. We show that the combined effects due to electrostatic correlations (caused by the coupling between the mean surface field and the multivalent, monopolar, charge valency of counterions) as well as the disorder-induced interactions (caused by the coupling between the surface disorder field and the quadrupolar moment of counterions) lead to much stronger attractive interactions between two randomly charged surfaces. The interaction profile turns out to be a nonmonotonic function of the intersurface separation, displaying an attractive minimum at relatively small separations, where the ensuing attraction can exceed the maximum strong-coupling attraction (produced by multivalent monopolar counterions between uniformly charged surfaces) by more than an order of magnitude.

cond-mat.soft