arXiv subjects

Sara Jabbari-Farouji

Publications and source records attributed to Sara Jabbari-Farouji.

At least 19 recordsLinked to original sources

arXiv2026

Flexibility Controls Active-Filament Transport in Crowded Landscapes

Active filaments, ranging from motor-driven biopolymers to elongated bacteria and worms, are paradigmatic examples of deformable active matter. How filament flexibility interacts with environmental heterogeneity to control their transport in crowded environments, however, remains poorly understood. Here, we perform large-scale Brownian dynamics simulations of tangentially driven active polymers moving through ordered and disordered obstacle arrays to map the long-time diffusion as a function of obstacle density and filament flexibility. We find that flexibility can either enhance or hinder transport depending on the structure of the medium. In disordered environments, transport is optimized at intermediate filament flexibility, whereas both highly flexible and semiflexible filaments diffuse more slowly. In contrast, dense ordered arrays enhance the mobility of semiflexible filaments by promoting directed motion along periodic channels. We identify three distinct transport regimes: (i) tortuosity-controlled diffusion of highly flexible filaments, characterized by trapping-and-hopping dynamics; (ii) confinement-assisted transport of moderately flexible filaments, which enhances diffusion in dense media; and (iii) persistence-controlled transport of semiflexible filaments, which facilitates diffusion in dense ordered media, but suppresses it in disordered media. Combining theory and simulations, we show that long-time diffusion is governed by confinement-induced changes in filament conformation and reorientation dynamics. Our work uncovers general transport principles for deformable active agents in heterogeneous environments and provides a predictive framework for active-filament navigation in complex porous landscapes.

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arXiv2025

Modulation of Non-equilibrium Structures of Active Dipolar Particles by an External Field

We study the impact of an external alignment field on the structure formation and polarization behavior of low-density dipolar active particles in three dimensions. Performing extensive Brownian dynamics simulations, we characterize the interplay between long-range dipolar interactions, field alignment, and self-propulsion. We find that the competition between activity (favoring bond breaking) and the field's orientational constraint (promoting bond formation) gives rise to a rich variety of self-assembled, actuated structures. At low to intermediate field strengths, disordered fluids composed of active chains and active percolated networks can emerge, whereas strong fields drive the formation of polarized columnar clusters. Counterintuitively, low activity levels significantly extend the range of field strengths over which percolated networks persist. This structural evolution manifests in the polarization response of strongly dipolar systems, which exhibit a transition from super-Langevin to sub-Langevin behavior with increasing activity, as a result of the coupling between structure formation and activity-induced bond breaking.

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arXiv2025

Emergent Isotropic-Nematic Transition in 3D Semiflexible Active Polymers

Active semiflexible filament collectives, ranging from motor-driven cytoskeletal filaments to slender organisms such as cyanobacteria and worm aggregates, abound in nature. Yet how activity and flexibility jointly govern their organization, especially Isotropic-Nematic (I-N) transition, remains poorly understood. Performing large-scale Brownian dynamics simulations of 3D active semiflexible polymers with varying flexibility degrees, we show that tangential active forces systematically shift the I-N transition to higher densities, with the shift controlled by the flexibility degree and activity strength. Strikingly, activity alters the nature of the transition: discontinuous at low strengths, continuous at moderate strengths, and ultimately suppressed at high activity levels. The delayed I-N transition originates from enhanced collective bending fluctuations, resulting in chain shrinkage and enlargement of effective confinement tube. At moderate activity levels, these fluctuations can trigger large-scale excitations that stochastically drive temporal transitions between nematic and isotropic states, indicating an activity-induced instability of the nematic field. We summarize this behavior in non-equilibrium state diagrams of density and activity for different flexibility degrees.

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arXiv2025

Locomotion of Active Polymerlike Worms in Porous Media

We investigate the locomotion of thin, living T. tubifex worms, which display active polymerlike behavior, within quasi-2D arrays of cylindrical pillars, examining varying spatial arrangements and densities. These active worms spread in crowded environments, with a dynamics dependent on both the concentration and arrangement of obstacles. In contrast to passive polymers, our results reveal that in disordered configurations, increasing the pillar density enhances the long-time diffusion of our active polymer-like worms, while we observe the opposite trend in ordered pillar arrays. We found that in disordered media, living worms reptate through available curvilinear tubes, whereas they become trapped within pores of ordered media. Intriguingly, we show that reducing the worm's activity significantly boosts its spread, enabling passive sorting of worms by activity level. Our experimental observations are corroborated through simulations of the tangentially driven polymer model with matched persistence length predicting the same trends.

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arXiv2025

Pore network models for the evaporation of complex fluids in porous media

Drying of fluids undergoing sol-gel transition in porous media, a process crucial for the consolidation of damaged porous structures in cultural heritage, often leads to skin formation at the surface. This phenomenon significantly hinders evaporation, yet its precise impact on drying kinetics remains poorly understood. To uncover the governing mechanisms, we develop a novel pore network model that closely replicates quasi-2D experimental porous media, incorporating spatial gradients in pore size distribution, with smaller pores near the evaporation side. We demonstrate that this pore distribution dictates the air invasion path and extends the constant-rate period of drying in Newtonian liquids, reproducing the experimental drying curves for water. We further extend our model to capture the interplay of capillary-driven liquid flows, space-dependent viscosity increases, and localized skin formation. To incorporate skin formation, we implement a viscosity-dependent evaporation pressure rule derived from experimental data on evaporation-induced sol-gel transition within a capillary tube. We identify a simple relationship: vapor pressure decreases once the meniscus fluid viscosity exceeds a critical threshold. By accounting for localized skin formation through reduced evaporation pressure at high-viscosity throats, our model successfully captures the slowdown of drying kinetics, achieving remarkable agreement with experimental drying curve.

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arXiv2024

Conformation and dynamics of wet tangentially-driven active filaments

We explore the impact of hydrodynamic interactions on the conformational and dynamical properties of wet tangentially-driven active polymers using multiparticle collision dynamics simulations. By analyzing active filaments with varying degrees of flexibility, we find that fluid-mediated interactions significantly influence both their conformation and dynamics. These interactions cause polymer conformations to shrink relative to their dry counterparts, especially for semiflexible polymers at high activity levels, where the average size of wet chains becomes nearly three times smaller, due to local buckling of wet polymers. This hydrodynamic-induced shrinkage is a hallmark of active polymers, as fluid-mediated interactions do not affect conformational properties of passive polymers. Furthermore, for tangentially-driven polymers where activity and conformation are coupled, hydrodynamic interactions significantly enhance the orientational and translational dynamics compared to their dry counterparts.

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arXiv2024

Sol-gel transition by evaporation in porous media

Historical monuments, outdoor stone sculptures and artworks made of porous materials are exposed to chemical and physical degradation over time. Presently, the most promising route for consolidation of weakened porous materials is the injection of viscoelastic solutions of polymerizing compounds. Those compounds, after injection, undergo a sol-gel transition inside the porous media through evaporation of the solvent. Finding a suitable gelifying solution as a consolidant calls for understanding the drying kinetics of viscoelastic fluids in porous media. Here, we present a multiscale study of the drying kinetics of solutions during the sol-gel transition. We investigate the drying dynamics and subsequent water uptake of a gel using NMR and X-ray microtomography techniques in porous materials. We find that during drying, a distinct front develops which separates the liquid region from the gelled region. This front advances from the free surface of evaporation towards the inner parts of the stone. We identify different drying periods which appear to be dependent on the intrinsic properties of the porous medium influencing strongly the homogeneity of the final gel distribution within a treated stone. Our findings not only are relevant for the consolidation of porous artworks but also for civil and soil engineering processes where the fluids considered are generally more complex than water.

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arXiv2023

Active motion of tangentially-driven polymers in periodic array of obstacles

We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational changes and distinct modes of transport for flexible and stiff active filaments. It leads to localization and caging of flexible polymers inside the inter-obstacle pores, while promoting more elongated conformations and enhanced diffusion for stiff polymers at low to moderate activity levels. The migration of flexible active polymers occurs via hopping events, where they unfold to move from one cage to another. In contrast, stiff chains travel mainly in straight paths within inter-obstacle channels, while occasionally changing their direction of motion. Both the duration of caging and persistent directed migration within the channels decrease with increasing the activity level. As a consequence, at high active forces polymers overcome confinement effects and transport within inter-obstacle pores as swiftly as those in free space. We explain the center of mass dynamics of semiflexible polymers in terms of active force and obstacle packing fraction by developing an approximate analytical theory.

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arXiv2023

Effects of inertia on conformation and dynamics of tangentially-driven active filaments

Active filament-like systems propelling along their backbone exist across the scales ranging from motor-driven bio-filaments to worms and robotic chains. In macroscopic active filaments such as chain of robots, in contrast to their microscopic counterparts, inertial effects on their motion cannot be ignored. Nonetheless, consequences of interplay between inertia and flexibility on shape and dynamics of active filaments remain unexplored. Here, we examine inertial effects on flexible tangentially-driven active polymer model pertinent to above examples and we determine the conditions under which inertia becomes important. Performing Langevin dynamics simulations of active polymers with underdamped and overdamped dynamics for a wide range of contour lengths and activities, we uncover striking inertial effects on conformation and dynamics at high activities. Inertial collisions increase the persistence length of active polymers and remarkably alter their scaling behavior. In stark contrast to passive polymers, inertia leaves its fingerprint at long times by an enhanced diffusion of the center of mass. We rationalize inertia-induced enhanced dynamics by analytical calculations of center of mass velocity correlations, applicable to any active polymer model, which reveal significant contributions from active force fluctuations convoluted by inertial relaxation.

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arXiv2022

Dynamical steady-states of active colloids interacting via chemical fields

We study the dynamical steady-states of a monolayer of chemically active self-phoretic colloids as a function of packing fraction and self-propulsion speed by means of Brownian dynamics simulations. We focus on the case that a chemical field induces competing attractive positional and repulsive orientational interactions. Analyzing the distribution of cluster size and local density as well as the hexatic order parameter, we distinguish four distinct dynamical states which include collapsed, active gas, dynamical clustering, and motility-induced phase-separated states. The long-range chemical field-induced interactions shift the onset of motility-induced phase separation (MIPS) to very low packing fractions at intermediate self-propulsion speeds. We also find that the fraction of particles in the largest clusters is a suitable order parameter characterizing the dynamical phase transitions from an active gas or dynamical clustering steady-state to a phase-separated state upon increase of the packing fraction. The order parameter changes discontinuously when going from an active gas to a MIPS-like state at intermediate self-propulsion speeds, whereas it changes continuously at larger activities where the system undergoes a transition from a dynamical clustering state to MIPS-like state.

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arXiv2020

Emergent pattern formation of active magnetic suspensions in an external field

We study collective self-organization of weakly magnetic active suspensions in a uniform external field by analyzing a mesoscopic continuum model that we have recently developed. Our model is based on a Smoluchowski equation for a particle probability density function in an alignment field coupled to a mean-field description of the flow arising from the activity and the alignment torque. Performing linear stability analysis of the Smoluchowski equation and the resulting orientational moment equations combined with non-linear 3D simulations, we provide a comprehensive picture of instability patterns as a function of strengths of activity and magnetic field. For sufficiently high activity and moderate magnetic field strengths, the competition between the activity-induced flow and external magnetic torque renders a homogeneous polar steady state unstable. As a result, four distinct dynamical patterns of collective motion emerge. The instability patterns for pushers include traveling bands governed by bend-twist instabilities and dynamical aggregates. For pullers, finite-sized and system spanning pillar-like concentrated regions predominated by splay deformations emerge which migrate in the field direction. Notably, at very strong magnetic fields, we observe a reentrant hydrodynamic stability of the polar steady state.

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arXiv2019

Chain level insights into tensile-compressive asymmetry in glassy and semicrystalline polymers

Using molecular dynamics simulations, we provide chain-level insights into the dissimilarities in rearrangements of polymers under uniaxial tensile and compressive deformation in glassy and semicrystalline samples of varying chain lengths. The organization of polymers under tension and compression is distinctively different. The chains align themselves along the tensile axis leading to a net global nematic ordering of their bonds and end-to-end vectors whereas under compression, the polymers arrange themselves in a plane perpendicular to the compressive axis resulting in emergence of an anti-nematic ordering of the bonds and the chain end-to-end vectors. Moreover, the degree of polymers unfolding is greater under tension and they deform less affinely when compared to chains under compression. The difference between the two responses strongly depends on the chain length and is the largest at intermediate chain lengths.

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arXiv2018

Supramolecular copolymers predominated by alternating order: theory and application

We investigate the copolymerization behavior of a two-component system into quasi-linear self-assemblies under conditions that interspecies binding is favored over identical species binding. The theoretical framework is based on a coarse-grained self-assembled Ising model with nearest neighbor interactions. In Ising language, such conditions correspond to the anti-ferromagnetic case giving rise to copolymers with predominantly alternating configurations. In the strong coupling limit, we show that the maximum fraction of polymerized material and the average length of strictly alternating copolymers depend on the stoichiometric ratio and the activation free energy of the more abundant species. They are substantially reduced when the stoichiometric ratio noticeably differs from unity. Moreover, for stoichiometric ratios close to unity, the copolymerization critical concentration is remarkably lower than the homopolymerization critical concentration of either species. We further analyze the polymerization behavior for a finite and negative coupling constant and characterize the composition of supramolecular copolymers. Our theoretical insights rationalize experimental results of supramolecular polymerization of oppositely charged monomeric species in aqueous solutions.

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arXiv2018

Static and dynamic scaling behavior of a polymer melt model with triple-well bending potential

We perform molecular-dynamics simulations for polymer melts of the coarse-grained polyvinyl alcohol model that crystallizes upon slow cooling. To establish the properties of its high temperature liquid state as a reference point, we characterize in detail the structural features of equilibrated polymer melts with chain lengths $5\le N \le 1000$ at a temperature slightly above their crystallization temperature. We find that the conformations of sufficiently long polymers with $N >50$ obey essentially the Flory's ideality hypothesis. The chain length dependence of the end-to-end distance and the gyration radius follow the scaling predictions of ideal chains and the probability distributions of the end-to-end distance, and form factors are in good agreement with those of ideal chains. The intrachain correlations reveal evidences for incomplete screening of self-interactions. However, the observed deviations are small. Our results rule out any pre-ordering or mesophase structure formation that are proposed as precursors of polymer crystallization in the melt. Moreover, we characterize in detail primitive paths of long entangled polymer melts and we examine scaling predictions of Rouse and the reptation theory for the mean squared displacement of monomers and polymers center of mass.

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arXiv2018

Controlling stability and transport of magnetic microswimmers by an external field

We investigate the hydrodynamic stability and transport of magnetic microswimmers in an external field using a kinetic theory framework. Combining linear stability analysis and nonlinear 3D continuum simulations, we show that for sufficiently large activity and magnetic field strengths, a homogeneous polar steady state is unstable for both puller and pusher swimmers. This instability is caused by the amplification of anisotropic hydrodynamic interactions due to the external alignment and leads to a partial depolarization and a reduction of the average transport speed of the swimmers in the field direction. Notably, at higher field strengths a reentrant hydrodynamic stability emerges where the homogeneous polar state becomes stable and a transport efficiency identical to that of active particles without hydrodynamic interactions is restored.

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arXiv2017

Flow properties and hydrodynamic interactions of rigid spherical microswimmers

We analyze a minimal model for a rigid spherical microswimmer and explore the consequences of its extended surface on the interplay between its self-propulsion and flow properties. The model is the first order representation of microswimmers, such as bacteria and algae, with rigid bodies and flexible propelling appendages. The flow field of such a microswimmer at finite distances significantly differs from that of a point-force (Stokeslet) dipole. For a suspension of microswimmers, we derive the grand mobility matrix that connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers. Our investigation of the mobility tensors reveals that hydrodynamic interactions among rigid-bodied microswimmers differ considerably from those among the corresponding point-force dipoles. Our results are relevant for the study of collective behavior of hydrodynamically interacting microswimmers by means of Stokesian dynamics simulations at moderate concentrations.

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arXiv2014

Interplay of anisotropy in shape and interactions in charged platelet suspensions

Motivated by the intriguing phase behavior of charged colloidal platelets, we investigate the structure and dynamics of charged repulsive disks by means of Monte-Carlo simulations. The electrostatic interactions are taken into account through an effective two-body potential, obtained within the non-linear Poisson-Boltzmann formalism, which has the form of anisotropic screened Coulomb potential. Recently, we showed that the original intrinsic anisotropy of the electrostatic potential in competition with excluded volume effects leads to a rich phase behavior that not only includes various liquid-crsytalline phases but also predicts the existence of novel structures composed of alternating nematic-antinematic sheets. Here, we examine the structural and dynamical signatures of each of the observed structures for both translational and rotational degrees of freedom. Finally, we discuss the influence of effective charge value and our results in relation to experimental findings on charged platelet suspensions.

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arXiv2012

Random, blocky and alternating ordering in supramolecular polymers of chemically bidisperse monomers

As a first step to understanding the role of molecular or chemical polydispersity in self-assembly, we put forward a coarse-grained model that describes the spontaneous formation of quasi-linear polymers in solutions containing two self-assembling species. Our theoretical framework is based on a two-component self-assembled Ising model in which the bidispersity is parameterized in terms of the strengths of the binding free energies that depend on the monomer species involved in the pairing interaction. Depending upon the relative values of the binding free energies involved, different morphologies of assemblies that include both components are formed, exhibiting paramagnetic-, ferromagnetic- or anti ferromagnetic-like order, i.e., random, blocky or alternating ordering of the two components in the assemblies. Analyzing the model for the case of ferromagnetic ordering, which is of most practical interest, we find that the transition from conditions of minimal assembly to those characterized by strong polymerization can be described by a critical concentration that depends on the concentration ratio of the two species. Interestingly, the distribution of monomers in the assemblies is different from that in the original distribution, i.e., the ratio of the concentrations of the two components put into the system. The monomers with a smaller binding free energy are more abundant in short assemblies and monomers with a larger binding affinity are more abundant in longer assemblies. Under certain conditions the two components congregate into separate supramolecular polymeric species and in that sense phase separate. We find strong deviations from the expected growth law for supramolecular polymers even for modest amounts of a second component, provided it is chemically sufficiently distinct from the main one.

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