arXiv subjects

Ehssan Nazockdast

Publications and source records attributed to Ehssan Nazockdast.

13 recordsLinked to original sources

arXiv2025

Self-organization of active rod suspensions on fluid membranes and thin viscous films

Many biological processes involve transport and organization of inclusions in thin fluid interfaces. A key aspect of these assemblies is the active dissipative stresses applied from the inclusions to the fluid interface, resulting in long-range active interfacial flows. We study the effect of these active flows on the self-organization of rod-like inclusions in the interface. Specifically, we consider a dilute suspension of Brownian rods of length $L$, embedded in a thin fluid interface of 2D viscosity $\eta_m$ and surrounded on both sides with 3D fluid domains of viscosity $\eta_f$. The momentum transfer from the interfacial flows to the surrounding fluids occurs over length $\ell_0=\eta_m/\eta_f$, known as Saffman-Delbr\"uck length. We use zeroth, first and second moments of Smoluchowski equation to obtain the conservation equations for concentration, polar order and nematic order fields, and use linear stability analysis and continuum simulations to study the dynamic variations of these fields as a function of $L/\ell_0$, the ratio of active to thermal stresses, and the dimensionless self-propulsion velocity of the embedded particles. We find that at sufficiently large activities, the suspensions of active extensile stress (pusher) with no directed motion undergo a finite wavelength nematic ordering, with the length of the ordered domains decreasing with increasing $L/\ell_0$. The ordering transition is hindered with further increases in $L/\ell_0$. In contrast, the suspensions with active contractile stress (puller) remain uniform with variations of activity. We notice that the self-propulsion velocity results in significant concentration fluctuations and changes in the size of the order domains that depend on $L/\ell_0$. Our research highlights the role of hydrodynamic interactions in the self-organization of active inclusions on biological interfaces.

cond-mat.soft↗

arXiv2024

Using Activity to Compartmentalize Binary Mixtures

We computationally study suspensions of slow and fast active Brownian particles that have undergone motility induced phase separation and are at steady state. Such mixtures, of varying non-zero activity, remain largely unexplored even though they are relevant for a plethora of systems and applications ranging from cellular biophysics to drone swarms. Our mixtures are modulated by their activity ratios ($\mathrm{Pe}^\mathrm{R}$), which we find to encode information by giving rise to three regimes, each of which display their unique emergent behaviors. Specifically, we found non-monotonic behavior of macroscopic properties, e.g. density and pressure, as a function of activity ratio, microphase separation of fast and slow particle domains, increased fluctuations on the interface and severe avalanche events compared to monodisperse active systems. Our approach of simultaneously varying the two activities of the particle species allowed us to discover these behaviors and explain the microscopic physical mechanisms that drive them.

cond-mat.soft↗

arXiv2023

Reciprocal theorem for linear poro-viscoelastic materials

In studying the transport of particles and inclusions in multi-phase systems we are often interested in integrated quantities such as the total force and the net velocity of the particles. Here, we derive a reciprocal formulation for linear poro-viscoelastic (PVE) materials, which are composed of a linear compressible viscoelastic phase, i.e. the network phase, permeated by a viscous fluid. As an application of the reciprocal theorem, we analytically calculate the time-dependent net force on a rigid stationary sphere in response to point-forces applied to the elastic network and Newtonian fluid phases of a PVE material. We show that the net force on the sphere in response to a point-force in the fluid phase evolves over timescales that are independent of the distance of the point-force to the sphere; in comparison, when the point-force is applied to the network phase the timescale for force development becomes distance-dependent. We discuss how in both cases these relaxation times are related to the physical timescales that are determined by mechanical properties of both phases -- such as the network's Poisson ratio, permeability and shear modules, and the fluid viscosity -- as well as geometric factors, including the size of the spherical inclusion and its distance from point-forces. The reciprocal theorem presented here can be applied to a wide range of problems involving the transport of cells, organelles and condensates in biological systems composed of filamentous networks permeated by viscous fluids.

cond-mat.soft↗

arXiv2023

The drag of a filament moving in a supported spherical bilayer

Many of the cell membrane vital functions are achieved by the self-organization of the proteins and biopolymers embedded in it. The protein dynamics are in part determined by its drag. A large number of these proteins can polymerize to form filaments. In-vitro studies of protein-membrane interactions often involve using rigid beads coated with lipid bilayers, as a model for the cell membrane. Motivated by this, we use slender-body theory to compute the translational and rotational resistance of a single filamentous protein embedded in the outer layer of a supported bilayer membrane and surrounded on the exterior by a Newtonian fluid. We first consider the regime, where the two layers are strongly coupled through their inter-leaflet friction. We find that the drag along the parallel direction grows linearly with the filament length and quadratically with the length for perpendicular and the rotational drag coefficients. These findings are explained using scaling arguments and by analyzing the velocity fields around the moving filament. We, then, present and discuss the qualitative differences between the drag of a filament moving in a freely suspended bilayer and a supported membrane as a function of the membrane inter-leaflet friction. Finally, we briefly discuss how these findings can be used in experiments to determine membrane rheology. In summary, we present a formulation that allows computing the effects of membrane properties (its curvature, viscosity, and inter-leaflet friction), and the exterior and interior 3D fluids depth and viscosity on the drag of a rod-like or filamentous protein, all in a unified theoretical framework.

physics.flu-dyn↗

arXiv2022

Hydrodynamics of a single filament moving in a fluid spherical membrane

Dynamic organization of the cytoskeletal filaments and rod-like proteins in the cell membrane and other biological interfaces occurs in many cellular processes. Previous modeling studies have considered the dynamics of a single rod on fluid planar membranes. We extend these studies to the more physiologically relevant case of a single filament moving in a spherical membrane. Specifically, we use a slender-body formulation to compute the translational and rotational resistance of a single filament of length $L$ moving in a membrane of radius $R$ and 2D viscosity $η_m$, and surrounded on its interior and exterior with Newtonian fluids of viscosities $η^{-}$ and $η^{+}$. We first discuss the case where the filament's curvature is at its minimum $κ=1/R$. We show that the boundedness of spherical geometry gives rise to flow confinement effects that increase in strength with increasing the ratio of filament's length to membrane radius $L/R$. These confinement flows only result in a mild increase in filament's resistance along its axis, $ξ_{\parallel}$, and its rotational resistance, $ξ_Ω$. As a result, our predictions of $ξ_\parallel$ and $ξ_Ω$ can be quantitatively mapped to the results on a planar membrane. In contrast, we find that the drag in perpendicular direction, $ξ_\perp$, increases superlinearly with the filament's length, when $L/R >1$ and ultimately $ξ_\perp \to \infty$ as $L/R \to π$. Next, we consider the effect of the filament's curvature, $κ$, on its parallel motion, while fixing the membrane's radius. We show that the flow around the filament becomes increasingly more asymmetric with increasing its curvature. These flow asymmetries induce a net torque on the filament, coupling its parallel and rotational dynamics. This coupling becomes stronger with increasing $L/R$ and $κ$.

physics.flu-dyn↗

arXiv2021

The Projection Extension Method: A Spectrally Accurate Technique for Complex Domains

An essential ingredient of a spectral method is the choice of suitable bases for test and trial spaces. On complex domains, these bases are harder to devise, necessitating the use of domain partitioning techniques such as the spectral element method. In this study, we introduce the Projection Extension (PE) method, an approach that yields spectrally accurate solutions to various problems on complex geometries without requiring domain decomposition. This technique builds on the insights used by extension methodologies such as the immersed boundary smooth extension and Smooth Forcing Extension (SFE) methods that are designed to improve the order of accuracy of the immersed boundary method. In particular, it couples an accurate extension procedure, that functions on arbitrary domains regardless of connectedness or regularity, with a least squares minimization of the boundary conditions. The resulting procedure is stable under iterative application and straightforward to generalize to higher dimensions. Moreover, it rapidly and robustly yields exponentially convergent solutions to a number of challenging test problems, including elliptic, parabolic, Newtonian fluid flow, and viscoelastic problems.

math.NA↗

arXiv2021

General solutions of poroelastic equations with viscous stress

Mechanical properties of cellular structures, including the cell cytoskeleton, are increasingly used as biomarkers for disease diagnosis and fundamental studies in cell biology. Recent experiments suggest that the cell cytoskeleton and its permeating cytosol, can be described as a poroelastic (PE) material. Biot theory is the standard model used to describe PE materials. Yet, this theory does not account for the fluid viscous stress, which can lead to inaccurate predictions of the mechanics in the dilute filamentous network of the cytoskeleton. Here, we adopt a two-phase model that extends Biot theory by including the fluid viscous stresses in the fluid's momentum equation. We use generalized linear viscoelastic (VE) constitutive equations to describe the permeating fluid and the network stresses and assume a constant friction coefficient that couples the fluid and network displacement fields. As the first step in developing a computational framework for solving the resulting equations, we derive closed-form general solutions of the fluid and network displacement fields in spherical coordinates. To demonstrate the applicability of our results, we study the motion of a rigid sphere moving under a constant force inside a PE medium, composed of a linear elastic network and a Newtonian fluid. We find that the network compressibility introduces a slow relaxation of the sphere and a non-monotonic network displacements with time along the direction of the applied force. These novel features cannot be predicted if VE constitutive equation is used for the medium. We show that our results can be applied to particle-tracking microrheology to differentiate between PE and VE materials and to independently measure the permeability and VE properties of the fluid and the network phases.

cond-mat.soft↗

arXiv2021

Dependence of phase behavior and surface tension on particle stiffness for active Brownian particles

We study quasi two-dimensional, monodisperse systems of active Brownian particles (ABPs) for a range of activities, stiffnesses, and densities. We develop a microscopic, analytical method for predicting the dense phase structure formed after motility-induced phase separation (MIPS) has occurred, including the dense cluster's area fraction, interparticle pressure, and radius. Our predictions are in good agreement with our Brownian dynamics simulations. We, then, derive a continuum model to investigate the relationship between the predicted interparticle pressure, the swim pressure, and the macroscopic pressure in the momentum equation. We find that formulating the point-wise macroscopic pressure as the interparticle pressure and modeling the particle activity through a spatially variant body force -- as opposed to a volume-averaged swim pressure -- results in consistent predictions of pressure in both the continuum model and the microscopic theory. This formulation of pressure also results in nearly zero surface tension for the phase separated domains, irrespective of activity, stiffness, and area fraction. Furthermore, using Brownian dynamics simulations and our continuum model, we showed that both the interface width and surface tension, are intrinsic characteristics of the system. On the other hand, if we were to exclude the body force induced by activity, we find that the resulting surface tension values are linearly dependent on the size of the simulation, in contrast to the statistical mechanical definition of surface tension.

cond-mat.soft↗

arXiv2020

Cell nucleus as a microrheological probe to study the rheology of the cytoskeleton

Mechanical properties of the cell are important biomarkers for probing its architectural changes caused by cellular processes and/or pathologies. The development of microfluidic technologies have enabled measuring cell mechanics at high-throughput, so that mechanical phenotyping can be applied to large samples in reasonable time-scales. These studies typically measure the stiffness of the cell as the only mechanical biomarker, and cannot disentangle the rheological contribution of different structural components of the cell, including the cell cortex, the interior cytoplasm and its immersed cytoskeletal structures, and the nucleus. Recent advancements in high-speed fluorescent imaging have enabled probing the deformations of the cell cortex, while also tracking different intracellular components in rates applicable to microfluidic platforms. We present a novel method to decouple the mechanics of the cell cortex and the cytoplasm by analyzing the correlation between the cortical deformations that are induced by external microfluidic flows, and the nucleus displacements induced by those cortical deformations; i.e. we use the nucleus as a high-throughput microrheological probe to study the rheology of the cytoplasm, independent of the cell cortex mechanics. To demonstrate the applicability of this method, we consider a proof of concept model consisting of a rigid spherical nucleus centered in a spherical cell. We obtain analytical expressions for time-dependent nucleus velocity as a function of the cell deformations, when the interior cytoplasm is modeled as a viscous, viscoelastic, porous and poroelastic materials, and demonstrate how the nucleus velocity can be used to characterize the linear rheology of the cytoplasm over a wide range of forces and time-scales/frequencies.

cond-mat.soft↗

arXiv2019

An integral equation method for the simulation of doubly-periodic suspensions of rigid bodies in a shearing viscous flow

With rheology applications in mind, we present a fast solver for the time-dependent effective viscosity of an infinite lattice containing one or more neutrally buoyant smooth rigid particles per unit cell, in a two-dimensional Stokes fluid with given shear rate. At each time, the mobility problem is reformulated as a 2nd-kind boundary integral equation, then discretized to spectral accuracy by the Nystrom method and solved iteratively, giving typically 10 digits of accuracy. Its solution controls the evolution of particle locations and angles in a first-order system of ordinary differential equations. The formulation is placed on a rigorous footing by defining a generalized periodic Green's function for the skew lattice. Numerically, the periodized integral operator is split into a near image sum|applied in linear time via the fast multipole method|plus a correction field solved cheaply via proxy Stokeslets. We use barycentric quadratures to evaluate particle interactions and velocity fields accurately, even at distances much closer than the node spacing. Using first-order time-stepping we simulate, eg, 25 ellipses per unit cell to 3-digit accuracy on a desktop in 1 hour per shear time. Our examples show equilibration at long times, force chains, and two types of blow-ups (jamming) whose power laws match lubrication theory asymptotics.

math.NA↗

arXiv2016

A fast platform for simulating flexible fiber suspensions applied to cell mechanics

We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular fiber assemblies. We use the non-local slender body theory to compute the fluid-structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multiple method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by the nonlinear Euler--Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit HIs in the time-stepping to resolve large fiber deformations, and to allow time-steps not constrained by temporal stiffness or fiber-fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries.

math.NA↗

arXiv2015

Cytoplasmic flows as signatures for the mechanics of mitotic positioning

The proper positioning of the mitotic spindle is crucial for asymmetric cell division and generating cell diversity during development. Proper position in the single-cell embryo of Caenorhabditis elegans is achieved initially by the migration and rotation of the pronuclear complex (PNC) and its two associated centrosomal arrays of microtubules (MTs). We present here the first systematic theoretical study of how these $O(1000)$ centrosomal microtubules (MTs) interact through the immersing cytoplasm, the cell periphery and PNC, and with each other, to achieve proper position. This study is made possible through our development of a highly efficient and parallelized computational framework that accounts explicitly for long-ranged hydrodynamic interactions (HIs) between the MTs, while also capturing their flexibility, dynamic instability, and interactions with molecular motors and boundaries. First, we show through direct simulation that previous estimates of the PNC drag coefficient, based on either ignoring or partially including HIs, lead to misprediction of the active forces and time-scales of migration. We then directly study the dynamics of PNC migration under various force-transduction models, including the pushing or pulling of MTs at the cortex, and the pulling of MTs by cytoplasmically-bound force generators. While achieving proper position and orientation on physiologically reasonable time-scales does not uniquely choose a model, we find that each model produces a different signature in its induced cytoplasmic flow and MT conformations. We suggest then that cytoplasmic flows and MT conformations can be used to differentiate between mechanisms and to determine their contribution to the migration process.

physics.bio-ph↗

arXiv2015

Active microrheology of colloidal suspensions: simulation and microstructural theory

Accelerated Stokesian Dynamics (ASD) simulation and a microstructural theory are applied to study structure and the viscosity of hard-sphere Brownian suspensions in active microrheology (MR).We consider moderate to dense suspensions, from near to far from equilibrium conditions.The theory explicitly considers many-body hydrodynamic interactions (HIs) in active MR, and is compared with ASD.Two conditions of moving the probe with constant force (CF) and constant velocity (CV) are considered.The structure is quantified using the probability distribution of colloidal particles around the probe, g(r), which is computed as a solution to the pair Smoluchowski equation (SE) for 0.2<ϕ<0.50, and a range of Peclet numbers (Pe), describing the ratio of external force on the probe to thermal forces.Results of ASD and theory demonstrate that a wake zone depleted of bath particles behind the moving probe forms at large Pe, while a boundary-layer accumulation develops upstream.The wake length saturates at Pe>>1 for CF while it continuously grows in CV.This contrast in behavior is related to the dispersion in the motion of the probe under CF conditions, while CV motion has no dispersion.This effect is incorporated in the theory as a force-induced hydrodynamic diffusion flux in the pair SE. We also demonstrate that, despite this difference of structure in CF and CV, g(r) near the probe is set by Pe, for both CF and CV resulting in similar values for their viscosity.Using the theory, the structural anisotropy and Brownian viscosity near equilibrium are shown to be quantitatively similar in both CF and CV motions, which is in contrast with the dilute theory which predict distortions and Brownian viscosities twice as large in CV, relative to CF.This difference arises due to the many-body interactions associated with the equilibrium structure in the moderate to dense regime.

cond-mat.soft↗