arXiv subjects

Mohammad Abu Hamed

Publications and source records attributed to Mohammad Abu Hamed.

7 recordsLinked to original sources

arXiv2023

Physical phase field model for phagocytosis

We propose and study a simple, physical model for phagocytosis, i.e. the active, actin-mediated uptake of micron-sized particles by biological cells. The cell is described by the phase field method and the driving mechanisms of uptake are actin ratcheting, modeled by a dynamic vector field, as well as cell-particle adhesion due to receptor-ligand binding. We first test the modeling framework for the symmetric situation of a spherical cell engulfing a fixed spherical particle. We then exemplify its versatility by studying various asymmetric situations like different particle shapes and orientations, as well as the simultaneous uptake of two particles. In addition, we perform a perturbation theory of a slightly modified model version in the symmetric setting, allowing to derive a reduced model, shedding light on the effective driving forces and being easier to solve. This work is meant as a first step in describing phagocytosis and we discuss several effects that are amenable to future modeling within the same framework.

cond-mat.soft↗

arXiv2021

Phase field model for phagocytosis dynamics

The basic process of the innate immune system when phagocyte (white blood cell) engulf or swallow a target particle (bacterium or dead cell), is called phagocytosis. We apply the phase field approach in the spirit of [1], that couples the order parameter $u$ with 3D polarization (orientation) vector field $\textbf{P}$ of the actin network of the phagocyte cytoskeleton. We derive a single closed scalar integro-differential equation governing the 3D phagocyte membrane dynamics during bead engulfment, which includes the normal velocity of the membrane, curvature, volume relaxation rate, a function determined by the molecular effects of the subcell level, and the adhesion effect of the motionless rigid spherical bead. This equation is easily solved numerically. The simulation manifests the pedestal and the cup phases but not the final complete bead internalization.

physics.bio-ph↗

arXiv2021

Phase field model for cell spreading dynamics

We suggest a 3D phase field model to describe 3D cell spreading on a flat substrate. The model is a simplified version of a minimal model that was developed in [1]. Our model couples the order parameter $u$ with 3D polarization (orientation) vector field $\textbf{P}$ of the actin network. We derive a closed integro-differential equation governing the 3D cell spreading dynamics on a flat substrate, which includes the normal velocity of the membrane, curvature, volume relaxation rate, a function determined by the molecular effects of the subcell level, and the adhesion effect. This equation is easily solved numerically. The results are in agreement with the early fast phase observed experimentally in [2]. Also we find agreement with the universal power law [3] which suggest that cell adhesion or contact area versus time behave as $\sim t^{1/2}$ in the early stage of cell spreading dynamics, and slow down at the next stages.

physics.bio-ph↗

arXiv2021

Three-dimensional phase field model for actin-based cell membrane dynamics

The interface dynamics of a 3D cell immersed in a 3D extracellular matrix is investigated. We suggest a 3D generalization of a known 2D minimal phase field model suggested in [1] for the description of keratocyte motility. Our model consists of two coupled evolution equations for the order parameter and a three-dimensional vector field describing the actin network polarization (orientation). We derive a closed evolutionary integro-differential equation governing the interface dynamics of a 3D cell. The equation includes the normal velocity of the membrane, its curvature, cell volume relaxation, and a parameter that is determined by the non-equilibrium effects in the cytoskeleton. This equation can be considered as a 3D generalization of the 2D case that was derived in [2].

physics.bio-ph↗

arXiv2019

A simple model of Keratocyte membrane dynamics

We perform an analytical investigation of the cell interface dynamics in the framework of a minimal phase field model of cell motility suggested in [1], which consists of two coupled evolution equations for the order parameter and a two-dimensional vector field describing the actin network polarization (orientation). We derive a closed evolutionary integro-differential equation governing the cell interface dynamics. The equation includes the normal velocity of the membrane, curvature, volume relaxation, and a parameter that is determined by the non-equilibrium effects in the cytoskeleton. This equation can be simplified to obtain a Burgers-like equation. A condition on the system parameters for the existence of a stationary cell shape is obtained.

physics.bio-ph↗

arXiv2018

Longwave nonlinear theory for chemically active droplet division instability

It has been suggested recently that growth and division of a protocell could be modeled by a chemically active droplet with simple chemical reactions driven by an external fuel supply. This model is called the continuum model. Indeed it's numerical simulation reveals a shape instability which results in droplet division into two smaller droplets of equal size resembling cell division [1]. In this paper, we investigate the reduced version of the continuum model, which is called the effective model. This model is studied both in the linear and nonlinear regime. First, we perform a linear stability analysis for the flat interface, and then we develop a nonlinear theory using the longwave approach. We find that the interface at the leading order is governed by the modified Kuramoto-Sivashinsky equation. Therefore the interface is subject to a logarithmic blow up after a finite time. In addition, an expression for the interface local velocity is obtained.

physics.bio-ph↗

arXiv2014

Inertial Manifolds for Certain Sub-Grid Scale $α$-Models of Turbulence

In this note we prove the existence of an inertial manifold, i.e., a global invariant, exponentially attracting, finite-dimensional smooth manifold, for two different sub-grid scale $α$-models of turbulence: the simplified Bardina model and the modified Leray-$α$ model, in two-dimensional space. That is, we show the existence of an exact rule that parameterizes the dynamics of small spatial scales in terms of the dynamics of the large ones. In particular, this implies that the long-time dynamics of these turbulence models is equivalent to that of a finite-dimensional system of ordinary differential equations.

math.DS↗