Related papers: Parametric FEM for Shape Optimization applied to G…
The Golgi apparatus has intrigued researchers since its discovery and despite the advances, there are still many open questions in regards to its shape and function. Here, we propose a mechanical model of Golgi apparatus stack and explain…
The generation of two non-identical membrane compartments via exchange of vesicles is considered to require two types of vesicles specified by distinct cytosolic coats that selectively recruit cargo and two membrane-bound SNARE pairs that…
We conduct a systematic exploration of the energy landscape of vesicle morphologies within the framework of the Helfrich model. Vesicle shapes are determined by minimizing the elastic energy subject to constraints of constant area and…
Organelle patterning and its heritability remain central mysteries in cell biology, highlighting the fundamental tension between genetic inheritance and self-assembly. Here, we explore the nonequilibrium assembly and emdedded size control…
This paper presents a phase-field model for simulating the three-dimensional deformation of vesicle membranes, incorporating area-difference elasticity, with constraints on bulk volume and surface area. We develop efficient numerical…
The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative…
The Cellular Potts model, also known as the Glazier-Graner-Hogeweg model, is a lattice-based approach by which biological tissues at the level of individual cells can be numerically studied. Traditionally, a square or hexagonal underlying…
From the Golgi apparatus to endosomes, organelles in the endomembrane system exhibit complex and varied morphologies that are often related to their function. Such membrane-bound organelles operate far from equilibrium due to directed…
The Helfrich model is a fundamental tool for determining the morphology of biological membranes. We relate the geometry of an important class of its equilibria to the geometry of sessile and pendant drops in the hyperbolic space ${\bf…
A phase-field model that takes into account the bending energy of fluid vesicles is presented. The Canham-Helfrich model is derived in the sharp-interface limit. A dynamic equation for the phase-field has been solved numerically to find…
A thermodynamically consistent phase-field model is introduced for simulating motion and shape transformation of vesicles under flow conditions. In particular, a general slip boundary condition is used to describe the interaction between…
We present an immersed boundary method to simulate the creeping motion of a rigid particle in a fluid described by the Stokes equations discretized thanks to a finite element strategy on unfitted meshes, called Phi-FEM, that uses the…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
One of the major issues in the computational mechanics is to take into account the geometrical complexity. To overcome this difficulty and to avoid the expensive mesh generation, geometrically unfitted methods, i.e. the numerical methods…
A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically…
In this paper, we study applications of the virtual element method (VEM) for simulating the deformation of multiphase composites. The VEM is a Galerkin approach that is applicable to meshes that consist of arbitrarily-shaped polygonal and…
Tubular and membranous shapes display a wide range of morphologies that are difficult to analyze within a common framework. By generalizing the classical Helfrich energy of biomembranes, we model them as solutions to a curvature…
We consider the shape optimization of flow fields for electrochemical cells. Our goal is to improve the cell by modifying the shape of its flow field. To do so, we introduce simulation models of the flow field with and without the porous…
A phase field model for dealing with shape instabilities in fluid membrane vesicles is presented. This model takes into account the Canham-Helfrich bending energy with spontaneous curvature. A dynamic equation for the phase-field is also…
In this paper we consider the topology optimization for a bipolar plate of a hydrogen electrolysis cell. We present a model for the bipolar plate using the Stokes equation with an additional drag term, which models the influence of fluid…