Viscous regularization and r-adaptive remeshing for finite element analysis of lipid membrane mechanics

As two-dimensional fluid shells, lipid bilayer membranes resist bending and stretching but are unable to sustain shear stresses. This property gives membranes the ability to adopt dramatic shape changes. In this paper, a finite element model is developed to study static equilibrium mechanics of membranes. In particular, a viscous regularization method is proposed to stabilize tangential mesh deformations and improve the convergence rate of nonlinear solvers. The Augmented Lagrangian method is used to enforce global constraints on area and volume during membrane deformations. As a validation of the method, equilibrium shapes for a shape-phase diagram of lipid bilayer vesicle are calculated. These numerical techniques are also shown to be useful for simulations of three-dimensional large-deformation problems: the formation of tethers (long tube-like exetensions); and Ginzburg-Landau phase separation of a two-lipid-component vesicle. To deal with the large mesh distortions of the two-phase model, modification of vicous regularization is explored to achieve r-adaptive mesh optimization

A computational method for the coupled solution of reaction–diffusion equations on evolving domains and manifolds: application to a model of cell migration and chemotaxis

In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk–surface reaction–diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk–surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane

Interactive Geometry Remeshing

We present a novel technique, both flexible and efficient, for interactive remeshing of irregular geometry. First, the original (arbitrary genus) mesh is substituted by a series of 2D maps in parameter space. Using these maps, our algorithm is then able to take advantage of established signal processing and halftoning tools that offer real-time interaction and intricate control. The user can easily combine these maps to create a control map – a map which controls the sampling density over the surface patch. This map is then sampled at interactive rates allowing the user to easily design a tailored resampling. Once this sampling is complete, a Delaunay triangulation and fast optimization are performed to perfect the final mesh. As a result, our remeshing technique is extremely versatile and general, being able to produce arbitrarily complex meshes with a variety of properties including: uniformity, regularity, semiregularity, curvature sensitive resampling, and feature preservation. We provide a high level of control over the sampling distribution allowing the user to interactively custom design the mesh based on their requirements thereby increasing their productivity in creating a wide variety of meshes

Geometric Surface Processing and Virtual Modeling

In this work we focus on two main topics "Geometric Surface Processing" and "Virtual Modeling". The inspiration and coordination for most of the research work contained in the thesis has been driven by the project New Interactive and Innovative Technologies for CAD (NIIT4CAD), funded by the European Eurostars Programme. NIIT4CAD has the ambitious aim of overcoming the limitations of the traditional approach to surface modeling of current 3D CAD systems by introducing new methodologies and technologies based on subdivision surfaces in a new virtual modeling framework. These innovations will allow designers and engineers to transform quickly and intuitively an idea of shape in a high-quality geometrical model suited for engineering and manufacturing purposes. One of the objective of the thesis is indeed the reconstruction and modeling of surfaces, representing arbitrary topology objects, starting from 3D irregular curve networks acquired through an ad-hoc smart-pen device. The thesis is organized in two main parts: "Geometric Surface Processing" and "Virtual Modeling". During the development of the geometric pipeline in our Virtual Modeling system, we faced many challenges that captured our interest and opened new areas of research and experimentation. In the first part, we present these theories and some applications to Geometric Surface Processing. This allowed us to better formalize and give a broader understanding on some of the techniques used in our latest advancements on virtual modeling and surface reconstruction. The research on both topics led to important results that have been published and presented in articles and conferences of international relevance

Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko

Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term observations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial distribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending.Comment: 17 pages, with 7 figures. To appear in Advances in Physics X (2018

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Finite element model of primary recrystallization in polycrystalline aggregates using a level set framework

International audienceThe paper describes a robust finite element model of interface motion in media with multiple domains and junctions, as is the case in polycrystalline materials. The adopted level set framework describes each domain (grain) with a single level set function, while avoiding the creation of overlap or vacuum between these domains. The finite element mesh provides information on stored energies, calculated from a previous deformation step. Nucleation and growth of new grains are modelled by inserting additional level set functions around chosen nodes of the mesh. The kinetics and topological evolutions induced by primary recrystallization are discussed from simple test cases to more complex configurations and compared with the Johnson-Mehl-Avrami-Kolmogorov theory

Numerical simulation of multifluid flows with the particle finite element method

In this monograph we have focused on understanding the basic physical principles of multi-fluid flows and the difficulties that arise in their numerical simulation. We have extended the Particle Finite Element Method to problems involving several different fluids with the aim of exploiting the fact that Lagrangian methods are specially well suited for tracking any kind of interfaces. We have developed a numerical scheme able to deal with large jumps in the physical properties (density and viscosity), include surface tension, and accurately represent all types of discontinuities in the flow variables at the interface. The scheme is based on decoupling the nodes position, velocity and pressure variables through the Picard linearization and a pressure segregation method which takes into account the interface conditions. The interface has been defined to be aligned with the moving mesh, so that it remains sharp along time. Furthermore, pressure degrees of freedom have been duplicated at the interface nodes to represent the discontinuity of this variable due to surface tension and variable viscosity, and the mesh has been refined in the vicinity of the interface to improve the accuracy of the computations. We have applied the resulting scheme to several academic and geological problems,such as the two-fluid sloshing, extrusion of viscous fluids, bubble rise and breakup,mixing of magmatic liquids and negatively buoyant jets.Postprint (published version