This thesis is devoted to the problem of finding a suitable geometrical de- scription of the domain for the Finite Element Method (FEM). We present the most important methods used in generation and improvement of unstructured triangular meshes (grids) for two dimensional FEM. Possible measures of mesh quality are discussed with respect to their usage in linear Lagrange FEM. The relationship between mesh geometry (especially angles of particular triangles), discretization error and stiffness matrix condition number is examined. Two methods of mesh improvement, based on Centroidal Voronoi Tessellations (CVT) and Optimal Delaunay Triangulations (ODT), are discussed in detail and some results on convergence of CVT based methods are reviewed. Some aspects of these methods, e.g. the relation between density of boundary points and interior mesh vertices and the treatment of the boundary triangles is reconsidered in a new way. We have implemented these two methods and we discuss possible im- provements and new algorithms. A geometrically very interesting idea of recent alternative to FEM, Isogeometric Analysis (IGA), is outlined and demonstrated on a simple example. Several numerical tests are made in order to the compare the accuracy of solutions of isotropic PDEs obtained by FEM on bad mesh, mesh improved...

Epithelial tissues, one of the four primary tissue structures found in our human body, are known to comprise of tiny cells interconnected in a unique continuous pattern. In most cases, they serve a dual purpose of protecting the internal organs from physical damage, and at the same time, enable in facilitating inter-cellular activities and prevent pathogen break ins. While the tissue mechanics and its proliferation have been scrutinized to great detail, it is their geometric uniqueness, that has remained more or less unexplored. With an intent of doing the same, this thesis identifies and explores those geometric properties/parameters that have an influence on the micro structure’s homogenized and localized response. However, it does so by extracting the microstructures profile and representing its cell edges via three dimensional beam elements - hence the name, bio-inspired structures. The analysis is carried out by first developing a staggered Representative Volume Element (RVE)using finite elements, and identifying its appropriate size. The staggered assembly aids in minimizing boundary effects from creeping in, and at the same time, provides the requisite statistical homogeneity. This is followed by the geometry study. A wide range of epithelial geometries are considered for the study, ranging from completely isotropic skin models, to in plane anisotropic cuboidal structures and out of plane anisotropic stratified geometries. The effects of orientation, relative density and edge length are extracted and studied in great detail. It is observed that cell edges initial orientation has a direct dependence on the particle distribution, whereas the change in orientation is largely dependent on the deformation the microstructure is subjected to. Relative density is documented to show a direct correlation to a materials homogenized response i.e. larger the relative density, greater is the microstructures stiffness and homogenized stress response to the same deformation. Edge length, on the other hand is observed to showcase a downward trend on the cell edge’s axial stress. On average, in any kind of distribution and any kind of deformation, smaller cell edges are known to showcase larger stresses, as compared to the larger cell edges.

Data loss has always been a side effect of sharing 3D models between different CAD systems. Continuous research and new frameworks have been implemented to minimise the data loss in CAD and in other downstream applications separately like 3D visual graphics applications (eg. 3DS Max, Blender etc.). As a first step into this research area, the thesis is an explorative study on understanding the problem of CAD data loss while exchanging models between a CAD application and a visual application. The thesis is performed at Tacton systems which provides product configurations to their customers in both CAD and visual environments and hence the research is focussed on reusing the CAD data in visual applications or restoring the data after exchange. The research questions are framed to answer the reasons of data loss and address the possible implementation techniques at the company. Being a niche topic, the thesis required inputs from different perspectives and knowledge sharing from people outside the company which proves the significance of open innovation in technology-oriented companies. Ten different ideas were brainstormed and developed into concepts to solve the problem of data loss. All the concepts are analysed and evaluated to check the functionality and feasibility of implementing it within the company workflow. The evaluations resulted in different concepts that are capable of solving the research problem. They have also been verified with various people internal and external to the company. The results also highlight the strengths and weaknesses of each of these concepts giving clear instructions to the company on the next steps. / Dataförluster har alltid varit en följd av att dela 3D-modeller mellan olika CAD-system. I forskning har nya metoder utvecklats och implementerats för att minimera dataförlusten i CAD och andra program, som t.ex. visuella 3D-grafikapplikationer (3DS Max, Blender etc.). Denna rapport är resultatet av en studie kring CAD-dataförluster när man överför modeller mellan ett CAD-program och ett visualiseringsprogram. Studien har utförts vid Tacton Systems AB, som tillhandahåller produktkonfigureringslösningar både i CAD-program och i visuella miljöer och därför har studien haft fokus på att återanvända eller återskapa CAD-data i visualiseringsprogramvaror. Forskningsfrågorna är inriktade på att hitta orsaker till dataförlusterna och möjliga lösningar för företaget. Eftersom detta är ett högspecialiserat ämne krävde arbetet insatser från olika perspektiv och kunskapsinhämtning från människor också utanför företaget, vilket visar på betydelsen av öppen innovation i teknikorienterade företag. Tio olika idéer togs fram och utvecklades till koncept för att lösa problemet med dataförluster. Alla koncept har analyserats och utvärderats för att bedöma deras funktionalitet och genomförbarhet, för att implementera dem inom företagets arbetsflöde. Utvärderingarna resulterade i sex olika koncept som skulle kunna lösa problemet. Dessa koncept har diskuterats och verifierats med olika personer inom och utanför företaget. Resultatet visar styrkor och svagheter i vart och ett av dessa koncept och ger tydliga rekommendationer till företaget om nästa steg.

Understanding and characterising the diffusive transport of capillary oxygen and nutrients in striated muscles is key to assessing angiogenesis and investigating the efficacy of experimental and therapeutic interventions for numerous pathological conditions, such as chronic ischaemia. In articular, the influence of both muscle tissue and microvascular heterogeneities on capillary oxygen supply is poorly understood. The objective of this thesis is to develop mathematical and computational modelling frameworks for the purpose of extending and generalising the current use of histology in estimating the regions of tissue supplied by individual capillaries to facilitate the exploration of functional capillary oxygen supply in striated muscles. In particular, we aim to investigate the balance between local capillary supply of oxygen and oxygen demand in the presence of various anatomical and functional heterogeneities, by capturing tissue details from histological imaging and estimating or predicting regions of capillary supply. Our computational method throughout is based on a finite element framework that captures the anatomical details of tissue cross sections. In Chapter 1 we introduce the problem. In Chapter 2 we develop a theoretical model to describe oxygen transport from capillaries to uniform muscle tissues (e.g. cardiac muscle). Transport is then explored in terms of oxygen levels and capillary supply regions. In Chapter 3 we extend this modelling framework to explore the influence of the surrounding tissue by accounting for the spatial anisotropies of fibre oxygen demand and diffusivity and the heterogeneity in fibre size and shape, as exemplified by mixed muscle tissues (e.g. skeletal muscle). We additionally explore the effects of diffusion through the interstitium, facilitated--diffusion by myoglobin, and Michaelis--Menten kinetics of tissue oxygen consumption. In Chapter 4, a further extension is pursued to account for intracellular heterogeneities in mitochondrial distribution and diffusive parameters. As a demonstration of the potential of the models derived in Chapters 2--4, in Chapter 5 we simulate oxygen transport in myocardial tissue biopsies from rats with either impaired angiogenesis or impaired arteriolar perfusion. Quantitative predictions are made to help explain and support experimental measurements of cardiac performance and metabolism. In the final chapter we summarize the main results and indicate directions for further work.

Les tessellations, aussi appelées mosaïques, permettent de modéliser de nombreuses structures, comme des assemblages de cellules en biologie ou de grains en science des matériaux. La tessellation aléatoire la plus connue est le diagramme de Voronoï qui à partir d'un ensemble de points, appelés germes, partitionne le plan. L'approche innovante de cette thèse est d'utiliser des champs aléatoires gaussiens pour générer des germes et des distances aléatoires, qui vont permettre de simuler une grande variété de tessellations en termes de formes et de tailles des cellules.Pour connaître les propriétés des tessellations simulées à partir de champs aléatoires gaussiens, celles-ci vont être caractérisées et comparées à d'autres tessellations. Tout d'abord par une approche ponctuelle en étudiant les germes, dont leur distribution spatiale. Puis par une approche par région, en étudiant la géométrie et la morphométrie des cellules.L'endothélium cornéen humain est une monocouche de cellules formant un pavage hexagonal régulier à la naissance, et perdant de sa régularité ensuite. La qualité du greffon cornéen est donnée par certaines observations, comme la densité, l'homogénéité de la forme et des tailles des cellules endothéliales.L'évolution avec l'âge de cette mosaïque cornéenne va être caractérisée à partir d’une base d’images de l’endothélium. L'originalité est ensuite d'effectuer une estimation de l'âge d’un endothélium à partir des différentes mesures permettant de caractériser les tessellations, et enfin de mettre en place une méthode prometteuse afin de savoir si une cornée a une évolution normale. / Tessellations, also called mosaics, are used to model many structures, for example cellular arrangements in biology or grains in material science. The most known tessellation is the Voronoï diagram which partitions the space from a set of points, called germs. The innovative approach of this thesis is to use Gaussian random fields to generate germs and random distances. The use of random fields allows to simulate a great variety of tessellations in terms of cells forms and sizes.To study the properties of each type of tessellation, they are characterized: first, by studying the germs, including their spatial distribution, and then by analyzing the cells geometry and morphometry. These tessellations are also compared to other known tessellations.The human corneal endothelium is a mono-layer of cells forming a regular hexagonal mosaic at birth, and losing his regularity later. The corneal graft quality is given by some observations made on the endothelial mosaic (cells density, the homogeneity of cells sizes and shapes).A database of endothelium images allows to characterize the evolution with age of the corneal mosaic. The originality is to estimate the age of an endothelium based on the measures computed to characterize the tessellations, and finally to set up a promising method to evaluate if a corneal evolution is normal.