The work developed in this thesis focusses on the electrical activity of the heart, from the modeling of the action potential originating from cardiac cells and propagating through the heart, as well as its electrical manifestation at the body surface. The study is divided in two main parts: modeling the action potential, and numerical simulations. For modeling the action potential a dimensional and asymptotic analysis is done. The key advance in this part of the work is that this analysis gives the steps to reliably control the action potential. It allows predicting the time/space scales and speed of any action potential that is to say the shape of the action potential and its propagation. This can be done as the explicit relations on all the physiological constants are defined precisely. This method facilitates the integrative modeling of a complete human heart with tissue-specific ionic models. It even proves that using a single model for the cardiac action potential is enough in many situations. For efficient numerical simulations, a numerical method for solving the heart-torso coupling problem is explored according to a level set description of the domains. This is done in the perspective of using directly medical images for building computational domains. A finite element method is then developed to manage meshes not adapted to internal interfaces. Finally, an anisotropic adaptive remeshing methods for unstructured finite element meshes is used to efficiently capture propagating action potentials within complex, realistic two dimensional geometries.

The work developed in this thesis focusses on the electrical activity of the heart, from the modeling of the action potential originating from cardiac cells and propagating through the heart, as well as its electrical manifestation at the body surface. The study is divided in two main parts: modeling the action potential, and numerical simulations. For modeling the action potential a dimensional and asymptotic analysis is done. The key advance in this part of the work is that this analysis gives the steps to reliably control the action potential. It allows predicting the time/space scales and speed of any action potential that is to say the shape of the action potential and its propagation. This can be done as the explicit relations on all the physiological constants are defined precisely. This method facilitates the integrative modeling of a complete human heart with tissue-specific ionic models. It even proves that using a single model for the cardiac action potential is enough in many situations. For efficient numerical simulations, a numerical method for solving the heart-torso coupling problem is explored according to a level set description of the domains. This is done in the perspective of using directly medical images for building computational domains. A finite element method is then developed to manage meshes not adapted to internal interfaces. Finally, an anisotropic adaptive remeshing methods for unstructured finite element meshes is used to efficiently capture propagating action potentials within complex, realistic two dimensional geometries.

The work developed in this thesis focusses on the electrical activity of the heart, from the modeling of the action potential originating from cardiac cells and propagating through the heart, as well as its electrical manifestation at the body surface. The study is divided in two main parts: modeling the action potential, and numerical simulations. For modeling the action potential a dimensional and asymptotic analysis is done. The key advance in this part of the work is that this analysis gives the steps to reliably control the action potential. It allows predicting the time/space scales and speed of any action potential that is to say the shape of the action potential and its propagation. This can be done as the explicit relations on all the physiological constants are defined precisely. This method facilitates the integrative modeling of a complete human heart with tissue-specific ionic models. It even proves that using a single model for the cardiac action potential is enough in many situations. For efficient numerical simulations, a numerical method for solving the heart-torso coupling problem is explored according to a level set description of the domains. This is done in the perspective of using directly medical images for building computational domains. A finite element method is then developed to manage meshes not adapted to internal interfaces. Finally, an anisotropic adaptive remeshing methods for unstructured finite element meshes is used to efficiently capture propagating action potentials within complex, realistic two dimensional geometries.

Aquesta tesi proposa una estructura de dades per emmagatzemar imatges tridimensionals. L'estructura da dades té forma d'arbre i codifica les components connexes dels conjunts de nivell de la imatge. Aquesta estructura és la eina bàsica per moltes aplicacions proposades: operadors morfològics tridimensionals, visualització d'imatges mèdiques, anàlisi d'histogrames de color, seguiment d'objectes en vídeo i detecció de vores. Motivada pel problema de la completació de vores, la tesi conté un estudi de com l'eliminació de soroll mitjançant variació total anisòtropa es pot fer servir per calcular conjunts de Cheeger en mètriques anisòtropes. Aquests conjunts de Cheeger anisòtrops es poden utilitzar per trobar òptims globals d'alguns funcionals per completar vores. També estan relacionats amb certs invariants afins que s'utilitzen en reconeixement d'objectes, i en la tesi s'explicita aquesta relació. / This thesis proposes a tree data structure to encode the connected components of level sets of 3D images. This data structure is applied as a main tool in several proposed applications: 3D morphological operators, medical image visualization, analysis of color histograms, object tracking in videos and edge detection. Motivated by the problem of edge linking, the thesis contains also an study of anisotropic total variation denoising as a tool for computing anisotropic Cheeger sets. These anisotropic Cheeger sets can be used to find global optima of a class of edge linking functionals. They are also related to some affine invariant descriptors which are used in object recognition, and this relationship is laid out explicitly.

Cette thèse présente un nouveau concept pour l’évaluation des déformations cardiaques à partir de ciné-IRM standard sans avoir recours aux images IRM marquées. Nous avons adapté la méthode des ensembles de niveaux afin de segmenter le myocarde et évalué le déplacement des contours endo et épicardique. Le processus de segmentation est appliqué directement sur un ensemble d’images pseudo-volumique 2D + t. Cela conduit à une méthode de segmentation efficace tenant compte à la fois des contraintes de continuité spatiale et temporelle. Puis, nous avons évalué le déplacement des contours endo et épicardique détectés avec une technique de mise en correspondance fondée sur les ensembles de niveaux. La vitesse de déplacement au sein de la paroi myocardique est évaluée par une méthode de flot optique, contrainte avec le déplacement des contours. Enfin, de ce champ de vitesses du myocarde, nous tirons des mesures pertinentes de la contraction cardiaque. La validation de la méthode proposée est effectuée sur des séquences d'images synthétiques, et en comparant sur les mêmes patients nos mesures à celles obtenues avec la méthode de référence HARP appliquée sur des images IRM taggées correspondantes. Les résultats de la méthode sont encourageants, ils sont pratiquement identiques à ceux de l’approche HARP. Cette méthode présente deux avantages principaux: premièrement elle exploite les ciné-IRM standard non taggées, deuxièmement elle permet des évaluations des déformations à haute résolution spatiale. Cette méthode est déjà disponible et peut rendre accessible l’évaluation des déformations du ventricule gauche du myocarde en routine clinique à partir des séquences ciné-IRM / This thesis presents a new concept for the assessment of cardiac deformation from standard cine-MRI without requiring tagged MRI. We have adapted the level set method to segment the myocardium and to evaluate the endocardial and epicardial velocity contours. The segmentation process is directly applied on a pseudo-volumic 2D+t set of images. This leads to an efficient segmentation method that both take into account spatial and temporal continuity constraints. Then, we evaluated the displacement of detected endocardial and epicardial contours by a levelset based matching procedure. The velocity flow in the myocardial wall is assessed by an optical flow method constrained with the contour displacement. Finally, from the velocity flow, we derive relevant measurements of the cardiac contraction. The validation of the method is performed on synthetic image sequences, and by comparing our measurements to those obtained on the same patients with the HARmonic Phase reference (HARP) method applied on matched tagged MR images. The results of this method are encouraging, they are practically identical to those HARP approach. This method presents two main advantages: first it exploits standard untagged cine-MRI, secondly it leads to high spatial resolution strain assessments. This method is readily available and has potential to make the assessment of left ventricular myocardial deformation accessible for clinical use from a set of cardiac cine MR acquisitions

The work developed in this thesis focusses on the electrical activity of the heart, from the modeling of the action potential originating from cardiac cells and propagating through the heart, as well as its electrical manifestation at the body surface. The study is divided in two main parts: modeling the action potential, and numerical simulations. For modeling the action potential a dimensional and asymptotic analysis is done. The key advance in this part of the work is that this analysis gives the steps to reliably control the action potential. It allows predicting the time/space scales and speed of any action potential that is to say the shape of the action potential and its propagation. This can be done as the explicit relations on all the physiological constants are defined precisely. This method facilitates the integrative modeling of a complete human heart with tissue-specific ionic models. It even proves that using a single model for the cardiac action potential is enough in many situations. For efficient numerical simulations, a numerical method for solving the heart-torso coupling problem is explored according to a level set description of the domains. This is done in the perspective of using directly medical images for building computational domains. A finite element method is then developed to manage meshes not adapted to internal interfaces. Finally, an anisotropic adaptive remeshing methods for unstructured finite element meshes is used to efficiently capture propagating action potentials within complex, realistic two dimensional geometries.

Level-set methods have become a valuable and well-established field of visualization over the last decades. Different implementations addressing different design goals and different data types exist. In particular, level sets can be used to extract isosurfaces from scalar volume data that fulfill certain smoothness criteria. Recently, such an approach has been generalized to operate on unstructured point-based volume data, where data points are not arranged on a regular grid nor are they connected in form of a mesh. Utilizing this new development, one can avoid an interpolation to a regular grid which inevitably introduces interpolation errors. However, the global processing of the level-set function can be slow when dealing with unstructured point-based volume data sets containing several million data points. We propose an improved level-set approach that performs the process of the level-set function locally. As for isosurface extraction we are only interested in the zero level set, values are only updated in regions close to the zero level set. In each iteration of the level-set process, the zero level set is extracted using direct isosurface extraction from unstructured point-based volume data and a narrow band around the zero level set is constructed. The band consists of two parts: an inner and an outer band. The inner band contains all data points within a small area around the zero level set. These points are updated when executing the level set step. The outer band encloses the inner band providing all those neighbors of the points of the inner band that are necessary to approximate gradients and mean curvature. Neighborhood information is obtained using an efficient kd-tree scheme, gradients and mean curvature are estimated using a four-dimensional least-squares fitting approach. Comparing ourselves to the global approach, we demonstrate that this local level-set approach for unstructured point-based volume data achieves a significant speed-up of one order of magnitude for data sets in the range of several million data points with equivalent quality and robustness.

Interface balance laws are derived to describe transport across a phase interface. This is used to derive generalized conditions for phase nucleation and growth, valid even for solids with inhomogeneous surface stress.<div><br></div><div>An explicit interface tracking approach called Enriched Isogeometric Analysis (EIGA) is used to simulate phase evolution. Algebraic level sets are used as a measure of distance and for point projection, both necessary operations in EIGA. Algebraic level sets are observed to often fail for surfaces. Rectification measures are developed to make algebraic level sets more robust and applicable for general surfaces. The proposed methods are demonstrated on electromigration problems. The simulations are validated by modeling electromigration experiments conducted on Cu-TiN line structures.</div><div><br></div><div>To model topological changes, common in phase evolution problems, Boolean operations are performed on the algebraic level sets using R-functions. This is demonstrated on electromigration simulations on solids with multiple voids, and on a bubble coalescence problem. </div>

<p>Moving boundary problems such as solidification, crack propagation, multi-body contact or shape optimal design represent an important class of engineering problems. Common to these problems are one or more moving interfaces or boundaries. One of the main challenges associated with boundary evolution is the difficulty that arises when the topology of the geometry changes. Other geometric issues such as distance to the boundary, projected point on the boundary and intersection between surfaces are also important and need to be efficiently solved. In general, the present thesis is concerned with the geometric arrangement and behavioral analysis of evolving parametric boundaries immersed in a domain. </p> <p>The first problem addressed in this thesis is the packing of ellipsoidal fillers in a regular domain and to estimate their effective physical behavior. Particle packing problem arises when one generates simulated microstructures of particulate composites. Such particulate composites used as thermal interface materials (TIMs) motivates this work. The collision detection and distance calculation between ellipsoids is much more difficult than other regular shapes such as spheres or polyhedra.  While many existing methods address the spherical packing problems, few appear to achieve volume loading exceeding 60%. The packing of ellipsoidal particles is even more difficult than that of spherical particles due to the need to detect contact between the particles. In this thesis, an efficient and robust ultra-packing algorithm termed Modified Drop-Fall-Shake is developed. The algorithm is used to simulate the real mixing process when manufacturing TIMs with hundreds of thousands ellipsoidal particles. The effective thermal conductivity of the particulate system is evaluated using an algorithm based on Random Network Model. </p> <p><br></p> <p>In problems where general free-form parametric surfaces (as opposed to the ellipsoidal fillers) need to be evolved inside a regular domain, the geometric distance from a point in the domain to the boundary is necessary to determine the influence of the moving boundary on the underlying domain approximation. Furthermore, during analysis, since the driving force behind interface evolution depends on locally computed curvatures and normals, it is ideal if the parametric entity is not approximated as piecewise-linear. To address this challenge,  an algebraic procedure is presented here to find the level sets of rational parametric surfaces commonly utilized by commercial CAD systems. The developed technique utilizes the resultant theory to construct implicit forms of parametric Bezier patches, level sets of which are termed algebraic level sets (ALS). Boolean compositions of the algebraic level sets are carried out using the theory of R-functions. The algebraic level sets and their gradients at a given point on the domain can also be used to project the point onto the immersed boundary. Beginning with a first-order algorithm, sequentially refined procedures culminating in a second-order projection algorithm are described for NURBS curves and surfaces. Examples are presented to illustrate the efficiency and robustness of the developed method. More importantly, the method is shown to be robust and able to generate valid solutions even for curves and surfaces with high local curvature or G₀ continuity---problems where the Newton--Raphson method fails due to discontinuity in the projected points or because the numerical iterations fail to converge to a solution, respectively. </p> <p><br></p> <p>Next, ALS is also extended for boundary representation (B-rep) models that are popularly used in CAD systems for modeling solids. B-rep model generally contains multiple NURBS patches due to the trimming feature used to construct such models, and as a result are not ``watertight" or mathematically compatible at patch edges. A time consuming geometry clean-up procedure is needed to preprocess geometry prior to finite element mesh generation using a B-rep model, which can take up to 70% of total analysis time according to literature. To avoid the need to clean up geometry and directly provide link between CAD and CAE integration,  signed algebraic level sets using novel inner/outer bounding box strategy is proposed for point classification of B-rep model. Several geometric examples are demonstrated, showing that this technique naturally models single patch NURBS geometry as well, and can deal with multiple patches involving planar trimming feature and Boolean operation. During the investigation of algebraic level sets, a complex self-intersection problem is also reported, especially for three-dimensional surface. The self-intersection may occur within an interval of interest during implicitization of a curve or surface since the implicitized curve or surface is not trimmed and extends to infinity. Although there is no robust and universal solution the problem, two potential solutions are provided and discussed in this thesis.</p> <p><br></p> <p>In order to improve the computational efficiency of analysis in immersed boundary problems, an efficient local refinement technique for both mesh and quadrature  using the kd-tree data structure is further proposed. The kd-tree sub-division is theoretically proved to be more efficient against traditional quad-/oct-tree subdivision methods. In addition, an efficient local refinement strategy based on signed algebraic level sets is proposed to divide the cells. The efficiency of kd-tree based mesh refinement and adaptive quadrature is later shown through numerical examples comparing with oct-tree subdivision, revealing significant reduction of degrees of freedom and quadrature points.</p> <p><br></p> <p>Towards analysis of moving boundaries problems, an explicit interface tracking method termed enriched isogeometric analysis (EIGA) is adopted in this thesis. EIGA utilizes NURBS shape function for both geometry representation and field approximation. The behavior field is modeled by a weighted blending of the underlying domain approximation and enriching field, allowing high order continuity naturally. Since interface is explicitly represented, EIGA provides direct geometric information such as normals and curvatures. In addition, the blending procedure ensures strong enforced boundary conditions. An important moving boundary problem, namely, reaction-diffusion problem, is investigated using EIGA. In reaction-diffusion problems, the phase interfaces evolve due to chemical reaction and diffusion under multi-physics driven forces, such as mechanical, electrical, thermal, etc. Typical failure phenomenon due to reaction-diffusion problems include void formation and intermetallic compound (IMC) growth. EIGA is applied to study factors and behavior patterns in these failure phenomenon, including void size, current direction, current density, etc. A full joint simulation is also conducted to study the degradation of solder joint under thermal aging and electromigration. </p>

No description available.