an anisoptropic surface remeshing strategy combining higher dimensional embedding with radial basis functions

Abstract Many applications heavily rely on piecewise triangular meshes to describe complex surface geometries. High-quality meshes significantly improve numerical simulations. In practice, however, one often has to deal with several challenges. Some regions in the initial mesh may be overrefined, others too coarse. Additionally, the triangles may be too thin or not properly oriented. We present a novel mesh adaptation procedure which greatly improves the problematic input mesh and overcomes all of these drawbacks. By coupling surface reconstruction via radial basis functions with the higher dimensional embedding surface remeshing technique, we can automatically generate anisotropic meshes. Moreover, we are not only able to fill or coarsen certain mesh regions but also align the triangles according to the curvature of the reconstructed surface. This yields an acceptable trade-off between computational complexity and accuracy

A novel surface remeshing scheme via higher dimensional embedding and radial basis functions

Many applications heavily rely on piecewise triangular meshes to describe complex surface geometries. High-quality meshes significantly improve numerical simulations. In practice, however, one often has to deal with several challenges. Some regions in the initial mesh may be overrefined, others too coarse. Additionally, the triangles may be too thin or not properly oriented. We present a novel mesh adaptation procedure which greatly improves the problematic input mesh and overcomes all of these drawbacks. By coupling surface reconstruction via radial basis functions with the higher dimensional embedding surface remeshing technique, we can automatically generate anisotropic meshes. Moreover, we are not only able to fill or coarsen certain mesh regions but also align the triangles according to the curvature of the reconstructed surface. This yields an acceptable trade-off between computational complexity and accuracy

Very high-order method on immersed curved domains for finite difference schemes with regular Cartesian grids

A new very high-order technique for solving conservation laws with curved boundary domains is proposed. A Finite Difference scheme on Cartesian grids is coupled with an original ghost cell method that provide accurate approximations for smooth solutions. The technology is based on a specific least square method with restrictions that enables to handle general Robin conditions. Several examples in two-dimensional geometries are presented for the unsteady Convection–Diffusion equation and the Euler equations. A fifth-order WENO scheme is employed with matching fifth-order reconstruction at the boundaries. Arbitrary high-order reconstruction for smooth flows is achievable independently of the underlying differential equation since the method works as a black-box dedicated to boundary condition treatment.This work has been partially supported by the Ministerio de Economı́a y Competitividad (grant #DPI2015- 68431-R) and #RTI2018-093366-B-I00 of the Ministerio de Ciencia, Innovación y Universidades of the Spanish Government and by the Consellerı́a de Educación e Ordenación Universitaria of the Xunta de Galicia (grants #GRC2014/039 and #ED431C 2018/41), cofinanced with FEDER, Spain funds and the Universidade da Coruña, Spain. J. Fernandez-Fidalgo gratefully acknowledges the contributions of the IACOBUS Program, Spain and the INDITEX-UDC, Spain grant that have partially financed the present work. S. Clain acknowledges the financial support by FEDER – Fundo Europeu de Desenvolvimento Regional, Portugal, through COMPETE 2020 – Programa Operational Fatores de Competitividade, and the National Funds through FCT — Fundação para a Ciência e a Tecnologia, Portugal, project No. UID/FIS/04650/2013 and project No. POCI-01-0145-FEDER-02811

Image Processing Techniques for Detecting Chromosome Abnormalities

With the increasing use of Fluorescence In Situ Hybridization (FISH) probes as markers for certain genetic sequences, the requirement of a proper image processing framework is becoming a necessity to accurately detect these probe signal locations in relation to the centerline of the chromosome. Automated detection and length measurements based on the centerline relative to the centromere and the telomere coordinates would highly assist in clinical diagnosis of genetic disorders and thus improve its efficiency significantly. Although many image processing techniques have been developed for chromosomal analysis such as ’’karyotype analysis” to assist in laboratory diagnosis, they fail to provide reliable results in segmenting and extracting the centerline of chromosomes due to the high variability in shape of chromosomes on microscope slides. In this thesis we propose a hybrid algorithm that utilizes Gradient Vector Flow active contours, Discrete Curve Evolution based skeleton pruning and morphological thinning to provide a robust and accurate centerline of the chromosome, which is then used for the measurement of the FISH probe signals. Then this centerline information is used to detect the centromere location of the chromosome and the probe signal location distances were measured with respective to these landmarks. The ability to accurately detect FISH probe locations with respective to its centerline and other landmarks can provide the cytogeneticists with detailed information that could lead to a faster diagnosis

Modelling of two-phase flow with surface active particles

Kolloidpartikel die von zwei nicht mischbaren Fluiden benetzt werden, tendieren dazu sich an der fluiden Grenzfläche aufzuhalten um die Oberflächenspannung zu minimieren. Bei genügender Anzahl solcher Kolloide werden diese zusammengedrückt und lassen die fluide Grenzfläche erstarren. Das gesamte System aus Fluiden und Kolloiden bildet dann eine spezielle Emulsion mit interessanten Eigenschaften. In dieser Arbeit wird ein kontinuum Model für solche Systeme entwickelt, basierend auf den Prinzipien der Massenerhaltung und der themodynamischen Konsistenz. Dabei wird die makroskopische Zwei-Phasen-Strömung durch eine Navier-Stokes Cahn-Hilliard Gleichung modelliert und die mikroskopischen Partikel an der fluiden Grenzfläche durch einen Phase-Field-Crystal Ansatz beschrieben. Zur Evaluation des verwendeten Strömungsmodells wird ein Test verschiedener Navier-Stokes Cahn-Hilliard Modelle anhand eines bekannten Benchmark Szenarios durchgeführt. Die Ergebnisse werden mit denen von anderen Methoden zur Simulation von Zwei-Phasen-Strömungen verglichen. Desweiteren wird eine neue Methode zur Simulation von Zwei-Phasen-Strömungen in komplexen Gebieten vorgestellt. Dabei wird die komplexe Geometrie implizit durch eine Phasenfeldvariable beschrieben, welche die charakteristische Funktion des Gebietes approximiert. Die Strömungsgleichungen werden dementsprechend so umformuliert, dass sie in einem größeren und einfacheren Gebiet gelten, wobei die Randbedingungen implizit durch zusätzliche Quellterme eingebracht werden. Zur Einarbeitung der Oberflächenkolloide in das Strömungsmodell wird schließlich die Variation der freien Energie des Gesamtsystems betrachtet. Dabei wird die Energie der Partikel durch die Phase-Field-Crystal Energie approximiert und die Energie der Oberfläche durch die Ginzburg-Landau Energie. Eine Variation der Gesamtenergie liefert dann die Phase-Field-Crystal Gleichung und die Navier-Stokes Cahn-Hilliard Gleichungen mit zusätzlichen elastischen Spannunngen. Zur Validierung des Ansatzes wird auch eine sharp interface Version der Gleichungen hergeleitet und mit der zuvor hergeleiteten diffuse interface Version abgeglichen. Die Diskretisierung der erhaltenen Gleichungen erfolgt durch Finiten Elemente in Kombination mit einem semi-impliziten Euler Verfahren. Durch numerische Simulationen wird die Anwendbarkeit des Modells gezeigt und bestätigt, dass die oberflächenaktiven Kolloide die fluide Grenzfläche hinreichend steif machen können um externen Kräften entgegenzuwirken und das gesamte System zu stabilisieren.Colloid particles that are partially wetted by two immiscible fluids can become confined to fluidfluid interfaces. At sufficiently high volume fractions, the colloids may jam and the interface may crystallize. The fluids together with the interfacial colloids compose an emulsion with interesting new properties and offer an important route to new soft materials. Based on the principles of mass conservation and thermodynamic consistency, we develop a continuum model for such systems which combines a Cahn-Hilliard-Navier-Stokes model for the macroscopic two-phase fluid system with a surface Phase-Field-Crystal model for the microscopic colloidal particles along the interface. We begin with validating the used flow model by testing different diffuse interface models on a benchmark configuration for a two-dimensional rising bubble and compare the results with reference solutions obtained by other two-phase flow models. Furthermore, we present a new method for simulating two-phase flows in complex geometries, taking into account contact lines separating immiscible incompressible components. In this approach, the complex geometry is described implicitly by introducing a new phase-field variable, which is a smooth approximation of the characteristic function of the complex domain. The fluid and component concentration equations are reformulated and solved in larger regular domain with the boundary conditions being implicitly modeled using source terms. Finally, we derive the thermodynamically consistent diffuse interface model for two-phase flow with interfacial particles by taking into account the surface energy and the energy associated with surface colloids from the surface PFC model. The resulting governing equations are the phase field crystal equations and Navier-Stokes Cahn-Hilliard equations with an additional elastic stress. To validate our approach, we derive a sharp interface model and show agreement with the diffuse interface model. We demonstrate the feasibility of the model and present numerical simulations that confirm the ability of the colloids to make the interface sufficiently rigid to resist external forces and to stabilize interfaces for long times

Three-dimensional modeling of natural heterogeneous objects

En la medicina y otros campos relacionados cuando se va a estudiar un objeto natural, se toman imágenes de tomografía computarizada a través de varios cortes paralelos. Estos cortes se apilan en datos de volumen y se reconstruyen en modelos computacionales con el fin de estudiar la estructura de dicho objeto. Para construir con éxito modelos tridimensionales es importante la identificación y extracción precisa de todas las regiones que comprenden el objeto heterogéneo natural. Sin embargo, la construcción de modelos tridimensionales por medio del computador a partir de imágenes médicas sigue siendo un problema difícil y plantea dos problemas relacionados con las inexactitudes que surgen de, y son inherentes al proceso de adquisición de datos. El primer problema es la aparición de artefactos que distorsionan el límite entre las regiones. Este es un problema común en la generación de mallas a partir de imágenes médicas, también conocido como efecto de escalón. El segundo problema es la extracción de mallas suaves 3D que se ajustan a los límites de las región que conforman los objetos heterogéneos naturales descritos en las imágenes médicas. Para resolver estos problemas, se propone el método CAREM y el método RAM. El énfasis de esta investigación está puesto en la exactitud y fidelidad a la forma de las regiones necesaria en las aplicaciones biomédicas. Todas las regiones representadas de forma implícita que componen el objeto heterogéneo natural se utilizan para generar mallas adaptadas a los requisitos de los métodos de elementos finitos a través de un enfoque de modelado de ingeniería reversa, por lo tanto, estas regiones se consideran como un todo en lugar de piezas aisladas ensambladas.In medicine and other related fields when a natural object is going to be studied, computed tomography images are taken through several parallel slices. These slices are then stacked in volume data and reconstructed into 3D computer models. In order to successfully build 3D computer models of natural heterogeneous objects, accurate identification and extraction of all regions comprising the natural heterogeneous object is important. However, building 3D computer models of natural heterogeneous objects from medical images is still a challenging problem, and poses two issues related to the inaccuracies which arise from and are inherent to the data acquisition process. The first issue is the appearance of aliasing artifacts in the boundary between regions, a common issue in mesh generation from medical images, also known as stair-stepped artifacts. The second issue is the extraction of smooth 3D multi-region meshes that conform to the region boundaries of natural heterogeneous objects described in the medical images. To solve these issues, the CAREM method and the RAM method are proposed. The emphasis of this research is placed on accuracy and shape fidelity needed for biomedical applications. All implicitly represented regions composing the natural heterogeneous object are used to generate meshes adapted to the requirements of finite element methods through a reverse engineering modeling approach, thus these regions are considered as whole rather than loosely assembled parts.Doctor en IngenieríaDoctorad