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Belyaeva, Anastasiya. "Computational methods for analyzing and modeling gene regulation and 3D genome organization." Thesis, Massachusetts Institute of Technology, 2021. https://hdl.handle.net/1721.1/130828.
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Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, February, 2021Cataloged from the official PDF of thesis.
Includes bibliographical references (pages 261-281).
Biological processes from differentiation to disease progression are governed by gene regulatory mechanisms. Currently large-scale omics and imaging data sets are being collected to characterize gene regulation at every level. Such data sets present new opportunities and challenges for extracting biological insights and elucidating the gene regulatory logic of cells. In this thesis, I present computational methods for the analysis and integration of various data types used for cell profiling. Specifically, I focus on analyzing and linking gene expression with the 3D organization of the genome. First, I describe methodologies for elucidating gene regulatory mechanisms by considering multiple data modalities. I design a computational framework for identifying colocalized and coregulated chromosome regions by integrating gene expression and epigenetic marks with 3D interactions using network analysis.
Then, I provide a general framework for data integration using autoencoders and apply it for the integration and translation between gene expression and chromatin images of naive T-cells. Second, I describe methods for analyzing single modalities such as contact frequency data, which measures the spatial organization of the genome, and gene expression data. Given the important role of the 3D genome organization in gene regulation, I present a methodology for reconstructing the 3D diploid conformation of the genome from contact frequency data. Given the ubiquity of gene expression data and the recent advances in single-cell RNA-sequencing technologies as well as the need for causal modeling of gene regulatory mechanisms, I then describe an algorithm as well as a software tool, difference causal inference (DCI), for learning causal gene regulatory networks from gene expression data.
DCI addresses the problem of directly learning differences between causal gene regulatory networks given gene expression data from two related conditions. Finally, I shift my focus from basic biology to drug discovery. Given the current COVID19 pandemic, I present a computational drug repurposing platform that enables the identification of FDA approved compounds for drug repurposing and investigation of potential causal drug mechanisms. This framework relies on identifying drugs that reverse the signature of the infection in the space learned by an autoencoder and then uses causal inference to identify putative drug mechanisms.
by Anastasiya Belyaeva.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Computational and Systems Biology Program
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Wang, Junle. "From 2D to stereoscopic-3D visual saliency : revisiting psychophysical methods and computational modeling." Nantes, 2012. http://www.theses.fr/2012NANT2072.
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L’attention visuelle est l’un des mécanismes les plus importants mis en oeuvre par le système visuel humain (SVH) afin de réduire la quantité d’information que le cerveau a besoin de traiter pour appréhender le contenu d’une scène. Un nombre croissant de travaux est consacré à l’étude de l’attention visuelle, et en particulier à sa modélisation computationnelle. Dans cette thèse, nous présentons des études portant sur plusieurs aspects de cette recherche. Nos travaux peuvent être classés globalement en deux parties. La première concerne les questions liées à la vérité de terrain utilisée, la seconde est relative à la modélisation de l’attention visuelle dans des conditions de visualisation 3D. Dans la première partie, nous analysons la fiabilité de cartes de densité de fixation issues de différentes bases de données occulométriques. Ensuite, nous identifions quantitativement les similitudes et les différences entre carte de densité de fixation et carte d’importance visuelle, ces deux types de carte étant les vérités de terrain communément utilisées par les applications relatives à l’attention. Puis, pour faire face au manque de vérité de terrain exploitable pour la modélisation de l’attention visuelle 3D, nous procédons à une expérimentation oculométrique binoculaire qui aboutit à la création d’une nouvelle base de données avec des images stéréoscopiques 3D. Dans la seconde partie, nous commençons par examiner l’impact de la profondeur sur l’attention visuelle dans des conditions de visualisation 3D. Nous quantifions d’abord le " biais de profondeur " lié à la visualisation de contenus synthétiques 3D sur écran plat stéréoscopique. Ensuite, nous étendons notre étude avec l’usage d’images 3D au contenu naturel. Nous proposons un modèle de l’attention visuelle 3D basé saillance de profondeur, modèle qui repose sur le contraste de profondeur de la scène. Deux façons différentes d’exploiter l’information de profondeur par notre modèle sont comparées. Ensuite, nous étudions le biais central et les différences qui existent selon que les conditions de visualisation soient 2D ou 3D. Nous intégrons aussi le biais central à notre modèle de l’attention visuelle 3D. Enfin, considérant que l’attention visuelle combinée à une technique de floutage peut améliorer la qualité d’expérience de la TV-3D, nous étudions l’influence de flou sur la perception de la profondeur, et la relation du flou avec la disparité binoculaireVisual attention is one of the most important mechanisms deployed in the human visual system to reduce the amount of information that our brain needs to process. An increasing amount of efforts are being dedicated in the studies of visual attention, particularly in computational modeling of visual attention. In this thesis, we present studies focusing on several aspects of the research of visual attention. Our works can be mainly classified into two parts. The first part concerns ground truths used in the studies related to visual attention ; the second part contains studies related to the modeling of visual attention for Stereoscopic 3D (S-3D) viewing condition. In the first part, our work starts with identifying the reliability of FDM from different eye-tracking databases. Then we quantitatively identify the similarities and difference between fixation density maps and visual importance map, which have been two widely used ground truth for attention-related applications. Next, to solve the problem of lacking ground truth in the community of 3D visual attention modeling, we conduct a binocular eye-tracking experiment to create a new eye-tracking database for S-3D images. In the second part, we start with examining the impact of depth on visual attention in S-3D viewing condition. We firstly introduce a so-called “depth-bias” in the viewing of synthetic S-3D content on planar stereoscopic display. Then, we extend our study from synthetic stimuli to natural content S-3D images. We propose a depth-saliency-based model of 3D visual attention, which relies on depth contrast of the scene. Two different ways of applying depth information in S-3D visual attention model are also compared in our study. Next, we study the difference of center-bias between 2D and S-3D viewing conditions, and further integrate the center-bias with S-3D visual attention modeling. At the end, based on the assumption that visual attention can be used for improving Quality of Experience of 3D-TV when collaborating with blur, we study the influence of blur on depth perception and blur’s relationship with binocular disparity
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Vaterlaus, Austin C. "Development of a 3D Computational Vocal Fold Model Optimization Tool." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8468.
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One of the primary objectives of voice research is to better understand the biomechanics of voice production and how changes in properties of the vocal folds (VFs) affect voice ability and quality. Synthetic VF models provide a way to observe how changes in geometry and material property affect voice biomechanics. This thesis seeks to evaluate an approach of using a genetic algorithm to design synthetic VF models in three ways: first, through the development of a computationally cost-effective 3D vocal fold model; second, by creating and optimizing a variation of this model; and third, by validating the approach. To reduce computation times, a user-defined function (UDF) was implemented in low-fidelity 2D and 3D computational VF models. The UDF replaced the conventional meshed fluid domain with the mechanical energy equation. The UDF was implemented in the commercial finite element code ADINA and verified to produce results that were similar to those of 2D and 3D VF models with meshed fluid domains. Computation times were reduced by 86% for 2D VF models and 74% for 3D VF models while core vibratory characteristic changes were less than 5%. The results from using the UDF demonstrate that computation times could be reduced while still producing acceptable results. A genetic algorithm optimizer was developed to study the effects of altering geometry and material elasticity on frequency, closed quotient (CQ), and maximum flow declination rate (MFDR). The objective was to achieve frequency and CQ values within the normal human physiological range while maximizing MFDR. The resulting models enabled an exploration of trends between objective and design variables. Significant trends and aspects of model variability are discussed. The results demonstrate the benefit of using a structured model exploration method to create models with desirable characteristics. Two synthetic VF models were fabricated to validate predictions made by models produced by the genetic algorithm. Fabricated models were subjected to tests where frequency, CQ, and sound pressure level were measured. Trends between computational and synthetic VF model responses are discussed. The results show that predicted frequency trends between computational and synthetic models were similar, trends for closed quotient were inconclusive, and relationships between MFDR and sound pressure level remained consistent. Overall, while discrepancies between computational and synthetic VF model results were observed and areas in need of further study are noted, the study results provide evidence of potential for using the present optimization method to design synthetic VF models.
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Fadeel, Abdalsalam. "Development and Application of a Computational Modeling Scheme for Periodic Lattice Structures." Wright State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=wright162248153014535.
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Collar, Catharine Jane. "Rational Drug Design for Neglected Diseases: Implementation of Computational Methods to Construct Predictive Devices and Examine Mechanisms." Digital Archive @ GSU, 2010. http://digitalarchive.gsu.edu/chemistry_diss/48.
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Over a billion individuals worldwide suffer from neglected diseases. This equates to approximately one-sixth of the human population. These infections are often endemic in remote tropical regions of impoverished populations where vectors can flourish and infected individuals cannot be effectively treated due to a lack of hospitals, medical equipment, drugs, and trained personnel. The few drugs that have been approved for the treatments of such illnesses are not widely used because they are riddled with inadequate implications of cost, safety, drug availability, administration, and resistance. Hence, there exists an eminent need for the design and development of improved new therapeutics. Influential world-renowned scientists in the Consortium for Parasitic Drug Development (CPDD) have preformed extensive biological testing for compounds active against parasites that cause neglected diseases. These data were acquired through several collaborations and found applicable to computational studies that examine quantitative structure-activity relationships through the development of predictive models and explore structural relationships through docking. Both of these in silico tools can contribute to an understanding of compound structural importance for specific targets. The compilation of manuscripts presented in this dissertation focus on three neglected diseases: trypanosomiasis, Chagas disease, and leishmaniasis. These diseases are caused by kinetoplastid parasites Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp., respectively. Statistically significant predictive devices were developed for the inhibition of the: (1) T. brucei P2 nucleoside transporter, (2) T. cruzi parasite at two temperatures, and (3) two species of Leishmania. From these studies compound structural importance was assessed for the targeting of each parasitic system. Since these three parasites are all from the Order Kinetoplastida and the kinetoplast DNA has been determined a viable target, compound interactions with DNA were explored to gain insight into binding modes of known and novel compounds.
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White, Douglas. "Analyzing multicellular interactions: A hybrid computational and biological pattern recognition approach." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/54876.
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Pluripotent embryonic stem cells (ESCs) can differentiate into all somatic cell types, making them a useful platform for studying a variety of cellular phenomenon. Furthermore, ESCs can be induced to form aggregates called embryoid bodies (EBs) which recapitulate the dynamics of development and morphogenesis. However, many different factors such as gradients of soluble morphogens, direct cell-to-cell signaling, and cell-matrix interactions have all been implicated in directing ESC differentiation. Though the effects of individual factors have often been investigated independently, the inherent difficulty in assaying combinatorial effects has made it difficult to ascertain the concerted effects of different environmental parameters, particularly due to the spatial and temporal dynamics associated with such cues. Dynamic computational models of ESC differentiation can provide powerful insight into how different cues function in combination both spatially and temporally. By combining particle based diffusion models, cellular agent based approaches, and physical models of morphogenesis, a multi-scale, rules-based modeling framework can provide insight into how each component contributes to differentiation. I propose to investigate the complex regulatory cues which govern complex morphogenic behavior in 3D ESC systems via a computational rules based modeling approach. The objective of this study is to examine how spatial patterns of differentiation by ESCs arise as a function of the microenvironment. The central hypothesis is that spatial control of soluble morphogens and cell-cell signaling will allow enhanced control over the patterns and efficiency of stem cell differentiation in embryoid bodies.
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Borrman, Tyler M. "Measuring Stability of 3D Chromatin Conformations and Identifying Neuron Specific Chromatin Loops Associated with Schizophrenia Risk." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1111.
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The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization.
At a finer resolution within compartments, chromatin forms loop structures capable of regulating gene expression. Genome wide association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with the neuropsychiatric disease schizophrenia. When these SNPs are not located within a gene it is difficult to gain insight into disease pathology; however, in some cases chromatin loops may link these noncoding schizophrenia risk variants to their pathological gene targets. By generating 3D genome maps, we identified and analyzed loops of glial cells, neural progenitor cells, and neurons thereby expanding the set of genes conferring schizophrenia risk.
The binding of T-cell receptors (TCRs) to foreign peptides on the surface of diseased cells triggers an immune response against the foreign invader. Utilizing available structural information of the TCR antigen interface, we developed computational methods for successful prediction of TCR-antigen binding. As this binding is a prerequisite for immune response, such improvements in binding prediction could lead to important advancements in the fields of autoimmunity and TCR design for cancer therapeutics.
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Lanterne, Célestin. "Réparation et optimisation de maillages 3D pour l'impression 3D." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0454.
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Les imprimantes 3D utilisent des modèles 3D sous la forme de maillages pour définir la géométrie et l'apparence des objets à imprimer. Un maillage 3D doit posséder certaines propriétés topologiques pour que la géométrie qu'il représente soit imprimable, et la géométrie elle même doit respecter certaines conditions pour être imprimable. Ces propriétés et conditions peuvent varier selon la technologie d'impression 3D utilisée.De nombreux maillages 3D utilisés pour l'impression n'ont dans un premier temps pas été conçus pour cette application. La principale utilisation première de ces maillages est la visualisation, qui ne nécessite pas les mêmes propriétés topologiques et conditions géométriques. Le sujet de cette thèse est la réparation de ces maillages afin de les rendre imprimables.Une chaîne de réparation comprenant plusieurs étapes a été conçue dans ce but. Les conditions de non-variété sont réparées en réalisant une extraction de composantes connexes (surfaces). Les bords des surfaces sont détectés et classés en fonction de la meilleure réparation à appliquer sur chaque. Les bords des surfaces sont réparés suivant leurs classement soit par une méthode de remplissage soit par une méthode d'épaississement. La fragilité de la géométrie est détectée et contrôlée3D printers use 3D models in the form of meshes to define the geometry and the appearance of objects to be printed. A 3D mesh must have some topological properties so that the geometry it represents could be printable and the geometry itself must respect certain conditions to be printable. These properties and conditions may vary depending on the 3D printing technologies in use.Many 3D meshes used for printing were not initially designed for this purpose application. The main primary use of these meshes is visualization, which does not require the same topological properties and geometric conditions. The subject of this thesis is the repair of these meshes to make them printable.A repair chain including several steps was designed for this purpose. Non-manifold conditions are repaired by extracting related components (surfaces). The boundaries of surfaces are detected and classified according to the best repair to be applied on each. The boundaries of surfaces are repaired according to their classification either by a filling method or by an offset method. The weakness of the geometry is detected and controlled
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Michálek, Mojmír Cyril. "Výpočtové modelování procesu 3D tisku součástí z PET-G materiálu." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2020. http://www.nusl.cz/ntk/nusl-418192.
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Master’s thesis deals with computational modeling of 3D printing process done by FDM method made from PETG material using finite element method. Research section contains a brief description of 3D printing process modeling possibilities using finite element method and summarizes fundamental mechanical properties of thermoplastics. In practical section there is an evaluation of specimens printed of PETG material tensile tests. Further there is performed a sensitivity analysis of various influences on vertical imperfection of printed part Idler and is done its design modification, which is based on results of this analysis.
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Hartl, Alexander Verfasser], Nassir [Akademischer Betreuer] [Navab, and Sibylle [Akademischer Betreuer] Ziegler. "Computational modeling of detection physics for 3D intraoperative imaging with navigated nuclear probes / Alexander Hartl. Betreuer: Nassir Navab. Gutachter: Nassir Navab ; Sibylle Ziegler." München : Universitätsbibliothek der TU München, 2015. http://d-nb.info/1079655190/34.
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Sköld, Christian. "Computational Modeling of the AT2 Receptor and AT2 Receptor Ligands : Investigating Ligand Binding, Structure–Activity Relationships, and Receptor-Bound Models." Doctoral thesis, Uppsala universitet, Avdelningen för organisk farmaceutisk kemi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7823.
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Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT2 receptor. The bioactive conformation of a peptide can provide important guidance in peptidomimetic design. By designing and introducing well-defined secondary structure mimetics into Ang II the bioactive conformation can be addressed. In this work, both γ- and β-turn mimetic scaffolds have been designed and characterized for incorporation into Ang II. Using conformational analysis and the pharmacophore recognition method DISCO, a model was derived of the binding mode of the pseudopeptide Ang II analogues. This model indicated that the positioning of the Arg side chain was important for AT2 receptor binding, which was also supported when the structure–activity relationship of Ang II was investigated by performing a glycine scan. To further examine ligand binding, a 3D model of the AT2 receptor was constructed employing homology modeling. Using this receptor model in a docking study of the ligands, binding modes were identified that were in agreement with data from point-mutation studies of the AT2 receptor. By investigating truncated Ang II analogues, small pseudopeptides were developed that were structurally similar to nonpeptide AT2 receptor ligands. For further guidance in ligand design of nonpeptide compounds, three-dimensional quantitative structure–activity relationship models for AT1 and AT2 receptor affinity as well as selectivity were derived.
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Ravel, Guillaume. "Three-dimensional modeling and experiment-driven numerical simulation of zebrafish escape swimming for biological applications." Thesis, Bordeaux, 2020. http://www.theses.fr/2020BORD0330.
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Les biologistes utilisent le poisson-zèbre comme modèle animal pour étudier les effets des facteurs génétiques ou environnementaux liés aux maladies locomotrices humaines afin de développer des traitements pharmacologiques. Les objectifs généraux du projet étaient 1) de développer un modèle numérique basé sur des données réelles capable de simuler avec précision la nage de fuite de l’eleuthéro-embryon de poisson-zèbre et 2) de fournir, en plus des paramètres cinématiques de nage, une estimation fine des performances énergétiques du comportement locomoteur pour enrichir les études expérimentales sur la locomotion. En outre, une modélisation numérique basée sur l'expérience pourrait améliorer la compréhension du comportement locomoteur. Pour cela, un code de calcul de dynamique des fluides décrivant l'écoulement des fluides autour d'un corps immergé, mobile et déformable a été utilisé pour reproduire in silico la réponse de fuite expérimentale d'un éleuthéro-embryon de cinq jours post-fécondation. La solution du modèle mécaniste, régie par les équations de Navier-Stokes incompressible et les lois de Newton, a été approchée sur un maillage cartésien tandis que le corps solide, représenté par une fonction level-set, a été décrit implicitement par une méthode de pénalisation. Quant à la cinématique de déformation, elle a été estimée directement à partir de vidéos expérimentales de locomotion par une Procrustes analysis. Une première approche a été envisagée pour en extraire la vitesse de déformation, en deux dimensions, basée sur le transport optimal. Afin d'être fidèle à la physique tridimensionnelle (3D), la morphologie de l’eleuthéro-embryon de poisson-zèbre et la cinématique de fuite expérimentale ont été reconstruites en 3D, par le suivi de marqueurs lagrangiens à la surface du corps du poisson-zèbre. Ainsi, une nouvelle approche a été développée pour estimer la vitesse de déformation à partir de données réelles expérimentales obtenues par imagerie ultra-rapide après stimulation par impulsion de champ électrique. L’eleuthéro-embryon de poisson-zèbre présente un comportement de fuite très stéréotypé et complexe, composé de trois modules de nage : courbure en C, contre-courbure et phase de nage cyclique rapide. L'approche développée permet de réaliser des simulations numériques haute-performance et réalistes de la locomotion réelle. Après avoir effectué une validation numérique du modèle qui repose sur chacune de ses composantes, une étude a été menée sur la performance énergétique de la réponse de fuite du poisson-zèbre, altérée par un changement de la viscosité du fluide. Une réponse linéaire du coût du transport, associée à une dépense d’énergie constante, indépendamment du milieu, a ainsi été montrée. Cette étude énergétique peut être étendue à tout corps immergé, en mouvement et déformable, et en particulier à toute expérience biologique comme l'exposition à un neuro-toxique, qui altérerait le comportement locomoteur de l’éleuthéro-embryon. Ainsi, la simulation numérique peut enrichir l’évaluation quantitative des conditions biologiques et des traitements pharmacologiques qui conduisent à perturber ou à restaurer le comportement locomoteurBiologists use zebrafish as an animal model to study the effects of genetic or environmental factors related to human locomotor diseases in order to develop pharmacological treatments. The general objectives of the project were 1) to develop a numerical model based on real-world data capable of accurately simulating the escape swimming of the zebrafish eleuthero-embryo and 2) to provide, in addition to swimming kinematic parameters, a fine estimate of the energetic performance of locomotor behavior to enrich experimental studies on locomotion. Furthermore, an experiment-based numerical modeling might enhance the understanding of locomotor behavior. For this purpose, a computational fluid dynamics code describing the fluid flow around a moving and deforming immersed body was used to reproduce in silico the experimental escape response of a five-day post-fertilization eleuthero-embryo. The solution of the mechanistic model, governed by the incompressible Navier-Stokes equations and Newton's laws was approximated on a Cartesian mesh while the solid body represented by a level-set function, was described implicitly by a penalization method. As for the deformation kinematics, it was estimated directly from experimental locomotion videos by a Procrustes analysis. A first approach has been considered to extract the deformation velocity, in two dimensions, based on optimal transportation. In order to be faithful to three-dimensional (3D) physics, the morphology of the zebrafish eleuthero-embryo and the experimental escape kinematics were reconstructed in 3D, by tracking Lagrangian markers on the surface of the zebrafish body. Thus, a new approach has been developed to estimate the deformation velocity from experimental real data obtained by ultra-high-speed imaging after electric field pulse stimulation. Zebrafish eleuthero-embryo exhibits a highly stereotyped and complex escape behavior consisting of three swimming modules: C-bend, counter-bend and fast-swimming cyclic phase. The developed approach enables high-performance and realistic numerical simulations of real locomotion. After performing a numerical validation of the model based on each component, a study was conducted on the energetic performance of the zebrafish's escape response, challenged by a change in fluid viscosity. A linear response of the cost of transport, associated with a constant energy expenditure, regardless the fluid environment, was thus demonstrated. This energy study can be extended to any immersed, moving and deformable body and in particular, to any biological experiment such as exposure to a neuro-toxicant, which would alter the locomotor behavior of the eleuthero-embryo. Thus, numerical simulation may enrich the quantitative assessments of biological conditions and pharmacological treatments which lead to disturbing or recovering the locomotor behavior
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Sköld, Christian. "Computational Modeling of the AT2 Receptor and AT2 Receptor Ligands : Investigating Ligand Binding, Structure–Activity Relationships, and Receptor-Bound Models." Doctoral thesis, Uppsala University, Organic Pharmaceutical Chemistry, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7823.
Full textAbstract:
Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT2 receptor.
The bioactive conformation of a peptide can provide important guidance in peptidomimetic design. By designing and introducing well-defined secondary structure mimetics into Ang II the bioactive conformation can be addressed. In this work, both γ- and β-turn mimetic scaffolds have been designed and characterized for incorporation into Ang II. Using conformational analysis and the pharmacophore recognition method DISCO, a model was derived of the binding mode of the pseudopeptide Ang II analogues. This model indicated that the positioning of the Arg side chain was important for AT2 receptor binding, which was also supported when the structure–activity relationship of Ang II was investigated by performing a glycine scan.
To further examine ligand binding, a 3D model of the AT2 receptor was constructed employing homology modeling. Using this receptor model in a docking study of the ligands, binding modes were identified that were in agreement with data from point-mutation studies of the AT2 receptor.
By investigating truncated Ang II analogues, small pseudopeptides were developed that were structurally similar to nonpeptide AT2 receptor ligands. For further guidance in ligand design of nonpeptide compounds, three-dimensional quantitative structure–activity relationship models for AT1 and AT2 receptor affinity as well as selectivity were derived.
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Brailo, Courtney M. "A Light Detecting and Ranging (LiDAR) and Global Positioning System (GPS) Study of the Truckee Meadows, NV. Quaternary Fault Mapping with ArcGIS, 3D Visualization and Computational Block Modeling of the Greater Reno area." Thesis, University of Nevada, Reno, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10126167.
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The Truckee Meadows (Reno, NV) sits in a tectonically complex area of western Nevada, where Walker Lane-style transtension is dominant throughout the region. A new Light Detection and Ranging (LiDAR) study focuses on the Truckee Meadows region of western Nevada, including the Reno/Sparks metropolitan area in Washoe County. We use the airborne LiDAR imagery (1485 sq. km) to create high quality, bare-earth topographic maps that were previously unattainable in vegetated, populated or alpine terrain. This approach gives us an opportunity to improve fault maps that may be outdated or incomplete in the area. Here we provide LiDAR imagery of a large section of Washoe County and an updated fault map of the greater Truckee Meadows region.
We also use this new LiDAR survey of the Truckee Meadows and nearby basins to constrain geometry, length, distribution, and slip rates along faults imaged by this new dataset. Estimated slip rates are compared to those derived from a geodetic block model constrained by Global Positioning Station (GPS) data to test for consistency. GPS station data and geologic mapping show that both east-west oriented extension and northwest-oriented right-lateral strike slip accommodate transtension as a backdrop for tectonics studies of region, with some northeast-oriented left-lateral strike slip. This study aims to better understand how this transtension is partitioned along remapped faults and newly identified structures in this urban setting, as the framework for strain accommodation in this area remains poorly understood.
Faults with normal offset were measured along strike using bare-earth LiDAR returns to determine the amount of vertical separation across geomorphic surfaces, and then converted to extension assuming a fault dip of 60 (+/-10) degrees. Since the primary geomorphic surfaces in this region are the result of Sierra Nevadan glacial outwash episodes, we use previously published geologic maps to link each surface to an associated date. When integrated across several basin perpendicular transects within the Mt. Rose pediment, we calculate a total extension rate of 0.87 (+0.40/-0.48) mm/yr for the southern Truckee Meadows basin. Integrated slip rates from fault scarp offsets are within the bounds of 1.23 (+/-0.70) mm/yr suggested by geodetic modeling. Block modeling highlights that north-striking faults primarily accommodate east-west extension, and so northwest-striking faults and/or block rotations must accommodate the northwest-directed shear seen in GPS velocities. This trend is bolstered by the discovery of a new northwest-oriented fault on Peavine Mountain 6 km east of the Mogul (2008) seismicity trend. Our study provides further evidence that the Truckee Meadows sits at a critical transition from north-striking normal faults in the southern part of the basin to northwest-oriented strike-slip faults to the north, an observation that mimics regional tectonics and geomorphology of the adjacent Lake Tahoe/Truckee system to the west.
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Ozturk, Tugce. "Experimental and Computational Investigation of the Microstructure-Mechanical Deformation Relationship in Polycrystalline Materials, Applied to Additively Manufactured Titanium Alloys." Research Showcase @ CMU, 2017. http://repository.cmu.edu/dissertations/900.
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Parts made out of titanium alloys demonstrate anisotropic mechanical properties when manufactured by electron beam melting, an emerging additive manufacturing technique. Understanding the process history dependent heterogeneous microstructure, and its effect on mechanical properties is crucial in determining the performance of additively manufactured titanium alloys as the mechanical behavior heavily relies on the underlying microstructural features. This thesis work focuses on combined experimental and computational techniques for microstructure characterization, synthetic microstructure generation, mechanical property measurement, and mechanical behavior modeling of polycrystalline materials, with special focus on dual phase titanium alloys. Macroscopic mechanical property measurements and multi-modal microstructure characterizations (high energy X-ray diffraction, computed tomography and optical microscopy) are performed on additively manufactured Ti-6Al-4V parts, revealing the heterogeneity of the microstructure and properties with respect to the build height. Because characterizing and testing every location within a build is not practical, a computational methodology is established in order to reduce the time and cost spent on microstructure-property database creation. First a statistical volume element size is determined for the Fast Fourier Transform based micromechanical modeling technique through a sensitivity study performed on an experimental Ni-based superalloy and syntheticW, Cu, Ni and Ti structures, showing that as the contrast of properties (e.g., texture, field localization, anisotropy, rate-sensitivity) increases, so does the minimum simulation domain size requirement. In all deformation regimes a minimum volume element is defined for both single and dual phase materials. The database is then expanded by generating statistically representative Ti structures which are modified for features of interest, e.g., lath thickness, grain size and orientation distribution, to be used in spectral full-field micromechanical modeling. The relative effect of the chosen microstructural features is quantified through comparisons of average and local field distributions. Fast Fourier transform based technique, being a spectral, full-field deformation modeling tool, is shown to be capable of capturing the relative contribution from varying microstructural features such as phase fractions, grain morphology/ size and texture on the overall mechanical properties as the results indicate that the mean field behavior is predominantly controlled by the alpha phase fraction and the prior beta phase orientation.
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Preuksakarn, Chakkrit. "Acquisition et validation de modèles architecturaux virtuels de plantes." Phd thesis, Université Montpellier II - Sciences et Techniques du Languedoc, 2012. http://tel.archives-ouvertes.fr/tel-00859843.
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Les modèles virtuels de plantes sont visuellement de plus en plus réalistes dans les applications infographiques. Cependant, dans le contexte de la biologie et l'agronomie, l'acquisition de modèles précis de plantes réelles reste un problème majeur pour la construction de modèles quantitatifs du développement des plantes.Récemment, des scanners laser 3D permettent d'acquérir des images 3D avec pour chaque pixel une profondeur correspondant à la distance entre le scanner et la surface de l'objet visé. Cependant, une plante est généralement un ensemble important de petites surfaces sur lesquelles les méthodes classiques de reconstruction échouent. Dans cette thèse, nous présentons une méthode pour reconstruire des modèles virtuels de plantes à partir de scans laser. Mesurer des plantes avec un scanner laser produit des données avec différents niveaux de précision. Les scans sont généralement denses sur la surface des branches principales mais recouvrent avec peu de points les branches fines. Le cœur de notre méthode est de créer itérativement un squelette de la structure de la plante en fonction de la densité locale de points. Pour cela, une méthode localement adaptative a été développée qui combine une phase de contraction et un algorithme de suivi de points.Nous présentons également une procédure d'évaluation quantitative pour comparer nos reconstructions avec des structures reconstruites par des experts de plantes réelles. Pour cela, nous explorons d'abord l'utilisation d'une distance d'édition entre arborescence. Finalement, nous formalisons la comparaison sous forme d'un problème d'assignation pour trouver le meilleur appariement entre deux structures et quantifier leurs différences.
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Bui, Cao Vu. "Modélisation d'environnements intérieurs par reconstruction 3D en temps réel et extraction de plans architecturaux 2D." Thesis, Troyes, 2018. http://www.theses.fr/2018TROY0032.
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Nous explorons le problème de la reconstruction complète d’un environnement intérieur en utilisant des données mixtes issues de la caméra RGB-D (couleur plus profondeur) de faible coût et de la centrale inertielle. Le processus de numérisation est réalisé en temps réel, en déplacement avec 6 degrés de liberté du système de numérisation. Nous nous concentrons sur les systèmes mobiles avec des contraintes informatiques, tels que les smartphones ou les tablettes. Les problèmes problématiques présentent un ensemble de défis fondamentaux : l'estimation du positionnement et de la trajectoire du périphérique lorsqu'il se déplace pendant l'acquisition de l'environnement et l'utilisation de structures de données légères pour stocker la représentation de la scène reconstruite. Le système doit être optimisé et efficace pour la mémoire, de sorte qu'il puisse fonctionner en temps réel, à bord de l'équipement mobile. Nous proposons également une nouvelle méthode de reconstruction de la surface, nommé Dodécaèdre Mapping, une solution de triangulation discrète pour la surface complète de l'environnement intérieur. L’algorithme tente d'approximer le maillage surfacique en déformant et en collant la surface affinée du dodécaèdre sur le nuage de points numérisé. Le dernier module de cette mission de recherche consiste à développer des outils de l'extraction automatique / semi-automatique de plans architecturaux 2D à partir de la reconstruction 3D de la scène scannée. Ce processus d'extraction est possible à partir du nuage de points 3D ou du maillage en définissant un plan de coupeScene reconstruction is the process of building an accurate geometric model of one's environment from We explore the problem of complete scene reconstruction in indoor environments using mixed - data from the low-cost RGB-D camera and the inertial unit. The scanning process is realized in real-time, on the move with 6DoF of the numerizing system. We focus on computationally-constrained mobile systems, such as smartphone or tablet devices. Problematic issues present a set of fundamental challenges - estimating the state and trajectory of the device as it moves while scanning environment and utilizing lightweight data structures to hold the representation of the reconstructed scene. The system needs to be computationally and memory-efficient, so that it can run in real time, on-board the mobile device. The point-cloud resulted in the above module, which is non-structured and noisy cause of the quality of the low-cost sensor, needed a new method for the surface reconstruction. Our Dodecahedron Mapping is presented like a triangulation solution for the completed indoor environment scanning. After filtering and smoothing the point cloud, the algorithm tries to approximating the surface mesh by deforming and pasting the dodecahedron surface to the scanned point cloud. And the last stage of this research mission is to developing tools for the automatic extraction of 2D architectural plans from the 3D scanned building scene. This extracting process is also possible from the 3D point cloud or mesh by defining a section plane
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Skrip, Betsy. "Imaging the airways : 3D modeling of a complete respiratory airway for use in computational flow dynamics studies of particle deposition in the lungs ; Creation of an educational animation about the respiratory system for use in the Human Visualization Project and CollaboRITorium /." Online version of thesis, 2008. http://hdl.handle.net/1850/7744.
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Ielina, Tetiana, Liudmyla Halavska, Daiva Mikucioniene, and Rimvidas Milasius. "Information models of knitwear in computational science and engineering." Thesis, Київський національний університет технологій та дизайну, 2021. https://er.knutd.edu.ua/handle/123456789/19105.
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Moore, Stephen Michael. "Computational 3D Modelling of Hemodynamics in the Circle of Willis." Thesis, University of Canterbury. Mechanical Engineering, 2007. http://hdl.handle.net/10092/1168.
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The Circle of Willis (CoW) is a ring-like arterial structure forming the major anastomotic connection between arterial supply systems in the brain, and is responsible for the distribution of oxygenated blood throughout the cerebral mass. Among the general population, only approximately 50% have a complete CoW, where absent or hypoplastic vessels are common among a multitude of possible anatomical variations, reducing the degree to which blood may be rerouted. While an individual with one of these variations may under normal circumstances suffer no ill effects, there are certain pathological conditions which can present a risk to the person's health and increase the possibility of suffering an ischaemic stroke when compounded with an anatomical variation. This body of work presents techniques for generating 3D models of the cerebral vasculature using magnetic resonance imaging (MRI) and performing computational fluid dynamics (CFD) simulations in order to simulate the flow patterns throughout a circle of Willis. Incorporated with the simulations is a mathematical model of the cerebral autoregulation mechanism, simulating the ability of the smaller arteries and arterioles in the brain to either constrict or dilate in response to alterations in cerebral blood flow, thereby altering the cerebrovascular resistance of each major brain territory and regulating the amount of blood flow within a physiological range of cerebral perfusion pressure. The CFD simulations have the ability to predict the amount of collateral flow rerouted via the communicating arteries in response to a stenosis or occlusion, and the major objective of this study has been the investigation of how anatomical variations of the circle of Willis affect the capacity to provide this collateral flow. Initial work began with the development of three idealized models of common anatomical variations, created using computer aided design software (CAD) and based on the results of MRI scans. The research then shifted to developing a technique whereby patient specific models of the circle of Willis could be directly segmented from the MRI data. As a result of this shift, an interactive GUI-based tool was developed for the processing of the MRI datasets, allowing for rapid data enhancement and creation of a surface topology representing the arterial wall of the circle of Willis, suitable for a CFD simulation. The results of both sets of simulations illustrate that there exist a number of variables associated with a patients circle of Willis geometry, such as cerebral blood flow and combinations and degrees of stenosis, implying that the initial goal of drawing generalized conclusions was perhaps flawed. Instead, a crucial outcome of this body of work is that the future research should be directed toward extending the physiological complexity of both the geometry and the autoregulation model, with the intention of a patient specific application rather than producing large datasets with which to make broad generalizations.
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Lien, Fue-Sang. "Computational modelling of 3D flow in complex ducts and passages." Thesis, University of Manchester, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304550.
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Burkitt, Mark. "Computational modelling of sperm behaviour in a 3D virtual oviduct." Thesis, University of Sheffield, 2011. http://etheses.whiterose.ac.uk/2246/.
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The processes by which individual sperm cells navigate the length and complexity of the female reproductive tract and then reach and fertilise the oocyte are fascinating. Numerous complex processes potentially influence the movement of spermatozoa within the tract, resulting in a regulated supply of spermatozoa to the oocytes at the site of fertilisation. Despite significant differences between species, breeds and individuals, these processes converge to ensure that an optimal number of high quality spermatozoa reach the oocytes, resulting in successful fertilisation without a significant risk of polyspermy. Computational modelling provides a useful method for combining knowledge about the individual processes in complex systems to help understand the relative significance of each factor. In this thesis, the first agent based computational model of sperm behaviour within the oviductal environment has been created. First, a generic conceptual model of sperm behaviour within the 3D oviduct is presented. Sperm are modelled as individual cells with a set of behavioural rules defining how they interact with their local environment and regulate their internal state. Secondly, a set of 3D models of the mammalian oviduct were constructed. Histology images of the mouse oviduct were obtained and the path that the oviductal tube follows through the tissue was identified using CUDA based image analysis. This was used to determine cross-sectional topology, and measurements from the cross sections were used to generate a set of accurately scaled 3D models of the oviduct. The process of constructing and validating the agent-based computational model of sperm movement and transport within the oviductal environment is described. The model is grounded in reality, with accurate space and time scales used throughout, and parameters and mechanisms from literature where available. Sensitivity analysis is performed on all parameters, and those which are most sensitive to variation have been identified. The model has been validated against literature were possible, and the limitations of the model, validation and assumptions made are clearly stated. The model has been used to investigate the significance of the oviductal environment on the regulation of sperm distribution and progression to the site of fertilisation, and how changes to that environment alter the distribution. Finally, the potential use for the model and how more complex mechanisms could be integrated in the future are discussed.
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Fisher, Matthew Jackson. "Parametric Optimization Design System for a Fluid Domain Assembly." Diss., CLICK HERE for online access, 2008. http://contentdm.lib.byu.edu/ETD/image/etd2373.pdf.
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Abed, Mohamad Samir, and Azita Hosseinzade. "Parameterstyrd projektering av broar : Koppling mellan Rhinoceros-Grasshopper och Tekla Structures." Thesis, KTH, Byggteknik och design, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-215192.
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I byggbranschen har nya metoder för projektering utvecklats genom införandet av moderna och mer kraftfulla BIM-verktyg. Flera av dagens konstruktioner modelleras enligt tredimensionella principer.Tekla Structures är ett kraftfullt BIM-verktyg som klarar av att hantera både huskonstruktioner och anläggningskonstruktioner. Trots detta kan programmet inte hantera broar med dubbelkrökning på ett effektivt sätt. Projektörer behöver därför utgå från flera program för att kunna hantera komplexa brokonstruktioner.För att kunna utnyttja fördelar med Tekla Structures, behöver programmet att utvecklas eller kompletteras med andra tredjepartsprogram. Detta projekt syftar till att integrera nya arbetssätt och införa en metodik, i form av parametriserade modellering i Tekla Structures. En sådan form av modellering tillåter användaren att modifiera parametrar för en önskad modell.Ett skript är skapad genom ett visuellt programmeringstillägg, som genererar parametriskbaserade bromodeller. Brokonstruktionstyp som modellerades i detta projekt är en plattrambro.Resultatet av projektet pekar mot att parametriserad modellering är ett effektivt sätt att modellera och en lösning för att bland annat hantera broar med dubbelkrökningar.New methods for project designing in the building construction industry have been developed by introducing modern and powerful BIM tools. Several of today’s constructions are designed according to three-dimensional principles.Tekla Structures is a powerful BIM tool that is capable of managing both house and infrastructure constructions. Despite this, the program cannot handle bridges with a horizontal and vertical curvature efficiently. The designers must instead rely on several other applications to manage complex bridge constructions.In order to use the advantages of Tekla Structures, the software needs to be evolved or complimented by other third party softwares. This project aims to integrate new working technics and introduce a method based on parametric design in Tekla Structures. Such form of modeling enables the modification of parameters to a desired model for the user.A script is created through a visual programming extension that generates a parametric based bridge models. The bridge type in this project was designed, is an integral bridge.The project has proved that parametric based design is more effectively and a solution to manage bridges with horizontal and vertical curvature.
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Aybar, Akin. "Computational Modelling Of Free Surface Flow In Intake Structures Using Flow 3d Software." Master's thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614377/index.pdf.
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Intakes are inlet structures where fluid is accelerated to a certain flow velocity to provide required amount of water into a hydraulic system. Intake size and geometry affects the formation of flow patterns, which can be influential for hydraulic performance of the whole system. An experimental study is conducted by measuring velocity field in the hydraulic model of the head pond of a hydropower plant to investigate vortex formation. Vortex strength based on potential flow theory is calculated from the measured velocity field. It was shown that vortex strength increases with the submergence Froude number. The free surface flow in the head pond is simulated using Flow-3D software. Vortex strength calculations are repeated using the computational velocity distributions and compared to experimentally obtained values. Similar computations were carried on with some idealized pond geometries such as rectangular and circular.
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Hammer, Steven James. "Engineering a 3D ultrasound system for image-guided vascular modelling." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/4253.
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Atherosclerosis is often diagnosed using an ultrasound (US) examination in the carotid and femoral arteries and the abdominal aorta. A decision to operate requires two measures of disease severity: the degree of stenosis measured using B-mode US; and the blood flow patterns in the artery measured using spectral Doppler US. However other biomechanical factors such as wall shear stress (WSS) and areas of flow recirculation are also important in disease development and rupture. These are estimated using an image-guided modelling approach, where a three-dimensional computational mesh of the artery is simulated. To generate a patient-specific arterial 3D computational mesh, a 3D ultrasound (3DUS) system was developed. This system uses a standard clinical US scanner with an optical position sensor to measure the position of the transducer; a video capture card to record video images from the scanner; and a PC running Stradwin software to reconstruct 3DUS data. The system was characterised using an industry-standard set of calibration phantoms, giving a reconstruction accuracy of ± 0.17 mm with a 12MHz linear array transducer. Artery movements from pulsatile flow were reduced using a retrospective gating technique. The effect of pressure applied to the transducer moving and deforming the artery was reduced using an image-based rigid registration technique. The artery lumen found on each 3DUS image was segmented using a semi-automatic segmentation technique known as ShIRT (the Sheffield Image Registration Toolkit). Arterial scans from healthy volunteers and patients with diagnosed arterial disease were segmented using the technique. The accuracy of the semi-automatic technique was assessed by comparing it to manual segmentation of each artery using a set of segmentation metrics. The mean accuracy of the semi-automatic technique ranged from 85% to 99% and depended on the quality of the images and the complexity of the shape of the lumen. Patient-specific 3D computational artery meshes were created using ShIRT. An idealised mesh was created using key features of the segmented 3DUS scan. This was registered and deformed to the rest of the segmented dataset, producing a mesh that represents the shape of the artery. Meshes created using ShIRT were compared to meshes created using the Rhino solid modelling package. ShIRT produced smoother meshes; Rhino reproduced the shape of arterial disease more accurately. The use of 3DUS with image-guided modelling has the potential to be an effective tool in the diagnosis of atherosclerosis. Simulations using these data reflect in vivo studies of wall shear stress and recirculation in diseased arteries and are comparable with results in the literature created using MRI and other 3DUS systems.
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Duan, Liuyun. "Modélisation géométrique de scènes urbaines par imagerie satellitaire." Thesis, Université Côte d'Azur (ComUE), 2017. http://www.theses.fr/2017AZUR4025.
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La modélisation automatique de villes à partir d’images satellites est l'un des principaux défis en lien avec la reconstruction urbaine. Son objectif est de représenter des villes en 3D de manière suffisamment compacte et précise. Elle trouve son application dans divers domaines, qui vont de la planification urbaine aux télécommunications, en passant par la gestion des catastrophes. L'imagerie satellite offre plusieurs avantages sur l'imagerie aérienne classique, tels qu'un faible coût d'acquisition, une couverture mondiale et une bonne fréquence de passage au-dessus des sites visités. Elle impose toutefois un certain nombre de contraintes techniques. Les méthodes existantes ne permettent que la synthèse de DSM (Digital Surface Models), dont la précision est parfois inégale. Cette dissertation décrit une méthode entièrement automatique pour la production de modèles 3D compacts, précis et répondant à une sémantique particulière, à partir de deux images satellites en stéréo. Cette méthode repose sur deux grands concepts. D'une part, la description géométrique des objets et leur assimilation à des catégories génériques sont effectuées simultanément, conférant ainsi une certaine robustesse face aux occlusions partielles ainsi qu'à la faible qualité des images. D'autre part, la méthode opère à une échelle géométrique très basse, ce qui permet la préservation de la forme des objets, avec finalement, une plus grande efficacité et un meilleur passage à l'échelle. Pour générer des régions élémentaires, un algorithme de partitionnement de l'image en polygones convexes est présentéAutomatic city modeling from satellite imagery is one of the biggest challenges in urban reconstruction. The ultimate goal is to produce compact and accurate 3D city models that benefit many application fields such as urban planning, telecommunications and disaster management. Compared with aerial acquisition, satellite imagery provides appealing advantages such as low acquisition cost, worldwide coverage and high collection frequency. However, satellite context also imposes a set of technical constraints as a lower pixel resolution and a wider that challenge 3D city reconstruction. In this PhD thesis, we present a set of methodological tools for generating compact, semantically-aware and geometrically accurate 3D city models from stereo pairs of satellite images. The proposed pipeline relies on two key ingredients. First, geometry and semantics are retrieved simultaneously providing robust handling of occlusion areas and low image quality. Second, it operates at the scale of geometric atomic regions which allows the shape of urban objects to be well preserved, with a gain in scalability and efficiency. Images are first decomposed into convex polygons that capture geometric details via Voronoi diagram. Semantic classes, elevations, and 3D geometric shapes are then retrieved in a joint classification and reconstruction process operating on polygons. Experimental results on various cities around the world show the robustness, scalability and efficiency of the proposed approach
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Afzelius, Lovisa. "Computational Modelling of Structures and Ligands of CYP2C9." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4016.
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Santos, Clayton Eduardo dos. "Modelagem computacional de estruturas anatômicas em 3D e simulação de suas imagens radiográficas." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/18/18133/tde-15102008-141521/.
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Os métodos de controle de qualidade tradicionais aplicados ao radiodiagnóstico, é a melhor maneira de garantir a boa qualidade das imagens produzidas. No entanto, a investigação de particularidades oriundas do processo de formação de imagens radiológicas requer ferramentas computacionais complementares, em função do número de variáveis envolvidas. Entretanto, os fantomas computacionais baseados em voxels não conseguem representar as variações morfométricas necessárias para a simulação de exames cujo diagnóstico é baseado em imagem. Neste trabalho foi desenvolvido um novo tipo de fantoma computacional, baseado em modelagem 3D, que possui as vantagens apresentadas pelos fantomas computacionais tradicionais sem os problemas encontados nestes. A ferramenta de modelagem utilizada, o Blender, é disponibilizada gratuitamente na internet. A técnica utilizada foi a box modeling, que consiste na deformação de uma primitiva básica, nesse caso um cubo, até que apresente a forma da estrutura que se deseja modelar. Para tanto, foram utilizadas como referencia, imagens obtidas de atlas de anatomia e fotografias de um esqueleto fornecido pela Universidade de Mogi das Cruzes. Foram modelados o sistema ósseo, os órgãos internos e a anatomia externa do corpo humano. A metodologia empregada permitiu a alteração de parâmetros do modelo dentro da ferramenta da modelagem. Essa possibilidade foi mostrada através da variação, dos formatos do intestino e do aumento da quantidade de tecido adiposo da malha referente a pele. A simulação das imagens radiológicas foi realizada a partir de coeficientes de atenuação de massa de materiais, ossos e tecidos e de modelos com diversas características físicas. Essa versatilidade permite prever a influência que as diferenças morfométricas entre os indivíduos provocam nas imagens, propriciando dessa forma, uma ferramenta relevante complementar aos métodos de controle de qualidade tradicionais.The conventional methods of quality control applied to radio diagnosis are the best way to have assured good quality of the produced images. Due the amount of variables to consider, the study of particular issues of the process of formation of radiological images requires complementary computational tools. However, the computational voxel based phantoms are not suitable to represent the morphometrical variations, intended for test simulations with image based diagnosis. This work developed a new type of computational phantom, based on 3D modelling. It has the same advantages of the conventional ones, without some of their restrictions. The modeling tool employed, Blender, is available on internet for free download. The project uses the technique called box modeling, which consists in the deformation of a primitive form (a cube, in this case) until it presents a similar form to that it is wanted to model. In order to achieve it, some images, obtained from anatomy atlas and a skeleton pictures obtained from University of Mogi das Cruzes, were used as reference. Were built models from skeletal system, internal organs and external human body anatomy. The applied methodology allowed model´s parameter settings on the modelling tool. This option was presented by means of intestine format variation and increase of adipose tissue on the mesh that represents skin. The simulation of radiological images was done by means of x-ray mass attenuation coefficients, bones and tissues and models with diferent physical characteristics. This flexibility allows the analysis and forecasting of the influences that morphometrical differences of individual implies on images, revealing an important tool that complements the conventional quality control tools.
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Aldehani, Mohammed. "Hydrogen-water isotope exchange in a trickle bed column by process simulation and 3D computational fluid dynamics modelling." Thesis, Lancaster University, 2016. http://eprints.lancs.ac.uk/82667/.
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Hydrogen is the most abundant chemical element in the universe and exists under three isotopic forms: protium, deuterium and tritium. Protium is commonly used in a variety of industries including electronics, metallurgy, chemistry and petrochemistry. Deuterium and tritium have taken more roles in both civil and defence nuclear industries and biomedical sciences. Today water treatment systems at nuclear sites remove many contaminating debris isotopes, with the exception of tritium. This is because tritiated waters have traditionally been particularly difficult and expensive to treat while they can spread easily if they escape into the environment. The topic of separation and purification of tritium and deuterium has a considerable value. Among the numerous separation methods of hydrogen isotopes, H2-H2O liquid catalytic exchange has attracted interest because of its mild operating conditions, high efficiency, limited corrosion and toxicity. The method of hydrogen-water liquid catalytic exchange has many possible applications such as; producing and upgrading heavy water, producing light water and removing tritium from light and heavy waters for recycling to fusion reactors or for low level nuclear deposits. This thesis presents the hydrogen-water isotope exchange reaction that is taking place co-currently and counter-currently through a trickle bed column. Numerical simulations were performed by process design and fluid flow modelling. The missing physical properties of deuterium, and particularly of tritium isotopologues in gaseous and water forms, were predicted and validated with existing literature data. Moreover, suitable operating parameters were approached allowing isotopic exchange to be performed under favourable performance. Intrinsic fluid flow studies by 3D modelling offered more understanding of various underlying phenomena taking place at the local scale and provided identification of main hydrodynamic characteristics in a trickle bed reactor including trends of pressure drop, liquid holdup and catalyst wetting efficiency. The activity of the catalytic process in terms of rate of conversion was discussed through the effect of operating conditions and was validated by a comparison with experimental data and literature.
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Renberg, Ulrica. "1D engine simulation of a turbocharged SI engine with CFD computation on components." Licentiate thesis, KTH, Machine Design (Div.), 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-9162.
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1D engine simulations of turbocharged engines are difficult to
Techniques that can increase the SI- engine efficiency while keeping the emissions very low is to reduce the engine displacement volume combined with a charging system. Advanced systems are needed for an effective boosting of the engine and today 1D engine simulation tools are often used for their optimization.
This thesis concerns 1D engine simulation of a turbocharged SI engine and the introduction of CFD computations on components as a way to assess inaccuracies in the 1D model.
1D engine simulations have been performed on a turbocharged SI engine and the results have been validated by on-engine measurements in test cell. The operating points considered have been in the engine’s low speed and load region, with the turbocharger’s waste-gate closed.
The instantaneous on-engine turbine efficiency was calculated for two different turbochargers based on high frequency measurements in test cell. Unfortunately the instantaneous mass flow rates and temperatures directly upstream and downstream of the turbine could not be measured and simulated values from the calibrated engine model were used. The on-engine turbine efficiency was compared with the efficiency computed by the 1D code using steady flow data to describe the turbine performance.
The results show that the on-engine turbine efficiency shows a hysteretic effect over the exhaust pulse so that the discrepancy between measured and quasi-steady values increases for decreasing mass flow rate after a pulse peak.
Flow modeling in pipe geometries that can be representative to those of an exhaust manifold, single bent pipes and double bent pipes and also the outer runners of an exhaust manifold, have been computed in both 1D and 3D under steady and pulsating flow conditions. The results have been compared in terms of pressure losses.
The results show that calculated pressure gradient for a straight pipe under steady flow is similar using either 1D or 3D computations. The calculated pressure drop over a bend is clearly higher1D engine simulations of turbocharged engines are difficult to using 1D computations compared to 3D computations, both for steady and pulsating flow. Also, the slow decay of the secondary flow structure that develops over a bend, gives a higher pressure gradient in the 3D calculations compared to the 1D calculation in the straight pipe parts downstream of a bend.
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Hermosa, Hidalgo Daniel Hernán. "Three-dimensional computational fluid dynamics with sediment transport modelling in hydropower reservoir: the Binga study case in The Philippines." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/19691/.
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The Binga reservoir was rapidly filled with sediments due to an underestimation of the sediment load and the absence of any sediment management strategy. The Binga reservoir is gradually losing its remaining ability to regulate the flow of Agno river as the water storage capacity is reduced year by year due to sedimentation. The sediment inflow is expected to increase over the coming years because the sedimentation that takes place in the upstream reservoir, Ambuklao reservoir, and its associated reduction of sediment trapping efficiency will increase the sediment load released to Binga reservoir. Also, the Binga tributaries, Adonot/Leboy and Bisal rivers, carry very high sediment loads to the reservoir. The Binga reservoir will therefore lose most of its remaining flow regulating capacity and the sediment trapping ability approaches zero.
Sediment management is crucial to maintain the plant as a run-of-river project. There must be provided a safe passage of floods, maintaining a sustainable ability to dampen the peak of the floods as much as possible, keeping the safety and integrity of the dam and the spillway, and the ability to produce power, providing always a safe passage of all incoming sediment loads. It is extremely important to stop the progression of the delta towards the intake, otherwise it can be clogged since the delta is more likely to develop a fan shape deposition pattern further in the direction towards the intake rather than the spillway. An alternative is proposed to direct the sediment load straight towards the spillway. It consists in the placement of a shortcut or canal in the right bank peninsula, considering the flow patterns in the first curve just before the peninsula. Simulations are carried out with SSIIM, for sediment transport evaluation after the implemented design. These evaluations will show if the canal will shorten the distance to the spillway with a straight path, thus avoiding the possible obstruction of the intake.
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Kyffin, J. A. "Establishing species-specific 3D liver microtissues for repeat dose toxicology and advancing in vitro to in vivo translation through computational modelling." Thesis, Liverpool John Moores University, 2018. http://researchonline.ljmu.ac.uk/9707/.
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The scientific basis of xenobiotic safety is complicated because of the variance in predictability of the primary and secondary pharmacology of foreign chemical substances, as well as variability in individual susceptibility within the population [1]. Despite a wealth of research into this field, our understanding of the mechanisms underpinning the occurrence of adverse effects from xenobiotics remains limited [2]. Adverse drug reactions (ADRs) represent a major encumbrance to the development of new therapeutics with approximately 21% of drug attrition attributed to toxicity during the development process [3]. The in vivo/ex vivo use of animals in science, and in particular drug development, is a global practice and the main purposes of animal experiments are; (i) to gain basic biological knowledge, (ii) for fundamental medical research, (iii) for the discovery and development of drugs, vaccines and medical devices, and (iv) for the toxicity testing of xenobiotics/drugs [4]. However, with there being species-species differences in mechanistic responses, it is difficult to assess results in animal trials and translate these findings in order to predict the in-vivo response in humans [5]. Current in vitro model systems developed to assess ADRs have a number of down falls including; (i) the isolating procedure of primary hepatocytes, (ii) their cost, (iii) inter-donor differences, (iv) limited availability, (v) as well as increasing ethical pressure to implement the 3R's (Replacement, Reduction and Refinement) in research [6]. The emphasis on producing a relevant and representative in vitro model for hepatotoxicity has therefore expanded. The aim of this thesis is to characterise a novel 3D microtissue model that, in the future, aims to provide a better in vitro platform to assess liver toxicity after repeat-dose exposure to xenobiotics. This is particularly important because the processes of hepatotoxicity manifest themselves over several hours and even days, and therefore in vitro models need to be able to comprehensively assess toxic potential for repeat-dose scenarios as well as chronic exposures. Computational modelling is implemented to 14 allow translation of results and to better bridge the gap between in vitro and in vivo approaches and to exploit the knowledge gained from experimental work. Chapter 1 is a critical review of culture techniques and cell types that are used during the development stages of xenobiotic discovery. A number of in vitro models are evaluated with regards to the determination of hepatotoxic potential of compounds. This review has been previously published [7]. Chapter 1 also includes an introduction to mathematical modelling of hepatic clearance and other pharmacokinetic approaches. Chapter 2 describes the experimental characterisation of a primary rat hepatocyte (PRH) spheroid model. The application of the liquid-overlay technique (LOT) [8] with PRH results in the production of viable and reproducible microtissues, amenable for high-throughput investigations. I show that our in vitro system mimics the in vivo cellular morphology, exhibiting both structural and functional polarisation, along with active and functional transporters. Chapter 3 describes the construction of a mathematical model of oxygen diffusion for my experimental in vitro spheroid system. This model is utilised to predict oxygen profiles within the spheroids and to propose optimised operating conditions in order to recapitulate healthy sinusoidal oxygen tensions. This optimisation is based on initial cell seeding densities and experimentally derived oxygen consumption rates (OCR). Chapter 4 describes the construction of a mathematical model to predict the diffusion of xenobiotics based on their inherent physicochemical properties. The in silico system incorporates specific parameters from the experimental spheroid system including paracellular transport features, namely tortuosity and pore fraction properties. The model describes how these spatiotemporal characteristics vary over the duration of the culture period and what effect these have on the transport of xenobiotics.
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Jeffcoate, Penelope. "Experimental and computational modelling of 3-D flow and bed shear stresses downstream from a multiple duct tidal barrage." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/experimental-and-computational-modelling-of-3d-flow-and-bed-shear-stresses-downstream-from-a-multiple-duct-tidal-barrage(13b4b1d2-d144-4510-bc46-50a25739e41c).html.
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The near-field depth-varying velocities and resulting bed stresses downstream from a tidal barrage have not previously been studied. The flow through and downstream of a row of seven open draft tubes in a barrage has been investigated through laboratory experiment in a wide flume, 3-D RANS CFD simulation and 2-D depth-averaged computation. When there is no turbine representation and hence negligible swirl in the draft tubes, agreement between the experiments and 3-D modelling is shown to be good, including the prediction of an asymmetric Coandă effect. With the addition of bulb bodies and vanes creating swirl in the draft tubes the velocity profiles are changed, with increased swirl directly downstream from the draft tubes and throughout the entire flume cross-section further from the barrage. The addition of rotors did not significantly alter the flow field patterns, for the stator/rotor combinations presented here. 3-D CFD could not accurately predict the velocity profiles resulting from the swirl in the ducts. The experiments and 3-D model shows that bed shear stress can be magnified markedly near the barrage particularly where the jets become attached to the bed. At full-scale this would result in a fully mobile bed with sand of typical grain size 1mm. One aim was to determine the distance downstream where depth-averaged modelling gives reasonable prediction and this is shown to occur around 20 tube diameters (20D) downstream of the barrage. Upstream of this, the depth-averaged modelling inaccurately predicts water level and bed shear as well as the 3-D flow field. The addition of swirl cannot be modelled using 2-D modelling, but by 20D downstream there is minimal velocity variation transversely and throughout the depth, indicating depth-averaged modelling would be applicable from this distance.
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Schaal, Wesley. "Computational Studies of HIV-1 Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2002. http://publications.uu.se/theses/91-554-5213-2/.
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Chykeyuk, Kiryl. "Analysis of 3D echocardiography." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:823cd243-5d48-4ecc-90e7-f56d49145be8.
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Heart disease is the major cause of death in the developed world. Due to its fast, portable, low-cost and harmless way of imaging the heart, echocardiography has become the most frequent tool for diagnosis of cardiac function in clinical routine. However, visual assessment of heart function from echocardiography is challenging, highly operatordependant and is subject to intra- and inter observer errors. Therefore, development of automated methods for echocardiography analysis is important towards accurate assessment of cardiac function. In this thesis we develop new ways to model echocardiography data using Bayesian machine learning methods and concern three problems: (i) wall motion analysis in 2D stress echocardiography, (ii) segmentation of the myocardium in 3D echocardiography, and (iii) standard views extraction from 3D echocardiography. Firstly, we propose and compare four discriminative methods for feature extraction and wall motion classification of 2D stress echocardiography (images of the heart taken at rest and after exercise or pharmalogical stress). The four methods are based on (i) Support Vector Machines, (ii) Relevance Vector Machines, (iii) Lasso algorithm and Regularised Least Squares, (iv) Elastic Net regularisation and Regularised Least Squares. Although all the methods are shown to have superior performance to the state-of-the-art, one conclusion is that good segmentation of the myocardium in echocardiography is key for accurate assessment of cardiac wall motion. We investigate the application of one of the most promising current machine learning techniques, called Decision Random Forests, to segment the myocardium from 3D echocardiograms. We demonstrate that more reliable and ultrasound specific descriptors are needed in order to achieve the best results. Specifically, we introduce two sets of new features to improve the segmentation results: (i) LoCo and GloCo features with a local and a global shape constraint on coupled endoand epicardial boundaries, and (ii) FA features, which use the Feature Asymmetry measure to highlight step-like edges in echocardiographic images. We also reinforce the traditional features such as Haar and Rectangular features by aligning 3D echocardiograms. For that we develop a new registration technique, which is based on aligning centre lines of the left ventricles. We show that with alignment performance is boosted by approximately 15%. Finally, a novel approach to detect planes in 3D images using regression voting is proposed. To the best of our knowledge we are the first to use a one-step regression approach for the task of plane detection in 3D images. We investigate the application to standard views extraction from 3D echocardiography to facilitate efficient clinical inspection of cardiac abnormalities and diseases. We further develop a new method, called the Class- Specific Regression Forest, where class label information is incorporating into the training phase to reinforce the learning from semantically relevant to the problem classes. During testing the votes from irrelevant classes are excluded from voting to maximise the confidence of output predictors. We demonstrate that the Class-Specific Regression Random Forest outperforms the classic Regression Random Forest and produces results comparable to the manual annotations.
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Martínez, Mateu Laura. "Mapping of the electrical activity of human atria. Multiscale modelling and simulations." Doctoral thesis, Universitat Politècnica de València, 2018. http://hdl.handle.net/10251/104604.
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La fibrilación auricular es una de las arritmias cardíacas más comunes observadas en la práctica clínica. Por lo tanto, es de vital importancia desarrollar nuevas tecnologías destinadas a diagnosticar y acabar con este tipo de arritmia, para mejorar la calidad de vida de los pacientes y reducir los costes de los sistemas nacionales de salud.
En los últimos años ha aumentado el uso de las nuevas técnicas de mapeo auricular, basadas en sistemas multi-electrodo para mapear la actividad eléctrica en humanos. Dichas técnicas permiten localizar y ablacionar los impulsores de la fibrilación auricular, como son las fuentes focales o los rotores. Sin embargo, todavía existe incertidumbre sobre su precisión y los procedimientos experimentales para su análisis están limitados debido a su carácter invasivo. Por lo tanto, las simulaciones computacionales son una herramienta muy útil para superar estas limitaciones, al permitir reproducir con fidelidad las observaciones experimentales, dividir el problema bajo estudio en sub-estudios más simples, y realizar investigaciones preliminares imposibles de llevar a cabo en el práctica clínica.
Esta tesis doctoral se centra en el análisis de la precisión de los sistemas de mapeo multi-electrodo a través de modelos y simulaciones computacionales. Para ello, desarrollamos modelos realistas multi-escala con el objetivo de simular actividad eléctrica auricular reentrante, en primer lugar en una lámina de tejido auricular, y en segundo lugar en las aurículas completas. Posteriormente, analizamos los efectos de las configuraciones geométricas multi-electrodo en la precisión de la localización de los rotores, mediante el uso de agrupaciones multi-electrodo con distancias inter-electrodo equidistantes, así como a través de catéteres de tipo basket con distancias inter-electrodo no equidistantes. Después de calcular los electrogramas unipolares intracavitarios, realizamos mapas de fase, detecciones de singularidad de fase para rastrear los rotores, y mapas de frecuencia dominantes. Finalmente, descubrimos que la precisión de los sistemas de mapeo multi-electrodo depende de su posición dentro de la cavidad auricular, de la distancia entre los electrodos y el tejido, de la distancia inter-electrodo, y de la contribución de las fuentes de campo lejano. Además, como consecuencia de estos factores que pueden afectar a la precisión de los sistemas de mapeo multi-electrodo, observamos la aparición de rotores falsos que podrían contribuir al fracaso de los procesos de ablación de la fibrilación auricular.Atrial fibrillation is one of the most common cardiac arrhythmias seen in clinical practice. Therefore, it is of vital importance to develop new technologies aimed at diagnosing and terminating this kind of arrhythmia, to improve the quality of life of patients and to reduce costs to national health systems. In the last years, new atrial mapping techniques based on multi-electrode systems are increasingly being used to map the atrial electrical activity in humans and localise and target atrial fibrillation drivers in the form of focal sources or rotors. However, significant concerns remain about their accuracy and experimental approaches to analyse them are limited due to their invasive character. Therefore, computer simulations are a helpful tool to overcome these limitations since they can reproduce with fidelity experimental observations, permit to split the problem to treat into more simple substudies, and allow the possibility of performing preliminary investigations impossible to carry out in the clinical practice. This PhD thesis is focused on the analysis for accuracy of the multielectrode mapping systems through computational models and simulations. For this purpose, we developed realistic multiscale models in order to simulate atrial electrical reentrant activity, first in a sheet of atrial tissue and, then, in the whole atria. Then, we analysed the effects of the multi-electrode geometrical configurations on the accuracy of localizing rotors, by using multi-electrode arrays with equidistant inter-electrode distances, as well as multi-electrode basket catheters with non-equidistant inter-electrode distances. After computing the intracavitary unipolar electrograms, we performed phase maps, phase singularity detections to track rotors, and dominant frequency maps. We finally found out that the accuracy of multi-electrode mapping systems depends on their position inside the atrial cavity, the electrode-to-tissue distance, the inter-electrode distance, and the contribution of far field sources. Furthermore, as a consequence of these factors, false rotors might appear and could contribute to failure of atrial fibrillation ablation procedures.
La fibril·lació auricular és una de les arítmies cardíaques més comuns observades en la pràctica clínica. Per tant, és de vital importància desenvolupar noves tecnologies destinades a diagnosticar i acabar amb aquest tipus d'arítmia, per tal de millorar la qualitat de vida dels pacients i reduir els costos dels sistemes nacionals de salut. En els últims anys, ha augmentat l'ús de les noves tècniques de mapeig auricular, basades en sistemes multielèctrode per a mapejar l'activitat elèctrica auricular en humans. Aquestes tècniques permeten localitzar i ablacionar els impulsors de la fibril·lació auricular, com són les fonts focals o els rotors. No obstant això, encara hi ha incertesa sobre la seua precisió i els procediments experimentals per al seu anàlisi estan limitats a causa del seu caràcter invasiu. Per tant, les simulacions computacionals són una eina molt útil per a superar aquestes limitacions, en permetre reproduir amb fidelitat les observacions experimentals, dividir el problema sota estudi en subestudis més simples, i realitzar investigacions preliminars impossibles de dur a terme en el pràctica clínica. Aquesta tesi doctoral es centra en l'anàlisi de la precisió del sistemes de mapeig multielèctrode mitjançant els models i les simulacions computacionals. Per a això, desenvolupàrem models realistes multiescala per tal de simular activitat elèctrica auricular reentrant, en primer lloc en una làmina de teixit auricular, i en segon lloc a les aurícules completes. Posteriorment, analitzàrem els efectes de les configuracions geomètriques multielèctrode en la precisió de la localització dels rotors, mitjançant l'ús d'agrupacions multielèctrode amb distàncies interelèctrode equidistants, així com catèters de tipus basket amb distàncies interelèctrode no equidistants. Després de calcular els electrogrames unipolars intracavitaris, vam realitzar mapes de fase, deteccions de singularitat de fase per a rastrejar els rotors, i mapes de freqüència dominants. Finalment, vam descobrir que la precisió dels sistemes de mapeig multielèctrode depèn de la seua posició dins de la cavitat auricular, de la distància entre els elèctrodes i el teixit, de la distància interelèctrode, i de la contribució de les fonts de camp llunyà. A més, com a conseqüència d'aquests factors, es va observar l'aparició de rotors falsos que podrien contribuir al fracàs de l'ablació de la fibril·lació auricular.
Martínez Mateu, L. (2018). Mapping of the electrical activity of human atria. Multiscale modelling and simulations [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/104604
TESIS
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Linde, Florian. "3D modelling of ship resistance in restricted waterways and application to an inland eco-driving prototype." Thesis, Compiègne, 2017. http://www.theses.fr/2017COMP2389/document.
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Les travaux de cette thèse ont pour but de développer un prototype d’éco-pilote, nommé EcoNav, permettant d’optimiser la vitesse d’un bateau afin de réduire sa consommation de carburant. EcoNav est composé de plusieurs modules dont : un modèle hydraulique 2D simulant l’écoulement hydrodynamique (vitesse du courant et hauteur d’eau) le long du trajet du bateau; - un modèle de résistance à l’avancement servant à alimenter un modèle de prédiction de la consommation de carburant; - un algorithme d’optimisation permettant de trouver le profil optimal de vitesse. Afin de pouvoir estimer la consommation de carburant, un modèle numérique de la résistance à l’avancement en milieu confiné a été développé durant la première partie de cette thèse. Ce modèle numérique 3D simule l’écoulement du fluide autour du bateau et permet de calculer les forces agissant sur sa coque. La résolution des équations RANS est couplée avec un algorithme de quasi-Newton afin de trouver la position d’équilibre du bateau et calculer son enfoncement. Cette méthode est validée en comparant les résultats numériques avec des résultats expérimentaux issus d’essais en bassin de traction. L’influence de l’enfoncement sur la résistance à l’avancement et la précision de la méthode est étudiée en comparant les résultats numériques obtenus avec et sans enfoncement. La précision des modèles empiriques de prédiction de la résistance à l’avancement est également comparée à celle du modèle numérique. Enfin, le modèle numérique est utilisé afin de déterminer si le confinement en largeur ou en profondeur ont une influence identique sur l’augmentation de résistance à l’avancement. Les résultats de cette étude permettent d’établir si le confinement de la voie d’eau peut être caractérisé à l’aide d’un paramètre unique (coefficient de blocage par exemple) ou bien deux paramètres permettant de distinguer le confinement latéral et vertical. Dans la seconde partie de cette thèse, les méthodes numériques utilisées pour le modèle d’éco-pilote sont décrites et comparées afin de sélectionner celles qui sont le plus adaptées à chaque module. EcoNav est ensuite utilisé afin de modéliser un cas réel : celui du bateau automoteur Oural navigant sur la Seine entre Chatou et Poses (153 km). La consommation optimisée est comparée à la consommation non optimisée, calculée à partir des vitesses AIS observées sur le tronçon étudié. L’influence de la trajectoire du bateau et de son temps de parcours sur sa consommation sont également étudiés. Les résultats de ces investigations ont montré qu’optimiser la vitesse du bateau permet d’obtenir une réduction de la consommation de carburant de l’ordre de 8 % et qu’optimiser la trajectoire du bateau ainsi que prendre en compte des informations en temps réel (disponibilité des écluses, trafic sur le fleuve) peuvent permettre de réaliser des économies de carburant supplémentairesAn eco-driving prototype, named EcoNav, is developed with the aim of optimizing a vessel speed in order to reduce fuel consumption for a given itinerary. EcoNav is organized in several modules : - a 2D hydraulic model simulating the flow conditions (current speed and water depth) along the itinerary; - a ship resistance model calculating the thrust necessary to counteract the hydrodynamic forces ; - a fuel consumption model calculating the fuel consumption corresponding to the thrust input; - a non linear optimization algorithm calculating the optimal speed profile. In order to evaluate the fuel consumption of an inland vessel, a ship resistance numerical model is developed in the first part of this PhD. This 3D numerical model simulates the flow around an inland self-propelled vessel and evaluates the hydrodynamic forces acting on the hull. A RANS solver is coupled with a quasi-Newton approach to find the equilibrium position and calculate ship sinkage. This method is validated by comparing the results of numerical simulations to towing tank tests. The numerical results with and without sinkage are also compared to study the influence of sinkage on ship resistance and on the accuracy of the method. Additionally, some empirical models are investigated and compared with the accuracy of the numerical method. Finally, the numerical model is used to determine if channel with and water depth restriction contribute to the same amount of ship resistance increase for the same level of restriction. The results of that investigation give insight to whether channel restriction can be characterized by a unique parameter (for instance the blockage ratio) or two parameters to distinguish water depth and channel with effects. In the second part of this PhD, the numerical methods used in the speed optimization model are described and validated. The speed optimization model is then used to simulate a real case: the itinerary of the self-propelled ship Oural on river Seine, between Chatou and Poses (153 km). The optimized fuel consumption is compared with the non-optimized fuel consumption, based on AIS speed profile retrieved on this itinerary. The effects of the ship trajectory and travel duration on fuel consumption are also investigated. The results of those investigations showed that optimizing the ship speed lead to an average fuel saving of 8 % and that using an optimal track and including real time information such as lock availability and river traffic can lead to additional fuel savings
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Pires, David da Silva. "Rastreamento de componentes conexas em vídeo 3D para obtenção de estruturas tridimensionais." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-06072009-173738/.
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Este documento apresenta uma dissertação sobre o desenvolvimento de um sistema de integração de dados para geração de estruturas tridimensionais a partir de vídeo 3D. O trabalho envolve a extensão de um sistema de vídeo 3D em tempo real proposto recentemente. Esse sistema, constituído por projetor e câmera, obtém imagens de profundidade de objetos por meio da projeção de slides com um padrão de faixas coloridas. Tal procedimento permite a obtenção, em tempo real, tanto do modelo 2,5 D dos objetos quanto da textura dos mesmos, segundo uma técnica denominada luz estruturada. Os dados são capturados a uma taxa de 30 quadros por segundo e possuem alta qualidade: resoluções de 640 x 480 pixeis para a textura e de 90 x 240 pontos (em média) para a geometria. A extensão que essa dissertação propõe visa obter o modelo tridimensional dos objetos presentes em uma cena por meio do registro dos dados (textura e geometria) dos diversos quadros amostrados. Assim, o presente trabalho é um passo intermediário de um projeto maior, no qual pretende-se fazer a reconstrução dos modelos por completo, bastando para isso apenas algumas imagens obtidas a partir de diferentes pontos de observação. Tal reconstrução deverá diminuir a incidência de pontos de oclusão (bastante comuns nos resultados originais) de modo a permitir a adaptação de todo o sistema para objetos móveis e deformáveis, uma vez que, no estado atual, o sistema é robusto apenas para objetos estáticos e rígidos. Até onde pudemos averiguar, nenhuma técnica já foi aplicada com este propósito. Este texto descreve o trabalho já desenvolvido, o qual consiste em um método para detecção, rastreamento e casamento espacial de componentes conexas presentes em um vídeo 3D. A informação de imagem do vídeo (textura) é combinada com posições tridimensionais (geometria) a fim de alinhar partes de superfícies que são vistas em quadros subseqüentes. Esta é uma questão chave no vídeo 3D, a qual pode ser explorada em diversas aplicações tais como compressão, integração geométrica e reconstrução de cenas, dentre outras. A abordagem que adotamos consiste na detecção de características salientes no espaço do mundo, provendo um alinhamento de geometria mais completo. O processo de registro é feito segundo a aplicação do algoritmo ICP---Iterative Closest Point---introduzido por Besl e McKay em 1992. Resultados experimentais bem sucedidos corroborando nosso método são apresentados.This document presents a MSc thesis focused on the development of a data integration system to generate tridimensional structures from 3D video. The work involves the extension of a recently proposed real time 3D video system. This system, composed by a video camera and a projector, obtains range images of recorded objects using slide projection of a coloured stripe pattern. This procedure allows capturing, in real time, objects´ texture and 2,5 D model, at the same time, by a technique called structured light. The data are acquired at 30 frames per second, being of high quality: the resolutions are 640 x 480 pixels and 90 x 240 points (in average), respectively. The extension that this thesis proposes aims at obtaining the tridimensional model of the objects present in a scene through data matching (texture and geometry) of various sampled frames. Thus, the current work is an intermediary step of a larger project with the intent of achieving a complete reconstruction from only a few images obtained from different viewpoints. Such reconstruction will reduce the incidence of occlusion points (very common on the original results) such that it should be possible to adapt the whole system to moving and deformable objects (In the current state, the system is robust only to static and rigid objects.). To the best of our knowledge, there is no method that has fully solved this problem. This text describes the developed work, which consists of a method to perform detection, tracking and spatial matching of connected components present in a 3D video. The video image information (texture) is combined with tridimensional sites (geometry) in order to align surface portions seen on subsequent frames. This is a key step in the 3D video that may be explored in several applications such as compression, geometric integration and scene reconstruction, to name but a few. Our approach consists of detecting salient features in both image and world spaces, for further alignment of texture and geometry. The matching process is accomplished by the application of the ICP---Iterative Closest Point---algorithm, introduced by Besl and McKay in 1992. Succesful experimental results corroborating our method are shown.
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Alzahrani, Faris. "3D modelling by computational fluid dynamics of local interactions of momentum, mass and heat transfers with catalyst deactivation in gas-solid catalytic reactors of low aspect ratios." Thesis, Lancaster University, 2016. http://eprints.lancs.ac.uk/82666/.
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Packed beds of gas-solid systems are extensively used as reactors, separators, dryers, filters, heat exchangers and combustors. The design of packed beds requires a detailed knowledge of local dynamics of flow, composition and temperature. Unfortunately, investigations for the development of 3D modelling codes by computational fluid dynamics are still not sufficiently mature compared with those relying on 2D modelling or simplified pseudo-homogenous models. This project investigates non-uniform catalyst deactivation in packed bed reactors of low aspect ratios under steady-state and dynamic operations. Low aspect ratio packed beds were selected as they are known to generate non-uniform distribution of local flow. Detailed knowledge of flow dynamics in terms of local structure of the packed bed, pressure drops, interstitial flow, heat and mass rate distributions was examined. The discrete element method was used to generate various packing configurations and the results of profiles of porosity were in a good agreement with the semi-analytical models, especially, in the vicinity of the wall. Similar oscillation trends with damping profiles towards the centre of the packed beds were observed. Flow heterogeneity was assessed by tests of mass transfer dispersion through a Lagrangian approach. Interactions of fluid flow, mass and heat transfers, and local deactivation of alumina catalyst Al2O3 of CO oxidation were investigated under design and operating conditions. An increase in the activation energy of deactivation promoted the deactivation by accelerating the reaction rate and releasing additional thermal energy, which in turn accelerated the deactivation. The 3D modelling allowed observation of local catalyst deactivation at packing pore level which is typically not accessible by the 2D modelling or pseudo-homogeneous models. In addition, the deactivation was quite asymmetrical along axial and radial directions, leading to uneven rates of thermal expansion and contraction and causing local deactivation associated with temperature runaways.
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Fajardo, Peña Pablo. "Methodology for the Numerical Characterization of a Radial Turbine under Steady and Pulsating Flow." Doctoral thesis, Universitat Politècnica de València, 2012. http://hdl.handle.net/10251/16878.
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The increasing use of turbochargers is leading to an outstanding research to understand the internal flow in turbomachines. In this frame, computational fluid dynamics (CFD) is one of the tools that can be applied to contribute to the analysis of the fluid-dynamic processes occurring in a turbine. The objective of this thesis is the development of a methodology for performing simulations of radial turbomachinery optimizing the available computational resources. This methodology is used for the characterization of a vaned-nozzle turbine under steady and pulsating flow conditions.
An important effort has been devoted in adjusting the case configuration to maximize the accuracy achievable with a certain computational cost. Concerning the cell size, a local mesh independence analysis is proposed as a procedure to optimize the distribution of cells in the domain, thus allowing to use a finer mesh in the most suitable places. Particularly important in turbomachinery simulations is the influence of the approach for simulating rotor motion. In this thesis two models have been compared: multiple reference frame and sliding mesh. The differences obtained using both methods were found to be significant in off-design regions. Steady flow CFD results have been validated against global measurements taken on a gas-stand.
The modeling of a turbine, installed either on a turbocharger test rig or an engine, requires the calculation of the flow in the ducts composing the system. Those ducts could be simulated assuming a one-dimensional (1D) approximation, and thus reducing the computational cost. In this frame of ideas, two CFD boundary conditions have been developed. The first one allows performing coupled 1D-3D simulations, communicating the flow variables from each domain through the boundary. The second boundary condition is based in a new formulation for a stand-alone anechoic end, which intends to represent the flow behavior of an infinite duct.
Finally, the turbine was simulatFajardo Peña, P. (2012). Methodology for the Numerical Characterization of a Radial Turbine under Steady and Pulsating Flow [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/16878
Palancia
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Maasdorp, Lynndle Caroline. "Temperature proton exchange membrane fuel cells in a serpentine design." Thesis, University of the Western Cape, 2010. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_1316_1307961639.
Full textAbstract:
The aim of my work is to model a segment of a unit cell of a fuel cell stack using numerical methods which is classified as computational fluid dynamics and implementing the work in a commercial computational fluid dynamics package, FLUENT. The focus of my work is to study the thermal distribution within this segment. The results of the work aid in a better understanding of the fuel cell operation in this temperature range. At the time of my investigation experimental results were unavailable for validation and therefore my results are compared to previously published results published. The outcome of the results corresponds to this, where the current flux density increases with the increasing of operating temperature and fixed operating voltage and the temperature variation across the fuel cell at varying operating voltages. It is in the anticipation of determining actual and or unique material input parameters that this work is done and at which point this studies results would contribute to the understanding high temperature PEM fuel cell thermal behaviour, significantly.
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Yirci, Murat. "Arrangements 2D pour la Cartographie de l’Espace Public et des Transports." Thesis, Paris Est, 2016. http://www.theses.fr/2016PESC1075/document.
Full textAbstract:
Cette thèse porte sur le développement facilité d'applications de cartographie et de transport, plus particulièrement sur la génération de réseaux piétonniers pour des applications telles que la navigation, le calcul d'itinéraires, l'analyse d'accessibilité et l'urbanisme. Afin d'atteindre ce but, nous proposons un modèle de données à deux couches qui cartographie l'espace public dans une hiérarchie d'objets géospatiaux sémantisés. A bas niveau, la géométrie 2D des objets géospatiaux est représentée par une partition planaire, modélisée par une structure topologique d'arrangement 2D. Cette représentation permet des traitements géométriques efficaces et efficients, ainsi qu'une maintenance et une validation aisée au fur et à mesure des éditions lorsque la géométrie ou la topologie d'un objet sont modifiées. A haut niveau, les aspects sémantiques et thématiques des objets géospatiaux sont modélisés et gérés. La hiérarchie entre ces objets est maintenue à travers un graphe dirigé acyclique dans lequel les feuilles correspondent à des primitives géométriques de l'arrangement 2D et les noeuds de plus haut niveau représentent les objets géospatiaux sémantiques plus ou moins aggrégés. Nous avons intégré le modèle de données proposé dans un framework SIG nommé StreetMaker en complément d'un ensemble d'algorithmes génériques et de capacités SIG basiques. Ce framework est alors assez riche pour générer automatiquement des graphes de réseau piétonnier. En effet, dans le cadre d'un projet d'analyse d'accessibilité, le flux de traitement proposé a permis de produire avec succès sur deux sites un graphe de réseau piétonnier à partir de données en entrées variées : des cartes vectorielles existantes, des données vectorielles créées semi-automatiquement et des objets vectoriels extraits d'un nuage de points lidar issu d'une acquisition de cartographie mobile.Alors que la modélisation 2D de la surface du sol est suffisante pour les applications SIG 2D, les applications SIG 3D nécessitent des modèles 3D de l'environnement. La modélisation 3D est un sujet très large mais, dans un premier pas vers cette modélisation 3D, nous nous sommes concentrés sur la modélisation semi-automatique d'objets de type cylindre généralisé (tels que les poteaux, les lampadaires, les troncs d'arbre, etc) à partir d'une seule image. Les méthodes et techniques développées sont présentées et discutéesThis thesis addresses easy and effective development of mapping and transportation applications which especially focuses on the generation of pedestrian networks for applications like navigation, itinerary calculation, accessibility analysis and urban planning. In order to achieve this goal, we proposed a two layered data model which encodes the public space into a hierarchy of semantic geospatial objects. At the lower level, the 2D geometry of the geospatial objects are captured using a planar partition which is represented as a topological 2D arrangement. This representation of a planar partition allows efficient and effective geometry processing and easy maintenance and validation throughout the editions when the geometry or topology of an object is modified. At the upper layer, the semantic and thematic aspects of geospatial objects are modelled and managed. The hierarchy between these objects is maintained using a directed acyclic graph (DAG) in which the leaf nodes correspond to the geometric primitives of the 2D arrangement and the higher level nodes represent the aggregated semantic geospatial objects at different levels. We integrated the proposed data model into our GIS framework called StreetMaker together with a set of generic algorithms and basic GIS capabilities. This framework is then rich enough to generate pedestrian network graphs automatically. In fact, within an accessibility analysis project, the full proposed pipeline was successfully used on two sites to produce pedestrian network graphs from various types of input data: existing GIS vector maps, semi-automatically created vector data and vector objects extracted from Mobile Mapping lidar point clouds.While modelling 2D ground surfaces may be sufficient for 2D GIS applications, 3D GIS applications require 3D models of the environment. 3D modelling is a very broad topic but as a first step to such 3D models, we focused on the semi-automatic modelling of objects which can be modelled or approximated by generalized cylinders (such as poles, lampposts, tree trunks, etc.) from single images. The developed methods and techniques are presented and discussed
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Eriksson, Emil. "Simulation of Biological Tissue using Mass-Spring-Damper Models." Thesis, Örebro universitet, Institutionen för naturvetenskap och teknik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-27663.
Full textAbstract:
The goal of this project was to evaluate the viability of a mass-spring-damper based model for modeling of biological tissue. A method for automatically generating such a model from data taken from 3D medical imaging equipment including both the generation of point masses and an algorithm for generating the spring-damper links between these points is presented. Furthermore, an implementation of a simulation of this model running in real-time by utilizing the parallel computational power of modern GPU hardware through OpenCL is described. This implementation uses the fourth order Runge-Kutta method to improve stability over similar implementations. The difficulty of maintaining stability while still providing rigidness to the simulated tissue is thoroughly discussed. Several observations on the influence of the structure of the model on the consistency of the simulated tissue are also presented. This implementation also includes two manipulation tools, a move tool and a cut tool for interaction with the simulation. From the results, it is clear that the mass-springdamper model is a viable model that is possible to simulate in real-time on modern but commoditized hardware. With further development, this can be of great benefit to areas such as medical visualization and surgical simulation.Målet med detta projekt var att utvärdera huruvida en modell baserad på massa-fjäderdämpare är meningsfull för att modellera biologisk vävnad. En metod för att automatiskt generera en sådan modell utifrån data tagen från medicinsk 3D-skanningsutrustning presenteras. Denna metod inkluderar både generering av punktmassor samt en algoritm för generering av länkar mellan dessa. Vidare beskrivs en implementation av en simulering av denna modell som körs i realtid genom att utnyttja den parallella beräkningskraften hos modern GPU-hårdvara via OpenCL. Denna implementation använder sig av fjärde ordningens Runge-Kutta-metod för förbättrad stabilitet jämfört med liknande implementationer. Svårigheten att bibehålla stabiliteten samtidigt som den simulerade vävnaden ges tillräcklig styvhet diskuteras genomgående. Flera observationer om modellstrukturens inverkan på den simulerade vävnadens konsistens presenteras också. Denna implementation inkluderar två manipuleringsverktyg, ett flytta-verktyg och ett skärverktyg för att interagera med simuleringen. Resultaten visar tydligt att en modell baserad på massa-fjäder-dämpare är en rimlig modell som är möjlig att simulera i realtid på modern men lättillgänglig hårdvara. Med vidareutveckling kan detta bli betydelsefullt för områden så som medicinsk bildvetenskap och kirurgisk simulering.
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Taileb, Saïd. "Vers des simulations numériques prédictives des détonations gazeuses : influence de la cinétique chimique, de l’equation d’etat et des effets tridimensionnels Influence of the chemical modeling on the quenching limits of gaseous detonation waves confined by an inert layer Computation of the mean hydrodynamic structure of gaseous detonations with losses Numerical study of 3D gaseous detonations in a square channel." Thesis, Chasseneuil-du-Poitou, Ecole nationale supérieure de mécanique et d'aérotechnique, 2020. http://www.theses.fr/2020ESMA0012.
Full textAbstract:
La présente étude s’inscrit dans le cadre général des simulations numériques des détonations dans des conditions non-idéales. Les configurations abordées correspondent à des écoulements rencontrés dans les accidents industriels ainsi que dans les moteurs à détonation rotative, dans lequel le combustible est injecté à des pressions élevées dans un milieu confiné par des gaz inertes. Les simulations conduites reposent sur un code de simulation numérique RESIDENT (REcycling mesh SImulation of DEtonations) développé à l’Institut Pprime. Il s’appuie sur des schémas numériques d’ordre élevé adaptés à la capture des chocs, avec un schéma d’interpolation MP d’ordre 9, un solveur HLLC-M et une intégration temporelle de Runge-Kutta d’ordre 3. Dans un premier temps, l’influence des équations d’état (EOS) sur la structure cellulaire de la détonation a été étudiée avec les deux EOS : gaz parfaits et Noble-Abel. Les résultats ont montré que l’interaction d’une ligne de glissement avec un ensemble de points triples est responsable de la création d’un nouveau point triple. L’augmentation du coefficient isentropique post-choc inhibe l’apparition de ces instabilités et régularise la structure cellulaire. Ce résultat tire son importance du fait que la structure cellulaire conditionne les règles empiriques de dimensionnement. Dans un second temps, l’influence de la modélisation de la cinétique chimique sur la structure de la détonation et ses limites d’extinction a été étudiée à l’aide de trois schémas cinétiques de complexité croissante : chimie à une étape globale, à trois étapes et chimie détaillée. Malgré les similitudes sur la dynamique du front et sur la structure cellulaire, les résultats présentent des différences significatives lorsque la détonation est soumise à des pertes latérales par un confinement par gaz inerte.Cette étude met en évidence l’impact du modèle cinétique sur la prédiction des limites d’extinction des détonations observées expérimentalement. Finalement, l’influence des effets tridimensionnels sur la dynamique de la détonation a été étudiée. Des comparaisons de simulations 2-D et 3-D ont été effectuées dans le cas d’une configuration d’une détonation marginale et d’une détonation semi-confinée. Malgré les différences dans la topologie de l’écoulement,des similitudes ont été observées dans la structure moyenne lorsque la détonation est idéale. L’analyse de l’énergie des fluctuations totale a révélé que les fluctuations d’entropie sont plus importantes que les fluctuations totales de pression. Dans le cas de la détonation semi-confinée, les effets 3-D se manifestent par un déficit de vitesse moindre qu’en 2-D lorsque la détonation se propage à la même hauteur réactive. Le déficit de vitesse est alors corrélé au rapport de l’épaisseur hydrodynamique avec le rayon de courbure, malgré une courbure moyenne plus importante du front en 3-DThis study is part of the general framework of numerical simulations of detonations under non-ideal conditions.The configurations discussed correspond to flows encountered in industrial hazards and rotating detonation engines.Simulations are based on an inhouse code RESIDENT (REcycling mesh SImulation of DEtonations) developed at the Pprime Institute. It is based on high-order shock capturing schemes, with a MP9 interpolation scheme, a HLLC-M solver and a 3rd Runge-Kutta time integration. At first, the influence of the equation of state (EOS) on the cellular detonation structure has been studied with two EOS : Perfect gas and Noble-Abel. The numerical results have shown that new triples points are generated from the interaction of a slip line with already existing triple points. The increase of the post-shock isentropic coeffient has inhibited the appearance of these instabilities and has regularized the cell structure. This results may be important as engineering correlations are based on the cell size and regularity. Secondly, the influence of chemical modelling on the structure of the detonation and its extinction limits were studied using three kinetic models of increasing complexity : single-step, three-step chain-branching and detailed chemistry. Despite the macroscopic features are similar, the outcome of the critical height of a detonation confined by an inert layer is significantly different, highlighting the impact of the kinetics in predicting the extinction limits observed in experiments. Finally, the influence of three-dimensional effects on the dynamics of detonation was studied. Comparisons of 2-D and 3-D simulations are carried out in the case of marginal and semi-confined detonations. Despite the differences observed in the flow topology, similarities were found in the mean structure when the detonation propagation is ideal. The analysis of the total fluctuation energy revealed that entropy fluctuations are more important than pressure fluctuations. In the case of semi-confined detonation, 3-D effects manifests a smaller velocity deficit than in 2-D when the detonation propagates at the same reactive height. The velocity deficitis correlated to the ratio of the hydrodynamic thickness to the radius of curvature, despite the higher average curvature of the 3-D front
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Gerver, Rachel Ellen. "3D thermal-electrochemical lithium-ion battery computational modeling." Thesis, 2009. http://hdl.handle.net/2152/ETD-UT-2009-08-373.
Full textAbstract:
The thesis presents a modeling framework for simulating three dimensional effects in lithium-ion batteries. This is particularly important for understanding the performance of large scale batteries used under high power conditions such as in hybrid electric vehicle applications. While 1D approximations may be sufficient for the smaller scale batteries used in cell phones and laptops, they are severely limited when scaled up to larger batteries, where significant 3D gradients can develop in concentration, current, temperature, and voltage. Understanding these 3D effects is critical for designing lithium-ion batteries for improved safety and long term durability, as well as for conducting effective design optimization studies. The model couples an electrochemical battery model with a thermal model to understand how thermal effects will influence electrochemical behavior and to determine temperature distributions throughout the battery. Several modeling example results are presented including thermal influences on current distribution, design optimization of current collector thickness and current collector tab placement, and investigation of lithium plating risk in three dimensions.text
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Martin, Michael. "Modeling of Transport in Lithium Ion Battery Electrodes." Thesis, 2012. http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11178.
Full textAbstract:
Lithium ion battery systems are promising solutions to current energy storage needs due to their high operating voltage and capacity. Numerous efforts have been conducted to model these systems in order to aid the design process and avoid expensive and time consuming prototypical experiments. Of the numerous processes occurring in these systems, solid state transport in particular has drawn a large amount of attention from the research community, as it tends to be one of the rate limiting steps in lithium ion battery performance. Recent studies have additionally indicated that purposeful design of battery electrodes using 3D microstructures offers new freedoms in design, better use of available cell area, and increased battery performance.
The following study is meant to serve as a first principles investigation into the behaviors of 3D electrode architectures by monitoring concentration and cycle behaviors under realistic operating conditions. This was accomplished using computational tools to model the solid state diffusion behavior in several generated electrode morphologies. Developed computational codes were used to generate targeted structures under prescribed conditions of particle shape, size, and overall morphology. The diffusion processes in these morphologies were simulated under conditions prescribed from literature.
Primary results indicate that parameters usually employed to describe electrode geometry, such as volume to surface area ratio, cannot be solely relied upon to predict or characterize performance. Additionally, the interaction between particle shapes implies some design aspects that may be exploited to improve morphology behavior. Of major importance is the degree of particle isolation and overlap in 3D architectures, as these govern gradient development and lithium depletion within the electrode structures. The results of this study indicate that there are optimum levels of these parameters, and so purposeful design must make use of these behaviors.
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Liu, Ming-Chung, and 劉明宗. "3D Modeling Computation on Web-based Environment." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/11484968461085365266.
Full textAbstract:
碩士國立中正大學
資訊工程研究所
88
Modeling of 3D objects from image pairs is a challenging problem and has been a research topic for many years. Stereo matching is the key technique of 3D objects modeling from image pairs. In this thesis, a hierarchical area-based stereo matching algorithm is proposed. The application of the stereo matching algorithm on the WWW environment is also implemented. By using the method we proposed, the disparity map and 3D mesh of an object can be constructed from one pair of its stereo images. In order to reduce the time complexity of stereo matching, a hierarchical stereo matching architecture is adopted. In other words, the hierarchical stereo matching algorithm matches image-blocks from coarser to finer resolution. In our algorithm, the image-blocks are matched according to correlation coefficient. If some image blocks do not match any block or they match blocks with small correlation coefficient, interpolations are used to reduce the noise in the 3D mesh.
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Hu, Xin. "Multiscale Modeling and Computation of 3D Incompressible Turbulent Flows." Thesis, 2012. https://thesis.library.caltech.edu/7093/2/Xin_HU_2012_ACM_thesis_Multiscale_Modeling_of_Turbulence-corrected_version.pdf.
Full textAbstract:
In the first part, we present a mathematical derivation of a closure relating the Reynolds stress to the mean strain rate for incompressible turbulent flows. This derivation is based on a systematic multiscale analysis that expresses the Reynolds stress in terms of the solutions of local periodic cell problems. We reveal an asymptotic structure of the Reynolds stress by invoking the frame invariant property of the cell problems and an iterative dynamic homogenization of large- and small-scale solutions. The Smagorinsky model for homogeneous turbulence is recovered as an example to illustrate our mathematical derivation. Another example is turbulent channel flow, where we derive a simplified turbulence model based on the asymptotic flow structure near the wall. Additionally, we obtain a nonlinear model by using a second order approximation of the inverse flow map function. This nonlinear model captures the effects of the backscatter of kinetic energy and dispersion and is consistent with other models, such as a mixed model that combines the Smagorinsky and gradient models, and the generic nonlinear model of Lund and Novikov.
Numerical simulation results at two Reynolds numbers using our simplified turbulence model are in good agreement with both experiments and direct numerical simulations in turbulent channel flow. However, due to experimental and modeling errors, we do observe some noticeable differences, e.g. , root mean square velocity fluctuations at Reτ = 180.
In the second part, we present a new perspective on calculating fully developed turbulent flows using a data-driven stochastic method. General polynomial chaos (gPC) bases are obtained based on the mean velocity profile of turbulent channel flow in the offline part. The velocity fields are projected onto the subspace spanned by these gPC bases and a coupled system of equations is solved to compute the velocity components in the Karhunen-Loeve expansion in the online part. Our numerical results have shown that the data-driven stochastic method for fully developed turbulence offers decent approximations of statistical quantities with a coarse grid and a relatively small number of gPC base elements.
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Rami, Mehdi Habibnia. "CFD Modelling of 3D Effects in Cycloidal Rotors." Doctoral thesis, 2021. http://hdl.handle.net/10400.6/12084.
Full textAbstract:
The cycloidalrotor
(cyclorotor) is a revolutionary propulsion system that has not been
systematically studied in the past in terms of its different aspects and applications. Therefore,
the current research presents the viability of the cyclorotor concept for powering a
hoveringcapable
unmanned scale aerial vehicle (UAV) through both computational fluid
dynamics (CFD) and also artificial neural network (ANN) analysis. Numerical or CFD
simulations included both performance and flow field measurements on a cyclorotor of
span and diameter equal to 0.8 meter. The simulations consist of diverse operating conditions
and under various flight phases. Hovering capabilities, forwardflight
and liftup
phases, operating under at closeground
flight levels, and threedimensional
(3D) effects
of the endplates
in the sides of cyclorotor in this scale. Furthermore, a novel propulsion
system by using a coupled combination of two cyclorotors and pairwing
system by using
plasma actuators is also presented in the current study as a recent patent. Numerous simulations
for various types of flight strategies and operating conditions are performed and
recorded as a database from the CFD phase. Subsequently, all the data from the numerical
computations are processed in ANN algorithms for further analysis and optimizations for
all of the assessed operating conditions in all modes. The ANN analysis could effectively
propose an optimal condition for all the abovementioned
operations on the basis of the
loading parameters, force coefficients, and figure of merit for efficiency analysis. The operating
conditions in the current study refers to the ranged of pitching oscillation angles,
and rotation speed, and the flight mode defines the different flying regimes such as hovering,
closeground,
or liftup
and forwardflight
concepts. Systematic and aerodynamic
performance measurements and analysis have been conducted to understand the effect
of the rotational speed, blade pitching amplitude, pitching axis location, forward/cruise
speed, takeoff
speed, different ground heightlevels.
Force measurements showed to be
distinctive in different regions on the circular trace of the traversing blades. The NACA
0012 profile is considered constantly for all the simulations in the current work. On the
basis of ANN analysis, an active control methodology, meaning that smart pitching schedules
are proposed for each of the operating conditions, that results in higher aerodynamic
performance and efficiency augmentation. This happens by keeping the cycloidal definition
in these rotor types, but instead of running the blades in a constant schedule over
cycles, we proposed an alternative varying pitch schedule in accordance to the blade position
which is called azimuth angle. This revealed significant enhancement in the overall
cyclorotor efficiency at each flight mode and operating condition. Concerning the attraction
of downwash jet flow from the bottom region of the cyclorotors, the present patent
illustrates to guide the downwash jet through a nozzle duct which is consisted of double
wings in the middle of two cyclorotors in the front and rear part of the propulsion mechanism.
Thus, instead of washing away the downwash jet, we process it and make a possible
running flow to face the rear rotor which operates at higher angular velocities and smaller
scale compared with that of front cyclorotor.O rotor cicloidal (ciclorotor) é um sistema propulsivo revolucionário que, até à data, não foi alvo de um estudo suficientemente sistemático, em particular no que diz respeito aos seus diferentes aspetos de projeto e aplicações. Como tal, a presente investigação apresenta um estudo sobre a viabilidade do conceito de propulsão a ciclorotor para um veículo aéreo não tripulado (UAV) capaz de pairar, sendo este estudo feito a partir de modelação usando dinâmica de fluidos computacional (CFD) e uma rede neural artificial (ANN). As simulações numéricas ou CFD incluem medições do desempenho e do campo de escoamento de um ciclorotor com 0,8 metros de envergadura e igual diâmetro. As simulações consideram diversas condições de operação e várias fases de voo. A capacidade de pairar, as fases de descolagem e de voo horizontal, o funcionamento a baixa altitude, e ainda os efeitos tridimensionais (3D), neste caso produzidos pelas placas finais nas laterais do ciclorotor estudados para esta escala. Para além disso, é proposto um sistema inovador de propulsão que recorre à combinação de dois ciclorotores e de um sistema de asa dupla com atuadores a plasma, o qual foi objeto de submissão de patente. São apresentadas numerosas simulações para os diferentes tipos de estratégias de voo, e de condições de funcionamento, as quais foram realizadas e gravadas numa base de dados de resultados de CFD. Subsequentemente, toda a informação obtida a partir do cálculo numérico é processadas em algoritmos ANN, tendo em vista uma análise e otimização adicional, em particular sobre todas as condições e modos de funcionamento avaliados. A análise ANN permite propor, com elevada eficácia computacional, as condições ótimas de operação para os vários tipos de funcionamento já mencionados, tendo por base os parâmetros de carga, os coeficientes das forças, e de figura de mérito, com vista a analisar o desempenho. As condições de operação do presente estudo incluem ainda uma gama de ângulos de oscilação da inclinação das pás, e de velocidades de rotação, as quais são definidas em função do modo de voo, o qual define os diferentes regimes, onde se incluem o pairar, o voo de baixa altitude, ou ainda descolagem e voo horizontal. Através de medições sistemáticas e de análise das variáveis de desempenho aerodinâmico foi possível compreender o efeito da velocidade de rotação, amplitude de inclinação das pás, a posição do eixo de inclinação das pás, a velocidade de cruzeiro/voo horizontal, a velocidade de decolagem, isto tudo a diferentes níveis de altitude. As medições de tração demonstraram ser distintas para diferentes regiões do trajeto circunferencial do ciclorotor. O perfil de NACA 0012 foi utilizado para todas as simulações realizadas durante o presente trabalho. Na base da análise ANN, foi considerada uma metodologia de controlo ativo, o que significa que tempos de oscilação de pás, definidos de forma inteligente, são propostos para cada uma das condições de funcionamento, o que resulta num maior desempenho aerodinâmico e num aumento de eficiência propulsiva. Isto é conseguido mantendo a geometria de ciclorotor mas, ao invés de modificar a inclinação das pás em tempos fixos do ciclo de rotação, propõese um funcionamento alternativo com variação dos tempos de oscilação dos respetivos ângulos de inclinação de acordo com o posicionamento azimutal da pá. Esta estratégia permitiu obter um incremento significativo no rendimento global do ciclorotor para cada modo de voo e respetivas condições de funcionamento. No que diz respeito à atração do jato de escoamento descendente, o qual é libertado pela parte inferior do ciclorotor, é apresentada uma patente que pretende direcionar o jato descendente para um canal, o qual é constituído por um sistema de asa dupla que é colocado entre os ciclorotores frontal e traseiro, sendo estes dois os constituintes do inovador sistema de propulsão. Portanto, ao invés de simplesmente libertar o jato descendente como num ciclorotor tradicional, este é aqui processado e conduzido pelas asas para o rotor traseiro, o qual funciona a maior velocidade angulares e tem uma menor escala comparativamente ao ciclorotor frontal.