Incorporating Inductances in Tissue-Scale Models of Cardiac Electrophysiology

In standard models of cardiac electrophysiology, including the bidomain and monodomain models, local perturbations can propagate at infinite speed. We address this unrealistic property by developing a hyperbolic bidomain model that is based on a generalization of Ohm's law with a Cattaneo-type model for the fluxes. Further, we obtain a hyperbolic monodomain model in the case that the intracellular and extracellular conductivity tensors have the same anisotropy ratio. In one spatial dimension, the hyperbolic monodomain model is equivalent to a cable model that includes axial inductances, and the relaxation times of the Cattaneo fluxes are strictly related to these inductances. A purely linear analysis shows that the inductances are negligible, but models of cardiac electrophysiology are highly nonlinear, and linear predictions may not capture the fully nonlinear dynamics. In fact, contrary to the linear analysis, we show that for simple nonlinear ionic models, an increase in conduction velocity is obtained for small and moderate values of the relaxation time. A similar behavior is also demonstrated with biophysically detailed ionic models. Using the Fenton-Karma model along with a low-order finite element spatial discretization, we numerically analyze differences between the standard monodomain model and the hyperbolic monodomain model. In a simple benchmark test, we show that the propagation of the action potential is strongly influenced by the alignment of the fibers with respect to the mesh in both the parabolic and hyperbolic models when using relatively coarse spatial discretizations. Accurate predictions of the conduction velocity require computational mesh spacings on the order of a single cardiac cell. We also compare the two formulations in the case of spiral break up and atrial fibrillation in an anatomically detailed model of the left atrium, and [...].Comment: 20 pages, 12 figure

Rekonstruktion und skalierbare Detektion und Verfolgung von 3D Objekten

The task of detecting objects in images is essential for autonomous systems to categorize, comprehend and eventually navigate or manipulate its environment. Since many applications demand not only detection of objects but also the estimation of their exact poses, 3D CAD models can prove helpful since they provide means for feature extraction and hypothesis refinement. This work, therefore, explores two paths: firstly, we will look into methods to create richly-textured and geometrically accurate models of real-life objects. Using these reconstructions as a basis, we will investigate on how to improve in the domain of 3D object detection and pose estimation, focusing especially on scalability, i.e. the problem of dealing with multiple objects simultaneously.Objekterkennung in Bildern ist für ein autonomes System von entscheidender Bedeutung, um seine Umgebung zu kategorisieren, zu erfassen und schließlich zu navigieren oder zu manipulieren. Da viele Anwendungen nicht nur die Erkennung von Objekten, sondern auch die Schätzung ihrer exakten Positionen erfordern, können sich 3D-CAD-Modelle als hilfreich erweisen, da sie Mittel zur Merkmalsextraktion und Verfeinerung von Hypothesen bereitstellen. In dieser Arbeit werden daher zwei Wege untersucht: Erstens werden wir Methoden untersuchen, um strukturreiche und geometrisch genaue Modelle realer Objekte zu erstellen. Auf der Grundlage dieser Konstruktionen werden wir untersuchen, wie sich der Bereich der 3D-Objekterkennung und der Posenschätzung verbessern lässt, wobei insbesondere die Skalierbarkeit im Vordergrund steht, d.h. das Problem der gleichzeitigen Bearbeitung mehrerer Objekte

Non-linear finite element analysis of flexible pipes for deep-water applications

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonFlexible pipes are essential components in the subsea oil and gas industry, where they are used to convey fluids under conditions of extreme external pressure and (often) axial load, while retaining low bending stiffness. This is made possible by their complex internal structure, consisting of unbonded components that are, to a certain extent, free to move internally relative to each other. Due to the product's high value and high cost of testing facilities, much e ort has been invested in the development of analytical and numerical models for simulating flexible pipe behaviour, which includes bulk response to various loading actions, calculation of component stresses and use of this data for component fatigue calculations. In this work, it is proposed that the multi-scale methods currently in widespread use for the modelling of composite materials can be applied to the modelling of flexible pipe. This allows the large-scale dynamics of an installed pipe (often several kilometers in length) to be related to the behaviour of its internal components (with characteristic lengths in millimeters). To do this, a formal framework is developed for an extension of the computational homogenisation procedure that allows multiscale models to be constructed in which models at both the large and small scales are composed of different structural elements. Within this framework, a large-scale flexible pipe model is created, using a two-dimensional corotational beam formulation with a constitutive model representative of flexible pipe bulk behaviour, which was obtained by further development of a recently proposed formulation inspired by the analogy between the flexible pipe structural behaviour and that of plastic materials with non-associative flow rules. A three-dimensional corotational formulation is also developed. The model is shown to perform adequately for practical analyses. Next, a detailed finite element (FE) model of a flexible pipe was created, using shell finite elements, generalised periodic boundary conditions and an implicit solution method. This model is tested against two analytical flexible pipe models for several basic load cases. Finally, the two models are used to carry out a sequential multi-scale analysis, in which a set of simulations using the detailed FE model is carried out in order to find the most appropriate coefficients for the large-scale model.EPSRC CASE studentship, with Lloyd's Register EME

Microstructural-Based Modeling Framework for High Temperature Behavior of Ferritic-Martensitic Steels Using Crystal Plasticity and Grain Boundary Finite Element Approaches

Ferritic/martensitic 9-12Cr steel alloys, have had widespread use as structural materials in power plants. Among this family of alloys, Grade 91 (Gr91) steel was a landmark in the development of 9-12Cr alloys. However, the unique microstructure complexity of the alloy has raised doubt regarding the techniques of data extrapolation in estimating its service-life for operation in next-generation power plants at higher temperatures and presssures. Conservatism becomes essential when the alloy is to be used in components lasting the life-cycle of power plants without replacement.This dissertation develops a physically-based microstructural model for creep rupture at 600 degrees Celsius for Gr91 steel as well as fundamental modeling tools that apply more broadly to microstructural modeling in metals. Key features of the Gr91 modeling framework capture the mechanical behavior of its prior austenite grains (PAG) and grain boundaries. Ultimately, a constitutive expression was adopted that captured the response from experiments conducted in the creep strain rate regime.An initial model intended to simulate low-cycle fatigue was first developed using the idea of geometrically necessary dislocations (GNDs) in crystal plasticity (CP) framework. That necessitated evaluating strain gradients and a patch-recovery method was implemented to recover a linear elastic deformation gradient field across the domain in linear elements. A Lie-group to Lie-algebra mapping was used to preserve orthogonality when projecting the rotation tensor from the elements’ Gauss points to the nodes.A statistically-stored dislocation density model was investigated to span the regimes of moderate strain rates (tension tests) to low strain rates (creep tests). Calibration of this model was possible against tension tests, but its application to creept tests suggested that other dislocation mechanisms were present during the primary creep regime of Gr91. Therefore, the CP model in the PAGs was changed to represent dislocation climb-glide motion and recovery along with linear viscous diffusional creep for point defect diffusion. This revised model more closely captured the measurements of creep response.Lastly, a robust Discontinuous Galerkin method is proposed to model the grain boundary interface elements to address traction oscillations observed for cohesive models. Stability and convergence are assessed along with non-conforming meshes

Exploiting Spatio-Temporal Coherence for Video Object Detection in Robotics

This paper proposes a method to enhance video object detection for indoor environments in robotics. Concretely, it exploits knowledge about the camera motion between frames to propagate previously detected objects to successive frames. The proposal is rooted in the concepts of planar homography to propose regions of interest where to find objects, and recursive Bayesian filtering to integrate observations over time. The proposal is evaluated on six virtual, indoor environments, accounting for the detection of nine object classes over a total of ∼ 7k frames. Results show that our proposal improves the recall and the F1-score by a factor of 1.41 and 1.27, respectively, as well as it achieves a significant reduction of the object categorization entropy (58.8%) when compared to a two-stage video object detection method used as baseline, at the cost of small time overheads (120 ms) and precision loss (0.92).</p

Fotofacesua: sistema de gestão fotográfica da Universidade de Aveiro

Nowadays, automation is present in basically every computational system. With the raise of Machine Learning algorithms through the years, the necessity of a human being to intervene in a system has dropped a lot. Although, in Universities, Companies and even governmental Institutions there are some systems that are have not been automatized. One of these cases, is the profile photo management, that stills requires human intervention to check if the image follows the Institution set of criteria that are obligatory to submit a new photo. FotoFaces is a system for updating the profile photos of collaborators at the University of Aveiro that allows the collaborator to submit a new photo and, automatically, through a set of image processing algorithms, decide if the photo meets a set of predifined criteria. One of the main advantages of this system is that it can be used in any institution and can be adapted to different needs by just changing the algorithms or criteria considered. This Dissertation describes some improvements implemented in the existing system, as well as some new features in terms of the available algorithms. The main contributions to the system are the following: sunglasses detection, hat detection and background analysis. For the first two, it was necessary to create a new database and label it to train, validate and test a deep transfer learning network, used to detect sunglasses and hats. In addition, several tests were performed varying the parameters of the network and using some machine learning and pre-processing techniques on the input images. Finally, the background analysis consists of the implementation and testing of 2 existing algorithms in the literature, one low level and the other deep learning. Overall, the results obtained in the improvement of the existing algorithms, as well as the performance of the new image processing modules, allowed the creation of a more robust (improved production version algorithms) and versatile (addition of new algorithms to the system) profile photo update system.Atualmente, a automação está presente em basicamente todos os sistemas computacionais. Com o aumento dos algoritmos de Aprendizagem Máquina ao longo dos anos, a necessidade de um ser humano intervir num sistema caiu bastante. Embora, em Universidades, Empresas e até Instituições governamentais, existam alguns sistemas que não foram automatizados. Um desses casos, é a gestão de fotos de perfil, que requer intervenção humana para verificar se a imagem segue o conjunto de critérios da Instituição que são obrigatórios para a submissão de uma nova foto. O FotoFaces é um sistema de atualização de fotos do perfil dos colaboradores na Universidade de Aveiro que permite ao colaborador submeter uma nova foto e, automaticamente, através de um conjunto de algoritmos de processamnto de imagem, decidir se a foto cumpre um conjunto de critérios predefinidos. Uma das principais vantagens deste sistema é que pode ser utilizado em qualquer Instituição e pode ser adaptado às diferentes necessidades alterando apenas os algoritmos ou os critérios considerados. Esta Dissertação descreve algumas melhorias implementadas no sistema existente, bem como algumas funcionalidades novas ao nível dos algoritmos disponíveis. As principais contribuições para o sistema são as seguintes: detecção de óculos de sol, detecção de chapéus e análise de background. Para as duas primeiras, foi necessário criar uma nova base de dados e rotulá-la para treinar, validar e testar uma rede de aprendizagem profunda por transferência, utilizada para detectar os óculos de sol e chapéus. Além disso, foram feitos vários testes variando os parâmetros da rede e usando algumas técnicas de aprendizagem máquina e pré-processamento sobre as imagens de entrada. Por fim, a análise do fundo consiste na implementação e teste de 2 algoritmos existentes na literatura, um de baixo nível e outro de aprendizagem profunda. Globalmente, os resultados obtidos na melhoria dos algoritmos existentes, bem como o desempenho dos novos módulos de processamneto de imagem, permitiram criar um sistema de atualização de fotos do perfil mais robusto (melhoria dos algoritmos da versão de produção) e versátil (adição de novos algoritmos ao sistema).Mestrado em Engenharia Eletrónica e Telecomunicaçõe

Biomimetic Manipulator Control Design for Bimanual Tasks in the Natural Environment

As robots become more prolific in the human environment, it is important that safe operational procedures are introduced at the same time; typical robot control methods are often very stiff to maintain good positional tracking, but this makes contact (purposeful or accidental) with the robot dangerous. In addition, if robots are to work cooperatively with humans, natural interaction between agents will make tasks easier to perform with less effort and learning time. Stability of the robot is particularly important in this situation, especially as outside forces are likely to affect the manipulator when in a close working environment; for example, a user leaning on the arm, or task-related disturbance at the end-effector. Recent research has discovered the mechanisms of how humans adapt the applied force and impedance during tasks. Studies have been performed to apply this adaptation to robots, with promising results showing an improvement in tracking and effort reduction over other adaptive methods. The basic algorithm is straightforward to implement, and allows the robot to be compliant most of the time and only stiff when required by the task. This allows the robot to work in an environment close to humans, but also suggests that it could create a natural work interaction with a human. In addition, no force sensor is needed, which means the algorithm can be implemented on almost any robot. This work develops a stable control method for bimanual robot tasks, which could also be applied to robot-human interactive tasks. A dynamic model of the Baxter robot is created and verified, which is then used for controller simulations. The biomimetic control algorithm forms the basis of the controller, which is developed into a hybrid control system to improve both task-space and joint-space control when the manipulator is disturbed in the natural environment. Fuzzy systems are implemented to remove the need for repetitive and time consuming parameter tuning, and also allows the controller to actively improve performance during the task. Experimental simulations are performed, and demonstrate how the hybrid task/joint-space controller performs better than either of the component parts under the same conditions. The fuzzy tuning method is then applied to the hybrid controller, which is shown to slightly improve performance as well as automating the gain tuning process. In summary, a novel biomimetic hybrid controller is presented, with a fuzzy mechanism to avoid the gain tuning process, finalised with a demonstration of task-suitability in a bimanual-type situation.EPSR

Modified mass-spring system for physically based deformation modeling

Mass-spring systems are considered the simplest and most intuitive of all deformable models. They are computationally efficient, and can handle large deformations with ease. But they suffer several intrinsic limitations. In this book a modified mass-spring system for physically based deformation modeling that addresses the limitations and solves them elegantly is presented. Several implementations in modeling breast mechanics, heart mechanics and for elastic images registration are presented

Modified mass-spring system for physically based deformation modeling

Mass-spring systems are considered the simplest and most intuitive of all deformable models. They are computationally efficient, and can handle large deformations with ease. But they suffer several intrinsic limitations. In this book a modified mass-spring system for physically based deformation modeling that addresses the limitations and solves them elegantly is presented. Several implementations in modeling breast mechanics, heart mechanics and for elastic images registration are presented

Mathematical models and numerical simulation of mechanochemical pattern formation in biological tissues

Mechanical and chemical pattern formation in the development of biological tissue is a fundamental and fascinating process of self-complexation and self-organization. Yet, the understanding of the underlying mechanisms and their mathematical description still lacks in many interesting cases such as embryogenesis. In this thesis, we combine recent experimental and theoretical insights and numerically investigate the capacity of mechano-chemical processes to spontaneously generate patterns in biological tissue. Firstly, we develop and numerically analyze a prototypical system of partial differential equations (PDEs) leading to mechanochemical pattern formation in evolving tissues. Based on recent experimental data, we propose a novel coupling by tensor invariants describing stretch, stress or strain of tissue mechanics on the production of signaling molecules (morphogens). In turn, morphogen leads to piecewise-defined active deformations of individual biological cells. The presented approach is flexible and applied to two prominent examples of evolving tissue: We show how these simple interaction rules (“feedback loops”) lead to spontaneous, robust mechanochemical patterns in the applications to embryogenesis and to symmetry breaking in the sweet water polyp Hydra. Our results reveal that the full 3D model geometry is essential to obtain realistic results such as gastrulation events. Also, we highlight predictive numerical experiments that assess the sensitivity of biological tissue with regard to mechanical stimuli, namely to micropipette aspiration. These numerical experiments allow for a cross-validation with experimental observations. Besides, we apply our modeling approach to growing tips in colonial hydroids and investigate the role of rotational and shearing active deformations by comparison to experimental data. Secondly, we develop an efficient, numerical method to reliably solve these strongly coupled, prototypical systems of PDEs that model mechanochemical long-term problems. We employ state-of-the-art finite element methods, parallel geometric multigrid solvers and present a simple, local mesh refinement strategy to obtain an efficient solution approach. Parallel solvers are essential to deal with the huge problem size in 3D and were modified to keep track of biological cells. Further, we propose a stabilization of the structural equation to deal with the strongly coupled system of equations and the challenges of the different timescales of growth (days) and nonlinear elasticity (seconds). Also, this addresses the instabilities which result form the description of homogeneous Neumann values on the entire boundary that is necessary since the locations of patterns is a priori unknown