Statistical modeling of the eye for multimodal treatment planning for external beam radiation therapy of intraocular tumors

Ocular anatomy and radiation-associated toxicities provide unique challenges for external beam radiation therapy. For treatment planning, precise modeling of organs at risk and tumor volume are crucial. Development of a precise eye model and automatic adaptation of this model to patients' anatomy remain problematic because of organ shape variability. This work introduces the application of a 3-dimensional (3D) statistical shape model as a novel method for precise eye modeling for external beam radiation therapy of intraocular tumors.

Correspondence establishment in statistical modeling of shapes with arbitrary topology

Correspondence establishment is a key step in statistical shape model building. There are several automated methods for solving this problem in 3D, but they usually can only handle objects with simple topology, like that of a sphere or a disc. We propose an extension to correspondence establishment over a population based on the optimization of the minimal description length function, allowing considering objects with arbitrary topology. Instead of using a fixed structure of kernel placement on a sphere for the systematic manipulation of point landmark positions, we rely on an adaptive, hierarchical organization of surface patches. This hierarchy can be built on surfaces of arbitrary topology and the resulting patches are used as a basis for a consistent, multi-scale modification of the surfaces' parameterization, based on point distribution models. The feasibility of the approach is demonstrated on synthetic models with different topologies.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

A static heap analysis for shape and connectivity: Unified memory analysis: The base framework

Modeling the evolution of the state of program memory during program execution is critical to many parallehzation techniques. Current memory analysis techniques either provide very accurate information but run prohibitively slowly or produce very conservative results. An approach based on abstract interpretation is presented for analyzing programs at compile time, which can accurately determine many important program properties such as aliasing, logical data structures and shape. These properties are known to be critical for transforming a single threaded program into a versión that can be run on múltiple execution units in parallel. The analysis is shown to be of polynomial complexity in the size of the memory heap. Experimental results for benchmarks in the Jolden suite are given. These results show that in practice the analysis method is efflcient and is capable of accurately determining shape information in programs that créate and manipúlate complex data structures.

Microstructure-based numerical modeling of the mechanical behavior of Mg alloys

Dentro de los materiales estructurales, el magnesio y sus aleaciones están siendo el foco de una de profunda investigación. Esta investigación está dirigida a comprender la relación existente entre la microestructura de las aleaciones de Mg y su comportamiento mecánico. El objetivo es optimizar las aleaciones actuales de magnesio a partir de su microestructura y diseñar nuevas aleaciones. Sin embargo, el efecto de los factores microestructurales (como la forma, el tamaño, la orientación de los precipitados y la morfología de los granos) en el comportamiento mecánico de estas aleaciones está todavía por descubrir. Para conocer mejor de la relación entre la microestructura y el comportamiento mecánico, es necesaria la combinación de técnicas avanzadas de caracterización experimental como de simulación numérica, a diferentes longitudes de escala. En lo que respecta a las técnicas de simulación numérica, la homogeneización policristalina es una herramienta muy útil para predecir la respuesta macroscópica a partir de la microestructura de un policristal (caracterizada por el tamaño, la forma y la distribución de orientaciones de los granos) y el comportamiento del monocristal. La descripción de la microestructura se lleva a cabo mediante modernas técnicas de caracterización (difracción de rayos X, difracción de electrones retrodispersados, así como con microscopia óptica y electrónica). Sin embargo, el comportamiento del cristal sigue siendo difícil de medir, especialmente en aleaciones de Mg, donde es muy complicado conocer el valor de los parámetros que controlan el comportamiento mecánico de los diferentes modos de deslizamiento y maclado. En la presente tesis se ha desarrollado una estrategia de homogeneización computacional para predecir el comportamiento de aleaciones de magnesio. El comportamiento de los policristales ha sido obtenido mediante la simulación por elementos finitos de un volumen representativo (RVE) de la microestructura, considerando la distribución real de formas y orientaciones de los granos. El comportamiento del cristal se ha simulado mediante un modelo de plasticidad cristalina que tiene en cuenta los diferentes mecanismos físicos de deformación, como el deslizamiento y el maclado. Finalmente, la obtención de los parámetros que controlan el comportamiento del cristal (tensiones críticas resueltas (CRSS) así como las tasas de endurecimiento para todos los modos de maclado y deslizamiento) se ha resuelto mediante la implementación de una metodología de optimización inversa, una de las principales aportaciones originales de este trabajo. La metodología inversa pretende, por medio del algoritmo de optimización de Levenberg-Marquardt, obtener el conjunto de parámetros que definen el comportamiento del monocristal y que mejor ajustan a un conjunto de ensayos macroscópicos independientes. Además de la implementación de la técnica, se han estudiado tanto la objetividad del metodología como la unicidad de la solución en función de la información experimental. La estrategia de optimización inversa se usó inicialmente para obtener el comportamiento cristalino de la aleación AZ31 de Mg, obtenida por laminado. Esta aleación tiene una marcada textura basal y una gran anisotropía plástica. El comportamiento de cada grano incluyó cuatro mecanismos de deformación diferentes: deslizamiento en los planos basal, prismático, piramidal hc+ai, junto con el maclado en tracción. La validez de los parámetros resultantes se validó mediante la capacidad del modelo policristalino para predecir ensayos macroscópicos independientes en diferentes direcciones. En segundo lugar se estudió mediante la misma estrategia, la influencia del contenido de Neodimio (Nd) en las propiedades de una aleación de Mg-Mn-Nd, obtenida por extrusión. Se encontró que la adición de Nd produce una progresiva isotropización del comportamiento macroscópico. El modelo mostró que este incremento de la isotropía macroscópica era debido tanto a la aleatoriedad de la textura inicial como al incremento de la isotropía del comportamiento del cristal, con valores similares de las CRSSs de los diferentes modos de deformación. Finalmente, el modelo se empleó para analizar el efecto de la temperatura en el comportamiento del cristal de la aleación de Mg-Mn-Nd. La introducción en el modelo de los efectos non-Schmid sobre el modo de deslizamiento piramidal hc+ai permitió capturar el comportamiento mecánico a temperaturas superiores a 150_C. Esta es la primera vez, de acuerdo con el conocimiento del autor, que los efectos non-Schmid han sido observados en una aleación de Magnesio. The study of Magnesium and its alloys is a hot research topic in structural materials. In particular, special attention is being paid in understanding the relationship between microstructure and mechanical behavior in order to optimize the current alloy microstructures and guide the design of new alloys. However, the particular effect of several microstructural factors (precipitate shape, size and orientation, grain morphology distribution, etc.) in the mechanical performance of a Mg alloy is still under study. The combination of advanced characterization techniques and modeling at several length scales is necessary to improve the understanding of the relation microstructure and mechanical behavior. Respect to the simulation techniques, polycrystalline homogenization is a very useful tool to predict the macroscopic response from polycrystalline microstructure (grain size, shape and orientation distributions) and crystal behavior. The microstructure description is fully covered with modern characterization techniques (X-ray diffraction, EBSD, optical and electronic microscopy). However, the mechanical behaviour of single crystals is not well-known, especially in Mg alloys where the correct parameterization of the mechanical behavior of the different slip/twin modes is a very difficult task. A computational homogenization framework for predicting the behavior of Magnesium alloys has been developed in this thesis. The polycrystalline behavior was obtained by means of the finite element simulation of a representative volume element (RVE) of the microstructure including the actual grain shape and orientation distributions. The crystal behavior for the grains was accounted for a crystal plasticity model which took into account the physical deformation mechanisms, e.g. slip and twinning. Finally, the problem of the parametrization of the crystal behavior (critical resolved shear stresses (CRSS) and strain hardening rates of all the slip and twinning modes) was obtained by the development of an inverse optimization methodology, one of the main original contributions of this thesis. The inverse methodology aims at finding, by means of the Levenberg-Marquardt optimization algorithm, the set of parameters defining crystal behavior that best fit a set of independent macroscopic tests. The objectivity of the method and the uniqueness of solution as function of the input information has been numerically studied. The inverse optimization strategy was first used to obtain the crystal behavior of a rolled polycrystalline AZ31 Mg alloy that showed a marked basal texture and a strong plastic anisotropy. Four different deformation mechanisms: basal, prismatic and pyramidal hc+ai slip, together with tensile twinning were included to characterize the single crystal behavior. The validity of the resulting parameters was proved by the ability of the polycrystalline model to predict independent macroscopic tests on different directions. Secondly, the influence of Neodymium (Nd) content on an extruded polycrystalline Mg-Mn-Nd alloy was studied using the same homogenization and optimization framework. The effect of Nd addition was a progressive isotropization of the macroscopic behavior. The model showed that this increase in the macroscopic isotropy was due to a randomization of the initial texture and also to an increase of the crystal behavior isotropy (similar values of the CRSSs of the different modes). Finally, the model was used to analyze the effect of temperature on the crystal behaviour of a Mg-Mn-Nd alloy. The introduction in the model of non-Schmid effects on the pyramidal hc+ai slip allowed to capture the inverse strength differential that appeared, between the tension and compression, above 150_C. This is the first time, to the author's knowledge, that non-Schmid effects have been reported for Mg alloys.

Urban wind energy: empirical optimization of high-rise building roof shape for the wind energy exploitation

El programa Europeo HORIZON2020 en Futuras Ciudades Inteligentes establece como objetivo que el 20% de la energía eléctrica sea generada a partir de fuentes renovables. Este objetivo implica la necesidad de potenciar la generación de energía eólica en todos los ámbitos. La energía eólica reduce drásticamente las emisiones de gases de efecto invernadero y evita los riesgos geo-políticos asociados al suministro e infraestructuras energéticas, así como la dependencia energética de otras regiones. Además, la generación de energía distribuida (generación en el punto de consumo) presenta significativas ventajas en términos de elevada eficiencia energética y estimulación de la economía. El sector de la edificación representa el 40% del consumo energético total de la Unión Europea. La reducción del consumo energético en este área es, por tanto, una prioridad de acuerdo con los objetivos "20-20-20" en eficiencia energética. La Directiva 2010/31/EU del Parlamento Europeo y del Consejo de 19 de mayo de 2010 sobre el comportamiento energético de edificaciones contempla la instalación de sistemas de suministro energético a partir de fuentes renovables en las edificaciones de nuevo diseño. Actualmente existe una escasez de conocimiento científico y tecnológico acerca de la geometría óptima de las edificaciones para la explotación de la energía eólica en entornos urbanos. El campo tecnológico de estudio de la presente Tesis Doctoral es la generación de energía eólica en entornos urbanos. Específicamente, la optimization de la geometría de las cubiertas de edificaciones desde el punto de vista de la explotación del recurso energético eólico. Debido a que el flujo del viento alrededor de las edificaciones es exhaustivamente investigado en esta Tesis empleando herramientas de simulación numérica, la mecánica de fluidos computacional (CFD en inglés) y la aerodinámica de edificaciones son los campos científicos de estudio. El objetivo central de esta Tesis Doctoral es obtener una geometría de altas prestaciones (u óptima) para la explotación de la energía eólica en cubiertas de edificaciones de gran altura. Este objetivo es alcanzado mediante un análisis exhaustivo de la influencia de la forma de la cubierta del edificio en el flujo del viento desde el punto de vista de la explotación energética del recurso eólico empleando herramientas de simulación numérica (CFD). Adicionalmente, la geometría de la edificación convencional (edificio prismático) es estudiada, y el posicionamiento adecuado para los diferentes tipos de aerogeneradores es propuesto. La compatibilidad entre el aprovechamiento de las energías solar fotovoltaica y eólica también es analizado en este tipo de edificaciones. La investigación prosigue con la optimización de la geometría de la cubierta. La metodología con la que se obtiene la geometría óptima consta de las siguientes etapas: - Verificación de los resultados de las geometrías previamente estudiadas en la literatura. Las geometrías básicas que se someten a examen son: cubierta plana, a dos aguas, inclinada, abovedada y esférica. - Análisis de la influencia de la forma de las aristas de la cubierta sobre el flujo del viento. Esta tarea se lleva a cabo mediante la comparación de los resultados obtenidos para la arista convencional (esquina sencilla) con un parapeto, un voladizo y una esquina curva. - Análisis del acoplamiento entre la cubierta y los cerramientos verticales (paredes) mediante la comparación entre diferentes variaciones de una cubierta esférica en una edificación de gran altura: cubierta esférica estudiada en la literatura, cubierta esférica integrada geométricamente con las paredes (planta cuadrada en el suelo) y una cubierta esférica acoplada a una pared cilindrica. El comportamiento del flujo sobre la cubierta es estudiado también considerando la posibilidad de la variación en la dirección del viento incidente. - Análisis del efecto de las proporciones geométricas del edificio sobre el flujo en la cubierta. - Análisis del efecto de la presencia de edificaciones circundantes sobre el flujo del viento en la cubierta del edificio objetivo. Las contribuciones de la presente Tesis Doctoral pueden resumirse en: - Se demuestra que los modelos de turbulencia RANS obtienen mejores resultados para la simulación del viento alrededor de edificaciones empleando los coeficientes propuestos por Crespo y los propuestos por Bechmann y Sórensen que empleando los coeficientes estándar. - Se demuestra que la estimación de la energía cinética turbulenta del flujo empleando modelos de turbulencia RANS puede ser validada manteniendo el enfoque en la cubierta de la edificación. - Se presenta una nueva modificación del modelo de turbulencia Durbin k — e que reproduce mejor la distancia de recirculación del flujo de acuerdo con los resultados experimentales. - Se demuestra una relación lineal entre la distancia de recirculación en una cubierta plana y el factor constante involucrado en el cálculo de la escala de tiempo de la velocidad turbulenta. Este resultado puede ser empleado por la comunidad científica para la mejora del modelado de la turbulencia en diversas herramientas computacionales (OpenFOAM, Fluent, CFX, etc.). - La compatibilidad entre las energías solar fotovoltaica y eólica en cubiertas de edificaciones es analizada. Se demuestra que la presencia de los módulos solares provoca un descenso en la intensidad de turbulencia. - Se demuestran conflictos en el cambio de escala entre simulaciones de edificaciones a escala real y simulaciones de modelos a escala reducida (túnel de viento). Se demuestra que para respetar las limitaciones de similitud (número de Reynolds) son necesarias mediciones en edificaciones a escala real o experimentos en túneles de viento empleando agua como fluido, especialmente cuando se trata con geometrías complejas, como es el caso de los módulos solares. - Se determina el posicionamiento más adecuado para los diferentes tipos de aerogeneradores tomando en consideración la velocidad e intensidad de turbulencia del flujo. El posicionamiento de aerogeneradores es investigado en las geometrías de cubierta más habituales (plana, a dos aguas, inclinada, abovedada y esférica). - Las formas de aristas más habituales (esquina, parapeto, voladizo y curva) son analizadas, así como su efecto sobre el flujo del viento en la cubierta de un edificio de gran altura desde el punto de vista del aprovechamiento eólico. - Se propone una geometría óptima (o de altas prestaciones) para el aprovechamiento de la energía eólica urbana. Esta optimización incluye: verificación de las geometrías estudiadas en el estado del arte, análisis de la influencia de las aristas de la cubierta en el flujo del viento, estudio del acoplamiento entre la cubierta y las paredes, análisis de sensibilidad del grosor de la cubierta, exploración de la influencia de las proporciones geométricas de la cubierta y el edificio, e investigación del efecto de las edificaciones circundantes (considerando diferentes alturas de los alrededores) sobre el flujo del viento en la cubierta del edificio objetivo. Las investigaciones comprenden el análisis de la velocidad, la energía cinética turbulenta y la intensidad de turbulencia en todos los casos. ABSTRACT The HORIZON2020 European program in Future Smart Cities aims to have 20% of electricity produced by renewable sources. This goal implies the necessity to enhance the wind energy generation, both with large and small wind turbines. Wind energy drastically reduces carbon emissions and avoids geo-political risks associated with supply and infrastructure constraints, as well as energy dependence from other regions. Additionally, distributed energy generation (generation at the consumption site) offers significant benefits in terms of high energy efficiency and stimulation of the economy. The buildings sector represents 40% of the European Union total energy consumption. Reducing energy consumption in this area is therefore a priority under the "20-20-20" objectives on energy efficiency. The Directive 2010/31/EU of the European Parliament and of the Council of 19 May 2010 on the energy performance of buildings aims to consider the installation of renewable energy supply systems in new designed buildings. Nowadays, there is a lack of knowledge about the optimum building shape for urban wind energy exploitation. The technological field of study of the present Thesis is the wind energy generation in urban environments. Specifically, the improvement of the building-roof shape with a focus on the wind energy resource exploitation. Since the wind flow around buildings is exhaustively investigated in this Thesis using numerical simulation tools, both computational fluid dynamics (CFD) and building aerodynamics are the scientific fields of study. The main objective of this Thesis is to obtain an improved (or optimum) shape of a high-rise building for the wind energy exploitation on the roof. To achieve this objective, an analysis of the influence of the building shape on the behaviour of the wind flow on the roof from the point of view of the wind energy exploitation is carried out using numerical simulation tools (CFD). Additionally, the conventional building shape (prismatic) is analysed, and the adequate positions for different kinds of wind turbines are proposed. The compatibility of both photovoltaic-solar and wind energies is also analysed for this kind of buildings. The investigation continues with the buildingroof optimization. The methodology for obtaining the optimum high-rise building roof shape involves the following stages: - Verification of the results of previous building-roof shapes studied in the literature. The basic shapes that are compared are: flat, pitched, shed, vaulted and spheric. - Analysis of the influence of the roof-edge shape on the wind flow. This task is carried out by comparing the results obtained for the conventional edge shape (simple corner) with a railing, a cantilever and a curved edge. - Analysis of the roof-wall coupling by testing different variations of a spherical roof on a high-rise building: spherical roof studied in the litera ture, spherical roof geometrically integrated with the walls (squared-plant) and spherical roof with a cylindrical wall. The flow behaviour on the roof according to the variation of the incident wind direction is commented. - Analysis of the effect of the building aspect ratio on the flow. - Analysis of the surrounding buildings effect on the wind flow on the target building roof. The contributions of the present Thesis can be summarized as follows: - It is demonstrated that RANS turbulence models obtain better results for the wind flow around buildings using the coefficients proposed by Crespo and those proposed by Bechmann and S0rensen than by using the standard ones. - It is demonstrated that RANS turbulence models can be validated for turbulent kinetic energy focusing on building roofs. - A new modification of the Durbin k — e turbulence model is proposed in order to obtain a better agreement of the recirculation distance between CFD simulations and experimental results. - A linear relationship between the recirculation distance on a flat roof and the constant factor involved in the calculation of the turbulence velocity time scale is demonstrated. This discovery can be used by the research community in order to improve the turbulence modeling in different solvers (OpenFOAM, Fluent, CFX, etc.). - The compatibility of both photovoltaic-solar and wind energies on building roofs is demonstrated. A decrease of turbulence intensity due to the presence of the solar panels is demonstrated. - Scaling issues are demonstrated between full-scale buildings and windtunnel reduced-scale models. The necessity of respecting the similitude constraints is demonstrated. Either full-scale measurements or wind-tunnel experiments using water as a medium are needed in order to accurately reproduce the wind flow around buildings, specially when dealing with complex shapes (as solar panels, etc.). - The most adequate position (most adequate roof region) for the different kinds of wind turbines is highlighted attending to both velocity and turbulence intensity. The wind turbine positioning was investigated for the most habitual kind of building-roof shapes (flat, pitched, shed, vaulted and spherical). - The most habitual roof-edge shapes (simple edge, railing, cantilever and curved) were investigated, and their effect on the wind flow on a highrise building roof were analysed from the point of view of the wind energy exploitation. - An optimum building-roof shape is proposed for the urban wind energy exploitation. Such optimization includes: state-of-the-art roof shapes test, analysis of the influence of the roof-edge shape on the wind flow, study of the roof-wall coupling, sensitivity analysis of the roof width, exploration of the aspect ratio of the building-roof shape and investigation of the effect of the neighbouring buildings (considering different surrounding heights) on the wind now on the target building roof. The investigations comprise analysis of velocity, turbulent kinetic energy and turbulence intensity for all the cases.

Modeling of Self-similar Traffic

Modeling of self-similar traffic is performed for the queuing system of G/M/1/K type using Weibull distribution. To study the self-similar traffic the simulation model is developed by using SIMULINK software package in MATLAB environment. Approximation of self-similar traffic on the basis of spline functions. Modeling self-similar traffic is carried outfor QS of W/M/1/K type using the Weibull distribution. Initial data are: the value of Hurst parameter H=0,65, the shape parameter of the distribution curve α≈0,7 and distribution parameter β≈0,0099. Considering that the self-similar traffic is characterized by the presence of "splashes" and long-termdependence between the moments of requests arrival in this study under given initial data it is reasonable to use linear interpolation splines.

Electromagnetic modeling of conformal wideband and multi-band patch antennas by bridging a solid-object modeler with MoM software

The advantages of antennas that can resemble the shape of the body to which they are attached are obvious. However, electromagnetic modeling of such unusually shaped antennas can be difficult. In this paper, the commercially available software SolidWorks(TM) is used for accurately drawing complex shapes in conjunction with the electromagnetic software FEKO(TM) to model the EM behavior of conformal antennas. The application of SolidWorks and custom-written software allows all the required information that forms the analyzed structure to be automatically inserted into FEKO, and gives the user complete control over the antenna being modeled. This approach is illustrated by a number of simulation examples of single, wideband, multi-band planar and curved patch antennas.

Biomechanics of the rostrum in crocodilians: A comparative analysis using finite-element modeling

This article reports the use of simple beam and finite-element models to investigate the relationship between rostral shape and biomechanical performance in living crocodilians under a range of loading conditions. Load cases corresponded to simple biting, lateral head shaking, and twist feeding behaviors. The six specimens were chosen to reflect, as far as possible, the full range of rostral shape in living crocodilians: a juvenile Caiman crocodilus, subadult Alligator mississippiensis and Crocodylus johnstoni, and adult Caiman crocodilus, Melanosuchus niger, and Paleosuchus palpebrosus. The simple beam models were generated using morphometric landmarks from each specimen. Three of the finite-element models, the A. mississippiensis, juvenile Caiman crocodilus, and the Crocodylus johnstoni, were based on CT scan data from respective specimens, but these data were not available for the other models and so these-the adult Caiman crocodilus, M. niger, and P. palpebrosus-were generated by morphing the juvenile Caiman crocodilus mesh with reference to three-dimensional linear distance measured from specimens. Comparison of the mechanical performance of the six finite-element models essentially matched results of the simple beam models: relatively tall skulls performed best under vertical loading and tall and wide skulls performed best under torsional loading. The widely held assumption that the platyrostral (dorsoventrally flattened) crocodilian skull is optimized for torsional loading was not supported by either simple beam theory models or finite-element modeling. Rather than being purely optimized against loads encountered while subduing and processing food, the shape of the crocodilian rostrum may be significantly affected by the hydrodynamic constraints of catching agile aquatic prey. This observation has important implications for our understanding of biomechanics in crocodilians and other aquatic reptiles.

Three-dimensional modeling of the human eye based on magnetic resonance imaging

PURPOSE. A methodology for noninvasively characterizing the three-dimensional (3-D) shape of the complete human eye is not currently available for research into ocular diseases that have a structural substrate, such as myopia. A novel application of a magnetic resonance imaging (MRI) acquisition and analysis technique is presented that, for the first time, allows the 3-D shape of the eye to be investigated fully. METHODS. The technique involves the acquisition of a T2-weighted MRI, which is optimized to reveal the fluid-filled chambers of the eye. Automatic segmentation and meshing algorithms generate a 3-D surface model, which can be shaded with morphologic parameters such as distance from the posterior corneal pole and deviation from sphericity. Full details of the method are illustrated with data from 14 eyes of seven individuals. The spatial accuracy of the calculated models is demonstrated by comparing the MRI-derived axial lengths with values measured in the same eyes using interferometry. RESULTS. The color-coded eye models showed substantial variation in the absolute size of the 14 eyes. Variations in the sphericity of the eyes were also evident, with some appearing approximately spherical whereas others were clearly oblate and one was slightly prolate. Nasal-temporal asymmetries were noted in some subjects. CONCLUSIONS. The MRI acquisition and analysis technique allows a novel way of examining 3-D ocular shape. The ability to stratify and analyze eye shape, ocular volume, and sphericity will further extend the understanding of which specific biometric parameters predispose emmetropic children subsequently to develop myopia. Copyright © Association for Research in Vision and Ophthalmology.

CFD-modeling and experiments of insulation debris transport phenomena in water flow

The investigation of insulation debris generation, transport, and sedimentation becomes more important with regard to reactor safety research for pressurized water reactors and boiling water reactors when considering the long-term behavior of emergency core coolant systems during all types of loss-of-coolant accidents (LOCAs). The insulation debris released near the break during a LOCA incident consists of a mixture of disparate particle populations that varies with size, shape, consistency, and other properties. Some fractions of the released insulation debris can be transported into the reactor sump, where it may perturb/impinge on the emergency core cooling systems. Open questions of generic interest are, for example, the particle load on strainers and corresponding pressure drop, the sedimentation of the insulation debris in a water pool, and its possible resuspension and transport in the sump water flow. A joint research project on such questions is being performed in cooperation with the University of Applied Sciences Zittau/Görlitz. The project deals with the experimental investigation and the development of computational fluid dynamics (CFD) models for the description of particle transport phenomena in coolant flow. While the experiments are performed at the University of Applied Sciences Zittau/Görlitz, the theoretical work is concentrated at Forschungszentrum Dresden-Rossendorf. In the current paper the basic concepts for CFD modeling are described and feasibility studies including the conceptual design of the experiments are presented.

CFD-modeling of insulation debris transport phenomena in water flow

The investigation of insulation debris generation, transport and sedimentation becomes important with regard to reactor safety research for PWR and BWR, when considering the long-term behavior of emergency core cooling systems during all types of loss of coolant accidents (LOCA). The insulation debris released near the break during a LOCA incident consists of a mixture of disparate particle population that varies with size, shape, consistency and other properties. Some fractions of the released insulation debris can be transported into the reactor sump, where it may perturb/impinge on the emergency core cooling systems. Open questions of generic interest are the sedimentation of the insulation debris in a water pool, its possible re-suspension and transport in the sump water flow and the particle load on strainers and corresponding pressure drop. A joint research project on such questions is being performed in cooperation between the University of Applied Sciences Zittau/Görlitz and the Forschungszentrum Dresden-Rossendorf. The project deals with the experimental investigation of particle transport phenomena in coolant flow and the development of CFD models for its description. While the experiments are performed at the University at Zittau/Görlitz, the theoretical modeling efforts are concentrated at Forschungszentrum Dresden-Rossendorf. In the current paper the basic concepts for CFD-modeling are described and feasibility studies including the conceptual design of the experiments are presented. © 2009 Elsevier B.V. All rights reserved.

CFD-modeling and Experiments of insulation debris transport phenomena in water flow

The investigation of insulation debris generation, transport and sedimentation becomes important with regard to reactor safety research for PWR and BWR, when considering the long-term behavior of emergency core cooling systems during all types of loss of coolant accidents (LOCA). The insulation debris released near the break during a LOCA incident consists of a mixture of disparate particle population that varies with size, shape, consistency and other properties. Some fractions of the released insulation debris can be transported into the reactor sump, where it may perturb/impinge on the emergency core cooling systems. Open questions of generic interest are the sedimentation of the insulation debris in a water pool, its possible re-suspension and transport in the sump water flow and the particle load on strainers and corresponding pressure drop. A joint research project on such questions is being performed in cooperation between the University of Applied Sciences Zittau/Görlitz and the Forschungszentrum Dresden-Rossendorf. The project deals with the experimental investigation of particle transport phenomena in coolant flow and the development of CFD models for its description. While the experiments are performed at the University at Zittau/Görlitz, the theoretical modeling efforts are concentrated at Forschungszentrum Dresden-Rossendorf. In the current paper the basic concepts for CFD modeling are described and feasibility studies including the conceptual design of the experiments are presented.

Modeling of CW Yb-doped fiber lasers with highly nonlinear cavity dynamics

We develop a theoretical framework for modeling of continuous wave Yb-doped fiber lasers with highly nonlinear cavity dynamics. The developed approach has shown good agreement between theoretical predictions and experimental results for particular scheme of Yb-doped laser with large spectral broadening during single round trip. The model is capable to accurately describe main features of the experimentally measured laser outputs such as power efficiency slope, power leakage through fibre Bragg gratings, spectral broadening and spectral shape of generated radiation. © 2011 Optical Society of America.