Purpose: 1) To estimate the threshold dose and the time evolution for cataract induction by near infrared radiation (IRR) in seconds exposure time domain; 2) to determine the ocular temperature development during the threshold exposure; 3) to investigate if near IRR induces cumulative lens damage considering irradiance exposure time reciprocity; 4) to experimentally estimate the temperature in the lens indirectly from the measurement of temperature-induced light scattering increase. Methods: Before exposure, 6-weeks-old albino rats were anesthetized and the pupils of both eyes were dilated. Then the animals were unilaterally exposed to 1090 nm IRR within the pupil area. Temperature was recorded with thermocouples placed in the selected positions of the eye. At the planned post-exposure time, the animal was sacrificed and the lenses were extracted for measurements of forward light scattering and macroscopic imaging (Paper I-III). In Paper IV, the lens was extracted from six-weeks-old albino Sprague-Dawley female rats and put into a temperature-controlled cuvette filled with balanced salt solution. Altogether, 80 lenses were equally divided on four temperature groups, 37, 40, 43 and 46 ºC. Each lens was exposed for 5 minutes to temperature depending on group belonging while the intensity of forward light scattering was recorded. Results: The in vivo exposure to 197 W/cm2 1090 nm IRR required a minimum 8 s for cataract induction. There was approximately 16 h delay between exposure and light scattering development in the lens. The same radiant exposure was found to cause a temperature increase of 10 °C at the limbus and 26 °C close to the retina. The in vivo exposure to 96 W/cm2 1090 nm IRR with exposure time up to 1 h resulted in an average temperature elevation of 7 °C at the limbus with the cornea humidified and no significant light scattering was induced one week after exposure. Arrhenius equation implies that the natural logarithm of the inclination coefficient for light scattering increase is linearly dependent on the inverse of the temperature. The proportionality constant and the intercept, estimated as CI(0.95)s, were 9.6±2.4 x103 K and 22.8±7.7. Further, it implies that if averaging 20 measurements of inclination coefficients in a new experiment at constant heat load, the confidence limits for prediction of temperature correspond to ±1.9 °C. Conclusions: It is indicated that IRR at 1090 nm produces thermal but not cumulatively photochemical cataract, probably by indirect heat conduction from absorption in tissues surrounding the lens. Applying the Arrhenius equation the in vivo temperature in the lens can be determined retrospectively with sufficient resolution.

Dans cette thèse a été développé un modèle numérique simulant la lumière réfléchie et l'émission thermique d'exoplanètes telluriques ne possédant pas d'atmosphère, au cours de leur orbite. Ce modèle est constituée de plusieurs éléments. Le code calcule tout d'abord le flux stellaire incident en tout point de la planète et en fonction du temps en prenant en compte le mouvement orbital et la rotation de la planète. Si nécessaire, le modèle peut calculer la dissipation associée aux forces de marées et le flux de chaleur interne associé. Ces flux radiatif et interne servent de conditions aux limites à un modèle qui traite la diffusion de la chaleur dans la subsurface et calcule la température de surface. Enfin, le code calcule le flux, et sa variation avec la phase orbitale, reçu par un observateur distant dans une ou plusieurs bandes spectrales. Ce flux peut inclure les sources de bruits associés à la méthode d'observation de façon à produire une observable réaliste.Une première étude a été consacrée aux planètes en orbite circulaire et en rotation synchrone, c'est à dire recevant un flux d'illumination constant avec le temps. Cette étude a montré qu'il était possible de contraindre, à partir d'observations bruitées simulées effectuées avec les télescopes de la prochaine génération (JWST, EChO) leur albédo de Bond, leur rayon, et l'inclinaison de l'orbite par rapport à l'observateur. Associée à des mesures de vitesse radiale, cette technique pourra permettre de déterminer masse et rayon d'exoplanètes ne transitant pas.Une seconde étude traite de l'influence de la rotation et de la force maréale pour des planètes recevant un flux d'illumination non constant (excentriques et/ou en rotation). Il est montré qu'il est possible de détecter par photométrie orbitale la signature de ces deux effets dans la courbe de lumière et ainsi de mieux contraindre les modèles de marées existants. De multiples possibilités d'applications de ce modèle numérique sont en cours, et se prolongent au-delà de cette thèse. / We have developed a numerical model that computes the reflected light and thermal emission of an airless rocky exoplanets during its orbit. This code first computes the stellar incident flux over the planetary surface as a function of time for any Keplerian orbit and rotation. The code can compute the tidal dissipation and the associated internal heat flux. Those illumination and internal flux are the boundary conditions for a heat diffusion model, which calculates time-dependent surface and subsurface temperatures. Eventually, the model computes the flux received by a distant observer, in one or several spectral bands. A realistic observation can be simulated adding the various sources of noise noise associated with the observation method.A first study was dedicated to synchronous planets on a circular orbit that receive a constant illumination flux. This study showed that it is possible to constrain their Bond albedo, radius and inclination from observations done with the JWST or EChO. Associated with radial velocity measurements, mass and radius of nontransiting planets can be inferred. In another work on planets receiving a non constant illumination flux (eccentric orbits or non synchronous planets) we study the signature of rotation period the tidal dissipation in the orbital photometry. We show that rotation period can be inferred providing a novel method to test tidal models. Many possibles applications of this model are already in progress and continue to be developed beyond this thesis.

Simulação computacional de ambientes cirúrgicos têm sido amplamente utilizados, normalmente para treinamentos, ajudando no desenvolvimento de habilidades essenciais e minimizando erros em procedimentos cirúrgicos. Para estes ambientes, é essencial a obtenção de um comportamento mais realista, sendo importante o uso de técnicas com alta precisão, além de uma simulação em tempo real. A fim de melhor controlar este trade-off entre eficiência e eficácia, apresentamos um ambiente híbrido e adaptativo que combina um conjunto de métodos para alcançar uma boa precisão e desempenho na simulação. Nosso sistema mescla métodos físicos de deformação (Método de Elementos Finitos e Mass-Mola) com um método não-físico que aproxima o comportamento dos primeiros (Green Coordinates), sendo capaz de utilizar o método apropriado dependendo da situação. Para melhor simular um ambiente cirúrgico completo, foram implementadas ferramentas adicionais para interação, permitindo pegar e manipular, queimar, e sentir os objetos do cenário. Nosso sistema proporciona grande imersão ao usuário, consumindo menos recursos computacionais e aumentando as taxas de atualização da simulação. / Computational simulation of surgical environments have been widely used usually for trainings, improving essential skills and minimizing errors in surgical procedures. As these environments are always looking for a more realistic behavior, it is important to use high-precision techniques while ensuring a real-time simulation. In order to better manage this trade-off between efficiency and effectiveness, we present a hybrid and adaptive environment that combines a set of methods to achieve good accuracy and performance for a simulation. Our system merges physically deformation methods (Finite Elements Method and Mass Spring Damper) with a non-physical method that approximates the formers behavior (Green Coordinates), being able to use the appropriate method depending on the situation. To simulate an approximation of a complete surgical environment, we also implement interaction tools, such as picking, burning, and haptic feedback. Our system provides great immersion for the user, consuming less computational resources and increasing update rates.

Simulação computacional de ambientes cirúrgicos têm sido amplamente utilizados, normalmente para treinamentos, ajudando no desenvolvimento de habilidades essenciais e minimizando erros em procedimentos cirúrgicos. Para estes ambientes, é essencial a obtenção de um comportamento mais realista, sendo importante o uso de técnicas com alta precisão, além de uma simulação em tempo real. A fim de melhor controlar este trade-off entre eficiência e eficácia, apresentamos um ambiente híbrido e adaptativo que combina um conjunto de métodos para alcançar uma boa precisão e desempenho na simulação. Nosso sistema mescla métodos físicos de deformação (Método de Elementos Finitos e Mass-Mola) com um método não-físico que aproxima o comportamento dos primeiros (Green Coordinates), sendo capaz de utilizar o método apropriado dependendo da situação. Para melhor simular um ambiente cirúrgico completo, foram implementadas ferramentas adicionais para interação, permitindo pegar e manipular, queimar, e sentir os objetos do cenário. Nosso sistema proporciona grande imersão ao usuário, consumindo menos recursos computacionais e aumentando as taxas de atualização da simulação. / Computational simulation of surgical environments have been widely used usually for trainings, improving essential skills and minimizing errors in surgical procedures. As these environments are always looking for a more realistic behavior, it is important to use high-precision techniques while ensuring a real-time simulation. In order to better manage this trade-off between efficiency and effectiveness, we present a hybrid and adaptive environment that combines a set of methods to achieve good accuracy and performance for a simulation. Our system merges physically deformation methods (Finite Elements Method and Mass Spring Damper) with a non-physical method that approximates the formers behavior (Green Coordinates), being able to use the appropriate method depending on the situation. To simulate an approximation of a complete surgical environment, we also implement interaction tools, such as picking, burning, and haptic feedback. Our system provides great immersion for the user, consuming less computational resources and increasing update rates.

Simulação computacional de ambientes cirúrgicos têm sido amplamente utilizados, normalmente para treinamentos, ajudando no desenvolvimento de habilidades essenciais e minimizando erros em procedimentos cirúrgicos. Para estes ambientes, é essencial a obtenção de um comportamento mais realista, sendo importante o uso de técnicas com alta precisão, além de uma simulação em tempo real. A fim de melhor controlar este trade-off entre eficiência e eficácia, apresentamos um ambiente híbrido e adaptativo que combina um conjunto de métodos para alcançar uma boa precisão e desempenho na simulação. Nosso sistema mescla métodos físicos de deformação (Método de Elementos Finitos e Mass-Mola) com um método não-físico que aproxima o comportamento dos primeiros (Green Coordinates), sendo capaz de utilizar o método apropriado dependendo da situação. Para melhor simular um ambiente cirúrgico completo, foram implementadas ferramentas adicionais para interação, permitindo pegar e manipular, queimar, e sentir os objetos do cenário. Nosso sistema proporciona grande imersão ao usuário, consumindo menos recursos computacionais e aumentando as taxas de atualização da simulação. / Computational simulation of surgical environments have been widely used usually for trainings, improving essential skills and minimizing errors in surgical procedures. As these environments are always looking for a more realistic behavior, it is important to use high-precision techniques while ensuring a real-time simulation. In order to better manage this trade-off between efficiency and effectiveness, we present a hybrid and adaptive environment that combines a set of methods to achieve good accuracy and performance for a simulation. Our system merges physically deformation methods (Finite Elements Method and Mass Spring Damper) with a non-physical method that approximates the formers behavior (Green Coordinates), being able to use the appropriate method depending on the situation. To simulate an approximation of a complete surgical environment, we also implement interaction tools, such as picking, burning, and haptic feedback. Our system provides great immersion for the user, consuming less computational resources and increasing update rates.

Darbo tikslas ‒ ištirti drėgnio įtaką susmulkinto gluosninio žilvičio savaiminiam kaitimui ir šilumos sklaidai pjaustinio sampile. Atlikti tyrimai ir literatūros analizė leidžia teigti, kad didelis drėgmės kiekis lemia pjaustinio biologinį aktyvumą, taip pat jo tankį, poringumą ir kitas savybes. Susidaro palankios sąlygos pjaustinio savaiminio kaitimo procesui, kuris siejamas su medienos audinių kvėpavimu, grybų ir bakterijų veikla, biodegradacijos proceso intensyvumu bei medienos pjaustinio savaiminio užsiliepsnojimo rizika. Atlikus tyrimus nustatyta, jog didžiausiu biologiniu aktyvumu (800 ÷ 340 W/(t•h)) pasižymi nuo 50 % iki 33 % drėgnio gluosninio žilvičio pjaustinys. Jam džiūstant toliau, išskiriamas šilumos srautas intensyviai mažėja ir išdžiūvus iki 12 % drėgnio, tampa visiškai biologiškai neaktyvus. Nustatyta, jog medienos pjaustinio temperatūrinis laidis nevienodas įvairuojant jo drėgniui. Temperatūrinio laidžio maksimali vertė 21,6 m2/s fiksuota, kai gluosnių pjaustinio drėgnis siekė 30 %. / The aim of this paper is to explore the influence of humidity to self‒heating and thermal dissipation pile chaff to cut Salicaceae osier. Performed research and analysis of literature suggests that high moisture content determines the biological activity of carving its density, porosity and other properties. It creates favourable conditions for self‒heating process of carving, which is associated with the wood tissue of breath, fungi and bacteria activity, biodegradation process, the intensity of wood carving and the risk of spontaneous ignition. The investigation revealed that the highest biological activity (800 ÷ 340 W/(t•h)) have between 50 % and 33 % of humidity Oyster osier chops. Further drying, heat flow decreases intensively and drying up to 12 % humidity, it is completely becoming biological inactive. It was found that the conductivity of wood carving temperature difference of unequal moisture. Thermal conductivity maximum value of 21,6 m2/s fixed, the willow carving moisture content was 30 %.

La problématique entourant la mise en oeuvre, la conception et le conditionnement de micro-capteurs au sein d'une application embarquée représente un enjeu industriel majeur, consiste en un vaste ensemble de défis techniques et touche à de nombreux champs de recherche scientifiques comme d'applications commerciales. Ce mémoire de thèse compile de manière pédagogique et détaillée la conception, la réalisation et l'évaluation expérimentale d'un capteur MEMS constitué d'un simple micro-filament destiné à la mesure, mutuellement, de la température, de la pression et de l'humidité d'une ambiance gazeuse, en utilisant un même et mutuel étage de conditionnement du signal – ce qui en tant que tel constitue une méthode d'intégration particulièrement originale qui est arbitrairement référencée comme "intégration totale". Aussi, le principe physique sous jacent à ce triplet de mesurage est la diffusion par conduction de la chaleur, produite par effet Joule dans l'élément sensible, à travers l'échantillon gazeux l'environnant. Ainsi, le principe de fonctionnement consiste en ce que, la réponse transitoire d'un tel ensemble permet d'une part de mettre en évidence, simultanément et de manière diagonalisable, à une température donnée, l'influence de la pression et de l'humidité sur la conductivité thermique et la capacité calorifique du couple sonde/échantillon. D'autre part, l'élément sensible est spécifiquement prévu pour que dans les conditions initiales du régime transitoire de l'échauffement, sa résistance électrique ne soit sensible qu'à la seule température ambiante, indépendamment des deux mesurandes. / Integration of micro sensors within an embedded system is a challenging task in terms of commercial application and deals with many fields of research. This report compiles a novel methodology of multi-sensor integration, from the design to the experimental evaluation. The reported MEMS gas sensor is made from a resistive micro-wire. It is designed to the sensing of temperature, pressure and humidity of a gaseous sample, at the same time, in using only a single sensing part as well as a single conditioning principle – which is by itself a new feature arbitrarily called "total integration". The physical principle involved here is heat-diffusion, where heat is produced by Joule effect within the resistive sensing part, sinking through the gaseous sample. The key is that the transient response of such a sensor enables the reading of both the sample thermal conductivity and heat capacity, depending on both humidity and pressure at a given temperature, the later being only depending upon the initial response of the sensor transient response.

Proteins and the formation of large protein complexes are essential parts of living organisms. Proteins are present in all aspects of life processes, performing a multitude of various functions ranging from being structural components of cells, to facilitating the passage of certain molecules between various regions of cells. The 'protein docking problem' refers to the computational method of predicting the appropriate matching pair of a protein (receptor) with respect to another protein (ligand), when attempting to bind to one another to form a stable complex. Research shows that matching the three-dimensional (3D) geometric structures of candidate proteins plays a key role in determining a so-called docking pair, which is one of the key aspects of the Computer Aided Drug Design process. However, the active sites which are responsible for binding do not always present a rigid-body shape matching problem. Rather, they may undergo sufficient deformation when docking occurs, which complicates the problem of finding a match. To address this issue, we present an isometry-invariant and topologically robust partial shape matching method for finding complementary protein binding sites, which we call the ProtoDock algorithm. The ProtoDock algorithm comes in two variations. The first version performs a partial shape complementarity matching by initially segmenting the underlying protein object mesh into smaller portions using a spectral mesh segmentation approach. The Heat Kernel Signature (HKS), the underlying basis of our shape descriptor, is subsequently computed for the obtained segments. A final descriptor vector is constructed from the Heat Kernel Signatures and used as the basis for the segment matching. The three different descriptor methods employed are, the accepted Bag of Features (BoF) technique, and our two novel approaches, Closest Medoid Set (CMS) and Medoid Set Average (MSA). The second variation of our ProtoDock algorithm aims to perform the partial matching by utilizing the pointwise HKS descriptors. The use of the pointwise HKS is mainly motivated by the suggestion that, at adequate times, the Heat Kernel Signature of a point on a surface sufficiently describes its neighbourhood. Hence, the HKS of a point may serve as the representative descriptor of its given region of which it forms a part. We propose three (3) sampling methods---Uniform, Random, and Segment-based Random sampling---for selecting these points for the partial matching. Random and Segment-based Random sampling both prove superior to the Uniform sampling method. Our experimental results, run against the Protein-Protein Benchmark 4.0, demonstrate the viability of our approach, in that, it successfully returns known binding segments for known pairing proteins. Furthermore, our ProtoDock-1 algorithm still still yields good results for low resolution protein meshes. This results in even faster processing and matching times with sufficiently reduced computational requirements when obtaining the HKS.

Submitted by Maria Medeiros (maria.dilva1@ufcg.edu.br) on 2018-09-25T11:56:53Z No. of bitstreams: 1 MARCOS ANTÔNIO AMARAL LINS - TESE (PPGEP) 2013.pdf: 2840885 bytes, checksum: 13b6f2695a2ffd6be9d615430752bc2d (MD5) / Made available in DSpace on 2018-09-25T11:56:53Z (GMT). No. of bitstreams: 1 MARCOS ANTÔNIO AMARAL LINS - TESE (PPGEP) 2013.pdf: 2840885 bytes, checksum: 13b6f2695a2ffd6be9d615430752bc2d (MD5) Previous issue date: 2013-07-05 / Para muitos gêneros alimentícios, o processo de transferência de calor é essencial para se chegar à condição de consumo humano. O presente trabalho teve como objetivo estudar o fenômeno da difusão transiente de calor em alimentos pastosos contidos em recipientes cilíndricos. O estudo apresenta soluções para a equação de difusão com condição de contorno do primeiro tipo. Foram desenvolvidas ferramentas analíticas (otimizador acoplado à solução analítica) para a descrição da difusão de calor em produtos pastosos com as formas mencionadas. As ferramentas analíticas foram validadas através de dados obtidos por simulação numérica tanto para o cilindro infinito quanto para o finito. Os erros cometidos com as ferramentas desenvolvidas no cálculo da difusividade térmica aparente para os dados simulados são aceitáveis quando o sensor de temperatura é colocado na região mais interna do cilindro. Os resultados obtidos para a difusividade térmica aparente de agar gel, purê de tomate e creme custard são compatíveis com os resultados encontrados na literatura para esses produtos. O software Finite Cylinder First Kind foi desenvolvido, validado e aplicado aos dados do purê de tomate, creme custard e agar gel para várias posições no interior do cilindro finito onde estes gêneros alimentícios se encontravam. Todos os resultados obtidos por otimização e simulação tiveram uma excelente concordância com os resultados experimentais. O método numérico se mostrou mais eficiente do que o analítico, na descrição do processo de difusão de calor nos produtos estudados, devido sua versatilidade de permitir a obtenção da solução da equação de difusão considerando a difusividade térmica variável com a temperatura local. / For many foodstuffs, the process of heat transfer is essential to reach the condition human consumption. The present work aims to study the phenomenon of transient diffusion of heat in pasty foodstuffs contained in cylindrical containers. The study presents solutions for the diffusion equation with boundary condition of the first kind. Analytical tools were developed - optimizer coupled to the analytical solution - to describe the diffusion of heat into products with the forms mentioned. Analytical tools were validated using data obtained by numerical simulation for both the cylinder the infinite and finite. The tools developed minimize errors in calculating the thermal diffusivity for the simulated data are acceptable when the temperature sensor is placed in the innermost region of the cylinder. The results obtained for the thermal diffusivity of agar gel, tomato puree and cream custard are consistents with the results found in the literature for these products. The software finite cylinder first kind was developed, validated and applied to data of tomato puree, cream custard and agar gel for various positions within the finite and infinite cylinder filled with these foodstuffs. All results obtained by simulation and optimization had an excellent agreement with the experimental results. The numerical method is more efficient than the analytical description of the heat diffusion process in the products, due to their versatility that allows obtaining the solution of the diffusion equation considering the thermal diffusivity varies with local temperature.

Proteins and the formation of large protein complexes are essential parts of living organisms. Proteins are present in all aspects of life processes, performing a multitude of various functions ranging from being structural components of cells, to facilitating the passage of certain molecules between various regions of cells. The 'protein docking problem' refers to the computational method of predicting the appropriate matching pair of a protein (receptor) with respect to another protein (ligand), when attempting to bind to one another to form a stable complex. Research shows that matching the three-dimensional (3D) geometric structures of candidate proteins plays a key role in determining a so-called docking pair, which is one of the key aspects of the Computer Aided Drug Design process. However, the active sites which are responsible for binding do not always present a rigid-body shape matching problem. Rather, they may undergo sufficient deformation when docking occurs, which complicates the problem of finding a match. To address this issue, we present an isometry-invariant and topologically robust partial shape matching method for finding complementary protein binding sites, which we call the ProtoDock algorithm. The ProtoDock algorithm comes in two variations. The first version performs a partial shape complementarity matching by initially segmenting the underlying protein object mesh into smaller portions using a spectral mesh segmentation approach. The Heat Kernel Signature (HKS), the underlying basis of our shape descriptor, is subsequently computed for the obtained segments. A final descriptor vector is constructed from the Heat Kernel Signatures and used as the basis for the segment matching. The three different descriptor methods employed are, the accepted Bag of Features (BoF) technique, and our two novel approaches, Closest Medoid Set (CMS) and Medoid Set Average (MSA). The second variation of our ProtoDock algorithm aims to perform the partial matching by utilizing the pointwise HKS descriptors. The use of the pointwise HKS is mainly motivated by the suggestion that, at adequate times, the Heat Kernel Signature of a point on a surface sufficiently describes its neighbourhood. Hence, the HKS of a point may serve as the representative descriptor of its given region of which it forms a part. We propose three (3) sampling methods---Uniform, Random, and Segment-based Random sampling---for selecting these points for the partial matching. Random and Segment-based Random sampling both prove superior to the Uniform sampling method. Our experimental results, run against the Protein-Protein Benchmark 4.0, demonstrate the viability of our approach, in that, it successfully returns known binding segments for known pairing proteins. Furthermore, our ProtoDock-1 algorithm still still yields good results for low resolution protein meshes. This results in even faster processing and matching times with sufficiently reduced computational requirements when obtaining the HKS.