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Assurance Cases have been effectively used for improving the safety of real-time safety systems. However, until now, Assurance Case techniques have not been applied to building confidence in the correctness of Scientific Computing (SC) software. Our approach is to employ Assurance Case techniques to the case of a specific medical image analysis software, 3dfim+, and then generalize the results/template for other medical and SC software. Using the Goal Structuring Notation (GSN), we develop an Assurance Case to support the top goal that "Program 3dfim+ delivers correct outputs when used for its intended use/purpose in its intended environment." This claim is supported by several sub-claims, including the claims that high-quality requirements exist and that the implementation complies with the requirements. The full argument decomposes each sub-claim further until at the bottom level evidence is provided. The evidence provided includes the requirements documentation, test cases and expert review. To simplify the Assurance Case diagram, a new generic module, parameterized over quality, was developed to argue that each quality has been achieved. Evaluation of the full Assurance Case shows that this approach is feasible for building confidence in SC software, even in the practical situation where confidence is sought, but redesign and reimplementation are not possible. The exercise uncovered issues with the original documentation for 3dfim+, including missing assumptions, and ambiguity with the chosen sign convention. Furthermore, although no errors in output were found, the Assurance Case highlights that confidence in the original 3dfim+ software could be improved through additional checks for input validity. / Thesis / Master of Science (MSc)

Tesis por compendio / [ES] El género de copépodos Tigriopus Norman, 1869 se distribuye en todo el mundo en piscinas costeras de rocas y actualmente se considera que incluye 15 especies válidas. Tigriopus fulvus (Fischer, 1860), con su subespecie Tigriopus fulvus adriaticus Van Douwe 1913 y Tigriopus fulvus algiricus Monard 1935, actualmente se informa que ocurren en el área mediterránea, pero actualmente se desconoce la diversidad real del género. Nuestro objetivo fue evaluar la identidad real de las poblaciones mediterráneas de Tigriopus y dilucidar su taxonomía y patrón de diversidad genética. Para alcanzar estos objetivos, utilizamos dos enfoques diferentes. El primero, basado en la morfología, donde las posibles diferencias morfológicas entre muestras topotípicas de Tigriopus fulvus s.s. y muestras topotípicas de las dos subespecies fueron investigadas. Un segundo, sobre una base molecular, donde se secuenciaron fragmentos de dos genes de ADN mitocondrial (subunidad I de citocromo c oxidasa, COI y subunidad de ARN ribosómico pequeño, 12S) y un gen de ADN nuclear (28S) para ser usados como marcador de referencia. En este marco, se utilizaron enfoques taxonómicos moleculares, como el descubrimiento automático de brechas de código de barras (ABGD), bPTP (procesos de árbol de Poisson bayesianos) y la relación K / ¿, para investigar la existencia de las supuestas subespecies de Tigriopus a través de la identificación de Operacional Unidades Taxonómicas (OTU). Nuestros datos sugieren la presencia de una sola especie caracterizada por una notable estructura genética basada en la geografía en toda el área de estudio. El patrón de diversidad observado se atribuye tentativamente aquí a una fuerte monopolización de los estanques de rocas por parte de los primeros inmigrantes que los alcanzan. Sin embargo, tal monopolización se ve interrumpida periódicamente por los eventos de extinción locales, que son frecuentes en los hábitats intrínsecamente inestables de las piscinas de rocas Aquí proponemos para este patrón el nombre de "monopolización periódica" ("Clockwork monopolization"). / [CA] El género de copépodos Tigriopus Norman, 1869 se distribuix en tot el mon en piscines costeres de roques i actualment se considera que inclou 15 especies valides. Tigriopus fulvus (Fischer, 1860), en la seua subespecie Tigriopus fulvus adriaticus Van Douwe 1913 i Tigriopus fulvus algiricus Monard 1935, actualment s'informa que ocorren en l'area mediterranea, pero actualment se desconeix la diversitat real del género. Nostre objectiu fon evaluar l'identitat real de les poblacions mediterranees de Tigriopus i dilucidar la seua taxonomia i patrón de diversitat genetica. Per a alcançar estos objectius, utilisem dos enfocaments diferents. El primer, basat en la morfologia, a on les possibles diferencies morfologiques entre mostres topotípicas de Tigriopus fulvus s.s. i mostres topotípicas dels dos subespecies foren investigades. Un segon, sobre una base molecular, a on se secuenciaron fragments de dos gens d'adn mitocondrial (subunidad i de citocromo c oxidasa, coi i subunidad d'arn ribosómico menut, 12s) i un gen d'adn nuclear (28s) per a ser amprats com marcador de referencia. En este marc, s'utilisaren enfocaments taxonomics moleculars, com el descobriment automatic de breches de codic de barres (ABGD), bPTP (processos d'arbre de poisson bayesianos) i la relacio K/¿, per a investigar l'existencia de les supostes subespecies de Tigriopus a través de l'identificacio d'operacional unitats taxonomiques (OTU). Nostres senyes sugerixen la presencia d'una sola especie caracterisada per una notable estructura genetica basada en la geografia en tota l'area d'estudi. El patrón de diversitat observat s'atribuix tentativament aci a una forta monopolisacio dels safarejos de roques per part dels primers immigrants que els alcancen. No obstant, tal monopolisacio se veu interrompuda periodicament pels events d'extincio locals, que son freqüents en els hábitats intrinsecament inestables de les piscines de roques aci proponem per a este patrón el nom de "Monopolisacio Periodica" ("Clockwork Monopolization"). / [EN] The copepod genus Tigriopus Norman, 1869 is distributed worldwide in coastal rock-pools and it is currently considered to include 15 valid species. Tigriopus fulvus (Fischer, 1860), with its subspecies Tigriopus fulvus adriaticus Van Douwe, 1913 and Tigriopus fulvus algiricus Monard, 1935, are currently reported to occur in the Mediterranean area, but the actual diversity of the genus is currently unknown. We aimed to assess the actual identity of Mediterranean Tigriopus populations and to elucidate their taxonomy and pattern of genetic diversity. In order to reach these goals, we use two different approaches. The first, based on morphology, where the possible morphological differences among topotypical samples of Tigriopus fulvus s.s. and topotypical samples of the two subspecies were investigated. A second, on a molecular basis, where fragments of two mitochondrial DNA genes (cytochrome c oxidase subunit I, COI and small ribosomal RNA subunit, 12S) and a nuclear DNA gene (28S) were sequenced to be used as a reference marker. In this frame, molecular taxonomical approaches, such as Automatic Barcode Gap Discovery (ABGD), bPTP (bayesian Poisson Tree Processes) and K/¿ ratio, were used in order to investigate the existences of the alleged subspecies of Tigriopus through the identification of Operational Taxonomic Units (OTUs). Our data suggest the presence of a single species characterized by a noteworthy geographically-based genetic structure in the whole study area. The observed diversity pattern is tentatively ascribed here to a strong monopolization of the rock pools by the first immigrants that reach them. However, such a monopolization is periodically disrupted by local extinction events, which are frequent in the intrinsically unstable rock pool habitats. We propose the name "clockwork monopolization" for this pattern. / Vecchioni, L. (2020). Systematics and phylogeography of the genus Tigriopus (Copepoda, Harpacticoida, Harpacticidae) in the basin of the Mediterranean Sea [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/144122 / Compendio

Le travail présenté dans ce mémoire consiste à élaborer en une seule étape une couche mince organique ayant les propriétés chimiques et/ou morphologiques souhaitées. Cette démarche vise à copolymériser par voie plasma (PECVD) deux monomères antagonistes (apolaire et polaire) afin de contrôler la répartition et la taille des nodules de l’un des polymères dispersé dans l’autre phase et d’obtenir ainsi une structuration chimique et/ou morphologique. Pour ce faire, six précurseurs ont été sélectionnés de façon à couvrir une large gamme de polarité: l’alcool allylique (AA), l’acide acrylique (AAc), l’aniline (ANi), le diéthylèneglycol diméthyl éther (DEGDME), le 1H,1H,2H-perfluoro-1-décène (HDFD) et le 2-(diméthylamino) éthyle méthacrylate (DMAEMA).La première partie de ce travail est centrée sur l’étude des mécanismes de croissance des différents homopolymères par voie plasma pulsé. Les cinétiques de dépôt, les structures chimiques et les morphologies sont plus spécifiquement détaillées pour deux monomères, les HDFD et DMAEMA en fonction des paramètres du procédé plasma, la polymérisation plasma de ces deux précurseurs étant pour la première fois décrite. La caractérisation des couches minces obtenues repose sur la spectroscopie Infrarouge à Transformée de Fourier (FTIR), la spectroscopie de photoélectrons X (XPS) et la microscopie à force atomique (AFM). Cette étude a montré le rôle catalytique des groupements fluorés induisant des vitesses de dépôt plus conséquentes. Même si la croissance est prépondérante durant le temps de décharge, le dépôt est non négligeable pendant la post-décharge. La structure chimique des polymères plasma est fortement dépendante des paramètres de la décharge et notamment la puissance et le temps de décharge. La spectroscopie FTIR s’est révélée comme un outil performant pour l’évaluation de la rétention de la structure chimique de l’entité monomère initiale dans le polymère plasma. Ces homopolymères présentent une morphologie homogène sans rugosité.Dans la deuxième partie, nous abordons la copolymérisation plasma pulsé. Les différents copolymères synthétisés sont p-AA-co-HDFD, p-AAc-co-HDFD, p-ANi-co-HDFD, p-DEGDME-co-HDFD, p-DMAEMA-co-HDFD, p-DMAEMA-co-ANi. La plupart sont issus de comonomères hydrophiles et hydrophobes à l’exception d’un synthétisé à partir de deux précurseurs polaires. Les cinétiques de dépôt, les propriétés chimiques et morphologiques sont discutées en fonction des paramètres plasma tels que la puissance injectée mais aussi des proportions relatives des différents comonomères. Les différentes analyses chimiques entreprises montrent plutôt la formation d’un mélange d’homopolymères ou d’un copolymère à bloc plutôt que la croissance d’un nouveau matériau. Cette hypothèse est étayée par la mise en évidence d’une structuration morphologique correspondant à la présence d’îlots à la surface. / The work presented in this thesis consists to elaborate only in one step a thin organic layer having the required chemical and/or morphological properties. This approach aims to plasma copolymerize (PECVD) two antagonistic monomers (nonpolar and polar) in order of controlling the repartition and the size of nodules of one of the polymers dispersed in the other phase and thus, of inducting a chemical and/or morphological structuring. For this, six precursors have been selected to cover a large range of polarity: allyl alcohol (AA), acrylic acid (AAc), aniline (ANi), the diethylene glycol dimethyl ether (DEGDME), the 1H,1H,2H-perfluor-1-decene (HDFD) and 2-(dimethylamino)ethyl methacrylate (DMAEMA).The first part of this work is centered on studying the growth mechanism of different homo-polymers through pulsed plasma. The kinetics of deposition, the chemical structures and morphologies are more specifically detailed for two monomers, HDFD and DMAEMA in function of plasma parameters, the plasma polymerization of these two precursors being described for the first time. The thin layers were characterized through Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). This study showed the catalytic role of fluorine groups inducing more consequent deposit rates. Even if the growth is significant during the plasma on-time, the deposit is not negligible during the plasma off-time. The chemical structure of plasma polymers is highly dependent on the discharge parameters and mainly the power and the pulse period. The FTIR spectroscopy was shown to be a relevant tool for evaluating the chemical structure’s retention of the initial monomer entity in the plasma polymer. These homopolymers present a homogenous morphology without roughness.In the second part, the pulsed plasma copolymerization is described. The different synthesized copolymers are p-AA-co-HDFD, p-AAc-co-HDFD, p-ANi-co-HDFD, p-DEGDME-co-HDFD, p-DMAEMA-co-HDFD, p-DMAEMA-co-ANi. The majorities are issued from hydrophilic and hydrophobic co-monomers excepted for one synthesized from two polar precursors. The kinetics of deposits, the chemical and morphological properties were discussed in function to plasma parameters such as the injected power as well as the relative proportions of different co-monomers. The different chemical analyses showed the formation of a mixture of homopolymers or of a block copolymer rather than the growth of a new material. This hypothesis is unsubstantiated by evidencing a morphological structuring corresponding to the presence of spherical nanostructure at the surface.

Aus Punkt 1. Die Deutsch-Chinesische Technische Fakultät: "Seit Mitte der 90er Jahre besteht zwischen der Universität Paderborn und der Qingdao University of Science and Technology (QUST) eine rege Kooperation. Qingdao, übersetzt „Grüne Insel“, liegt im Osten Chinas am Gelben Meer, gut eine Flugstunde von Peking entfernt.1 Im sowohl touristisch als auch industriell attraktiven Großraum Qingdao leben derzeit ca. 7 Millionen Einwohner. Die stark expandierende QUST besitzt ca. 20.000 Studierende in meist natur- und ingenieurwissenschaftlichen Fächern."

Fine-pitch ferroelectric domain gratings are extensively used for generation of light in the visible and near-infrared spectral regions through quasi-phase matched (QPM) frequency conversion. Sub-μm QPM devices enables demonstration of nonlinear optics with counterpropagating waves, a field of nonlinear optics which remains sparsely explored due to the difficulty of fabricatinghigh quality gratings. In recent years, bulk Rb-doped KTiOPO4 (RKTP) has emerged as a highly promising nonlinear materials for fabrication of fine-pitch QPM devices through periodic electric-field poling. RKTP possesses large optical nonlinearity and high resistance to optical damage, while demonstrating improved material homogeneity and lower ionic conductivity than its isomorphs, which are important features for poling. Although fine-pitch QPM gratings, as well as large aperture QPM devices, have been demonstrated, fabrication of sub-μm high quality QPM devices remains a challenge. The primary aim of this research was to develop a reliable method to fabricate high-quality sub-μm periodically poled RKTP crystals (PPRKTP) and exploit them in novel optical applications. For this purpose, a novel poling method was developed. It was based on periodic modulation of the coercive field through ion exchange, where K+ ions are exchanged with Rb+ in the crystal, to modulate the coercive field and the ionic conductivity. This enables periodic poling of higher quality and with shorter period than ever before. High quality PPRKTP with a period of 755 nm were fabricated and used to demonstrate the first cascaded mirrorless optical parametric oscillator (MOPO), as well as the first MOPO pumped by a Q-switched laser. PPRKTP samples for blue light generation were fabricated, and second harmonic generation (SHG) was investigated with a high power 946 nm fiber laser. Up to 2 W of blue power was demonstrated for bulk samples, where the output power was limited by absorption of the SHG, leading to thermal dephasing of the devices. Laser-written waveguides were fabricated in PPRKTP for the first time, and a record high SHG power of 76 mW was obtained. Finally, the high-temperature stability of ferroelectric domain gratings was investigated. This is of utmost importance when a PPRKTP crystal is used as a seed for crystal growth. It was found that for charged domains walls, the domain-wall motion was highly anisotropic with rapid movement in y-direction while only small movements were observed in the x-direction of the crystal. / Ickelinjära ferroelektriska kristaller med artificiella domängitter med perioder av några mikrometer används idag för generering av ljus i de synliga och nära-infraröda våglängdsområdena, genom kvasifasmatchad (QPM) frekvenskonvertering. Med sub-μm QPM domängitter kan man åstadkomma ickelinjära optiska effekter med motpropagerande parametriska ljusvågor. Detta är ett område av den ickelinjära optiken som fortfarande är tämligen outforskat på grund av svårigheten med att tillverka högkvalitativa domängitter.  Under de senaste åren har Rb-dopat KTiOPO4 (RKTP) blivit ett mycket lovande ickelinjärt material för tillverkning av QPM-gitter med mycket korta perioder genom periodisk elektrisk fält polning. RKTP kristallen har en hög optisk ickelinejäritet och den tål höga optiska intensiteter, samtidigt som materialet har bättre materialhomogenitet och lägre jonledningsförmåga än vad dess isomorfa kristaller har. De två senare egenskaperna har visat sig viktiga för att få en lyckad polning. Fastän QPM-gitter med kort periodicitet, liksom QPM-gitter med stor apertur, har demonstrerats, är tillverkningen av högkvalitativa QPM-kristaller med sub-µm perioder fortfarande en utmaning. Det primära syftet med denna avhandling var att utveckla en pålitlig metod för att tillverka högkvalitativa sub-μm periodiskt polade RKTP kristaller (PPRKTP) och utnyttja dem i nya optiska tillämpningar. I detta syfte utvecklades en ny polningsmetod. Den baseras på periodiskt jonutbyte, där K+ joner byts mot Rb+ i kristallen, vilket resulterar i en samtidig modulation av materialets koerciva fält och jonledningsförmåga. Detta möjliggör i sin tur periodisk polning av högre kvalitet och med kortare perioder än någonsin tidigare har uppnåtts. Högkvalitativa PPRKTP kristaller med en period på 755 nm tillverkades och användes för att demonstrera den första kaskaderade spegelfria optiska parametriska oscillatorn (MOPO), liksom den första MOPO processen pumpad av en Q-switchad laser. Vidare utvecklades PPRKTP-kristaller för generering av blått ljus via frekvensdubbling. Dessa utvärderades med hjälp av en högeffekts-fiberlaser vid 946 nm. Upp till 2 W av blått ljus erhölls för bulkkristallerna. Uteffekten begränsades av absorption av det blåa frekvensdubblade ljuset, vilket ledde till urfasning i QPM-gittret p.g.a. termiska effekter. Laserskrivna vågledare tillverkades sedan i PPRKTP för första gången, och en rekordhög effekt på 76 mW erhölls via frekvensdubbling. Slutligen undersöktes stabiliteten hos de periodiskt polade domängitterna vid höga temperaturer. Det är viktigt att domängittrena är stabila när PPRKTP kristallerna används som ympämne för kristalltillväxt. Det visade sig att instabila domänväggar flyttade sig mycket anisotropt, med en snabb rörelse i kristallens y-riktning och en långsam rörelse i kristallens x-riktning. / <p>QC 20170519</p>