Inaug.-Diss.--Bonn.

We study the properties of m-plane GaN structure on LiAlO 2 substrate grown by plasma-assisted molecular-beam epitaxy (PAMBE). Lattice parameters of LiAlO 2 are close to GaN, the interface between LiAlO 2 and GaN showed a good lattice matching. Low lattice mismatch can reduce the defect generation, improve crystal quality. However, lattice mismatch still exist, more or less density of defect still can be observed. The density of defect was reduced in the sample at high temperature. In this study, we investigate GaN on LiAlO 2 by scanning electron microscope (SEM), atomic force microscope (AFM), photoluminescence (PL) and X-ray diffraction (XRD) for different growth temperatures.

GaP ist ein Halbleiter mit einer großen Bandlückenenergie und infolgedessen transparent im größten Teil der sichtbaren Wellenlängen. GaP hat außerdem die kleinste Gitterfehlanpasung zu Si (weniger als 0.4%). Das macht GaP ein interessantes Material für monolithische Integration zu III–V Lichtsender auf Si. Diese Arbeit ist eine Untersuchung über die strukturellen und optische Eigenschaften von (Al, Ga) (As, P) Heterostrukturen auf GaP (001) -Substrat aufgewachsen. Die Einflüsse des PH3 Fluss und Wachstumstemperatur untersucht auf dem Kristallqualität und Oberflächenqualität von AlGaP/GaP Heterostructure. Experimentelle Ergebnisse deuten darauf hin, dass eine Wachstumstemperatur von 490 oC und ein geknackter (engl. cracked) PH3 Fluss von 2.7 sccm zur besten AlGaP Qualität und gleichzeitig zur guten GaP Qualität führen. Um die ineffiziente Lichtemission von GaP zu überwinden wurde GaAs in der GaP-Matrix gewachsen. Die Entstehung der Quantenpunkte wurde durch die 3.7% Gitterfehlanpassung zwischen GaAs und GaP für GaAs Nenndicke über 1,2 ML. Die optischen Messungen zeigen zwei Peaks im Bereich von 1,7 bis 2,1 eV und die Lumineszenz auf Raumtemperatur für 2,7 und 3,6 ML-Proben. Die hohe Energieemission wird der indirekten Rekombination in den dünnen Quantentröge oder kleine gespannte Quantenpunkte zurückzuführen, Während die niedrige Energie Emission ist aufgrund der direkten Elektron-Loch- Rekombination in der entspannten Quantenpunkte. Die Wirkung von Al wird untersucht auf die energetische Bandausrichtung und auf die elektronische Struktur der (Al,Ga)As Quantenstrukturen. Die optische Spektren zeigten einen blaue Verschiebung (engl. blue shift) mit wachsendem Al-Inhalt und die höchste missionsenergie für die (Al,Ga)As/GaP- Heterostruktur war 2.17 eV die zum indirekten Typ-II-Rekombination zusammenhängt. / Transparency of GaP due to the large indirect bandgap energy and its small lattice mismatch with Si make GaP an interesting candidate for optoelectronic devices in visible wavelength. This thesis is an investigation on the structural and optical characteristics of (Al,Ga)(As,P) heterostructures grown on GaP (001) substrates. The influences of the PH3 flux and growth temperature are studied on the crystal and surface quality of AlGaP/GaP heterostructure. The results indicate the narrow growth window of PH3 = 2.7 sccm and growth temperature = 490oC as the optimized conditions. To overcome the inefficient light emission of indirect GaP, direct bandgap GaAs was grown as the quantum structures in the GaP matrix. The QD formation is driven by the 3.7% lattice mismatch between GaAs and GaP for GaAs nominal thickness above 1.2 ML. The optical measurements show two peaks in the range of 1.7 to 2.1 eV and the luminescence up to room temperature for 2.7 and 3.6 ML samples. The high energy emission is attributed to indirect carrier recombination in the thin quantum wells or small strained quantum dots, whereas the low energy red emission is due to the direct electron-hole recombination in the relaxed quantum dots. The influence of the Al content on the band alignment and electronic structure of (Al,Ga)As quantum structures is studied. The optical spectra illustrate the blueshift of the radiative emission with increasing the Al content and the highest emission energy of 2.17 eV is observed for the (Al,Ga)As/GaP system that is related to the indirect type-II radiative recombination.

Field and laboratory studies were used to elucidate the factors affecting temporal and spatial variations of species abundance and structure of macroalgal assemblage and environmental variables between fish farming (FFA) and non-fish farming (NFFA) areas in Hsiao-Lu-Chiao island, a coral island in southwestern Taiwan. Four experiments have been approached: 1. field surveys of macroalgal assemblage structure on 5-m and 10-m depth at 3 sampling sites at FFA (FFA1, FFA2 and FFA3) and 1 sampling site at NFFA from September 2004, January 2005 and April 2005; 2.the relationship between abiotic (monthly maximum air temperature, monthly minimum air temperature, monthly mean air temperature, monthly cumulative precipitation, monthly cumulative irradiance, seawater temperature, light extinction coefficient, water motion, and nutrient (NO3-, NO2-, NH4+, SRP, DON, and DOP) and biotic (seaurchin density) factors and spatio-temporal variations in macroalgal structures analyzed by non-parametric multivariate model; 3. Factors affecting macroalgal abundance and structure: (1). Comparison of growth temperature ranges in different species to field temperature fluctuation; (2).Comparison of growth irradiance ranges in different species to field irradiance fluctuation; 4.Herbivore pressure: (1). Spatio-temporal variations of sea urchin abundance and structure of assemblage; (2). Gut contents and food preference of sea urchin experiment; (3). Herbivore exclusion experiment. Macroalgal %cover, biomass, species richness, diversity (H¡¦) and evenness (J¡¦) showed temporal and spatial variations, low values in January 2005 and also low values in the 5 m- and 10 m-depth areas of FFA1 and the 10 m-depth areas of FFA2. The data of k-dominance curve, hierarchical cluster and ANOSIM tests indicate that macroalgal assemblage is different between 4 sampling sites, between 2 depths and between 3 seasons. Ceratodictyon spongiosum is the most important species that separates September and January assemblages from April assemblage and separates the FFA1 and FFA2 assemblages from the FFA3 and NFFA assemblages. BVSTEP analysis shows that nutrients (NO3-, DON, DOP), temperature, monthly cumulative precipitation, and sea urchin density are the factors corresponding to variations of macroalgal assemblages, this correlation is more significant for 5 m-depth assemblage. Fish farming area FFA1and FFA2 assemblage are affect by sea urchin density, temperature and DON. Sea urchin influnces macroalgal abundance and assemblage structure in FFA1 and FFA2. Macroalgal %cover in 5 m-depth area shows a reversal relationship with sea urchin density; however, this relationship is not observed for 10 m-depth area. FFA1 and FFA2 are belong to high grazing pressure sites as indicated by high sea urchin density and exclusion experiment. Sea urchin gut contents and feeding preference test show that sea urchin has strong food selectivity with Hypnea charoides and Gracilaria coronopifolia as the most preferred species. Herbivore exclusion experiment shows that Hypnea charoides and Gracilaria coronopifolia are the species recruited in the cages. Ceratodictyon spongiosum had high biomass in FFA1 and FFA2 in January, which was ¡¥low DOP/high DON¡¦. The coindicence of temporal variations in FFA3 assemblage structure with a change from ¡¦Halimeda opuntia and Boodlea compostia¡¦ ¡÷ ¡¦Amphiroa fragilissima, Corallina phhulifera and Galaxaura oblongata¡¦ ¡÷¡¦Halimeda opuntia and Boodlea compostia¡¦ with low nitrogen/ high phosphorous¡¦ ¡÷¡¦ high nitrogen/ low phosphorous¡¦ ¡÷ ¡¦low nitrogen/ high phosphorous¡¦ suggest a role of ¡¦low nitrogen (NO3-)/high phosphorous (DOP)¡¦ for FFA3 structure modification. NFFA assemblage is controlled by temperature and monthly cumulative precipitation. Monthly cumulative precipitation in September was higher than January and April, in which Boodlea compostia and Gracilaria coronopifolia were dominant algae in September. The temperature growth responses of algae using the continuous-flow outdoor laboratory tank culture system fit their seasonal growth, reflecting the temperature-dependent manner of seasonal variations in abundance. It could be concluded from the present investigation that the structure of benthic macroalgal assemblage in Hsiao-Lu-Chiao island in southwestern Taiwan is affected by predicted natural and pulse disturbances. Temperature fluctuations involve in overall temporal variations in structure. Sea urchin herbivory and nutrient as pulse nutrient modulate the structure in fish farming area while monthly cumulative precipitation is associated with algal structure in non-fish farming area.

La reconstruction et la résurrection moléculaire de protéines ancestrales est au coeur de cette thèse. Alors que les données moléculaires fossiles sont quasi inexistantes, il est possible d'estimer quelles étaient les séquences ancestrales les plus probables le long d'un arbre phylogénétique décrivant les relations de parentés entre séquences actuelles. Avoir accès à ces séquences ancestrales permet alors de tester de nombreuses hypothèses biologiques, de la fonction des protéines ancestrales à l'adaptation des organismes à leur environnement. Cependant, ces inférences probabilistes de séquences ancestrales sont dépendantes de modèles de substitution fournissant les probabilités de changements entre acides aminés. Ces dernières années ont vu le développement de nouveaux modèles de substitutions d'acides aminés, permettant de mieux prendre en compte les phénomènes biologiques agissant sur l'évolution des séquences protéiques. Classiquement, les modèles supposent que le processus évolutif est à la fois le même pour tous les sites d'un alignement protéique et qu'il est resté constant au cours du temps lors de l'évolution des lignées. On parle alors de modèle homogène en temps et en sites. Les modèles récents, dits hétérogènes, ont alors permis de lever ces contraintes en permettant aux sites et/ou aux lignées d'évoluer selon différents processus. Durant cette thèse, de nouveaux modèles hétérogènes en temps et sites ont été développés en Maximum de Vraisemblance. Il a notamment été montré qu'ils permettent d'améliorer considérablement l'ajustement aux données et donc de mieux prendre en compte les phénomènes régissant l'évolution des séquences protéiques afin d'estimer de meilleurs séquences ancestrales. A l'aide de ces modèles et de reconstruction ou résurrection de protéines ancestrales en laboratoire, il a été montré que l'adaptation à la température est un déterminant majeur de la variation des taux évolutifs entre lignées d'Archées. De même, en appliquant ces modèles hétérogènes le long de l'arbre universel du vivant, il a été possible de mieux comprendre la nature du signal évolutif informant de manière non-parcimonieuse un ancêtre universel vivant à plus basse température que ses deux descendants, à savoir les ancêtres bactériens et archéens. Enfin, il a été montré que l'utilisation de tels modèles pouvait permettre d'améliorer la fonctionnalité des protéines ancestrales ressuscitées en laboratoire, ouvrant la voie à une meilleure compréhension des mécanismes évolutifs agissant sur les séquences biologiques / The molecular reconstruction and resurrection of ancestral proteins is the major issue tackled in this thesis manuscript. While fossil molecular data are almost nonexistent, phylogenetic methods allow to estimate what were the most likely ancestral protein sequences along a phylogenetic tree describing the relationships between extant sequences. With these ancestral sequences, several biological hypotheses can be tested, from the evolution of protein function to the inference of ancient environments in which the ancestors were adatapted. These probabilistic estimations of ancestral sequences depend on substitution models giving the different probabilities of substitution between all pairs of amino acids. Classicaly, substitution models assume in a simplistic way that the evolutionary process remains homogeneous (constant) among sites of the multiple sequence alignment or between lineages. During the last decade, several methodological improvements were realised, with the description of substitution models allowing to account for the heterogeneity of the process among sites and in time. During my thesis, I developed new heterogeneous substitution models in Maximum Likelihood that were proved to better fit the data than any other homogeneous or heterogeneous models. I also demonstrated their better performance regarding the accuracy of ancestral sequence reconstruction. With the use of these models to reconstruct or resurrect ancestral proteins, my coworkers and I showed the adapation to temperature is a major determinant of evolutionary rates in Archaea. Furthermore, we also deciphed the nature of the phylogenetic signal informing substitution models to infer a non-parsimonious scenario for the adaptation to temperature during early Life on Earth, with a non-hyperthermophilic last universal common ancestor living at lower temperatures than its two descendants. Finally, we showed that the use of heterogeneous models allow to improve the functionality of resurrected proteins, opening the way to a better understanding of evolutionary mechanisms acting on biological sequences