Approved for public release; distribution in unlimited. / OFDM is a modulation technique that achieves high data rates, increased bandwidth efficiency and robustness in multipath environments. However, OFDM has some disadvantages, such as sensitivity to channel fading, large peak to average ratio and sensitivity to frequency offset. The latter causes intercarrier interference (ICI) and a reduction in the amplitude of the desired subcarrier which results in loss of orthogonality. In this thesis, the effects of frequency offset are studied in terms of loss of orthogonality. A number of techniques for frequency offset estimation are presented and tested in computer simulations. / Lieutenant Junior Grade, Turkish Navy

In this study, two major internal erosion initiation processes, suffusion and concentrated leak mechanisms, which lead to both defect formation in a dam’s body and its foundation and high throughflow in dams subjected to internal erosion were studied. This understanding has the potential to facilitate numerical modelling and expedite dam safety assessment studies.  The throughflow properties of coarse rockfill material were studied by; analysing filed pump test data, performing extensive laboratory experiments with a large-scale apparatus and numerically simulating the three-dimensional flow through coarse rock materials, replicating the material used in the laboratory experiments. Results from the tests demonstrate that the parameters of the nonlinear momentum equation of the flow depend on the Reynolds number for pore Reynolds numbers lower than 60000.  Numerical studies were also carried out to conduct numerical experiments. By applying a Lagrangian particle tracking method, a model for estimating the lengths of the flow channels in the porous media was developed.  The shear forces exerted on the coarse particles in the porous media were found to be significantly dependent on the inertial forces of the flow. Suffusion and concentrated leak mechanisms were also studied by means of laboratory experiments to develop a theoretical framework for continuum-based numerical modelling. An erosion apparatus was designed and constructed with the capability of applying hydraulic and mechanical loading. Results were then used to develop constitutive laws of the soil erosion as a function of the applied hydromechanical load for both suffusion and concentrated leak mechanisms. Both the initiation and mass removal rate of were found to be dependent on the soil in-situ stresses. A three-dimensional electrical-resistivity-based tomography method was also adopted for the internal erosion apparatus and was found to be successful in visualising the porosity evolution due to suffusion. / <p>QC 20161006</p>

Das Enzym Tryptophan Synthase ist ein ausgezeichnetes Beispiel einer molekularen Fabrik auf der Nanoskala mit zwei katalytischen Zentren. Der katalytische Zyklus des Moleküls beruht zudem auf zahlreichen allosterischen Wechselwirkungen sowie der Übertragung des Intermediats Indol durch einen intramolekularen Tunnel. In dieser Arbeit wird das erste kinetische Modell eines einzelnen Tryptophan Synthase Moleküls konstruiert und analysiert. Simulationen zeigen starke Korrelationen zwischen den Zuständen der Katalysezentren sowie die Ausbildung von Synchronisation. Mit stochastischer Thermodynamik wird die experimentell unzugängliche Reaktionskonstante für die Rückübertragung des Indols aus Messdaten rekonstuiert. Methoden, die den Informationsaustausch in bipartiten Markovnetzwerken charakterisieren, werden auf beliebige Markovnetzwerke verallgemeinert und auf das Modell angewendet. Der abschließende Teil befasst sich mit chemischen Reaktionsnetzwerken von Metaboliten und Enzymen. Es werden algebraische Modelle (Halbgruppen) konstruiert, welche aufeinanderfolgende und simultane katalytische Funktionen von Enzymen und von Unternetzwerken erfassen. Diese Funktionen werden genutzt, um eine natürliche Dynamikum sowie hinreichende und notwendige Bedingungen für seine Selbsterhaltung zu formulieren. Anschließend werden die algebraischen Modelle dazu genutzt, um eine Korrespondenz zwischen Halbgruppenkongruenzen und Skalenübergängen auf den Reaktionsnetzwerken herzustellen. Insbesondere wird eine Art von Kongruenzen erörtert, welche dem Ausspuren der globalen Struktur des Netzwerkes unter vollständiger Beibehaltung seiner lokalen Komponenten entspicht. Während klassische Techniken eine bestimmte lokale Komponente fixieren und sämtliche Informationen über ihre Umgebung ausspuren, sind bei dem algebraischen Verfahren alle lokalen Komponenten zugleich sichtbar und eine Verknüpfung von Funktionen aus verschiedenen Komponenten ist problemlos möglich. / The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine with two distinct catalytic subunits. It catalyzes the biosynthesis of tryptophan, whereby the catalytic activity in a subunit is enhanced or inhibited depending on the state of the other subunit, gates control the accessibility of the reactive sites and the intermediate product indole is directly channeled within the protein. The first single-molecule kinetic model of the enzyme is constructed. Simulations reveal strong correlations in the states of the active centers and the emergent synchronization. Thermodynamic data is used to calculate the rate constant for the reverse indole channeling. Using the fully reversible single-molecule model, the stochastic thermodynamics of the enzyme is closely examined. The current methods describing information exchange in bipartite systems are extended to arbitrary Markov networks and applied to the kinetic model. They allow the characterization of the information exchange between the subunits resulting from allosteric cross-regulations and channeling. The final part of this work is focused on chemical reaction networks of metabolites and enzymes. Algebraic semigroup models are constructed based on a formalism that emphasizes the catalytic function of reactants within the network. A correspondence between coarse-graining procedures and semigroup congruences respecting the functional structure is established. A family of congruences that leads to a rather unusual coarse-graining is analyzed: The network is covered with local patches in a way that the local information on the network is fully retained, but the environment of each patch is not resolved. Whereas classical coarse-graining procedures would fix a particular patch and delete information about the environment, the algebraic approach keeps the structure of all local patches and allows the interaction of functions within distinct patches.

Les mosaïques de paysages dessinées par les cours d’eau sont le fruit de fonctionnements complexes. Ces fonctionnements sont appréhendés à divers échelles spatio-temporelles (e.g, bassin versant, secteurs fonctionnels, macroformes alluviales ou particules sédimentaires) décrites au sein du concept de système fluvial. Le fonctionnement des systèmes fluviaux s’établissent autour d’équilibres sédimentaires mettant en balance les flux liquides et solides. C’est pourquoi, l’état géomorphologique des cours d’eau à charge sédimentaire graveleuse peut être décrit au travers d’un prisme sédimentaire par l’observation de tendances générales à large échelles, de phénomènes plus ou moins localisés tels que l’incision, l’engravement, la migration des formes sédimentaires ou des modifications des propriétés géométriques des particules constituant la charge sédimentaire. Ainsi, la meilleure connaissance du rôle des flux sédimentaires actuels et passés dans l’état géomorphologique pour la prédiction des trajectoires hydrosédimentaires des cours, répond à des objectifs à la fois écologiques (la perméabilité de la nappe d’alluvions et de la zone hyporhéique exercent des fonctions auto-épuratrices (Datry et al., 2008), la faune benthique est la base de la chaîne alimentaire des écosystèmes fluviaux), politiques (liés à la gestion des risques d’inondation et d’érosion des terres ou d’ouvrages d’ingénierie) ou encore philosophiques (quel fonctionnement de référence pour quel système fluvial ? Quelle implication et quel rôle pour l’Homme dans le fonctionnement de ces systèmes anthropisés à divers degrés ?). Aussi, le développement d’outils et de méthodologie(s) pour la caractérisation des flux sédimentaires ou des processus observés en rivières constitue un axe de recherche important en constante émulsion. Les recherches que nous avons engagés sont articulées autour de trois axes interdépendants : (1) les propriétés physiques des particules sédimentaires, (2) leur mobilité et (3) leur transformation par abrasion. Dans le cadre de ce typique, nous avons cherché à lever le doute subsistant concernant le rôle de la fracturation de traceurs naturels (calcaires) équipés de transpondeurs passifs basses fréquences (PIT-tag) et à tester l’intérêt de l’utilisation de galets synthétiques pour la conception de nouveaux traceurs équipés de transpondeurs actifs ultra hautes fréquences (a-UHF). Nous avons ensuite testé le potentiel de ces transpondeurs (a-UHF), dont les caractéristiques d’émission sont mieux adaptées que celles des PIT-tag à l’étude du fonctionnement des macroformes fluviale à l’échelle de tronçons fonctionnels, puis avons développé une méthodologie de recherche en rivière spécifique à ces nouveaux traceurs. Par ailleurs, Nous avons testé la sensibilité à divers paramètres d’entrée d’un programme de calcul d’émoussé de particules sédimentaires grossières, en avons validé son intérêt pour l’analyse (1) des relations entre évolution des indices d’émoussé et abrasion de la masse sédimentaire et (2) du fonctionnement hydrosédimentaire d’un bassin versant et avons formulé les recommandations nécessaires de respecter pour sa bonne utilisation. Enfin, nous avons cherché à comparer les influences respectives de la densité et de la forme des particules sédimentaires pendant leur transport par charriage. Ces résultats soulignent l’influence au moins aussi grande de la forme comparée à la mobilité, sur le déplacement des particules sédimentaires. / The influence of fluvial systems dynamics on riverine landscape patterns is the consequence of complex ecosystem dynamics. These driving factors can be analysed at different spatiotemporal scales of the fluvial system (for example: river basin, functional units, alluvial megaforms or sedimentary particles). The dynamic of fluvial systems depends on the equilibrium between solid and liquid fluids. For this reason, the geomorphological status of watercourses can be described from a sedimentary perspective taking into account general trends at large scale, local characteristics such as incision, aggradation, sedimentary migration or the alteration of particles’ geometrical properties that constitute bed load. Thus, a better understanding of the influence of past and present sedimentary flows on the geomorphological status of watercourses has at the same time an ecological impact (permeability of both the alluvial layer and the hyporheic zone and its self-filtration function (Datry et al., 2008)), a political impact (related to flood management, erosion risks and issues or hydraulic facilities) or even a philosophical issue (what is the appropriate reference for what fluvial system? What is the role of Humanity on these anthropized environments and at what extent?).Thus, the development of methodological tools to characterize sedimentary flows or the observed dynamics on rivers, is considered a major and rising research issue. The research studies described in this thesis are structured in three distinct topics: (1) physical properties of sedimentary particles; (2) their mobility; (3) their transformation as a consequence of abrasion.In this context, we have analysed the relationship between breakage and low recovery rates for natural tracers (limestone pebbles) equipped with low frequency passive transponders (PIT-tag). In addition, we have tested the use of synthetic pebbles to create new tracers equipped with high frequency active transponders (a-UHF), more performant than PIT-tags. Secondly, we have developed a new search and location field methodology specially, adapted to these new transponders. Thirdly, we have tested the sensibility of the toolbox developed by Roussillon et al. (2009), design to measure the roundness of coarse sedimentary particles, to different entry parameters. We have confirmed its interest to (1) analyse the relationship between particles normalized abrasion and its roundness trends; (2) analyse the hydrosedimentary dynamics at a river basin scale. We have included several recommendations to apply this toolbox in the appropriate conditions. Finally, we have performed a comparative analysis between particles’ density and shape and its influence on bedrock transport. These results highlight the significant influence of shape on travelled distance in comparison with density.

Theoretical studies of the molecular mechanisms responsible for the formation and stability of protein complexes have gained importance due to their practical applications in the understanding of the molecular basis of several diseases, in protein engineering and biotechnology. The objective of this project is to critically analyze and refine a coarse-grained force field for protein-protein interactions based on experimental thermodynamic properties and to apply it to cancer-related S100A4 protein system. Our ultimate goal is to generate knowledge for a better understanding of the physical mechanisms responsible for the association of particular proteins in different environments. We studied the role of short and long-range interactions on the complexation of homo-associations. Furthermore, we analyzed the influence of the pH and its correlation with the charge regulation mechanism. We analyzed and refined the adjustable Lennard-Jones parameter for a mesoscopic model based on experimental second virial data for lysozyme, chymotrypsinogen, and ribonuclease A via Monte Carlo simulations. From of that, the S100A3 protein was used to test the new calibrated parameters. Finally, we evaluated the dimerization process of S100A4 proteins, observing the role of physical-chemistry variables involved in the thermodynamical stability of different oligomers. / Estudos teóricos dos mecanismos moleculares responsáveis pela formação e estabilidade dos complexos de proteínas vêm ganhando importância devido às suas aplicações práticas no entendimento da base molecular de várias doenças, em engenharia de proteínas e biotecnologia. O objetivo deste projeto é analisar criticamente e aperfeiçoar um campo de força de granulidade grossa para interação proteína-proteína com base em propriedades termodinâmicas experimentais e aplicá-lo ao sistema proteico S100A4 relacionado com o câncer. Nosso objetivo final é gerar conhecimento para uma melhor compreensão dos mecanismos físicos responsáveis pelas associações de proteínas particulares em diferentes ambientes. Estudamos o papel das interações de curto e longo alcance na complexação de homo-associações. Além disso, analisamos a influência do pH e sua correlação com o mecanismo de regulação de cargas. Por meio de simulações Monte Carlo, analisamos e refinamos o parametro ajustável de Lennard-Jones para um modelo mesoscópico, usando dados experimentais do segundo virial para a lisozima, o quimotripsinogênio e a ribonuclease A. A partir disso, a proteína S100A3 foi usada para testar os novos parâmetros calibrados. Finalmente, foi avaliado o processo de dimerização das proteínas S100A4, observando o papel de algumas variáveis físico-químicas envolvidas na estabilidade termondinâmica de diferentes oligómeros.

The objective of this study was to test the line intersect sampling (LIS) methodology using the design-based inference with stratified systematic sampling and two transect shapes: a straight line and a cross shape, both with three different lengths (100, 150, and 200 m) to estimate the number of coarse woody debris (CWD) elements, their volume, biomass and carbon stocks; by decay class; furthermore, we fit and select CWD biomass and carbon models. The study area includes two types of native forest in the State of São Paulo, Brazil: a Seasonal Semi-deciduous Forest (SSF) and a Cerrado sensu-stricto (CSS). Two strata were chosen in each area, and in each stratum ten sampling units were installed according to a systematic sampling protocol. Each sampling unit had one North- South line of 200 m superimposed over the other lengths (100 and 150 m) and three lines (one for each length) in the East-West direction forming the cross shapes, for a total 650 m per sampling unit. All CWD elements with a diameter _ 10 cm that crossed the transect were tallied. For each element, the diameter, length, perpendicular width, decay class, and (when possible) species was recorded. Disc samples were taken from each element, from which cylinder samples were extracted then oven dried to determine density. These cylinders were milled and analyzed to determine carbon content (%). The volume of each element was calculated by taking the difference between cross-sectional area and any hollowed area, then multiplying by the element\'s length. Biomass was calculated by multiplying volume values by density values, and carbon stocks were calculated by multiplying biomass by the carbon percentage factors computed via lab analysis. Total estimators were calculated by area and per hectare for the number of CWD elements, their volume, biomass, and carbon stocks. These estimators were calculated by stratum then combined across the entire sample population. The data from each sampling unit was also used to calculate the wood density and carbon concentration by decay class, as well as to fit linear and nonlinear models. For the SSF area, the most accurate transect design was the 200 m cross shaped; and for the CSS area was selected the 150 m cross shape. Both areas showed lower biomass values (1.3 and 6.7 Mg/ha for the CSS and SSF areas, respectively) than other studies in the Amazon Forest where CWD research has been conducted. In both areas, as the decay class increased (from least to most rotten material), wood density decreased, which follows the same pattern as other literature. Carbon concentration barely changed within decay classes. Using a conversion constant of 50%, similar carbon stock results were obtained. Nonlinear models (using diameter and length as predictor variables) proved an efficient tool for predicting CWD biomass at an element level. As expected, biomass data exhibited heteroscedasticity, which was mitigated by modeling the variance of the residuals with a power function of the combined variable. Adding decay class as an indicator variable also resulted in model improvement. / Este estudo buscou testar a metodologia de amostragem pela linha interceptadora (LIS), usando a inferência baseada no design, com amostragem sistemática estratificada em duas formas de transectos: linha reta e forma de cruz, ambos com três diferentes comprimentos de transectos: 100, 150 e 200 m para estimar o número de elementos, volume, biomassa e estoque de carbono de madeira morta; investigar a densidade da madeira e a concentração de carbono da madeira morta pela classe de decomposição; e, ajustar e selecionar modelos de biomassa e carbono de madeira morta, em dois tipos de floresta nativa no estado de São Paulo, Brasil: uma Floresta Estacional Semidecidual (SSF) e um Cerrado sensu-stricto (CSS). Em cada tipo florestal foram selecionados dois estratos e localidas dez unidades de amostragem em cada. A unidade de amostragem é um transecto Norte-Sul, com 200 m, que sobrepõe os outros comprimentos (100 e 150 m), e três transectos (para cada comprimento) na direção Leste-Oeste, formando a cruz, totalizando 650m. Foram medidos todos os elementos de madeira morta grossa (CWD) que cruzaram o transecto com um diâmetro _10 cm. Foi medido o diâmetro na interseção, o comprimento, a largura perpendicular, o elemento foi classificado de acordo com a classe de decomposição e, quando possível, a espécie foi identificada. De cada elemento foi retirado um disco de amostra na interseção, este foi fotografado para o cálculo da área oca. De cada disco foram extraídos cilindros, secos em estufa para determinação da densidade, estes foram moídos e analisados para determinação do teor de carbono (%). O volume de cada elemento foi calculado pela diferença da área seccional e área oca, multiplicada pelo comprimento; a biomassa foi calculada multiplicando o volume pela densidade; e o estoque de carbono foi calculado multiplicando a biomassa pela concentração de carbono. Os estimadores do total foram calculados por área e por hectare para o número de elementos de CWD, volume, biomassa e estoque de carbono; foram calculados por estrato, e combinados para a população. Os dados dos 650m de cada unidade foram utilizados para calcular as médias da densidade da madeira e concentração de carbono por classe de decomposição e, para construção de modelos lineares e não-lineares. Para a SSF, o design mais preciso foi transectos em forma de cruz, com 200 m. Para CSS foram selecionados transectos em cruz, com 150 m. As áreas apresentaram valores de biomassa 1.3-6.7 Mg/ha para CSS e SSF, respectivamente. Em ambos tipos florestais foi encontrado que à medida que a classe de decomposição aumenta (mais fresco para mais podre), a densidade da madeira diminui, seguindo os mesmos padrões encontrados na literatura. A concentração de carbono não apresentou mudança dentro das classes de decomposição. Modelos nãolineares com diâmetro e comprimento como variáveis preditoras provaram ser uma ferramenta eficiente para predizer a biomassa e carbono de CWD. Como esperado, os dados de biomassa apresentaram heterocedasticidade, mitigada pela modelagem da variância dos resíduos com uma função de potência. A adição da classe de decomposição como variável indicadora também mostrou melhora nos modelos.

Jusqu’à présent, la dynamique des fractions végétales n’avait jamais été étudiée dans les estuaires macrotidaux en raison de leur faible quantité, par rapports aux fortes charges en matières en suspension fines, et du manque de protocoles d’étude et d’échantillonnage adéquats. Les débris végétaux sont toutefois à l’origine de perturbations d’activités économiques qui impliquent la filtration de larges volumes d’eau. L’objectif de cette thèse était ainsi de comprendre la dynamique d’apport et de transit de ces débris végétaux dans l’estuaire de la Gironde par la mise en oeuvre d’un suivi spatio-temporel de leur distribution et de techniques nouvelles pour un tel estuaire hyper-turbide (incubations in-situ litter-bag, caractérisation biogéochimique, identification des sources). Les résultats principaux sont la mise en évidence du contrôle du régime hydrologique sur leur distribution et la détermination des échelles de temps de leur persistance dans l’estuaire de la Gironde. / Up to now, vegetal fraction dynamics has not been studied in macrotidal estuaries, due to its low quantity in comparison to the strong charge of suspended particulate matter, and due to the lack of appropriate protocols to sample and examine it. Nevertheless, vegetal debris have been identified as a factor able to disrupt a wide range of stakeholder activities that require huge volumes of water to filter. The objective of this PhD was to understand the input and transfer dynamics of vegetal debris in the Gironde Estuary by the implementation of a spatiotemporal btrack of their distribution and by the development of new techniques for this hyper-turbide estuary (in situ litter-bag incubations, biogeochemical characterization, and identification of the sources). Mean results highlight the influence of the hydrological regime in their distribution and reveal time scales of their persistence in the Gironde Estuary.

In this thesis I present and test a methodology for developing a stand scale index of structural complexity. If properly designed such an index can act as a summary variable for a larger set of stand structural attributes, providing a means of ranking stands in terms of their structural complexity, and by association, their biodiversity and vegetation condition. This type of index can also facilitate the use of alternative policy instruments for biodiversity conservation, such as mitigation banking, auctions and offsets, that rely on a common currency – the index value – that can be compared or traded between sites. My intention was to establish a clear and documentable methodology for developing a stand scale index of structural complexity, and to test this methodology using data from real stands.¶ As a starting point, I reviewed the literature concerning forest and woodland structure and found there was no clear definition of stand structural complexity, or definitive suite of structural attributes for characterising it. To address this issue, I defined stand structural complexity as a combined measure of the number of different structural attributes present in a stand, and the relative abundance of each of these attributes. This was analogous to approaches that have quantified diversity in terms of the abundance and richness of elements. It was also concluded from the review, that stand structural complexity should be viewed as a relative, rather than absolute concept, because the potential levels of different structural attributes are bound within certain limits determined by the inherent characteristics of the site in question, and the biota of the particular community will have evolved to reflect this range of variation. This implied that vegetation communities with naturally simple structures should have the potential to achieve high scores on an index of structural complexity.¶ I proposed the following five-stage methodology for developing an index of stand structural complexity: 1. Establish a comprehensive suite of stand structural attributes as a starting point for developing the index, by reviewing studies in which there is an established relationship between elements of biodiversity and structural attributes. 2. Develop a measurement system for quantifying the different attributes included in the comprehensive suite. 3. Use this measurement system to collect data from a representative set of stands across the range of vegetation condition (highly modified to unmodified) and developmental stages (regrowth to oldgrowth) occurring in the vegetation communities in which the index is intended to operate. 4. Identify a core set of structural attributes from an analysis of these data. 5. Combine the core attributes in a simple additive index, in which attributes are scored relative to their observed levels in each vegetation community.¶ Stage one of this methodology was addressed by reviewing a representative sample of the literature concerning fauna habitat relationships in temperate Australian forests and woodlands. This review identified fifty-five studies in south-east and south-west Australia, in which the presence or abundance of different fauna were significantly (p&lt0.05) associated with vegetation structural attributes. The majority of these studies concerned bird, arboreal mammal, and ground mammal habitat requirements, with relatively fewer studies addressing the habitat requirements of reptiles, invertebrates, bats or amphibians. Thirty four key structural attributes were identified from these fifty-five studies, by grouping similar attributes, and then representing each group with a single generic attribute. This set, in combination with structural attributes identified in the earlier review, provided the basis for developing an operational set of stand level attributes for the collection of data from study sites.¶ To address stages two and three of the methodology, data were collected from one woodland community –Yellow Box-Red Gum (E. melliodora-E. Blakelyi ) – and two dry sclerophyll forest communities – Broadleaved Peppermint-Brittle Gum (E. dives-E. mannifera ), Scribbly Gum-Red Stringybark (E. rossii E. macrorhyncha ) – in a 15,000 km2 study area in the South eastern Highlands Bioregion of Australia. A representative set of 48 sites was established within this study area, by identifying 24 strata, on the basis of the three vegetation communities, two catchments, two levels of rainfall and two levels of condition, and then locating two sites (replicates) within each stratum. At each site, three plots were systematically established, to provide an unbiased estimate of stand level means for 75 different structural attributes.¶ I applied a three-stage analysis to identify a core set of attributes from these data. The first stage – a preliminary analysis – indicated that the 48 study sites represented a broad range of condition, and that the two dry sclerophyll communities could be treated as a single community, which was structurally distinct from the woodland community. In the second stage of the analysis, thirteen core attributes were dentified using the criteria that a core attribute should:¶ 1. Be either, evenly or approximately normally distributed amongst study sites; 2. Distinguish between woodland and dry sclerophyll communities; 3. Function as a surrogate for other attributes; 4. Be efficient to measure in the field. The core attributes were: Vegetation cover &lt0.5m Vegetation cover 0.5-6.0m; Perennial species richness; Lifeform richness; Stand basal area of live trees; Quadratic mean diameter of live stems; ln(number of regenerating stems per ha+1); ln(number of hollow bearing trees per ha+1);ln(number of dead trees per ha+1);sqrt(number of live stems per ha &gt40cm dbh); sqrt(total log length per ha); sqrt(total largelog length per ha); Litter dry weight per ha. This analysis also demonstrated that the thirteen core attributes could be modelled as continuous variables, and that these variables were indicative of the scale at which the different attributes operated.¶ In the third and final stage of the analysis, Principal Components Analysis was used to test for redundancy amongst the core attributes. Although this analysis highlighted six groupings, within which attributes were correlated to some degree, these relationships were not considered sufficiently robust to justify reducing the number of core attributes.¶ The thirteen core attributes were combined in a simple additive index, in which, each attribute accounted for 10 points in a total index value of 130. Attributes were rescaled as a score from 0-10, using equations that modelled attribute score as a function of the raw attribute data. This maintained a high correlation (r > 0.97, p< 0.0001) between attribute scores and the original attribute data. Sensitivity analysis indicated that the index was not sensitive to attribute weightings, and on this basis attributes carried equal weight. In this form my index was straightforward to apply, and approximately normally distributed amongst study sites.¶ I demonstrated the practical application of the index in a user-friendly spreadsheet, designed to allow landowners and managers to assess the condition of their vegetation, and to identify management options. This spreadsheet calculated an index score from field data, and then used this score to rank the site relative to a set of reference sites. This added a regional context to the operation of the index, and is a potentially useful tool for identifying sites of high conservation value, or for identifying sites where management actions have maintained vegetation quality. The spreadsheet also incorporated the option of calculating an index score using a subset of attributes, and provided a measure of the uncertainty associated with this score.¶ I compared the proposed index with five prominent indices used to quantify vegetation condition or habitat value in temperate Australian ecosystems. These were: Newsome and Catling’s (1979) Habitat Complexity Score, Watson et al.’s (2001) Habitat Complexity Score, the Site Condition Score component of the Habitat Hectares Index of Parkes et al. (2003), the Vegetation Condition Score component of the Biodiversity Benefits Index of Oliver and Parkes (2003), and the Vegetation Condition Score component of the BioMetric Assessment Tool of Gibbons et al. (2004). I found that my index differentiated between study sites better than each of these indices. However, resource and time constraints precluded the use of a new and independent data set for this testing, so that the superior performance of my index must be interpreted cautiously.¶ As a group, the five indices I tested contained attributes describing compositional diversity, coarse woody debris, regeneration, large trees and hollow trees – these were attributes that I also identified as core ones. However, unlike these indices, I quantified weeds indirectly through their effect on indigenous plant diversity, I included the contribution of non-indigenous species to vegetation cover and did not apply a discount to this contribution, I limited the direct assessment of regeneration to long-lived overstorey species, I used stand basal area as a surrogate for canopy cover, I quantified litter in terms of biomass (dry weight) rather than cover, and I included the additional attributes of quadratic mean diameter and the number of dead trees.¶ I also concluded that Parkes et al. (2003), Oliver and Parkes (2003), and Gibbons et al. (2004), misapplied the concept of benchmarking, by characterising attributes in terms of a benchmark range or average level. This ignored processes that underpin variation at the stand level, such as the increased development of some attributes at particular successional stages, and the fact that attributes can respond differently to disturbance agents. It also produced indices that were not particularly sensitive to the differences in attribute levels occurring between stands. I suggested that a more appropriate application of benchmarking would be at the overarching level of stand structural complexity, using a metric such as the index developed in this thesis. These benchmarks could reflect observed levels of structural complexity in unmodified natural stands at different successional stages, or thresholds for structural complexity at which a wide range of biota are present, and would define useful goals for guiding on-ground management.

The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. Accordingly, breeding sites should exhibit predictable habitat features linked to these components. In this study, I evaluated the relative influences of habitat features linked to fitness components on selection of breeding sites by coho salmon (Oncorhynchus kisutch). I also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. I used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. The relative likelihood of each of these models was then evaluated based on how coho salmon were observed to select breeding sites. Specific variables examined within these models included depth at the redd, width to depth ratio, stream network location, proximity to other redds, maximum depth, proximity to a pool tail, and the count of naturally occurring and artificially placed large wood. Results of this work suggest that female coho salmon most likely select breeding sites based on habitat features linked to all four hypothesized fitness components. Linkages between large wood and breeding site selection were less clear, likely due to mismatches between the scale at which availability was quantified relative to the geomorphic influences of wood, insufficient time for wood to have geomorphic influences on habitat, or the directionality in which geomorphic effects are currently manifested (i.e., upstream, downstream, or bi-directional influences). Future work focused on geomorphic processes in this system could reveal stronger linkages between instream wood and the habitat features that coho salmon select for breeding. / Graduation date: 2013

Four different trials of stratified three-layered fine paper, of sulphate pulp, were performed to investigate if stratified fine fraction or fibres from birch can improve the properties of a paper compared to a reference sheet. All trials had five different scenarios and each scenario was calendered with different linear load. All sheets had a grammage of 80 g/m2.In the first trial, the paper contained birch, pine and filler of calciumcarbonate (marble), and was manufactured with the pilot paper machine XPM and the stratified headbox Formator at RCF (Stora Enso Research Center in Falun). The furnish consisted of 75% birch and 25% pine.The second trial contained coated sheets with paper from trial one as the base paper. The coating slip contained calciumcarbonate and clay and the amount was approximately 10-12 g/m2.The third trial, also with birch and pine but without filler, was performed at STFI (Skogsindustrins Tekniska Forskningsinstitut in Stockholm) with the laboratory scaled paper machine StratEx and the stratified headbox AQ-vanes. The furnish consisted of 75% birch and 25% pine, except for one scenario which contained of 75% pine and 25% birch.The last trial contained fractionated pulp of birch and pine and was performed at STFI. 50% was fine fraction and 50% was coarse fraction.This test does not show any clear benefits of making stratified sheets of birch and pine when it comes to properties such as bending stiffness, tensile index and surface smoothness. The retention can be improved with birch in the surface plies. It is possible that the formation can be improved with birch in the surface plies and pine in the middle ply. It is also possible that fine fraction in the surface plies and coarse fraction in the middle ply can improve both surface smoothness and bending stiffness. The results in this test are shown with confidence intervals which points out the difficulties of analysing sheets manufactured with a pilot paper machine or a laboratory scaled paper machine.