Using a Combination of Phylogenetic Comparative and Paleobotanical Methods to Elucidate Patterns of Lineage Selection in Rosales (Plantae: Anthophyta)

An increasing focus in evolutionary biology is on the interplay between mesoscale ecological and evolutionary processes such as population demographics, habitat tolerance, and especially geographic distribution, as potential drivers responsible for patterns of diversification and extinction over geologic time. However, few studies to date connect organismal processes such as survival and reproduction through mesoscale patterns to long-term macroevolutionary trends. In my dissertation, I investigate how mechanism of seed dispersal, mediated through geographic range size, influences diversification rates in the Rosales (Plantae: Anthophyta). In my first chapter, I validate the phylogenetic comparative methods that I use in my second and third chapters. Available state speciation and extinction (SSE) models assumptions about evolution known to be false through fossil data. I show, however, that as long as net diversification rates remain positive – a condition likely true for the Rosales – these violations of SSE’s assumptions do not cause significantly biased results. With SSE methods validated, my second chapter reconstructs three associations that appear to increase diversification rate for Rosalean genera: (1) herbaceous habit; (2) a three-way interaction combining animal dispersal, high within-genus species richness, and geographic range on multiple continents; (3) a four-way interaction combining woody habit with the other three characteristics of (2). I suggest that the three- and four-way interactions represent colonization ability and resulting extinction resistance in the face of late Cenozoic climate change; however, there are other possibilities as well that I hope to investigate in future research. My third chapter reconstructs the phylogeographic history of the Rosales using both non-fossil-assisted SSE methods as well as fossil-informed traditional phylogeographic analysis. Ancestral state reconstructions indicate that the Rosaceae diversified in North America while the other Rosalean families diversified elsewhere, possibly in Eurasia. SSE is able to successfully identify groups of genera that were likely to have been ancestrally widespread, but has poorer taxonomic resolution than methods that use fossil data. In conclusion, these chapters together suggest several potential causal links between organismal, mesoscale, and geologic scale processes, but further work will be needed to test the hypotheses that I raise here.

Multiscale Modeling and Simulation of Stepped Crystal Surfaces

A primary goal of this dissertation is to understand the links between mathematical models that describe crystal surfaces at three fundamental length scales: The scale of individual atoms, the scale of collections of atoms forming crystal defects, and macroscopic scale. Characterizing connections between different classes of models is a critical task for gaining insight into the physics they describe, a long-standing objective in applied analysis, and also highly relevant in engineering applications. The key concept I use in each problem addressed in this thesis is coarse graining, which is a strategy for connecting fine representations or models with coarser representations. Often this idea is invoked to reduce a large discrete system to an appropriate continuum description, e.g. individual particles are represented by a continuous density. While there is no general theory of coarse graining, one closely related mathematical approach is asymptotic analysis, i.e. the description of limiting behavior as some parameter becomes very large or very small. In the case of crystalline solids, it is natural to consider cases where the number of particles is large or where the lattice spacing is small. Limits such as these often make explicit the nature of links between models capturing different scales, and, once established, provide a means of improving our understanding, or the models themselves. Finding appropriate variables whose limits illustrate the important connections between models is no easy task, however. This is one area where computer simulation is extremely helpful, as it allows us to see the results of complex dynamics and gather clues regarding the roles of different physical quantities. On the other hand, connections between models enable the development of novel multiscale computational schemes, so understanding can assist computation and vice versa. Some of these ideas are demonstrated in this thesis. The important outcomes of this thesis include: (1) a systematic derivation of the step-flow model of Burton, Cabrera, and Frank, with corrections, from an atomistic solid-on-solid-type models in 1+1 dimensions; (2) the inclusion of an atomistically motivated transport mechanism in an island dynamics model allowing for a more detailed account of mound evolution; and (3) the development of a hybrid discrete-continuum scheme for simulating the relaxation of a faceted crystal mound. Central to all of these modeling and simulation efforts is the presence of steps composed of individual layers of atoms on vicinal crystal surfaces. Consequently, a recurring theme in this research is the observation that mesoscale defects play a crucial role in crystal morphological evolution.

Chiroptical spectroscopy of biomolecules using chiral plasmonic nanostructures

This thesis explores the potential of chiral plasmonic nanostructures for the ultrasensitive detection of protein structure. These nanostructures support the generation of fields with enhanced chirality relative to circularly polarised light and are an extremely incisive probe of protein structure. In chapter 4 we introduce a nanopatterned Au film (Templated Plasmonic Substrate, TPS) fabricated using a high through-put injection moulding technique which is a viable alternative to expensive lithographically fabricated nanostructures. The optical and chiroptical properties of TPS nanostructures are found to be highly dependent on the coupling between the electric and magnetic modes of the constituent solid and inverse structures. Significantly, refractive index based measurements of strongly coupled TPSs display a similar sensitivity to protein structure as previous lithographic nanostructures. We subsequently endeavour to improve the sensing properties of TPS nanostructures by developing a high through-put nanoscale chemical functionalisation technique. This process involves a chemical protection/deprotection strategy. The protection step generates a self-assembled monolayer (SAM) of a thermally responsive polymer on the TPS surface which inhibits protein binding. The deprotection step exploits the presence of nanolocalised thermal gradients in the water surrounding the TPS upon irradiation with an 8ns pulsed laser to modify the SAM conformation on surfaces with high net chirality. This allows binding of biomaterial in these regions and subsequently enhances the TPS sensitivity levels. In chapter 6 an alternative method for the detection of protein structure using TPS nanostructures is introduced. This technique relies on mediation of the electric/magnetic coupling in the TPS by the adsorbed protein. This phenomenon is probed through both linear reflectance and nonlinear second harmonic generation (SHG) measurements. Detection of protein structure using this method does not require the presence of fields of enhanced chirality whilst it is also sensitive to a larger array of secondary structure motifs than the measurements in chapters 4 and 5. Finally, a preliminary investigation into the detection of mesoscale biological structure is presented. Sensitivity to the mesoscale helical pitch of insulin amyloid fibrils is displayed through the asymmetry in the circular dichroism (CD) of lithographic gammadions of varying thickness upon adsorption of insulin amyloid fibril spherulites and fragmented fibrils. The proposed model for this sensitivity to the helical pitch relies on the vertical height of the nanostructures relative to this structural property as well as the binding orientation of the fibrils.

Perspetivas de utilização do potencial eólico em Timor-Leste

A exigência energética global está mais orientada para a utilização das fontes de Energias Renováveis (FERs), comprometendo e garantindo um desenvolvimento sustentável. Este trabalho tem como objetivo contribuir para o atingir das metas do PED 2011-2030, no que refere à utilização das FER, em particular do potencial eólico em Timor-Leste. Timor-Leste tem apresentado um grande interesse na política de aproveitamento de FER para alcançar a meta de longo prazo de PED 2030, comprometendo-se com o desenvolvimento sustentável através de ERs. Este trabalho pretende contribuir em particular com o estudo do aproveitamento de energia eólica. Com base no clima do vento de longo termo entre 2004 – 2012, da estação meteorológica (EM) de Díli e conjugando estes com os dados da campanha experimental de Martifer cedidos, de Dezembro 2008 - Novembro 2009, obteve-se o coeficiente de variabilidade (Cvariab.) inter-anual. Foi assim possível construir o mapa médio do vento de longo termo, com modelo atmosférico de mesoscala, numa resolução refinada de 3×3 km. Para a identificação dos locais mais favoráveis do vento, foi utilizado o modelo ArcGIS para georreferenciação do recurso. A filtragem das restrições e os constrangimentos do terreno permitiu construir o mapa do vento sustentável de Timor-Leste, por distritos, subdistritos, sucos, do enclave de Oecússi e a ilha de Atauro, o que conduziu à hierarquização de cinco zonas favoráveis (zona 1 - 5). A contribuição para o plano energético de Timor-Leste consiste em duas fases: - a 1ª fase o aproveitamento eólico em três PEs nas zonas monitorizadas (3 e 5) oriundo de dados cedidos pela Martifer, contabilizou-se um total de 424.694 MWh de produção de energia anual, tendo-se verificado o custo normalizado de energia (LCOE) no valor médio calculado de 0,046 €/kWh; - na 2ª fase a construção de acesso e o desenvolvimento de PEs nas zonas 1, 2 e 4 para o Cenário de Max-Renovável. Assim sendo, viabilizam a "Perspetiva de Utilização da Energia Eólica" no quadro do PED 2011 - 2030 de Timor-Leste, que viria reduzir o custo de produção de energia atual, e a emissão de CO2; Abstract: Prospects of Using Wind Energy in Timor-Leste The demand for global energy is more focused on the use of Reneweable Energy sources (REs), ensuring and committing itself to sustainable development. This study was prompted by the wish to contribute to the achievement the goals of the Strategic Development Plan (PED 2011-2030) regarding the use of REs, particularly the wind energy in Timor-Leste. Timor-Leste has presented a great interest in the use of renewable energy sources policy to achieve the long term goal of the PED 2030, committing to a sustainable development through renewable energy. This thesis intends to contribute in particular with the study of the use of wind energy. Based on the long term wind climate between 2004 and 2012 of the Díli weather station and combining these data with the Martifer campaign experimental data of December 2008 - November 2009, the interannual variation coefficient (Cv) was obtained. Thus, it was possible to build the map of long term average wind with atmospheric mesoscale model in a refined resolution of 3×3 km. The ArcGIS model was used for the identification of the most favorable locations of the wind for its georeferencing. The constraining of filtering and the constraints of the terrain allowed to construe the sustainable wind map of Timor-Leste in distritos, subdistritos, sucos, and also of the enclave of Oecussi and Atauro island, which led to the ranking of five favorable areas (zone 1-5) for an immediate experimental campaign of wind characterization and utilization of this resource in wind parks. The contribution to Timor-Leste's energy plan consists of two phases: - the first phase of three wind farms in zone (3 and 5) from data provided by Martifer, a total of 424,694 MWh, and levelyzed cost of electricity (LCOE) in the calculated average value of 0.046 €/kWh; - in the second phase the construction of access and development of wind farms in zones 1, 2 and 4 for the Max-Renewable Scenario. As such, they make possible the "Perspective of Wind Energy Use" in Timor Leste’s PED 2011 - 2030, which would reduce current energy production costs and CO2 emissions.

Understanding significant precipitation in Madeira island using high-resolution numerical simulations of real cases

In order to advance the knowledge about precipitation development over Madeira island, four rainfall patterns are investigated based on high-resolution numerical simulations performed with the MESO-NH model. The main environmental conditions during these precipitation periods are examined, and important factors leading to significant accumulated precipitation in Madeira are shown. We found that the combination of orographic effect and atmospheric conditions is essential for the establishment of each situation. Under a moist and conditionally unstable atmosphere, convection over the island is triggered, and its location was determined mainly by variations of the ambient flow, which was also associated with different moist Froude numbers. Interestingly, our results showed some similarities with situations discussed in idealized studies. However, the real variations of the atmospheric configuration confirm the complexity of significant precipitation development in mountainous regions. In addition, precipitating systems initially formed over the ocean were simulated reaching the island. The four periods were characterised by different time durations, and the local terrain interacting with the mesoscale circulation was decisive in producing a large part of the precipitation, which concentrated in distinct regions of the island induced by the airflow dynamic.