Climate sensitivity across marine domains of life: limits to evolutionary adaptation shape species interactions, supplementary material

Organisms in all domains, Archaea, Bacteria, and Eukarya will respond to climate change with differential vulnerabilities resulting in shifts in species distribution, coexistence, and interactions. The identification of unifying principles of organism functioning across all domains would facilitate a cause and effect understanding of such changes and their implications for ecosystem shifts. For example, the functional specialization of all organisms in limited temperature ranges leads us to ask for unifying functional reasons. Organisms also specialize in either anoxic or various oxygen ranges, with animals and plants depending on high oxygen levels. Here, we identify thermal ranges, heat limits of growth, and critically low (hypoxic) oxygen concentrations as proxies of tolerance in a meta-analysis of data available for marine organisms, with special reference to domain-specific limits. For an explanation of the patterns and differences observed, we define and quantify a proxy for organismic complexity across species from all domains. Rising complexity causes heat (and hypoxia) tolerances to decrease from Archaea to Bacteria to uni- and then multicellular Eukarya. Within and across domains, taxon-specific tolerance limits likely reflect ultimate evolutionary limits of its species to acclimatization and adaptation. We hypothesize that rising taxon-specific complexities in structure and function constrain organisms to narrower environmental ranges. Low complexity as in Archaea and some Bacteria provide life options in extreme environments. In the warmest oceans, temperature maxima reach and will surpass the permanent limits to the existence of multicellular animals, plants and unicellular phytoplankter. Smaller, less complex unicellular Eukarya, Bacteria, and Archaea will thus benefit and predominate even more in a future, warmer, and hypoxic ocean.

A static heap analysis for shape and connectivity: Unified memory analysis: The base framework

Modeling the evolution of the state of program memory during program execution is critical to many parallehzation techniques. Current memory analysis techniques either provide very accurate information but run prohibitively slowly or produce very conservative results. An approach based on abstract interpretation is presented for analyzing programs at compile time, which can accurately determine many important program properties such as aliasing, logical data structures and shape. These properties are known to be critical for transforming a single threaded program into a versión that can be run on múltiple execution units in parallel. The analysis is shown to be of polynomial complexity in the size of the memory heap. Experimental results for benchmarks in the Jolden suite are given. These results show that in practice the analysis method is efflcient and is capable of accurately determining shape information in programs that créate and manipúlate complex data structures.

Geometric diagnostics of complex patterns: Spiral defect chaos

Motivated by the observation of spiral patterns in a wide range of physical, chemical, and biological systems, we present an automated approach that aims at characterizing quantitatively spiral-like elements in complex stripelike patterns. The approach provides the location of the spiral tip and the size of the spiral arms in terms of their arc length and their winding number. In addition, it yields the number of pattern components (Betti number of order 1), as well as their size and certain aspects of their shape. We apply the method to spiral defect chaos in thermally driven Rayleigh- Bénard convection and find that the arc length of spirals decreases monotonically with decreasing Prandtl number of the fluid and increasing heating. By contrast, the winding number of the spirals is nonmonotonic in the heating. The distribution function for the number of spirals is significantly narrower than a Poisson distribution. The distribution function for the winding number shows approximately an exponential decay. It depends only weakly on the heating, but strongly on the Prandtl number. Large spirals arise only for larger Prandtl numbers. In this regime the joint distribution for the spiral length and the winding number exhibits a three-peak structure, indicating the dominance of Archimedean spirals of opposite sign and relatively straight sections. For small Prandtl numbers the distribution function reveals a large number of small compact pattern components.

Urban wind energy: empirical optimization of high-rise building roof shape for the wind energy exploitation

El programa Europeo HORIZON2020 en Futuras Ciudades Inteligentes establece como objetivo que el 20% de la energía eléctrica sea generada a partir de fuentes renovables. Este objetivo implica la necesidad de potenciar la generación de energía eólica en todos los ámbitos. La energía eólica reduce drásticamente las emisiones de gases de efecto invernadero y evita los riesgos geo-políticos asociados al suministro e infraestructuras energéticas, así como la dependencia energética de otras regiones. Además, la generación de energía distribuida (generación en el punto de consumo) presenta significativas ventajas en términos de elevada eficiencia energética y estimulación de la economía. El sector de la edificación representa el 40% del consumo energético total de la Unión Europea. La reducción del consumo energético en este área es, por tanto, una prioridad de acuerdo con los objetivos "20-20-20" en eficiencia energética. La Directiva 2010/31/EU del Parlamento Europeo y del Consejo de 19 de mayo de 2010 sobre el comportamiento energético de edificaciones contempla la instalación de sistemas de suministro energético a partir de fuentes renovables en las edificaciones de nuevo diseño. Actualmente existe una escasez de conocimiento científico y tecnológico acerca de la geometría óptima de las edificaciones para la explotación de la energía eólica en entornos urbanos. El campo tecnológico de estudio de la presente Tesis Doctoral es la generación de energía eólica en entornos urbanos. Específicamente, la optimization de la geometría de las cubiertas de edificaciones desde el punto de vista de la explotación del recurso energético eólico. Debido a que el flujo del viento alrededor de las edificaciones es exhaustivamente investigado en esta Tesis empleando herramientas de simulación numérica, la mecánica de fluidos computacional (CFD en inglés) y la aerodinámica de edificaciones son los campos científicos de estudio. El objetivo central de esta Tesis Doctoral es obtener una geometría de altas prestaciones (u óptima) para la explotación de la energía eólica en cubiertas de edificaciones de gran altura. Este objetivo es alcanzado mediante un análisis exhaustivo de la influencia de la forma de la cubierta del edificio en el flujo del viento desde el punto de vista de la explotación energética del recurso eólico empleando herramientas de simulación numérica (CFD). Adicionalmente, la geometría de la edificación convencional (edificio prismático) es estudiada, y el posicionamiento adecuado para los diferentes tipos de aerogeneradores es propuesto. La compatibilidad entre el aprovechamiento de las energías solar fotovoltaica y eólica también es analizado en este tipo de edificaciones. La investigación prosigue con la optimización de la geometría de la cubierta. La metodología con la que se obtiene la geometría óptima consta de las siguientes etapas: - Verificación de los resultados de las geometrías previamente estudiadas en la literatura. Las geometrías básicas que se someten a examen son: cubierta plana, a dos aguas, inclinada, abovedada y esférica. - Análisis de la influencia de la forma de las aristas de la cubierta sobre el flujo del viento. Esta tarea se lleva a cabo mediante la comparación de los resultados obtenidos para la arista convencional (esquina sencilla) con un parapeto, un voladizo y una esquina curva. - Análisis del acoplamiento entre la cubierta y los cerramientos verticales (paredes) mediante la comparación entre diferentes variaciones de una cubierta esférica en una edificación de gran altura: cubierta esférica estudiada en la literatura, cubierta esférica integrada geométricamente con las paredes (planta cuadrada en el suelo) y una cubierta esférica acoplada a una pared cilindrica. El comportamiento del flujo sobre la cubierta es estudiado también considerando la posibilidad de la variación en la dirección del viento incidente. - Análisis del efecto de las proporciones geométricas del edificio sobre el flujo en la cubierta. - Análisis del efecto de la presencia de edificaciones circundantes sobre el flujo del viento en la cubierta del edificio objetivo. Las contribuciones de la presente Tesis Doctoral pueden resumirse en: - Se demuestra que los modelos de turbulencia RANS obtienen mejores resultados para la simulación del viento alrededor de edificaciones empleando los coeficientes propuestos por Crespo y los propuestos por Bechmann y Sórensen que empleando los coeficientes estándar. - Se demuestra que la estimación de la energía cinética turbulenta del flujo empleando modelos de turbulencia RANS puede ser validada manteniendo el enfoque en la cubierta de la edificación. - Se presenta una nueva modificación del modelo de turbulencia Durbin k — e que reproduce mejor la distancia de recirculación del flujo de acuerdo con los resultados experimentales. - Se demuestra una relación lineal entre la distancia de recirculación en una cubierta plana y el factor constante involucrado en el cálculo de la escala de tiempo de la velocidad turbulenta. Este resultado puede ser empleado por la comunidad científica para la mejora del modelado de la turbulencia en diversas herramientas computacionales (OpenFOAM, Fluent, CFX, etc.). - La compatibilidad entre las energías solar fotovoltaica y eólica en cubiertas de edificaciones es analizada. Se demuestra que la presencia de los módulos solares provoca un descenso en la intensidad de turbulencia. - Se demuestran conflictos en el cambio de escala entre simulaciones de edificaciones a escala real y simulaciones de modelos a escala reducida (túnel de viento). Se demuestra que para respetar las limitaciones de similitud (número de Reynolds) son necesarias mediciones en edificaciones a escala real o experimentos en túneles de viento empleando agua como fluido, especialmente cuando se trata con geometrías complejas, como es el caso de los módulos solares. - Se determina el posicionamiento más adecuado para los diferentes tipos de aerogeneradores tomando en consideración la velocidad e intensidad de turbulencia del flujo. El posicionamiento de aerogeneradores es investigado en las geometrías de cubierta más habituales (plana, a dos aguas, inclinada, abovedada y esférica). - Las formas de aristas más habituales (esquina, parapeto, voladizo y curva) son analizadas, así como su efecto sobre el flujo del viento en la cubierta de un edificio de gran altura desde el punto de vista del aprovechamiento eólico. - Se propone una geometría óptima (o de altas prestaciones) para el aprovechamiento de la energía eólica urbana. Esta optimización incluye: verificación de las geometrías estudiadas en el estado del arte, análisis de la influencia de las aristas de la cubierta en el flujo del viento, estudio del acoplamiento entre la cubierta y las paredes, análisis de sensibilidad del grosor de la cubierta, exploración de la influencia de las proporciones geométricas de la cubierta y el edificio, e investigación del efecto de las edificaciones circundantes (considerando diferentes alturas de los alrededores) sobre el flujo del viento en la cubierta del edificio objetivo. Las investigaciones comprenden el análisis de la velocidad, la energía cinética turbulenta y la intensidad de turbulencia en todos los casos. ABSTRACT The HORIZON2020 European program in Future Smart Cities aims to have 20% of electricity produced by renewable sources. This goal implies the necessity to enhance the wind energy generation, both with large and small wind turbines. Wind energy drastically reduces carbon emissions and avoids geo-political risks associated with supply and infrastructure constraints, as well as energy dependence from other regions. Additionally, distributed energy generation (generation at the consumption site) offers significant benefits in terms of high energy efficiency and stimulation of the economy. The buildings sector represents 40% of the European Union total energy consumption. Reducing energy consumption in this area is therefore a priority under the "20-20-20" objectives on energy efficiency. The Directive 2010/31/EU of the European Parliament and of the Council of 19 May 2010 on the energy performance of buildings aims to consider the installation of renewable energy supply systems in new designed buildings. Nowadays, there is a lack of knowledge about the optimum building shape for urban wind energy exploitation. The technological field of study of the present Thesis is the wind energy generation in urban environments. Specifically, the improvement of the building-roof shape with a focus on the wind energy resource exploitation. Since the wind flow around buildings is exhaustively investigated in this Thesis using numerical simulation tools, both computational fluid dynamics (CFD) and building aerodynamics are the scientific fields of study. The main objective of this Thesis is to obtain an improved (or optimum) shape of a high-rise building for the wind energy exploitation on the roof. To achieve this objective, an analysis of the influence of the building shape on the behaviour of the wind flow on the roof from the point of view of the wind energy exploitation is carried out using numerical simulation tools (CFD). Additionally, the conventional building shape (prismatic) is analysed, and the adequate positions for different kinds of wind turbines are proposed. The compatibility of both photovoltaic-solar and wind energies is also analysed for this kind of buildings. The investigation continues with the buildingroof optimization. The methodology for obtaining the optimum high-rise building roof shape involves the following stages: - Verification of the results of previous building-roof shapes studied in the literature. The basic shapes that are compared are: flat, pitched, shed, vaulted and spheric. - Analysis of the influence of the roof-edge shape on the wind flow. This task is carried out by comparing the results obtained for the conventional edge shape (simple corner) with a railing, a cantilever and a curved edge. - Analysis of the roof-wall coupling by testing different variations of a spherical roof on a high-rise building: spherical roof studied in the litera ture, spherical roof geometrically integrated with the walls (squared-plant) and spherical roof with a cylindrical wall. The flow behaviour on the roof according to the variation of the incident wind direction is commented. - Analysis of the effect of the building aspect ratio on the flow. - Analysis of the surrounding buildings effect on the wind flow on the target building roof. The contributions of the present Thesis can be summarized as follows: - It is demonstrated that RANS turbulence models obtain better results for the wind flow around buildings using the coefficients proposed by Crespo and those proposed by Bechmann and S0rensen than by using the standard ones. - It is demonstrated that RANS turbulence models can be validated for turbulent kinetic energy focusing on building roofs. - A new modification of the Durbin k — e turbulence model is proposed in order to obtain a better agreement of the recirculation distance between CFD simulations and experimental results. - A linear relationship between the recirculation distance on a flat roof and the constant factor involved in the calculation of the turbulence velocity time scale is demonstrated. This discovery can be used by the research community in order to improve the turbulence modeling in different solvers (OpenFOAM, Fluent, CFX, etc.). - The compatibility of both photovoltaic-solar and wind energies on building roofs is demonstrated. A decrease of turbulence intensity due to the presence of the solar panels is demonstrated. - Scaling issues are demonstrated between full-scale buildings and windtunnel reduced-scale models. The necessity of respecting the similitude constraints is demonstrated. Either full-scale measurements or wind-tunnel experiments using water as a medium are needed in order to accurately reproduce the wind flow around buildings, specially when dealing with complex shapes (as solar panels, etc.). - The most adequate position (most adequate roof region) for the different kinds of wind turbines is highlighted attending to both velocity and turbulence intensity. The wind turbine positioning was investigated for the most habitual kind of building-roof shapes (flat, pitched, shed, vaulted and spherical). - The most habitual roof-edge shapes (simple edge, railing, cantilever and curved) were investigated, and their effect on the wind flow on a highrise building roof were analysed from the point of view of the wind energy exploitation. - An optimum building-roof shape is proposed for the urban wind energy exploitation. Such optimization includes: state-of-the-art roof shapes test, analysis of the influence of the roof-edge shape on the wind flow, study of the roof-wall coupling, sensitivity analysis of the roof width, exploration of the aspect ratio of the building-roof shape and investigation of the effect of the neighbouring buildings (considering different surrounding heights) on the wind now on the target building roof. The investigations comprise analysis of velocity, turbulent kinetic energy and turbulence intensity for all the cases.

Vortex-induced vibrations on bridges : the interaction mechanism in complex sections and a new proposed semi-empirical model

El presente trabajo de investigación se ocupa del estudio de las vibraciones verticales inducidas por vórtices (VIV) en aquellos puentes que, por sus características geométricas y propiedades dinámicas, muestran cierta sensibilidad este tipo de fenómeno aeroelástico. El objeto principal es el análisis del mecanismo de interacción viento-estructura sobre secciones no fuseladas de geometría simple, con objeto de realizar una adecuada caracterización del problema y poder abordar posteriormente el análisis de otras secciones de geometría más compleja, representativas de los principales elementos estructurales de los puentes, como arcos, tableros, torres y pilas. Este aspecto es fundamental durante la fase de diseño del puente, donde deberán tenerse en cuenta también una serie de detalles que pueden influir significativamente su sensibilidad ante problemas aerodinámicos, como la morfología y dimensiones principales de la sección transversal del tablero, la disposición de barreras de seguridad y barreras cortaviento, o las riostras que unen diferentes elementos estructurales. La configuración de dos elementos en tándem o la construcción de un puente en las inmediaciones de otro existente son otros aspectos a considerar respecto a la sensibilidad frente a efectos aeroelásticos. El estudio se ha llevado a cabo principalmente mediante la implementación de simulaciones numéricas que reproducen la interacción entre la corriente de aire y secciones representativas de modelos estructurales, a partir de un código CFD basado en el método de las partículas de vórtices (VPM), siguiendo por tanto un esquema Lagrangiano. Los resultados han sido validados con datos experimentales existentes, valores procedentes de ensayos en túnel de viento y registros reales a partir de diferentes casos de estudio: Alconétar (2006), Niterói (1980), Trans- Tokyo Bay (1995) y Volgogrado (2010). Finalmente, se propone un modelo semi-empírico para la estimación del rango de velocidades críticas y amplitudes de oscilación basado en la utilización de las derivadas de flameo de Scanlan, y la densidad espectral de las fuerzas aerodinámicas en el dominio de la frecuencia. The present research work concerns the study of vertical vortex-induced vibrations (VIV) in bridges which show certain sensitivity to this type of aeroelastic phenomenon. It focuses on the analysis of the wind-structure interaction mechanism on bluff sections, with the objective of making a good characterisation of the problem and subsequently addressing the analysis of sections with a complex geometry, which are representative of the bridge structural elements, such as arches, decks, towers and piers. This issue is of relative importance during the bridge design phase, since minor details of the aforementioned elements can significantly influence its sensitivity to aerodynamic problems. The shape and main dimensions of the deck cross section, the addition of safety barriers and windshields, the presence of braces to enhance the structure mechanical properties, the utilisation of cross sections in tandem arrangement, or the erection of a new bridge in the vicinity of another existing one are some of the aspects to be considered regarding the sensitivity to the aeroelastic effects. The study has been carried out mainly through the implementation of numerical simulations that reproduces the interaction between the airflow and the representative cross section of a structural bridge model, by the use of a CFD code based on the vortex particle method (VPM), thus following a Lagrangian scheme. The results have been validated with existing experimental data, values from wind tunnel tests and full scale observations from the different case studies: Alconétar (2006), Niterói (1980), Trans-Tokyo Bay (1995) and Volgograd (2010). Finally, a new semi-empirical model is proposed for the estimation of the critical wind velocity ranges and oscillation amplitudes based on the use of the Scanlan’s flutter derivatives and the power spectral density of aerodynamic force time history in the frequency domain.

Nuclear Pore Complex Number and Distribution throughout the Saccharomyces cerevisiae Cell Cycle by Three-Dimensional Reconstruction from Electron Micrographs of Nuclear Envelopes

The number of nuclear pore complexes (NPCs) in individual nuclei of the yeast Saccharomyces cerevisiae was determined by computer-aided reconstruction of entire nuclei from electron micrographs of serially sectioned cells. Nuclei of 32 haploid cells at various points in the cell cycle were modeled and found to contain between 65 and 182 NPCs. Morphological markers, such as cell shape and nuclear shape, were used to determine the cell cycle stage of the cell being examined. NPC number was correlated with cell cycle stage to reveal that the number of NPCs increases steadily, beginning in G1-phase, suggesting that NPC assembly occurs continuously throughout the cell cycle. However, the accumulation of nuclear envelope observed during the cell cycle, indicated by nuclear surface area, is not continuous at the same rate, such that the density of NPCs per unit area of nuclear envelope peaks in apparent S-phase cells. Analysis of the nuclear envelope reconstructions also revealed no preferred NPC-to-NPC distance. However, NPCs were found in large clusters over regions of the nuclear envelope. Interestingly, clusters of NPCs were most pronounced in early mitotic nuclei and were found to be associated with the spindle pole bodies, but the functional significance of this association is unknown.

Oxidation states of the manganese cluster during the flash-induced S-state cycle of the photosynthetic oxygen-evolving complex.

The Mn K-edge x-ray absorption spectra for the pure S states of the tetranuclear Mn cluster of the oxygen-evolving complex of photosystem II during flash-induced S-state cycling have been determined. The relative S-state populations in samples given 0, 1, 2, 3, 4, or 5 flashes were determined from fitting the flash-induced electron paramagnetic resonance (EPR) multiline signal oscillation pattern to the Kok model. The edge spectra of samples given 0, 1, 2, or 3 flashes were combined with EPR information to calculate the pure S-state edge spectra. The edge positions (defined as the zero-crossing of the second derivatives) are 6550.1, 6551.7, 6553.5, and 6553.8 eV for S0, S1, S2, and S3, respectively. In addition to the shift in edge position, the S0--> S1 and S1--> S2 transitions are accompanied by characteristic changes in the shape of the edge, both indicative of Mn oxidation. The edge position shifts very little (0.3 eV) for the S2--> S3 transition, and the edge shape shows only subtle changes. We conclude that probably no direct Mn oxidation is involved in this transition. The proposed Mn oxidation state assignments are as follows: S0 (II, III, IV, IV) or (III, III, III, IV), S1 (III, III, IV, IV), S2 (III, IV, IV, IV), S3 (III, IV, IV, IV).

Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.

Non-rigid object tracking in complex scenes

A recently proposed colour based tracking algorithm has been established to track objects in real circumstances [Zivkovic, Z., Krose, B. 2004. An EM-like algorithm for color-histogram-based object tracking. In: Proc, IEEE Conf. on Computer Vision and Pattern Recognition, pp. 798-803]. To improve the performance of this technique in complex scenes, in this paper we propose a new algorithm for optimally adapting the ellipse outlining the objects of interest. This paper presents a Lagrangian based method to integrate a regularising component into the covariance matrix to be computed. Technically, we intend to reduce the residuals between the estimated probability distribution and the expected one. We argue that, by doing this, the shape of the ellipse can be properly adapted in the tracking stage. Experimental results show that the proposed method has favourable performance in shape adaption and object localisation.

Contrast sensitivity for complex and random gratings

This thesis studied the effect of (i) the number of grating components and (ii) parameter randomisation on root-mean-square (r.m.s.) contrast sensitivity and spatial integration. The effectiveness of spatial integration without external spatial noise depended on the number of equally spaced orientation components in the sum of gratings. The critical area marking the saturation of spatial integration was found to decrease when the number of components increased from 1 to 5-6 but increased again at 8-16 components. The critical area behaved similarly as a function of the number of grating components when stimuli consisted of 3, 6 or 16 components with different orientations and/or phases embedded in spatial noise. Spatial integration seemed to depend on the global Fourier structure of the stimulus. Spatial integration was similar for sums of two vertical cosine or sine gratings with various Michelson contrasts in noise. The critical area for a grating sum was found to be a sum of logarithmic critical areas for the component gratings weighted by their relative Michelson contrasts. The human visual system was modelled as a simple image processor where the visual stimuli is first low-pass filtered by the optical modulation transfer function of the human eye and secondly high-pass filtered, up to the spatial cut-off frequency determined by the lowest neural sampling density, by the neural modulation transfer function of the visual pathways. The internal noise is then added before signal interpretation occurs in the brain. The detection is mediated by a local spatially windowed matched filter. The model was extended to include complex stimuli and its applicability to the data was found to be successful. The shape of spatial integration function was similar for non-randomised and randomised simple and complex gratings. However, orientation and/or phase randomised reduced r.m.s contrast sensitivity by a factor of 2. The effect of parameter randomisation on spatial integration was modelled under the assumption that human observers change the observer strategy from cross-correlation (i.e., a matched filter) to auto-correlation detection when uncertainty is introduced to the task. The model described the data accurately.

Numerical modelling of complex femtosecond laser inscribed fiber gratings - comparison wih experiment

We present experimental studies and numerical modeling based on a combination of the Bidirectional Beam Propagation Method and Finite Element Modeling that completely describes the wavelength spectra of point by point femtosecond laser inscribed fiber Bragg gratings, showing excellent agreement with experiment. We have investigated the dependence of different spectral parameters such as insertion loss, all dominant cladding and ghost modes and their shape relative to the position of the fiber Bragg grating in the core of the fiber. Our model is validated by comparing model predictions with experimental data and allows for predictive modeling of the gratings. We expand our analysis to more complicated structures, where we introduce symmetry breaking; this highlights the importance of centered gratings and how maintaining symmetry contributes to the overall spectral quality of the inscribed Bragg gratings. Finally, the numerical modeling is applied to superstructure gratings and a comparison with experimental results reveals a capability for dealing with complex grating structures that can be designed with particular wavelength characteristics.

Numerical modelling of complex femtosecond laser inscribed fiber gratings - comparison wih experiment

We present experimental studies and numerical modeling based on a combination of the Bidirectional Beam Propagation Method and Finite Element Modeling that completely describes the wavelength spectra of point by point femtosecond laser inscribed fiber Bragg gratings, showing excellent agreement with experiment. We have investigated the dependence of different spectral parameters such as insertion loss, all dominant cladding and ghost modes and their shape relative to the position of the fiber Bragg grating in the core of the fiber. Our model is validated by comparing model predictions with experimental data and allows for predictive modeling of the gratings. We expand our analysis to more complicated structures, where we introduce symmetry breaking; this highlights the importance of centered gratings and how maintaining symmetry contributes to the overall spectral quality of the inscribed Bragg gratings. Finally, the numerical modeling is applied to superstructure gratings and a comparison with experimental results reveals a capability for dealing with complex grating structures that can be designed with particular wavelength characteristics.

The role of impurities in the shape, structure and physical properties of semiconducting oxide nanostructures grown by thermal evaporation

A thermal evaporation method developed in the research group enables to grow and design several morphologies of semiconducting oxide nanostructures, such as Ga_2O_3, GeO_2 or Sb_2O_3, among others, and some ternary oxide compounds (ZnGa_2O_4, Zn_2GeO_4). In order to tailor physical properties, a successful doping of these nanostructures is required. However, for nanostructured materials, doping may affect not only their physical properties, but also their morphology during the thermal growth process. In this paper, we will show some examples of how the addition of impurities may result into the formation of complex structures, or changes in the structural phase of the material. In particular, we will consider the addition of Sn and Cr impurities into the precursors used to grow Ga_2O_3, Zn_2GeO_4 and Sb_2O_3 nanowires, nanorods or complex nanostructures, such as crossing wires or hierarchical structures. Structural and optical properties were assessed by electron microscopy (SEM and TEM), confocal microscopy, spatially resolved cathodoluminescence (CL), photoluminescence, and Raman spectroscopies. The growth mechanisms, the luminescence bands and the optical confinement in the obtained oxide nanostructures will be discussed. In particular, some of these nanostructures have been found to be of interest as optical microcavities. These nanomaterials may have applications in optical sensing and energy devices.

The Roles of Phenotypic Plasticity and Plant-Microbe Interactions in the Evolution of Complex Traits in Boechera stricta

All organisms live in complex habitats that shape the course of their evolution by altering the phenotype expressed by a given genotype (a phenomenon known as phenotypic plasticity) and simultaneously by determining the evolutionary fitness of that phenotype. In some cases, phenotypic evolution may alter the environment experienced by future generations. This dissertation describes how genetic and environmental variation act synergistically to affect the evolution of glucosinolate defensive chemistry and flowering time in Boechera stricta, a wild perennial herb. I focus particularly on plant-associated microbes as a part of the plant’s environment that may alter trait evolution and in turn be affected by the evolution of those traits. In the first chapter I measure glucosinolate production and reproductive fitness of over 1,500 plants grown in common gardens in four diverse natural habitats, to describe how patterns of plasticity and natural selection intersect and may influence glucosinolate evolution. I detected extensive genetic variation for glucosinolate plasticity and determined that plasticity may aid colonization of new habitats by moving phenotypes in the same direction as natural selection. In the second chapter I conduct a greenhouse experiment to test whether naturally-occurring soil microbial communities contributed to the differences in phenotype and selection that I observed in the field experiment. I found that soil microbes cause plasticity of flowering time but not glucosinolate production, and that they may contribute to natural selection on both traits; thus, non-pathogenic plant-associated microbes are an environmental feature that could shape plant evolution. In the third chapter, I combine a multi-year, multi-habitat field experiment with high-throughput amplicon sequencing to determine whether B. stricta-associated microbial communities are shaped by plant genetic variation. I found that plant genotype predicts the diversity and composition of leaf-dwelling bacterial communities, but not root-associated bacterial communities. Furthermore, patterns of host genetic control over associated bacteria were largely site-dependent, indicating an important role for genotype-by-environment interactions in microbiome assembly. Together, my results suggest that soil microbes influence the evolution of plant functional traits and, because they are sensitive to plant genetic variation, this trait evolution may alter the microbial neighborhood of future B. stricta generations. Complex patterns of plasticity, selection, and symbiosis in natural habitats may impact the evolution of glucosinolate profiles in Boechera stricta.

Shape and chemically anisotropic colloidal particles: A theoretical study of their structure, phase behavior, and slow dynamics

A detailed non-equilibrium state diagram of shape-anisotropic particle fluids is constructed. The effects of particle shape are explored using Naive Mode Coupling Theory (NMCT), and a single particle Non-linear Langevin Equation (NLE) theory. The dynamical behavior of non-ergodic fluids are discussed. We employ a rotationally frozen approach to NMCT in order to determine a transition to center of mass (translational) localization. Both ideal and kinetic glass transitions are found to be highly shape dependent, and uniformly increase with particle dimensionality. The glass transition volume fraction of quasi 1- and 2- dimensional particles fall monotonically with the number of sites (aspect ratio), while 3-dimensional particles display a non-monotonic dependence of glassy vitrification on the number of sites. Introducing interparticle attractions results in a far more complex state diagram. The ideal non-ergodic boundary shows a glass-fluid-gel re-entrance previously predicted for spherical particle fluids. The non-ergodic region of the state diagram presents qualitatively different dynamics in different regimes. They are qualified by the different behaviors of the NLE dynamic free energy. The caging dominated, repulsive glass regime is characterized by long localization lengths and barrier locations, dictated by repulsive hard core interactions, while the bonding dominated gel region has short localization lengths (commensurate with the attraction range), and barrier locations. There exists a small region of the state diagram which is qualified by both glassy and gel localization lengths in the dynamic free energy. A much larger (high volume fraction, and high attraction strength) region of phase space is characterized by short gel-like localization lengths, and long barrier locations. The region is called the attractive glass and represents a 2-step relaxation process whereby a particle first breaks attractive physical bonds, and then escapes its topological cage. The dynamic fragility of fluids are highly particle shape dependent. It increases with particle dimensionality and falls with aspect ratio for quasi 1- and 2- dimentional particles. An ultralocal limit analysis of the NLE theory predicts universalities in the behavior of relaxation times, and elastic moduli. The equlibrium phase diagram of chemically anisotropic Janus spheres and Janus rods are calculated employing a mean field Random Phase Approximation. The calculations for Janus rods are corroborated by the full liquid state Reference Interaction Site Model theory. The Janus particles consist of attractive and repulsive regions. Both rods and spheres display rich phase behavior. The phase diagrams of these systems display fluid, macrophase separated, attraction driven microphase separated, repulsion driven microphase separated and crystalline regimes. Macrophase separation is predicted in highly attractive low volume fraction systems. Attraction driven microphase separation is charaterized by long length scale divergences, where the ordering length scale determines the microphase ordered structures. The ordering length scale of repulsion driven microphase separation is determined by the repulsive range. At the high volume fractions, particles forgo the enthalpic considerations of attractions and repulsions to satisfy hard core constraints and maximize vibrational entropy. This results in site length scale ordering in rods, and the sphere length scale ordering in Janus spheres, i.e., crystallization. A change in the Janus balance of both rods and spheres results in quantitative changes in spinodal temperatures and the position of phase boundaries. However, a change in the block sequence of Janus rods causes qualitative changes in the type of microphase ordered state, and induces prominent features (such as the Lifshitz point) in the phase diagrams of these systems. A detailed study of the number of nearest neighbors in Janus rod systems reflect a deep connection between this local measure of structure, and the structure factor which represents the most global measure of order.