Optimisation of algorithms to compute information theoretic indexes

Analysis of big amount of data is a field with many years of research. It is centred in getting significant values, to make it easier to understand and interpret data. Being the analysis of interdependence between time series an important field of research, mainly as a result of advances in the characterization of dynamical systems from the signals they produce. In the medicine sphere, it is easy to find many researches that try to understand the brain behaviour, its operation mode and its internal connections. The human brain comprises approximately 1011 neurons, each of which makes about 103 synaptic connections. This huge number of connections between individual processing elements provides the fundamental substrate for neuronal ensembles to become transiently synchronized or functionally connected. A similar complex network configuration and dynamics can also be found at the macroscopic scales of systems neuroscience and brain imaging. The emergence of dynamically coupled cell assemblies represents the neurophysiological substrate for cognitive function such as perception, learning, thinking. Understanding the complex network organization of the brain on the basis of neuroimaging data represents one of the most impervious challenges for systems neuroscience. Brain connectivity is an elusive concept that refers to diferent interrelated aspects of brain organization: structural, functional connectivity (FC) and efective connectivity (EC). Structural connectivity refers to a network of physical connections linking sets of neurons, it is the anatomical structur of brain networks. However, FC refers to the statistical dependence between the signals stemming from two distinct units within a nervous system, while EC refers to the causal interactions between them. This research opens the door to try to resolve diseases related with the brain, like Parkinson’s disease, senile dementia, mild cognitive impairment, etc. One of the most important project associated with Alzheimer’s research and other diseases are enclosed in the European project called Blue Brain. The center for Biomedical Technology (CTB) of Universidad Politecnica de Madrid (UPM) forms part of the project. The CTB researches have developed a magnetoencephalography (MEG) data processing tool that allow to visualise and analyse data in an intuitive way. This tool receives the name of HERMES, and it is presented in this document. Analysis of big amount of data is a field with many years of research. It is centred in getting significant values, to make it easier to understand and interpret data. Being the analysis of interdependence between time series an important field of research, mainly as a result of advances in the characterization of dynamical systems from the signals they produce. In the medicine sphere, it is easy to find many researches that try to understand the brain behaviour, its operation mode and its internal connections. The human brain comprises approximately 1011 neurons, each of which makes about 103 synaptic connections. This huge number of connections between individual processing elements provides the fundamental substrate for neuronal ensembles to become transiently synchronized or functionally connected. A similar complex network configuration and dynamics can also be found at the macroscopic scales of systems neuroscience and brain imaging. The emergence of dynamically coupled cell assemblies represents the neurophysiological substrate for cognitive function such as perception, learning, thinking. Understanding the complex network organization of the brain on the basis of neuroimaging data represents one of the most impervious challenges for systems neuroscience. Brain connectivity is an elusive concept that refers to diferent interrelated aspects of brain organization: structural, functional connectivity (FC) and efective connectivity (EC). Structural connectivity refers to a network of physical connections linking sets of neurons, it is the anatomical structur of brain networks. However, FC refers to the statistical dependence between the signals stemming from two distinct units within a nervous system, while EC refers to the causal interactions between them. This research opens the door to try to resolve diseases related with the brain, like Parkinson’s disease, senile dementia, mild cognitive impairment, etc. One of the most important project associated with Alzheimer’s research and other diseases are enclosed in the European project called Blue Brain. The center for Biomedical Technology (CTB) of Universidad Politecnica de Madrid (UPM) forms part of the project. The CTB researches have developed a magnetoencephalography (MEG) data processing tool that allow to visualise and analyse data in an intuitive way. This tool receives the name of HERMES, and it is presented in this document.

Functional and effective connectivity in MEG. Application to the study of epilepsy

Nuestro cerebro contiene cerca de 1014 sinapsis neuronales. Esta enorme cantidad de conexiones proporciona un entorno ideal donde distintos grupos de neuronas se sincronizan transitoriamente para provocar la aparición de funciones cognitivas, como la percepción, el aprendizaje o el pensamiento. Comprender la organización de esta compleja red cerebral en base a datos neurofisiológicos, representa uno de los desafíos más importantes y emocionantes en el campo de la neurociencia. Se han propuesto recientemente varias medidas para evaluar cómo se comunican las diferentes partes del cerebro a diversas escalas (células individuales, columnas corticales, o áreas cerebrales). Podemos clasificarlos, según su simetría, en dos grupos: por una parte, la medidas simétricas, como la correlación, la coherencia o la sincronización de fase, que evalúan la conectividad funcional (FC); mientras que las medidas asimétricas, como la causalidad de Granger o transferencia de entropía, son capaces de detectar la dirección de la interacción, lo que denominamos conectividad efectiva (EC). En la neurociencia moderna ha aumentado el interés por el estudio de las redes funcionales cerebrales, en gran medida debido a la aparición de estos nuevos algoritmos que permiten analizar la interdependencia entre señales temporales, además de la emergente teoría de redes complejas y la introducción de técnicas novedosas, como la magnetoencefalografía (MEG), para registrar datos neurofisiológicos con gran resolución. Sin embargo, nos hallamos ante un campo novedoso que presenta aun varias cuestiones metodológicas sin resolver, algunas de las cuales trataran de abordarse en esta tesis. En primer lugar, el creciente número de aproximaciones para determinar la existencia de FC/EC entre dos o más señales temporales, junto con la complejidad matemática de las herramientas de análisis, hacen deseable organizarlas todas en un paquete software intuitivo y fácil de usar. Aquí presento HERMES (http://hermes.ctb.upm.es), una toolbox en MatlabR, diseñada precisamente con este fin. Creo que esta herramienta será de gran ayuda para todos aquellos investigadores que trabajen en el campo emergente del análisis de conectividad cerebral y supondrá un gran valor para la comunidad científica. La segunda cuestión practica que se aborda es el estudio de la sensibilidad a las fuentes cerebrales profundas a través de dos tipos de sensores MEG: gradiómetros planares y magnetómetros, esta aproximación además se combina con un enfoque metodológico, utilizando dos índices de sincronización de fase: phase locking value (PLV) y phase lag index (PLI), este ultimo menos sensible a efecto la conducción volumen. Por lo tanto, se compara su comportamiento al estudiar las redes cerebrales, obteniendo que magnetómetros y PLV presentan, respectivamente, redes más densamente conectadas que gradiómetros planares y PLI, por los valores artificiales que crea el problema de la conducción de volumen. Sin embargo, cuando se trata de caracterizar redes epilépticas, el PLV ofrece mejores resultados, debido a la gran dispersión de las redes obtenidas con PLI. El análisis de redes complejas ha proporcionado nuevos conceptos que mejoran caracterización de la interacción de sistemas dinámicos. Se considera que una red está compuesta por nodos, que simbolizan sistemas, cuyas interacciones se representan por enlaces, y su comportamiento y topología puede caracterizarse por un elevado número de medidas. Existe evidencia teórica y empírica de que muchas de ellas están fuertemente correlacionadas entre sí. Por lo tanto, se ha conseguido seleccionar un pequeño grupo que caracteriza eficazmente estas redes, y condensa la información redundante. Para el análisis de redes funcionales, la selección de un umbral adecuado para decidir si un determinado valor de conectividad de la matriz de FC es significativo y debe ser incluido para un análisis posterior, se convierte en un paso crucial. En esta tesis, se han obtenido resultados más precisos al utilizar un test de subrogadas, basado en los datos, para evaluar individualmente cada uno de los enlaces, que al establecer a priori un umbral fijo para la densidad de conexiones. Finalmente, todas estas cuestiones se han aplicado al estudio de la epilepsia, caso práctico en el que se analizan las redes funcionales MEG, en estado de reposo, de dos grupos de pacientes epilépticos (generalizada idiopática y focal frontal) en comparación con sujetos control sanos. La epilepsia es uno de los trastornos neurológicos más comunes, con más de 55 millones de afectados en el mundo. Esta enfermedad se caracteriza por la predisposición a generar ataques epilépticos de actividad neuronal anormal y excesiva o bien síncrona, y por tanto, es el escenario perfecto para este tipo de análisis al tiempo que presenta un gran interés tanto desde el punto de vista clínico como de investigación. Los resultados manifiestan alteraciones especificas en la conectividad y un cambio en la topología de las redes en cerebros epilépticos, desplazando la importancia del ‘foco’ a la ‘red’, enfoque que va adquiriendo relevancia en las investigaciones recientes sobre epilepsia. ABSTRACT There are about 1014 neuronal synapses in the human brain. This huge number of connections provides the substrate for neuronal ensembles to become transiently synchronized, producing the emergence of cognitive functions such as perception, learning or thinking. Understanding the complex brain network organization on the basis of neuroimaging data represents one of the most important and exciting challenges for systems neuroscience. Several measures have been recently proposed to evaluate at various scales (single cells, cortical columns, or brain areas) how the different parts of the brain communicate. We can classify them, according to their symmetry, into two groups: symmetric measures, such as correlation, coherence or phase synchronization indexes, evaluate functional connectivity (FC); and on the other hand, the asymmetric ones, such as Granger causality or transfer entropy, are able to detect effective connectivity (EC) revealing the direction of the interaction. In modern neurosciences, the interest in functional brain networks has increased strongly with the onset of new algorithms to study interdependence between time series, the advent of modern complex network theory and the introduction of powerful techniques to record neurophysiological data, such as magnetoencephalography (MEG). However, when analyzing neurophysiological data with this approach several questions arise. In this thesis, I intend to tackle some of the practical open problems in the field. First of all, the increase in the number of time series analysis algorithms to study brain FC/EC, along with their mathematical complexity, creates the necessity of arranging them into a single, unified toolbox that allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of them. I developed such a toolbox for this aim, it is named HERMES (http://hermes.ctb.upm.es), and encompasses several of the most common indexes for the assessment of FC and EC running for MatlabR environment. I believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis and will entail a great value for the scientific community. The second important practical issue tackled in this thesis is the evaluation of the sensitivity to deep brain sources of two different MEG sensors: planar gradiometers and magnetometers, in combination with the related methodological approach, using two phase synchronization indexes: phase locking value (PLV) y phase lag index (PLI), the latter one being less sensitive to volume conduction effect. Thus, I compared their performance when studying brain networks, obtaining that magnetometer sensors and PLV presented higher artificial values as compared with planar gradiometers and PLI respectively. However, when it came to characterize epileptic networks it was the PLV which gives better results, as PLI FC networks where very sparse. Complex network analysis has provided new concepts which improved characterization of interacting dynamical systems. With this background, networks could be considered composed of nodes, symbolizing systems, whose interactions with each other are represented by edges. A growing number of network measures is been applied in network analysis. However, there is theoretical and empirical evidence that many of these indexes are strongly correlated with each other. Therefore, in this thesis I reduced them to a small set, which could more efficiently characterize networks. Within this framework, selecting an appropriate threshold to decide whether a certain connectivity value of the FC matrix is significant and should be included in the network analysis becomes a crucial step, in this thesis, I used the surrogate data tests to make an individual data-driven evaluation of each of the edges significance and confirmed more accurate results than when just setting to a fixed value the density of connections. All these methodologies were applied to the study of epilepsy, analysing resting state MEG functional networks, in two groups of epileptic patients (generalized and focal epilepsy) that were compared to matching control subjects. Epilepsy is one of the most common neurological disorders, with more than 55 million people affected worldwide, characterized by its predisposition to generate epileptic seizures of abnormal excessive or synchronous neuronal activity, and thus, this scenario and analysis, present a great interest from both the clinical and the research perspective. Results revealed specific disruptions in connectivity and network topology and evidenced that networks’ topology is changed in epileptic brains, supporting the shift from ‘focus’ to ‘networks’ which is gaining importance in modern epilepsy research.

Photovoltaic LiNbO3particles: Applications to Biomedicine/Biophotonics

Recently, a novel method to trap and pattern ensembles of nanoparticles has been proposed and tested. It relies on the photovoltaic (PV) properties of certain ferroelectric crystals such as LiNbO3 [1,2]. These crystals, when suitably doped, develop very high electric fields in response to illumination with light of suitable wavelength. The PV effect lies in the asymmetrical excitation of electrons giving rise to PV currents and associated space-charge fields (photorefractive effect). The field generated in the bulk of the sample propagates to the surrounding medium as evanescent fields. When dielectric or metal nanoparticles are deposited on the surface of the sample the evanescent fields give rise to either electrophoretic or dielectrophoretic forces, depending on the charge state of the particles, that induce the trapping and patterning effects [3,4]. The purpose of this work has been to explore the effects of such PV fields in the biology and biomedical areas. A first work was able to show the necrotic effects induced by such fields on He-La tumour cells grown on the surface of an illuminated iron-doped LiNbO3 crystal [5]. In principle, it is conceived that LiNbO3 nanoparticles may be advantageously used for such biomedical purposes considering the possibility of such nanoparticles being incorporated into the cells. Previous experiments using microparticles have been performed [5] with similar results to those achieved with the substrate. Therefore, the purpose of this work has been to fabricate and characterize the LiNbO3 nanoparticles and assess their necrotic effects when they are incorporated on a culture of tumour cells. Two different preparation methods have been used: 1) mechanical grinding from crystals, and 2) bottom-up sol-gel chemical synthesis from metal-ethoxide precursors. This later method leads to a more uniform size distribution of smaller particles (down to around 50 nm). Fig. 1(a) and 1(b) shows SEM images of the nanoparticles obtained with both method. An ad hoc software taking into account the physical properties of the crystal, particullarly donor and aceptor concentrations has been developped in order to estimate the electric field generated in noparticles. In a first stage simulations of the electric current of nanoparticles, in a conductive media, due to the PV effect have been carried out by MonteCarlo simulations using the Kutharev 1-centre transport model equations [6] . Special attention has been paid to the dependence on particle size and [Fe2+]/[Fe3+]. First results on cubic particles shows large dispersion for small sizes due to the random number of donors and its effective concentration (Fig 2). The necrotic (toxicity) effect of nanoparticles incorporated into a tumour cell culture subjected to 30 min. illumination with a blue LED is shown in Fig.3. For each type of nanoparticle the percent of cell survival in dark and illumination conditions has been plot as a function of the particle dilution factor. Fig. 1a corresponds to mechanical grinding particles whereas 1b and 1c refer to chemically synthesized particles with two oxidation states. The light effect is larger with mechanical grinding nanoparticles, but dark toxicity is also higher. For chemically synthesized nanoparticles dark toxicity is low but only in oxidized samples, where the PV effect is known to be larger, the light effect is appreciable. These preliminary results demonstrate that Fe:LiNbO· nanoparticles have a biological damaging effect on cells, although there are many points that should be clarified and much space for PV nanoparticles optimization. In particular, it appears necessary to determine the fraction of nanoparticles that become incorporated into the cells and the possible existence of threshold size effects. This work has been supported by MINECO under grant MAT2011-28379-C03.

Representing microstates of static granular matter in a stress phase space

A stress phase space is proposed to compare the static packings of a granular system (microstates) that are compatible to a macrostate described by external stresses. The equivalent stress of each particle of a static packing can be obtained from the mechanical interaction forces, and the associated volume is given by the respective Voronoi cell. Therefore, particles can be located at different stress levels and grouped into categories or configurations, which are defined in base of the geometrical features of the local arrangement (in particular, of the number of forces that keep them force-balanced). They can be represented as points in a stress phase space. The nature of this space is analyzed in detail. The integration limits of the stress variables that avoid or limit tensile states and the capability of each configuration to represent specific stress states establish its main features. Furthermore, if some stress variables are used, instead of the usual components of the Cauchy stress tensor, then some symmetries can be found. Results obtained from molecular dynamics simulations are used to check this nature. Finally, some statistical ensembles are written in terms of the coordinates of this phase space. These require some assumptions that are made in base on continuum mechanics principles.

Time-multiscale methods for the simulation of slow transport problems in atomistic systems

En esta tesis presentamos una teoría adaptada a la simulación de fenómenos lentos de transporte en sistemas atomísticos. En primer lugar, desarrollamos el marco teórico para modelizar colectividades estadísticas de equilibrio. A continuación, lo adaptamos para construir modelos de colectividades estadísticas fuera de equilibrio. Esta teoría reposa sobre los principios de la mecánica estadística, en particular el principio de máxima entropía de Jaynes, utilizado tanto para sistemas en equilibrio como fuera de equilibrio, y la teoría de las aproximaciones del campo medio. Expresamos matemáticamente el problema como un principio variacional en el que maximizamos una entropía libre, en lugar de una energía libre. La formulación propuesta permite definir equivalentes atomísticos de variables macroscópicas como la temperatura y la fracción molar. De esta forma podemos considerar campos macroscópicos no uniformes. Completamos el marco teórico con reglas de cuadratura de Monte Carlo, gracias a las cuales obtenemos modelos computables. A continuación, desarrollamos el conjunto completo de ecuaciones que gobiernan procesos de transporte. Deducimos la desigualdad de disipación entrópica a partir de fuerzas y flujos termodinámicos discretos. Esta desigualdad nos permite identificar la estructura que deben cumplir los potenciales cinéticos discretos. Dichos potenciales acoplan las tasas de variación en el tiempo de las variables microscópicas con las fuerzas correspondientes. Estos potenciales cinéticos deben ser completados con una relación fenomenológica, del tipo definido por la teoría de Onsanger. Por último, aportamos validaciones numéricas. Con ellas ilustramos la capacidad de la teoría presentada para simular propiedades de equilibrio y segregación superficial en aleaciones metálicas. Primero, simulamos propiedades termodinámicas de equilibrio en el sistema atomístico. A continuación evaluamos la habilidad del modelo para reproducir procesos de transporte en sistemas complejos que duran tiempos largos con respecto a los tiempos característicos a escala atómica. ABSTRACT In this work, we formulate a theory to address simulations of slow time transport effects in atomic systems. We first develop this theoretical framework in the context of equilibrium of atomic ensembles, based on statistical mechanics. We then adapt it to model ensembles away from equilibrium. The theory stands on Jaynes' maximum entropy principle, valid for the treatment of both, systems in equilibrium and away from equilibrium and on meanfield approximation theory. It is expressed in the entropy formulation as a variational principle. We interpret atomistic equivalents of macroscopic variables such as the temperature and the molar fractions, wich are not required to be uniform, but can vary from particle to particle. We complement this theory with Monte Carlo summation rules for further approximation. In addition, we provide a framework for studying transport processes with the full set of equations driving the evolution of the system. We first derive a dissipation inequality for the entropic production involving discrete thermodynamic forces and fluxes. This discrete dissipation inequality identifies the adequate structure for discrete kinetic potentials which couple the microscopic field rates to the corresponding driving forces. Those kinetic potentials must finally be expressed as a phenomenological rule of the Onsanger Type. We present several validation cases, illustrating equilibrium properties and surface segregation of metallic alloys. We first assess the ability of a simple meanfield model to reproduce thermodynamic equilibrium properties in systems with atomic resolution. Then, we evaluate the ability of the model to reproduce a long-term transport process in complex systems.

Self assembled and ordered group III nitride nanocolumnar structures for light emitting applications

El objetivo de este trabajo es un estudio profundo del crecimiento selectivo de nanoestructuras de InGaN por epitaxia de haces moleculares asistido por plasma, concentrandose en el potencial de estas estructuras como bloques constituyentes en LEDs de nueva generación. Varias aproximaciones al problema son discutidas; desde estructuras axiales InGaN/GaN, a estructuras core-shell, o nanoestructuras crecidas en sustratos con orientaciones menos convencionales (semi polar y no polar). La primera sección revisa los aspectos básicos del crecimiento auto-ensamblado de nanocolumnas de GaN en sustratos de Si(111). Su morfología y propiedades ópticas son comparadas con las de capas compactas de GaN sobre Si(111). En el caso de las columnas auto-ensambladas de InGaN sobre Si(111), se presentan resultados sobre el efecto de la temperatura de crecimiento en la incorporación de In. Por último, se discute la inclusión de nanodiscos de InGaN en las nanocolumnas de GaN. La segunda sección revisa los mecanismos básicos del crecimiento ordenado de nanoestructuras basadas en GaN, sobre templates de GaN/zafiro. Aumentando la relación III/V localmente, se observan cambios morfológicos; desde islas piramidales, a nanocolumnas de GaN terminadas en planos semipolares, y finalmente, a nanocolumnas finalizadas en planos c polares. Al crecer nanodiscos de InGaN insertados en las nanocolumnas de GaN, las diferentes morfologias mencionadas dan lugar a diferentes propiedades ópticas de los nanodiscos, debido al diferente carácter (semi polar o polar) de los planos cristalinos involucrados. La tercera sección recoge experimentos acerca de los efectos que la temperatura de crecimiento y la razón In/Ga tienen en la morfología y emisión de nanocolumnas ordenadas de InGaN crecidas sobre templates GaN/zafiro. En el rango de temperaturas entre 650 y 750 C, la incorporacion de In puede modificarse bien por la temperatura de crecimiento, o por la razón In/Ga. Controlar estos factores permite la optimización de la longitud de onda de emisión de las nanocolumnas de InGaN. En el caso particular de la generación de luz blanca, se han seguidos dos aproximaciones. En la primera, se obtiene emisión amarilla-blanca a temperatura ambiente de nanoestructuras donde la región de InGaN consiste en un gradiente de composiciones de In, que se ha obtenido a partir de un gradiente de temperatura durante el crecimiento. En la segunda, el apilamiento de segmentos emitiendo en azul, verde y rojo, consiguiendo la integración monolítica de estas estructuras en cada una de las nanocolumnas individuales, da lugar a emisores ordenados con un amplio espectro de emisión. En esta última aproximación, la forma espectral puede controlarse con la longitud (duración del crecimiento) de cada uno de los segmentos de InGaN. Más adelante, se presenta el crecimiento ordenado, por epitaxia de haces moleculares, de arrays de nanocolumnas que son diodos InGaN/GaN cada una de ellas, emitiendo en azul (441 nm), verde (502 nm) y amarillo (568 nm). La zona activa del dispositivo consiste en una sección de InGaN, de composición constante nominalmente y longitud entre 250 y 500 nm, y libre de defectos extendidos en contraste con capas compactas de InGaN de similares composiciones y espesores. Los espectros de electroluminiscencia muestran un muy pequeño desplazamiento al azul al aumentar la corriente inyectada (desplazamiento casi inexistente en el caso del dispositivo amarillo), y emisiones ligeramente más anchas que en el caso del estado del arte en pozos cuánticos de InGaN. A continuación, se presenta y discute el crecimiento ordenado de nanocolumnas de In(Ga)N/GaN en sustratos de Si(111). Nanocolumnas ordenadas emitiendo desde el ultravioleta (3.2 eV) al infrarrojo (0.78 eV) se crecieron sobre sustratos de Si(111) utilizando una capa compacta (“buffer”) de GaN. La morfología y eficiencia de emisión de las nanocolumnas emitiendo en el rango espectral verde pueden ser mejoradas ajustando las relaciones In/Ga y III/N, y una eficiencia cuántica interna del 30% se deriva de las medidas de fotoluminiscencia en nanocolumnas optimizadas. En la siguiente sección de este trabajo se presenta en detalle el mecanismo tras el crecimiento ordenado de nanocolumnas de InGaN/GaN emitiendo en el verde, y sus propiedades ópticas. Nanocolumnas de InGaN/GaN con secciones largas de InGaN (330-830 nm) se crecieron tanto en sustratos GaN/zafiro como GaN/Si(111). Se encuentra que la morfología y la distribución espacial del In dentro de las nanocolumnas dependen de las relaciones III/N e In/Ga locales en el frente de crecimiento de las nanocolumnas. La dispersión en el contenido de In entre diferentes nanocolumnas dentro de la misma muestra es despreciable, como indica las casi identicas formas espectrales de la catodoluminiscencia de una sola nanocolumna y del conjunto de ellas. Para las nanocolumnas de InGaN/GaN crecidas sobre GaN/Si(111) y emitiendo en el rango espectral verde, la eficiencia cuántica interna aumenta hasta el 30% al disminuir la temperatura de crecimiento y aumentar el nitrógeno activo. Este comportamiento se debe probablemente a la formación de estados altamente localizados, como indica la particular evolución de la energía de fotoluminiscencia con la temperatura (ausencia de “s-shape”) en muestras con una alta eficiencia cuántica interna. Por otro lado, no se ha encontrado la misma dependencia entre condiciones de crecimiento y efiencia cuántica interna en las nanoestructuras InGaN/GaN crecidas en GaN/zafiro, donde la máxima eficiencia encontrada ha sido de 3.7%. Como alternativa a las nanoestructuras axiales de InGaN/GaN, la sección 4 presenta resultados sobre el crecimiento y caracterización de estructuras core-shell de InGaN/GaN, re-crecidas sobre arrays de micropilares de GaN fabricados por ataque de un template GaN/zafiro (aproximación top-down). El crecimiento de InGaN/GaN es conformal, con componentes axiales y radiales en el crecimiento, que dan lugar a la estructuras core-shell con claras facetas hexagonales. El crecimiento radial (shell) se ve confirmado por medidas de catodoluminiscencia con resolución espacial efectuadas en un microscopio electrónico de barrido, asi como por medidas de microscopía de transmisión de electrones. Más adelante, el crecimiento de micro-pilares core-shell de InGaN se realizó en pilares GaN (cores) crecidos selectivamente por epitaxia de metal-orgánicos en fase vapor. Con el crecimiento de InGaN se forman estructuras core-shell con emisión alrededor de 3 eV. Medidas de catodoluminiscencia resuelta espacialmente indican un aumento en el contenido de indio del shell en dirección a la parte superior del pilar, que se manifiesta en un desplazamiento de la emisión de 3.2 eV en la parte inferior, a 3.0 eV en la parte superior del shell. Este desplazamiento está relacionado con variaciones locales de la razón III/V en las facetas laterales. Finalmente, se demuestra la fabricación de una estructura pin basada en estos pilares core-shell. Medidas de electroluminiscencia resuelta espacialmente, realizadas en pilares individuales, confirman que la electroluminiscencia proveniente del shell de InGaN (diodo lateral) está alrededor de 3.0 eV, mientras que la emisión desde la parte superior del pilar (diodo axial) está alrededor de 2.3 eV. Para finalizar, se presentan resultados sobre el crecimiento ordenado de GaN, con y sin inserciones de InGaN, en templates semi polares (GaN(11-22)/zafiro) y no polares (GaN(11-20)/zafiro). Tras el crecimiento ordenado, gran parte de los defectos presentes en los templates originales se ven reducidos, manifestándose en una gran mejora de las propiedades ópticas. En el caso de crecimiento selectivo sobre templates con orientación GaN(11-22), no polar, la formación de nanoestructuras con una particular morfología (baja relación entre crecimiento perpedicular frente a paralelo al plano) permite, a partir de la coalescencia de estas nanoestructuras, la fabricación de pseudo-templates no polares de GaN de alta calidad. ABSTRACT The aim of this work is to gain insight into the selective area growth of InGaN nanostructures by plasma assisted molecular beam epitaxy, focusing on their potential as building blocks for next generation LEDs. Several nanocolumn-based approaches such as standard axial InGaN/GaN structures, InGaN/GaN core-shell structures, or InGaN/GaN nanostructures grown on semi- and non-polar substrates are discussed. The first section reviews the basics of the self-assembled growth of GaN nanocolumns on Si(111). Morphology differences and optical properties are compared to those of GaN layer grown directly on Si(111). The effects of the growth temperature on the In incorporation in self-assembled InGaN nanocolumns grown on Si(111) is described. The second section reviews the basic growth mechanisms of selectively grown GaNbased nanostructures on c-plane GaN/sapphire templates. By increasing the local III/V ratio morphological changes from pyramidal islands, to GaN nanocolumns with top semi-polar planes, and further to GaN nanocolumns with top polar c-planes are observed. When growing InGaN nano-disks embedded into the GaN nanocolumns, the different morphologies mentioned lead to different optical properties, due to the semipolar and polar nature of the crystal planes involved. The third section reports on the effect of the growth temperature and In/Ga ratio on the morphology and light emission characteristics of ordered InGaN nanocolumns grown on c-plane GaN/sapphire templates. Within the growth temperature range of 650 to 750oC the In incorporation can be modified either by the growth temperature, or the In/Ga ratio. Control of these factors allows the optimization of the InGaN nanocolumns light emission wavelength. In order to achieve white light emission two approaches are used. First yellow-white light emission can be obtained at room temperature from nanostructures where the InGaN region is composition-graded by using temperature gradients during growth. In a second approach the stacking of red, green and blue emitting segments was used to achieve the monolithic integration of these structures in one single InGaN nanocolumn leading to ordered broad spectrum emitters. With this approach, the spectral shape can be controlled by changing the thickness of the respective InGaN segments. Furthermore the growth of ordered arrays of InGaN/GaN nanocolumnar light emitting diodes by molecular beam epitaxy, emitting in the blue (441 nm), green (502 nm), and yellow (568 nm) spectral range is reported. The device active region, consisting of a nanocolumnar InGaN section of nominally constant composition and 250 to 500 nm length, is free of extended defects, which is in strong contrast to InGaN layers (planar) of similar composition and thickness. Electroluminescence spectra show a very small blue shift with increasing current, (almost negligible in the yellow device) and line widths slightly broader than those of state-of-the-art InGaN quantum wells. Next the selective area growth of In(Ga)N/GaN nanocolumns on Si(111) substrates is discussed. Ordered In(Ga)N/GaN nanocolumns emitting from ultraviolet (3.2 eV) to infrared (0.78 eV) were then grown on top of GaN-buffered Si substrates. The morphology and the emission efficiency of the In(Ga)N/GaN nanocolumns emitting in the green could be substantially improved by tuning the In/Ga and total III/N ratios, where an estimated internal quantum efficiency of 30 % was derived from photoluminescence data. In the next section, this work presents a study on the selective area growth mechanisms of green-emitting InGaN/GaN nanocolumns and their optical properties. InGaN/GaN nanocolumns with long InGaN sections (330-830nm) were grown on GaN/sapphire and GaN-buffered Si(111). The nanocolumn’s morphology and spatial indium distribution is found to depend on the local group (III)/N and In/Ga ratios at the nanocolumn’s top. A negligible spread of the average indium incorporation among different nanostructures is found as indicated by similar shapes of the cathodoluminescence spectra taken from single nanocolumns and ensembles of nanocolumns. For InGaN/GaN nanocolumns grown on GaN-buffered Si(111), all emitting in the green spectral range, the internal quantum efficiency increases up to 30% when decreasing growth temperature and increasing active nitrogen. This behavior is likely due to the formation of highly localized states, as indicated by the absence of a complete s-shape behavior of the PL peak position with temperature (up to room temperature) in samples with high internal quantum efficiency. On the other hand, no dependence of the internal quantum efficiency on the growth conditions is found for InGaN/GaN nanostructures grown on GaN/sapphire, where the maximum achieved efficiency is 3.7%. As alternative to axial InGaN/GaN nanostructures, section 4 reports on the growth and characterization of InGaN/GaN core-shell structures on an ordered array of top-down patterned GaN microrods etched from a GaN/sapphire template. Growth of InGaN/GaN is conformal, with axial and radial growth components leading to core-shell structures with clear hexagonal facets. The radial InGaN growth (shell) is confirmed by spatially resolved cathodoluminescence performed in a scanning electron microscopy as well as in scanning transmission electron microscopy. Furthermore the growth of InGaN core-shell micro pillars using an ordered array of GaN cores grown by metal organic vapor phase epitaxy as a template is demonstrated. Upon InGaN overgrowth core-shell structures with emission at around 3.0 eV are formed. With spatially resolved cathodoluminescence, an increasing In content towards the pillar top is found to be present in the InGaN shell, as indicated by a shift of CL peak position from 3.2 eV at the shell bottom to 3.0 eV at the shell top. This shift is related to variations of the local III/V ratio at the side facets. Further, the successful fabrication of a core-shell pin diode structure is demonstrated. Spatially resolved electroluminescence measurements performed on individual micro LEDs, confirm emission from the InGaN shell (lateral diode) at around 3.0 eV, as well as from the pillar top facet (axial diode) at around 2.3 eV. Finally, this work reports on the selective area growth of GaN, with and without InGaN insertion, on semi-polar (11-22) and non-polar (11-20) templates. Upon SAG the high defect density present in the GaN templates is strongly reduced as indicated by TEM and a dramatic improvement of the optical properties. In case of SAG on non-polar (11-22) templates the formation of nanostructures with a low aspect ratio took place allowing for the fabrication of high-quality, non-polar GaN pseudo-templates by coalescence of the nanostructures.

Multiscale modeling of the plastic behaviour in single crystal tungsten: from atomistic to crystal plasticity simulations

En una planta de fusión, los materiales en contacto con el plasma así como los materiales de primera pared experimentan condiciones particularmente hostiles al estar expuestos a altos flujos de partículas, neutrones y grandes cargas térmicas. Como consecuencia de estas diferentes y complejas condiciones de trabajo, el estudio, desarrollo y diseño de estos materiales es uno de los más importantes retos que ha surgido en los últimos años para la comunidad científica en el campo de los materiales y la energía. Debido a su baja tasa de erosión, alta resistencia al sputtering, alta conductividad térmica, muy alto punto de fusión y baja retención de tritio, el tungsteno (wolframio) es un importante candidato como material de primera pared y como posible material estructural avanzado en fusión por confinamiento magnético e inercial. Sin embargo, el tiempo de vida del tungsteno viene controlado por diversos factores como son su respuesta termo-mecánica en la superficie, la posibilidad de fusión y el fallo por acumulación de helio. Es por ello que el tiempo de vida limitado por la respuesta mecánica del tungsteno (W), y en particular su fragilidad, sean dos importantes aspectos que tienes que ser investigados. El comportamiento plástico en materiales refractarios con estructura cristalina cúbica centrada en las caras (bcc) como el tungsteno está gobernado por las dislocaciones de tipo tornillo a escala atómica y por conjuntos e interacciones de dislocaciones a escalas más grandes. El modelado de este complejo comportamiento requiere la aplicación de métodos capaces de resolver de forma rigurosa cada una de las escalas. El trabajo que se presenta en esta tesis propone un modelado multiescala que es capaz de dar respuestas ingenieriles a las solicitudes técnicas del tungsteno, y que a su vez está apoyado por la rigurosa física subyacente a extensas simulaciones atomísticas. En primer lugar, las propiedades estáticas y dinámicas de las dislocaciones de tipo tornillo en cinco potenciales interatómicos de tungsteno son comparadas, determinando cuáles de ellos garantizan una mayor fidelidad física y eficiencia computacional. Las grandes tasas de deformación asociadas a las técnicas de dinámica molecular hacen que las funciones de movilidad de las dislocaciones obtenidas no puedan ser utilizadas en los siguientes pasos del modelado multiescala. En este trabajo, proponemos dos métodos alternativos para obtener las funciones de movilidad de las dislocaciones: un modelo Monte Cario cinético y expresiones analíticas. El conjunto de parámetros necesarios para formular el modelo de Monte Cario cinético y la ley de movilidad analítica son calculados atomísticamente. Estos parámetros incluyen, pero no se limitan a: la determinación de las entalpias y energías de formación de las parejas de escalones que forman las dislocaciones, la parametrización de los efectos de no Schmid característicos en materiales bcc,etc. Conociendo la ley de movilidad de las dislocaciones en función del esfuerzo aplicado y la temperatura, se introduce esta relación como ecuación de flujo dentro de un modelo de plasticidad cristalina. La predicción del modelo sobre la dependencia del límite de fluencia con la temperatura es validada experimentalmente con ensayos uniaxiales en tungsteno monocristalino. A continuación, se calcula el límite de fluencia al aplicar ensayos uniaxiales de tensión para un conjunto de orientaciones cristalográticas dentro del triángulo estándar variando la tasa de deformación y la temperatura de los ensayos. Finalmente, y con el objetivo de ser capaces de predecir una respuesta más dúctil del tungsteno para una variedad de estados de carga, se realizan ensayos biaxiales de tensión sobre algunas de las orientaciones cristalográficas ya estudiadas en función de la temperatura.-------------------------------------------------------------------------ABSTRACT ----------------------------------------------------------Tungsten and tungsten alloys are being considered as leading candidates for structural and functional materials in future fusion energy devices. The most attractive properties of tungsten for the design of magnetic and inertial fusion energy reactors are its high melting point, high thermal conductivity, low sputtering yield and low longterm disposal radioactive footprint. However, tungsten also presents a very low fracture toughness, mostly associated with inter-granular failure and bulk plasticity, that limits its applications. As a result of these various and complex conditions of work, the study, development and design of these materials is one of the most important challenges that have emerged in recent years to the scientific community in the field of materials for energy applications. The plastic behavior of body-centered cubic (bcc) refractory metals like tungsten is governed by the kink-pair mediated thermally activated motion of h¿ (\1 11)i screw dislocations on the atomistic scale and by ensembles and interactions of dislocations at larger scales. Modeling this complex behavior requires the application of methods capable of resolving rigorously each relevant scale. The work presented in this thesis proposes a multiscale model approach that gives engineering-level responses to the technical specifications required for the use of tungsten in fusion energy reactors, and it is also supported by the rigorous underlying physics of extensive atomistic simulations. First, the static and dynamic properties of screw dislocations in five interatomic potentials for tungsten are compared, determining which of these ensure greater physical fidelity and computational efficiency. The large strain rates associated with molecular dynamics techniques make the dislocation mobility functions obtained not suitable to be used in the next steps of the multiscale model. Therefore, it is necessary to employ mobility laws obtained from a different method. In this work, we suggest two alternative methods to get the dislocation mobility functions: a kinetic Monte Carlo model and analytical expressions. The set of parameters needed to formulate the kinetic Monte Carlo model and the analytical mobility law are calculated atomistically. These parameters include, but are not limited to: enthalpy and energy barriers of kink-pairs as a function of the stress, width of the kink-pairs, non-Schmid effects ( both twinning-antitwinning asymmetry and non-glide stresses), etc. The function relating dislocation velocity with applied stress and temperature is used as the main source of constitutive information into a dislocation-based crystal plasticity framework. We validate the dependence of the yield strength with the temperature predicted by the model against existing experimental data of tensile tests in singlecrystal tungsten, with excellent agreement between the simulations and the measured data. We then extend the model to a number of crystallographic orientations uniformly distributed in the standard triangle and study the effects of temperature and strain rate. Finally, we perform biaxial tensile tests and provide the yield surface as a function of the temperature for some of the crystallographic orientations explored in the uniaxial tensile tests.

Evolution of extreme temperature events in short term climate projection for Iberian Peninsula

Extreme events of maximum and minimum temperatures are a main hazard for agricultural production in Iberian Peninsula. For this purpose, in this study we analyze projections of their evolution that could be valid for the next decade, represented in this study by the 30-year period 2004-2034 (target period). For this purpose two kinds of data were used in this study: 1) observations from the station network of AEMET (Spanish National Meteorological Agency) for five Spanish locations, and 2) simulated data at a resolution of 50 50 km horizontal grid derived from the outputs of twelve Regional Climate Models (RCMs) taken from project ENSEMBLES (van der Linden and Mitchell, 2009), with a bias correction (Dosio and Paruolo, 2011; Dosio et al., 2012) regarding the observational dataset Spain02 (Herrera et al., 2012). To validate the simulated climate, the available period of observations was compared to a baseline period (1964-1994) of simulated climate for all locations. Then, to analyze the changes for the present/very next future, probability of extreme temperature events for 2004-2034 were compared to that of the baseline period. Although only minor changes are expected, small variations in variability may have a significant impact in crop performance.

Urban Archaeology in Madrid. Experiences and Opportunities to Understand Historical City

In 2015, it will be thirty years since Spanish Historic Heritage Law from 1985 was approved. The results after three decades under this law are necessarily positive and witness how the complex autonomous regional legislation has been promoted, guided and organized in this Heritage field. In addition, the law enforcement has brought into the scene how the numerous public and private initiatives involved in caring, managing, protecting and restoring our cultural heritage have been channeled and regulated, as well as monitoring the impact these initiatives produce on urban archaeology. During this long period of Spanish recent history, cultural heritage -understood as an important development tool, especially when related to cultural tourism- has succeeded in channeling resources for developing the historical research projects, both documental and archaeological, that the Spanish monumental urban ensembles were requiring. In this context, the case of the city of Madrid is a clear example of the significant development that urban Historical Archaeology has experienced in Spain over the last thirty years, especially when dealing with the study of the Middle Ages (8th to 15th centuries) and the Modern Age (16th to 18th centuries). Given the number of interventions and the important results obtained by many of them, Madrid urban archaeology is an extraordinary example of the consequences of implementing new management models, changing criteria and operating procedures, and also, of course, of the conflicts and debates raised regarding heritage, as well as the importance these interventions have implied, which is the main aim of this work.

Selecting crop models for decision making in wheat insurance

In crop insurance, the accuracy with which the insurer quantifies the actual risk is highly dependent on the availability on actual yield data. Crop models might be valuable tools to generate data on expected yields for risk assessment when no historical records are available. However, selecting a crop model for a specific objective, location and implementation scale is a difficult task. A look inside the different crop and soil modules to understand how outputs are obtained might facilitate model choice. The objectives of this paper were (i) to assess the usefulness of crop models to be used within a crop insurance analysis and design and (ii) to select the most suitable crop model for drought risk assessment in semi-arid regions in Spain. For that purpose first, a pre-selection of crop models simulating wheat yield under rainfed growing conditions at the field scale was made, and second, four selected models (Aquacrop, CERES- Wheat, CropSyst and WOFOST) were compared in terms of modelling approaches, process descriptions and model outputs. Outputs of the four models for the simulation of winter wheat growth are comparable when water is not limiting, but differences are larger when simulating yields under rainfed conditions. These differences in rainfed yields are mainly related to the dissimilar simulated soil water availability and the assumed linkages with dry matter formation. We concluded that for the simulation of winter wheat growth at field scale in such semi-arid conditions, CERES-Wheat and CropSyst are preferred. WOFOST is a satisfactory compromise between data availability and complexity when detail data on soil is limited. Aquacrop integrates physiological processes in some representative parameters, thus diminishing the number of input parameters, what is seen as an advantage when observed data is scarce. However, the high sensitivity of this model to low water availability limits its use in the region considered. Contrary to the use of ensembles of crop models, we endorse that efforts be concentrated on selecting or rebuilding a model that includes approaches that better describe the agronomic conditions of the regions in which they will be applied. The use of such complex methodologies as crop models is associated with numerous sources of uncertainty, although these models are the best tools available to get insight in these complex agronomic systems.

Evaluación del impacto del programa Monumenta en los centros históricos del sur de Brasil : los casos de Pelotas, Porto Alegre (Rio Grande do Sul) y São Francisco do Sul (Santa Catarina)

Esta Tesis tiene como objetivo demostrar que los programas de preservación del patrimonio, durante su fase de implementación, deben someterse a un análisis multidisciplinar que haga un balance de su ejecución. Dicho análisis permitirá identificar resultados significativos, capaces de fundamentar la rectificación de las bases conceptuales de la política pública en cuestión. Este reajuste podrá darse, por lo tanto, durante su vigencia y, de forma más relevante, posteriormente, sus motivos y resultados permitirán elaborar nuevas estrategias que serán aplicadas en futuros programas de intervención. Por otro lado se indagó, además, si las ciudades participantes en un programa nacional de preservación del patrimonio, regidas por normas y metas comunes, podrían alcanzar resultados diferentes. Para atender a estos objetivos, la investigación se encuentra enfocada a la realidad brasileña, siendo seleccionado como objeto de estudio el Programa Monumenta. Este Programa formó parte de la política pública cultural del Ministerio de Cultura con una importante implicación del Banco Interamericano de Desarrollo. Implementado a partir de 1999, procuró promover un proceso de recuperación urbana sostenible y de preservación del patrimonio de 26 Sitios Históricos Urbanos o Conjuntos de Monumentos Urbanos protegidos por el Instituto del Patrimonio Histórico y Artístico Nacional (Iphan). El Programa contó con el apoyo de la Unesco y del Iphan, así como con la participación de las Administraciones Municipales y/o Estatales, sectores privados y la sociedad civil. Las hipótesis planteadas en esta Tesis Doctoral fueron: (a) el análisis de los resultados en la fase de implementación de un programa de preservación del patrimonio es imprescindible, porque permite extraer conclusiones preliminares y orientar sus reformas; (b) los objetivos a corto plazo establecidos por el Programa Monumenta fueron alcanzados de modo diferenciado en las distintas ciudades beneficiadas; (c) a pesar de las diferencias, el Programa Monumenta presentó resultados preliminares positivos y significativos en la preservación del patrimonio histórico urbano brasileño. Los procedimientos metodológicos se centraron en un análisis cuantitativo, cualitativo y comparativo de los resultados alcanzados por tres ciudades beneficiadas por el Programa Monumenta, seleccionadas según su tamaño poblacional: Pelotas, Porto Alegre (Estado de Rio Grande do Sul) y São Francisco do Sul (Estado de Santa Catarina). Estos procedimientos fueron aplicados en los siguientes indicadores: utilización de los equipamientos culturales, características de la población y de los domicilios, variación de las actividades económicas, financiación destinada al sector privado para la recuperación de inmuebles y el fomento de la seguridad urbana. La Tesis ha englobado discusiones y conceptos abordados en las disciplinas de la Sociología Urbana, Geografía Urbana, Historia, Economía y Estadística de modo que se atribuye al objeto de investigación una visión interdisciplinar que ayudará a la comprensión de la teoría y la práctica preservacionistas. El análisis de la varianza, la regresión lineal y el análisis factorial fueron las herramientas estadísticas aplicadas sobre los datos con el objetivo de constatar la significación de los resultados y la relación de correspondencia entre algunas variables. Esta Tesis contribuye a la elaboración de una metodología analítica que puede ser aplicada en el cálculo de la superficie ocupada por las actividades económicas, con base en el método estadístico del Diagrama de Caja y Bigotes, de John Wilder Tukey. Las conclusiones corroboran las hipótesis planteadas y pretenden contribuir al diseño de las nuevas políticas públicas de preservación de sitios históricos de carácter urbano, enfatizando, con ello, la necesidad de evaluaciones más profundas de los resultados durante su fase de implementación. ---------------------------------------------------------------------------------- RESUMO--------------------------------------------------------------------------- A presente Tese apresenta como objetivo principal demonstrar que os programas de preservação do patrimônio histórico, durante a sua fase de implementação, necessitam de uma análise multidisciplinar sobre a sua execução. Essa análise permite identificar resultados significativos, capazes de fundamentar a retificação das bases conceituais da política pública em questão. A correção poderá, portanto, ser realizada tanto durante a sua vigência como posteriormente, ao permitir a elaboração de novas estratégias a serem aplicadas nos futuros programas de intervenção. Por outro lado, indagou-se se cidades participantes de um mesmo programa nacional de preservação do patrimônio histórico, regidas por normas e metas comuns, poderiam alcançar resultados não similares. Para atender tais objetivos, a investigação enfoca a realidade brasileira, tendo sido selecionado o Programa Monumenta como objeto de estudo. Esse Programa fez parte de uma política pública cultural do Ministério da Cultura, que atuou em parceria com o Banco Interamericano de Desenvolvimento. Implantado em nível nacional, a partir de 1999, visava promover um processo de recuperação urbana sustentável, bem como a preservação do patrimônio de 26 Sítios Urbanos Históricos ou Conjuntos de Monumentos Urbanos, protegidos pelo Instituto do Patrimônio Histórico e Artístico Nacional (Iphan). O Programa contou com o apoio da Unesco e do Iphan, além da participação das Administrações Municipais e/ou Estaduais, setores privados e sociedade civil. As hipóteses estabelecidas nesta Tese Doutoral foram: (a) a análise dos resultados na fase de implementação de um programa de preservação do patrimônio é imprescindível, pois permite extrair conclusões preliminares e orientar as suas reformulações; (b) os objetivos em curto prazo, estabelecidos pelo Programa Monumenta, foram alcançados de modo diferente pelas cidades beneficiadas; (c) apesar das diferenças, o Programa Monumenta apresentou resultados preliminares positivos e significativos sobre a preservação do patrimônio histórico urbano brasileiro. Os procedimentos metodológicos se centraram em análises quantitativa, qualitativa e comparativa dos resultados alcançados em três cidades beneficiadas pelo Programa Monumenta, selecionadas de acordo com o tamanho populacional: Pelotas, Porto Alegre (Estado do Rio Grande do Sul) e São Francisco do Sul (Estado de Santa Catarina). Esses procedimentos foram aplicados nos seguintes indicadores: utilização dos equipamentos culturais, características da população e dos domicílios, atividades econômicas, financiamento destinado ao setor privado para a recuperação dos imóveis e, ainda, o fomento da segurança urbana. A Tese inclui discussões e conceitos abordados nas disciplinas de Sociologia Urbana, Geografia Urbana, História, Economia e Estatística, de modo a atribuir ao objeto de investigação uma visão interdisciplinar e uma compreensão entre a teoria e a prática preservacionista. A análise de variância, regressão linear e análise fatorial foram as técnicas estatísticas aplicadas sobre os dados, com o objetivo de constatar a significação dos resultados e a relação de correspondência entre algumas variáveis. Esta Tese contribui com a elaboração de uma metodologia aplicada no cálculo da superfície ocupada pelas atividades econômicas, utilizando como método estatístico o Diagrama de Caixa e Bigodes, de John Wilder Tukey. As conclusões corroboram com as hipóteses estabelecidas e pretendem contribuir para o desenho de novas políticas públicas de preservação de sítios históricos de caráter urbano, enfatizando a necessidade de avaliações mais profundas dos resultados durante a sua fase de implementação. ---------------------------------------------------------------------------------- ABSTRACT ---------------------------------------------------------------------------------- The main goal of this PhD. Thesis is to demonstrate that a multidisciplinary analysis is needed during the implementation phase of preservation of heritage programmes. Such analysis allows the identification of significant results, which in turn can serve as the foundation for the conceptual bases of the public policy at hand. Thus, any corrections can be made both during the programme and afterward, by introducing new strategies to be applied in future intervention programmes. On the other hand, this project also asks whether cities participating in the same national preservation of heritage programme with common rules and goals can achieve distinct results. In order to meet these objectives, the project chose Brazil as its focus and Monumenta Programme for its object of study. This Programme is part of the Ministry of Culture’s public cultural policy, and was developed with cooperation by the Inter-American Development Bank. Implemented at the national level in 1999, the Programme aimed at promoting a process of sustainable urban renewal and the preservation of 26 urban historic sites or urban monumental ensembles, protected by the National Historic and Artistic Heritage Institute (IPHAN). UNESCO and IPHAN supported the Programme, and participants included municipal and state offices, private businesses, and local residents. The hypotheses established in this Doctoral Thesis were: (a) the analysis of the results in the implementation phase of a cultural public policy is imperative, because it enables preliminary conclusions to be drawn and orientate reforms; (b) the short-term objectives set out in the Monumenta Programme were achieved differently in the benefitted cities; (c) despite the differences, the Monumenta Programme displayed significant positive preliminary results in the conservation of the urban historic heritage in Brazil. Methodology procedures centered around quantitative, qualitative, and comparative analyses of the results achieved in three benefiting cities, selected according to population size: Pelotas, Porto Alegre (Rio Grande do Sul State) and São Francisco do Sul (Santa Catarina State). These procedures were applied to the following indicators: the use of the cultural facilities, characteristics of the population and the residential housing, variation of the economic activities, financing destined for the recovery of real estate, and promoting urban safety. The Thesis includes discussions and concepts addressed in urban sociology, urban geography, history, economics, and statistics, in order to examine the object of study with an interdisciplinary eye and an understanding between preservation theory and practice. Variance analysis, linear regression, and factorial analysis were the statistical techniques applied to the data, with the goal of defining the significance of the results and the correspondence ratio between some of the variables. This Thesis attempted to elaborate an applied methodology for calculating the space occupied by economic activities, using John Wilder Tukey's statistical method of Box-and-Whisker Plot. The conclusions corroborated the hypotheses established and are meant to contribute to the design of new public policies of historical site preservation in urban settings, emphasizing the need for deeper evaluations of the results during the implementation phase.

Agrupaciones heterogéneas e intervención en arquitecturas existentes

Esta tesis doctoral profundiza, dentro del campo de la práctica del proyecto arquitectónico, en aquellas técnicas proyectuales que al intervenir sobre lo ya construido son capaces de cambiar su valor y su significado. La investigación tiene como objetivo demostrar que es posible revertir la obsolescencia de las arquitecturas ordinaras existentes mediante una técnica proyectual que hemos llamado agrupaciones heterogéneas. En ellas, la preexistencia y lo aportado inauguran un tiempo de convivencia que obliga a reinterpretar a la primera mientras que la segunda es forzada a traducir sus imaginarios. Esta investigación se conecta con el mundo del conocimiento a través de dos vectores, uno que lo enlaza con el estudio de las agrupaciones heterogéneas y otro con la intervención sobre arquitecturas ordinarias. Para el desarrollo de los trabajos, en una primera parte, se ha procedido al análisis de cada campo por separado a través del estudio de casos concretos: la plastic furniture de Charles y Ray Eames para el caso de las agrupaciones heterogéneas y el libro-manifiesto Plus de Frédéric Druot, Anne Lacaton y Jean-Philippe Vassal para la intervención sobre arquitecturas ordinarias. En cada estudio hemos obtenido unas conclusiones parciales: la arquitectura entendida como estado de encuentro y la teoría de la resistencia a los imaginarios. La segunda parte de la tesis toma el proyecto de Frank Gehry para su casa en Santa Mónica como un ejemplo en el que se ha revertido con éxito la obsolescencia de una arquitectura ordinaria a través de la técnica de las agrupaciones heterogéneas. A partir de ese ejemplo, y bajo la perspectiva de los dos campos estudiados, se propone una cartografía teórica para leer los procesos de innovación que tienen lugar al utilizar esta estrategia en diseño del proyecto. ABSTRACT This PhD thesis will provide an in-depth view of the techniques in practice in architectural projects, with proposals that are able to change the value and meaning of work that has already been built. The research is aimed at proving that it is possible to revert the obsolescence of the existing ordinary architecture using a project technique that we have called “heterogeneous ensembles”. In these ensembles, what existed beforehand and what has been contributed afterwards have brought about a new form of co-existence which forces the former to be reinterpreted and the latter to clarify its archetypes. This research connects to the world of knowledge through two vectors: one which links it to the study of the heterogeneous ensembles and the other to the work carried out on the ordinary architecture. To carry out this work, firstly we analysed each field separately by studying specific cases: the Charles and Ray Eames plastic furniture for the heterogeneous ensembles and the book and manifesto Plus by Frédéric Druot, Anne Lacaton and Jean- Philippe Vassal for the work carried out on the ordinary architecture. We drew partial conclusions in each study: architecture understood as a state of encounter and the theory of resistance to the archetypes. The second part of the thesis takes Frank Gehry’s project for his Santa Monica house as an example in which the obsolescence of ordinary architecture has been successfully reverted using the heterogeneous ensembles technique. Based on this example and from the standpoint of the two fields in question, we propose a theoretical cartography to read the innovation processes that take place when using this strategy in project design.

Strategies for adapting maize to climate change and extreme temperatures in Andalusia, Spain

Climate projections indicate that rising temperatures will affect summer crops in the southern Iberian Peninsula. The aim of this study was to obtain projections of the impacts of rising temperatures, and of higher frequency of extreme events on irrigated maize, and to evaluate some adaptation strategies. The study was conducted at several locations in Andalusia using the CERES-Maize crop model, previously calibrated/validated with local experimental datasets. The simulated climate consisted of projections from regional climate models from the ENSEMBLES project; these were corrected for daily temperature and precipitation with regard to the E-OBS observational dataset. These bias-corrected projections were used with the CERES-Maize model to generate future impacts. Crop model results showed a decrease in maize yield by the end of the 21st century from 6 to 20%, a decrease of up to 25% in irrigation water requirements, and an increase in irrigation water productivity of up to 22%, due to earlier maturity dates and stomatal closure caused by CO2 increase. When adaptation strategies combining earlier sowing dates and cultivar changes were considered, impacts were compensated, and maize yield increased up to 14%, compared with the baseline period (1981-2010), with similar reductions in crop irrigation water requirements. Effects of extreme maximum temperatures rose to 40% at the end of the 21st century, compared with the baseline. Adaptation resulted in an overall reduction in extreme Tmax damages in all locations, with the exception of Granada, where losses were limited to 8%.

Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy

We have investigated the pH dependence of the dynamics of conformational fluctuations of green fluorescent protein mutants EGFP (F64L/S65T) and GFP-S65T in small ensembles of molecules in solution by using fluorescence correlation spectroscopy (FCS). FCS utilizes time-resolved measurements of fluctuations in the molecular fluorescence emission for determination of the intrinsic dynamics and thermodynamics of all processes that affect the fluorescence. Fluorescence excitation of a bulk solution of EGFP decreases to zero at low pH (pKa = 5.8) paralleled by a decrease of the absorption at 488 nm and an increase at 400 nm. Protonation of the hydroxyl group of Tyr-66, which is part of the chromophore, induces these changes. When FCS is used the fluctuations in the protonation state of the chromophore are time resolved. The autocorrelation function of fluorescence emission shows contributions from two chemical relaxation processes as well as diffusional concentration fluctuations. The time constant of the fast, pH-dependent chemical process decreases with pH from 300 μs at pH 7 to 45 μs at pH 5, while the time-average fraction of molecules in a nonfluorescent state increases to 80% in the same range. A second, pH-independent, process with a time constant of 340 μs and an associated fraction of 13% nonfluorescent molecules is observed between pH 8 and 11, possibly representing an internal proton transfer process and associated conformational rearrangements. The FCS data provide direct measures of the dynamics and the equilibrium properties of the protonation processes. Thus FCS is a convenient, intrinsically calibrated method for pH measurements in subfemtoliter volumes with nanomolar concentrations of EGFP.

Deciphering a neural code for vision

Deciphering the information that eyes, ears, and other sensory organs transmit to the brain is important for understanding the neural basis of behavior. Recordings from single sensory nerve cells have yielded useful insights, but single neurons generally do not mediate behavior; networks of neurons do. Monitoring the activity of all cells in a neural network of a behaving animal, however, is not yet possible. Taking an alternative approach, we used a realistic cell-based model to compute the ensemble of neural activity generated by one sensory organ, the lateral eye of the horseshoe crab, Limulus polyphemus. We studied how the neural network of this eye encodes natural scenes by presenting to the model movies recorded with a video camera mounted above the eye of an animal that was exploring its underwater habitat. Model predictions were confirmed by simultaneously recording responses from single optic nerve fibers of the same animal. We report here that the eye transmits to the brain robust “neural images” of objects having the size, contrast, and motion of potential mates. The neural code for such objects is not found in ambiguous messages of individual optic nerve fibers but rather in patterns of coherent activity that extend over small ensembles of nerve fibers and are bound together by stimulus motion. Integrative properties of neurons in the first synaptic layer of the brain appear well suited to detecting the patterns of coherent activity. Neural coding by this relatively simple eye helps explain how horseshoe crabs find mates and may lead to a better understanding of how more complex sensory organs process information.