Spatial analysis of geometric design consistency and road sight distance

Because of the high number of crashes occurring on highways, it is necessary to intensify the search for new tools that help in understanding their causes. This research explores the use of a geographic information system (GIS) for an integrated analysis, taking into account two accident-related factors: design consistency (DC) (based on vehicle speed) and available sight distance (ASD) (based on visibility). Both factors require specific GIS software add-ins, which are explained. Digital terrain models (DTMs), vehicle paths, road centerlines, a speed prediction model, and crash data are integrated in the GIS. The usefulness of this approach has been assessed through a study of more than 500 crashes. From a regularly spaced grid, the terrain (bare ground) has been modeled through a triangulated irregular network (TIN). The length of the roads analyzed is greater than 100 km. Results have shown that DC and ASD could be related to crashes in approximately 4% of cases. In order to illustrate the potential of GIS, two crashes are fully analyzed: a car rollover after running off road on the right side and a rear-end collision of two moving vehicles. Although this procedure uses two software add-ins that are available only for ArcGIS, the study gives a practical demonstration of the suitability of GIS for conducting integrated studies of road safety.

Mycorrhizal preferences and fine spatial structure of the epiphytic orchid Epidendrum rhopalostele

• Premise of the study: The presence of compatible fungi is necessary for epiphytic orchid recruitment. Thus, identifying associated mycorrhizal fungi at the population level is essential for orchid conservation. Recruitment patterns may also be conditioned by factors such as seed dispersal range and specific environmental characteristics. • Methods: In a forest plot, all trees with a diameter at breast height >1 cm and all individuals of the epiphytic orchid Epidendrum rhopalostele were identified and mapped. Additionally, one flowering individual of E. rhopalostele per each host tree was randomly selected for root sampling and DNA extraction. • Key results: A total of 239 E. rhopalostele individuals were located in 25 of the 714 potential host trees. Light microscopy of sampled roots showed mycorrhizal fungi in 22 of the 25 sampled orchids. Phylogenetic analysis of ITS1-5.8S-ITS2 sequences yielded two Tulasnella clades. In four cases, plants were found to be associated with both clades. The difference between univariate and bivariate K functions was consistent with the random labeling null model at all spatial scales, indicating that trees hosting clades A and B of Tulasnella are not spatially segregated. The analysis of the inhomogenous K function showed that host trees are not clustered, suggesting no limitations to population-scale dispersal. χ2 analysis of contingency tables showed that E. rhopalostele is more frequent on dead trees than expected. • Conclusions: Epidendrum rhopalostele establishes mycorrhizal associations with at least two different Tulasnella species. The analysis of the distribution patterns of this orchid suggests a microsite preference for dead trees and no seed dispersal limitation.

Methods for the analysis of multi-scale cell dynamics from fluorescence microscopy images

La embriogénesis es el proceso mediante el cual una célula se convierte en un ser un vivo. A lo largo de diferentes etapas de desarrollo, la población de células va proliferando a la vez que el embrión va tomando forma y se configura. Esto es posible gracias a la acción de varios procesos genéticos, bioquímicos y mecánicos que interaccionan y se regulan entre ellos formando un sistema complejo que se organiza a diferentes escalas espaciales y temporales. Este proceso ocurre de manera robusta y reproducible, pero también con cierta variabilidad que permite la diversidad de individuos de una misma especie. La aparición de la microscopía de fluorescencia, posible gracias a proteínas fluorescentes que pueden ser adheridas a las cadenas de expresión de las células, y los avances en la física óptica de los microscopios han permitido observar este proceso de embriogénesis in-vivo y generar secuencias de imágenes tridimensionales de alta resolución espacio-temporal. Estas imágenes permiten el estudio de los procesos de desarrollo embrionario con técnicas de análisis de imagen y de datos, reconstruyendo dichos procesos para crear la representación de un embrión digital. Una de las más actuales problemáticas en este campo es entender los procesos mecánicos, de manera aislada y en interacción con otros factores como la expresión genética, para que el embrión se desarrolle. Debido a la complejidad de estos procesos, estos problemas se afrontan mediante diferentes técnicas y escalas específicas donde, a través de experimentos, pueden hacerse y confrontarse hipótesis, obteniendo conclusiones sobre el funcionamiento de los mecanismos estudiados. Esta tesis doctoral se ha enfocado sobre esta problemática intentando mejorar las metodologías del estado del arte y con un objetivo específico: estudiar patrones de deformación que emergen del movimiento organizado de las células durante diferentes estados del desarrollo del embrión, de manera global o en tejidos concretos. Estudios se han centrado en la mecánica en relación con procesos de señalización o interacciones a nivel celular o de tejido. En este trabajo, se propone un esquema para generalizar el estudio del movimiento y las interacciones mecánicas que se desprenden del mismo a diferentes escalas espaciales y temporales. Esto permitiría no sólo estudios locales, si no estudios sistemáticos de las escalas de interacción mecánica dentro de un embrión. Por tanto, el esquema propuesto obvia las causas de generación de movimiento (fuerzas) y se centra en la cuantificación de la cinemática (deformación y esfuerzos) a partir de imágenes de forma no invasiva. Hoy en día las dificultades experimentales y metodológicas y la complejidad de los sistemas biológicos impiden una descripción mecánica completa de manera sistemática. Sin embargo, patrones de deformación muestran el resultado de diferentes factores mecánicos en interacción con otros elementos dando lugar a una organización mecánica, necesaria para el desarrollo, que puede ser cuantificado a partir de la metodología propuesta en esta tesis. La metodología asume un medio continuo descrito de forma Lagrangiana (en función de las trayectorias de puntos materiales que se mueven en el sistema en lugar de puntos espaciales) de la dinámica del movimiento, estimado a partir de las imágenes mediante métodos de seguimiento de células o de técnicas de registro de imagen. Gracias a este esquema es posible describir la deformación instantánea y acumulada respecto a un estado inicial para cualquier dominio del embrión. La aplicación de esta metodología a imágenes 3D + t del pez zebra sirvió para desvelar estructuras mecánicas que tienden a estabilizarse a lo largo del tiempo en dicho embrión, y que se organizan a una escala semejante al del mapa de diferenciación celular y con indicios de correlación con patrones de expresión genética. También se aplicó la metodología al estudio del tejido amnioserosa de la Drosophila (mosca de la fruta) durante el cierre dorsal, obteniendo indicios de un acoplamiento entre escalas subcelulares, celulares y supracelulares, que genera patrones complejos en respuesta a la fuerza generada por los esqueletos de acto-myosina. En definitiva, esta tesis doctoral propone una estrategia novedosa de análisis de la dinámica celular multi-escala que permite cuantificar patrones de manera inmediata y que además ofrece una representación que reconstruye la evolución de los procesos como los ven las células, en lugar de como son observados desde el microscopio. Esta metodología por tanto permite nuevas formas de análisis y comparación de embriones y tejidos durante la embriogénesis a partir de imágenes in-vivo. ABSTRACT The embryogenesis is the process from which a single cell turns into a living organism. Through several stages of development, the cell population proliferates at the same time the embryo shapes and the organs develop gaining their functionality. This is possible through genetic, biochemical and mechanical factors that are involved in a complex interaction of processes organized in different levels and in different spatio-temporal scales. The embryogenesis, through this complexity, develops in a robust and reproducible way, but allowing variability that makes possible the diversity of living specimens. The advances in physics of microscopes and the appearance of fluorescent proteins that can be attached to expression chains, reporting about structural and functional elements of the cell, have enabled for the in-vivo observation of embryogenesis. The imaging process results in sequences of high spatio-temporal resolution 3D+time data of the embryogenesis as a digital representation of the embryos that can be further analyzed, provided new image processing and data analysis techniques are developed. One of the most relevant and challenging lines of research in the field is the quantification of the mechanical factors and processes involved in the shaping process of the embryo and their interactions with other embryogenesis factors such as genetics. Due to the complexity of the processes, studies have focused on specific problems and scales controlled in the experiments, posing and testing hypothesis to gain new biological insight. However, methodologies are often difficult to be exported to study other biological phenomena or specimens. This PhD Thesis is framed within this paradigm of research and tries to propose a systematic methodology to quantify the emergent deformation patterns from the motion estimated in in-vivo images of embryogenesis. Thanks to this strategy it would be possible to quantify not only local mechanisms, but to discover and characterize the scales of mechanical organization within the embryo. The framework focuses on the quantification of the motion kinematics (deformation and strains), neglecting the causes of the motion (forces), from images in a non-invasive way. Experimental and methodological challenges hamper the quantification of exerted forces and the mechanical properties of tissues. However, a descriptive framework of deformation patterns provides valuable insight about the organization and scales of the mechanical interactions, along the embryo development. Such a characterization would help to improve mechanical models and progressively understand the complexity of embryogenesis. This framework relies on a Lagrangian representation of the cell dynamics system based on the trajectories of points moving along the deformation. This approach of analysis enables the reconstruction of the mechanical patterning as experienced by the cells and tissues. Thus, we can build temporal profiles of deformation along stages of development, comprising both the instantaneous events and the cumulative deformation history. The application of this framework to 3D + time data of zebrafish embryogenesis allowed us to discover mechanical profiles that stabilized through time forming structures that organize in a scale comparable to the map of cell differentiation (fate map), and also suggesting correlation with genetic patterns. The framework was also applied to the analysis of the amnioserosa tissue in the drosophila’s dorsal closure, revealing that the oscillatory contraction triggered by the acto-myosin network organized complexly coupling different scales: local force generation foci, cellular morphology control mechanisms and tissue geometrical constraints. In summary, this PhD Thesis proposes a theoretical framework for the analysis of multi-scale cell dynamics that enables to quantify automatically mechanical patterns and also offers a new representation of the embryo dynamics as experienced by cells instead of how the microscope captures instantaneously the processes. Therefore, this framework enables for new strategies of quantitative analysis and comparison between embryos and tissues during embryogenesis from in-vivo images.

Paisaje de energías: conocimiento estético en el enfoque ambiental del proyecto

Desde hace ya varias décadas la praxis de la ecología ha venido reconociendo la necesidad de estudiar los múltiples sistemas de interacción del ser humano, como especie viva, y su entorno. Entidades espaciales como el paisaje geográfico son empleadas para delimitar sistemas territoriales operados por la sociedad, precisando campos concretos de su acción física, biológica y cultural. La ecología aborda así el conocimiento científico del territorio como asentamiento humano, rastrea sus patrones espaciales y analiza su compleja estructura funcional. En ese contexto, la transferencia de herramientas e instrumentos desde la ecología al ámbito proyectivo posee ya un bagaje de más de cinco décadas. Cada vez con más frecuencia el proyecto emplea parámetros, inventarios, fórmulas, indicadores y tecnologías que tratan de dar una respuesta ambientalmente adecuada a los condicionantes de contorno, por ejemplo aprovechando las condiciones climáticas en la optimización energética o proponiendo programas de usos del suelo que eviten perturbaciones en ecosistemas de interés. Con todo, en el momento presente surgen voces que, ante el dominio indiscutible de los enfoques netamente deterministas, tratan de recordar que los principios del pensamiento ecológico van más allá del mero control cuantitativo de los procesos biofísicos. Recuerdan que la etología demostró a principios del XX que el ser humano, como ser consciente, inviste una relación de intimidad con su entorno que supera tales perspectivas: a través de la correspondencia entre percepción y significación, entre lo físico y lo psíquico, entre interioridad y exterioridad, las personas abrazan la plenitud de aquello que les rodea en un acto de profunda conciliación afectiva. De tal ligadura de intimidad depende, sí o sí, y en toda su profundidad, la aceptación humana del entorno construido. A través de la noción de ambiente [Umwelt] se demuestra que la relación del hombre con su entorno es inseparable, bidireccional y coordinada y, por lo tanto, desde una posición coherente, la experiencia del espacio puede ser examinada a partir de la reciprocidad que constituyen, en continuidad, la persona y el lugar. De esta forma, la tesis dirige su objetivo principal a explorar y considerar, desde el proyecto, el significado y la influencia de la experiencia ambiental del espacio construido en la vida humana. Es más que probable que buena parte de los problemas de desafección del hombre con los paisajes transformados de su contemporaneidad tenga que ver con que tanto las intensidades de la experiencia y percepción humana, como la potestad interpretativa de sus productos culturales, incluyendo la arquitectura, han sido fuertemente reducidas. Ante este problema, la investigación toma como hipótesis la oportunidad que ofrece el pensamiento ecológico de reformular la experiencia estética como un acto de conocimiento, como un evento donde se da el encuentro físico y se construyen significados, donde se sancionan valores sociales y se mira hacia el futuro. Se ha de señalar que la presente tesis doctoral arranca en el Laboratorio de Paisaje del Grupo de Investigación Paisaje Cultural de la Universidad Politécnica de Madrid dirigido por Concha Lapayese y Darío Gazapo, y por tanto hace suyos para el estado del arte los principales conceptos e ideas bajo los que el trabajo teórico y práctico del grupo se viene orientando desde hace años: la consideración del paisaje como acontecimiento; la oscilación de la interpretación entre un paisaje específico y un paisaje genérico en un mundo globalizado; el reconocimiento de la experiencia estética del paisaje como una toma de conciencia social; y en definitiva, la reivindicación de la interioridad en el proyecto contemporáneo. La investigación profundiza en una línea de oportunidad que se abre al promover lo que se ha llamado un conocimiento por lo sentido como estrategia ambiental que permite contrarrestar mitos profundamente arraigados en las estructuras sociales. El primer paso en ese recorrido sería explorar ecológicamente el aporte de la experiencia estética; esto es, su consideración como forma de conocimiento específico. Resultaría pertinente impulsar la idea de la inmersión en el paisaje como fenómeno experiencial, sensual y corporal, y enfrentar, desde ahí, el problema de la aceptación social de lo nuevo y lo trasformado de acuerdo con el momento actual. La exploración sobre la afectividad en el ambiente no es, en cualquier caso, un asunto nuevo. Sin pretensiones de historiografía, dos momentos del siglo XX concentran el interés de la investigación. La primera se corresponde fundamentalmente con la segunda década del siglo, en relación a una serie de influencias que desde los avances científicos determinaron singulares aventuras del arte más experimental. La segunda se posiciona en el entorno de 1970, época en la que es conocido el interés que despertaron las cuestiones ambientales. En ambos casos se han estudiado aportaciones que desvelan conceptos determinantes en la definición de la experiencia estética como un evento de adquisición de conocimiento por lo sentido. Es conveniente adelantar el rol de centralidad que para la investigación tiene el concepto de energía, tal como el propio título subraya. La energía como realidad material y sensible es el sustrato que permite navegar por el principio de unidad epistemológica que subyace al pensamiento ecológico. Sus continuas referencias simbólicas, físicas y metafóricas entre los artistas estudiados no son un mero recurso iconográfico: mantienen inherente el principio de continuidad ambiental en el cual el ser humano y la inmensidad del cosmos navegan indisociables. Un discurso unificado y consistente sobre los aportes de la experiencia estética enfocada como forma de conocimiento por lo sentido hila la lectura histórica, conceptual y práctica de toda la investigación. Con ello se alcanza a hilvanar un diagrama conceptual, modelo de análisis proyectivo, que recoge ideas científicas, filosóficas y proyectivas. De alguna manera, el diagrama trata de dibujar, desde los principios del pensamiento ecológico, la correlación de continuidad que, vacilante, tensa, sutil y frágil se desplaza incesante e irresuelta entre interioridad y exterioridad. ABSTRACT Over the last few decades ecological practice has come to acknowledge a need for studying the multiple systems of interaction between the human being - inasmuch as it is a living species - and its environment. Spatial entities such as the geographic notion of landscape have been used to delimitate the territorial systems operated by society and to describe in detail specific fields of its physical, biological and cultural action. Ecology has thus managed to address the scientific knowledge of the territory as a human settlement, tracking its spatial patterns and analysing its complex functional structure. In this context, the transfer of tools and instruments from the field of ecology to that of design has a tradition already going back more than fifty years. Increasingly more often, design makes use of parameters, inventories, formulas, indicators and technologies to give an environmentally sound response to contour conditions: for instance, taking advantage of the local climate for the optimisation of energy consumption or proposing land uses that avoid disturbing valuable ecosystems. Yet in the present day some voices have arisen that, against the uncontested domination of purely positivistic approaches, are trying to draw attention to the fact that the principles of ecological thought go beyond mere quantitative control of biophysical processes. They point out that, in the early 20th century, ethology proved that the human being, as a conscious entity, invests itself into a relationship of intimacy with its environment that surpasses such perspectives: through the correspondences between perception and signification, between physical and psychological or between inside and outside, people embrace the entirety of their surroundings in an action of deep affective conciliation. It is on this link of intimacy that - fully and unquestionably - human acceptance of the built environment depends. Through the notion of environment [Umwelt] it can be proven that the relationship between the human being and its environment is inseparable, bidirectional and coordinated; and that, therefore, from a coherent position the experience of space can be examined through the reciprocity constituted continuously by person and place. Thus, the main goal in this thesis is to explore and acknowledge, from the standpoint of design, the meaning and influence of the environmental experience in human life. It is extremely likely that many of the issues with mankind’s alienation from the transformed landscapes of the present day arise from the fact that both the intensity of human perception and experience and the interpretive capacity of its cultural products –including architecture - have been greatly reduced. Facing this issue, research has taken as hypothesis the opportunity offered by ecological thought of reformulating aesthetic experience as an act of knowledge – as an event where physical encounter takes place and meanings are constructed; where social values are sanctioned and the path towards the future is drawn. This notwithstanding, the present thesis began in the Landscape Laboratory of the Technical University of Madrid Cultural Landscape Research Group (GIPC-UPM), led by Concha Lapayese and Darío Gazapo; and has therefore appropriated for its state of the art the main concepts and ideas that have been orienting the practical and theoretical work of the latter: the understanding of landscape as an event, the oscillation of interpretation between a specific and a generic landscape within a globalised world; the acknowledgement of the aesthetic experience of landscape as a way of acquiring social awareness; and, all in all, a vindication of interiority in contemporary design. An exploration has been made of the line of opportunity that is opened when promoting what has been termed knowledge through the senses as an environmental strategy allowing to counter myths deeply rooted in social structures. The first step in this path would be an ecological exploration of the contribution of the aesthetic experience; that is, its consideration as a type of specific knowledge. It would be pertinent to further the idea of immersion into the landscape as an experiential, sensual and corporeal phenomenon and, from that point, to face the issue of social acceptance of what is new and transformed according to the values of the present day. The exploration of affectivity in the environment is not, at any rate, a new topic. Without aspiring to make a history of it, we can mark two points in the 20th century that have concentrated the interest of this research. The first coincides with the second decade of the century and relates to a number of influences that, arising from scientific progress, determined the singular adventures of the more experimental tendencies in art. The second is centred around 1970: a period in which the interest drawn by environmental matters is well known. In both cases, contributions have been studied that reveal crucial concepts in defining the aesthetic experience as an event for the acquisition of knowledge through the senses. It is necessary to highlight the role of centrality that the concept of energy has throughout this research, as is evident even in its title. Energy as a material, sensitive reality is the substrate making it possible to navigate through the principle of epistemological unity underlying ecological thought. The continuous symbolic, physical and metaphorical references to it among the artists studied here are not a mere iconographic source: they remind of the inherency of the principle of environmental continuity within which the human being and the immensity of cosmos travel indissociably. A unified, consistent discourse on the contributions of the aesthetic experience addressed as knowledge through the senses weaves together the historic, conceptual and practical reading of the whole research. With it, a conceptual diagram is constructed – a model of design analysis – gathering together scientific, philosophical and design ideas. Somehow, the diagram tries to draw from the principles of ecological thought the correlation of continuity that, vacillating, tense, subtle and fragile, shifts incessantly and unresolved between interiority and exteriority.

Global instability analysis and control of three-dimensional long open cavity flow

The three-dimensional wall-bounded open cavity may be considered as a simplified geometry found in industrial applications such as leading gear or slotted flats on the airplane. Understanding the three-dimensional complex flow structure that surrounds this particular geometry is therefore of major industrial interest. At the light of the remarkable former investigations in this kind of flows, enough evidences suggest that the lateral walls have a great influence on the flow features and hence on their instability modes. Nevertheless, even though there is a large body of literature on cavity flows, most of them are based on the assumption that the flow is two-dimensional and spanwise-periodic. The flow over realistic open cavity should be considered. This thesis presents an investigation of three-dimensional wall-bounded open cavity with geometric ratio 6:2:1. To this aim, three-dimensional Direct Numerical Simulation (DNS) and global linear instability have been performed. Linear instability analysis reveals that the onset of the first instability in this open cavity is around Recr 1080. The three-dimensional shear layer mode with a complex structure is shown to be the most unstable mode. I t is noteworthy that the flow pattern of this high-frequency shear layer mode is similar to the observed unstable oscillations in supercritical unstable case. DNS of the cavity flow carried out at different Reynolds number from steady state until a nonlinear saturated state is obtained. The comparison of time histories of kinetic energy presents a clearly dominant energetic mode which shifts between low-frequency and highfrequency oscillation. A complete flow patterns from subcritical cases to supercritical case has been put in evidence. The flow structure at the supercritical case Re=1100 resembles typical wake-shedding instability oscillations with a lateral motion existed in the subcritical cases. Also, This flow pattern is similar to the observations in experiments. In order to validate the linear instability analysis results, the topology of the composite flow fields reconstructed by linear superposition of a three-dimensional base flow and its leading three-dimensional global eigenmodes has been studied. The instantaneous wall streamlines of those composited flows display distinguish influence region of each eigenmode. Attention has been focused on the leading high-frequency shear layer mode; the composite flow fields have been fully recognized with respect to the downstream wave shedding. The three-dimensional shear layer mode is shown to give rise to a typical wake-shedding instability with a lateral motions occurring downstream which is in good agreement with the experiment results. Moreover, the spanwise-periodic, open cavity with the same length to depth ratio has been also studied. The most unstable linear mode is different from the real three-dimensional cavity flow, because of the existence of the side walls. Structure sensitivity of the unstable global mode is analyzed in the flow control context. The adjoint-based sensitivity analysis has been employed to localized the receptivity region, where the flow is more sensible to momentum forcing and mass injection. Because of the non-normality of the linearized Navier-Stokes equations, the direct and adjoint field has a large spatial separation. The strongest sensitivity region is locate in the upstream lip of the three-dimensional cavity. This numerical finding is in agreement with experimental observations. Finally, a prototype of passive flow control strategy is applied.