Geological control of physiography in Southeast Queensland: A multi-scale analysis using GIS

The study reported here, constitutes a full review of the major geological events that have influenced the morphological development of the southeast Queensland region. Most importantly, it provides evidence that the region’s physiography continues to be geologically ‘active’ and although earthquakes are presently few and of low magnitude, many past events and tectonic regimes continue to be strongly influential over drainage, morphology and topography. Southeast Queensland is typified by highland terrain of metasedimentary and igneous rocks that are parallel and close to younger, lowland coastal terrain. The region is currently situated in a passive margin tectonic setting that is now under compressive stress, although in the past, the region was subject to alternating extensional and compressive regimes. As part of the investigation, the effects of many past geological events upon landscape morphology have been assessed at multiple scales using features such as the location and orientation of drainage channels, topography, faults, fractures, scarps, cleavage, volcanic centres and deposits, and recent earthquake activity. A number of hypotheses for local geological evolution are proposed and discussed. This study has also utilised a geographic information system (GIS) approach that successfully amalgamates the various types and scales of datasets used. A new method of stream ordination has been developed and is used to compare the orientation of channels of similar orders with rock fabric, in a topologically controlled approach that other ordering systems are unable to achieve. Stream pattern analysis has been performed and the results provide evidence that many drainage systems in southeast Queensland are controlled by known geological structures and by past geological events. The results conclude that drainage at a fine scale is controlled by cleavage, joints and faults, and at a broader scale, large river valleys, such as those of the Brisbane River and North Pine River, closely follow the location of faults. These rivers appear to have become entrenched by differential weathering along these planes of weakness. Significantly, stream pattern analysis has also identified some ‘anomalous’ drainage that suggests the orientations of these watercourses are geologically controlled, but by unknown causes. To the north of Brisbane, a ‘coastal drainage divide’ has been recognized and is described here. The divide crosses several lithological units of different age, continues parallel to the coast and prevents drainage from the highlands flowing directly to the coast for its entire length. Diversion of low order streams away from the divide may be evidence that a more recent process may be the driving force. Although there is no conclusive evidence for this at present, it is postulated that the divide may have been generated by uplift or doming associated with mid-Cenozoic volcanism or a blind thrust at depth. Also north of Brisbane, on the D’Aguilar Range, an elevated valley (the ‘Kilcoy Gap’) has been identified that may have once drained towards the coast and now displays reversed drainage that may have resulted from uplift along the coastal drainage divide and of the D’Aguilar blocks. An assessment of the distribution and intensity of recent earthquakes in the region indicates that activity may be associated with ancient faults. However, recent movement on these faults during these events would have been unlikely, given that earthquakes in the region are characteristically of low magnitude. There is, however, evidence that compressive stress is building and being released periodically and ancient faults may be a likely place for this stress to be released. The relationship between ancient fault systems and the Tweed Shield Volcano has also been discussed and it is suggested here that the volcanic activity was associated with renewed faulting on the Great Moreton Fault System during the Cenozoic. The geomorphology and drainage patterns of southeast Queensland have been compared with expected morphological characteristics found at passive and other tectonic settings, both in Australia and globally. Of note are the comparisons with the East Brazilian Highlands, the Gulf of Mexico and the Blue Ridge Escarpment, for example. In conclusion, the results of the study clearly show that, although the region is described as a passive margin, its complex, past geological history and present compressive stress regime provide a more intricate and varied landscape than would be expected along typical passive continental margins. The literature review provides background to the subject and discusses previous work and methods, whilst the findings are presented in three peer-reviewed, published papers. The methods, hypotheses, suggestions and evidence are discussed at length in the final chapter.

Multi-scale analysis of AFM tip and surface interactions

Thoroughly understanding AFM tip-surface interactions is crucial for many experimental studies and applications. It is important to realize that despite its simple appearance, the system of tip and sample surface involves multiscale interactions. In fact, the system is governed by a combination of molecular force (like the van der Waals force), its macroscopic representations (such as surface force) and gravitational force (a macroscopic force). Hence, in the system, various length scales are operative, from sub-nanoscale (at the molecular level) to the macroscopic scale. By integrating molecular forces into continuum equations, we performed a multiscale analysis and revealed the nonlocality effect between a tip and a rough solid surface and the mechanism governing liquid surface deformation and jumping. The results have several significant implications for practical applications. For instance, nonlocality may affect the measurement accuracy of surface morphology. At the critical state of liquid surface jump, the ratio of the gap between a tip and a liquid dome (delta) over the dome height (y(o)) is approximately (n-4) (for a large tip), which depends on the power law exponent n of the molecular interaction energy. These findings demonstrate that the multiscale analysis is not only useful but also necessary in the understanding of practical phenomena involving molecular forces. (c) 2007 Elsevier Ltd. All rights reserved.

Multi-scale analysis of connectivity for image retrieval

Previously, we proposed the concept of connectivity to obtain discriminating shape descriptors. In this paper, we use connectivity to obtain superior distance histograms for multi-scale images. Experiments are performed to evaluate the distance histograms, based on connectivity, for shape-based retrieval of multi-scale images. Item S8 within the MPEG-7 still images content set is used for performing experiments. Experimental results show that the proposed method enhances retrieval performance significantly.

Development of the multi-scale analysis model to simulate strain localization occurring during material processing

Abstract A detailed description of possibilities given by the developed Cellular Automata—Finite Element (CAFE) multi scale model for prediction of the initiation and propagation of micro shear bands and shear bands in metallic materials subjected to plastic deformation is presented in the work. Particular emphasis in defining the criterion for initiation of micro shear and shear bands, as well as in defining the transition rules for the cellular automata, is put on accounting for the physical aspects of these phenomena occurring in two different scales in the material. The proposed approach led to the creation of the real multi scale model of strain localization phenomena. This model predicts material behavior in various thermo-mechanical processes. Selected examples of applications of the developed model to simulations of metal forming processes, which involve strain localization, are presented in the work. An approach based on the Smoothed Particle Hydrodynamic, which allows to overcome difficulties with remeshing in the traditional CAFE method, is a subject of this work as well. In the developed model remeshing becomes possible and difficulties limiting application of the CAFE method to simple deformation processes are solved. Obtained results of numerical simulaA detailed description of possibilities given by the developed Cellular Automata—Finite Element (CAFE) multi scale model for prediction of the initiation and propagation of micro shear bands and shear bands in metallic materials subjected to plastic deformation is presented in the work. Particular emphasis in defining the criterion for initiation of micro shear and shear bands, as well as in defining the transition rules for the cellular automata, is put on accounting for the physical aspects of these phenomena occurring in two different scales in the material. The proposed approach led to the creation of the real multi scale model of strain localization phenomena. This model predicts material behavior in various thermo-mechanical processes. Selected examples of applications of the developed model to simulations of metal forming processes, which involve strain localization, are presented in the work. An approach based on the Smoothed Particle Hydrodynamic, which allows to overcome difficulties with remeshing in the traditional CAFE method, is a subject of this work as well. In the developed model remeshing becomes possible and difficulties limiting application of the CAFE method to simple deformation processes are solved. Obtained results of numerical simulations are compared with the experimental results of cold rolling process to show good predicative capabilities of the developed model.tions are compared with the experimental results of cold rolling process to show good predicative capabilities of the developed model.

Techniques and Methods for a multi-scale analysis of neuromuscular fatigue

This thesis proposes an integrated holistic approach to the study of neuromuscular fatigue in order to encompass all the causes and all the consequences underlying the phenomenon. Starting from the metabolic processes occurring at the cellular level, the reader is guided toward the physiological changes at the motorneuron and motor unit level and from this to the more general biomechanical alterations. In Chapter 1 a list of the various definitions for fatigue spanning several contexts has been reported. In Chapter 2, the electrophysiological changes in terms of motor unit behavior and descending neural drive to the muscle have been studied extensively as well as the biomechanical adaptations induced. In Chapter 3 a study based on the observation of temporal features extracted from sEMG signals has been reported leading to the need of a more robust and reliable indicator during fatiguing tasks. Therefore, in Chapter 4, a novel bi-dimensional parameter is proposed. The study on sEMG-based indicators opened a scenario also on neurophysiological mechanisms underlying fatigue. For this purpose, in Chapter 5, a protocol designed for the analysis of motor unit-related parameters during prolonged fatiguing contractions is presented. In particular, two methodologies have been applied to multichannel sEMG recordings of isometric contractions of the Tibialis Anterior muscle: the state-of-the-art technique for sEMG decomposition and a coherence analysis on MU spike trains. The importance of a multi-scale approach has been finally highlighted in the context of the evaluation of cycling performance, where fatigue is one of the limiting factors. In particular, the last chapter of this thesis can be considered as a paradigm: physiological, metabolic, environmental, psychological and biomechanical factors influence the performance of a cyclist and only when all of these are kept together in a novel integrative way it is possible to derive a clear model and make correct assessments.

A multi-scale analysis of transforming agricultural markets in the context of globalization: implications for natural resources, food prices and rural poverty in Latin America

Vivimos una época en la que el mundo se transforma aceleradamente. La globalización está siguiendo un curso imparable, la población mundial así como la población urbana siguen creciendo, y en los países emergentes los ingresos promedios aumentan, resultando en un cambio también acelerado de las dietas y hábitos alimentarios. En conjunto esos factores están causando un aumento fundamental de la demanda de alimentos. Junto con la apertura de los mercados agrícolas, estos procesos han provocado un crecimiento del comercio internacional de alimentos durante la última década. Dado que muchos países de América Latina están dotados de abundancia de recursos naturales, estas tendencias han producido un crecimiento rápido de las exportaciones de bienes primarios desde América Latina al resto del mundo. En sólo 30 años la participación en el mercado agrícola de América Latina casi se ha duplicado, desde 10% en 1980 a 18% en 2010. Este aumento del comercio agrícola ha dado lugar a un debate sobre una serie de cuestiones cruciales relacionadas con los impactos del comercio en la seguridad alimentaria mundial, en el medio ambiente o en la reducción de la pobreza rural en países en desarrollo. Esta tesis aplica un marco integrado para analizar varios impactos relacionados con la transformación de los mercados agrícolas y los mercados rurales debidos a la globalización y, en particular, al progresivo aumento del comercio internacional. En concreto, la tesis aborda los siguientes temas: En primer lugar, la producción mundial de alimentos tendrá que aumentar considerablemente para poder satisfacer la demanda de una población mundial de 9000 millones personas en 2050, lo cual plantea grandes desafíos sobre los sistemas de la producción de alimentos. Alcanzar este logro, sin comprometer la integridad del medio ambiente en regiones exportadoras, es un reto aún mayor. En este contexto, la tesis analiza los efectos de la liberalización del comercio mundial, considerando distintas tecnologías de producción agraria, sobre unos indicadores de seguridad alimentaria en diferentes regiones del mundo y sobre distintos indicadores ambientales, teniendo en cuenta escalas diferentes en América Latina y el Caribe. La tesis utiliza el modelo “International Model for Policy Analysis of Agricultural Commodities and Trade (IMPACT)” – un modelo dinámico de equilibrio parcial del sector agrícola a escala global – para modelar la apertura de los mercados agrícolas así como diferentes escenarios de la producción hasta el año 2050. Los resultados del modelo están vinculados a modelos biofísicos para poder evaluar los cambios en la huella hídrica y la calidad del agua, así como para cuantificar los impactos del cambio en el uso del suelo sobre la biodiversidad y los stocks de carbono en 2050. Los resultados indican que la apertura de los mercados agrícolas es muy importante para mejorar la seguridad alimentaria a nivel mundial, sin embargo, produce también presiones ambientales indeseables en algunas regiones de América Latina. Contrastando dos escenarios que consideran distintas modos de producción, la expansión de la tierra agrícola frente a un escenario de la producción más intensiva, se demuestra que las mejoras de productividad son generalmente superiores a la expansión de las tierras agrícolas, desde un punto de vista económico e ambiental. En cambio, los escenarios de intensificación sostenible no sólo hacen posible una mayor producción de alimentos, sino que también generan menos impactos medioambientales que los otros escenarios futuros en todas sus dimensiones: biodiversidad, carbono, emisiones de nitratos y uso del agua. El análisis muestra que hay un “trade-off” entre el objetivo de alcanzar la sostenibilidad ambiental y el objetivo de la seguridad alimentaria, independiente del manejo agrícola en el futuro. En segundo lugar, a la luz de la reciente crisis de los precios de alimentos en los años 2007/08, la tesis analiza los impactos de la apertura de los mercados agrícolas en la transmisión de precios de los alimentos en seis países de América Latina: Argentina, Brasil, Chile, Colombia, México y el Perú. Para identificar las posibles relaciones de cointegración entre los índices de precios al consumidor de alimentos y los índices de precios de agrarios internacionales, sujetos a diferentes grados de apertura de mercados agrícolas en los seis países de América Latina, se utiliza un modelo simple de corrección de error (single equation error correction). Los resultados indican que la integración global de los mercados agrícolas ha dado lugar a diferentes tasas de transmisión de precios en los países investigados. Sobre todo en el corto plazo, las tasas de transmisión dependen del grado de apertura comercial, mientras que en el largo plazo las tasas de transmisión son elevadas, pero en gran medida independientes del régimen de comercio. Por lo tanto, durante un período de shocks de precios mundiales una mayor apertura del comercio trae consigo más inestabilidad de los precios domésticos a corto plazo y la resultante persistencia en el largo plazo. Sin embargo, estos resultados no verifican necesariamente la utilidad de las políticas comerciales, aplicadas frecuentemente por los gobiernos para amortiguar los shocks de precios. Primero, porque existe un riesgo considerable de volatilidad de los precios debido a cambios bruscos de la oferta nacional si se promueve la autosuficiencia en el país; y segundo, la política de proteccionismo asume el riesgo de excluir el país de participar en las cadenas de suministro de alto valor del sector agrícola, y por lo tanto esa política podría obstaculizar el desarrollo económico. Sin embargo, es indispensable establecer políticas efectivas para reducir la vulnerabilidad de los hogares a los aumentos repentinos de precios de alimentos, lo cual requiere una planificación gubernamental precisa con el presupuesto requerido disponible. En tercer lugar, la globalización afecta a la estructura de una economía y, por medios distintos, la distribución de los ingreso en un país. Perú sirve como ejemplo para investigar más profundamente las cuestiones relacionadas con los cambios en la distribución de los ingresos en zonas rurales. Perú, que es un país que está cada vez más integrado en los mercados mundiales, consiguió importantes descensos en la pobreza extrema en sus zonas rurales, pero a la vez adolece de alta incidencia de pobreza moderada y de desigualdad de los ingresos en zonas rural al menos durante el periodo comprendido entre 2004 y 2012. Esta parte de la tesis tiene como objetivo identificar las fuerzas impulsoras detrás de estas dinámicas en el Perú mediante el uso de un modelo de microsimulación basado en modelos de generación de ingresos aplicado a nivel los hogares rurales. Los resultados indican que la fuerza principal detrás de la reducción de la pobreza ha sido el crecimiento económico general de la economía, debido a las condiciones macroeconómicas favorables durante el periodo de estudio. Estos efectos de crecimiento beneficiaron a casi todos los sectores rurales, y dieron lugar a la disminución de la pobreza rural extrema, especialmente entre los agricultores de papas y de maíz. En parte, estos agricultores probablemente se beneficiaron de la apertura de los mercados agrícolas, que es lo que podría haber provocado un aumento de los precios al productor en tiempos de altos precios mundiales de los alimentos. Sin embargo, los resultados también sugieren que para una gran parte de la población más pobre existían barreras de entrada a la hora de poder participar en el empleo asalariado fuera de la agricultura o en la producción de cultivos de alto valor. Esto podría explicarse por la falta de acceso a unos activos importantes: por ejemplo, el nivel de educación de los pobres era apenas mejor en 2012 que en 2004; y también las dotaciones de tierra y de mano de obra, sobre todo de los productores pobres de maíz y patata, disminuyeron entre 2004 y 2012. Esto lleva a la conclusión de que aún hay margen para aplicar políticas para facilitar el acceso a estos activos, que podría contribuir a la erradicación de la pobreza rural. La tesis concluye que el comercio agrícola puede ser un importante medio para abastecer una población mundial creciente y más rica con una cantidad suficiente de calorías. Para evitar adversos efectos ambientales e impactos negativos para los consumidores y de los productores pobres, el enfoque debe centrarse en las mejoras de la productividad agrícola, teniendo en cuenta los límites ambientales y ser socialmente inclusivo. En este sentido, será indispensable seguir desarrollando soluciones tecnológicas que garanticen prácticas de producción agrícola minimizando el uso de recursos naturales. Además, para los pequeños pobres agricultores será fundamental eliminar las barreras de entrada a los mercados de exportación que podría tener efectos indirectos favorables a través de la adopción de nuevas tecnologías alcanzables a través de mercados internacionales. ABSTRACT The world is in a state of rapid transition. Ongoing globalization, population growth, rising living standards and increasing urbanization, accompanied by changing dietary patterns throughout the world, are increasing the demand for food. Together with more open trade regimes, this has triggered growing international agricultural trade during the last decade. For many Latin American countries, which are gifted with relative natural resource abundance, these trends have fueled rapid export growth of primary goods. In just 30 years, the Latin American agricultural market share has almost doubled from 10% in 1980 to 18% in 2010. These market developments have given rise to a debate around a number of crucial issues related to the role of agricultural trade for global food security, for the environment or for poverty reduction in developing countries. This thesis uses an integrated framework to analyze a broad array of possible impacts related to transforming agricultural and rural markets in light of globalization, and in particular of increasing trade activity. Specifically, the following issues are approached: First, global food production will have to rise substantially by the year 2050 to meet effective demand of a nine billion people world population which poses major challenges to food production systems. Doing so without compromising environmental integrity in exporting regions is an even greater challenge. In this context, the thesis explores the effects of future global trade liberalization on food security indicators in different world regions and on a variety of environmental indicators at different scales in Latin America and the Caribbean, in due consideration of different future agricultural production practices. The International Model for Policy Analysis of Agricultural Commodities and Trade (IMPACT) –a global dynamic partial equilibrium model of the agricultural sector developed by the International Food Policy Research Institute (IFPRI)– is applied to run different future production scenarios, and agricultural trade regimes out to 2050. Model results are linked to biophysical models, used to assess changes in water footprints and water quality, as well as impacts on biodiversity and carbon stocks from land use change by 2050. Results indicate that further trade liberalization is crucial for improving food security globally, but that it would also lead to more environmental pressures in some regions across Latin America. Contrasting land expansion versus more intensified agriculture shows that productivity improvements are generally superior to agricultural land expansion, from an economic and environmental point of view. Most promising for achieving food security and environmental goals, in equal measure, is the sustainable intensification scenario. However, the analysis shows that there are trade-offs between environmental and food security goals for all agricultural development paths. Second, in light of the recent food price crisis of 2007/08, the thesis looks at the impacts of increasing agricultural market integration on food price transmission from global to domestic markets in six Latin American countries, namely Argentina, Brazil, Chile, Colombia, Mexico and Peru. To identify possible cointegrating relationships between the domestic food consumer price indices and world food price levels, subject to different degrees of agricultural market integration in the six Latin American countries, a single equation error correction model is used. Results suggest that global agricultural market integration has led to different levels of price path-through in the studied countries. Especially in the short-run, transmission rates depend on the degree of trade openness, while in the long-run transmission rates are high, but largely independent of the country-specific trade regime. Hence, under world price shocks more trade openness brings with it more price instability in the short-term and the resulting persistence in the long-term. However, these findings do not necessarily verify the usefulness of trade policies, often applied by governments to buffer such price shocks. First, because there is a considerable risk of price volatility due to domestic supply shocks if self-sufficiency is promoted. Second, protectionism bears the risk of excluding a country from participating in beneficial high-value agricultural supply chains, thereby hampering economic development. Nevertheless, to reduce households’ vulnerability to sudden and large increases of food prices, effective policies to buffer food price shocks should be put in place, but must be carefully planned with the required budget readily available. Third, globalization affects the structure of an economy and, by different means, the distribution of income in a country. Peru serves as an example to dive deeper into questions related to changes in the income distribution in rural areas. Peru, a country being increasingly integrated into global food markets, experienced large drops in extreme rural poverty, but persistently high rates of moderate rural poverty and rural income inequality between 2004 and 2012. The thesis aims at disentangling the driving forces behind these dynamics by using a microsimulation model based on rural household income generation models. Results provide evidence that the main force behind poverty reduction was overall economic growth of the economy due to generally favorable macroeconomic market conditions. These growth effects benefited almost all rural sectors, and led to declines in extreme rural poverty, especially among potato and maize farmers. In part, these farmers probably benefited from policy changes towards more open trade regimes and the resulting higher producer prices in times of elevated global food price levels. However, the results also suggest that entry barriers existed for the poorer part of the population to participate in well-paid wage-employment outside of agriculture or in high-value crop production. This could be explained by a lack of sufficient access to important rural assets. For example, poor people’s educational attainment was hardly better in 2012 than in 2004. Also land and labor endowments, especially of (poor) maize and potato growers, rather decreased than increased over time. This leads to the conclusion that there is still scope for policy action to facilitate access to these assets, which could contribute to the eradication of rural poverty. The thesis concludes that agricultural trade can be one important means to provide a growing and richer world population with sufficient amounts of calories. To avoid adverse environmental effects and negative impacts for poor food consumers and producers, the focus should lie on agricultural productivity improvements, considering environmental limits and be socially inclusive. In this sense, it will be crucial to further develop technological solutions that guarantee resource-sparing agricultural production practices, and to remove entry barriers for small poor farmers to export markets which might allow for technological spill-over effects from high-value global agricultural supply chains.

Multi-scale simulation using a hybrid mass-spring system and finite element model

Ply-scale finite element (FE) models are widely used to predict the performance of a composite structure based on material properties of individual plies. When simulating damage, these models neglect microscopic fracture processes which may have a significant effect on how a crack progresses within and between plies of a multidirectional laminate. To overcome this resolution limitation a multi-scale modelling technique is employed to simulate the effect micro-scale damage events have on the macro-scale response of a structure. The current paper discusses the development and validation of a hybrid mass-spring system and finite element modelling technique for multi-scale analysis. The model developed here is limited to elastic deformations; however, it is the first key step towards an efficient multi-scale damage model well suited to simulation of fracture in fibre reinforced composite materials. Various load cases have been simulated using the model developed here which show excellent accuracy compared to analytical and FE results. Future work is discussed, including extension of the model to incorporate damage modelling.

Multi-time scale analysis applied to long time simulation of power systems

The results are presented of applying multi-time scale analysis using the singular perturbation technique for long time simulation of power system problems. A linear system represented in state-space form can be decoupled into slow and fast subsystems. These subsystems can be simulated with different time steps and then recombined to obtain the system response. Simulation results with a two-time scale analysis of a power system show a large saving in computational costs.

Multi-scale structural and chemical analysis of sugarcane bagasse in the process of sequential acid-base pretreatment and ethanol production by Scheffersomyces shehatae and Saccharomyces cerevisiae

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Multi-Scale Modeling for Image Analysis of Brain Tumor Studies

Image-based modeling of tumor growth combines methods from cancer simulation and medical imaging. In this context, we present a novel approach to adapt a healthy brain atlas to MR images of tumor patients. In order to establish correspondence between a healthy atlas and a pathologic patient image, tumor growth modeling in combination with registration algorithms is employed. In a first step, the tumor is grown in the atlas based on a new multi-scale, multi-physics model including growth simulation from the cellular level up to the biomechanical level, accounting for cell proliferation and tissue deformations. Large-scale deformations are handled with an Eulerian approach for finite element computations, which can operate directly on the image voxel mesh. Subsequently, dense correspondence between the modified atlas and patient image is established using nonrigid registration. The method offers opportunities in atlasbased segmentation of tumor-bearing brain images as well as for improved patient-specific simulation and prognosis of tumor progression.

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.