Coral calcification under daily oxygen saturation and pH dynamics reveals the important role of oxygen

Coral reefs are essential to many nations, and are currently in global decline. Although climate models predict decreases in seawater pH (0.3 units) and oxygen saturation (5 percentage points), these are exceeded by the current daily pH and oxygen fluctuations on many reefs (pH 7.8-8.7 and 27-241% O2 saturation). We investigated the effect of oxygen and pH fluctuations on coral calcification in the laboratory using the model species Acropora millepora. Light calcification rates were greatly enhanced (+178%) by increased seawater pH, but only at normoxia; hyperoxia completely negated this positive effect. Dark calcification rates were significantly inhibited (51-75%) at hypoxia, whereas pH had no effect. Our preliminary results suggest that within the current oxygen and pH range, oxygen has substantial control over coral growth, whereas the role of pH is limited. This has implications for reef formation in this era of rapid climate change, which is accompanied by a decrease in seawater oxygen saturation owing to higher water temperatures and coastal eutrophication.

Trade, Exchange Rates, and Macroeconomic Dynamics in East Asia: Why the Electronics Cycle Matters

Against the background of increasing regional trade and investment, there is growing interest in monetary and macroeconomic policy coordination in East Asia. Although there is a sizable literature on macroeconomic linkages among East Asian countries and the potential merit of policy coordination in the region, the existing studies tend to examine these issues exclusively in terms of macroeconomic variables and do not consider how these aggregate variables are influenced by one prominent feature of a number of East Asian economies: their heavy dependence on the electronics industry. Although active engagement in the global electronics industry has been a powerful growth engine for the Asian countries, it has also left their economies vulnerable to cyclical fluctuations in the world electronics market. As the cycle of the global electronics industry exerts profound impacts on the medium-term dynamics of the Asian economies, it is imperative to take an explicit account of its influence when studying the way in which the regional economies are linked to one another and how this relationship can be altered by a specific policy initiative. We illustrate the importance of this point by examining recent studies on: (1) trade competition between China andother Asian countries and the role of the Chinese renminbi therein; and (2) the effect offluctuations in the yen/dollar exchange rate on the regional economies.

Influence of termal fluctuations in radiation damage cascade production and defect dynamics in tungsten

The detailed study of the deterioration suffered by the materials of the components of a nuclear facility, in particular those forming part of the reactor core, is a topic of great interest which importance derives in large technological and economic implications. Since changes in the atomic-structural properties of relevant components pose a risk to the smooth operation with clear consequences for security and life of the plant, controlling these factors is essential in any development of engineering design and implementation. In recent times, tungsten has been proposed as a structural material based on its good resistance to radiation, but still needs to be done an extensive study on the influence of temperature on the behavior of this material under radiation damage. This work aims to contribute in this regard. Molecular Dynamics (MD) simulations were carried out to determine the influence of temperature fluctuations on radiation damage production and evolution in Tungsten. We have particularly focused our study in the dynamics of defect creation, recombination, and diffusion properties. PKA energies were sampled in a range from 5 to 50 KeV. Three different temperature scenarios were analyzed, from very low temperatures (0-200K), up to high temperature conditions (300-500 K). We studied the creation of defects, vacancies and interstitials, recombination rates, diffusion properties, cluster formation, their size and evolution. Simulations were performed using Lammps and the Zhou EAM potential for W

Low-dimensional modeling of streaks in a wedge flow boundary layer

This paper is concerned with the low dimensional structure of optimal streaks in a wedge flow boundary layer, which have been recently shown to consist of a unique (up to a constant factor) three-dimensional streamwise evolving mode, known as the most unstable streaky mode. Optimal streaks exhibit a still unexplored/unexploited approximate self-similarity (not associated with the boundary layer self-similarity), namely the streamwise velocity re-scaled with their maximum remains almost independent of both the spanwise wavenumber and the streamwise coordinate; the remaining two velocity components instead do not satisfy this property. The approximate self-similar behavior is analyzed here and exploited to further simplify the description of optimal streaks. In particular, it is shown that streaks can be approximately described in terms of the streamwise evolution of the scalar amplitudes of just three one-dimensional modes, providing the wall normal profiles of the streamwise velocity and two combinations of the cross flow velocity components; the scalar amplitudes obey a singular system of three ordinary differential equations (involving only two degrees of freedom), which approximates well the streamwise evolution of the general streaks.

Efficient adaptive methods based on adjoint equations and truncation error estimation for unstructured grids

El propósito de esta tesis es la implementación de métodos eficientes de adaptación de mallas basados en ecuaciones adjuntas en el marco de discretizaciones de volúmenes finitos para mallas no estructuradas. La metodología basada en ecuaciones adjuntas optimiza la malla refinándola adecuadamente con el objetivo de mejorar la precisión de cálculo de un funcional de salida dado. El funcional suele ser una magnitud escalar de interés ingenieril obtenida por post-proceso de la solución, como por ejemplo, la resistencia o la sustentación aerodinámica. Usualmente, el método de adaptación adjunta está basado en una estimación a posteriori del error del funcional de salida mediante un promediado del residuo numérico con las variables adjuntas, “Dual Weighted Residual method” (DWR). Estas variables se obtienen de la solución del problema adjunto para el funcional seleccionado. El procedimiento habitual para introducir este método en códigos basados en discretizaciones de volúmenes finitos involucra la utilización de una malla auxiliar embebida obtenida por refinamiento uniforme de la malla inicial. El uso de esta malla implica un aumento significativo de los recursos computacionales (por ejemplo, en casos 3D el aumento de memoria requerida respecto a la que necesita el problema fluido inicial puede llegar a ser de un orden de magnitud). En esta tesis se propone un método alternativo basado en reformular la estimación del error del funcional en una malla auxiliar más basta y utilizar una técnica de estimación del error de truncación, denominada _ -estimation, para estimar los residuos que intervienen en el método DWR. Utilizando esta estimación del error se diseña un algoritmo de adaptación de mallas que conserva los ingredientes básicos de la adaptación adjunta estándar pero con un coste computacional asociado sensiblemente menor. La metodología de adaptación adjunta estándar y la propuesta en la tesis han sido introducidas en un código de volúmenes finitos utilizado habitualmente en la industria aeronáutica Europea. Se ha investigado la influencia de distintos parámetros numéricos que intervienen en el algoritmo. Finalmente, el método propuesto se compara con otras metodologías de adaptación de mallas y su eficiencia computacional se demuestra en una serie de casos representativos de interés aeronáutico. ABSTRACT The purpose of this thesis is the implementation of efficient grid adaptation methods based on the adjoint equations within the framework of finite volume methods (FVM) for unstructured grid solvers. The adjoint-based methodology aims at adapting grids to improve the accuracy of a functional output of interest, as for example, the aerodynamic drag or lift. The adjoint methodology is based on the a posteriori functional error estimation using the adjoint/dual-weighted residual method (DWR). In this method the error in a functional output can be directly related to local residual errors of the primal solution through the adjoint variables. These variables are obtained by solving the corresponding adjoint problem for the chosen functional. The common approach to introduce the DWR method within the FVM framework involves the use of an auxiliary embedded grid. The storage of this mesh demands high computational resources, i.e. over one order of magnitude increase in memory relative to the initial problem for 3D cases. In this thesis, an alternative methodology for adapting the grid is proposed. Specifically, the DWR approach for error estimation is re-formulated on a coarser mesh level using the _ -estimation method to approximate the truncation error. Then, an output-based adaptive algorithm is designed in such way that the basic ingredients of the standard adjoint method are retained but the computational cost is significantly reduced. The standard and the new proposed adjoint-based adaptive methodologies have been incorporated into a flow solver commonly used in the EU aeronautical industry. The influence of different numerical settings has been investigated. The proposed method has been compared against different grid adaptation approaches and the computational efficiency of the new method has been demonstrated on some representative aeronautical test cases.

Simulación numérica de un problema de contaminación atmosférica

La ecuación en derivadas parciales de advección difusión con reacción química es la base de los modelos de dispersión de contaminantes en la atmósfera, y los diferentes métodos numéricos empleados para su resolución han sido objeto de amplios estudios a lo largo de su desarrollo. En esta Tesis se presenta la implementación de un nuevo método conservativo para la resolución de la parte advectiva de la ecuación en derivadas parciales que modela la dispersión de contaminantes dentro del modelo mesoescalar de transporte químico CHIMERE. Este método está basado en una técnica de volúmenes finitos junto con una interpolación racional. La ventaja de este método es la conservación exacta de la masa transportada debido al empleo de la ley de conservación de masas. Para ello emplea una formulación de flujo basado en el cálculo de la integral ponderada dentro de cada celda definida para la discretización del espacio en el método de volúmenes finitos. Los resultados numéricos obtenidos en las simulaciones realizadas (implementando el modelo conservativo para la advección en el modelo CHIMERE) se han comparado con los datos observados de concentración de contaminantes registrados en la red de estaciones de seguimiento y medición distribuidas por la Península Ibérica. Los datos estadísticos de medición del error, la media normalizada y la media absoluta normalizada del error, presentan valores que están dentro de los rangos propuestos por la EPA para considerar el modelo preciso. Además, se introduce un nuevo método para resolver la parte advectivadifusiva de la ecuación en derivadas parciales que modeliza la dispersión de contaminantes en la atmósfera. Se ha empleado un método de diferencias finitas de alto orden para resolver la parte difusiva de la ecuación de transporte de contaminantes junto con el método racional conservativo para la parte advectiva en una y dos dimensiones. Los resultados obtenidos de la aplicación del método a diferentes situaciones incluyendo casos académicos y reales han sido comparados con la solución analítica de la ecuación de advección-difusión, demostrando que el nuevo método proporciona un resultado preciso para aproximar la solución. Por último, se ha desarrollado un modelo completo que contempla los fenómenos advectivo y difusivo con reacción química, usando los métodos anteriores junto con una técnica de diferenciación regresiva (BDF2). Esta técnica consiste en un método implícito multipaso de diferenciación regresiva de segundo orden, que nos permite resolver los problemas rígidos típicos de la química atmosférica, modelizados a través de sistemas de ecuaciones diferenciales ordinarias. Este método hace uso de la técnica iterativa Gauss- Seidel para obtener la solución de la parte implícita de la fórmula BDF2. El empleo de la técnica de Gauss-Seidel en lugar de otras técnicas comúnmente empleadas, como la iteración por el método de Newton, nos proporciona rapidez de cálculo y bajo consumo de memoria, ideal para obtener modelos operativos para la resolución de la cinética química atmosférica. ABSTRACT Extensive research has been performed to solve the atmospheric chemicaladvection- diffusion equation and different numerical methods have been proposed. This Thesis presents the implementation of an exactly conservative method for the advection equation in the European scale Eulerian chemistry transport model CHIMERE based on a rational interpolation and a finite volume algorithm. The advantage of the method is that the cell-integrated average is predicted via a flux formulation, thus the mass is exactly conserved. Numerical results are compared with a set of observation registered at some monitoring sites in Spain. The mean normalized bias and the mean normalized absolute error present values that are inside the range to consider an accurate model performance. In addition, it has been introduced a new method to solve the advectiondiffusion equation. It is based on a high-order accurate finite difference method to solve de diffusion equation together with a rational interpolation and a finite volume to solve the advection equation in one dimension and two dimensions. Numerical results obtained from solving several problems include academic and real atmospheric problems have been compared with the analytical solution of the advection-diffusion equation, showing that the new method give an efficient algorithm for solving such problems. Finally, a complete model has been developed to solve the atmospheric chemical-advection-diffusion equation, adding the conservative method for the advection equation, the high-order finite difference method for the diffusion equation and a second-order backward differentiation formula (BDF2) to solve the atmospheric chemical kinetics. The BDF2 is an implicit, second order multistep backward differentiation formula used to solve the stiff systems of ordinary differential equations (ODEs) from atmospheric chemistry. The Gauss-Seidel iteration is used for approximately solving the implicitly defined BDF solution, giving a faster tool than the more commonly used iterative modified Newton technique. This method implies low start-up costs and a low memory demand due to the use of Gauss-Seidel iteration.

Relation of Lagragian structures and drifter dynamics in the Gulf of Mexico

We use a Lagrangian descriptor (the so called function M) which measures the length of particle trajectories on the ocean surface over a given interval of time. With this tool we identify the Lagrangian skeleton of the flow and compare it on three datasets over the Gulf of Mexico during the year 2010. The satellite altimetry data used come from AVISO and simulations from HYCOM GOMl0.04 experiments 30.1 and 31.0. We contrast the Lagrangian structure and transport using the evolution of several surface drifters. We show that the agreement in relevant cases between Lagrangian structures and dynamics of drifters depends on the quality of the data on the studied area.

Modeling GHG emissions, N and C dynamics in Spanish agricultural soils.

To date, only few initiatives have been carried out in Spain in order to use mathematical models (e.g. DNDC, DayCent, FASSET y SIMSNIC) to estimate nitrogen (N) and carbon (C) dynamics as well as greenhouse gases (GHG) in Spanish agrosystems. Modeling at this level may allow to gain insight on both the complex relationships between biological and physicochemical processes, controlling the processes leading to GHG production and consumption in soils (e.g. nitrification, denitrification, decomposing, etc.), and the interactions between C and N cycles within the different components of the continuum plant-soil-environment. Additionally, these models can simulate the processes behind production, consumition and transport of GHG (e.g. nitrous oxide, N2O, and carbon dioxide, CO2) in the short and medium term and at different scales. Other sources of potential pollution from soils can be identified and quantified using these process-based models (e.g. NO3 y NH3).

An experimental analysis od the stability and the dynamics of asixymmetric liquid bridges between unequal disks

In this paper experimental results related to both stability an the dynamic of a asiximmetric liquid bridge between unequal disk are presented. Experiments have been performed by using a drop tower facility and the response of the liquid bridge to a sudden change of the acceleration level acting on it has bee obtained.

Simulación eficiente de mecanismos flexibles mediante formulaciones topológicas

El objetivo de esta Tesis es presentar un método eficiente para la evaluación de sistemas multi-cuerpo con elementos flexibles con pequeñas deformaciones, basado en métodos topológicos para la simulación de sistemas tan complejos como los que se utilizan en la práctica y en tiempo real o próximo al real. Se ha puesto un especial énfasis en la resolución eficiente de aquellos aspectos que conllevan mayor coste computacional, tales como la evaluación de las ecuaciones dinámicas y el cálculo de los términos de inercia. Las ecuaciones dinámicas se establecen en función de las variables independientes del sistema, y la integración de las mismas se realiza mediante formulaciones implícitas de index-3. Esta Tesis se articula en seis Capítulos. En el Capítulo 1 se realiza una revisión bibliográfica de la simulación de sistemas flexibles y los métodos más relevantes de integración de las ecuaciones diferenciales del movimiento. Asimismo, se presentan los objetivos de esta Tesis. En el Capítulo 2 se presenta un método semi-recursivo para la evaluación de las ecuaciones de los sistemas multi-cuerpo con elementos flexibles basado en formulaciones topológicas y síntesis modal. Esta Tesis determina la posición de cada punto del cuerpo flexible en función de un sistema de referencia flotante que se mueve con dicho cuerpo y de las amplitudes de ciertos modos de deformación calculados a partir de un mallado obtenido mediante el Método de Elementos Finitos. Se presta especial atención en las condiciones de contorno que se han de tener en cuenta a la hora de establecer las variables que definen la deformación del cuerpo flexible. El Capítulo 3 se centra en la evaluación de los términos de inercia de los sistemas flexibles que generalmente conllevan un alto coste computacional. Se presenta un método que permite el cálculo de dichos términos basado en el uso de 24 matrices constantes que pueden ser calculadas previamente al proceso de integración. Estas matrices permiten evaluar la matriz de masas y el vector de fuerzas de inercia dependientes de la velocidad sin que sea necesario evaluar la posición deformada de todos los puntos del cuerpo flexible. Se realiza un análisis pormenorizado de dichas matrices con el objetivo de optimizar su cálculo estableciendo aproximaciones que permitan reducir el número de dichos términos y optimizar aún más su evaluación. Se analizan dos posibles simplificaciones: la primera utiliza una discretización no-consistente basada en elementos finitos en los que se definen únicamente los desplazamientos axiales de los nodos; en la segunda propuesta se hace uso de una matriz de masas concentradas (Lumped Mass). Basándose en la formulación presentada, el Capítulo 4 aborda la integración eficiente de las ecuaciones dinámicas. Se presenta un método iterativo para la integración con fórmulas de index-3 basado en la proyección de las ecuaciones dinámicas según las variables independientes del sistema multi-cuerpo. El cálculo del residuo del sistema de ecuaciones no lineales que se ha de resolver de modo iterativo se realiza mediante un proceso recursivo muy eficiente que aprovecha la estructura topológica del sistema. Se analizan tres formas de evaluar la matriz tangente del citado sistema no lineal: evaluación aproximada, numérica y recursiva. El método de integración presentado permite el uso de distintas fórmulas. En esta Tesis se analizan la Regla Trapezoidal, la fórmula BDF de segundo orden y un método híbrido TR-BDF2. Para este último caso se presenta un algoritmo de paso variable. En el Capítulo 5 plantea la implementación del método propuesto en un programa general de simulación de mecanismos que permita la resolución de cualquier sistema multi-cuerpo definiéndolo mediante un fichero de datos. La implementación de este programa se ha realizado tanto en C++ como en Java. Se muestran los resultados de las formulaciones presentadas en esta Tesis mediante la simulación de cuatro ejemplos de distinta complejidad. Mediante análisis concretos se comparan la formulación presentada con otras existentes. También se analiza el efecto del lenguaje de programación utilizado en la implementación y los efectos de las posibles simplificaciones planteadas. Por último, el Capítulo 6 resume las principales conclusiones alcanzadas en la Tesis y las futuras líneas de investigación que con ella se abren. ABSTRACT This Thesis presents an efficient method for solving the forward dynamics of a multi-body sys-tem formed by rigid and flexible bodies with small strains for real-time simulation of real-life models. It is based on topological formulations. The presented work focuses on the efficient solution of the most time-consuming tasks of the simulation process, such as the numerical integration of the motion differential equations and in particular the evaluation of the inertia terms corresponding to the flexible bodies. The dynamic equations are formulated in terms of independent variables of the muti-body system, and they are integrated by means of implicit index-3 formulae. The Thesis is arranged in six chapters. Chapter 1 presents a review of the most relevant and recent contributions related to the modelization of flexible multi-body systems and the integration of the corresponding dynamic equations. The main objectives of the Thesis are also presented in detail. Chapter 2 presents a semi-recursive method for solving the equations of a multi-body system with flexible bodies based on topological formulations and modal synthesis. This Thesis uses the floating frame approach and the modal amplitudes to define the position of any point at the flexible body. These modal deformed shapes are obtained by means of the Finite Element Method. Particular attention has been taken to the boundary conditions used to define the deformation of the flexible bodies. Chapter 3 focuses on the evaluation of the inertia terms, which is usually a very time-consuming task. A new method based on the use of 24 constant matrices is presented. These matrices are evaluated during the set-up step, before the integration process. They allow the calculation of the inertia terms in terms of the position and orientation of the local coordinate system and the deformation variables, and there is no need to evaluate the position and velocities of all the nodes of the FEM mesh. A deep analysis of the inertia terms is performed in order to optimize the evaluation process, reducing both the terms used and the number of arithmetic operations. Two possible simplifications are presented: the first one uses a non-consistent approach in order to define the inertia terms respect to the Cartesian coordinates of the FEM mesh, rejecting those corresponding to the angular rotations; the second approach makes use of lumped mass matrices. Based on the previously presented formulation, Chapter 4 is focused on the numerical integration of the motion differential equations. A new predictor-corrector method based on index-3 formulae and on the use of multi-body independent variables is presented. The evaluation of the dynamic equations in a new time step needs the solution of a set on nonlinear equations by a Newton-Raphson iterative process. The computation of the corresponding residual vector is performed efficiently by taking advantage of the system’s topological structure. Three methods to compute the tangent matrix are presented: an approximated evaluation that considers only the most relevant terms, a numerical approach based on finite differences and a recursive method that uses the topological structure. The method presented for integrating the dynamic equations can use a variety of integration formulae. This Thesis analyses the use of the trapezoidal rule, the 2nd order BDF formula and the hybrid TR-BDF2 method. A variable-time step strategy is presented for the last one. Chapter 5 describes the implementation of the proposed method in a general purpose pro-gram for solving any multibody defined by a data file. This program is implemented both in C++ and Java. Four examples are used to check the validity of the formulation and to compare this method with other methods commonly used to solve the dynamic equations of multi-body systems containing flexible bodies. The efficiency of the programming methodology used and the effect of the possible simplifications proposed are also analyzed. Chapter 6 summarizes the main Conclusions obtained in this Thesis and the new lines of research that have been opened.

Conceptual modelling to assess how the interplay of hydrological connectivity, catchment storage and tracer dynamics controls nonstationary water age estimates

Acknowledgements We would like to gratefully acknowledge the data provided by SEPA, Iain Malcolm. Mark Speed, Susan Waldron and many MSS staff helped with sample collection and lab analysis. We thank the European Research Council (project GA 335910 VEWA) for funding and are grateful for the constructive comments provided by three anonymous reviewers.