Los paisajes del desecho: reactivación de los lugares del deterioro

Actualmente en nuestro planeta producimos 1.300 millones de toneladas de residuos urbanos al año. Si los extendemos sobre la superficie de un cuadrado de lado 100 m (una hectárea) alcanzarían una altura de 146 km. ¿Cuál es el origen de nuestros residuos? ¿A dónde va esta basura? ¿Cómo nos afecta? ¿Tiene alguna utilidad? Se trata de un problema antiguo que, en los últimos tiempos, ha adquirido una nueva dimensión por el tipo y la cantidad de residuos generados. Las primeras preocupaciones de la ciudad por ordenar estos problemas dieron lugar al establecimiento de espacios o lugares específicos para la acumulación de los residuos urbanos: los vertederos. Los desechos hoy se generan más rápidamente que los medios disponibles para reciclarlos o tratarlos. Los vertederos de residuos urbanos son y seguirán siendo, a corto y medio plazo, soluciones válidas por ser un método de gestión relativamente barato, sobre todo en los países en vías de desarrollo. Como consecuencia y necesidad de lo anterior, se plantea demostrar que la recuperación y la transformación de estos vertederos de residuos urbanos (lugares del deterioro), una vez abandonados, es posible y que además pueden dar lugar a nuevos espacios públicos estratégicos de la ciudad contemporánea. Son espacios de oportunidad, vacíos monumentales producto de una reactivación arquitectónica y paisajística realizada a partir de complejos procesos de ingeniería medioambiental. Pero las soluciones aplicadas a los vertederos de residuos urbanos desde mediados del siglo XX se han realizado exclusivamente desde la ingeniería para tratar de resolver cuestiones técnicas, un modelo agotado que ya no puede gestionar la magnitud que este problema ha alcanzado, haciéndose necesaria e inevitable la participación de la arquitectura para abrir nuevas líneas de investigación y de acción. En estos primeros compases del siglo XXI existe una “nueva” preocupación, un “nuevo” interés en los paradigmas de lo ecológico y de la sostenibilidad, también un interés filosófico (que igualmente otorga un nuevo valor al residuo como recurso), que dirigen su mirada hacia un concepto de paisaje abierto y diferente a modelos anteriores más estáticos, recuperando como punto de partida el ideal pintoresco. El landscape urbanism se consolida como una disciplina capaz de dar respuesta a lo natural y artificial simultáneamente, que sustituye a las herramientas tradicionales de la arquitectura para solucionar los problemas de la ciudad contemporánea, incorporando las infraestructuras de gran escala, como un vertedero de residuos urbanos, y los paisajes públicos que generan como el verdadero mecanismo de organización del urbanismo de hoy. No se trata solo de un modelo formal sino, lo que es más importante: de un modelo de procesos. Esta nueva preocupación permite abordar la cuestión del paisaje de manera amplia, sin restricciones, con un alto grado de flexibilidad en las nuevas propuestas que surgen como consecuencia de estos conceptos, si bien los esfuerzos, hasta la fecha, parecen haberse dirigido más hacia el fenómeno de lo estético, quedando todavía por explorar las consecuencias políticas, sociales, económicas y energéticas derivadas de los residuos. También las arquitectónicas. El proyecto del landscape urbanism se ocupa de la superficie horizontal, del plano del suelo. Desde siempre, la preparación de este plano para desarrollar cualquier actividad humana ha sido un gesto fundacional, un gesto propio necesario de toda arquitectura, que además ahora debe considerarlo como un medio o soporte biológicamente activo. En términos contemporáneos, el interés disciplinar radica en la continuidad y en la accesibilidad del suelo, diluyendo los límites; en que funcione a largo plazo, que se anticipe al cambio, a través de la flexibilidad y de la capacidad de negociación, y que sea público. La recuperación de un vertedero de residuos urbanos ofrece todas estas condiciones. Un breve recorrido por la historia revela los primeros ejemplos aislados de recuperación de estos lugares del deterioro, que han pasado por distintas fases en función de la cantidad y el tipo de los desechos producidos, evolucionando gracias a la tecnología y a una nueva mirada sobre el paisaje, hasta desarrollar una verdadera conciencia de lo ecológico (nacimiento de una ideología). El Monte Testaccio en Roma (siglos I-III d.C.) constituye un caso paradigmático y ejemplar de vertedero planificado a priori no solo como lugar en el que depositar los residuos, sino como lugar que será recuperado posteriormente y devuelto a la ciudad en forma de espacio público. Una topografía de desechos generada por acumulación, organizada y planificada durante tres siglos, que nos hace reflexionar sobre los temas de producción, consumo y proyecto arquitectónico. El Monte Testaccio revela una fuente de inspiración, un arquetipo de gestión sostenible de los recursos y del territorio. A través de la experiencia en la recuperación y transformación en espacios públicos de casos contemporáneos, como el antiguo vertedero de Valdemingómez en Madrid o el de El Garraf en Barcelona, se han analizado las técnicas y las soluciones empleadas para establecer nuevas herramientas de proyecto planteadas en clave de futuro, que revelan la importancia de los procesos frente a la forma, en los cuales intervienen muchos factores (tanto naturales como artificiales), entre ellos la vida y el tiempo de la materia viva acumulada. Son lugares para nuevas oportunidades y ejemplos de una nueva relación con la naturaleza. La reactivación de los vertederos de residuos, a través del proyecto, nos propone una nueva topografía construida en el tiempo, el suelo como soporte, como punto de encuentro de la naturaleza y los sistemas tecnológicos de la ciudad que posibilitan nuevos modos de vida y nuevas actividades. Los vertederos de residuos son inmensas topografías naturales surgidas de procesos artificiales, atalayas desde las que divisar un nuevo horizonte, un nuevo mundo, un nuevo futuro donde sea posible lograr la reversibilidad de nuestros actos del deterioro. Pero la voluntad de estas recuperaciones y transformaciones no consiste exclusivamente en su reintegración al paisaje, sino que han servido como muestra de las nuevas actitudes que la sociedad ha de emprender en relación a los temas medio ambientales. ABSTRACT Here on our planet we currently produce 1.3 billion tonnes of urban waste per year. If we were to spread this over a surface of 100m2 (one hectare), it would reach a height of 146km. What is the origin of this waste? Where does our refuse go? How does it affect us? Does it have any uses? We are dealing with an old problem which, in recent times, has taken on a new dimension due to the type of waste and the amount generated. Cities’ first concerns in resolving these problems gave rise to the establishment of areas or specific places for the accumulation of urban waste: landfills. These days, waste is generated more quickly than the available resources can recycle or process it. Urban waste landfills are and will continue to be, in the short and mid-term, valid solutions, given that they constitute a relatively cheap method for waste management, especially in developing countries. Consequently and necessarily, we plan to demonstrate that it is possible to recover and transform these urban waste landfills (areas of deterioration) once they have been abandoned and that they can give rise to new strategic public areas in contemporary cities. They are areas of opportunity, monumental vacancies produced by an architectural reactivation of the landscape, which is achieved using complex processes of environmental engineering. But the solutions applied to urban waste landfills throughout the 20th century have used engineering exclusively in the attempt to resolve the technical aspects. This is a worn-out model which can no longer handle the magnitude which the problem has attained and therefore, there is an inevitable need for the participation of architecture, which can open new lines of research and action. In these first steps into the 21st century, there is a “new” concern, a “new” interest in the paradigms of environmentalism and sustainability. There is also a philosophical interest (which assigns the new value of ‘resource’ to waste) and all is aimed towards the concept of an open landscape, unlike the previous, more static models, and the intention is to recover picturesque ideals as the starting point. Landscape urbanism has been established as a discipline capable of simultaneously responding to the natural and the artificial, replacing the traditional tools of architecture in order to resolve contemporary cities’ problems. It incorporates large scale infrastructures, such as urban waste landfills, and public landscapes which are generated as the true organisational mechanism of modern day urbanism. It is not merely a formal model, it is more important than that: it is a model of processes. This new concern allows us to address the matter of landscape in a broad way, without restrictions, and with a great degree of flexibility in the new proposals which come about as a consequence of these concepts. However, efforts to date seem to have been more directed at aesthetic aspects and we have yet to explore the political, social, economic and energetic consequences derived from waste – nor have we delved into the architectural consequences. The landscape urbanism project is involved with the horizontal surface, the ground plane. Traditionally, the preparation of this plane for the development of any human activity has been a foundational act, a necessary act of all architecture, but now this plane must be considered as a biologically active medium or support. In contemporary terms, the discipline’s interest lies in the continuity and accessibility of the land, diffusing the limits; in long term functionality; in the anticipation of change, via flexibility and the ability to negotiate; and in it being a public space. The recovery of an urban waste landfill offers all of these conditions. A brief look through history reveals the first isolated examples of recovery of these spaces of deterioration. They have gone through various phases based on the quantity and type of waste produced, they have evolved thanks to technology and a new outlook on the landscape, and a real environmental awareness has been developed (the birth of an ideology). Monte Testaccio in Rome (1st to 3rd Century AD) constitutes a paradigmatic and exemplary case of a landfill that was planned a priori not only as a place to deposit waste but also as a place that would be subsequently recovered and given back to the city in the form of a public space. This spoil mound, generated by organised and planned accumulation over three centuries, makes us reflect on the themes of production, consumption and architectural planning. Monte Testaccio reveals a source of inspiration, an archetype of the sustainable management of resources and land. Using our experience of contemporary cases of land recovery and its transformation into public spaces, such as the former Valdemingómez landfill in Madrid or the Garraf in Barcelona, we analysed the techniques and solutions used in order to establish new project tools. These are proposed with an eye on the future, seeing as they reveal the importance of the processes over the form and involve many factors (both natural and artificial), including the life and age of the accumulated living matter. They are places for new opportunities and examples of our new relationship with nature. The reactivation of landfills, via this project, is a proposal for a new topography built within time, using the ground as the support, as the meeting point between nature and the technological systems of the city which make it possible for new ways of life and new activities to come about. Landfills are immense natural topographical areas produced by artificial processes, watchtowers from which to discern a new horizon, a new world, a new future in which it will be possible to reverse our acts of deterioration. But the intention behind these recoveries and transformations does not only hope for landscape reintegration but it also hopes that they will also serve as a sign of the new attitudes that must be adopted by society with regard to environmental matters.

Engineering Computational Emotion - A Reference Model for Emotion in Artificial Systems

Emotion is generally argued to be an influence on the behavior of life systems, largely concerning flexibility and adaptivity. The way in which life systems acts in response to a particular situations of the environment, has revealed the decisive and crucial importance of this feature in the success of behaviors. And this source of inspiration has influenced the way of thinking artificial systems. During the last decades, artificial systems have undergone such an evolution that each day more are integrated in our daily life. They have become greater in complexity, and the subsequent effects are related to an increased demand of systems that ensure resilience, robustness, availability, security or safety among others. All of them questions that raise quite a fundamental challenges in control design. This thesis has been developed under the framework of the Autonomous System project, a.k.a the ASys-Project. Short-term objectives of immediate application are focused on to design improved systems, and the approaching of intelligence in control strategies. Besides this, long-term objectives underlying ASys-Project concentrate on high order capabilities such as cognition, awareness and autonomy. This thesis is placed within the general fields of Engineery and Emotion science, and provides a theoretical foundation for engineering and designing computational emotion for artificial systems. The starting question that has grounded this thesis aims the problem of emotion--based autonomy. And how to feedback systems with valuable meaning has conformed the general objective. Both the starting question and the general objective, have underlaid the study of emotion, the influence on systems behavior, the key foundations that justify this feature in life systems, how emotion is integrated within the normal operation, and how this entire problem of emotion can be explained in artificial systems. By assuming essential differences concerning structure, purpose and operation between life and artificial systems, the essential motivation has been the exploration of what emotion solves in nature to afterwards analyze analogies for man--made systems. This work provides a reference model in which a collection of entities, relationships, models, functions and informational artifacts, are all interacting to provide the system with non-explicit knowledge under the form of emotion-like relevances. This solution aims to provide a reference model under which to design solutions for emotional operation, but related to the real needs of artificial systems. The proposal consists of a multi-purpose architecture that implement two broad modules in order to attend: (a) the range of processes related to the environment affectation, and (b) the range or processes related to the emotion perception-like and the higher levels of reasoning. This has required an intense and critical analysis beyond the state of the art around the most relevant theories of emotion and technical systems, in order to obtain the required support for those foundations that sustain each model. The problem has been interpreted and is described on the basis of AGSys, an agent assumed with the minimum rationality as to provide the capability to perform emotional assessment. AGSys is a conceptualization of a Model-based Cognitive agent that embodies an inner agent ESys, the responsible of performing the emotional operation inside of AGSys. The solution consists of multiple computational modules working federated, and aimed at conforming a mutual feedback loop between AGSys and ESys. Throughout this solution, the environment and the effects that might influence over the system are described as different problems. While AGSys operates as a common system within the external environment, ESys is designed to operate within a conceptualized inner environment. And this inner environment is built on the basis of those relevances that might occur inside of AGSys in the interaction with the external environment. This allows for a high-quality separate reasoning concerning mission goals defined in AGSys, and emotional goals defined in ESys. This way, it is provided a possible path for high-level reasoning under the influence of goals congruence. High-level reasoning model uses knowledge about emotional goals stability, letting this way new directions in which mission goals might be assessed under the situational state of this stability. This high-level reasoning is grounded by the work of MEP, a model of emotion perception that is thought as an analogy of a well-known theory in emotion science. The work of this model is described under the operation of a recursive-like process labeled as R-Loop, together with a system of emotional goals that are assumed as individual agents. This way, AGSys integrates knowledge that concerns the relation between a perceived object, and the effect which this perception induces on the situational state of the emotional goals. This knowledge enables a high-order system of information that provides the sustain for a high-level reasoning. The extent to which this reasoning might be approached is just delineated and assumed as future work. This thesis has been studied beyond a long range of fields of knowledge. This knowledge can be structured into two main objectives: (a) the fields of psychology, cognitive science, neurology and biological sciences in order to obtain understanding concerning the problem of the emotional phenomena, and (b) a large amount of computer science branches such as Autonomic Computing (AC), Self-adaptive software, Self-X systems, Model Integrated Computing (MIC) or the paradigm of models@runtime among others, in order to obtain knowledge about tools for designing each part of the solution. The final approach has been mainly performed on the basis of the entire acquired knowledge, and described under the fields of Artificial Intelligence, Model-Based Systems (MBS), and additional mathematical formalizations to provide punctual understanding in those cases that it has been required. This approach describes a reference model to feedback systems with valuable meaning, allowing for reasoning with regard to (a) the relationship between the environment and the relevance of the effects on the system, and (b) dynamical evaluations concerning the inner situational state of the system as a result of those effects. And this reasoning provides a framework of distinguishable states of AGSys derived from its own circumstances, that can be assumed as artificial emotion.

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

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

Sistema multiplataforma de gestión integral de huertos urbanos

En este Proyecto Fin de Grado se construirá una herramienta de gestión integral de centros hortícolas donde una serie de huertos cuidados por personas en situación de discapacidad son alquilados a terceros. Esta iniciativa se lleva a cabo gracias a la iniciativa “La Huerta de Montecarmelo” de la Fundación Carmen Pardo-Valcarce de Madrid. Este proyecto es el resultado de la colaboración entre la Escuela Técnica Superior de Ingeniería de Sistemas Informáticos y la Fundación, a través de un programa de Prácticas Externas que duró doce meses. Por una parte, tras años de trabajo en esta Obra Social, se encontró que muchos de los clientes, pasado el verano, se desvinculaban de las tareas y del medio. A fin de solucionar esos problemas, se propuso construir una aplicación web, comunicada con otros dispositivos, como Smartphones, permitiendo un flujo de trabajo más ágil y notificando a los arrendatarios de cada cambio en sus huertos, por ejemplo: fotos recientes, notificaciones de recolecta o futuros cursos. El proyecto se llevó a cabo con éxito a lo largo de 2012 y 2013. Abstract In this Final Degree Project we build a complete horticulture center management tool where a set of gardens, which are kept by people with disabilities, are leased to third parties. This project is carried out within the La Huerta Montecarmelo initiative of the Carmen Pardo-Valcarce Foundation in Madrid. The project was the result of collaboration between the School of Computer Systems Engineering of the Technical University of Madrid and that Foundation through an External Practices program that lasted twelve months. By one hand, over the years of Social Work in this initiative, it was found that some clients after spring were easily disconnected from the tasks involved to the garden. By the other, all the management of more than two hundred of gardens becomes a very complex task due to lots of paperwork. To solve these problems and more, we proposed to build a web application, relying on other devices, such as Smartphones, allowing a more agile workflow and notifying customers of any change related to its garden, for example: recent photographs, notifications of harvest or future courses. The project was successfully carried out throughout 2012 and 2013.

Caracterización de sistemas vibroacústicos mediante análisis estadístico de energía

Hoy día nadie discute la importancia de predecir el comportamiento vibroacústico de estructuras (edificios, vehículos aeronaves, satélites). También se ha hecho patente, con el tiempo, que el rango espectral en el que la respuesta es importante se ha desplazado hacia alta frecuencia en prácticamente todos los campos. Esto ha hecho que los métodos de análisis en este rango alto de frecuencias cobren importancia y actualidad. Uno de los métodos más extendidos para este fin es el basado en el Análisis Estadístico de la Energía, SEA. Es un método que ha mostrado proporcionar un buen equilibrio entre potencia de calculo, precisión y fiabilidad. En un SEA el sistema (estructura, cavidades o aire circundante) se modela mediante una matriz de coeficientes que dependen directamente de los factores de pérdidas de las distintas partes del sistema. Formalmente es un método de análisis muy cómodo e intuitivo de manejar cuya mayor dificultad es precisamente la determinación de esos factores de pérdidas. El catálogo de expresiones analíticas o numéricas para su determinación no es suficientemente amplio por lo que normalmente siempre se suele acabar necesitando hacer uso de herramientas experimentales, ya sea para su obtención o la comprobación de los valores utilizados. La determinación experimental tampoco está exenta de problemas, su obtención necesita de configuraciones experimentales grandes y complejas con requisitos que pueden llegar a ser muy exigentes y en las que además, se ven involucrados problemas numéricos relacionados con los valores de los propios factores de pérdidas, el valor relativo entre ellos y las características de las matrices que conforman. Este trabajo estudia la caracterización de sistemas vibroacústicos mediante el análisis estadístico de energía. Se centra en la determinación precisa de los valores de los factores de pérdidas. Dados los problemas que puede presentar un sistema experimental de estas características, en una primera parte se estudia la influencia de todas las magnitudes que intervienen en la determinación de los factores de pérdidas mediante un estudio de incertidumbres relativas, que, por medio de los coeficientes de sensibilidad normalizados, indicará la importancia de cada una de las magnitudes de entrada (esencialmente energías y potencias) en los resultados. De esta parte se obtiene una visión general sobre a qué mensurados se debe prestar más atención, y de qué problemas pueden ser los que más influyan en la falta de estabilidad (o incoherencia) de los resultados. Además, proporciona un modelo de incertidumbres válido para los casos estudiados y ha permitido evaluar el error cometido por algún método utilizado habitualmente para la caracterización de factores de pérdidas como la aproximación a 2 subsistemas En una segunda parte se hace uso de las conclusiones obtenidas en la primera, de forma que el trabajo se orienta en dos direcciones. Una dirigida a la determi nación suficientemente fiel de la potencia de entrada que permita simplificar en lo posible la configuración experimental. Otra basada en un análisis detallado de las propiedades de la matriz que caracteriza un SEA y que conduce a la propuesta de un método para su determinación robusta, basada en un filtrado de Montecarlo y que, además, muestra cómo los problemas numéricos de la matriz SEA pueden no ser tan insalvables como se apunta en la literatura. Por último, además, se plantea una solución al caso en el que no todos los subsistemas en los que se divide el sistema puedan ser excitados. El método propuesto aquí no permite obtener el conjunto completo de coeficientes necesarios para definir un sistema, pero el solo hecho de poder obtener conjuntos parciales ya es un avance importante y, sobre todo, abre la puerta al desarrollo de métodos que permitan relajar de forma importante las exigencias que la determinación experimental de matrices SEA tiene. ABSTRACT At present there is an agreement about the importance to predict the vibroacoustic response of structures (buildings, vehicles, aircrafts, satellites, etc.). In addition, there has become clear over the time that the frequency range over which the response is important has been shift to higher frequencies in almost all the engineering fields. As a consequence, the numerical methods for high frequency analysis have increase in importance. One the most widespread methods for this type of analysis is the one based on the Statistical Energy Analysis, SEA. This method has shown to provide a good balance among calculation power, accuracy and liability. Within a SEA, a system (structure, cavities, surrounding air) is modeled by a coefficients matrix that depends directly on the loss factors of the different parts of the system. Formally, SEA is a very handy and intuitive analysis method whose greatest handicap is precisely the determination of the loss factors. The existing set of analytical or numerical equations to obtain the loss factor values is not enough, so that usually it is necessary to use experimental techniques whether it is to its determination to to check the estimated values by another mean. The experimental determination presents drawbacks, as well. To obtain them great and complex experimental setups are needed including requirements that can be very demanding including numerical problems related to the values of the loss factors themselves, their relative value and the characteristics of the matrices they define. The present work studies the characterization of vibroacousti systems by this SEA method. It focuses on the accurate determination of the loss factors values. Given all the problems an experimental setup of these characteristics can show, the work is divided in two parts. In the first part, the influence of all the quantities involved on the determination of the loss factors is studied by a relative uncertainty estimation, which, by means of the normalised sensitivity coefficients, will provide an insight about the importance of every input quantities (energies and input powers, mainly) on the final result. Besides, this part, gives an uncertainty model that has allowed assessing the error of one of the methods more widely used to characterize the loss factors: the 2-subsystem approach. In the second part, use of the former conclusions is used. An equation for the input power into the subsystems is proposed. This equation allows simplifying the experimental setup without changing the liability of the test. A detailed study of the SEA matrix properties leads to propose a robust determination method of this SEA matrix by a Monte Carlo filtering. In turn, this new method shows how the numerical problems of the SEA matrix can be overcome Finally, a solution is proposed for the case where not all the subsystems are excited. The method proposed do not allows obtaining the whole set of coefficients of the SEA matrix, but the simple fact of getting partial sets of loss factors is a significant advance and, over all, it opens the door to the development of new methods that loosen the requirements that an experimental determination of a SEA matrix have.

Co-simulation Methodologies for Hybrid and Electric Vehicle Dynamics

In recent decades, full electric and hybrid electric vehicles have emerged as an alternative to conventional cars due to a range of factors, including environmental and economic aspects. These vehicles are the result of considerable efforts to seek ways of reducing the use of fossil fuel for vehicle propulsion. Sophisticated technologies such as hybrid and electric powertrains require careful study and optimization. Mathematical models play a key role at this point. Currently, many advanced mathematical analysis tools, as well as computer applications have been built for vehicle simulation purposes. Given the great interest of hybrid and electric powertrains, along with the increasing importance of reliable computer-based models, the author decided to integrate both aspects in the research purpose of this work. Furthermore, this is one of the first final degree projects held at the ETSII (Higher Technical School of Industrial Engineers) that covers the study of hybrid and electric propulsion systems. The present project is based on MBS3D 2.0, a specialized software for the dynamic simulation of multibody systems developed at the UPM Institute of Automobile Research (INSIA). Automobiles are a clear example of complex multibody systems, which are present in nearly every field of engineering. The work presented here benefits from the availability of MBS3D software. This program has proven to be a very efficient tool, with a highly developed underlying mathematical formulation. On this basis, the focus of this project is the extension of MBS3D features in order to be able to perform dynamic simulations of hybrid and electric vehicle models. This requires the joint simulation of the mechanical model of the vehicle, together with the model of the hybrid or electric powertrain. These sub-models belong to completely different physical domains. In fact the powertrain consists of energy storage systems, electrical machines and power electronics, connected to purely mechanical components (wheels, suspension, transmission, clutch…). The challenge today is to create a global vehicle model that is valid for computer simulation. Therefore, the main goal of this project is to apply co-simulation methodologies to a comprehensive model of an electric vehicle, where sub-models from different areas of engineering are coupled. The created electric vehicle (EV) model consists of a separately excited DC electric motor, a Li-ion battery pack, a DC/DC chopper converter and a multibody vehicle model. Co-simulation techniques allow car designers to simulate complex vehicle architectures and behaviors, which are usually difficult to implement in a real environment due to safety and/or economic reasons. In addition, multi-domain computational models help to detect the effects of different driving patterns and parameters and improve the models in a fast and effective way. Automotive designers can greatly benefit from a multidisciplinary approach of new hybrid and electric vehicles. In this case, the global electric vehicle model includes an electrical subsystem and a mechanical subsystem. The electrical subsystem consists of three basic components: electric motor, battery pack and power converter. A modular representation is used for building the dynamic model of the vehicle drivetrain. This means that every component of the drivetrain (submodule) is modeled separately and has its own general dynamic model, with clearly defined inputs and outputs. Then, all the particular submodules are assembled according to the drivetrain configuration and, in this way, the power flow across the components is completely determined. Dynamic models of electrical components are often based on equivalent circuits, where Kirchhoff’s voltage and current laws are applied to draw the algebraic and differential equations. Here, Randles circuit is used for dynamic modeling of the battery and the electric motor is modeled through the analysis of the equivalent circuit of a separately excited DC motor, where the power converter is included. The mechanical subsystem is defined by MBS3D equations. These equations consider the position, velocity and acceleration of all the bodies comprising the vehicle multibody system. MBS3D 2.0 is entirely written in MATLAB and the structure of the program has been thoroughly studied and understood by the author. MBS3D software is adapted according to the requirements of the applied co-simulation method. Some of the core functions are modified, such as integrator and graphics, and several auxiliary functions are added in order to compute the mathematical model of the electrical components. By coupling and co-simulating both subsystems, it is possible to evaluate the dynamic interaction among all the components of the drivetrain. ‘Tight-coupling’ method is used to cosimulate the sub-models. This approach integrates all subsystems simultaneously and the results of the integration are exchanged by function-call. This means that the integration is done jointly for the mechanical and the electrical subsystem, under a single integrator and then, the speed of integration is determined by the slower subsystem. Simulations are then used to show the performance of the developed EV model. However, this project focuses more on the validation of the computational and mathematical tool for electric and hybrid vehicle simulation. For this purpose, a detailed study and comparison of different integrators within the MATLAB environment is done. Consequently, the main efforts are directed towards the implementation of co-simulation techniques in MBS3D software. In this regard, it is not intended to create an extremely precise EV model in terms of real vehicle performance, although an acceptable level of accuracy is achieved. The gap between the EV model and the real system is filled, in a way, by introducing the gas and brake pedals input, which reflects the actual driver behavior. This input is included directly in the differential equations of the model, and determines the amount of current provided to the electric motor. For a separately excited DC motor, the rotor current is proportional to the traction torque delivered to the car wheels. Therefore, as it occurs in the case of real vehicle models, the propulsion torque in the mathematical model is controlled through acceleration and brake pedal commands. The designed transmission system also includes a reduction gear that adapts the torque coming for the motor drive and transfers it. The main contribution of this project is, therefore, the implementation of a new calculation path for the wheel torques, based on performance characteristics and outputs of the electric powertrain model. Originally, the wheel traction and braking torques were input to MBS3D through a vector directly computed by the user in a MATLAB script. Now, they are calculated as a function of the motor current which, in turn, depends on the current provided by the battery pack across the DC/DC chopper converter. The motor and battery currents and voltages are the solutions of the electrical ODE (Ordinary Differential Equation) system coupled to the multibody system. Simultaneously, the outputs of MBS3D model are the position, velocity and acceleration of the vehicle at all times. The motor shaft speed is computed from the output vehicle speed considering the wheel radius, the gear reduction ratio and the transmission efficiency. This motor shaft speed, somehow available from MBS3D model, is then introduced in the differential equations corresponding to the electrical subsystem. In this way, MBS3D and the electrical powertrain model are interconnected and both subsystems exchange values resulting as expected with tight-coupling approach.When programming mathematical models of complex systems, code optimization is a key step in the process. A way to improve the overall performance of the integration, making use of C/C++ as an alternative programming language, is described and implemented. Although this entails a higher computational burden, it leads to important advantages regarding cosimulation speed and stability. In order to do this, it is necessary to integrate MATLAB with another integrated development environment (IDE), where C/C++ code can be generated and executed. In this project, C/C++ files are programmed in Microsoft Visual Studio and the interface between both IDEs is created by building C/C++ MEX file functions. These programs contain functions or subroutines that can be dynamically linked and executed from MATLAB. This process achieves reductions in simulation time up to two orders of magnitude. The tests performed with different integrators, also reveal the stiff character of the differential equations corresponding to the electrical subsystem, and allow the improvement of the cosimulation process. When varying the parameters of the integration and/or the initial conditions of the problem, the solutions of the system of equations show better dynamic response and stability, depending on the integrator used. Several integrators, with variable and non-variable step-size, and for stiff and non-stiff problems are applied to the coupled ODE system. Then, the results are analyzed, compared and discussed. From all the above, the project can be divided into four main parts: 1. Creation of the equation-based electric vehicle model; 2. Programming, simulation and adjustment of the electric vehicle model; 3. Application of co-simulation methodologies to MBS3D and the electric powertrain subsystem; and 4. Code optimization and study of different integrators. Additionally, in order to deeply understand the context of the project, the first chapters include an introduction to basic vehicle dynamics, current classification of hybrid and electric vehicles and an explanation of the involved technologies such as brake energy regeneration, electric and non-electric propulsion systems for EVs and HEVs (hybrid electric vehicles) and their control strategies. Later, the problem of dynamic modeling of hybrid and electric vehicles is discussed. The integrated development environment and the simulation tool are also briefly described. The core chapters include an explanation of the major co-simulation methodologies and how they have been programmed and applied to the electric powertrain model together with the multibody system dynamic model. Finally, the last chapters summarize the main results and conclusions of the project and propose further research topics. In conclusion, co-simulation methodologies are applicable within the integrated development environments MATLAB and Visual Studio, and the simulation tool MBS3D 2.0, where equation-based models of multidisciplinary subsystems, consisting of mechanical and electrical components, are coupled and integrated in a very efficient way.

Estimación de la resistencia de estructuras de hormigón armado reforzadas a cortante mediante FRP

El empleo de refuerzos de FRP en vigas de hormigón armado es cada vez más frecuente por sus numerosas ventajas frente a otros métodos más tradicionales. Durante los últimos años, la técnica FRP-NSM, consistente en introducir barras de FRP sobre el recubrimiento de una viga de hormigón, se ha posicionado como uno de los mejores métodos de refuerzo y rehabilitación de estructuras de hormigón armado, tanto por su facilidad de montaje y mantenimiento, como por su rendimiento para aumentar la capacidad resistente de dichas estructuras. Si bien el refuerzo a flexión ha sido ampliamente desarrollado y estudiado hasta la fecha, no sucede lo mismo con el refuerzo a cortante, debido principalmente a su gran complejidad. Sin embargo, se debería dedicar más estudio a este tipo de refuerzo si se pretenden conservar los criterios de diseño en estructuras de hormigón armado, los cuales están basados en evitar el fallo a cortante por sus consecuencias catastróficas Esta ausencia de información y de normativa es la que justifica esta tesis doctoral. En este pro-yecto se van a desarrollar dos metodologías alternativas, que permiten estimar la capacidad resistente de vigas de hormigón armado, reforzadas a cortante mediante la técnica FRP-NSM. El primer método aplicado consiste en la implementación de una red neuronal artificial capaz de predecir adecuadamente la resistencia a cortante de vigas reforzadas con este método a partir de experimentos anteriores. Asimismo, a partir de la red se han llevado a cabo algunos estudios a fin de comprender mejor la influencia real de algunos parámetros de la viga y del refuerzo sobre la resistencia a cortante con el propósito de lograr diseños más seguros de este tipo de refuerzo. Una configuración óptima de la red requiere discriminar adecuadamente de entre los numerosos parámetros (geométricos y de material) que pueden influir en el compor-tamiento resistente de la viga, para lo cual se han llevado a cabo diversos estudios y pruebas. Mediante el segundo método, se desarrolla una ecuación de proyecto que permite, de forma sencilla, estimar la capacidad de vigas reforzadas a cortante con FRP-NSM, la cual podría ser propuesta para las principales guías de diseño. Para alcanzar este objetivo, se plantea un pro-blema de optimización multiobjetivo a partir de resultados de ensayos experimentales llevados a cabo sobre vigas de hormigón armado con y sin refuerzo de FRP. El problema multiobjetivo se resuelve mediante algoritmos genéticos, en concreto el algoritmo NSGA-II, por ser más apropiado para problemas con varias funciones objetivo que los métodos de optimización clásicos. Mediante una comparativa de las predicciones realizadas con ambos métodos y de los resulta-dos de ensayos experimentales se podrán establecer las ventajas e inconvenientes derivadas de la aplicación de cada una de las dos metodologías. Asimismo, se llevará a cabo un análisis paramétrico con ambos enfoques a fin de intentar determinar la sensibilidad de aquellos pa-rámetros más sensibles a este tipo de refuerzo. Finalmente, se realizará un análisis estadístico de la fiabilidad de las ecuaciones de diseño deri-vadas de la optimización multiobjetivo. Con dicho análisis se puede estimar la capacidad resis-tente de una viga reforzada a cortante con FRP-NSM dentro de un margen de seguridad espe-cificado a priori. ABSTRACT The use of externally bonded (EB) fibre-reinforced polymer (FRP) composites has gained acceptance during the last two decades in the construction engineering community, particularly in the rehabilitation of reinforced concrete (RC) structures. Currently, to increase the shear resistance of RC beams, FRP sheets are externally bonded (EB-FRP) and applied on the external side surface of the beams to be strengthened with different configurations. Of more recent application, the near-surface mounted FRP bar (NSM-FRP) method is another technique successfully used to increase the shear resistance of RC beams. In the NSM method, FRP rods are embedded into grooves intentionally prepared in the concrete cover of the side faces of RC beams. While flexural strengthening has been widely developed and studied so far, the same doesn´t occur to shearing strength mainly due to its great complexity. Nevertheless, if design criteria are to be preserved more research should be done to this sort of strength, which are based on avoiding shear failure and its catastrophic consequences. However, in spite of this, accurately calculating the shear capacity of FRP shear strengthened RC beams remains a complex challenge that has not yet been fully resolved due to the numerous variables involved in the procedure. The objective of this Thesis is to develop methodologies to evaluate the capacity of FRP shear strengthened RC beams by dealing with the problem from a different point of view to the numerical modeling approach by using artificial intelligence techniques. With this purpose two different approaches have been developed: one concerned with the use of artificial neural networks and the other based on the implementation of an optimization approach developed jointly with the use of artificial neural networks (ANNs) and solved with genetic algorithms (GAs). With these approaches some of the difficulties concerned regarding the numerical modeling can be overcome. As an alternative tool to conventional numerical techniques, neural networks do not provide closed form solutions for modeling problems but do, however, offer a complex and accurate solution based on a representative set of historical examples of the relationship. Furthermore, they can adapt solutions over time to include new data. On the other hand, as a second proposal, an optimization approach has also been developed to implement simple yet accurate shear design equations for this kind of strengthening. This approach is developed in a multi-objective framework by considering experimental results of RC beams with and without NSM-FRP. Furthermore, the results obtained with the previous scheme based on ANNs are also used as a filter to choose the parameters to include in the design equations. Genetic algorithms are used to solve the optimization problem since they are especially suitable for solving multi-objective problems when compared to standard optimization methods. The key features of the two proposed procedures are outlined and their performance in predicting the capacity of NSM-FRP shear strengthened RC beams is evaluated by comparison with results from experimental tests and with predictions obtained using a simplified numerical model. A sensitivity study of the predictions of both models for the input parameters is also carried out.

A time-domain finite element method for seakeeping and wave resistance problems

El objetivo de la tesis es la investigación de algoritmos numéricos para el desarrollo de herramientas numéricas para la simulación de problemas tanto de comportamiento en la mar como de resistencia al avance de buques y estructuras flotantes. La primera herramienta desarrollada resuelve el problema de difracción y radiación de olas. Se basan en el método de los elementos finitos (MEF) para la resolución de la ecuación de Laplace, así como en esquemas basados en MEF, integración a lo largo de líneas de corriente, y en diferencias finitas desarrollados para la condición de superficie libre. Se han desarrollado herramientas numéricas para la resolución de la dinámica de sólido rígido en sistemas multicuerpos con ligaduras. Estas herramientas han sido integradas junto con la herramienta de resolución de olas difractadas y radiadas para la resolución de problemas de interacción de cuerpos con olas. También se han diseñado algoritmos de acoplamientos con otras herramientas numéricas para la resolución de problemas multifísica. En particular, se han realizado acoplamientos con una herramienta numérica basada de cálculo de estructuras con MEF para problemas de interacción fluido-estructura, otra de cálculo de líneas de fondeo, y con una herramienta numérica de cálculo de flujos en tanques internos para problemas acoplados de comportamiento en la mar con “sloshing”. Se han realizado simulaciones numéricas para la validación y verificación de los algoritmos desarrollados, así como para el análisis de diferentes casos de estudio con aplicaciones diversas en los campos de la ingeniería naval, oceánica, y energías renovables marinas. ABSTRACT The objective of this thesis is the research on numerical algorithms to develop numerical tools to simulate seakeeping problems as well as wave resistance problems of ships and floating structures. The first tool developed is a wave diffraction-radiation solver. It is based on the finite element method (FEM) in order to solve the Laplace equation, as well as numerical schemes based on FEM, streamline integration, and finite difference method tailored for solving the free surface boundary condition. It has been developed numerical tools to solve solid body dynamics of multibody systems with body links across them. This tool has been integrated with the wave diffraction-radiation solver to solve wave-body interaction problems. Also it has been tailored coupling algorithms with other numerical tools in order to solve multi-physics problems. In particular, it has been performed coupling with a MEF structural solver to solve fluid-structure interaction problems, with a mooring solver, and with a solver capable of simulating internal flows in tanks to solve couple seakeeping-sloshing problems. Numerical simulations have been carried out to validate and verify the developed algorithms, as well as to analyze case studies in the areas of marine engineering, offshore engineering, and offshore renewable energy.

Discourses and values underpin public debate on fracking in Spain: a case study at the crossroad

In the EU context extraction of shale and oil gas by hydraulic fracturing (fracking) differs from country to country in terms of legislation and implementation. While fossil fuel extraction using this technology is currently taking place in the UK, Germany and France have adopted respective moratoria. In between is the Spanish case, where hydrocarbon extraction projects through fracking have to undergo mandatory and routine environmental assessment in accordance with the last changes to environmental regulations. Nowadays Spain is at the crossroad with respect to the future of this technology. We presume a social conflictt in our country since the position and strategy of the involved and confronted social actors -national, regional and local authorities, energy companies, scientists, NGO and other social organization- are going to play key and likely divergent roles in its industrial implementation and public acceptance. In order to improve knowledge on how to address these controverted situations from the own engineering context, the affiliated units from the Higher Technical School of Mines and Energy Engineering at UPM have been working on a transversal program to teach values and ethics. Over the past seven years, this pioneering experience has shown the usefulness of applying a consequentialist ethics, based on a case-by-case approach and costs-benefits analysis both for action and inaction. As a result of this initiative a theoretical concept has arisen and crystallized in this field: it is named Inter-ethics. This theoretical perspective can be very helpful in complex situations, with multi-stakeholders and plurality of interests, when ethical management requires the interaction between the respective ethics of each group; professional ethics of a single group is not enough. Under this inter-ethics theoretical framework and applying content analysis techniques, this paper explores the articulation of the discourse in favour and against fracking technology and its underlying values as manifested in the Spanish traditional mass media and emerging social media such as Youtube. Results show that Spanish public discourse on fracking technology includes the costs-benefits analysis to communicate how natural resources from local communities may be affected by these facilities due to environmental, health and economic consequences. Furthermore, this technology is represented as a solution to the "demand of energy" according to the optimistic discourse while, from a pessimistic view, fracking is often framed as a source "environmental problems" and even natural disasters as possible earthquakes. In this latter case, this negative representation could have been influenced by the closure of a macro project to store injected natural gas in the Mediterranean Sea using the old facilities of an oil exploitation in Amposta (Proyecto Cástor). The closure of this project was due to the occurrence of earthquakes whose intensity was higher than the originally expected by the experts in the assessment stage of the project.

Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo

In an effort to expand the scope of protein mutagenesis, we have completed the first steps toward a general method to allow the site-specific incorporation of unnatural amino acids into proteins in vivo. Our approach involves the generation of an “orthogonal” suppressor tRNA that is uniquely acylated in Escherichia coli by an engineered aminoacyl-tRNA synthetase with the desired unnatural amino acid. To this end, eight mutations were introduced into tRNA2Gln based on an analysis of the x-ray crystal structure of the glutaminyl-tRNA aminoacyl synthetase (GlnRS)–tRNA2Gln complex and on previous biochemical data. The resulting tRNA satisfies the minimal requirements for the delivery of an unnatural amino acid: it is not acylated by any endogenous E. coli aminoacyl-tRNA synthetase including GlnRS, and it functions efficiently in protein translation. Repeated rounds of DNA shuffling and oligonucleotide-directed mutagenesis followed by genetic selection resulted in mutant GlnRS enzymes that efficiently acylate the engineered tRNA with glutamine in vitro. The mutant GlnRS and engineered tRNA also constitute a functional synthetase–tRNA pair in vivo. The nature of the GlnRS mutations, which occur both at the protein–tRNA interface and at sites further away, is discussed.

Nonlinear indicial response of complex nonstationary oscillations as pulmonary hypertension responding to step hypoxia

This paper is devoted to the quantization of the degree of nonlinearity of the relationship between two biological variables when one of the variables is a complex nonstationary oscillatory signal. An example of the situation is the indicial responses of pulmonary blood pressure (P) to step changes of oxygen tension (ΔpO2) in the breathing gas. For a step change of ΔpO2 beginning at time t1, the pulmonary blood pressure is a nonlinear function of time and ΔpO2, which can be written as P(t-t1 | ΔpO2). An effective method does not exist to examine the nonlinear function P(t-t1 | ΔpO2). A systematic approach is proposed here. The definitions of mean trends and oscillations about the means are the keys. With these keys a practical method of calculation is devised. We fit the mean trends of blood pressure with analytic functions of time, whose nonlinearity with respect to the oxygen level is clarified here. The associated oscillations about the mean can be transformed into Hilbert spectrum. An integration of the square of the Hilbert spectrum over frequency yields a measure of oscillatory energy, which is also a function of time, whose mean trends can be expressed by analytic functions. The degree of nonlinearity of the oscillatory energy with respect to the oxygen level also is clarified here. Theoretical extension of the experimental nonlinear indicial functions to arbitrary history of hypoxia is proposed. Application of the results to tissue remodeling and tissue engineering of blood vessels is discussed.

A first trial of retrospective collaboration for positional cloning in complex inheritance: Assay of the cytokine region on chromosome 5 by the Consortium on Asthma Genetics (COAG)

The central problem of complex inheritance is to map oligogenes for disease susceptibility, integrating linkage and association over samples that differ in several ways. Combination of evidence over multiple samples with 1,037 families supports loci contributing to asthma susceptibility in the cytokine region on 5q [maximum logarithm of odds (lod) = 2.61 near IL-4], but no evidence for atopy. The principal problems with retrospective collaboration on linkage appear to have been solved, providing far more information than a single study. A multipoint lod table evaluated at commonly agreed reference loci is required for both collaboration and metaanalysis, but variations in ascertainment, pedigree structure, phenotype definition, and marker selection are tolerated. These methods are invariant with statistical methods that increase the power of lods and are applicable to all diseases, motivating collaboration rather than competition. In contrast to linkage, positional cloning by allelic association has yet to be extended to multiple samples, a prerequisite for efficient combination with linkage and the greatest current challenge to genetic epidemiology.

Tissue-engineered cells producing complex recombinant proteins inhibit ovarian cancer in vivo

Techniques of tissue engineering and cell and molecular biology were used to create a biodegradable scaffold for transfected cells to produce complex proteins. Mullerian Inhibiting Substance (MIS) causes regression of Mullerian ducts in the mammalian embryo. MIS also causes regression in vitro of ovarian tumor cell lines and primary cells from ovarian carcinomas, which derive from Mullerian structures. In a strategy to circumvent the complicated purification protocols for MIS, Chinese hamster ovary cells transfected with the human MIS gene were seeded onto biodegradable polymers of polyglycolic acid fibers and secretion of MIS confirmed. The polymer-cell graft was implanted into the right ovarian pedicle of severe combined immunodeficient mice. Serum MIS in the mice rose to supraphysiologic levels over time. One week after implantation of the polymer-cell graft, IGROV-1 human tumors were implanted under the renal capsule of the left kidney. Growth of the IGROV-1 tumors was significantly inhibited in the animals with a polymer-cell graft of MIS-producing cells, compared with controls. This novel MIS delivery system could have broader applications for other inhibitory agents not amenable to efficient purification and provides in vivo evidence for a role of MIS in the treatment of ovarian cancer.

High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides

Homologous DNA recombination is a fundamental, regenerative process within living organisms. However, in most organisms, homologous recombination is a rare event, requiring a complex set of reactions and extensive homology. We demonstrate in this paper that Beta protein of phage λ generates recombinants in chromosomal DNA by using synthetic single-stranded DNAs (ssDNA) as short as 30 bases long. This ssDNA recombination can be used to mutagenize or repair the chromosome with efficiencies that generate up to 6% recombinants among treated cells. Mechanistically, it appears that Beta protein, a Rad52-like protein, binds and anneals the ssDNA donor to a complementary single-strand near the DNA replication fork to generate the recombinant. This type of homologous recombination with ssDNA provides new avenues for studying and modifying genomes ranging from bacterial pathogens to eukaryotes. Beta protein and ssDNA may prove generally applicable for repairing DNA in many organisms.

Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.