Improving probabilistic flood forecasting through a data assimilation scheme based on genetic programming

Opportunities offered by high performance computing provide a significant degree of promise in the enhancement of the performance of real-time flood forecasting systems. In this paper, a real-time framework for probabilistic flood forecasting through data assimilation is presented. The distributed rainfall-runoff real-time interactive basin simulator (RIBS) model is selected to simulate the hydrological process in the basin. Although the RIBS model is deterministic, it is run in a probabilistic way through the results of calibration developed in a previous work performed by the authors that identifies the probability distribution functions that best characterise the most relevant model parameters. Adaptive techniques improve the result of flood forecasts because the model can be adapted to observations in real time as new information is available. The new adaptive forecast model based on genetic programming as a data assimilation technique is compared with the previously developed flood forecast model based on the calibration results. Both models are probabilistic as they generate an ensemble of hydrographs, taking the different uncertainties inherent in any forecast process into account. The Manzanares River basin was selected as a case study, with the process being computationally intensive as it requires simulation of many replicas of the ensemble in real time.

Edge Detection by Adaptive Splitting II. The Three-Dimensional Case

In Llanas and Lantarón, J. Sci. Comput. 46, 485–518 (2011) we proposed an algorithm (EDAS-d) to approximate the jump discontinuity set of functions defined on subsets of ℝ d . This procedure is based on adaptive splitting of the domain of the function guided by the value of an average integral. The above study was limited to the 1D and 2D versions of the algorithm. In this paper we address the three-dimensional problem. We prove an integral inequality (in the case d=3) which constitutes the basis of EDAS-3. We have performed detailed computational experiments demonstrating effective edge detection in 3D function models with different interface topologies. EDAS-1 and EDAS-2 appealing properties are extensible to the 3D case

Effectiveness of safety-based incentives in Public Private Partnerships: Evidence from the case of Spain

Many countries around the world are implementing Public?Private?Partnership (PPP) contacts to manage road infrastructure. In some of these contracts the public sector introduces economic incentives to the private operator to foster the accomplishment of social goals. One of the incentives that have been introduced in some PPP contracts is related to safety in such a way that the better the safety outcome the greater will be the economic reward to the contractor. The aim of this paper is at identify whether the incentives to improve road safety in highway PPPs are ultimately effective in improving safety ratios. To this end Poisson and negative binomial regression models have been applied using information from highway sections in Spain. The findings indicate that even though road safety is highly influenced by variables that are not much controllable by the contractor such as the Average Annual Daily Traffic and the percentage of heavy vehicles, the implementation of safety incentives in PPPs has a positive influence in the reduction of fatalities, injuries and accidents.

Analysis of irregular behaviour on an optical computing logic cell

A new methodology to study irregular behaviours in logic cells is reported. It is based on two types of diagrams, namely phase and working diagrams. Sets of four bits are grouped and represented by their hexadecimal equivalent. Some hexadecimal numbers correspond to certain logic functions. The influence of the internal and external tolerances, namely those appearing in the employed devices and in the working signals, may be analysed with this method. Its importance in the case of logic structures with chaotic behaviours is studied.

Analysis of safety-based incentives in public private partnerships. The case of Spain

OUTLINE: • Introduction • Experimental Setup • Experimental Procedure • Experimental Results - Surface Roughness - Residual Stresses - Friction - Wear - EDX • Conclusions

Teaching based on the case method of building collective protection

One of the fundamental aspects in the adaptation of the teaching to the European higher education is changing based models of teacher education to models based on student learning. In this work we present an educational experience developed with the teaching method based on the case method, with a clearly multidisciplinary. The experience has been developed in the teaching of analysis and verification of safety rails. This is a multidisciplinary field that presents great difficulties during their teaching. The use of the case method has given good results in the competences achieved by students

Analysis of teaching experience based on teaching by the case method. Application to reinforcing wooden floors

The technique of reinforcement of wooden floors is a matter clearly multidisciplinary. The teaching of the subject using the "traditional" method, explaining the theory first and then proposing and solving problems has not been successful. This paper discusses the results of a teaching experiencie. It has been the teaching of the subject by the case method. The results are clearly superior to those obtained with the traditional methodology.

A sharing-based approach to supporting adaptation in service compositions

Data-related properties of the activities involved in a service composition can be used to facilitate several design-time and run-time adaptation tasks, such as service evolution, distributed enactment, and instance-level adaptation. A number of these properties can be expressed using a notion of sharing. We present an approach for automated inference of data properties based on sharing analysis, which is able to handle service compositions with complex control structures, involving loops and sub-workflows. The properties inferred can include data dependencies, information content, domain-defined attributes, privacy or confidentiality levels, among others. The analysis produces characterizations of the data and the activities in the composition in terms of minimal and maximal sharing, which can then be used to verify compliance of potential adaptation actions, or as supporting information in their generation. This sharing analysis approach can be used both at design time and at run time. In the latter case, the results of analysis can be refined using the composition traces (execution logs) at the point of execution, in order to support run-time adaptation.

Towards cost reduction in concentrating solar power: innovative design for an efficient fresnel based solar field

Energía termosolar (de concentración) es uno de los nombres que hacen referencia en español al término inglés “concentrating solar power”. Se trata de una tecnología basada en la captura de la potencia térmica de la radiación solar, de forma que permita alcanzar temperaturas capaces de alimentar un ciclo termodinámico convencional (o avanzado); el futuro de esta tecnología depende principalmente de su capacidad para concentrar la radiación solar de manera eficiente y económica. La presente tesis está orientada hacia la resolución de ciertos problemas importantes relacionados con este objetivo. La mencionada necesidad de reducir costes en la concentración de radiación solar directa, asegurando el objetivo termodinámico de calentar un fluido hasta una determinada temperatura, es de vital importancia. Los colectores lineales Fresnel han sido identificados en la literatura científica como una tecnología con gran potencial para alcanzar esta reducción de costes. Dicha tecnología ha sido seleccionada por numerosas razones, entre las que destacan su gran libertad de diseño y su actual estado inmaduro. Con el objetivo de responder a este desafío se desarrollado un detallado estudio de las propiedades ópticas de los colectores lineales Fresnel, para lo cual se han utilizado métodos analíticos y numéricos de manera combinada. En primer lugar, se han usado unos modelos para la predicción de la localización y la irradiación normal directa del sol junto a unas relaciones analíticas desarrolladas para estudiar el efecto de múltiples variables de diseño en la energía incidente sobre los espejos. Del mismo modo, se han obtenido analíticamente los errores debidos al llamado “off-axis aberration”, a la apertura de los rayos reflejados en los espejos y a las sombras y bloqueos entre espejos. Esto ha permitido la comparación de diferentes formas de espejo –planos, circulares o parabólicos–, así como el diseño preliminar de la localización y anchura de los espejos y receptor sin necesidad de costosos métodos numéricos. En segundo lugar, se ha desarrollado un modelo de trazado de rayos de Monte Carlo con el objetivo de comprobar la validez del estudio analítico, pero sobre todo porque este no es preciso en el estudio de la reflexión en espejos. El código desarrollado está específicamente ideado para colectores lineales Fresnel, lo que ha permitido la reducción del tiempo de cálculo en varios órdenes de magnitud en comparación con un programa comercial más general. Esto justifica el desarrollo de un nuevo código en lugar de la compra de una licencia de otro programa. El modelo ha sido usado primeramente para comparar la intensidad de flujo térmico y rendimiento de colectores Fresnel, con y sin reflector secundario, con los colectores cilíndrico parabólicos. Finalmente, la conjunción de los resultados obtenidos en el estudio analítico con el programa numérico ha sido usada para optimizar el campo solar para diferentes orientaciones –Norte-Sur y Este-Oeste–, diferentes localizaciones –Almería y Aswan–, diferentes inclinaciones hacia el Trópico –desde 0 deg hasta 32 deg– y diferentes mínimos de intensidad del flujo en el centro del receptor –10 kW/m2 y 25 kW/m2–. La presente tesis ha conducido a importantes descubrimientos que deben ser considerados a la hora de diseñar un campo solar Fresnel. En primer lugar, los espejos utilizados no deben ser plano, sino cilíndricos o parabólicos, ya que los espejos curvos implican mayores concentraciones y rendimiento. Por otro lado, se ha llegado a la conclusión de que la orientación Este-Oeste es más propicia para localizaciones con altas latitudes, como Almería, mientras que en zonas más cercanas a los trópicos como Aswan los campos Norte-Sur conducen a mayores rendimientos. Es de destacar que la orientación Este-Oeste requiere aproximadamente la mitad de espejos que los campos Norte-Sur, puediendo estar inclinados hacia los Trópicos para mejorar el rendimiento, y que alcanzan parecidos valores de intensidad térmica en el receptor todos los días a mediodía. Sin embargo, los campos con orientación Norte-Sur permiten un flujo más constante a lo largo de un día. Por último, ha sido demostrado que el uso de diseños pre-optimizados analíticamente, con anchura de espejos y espaciado entre espejos variables a lo ancho del campo, pueden implicar aumentos de la energía generada por metro cuadrado de espejos de hasta el 6%. El rendimiento óptico anual de los colectores cilíndrico parabólicos es 23 % mayor que el rendimiento de los campos Fresnel en Almería, mientras que la diferencia es de solo 9 % en Aswan. Ello implica que, para alcanzar el mismo precio de electricidad que la tecnología de referencia, la reducción de costes de instalación por metro cuadrado de espejo debe estar entre el 10 % y el 25 %, y que los colectores lineales Fresnel tienen más posibilidades de ser desarrollados en zonas de bajas latitudes. Como consecuencia de los estudios desarrollados en esta tesis se ha patentado un sistema de almacenamiento que tiene en cuenta la variación del flujo térmico en el receptor a lo largo del día, especialmente para campos con orientación Este-Oeste. Este invento permitiría el aprovechamiento de la energía incidente durante más parte del año, aumentando de manera apreciable los rendimientos óptico y térmico. Abstract Concentrating solar power is the common name of a technology based on capturing the thermal power of solar radiation, in a suitable way to reach temperatures able to activate a conventional (or advanced) thermodynamic cycle to generate electricity; this quest mainly depends on our ability to concentrate solar radiation in a cheap and efficient way. The present thesis is focused to highlight and help solving some of the important issues related to this problem. The need of reducing costs in concentrating the direct solar radiation, but without jeopardizing the thermodynamic objective of heating a fluid up to the required temperature, is of prime importance. Linear Fresnel collectors have been identified in the scientific literature as a technology with high potential to reach this cost reduction. This technology has been selected because of a number of reasons, particularly the degrees of freedom of this type of concentrating configuration and its current immature state. In order to respond to this challenge, a very detailed exercise has been carried out on the optical properties of linear Fresnel collectors. This has been done combining analytic and numerical methods. First, the effect of the design variables on the ratio of energy impinging onto the reflecting surface has been studied using analytically developed equations, together with models that predict the location and direct normal irradiance of the sun at any moment. Similarly, errors due to off-axis aberration, to the aperture of the reflected energy beam and to shading and blocking effects have been obtained analytically. This has allowed the comparison of different shapes of mirrors –flat, cylindrical or parabolic–, as well as a preliminary optimization of the location and width of mirrors and receiver with no need of time-consuming numerical models. Second, in order to prove the validity of the analytic results, but also due to the fact that the study of the reflection process is not precise enough when using analytic equations, a Monte Carlo Ray Trace model has been developed. The developed code is designed specifically for linear Fresnel collectors, which has reduced the computing time by several orders of magnitude compared to a wider commercial software. This justifies the development of the new code. The model has been first used to compare radiation flux intensities and efficiencies of linear Fresnel collectors, both multitube receiver and secondary reflector receiver technologies, with parabolic trough collectors. Finally, the results obtained in the analytic study together with the numeric model have used in order to optimize the solar field for different orientations –North-South and East-West–, different locations –Almería and Aswan–, different tilts of the field towards the Tropic –from 0 deg to 32 deg– and different flux intensity minimum requirements –10 kW/m2 and 25 kW/m2. This thesis work has led to several important findings that should be considered in the design of Fresnel solar fields. First, flat mirrors should not be used in any case, as cylindrical and parabolic mirrors lead to higher flux intensities and efficiencies. Second, it has been concluded that, in locations relatively far from the Tropics such as Almería, East-West embodiments are more efficient, while in Aswan North- South orientation leads to a higher annual efficiency. It must be noted that East-West oriented solar fields require approximately half the number of mirrors than NS oriented fields, can be tilted towards the Equator in order to increase the efficiency and attain similar values of flux intensity at the receiver every day at midday. On the other hand, in NS embodiments the flux intensity is more even during each single day. Finally, it has been proved that the use of analytic designs with variable shift between mirrors and variable width of mirrors across the field can lead to improvements in the electricity generated per reflecting surface square meter up to 6%. The annual optical efficiency of parabolic troughs has been found to be 23% higher than the efficiency of Fresnel fields in Almería, but it is only around 9% higher in Aswan. This implies that, in order to attain the same levelized cost of electricity than parabolic troughs, the required reduction of installation costs per mirror square meter is in the range of 10-25%. Also, it is concluded that linear Fresnel collectors are more suitable for low latitude areas. As a consequence of the studies carried out in this thesis, an innovative storage system has been patented. This system takes into account the variation of the flux intensity along the day, especially for East-West oriented solar fields. As a result, the invention would allow to exploit the impinging radiation along longer time every day, increasing appreciably the optical and thermal efficiencies.

A Novel Approach to Context-Aware Content-Based Middleware

La computación ubicua está extendiendo su aplicación desde entornos específicos hacia el uso cotidiano; el Internet de las cosas (IoT, en inglés) es el ejemplo más brillante de su aplicación y de la complejidad intrínseca que tiene, en comparación con el clásico desarrollo de aplicaciones. La principal característica que diferencia la computación ubicua de los otros tipos está en como se emplea la información de contexto. Las aplicaciones clásicas no usan en absoluto la información de contexto o usan sólo una pequeña parte de ella, integrándola de una forma ad hoc con una implementación específica para la aplicación. La motivación de este tratamiento particular se tiene que buscar en la dificultad de compartir el contexto con otras aplicaciones. En realidad lo que es información de contexto depende del tipo de aplicación: por poner un ejemplo, para un editor de imágenes, la imagen es la información y sus metadatos, tales como la hora de grabación o los ajustes de la cámara, son el contexto, mientras que para el sistema de ficheros la imagen junto con los ajustes de cámara son la información, y el contexto es representado por los metadatos externos al fichero como la fecha de modificación o la de último acceso. Esto significa que es difícil compartir la información de contexto, y la presencia de un middleware de comunicación que soporte el contexto de forma explícita simplifica el desarrollo de aplicaciones para computación ubicua. Al mismo tiempo el uso del contexto no tiene que ser obligatorio, porque si no se perdería la compatibilidad con las aplicaciones que no lo usan, convirtiendo así dicho middleware en un middleware de contexto. SilboPS, que es nuestra implementación de un sistema publicador/subscriptor basado en contenido e inspirado en SIENA [11, 9], resuelve dicho problema extendiendo el paradigma con dos elementos: el Contexto y la Función de Contexto. El contexto representa la información contextual propiamente dicha del mensaje por enviar o aquella requerida por el subscriptor para recibir notificaciones, mientras la función de contexto se evalúa usando el contexto del publicador y del subscriptor. Esto permite desacoplar la lógica de gestión del contexto de aquella de la función de contexto, incrementando de esta forma la flexibilidad de la comunicación entre varias aplicaciones. De hecho, al utilizar por defecto un contexto vacío, las aplicaciones clásicas y las que manejan el contexto pueden usar el mismo SilboPS, resolviendo de esta forma la incompatibilidad entre las dos categorías. En cualquier caso la posible incompatibilidad semántica sigue existiendo ya que depende de la interpretación que cada aplicación hace de los datos y no puede ser solucionada por una tercera parte agnóstica. El entorno IoT conlleva retos no sólo de contexto, sino también de escalabilidad. La cantidad de sensores, el volumen de datos que producen y la cantidad de aplicaciones que podrían estar interesadas en manipular esos datos está en continuo aumento. Hoy en día la respuesta a esa necesidad es la computación en la nube, pero requiere que las aplicaciones sean no sólo capaces de escalar, sino de hacerlo de forma elástica [22]. Desgraciadamente no hay ninguna primitiva de sistema distribuido de slicing que soporte un particionamiento del estado interno [33] junto con un cambio en caliente, además de que los sistemas cloud actuales como OpenStack u OpenNebula no ofrecen directamente una monitorización elástica. Esto implica que hay un problema bilateral: cómo puede una aplicación escalar de forma elástica y cómo monitorizar esa aplicación para saber cuándo escalarla horizontalmente. E-SilboPS es la versión elástica de SilboPS y se adapta perfectamente como solución para el problema de monitorización, gracias al paradigma publicador/subscriptor basado en contenido y, a diferencia de otras soluciones [5], permite escalar eficientemente, para cumplir con la carga de trabajo sin sobre-provisionar o sub-provisionar recursos. Además está basado en un algoritmo recientemente diseñado que muestra como añadir elasticidad a una aplicación con distintas restricciones sobre el estado: sin estado, estado aislado con coordinación externa y estado compartido con coordinación general. Su evaluación enseña como se pueden conseguir notables speedups, siendo el nivel de red el principal factor limitante: de hecho la eficiencia calculada (ver Figura 5.8) demuestra cómo se comporta cada configuración en comparación con las adyacentes. Esto permite conocer la tendencia actual de todo el sistema, para saber si la siguiente configuración compensará el coste que tiene con la ganancia que lleva en el throughput de notificaciones. Se tiene que prestar especial atención en la evaluación de los despliegues con igual coste, para ver cuál es la mejor solución en relación a una carga de trabajo dada. Como último análisis se ha estimado el overhead introducido por las distintas configuraciones a fin de identificar el principal factor limitante del throughput. Esto ayuda a determinar la parte secuencial y el overhead de base [26] en un despliegue óptimo en comparación con uno subóptimo. Efectivamente, según el tipo de carga de trabajo, la estimación puede ser tan baja como el 10 % para un óptimo local o tan alta como el 60 %: esto ocurre cuando se despliega una configuración sobredimensionada para la carga de trabajo. Esta estimación de la métrica de Karp-Flatt es importante para el sistema de gestión porque le permite conocer en que dirección (ampliar o reducir) es necesario cambiar el despliegue para mejorar sus prestaciones, en lugar que usar simplemente una política de ampliación. ABSTRACT The application of pervasive computing is extending from field-specific to everyday use. The Internet of Things (IoT) is the shiniest example of its application and of its intrinsic complexity compared with classical application development. The main characteristic that differentiates pervasive from other forms of computing lies in the use of contextual information. Some classical applications do not use any contextual information whatsoever. Others, on the other hand, use only part of the contextual information, which is integrated in an ad hoc fashion using an application-specific implementation. This information is handled in a one-off manner because of the difficulty of sharing context across applications. As a matter of fact, the application type determines what the contextual information is. For instance, for an imaging editor, the image is the information and its meta-data, like the time of the shot or camera settings, are the context, whereas, for a file-system application, the image, including its camera settings, is the information and the meta-data external to the file, like the modification date or the last accessed timestamps, constitute the context. This means that contextual information is hard to share. A communication middleware that supports context decidedly eases application development in pervasive computing. However, the use of context should not be mandatory; otherwise, the communication middleware would be reduced to a context middleware and no longer be compatible with non-context-aware applications. SilboPS, our implementation of content-based publish/subscribe inspired by SIENA [11, 9], solves this problem by adding two new elements to the paradigm: the context and the context function. Context represents the actual contextual information specific to the message to be sent or that needs to be notified to the subscriber, whereas the context function is evaluated using the publisher’s context and the subscriber’s context to decide whether the current message and context are useful for the subscriber. In this manner, context logic management is decoupled from context management, increasing the flexibility of communication and usage across different applications. Since the default context is empty, context-aware and classical applications can use the same SilboPS, resolving the syntactic mismatch that there is between the two categories. In any case, the possible semantic mismatch is still present because it depends on how each application interprets the data, and it cannot be resolved by an agnostic third party. The IoT environment introduces not only context but scaling challenges too. The number of sensors, the volume of the data that they produce and the number of applications that could be interested in harvesting such data are growing all the time. Today’s response to the above need is cloud computing. However, cloud computing applications need to be able to scale elastically [22]. Unfortunately there is no slicing, as distributed system primitives that support internal state partitioning [33] and hot swapping and current cloud systems like OpenStack or OpenNebula do not provide elastic monitoring out of the box. This means there is a two-sided problem: 1) how to scale an application elastically and 2) how to monitor the application and know when it should scale in or out. E-SilboPS is the elastic version of SilboPS. I t is the solution for the monitoring problem thanks to its content-based publish/subscribe nature and, unlike other solutions [5], it scales efficiently so as to meet workload demand without overprovisioning or underprovisioning. Additionally, it is based on a newly designed algorithm that shows how to add elasticity in an application with different state constraints: stateless, isolated stateful with external coordination and shared stateful with general coordination. Its evaluation shows that it is able to achieve remarkable speedups where the network layer is the main limiting factor: the calculated efficiency (see Figure 5.8) shows how each configuration performs with respect to adjacent configurations. This provides insight into the actual trending of the whole system in order to predict if the next configuration would offset its cost against the resulting gain in notification throughput. Particular attention has been paid to the evaluation of same-cost deployments in order to find out which one is the best for the given workload demand. Finally, the overhead introduced by the different configurations has been estimated to identify the primary limiting factor for throughput. This helps to determine the intrinsic sequential part and base overhead [26] of an optimal versus a suboptimal deployment. Depending on the type of workload, this can be as low as 10% in a local optimum or as high as 60% when an overprovisioned configuration is deployed for a given workload demand. This Karp-Flatt metric estimation is important for system management because it indicates the direction (scale in or out) in which the deployment has to be changed in order to improve its performance instead of simply using a scale-out policy.

A real case of a cognitive multiplayer game: design and development of the iOS client in Swift and its cloud architecture

as tecnologías emergentes como el cloud computing y los dispositivos móviles están creando una oportunidad sin precedentes para mejorar el sistema educativo, permitiendo tanto a los educadores personalizar y mejorar la experiencia de aprendizaje, como facilitar a los estudiantes que adquieran conocimientos sin importar dónde estén. Por otra parte, a través de técnicas de gamificacion será posible promover y motivar a los estudiantes a que aprendan materias arduas haciendo que la experiencia sea más motivadora. Los juegos móviles pueden ser el camino correcto para dar soporte a esta experiencia de aprendizaje mejorada. Este proyecto integra el diseño y desarrollo de una arquitectura en la nube altamente escalable y con alto rendimiento, así como el propio cliente de iOS, para dar soporte a una nueva version de Temporis, un juego móvil multijugador orientado a reordenar eventos históricos en una línea temporal (e.j. historia, arte, deportes, entretenimiento y literatura). Temporis actualmente está disponible en Google Play. Esta memoria describe el desarrollo de la nueva versión de Temporis (Temporis v.2.0) proporcionando detalles acerca de la mejora y adaptación basados en el Temporis original. En particular se describe el nuevo backend hecho en Go sobre Google App Engine creado para soportar miles de usuarios, asó como otras características por ejemplo como conseguir enviar noticaciones push desde la propia plataforma. Por último, el cliente de iOS en Temporis v.2.0 se ha desarrollado utilizando las últimas y más relevantes tecnologías, prestando especial atención a Swift (el lenguaje de programación nuevo de Apple, que es seguro y rápido), el Paradigma Funcional Reactivo (que ayuda a construir aplicaciones altamente interactivas además de a minimizar errores) y la arquitectura VIPER (una arquitectura que sigue los principios SOLID, se centra en la separación de asuntos y favorece la reutilización de código en otras plataformas). ABSTRACT Emerging technologies such as cloud computing and mobile devices are creating an unprecedented opportunity for enhancing the educational system, letting both educators customize and improve the learning experience, and students acquire knowledge regardless of where they are. Moreover, through gamification techniques it would be possible to encourage and motivate students to learn arduous subjects by making the experience more motivating. Mobile games can be a perfect vehicle to support this enhanced learning experience. This project integrates the design and development of a highly scalable and performant cloud architecture, as well as the iOS client that uses it, in order to provide support to a new version of Temporis, a mobile multiplayer game focused on ordering time-based (e.g. history, art, sports, entertainment and literature) in a timeline that currently is available on Google Play. This work describes the development of the new Temporis version (Temporis v.2.0), providing details about improvements and details on the adaptation of the original Temporis. In particular, the new Google App Engine backend is described, which was created to support thousand of users developed in Go language are provided, in addition to other features like how to achieve push notications in this platform. Finally, the mobile iOS client developed using the latest and more relevant technologies is explained paying special attention to Swift (Apple's new programming language, that is safe and fast), the Functional Reactive Paradigm (that helps building highly interactive apps while minimizing bugs) and the VIPER architecture (a SOLID architecture that enforces separation of concerns and makes it easy to reuse code for other platforms).

Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics

Many small bacterial, archaebacterial, and eukaryotic genomes have been sequenced, and the larger eukaryotic genomes are predicted to be completely sequenced within the next decade. In all genomes sequenced to date, a large portion of these organisms’ predicted protein coding regions encode polypeptides of unknown biochemical, biophysical, and/or cellular functions. Three-dimensional structures of these proteins may suggest biochemical or biophysical functions. Here we report the crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-Å resolution. The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an ATP-mediated molecular switch, which we confirm by biochemical experiments. Furthermore, the structure reveals different ATP binding motifs that are shared among many homologous hypothetical proteins in this family. This result indicates that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.