Implementation of a building automation system based on semantic modeling

This paper presents an Ontology-Based multi-technology platform designed to avoid some issues of Building Automation Systems. The platform allows the integration of several building automation protocols, eases the development and implementation of different kinds of services and allows sharing information related to the infrastructure and facilities within a building. The system has been implemented and tested in the Energy Efficiency Research Facility at CeDInt-UPM.

A Web-based Support System for Providing Effective Monitoring, Feedback and Evaluation in Project Management Education

This work introduces a web-based learning environment to facilitate learning in Project Management. The proposed web-based support system integrates methodological procedures and information systems, allowing to promote learning among geographically-dispersed students. Thus, students who are enrolled in different universities at different locations and attend their own project management courses, share a virtual experience in executing and managing projects. Specific support systems were used or developed to automatically collect information about student activities, making it possible to monitor the progress made on learning and assess learning performance as established in the defined rubric.

Proof of concept of an imaging system demonstrator for PET applications with SiPM

A PET imaging system demonstrator based on LYSO crystal arrays coupled to SiPM matrices is under construction at the University and INFN of Pisa. Two SiPM matrices, composed of 8×8 SiPM pixels, and 1,5 mm pitch, have been coupled one to one to a LYSO crystals array and read out by a custom electronics system. front-end ASICs were used to read 8 channels of each matrix. Data from each front-end were multiplexed and sent to a DAQ board for the digital conversion; a motherboard collects the data and communicates with a host computer through a USB port for the storage and off-line data processing. In this paper we show the first preliminary tomographic image of a point-like radioactive source acquired with part of the two detection heads in time coincidence.

3D Videoconferencing system using spatial scalability

An implementation of a real-time 3D videoconferencing system using the currently available technology is presented. This appr oach is based on the side by side spatial compression of the stereoscopic images . The encoder and the decoder have b een implemented in a standard personal computer and a conventional 3D comp atible TV has been used to present the frames. Moreover, the users without 3D technology can use the system because 2D compatibility mode has been implemented in the decoder. The performance res ults show that a conventional computer can be used for encod ing/decoding audio and video streams and the delay in the transmission is lower than 200 ms.

AquaData and AquaGIS: Two computer utilities for temporal and spatial simulations of water-limited yield with AquaCrop.

The crop simulation model AquaCrop, recently developed by FAO can be used for a wide range of purposes. However, in its present form, its use over large areas or for applications that require a large number of simulations runs (e.g., long-term analysis), is not practical without developing software to facilitate such applications. Two tools for managing the inputs and outputs of AquaCrop, named AquaData and AquaGIS, have been developed for this purpose and are presented here. Both software utilities have been programmed in Delphi v. 5 and in addition, AquaGIS requires the Geographic Information System (GIS) programming tool MapObjects. These utilities allow the efficient management of input and output files, along with a GIS module to develop spatial analysis and effect spatial visualization of the results, facilitating knowledge dissemination. A sample of application of the utilities is given here, as an AquaCrop simulation analysis of impact of climate change on wheat yield in Southern Spain, which requires extensive input data preparation and output processing. The use of AquaCrop without the two utilities would have required approximately 1000 h of work, while the utilization of AquaData and AquaGIS reduced that time by more than 99%. Furthermore, the use of GIS, made it possible to perform a spatial analysis of the results, thus providing a new option to extend the use of the AquaCrop model to scales requiring spatial and temporal analyses.

Computer workstation vetting by supply current monitoring

It is our goal within this project to develop a powerful electronic system capable to claim, with high certainty, that a malicious software is running (or not) along with the workstations’ normal activity. The new product will be based on measurement of the supply current taken by a workstation from the grid. Unique technique is proposed within these proceedings that analyses the supply current to produce information about the state of the workstation and to generate information of the presence of malicious software running along with the rightful applications. The testing is based on comparison of the behavior of a fault-free workstation (established i advance) and the behavior of the potentially faulty device.

Context modelling for natural Human Computer Interaction applications in e-health

The conception of IoT (Internet of Things) is accepted as the future tendency of Internet among academia and industry. It will enable people and things to be connected at anytime and anyplace, with anything and anyone. IoT has been proposed to be applied into many areas such as Healthcare, Transportation，Logistics, and Smart environment etc. However, this thesis emphasizes on the home healthcare area as it is the potential healthcare model to solve many problems such as the limited medical resources, the increasing demands for healthcare from elderly and chronic patients which the traditional model is not capable of. A remarkable change in IoT in semantic oriented vision is that vast sensors or devices are involved which could generate enormous data. Methods to manage the data including acquiring, interpreting, processing and storing data need to be implemented. Apart from this, other abilities that IoT is not capable of are concluded, namely, interoperation, context awareness and security & privacy. Context awareness is an emerging technology to manage and take advantage of context to enable any type of system to provide personalized services. The aim of this thesis is to explore ways to facilitate context awareness in IoT. In order to realize this objective, a preliminary research is carried out in this thesis. The most basic premise to realize context awareness is to collect, model, understand, reason and make use of context. A complete literature review for the existing context modelling and context reasoning techniques is conducted. The conclusion is that the ontology-based context modelling and ontology-based context reasoning are the most promising and efficient techniques to manage context. In order to fuse ontology into IoT, a specific ontology-based context awareness framework is proposed for IoT applications. In general, the framework is composed of eight components which are hardware, UI (User Interface), Context modelling, Context fusion, Context reasoning, Context repository, Security unit and Context dissemination. Moreover, on the basis of TOVE (Toronto Virtual Enterprise), a formal ontology developing methodology is proposed and illustrated which consists of four stages: Specification & Conceptualization, Competency Formulation, Implementation and Validation & Documentation. In addition, a home healthcare scenario is elaborated by listing its well-defined functionalities. Aiming at representing this specific scenario, the proposed ontology developing methodology is applied and the ontology-based model is developed in a free and open-source ontology editor called Protégé. Finally, the accuracy and completeness of the proposed ontology are validated to show that this proposed ontology is able to accurately represent the scenario of interest.

A proposal for enhancing the motivation in students of computer programming

Computer programming is known to be one of the most difficult courses for students in the first year of engineering. They are faced with the challenge of abstract thinking and gaining programming skills for the first time. These skills are acquired by continuous practicing from the start of the course. In order to enhance the motivation and dynamism of the learning and assessment processes, we have proposed the use of three educational resources namely screencasts, self-assessment questionnaires and automated grading of assignments. These resources have been made available in Moodle which is a Learning Management System widely used in education environments and adopted by the Telecommunications Engineering School at the Universidad Politécnica de Madrid (UPM). Both teachers and students can enhance the learning and assessment processes through the use of new educational activities such as self-assessment questionnaires and automated grading of assignments. On the other hand, multimedia resources such as screencasts can guide students in complex topics. The resources proposed allow teachers to improve their tutorial actions since they provide immediate feedback and comments to students without the enormous effort of manual correction and evaluation by teachers specially taking into account the large number of students enrolled in the course. In this paper we present the case study where three proposed educational resources were applied. We describe the special features of the course and explain why the use of these resources can both enhance the students? motivation and improve the teaching and learning processes. Our research work was carried out on students attending the "Computer programming" course offered in the first year of a Telecommunications Engineering degree at UPM. This course is mandatory and has more than 450 enrolled students. Our purpose is to encourage the motivation and dynamism of the learning and assessment processes.

Persuasive system design methods to deliver a cardio-rehabilitation program of post mi outpatients

Las enfermedades no transmisibles provocan cada ano 38 millones de fallecimientos en el mundo. Entre ellas, tan solo cuatro enfermedades son responsables del 82% de estas muertes: las enfermedades cardiovasculares, las enfermedades crónicas respiratorias, la diabetes, y el cáncer. Se prevé que estas cifras aumenten en los próximos anos, ya que las tendencias indican que en el año 2030 las muertes por esta causa ascenderán a 53 millones de personas. La Organización Mundial de la Salud (OMS) considera importante buscar soluciones para afrontar esta situación y ha solicitado a los gobiernos del mundo la implementación de intervenciones para mejorar los hábitos de vida de las personas y reducir así el riesgo de desarrollo de enfermedades no trasmisibles. Cada año se producen 32 millones de infartos de miocardio y derrames celebrales, de los cuales 12.5 son mortales. En el mundo entre el 40% y 75% de la víctimas de un infarto de miocardio mueren antes de su ingreso en el hospital. En los casos que sobreviven, la adopción de un estilo de vida saludable puede evitar infartos sucesivo, y supone un ahorro potencial de 6 billones de euros al año. La rehabilitación cardiaca es un programa individualizado que aplica un método multidisciplinar para ayudar al paciente a recuperar su condición física, a gestionar la enfermedad cardiovascular y sus comorbilidades, a adoptar hábitos de vida saludables, y a promover su salud mental. La rehabilitación cardiaca requiere la total involucración y motivación del paciente, solo de esta manera se podrán promover hábitos saludables y mejorar la gestión y prevención de su enfermedad. Aunque la participación en los programas de rehabilitación cardiaca es baja, hoy en día existen programas de rehabilitación cardiaca que el paciente puede realizar en su casa. Estos suponen una solución prometedora para aumentar la participación. La rehabilitación cardiaca se considera una intervención integral donde los modelos de psicología de la salud son aplicados para promover un cambio en el estilo de vida de las personas así como para ayudarles a afrontar su propia enfermedad. Existen métodos para implementar cambios de hábitos y de aptitud, y también se considera muy relevante promover no solo el bienestar físico sino también el mental. Existen tecnologías que promueven los cambios de comportamientos en los seres humanos. En concreto, las tecnologías persuasivas y los sistemas de apoyo al cambio de comportamientos modelan las características, las estrategias y los métodos de diseño para promover cambios usando la tecnología. Pero estos modelos tienen algunas limitaciones: todavía no se ha definido que rol tienen las emociones en el cambio de comportamientos y como traducir los métodos de la psicología de la salud en la tecnología. Esta tesis se centra en tres elementos que tienen un rol clave en los cambios de hábitos y actitud: el estado físico, el estado mental, y la tecnología. -Estado de salud: un estado de salud critico puede modificar la actitud del ser humano respecto al cambio. A la vez un buen estado de salud hace que la necesidad del cambio sea menos percibida. -Estado emocional: la actitud tiene un componente afectivo. Los estados emocionales negativos pueden reducir la habilidad de una persona para adoptar nuevos comportamientos. La salud mental es la situación ideal donde los individuos tienen predisposición a los cambios. La tecnología puede ayudar a las personas a adoptar nuevos hábitos, así como a mantener una salud física y mental. Este trabajo de investigación se centra en el diseño de tecnologías para la mejora del estado físico y emocional de las personas. Se ha propuesto un marco de diseño llamado “Well.Be.Sign”. El marco se basa en tres aspectos: El marco teórico: representa los elementos que se tienen que definir para diseñar tecnologías para promover el bienestar de las personas. -El diagrama de influencia: presenta las fuerzas de ‘persuasión’ en el contexto de la salud. El rol de las tecnologías persuasivas ha sido contextualizado en una dimensión donde otros elementos influencian el usuario.  El proceso de diseño: describe el proceso de diseño utilizando una metodología iterativa e incremental que aplica una combinación de métodos de diseño existentes (Diseño Orientado a Objetivos, Diseño de Sistemas Persuasivos) así como elementos originales de este trabajo de investigación. Los métodos se han aplicados para diseñar un sistema que ofrezca un programa de tele-rehabilitación cardiaca. Inicialmente se ha diseñado un prototipo de acuerdo con las necesidades del usuario. En segundo lugar, el prototipo se ha extendido especificando la intervención requerida para al programa de rehabilitación cardiaca. Finalmente el sistema se ha desarrollado y validado en un ensayo clínico con grupo control, donde se observaron las variaciones del estado cardiovascular, el nivel de conocimiento acerca de la enfermedad, la percepción de la enfermedad, la persistencia de hábitos saludables, y la aceptabilidad del sistema. Los resultados muestran que el grupo de intervención tiene una superior capacidad cardiovascular, mejor conocimiento acerca de la enfermedad, y más percepción de control de la enfermedad. Asimismo, en algunos casos se ha registrado persistencia de los hábitos de ejercicios 6 meses después del uso del sistema. Otros dos estudios se han presentado para demonstrar la relevancia del estado emocional del usuario en el diseño de aplicaciones para la promoción del bienestar.  En personas con una grave enfermedad crónica como la insuficiencia cardiaca, donde se ha presentado las conexiones entre estado de salud y estado emocional. En el estudio se ensena la relaciones que tienen los síntomas y las emociones negativas y como un estado negativo emocional puede empeorar la condición física del paciente. -Personas con trastornos del humor: el estudio muestra como las emociones pueden tener un impacto en la percepción de la tecnología por parte del usuario. ABSTRACT Noncommunicable diseases (NCDs) cause the death of 38 million people every year. Four major NCDs are responsible for 82% of these deaths: cardio vascular disease, chronic respiratory disease, diabetes and cancer. These pandemic numbers are projected to raise to 53 million deaths in 2030, and for this reason the assembly of the World Health Organization (WHO) considers communicable diseases as an urgent need to be addressed. It is also a trend to advocate the adoption of mobile technology to deliver health services and to promote healthy behaviours among citizens, but adopting healthS promoting lifestyle is still a difficult task facing human tendencies. Within this context, there is a promising opportunity: persuasive technologies. These technologies are intentionally designed to change a person’s attitudes or behaviours; when applied in this context, than can be used to change health-related attitudes, beliefs, and behaviours. Each year there are 32 million heart attacks and strokes globally, of which about 12.5 million are fatal. Worldwide between 40 and 75% of all heart-attack victims die before reaching hospital. Avoiding a second heart attack by improving adherence to lifestyle and medication regimens has a cost saving potential of around €6 billion per year. In most of the cases the cardiovascular event has been provoked by unhealthy lifestyle. Furthermore, after an MI event the patient's decision to adopt or not healthier behaviour will influence the progress of the disease. Cardio-rehabilitation is an individualized program that follows a multidisciplinary approach to support the user to recover from the Myocardial Infarction, manage the Cardio Vascular Disease and the comorbidities, adopt healthy habits, and cope with any emotional distress. Cardio- rehabilitation requires patient participation and willingness to perform behavioral modifications and change the attitude toward the management and prevention of the disease. Participation in the Cardio Rehabilitation program is not high; the home-based rehabilitation program is a promising solution to increase participation. Nowadays cardio rehabilitation is considered a comprehensive intervention in which models of health psychology are applied to promote the behaviour change of the individuals. Relevant methods that have been successfully applied to foster healthy habits include the Health Belief Model and the Trans Theoretical Model. Studies also demonstrate the importance to promote not only the physical but also the mental well being of the individuals. The idea of also promoting behaviour change using technologies has been defined by the literature as persuasive technologies or behaviour change support systems, in which the features, the strategies and the design method have been modelled to foster the behaviour change using technology. Limitations have been found in this model: there is still research to be done on the role of the emotions and how psychological health intervention can be translated into computer methods. This research focuses on three elements that could foster behaviour change in individuals: the physical and emotional status of the person, and the technology. Every component can influence the user's attitude and behaviour in the following ways: ' Physical status: bad physical status could change human attitude toward the necessity to adopt health behaviours; at the same time, good health status reduces the need to adopt healthy habits. ' Emotional status: the attitude has an affective component, negative emotional state can reduce the ability of a person to adopt new behaviours, and mental well being is the ideal situation in which individuals have a predisposition to adopt healthy behaviours. ' Technology: it can help users to adopt new behaviours and can also be support to promote physical and emotional status. Following this approach the idea driven in this research is that technology that is designed to improve the physical status and the emotional status of the individual could better foster behaviour change. According to this principle, the Well.Be.Sign framework has been proposed. The framework is based on three views: ' The theoretical framework: it represents the patterns that have to be defined to design the technologies to promote well being. ' The influence diagram: it shows the persuasive forces in the context of health care. The role of the persuasive technologies is contextualized in a wider universe where other factors and persuasive forces influence a patient. ' The design process: it shows the process of design using an iterative, incremental methodology that applies a combination of existing methodologies (Goal Directed Design and Persuasive System Design) and others that are original to this research. The methods have been applied to design a system to deliver cardio rehabilitation at home: first a prototype has been defined according to the user’s needs, then it has been extended with the specific intervention required for the cardio–rehabilitation, finally the system has been developed and validated in a controlled clinical study in which the cardiovascular fitness, the level of knowledge, the perception of the illness, the persistence of healthy habits and the system acceptance (only the intervention group) were measured. The results show that the intervention group increased cardiovascular capacity, knowledge, feeling of control of illness and perceived benefits of exercise at the end of the study. After six months of the study, a followSup of the exercise habits was performed. Some individuals of the intervention group continued to be engaged in the running exercise sessions promoted in the designed system. Two other cases have been presented to demonstrate the foundations of the Well.Be.Sign’s approach to promote both physical and emotional status: ' People affected by Heart Failure, in which a bidirectional connection between health status and emotions has been discussed with patients. Two correlations were demonstrated: the relationship between symptoms and negative emotional response, and that negative emotional status is correlated with worsening of chronic conditions. ' People with mood disorders: the study shows that emotions could also impact how the user perceives the technology.

Parallel Computer Vision Algorithms for Graphics Processing Units

La evolución de los teléfonos móviles inteligentes, dotados de cámaras digitales, está provocando una creciente demanda de aplicaciones cada vez más complejas que necesitan algoritmos de visión artificial en tiempo real; puesto que el tamaño de las señales de vídeo no hace sino aumentar y en cambio el rendimiento de los procesadores de un solo núcleo se ha estancado, los nuevos algoritmos que se diseñen para visión artificial han de ser paralelos para poder ejecutarse en múltiples procesadores y ser computacionalmente escalables. Una de las clases de procesadores más interesantes en la actualidad se encuentra en las tarjetas gráficas (GPU), que son dispositivos que ofrecen un alto grado de paralelismo, un excelente rendimiento numérico y una creciente versatilidad, lo que los hace interesantes para llevar a cabo computación científica. En esta tesis se exploran dos aplicaciones de visión artificial que revisten una gran complejidad computacional y no pueden ser ejecutadas en tiempo real empleando procesadores tradicionales. En cambio, como se demuestra en esta tesis, la paralelización de las distintas subtareas y su implementación sobre una GPU arrojan los resultados deseados de ejecución con tasas de refresco interactivas. Asimismo, se propone una técnica para la evaluación rápida de funciones de complejidad arbitraria especialmente indicada para su uso en una GPU. En primer lugar se estudia la aplicación de técnicas de síntesis de imágenes virtuales a partir de únicamente dos cámaras lejanas y no paralelas—en contraste con la configuración habitual en TV 3D de cámaras cercanas y paralelas—con información de color y profundidad. Empleando filtros de mediana modificados para la elaboración de un mapa de profundidad virtual y proyecciones inversas, se comprueba que estas técnicas son adecuadas para una libre elección del punto de vista. Además, se demuestra que la codificación de la información de profundidad con respecto a un sistema de referencia global es sumamente perjudicial y debería ser evitada. Por otro lado se propone un sistema de detección de objetos móviles basado en técnicas de estimación de densidad con funciones locales. Este tipo de técnicas es muy adecuada para el modelado de escenas complejas con fondos multimodales, pero ha recibido poco uso debido a su gran complejidad computacional. El sistema propuesto, implementado en tiempo real sobre una GPU, incluye propuestas para la estimación dinámica de los anchos de banda de las funciones locales, actualización selectiva del modelo de fondo, actualización de la posición de las muestras de referencia del modelo de primer plano empleando un filtro de partículas multirregión y selección automática de regiones de interés para reducir el coste computacional. Los resultados, evaluados sobre diversas bases de datos y comparados con otros algoritmos del estado del arte, demuestran la gran versatilidad y calidad de la propuesta. Finalmente se propone un método para la aproximación de funciones arbitrarias empleando funciones continuas lineales a tramos, especialmente indicada para su implementación en una GPU mediante el uso de las unidades de filtraje de texturas, normalmente no utilizadas para cómputo numérico. La propuesta incluye un riguroso análisis matemático del error cometido en la aproximación en función del número de muestras empleadas, así como un método para la obtención de una partición cuasióptima del dominio de la función para minimizar el error. ABSTRACT The evolution of smartphones, all equipped with digital cameras, is driving a growing demand for ever more complex applications that need to rely on real-time computer vision algorithms. However, video signals are only increasing in size, whereas the performance of single-core processors has somewhat stagnated in the past few years. Consequently, new computer vision algorithms will need to be parallel to run on multiple processors and be computationally scalable. One of the most promising classes of processors nowadays can be found in graphics processing units (GPU). These are devices offering a high parallelism degree, excellent numerical performance and increasing versatility, which makes them interesting to run scientific computations. In this thesis, we explore two computer vision applications with a high computational complexity that precludes them from running in real time on traditional uniprocessors. However, we show that by parallelizing subtasks and implementing them on a GPU, both applications attain their goals of running at interactive frame rates. In addition, we propose a technique for fast evaluation of arbitrarily complex functions, specially designed for GPU implementation. First, we explore the application of depth-image–based rendering techniques to the unusual configuration of two convergent, wide baseline cameras, in contrast to the usual configuration used in 3D TV, which are narrow baseline, parallel cameras. By using a backward mapping approach with a depth inpainting scheme based on median filters, we show that these techniques are adequate for free viewpoint video applications. In addition, we show that referring depth information to a global reference system is ill-advised and should be avoided. Then, we propose a background subtraction system based on kernel density estimation techniques. These techniques are very adequate for modelling complex scenes featuring multimodal backgrounds, but have not been so popular due to their huge computational and memory complexity. The proposed system, implemented in real time on a GPU, features novel proposals for dynamic kernel bandwidth estimation for the background model, selective update of the background model, update of the position of reference samples of the foreground model using a multi-region particle filter, and automatic selection of regions of interest to reduce computational cost. The results, evaluated on several databases and compared to other state-of-the-art algorithms, demonstrate the high quality and versatility of our proposal. Finally, we propose a general method for the approximation of arbitrarily complex functions using continuous piecewise linear functions, specially formulated for GPU implementation by leveraging their texture filtering units, normally unused for numerical computation. Our proposal features a rigorous mathematical analysis of the approximation error in function of the number of samples, as well as a method to obtain a suboptimal partition of the domain of the function to minimize approximation error.

Human-computer interaction based on visual hand-gesture recognition using volumetric spatiograms of local binary patterns

A more natural, intuitive, user-friendly, and less intrusive Human–Computer interface for controlling an application by executing hand gestures is presented. For this purpose, a robust vision-based hand-gesture recognition system has been developed, and a new database has been created to test it. The system is divided into three stages: detection, tracking, and recognition. The detection stage searches in every frame of a video sequence potential hand poses using a binary Support Vector Machine classifier and Local Binary Patterns as feature vectors. These detections are employed as input of a tracker to generate a spatio-temporal trajectory of hand poses. Finally, the recognition stage segments a spatio-temporal volume of data using the obtained trajectories, and compute a video descriptor called Volumetric Spatiograms of Local Binary Patterns (VS-LBP), which is delivered to a bank of SVM classifiers to perform the gesture recognition. The VS-LBP is a novel video descriptor that constitutes one of the most important contributions of the paper, which is able to provide much richer spatio-temporal information than other existing approaches in the state of the art with a manageable computational cost. Excellent results have been obtained outperforming other approaches of the state of the art.

Improved high-speed de-excitation system for brushless synchronous machines tested on a 20 MVA hydro-generator

Synchronous machines with brushless excitation have the disadvantage that the field winding is not accessible for the de-excitation of the machine. This means that, despite the proper operation of the protection system, the slow de-excitation time constant may produce severe damage in the event of an internal short circuit. A high-speed de-excitation system for these machines was developed, and this study presents the continuation of a previously published study. This study presents the design by computer simulation and the results of the first commissioning of this de-excitation system in a commercial 20 MVA hydro-generator. The de-excitation is achieved by inserting resistance in the field circuit, obtaining a dynamic response similar to that achieved in machines with static excitation. In this case, a non-linear discharge resistor was used, making the dynamic response even better.

Computer-based analysis of the binding steps in protein complex formation

Computer models were used to examine whether and under what conditions the multimeric protein complex is inhibited by high concentrations of one of its components—an effect analogous to the prozone phenomenon in precipitin tests. A series of idealized simple “ball-and-stick” structures representing small oligomeric complexes of protein molecules formed by reversible binding reactions were analyzed to determine the binding steps leading to each structure. The equilibrium state of each system was then determined over a range of starting concentrations and Kds and the steady-state concentration of structurally complete oligomer calculated for each situation. A strong inhibitory effect at high concentrations was shown by any protein molecule forming a bridge between two or more separable parts of the complex. By contrast, proteins linked to the outside of the complex by a single bond showed no inhibition whatsoever at any concentration. Nonbridging, multivalent proteins in the body of the complex could show an inhibitory effect or not depending on the structure of the complex and the strength of its bonds. On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation.

Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution

The origin of the catalytic power of enzymes is discussed, paying attention to evolutionary constraints. It is pointed out that enzyme catalysis reflects energy contributions that cannot be determined uniquely by current experimental approaches without augmenting the analysis by computer simulation studies. The use of energy considerations and computer simulations allows one to exclude many of the popular proposals for the way enzymes work. It appears that the standard approaches used by organic chemists to catalyze reactions in solutions are not used by enzymes. This point is illustrated by considering the desolvation hypothesis and showing that it cannot account for a large increase in kcat relative to the corresponding kcage for the reference reaction in a solvent cage. The problems associated with other frequently invoked mechanisms also are outlined. Furthermore, it is pointed out that mutation studies are inconsistent with ground state destabilization mechanisms. After considering factors that were not optimized by evolution, we review computer simulation studies that reproduced the overall catalytic effect of different enzymes. These studies pointed toward electrostatic effects as the most important catalytic contributions. The nature of this electrostatic stabilization mechanism is far from being obvious because the electrostatic interaction between the reacting system and the surrounding area is similar in enzymes and in solution. However, the difference is that enzymes have a preorganized dipolar environment that does not have to pay the reorganization energy for stabilizing the relevant transition states. Apparently, the catalytic power of enzymes is stored in their folding energy in the form of the preorganized polar environment.

Janus: an FPGA-based system for high-performance scientific computing

This paper describes JANUS, a modular massively parallel and reconfigurable FPGA-based computing system. Each JANUS module has a computational core and a host. The computational core is a 4x4 array of FPGA-based processing elements with nearest-neighbor data links. Processors are also directly connected to an I/O node attached to the JANUS host, a conventional PC. JANUS is tailored for, but not limited to, the requirements of a class of hard scientific applications characterized by regular code structure, unconventional data manipulation instructions and not too large data-base size. We discuss the architecture of this configurable machine, and focus on its use on Monte Carlo simulations of statistical mechanics. On this class of application JANUS achieves impressive performances: in some cases one JANUS processing element outperfoms high-end PCs by a factor ≈1000. We also discuss the role of JANUS on other classes of scientific applications.