MEIA SYSTEMS: Membrane Encrypted Information Applications Systems

Membrane computing is a recent area that belongs to natural computing. This field works on computational models based on nature's behavior to process the information. Recently, numerous models have been developed and implemented with this purpose. P-systems are the structures which have been defined,developed and implemented to simulate the behavior and the evolution of membrane systems which we find in nature. What we show in this paper is a new model that deals with encrypted information which provides security the membrane systems communication. Moreover we find non deterministic and random applications in nature that are suitable to MEIA systems. The inherent parallelism and non determinism make this applications perfect object to implement MEIA systems.

Atomic physics modeling and applications for ICF plasmas

The Atomic Physics Group at the Institute of Nuclear Fusion (DENIM) in Spain has accumulated experience over the years in developing a collection of computational models and tools for determining some relevant microscopic properties of, mainly, ICF and laser-produced plasmas in a variety of conditions. In this work several applications of those models in determining some relevant microscopic properties are presented.

Seismic modelling of bridges with semirigid connections

The need to modal semi-rigid behaviour of joints to analyze the seismic response of bridges arises when retrofitting devices such as cables or bolts are introduced in otherwise free joints or when the design takes advantage of the plastification of structural sections to impose energy dissipation though their ductile behaviour. The paper presents some preliminary results of a parametric study carried out using s1mplified computational models. Two instances where semirigid connection play a role in the seismic response of bridges have been discussed. The ongoing research from which this paper is extracted is intended to enhance understanding on the effectivness of various bridge retrofitting measures and to provide information that may be used to calibrate some ECS-2 rules. Finally, it is hoped that the development of reliable simplified techniques for nonlinear analysis will provide designers with useful tools to examine behavior and ultimately improve seismic safety in actual bridges.

Sensing Aeropolis. Urban air monitoring devices in Madrid, 2006-2010

Esta tesis examina las implicaciones técnicas, políticas y espaciales del aire urbano, y en concreto, de la calidad del aire, para tenerlo en cuenta desde una perspectiva arquitectónica. En oposición a formas de entender el aire como un vacío o como una metáfora, este proyecto propone abordarlo desde un acercamiento material y tecnológico, trayendo el entorno al primer plano y reconociendo sus múltiples agencias. Debido a la escasa bibliografía detectada en el campo de la arquitectura, el objetivo es construir un marco teórico-analítico para considerar el aire urbano. Para ello el trabajo construye Aeropolis, una metáfora heurística que describe el ensamblaje sociotecnico de la ciudad. Situada en la intersección de determinadas ramas de la filosofía de la cultura, los estudios sobre ciencia y tecnología y estudios feministas de la ciencia este nuevo paisaje conceptual ofrece una metodología y herramientas para abordar el objeto de estudio desde distintos ángulos. Estas herramientas metodológicas han sido desarrolladas en el contexto específico de Madrid, ciudad muy contaminada cuyo aire ha sido objeto de controversias políticas y sociales, y donde las políticas y tecnologías para reducir sus niveles no han sido exitosas. Para encontrar una implicación alternativa con el aire esta tesis propone un método de investigación de agentes invisibles a partir del análisis de sus dispositivos epistémicos. Se centra, en concreto, en los instrumentos que miden, visualizan y comunican la calidad del aire, proponiendo que no sólo lo representan, sino que son también instrumentos que diseñan el aire y la ciudad. La noción de “sensing” (en castellano medir y sentir) es expandida, reconociendo distintas prácticas que reconstruyen el aire de Madrid. El resultado de esta estrategia no es sólo la ampliación de los espacios desde los que relacionarnos con el aire, sino también la legitimación de prácticas existentes fuera de contextos científicos y administrativos, como por ejemplo prácticas relacionadas con el cuerpo, así como la redistribución de agencias entre más actores. Así, esta tesis trata sobre toxicidad, la Unión Europea, producción colaborativa, modelos de computación, dolores de cabeza, kits DIY, gases, cuerpos humanos, salas de control, sangre o políticos, entre otros. Los dispositivos que sirven de datos empíricos sirven como un ejemplo excepcional para investigar infraestructuras digitales, permitiendo desafiar nociones sobre Ciudades Inteligentes. La tesis pone especial atención en los efectos del aire en el espacio público, reconociendo los procesos de invisibilización que han sufrido sus infraestructuras de monitorización. Para terminar se exponen líneas de trabajo y oportunidades para la arquitectura y el diseño urbano a través de nuevas relaciones entre infraestructuras urbanas, el medio construido, espacios domésticos y públicos y humanos y no humanos, para crear nuevas ecologías políticas urbanas (queer). ABSTRACT This thesis examines the technical, political and spatial implications of urban air, and more specifically "air quality", in order to consider it from an architectural perspective. In opposition to understandings of the air either as a void or as a metaphor, this project proposes to inspect it from a material and technical approach, bringing the background to the fore and acknowledging its multiple agencies. Due to the scarce bibliography within the architectural field, its first aim is to construct a theoretical and analytical framework from which to consider urban air. For this purpose, the work attempts the construction of Aeropolis, a heuristic metaphor that describes the city's aero socio-material assemblage. Located at the intersection of certain currents in cultural philosophy, science and technology studies as well as feminist studies in technoscience, this framework enables a methodology and toolset to be extracted in order to approach the subject matter from different angles. The methodological tools stemming from this purpose-built framework were put to the test in a specific case study: Madrid, a highly polluted city whose air has been subject to political and social controversies, and where no effective policies or technologies have been successful in reducing its levels of pollution. In order to engage with the air, the thesis suggests a method for researching invisible agents by examining the epistemic devices involved. It locates and focuses on the instruments that sense, visualise and communicate urban air, claiming that they do not only represent it, but are also instruments that design the air and the city. The notion of "sensing" is then expanded by recognising different practices which enact the air in Madrid. The work claims that the result of this is not only the opening up of spaces for engagement but also the legitimisation of existing practices outside science and policymaking environments, such as embodied practices, as well as the redistribution of agency among more actors. So this is a thesis about toxicity, the European Union, collaborative production, scientific computational models, headaches, DIY kits, gases, human bodies, control rooms, blood, or politicians, among many others. The devices found throughout the work serve as an exceptional substrate for an investigation of digital infrastructures, enabling to challenge Smart City tropes. There is special attention paid to the effects of the air on the public space, acknowledging the silencing processes these infrastructures have been subjected to. Finally there is an outline of the opportunities arising for architecture and urban design when taking the air into account, to create new (queer) urban political ecologies between the air, urban infrastructures, the built environment, public and domestic spaces, and humans and more than humans.

Auto-Emergencia de Comunicación Sintáctica en Entornos Estáticos y Dinámicos para Grupos de Robots mediante Evolución Gramatical y Aprendizaje por Refuerzo

La idea de dotar a un grupo de robots o agentes artificiales de un lenguaje ha sido objeto de intenso estudio en las ultimas décadas. Como no podía ser de otra forma los primeros intentos se enfocaron hacia el estudio de la emergencia de vocabularios compartidos convencionalmente por el grupo de robots. Las ventajas que puede ofrecer un léxico común son evidentes, como también lo es que un lenguaje con una estructura más compleja, en la que se pudieran combinar palabras, sería todavía más beneficioso. Surgen así algunas propuestas enfocadas hacia la emergencia de un lenguaje consensuado que muestre una estructura sintáctica similar al lenguaje humano, entre las que se encuentra este trabajo. Tomar el lenguaje humano como modelo supone adoptar algunas de las hipótesis y teorías que disciplinas como la filosofía, la psicología o la lingüística entre otras se han encargado de proponer. Según estas aproximaciones teóricas el lenguaje presenta una doble dimension formal y funcional. En base a su dimensión formal parece claro que el lenguaje sigue unas reglas, por lo que el uso de una gramática se ha considerado esencial para su representación, pero también porque las gramáticas son un dispositivo muy sencillo y potente que permite generar fácilmente estructuras simbólicas. En cuanto a la dimension funcional se ha tenido en cuenta la teoría quizá más influyente de los últimos tiempos, que no es otra que la Teoría de los Actos del Habla. Esta teoría se basa en la idea de Wittgenstein por la que el significado reside en el uso del lenguaje, hasta el punto de que éste se entiende como una manera de actuar y de comportarse, en definitiva como una forma de vida. Teniendo presentes estas premisas en esta tesis se pretende experimentar con modelos computacionales que permitan a un grupo de robots alcanzar un lenguaje común de manera autónoma, simplemente mediante interacciones individuales entre los robots, en forma de juegos de lenguaje. Para ello se proponen tres modelos distintos de lenguaje: • Un modelo basado en gramáticas probabilísticas y aprendizaje por refuerzo en el que las interacciones y el uso del lenguaje son claves para su emergencia y que emplea una gramática generativa estática y diseñada de antemano. Este modelo se aplica a dos grupos distintos: uno formado exclusivamente por robots y otro que combina robots y un humano, de manera que en este segundo caso se plantea un aprendizaje supervisado por humanos. • Un modelo basado en evolución gramatical que permite estudiar no solo el consenso sintáctico, sino también cuestiones relativas a la génesis del lenguaje y que emplea una gramática universal a partir de la cual los robots pueden evolucionar por sí mismos la gramática más apropiada según la situación lingüística que traten en cada momento. • Un modelo basado en evolución gramatical y aprendizaje por refuerzo que toma aspectos de los anteriores y amplia las posibilidades de los robots al permitir desarrollar un lenguaje que se adapta a situaciones lingüísticas dinámicas que pueden cambiar en el tiempo y también posibilita la imposición de restricciones de orden muy frecuentes en las estructuras sintácticas complejas. Todos los modelos implican un planteamiento descentralizado y auto-organizado, de manera que ninguno de los robots es el dueño del lenguaje y todos deben cooperar y colaborar de forma coordinada para lograr el consenso sintáctico. En cada caso se plantean experimentos que tienen como objetivo validar los modelos propuestos, tanto en lo relativo al éxito en la emergencia del lenguaje como en lo relacionado con cuestiones paralelas de importancia, como la interacción hombre-máquina o la propia génesis del lenguaje. ABSTRACT The idea of giving a language to a group of robots or artificial agents has been the subject of intense study in recent decades. The first attempts have focused on the development and emergence of a conventionally shared vocabulary. The advantages that can provide a common vocabulary are evident and therefore a more complex language that combines words would be even more beneficial. Thus some proposals are put forward towards the emergence of a consensual language with a sintactical structure in similar terms to the human language. This work follows this trend. Taking the human language as a model means taking some of the assumptions and theories that disciplines such as philosophy, psychology or linguistics among others have provided. According to these theoretical positions language has a double formal and functional dimension. Based on its formal dimension it seems clear that language follows rules, so that the use of a grammar has been considered essential for representation, but also because grammars are a very simple and powerful device that easily generates these symbolic structures. As for the functional dimension perhaps the most influential theory of recent times, the Theory of Speech Acts has been taken into account. This theory is based on the Wittgenstein’s idea about that the meaning lies in the use of language, to the extent that it is understood as a way of acting and behaving. Having into account these issues this work implements some computational models in order to test if they allow a group of robots to reach in an autonomous way a shared language by means of individual interaction among them, that is by means of language games. Specifically, three different models of language for robots are proposed: • A reinforcement learning based model in which interactions and language use are key to its emergence. This model uses a static probabilistic generative grammar which is designed beforehand. The model is applied to two different groups: one formed exclusively by robots and other combining robots and a human. Therefore, in the second case the learning process is supervised by the human. • A model based on grammatical evolution that allows us to study not only the syntactic consensus, but also the very genesis of language. This model uses a universal grammar that allows robots to evolve for themselves the most appropriate grammar according to the current linguistic situation they deal with. • A model based on grammatical evolution and reinforcement learning that takes aspects of the previous models and increases their possibilities. This model allows robots to develop a language in order to adapt to dynamic language situations that can change over time and also allows the imposition of syntactical order restrictions which are very common in complex syntactic structures. All models involve a decentralized and self-organized approach so that none of the robots is the language’s owner and everyone must cooperate and work together in a coordinated manner to achieve syntactic consensus. In each case experiments are presented in order to validate the proposed models, both in terms of success about the emergence of language and it relates to the study of important parallel issues, such as human-computer interaction or the very genesis of language.

Caracterización y simulación de arborizaciones dentríticas con redes bayesianas incluyendo variables angulares

El funcionamiento interno del cerebro es todavía hoy en día un misterio, siendo su comprensión uno de los principales desafíos a los que se enfrenta la ciencia moderna. El córtex cerebral es el área del cerebro donde tienen lugar los procesos cerebrales de más alto nivel, cómo la imaginación, el juicio o el pensamiento abstracto. Las neuronas piramidales, un tipo específico de neurona, suponen cerca del 80% de los cerca de los 10.000 millones de que componen el córtex cerebral, haciendo de ellas un objetivo principal en el estudio del funcionamiento del cerebro. La morfología neuronal, y más específicamente la morfología dendrítica, determina cómo estas procesan la información y los patrones de conexión entre neuronas, siendo los modelos computacionales herramientas imprescindibles para el estudio de su rol en el funcionamiento del cerebro. En este trabajo hemos creado un modelo computacional, con más de 50 variables relativas a la morfología dendrítica, capaz de simular el crecimiento de arborizaciones dendríticas basales completas a partir de reconstrucciones de neuronas piramidales reales, abarcando desde el número de dendritas hasta el crecimiento los los árboles dendríticos. A diferencia de los trabajos anteriores, nuestro modelo basado en redes Bayesianas contempla la arborización dendrítica en su conjunto, teniendo en cuenta las interacciones entre dendritas y detectando de forma automática las relaciones entre las variables morfológicas que caracterizan la arborización. Además, el análisis de las redes Bayesianas puede ayudar a identificar relaciones hasta ahora desconocidas entre variables morfológicas. Motivado por el estudio de la orientación de las dendritas basales, en este trabajo se introduce una regularización L1 generalizada, aplicada al aprendizaje de la distribución von Mises multivariante, una de las principales distribuciones de probabilidad direccional multivariante. También se propone una distancia circular multivariante que puede utilizarse para estimar la divergencia de Kullback-Leibler entre dos muestras de datos circulares. Comparamos los modelos con y sin regularizaci ón en el estudio de la orientación de la dendritas basales en neuronas humanas, comprobando que, en general, el modelo regularizado obtiene mejores resultados. El muestreo, ajuste y representación de la distribución von Mises multivariante se implementa en un nuevo paquete de R denominado mvCircular.---ABSTRACT---The inner workings of the brain are, as of today, a mystery. To understand the brain is one of the main challenges faced by current science. The cerebral cortex is the region of the brain where all superior brain processes, like imagination, judge and abstract reasoning take place. Pyramidal neurons, a specific type of neurons, constitute approximately the 80% of the more than 10.000 million neurons that compound the cerebral cortex. It makes the study of the pyramidal neurons crucial in order to understand how the brain works. Neuron morphology, and specifically the dendritic morphology, determines how the information is processed in the neurons, as well as the connection patterns among neurons. Computational models are one of the main tools for studying dendritic morphology and its role in the brain function. We have built a computational model that contains more than 50 morphological variables of the dendritic arborizations. This model is able to simulate the growth of complete dendritic arborizations from real neuron reconstructions, starting with the number of basal dendrites, and ending modeling the growth of dendritic trees. One of the main diferences between our approach, mainly based on the use of Bayesian networks, and other models in the state of the art is that we model the whole dendritic arborization instead of focusing on individual trees, which makes us able to take into account the interactions between dendrites and to automatically detect relationships between the morphologic variables that characterize the arborization. Moreover, the posterior analysis of the relationships in the model can help to identify new relations between morphological variables. Motivated by the study of the basal dendrites orientation, a generalized L1 regularization applied to the multivariate von Mises distribution, one of the most used distributions in multivariate directional statistics, is also introduced in this work. We also propose a circular multivariate distance that can be used to estimate the Kullback-Leibler divergence between two circular data samples. We compare the regularized and unregularized models on basal dendrites orientation of human neurons and prove that regularized model achieves better results than non regularized von Mises model. Sampling, fitting and plotting functions for the multivariate von Mises are implemented in a new R packaged called mvCircular.

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.

Modified PNA design and synthesis: a novel approach using Molecular Dynamics and Metadynamics

Gli acidi peptido nucleici sono potenti strumenti utilizzati in ambito biotecnologico per colpire DNA o RNA. PNA contenenti basi o backbone modificati sono attualmente studiati per migliorarne le proprietà in ambito biologico. Bersagliare i micro RNA (anti-miR) è particolarmente interessante nell’ottica di future applicazioni terapeutiche, ma strumenti computazionali che aiutino nel design di nuovi PNA anti-miR non sono stati ancora completamente sviluppati. Le proprietà conformazionali del singolo filamento di PNA (non modificato o recante modificazioni in γ) e dei duplex PNA:RNA e i processi di re-annealing e melting sono stati studiati tramite Dinamica Molecolare e Metadinamica. L’approccio computazionale consolidato, assieme a un programma modificato per la generazione delle strutture dei duplex contenenti PNA, è stato utilizzato per il virtual screening di PNA contenenti basi modificate. Sono state inoltre sintetizzate le unità per l’ottenimento del composto più promettente e una funzione idrolitica da legare al monomero finale.

Identificação de sistemas para o estudo de controle motor.

Qualquer tarefa motora ativa se dá pela ativação de uma população de unidades motoras. Porém, devido a diversas dificuldades, tanto técnicas quanto éticas, não é possível medir a entrada sináptica dos motoneurônios em humanos. Por essas razões, o uso de modelos computacionais realistas de um núcleo de motoneurônios e as suas respectivas fibras musculares tem um importante papel no estudo do controle humano dos músculos. Entretanto, tais modelos são complexos e uma análise matemática é difícil. Neste texto é apresentada uma abordagem baseada em identificação de sistemas de um modelo realista de um núcleo de unidades motoras, com o objetivo de obter um modelo mais simples capaz de representar a transdução das entradas do núcleo de unidades motoras na força do músculo associado ao núcleo. A identificação de sistemas foi baseada em um algoritmo de mínimos quadrados ortogonal para achar um modelo NARMAX, sendo que a entrada considerada foi a condutância sináptica excitatória dendrítica total dos motoneurônios e a saída foi a força dos músculos produzida pelo núcleo de unidades motoras. O modelo identificado reproduziu o comportamento médio da saída do modelo computacional realista, mesmo para pares de sinal de entrada-saída não usados durante o processo de identificação do modelo, como sinais de força muscular modulados senoidalmente. Funções de resposta em frequência generalizada do núcleo de motoneurônios foram obtidas do modelo NARMAX, e levaram a que se inferisse que oscilações corticais na banda-beta (20 Hz) podem influenciar no controle da geração de força pela medula espinhal, comportamento do núcleo de motoneurônios até então desconhecido.

Three-dimensional simulation of the rolling of a saturated fibro-porous media

This paper describes recent advances made in computational modelling of the sugar cane liquid extraction process. The saturated fibro-porous material is rolled between circumferentially grooved rolls, which enhance frictional grip and provide a low-resistance path for liquid flow during the extraction process. Previously reported two-dimensional (2D) computational models, account for the large deformation of the porous material by solving the fully coupled governing fibre stress and fluid-flow equations using finite element techniques. While the 2D simulations provide much insight into the overarching cause-effect relationships, predictions of mechanical quantities such as roll separating force and particularly torque as a function of roll speed and degree of compression are not satisfactory for industrial use. It is considered that the unsatisfactory response in roll torque prediction may be due to the stress levels that exist between the groove tips and roots which have been largely neglected in the geometrically simplified 2D model. This paper gives results for both two- and three-dimensional finite element models and highlights their strengths and weaknesses in predicting key milling parameters. (c) 2005 Elsevier B.V. All rights reserved.

Predictive vaccinology: Optimisation of predictions using support vector machine classifiers

Promiscuous human leukocyte antigen (HLA) binding peptides are ideal targets for vaccine development. Existing computational models for prediction of promiscuous peptides used hidden Markov models and artificial neural networks as prediction algorithms. We report a system based on support vector machines that outperforms previously published methods. Preliminary testing showed that it can predict peptides binding to HLA-A2 and -A3 super-type molecules with excellent accuracy, even for molecules where no binding data are currently available.

RatSLAM: A hippocampal model for simultaneous localisation and mapping

The work presents a new approach to the problem of simultaneous localization and mapping - SLAM - inspired by computational models of the hippocampus of rodents. The rodent hippocampus has been extensively studied with respect to navigation tasks, and displays many of the properties of a desirable SLAM solution. RatSLAM is an implementation of a hippocampal model that can perform SLAM in real time on a real robot. It uses a competitive attractor network to integrate odometric information with landmark sensing to form a consistent representation of the environment. Experimental results show that RatSLAM can operate with ambiguous landmark information and recover from both minor and major path integration errors.

Concept-based document readability in domain specific information retrieval

Domain specific information retrieval has become in demand. Not only domain experts, but also average non-expert users are interested in searching domain specific (e.g., medical and health) information from online resources. However, a typical problem to average users is that the search results are always a mixture of documents with different levels of readability. Non-expert users may want to see documents with higher readability on the top of the list. Consequently the search results need to be re-ranked in a descending order of readability. It is often not practical for domain experts to manually label the readability of documents for large databases. Computational models of readability needs to be investigated. However, traditional readability formulas are designed for general purpose text and insufficient to deal with technical materials for domain specific information retrieval. More advanced algorithms such as textual coherence model are computationally expensive for re-ranking a large number of retrieved documents. In this paper, we propose an effective and computationally tractable concept-based model of text readability. In addition to textual genres of a document, our model also takes into account domain specific knowledge, i.e., how the domain-specific concepts contained in the document affect the document’s readability. Three major readability formulas are proposed and applied to health and medical information retrieval. Experimental results show that our proposed readability formulas lead to remarkable improvements in terms of correlation with users’ readability ratings over four traditional readability measures.

Structure and dynamics of a gene network model incorporating small RNAs

As advances in molecular biology continue to reveal additional layers of complexity in gene regulation, computational models need to incorporate additional features to explore the implications of new theories and hypotheses. It has recently been suggested that eukaryotic organisms owe their phenotypic complexity and diversity to the exploitation of small RNAs as signalling molecules. Previous models of genetic systems are, for several reasons, inadequate to investigate this theory. In this study, we present an artificial genome model of genetic regulatory networks based upon previous work by Torsten Reil, and demonstrate how this model generates networks with biologically plausible structural and dynamic properties. We also extend the model to explore the implications of incorporating regulation by small RNA molecules in a gene network. We demonstrate how, using these signals, highly connected networks can display dynamics that are more stable than expected given their level of connectivity.

On the relation between dichoptic masking and binocular rivalry

When our two eyes view incompatible images, the brain invokes suppressive processes to inhibit one image, and favor the other. Two phenomena are typically observed: dichoptic masking (reduced sensitivity to one image) for brief presentations, and binocular rivalry (alternation between the two images), over longer exposures. However, it is not clear if these two phenomena arise from a common suppressive process. We investigated this by measuring both threshold elevation in simultaneous dichoptic masking and mean percept durations in rivalry, whilst varying relative stimulus orientation. Masking and rivalry showed significant correlations, such that strong masking was associated with long dominance durations. A second experiment suggested that individual differences across both measures are also correlated. These findings are consistent with varying the magnitude of interocular suppression in computational models of both rivalry and masking, and imply the existence of a common suppressive process. Since dichoptic masking has been localised to the monocular neurons of V1, this is a plausible first stage of binocular rivalry.