Influence of summertime mesoscale convective systems on the heat balance and surface mixed layer dynamics of a large Amazonian hydroelectric reservoir

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural properties and energetics of diffuse Rb-87 clusters in three-dimension

A correlated two-body basis function is used to describe the three-dimensional bosonic clusters interacting via two-body van der Waals potential. We calculate the ground state and the zero orbital angular momentum excited states for Rb-N clusters with up to N = 40. We solve the many-particle Schrodinger equation by potential harmonics expansion method, which keeps all possible two-body correlations in the calculation and determines the lowest effective many-body potential. We study energetics and structural properties for such diffuse clusters both at dimer and tuned scattering length. The motivation of the present study is to investigate the possibility of formation of N-body clusters interacting through the van der Waals interaction. We also compare the system with the well studied He, Ne, and Ar clusters. We also calculate correlation properties and observe the generalised Tjon line for large cluster. We test the validity of the shape-independent potential in the calculation of the ground state energy of such diffuse cluster. These are the first such calculations reported for Rb clusters. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4730972]

Characterization and modeling of the barrier properties in nanostructured systems

The object of the present study is the process of gas transport in nano-sized materials, i.e. systems having structural elements of the order of nanometers. The aim of this work is to advance the understanding of the gas transport mechanism in such materials, for which traditional models are not often suitable, by providing a correct interpretation of the relationship between diffusive phenomena and structural features. This result would allow the development new materials with permeation properties tailored on the specific application, especially in packaging systems. The methods used to achieve this goal were a detailed experimental characterization and different simulation methods. The experimental campaign regarded the determination of oxygen permeability and diffusivity in different sets of organic-inorganic hybrid coatings prepared via sol-gel technique. The polymeric samples coated with these hybrid layers experienced a remarkable enhancement of the barrier properties, which was explained by the strong interconnection at the nano-scale between the organic moiety and silica domains. An analogous characterization was performed on microfibrillated cellulose films, which presented remarkable barrier effect toward oxygen when it is dry, while in the presence of water the performance significantly drops. The very low value of water diffusivity at low activities is also an interesting characteristic which deals with its structural properties. Two different approaches of simulation were then considered: the diffusion of oxygen through polymer-layered silicates was modeled on a continuum scale with a CFD software, while the properties of n-alkanthiolate self assembled monolayers on gold were analyzed from a molecular point of view by means of a molecular dynamics algorithm. Modeling transport properties in layered nanocomposites, resulting from the ordered dispersion of impermeable flakes in a 2-D matrix, allowed the calculation of the enhancement of barrier effect in relation with platelets structural parameters leading to derive a new expression. On this basis, randomly distributed systems were simulated and the results were analyzed to evaluate the different contributions to the overall effect. The study of more realistic three-dimensional geometries revealed a prefect correspondence with the 2-D approximation. A completely different approach was applied to simulate the effect of temperature on the oxygen transport through self assembled monolayers; the structural information obtained from equilibrium MD simulations showed that raising the temperature, makes the monolayer less ordered and consequently less crystalline. This disorder produces a decrease in the barrier free energy and it lowers the overall resistance to oxygen diffusion, making the monolayer more permeable to small molecules.

Computer simulations of charged systems in partially periodic geometries

This work presents algorithms for the calculation of the electrostatic interaction in partially periodic systems. The framework for these algorithms is provided by the simulation package ESPResSo, of which the author was one of the main developers. The prominent features of the program are listed and the internal structure is described. In the following, algorithms for the calculation of the Coulomb sum in three dimensionally periodic systems are described. These methods are the foundations for the algorithms for partially periodic systems presented in this work. Starting from the MMM2D method for systems with one non-periodic coordinate, the ELC method for these systems is developed. This method consists of a correction term which allows to use methods for three dimensional periodicity also for the case of two periodic coordinates. The computation time of this correction term is neglible for large numbers of particles. The performance of MMM2D and ELC are demonstrated by results from the implementations contained in ESPResSo. It is also discussed, how different dielectric constants inside and outside of the simulation box can be realized. For systems with one periodic coordinate, the MMM1D method is derived from the MMM2D method. This method is applied to the problem of the attraction of like-charged rods in the presence of counterions, and results of the strong coupling theory for the equilibrium distance of the rods at infinite counterion-coupling are checked against results from computer simulations. The degree of agreement between the simulations at finite coupling and the theory can be characterized by a single parameter gamma_RB. In the special case of T=0, one finds under certain circumstances flat configurations, in which all charges are located in the rod-rod plane. The energetically optimal configuration and its stability are determined analytically, which depends on only one parameter gamma_z, similar to gamma_RB. These findings are in good agreement with results from computer simulations.

Validation of the CFD code NEPTUNE for a full scale simulator for decay heat removal systems with in-pool heat exchangers

In the present work, a multi physics simulation of an innovative safety system for light water nuclear reactor is performed, with the aim to increase the reliability of its main decay heat removal system. The system studied, denoted by the acronym PERSEO (in Pool Energy Removal System for Emergency Operation) is able to remove the decay power from the primary side of the light water nuclear reactor through a heat suppression pool. The experimental facility, located at SIET laboratories (PIACENZA), is an evolution of the Thermal Valve concept where the triggering valve is installed liquid side, on a line connecting two pools at the bottom. During the normal operation, the valve is closed, while in emergency conditions it opens, the heat exchanger is flooded with consequent heat transfer from the primary side to the pool side. In order to verify the correct system behavior during long term accidental transient, two main experimental PERSEO tests are analyzed. For this purpose, a coupling between the mono dimensional system code CATHARE, which reproduces the system scale behavior, with a three-dimensional CFD code NEPTUNE CFD, allowing a full investigation of the pools and the injector, is implemented. The coupling between the two codes is realized through the boundary conditions. In a first analysis, the facility is simulated by the system code CATHARE V2.5 to validate the results with the experimental data. The comparison of the numerical results obtained shows a different void distribution during the boiling conditions inside the heat suppression pool for the two cases of single nodalization and three volume nodalization scheme of the pool. Finaly, to improve the investigation capability of the void distribution inside the pool and the temperature stratification phenomena below the injector, a two and three dimensional CFD models with a simplified geometry of the system are adopted.

Evaluation of Human Exposure to Magnetic Fields Generated by Electric Power Systems in Complex Configurations

The international growing concern for the human exposure to magnetic fields generated by electric power lines has unavoidably led to imposing legal limits. Respecting these limits, implies being able to calculate easily and accurately the generated magnetic field also in complex configurations. Twisting of phase conductors is such a case. The consolidated exact and approximated theory regarding a single-circuit twisted three-phase power cable line has been reported along with the proposal of an innovative simplified formula obtained by means of an heuristic procedure. This formula, although being dramatically simpler, is proven to be a good approximation of the analytical formula and at the same time much more accurate than the approximated formula found in literature. The double-circuit twisted three-phase power cable line case has been studied following different approaches of increasing complexity and accuracy. In this framework, the effectiveness of the above-mentioned innovative formula is also examined. The experimental verification of the correctness of the twisted double-circuit theoretical analysis has permitted its extension to multiple-circuit twisted three-phase power cable lines. In addition, appropriate 2D and, in particularly, 3D numerical codes for simulating real existing overhead power lines for the calculation of the magnetic field in their vicinity have been created. Finally, an innovative ‘smart’ measurement and evaluation system of the magnetic field is being proposed, described and validated, which deals with the experimentally-based evaluation of the total magnetic field B generated by multiple sources in complex three-dimensional arrangements, carried out on the basis of the measurement of the three Cartesian field components and their correlation with the field currents via multilinear regression techniques. The ultimate goal is verifying that magnetic induction intensity is within the prescribed limits.

Evaluation of 3D cell culture systems for host-pathogen interaction studies

Traditional cell culture models have limitations in extrapolating functional mechanisms that underlie strategies of microbial virulence. Indeed during the infection the pathogens adapt to different tissue-specific environmental factors. The development of in vitro models resembling human tissue physiology might allow the replacement of inaccurate or aberrant animal models. Three-dimensional (3D) cell culture systems are more reliable and more predictive models that can be used for the meaningful dissection of host–pathogen interactions. The lung and gut mucosae often represent the first site of exposure to pathogens and provide a physical barrier against their entry. Within this context, the tracheobronchial and small intestine tract were modelled by tissue engineering approach. The main work was focused on the development and the extensive characterization of a human organotypic airway model, based on a mechanically supported co-culture of normal primary cells. The regained morphological features, the retrieved environmental factors and the presence of specific epithelial subsets resembled the native tissue organization. In addition, the respiratory model enabled the modular insertion of interesting cell types, such as innate immune cells or multipotent stromal cells, showing a functional ability to release pertinent cytokines differentially. Furthermore this model responded imitating known events occurring during the infection by Non-typeable H. influenzae. Epithelial organoid models, mimicking the small intestine tract, were used for a different explorative analysis of tissue-toxicity. Further experiments led to detection of a cell population targeted by C. difficile Toxin A and suggested a role in the impairment of the epithelial homeostasis by the bacterial virulence machinery. The described cell-centered strategy can afford critical insights in the evaluation of the host defence and pathogenic mechanisms. The application of these two models may provide an informing step that more coherently defines relevant molecular interactions happening during the infection.

Simple virtual reality display of fetal volume ultrasound

Three-dimensional (3D) ultrasound volume acquisition, analysis and display of fetal structures have enhanced their visualization and greatly improved the general understanding of their anatomy and pathology. The dynamic display of volume data generally depends on proprietary software, usually supplied with the ultrasound system, and on the operator's ability to maneuver the dataset digitally. We have used relatively simple tools and an established storage, display and manipulation format to generate non-linear virtual reality object movies of prenatal images (including moving sequences and 3D-rendered views) that can be navigated easily and interactively on any current computer. This approach permits a viewing or learning experience that is superior to watching a linear movie passively.

ANALYSIS AND VISUALIZATION OF FLOW FIELDS USING INFORMATION-THEORETIC TECHNIQUES AND GRAPH-BASED REPRESENTATIONS

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner. My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow patterns and how to pick good viewpoints to observe flow fields become critical. We treat streamline selection and viewpoint selection as symmetric problems and solve them simultaneously using the dual information channel [81]. To the best of my knowledge, this is the first attempt in flow visualization to combine these two selection problems in a unified approach. This work selects streamline in a view-independent manner and the selected streamlines will not change for all viewpoints. My another work [56] uses an information-theoretic approach to evaluate the importance of each streamline under various sample viewpoints and presents a solution for view-dependent streamline selection that guarantees coherent streamline update when the view changes gradually. When projecting 3D streamlines to 2D images for viewing, occlusion and clutter become inevitable. To address this challenge, we design FlowGraph [57, 58], a novel compound graph representation that organizes field line clusters and spatiotemporal regions hierarchically for occlusion-free and controllable visual exploration. We enable observation and exploration of the relationships among field line clusters, spatiotemporal regions and their interconnection in the transformed space. Most viewpoint selection methods only consider the external viewpoints outside of the flow field. This will not convey a clear observation when the flow field is clutter on the boundary side. Therefore, we propose a new way to explore flow fields by selecting several internal viewpoints around the flow features inside of the flow field and then generating a B-Spline curve path traversing these viewpoints to provide users with closeup views of the flow field for detailed observation of hidden or occluded internal flow features [54]. This work is also extended to deal with unsteady flow fields. Besides flow field visualization, some other topics relevant to visualization also attract my attention. In iGraph [31], we leverage a distributed system along with a tiled display wall to provide users with high-resolution visual analytics of big image and text collections in real time. Developing pedagogical visualization tools forms my other research focus. Since most cryptography algorithms use sophisticated mathematics, it is difficult for beginners to understand both what the algorithm does and how the algorithm does that. Therefore, we develop a set of visualization tools to provide users with an intuitive way to learn and understand these algorithms.

Molecular structure of antibodies against small ligands

Antibodies which bind bioactive ligands can serve as a template for the generation of a second antibody which may react with the physiological receptor. This phenomenon of molecular mimicry by antibodies has been described in a variety of systems. In order to understand the chemical and molecular mechanisms involved in these interactions, monoclonal antibodies directed against two pharmacologically active alkaloids, morphine and nicotine, were carefully studied using experimental and theoretical molecular modeling techniques. The molecular characterization of these antibodies involved binding studies with ligand analogs and determination of the variable region amino acid sequence. A three-dimensional model of the anti-morphine binding site was constructed using computational and graphics display techniques. The antibody response in BALB/c mice to morphine appears relatively restricted, in that all of the antibodies examined in this study contained a $\lambda$ light chain, which is normally found in only 5% of mouse immunoglobulins. This study represents the first use of theoretical and experimental modeling techniques to describe the antigen binding site of a mouse Fv region containing a $\lambda$ light chain. The binding site model indicates that a charged glutamic acid residue and aromatic side chains are key features in ionic and hydrophobic interactions with the ligand morphine. A glutamic acid residue is found in the identical position in the anti-nicotine antibody and may play a role in binding nicotine. ^

Adaptive fuzzy knowledge-based systems for control metabots' mobility on virtual environments

The confluence of three-dimensional (3D) virtual worlds with social networks imposes on software agents, in addition to conversational functions, the same behaviours as those common to human-driven avatars. In this paper, we explore the possibilities of the use of metabots (metaverse robots) with motion capabilities in complex virtual 3D worlds and we put forward a learning model based on the techniques used in evolutionary computation for optimizing the fuzzy controllers which will subsequently be used by metabots for moving around a virtual environment.

A method for revealing phase space structures of general time dependent dynamical systems

In this paper we develop new techniques for revealing geometrical structures in phase space that are valid for aperiodically time dependent dynamical systems, which we refer to as Lagrangian descriptors. These quantities are based on the integration, for a finite time, along trajectories of an intrinsic bounded, positive geometrical and/or physical property of the trajectory itself. We discuss a general methodology for constructing Lagrangian descriptors, and we discuss a “heuristic argument” that explains why this method is successful for revealing geometrical structures in the phase space of a dynamical system. We support this argument by explicit calculations on a benchmark problem having a hyperbolic fixed point with stable and unstable manifolds that are known analytically. Several other benchmark examples are considered that allow us the assess the performance of Lagrangian descriptors in revealing invariant tori and regions of shear. Throughout the paper “side-by-side” comparisons of the performance of Lagrangian descriptors with both finite time Lyapunov exponents (FTLEs) and finite time averages of certain components of the vector field (“time averages”) are carried out and discussed. In all cases Lagrangian descriptors are shown to be both more accurate and computationally efficient than these methods. We also perform computations for an explicitly three dimensional, aperiodically time-dependent vector field and an aperiodically time dependent vector field defined as a data set. Comparisons with FTLEs and time averages for these examples are also carried out, with similar conclusions as for the benchmark examples.

Desarrollo de tecnologías de telemanipulación con alto grado de escalado orientadas a la interacción hombre-robot en entornos nucleares

Esta tesis se centra en desarrollo de tecnologías para la interacción hombre-robot en entornos nucleares de fusión. La problemática principal del sector de fusión nuclear radica en las condiciones ambientales tan extremas que hay en el interior del reactor, y la necesidad de que los equipos cumplan requisitos muy restrictivos para poder aguantar esos niveles de radiación, magnetismo, ultravacío, temperatura... Como no es viable la ejecución de tareas directamente por parte de humanos, habrá que utilizar dispositivos de manipulación remota para llevar a cabo los procesos de operación y mantenimiento. En las instalaciones de ITER es obligatorio tener un entorno controlado de extrema seguridad, que necesita de estándares validados. La definición y uso de protocolos es indispensable para regir su buen funcionamiento. Si nos centramos en la telemanipulación con algo grado de escalado, surge la necesidad de definir protocolos para sistemas abiertos que permitan la interacción entre equipos y dispositivos de diversa índole. En este contexto se plantea la definición del Protocolo de Teleoperación que permita la interconexión entre dispositivos maestros y esclavos de distinta tipología, pudiéndose comunicar bilateralmente entre sí y utilizar distintos algoritmos de control según la tarea a desempeñar. Este protocolo y su interconectividad se han puesto a prueba en la Plataforma Abierta de Teleoperación (P.A.T.) que se ha desarrollado e integrado en la ETSII UPM como una herramienta que permita probar, validar y realizar experimentos de telerrobótica. Actualmente, este Protocolo de Teleoperación se ha propuesto a través de AENOR al grupo ISO de Telerobotics como una solución válida al problema existente y se encuentra bajo revisión. Con el diseño de dicho protocolo se ha conseguido enlazar maestro y esclavo, sin embargo con los niveles de radiación tan altos que hay en ITER la electrónica del controlador no puede entrar dentro del tokamak. Por ello se propone que a través de una mínima electrónica convenientemente protegida se puedan multiplexar las señales de control que van a través del cableado umbilical desde el controlador hasta la base del robot. En este ejercicio teórico se demuestra la utilidad y viabilidad de utilizar este tipo de solución para reducir el volumen y peso del cableado umbilical en cifras aproximadas de un 90%, para ello hay que desarrollar una electrónica específica y con certificación RadHard para soportar los enormes niveles de radiación de ITER. Para este manipulador de tipo genérico y con ayuda de la Plataforma Abierta de Teleoperación, se ha desarrollado un algoritmo que mediante un sensor de fuerza/par y una IMU colocados en la muñeca del robot, y convenientemente protegidos ante la radiación, permiten calcular las fuerzas e inercias que produce la carga, esto es necesario para poder transmitirle al operador unas fuerzas escaladas, y que pueda sentir la carga que manipula, y no otras fuerzas que puedan influir en el esclavo remoto, como ocurre con otras técnicas de estimación de fuerzas. Como el blindaje de los sensores no debe ser grande ni pesado, habrá que destinar este tipo de tecnología a las tareas de mantenimiento de las paradas programadas de ITER, que es cuando los niveles de radiación están en sus valores mínimos. Por otro lado para que el operador sienta lo más fielmente posible la fuerza de carga se ha desarrollado una electrónica que mediante el control en corriente de los motores permita realizar un control en fuerza a partir de la caracterización de los motores del maestro. Además para aumentar la percepción del operador se han realizado unos experimentos que demuestran que al aplicar estímulos multimodales (visuales, auditivos y hápticos) aumenta su inmersión y el rendimiento en la consecución de la tarea puesto que influyen directamente en su capacidad de respuesta. Finalmente, y en referencia a la realimentación visual del operador, en ITER se trabaja con cámaras situadas en localizaciones estratégicas, si bien el humano cuando manipula objetos hace uso de su visión binocular cambiando constantemente el punto de vista adecuándose a las necesidades visuales de cada momento durante el desarrollo de la tarea. Por ello, se ha realizado una reconstrucción tridimensional del espacio de la tarea a partir de una cámara-sensor RGB-D, lo cual nos permite obtener un punto de vista binocular virtual móvil a partir de una cámara situada en un punto fijo que se puede proyectar en un dispositivo de visualización 3D para que el operador pueda variar el punto de vista estereoscópico según sus preferencias. La correcta integración de estas tecnologías para la interacción hombre-robot en la P.A.T. ha permitido validar mediante pruebas y experimentos para verificar su utilidad en la aplicación práctica de la telemanipulación con alto grado de escalado en entornos nucleares de fusión. Abstract This thesis focuses on developing technologies for human-robot interaction in nuclear fusion environments. The main problem of nuclear fusion sector resides in such extreme environmental conditions existing in the hot-cell, leading to very restrictive requirements for equipment in order to deal with these high levels of radiation, magnetism, ultravacuum, temperature... Since it is not feasible to carry out tasks directly by humans, we must use remote handling devices for accomplishing operation and maintenance processes. In ITER facilities it is mandatory to have a controlled environment of extreme safety and security with validated standards. The definition and use of protocols is essential to govern its operation. Focusing on Remote Handling with some degree of escalation, protocols must be defined for open systems to allow interaction among different kind of equipment and several multifunctional devices. In this context, a Teleoperation Protocol definition enables interconnection between master and slave devices from different typologies, being able to communicate bilaterally one each other and using different control algorithms depending on the task to perform. This protocol and its interconnectivity have been tested in the Teleoperation Open Platform (T.O.P.) that has been developed and integrated in the ETSII UPM as a tool to test, validate and conduct experiments in Telerobotics. Currently, this protocol has been proposed for Teleoperation through AENOR to the ISO Telerobotics group as a valid solution to the existing problem, and it is under review. Master and slave connection has been achieved with this protocol design, however with such high radiation levels in ITER, the controller electronics cannot enter inside the tokamak. Therefore it is proposed a multiplexed electronic board, that through suitable and RadHard protection processes, to transmit control signals through an umbilical cable from the controller to the robot base. In this theoretical exercise the utility and feasibility of using this type of solution reduce the volume and weight of the umbilical wiring approximate 90% less, although it is necessary to develop specific electronic hardware and validate in RadHard qualifications in order to handle huge levels of ITER radiation. Using generic manipulators does not allow to implement regular sensors for force feedback in ITER conditions. In this line of research, an algorithm to calculate the forces and inertia produced by the load has been developed using a force/torque sensor and IMU, both conveniently protected against radiation and placed on the robot wrist. Scaled forces should be transmitted to the operator, feeling load forces but not other undesirable forces in slave system as those resulting from other force estimation techniques. Since shielding of the sensors should not be large and heavy, it will be necessary to allocate this type of technology for programmed maintenance periods of ITER, when radiation levels are at their lowest levels. Moreover, the operator perception needs to feel load forces as accurate as possible, so some current control electronics were developed to perform a force control of master joint motors going through a correct motor characterization. In addition to increase the perception of the operator, some experiments were conducted to demonstrate applying multimodal stimuli (visual, auditory and haptic) increases immersion and performance in achieving the task since it is directly correlated with response time. Finally, referring to the visual feedback to the operator in ITER, it is usual to work with 2D cameras in strategic locations, while humans use binocular vision in direct object manipulation, constantly changing the point of view adapting it to the visual needs for performing manipulation during task procedures. In this line a three-dimensional reconstruction of non-structured scenarios has been developed using RGB-D sensor instead of cameras in the remote environment. Thus a mobile virtual binocular point of view could be generated from a camera at a fixed point, projecting stereoscopic images in 3D display device according to operator preferences. The successful integration of these technologies for human-robot interaction in the T.O.P., and validating them through tests and experiments, verify its usefulness in practical application of high scaling remote handling at nuclear fusion environments.

Symmetry, stability, and dynamics of multidomain and multicomponent protein systems

Symmetry is commonly observed in many biological systems. Here we discuss representative examples of the role of symmetry in structural molecular biology. Point group symmetries are observed in many protein oligomers whose three-dimensional atomic structures have been elucidated by x-ray crystallography. Approximate symmetry also occurs in multidomain proteins. Symmetry often confers stability on the molecular system and results in economical usage of basic components to build the macromolecular structure. Symmetry is also associated with cooperativity. Mild perturbation from perfect symmetry may be essential in some systems for dynamic functions.

Identification of three gene candidates for multicellular resistance in colon carcinoma

Solid tumours display elevated resistance to chemo- and radiotherapies compared to individual tumour derived cells. This so-called multicellular resistance (MCR) phenomenon can only be partly explained by reduced diffusion and altered cell cycle status; even fast growing cells on the surface of solid tumours display MCR. Multicellular spheroids (MCS) recapture this phenomenon ex vivo and here we compare gene expression in exponentially growing MCS with gene expression in monolayer culture. Using an 18,664 gene microarray, we identified 42 differentially expressed genes and three of these genes can be linked to potential mechanisms of MCR. A group of interferon response genes were also up-regulated in MCS, as were a number of genes that that are indicative of greater differentiation in three-dimensional cultures.