Enhancing iDynoMiCS framework with a plasmid conjugation module

Actualmente existen aplicaciones que permiten simular el comportamiento de bacterias en distintos hábitats y los procesos que ocurren en estos para facilitar su estudio y experimentación sin la necesidad de un laboratorio. Una de las aplicaciones de software libre para la simulación de poblaciones bacteriológicas mas usada es iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), un simulador basado en agentes que permite trabajar con varios modelos computacionales de bacterias en 2D y 3D. Este simulador permite una gran libertad al configurar una numerosa cantidad de variables con respecto al entorno, reacciones químicas y otros detalles importantes. Una característica importante es el poder simular de manera sencilla la conjugación de plásmidos entre bacterias. Los plásmidos son moléculas de ADN diferentes del cromosoma celular, generalmente circularles, que se replican, transcriben y conjugan independientemente del ADN cromosómico. Estas están presentes normalmente en bacterias procariotas, y en algunas ocasiones en eucariotas, sin embargo, en este tipo de células son llamados episomas. Dado el complejo comportamiento de los plásmidos y la gama de posibilidades que estos presentan como mecanismos externos al funcionamiento básico de la célula, en la mayoría de los casos confiriéndole distintas ventajas evolutivas, como por ejemplo: resistencia antibiótica, entre otros, resulta importante su estudio y subsecuente manipulación. Sin embargo, el marco operativo del iDynoMiCS, en cuanto a simulación de plásmidos se refiere, es demasiado sencillo y no permite realizar operaciones más complejas que el análisis de la propagación de un plásmido en la comunidad. El presente trabajo surge para resolver esta deficiencia de iDynomics. Aquí se analizarán, desarrollarán e implementarán las modificaciones necesarias para que iDynomics pueda simular satisfactoriamente y mas apegado a la realidad la conjugación de plásmidos y permita así mismo resolver distintas operaciones lógicas, como lo son los circuitos genéticos, basadas en plásmidos. También se analizarán los resultados obtenidos de acuerdo a distintos estudios relevantes y a la comparación de los resultados obtenidos con el código original de iDynomics. Adicionalmente se analizará un estudio comparando la eficiencia de detección de una sustancia mediante dos circuitos genéticos distintos. Asimismo el presente trabajo puede tener interés para el grupo LIA de la Facultad de Informática de la Universidad Politécnica de Madrid, el cual está participando en el proyecto europeo BACTOCOM que se centra en el estudio de la conjugación de plásmidos y circuitos genéticos. --ABSTRACT--Currently there are applications that simulate the behavior of bacteria in different habitats and the ongoing processes inside them to facilitate their study and experimentation without the need for an actual laboratory. One of the most used open source applications to simulate bacterial populations is iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), an agent-based simulator that allows working with several computer models of 2D and 3D bacteria in biofilms. This simulator allows great freedom by means of a large number of configurable variables regarding environment, chemical reactions and other important details of the simulation. Within these characteristics there exists a very basic framework to simulate plasmid conjugation. Plasmids are DNA molecules physically different from the cell’s chromosome, commonly found as small circular, double-stranded DNA molecules that are replicated, conjugated and transcribed independently of chromosomal DNA. These bacteria are normally present in prokaryotes and sometimes in eukaryotes, which in this case these cells are called episomes. Plasmids are external mechanisms to the cells basic operations, and as such, in the majority of the cases, confer to the host cell various evolutionary advantages, like antibiotic resistance for example. It is mperative to further study plasmids and the possibilities they present. However, the operational framework of the iDynoMiCS plasmid simulation is too simple, and does not allow more complex operations that the analysis of the spread of a plasmid in the community. This project was conceived to resolve this particular deficiency in iDynomics, moreover, in this paper is discussed, developed and implemented the necessary changes to iDynomics simulation software so it can satisfactorily and realistically simulate plasmid conjugation, and allow the possibility to solve various ogic operations, such as plasmid-based genetic circuits. Moreover the results obtained will be analyzed and compared with other relevant studies and with those obtained with the original iDynomics code. Conjointly, an additional study detailing the sensing of a substance with two different genetic circuits will be presented. This work may also be relevant to the LIA group of the Faculty of Informatics of the Polytechnic University of Madrid, which is participating in the European project BACTOCOM that focuses on the study of the of plasmid conjugation and genetic circuits.

Energy Management Module for Mobile Robots in Hostile Environments

In hostile environments at CERN and other similar scientific facilities, having a reliable mobile robot system is essential for successful execution of robotic missions and to avoid situations of manual recovery of the robots in the event that the robot runs out of energy. Because of environmental constraints, such mobile robots are usually battery-powered and hence energy management and optimization is one of the key challenges in this field. The ability to know beforehand the energy consumed by various elements of the robot (such as locomotion, sensors, controllers, computers and communication) will allow flexibility in planning or managing the tasks to be performed by the robot.

SOPHIA CPV module round robin: power rating at CSOC

Within the European funded project SOPHIA, a Round Robin measurement on CPV module has been initiated. Seven different test laboratories located in Europe between 48°N and 37°N perform measurements of four SOITEC CPV modules. The modules are electrically characterized with different measurement equipment under various climatic conditions. One pyrheliometer and one spectral sensor based on component cells are shipped together with the modules. This ensures that the irradiance and spectrum, two factors with high impact on CPV module performance, are measured with the identical equipment at each site. The round robin activity is performed in closeco-operation with the IEC TC82 WG7 power rating team in order to support the work on the CPV module power rating draft standard 62670-3. The resultingrated module power outputs at CSOC (Concentrator Standard Operating Conditions) are compared amongst the power rating methods and amongst the test labs. In this manner, a deviation in rated power output between different test labs and power rating methods is determined.

Análisis de sistemas eléctricos en microsatélites. Desarrollo de módulos para una Concurrent Design Facility (CFD)para el desarrollo y análisis de misiones espaciales = Analysis of microsatellites power subsystems (battery testing). Development and programming of a new Propulsion Module for a space mission Concurrent Design Facility (CDF)

El objetivo de este proyecto es recoger y explicar el conjunto de tareas realizadas durante el proceso de colaboración llevado a cabo en el Instituto de Microgravedad “Ignacio Da Riva” durante el curso académico 2014/2015, las cuales han conformado las prácticas externas cursadas en la titulación de Grado en Ingeniería Aeroespacial, y el Trabajo de Fin de Grado de la misma titulación. En este documento se pretende,además, poner de manifiesto la rigurosidad con la que se trabaja en el ámbito espacial y la importancia de los protocolos y procedimientos para asegurar un resultado adecuado en los trabajos realizados. Una parte importante del proyecto detalla los procesos de monitorización y mantenimiento de la batería del satélite universitario UPMSat-2 cuyo lanzamiento está previsto para el año próximo y el cual será el segundo satélite del mundo en incorporar una batería de Ión-Litio.

Análisis de sistemas eléctricos en microsatélites. Desarrollo de módulos para una Concurrent Design Facility (CDF) para desarrollo y análisis de misiones espaciales = Analysis of microsatellites power subsystems (battery testing). Development and programming of a new Orbit Design Module for a space mission Concurrent Design Facility (CDF)

El presente proyecto se ha realizado durante las prácticas curriculares que han tenido lugar en el Instituto Universitario de Microgravedad “Ignacio Da Riva” (IDR/UPM). A lo largo de estas prácticas se han llevado a cabo trabajos en diversos campos, todos relacionados con el UPMSat-2, desde el subsistema de potencia (placas solares y baterías) hasta el desarrollo de módulos para la Sala de Diseño Concurrente (Concurrent Design Facility, CDF). En la realización de las mismas se ha trabajado en equipo, junto con otros dos alumnos. El objetivo del proyecto es recopilar las tareas realizadas, proporcionando el desarrollo teórico necesario para llevar a cabo todas ellas. Al ser un trabajo con varias partes claramente diferenciadas, se ha optado por comenzar con unas páginas dedicadas a las misiones espaciales. A continuación el trabajo se adentra en el subsistema de potencia de un satélite, particularizando para el UPMSat-2. Finalmente, se proporciona la teoría necesaria para el desarrollo del módulo de misión de la CDF del IDR/UPM, software que se ha desarrollado y tiene reservado un espacio al final, en el cual se describe el programa y se realizan comparaciones de los resultados que proporciona frente a casos reales.

Methodology of quantifying curvature of Fresnel lenses and its effect on CPV module performance

Fresnel lenses used as primary optics in concentrating photovoltaic modules may show warping produced by lens manufacturing or module assembly (e.g., stress during molding or weight load) or due to stress during operation (e.g., mismatch of thermal expansion between different materials). To quantify this problem, a simple method called “checkerboard method” is presented. The proposed method identifies shape errors on the front surface of primary lenses by analyzing the Fresnel reflections. This paper also deals with the quantification of the effects these curvatures have on their optical performance and on the electrical performance of concentrating modules incorporating them. This method can be used to perform quality control of Fresnel lenses in scenarios of high volume production.

Análisis en sistemas eléctricos en microsatélites. Desarrollo de módulos para una Concurrent Design Facility (CDF) para desarrollo y análisis de misiones espaciales = Analysis of microsatellites power subsystems (battery testing). Development and programming of a new Orbit Design Module for a space mission Concurrent Design Facility (CDF)

El objetivo de este trabajo de fin de grado es la exposición de los resultados y conclusiones, fruto de las tareas desarrolladas durante las practicas curriculares en el Instituto Universitario de Microgravedad “Ignacio Da Riva” (IDR/UPM) el presente curso académico. La estructura del trabajo se compone de dos bloques diferenciados entre sí: el seguimiento de una batería y el desarrollo de un módulo para una CDF.

Silicon PV module customization using laser technology for new BIPV applications

It is well known that lasers have helped to increase efficiency and to reduce production costs in the photovoltaic (PV) sector in the last two decades, appearing in most cases as the ideal tool to solve some of the critical bottlenecks of production both in thin film (TF) and crystalline silicon (c-Si) technologies. The accumulated experience in these fields has brought as a consequence the possibility of using laser technology to produce new Building Integrated Photovoltaics (BIPV) products with a high degree of customization. However, to produce efficiently these personalized products it is necessary the development of optimized laser processes able to transform standard products in customized items oriented to the BIPV market. In particular, the production of semitransparencies and/or freeform geometries in TF a-Si modules and standard c-Si modules is an application of great interest in this market. In this work we present results of customization of both TF a-Si modules and standard monocrystalline (m-Si) and policrystalline silicon (pc-Si) modules using laser ablation and laser cutting processes. A discussion about the laser processes parameterization to guarantee the functionality of the device is included. Finally some examples of final devices are presented with a full discussion of the process approach used in their fabrication.

Tritium permeation experiment at IFMIF Medium Flux Test Module

Tritium release experiments using different breeding material candidates are planned for the medium flux region of the IFMIF Test Cell. Nowadays, only ceramic breeder materials have been suggested to be tested in the Tritium Release Module located in the Medium Flux Test Module of IFMIF. Liquid breeder blankets are very promising and for that reason, several concepts will be tested in ITER. One of the main problems concerning the liquid blankets is the permeation of the generated tritium in the breeder throughout the walls. Since tritium permeation is highly influenced by irradiation conditions, IFMIF is a suitable scenario to perform tritium permeation related experiments. In this paper, a preliminary design of a tritium permeation experiment for the Medium Flux Test Module of IFMIF is proposed, in order to contribute to the progress of the liquid breeder blanket concept validation. The conceptual design of the capsule in which the experiment will be performed is carried out, taking into consideration the experiment necessities and its implementation in the Tritium Release Module. In addition to this, some thermal hydraulic calculations have been performed to evaluate the thermal behaviour of the irradiation capsule

Module optical analyzer: Identification of defects on the production line

The usefulness of the module optical analyzer when identifying module defects on production line is presented in this paper. Two different case studies performed with two different kind of CPV modules are presented to show the use of MOA both in IES-UPM and Daido Steel facilities.

SOPHIA CPV module round robin: power rating at CSOC

In the frame of the European project SOPHIA a concentrator photovoltaic (CPV) module measurement round robin has been initiated. The round robin includes measurements of four CPV modules at seven different test laboratories located in Europe. IV curves of the modules are measured with different measurement equipment under various climatic conditions. The aim of this activity is to perform at each site a rating of the modules at concentrator standard operating conditions CSOC according to IEC 62670-1. The outcome of the round robin is intended for direct feedback to the current draft standard IEC 62670-3 “Concentrator Photovoltaic (CPV) Performance Testing - Performance Measurements and Power Rating”. The paper discusses initial results from the first three partners that have already finished the measurements up to now.

Methodology for Dynamic Stability and Robustness Analysis of Commercial-Power-Module-Based DC-Distributed Systems

El propósito de esta tesis es presentar una metodología para realizar análisis de la dinámica en pequeña señal y el comportamiento de sistemas de alimentación distribuidos de corriente continua (CC), formados por módulos comerciales. Para ello se hace uso de un método sencillo que indica los márgenes de estabilidad menos conservadores posibles mediante un solo número. Este índice es calculado en cada una de las interfaces que componen el sistema y puede usarse para obtener un índice global que indica la estabilidad del sistema global. De esta manera se posibilita la comparación de sistemas de alimentación distribuidos en términos de robustez. La interconexión de convertidores CC-CC entre ellos y con los filtros EMI necesarios puede originar interacciones no deseadas que dan lugar a la degradación del comportamiento de los convertidores, haciendo el sistema más propenso a inestabilidades. Esta diferencia en el comportamiento se debe a interacciones entre las impedancias de los diversos elementos del sistema. En la mayoría de los casos, los sistemas de alimentación distribuida están formados por módulos comerciales cuya estructura interna es desconocida. Por ello los análisis presentados en esta tesis se basan en medidas de la respuesta en frecuencia del convertidor que pueden realizarse desde los terminales de entrada y salida del mismo. Utilizando las medidas de las impedancias de entrada y salida de los elementos del sistema, se puede construir una función de sensibilidad que proporciona los márgenes de estabilidad de las diferentes interfaces. En esta tesis se utiliza el concepto del valor máximo de la función de sensibilidad (MPC por sus siglas en inglés) para indicar los márgenes de estabilidad como un único número. Una vez que la estabilidad de todas las interfaces del sistema se han evaluado individualmente, los índices obtenidos pueden combinarse para obtener un único número con el que comparar la estabilidad de diferentes sistemas. Igualmente se han analizado las posibles interacciones en la entrada y la salida de los convertidores CC-CC, obteniéndose expresiones analíticas con las que describir en detalle los acoplamientos generados en el sistema. Los estudios analíticos realizados se han validado experimentalmente a lo largo de la tesis. El análisis presentado en esta tesis se culmina con la obtención de un índice que condensa los márgenes de estabilidad menos conservativos. También se demuestra que la robustez del sistema está asegurada si las impedancias utilizadas en la función de sensibilidad se obtienen justamente en la entrada o la salida del subsistema que está siendo analizado. Por otra parte, la tesis presenta un conjunto de parámetros internos asimilados a impedancias, junto con sus expresiones analíticas, que permiten una explicación detallada de las interacciones en el sistema. Dichas expresiones analíticas pueden obtenerse bien mediante las funciones de transferencia analíticas si se conoce la estructura interna, o utilizando medidas en frecuencia o identificación de las mismas a través de la respuesta temporal del convertidor. De acuerdo a las metodologías presentadas en esta tesis se puede predecir la estabilidad y el comportamiento de sistemas compuestos básicamente por convertidores CC-CC y filtros, cuya estructura interna es desconocida. La predicción se basa en un índice que condensa la información de los márgenes de estabilidad y que permite la obtención de un indicador de la estabilidad global de todo el sistema, permitiendo la comparación de la estabilidad de diferentes arquitecturas de sistemas de alimentación distribuidos. ABSTRACT The purpose of this thesis is to present dynamic small-signal stability and performance analysis methodology for dc-distributed systems consisting of commercial power modules. Furthermore, the objective is to introduce simple method to state the least conservative margins for robust stability as a single number. In addition, an index characterizing the overall system stability is obtained, based on which different dc-distributed systems can be compared in terms of robustness. The interconnected systems are prone to impedance-based interactions which might lead to transient-performance degradation or even instability. These systems typically are constructed using commercial converters with unknown internal structure. Therefore, the analysis presented throughout this thesis is based on frequency responses measurable from the input and output terminals. The stability margins are stated utilizing a concept of maximum peak criteria, derived from the behavior of impedance-based sensitivity function that provides a single number to state robust stability. Using this concept, the stability information at every system interface is combined to a meaningful number to state the average robustness of the system. In addition, theoretical formulas are extracted to assess source and load side interactions in order to describe detailed couplings within the system. The presented theoretical analysis methodologies are experimentally validated throughout the thesis. In this thesis, according to the presented analysis, the least conservative stability margins are provided as a single number guaranteeing robustness. It is also shown that within the interconnected system the robust stability is ensured only if the impedance-based minor-loop gain is determined at the very input or output of each subsystem. Moreover, a complete set of impedance-type internal parameters as well as the formulas according to which the interaction sensitivity can be fully explained and analyzed, is provided. The given formulation can be utilized equally either based on measured frequency responses, time-domain identified internal parameters or extracted analytic transfer functions. Based on the analysis methodologies presented in this thesis, the stability and performance of interconnected systems consisting of converters with unknown internal structure, can be predicted. Moreover, the provided concept to assess the least conservative stability margins enables to obtain an index to state the overall robust stability of distributed power architecture and thus to compare different systems in terms of stability.

Direct visualization of antigen-specific T cells: HTLV-1 Tax11–19- specific CD8+ T cells are activated in peripheral blood and accumulate in cerebrospinal fluid from HAM/TSP patients

Human T lymphotropic virus type 1 (HTLV-1) -associated myelopathy/tropic spastic paraparesis is a demyelinating inflammatory neurologic disease associated with HTLV-1 infection. HTLV-1 Tax11–19-specific cytotoxic T cells have been isolated from HLA-A2-positive patients. We have used a peptide-loaded soluble HLA-A2–Ig complex to directly visualize HTLV-1 Tax11–19-specific T cells from peripheral blood and cerebrospinal fluid without in vitro stimulation. Five of six HTLV-1-associated myelopathy/tropic spastic paraparesis patients carried a significant number (up to 13.87%) of CD8+ lymphocytes specific for the HTLV-1 Tax11–19 peptide in their peripheral blood, which were not found in healthy controls. Simultaneous comparison of peripheral blood and cerebrospinal fluid from one patient revealed 2.5-fold more Tax11–19-specific T cells in the cerebrospinal fluid (23.7% vs. 9.4% in peripheral blood lymphocyte). Tax11–19-specific T cells were seen consistently over a 9-yr time course in one patient as far as 19 yrs after the onset of clinical symptoms. Further analysis of HTLV-1 Tax11–19-specific CD8+ T lymphocytes in HAM/TSP patients showed different expression patterns of activation markers, intracellular TNF-α and γ-interferon depending on the severity of the disease. Thus, visualization of antigen-specific T cells demonstrates that HTLV-1 Tax11–19-specific CD8+ T cells are activated, persist during the chronic phase of the disease, and accumulate in cerebrospinal fluid, showing their pivotal role in the pathogenesis of this neurologic disease.

Intron positions correlate with module boundaries in ancient proteins

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of “linker regions” that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-Å modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters and show that, as the diameter varies, significant peaks of correlation appear for module diameters centered at 21.7, 27.6, and 32.9 Å. These preferred module diameters roughly correspond to predicted exon sizes of 15, 22, and 30 residues. Thus, there are significant correlations between introns, modules, and a quantized pattern of the lengths of polypeptide chains, which is the prediction of the “Exon Theory of Genes.”