Análisis térmico y de capacidad de transporte de un cable subterráneo de potencia

El presente proyecto tiene la finalidad de diseñar una herramienta mediante métodos numéricos implementados en Matlab que permita estudiar los fenómenos térmicos que tiene lugar en los cables subterráneos de potencia cuando se encuentran en carga. Y a partir de las soluciones obtenidas determinar la capacidad máxima del transporte del cable para un emplazamiento determinado.

Selected topics in the Hydrodynamics of floating offshore wind turbines: heave damping and second order surge motions

La Energía eléctrica producida mediante tecnología eólica flotante es uno de los recursos más prometedores para reducir la dependencia de energía proveniente de combustibles fósiles. Esta tecnología es de especial interés en países como España, donde la plataforma continental es estrecha y existen pocas áreas para el desarrollo de estructuras fijas. Entre los diferentes conceptos flotantes, esta tesis se ha ocupado de la tipología semisumergible. Estas plataformas pueden experimentar movimientos resonantes en largada y arfada. En largada, dado que el periodo de resonancia es largo estos puede ser inducidos por efectos de segundo orden de deriva lenta que pueden tener una influencia muy significativa en las cargas en los fondeos. En arfada las fuerzas de primer orden pueden inducir grandes movimientos y por tanto la correcta determinación del amortiguamiento es esencial para la analizar la operatividad de la plataforma. Esta tesis ha investigado estos dos efectos, para ello se ha usado como caso base el diseño de una plataforma desarrollada en el proyecto Europeo Hiprwind. La plataforma se compone de 3 columnas cilíndricas unidas mediante montantes estructurales horizontales y diagonales, Los cilindros proporcionan flotabilidad y momentos adrizante. A la base de cada columna se le ha añadido un gran “Heave Plate” o placa de cierre. El diseño es similar a otros diseños previos (Windfloat). Se ha fabricado un modelo a escala de una de las columnas para el estudio detallado del amortiguamiento mediante oscilaciones forzadas. Las dimensiones del modelo (1m diámetro en la placa de cierre) lo hacen, de los conocidos por el candidato, el mayor para el que se han publicado datos. El diseño del cilindro se ha realizado de tal manera que permite la fijación de placas de cierre planas o con refuerzo, ambos modelos se han fabricado y analizado. El modelo con refuerzos es una reproducción exacta del diseño a escala real incluyendo detalles distintivos del mismo, siendo el más importante la placa vertical perimetral. Los ensayos de oscilaciones forzadas se han realizado para un rango de frecuencias, tanto para el disco plano como el reforzado. Se han medido las fuerzas durante los ensayos y se han calculado los coeficientes de amortiguamiento y de masa añadida. Estos coeficientes son necesarios para el cálculo del fondeo mediante simulaciones en el dominio del tiempo. Los coeficientes calculados se han comparado con la literatura existente, con cálculos potenciales y por ultimo con cálculos CFD. Para disponer de información relevante para el diseño estructural de la plataforma se han medido y analizado experimentalmente las presiones en la parte superior e inferior de cada placa de cierre. Para la correcta estimación numérica de las fuerzas de deriva lenta en la plataforma se ha realizado una campaña experimental que incluye ensayos con modelo cautivo de la plataforma completa en olas bicromaticas. Pese a que estos experimentos no reproducen un escenario de oleaje realista, los mismos permiten una verificación del modelo numérico mediante la comparación de fuerzas medidas en el modelo físico y el numérico. Como resultados de esta tesis podemos enumerar las siguientes conclusiones. 1. El amortiguamiento y la masa añadida muestran una pequeña dependencia con la frecuencia pero una gran dependencia con la amplitud del movimiento. siendo coherente con investigaciones existentes. 2. Las medidas con la placa de cierre reforzada con cierre vertical en el borde, muestra un amortiguamiento significativamente menor comparada con la placa plana. Esto implica que para ensayos de canal es necesario incluir estos detalles en el modelo. 3. La masa añadida no muestra grandes variaciones comparando placa plana y placa con refuerzos. 4. Un coeficiente de amortiguamiento del 6% del crítico se puede considerar conservador para el cálculo en el dominio de la frecuencia. Este amortiguamiento es equivalente a un coeficiente de “drag” de 4 en elementos de Morison cuadráticos en las placas de cierre usadas en simulaciones en el dominio del tiempo. 5. Se han encontrado discrepancias en algunos valores de masa añadida y amortiguamiento de la placa plana al comparar con datos publicados. Se han propuesto algunas explicaciones basadas en las diferencias en la relación de espesores, en la distancia a la superficie libre y también relacionadas con efectos de escala. 6. La presión en la placa con refuerzos son similares a las de la placa plana, excepto en la zona del borde donde la placa con refuerzo vertical induce una gran diferencias de presiones entre la cara superior e inferior. 7. La máxima diferencia de presión escala coherentemente con la fuerza equivalente a la aceleración de la masa añadida distribuida sobre la placa. 8. Las masas añadidas calculadas con el código potencial (WADAM) no son suficientemente precisas, Este software no contempla el modelado de placas de pequeño espesor con dipolos, la poca precisión de los resultados aumenta la importancia de este tipo de elementos al realizar simulaciones con códigos potenciales para este tipo de plataformas que incluyen elementos de poco espesor. 9. Respecto al código CFD (Ansys CFX) la precisión de los cálculos es razonable para la placa plana, esta precisión disminuye para la placa con refuerzo vertical en el borde, como era de esperar dado la mayor complejidad del flujo. 10. Respecto al segundo orden, los resultados, en general, muestran que, aunque la tendencia en las fuerzas de segundo orden se captura bien con los códigos numéricos, se observan algunas reducciones en comparación con los datos experimentales. Las diferencias entre simulaciones y datos experimentales son mayores al usar la aproximación de Newman, que usa únicamente resultados de primer orden para el cálculo de las fuerzas de deriva media. 11. Es importante remarcar que las tendencias observadas en los resultados con modelo fijo cambiarn cuando el modelo este libre, el impacto que los errores en las estimaciones de fuerzas segundo orden tienen en el sistema de fondeo dependen de las condiciones ambientales que imponen las cargas ultimas en dichas líneas. En cualquier caso los resultados que se han obtenido en esta investigación confirman que es necesaria y deseable una detallada investigación de los métodos usados en la estimación de las fuerzas no lineales en las turbinas flotantes para que pueda servir de guía en futuros diseños de estos sistemas. Finalmente, el candidato espera que esta investigación pueda beneficiar a la industria eólica offshore en mejorar el diseño hidrodinámico del concepto semisumergible. ABSTRACT Electrical power obtained from floating offshore wind turbines is one of the promising resources which can reduce the fossil fuel energy consumption and cover worldwide energy demands. The concept is the most competitive in countries, such as Spain, where the continental shelf is narrow and does not provide space for fixed structures. Among the different floating structures concepts, this thesis has dealt with the semisubmersible one. Platforms of this kind may experience resonant motions both in surge and heave directions. In surge, since the platform natural period is long, such resonance can be excited with second order slow drift forces and may have substantial influence on mooring loads. In heave, first order forces can induce significant motion, whose damping is a crucial factor for the platform downtime. These two topics have been investigated in this thesis. To this aim, a design developed during HiPRWind EU project, has been selected as reference case study. The platform is composed of three cylindrical legs, linked together by a set of structural braces. The cylinders provide buoyancy and restoring forces and moments. Large circular heave plates have been attached to their bases. The design is similar to other documented in literature (e.g. Windfloat), which implies outcomes could have a general value. A large scale model of one of the legs has been built in order to study heave damping through forced oscillations. The final dimensions of the specimen (one meter diameter discs) make it, to the candidate’s knowledge, the largest for which data has been published. The model design allows for the fitting of either a plain solid heave plate or a flapped reinforced one; both have been built. The latter is a model scale reproduction of the prototype heave plate and includes some distinctive features, the most important being the inclusion of a vertical flap on its perimeter. The forced oscillation tests have been conducted for a range of frequencies and amplitudes, with both the solid plain model and the vertical flap one. Forces have been measured, from which added mass and damping coefficients have been obtained. These are necessary to accurately compute time-domain simulations of mooring design. The coefficients have been compared with literature, and potential flow and CFD predictions. In order to provide information for the structural design of the platform, pressure measurements on the top and bottom side of the heave discs have been recorded and pressure differences analyzed. In addition, in order to conduct a detailed investigation on the numerical estimations of the slow-drift forces of the HiPRWind platform, an experimental campaign involving captive (fixed) model tests of a model of the whole platform in bichromatic waves has been carried out. Although not reproducing the more realistic scenario, these tests allowed a preliminary verification of the numerical model based directly on the forces measured on the structure. The following outcomes can be enumerated: 1. Damping and added mass coefficients show, on one hand, a small dependence with frequency and, on the other hand, a large dependence with the motion amplitude, which is coherent with previously published research. 2. Measurements with the prototype plate, equipped with the vertical flap, show that damping drops significantly when comparing this to the plain one. This implies that, for tank tests of the whole floater and turbine, the prototype plate, equipped with the flap, should be incorporated to the model. 3. Added mass values do not suffer large alterations when comparing the plain plate and the one equipped with a vertical flap. 4. A conservative damping coefficient equal to 6% of the critical damping can be considered adequate for the prototype heave plate for frequency domain analysis. A corresponding drag coefficient equal to 4.0 can be used in time domain simulations to define Morison elements. 5. When comparing to published data, some discrepancies in added mass and damping coefficients for the solid plain plate have been found. Explanations have been suggested, focusing mainly on differences in thickness ratio and distance to the free surface, and eventual scale effects. 6. Pressures on the plate equipped with the vertical flap are similar in magnitude to those of the plain plate, even though substantial differences are present close to the edge, where the flap induces a larger pressure difference in the reinforced case. 7. The maximum pressure difference scales coherently with the force equivalent to the acceleration of the added mass, distributed over the disc surface. 8. Added mass coefficient values predicted with the potential solver (WADAM) are not accurate enough. The used solver does not contemplate modeling thin plates with doublets. The relatively low accuracy of the results highlights the importance of these elements when performing potential flow simulations of offshore platforms which include thin plates. 9. For the full CFD solver (Ansys CFX), the accuracy of the computations is found reasonable for the plain plate. Such accuracy diminishes for the disc equipped with a vertical flap, an expected result considering the greater complexity of the flow. 10. In regards to second order effects, in general, the results showed that, although the main trend in the behavior of the second-order forces is well captured by the numerical predictions, some under prediction of the experimental values is visible. The gap between experimental and numerical results is more pronounced when Newman’s approximation is considered, making use exclusively of the mean drift forces calculated in the first-order solution. 11. It should be observed that the trends observed in the fixed model test may change when the body is free to float, and the impact that eventual errors in the estimation of the second-order forces may have on the mooring system depends on the characteristics of the sea conditions that will ultimately impose the maximum loads on the mooring lines. Nevertheless, the preliminary results obtained in this research do confirm that a more detailed investigation of the methods adopted for the estimation of the nonlinear wave forces on the FOWT would be welcome and may provide some further guidance for the design of such systems. As a final remark, the candidate hopes this research can benefit the offshore wind industry in improving the hydrodynamic design of the semi-submersible concept.

RecA binding to a single double-stranded DNA molecule: A possible role of DNA conformational fluctuations

Most genetic regulatory mechanisms involve protein–DNA interactions. In these processes, the classical Watson–Crick DNA structure sometimes is distorted severely, which in turn enables the precise recognition of the specific sites by the protein. Despite its key importance, very little is known about such deformation processes. To address this general question, we have studied a model system, namely, RecA binding to double-stranded DNA. Results from micromanipulation experiments indicate that RecA binds strongly to stretched DNA; based on this observation, we propose that spontaneous thermal stretching fluctuations may play a role in the binding of RecA to DNA. This has fundamental implications for the protein–DNA binding mechanism, which must therefore rely in part on a combination of flexibility and thermal fluctuations of the DNA structure. We also show that this mechanism is sequence sensitive. Theoretical simulations support this interpretation of our experimental results, and it is argued that this is of broad relevance to DNA–protein interactions.

A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase

Editing of RNA changes the read-out of information from DNA by altering the nucleotide sequence of a transcript. One type of RNA editing found in all metazoans uses double-stranded RNA (dsRNA) as a substrate and results in the deamination of adenosine to give inosine, which is translated as guanosine. Editing thus allows variant proteins to be produced from a single pre-mRNA. A mechanism by which dsRNA substrates form is through pairing of intronic and exonic sequences before the removal of noncoding sequences by splicing. Here we report that the RNA editing enzyme, human dsRNA adenosine deaminase (DRADA1, or ADAR1) contains a domain (Zα) that binds specifically to the left-handed Z-DNA conformation with high affinity (KD = 4 nM). As formation of Z-DNA in vivo occurs 5′ to, or behind, a moving RNA polymerase during transcription, recognition of Z-DNA by DRADA1 provides a plausible mechanism by which DRADA1 can be targeted to a nascent RNA so that editing occurs before splicing. Analysis of sequences related to Zα has allowed identification of motifs common to this class of nucleic acid binding domain.

The conducting form of gramicidin A is a right-handed double-stranded double helix

The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDHℛ) reported here agree with 15N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs+ and K+ salts may be in error and that our evidence points to the DSDHℛ as the major conformer responsible for ion transport in membranes.

Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii

Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination, and repair in bacteria and eukarya. We report here the identification and characterization of the SSB of an archaeon, Methanococcus jannaschii. The M. jannaschii SSB (mjaSSB) has significant amino acid sequence similarity to the eukaryotic SSB, replication protein A (RPA), and contains four tandem repeats of the core single-stranded DNA (ssDNA) binding domain originally defined by structural studies of RPA. Homologous SSBs are encoded by the genomes of other archaeal species, including Methanobacterium thermoautotrophicum and Archaeoglobus fulgidus. The purified mjaSSB binds to ssDNA with high affinity and selectivity. The apparent association constant for binding to ssDNA is similar to that of RPA under comparable experimental conditions, and the affinity for ssDNA exceeds that for double-stranded DNA by at least two orders of magnitude. The binding site size for mjaSSB is ≈20 nucleotides. Given that RPA is related to mjaSSB at the sequence level and to Escherichia coli SSB at the structural level, we conclude that the SSBs of archaea, eukarya, and bacteria share a common core ssDNA-binding domain. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life.

Double-stranded RNA induces mRNA degradation in Trypanosoma brucei

Double-stranded RNA (dsRNA) recently has been shown to give rise to genetic interference in Caenorhabditis elegans and also is likely to be the basis for phenotypic cosuppression in plants in certain instances. While constructing a plasmid vector for transfection of trypanosome cells, we serendipitously discovered that in vivo expression of dsRNA of the α-tubulin mRNA 5′ untranslated region (5′ UTR) led to multinucleated cells with striking morphological alterations and a specific block of cytokinesis. Transfection of synthetic α-tubulin 5′ UTR dsRNA, but not of either strand individually, caused the same phenotype. On dsRNA transfection, tubulin mRNA, but not the corresponding pre-mRNA, was rapidly and specifically degraded, leading to a deficit of α-tubulin synthesis. The transfected cells were no longer capable of carrying out cytokinesis and eventually died. Analysis of cytoskeletal structures from these trypanosomes revealed defects in the microtubules of the flagellar axoneme and of the flagellar attachment zone, a complex cortical structure that we propose is essential for establishing the path of the cleavage furrow at cytokinesis. Last, dsRNA-mediated mRNA degradation is not restricted to α-tubulin mRNA but can be applied to other cellular mRNAs, thus establishing a powerful tool to genetically manipulate these important protozoan parasites.

An autonomous folding unit mediates the assembly of two-stranded coiled coils

Subunit oligomerization of many proteins is mediated by coiled-coil domains. Although the basic features contributing to the thermodynamic stability of coiled coils are well understood, the mechanistic details of their assembly have not yet been dissected. Here we report a 13-residue sequence pattern that occurs with limited sequence variations in many two-stranded coiled coils and that is absolutely required for the assembly of the Dictyostelium discoideum actin-bundling protein cortexillin I and the yeast transcriptional activator GCN4. The functional relationship between coiled-coil “trigger” sequences was manifested by replacing the intrinsic trigger motif of GCN4 with the related sequence from cortexillin I. We demonstrate that these trigger sequences represent autonomous helical folding units that, in contrast to arbitrarily chosen heptad repeats, can mediate coiled-coil formation. Aside from being of general interest for protein folding, trigger motifs should be of particular importance in the protein de novo design.

Interactions of RecF protein with RecO, RecR, and single-stranded DNA binding proteins reveal roles for the RecF–RecO–RecR complex in DNA repair and recombination

The products of the recF, recO, and recR genes are thought to interact and assist RecA in the utilization of single-stranded DNA precomplexed with single-stranded DNA binding protein (Ssb) during synapsis. Using immunoprecipitation, size-exclusion chromatography, and Ssb protein affinity chromatography in the absence of any nucleotide cofactors, we have obtained the following results: (i) RecF interacts with RecO, (ii) RecF interacts with RecR in the presence of RecO to form a complex consisting of RecF, RecO, and RecR (RecF–RecO–RecR); (iii) RecF interacts with Ssb protein in the presence of RecO. These data suggested that RecO mediates the interactions of RecF protein with RecR and with Ssb proteins. Incubation of RecF, RecO, RecR, and Ssb proteins resulted in the formation of RecF–RecO–Ssb complexes; i.e., RecR was excluded. Preincubation of RecF, RecO, and RecR proteins prior to addition of Ssb protein resulted in the formation of complexes consisting of RecF, RecO, RecR, and Ssb proteins. These data suggest that one role of RecF is to stabilize the interaction of RecR with RecO in the presence of Ssb protein. Finally, we found that interactions of RecF with RecO are lost in the presence of ATP. We discuss these results to explain how the RecF–RecO–RecR complex functions as an anti-Ssb factor.

Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage

A sensitive and rapid in situ method was developed to visualize sites of single-stranded (ss) DNA in cultured cells and in experimental test animals. Anti-bromodeoxyuridine antibody recognizes the halogenated base analog incorporated into chromosomal DNA only when substituted DNA is in the single strand form. After treatment of cells with DNA-damaging agents or γ irradiation, ssDNA molecules form nuclear foci in a dose-dependent manner within 60 min. The mammalian recombination protein Rad51 and the replication protein A then accumulate at sites of ssDNA and form foci, suggesting that these are sites of recombinational DNA repair.

Activation of target-tissue immune-recognition molecules by double-stranded polynucleotides

Abnormal expression of major histocompatibility complex (MHC) class I and class II in various tissues is associated with autoimmune disease. Autoimmune responses can be triggered by viral infections or tissue injuries. We show that the ability of a virus or a tissue injury to increase MHC gene expression is duplicated by any fragment of double-stranded (ds) DNA or dsRNA introduced into the cytoplasm of nonimmune cells. Activation is sequence-independent, is induced by ds polynucleotides as small as 25 bp in length, and is not duplicated by single-stranded polynucleotides. In addition to causing abnormal MHC expression, the ds nucleic acids increase the expression of genes necessary for antigen processing and presentation: proteasome proteins (e.g., LMP2), transporters of antigen peptides; invariant chain, HLA-DM, and the costimulatory molecule B7.1. The mechanism is different from and additive to that of γ-interferon (γIFN), i.e., ds polynucleotides increase class I much more than class II, whereas γIFN increases class II more than class I. The ds nucleic acids also induce or activate Stat1, Stat3, mitogen-activated protein kinase, NF-κB, the class II transactivator, RFX5, and the IFN regulatory factor 1 differently from γIFN. CpG residues are not responsible for this effect, and the action of the ds polynucleotides could be shown in a variety of cell types in addition to thyrocytes. We suggest that this phenomenon is a plausible mechanism that might explain how viral infection of tissues or tissue injury triggers autoimmune disease; it is potentially relevant to host immune responses induced during gene therapy.

Folding simulations of a three-stranded antiparallel β-sheet peptide

Protein folding is a grand challenge of the postgenomic era. In this paper, 58 folding events sampled during 47 molecular dynamics trajectories for a total simulation time of more than 4 μs provide an atomic detail picture of the folding of a 20-residue synthetic peptide with a stable three-stranded antiparallel β-sheet fold. The simulations successfully reproduce the NMR solution conformation, irrespective of the starting structure. The sampling of the conformational space is sufficient to determine the free energy surface and localize the minima and transition states. The statistically predominant folding pathway involves the formation of contacts between strands 2 and 3, starting with the side chains close to the turn, followed by association of the N-terminal strand onto the preformed 2–3 β-hairpin. The folding mechanism presented here, formation of a β-hairpin followed by consolidation, is in agreement with a computational study of the free energy surface of another synthetic three-stranded antiparallel β-sheet by Bursulaya and Brooks [(1999) J. Am. Chem. Soc. 121, 9947–9951]. Hence, it might hold in general for antiparallel β-sheets with short turns.

Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy

We report single-molecule measurements on the folding and unfolding conformational equilibrium distributions and dynamics of a disulfide crosslinked version of the two-stranded coiled coil from GCN4. The peptide has a fluorescent donor and acceptor at the N termini of its two chains and a Cys disulfide near its C terminus. Thus, folding brings the two N termini of the two chains close together, resulting in an enhancement of fluorescent resonant energy transfer. End-to-end distance distributions have thus been characterized under conditions where the peptide is nearly fully folded (0 M urea), unfolded (7.4 M urea), and in dynamic exchange between folded and unfolded states (3.0 M urea). The distributions have been compared for the peptide freely diffusing in solution and deposited onto aminopropyl silanized glass. As the urea concentration is increased, the mean end-to-end distance shifts to longer distances both in free solution and on the modified surface. The widths of these distributions indicate that the molecules are undergoing millisecond conformational fluctuations. Under all three conditions, these fluctuations gave nonexponential correlations on 1- to 100-ms time scale. A component of the correlation decay that was sensitive to the concentration of urea corresponded to that measured by bulk relaxation kinetics. The trajectories provided effective intramolecular diffusion coefficients as a function of the end-to-end distances for the folded and unfolded states. Single-molecule folding studies provide information concerning the distributions of conformational states in the folded, unfolded, and dynamically interconverting states.

The central structural feature of the membrane fusion protein subunit from the Ebola virus glycoprotein is a long triple-stranded coiled coil

The ectodomain of the Ebola virus Gp2 glycoprotein was solubilized with a trimeric, isoleucine zipper derived from GCN4 (pIIGCN4) in place of the hydrophobic fusion peptide at the N terminus. This chimeric molecule forms a trimeric, highly α-helical, and very thermostable molecule, as determined by chemical crosslinking and circular dichroism. Electron microscopy indicates that Gp2 folds into a rod-like structure like influenza HA2 and HIV-1 gp41, providing further evidence that viral fusion proteins from diverse families such as Orthomyxoviridae (Influenza), Retroviridae (HIV-1), and Filoviridae (Ebola) share common structural features, and suggesting a common membrane fusion mechanism.