Grain boundaries in vortex matter

We explore the statistical properties of grain boundaries in the vortex polycrystalline phase of type-II superconductors. Treating grain boundaries as arrays of dislocations interacting through linear elasticity, we show that self-interaction of a deformed grain boundary is equivalent to a nonlocal long-range surface tension. This affects the pinning properties of grain boundaries, which are found to be less rough than isolated dislocations. The presence of grain boundaries has an important effect on the transport properties of type-II superconductors as we show by numerical simulations: our results indicate that the critical current is higher for a vortex polycrystal than for a regular vortex lattice. Finally, we discuss the possible role of grain boundaries in vortex lattice melting. Through a phenomenological theory we show that melting can be preceded by an intermediate polycrystalline phase.

Photometric and fundamental plane studies of galaxies

Determining the morphological parameters that describe galaxies has always been a challenging task. The studies on the correlations between different photometric as well as spectroscopic parameters of the galaxies help in understanding their structure, properties of the stars and gas which constitute the galaxy, the various physical and chemical processes which determine the properties, and galaxy formation and evolution. In the last few decades, the advent of Charge Coupled Devices (CCDs) and near infrared arrays ha\·e provided quick and reliable digitized data acquisition, in the optical and near infrared bands. This has provided an avalanche of data, which can be processed using sophisticated image analysis techniques to obtain information about the morphology of galaxies. The photometric analysis performed in this thesis involve the extraction of structural parameters of early type gala.xies imaged in the near infrared K (2.2ttm) band, obtaining correlations between these, parameters and using them to constrain the large scale properties of galaxi,~s.

Underwater Target Localization, Tracking and Classification

Underwater target localization and tracking attracts tremendous research interest due to various impediments to the estimation task caused by the noisy ocean environment. This thesis envisages the implementation of a prototype automated system for underwater target localization, tracking and classification using passive listening buoy systems and target identification techniques. An autonomous three buoy system has been developed and field trials have been conducted successfully. Inaccuracies in the localization results, due to changes in the environmental parameters, measurement errors and theoretical approximations are refined using the Kalman filter approach. Simulation studies have been conducted for the tracking of targets with different scenarios even under maneuvering situations. This system can as well be used for classifying the unknown targets by extracting the features of the noise emanations from the targets.

A Multi-Objective Antenna Placement Genetic Algorithm for Matched Array Synthesis on Complex Platforms

A Multi-Objective Antenna Placement Genetic Algorithm (MO-APGA) has been proposed for the synthesis of matched antenna arrays on complex platforms. The total number of antennas required, their position on the platform, location of loads, loading circuit parameters, decoupling and matching network topology, matching network parameters and feed network parameters are optimized simultaneously. The optimization goal was to provide a given minimum gain, specific gain discrimination between the main and back lobes and broadband performance. This algorithm is developed based on the non-dominated sorting genetic algorithm (NSGA-II) and Minimum Spanning Tree (MST) technique for producing diverse solutions when the number of objectives is increased beyond two. The proposed method is validated through the design of a wideband airborne SAR

Modellierung und numerische Simulation der Thermoregulation von Früh- und Neugeborenen

Bei frühgeborenen Säuglingen spielt die Thermoregulation zur Aufrechterhaltung einer überlebenswichtigen Körpertemperatur durch Wärmeproduktion, -abgabe bzw. -aufnahme eine entscheidende Rolle. Der Einsatz moderner Inkubatoren soll die körpereigenen Thermoregulatoren unterstützen, und es ist im Hinblick auf verschiedene medizinische Fragestellungen wünschenswert, diesen Prozess modellieren zu können. Wir stellen ein einfaches Modell auf der Basis von partiellen Differentialgleichungen vor und beschreiben detailliert die numerische Simulation mit Hilfe einer Finite-Volumen-Methode. Dazu wird ein zweidimensionales Modell eines Frühgeborenen trianguliert und das Modell diskretisiert. Zahlreiche numerische Resultate zeigen die Qualität unseres Modells.

Heterochromatin und epigenetische Kontrolle der Centromere in Dictyostelium discoideum

Heterochromatin Protein 1 (HP1) is an evolutionarily conserved protein required for formation of a higher-order chromatin structures and epigenetic gene silencing. The objective of the present work was to functionally characterise HP1-like proteins in Dictyostelium discoideum, and to investigate their function in heterochromatin formation and transcriptional gene silencing. The Dictyostelium genome encodes three HP1-like proteins (hcpA, hcpB, hcpC), from which only two, hcpA and hcpB, but not hcpC were found to be expressed during vegetative growth and under developmental conditions. Therefore, hcpC, albeit no obvious pseudogene, was excluded from this study. Both HcpA and HcpB show the characteristic conserved domain structure of HP1 proteins, consisting of an N-terminal chromo domain and a C-terminal chromo shadow domain, which are separated by a hinge. Both proteins show all biochemical activities characteristic for HP1 proteins, such as homo- and heterodimerisation in vitro and in vivo, and DNA binding activtity. HcpA furthermore seems to bind to K9-methylated histone H3 in vitro. The proteins thus appear to be structurally and functionally conserved in Dictyostelium. The proteins display largely identical subnuclear distribution in several minor foci and concentration in one major cluster at the nuclear periphery. The localisation of this cluster adjacent to the nucleus-associated centrosome and its mitotic behaviour strongly suggest that it represents centromeric heterochromatin. Furthermore, it is characterised by histone H3 lysine-9 dimethylation (H3K9me2), which is another hallmark of Dictyostelium heterochromatin. Therefore, one important aspect of the work was to characterise the so-far largely unknown structural organisation of centromeric heterochromatin. The Dictyostelium homologue of inner centromere protein INCENP (DdINCENP), co-localized with both HcpA and H3K9me2 during metaphase, providing further evidence that H3K9me2 and HcpA/B localisation represent centromeric heterochromatin. Chromatin immunoprecipitation (ChIP) showed that two types of high-copy number retrotransposons (DIRS-1 and skipper), which form large irregular arrays at the chromosome ends, which are thought to contain the Dictyostelium centromeres, are characterised by H3K9me2. Neither overexpression of full-length HcpA or HcpB, nor deletion of single Hcp isoforms resulted in changes in retrotransposon transcript levels. However, overexpression of a C-terminally truncated HcpA protein, assumed to display a dominant negative effect, lead to an increase in skipper retrotransposon transcript levels. Furthermore, overexpression of this protein lead to severe growth defects in axenic suspension culture and reduced cell viability. In order to elucidate the proteins functions in centromeric heterochromatin formation, gene knock-outs for both hcpA and hcpB were generated. Both genes could be successfully targeted and disrupted by homologous recombination. Surprisingly, the degree of functional redundancy of the two isoforms was, although not unexpected, very high. Both single knock-out mutants did not show any obvious phenotypes under standard laboratory conditions and only deletion of hcpA resulted in subtle growth phenotypes when grown at low temperature. All attempts to generate a double null mutant failed. However, both endogenous genes could be disrupted in cells in which a rescue construct that ectopically expressed one of the isoforms either with N-terminal 6xHis- or GFP-tag had been introduced. The data imply that the presence of at least one Hcp isoform is essential in Dictyostelium. The lethality of the hcpA/hcpB double mutant thus greatly hampered functional analysis of the two genes. However, the experiment provided genetic evidence that the GFP-HcpA fusion protein, because of its ability to compensate the loss of the endogenous HcpA protein, was a functional protein. The proteins displayed quantitative differences in dimerisation behaviour, which are conferred by the slightly different hinge and chromo shadow domains at the C-termini. Dimerisation preferences in increasing order were HcpA-HcpA << HcpA-HcpB << HcpB-HcpB. Overexpression of GFP-HcpA or a chimeric protein containing the HcpA C-terminus (GFP-HcpBNAC), but not overexpression of GFP-HcpB or GFP-HcpANBC, lead to increased frequencies of anaphase bridges in late mitotic cells, which are thought to be caused by telomere-telomere fusions. Chromatin targeting of the two proteins is achieved by at least two distinct mechanisms. The N-terminal chromo domain and hinge of the proteins are required for targeting to centromeric heterochromatin, while the C-terminal portion encoding the CSD is required for targeting to several other chromatin regions at the nuclear periphery that are characterised by H3K9me2. Targeting to centromeric heterochromatin likely involves direct binding to DNA. The Dictyostelium genome encodes for all subunits of the origin recognition complex (ORC), which is a possible upstream component of HP1 targeting to chromatin. Overexpression of GFP-tagged OrcB, the Dictyostelium Orc2 homologue, showed a distinct nuclear localisation that partially overlapped with the HcpA distribution. Furthermore, GFP-OrcB localized to the centrosome during the entire cell cycle, indicating an involvement in centrosome function. DnmA is the sole DNA methyltransferase in Dictyostelium required for all DNA(cytosine-)methylation. To test for its in vivo activity, two different cell lines were established that ectopically expressed DnmA-myc or DnmA-GFP. It was assumed that overexpression of these proteins might cause an increase in the 5-methyl-cytosine(5-mC)-levels in the genomic DNA due to genomic hypermethylation. Although DnmA-GFP showed preferential localisation in the nucleus, no changes in the 5-mC-levels in the genomic DNA could be detected by capillary electrophoresis.

Nuclear organisation and epigenetic regulation of gene expression in Dictyostelium discoideum

A series of vectors for the over-expression of tagged proteins in Dictyostelium were designed, constructed and tested. These vectors allow the addition of an N- or C-terminal tag (GFP, RFP, 3xFLAG, 3xHA, 6xMYC and TAP) with an optimized polylinker sequence and no additional amino acid residues at the N or C terminus. Different selectable markers (Blasticidin and gentamicin) are available as well as an extra chromosomal version; these allow copy number and thus expression level to be controlled, as well as allowing for more options with regard to complementation, co- and super-transformation. Finally, the vectors share standardized cloning sites, allowing a gene of interest to be easily transfered between the different versions of the vectors as experimental requirements evolve. The organisation and dynamics of the Dictyostelium nucleus during the cell cycle was investigated. The centromeric histone H3 (CenH3) variant serves to target the kinetochore to the centromeres and thus ensures correct chromosome segregation during mitosis and meiosis. A number of Dictyostelium histone H3-domain containing proteins as GFP-tagged fusions were expressed and it was found that one of them functions as CenH3 in this species. Like CenH3 from some other species, Dictyostelium CenH3 has an extended N-terminal domain with no similarity to any other known proteins. The targeting domain, comprising α-helix 2 and loop 1 of the histone fold is required for targeting CenH3 to centromeres. Compared to the targeting domain of other known and putative CenH3 species, Dictyostelium CenH3 has a shorter loop 1 region. The localisation of a variety of histone modifications and histone modifying enzymes was examined. Using fluorescence in situ hybridisation (FISH) and CenH3 chromatin-immunoprecipitation (ChIP) it was shown that the six telocentric centromeres contain all of the DIRS-1 and most of the DDT-A and skipper transposons. During interphase the centromeres remain attached to the centrosome resulting in a single CenH3 cluster which also contains the putative histone H3K9 methyltransferase SuvA, H3K9me3 and HP1 (heterochromatin protein 1). Except for the centromere cluster and a number of small foci at the nuclear periphery opposite the centromeres, the rest of the nucleus is largely devoid of transposons and heterochromatin associated histone modifications. At least some of the small foci correspond to the distal telomeres, suggesting that the chromosomes are organised in a Rabl-like manner. It was found that in contrast to metazoans, loading of CenH3 onto Dictyostelium centromeres occurs in late G2 phase. Transformation of Dictyostelium with vectors carrying the G418 resistance cassette typically results in the vector integrating into the genome in one or a few tandem arrays of approximately a hundred copies. In contrast, plasmids containing a Blasticidin resistance cassette integrate as single or a few copies. The behaviour of transgenes in the nucleus was examined by FISH, and it was found that low copy transgenes show apparently random distribution within the nucleus, while transgenes with more than approximately 10 copies cluster at or immediately adjacent to the centromeres in interphase cells regardless of the actual integration site along the chromosome. During mitosis the transgenes show centromere-like behaviour, and ChIP experiments show that transgenes contain the heterochromatin marker H3K9me2 and the centromeric histone variant H3v1. This clustering, and centromere-like behaviour was not observed on extrachromosomal transgenes, nor on a line where the transgene had integrated into the extrachromosomal rDNA palindrome. This suggests that it is the repetitive nature of the transgenes that causes the centromere-like behaviour. A Dictyostelium homolog of DET1, a protein largely restricted to multicellular eukaryotes where it has a role in developmental regulation was identified. As in other species Dictyostelium DET1 is nuclear localised. In ChIP experiments DET1 was found to bind the promoters of a number of developmentally regulated loci. In contrast to other species where it is an essential protein, loss of DET1 is not lethal in Dictyostelium, although viability is greatly reduced. Loss of DET1 results in delayed and abnormal development with enlarged aggregation territories. Mutant slugs displayed apparent cell type patterning with a bias towards pre-stalk cell types.

Identifizierung und funktionelle Charakterisierung neuer A-Kinase-Ankerproteine (AKAPs) im Modellorganismus C. elegans

In dieser Arbeit sollten neue Interaktionspartner der regulatorischen Untereinheit (R-UE) der Proteinkinase A (PKA) und des Modellorganismus C. elegans identifiziert und funktionell charakterisiert werden. Im Gegensatz zu Säugern (vier Isoformen), exprimiert der Nematode nur eine PKA-R-Isoform. Mittels in silico Analysen und so genannten „Pulldown“ Experimenten, wurde insbesondere nach A Kinase Ankerproteinen (AKAP) in C. elegans gesucht. Aus in silico Recherchen resultiert das rgs5 Protein als mögliches Funktionshomolog des humanen AKAP10. Rgs5 enthält eine potenzielle, amphipathische Helix (AS 421-446, SwissProt ID A9Z1K0), die in Peptide-SPOT-Arrays (durchgeführt im Biotechnologie Zentrum in Oslo, AG Prof. K. Taskén) eine Bindung an RI und RII-UE zeigt. Eine ähnliche Lokalisation von rgs5 und hAKAP10 in der Zelle, sowie vergleichende BRET² Studien, weisen auf eine mögliche Funktionshomologie zwischen AKAP10 und rgs5 hin. Die hier durchgeführten Analysen deuten darauf hin, dass es sich bei rgs5 um ein neues, klassisches AKAP mit „RII bindender Domäne“ Motiv im Modellorganismus C. elegans handelt. Basierend auf so genannten „pulldown“ Versuchen können, neben „klassischen“ AKAPs (Interaktion über amphipathische Helices), auch Interaktionspartner ohne typische Helixmotive gefunden werden. Dazu gehört auch RACK1, ein multifunktionales Protein mit 7 WD40 Domänen, das ubiquitär exprimiert wird und bereits mehr als 70 Interaktionspartner in unterschiedlichsten Signalwegen komplexiert (Adams et al., 2011). Durch BRET² Interaktionsstudien und Oberflächenplasmonresonanz (SPR) Analysen konnten hRI und kin2 als spezifische Interaktionspartner von RACK1 verifiziert werden. Untersuchungen zur Identifikation der Interaktionsflächen der beiden Proteine RACK1 und hRI zeigten im BRET² System, dass RACK1 über die WD40 Domänen 1-2 und 6-7 interagiert. Die Analyse unterschiedlicher hRI-Deletionsmutanten deutet auf die DD-Domäne im N-Terminus und zusätzlich auf eine potenzielle BH3 Domäne im C-Terminus des Proteins als Interaktionsfläche mit RACK1 hin. Die Koexpression von hRI BH3 und RACK1 zeigt einen auffälligen ein Phänotyp in Cos7 Zellen. Dieser zeichnet sich unter anderem durch eine Degradation des Zellkerns, DNA Kondensation und eine starke Vakuolisierung aus, was beides als Anzeichen für einen programmierten Zelltod interpretiert werden könnte. Erste Untersuchungen zum Mechanismus des ausgelösten Zelltods deuten auf eine Caspase unabhängige Apoptose (Paraptose) hin und einen bislang unbekannten Funktionsmechanismus der PKA hin.

Abbildung von XML-Dokumenten auf SQL:2003-konforme Datentypen

Die Auszeichnungssprache XML dient zur Annotation von Dokumenten und hat sich als Standard-Datenaustauschformat durchgesetzt. Dabei entsteht der Bedarf, XML-Dokumente nicht nur als reine Textdateien zu speichern und zu transferieren, sondern sie auch persistent in besser strukturierter Form abzulegen. Dies kann unter anderem in speziellen XML- oder relationalen Datenbanken geschehen. Relationale Datenbanken setzen dazu bisher auf zwei grundsätzlich verschiedene Verfahren: Die XML-Dokumente werden entweder unverändert als binäre oder Zeichenkettenobjekte gespeichert oder aber aufgespalten, sodass sie in herkömmlichen relationalen Tabellen normalisiert abgelegt werden können (so genanntes „Flachklopfen“ oder „Schreddern“ der hierarchischen Struktur). Diese Dissertation verfolgt einen neuen Ansatz, der einen Mittelweg zwischen den bisherigen Lösungen darstellt und die Möglichkeiten des weiterentwickelten SQL-Standards aufgreift. SQL:2003 definiert komplexe Struktur- und Kollektionstypen (Tupel, Felder, Listen, Mengen, Multimengen), die es erlauben, XML-Dokumente derart auf relationale Strukturen abzubilden, dass der hierarchische Aufbau erhalten bleibt. Dies bietet zwei Vorteile: Einerseits stehen bewährte Technologien, die aus dem Bereich der relationalen Datenbanken stammen, uneingeschränkt zur Verfügung. Andererseits lässt sich mit Hilfe der SQL:2003-Typen die inhärente Baumstruktur der XML-Dokumente bewahren, sodass es nicht erforderlich ist, diese im Bedarfsfall durch aufwendige Joins aus den meist normalisierten und auf mehrere Tabellen verteilten Tupeln zusammenzusetzen. In dieser Arbeit werden zunächst grundsätzliche Fragen zu passenden, effizienten Abbildungsformen von XML-Dokumenten auf SQL:2003-konforme Datentypen geklärt. Darauf aufbauend wird ein geeignetes, umkehrbares Umsetzungsverfahren entwickelt, das im Rahmen einer prototypischen Applikation implementiert und analysiert wird. Beim Entwurf des Abbildungsverfahrens wird besonderer Wert auf die Einsatzmöglichkeit in Verbindung mit einem existierenden, ausgereiften relationalen Datenbankmanagementsystem (DBMS) gelegt. Da die Unterstützung von SQL:2003 in den kommerziellen DBMS bisher nur unvollständig ist, muss untersucht werden, inwieweit sich die einzelnen Systeme für das zu implementierende Abbildungsverfahren eignen. Dabei stellt sich heraus, dass unter den betrachteten Produkten das DBMS IBM Informix die beste Unterstützung für komplexe Struktur- und Kollektionstypen bietet. Um die Leistungsfähigkeit des Verfahrens besser beurteilen zu können, nimmt die Arbeit Untersuchungen des nötigen Zeitbedarfs und des erforderlichen Arbeits- und Datenbankspeichers der Implementierung vor und bewertet die Ergebnisse.

Multisensor Modeling Underwater with Uncertain Information

This thesis develops an approach to the construction of multidimensional stochastic models for intelligent systems exploring an underwater environment. It describes methods for building models by a three- dimensional spatial decomposition of stochastic, multisensor feature vectors. New sensor information is incrementally incorporated into the model by stochastic backprojection. Error and ambiguity are explicitly accounted for by blurring a spatial projection of remote sensor data before incorporation. The stochastic models can be used to derive surface maps or other representations of the environment. The methods are demonstrated on data sets from multibeam bathymetric surveying, towed sidescan bathymetry, towed sidescan acoustic imagery, and high-resolution scanning sonar aboard a remotely operated vehicle.

A Distributed Model for Mobile Robot Environment-Learning and Navigation

A distributed method for mobile robot navigation, spatial learning, and path planning is presented. It is implemented on a sonar-based physical robot, Toto, consisting of three competence layers: 1) Low-level navigation: a collection of reflex-like rules resulting in emergent boundary-tracing. 2) Landmark detection: dynamically extracts landmarks from the robot's motion. 3) Map learning: constructs a distributed map of landmarks. The parallel implementation allows for localization in constant time. Spreading of activation computes both topological and physical shortest paths in linear time. The main issues addressed are: distributed, procedural, and qualitative representation and computation, emergent behaviors, dynamic landmarks, minimized communication.

Bit-Width Analysis for General Applications

It has been widely known that a significant part of the bits are useless or even unused during the program execution. Bit-width analysis targets at finding the minimum bits needed for each variable in the program, which ensures the execution correctness and resources saving. In this paper, we proposed a static analysis method for bit-widths in general applications, which approximates conservatively at compile time and is independent of runtime conditions. While most related work focus on integer applications, our method is also tailored and applicable to floating point variables, which could be extended to transform floating point number into fixed point numbers together with precision analysis. We used more precise representations for data value ranges of both scalar and array variables. Element level analysis is carried out for arrays. We also suggested an alternative for the standard fixed-point iterations in bi-directional range analysis. These techniques are implemented on the Trimaran compiler structure and tested on a set of benchmarks to show the results.

SCAPA (Spacially Addressable Protein Array) – a Novel Protein Array for the Differential Profiling of Ligand-receptor Induced Signalling

While protein microarray technology has been successful in demonstrating its usefulness for large scale high-throughput proteome profiling, performance of antibody/antigen microarrays has been only moderately productive. Immobilization of either the capture antibodies or the protein samples on solid supports has severe drawbacks. Denaturation of the immobilized proteins as well as inconsistent orientation of antibodies/ligands on the arrays can lead to erroneous results. This has prompted a number of studies to address these challenges by immobilizing proteins on biocompatible surfaces, which has met with limited success. Our strategy relates to a multiplexed, sensitive and high-throughput method for the screening quantification of intracellular signalling proteins from a complex mixture of proteins. Each signalling protein to be monitored has its capture moiety linked to a specific oligo ‘tag’. The array involves the oligonucleotide hybridization-directed localization and identification of different signalling proteins simultaneously, in a rapid and easy manner. Antibodies have been used as the capture moieties for specific identification of each signaling protein. The method involves covalently partnering each antibody/protein molecule with a unique DNA or DNA derivatives oligonucleotide tag that directs the antibody to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array. Particular surface modifications and optimal conditions allowed high signal to noise ratio which is essential to the success of this approach.

Tubular Organization of SnO₂ Nanocrystallites for Improved Lithium Ion Battery Anode Performance

Porous tin oxide nanotubes were obtained by vacuum infiltration of tin oxide nanoparticles into porous aluminum oxide membranes, followed by calcination. The porous tin oxide nanotube arrays so prepared were characterized by FE-SEM, TEM, HRTEM, and XRD. The nanotubes are open-ended, highly ordered with uniform cross-sections, diameters and wall thickness. The tin oxide nanotubes were evaluated as a substitute anode material for the lithium ion batteries. The tin oxide nanotube anode could be charged and discharged repeatedly, retaining a specific capacity of 525 mAh/g after 80 cycles. This capacity is significantly higher than the theoretical capacity of commercial graphite anode (372 mAh/g) and the cyclability is outstanding for a tin based electrode. The cyclability and capacities of the tin oxide nanotubes were also higher than their building blocks of solid tin oxide nanoparticles. A few factors accounting for the good cycling performance and high capacity of tin oxide nanotubes are suggested.

Diseño y realización de servicios de presentación en entornos gráficos.

En cada unidad didáctica precede al tít.: Técnico Superior en Desarrollo de Aplicaciones Informáticas y consta en marbetes: Formación Profesional a Distancia y Ciclo Formativo de Grado Superior