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The size and morphology control of precipitated solid particles is a major economic issue for numerous industries. For instance, it is interesting for the nuclear industry, concerning the recovery of radioactive species from used nuclear fuel.
The precipitates features, which are a key parameter from the post-precipitate processing, depend on the process local mixing conditions. So far, the relationship between precipitation features and hydrodynamic conditions have not been investigated.
In this study, a new experimental configuration consisting of coalescing drops is set to investigate the link between reactive crystallization and hydrodynamics. Two configurations of aqueous drops are examined. The first one corresponds to high contact angle drops (>90°) in oil, as a model system for flowing drops, the second one correspond to sessile drops in air with low contact angle (<25°). In both cases, one reactive is dissolved in each drop, namely oxalic acid and cerium nitrate. When both drops get into contact, they may coalesce; the dissolved species mix and react to produce insoluble cerium oxalate. The precipitates features and effect on hydrodynamics are investigated depending on the solvent. In the case of sessile drops in air, the surface tension difference between the drops generates a gradient which induces a Marangoni flow from the low surface tension drop over the high surface tension drop. By setting the surface tension difference between the two drops and thus the Marangoni flow, the hydrodynamics conditions during the drop coalescence could be modified. Diols/water mixtures are used as solvent, in order to fix the surface tension difference between the liquids of both drops regardless from the reactant concentration. More precisely, the used diols, 1,2-propanediol and 1,3-propanediol, are isomer with identical density and close viscosity. By keeping the water volume fraction constant and playing with the 1,2-propanediol and 1,3-propanediol volume fractions of the solvents, the mixtures surface tensions differ up to 10 mN/m for identical/constant reactant concentration, density and viscosity. 3 precipitation behaviors were identified for the coalescence of water/diols/recatants drops depending on the oxalic excess. The corresponding precipitates patterns are visualized by optical microscopy and the precipitates are characterized by confocal microscopy SEM, XRD and SAXS measurements. In the intermediate oxalic excess regime, formation of periodic patterns can be observed. These patterns consist in alternating cerium oxalate precipitates with distinct morphologies, namely needles and “microflowers”. Such periodic fringes can be explained by a feedback mechanism between convection, reaction and the diffusion.
About the relation between implicit Theory of Mind & the comprehension of complement sentences
(2010)
Previous studies on the relation between language and social cognition have shown that children’s mastery of embedded sentential complements plays a causal role for the development of a Theory of Mind (ToM). Children start to succeed on complementation tasks in which they are required to report the content of an embedded clause in the second half of the fourth year. Traditional ToM tasks test the child’s ability to predict that a person who is holding a false belief (FB) about a situation will act "falsely". In these task, children do not represent FBs until the age of 4 years. According the linguistic determinism hypothesis, only the unique syntax of complement sentences provides the format for representing FBs. However, experiments measuring children’s looking behavior instead of their explicit predictions provided evidence that already 2-year olds possess an implicit ToM. This dissertation examined the question of whether there is an interrelation also between implicit ToM and the comprehension of complement sentences in typically developing German preschoolers. Two studies were conducted. In a correlational study (Study 1 ), 3-year-old children’s performance on a traditional (explicit) FB task, on an implicit FB task and on language tasks measuring children’s comprehension of tensed sentential complements were collected and tested for their interdependence. Eye-tracking methodology was used to assess implicit ToM by measuring participants’ spontaneous anticipatory eye movements while they were watching FB movies. Two central findings emerged. First, predictive looking (implicit ToM) was not correlated with complement mastery, although both measures were associated with explicit FB task performance. This pattern of results suggests that explicit, but not implicit ToM is language dependent. Second, as a group, 3-year-olds did not display implicit FB understanding. That is, previous findings on a precocious reasoning ability could not be replicated. This indicates that the characteristics of predictive looking tasks play a role for the elicitation of implicit FB understanding as the current task was completely nonverbal and as complex as traditional FB tasks. Study 2 took a methodological approach by investigating whether children display an earlier comprehension of sentential complements when using the same means of measurement as used in experimental tasks tapping implicit ToM, namely anticipatory looking. Two experiments were conducted. 3-year-olds were confronted either with a complement sentence expressing the protagonist’s FB (Exp. 1) or with a complex sentence expressing the protagonist’s belief without giving any information about the truth/ falsity of the belief (Exp. 2). Afterwards, their expectations about the protagonist’s future behavior were measured. Overall, implicit measures reveal no considerably earlier understanding of sentential complementation. Whereas 3-year-olds did not display a comprehension of complex sentences if these embedded a false proposition, children from 3;9 years on were proficient in processing complement sentences if the truth value of the embedded proposition could not be evaluated. This pattern of results suggests that (1) the linguistic expression of a person’s FB does not elicit implicit FB understanding and that (2) the assessment of the purely syntactic understanding of complement sentences is affected by competing reality information. In conclusion, this dissertation found no evidence that the implicit ToM is related to the comprehension of sentential complementation. The findings suggest that implicit ToM might be based on nonlinguistic processes. Results are discussed in the light of recently proposed dual-process models that assume two cognitive mechanisms that account for different levels of ToM task performance.
Many complex systems that we encounter in the world can be formalized using networks. Consequently, they have been in the focus of computer science for decades, where algorithms are developed to understand and utilize these systems.
Surprisingly, our theoretical understanding of these algorithms and their behavior in practice often diverge significantly. In fact, they tend to perform much better on real-world networks than one would expect when considering the theoretical worst-case bounds. One way of capturing this discrepancy is the average-case analysis, where the idea is to acknowledge the differences between practical and worst-case instances by focusing on networks whose properties match those of real graphs. Recent observations indicate that good representations of real-world networks are obtained by assuming that a network has an underlying hyperbolic geometry.
In this thesis, we demonstrate that the connection between networks and hyperbolic space can be utilized as a powerful tool for average-case analysis. To this end, we first introduce strongly hyperbolic unit disk graphs and identify the famous hyperbolic random graph model as a special case of them. We then consider four problems where recent empirical results highlight a gap between theory and practice and use hyperbolic graph models to explain these phenomena theoretically. First, we develop a routing scheme, used to forward information in a network, and analyze its efficiency on strongly hyperbolic unit disk graphs. For the special case of hyperbolic random graphs, our algorithm beats existing performance lower bounds. Afterwards, we use the hyperbolic random graph model to theoretically explain empirical observations about the performance of the bidirectional breadth-first search. Finally, we develop algorithms for computing optimal and nearly optimal vertex covers (problems known to be NP-hard) and show that, on hyperbolic random graphs, they run in polynomial and quasi-linear time, respectively.
Our theoretical analyses reveal interesting properties of hyperbolic random graphs and our empirical studies present evidence that these properties, as well as our algorithmic improvements translate back into practice.
In den letzten Jahren wurden relativ komplexe Erosionsmodelle entwickelt, deren Teilprozesse immer mehr auf physikalisch begründeten Ansätzen beruhen. Damit verbunden ist eine höhere Anzahl aktueller Eingangsparameter, deren Bestimmung im Feld arbeits- und kostenaufwendig ist. Zudem werden die Parameter punktuell, also an bestimmten Stellen und nicht flächenhaft wie bei der Fernerkundung, erfasst. Im Rahmen dieser Arbeit wird gezeigt, wie Satellitendaten als relativ kostengünstige Ergänzung oder Alternative zur konventionellen Parametererhebung genutzt werden können. Dazu werden beispielhaft der Blattflächenindex (LAI) und der Bedeckungsgrad für das physikalisch begründete Erosionsmodell EROSION 3D abgeleitet. Im Mittelpunkt des Interesses steht dabei das Aufzeigen von existierenden Methoden, die die Basis für eine operationelle Bereitstellung solcher Größen nicht nur für Erosions- sondern allgemein für Prozessmodelle darstellen. Als Untersuchungsgebiet dient das primär landwirtschaftlich genutzte Einzugsgebiet des Mehltheuer Baches, das sich im Sächsischen Lößgefilde befindet und für das Simulationsrechnungen mit konventionell erhobenen Eingangsparametern für 29 Niederschlagsereignisse im Jahr 1999 vorliegen [MICHAEL et al. 2000]. Die Fernerkundungsdatengrundlage bilden Landsat-5-TM-Daten vom 13.03.1999, 30.04.1999 und 19.07.1999. Da die Vegetationsparameter für alle Niederschlagsereignisse vorliegen sollen, werden sie basierend auf der Entwicklung des LAI zeitlich interpoliert. Dazu erfolgt zunächst die Ableitung des LAI für alle vorhandenen Fruchtarten nach den semi-empirischen Modellen von CLEVERS [1986] und BARET & GUYOT [1991] mit aus der Literatur entnommenen Koeffizienten. Des Weiteren wird eine Methode untersucht, nach der die Koeffizienten für das Clevers-Modell aus den TM-Daten und einem vereinfachten Wachstumsmodell bestimmt werden. Der Bedeckungsgrad wird nach ROSS [1981] aus dem LAI ermittelt. Die zeitliche Interpolation des LAI wird durch die schlagbezogene Anpassung eines vereinfachten Wachstumsmodells umgesetzt, das dem hydrologischen Modell SWIM [KRYSANOVA et al. 1999] entstammt und in das durchschnittliche Tagestemperaturen eingehen. Mit den genannten Methoden bleiben abgestorbene Pflanzenteile unberücksichtigt. Im Vergleich zur konventionellen terrestrischen Parametererhebung ermöglichen sie eine differenziertere Abbildung räumlicher Variabilitäten und des zeitlichen Verlaufes der Vegetationsparameter. Die Simulationsrechnungen werden sowohl mit den direkten Bedeckungsgraden aus den TM-Daten (pixelbezogen) als auch mit den zeitlich interpolierten Bedeckungsgraden für alle Ereignisse (schlagbezogen) durchgeführt. Bei beiden Vorgehensweisen wird im Vergleich zur bisherigen Abschätzung eine Verbesserung der räumlichen Verteilung der Parameter und somit eine räumliche Umverteilung von Erosions- und Depositionsflächen erreicht. Für die im Untersuchungsgebiet vorliegende räumliche Heterogenität (z. B. Schlaggröße) bieten Landsat-TM-Daten eine ausreichend genaue räumliche Auflösung. Damit wird nachgewiesen, dass die satellitengestützte Fernerkundung im Rahmen dieser Untersuchungen sinnvoll einsetzbar ist. Für eine operationelle Bereitstellung der Parameter mit einem vertretbaren Aufwand ist es erforderlich, die Methoden weiter zu validieren und möglichst weitestgehend zu automatisieren.
Die vorliegende Arbeit 'Abflußentwicklung in Teileinzugsgebieten des Rheins - Simulationen für den Ist-Zustand und für Klimaszenarien' untersucht Auswirkungen möglicher zukünftiger Klimaänderungen auf das Abflußgeschehen in ausgewählten, durch Mittelgebirge geprägten Teileinzugsgebieten des Rheins: Mosel (bis Pegel Cochem); Sieg (bis Pegel Menden 1) und Main (bis Pegel Kemmern).In einem ersten Schritt werden unter Verwendung des hydrologischen Modells HBV-D wichtige Modellprozesse entsprechend der Einzugsgebietscharakteristik parametrisiert und ein Abbild der Gebietshydrologie erzeugt, das mit Zeitreihen gemessener Tageswerte (Temperatur, Niederschlag) eine Zeitreihe der Pegeldurchflüsse simulieren kann. Die Güte der Simulation des Ist-Zustandes (Standard-Meßzeitraum 1.1.1961-31.12.1999) ist für die Kalibrierungs- und Validierungszeiträume in allen Untersuchungsgebieten gut bis sehr gut.Zur Erleichterung der umfangreichen, zeitaufwendigen einzugsgebietsbezogenen Datenaufbereitung für das hydrologische Modell HBV-D wurde eine Arbeitsumgebung auf Basis von Programmerweiterungen des Geoinformationssystems ArcView und zusätzlichen Hilfsprogrammen entwickelt. Die Arbeitsumgebung HBV-Params enthält eine graphische Benutzeroberfläche und räumt sowohl erfahrenen Hydrologen als auch hydrologisch geschulten Anwendern, z.B. Studenten der Vertiefungsrichtung Hydrologie, Flexibilität und vollständige Kontrolle bei der Ableitung von Parameterwerten und der Editierung von Parameter- und Steuerdateien ein. Somit ist HBV-D im Gegensatz zu Vorläuferversionen mit rudimentären Arbeitsumgebungen auch außerhalb der Forschung für Lehr- und Übungszwecke einsetzbar.In einem zweiten Schritt werden Gebietsniederschlagssummen, Gebietstemperaturen und simulierte Mittelwerte des Durchflusses (MQ) des Ist-Zustandes mit den Zuständen zweier Klimaszenarien für den Szenarienzeitraum 100 Jahre später (2061-2099) verglichen. Die Klimaszenarien beruhen auf simulierten Zirkulationsmustern je eines Modellaufes zweier Globaler Zirkulationsmodelle (GCM), die mit einem statistischen Regionalisierungsverfahren in Tageswertszenarien (Temperatur, Niederschlag) an Meßstationen in den Untersuchungsgebieten überführt wurden und als Eingangsdaten des hydrologischen Modells verwendet werden.Für die zweite Hälfte des 21. Jahrhunderts weisen beide regionalisierten Klimaszenarien eine Zunahme der Jahresmittel der Gebietstemperatur sowie eine Zunahme der Jahressummen der Gebietsniederschläge auf, die mit einer hohen Variabilität einhergeht. Eine Betrachtung der saisonalen (monatlichen) Änderungsbeträge von Temperatur, Niederschlag und mittlerem Durchfluß zwischen Szenarienzeitraum (2061-2099) und Ist-Zustand ergibt in allen Untersuchungsgebieten eine Temperaturzunahme (höher im Sommer als im Winter) und eine generelle Zunahme der Niederschlagssummen (mit starken Schwankungen zwischen den Einzelmonaten), die bei der hydrologischen Simulation zu deutlich höheren mittleren Durchflüssen von November bis März und leicht erhöhten mittleren Durchflüssen in den restlichen Monaten führen. Die Stärke der Durchflußerhöhung ist nach den individuellen Klimaszenarien unterschiedlich und im Sommer- bzw. Winterhalbjahr gegenläufig ausgeprägt. Hauptursache für die simulierte starke Zunahme der mittleren Durchflüsse im Winterhalbjahr ist die trotz Temperaturerhöhung der Klimaszenarien winterlich niedrige Evapotranspiration, so daß erhöhte Niederschläge direkt in erhöhten Durchfluß transformiert werden können.Der Vergleich der Untersuchungsgebiete zeigt in Einzelmonaten von West nach Ost abnehmende Änderungsbeträge der Niederschlagssummen, die als Hinweis auf die Bedeutung der Kontinentalitätseinflüsse auch unter geänderten klimatischen Bedingungen in Südwestdeutschland aufgefaßt werden könnten.Aus den regionalisierten Klimaszenarien werden Änderungsbeträge für die Modulation gemessener Zeitreihen mittels synthetischer Szenarien abgeleitet, die mit einem geringen Rechenaufwand in hydrologische Modellantworten überführt werden können. Die direkte Ableitung synthetischer Szenarien aus GCM-Ergebniswerten (bodennahe Temperatur und Gesamtniederschlag) an einzelnen GCM-Gitterpunkten erbrachte unbefriedigende Ergebnisse.Ob, in welcher Höhe und zeitlichen Verteilung die in den (synthetischen) Szenarien verwendeten Niederschlags- und Temperaturänderungen eintreten werden, kann nur die Zukunft zeigen. Eine Abschätzung, wie sich die Abflußverhältnisse und insbesondere die mittleren Durchflüsse der Untersuchungsgebiete bei möglichen Änderungen entwickeln würden, kann jedoch heute schon vorgenommen werden. Simulationen auf Szenariogrundlagen sind ein Weg, unbekannte zukünftige Randbedingungen sowie regionale Auswirkungen möglicher Änderungen des Klimasystems ausschnittsweise abzuschätzen und entsprechende Risikominderungsstrategien zu entwickeln. Jegliche Modellierung und Simulation natürlicher Systeme ist jedoch mit beträchtlichen Unsicherheiten verknüpft. Vergleichsweise große Unsicherheiten sind mit der zukünftigen Entwicklung des sozioökonomischen Systems und der Komplexität des Klimasystems verbunden. Weiterhin haben Unsicherheiten der einzelnen Modellbausteine der Modellkette Emissionsszenarien/Gaszyklusmodelle - Globale Zirkulationsmodelle/Regionalisierung - hydrologisches Modell, die eine Kaskade der Unsicherheiten ergeben, neben Datenunsicherheiten bei der Erfassung hydrometeorologischer Meßgrößen einen erheblichen Einfluß auf die Vertrauenswürdigkeit der Simulationsergebnisse, die als ein dargestellter Wert eines Ergebnisbandes zu interpretieren sind.Der Einsatz (1) robuster hydrologischer Modelle, die insbesondere temperaturbeeinflußte Prozesse adäquat beschreiben,(2) die Verwendung langer Zeitreihen (wenigsten 30 Jahre) von Meßwerten und(3) die gleichzeitige vergleichende Betrachtung von Klimaszenarien, die auf unterschiedlichen GCMs beruhen (und wenn möglich, verschiedene Emissionsszenarien berücksichtigen),sollte aus Gründen der wissenschaftlichen Sorgfalt, aber auch der besseren Vergleichbarkeit der Ergebnisse von Regionalstudien im noch jungen Forschungsfeld der Klimafolgenforschung beachtet werden.
Iron-sulfur clusters are essential enzyme cofactors. The most common and stable clusters are [2Fe-2S] and [4Fe-4S] that are found in nature. They are involved in crucial biological processes like respiration, gene regulation, protein translation, replication and DNA repair in prokaryotes and eukaryotes. In Escherichia coli, Fe-S clusters are essential for molybdenum cofactor (Moco) biosynthesis, which is a ubiquitous and highly conserved pathway. The first step of Moco biosynthesis is catalyzed by the MoaA protein to produce cyclic pyranopterin monophosphate (cPMP) from 5’GTP. MoaA is a [4Fe-4S] cluster containing radical S-adenosyl-L-methionine (SAM) enzyme. The focus of this study was to investigate Fe-S cluster insertion into MoaA under nitrate and TMAO respiratory conditions using E. coli as a model organism. Nitrate and TMAO respiration usually occur under anaerobic conditions, where oxygen is depleted. Under these conditions, E. coli uses nitrate and TMAO as terminal electron. Previous studies revealed that Fe-S cluster insertion is performed by Fe-S cluster carrier proteins. In E. coli, these proteins are known as A-type carrier proteins (ATC) by phylogenomic and genetic studies. So far, three of them have been characterized in detail in E. coli, namely IscA, SufA, and ErpA. This study shows that ErpA and IscA are involved in Fe-S cluster insertion into MoaA under nitrate and TMAO respiratory conditions. ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. SufA is not able to replace the functions of IscA or ErpA under nitrate respiratory conditions.
Nitrate reductase is a molybdoenzyme that coordinates Moco and Fe-S clusters. Under nitrate respiratory conditions, the expression of nitrate reductase is significantly increased in E. coli. Nitrate reductase is encoded in narGHJI genes, the expression of which is regulated by the transcriptional regulator, fumarate and nitrate reduction (FNR). The activation of FNR under conditions of nitrate respiration requires one [4Fe-4S] cluster. In this part of the study, we analyzed the insertion of Fe-S cluster into FNR for the expression of narGHJI genes in E. coli. The results indicate that ErpA is essential for the FNR-dependent expression of the narGHJI genes, a role that can be replaced partially by IscA and SufA when they are produced sufficiently under the conditions tested. This observation suggests that ErpA is indirectly regulating nitrate reductase expression via inserting Fe-S clusters into FNR.
Most molybdoenzymes are complex multi-subunit and multi-cofactor-containing enzymes that coordinate Fe-S clusters, which are functioning as electron transfer chains for catalysis. In E. coli, periplasmic aldehyde oxidoreductase (PaoAC) is a heterotrimeric molybdoenzyme that
consists of flavin, two [2Fe-2S], one [4Fe-4S] cluster and Moco. In the last part of this study, we investigated the insertion of Fe-S clusters into E. coli periplasmic aldehyde oxidoreductase (PaoAC). The results show that SufA and ErpA are involved in inserting [4Fe-4S] and [2Fe-2S] clusters into PaoABC, respectively under aerobic respiratory conditions.
In this thesis, I examine different A-bar movement dependencies in Igbo, a Benue-Congo language spoken in southern Nigeria. Movement dependencies are found in constructions where an element is moved to the left edge of the clause to express information-structural categories such as in questions, relativization and focus. I show that these constructions in Igbo are very uniform from a syntactic point of view. The constructions are built on two basic fronting operations: relativization and focus movement, and are biclausal. I further investigate several morphophonological effects that are found in these A-bar constructions. I propose that these effects are reflexes of movement that are triggered when an element is moved overtly in relativization or focus. This proposal helps to explain the tone patterns that have previously been assumed to be a property of relative clauses. The thesis adds to the growing body of tonal reflexes of A-bar movement reported for a few African languages. The thesis also provides an insight into the complementizer domain (C-domain) of Igbo.
A water quality model for shallow river-lake systems and its application in river basin management
(2007)
This work documents the development and application of a new model for simulating mass transport and turnover in rivers and shallow lakes. The simulation tool called 'TRAM' is intended to complement mesoscale eco-hydrological catchment models in studies on river basin management. TRAM aims at describing the water quality of individual water bodies, using problem- and scale-adequate approaches for representing their hydrological and ecological characteristics. The need for such flexible water quality analysis and prediction tools is expected to further increase during the implementation of the European Water Framework Directive (WFD) as well as in the context of climate change research. The developed simulation tool consists of a transport and a reaction module with the latter being highly flexible with respect to the description of turnover processes in the aquatic environment. Therefore, simulation approaches of different complexity can easily be tested and model formulations can be chosen in consideration of the problem at hand, knowledge of process functioning, and data availability. Consequently, TRAM is suitable for both heavily simplified engineering applications as well as scientific ecosystem studies involving a large number of state variables, interactions, and boundary conditions. TRAM can easily be linked to catchment models off-line and it requires the use of external hydrodynamic simulation software. Parametrization of the model and visualization of simulation results are facilitated by the use of geographical information systems as well as specific pre- and post-processors. TRAM has been developed within the research project 'Management Options for the Havel River Basin' funded by the German Ministry of Education and Research. The project focused on the analysis of different options for reducing the nutrient load of surface waters. It was intended to support the implementation of the WFD in the lowland catchment of the Havel River located in North-East Germany. Within the above-mentioned study TRAM was applied with two goals in mind. In a first step, the model was used for identifying the magnitude as well as spatial and temporal patterns of nitrogen retention and sediment phosphorus release in a 100~km stretch of the highly eutrophic Lower Havel River. From the system analysis, strongly simplified conceptual approaches for modeling N-retention and P-remobilization in the studied river-lake system were obtained. In a second step, the impact of reduced external nutrient loading on the nitrogen and phosphorus concentrations of the Havel River was simulated (scenario analysis) taking into account internal retention/release. The boundary conditions for the scenario analysis such as runoff and nutrient emissions from river basins were computed by project partners using the catchment models SWIM and ArcEGMO-Urban. Based on the output of TRAM, the considered options of emission control could finally be evaluated using a site-specific assessment scale which is compatible with the requirements of the WFD. Uncertainties in the model predictions were also examined. According to simulation results, the target of the WFD -- with respect to total phosphorus concentrations in the Lower Havel River -- could be achieved in the medium-term, if the full potential for reducing point and non-point emissions was tapped. Furthermore, model results suggest that internal phosphorus loading will ease off noticeably until 2015 due to a declining pool of sedimentary mobile phosphate. Mass balance calculations revealed that the lakes of the Lower Havel River are an important nitrogen sink. This natural retention effect contributes significantly to the efforts aimed at reducing the river's nitrogen load. If a sustainable improvement of the river system's water quality is to be achieved, enhanced measures to further reduce the immissions of both phosphorus and nitrogen are required.
This thesis discusses challenges in IT security education, points out a gap between e-learning and practical education, and presents a work to fill the gap. E-learning is a flexible and personalized alternative to traditional education. Nonetheless, existing e-learning systems for IT security education have difficulties in delivering hands-on experience because of the lack of proximity. Laboratory environments and practical exercises are indispensable instruction tools to IT security education, but security education in conventional computer laboratories poses particular problems such as immobility as well as high creation and maintenance costs. Hence, there is a need to effectively transform security laboratories and practical exercises into e-learning forms. In this thesis, we introduce the Tele-Lab IT-Security architecture that allows students not only to learn IT security principles, but also to gain hands-on security experience by exercises in an online laboratory environment. In this architecture, virtual machines are used to provide safe user work environments instead of real computers. Thus, traditional laboratory environments can be cloned onto the Internet by software, which increases accessibility to laboratory resources and greatly reduces investment and maintenance costs. Under the Tele-Lab IT-Security framework, a set of technical solutions is also proposed to provide effective functionalities, reliability, security, and performance. The virtual machines with appropriate resource allocation, software installation, and system configurations are used to build lightweight security laboratories on a hosting computer. Reliability and availability of laboratory platforms are covered by a virtual machine management framework. This management framework provides necessary monitoring and administration services to detect and recover critical failures of virtual machines at run time. Considering the risk that virtual machines can be misused for compromising production networks, we present a security management solution to prevent the misuse of laboratory resources by security isolation at the system and network levels. This work is an attempt to bridge the gap between e-learning/tele-teaching and practical IT security education. It is not to substitute conventional teaching in laboratories but to add practical features to e-learning. This thesis demonstrates the possibility to implement hands-on security laboratories on the Internet reliably, securely, and economically.
A task-based parallel elliptic solver for numerical relativity with discontinuous Galerkin methods
(2022)
Elliptic partial differential equations are ubiquitous in physics. In numerical relativity---the study of computational solutions to the Einstein field equations of general relativity---elliptic equations govern the initial data that seed every simulation of merging black holes and neutron stars. In the quest to produce detailed numerical simulations of these most cataclysmic astrophysical events in our Universe, numerical relativists resort to the vast computing power offered by current and future supercomputers. To leverage these computational resources, numerical codes for the time evolution of general-relativistic initial value problems are being developed with a renewed focus on parallelization and computational efficiency. Their capability to solve elliptic problems for accurate initial data must keep pace with the increasing detail of the simulations, but elliptic problems are traditionally hard to parallelize effectively.
In this thesis, I develop new numerical methods to solve elliptic partial differential equations on computing clusters, with a focus on initial data for orbiting black holes and neutron stars. I develop a discontinuous Galerkin scheme for a wide range of elliptic equations, and a stack of task-based parallel algorithms for their iterative solution. The resulting multigrid-Schwarz preconditioned Newton-Krylov elliptic solver proves capable of parallelizing over 200 million degrees of freedom to at least a few thousand cores, and already solves initial data for a black hole binary about ten times faster than the numerical relativity code SpEC. I also demonstrate the applicability of the new elliptic solver across physical disciplines, simulating the thermal noise in thin mirror coatings of interferometric gravitational-wave detectors to unprecedented accuracy. The elliptic solver is implemented in the new open-source SpECTRE numerical relativity code, and set up to support simulations of astrophysical scenarios for the emerging era of gravitational-wave and multimessenger astronomy.
In Systems Medicine, in addition to high-throughput molecular data (*omics), the wealth of clinical characterization plays a major role in the overall understanding of a disease. Unique problems and challenges arise from the heterogeneity of data and require new solutions to software and analysis methods. The SMART and EurValve studies establish a Systems Medicine approach to valvular heart disease -- the primary cause of subsequent heart failure.
With the aim to ascertain a holistic understanding, different *omics as well as the clinical picture of patients with aortic stenosis (AS) and mitral regurgitation (MR) are collected. Our task within the SMART consortium was to develop an IT platform for Systems Medicine as a basis for data storage, processing, and analysis as a prerequisite for collaborative research. Based on this platform, this thesis deals on the one hand with the transfer of the used Systems Biology methods to their use in the Systems Medicine context and on the other hand with the clinical and biomolecular differences of the two heart valve diseases. To advance differential expression/abundance (DE/DA) analysis software for use in Systems Medicine, we state 21 general software requirements and features of automated DE/DA software, including a novel concept for the simple formulation of experimental designs that can represent complex hypotheses, such as comparison of multiple experimental groups, and demonstrate our handling of the wealth of clinical data in two research applications DEAME and Eatomics. In user interviews, we show that novice users are empowered to formulate and test their multiple DE hypotheses based on clinical phenotype. Furthermore, we describe insights into users' general impression and expectation of the software's performance and show their intention to continue using the software for their work in the future. Both research applications cover most of the features of existing tools or even extend them, especially with respect to complex experimental designs. Eatomics is freely available to the research community as a user-friendly R Shiny application.
Eatomics continued to help drive the collaborative analysis and interpretation of the proteomic profile of 75 human left myocardial tissue samples from the SMART and EurValve studies. Here, we investigate molecular changes within the two most common types of valvular heart disease: aortic valve stenosis (AS) and mitral valve regurgitation (MR). Through DE/DA analyses, we explore shared and disease-specific protein alterations, particularly signatures that could only be found in the sex-stratified analysis. In addition, we relate changes in the myocardial proteome to parameters from clinical imaging. We find comparable cardiac hypertrophy but differences in ventricular size, the extent of fibrosis, and cardiac function. We find that AS and MR show many shared remodeling effects, the most prominent of which is an increase in the extracellular matrix and a decrease in metabolism. Both effects are stronger in AS. In muscle and cytoskeletal adaptations, we see a greater increase in mechanotransduction in AS and an increase in cortical cytoskeleton in MR. The decrease in proteostasis proteins is mainly attributable to the signature of female patients with AS. We also find relevant therapeutic targets.
In addition to the new findings, our work confirms several concepts from animal and heart failure studies by providing the largest collection of human tissue from in vivo collected biopsies to date. Our dataset contributing a resource for isoform-specific protein expression in two of the most common valvular heart diseases. Apart from the general proteomic landscape, we demonstrate the added value of the dataset by showing proteomic and transcriptomic evidence for increased expression of the SARS-CoV-2- receptor at pressure load but not at volume load in the left ventricle and also provide the basis of a newly developed metabolic model of the heart.
A systems biological approach towards the molecular basis of heterosis in Arabidopsis thaliana
(2011)
Heterosis is defined as the superiority in performance of heterozygous genotypes compared to their corresponding genetically different homozygous parents. This phenomenon is already known since the beginning of the last century and it has been widely used in plant breeding, but the underlying genetic and molecular mechanisms are not well understood. In this work, a systems biological approach based on molecular network structures is proposed to contribute to the understanding of heterosis. Hybrids are likely to contain additional regulatory possibilities compared to their homozygous parents and, therefore, they may be able to correctly respond to a higher number of environmental challenges, which leads to a higher adaptability and, thus, the heterosis phenomenon. In the network hypothesis for heterosis, presented in this work, more regulatory interactions are expected in the molecular networks of the hybrids compared to the homozygous parents. Partial correlations were used to assess this difference in the global interaction structure of regulatory networks between the hybrids and the homozygous genotypes. This network hypothesis for heterosis was tested on metabolite profiles as well as gene expression data of the two parental Arabidopsis thaliana accessions C24 and Col-0 and their reciprocal crosses. These plants are known to show a heterosis effect in their biomass phenotype. The hypothesis was confirmed for mid-parent and best-parent heterosis for either hybrid of our experimental metabolite as well as gene expression data. It was shown that this result is influenced by the used cutoffs during the analyses. Too strict filtering resulted in sets of metabolites and genes for which the network hypothesis for heterosis does not hold true for either hybrid regarding mid-parent as well as best-parent heterosis. In an over-representation analysis, the genes that show the largest heterosis effects according to our network hypothesis were compared to genes of heterotic quantitative trait loci (QTL) regions. Separately for either hybrid regarding mid-parent as well as best-parent heterosis, a significantly larger overlap between the resulting gene lists of the two different approaches towards biomass heterosis was detected than expected by chance. This suggests that each heterotic QTL region contains many genes influencing biomass heterosis in the early development of Arabidopsis thaliana. Furthermore, this integrative analysis led to a confinement and an increased confidence in the group of candidate genes for biomass heterosis in Arabidopsis thaliana identified by both approaches.
Actin is one of the most highly conserved proteins in eukaryotes and distinct actin-related proteins with filament-forming properties are even found in prokaryotes. Due to these commonalities, actin-modulating proteins of many species share similar structural properties and proposed functions. The polymerization and depolymerization of actin are critical processes for a cell as they can contribute to shape changes to adapt to its environment and to move and distribute nutrients and cellular components within the cell. However, to what extent functions of actin-binding proteins are conserved between distantly related species, has only been addressed in a few cases. In this work, functions of Coronin-A (CorA) and Actin-interacting protein 1 (Aip1), two proteins involved in actin dynamics, were characterized. In addition, the interchangeability and function of Aip1 were investigated in two phylogenetically distant model organisms. The flowering plant Arabidopsis thaliana (encoding two homologs, AIP1-1 and AIP1-2) and in the amoeba Dictyostelium discoideum (encoding one homolog, DdAip1) were chosen because the functions of their actin cytoskeletons may differ in many aspects. Functional analyses between species were conducted for AIP1 homologs as flowering plants do not harbor a CorA gene.
In the first part of the study, the effect of four different mutation methods on the function of Coronin-A protein and the resulting phenotype in D. discoideum was revealed in two genetic knockouts, one RNAi knockdown and a sudden loss-of-function mutant created by chemical-induced dislocation (CID). The advantages and disadvantages of the different mutation methods on the motility, appearance and development of the amoebae were investigated, and the results showed that not all observed properties were affected with the same intensity. Remarkably, a new combination of Selection-Linked Integration and CID could be established.
In the second and third parts of the thesis, the exchange of Aip1 between plant and amoeba was carried out. For A. thaliana, the two homologs (AIP1-1 and AIP1-2) were analyzed for functionality as well as in D. discoideum. In the Aip1-deficient amoeba, rescue with AIP1-1 was more effective than with AIP1-2. The main results in the plant showed that in the aip1-2 mutant background, reintroduced AIP1-2 displayed the most efficient rescue and A. thaliana AIP1-1 rescued better than DdAip1. The choice of the tagging site was important for the function of Aip1 as steric hindrance is a problem. The DdAip1 was less effective when tagged at the C-terminus, while the plant AIP1s showed mixed results depending on the tag position. In conclusion, the foreign proteins partially rescued phenotypes of mutant plants and mutant amoebae, despite the organisms only being very distantly related in evolutionary terms.
Today, it is well known that galaxies like the Milky Way consist not only of stars but also of gas and dust. The galactic halo, a sphere of gas that surrounds the stellar disk of a galaxy, is especially interesting. It provides a wealth of information about in and outflowing gaseous material towards and away from galaxies and their hierarchical evolution. For the Milky Way, the so-called high-velocity clouds (HVCs), fast moving neutral gas complexes in the halo that can be traced by absorption-line measurements, are believed to play a crucial role in the overall matter cycle in our Galaxy. Over the last decades, the properties of these halo structures and their connection to the local circumgalactic and intergalactic medium (CGM and IGM, respectively) have been investigated in great detail by many different groups. So far it remains unclear, however, to what extent the results of these studies can be transferred to other galaxies in the local Universe. In this thesis, we study the absorption properties of Galactic HVCs and compare the HVC absorption characteristics with those of intervening QSO absorption-line systems at low redshift. The goal of this project is to improve our understanding of the spatial extent and physical conditions of gaseous galaxy halos in the local Universe. In the first part of the thesis we use HST /STIS ultraviolet spectra of more than 40 extragalactic background sources to statistically analyze the absorption properties of the HVCs in the Galactic halo. We determine fundamental absorption line parameters including covering fractions of different weakly/intermediately/highly ionized metals with a particular focus on SiII and MgII. Due to the similarity in the ionization properties of SiII and MgII, we are able to estimate the contribution of HVC-like halo structures to the cross section of intervening strong MgII absorbers at z = 0. Our study implies that only the most massive HVCs would be regarded as strong MgII absorbers, if the Milky Way halo would be seen as a QSO absorption line system from an exterior vantage point. Combining the observed absorption-cross section of Galactic HVCs with the well-known number density of intervening strong MgII absorbers at z = 0, we conclude that the contribution of infalling gas clouds (i.e., HVC analogs) in the halos of Milky Way-type galaxies to the cross section of strong MgII absorbers is 34%. This result indicates that only about one third of the strong MgII absorption can be associated with HVC analogs around other galaxies, while the majority of the strong MgII systems possibly is related to galaxy outflows and winds. The second part of this thesis focuses on the properties of intervening metal absorbers at low redshift. The analysis of the frequency and physical conditions of intervening metal systems in QSO spectra and their relation to nearby galaxies offers new insights into the typical conditions of gaseous galaxy halos. One major aspect in our study was to regard intervening metal systems as possible HVC analogs. We perform a detailed analysis of absorption line properties and line statistics for 57 metal absorbers along 78 QSO sightlines using newly-obtained ultraviolet spectra obtained with HST /COS. We find clear evidence for bimodal distribution in the HI column density in the absorbers, a trend that we interpret as sign for two different classes of absorption systems (with HVC analogs at the high-column density end). With the help of the strong transitions of SiII λ1260, SiIII λ1206, and CIII λ977 we have set up Cloudy photoionization models to estimate the local ionization conditions, gas densities, and metallicities. We find that the intervening absorption systems studied by us have, on average, similar physical conditions as Galactic HVC absorbers, providing evidence that many of them represent HVC analogs in the vicinity of other galaxies. We therefore determine typical halo sizes for SiII, SiIII, and CIII for L = 0.01L∗ and L = 0.05L∗ galaxies. Based on the covering fractions of the different ions in the Galactic halo, we find that, for example, the typical halo size for SiIII is ∼ 160 kpc for L = 0.05L∗ galaxies. We test the plausibility of this result by searching for known galaxies close to the QSO sightlines and at similar redshifts as the absorbers. We find that more than 34% of the measured SiIII absorbers have galaxies associated with them, with the majority of the absorbers indeed being at impact parameters ρ ≤160 kpc.