Universität Stuttgart
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Item Open Access Dimensions of proximity and localisation of knowledge-intensive producer services : the case of software services for automotive industry in Stuttgart region(2009) Tözün, Reha; Gaebe, Wolf (Prof. Dr. rer. pol.)This thesis primarily examines the spatiality of knowledge-intensive producer services within the framework of knowledge tacitness and aspatial proximities notions. Additionally, based on an example of a West-European location, it links aspatial proximities and regional structural change discourses and explores the significance of lead firms for regional agglomerations. Globalization operates on the significantly lowered trade barriers and mobility of goods, persons and information. In such an environment, knowledge-production and innovation are critical elements of industrial competitiveness, especially for developed countries in Western Europe. As it has been suggested since late 1980's, innovation has a strong interactive component and the knowledge-creation processes tend to localize geographically. However, such processes are do function over geographical distance as well; therefore one needs to consider the non-geographical influences to understand the dynamics involved. The aspatial proximities, which are categorized by Boschma along cognitive, social, organisational and institutional dimensions, provide an intriguing framework to handle the issues regarding the spatiality of knowledge-producing relations between economic actors. Despite the awareness regarding the role of interaction, theories on regional agglomeration phenomenon tend to be more attentive to the supply-side matters. However, the impulses and incentives from demand side do co-define the direction and extent of knowledge production efforts. With the important roles it assigns to local demand and customers, Porter's industrial clusters concept offers a theoretical background for the research interests of this study. Beside aspatial proximities and industrial clusters, this thesis draws on learning regions, long-waves of technological change and regional structural change literatures for its framework of analysis. For the empirical investigation software services for automotive industry in the Stuttgart region were selected. In-depth interviews with regional experts were adopted for the purposes of data collection. The knowledge-intensive producer services relations fundamentally depend on application- and customer-specific knowledge, which is often change-prone and not market-traded. The study revealed that the well-maintained aspatial proximities allow service providers to have sustained access to such knowledge. It was also found that the creation and maintenance of aspatial proximities is related to the availability of spatial proximity between actors and groups. As such, geographical space has a subtle and indirect effect on knowledge production in that it influences cognitive, social and organisational space through which knowledge is generated and shared. The management of aspatial proximities is also a crucial factor for the path-dependant agglomeration of services activities around existing production locations. The study also found out that the coordination challenges induced by the cognitive dynamics of knowledge-production processes strongly affect the spatial proximity requirements of interactive relations. Cognitive dynamics is defined by the tacitness of knowledge content and the processes characteristics. While tacitness creates the need for face-to-face exchanges, time constraints and interfaces between knowledge-production processes compel actors to have more frequent meetings. Under conditions where highly tacit knowledge content has to be co-produced and shared in short time intervals across numerous processes run by different teams, groups of actors are compelled to engage in more frequent face-to-face interaction in order to avoid knowledge mismatches and miscomprehension. As such, the serviceability of such relations decreases with distance and increasing geographical space between partners escalates transaction costs, which in return impels parties to locate near each other. However, the codifiability of knowledge content and the manageability of processes change these dynamics and spatial proximity becomes a choice rather than a requirement. Provided that their operations contain active technology-oriented and knowledge-production functions, lead firms can act as the nodes of regional knowledge-production networks in clusters. The evidence collected for this study suggests that besides acting as demanding local customers à la Porter, they actively co-develop innovations and enrich knowledge capital of a cluster.Item Open Access Development of artificial single and double reading domains to analyze chromatin modification patterns(2018) Mauser, Rebekka; Jeltsch, Albert (Prof. Dr.)The unstructured N-terminal tails of histone proteins carry many different post-translational modifications (PTMs), like methylation, acetylation or phosphorylation. These PTMs can alter the chromatin structure, influence the interaction of adjacent nucleosomes and serve as specific binding sites for histone interacting domains. Currently, the investigation of histone tail PTMs is mainly based on antibodies, however concerns about the specificity of these antibodies and reproducibility of data arouse. Therefore, it was one aim of this thesis to develop alternative approaches to histone tail PTM antibodies. Previous studies already showed that histone modification interacting domains (HiMIDs) can replace histone tail antibodies in a highly effective manner. As part of this work, the TAF3 PHD domain was established as new H3K4me3 specific HiMID. In peptide array binding and Far-western blot assays, the domain showed a specific interaction with H3K4me3 modifications. Also in ChIP like experiments (CIDOP: Chromatin Interacting Domain Precipitation) coupled to qPCR and next generation sequencing, the domain showed a similar performance as validated H3K4me3 antibodies. With the proposal of the histone code hypothesis the question was raised if combinations of histone modifications carry specific biological functions. However, so far, the experimental analysis of the co-occurrence of histone modification on the same nucleosome in a genome-wide manner is a challenging task. For this reason, the main aim of this work was to develop double reading domains in which two histone reading domains are fused together with a flexible linker to achieve simultaneously readout of dual histone tail modifications in a single CIDOP experiment. To validate the concept, the Dnmt3a PWWP domain and the MPP8 Chromo domain were fused together and their specific recognitions of H3K36me2/3 and H3K9me3 histone tail modifications were analyzed. Biochemical investigations like peptide arrays, Far-western blot and western blot experiments showed that both domains specifically interact with their targets and preferentially interact with double modified chromatin. Additionally, the preferred interaction with double modified chromatin could be further verified with binding pocket mutants and methyl-lysine analogues. The newly generated double domain was used in chromatin precipitation experiments to identify genome regions where both modifications are present. The genome-wide distribution of the H3K36me2/3-H3K9me3 showed that this combination of histone marks represents a novel bivalent chromatin state, which is associated with weakly transcribed genes and is enriched for binding sites of ZNF274 and SetDB1. Also in this work, mixed peptide arrays were introduced as new screening method for the efficient analysis of double reading domains. The naturally occurring double reading domain of the BPTF protein was used to demonstrate the capability of this new screening tool. BPTF contains a PHD domain, which binds to H3K4me3 and a Bromo domain, which interacts with acetyl groups of the H4 tail. Synergistic binding to both peptides was shown using the newly developed mixed peptide arrays. Additionally, in the course of this work mixed peptide arrays were used to optimize several of the designed double reading domains. Furthermore, some other double reading domains were generated in this work, like PWWP-ATRX, MPP8 Chromo domain-L-double Tudor and CBX7 Chromo domain-L-MPP8 Chromo domain and analyzed for specific dual readout. Also double reading domains with dual specificity for DNA methylation and histone marks were generated. The firstly used methyl-DNA binding domain of the MBD2 protein showed a strong binding, dominating the effect of the HiMIDs. Therefore, the weaker but still specific methyl-DNA binding domain of the MBD1 protein was used. First experiments with this new fusion constructs showed a simultaneously interaction with chromatin which is associated with DNA methylation and histone PTMs. In summary, the studies with double reading domains showed that with this novel method precipitation of double modified chromatin is possible and that the genome-wide investigation of newly studied bivalent chromatin states is feasible. Therefore, this novel approach makes it possible to analyze many different combinations of histone modifications, investigate their influence on chromatin and gain a deeper understanding of the biological role behind histone tail modification patterns.Item Open Access High order interactions among environmental variables : diagnostics and initial steps towards modeling(2013) Rodríguez Fernández, Jhan Ignacio; Bárdossy, András (Prof. Dr. rer. nat. Dr.-Ing.)In the field of geostatistics and spatial statistics, variogram based models have proved a very flexible and useful tool. However, such spatial models take into account only interdependencies between pairs of variables, mostly in the form of covariances. In the present work, we point out to the necessity to extend the interdependence models beyond covariance modeling; we summarize some of the difficulties arising when attempting such extensions; and propose an approach to address these difficulties.Item Open Access Die Quellstärke in der Sickerwasserprognose : Möglichkeiten und Grenzen von Labor- und Freilanduntersuchungen(2010) Mackenberg, Sylvia; Metzger, Jörg W. (Prof. Dr. rer. nat. habil.)Den Umgang mit kontaminierten Böden und Standorten im Rahmen des Boden- und Grundwasserschutzes regeln in Deutschland das Bundes-Bodenschutzgesetz und die Bundes-Bodenschutz- und Altlastenverordnung (BBodSchV). Die Durchführung einer Sickerwasserprognose dient der Gefährdungsabschätzung einer Grundwasserkontamination durch Bodenbelastungen. Gemäß der BBodSchV umfasst sie Untersuchungen zur Mobilisierbarkeit von Stoffen durch das Bodensickerwasser sowie eine Transportbetrachtung der gelösten Stoffe bis zum Ort der Beurteilung, die Grenze zwischen der ungesättigten und der gesättigten Bodenzone. Neben dieser bundesweit geltenden Verordnung existieren landesinterne Regelungen sowie Verfahrensvorschläge in der Baustoffbranche zum Umgang mit Baustoff und Recyclingprodukten. Allen Fragestellungen gemein ist die Abschätzung der im Sickerwasser gelösten Stoffkomponenten sowie ihrer Konzentrationen nach dem Passieren eines kontaminierten Materials, was als Quellstärke bezeichnet wird. Ziel der vorliegenden Arbeit war es, Aussagen über die Vergleichbarkeit der in diesen Testverfahren erzielbaren Ergebnisse abzuleiten. Weiterhin stand die potenzielle Übertragbarkeit von Ergebnissen, die in Laborversuchen zur Bestimmung der Quellstärke im Rahmen einer Sickerwasserprognose ermittelt werden, auf reale Verhältnisse im Fokus der Untersuchungen. Basierend auf einer Beurteilung der Praxisrelevanz der einzelnen Laborverfahren sollte abschließend ein Verfahrensvorschlag zur Bestimmung der Quellstärke erarbeitet werden: In Batchversuchen wurden der Einfluss des Wasser-Feststoffverhältnisses (WFV) auf die qualitative und quantitative stoffliche Zusammensetzung des Eluats sowie die potenzielle Mobilisierbarkeit von Schadstoffe untersucht. Die Erhöhung des WFV bei anorganischen Stoffkomponenten führte in der Regel zu einer Verringerung der Stoffkonzentration. Im Gegensatz dazu wurden bei Materialien, die mit polycyclischen aromatischen Kohlenwasserstoffen (PAK) kontaminiert waren, unabhängig vom jeweiligen WFV immer konstante PAK-Konzentrationen gemessen. Vergleichbare Ergebnisse wurden in Laborsäulenversuchen bei voller Wassersättigung erzielt. Aufgetragen über das WFV nehmen die Konzentrationen der meisten anorganischen Stoffkomponenten bei stationären Versuchsbedingungen mit zunehmender Versuchsdauer ab. Die PAK-Konzentrationen wiesen konstante Werte auf. Im Rahmen der Untersuchungen zum Einfluss der Schichthöhe wurde die absolute Kontaktzeit zwischen dem Eluat und dem Untersuchungsmaterial (Aufenthaltsdauer des Eluats in der Säule) variiert. Bei gleichem WFV entstanden keine Konzentrationsunterschiede aufgrund einer größeren Schichthöhe. Auch die Verringerung der Flussrate und damit eine Erhöhung der spezifischen Kontaktzeit (direkter Kontakt zwischen Eluat und Bodenmatrix pro Wegstrecke) führte bei anorganischen Schadstoffen nur in wenigen Fällen zu einer Konzentrationsänderung. Für PAK wurden unterschiedliche Ergebnisse in Abhängigkeit des pH-Werts erzielt. Bei einem pH-Wert von 8 wurde eine Konzentrationsabnahme um mehrere Größenordnungen registriert, bei einem pH-Wert von 12 zeigte sich keine Änderung der Konzentration. Diese Unterschiede wurden auf mikrobiologische Aktivität bei einem pH-Wert von 8 zurückgeführt, die in einem basischen Milieu weitestgehend unterbunden wird. Um die Übertragbarkeit der Ergebnisse von Laboruntersuchungen auf Feldsituationen beurteilen zu können, wurden Versuche mit Laborlysimetern und Freilandsäulen unter Teilsättigung durchgeführt. Für PAK führen Laborversuche häufig zu einer Überschätzung des Gefährdungspotenzials, da ein biologischer Abbau bei vollständiger Wassersättigung stark gehemmt wird. Die im Labor ermittelten Konzentrationen anorganischer Stoffkomponenten stimmten größenordnungsmäßig mit den Konzentrationen der Freilandversuche überein. Infolge natürlich wechselnder Niederschläge und Temperaturschwankungen wichen die im Freiland gemessenen Konzentrationen bei gleichem WFV immer wieder von den Konzentrationen der Laborversuche unter stationären Bedingungen ab. Basierend auf den Ergebnissen der Untersuchungen wurde ein Vorschlag für ein praktisches Verfahren zur Bestimmung der Quellstärke ausgearbeitet, der die Aspekte Wirtschaftlichkeit und Praktikabilität der Durchführung, insbesondere im Hinblick auf eine akzeptable Versuchsdauer, vereint. Das stufenweise Vorgehen unterscheidet zwischen Materialien die mit anorganischen Schadstoffen bzw. Materialien die mit PAK belastet sind. Zu Beginn der Quellstärkebestimmung von Materialien mit anorganischen Schadstoffen stehen einfache Batchversuche. In Abhängigkeit der daraus erzielbaren Ergebnisse folgen gegebenenfalls Laborsäulenuntersuchungen mit variierbaren Fließbedingungen. Die Quellstärke PAK-haltiger Materialien wird in Abhängigkeit ihres jeweiligen pH-Werts ebenfalls anhand einfacher Batchversuche oder anhand von aufwändigeren Laborsäulenuntersuchungen mit einer Wasserteilsättigung der eingebauten Materialschicht ermittelt.Item Open Access Synthese und Charakterisierung von amphipolaren Blockcopolymeren und Untersuchung des Phasenverhaltens in Mischungen mit Polypropylen(2012) Curcic, Tamar; Eisenbach, Claus Dieter (Prof. Dr. )Um Polypropylen (PP) / Polyamid (PA)-Mehrschichtfolien mit verbesserten mechanischen, optischen und permeationstechnischen Eigenschaften ohne Verwendung von speziellen Haftvermittlerschichten herzustellen, wurden Diblockcopolymere eingesetzt. Diese können dem PP und/oder PA in einem Zweischneckenextruder als Additiv zugemisch werden. Bei diesem Konzept wird versucht, die Grenzflächenspannung an der PP/PAGrenzfläche herabzusetzen und dadurch nach der Zusammenführung der einzelnen Schichten eine Verbundhaftung zu erzielen. Da die Blendmorphologie die Eigenschaften der Materialien entscheidend beeinflusst, sollten zuerst das Phasenverhalten der PP / HV Blends sowie die Anreicherung der Blockcopolymere an der PP-Oberfläche untersucht werden. Ziel dieser Arbeit war es, das thermische Verhalten, das Phasenverhalten sowie die Oberflächeneigenschaften von Blends, bestehend aus PP und Blockcopolymeren Poly((ethylen-alt-propylen)-b-oxyethylen) (PEP-PEO), mit unterschiedlichen Blocklängenverhältniss zu untersuchen. Zu diesem Zweck wurden amphiphile Blockcopolymere PEP-PEO als Modelladditive mit definiertem Molekulargewicht und Blocklängenverhältnis des Poly(oxyethylen)- und C2-verzweigten Polyethylenblocks hergestellt und charakterisiert. Die Synthese des Blockcopolymers Poly((ethylen-alt-propylen)-b-oxyethylen) erfolgte durch anionische Polymerisation von Isopren und Ethylenoxid. Die Synthese stellte eine dreistufige Reaktion dar. Im ersten Schritt wurde Isopren polymerisiert. Danach wurde der Isoprenblock hydriert und im letzten Schritt wurde der Ethylenoxidblock aufgebaut. So hat man die Möglichkeit, die sequenzielle Analytik betreiben zu können und dazu noch die Verträglichkeit von PEP-Blöcken unterschiedlichen Molmassen mit Polypropylen zu prüfen. Die Versuche zur Bestimmung der Verträglichkeit von PP und PEP haben gezeigt, dass PEP mit Mn= 5000 nur bedingt in Polypropylen löslich ist. Hingegen zeigt PEP mit Mn=15000 uneingeschränkte Löslichkeit mit Polypropylen. PP/PEP(Mn=5000)-Blends waren ab 8 Gew. % an Blockcopolymerantel brüchig und trüb. Blends bestehend aus PP und PEP(Mn=15000 g/Mol) waren hingegen bis einschliesslich 20 Gew % an BP-Anteil durchsichtig und elastisch. Da Bulk- und Oberflächeneigenschaften im engen Zusammenhang stehen, wurden die PP/BP-Blends hinsichtlich dieser Eigenschaften charakterisiert. Für Bulkeigenschaften wurde das Mischungsverhalten der Blends mittels Wärmeflusskalorimetrie (DSC) untersucht. Für die Charakterisierung der Oberflächeneigenschaften kamen oberflächensensitive Methoden wie IRSpektroskopie mit ATR-Technik und Benetzungsanalyse zum Einsatz. Außerdem wurden wärmeflußkalorimetrische (DSC) und schmelzrheologische Studien für die Bestimmung des Phasenverhaltens der Systeme unter dynamischen Bedingungen eingesetzt. Am Beispiel des Blendsystems PP/PEP-PEO ist die Gültigkeit des Zeit-Temperatur-Superpositionsprinzips exemplarisch für die untersuchten Blends in dieser Arbeit untersucht worden. Die Analyse zeigt, dass das Modellblendsystem PP/BP-2b das Zeit-Temperatur-Superpositionsprinzip mit zunehmendem Diblockcopolymergehalt immer weniger erfüllt. Die Interpretation der Messergebnisse lässt sich auf Grundlage der Perkolationstheorie erklären. Beim Auftragen des Speichermoduls gegenüber dem Gewichtsanteil an Blockcopolymer resultierte eine Kurve, die sich mit Hilfe der error Funktion komplett wiedergeben ließ. Dieses Ergebnis lässt den Schluss zu, dass bei den untersuchten Polymerblends die beobachtete Änderung des Speichermoduls als Perkolationseffekt zu deuten ist und der Verlauf der Kurve den Perkolationsgesetzmäßigkeiten folgt. Der beobachtete Effekt korreliert sehr gut mit den in Kap. 7 erläuterten Abhängigkeiten des Phasenverhaltens von Blockcopolymergehalt im Blend.Item Open Access Biochemical characterisation of tRNA-Asp methyltransferase Dnmt2 and its physiological significance(2014) Shanmugam, Raghuvaran; Jeltsch, Albert (Prof. Dr.)Methylation of tRNA plays important roles in the stabilisation of tRNAs and accurate protein synthesis in cells. In eukaryotes various tRNA methyltransferases exist, among them DNMT2 which methylates tRNAAsp at position C38 in the anticodon loop. It is also called tRNA-aspartate methyltransferase 1 (Trdmt1) and the enzyme is highly conserved among eukaryotes. In this work, I investigated the mechanism of DNMT2 interaction with tRNAAsp, characterised the function of the only prokaryotic Dnmt2 homolog found in G. sulfurreducens and studied the physiological importance of the C38 methylation of tRNAAsp in mammalian cells. The molecular details of the interaction of DNMT2 and tRNAAsp are unknown due to lack of the co-crystal structure. Here, I characterised the important residues in DNMT2 required for the tRNA binding and catalysis. By site-directed mutagenesis of 20 conserved lysine and arginine residues in DNMT2, I show that 8 of them have a strong effect on the catalytic activity of the enzyme. They map to one side of the enzyme where the catalytic pocket of DNMT2 is located. The binding of most of the mutant enzymes to tRNA was unaffected suggesting a role of these residues in transition state stabilisation. Manual docking of tRNAAsp into the surface cleft decorated by the 8 residues suggested that DNMT2 interacts mainly with the anticodon stem/loop of tRNAAsp. In my second project, I characterised the function of Dnmt2 homolog found in G. sulfurreducens (GsDnmt2). Here, I show that GsDnmt2 methylates tRNAGlu more efficiently than tRNAAsp. I also report the molecular basis for the swapped substrate specificity of GsDnmt2 and show that the variable loops of G.sulfurreducens tRNAAsp and tRNAGlu of eukaryotes contain a -GG- dinucleotide which is not preferred by Dnmt2. Exchange of the variable loop of mouse tRNAAsp to that tRNAGlu led to dramatic decrease in the activity of human DNMT2. This identifies the variable loop of tRNA as a specificity determinant in the recognition by Dnmt2. In my final project, I investigated the physiological importance of the tRNAAsp C38 methylation in aminoacylation and cellular protein synthesis. Here, I report that C38 methylation enhances the rate of aspartylation on tRNAAsp by 4-5 folds. Concomitant with this, a decrease in the charging levels of tRNAAsp was observed in Dnmt2 knockout MEF cells, which also showed a reduced efficiency in the synthesis of proteins containing poly-Asp sequences. A gene ontology searches for proteins with poly-Asp sequences showed that a significant number of these proteins are associated with transcriptional regulation and gene expression functions. With this I propose that the mild phenotype observed with the Dnmt2 KO cells under stress condition could be correlated to a disregulation of protein synthesis.Item Open Access Enzymatic asymmetric dihydroxylation of alkenes(2016) Gally, Christine; Hauer, Bernhard (Prof. Dr.)The introduction of chirality into C=C double bonds is of special interest in organic synthesis. In particular, the catalytic asymmetric dihydroxylation (AD) of alkenes has attracted considerable attention due to the facile transformation of the chiral diol products into valuable derivatives. By chemical means, the metal-catalyzed AD of olefins provides both stereo- and regiospecific cis-diol moieties. Next to their toxicity, however, these metal catalysts can also lead to byproduct formation as a result of oxidative fission. In nature, Rieske non-heme iron oxygenases (ROs) represent promising biocatalysts for this reaction since they are the only enzymes known to catalyze the stereoselective formation of vicinal cis-diols in one step. ROs are key enzymes in the degradation of aromatic hydrocarbons and can target a wide variety of different arenes. Despite their broad substrate scope, limited data is available for the conversion of unnatural substrates by this class of enzymes. To explore their potential for alkene oxidation, three ROs were tested for the oxyfunctionalization of a set of structurally diverse olefins including linear and cyclic arene-substituted alkenes, cycloalkenes as well as several terpenes. Naphthalene- (NDO), benzene- (BDO) and cumene dioxygenases (CDO) from different Pseudomonas strains where selected as they are amongst the RO enzymes that have already been reported to catalyze the oxidation of a small number of olefins. The majority of compounds from the selected substrate panel could be converted by NDO, BDO or CDO and products were either isolated and identified by NMR analysis or using the authentic standards. Dependent on the substrate, allylic monohydroxylation was found in addition to the corresponding diol products, a reaction which is chemically still most reliably achieved by the use of SeO2 in stoichiometric amounts. However, having been evolved for the dihydroxylation of aromatic compounds, wild type ROs displayed low conversions (< 50%) and modest stereoselectivities (≤ 80% ee/de) for several of the tested olefins. To overcome these limitations, changes in the active site topology of RO catalysts were introduced. A single targeted point mutation that was identified based on sequence and structural comparisons with other members of the RO family proved to be sufficient to generate BDO and CDO variants displaying remarkable changes in regio- and stereoselectivity for various substrates. In particular biotransformations with CDO M232A gave excellent stereoselectivities (≥ 95% ee/de) and good activities (> 90%) also for linear alkenes, which have been reported to be challenging substrates for RO-catalyzed oxyfunctionalizations. Site-saturation mutagenesis at position 232 in CDO revealed a correlation between the steric demand of the amino acid side chain and its influence on regio- and/ or stereoselectivities for styrene and indene. While the wild type enzyme almost exclusively catalyzed the dihydroxylation of the aromatic ring, the regioselectivity was shifted with decreasing side chain size to the terminal vinyl group of styrene, yielding up to 96% of the alkene-1,2-diol. For cis-1,2-indandiol formation, enantiocomplementary enzymes could be generated, a fact further highlighting the importance of position 232 for the engineering of ROs. Moreover, site-saturation mutagenesis of additional residues in the substrate binding pocket of CDO (F278, I288, I336 and F378) identified further positions having an influence on selectivity and product formation for alkene oxidation. To proof the applicability of ROs for organic synthesis, semi-preparative scale biotransformations (70 mg) of selected substrates were performed with CDO M232A. Without further optimization of the reaction set-up, products were successfully isolated in > 30% yield. In addition, up-scaling of (R)-limonene hydroxylation to 4 L in a bioreactor with growing cells gave final isolated product titers of 0.4 g L-1 even though substrate volatility and product toxicity diminished the yield. In conclusion, these examples demonstrated that a single point mutation was sufficient to transform CDO wild type into an efficient catalyst, furthermore constituting the first example of the rational engineering of CDO and BDO enzymes for the oxyfunctionalization of a broad range of alkenes.Item Open Access Molecular dynamics simulations of Si, SiC and Si3N4 layered systems(2013) Prskalo, Alen-Pilip; Schmauder, Siegfried (Prof. Dr.)Experimental and empirical work in the field of nano-scale, functional multilayer coatings produced by physical (PVD) or chemical (CVD) vapor deposition are currently an object of international research. The research results have already been implemented in industrial products, however, the atomistic understanding of the underlying processes during deposition of these multilayer systems is still incomplete. In particular the correlation between the deposition parameters and the resulting coating structure needs further attention. To overcome the heuristic stage of the coating development and to facilitate targeted and efficient optimization of the coating structure and the resulting mechanical properties, a deeper understanding of the correlation between the substrate temperature, deposition rate and energy onto the growing coating structure is necessary. The same holds for the structure-properties correlation of these systems with a large number of interfaces as well as for the mechanical properties of individual layers. The aim of this work is the combination and mutual validation of modern molecular dynamics simulations (MD) with experimental methods of physical vapor deposition of silicon and silicon-based SiC- and Si3N4-protective coatings. This was done within the framework of the research project "Molecular dynamics modeling and validation of manufacturing and structure-property correlations of SiC/SiN nano laminates" funded by the German Research Foundation (DFG) and in a collaboration between the Institute for Materials Testing, Materials Science and Strength of Materials (IMWF) at the University of Stuttgart and the Institute for Applied Materials - Applied Materials Physics (IAM-AWP) at the Karlsruhe Institute of Technology (KIT). While molecular dynamics simulations were performed at the IMWF, experimental investigations took place at the IAM-AWP. Hereby, the results of MD studies served as input parameters for experimental investigations. In this way, time-consuming and expensive experimental investigations could be avoided, since only optimistic simulation predictions had to be verified experimentally. In return, the group at the IAM-AWP delivered experimental results which were used to validate the simulation model. In general, each experimental study was also represented by a MD simulation. Hence, the entire process of the coating deposition and characterization can be divided into three distinct stages: - Simulation and experimental investigation of the sputtering process of Si, SiC and Si3N4. - Simulation und experimental investigation of the deposition process of silicon substrates by Si, SiC and Si3N4. - Simulations and experimental characterisation of the correlation between the structure and properties of the deposited silicon and silicon-based SiC- and Si3N4- protective coatings.Item Open Access Hochfrequenzuntersuchungen an niedrigdimensionalen Supraleitern(2004) Thoms, Jürgen; Dressel, Martin (Prof. Dr.)Mit der BCS-Theorie lassen sich die Eigenschaften konventioneller Supraleiter sehr genau beschreiben. In unkonventionellen Supraleitern kann neben der Gestalt des Ordnungsparameters auch die Form des Paarungszustands von der klassischen Beschreibung abweichen: Im Unterschied zu den Singulett-Supraleitern mit einem Gesamtspin von Null ist hier ein Triplett-Supraleiter mit Gesamtspin Eins möglich. In den Bechgaard-Salzen und in Strontiumruthenat könnte diese exotische Form der Triplett-Supraleitung vorliegen. Die Frage nach der Natur und der Gestalt des Paarungszustands wird von der Frage nach der Vermittlung der Supraleitung begleitet. In den klassischen, konventionellen Supraleitern spielen Phononen die Rolle der Paarvermittler. Bei unkonventionellen Supraleitern können Spinfluktuationen oder andere Wechselwirkungen eine zusätzliche oder gar die alleinige Rolle der Paarvermittler spielen. Bei den in dieser Arbeit untersuchten Materialien handelt es sich um unkonventionelle Supraleiter mit stark anisotropen Eigenschaften. Sowohl die Gestalt des Ordnungsparameters als auch die Form des Paarungszustands der Materialien ist nicht eindeutig geklärt. Die untersuchten Materialien besitzen Sprungtemperaturen bis hinunter zu 1 K. Ihr supraleitender Zustand ist somit nicht mehr den optischen Messverfahren zugänglich. Untersuchungen der elektronischen Eigenschaften im niederfrequenten Bereich erfordern die Kontaktierung der Proben mittels Leitpasten, was die druckempfindlichen supraleitenden Eigenschaften beeinflussen kann. Bei Energien unterhalb 100 GHz bieten sich deshalb Messungen mit Mikrowellen an. Hochfrequenzmessungen in geschlossenen Resonatoren bringen den Vorteil der kontaktlosen Messung mit sich. Zudem können Kristalle untersucht werden, deren Ausdehnung deutlich unterhalb der Wellenlänge liegt. Vor allem bei organischen Materialien erwiesen sich kleine Einkristalle als qualitativ hochwertiger im Vergleich zu großen Proben. Im Resonator trifft die Strahlung mehrfach auf die Probe, was die Empfindlichkeit der Messungen an metallischen Materialien erhöht, die ohnehin nur wenig absorbieren. Zudem können beide Komponenten der komplexen optischen Parameter bestimmt werden, z.B. die komplexe Leitfähigkeit. Dies ermöglicht einerseits die Messung der Sprungtemperatur im Hochfrequenzbereich, andererseits kann über die Temperaturabhängigkeit der Eindringtiefe auf Nullstellen im Ordnungsparameter geschlossen werden. In der vorliegenden Arbeit wurde eine Messapparatur aufgebaut, mit der die komplexen Hochfrequenzeigenschaften sowie der spezifische Widerstand von anisotropen Materialien ermittelt werden können. Ein 3He-Kryostat erlaubt die Untersuchung bei Temperaturen zwischen 0,4 K und Raumtemperatur. Mit der Apparatur wurden unterschiedlich niedrigdimensionale Supraleiter analysiert: das quasi-eindimensionale Bechgaard-Salz (TMTSF)2ClO4, die zweidimensionalen organischen Ladungstransfersalze k-(BEDT-TTF)2I3 und k-(BEDT-TTF)2Cu[N(CN)2]Br sowie das strukturell und elektronisch den zweidimensionalen Hochtemperatursupraleitern verwandte Sr2RuO4. Mittels verschiedener Einsätze wurden die Hochfrequenzeigenschaften und der Gleichstrom-Widerstand der Proben im selben 3He-Kryostat untersucht. Der Gleichstrom-Einsatz ermöglicht die Bestimmung des Probenwiderstands nach der Vierpunktmethode. Bei den Messungen erwies sich Leit-Kohlenstoff als optimale Kontaktpaste. Die damit möglichen geometrisch kleinen Kontakte minimieren mechanische Spannungen und besitzen geringe Kontaktwiderstände ohne wesentliche Temperaturabhängigkeit. Der Mikrowellen-Einsatz arbeitet bei 35 GHz und erlaubt durch eine in-situ Positionierung der Probe im maximalen elektrischen Feld oder im maximalen magnetischen Feld. Das rechnergesteuerte Messsystem passt automatisch die Breite des Frequenzscans an die sich mit der Temperatur ändernde Mittenfrequenz sowie Halbwertsbreite an. Frequenz und Halbwertsbreite werden mit hoher Genauigkeit bestimmt. Die gleichzeitige Ermittlung von Halbwertsbreite und Mittenfrequenz des Resonators erlaubt die direkte Berechnung der komplexen Hochfrequenzeigenschaften (Oberflächenimpedanz bzw. Leitfähigkeit) aus den Messdaten. Im supraleitenden Zustand deutlich unterhalb der Sprungtemperatur lässt sich aus der Oberflächenreaktanz die Eindringtiefe ermitteln. Ihre Temperaturabhängigkeit kann mit verschiedenen Modellen verglichen werden und liefert Aufschluss über die Gestalt des supraleitenden Ordnungsparameters. Der Temperaturverlauf der Leitfähigkeit kann Rückschlüsse auf die Natur des supraleitenden Zustands liefern. Der Übergang in den supraleitenden Zustand bei 35 GHz konnte bei allen Materialien beobachtet werden. Erstmals wurde der supraleitende Zustand bei 35 GHz in Strontiumruthenat bzw. in (TMTSF)2ClO4 beobachtet.Item Open Access Using umbrella integration to find minimum free energy paths(2015) Bohner, Matthias Ulrich; Kästner, Johannes (Prof. Dr.)The analysis of the detailed mechanism of chemical reactions is a key task of computational chemistry. The detailed knowledge may help to improve known processes or even contribute to the development of new ones. In this way ecological and economic demands can be reduced. Furthermore, the course of a reaction path also plays an important role in the action of drugs. Understanding the binding of the active ingredient to receptors, such as proteins, can make it possible to optimize drugs by reducing side effects, or even to find new effects. Unfortunately, chemical reactions are usually too fast to observe intermediate states by experimental methods. This is where theoretical chemistry joins the game. In theoretical chemistry we combine the coordinates of all atoms with the configuration space. The potential energy forms a hypersurface in this space. Minima represent stable or metastable states. Saddle points represent transition states which are the most unfavourable configurations occurring on the most favourable path between two minima. If the path of a reaction is known, all intermediate states can be observed by theoretical methods. However, these calculations are usually computationally costly. This is the reason why, in contrast to experimental methods, it is in general impossible to sample the whole configuration space. This would in most cases exceed the available computational resources. It is therefore necessary to use techniques enabling a reaction path to be found without sampling the whole configuration space. In the case of a thermodynamic ensemble, e.g. the contents of a test tube, statistical information has to be included. The corresponding potential is the so-called free energy landscape, for which some degrees of freedom of the configuration space are thermostatistically integrated out. Consequently this function includes statistical and energetic properties. The free energy can in general only be calculated by statistical simulations (Monte--Carlo or molecular dynamics). Unfortunately, the transition states in which we have a special interest are rarely sampled. Special methods have to be applied to get sufficient sampling as well in areas of these rare events. In this work a non-physical quadratic potential is used to bias the equation of motion of the particles while doing molecular dynamics simulations. In this way unfavourable areas in the configuration space can also be sampled sufficiently. This technique is called umbrella sampling. The bias is applied to one or more coordinates which describe the reaction and therefore are called reaction coordinates. An umbrella sampling run will result in a distribution of the reaction coordinates. The expectation value of this distribution will be located close to the minimum of the bias function without in general corresponding to it. The difference between the minimum of the bias function and the expectation value can be used to calculate the gradient of the underlying free energy surface. Similarly, the covariance of the distribution of the reaction coordinate can be used to calculate the Hessian of the free energy surface. This method of interpreting the data gained by umbrella sampling is called umbrella integration. At first these values are used for an iterative search of the saddle points, which represent the transition states. From these configurations, free energy paths can be constructed by following the gradient down to the minima. This algorithm was successfully tested for the alanine dipeptide system. This simple method has the disadvantages that it works serially and that one needs good initial guesses for the saddle points in order to find them. Therefore, in a second part of the work, the established method of nudged elastic band optimization (NEB) is extended for use in the free energy surface. NEB optimization searches for a reaction path. This path is discretized into a number configurations, so-called images. For the sake of equal distribution of the images along the path a non-physical spring force between the images is used. The force, which is actually minimized during the NEB optimisation, consists of the projection of the real force of the underlying potential perpendicular to the path, and the projection of the spring force parallel to the path. An optimizer is developed which archives quadratic convergence of NEB optimizations in the noise-free potential energy surface of some test systems. This optimiser uses gradients and Hessians at each step. For the free energy surface both values can be calculated by umbrella integration as mentioned above. NEB optimizations within the free energy are performed in this work in the following way: at first a guess path is assumed, e.g. a straight line between two points in the configuration space, usually minima. This path is discretized into a number of images. Molecular dynamics umbrella sampling simulations are performed on each image. The gradient and Hessian from the umbrella integration are fed into the newly developed NEB optimizer. This way one does not need good starting guesses for the saddle points but an interpolation between the much more easily accessible minima is sufficient. Furthermore, the need for independent molecular dynamics runs at each image makes the method intrinsically parallel. The whole method is applied to the well-studied alanine dipeptide system and compared with the results from the serial method. Subsequently the algorithm is applied to a much more costly system of binding a ligand to its receptor in water.