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Jahresbericht 2008 - Universität Bayreuth Rechenzentrum (2009)

Universität Bayreuth Rechenzentrum Jahresbericht des Rechenzentrums

First principles phase diagram calculations in group IV carbides and Mg2SiO4 liquid from Molecular Dynamics (2009)

Omar Adjaoud

Atomistic simulations on stability and physical properties of Earth materials are playing an increasingly important role in high pressure mineralogy. Such computations can provide guidance for experimental studies and insight into underlying causes of observations, or explore conditions and properties that are inaccessible to experiments at the current time. A variety of approaches have been applied in such research, with density functional theory based methods having become a reliable tool in computational mineral sciences. Despite this progress there are interesting problems which density functional theory based methods are not able to tackle on a routine basis. These include computations of phase diagrams and transport properties in liquids. The sub-solidus phase diagrams of the binary systems TiC-ZrC, TiC-HfC, ZrC-HfC at ambient pressure are computed based on electronic structure and energy calculations within density functional theory. Formation energies for a large number of supercells with compositions of (M1,M2)C, M1, M2 = Ti, Zr, or Hf, are computed by a plane-wave pseudopotential method. The energies serve as a basis for fitting cluster expansion Hamiltonians that are used to explore the sub-solidus phase diagram, i.e. stability of ordered intermediate compounds and the degree of miscibility in the systems by Monte Carlo simulations. Hamiltonians can be fit to the formation energies of the cells directly or after taking into account vibrational free energy. As it is prohibitive to compute vibrational free energy for all configurations they are approximated by the transferable force constant scheme: nearest neighbor force constants are computed for the end-member crystals with imposed but varying lattice parameters. The resulting bond stiffness versus bond length relationships are applied to the superstructures, using the relaxed bond lengths and their chemical identities as predictor. Significant miscibility gaps were predicted for the binaries TiC-ZrC and HfC-TiC, with consolute temperature in excess of 2000 K, in good agreement with experiments. The system HfC-ZrC shows complete miscibility at room temperature. Approximately symmetric phase diagram for HfC-TiC and asymmetric phase diagrams for HfC-ZrC and TiC-ZrC were predicted. With the success of the method in the simple carbide systems similar computations can now be performed for geologically relevant mineral families. Mg2SiO4 liquid at high pressure is of central importance in our understanding of melts that occur in the deep Earth and in particular in the early history of our planet, when it was in a magma ocean stage. Due to high melting temperatures little is known experimentally about its high pressure thermodynamic and transport properties that govern magma ocean structure and dynamics. Molecular dynamics simulations now fill this gap. Currently, density functional theory based computations are restricted to a few hundred atoms and a few picoseconds. While such simulations allow for determination of thermodynamic properties, longer run durations and larger cells are necessary to obtain transport properties such as diffusivity and viscosity with sufficient precision. By contrast, semi-empirical pair potentials provide an efficient route to perform large-scale molecular dynamics simulations. They suffer, however, from the fact that the transferability of the potentials to different conditions is not guaranteed. The development of aspherical flexible potentials that are fit to density functional theory results bridge the gap between ab-initio methods and classical potentials. Comprehensive large-scale molecular dynamics simulations using the aspherical ionic model were performed on Mg2SiO4 melt to obtain thermodynamic properties as well as diffusivity and viscosity. The pressure-temperature range covered was 0-32 GPa and 2600-3200 K. The thermodynamic parameters agree well with density functional theory based results: the Grüneisen parameter $gamma$ was found to increase significantly with pressure. Diffusivity is predicted to decrease and viscosity to increase with pressure. Both transport properties were readily fit with closed Arrhenius expression. Independent estimates on diffusivity and viscosity allows an examination of their relation through the Eyring equation, often employed to compute viscosity from diffusivity data. The proportionality factor between them, the translation distance for a diffusion event $lambda$, is determined as $lambda$=18 AA at 0 GPa, and decreases with pressure. This is in good agreement with previous molecular dynamics simulations using classical potentials, but significantly larger than other estimates of $lambda$ based on experimental data that yield 2.8 AA $ < lambda < $ 5 AA. Combining the thermodynamic and viscosity fits a magma ocean adiabat and the associated viscosity profile were computed.

Characterization of phase transitions by the analysis of crystal structures (2009)

Joachim Angelkort

In this thesis results of the investigations of the mechanisms of solid-solid phase transitions are reported on basis of the exemplary characterization of the phase transition of the metalorganic compound Eu(SC36H49)2 and of the inorganic transition-metal compounds TiI3 and CrOCl. The phase transitions were surveyed temperature dependently by the performance of single-crystal X-ray diffraction experiments and measurements of the magnetic susceptibility. The X-ray diffraction experiments were carried out as data collections of integrated intensities of reflections and as measurements of profiles on selected reflections in so-called omega-2theta maps. The data sets of the integrated intensities were used to determine the crystal structures at different temperatures. By the comparison of the high- and the low-temperature crystal structures the mechanisms of the phase transitions of the compounds Eu(SC36H49)2 and TiI3 were determined. Furthermore the transition temperatures of all three compounds were determined by temperature-dependent measurements of intensities of superstructure reflections. From the omega-2theta maps the monoclinic lattice distortion of the low-temperature phase of CrOCl was determined.

In-situ measurements of the Liquid-Phase Sintering of Zinc Oxide (2009)

Mohammad Lutful Arefin

Polycrystalline ceramic semiconductor devices based on ZnO and several additive oxides show highly non-ohmic current-voltage behavior similar to the Zener diodes. The devices act as an insulator up to a certain electrical field called the breakdown field (EBR) but change into a highly conducting one just above it. Below and above the breakdown field they behave perfectly ohmic. This overall non- linear current-voltage characteristic together with the ability to withstand repeated high power pulses has made metal oxide varistors popular as "surge-arrestors" in electrical circuitry. ZnO doped with Bi2O3 and Sb2O3 (ZBS), is the basic system for ceramic varistors. Phase formation during sintering of ZBS was measured in situ, using 1 mm thick samples and synchrotron X-rays. Thermodynamic calculations were performed to explain phase formation, composition, stability of additive oxides and influence of the oxygen fugacity on sintering. Sb2O4, pyrochlore, trirutile and spinel were formed at temperatures of 500°C to 800°C. The oxidation of antimony was controlled by the oxygen partial pressure and affected both, phase formation and sintering kinetics, in the ZBS system. There are three well defined phases in the final microstructure e.g. the ZnO-grains, Pyrochlore and Spinel phases. The evolution of these phases with temperature and time are important facts to the understanding of the basic functionality of the ZnO varistor system. Liquid phase sintering kinetics in the system ZnO-Bi2O3-Sb2O3 was studied using closed crucibles and an optical dilatometer. The kinetic field technique was modified to compare densification rates with liquid phase sintering models. Grain growths data were derived directly from the kinetic field diagram and compared to microstructure analysis of quenched samples. A reasonable agreement was obtained between both techniques - demonstrating that the modified kinetic field technique is an efficient tool for process optimization.

Vegetation ecology of springs: ecological, spatial and temporal patterns (2009)

Volker Audorff

Acidification is a phenomenon, which affected the forested catchments of the northern hemisphere severely over recent decades. Acidic depositions depleted the buffering capacities of soil and groundwater, what lead to an impairment of forests, headwaters, and lakes. Even though the depositions were reduced considerably since the early 1990s, the recovery of catchments was found to occur time-delayed. The grade of recovery was found to vary significantly between regions. Biomonitoring is an appropriate tool to detect spatial and temporal patterns of ecosystem alterations, such as acidification and recovery. However, to know the interrelationships between organisms and their environment is an indispensable precondition for the identification of indicator species. The complexity of ecosystems and ecological processes hampers this quest oftentimes. Springs provide a natural setting that minimises such constraints. Compared to other habitat types, external factors are less relevant, which makes it easier to relate changes in species abundances to changes in their environment. Studying this species-environment relationship, here the response of plant species to the acidification of the spring waters was of particular interest. In a survey of five regions in Central Europe - taking spatial, hydrophysical as well as hydrochemical parameters of the springs into account - it was clearly shown that the species composition of springs is essentially determined by the spring water chemistry, and more precisely by the gradient of acidity and nutrient availability. This connection was reflected by spatial patterns within and between the regions. These patterns provide useful ecological information about spring water quality and in return about the acidity status of their forested catchments. Including catchment traits - like bedrock, climatic parameters, and forest vegetation - in the analyses, these emerged to be relevant for the species composition of springs, but less than the spring water chemistry. A path analysis showed that the catchments affect the vegetation of springs not directly, but indirectly via the determination of spring water quality. Hence, the catchments are a part of the functional chain, which is driven by the atmospheric depositions. The pH-value was found to represent the gradient of acidity and nutrient availability best. It can serve as a proxy measure that can be related to species occurrence and to species dynamics respectively, aiming to identify indicator species for assessing the status and alterations of spring water quality. With the aim to delineate niche optima and amplitudes, which in return can serve as indicator values, the realised niches of spring-inhabiting species were modelled with respect to pH. The niche attributes were found to be a matter of sampling scale. Larger plot sizes (grain) weakened the species-environment relationship, what consequently resulted in broader niche amplitudes. In contrast, the grain did not influence the species’ pH optima. Monitoring approaches that target to assess processes in time, such as acidification and recovery, are dependent on the response time of indicator species to changes in their environment. Investigating an interval of four consecutive years, inter-annual variability of the species composition could not be attributed to changes in the acidity of the spring waters. Looking at single species, bryophytes did not show a higher sensitivity to the inter-annual variability of the environment than vascular plants. Actually, only a minority of all species featured abundance changes which were significantly correlated to variations in spring water acidity. Our results suggest that the species inertia retards the vegetation dynamics of forest springs. A delayed or long-term integrating response of potential indicator species must be considered when evaluating their indicator suitability. In conclusion, the biomonitoring of spring water acidification or recovery is expedient only for longer time intervals. In a nutshell, the vegetation of springs is closely related to the hydrochemical traits of the spring waters, in particular to a gradient of acidity and nutrient availability. Individual species as well as whole plant communities are suitable indicators which allow for the monitoring of the acidity status of forested catchments. The results of this study contribute to a better understanding of the species-environment-relationships, and in return to an improvement of indicator systems.

A Survey on Reputation Systems for Artificial Societies (2009)

Tina Balke Stefan König Torsten Eymann

The Internet has caused a revolution in trading. Especially cheap items are now easy to buy and sell on the Internet. As a consequence, sellers nowadays offer a wide range of products on the web, creating an abundance of choice for consumers. Consumers have the opportunity to browse on different auction sites for the item they really want. Along with this success story, however, came the stories of people being cheated by fraudulent online sellers. These frauds cover a range from not delivering what has been promised, the overrating of a product´s condition, to deliberate acts of theft. They are a result of so-called asymmetric information. Trust and reputation mechanisms are intended to address this asymmetric information distribution. This article surveys the most common trust and reputation systems.

Proceedings of the 11th European Agent Systems Summer School Student Session (2009)

Tina Balke Serena Villata Daniel Villatoro

This volume contains the papers presented at the Student Session of the 11th European Agent Systems Summer School (EASSS) held on 2nd of September 2009 at Educatorio della Providenza, Turin, Italy. The Student Session, organised by students, is designed to encourage student interaction and feedback from the tutors. By providing the students with a conference-like setup, both in the presentation and in the review process, students have the opportunity to prepare their own submission, go through the selection process and present their work to each other and their interests to their fellow students as well as internationally leading experts in the agent field, both from the theoretical and the practical sector.

Analyse der physiologischen Funktion von Mitgliedern der Rieske-Typ Eisen-Schwefel-Proteinfamilie in der inneren Plastidenhülle (2009)

Sandra Bartsch

Höher entwickelte Pflanzen enthalten eine Superfamilie von non-Häm Oxygenasen, deren Mitglieder über identische, konservierte Rieske- und mononukleare Fe-Bindungsdomänen verfügen. Diese Familie umfasst Tic55, PAO, CAO, CMO und ein 52 kDa schweres Protein (PTC52), welches in Assoziation mit dem Präkursor NADPH:Protochlorophyllid (Pchlid) Oxidoreduktase A (pPORA) Translocon vorliegt. Die Expression von AtCAO cDNA in Synechocystis, welches kein CAO-Gen enthält, führte zur Bildung von Chlorophyll b (Chl b) und geringen Mengen an Pchlid b. Pulse labeling Experimente mit dem isolierten PTC-Komplex und dem Pchlid Präkursor 5-Aminolävulinsäure (5-ALA) zeigten, dass PTC52 als Pchlid a Oxygenase agiert. Die gekoppelte in vitro Transkription/Translation von Arabidopsis CAO (AtCAO) bzw. PTC52 (AtPTC52) cDNAs führte zur Bildung von katalytisch aktiven Proteinen, wobei CAO Chlid a in Chlid b umwandelte, wohingegen PTC52 die Umwandlung von Pchlid a zu Pchlid b katalysierte. In Kotyledonen von Gerste und Arabidopsis ist der Import von pPORA von Pchlid abhängig. Während der Membran-Passage interagiert pPORA mit Komponenten des PTC-Komplexes und bildet dabei sog. „junction“-Komplexe zwischen äußerer und innerer Plastidenhülle. CAO wird als größeres Präkursor-Protein synthetisiert, über den Standard-Import-Komplex in den Intermembran-Raum importiert und liegt in seiner prozessierten Form als intrinsisches Protein der Thylakoid-Membranen bzw. der inneren Plastidenhülle vor, wo es mit Tic40, Tic22 und Tic20 interagiert und einen neuen Tic-Subkomplex bildet. Weitere Analysen mit Chloroplasten der Chlorina Mutanten ch1-3 (kein funktionelles CAO-Gen; keine Akkumulation von Chl b bzw. LHC-Proteinen) zeigten keinen Import von pLhcb1 (= Präkursor des LHCII-Apoproteins) bzw. pLhcb4 (= Präkursor des CP29-Apoproteins). PTC52 wird als größeres, ca. 57 kDa schweres Vorstufenprotein synthetisiert, in Chloroplasten importiert und zur endgültigen Größe prozessiert. Das reife, 52 kDa schwere Protein wurde als intrinsisches Membranprotein der inneren Plastidenhülle identifiziert, wo es mit PTC130, PTC90, PTC16/Oep16 und PTC33/Toc33 interagiert und einen funktionellen Protein-Import-Komplex (PTC-Komplex) bildet. Während des substratabhängigen Imports von pPORA katalysiert PTC52 die Oxygenierung von Pchlid a zu Pchlid b. DEPC agiert, indem es konservierte His-Reste im Rieske-Fe-S-Cluster ethoxyformyliert. Während bei geringen DEPC-Konzentrationen allein der Import von pPORA inhibiert war, war dieser in Anwesenheit von 1 mM DEPC nicht nachweisbar, wohingegen die Translokation von Tic55-Import-Substraten um ca. 10 % verringert war. Dies bestätigte die Beteiligung der His-Reste am katalytischen Mechanismus von PTC52 und Teil des PTC-Komplexes. Anhand von zwei PTC52-knockout-Linien (SALK_011945 und SAIL_148.HC5) wurde gezeigt, dass loss-of-function-Mutationen im Arabidopsis PTC52-Gen zu einem embryoletalen Phänotyp führten, so dass heterozygote AtPTC52/Atptc52-Pflanzen zur Analyse der Bedeutung von PTC52 in planta herangezogen wurden. Diese Keimlinge waren empfindlicher gegenüber einer Belichtung, was durch die geringeren Mengen an „light-harvesting“ POR-Pchlid (LHPP) – Komplexen im Prolamellarkörper der Etioplasten erklärbar war. Durch Pigmentanalysen konnte sowohl Pchlid a als auch Pchlid b in Wildtyp-Keimlingen identifiziert werden, wobei deren relative Anteile in AtPTC52/Atptc52-Pflanzen in Richtung Pchlid a verschoben waren. Zusätzlich waren ein Rückgang der Chl-Akkumulation, ein verändertes Chl b/Chl a-Verhältnis und eine Verringerung der LHCII-Mengen während des frühen Ergrünens erkennbar. Mittels Affinitätschromatographie wurden Tic55, PTC52 und PAO als Thioredoxin (Trx)-Targets in der inneren Plastidenhülle identifiziert. Abgesehen von konservierten Rieske- und [2Fe-2S]-Clustern weisen diese Proteine ein CxxC-Motiv auf. Aktivitätsmessungen in An- bzw. Abwesenheit von stromalem Trx f bzw. Trx m lassen darauf schließen, dass PTC52 und PAO aus Gerste reversiblen Oxidations/Reduktionsvorgängen, vermittelt durch redox-aktive SH-Gruppen, unterliegen, wobei die reduzierte Form eine höhere Aktivität aufweist. Um zu verifizieren, ob Trx die Aktivität von Tic55, PTC52 und PAO als Reaktion auf die Licht-Dunkel-Regulation und/oder oxidativen Stress regulieren könnte, verglichen wir die In-Vitro-Import-Kapazitäten der verschiedenen Import-Komplexe in tigrina d12 – Chloroplasten, die aus Pflanzen stammten, die entweder unter kontinuierlichem Weiß-Licht angezogen oder vor der Plastiden-Isolierung verdunkelt bzw. einem Dunkel-Licht-Shift unterworfen worden waren. Tic55, PTC52 und PAO reagierten sensitiv gegenüber einer oxidativen Kontrolle und waren in wiederbelichteten tigrina d12 – Pflanzen inaktiv. In CAO ist kein CxxC-Motiv vorhanden, so dass CAO weder auf das Thioredoxin-System noch auf oxidativen Stress reagiert.

Synthese und Charakterisierung von Donor-Brücke-Akzeptor-Molekülen und photoschaltbaren Systemen für Energie- und Elektronentransferuntersuchungen (2009)

Peter Bauer

Neue DBA-Moleküle hergestellt und charakterisiert. N,N,N,N-Tetraphenylbenzidin-Chromophore (TPD = Donor D) und (1-Heptyloctyl)perylen-3,4:9,10-tetracarboxybisimid-Chromophore (PBI = Akzeptor A) wurden über Alkylketten unterschiedlicher Länge (C6H12, C12H24, C18C36) zu maßgeschneiderten Donor-Brücke-Akzeptor-Dyaden (DBA) verbrückt. Zum Vergleich wurde auch eine Dyade mit einer polaren 3,6,9-trioxaundecanyl-Brücke synthetisiert. Im Zuge der Untersuchung der photophysikalischen Eigenschaften zeigten die DBA-Systeme bei selektiver Donoranregung eine Donor-Fluoreszenzlöschung bei gleichzeitiger Akzeptoremission. Durch die Verbrückung von D und A in DBA wurde ein hocheffizienter intramolekularer strahlungsloser Energietransfer bis über 90% zwischen Donor und Akzeptor ermöglicht. Die Effizienz der Energieübertragung ist von der Brückenlänge abhängig, aber nicht von deren Polarität. Akzeptor-Fluoreszenzlöschung nach selektiver Anregung von A deutet auf Ladungstransfer von D nach A. Um Bausteine für photochrome Systeme zu erhalten wurden funktionalisierte 1,2-Bis(5´-phenyl-2´-methylthien-3´-yl)perfluorocyclopenten-Derivate (BTF) synthetisiert und deren optische und photochemische Eigenschaften sorgfältig untersucht. Ein neues Photoschalter-Chromophorsystem (PBI-BTF-PBI) wurde durch gezielte Verknüpfung von zwei PBI-Chromophoren einem BTF-Photoschalter hergestellt. Optische und elektrochemische Eigenschaften können durch selektive Anregung der Photoschalterbrücke mit Licht reversibel geschalten werden. Bei geschlossenem Photoschalter findet eine PBI-Fluoreszenzlöschung von 81% statt. Förster-Energietransfer vom angeregten PBI-Fluorophor auf den geschlossenen Photoschalter ist als nichtstrahlender Desaktivierungskanal anzunehmen. Cyclovoltammetriestudien zeigten, dass sich das HOMO-Niveau der BTF-Brücke lichtinduziert reversibel verändern lässt. Außerdem wurden neue photoschaltbare Polythienylvinylene (P3HTV) wurden erstmals synthetisiert. Die Systeme enthalten entweder eine alternierende Anordnung von 3-Hexylthienylen-Vinylen- und BTF-Grundbausteinen (Poly(3HTV-alt-BTF)) oder P3HTV-Segmente auf beiden Seiten eines BTF-Photoschalters (P3HTV-BTF-P3HTV). Auch ein symmetrisch aufgebautes System mit zwei Poly-3-hexylthiophen-Ketten (P3HT) mit jeweils 7 Wiederholungseinheiten an einem BTF-Photoschalter wurde erstmals synthetisiert (P3HT-BTF-P3HT). Um Energietransferprozesse zu studieren, wurden die optischen Eigenschaften der photoschaltbaren Polymere durch UV/Vis- und Fluoreszenzspektroskopie untersucht. Redoxpotentiale und HOMO-LUMO-Niveaus wurden durch CV-Messungen bestimmt. Um optische Eigenschaften reversibel verändern zu können, wurden erste Photoschalt-Experimente in Lösung und im Film durchgeführt. In P3HT-BTF-P3HT konnte nach einer photochemischen Ringschlussreaktion der BTF-Einheit die P3HT-Fluoreszenz reversibel um 70% gelöscht werden.

Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonate (PFOS) in an Aquatic Ecosystem - Distribution and Fate (2009)

Anna Maria Becker

Perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) belong to the family of perfluorinated surfactants (PFSs). They are widely distributed and persistent in the environment. For over 50 years, they have been used in numerous applications including paper and textile treatment, production of fluoropolymers, cosmetics and insecticides formulations, and fire fighting foams. They can enter the environment via direct and indirect emission sources such as manufacturing processes, use of commercial products containing PFSs, release of waste waters or degradation of precursor substances. Due to their physical-chemical properties, i.e. relatively good solubility, low volatility and stability under environmental conditions, water bodies are important sinks for these chemicals. The aim of this doctoral thesis was to elucidate sources, distribution and fate of PFOA and PFOS in an aquatic ecosystem that is not directly affected by fluorochemical production activity. The presented study was mainly focused on the river Roter Main, Bayreuth, Germany, and gives a good picture of the behaviour of PFOA and PFOS in such an aquatic ecosystem. In order to achieve the main goal, suitable analytical procedures for reliable quantification of trace amounts of the target analytes in different environmental matrices such as water, liquid and solid wastes, sediments, biological tissues, were developed or optimised. Each method included a solid-phase extraction step for analytes’ preconcentration and removal of interfering matrix, followed by quantitative determination via high performance liquid chromatography coupled to electrospray ionisation tandem mass spectrometery (HLPC-ESI-MS). Due to the possibility of ionisation suppression, isotope dilution or standard addition method was applied. Analysis of waste waters collected from four different waste water treatment plants (WWTPs) located in Upper Franconia, Bavaria, Germany, showed that the largest plant (Bayreuth) receiving waste waters of mostly commercial and industrial origin released the highest amount of PFOA and PFOS, whereas the smallest plant (Himmelkron) treating waste waters of only domestic source released the least. The monitoring of waste waters from the WWTP Bayreuth enabled to estimate the typical mass flows of PFOA and PFOS into river waters as about 1 and 5 g/day, respectively, showing that a plant of a medium-size, moderately industrialised city can be a major source of river pollution. Detailed investigation of PFOA and PFOS concentrations in liquid and solid wastes collected at different stages of the treatment process showed additional fluxes of these compounds inside the plant, likely due to the decomposition of their precursors. Analysis of sediments collected from the river receiving treated waste waters showed a significant increase in concentrations of both analytes downstream the outlet of the plant (up to 3- and 4-fold for PFOA and PFOS, respectively). PFOS concentrations were up to 40-fold higher in sediments than in river water, showing its higher adsorption potential in comparison to PFOA (max. sediment/water = 6). Once in the river, PFOS, and to a lower extent PFOA, can bioaccumulate in aquatic organisms. Although partially removed from water, they are still bioavailable for benthic organisms inhabiting the river thus entering the food chain. This was reflected in higher levels found in river goby - in comparison to chub - feeding on invertebrates living in the sediment. At the starting point of this doctoral thesis little information was available about environmental contamination with PFOA and PFOS in Germany, and it is the first study performed in Bavaria giving such a detailed picture of sources and fate of PFSs in a river ecosystem

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