High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

Abstract Background The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Functional in vitro studies are fundamental for the comprehension of their role; nevertheless results are highly dependable on the adopted cellular model. Next generation small RNA transcriptomic sequencing data of a tumor cell line and keratinocytes derived from primary culture was generated in order to characterize the microRNA content of these systems, thus helping in their understanding. Both constitute cell models for functional studies of microRNAs in head and neck squamous cell carcinoma (HNSCC), a smoking-related cancer. Known microRNAs were quantified and analyzed in the context of gene regulation. New microRNAs were investigated using similarity and structural search, ab initio classification, and prediction of the location of mature microRNAs within would-be precursor sequences. Results were compared with small RNA transcriptomic sequences from HNSCC samples in order to access the applicability of these cell models for cancer phenotype comprehension and for novel molecule discovery. Results Ten miRNAs represented over 70% of the mature molecules present in each of the cell types. The most expressed molecules were miR-21, miR-24 and miR-205, Accordingly; miR-21 and miR-205 have been previously shown to play a role in epithelial cell biology. Although miR-21 has been implicated in cancer development, and evaluated as a biomarker in HNSCC progression, no significant expression differences were seen between cell types. We demonstrate that differentially expressed mature miRNAs target cell differentiation and apoptosis related biological processes, indicating that they might represent, with acceptable accuracy, the genetic context from which they derive. Most miRNAs identified in the cancer cell line and in keratinocytes were present in tumor samples and cancer-free samples, respectively, with miR-21, miR-24 and miR-205 still among the most prevalent molecules at all instances. Thirteen miRNA-like structures, containing reads identified by the deep sequencing, were predicted from putative miRNA precursor sequences. Strong evidences suggest that one of them could be a new miRNA. This molecule was mostly expressed in the tumor cell line and HNSCC samples indicating a possible biological function in cancer. Conclusions Critical biological features of cells must be fully understood before they can be chosen as models for functional studies. Expression levels of miRNAs relate to cell type and tissue context. This study provides insights on miRNA content of two cell models used for cancer research. Pathways commonly deregulated in HNSCC might be targeted by most expressed and also by differentially expressed miRNAs. Results indicate that the use of cell models for cancer research demands careful assessment of underlying molecular characteristics for proper data interpretation. Additionally, one new miRNA-like molecule with a potential role in cancer was identified in the cell lines and clinical samples.

Theoretical and experimental studies on the electronic, optical, and structural properties of poly-pyrrole-2-carboxylic acid films

A theoretical approach is used here to explain experimental results obtained from the electrosynthesis of polypyrrole-2-carboxylic acid (PPY-2-COOH) films in nonaqueous medium. An analysis of the Fukui function (reactivity index) indicates that the monomer (pyrrole-2-carboxylic acid, PY-2-COOH), and dimers and trimers are oxidized in the C4 or C5 positions of the heterocyclic ring of the PY-2-COOH structure. After calculating the heat of formation using semiempirical Austin Model 1 post-Hartree-Fock parameterization for dimer species, both C4 and C5 positions adjacent to the aromatic rings of PPY-2-COOH were considered the most susceptible ones to oxidative coupling reactions. The ZINDO-S/CI semiempirical method was used to simulate the electronic transitions typically seen in the UV-VIS-NIR range in monomer and oligomers with different conjugation lengths. The use of an electrochemical quartz crystal microbalance provides sufficient information to propose a polymerization mechanism of PY-2-COOH based on molecular modeling and experimental results.

The coronal heating problem

The heating of the solar corona has been investigated during four of decades and several mechanisms able to produce heating have been proposed. It has until now not been possible to produce quantitative estimates that would establish any of these heating mechanism as the most important in the solar corona. In order to investigate which heating mechanism is the most important, a more detailed approach is needed. In this thesis, the heating problem is approached ”ab initio”, using well observed facts and including realistic physics in a 3D magneto-hydrodynamic simulation of a small part of the solar atmosphere. The ”engine” of the heating mechanism is the solar photospheric velocity field, that braids the magnetic field into a configuration where energy has to be dissipated. The initial magnetic field is taken from an observation of a typical magnetic active region scaled down to fit inside the computational domain. The driving velocity field is generated by an algorithm that reproduces the statistical and geometrical fingerprints of solar granulation. Using a standard model atmosphere as the thermal initial condition, the simulation goes through a short startup phase, where the initial thermal stratification is quickly forgotten, after which the simulation stabilizes in statistical equilibrium. In this state, the magnetic field is able to dissipate the same amount of energy as is estimated to be lost through radiation, which is the main energy loss mechanism in the solar corona. The simulation produces heating that is intermittent on the smallest resolved scales and hot loops similar to those observed through narrow band filters in the ultra violet. Other observed characteristics of the heating are reproduced, as well as a coronal temperature of roughly one million K. Because of the ab initio approach, the amount of heating produced in these simulations represents a lower limit to coronal heating and the conclusion is that such heating of the corona is unavoidable.

Molekulardynamik-Simulation zur Struktur von SiO 2-Oberflächen mit adsorbiertem Wasser

In der vorliegenden Arbeit werdenMolekulardynamik-Simulationen zur Untersuchung derstatischen Eigenschaften von amorphenSiliziumdioxidoberflächen (Siliziumdioxid) durchgeführt. Da das von van Beest, Kramer und van Santen vorgeschlagene,sogenannte BKS-Potential für Bulksysteme optimiert wurde und an Oberflächen deutlichandere Ladungsverteilungenauftreten als im Bulk, ist die Anwendbarkeit diesesPotentials für Oberflächensystemefraglich. Aus diesem Grund haben wir untersucht, inwieweitsich die Oberflächeneigenschaften von Systemen, die mit Hilfe des BKS-Potentials äquilibriertwurden, durch ein Nachrelaxieren mit einer ab-initio-Simulation (Car-Parrinello-Methode)ändern. Mit Hilfe der Kombination aus BKS- und Car-Parrinello-Methode (CPMD)konnten wir feststellen, daß sich die Systeme aufgrund des Nachrelaxierens in z-Richtungweiter ausdehnen. Desweiteren zeigte sich insbesondere bei kleinen Ringen (kommen nur ander Oberfläche vor), daß es deutliche Abweichungen in den Geometrien (Atomabstände,Winkel usw.) zwischen der reinen BKS- und der kombinierten BKS-CPMD-Methode gibt. Anhand vonCPMD-Simulationen konnten wir zeigen, daß es durch die Wechselwirkung eines Wassermolekülsmit einem 2er-Ring zum Aufbrechen dieser Ringstruktur und zur Bildung von zweiSilanolgruppen (SiOH) kommt. Desweiteren stellten wir fest, daß es sich hierbei um eineexotherme Reaktion (Energiedifferenz 1.6 eV) handelt, für die eineEnergiebarriere von 1.1 eV überwunden werden muß. Ferner ergab sich, daß die an der Bildung des2er-Ringes beteiligten, stark deformierten Tetraeder nach dem Aufbrechen dieserRingstruktur eine nahezu ideale Tetraederform annehmen.

Structure and dynamics of supramolecular assemblies studied by advanced solid-state NMR spectroscopy

Ziel der vorliegenden Arbeit ist die Aufklärung von Struktur und Dynamik komplexer supramolekularer Systeme mittels Festkörper NMR Spektroskopie. Die Untersuchung von pi-pi Wechselwirkungen, welche einen entscheidenden Einfluss auf die strukturellen und dynamischen Eigenschaften supra- molekularer Systeme haben, hilft dabei, die Selbst- organisationsprozesse dieser komplexen Materialien besser zu verstehen. Mit dipolaren 1H-1H and 1H-13C Wiedereinkopplungs NMR Methoden unter schnellem MAS können sowohl 1H chemische Verschiebungen als auch dipolare 1H-1H und 1H-13C Kopplungen untersucht werden, ohne dass eine Isotopenmarkierung erforderlich ist. So erhält man detaillierte Informationen über die Struktur und die Beweglichkeit einzelner Molekül- segmente. In Verbindung mit sogenannten nucleus independent chemical shift (NICS) maps (berechnet mit ab-initio Methoden) lassen sich Abstände von Protonen relativ zu pi-Elektronensystemen bestimmen und so Strukturvorschläge ableiten. Mit Hilfe von homo- und heteronuklearen dipolaren Rotationsseitenbandenmustern könnenaußerdem Ordnungs- parameter für verschiedene Molekülsegmente bestimmt werden. Die auf diese Weise gewonnenen Informationen über die strukturellen und dynamischen Eigenschaften supramolekularer Systeme tragen dazu bei, strukturbestimmende Molekül- einheiten und Hauptordnungsphänomene zu identifizieren sowie lokale Wechselwirkungen zu quantifizieren, um so den Vorgang der Selbstorganisation besser zu verstehen.

Tetracycline-inducible RNAi Knockdown of SCL (Stem Cell Leukaemia) in Mice

RNAi (RNA interference) is a powerful technology for sequence-specific targeting of mRNAs. This thesis was aimed at establishing conditions for conditional RNAi-mediated silencing first in vitro and subsequently also in transgenic mice. As a target the basic helix-loop-helix transcription factor encoding gene SCL (stem cell leukaemia also known as Tal-1 or TCL5) was used. SCL is a key regulator for haematopoietic development and ectopic expression of SCL is correlated with acute T-lymphoblastic leukaemias. Loss of SCL function studies demonstrated that ab initio deletion of SCL resulted in embryonic lethality around day E9 in gestation. To be able to conditionally inactivate SCL, RNAi technology was combined with the tetracycline-dependent regulatory system. This strategy allowed to exogenously control the induction of RNAi in a reversible fashion and consequently the generation of a completely switchable RNAi knockdown. First a suitable vector allowing for co-expression of tetracycline-controlled shRNAs (small hairpin RNAs) and constitutively active EGFP (enhanced green fluorescent protein) was generated. This novel vector, pRNAi-EGFP, was then evaluated for EGFP expression and tetracycline-mediated expression of shRNAs. Four sequences targeting different regions within the SCL mRNA were tested for their efficiency to specifically knockdown SCL. These experiments were performed in M1 murine leukaemia cells and subsequently in the HEK 293 cell line, expressing an engineered HA-tagged SCL protein. The second assay provided a solid experimental method for determining the efficiency of different SCL-siRNA knockdown constructs in tissue culture. Western blotting analyses revealed a down regulation of SCL protein for all four tested SCL-specific target sequences albeit with different knockdown efficiencies (between 25% and 100%). Furthermore, stringent tetracycline-dependent switchability of shRNA expression was confirmed by co-transfecting the SCL-specific pRNAi-EGFP vector (SCL-siRNA) together with the HA-tagged SCL expression plasmid into the HEK 293TR /T-REx cell line constitutively expressing the tetracycline repressor (TetR). These series of experiments demonstrated tight regulation of siRNA expression without background activity. To be able to control the SCL knockdown in vivo and especially to circumvent any possible embryonic lethality a transgenic mouse line with general expression of a tetracycline repressor was needed. Two alternative methods were used to generate TetR mice. The first approach was to co-inject the tetracycline-regulated RNAi vector together with a commercially available and here specifically modified T-REx expression vector (SCL-siRNA T-REx FRT LoxP mouse line). The second method involved the generation of a TetR expressor mouse line, which was then used for donating TetR-positive oocytes for pronuclear injection of the RNAi vector (SCL-siRNA T-REx mouse line). As expected, and in agreement with data from conditional Cre-controlled adult SCL knockout mice, post-transcriptional silencing of SCL by RNAi caused a shift in the maturation of red blood cell populations. This was shown in the bone marrow and peripheral blood by FACS analysis with the red blood cell-specific TER119 and CD71 markers which can be used to define erythrocyte differentiation (Lodish plot technique). In conclusion this study established conditions for effective SCL RNAi-mediated silencing in vitro and in vivo providing an important tool for further investigations into the role of SCL and, more generally, of its in vivo function in haematopoiesis and leukaemia. Most importantly, the here acquired knowledge will now allow the establishment of other completely conditional and reversible knockdown phenotypes in mice.

Development of empirical potentials for amorphous silica

Development of empirical potentials for amorphous silica Amorphous silica (SiO2) is of great importance in geoscience and mineralogy as well as a raw material in glass industry. Its structure is characterized as a disordered continuous network of SiO4 tetrahedra. Many efforts have been undertaken to understand the microscopic properties of silica by classical molecular dynamics (MD) simulations. In this method the interatomic interactions are modeled by an effective potential that does not take explicitely into account the electronic degrees of freedom. In this work, we propose a new methodology to parameterize such a potential for silica using ab initio simulations, namely Car-Parrinello (CP) method [Phys. Rev. Lett. 55, 2471 (1985)]. The new potential proposed is compared to the BKS potential [Phys. Rev. Lett. 64, 1955 (1990)] that is considered as the benchmark potential for silica. First, CP simulations have been performed on a liquid silica sample at 3600 K. The structural features so obtained have been compared to the ones predicted by the classical BKS potential. Regarding the bond lengths the BKS tends to underestimate the Si-O bond whereas the Si-Si bond is overestimated. The inter-tetrahedral angular distribution functions are also not well described by the BKS potential. The corresponding mean value of theSiOSi angle is found to be ≃ 147◦, while the CP yields to aSiOSi angle centered around 135◦. Our aim is to fit a classical Born-Mayer/Coulomb pair potential using ab initio calculations. To this end, we use the force-matching method proposed by Ercolessi and Adams [Europhys. Lett. 26, 583 (1994)]. The CP configurations and their corresponding interatomic forces have been considered for a least square fitting procedure. The classical MD simulations with the resulting potential have lead to a structure that is very different from the CP one. Therefore, a different fitting criterion based on the CP partial pair correlation functions was applied. Using this approach the resulting potential shows a better agreement with the CP data than the BKS ones: pair correlation functions, angular distribution functions, structure factors, density of states and pressure/density were improved. At low temperature, the diffusion coefficients appear to be three times higher than those predicted by the BKS model, however showing a similar temperature dependence. Calculations have also been carried out on crystalline samples in order to check the transferability of the potential. The equilibrium geometry as well as the elastic constants of α-quartz at 0 K are well described by our new potential although the crystalline phases have not been considered for the parameterization. We have developed a new potential for silica which represents an improvement over the pair potentials class proposed so far. Furthermore, the fitting methodology that has been developed in this work can be applied to other network forming systems such as germania as well as mixtures of SiO2 with other oxides (e.g. Al2O3, K2O, Na2O).

NMR studies on supramolecular aggregates in solution and the solid state

The aim of this work presented here is the characterization of structure and dynamics of different types of supramolecular systems by advanced NMR spectroscopy. One of the characteristic features of NMR spectroscopy is based on its high selectivity. Thus, it is desirable to exploit this technique for studying structure and dynamics of large supramolecular systems without isotopic enrichment. The observed resonance frequencies are not only isotope specific but also influenced by local fields, in particular by the distribution of electron density around the investigated nucleus. Barbituric acid are well known for forming strongly hydrogen-bonded complexes with variety of adenine derivatives. The prototropic tautomerism of this material facilitates an adjustment to complementary bases containing a DDA(A = hydrogen bond acceptor site, D = hydrogen bond donor site) or ADA sequences, thereby yielding strongly hydrogen-bonded complexes. In this contribution solid-state structures of the enolizable chromophor "1-n-butyl-5-(4-nitrophenyl)-barbituric acid" that features adjustable hydrogen-bonding properties and the molecular assemblies with three different strength of bases (Proton sponge, adenine mimetic 2,6-diaminopyridine (DAP) and 2,6-diacetamidopyridine (DAC)) are studied. Diffusion NMR spectroscopy gives information over such interactions and has become the method of choice for measuring the diffusion coefficient, thereby reflecting the effective size and shape of a molecular species. In this work the investigation of supramolecular aggregates in solution state by means of DOSY NMR techniques are performed. The underlying principles of DOSY NMR experiment are discussed briefly and more importantly two applications demonstrating the potential of this method are focused on. Calix[n]arenes have gained a rather prominent position, both as host materials and as platforms to design specific receptors. In this respect, several different capsular contents of tetra urea calix[4]arenes (benzene, benzene-d6, 1-fluorobenzene, 1-fluorobenzene-d5, 1,4-difluorobenzene, and cobaltocenium) are studied by solid state NMR spectroscopy. In the solid state, the study of the interaction between tetra urea calix[4]arenes and guest is simplified by the fact that the guests molecule remains complexed and positioned within the cavity, thus allowing a more direct investigation of the host-guest interactions.

Nuclear charge radius determination of 7,10 Be and the one-neutron halo nucleus 11 Be

The only nuclear model independent method for the determination of nuclear charge radii of short-lived radioactive isotopes is the measurement of the isotope shift. For light elements (Z < 10) extremely high accuracy in experiment and theory is required and was only reached for He and Li so far. The nuclear charge radii of the lightest elements are of great interest because they have isotopes which exhibit so-called halo nuclei. Those nuclei are characterized by a a very exotic nuclear structure: They have a compact core and an area of less dense nuclear matter that extends far from this core. Examples for halo nuclei are 6^He, 8^He, 11^Li and 11^Be that is investigated in this thesis. Furthermore these isotopes are of interest because up to now only for such systems with a few nucleons the nuclear structure can be calculated ab-initio. In the Institut für Kernchemie at the Johannes Gutenberg-Universität Mainz two approaches with different accuracy were developed. The goal of these approaches was the measurement of the isotope shifts between (7,10,11)^Be^+ and 9^Be^+ in the D1 line. The …first approach is laser spectroscopy on laser cooled Be^+ ions that are trapped in a linear Paul trap. The accessible accuracy should be in the order of some 100 kHz. In this thesis two types of linear Paul traps were developed for this purpose. Moreover, the peripheral experimental setup was simulated and constructed. It allows the efficient deceleration of fast ions with an initial energy of 60 keV down to some eV and an effcient transport into the ion trap. For one of the Paul traps the ion trapping could already be demonstrated, while the optical detection of captured 9^Be^+ ions could not be completed, because the development work was delayed by the second approach. The second approach uses the technique of collinear laser spectroscopy that was already applied in the last 30 years for measuring isotope shifts of plenty of heavier isotopes. For light elements (Z < 10), it was so far not possible to reach the accuracy that is required to extract information about nuclear charge radii. The combination of collinear laser spectroscopy with the most modern methods of frequency metrology …finally permitted the …first-time determination of the nuclear charge radii of (7,10)^Be and the one neutron halo nucleus 11^Be at the COLLAPS experiment at ISOLDE/ CERN. In the course of the work reported in this thesis it was possible to measure the absolute transition frequencies and the isotope shifts in the D1 line for the Be isotopes mentioned above with an accuracy of better than 2 MHz. Combination with the most recent calculations of the mass effect allowed the extraction of the nuclear charge radii of (7,10,11)^Be with an relative accuracy better than 1%. The nuclear charge radius decreases from 7^Be continuously to 10^Be and increases again for 11^Be. This result is compared with predictions of ab-initio nuclear models which reproduce the observed trend. Particularly the "Greens Function Monte Carlo" and the "Fermionic Molecular Dynamic" model show very good agreement.

Thiophene-containing organic semiconducting heteroacenes for electronic applications

Diese Studie verfolgt das Konzept der "Oligomer-Ansatz", die von Müllen angesprochen wurde et.al. vor etwa 10 Jahren. Der Schwerpunkt dieser Arbeit war die Synthese, Charakterisierung und Anwendung von halbleitenden konjugierten heteroacenes für organische Elektronik.rnZur weiteren Entwicklung der Familie von schwefelhaltigen Pentacene, zwei Moleküle (Benzo [1,2 - b :4,5-b '] bis [b] benzodithiophene und dithieno-[2,3-d: 2', 3'-d ']-benzo-[1,2-b :4,5-b'] dithiophene)rnfacilely wurden synthetisiert und charakterisiert durch eine Kombination verschiedener Methoden. Die beiden neue Moleküle weisen hervorragende ökologische Stabilität und angewendet OFETs Geräte als p-Kanal-Material. Die Vorversuche gaben Ladungsträgerbeweglichkeiten von 0,1 cm2 V-1 s-1 undrn1,6 cm2 V-1 s-1 bzw. aus den beiden Molekülen.rnAusgelöst durch die Frage "je länger desto besser?", Eine Reihe von neuen heteroheptacenes wurden synthetisiert und intensiv im Hinblick auf ihre feste Struktur, Selbst-assenbly auf der studierte Oberfläche, opto-elektro-Eigenschaften und Eigenschaften des Orbits Grenze. Einer derrnheteroheptacene Moleküle wurden als die aktiven Kanäle in OFET Geräten angewendet. Jedoch in Trotz der mehr verlängert Konjugationslänge die Geräte auf der Basis zeigten heptacenes viel schlimmer Ladungsträgerbeweglichkeiten als die heteropentacenes. Viele Faktoren können Festlegung der endgültigen Leistung der Produkte und der chemischen Struktur ist nur einer von ihnen.rnIn dieser Hinsicht scheint es, dass es auch sinnvoll, den Einfluss der Heteroatome Studie und Alkylsubstitution auf der soliden und elektronischen Strukturen. Daher mehr heteroheptacenes wurden synthetisiert. Abwechslungsreiches in der Anzahl und Art der heteroatomare Brücke,rndiese Oligoazene ausgestellt dramatisch anders feste Struktur und opto-elektronischernEigenschaften. Darüber hinaus wurde eine kombinierte DFT Berechnung der Molekülorbitale dieser heptacenes darauf hingewiesen, dass die Einführung von Stickstoff Brücken wird die π-Orbitale zu destabilisieren, während stabilisieren den Schwefel Brücken sowohl HOMO und LUMO Energien. Dies ist wichtig, wenn man will hoch π verlängert Oligoazene synthetisieren und dabei eine angemessene Stabilität.

Charge transport in amorphous organic semiconductors

Organic semiconductors with the unique combination of electronic and mechanical properties may offer cost-effective ways of realizing many electronic applications, e.g. large-area flexible displays, printed integrated circuits and plastic solar cells. In order to facilitate the rational compound design of organic semiconductors, it is essential to understand relevant physical properties e.g. charge transport. This, however, is not straightforward, since physical models operating on different time and length scales need to be combined. First, the material morphology has to be known at an atomistic scale. For this atomistic molecular dynamics simulations can be employed, provided that an atomistic force field is available. Otherwise it has to be developed based on the existing force fields and first principle calculations. However, atomistic simulations are typically limited to the nanometer length- and nanosecond time-scales. To overcome these limitations, systematic coarse-graining techniques can be used. In the first part of this thesis, it is demonstrated how a force field can be parameterized for a typical organic molecule. Then different coarse-graining approaches are introduced together with the analysis of their advantages and problems. When atomistic morphology is available, charge transport can be studied by combining the high-temperature Marcus theory with kinetic Monte Carlo simulations. The approach is applied to the hole transport in amorphous films of tris(8-hydroxyquinoline)aluminium (Alq3). First the influence of the force field parameters and the corresponding morphological changes on charge transport is studied. It is shown that the energetic disorder plays an important role for amorphous Alq3, defining charge carrier dynamics. Its spatial correlations govern the Poole-Frenkel behavior of the charge carrier mobility. It is found that hole transport is dispersive for system sizes accessible to simulations, meaning that calculated mobilities depend strongly on the system size. A method for extrapolating calculated mobilities to the infinite system size is proposed, allowing direct comparison of simulation results and time-of-flight experiments. The extracted value of the nondispersive hole mobility and its electric field dependence for amorphous Alq3 agree well with the experimental results.

Optimising thin-film solar cells by computer simulations

CIGS-Dünnschichtsolarzellen verbinden hohe Effizienz mit niedrigen Kosten und sind damit eine aussichtsreiche Photovoltaik-Technologie. Das Verständnis des Absorbermaterials CIGS ist allerdings noch lückenhaft und benötigt weitere Forschung. In dieser Dissertation werden Computersimulationen vorgestellt, die erheblich zum besseren Verständnis von CIGS beitragen. Es wurden die beiden Systeme Cu(In,Ga)Se2 und (Cu,In,Vac)Se betrachtet. Die Gesamtenergie der Systeme wurde in Clusterentwicklungen ausgedrückt, die auf der Basis von ab initio Dichtefunktionalrechnungen erstellt wurden. Damit war es möglich Monte Carlo (MC)-Simulationen durchzuführen. Kanonische MC-Simulationen von Cu(In,Ga)Se2 zeigen das temperaturabhängige Verhalten der In-Ga-Verteilung. In der Nähe der Raumtemperatur findet ein Übergang von einer geordneten zu einer ungeordneten Phase statt. Unterhalb separiert das System in CuInSe2 und CuGaSe2. Oberhalb existiert eine gemischte Phase mit inhomogen verteilten In- und Ga-Clustern. Mit steigender Temperatur verkleinern sich die Cluster und die Homogenität nimmt zu. Bei allen Temperaturen, bis hin zur Produktionstemperatur der Solarzellen (¼ 870 K), ist In-reiches CIGS homogener als Ga-reiches CIGS. Das (Cu,In,Vac)Se-System wurde mit kanonischen und großkanonischen MC-Simulationen untersucht. Hier findet sich für das CuIn5Se8-Teilsystem ein Übergang von einer geordneten zu einer ungeordneten Phase bei T0 = 279 K. Großkanonische Simulationen mit vorgegebenen Werten für die chemischen Potentiale von Cu und In wurden verwendet, um die Konzentrations- Landschaft und damit die sich ergebenden Stöchiometrien zu bestimmen. Stabilitätsbereiche wurden für stöchiometrisches CuInSe2 und für die Defektphasen CuIn5Se8 und CuIn3Se5 bei einer Temperatur von 174 K identifiziert. Die Bereiche für die Defektphasen sind bei T = 696 K verschwunden. Die Konzentrations-Landschaft reproduziert auch die leicht Cu-armen Stöchiometrien, die bei Solarzellen mit guten Effizienzen experimentell beobachtet werden. Die Simulationsergebnisse können verwendet werden, um den industriellen CIGS-Produktionspr

Electron spectroscopy of novel charge transfer systems based on polycyclic aromatic hydrocarbons

Organische Ladungstransfersysteme weisen eine Vielfalt von konkurrierenden Wechselwirkungen zwischen Ladungs-, Spin- und Gitterfreiheitsgraden auf. Dies führt zu interessanten physikalischen Eigenschaften, wie metallische Leitfähigkeit, Supraleitung und Magnetismus. Diese Dissertation beschäftigt sich mit der elektronischen Struktur von organischen Ladungstransfersalzen aus drei Material-Familien. Dabei kamen unterschiedliche Photoemissions- und Röntgenspektroskopietechniken zum Einsatz. Die untersuchten Moleküle wurden z.T. im MPI für Polymerforschung synthetisiert. Sie stammen aus der Familie der Coronene (Donor Hexamethoxycoronen HMC und Akzeptor Coronen-hexaon COHON) und Pyrene (Donor Tetra- und Hexamethoxypyren TMP und HMP) im Komplex mit dem klassischen starken Akzeptor Tetracyanoquinodimethan (TCNQ). Als dritte Familie wurden Ladungstransfersalze der k-(BEDT-TTF)2X Familie (X ist ein monovalentes Anion) untersucht. Diese Materialien liegen nahe bei einem Bandbreite-kontrollierten Mottübergang im Phasendiagramm.rnFür Untersuchungen mittels Ultraviolett-Photoelektronenspektroskopie (UPS) wurden UHV-deponierte dünne Filme erzeugt. Dabei kam ein neuer Doppelverdampfer zum Einsatz, welcher speziell für Milligramm-Materialmengen entwickelt wurde. Diese Methode wies im Ladungstransferkomplex im Vergleich mit der reinen Donor- und Akzeptorspezies energetische Verschiebungen von Valenzzuständen im Bereich weniger 100meV nach. Ein wichtiger Aspekt der UPS-Messungen lag im direkten Vergleich mit ab-initio Rechnungen.rnDas Problem der unvermeidbaren Oberflächenverunreinigungen von lösungsgezüchteten 3D-Kristallen wurde durch die Methode Hard-X-ray Photoelectron Spectroscopy (HAXPES) bei Photonenenergien um 6 keV (am Elektronenspeicherring PETRA III in Hamburg) überwunden. Die große mittlere freie Weglänge der Photoelektronen im Bereich von 15 nm resultiert in echter Volumensensitivität. Die ersten HAXPES Experimente an Ladungstransferkomplexen weltweit zeigten große chemische Verschiebungen (mehrere eV). In der Verbindung HMPx-TCNQy ist die N1s-Linie ein Fingerabdruck der Cyanogruppe im TCNQ und zeigt eine Aufspaltung und einen Shift zu höheren Bindungsenergien von bis zu 6 eV mit zunehmendem HMP-Gehalt. Umgekehrt ist die O1s-Linie ein Fingerabdruck der Methoxygruppe in HMP und zeigt eine markante Aufspaltung und eine Verschiebung zu geringeren Bindungsenergien (bis zu etwa 2,5eV chemischer Verschiebung), d.h. eine Größenordnung größer als die im Valenzbereich.rnAls weitere synchrotronstrahlungsbasierte Technik wurde Near-Edge-X-ray-Absorption Fine Structure (NEXAFS) Spektroskopie am Speicherring ANKA Karlsruhe intensiv genutzt. Die mittlere freie Weglänge der niederenergetischen Sekundärelektronen (um 5 nm). Starke Intensitätsvariationen von bestimmten Vorkanten-Resonanzen (als Signatur der unbesetzte Zustandsdichte) zeigen unmittelbar die Änderung der Besetzungszahlen der beteiligten Orbitale in der unmittelbaren Umgebung des angeregten Atoms. Damit war es möglich, präzise die Beteiligung spezifischer Orbitale im Ladungstransfermechanismus nachzuweisen. Im genannten Komplex wird Ladung von den Methoxy-Orbitalen 2e(Pi*) und 6a1(σ*) zu den Cyano-Orbitalen b3g und au(Pi*) und – in geringerem Maße – zum b1g und b2u(σ*) der Cyanogruppe transferiert. Zusätzlich treten kleine energetische Shifts mit unterschiedlichem Vorzeichen für die Donor- und Akzeptor-Resonanzen auf, vergleichbar mit den in UPS beobachteten Shifts.rn

Baryons in the chiral regime

Quantum Chromodynamics (QCD) is the theory of strong interactions, one of the four fundamental forces in our Universe. It describes the interaction of gluons and quarks which build up hadrons like protons and neutrons. Most of the visible matter in our universe is made of protons and neutrons. Hence, we are interested in their fundamental properties like their masses, their distribution of charge and their shape. \\rnThe only known theoretical, non-perturbative and {\it ab initio} method to investigate hadron properties at low energies is lattice Quantum Chromodynamics (lattice QCD). However, up-to-date simulations (especially for baryonic quantities) do not achieve the accuracy of experiments. In fact, current simulations do not even reproduce the experimental values for the form factors. The question arises wether these deviations can be explained by systematic effects in lattice QCD simulations.rnrnThis thesis is about the computation of nucleon form factors and other hadronic quantities from lattice QCD. So called Wilson fermions are used and the u- and d-quarks are treated fully dynamically. The simulations were performed using gauge ensembles with a range of lattice spacings, volumes and pion masses.\\rnFirst of all, the lattice spacing was set to be able to make contact between the lattice results and their experimental complement and to be able to perform a continuum extrapolation. The light quark mass has been computed and found to be $m_{ud}^{\overline{\text{MS}}}(2\text{ GeV}) = 3.03(17)(38)\text{ MeV}$. This value is in good agreement with values from experiments and other lattice determinations.\\rnElectro-magnetic and axial form factors of the nucleon have been calculated. From these form factors the nucleon radii and the coupling constants were computed. The different ensembles enabled us to investigate systematically the dependence of these quantities on the volume, the lattice spacing and the pion mass.\newpage Finally we perform a continuum extrapolation and chiral extrapolations to the physical point.\\rnIn addition, we investigated so called excited state contributions to these observables. A technique was used, the summation method, which reduces these effects significantly and a much better agreement with experimental data was achieved. On the lattice, the Dirac radius and the axial charge are usually found to be much smaller than the experimental values. However, due to the carefully investigation of all the afore-mentioned systematic effects we get $\langle r_1^2\rangle_{u-d}=0.627(54)\text{ fm}^2$ and $g_A=1.218(92)$, which is in agreement with the experimental values within the errors.rnrnThe first three chapters introduce the theoretical background of form factors of the nucleon and lattice QCD in general. In chapter four the lattice spacing is determined. The computation of nucleon form factors is described in chapter five where systematic effects are investigated. All results are presented in chapter six. The thesis ends with a summary of the results and identifies options to complement and extend the calculations presented. rn

Structure and properties of quaternary and tetragonal Heusler compounds for spintronics and spin transfer torque applications

Diese Dissertation ist in zwei Teile aufgeteilt: Teil 1 befasst sich mit der Vorhersage von Halb-Metallizität in quarternären Heuslerverbindungen und deren Potential für Spintronik-Anwendungen. Teil 2 befasst sich mit den strukturellen Eigenschaften der Mn2-basierenden Heuslerverbindungen und dem Tuning von ihrer magnetischen Eigenschaften bzgl. Koerzitivfeldstärke und Remanenz. Diese Verbindungen sind geeignet für Spin-Transfer Torque-Anwendungen.rnrnIn Teil 1 wurden die folgenden drei Probenserien quarternärer Heuslerverbindungen untersucht: XX´MnGa (X = Cu, Ni und X´ = Fe, Co), CoFeMnZ (Z = Al, Ga, Si, Ge) und Co2−xRhxMnZ (Z = Ga, Sn, Sb). Abgesehen von CuCoMnGa wurden alle diese Verbindungen mittels ab-initio Bandstrukturrechnungen als halbmetallische Ferromagnete prognostiziert. In der XX´MnGa-Verbindungsklasse besitzt NiFeMnGa zwar eine zu niedrige Curie-Temperatur für technologische Anwendungen, jedoch NiCoMnGa mit seiner hohen Spinpolarisation, einem hohen magnetischen Moment und einer hohen Curie-Temperatur stellt ein neues Material für Spintronik-Anwendungen dar. Alle CoFeMnZ-Verbindungen kristallisieren in der kubischen Heuslerstruktur und ihre magnetischen Momente folgen der Slater-Pauling-Regel, was Halbmetalizität und eine hohe Spinpolarisation impliziert. Die ebenfalls hohen Curie-Temperaturen ermöglichen einen Einsatz weit über Raumtemperatur hinaus. In der strukturellen Charakterisierung wurde festgestellt, dass sämtliche Co2−xRhxMnZ abgesehen von CoRhMnSn verschiedene Typen von Unordnung aufweisen; daher war die ermittelte Abweichung von der Slater-Pauling-Regel sowie von der 100%-igen Spinpolarisation dieser Verbindungen zu erwarten. Die Halbmetallizität der geordneten CoRhMnSn-Verbindung sollte nach den durchgeführten magnetischen Messungen vorhanden sein.rnrnIm zweiten Teil wurden Mn3−xCoxGa und Mn2−xRh1+xSn synthetisiert und charakterisiert. Es wurde gezeigt, dass Mn3−xCoxGa im Bereich x = 0.1 − 0.4 in einer tetragonal verzerrten inversen Heuslerstruktur kristallisiert und im Bereich x = 0.6−1 in einer kubisch inversen Heuslerstruktur. Während die tetragonalen Materialien hartmagnetisch sind und Charakeristika aufweisen, die typischerweise für Spin-Transfer Torque-Anwengungen attraktiv sind, repräsentieren die weichmagnetischen kubischen Vertreter die 100% spinpolarisierten Materialien, die der Slater-Pauling-Regel folgen. Mn2RhSn kristallisiert in der inversen tetragonal verzerrten Heuslerstruktur, weist einernhartmagnetische Hystereseschleife auf und folgt nicht der Slater-Pauling-Regel. Bei hohen Rh-Gehalt wird die kubische inverse Heuslerstruktur gebildet. Alle kubischen Proben sind weichmagnetisch und folgen der Slater-Pauling-Regel.