Thesis (doctoral)--Rijksuniversiteit Groningen, 1997. / Includes bibliographical references.

In this thesis we study a variety of two- and three-dimensional (2D and 3D, respectively) nodal semimetals, subjected to local electronic interactions or disorder. Such systems constitute a minimal model for various real materials and capture a plethora of interesting physical phenomena therein. Our methodology includes an unbiased renormalization group analysis controlled by epsilon expansions about the appropriate lower critical dimension, mean-field analysis, as well as complementary numerical analyses. First, we focus on emergent symmetries at various infrared unstable quantum critical points, appearing in a renormalization group flow of interaction couplings. We investigate a 3D chiral Dirac semimetal, which in a noninteracting system enjoys a microscopic U(1)⊗SU(2) global symmetry. Though the chiral symmetry is absent in the interacting model, it gets restored (partially or fully) at various fixed points as emergent phenomena. Subsequently, we study a collection of 3D interacting effective spin-3/2 biquadratic Luttinger fermions, and demonstrate the emergence of full rotational symmetry between the distinct nematic sectors (namely Eg and T2g ) of the corresponding octahedral group. We then investigate the effects of electronic interactions at zero and finite temperature and chemical doping in a collection of (i) 2D Dirac and Luttinger fermions, constituting the linearly and quadratically dispersing low-energy excitations in monolayer and bilayer graphene, respectively, and (ii) 3D Luttinger fermions, describing a biquadratic touching of Kramers degenerate conduction and valence bands, relevant in the normal state of 227 pyrochlore iridates, and half-Heusler compounds, for example. These systems exhibit a plethora of competing broken symmetry phases (both magnetic and superconducting) when tuning the strength of interactions, temperature, and chemical doping. In this context we propose the selection rules, identifying the broken symmetry phases promoted by a given interaction channel, and the organizing principle, ordering these preselected phases along the temperature axis based on a generalized energy-entropy argument. Finally, we explore topological aspects of nodal Fermi liquids. We propose an experimentally feasible way to engineer higher-order topological phases via the application of uniaxial strain on a 3D Luttinger semimetal. Favoring a direction, strain explicitly breaks cubic symmetry. We show that the corresponding nematic orderings of Luttinger fermions result in a topological insulator or Dirac semimetal, depending on the sign (compressive or tensile, respectively) of the strain. We show that both of these phases host 1D hinge modes, localized along the edges parallel to the direction of strain, that are therefore second-order topological in nature. We then investigate the effects of disorder on such a second-order Dirac semimetal, and show its stability for weak enough disorder. At a critical disorder strength the system goes through a quantum phase transition into a diffusive metal phase and the toplogical hinge states melt into the bulk. The methodology presented in this thesis can be extended to a large family of correlated multiband systems, such as Weyl and nodal-loop semimetal.

Understanding the conformational and dynamic changes of biomacromolecular complexes in different states, such as the membrane protein photoreceptor-transducer complex NpSRII/NpHtrII, is a key step to gaining insight into the functional mechanism of these important classes of protein complexes, since ~30 % of the human proteome are membrane proteins, yet they are largely underrepresented in terms of structural information with <1 % of all structures in the protein data bank. Hence for the development of methods suitable to study the conformation and dynamics of such complexes there is a strong demand and a vast potential field of applications. Here we combined method development at the interface between biomolecular simulations and model-based analysis of EPR- and fluorescence spectroscopic data with application studies using state-of-the-art spectroscopic techniques in conjunction with site-directed spin- or fluorescence labeling. In an initial benchmark study on the rigid globular protein complex Rpo4/7, we compared experimental inter fluorescence label distances or spin label distance distributions to a variety of predicted inter label distances based on molecular dynamics simulations, Monte Carlo sampling and a discrete rotamer library analysis. We found that while for the molecular dynamics simulations with explicit solvent considerable sampling challenges have to be overcome to reproduce the experimentally observed inter label distance distributions, the Monte Carlo sampling performed well when compared to the experimental data and was computationally less demanding. Significantly more efficient and equally accurate for our examples was the so-called rotamer library analysis available for the spin labels since it relies on a pre-calculated set of rotational isomers. In general, predictions for the mean distances were in agreement within the error margins while distribution shapes were more challenging to reproduce. Overall this study shows a positive evaluation for the assessed tools and the developed simulation protocols as well as their potential applications. Using the combination of EPR and fluorescence spectroscopy for distance determination we studied the structural influence of RNA binding on Rpo4/7, and showed that the protein complex stays conformationally rigid and thereby serves as a guiding rail for the nascent RNA chain that leaves the RNA polymerase along the Rpo4/7 RNA binding interface. To enhance the interpretation of experimentally determined changes of conformation and dynamics in protein complexes and to discuss the observed changes in terms of structural information, we built models of the two transcription factors TFE and the Spt4/5 complex, as well as of Argonaute, a 713 amino acid four-domain protein nuclease from Methanocaldococcus jannaschii. These structural models not only allowed a more accurate planning of fluorescence or EPR labeling experiments, but also the models enabled the discussion of the experimental data in structural terms. Based on such an initial structure further computational analysis techniques may be applied to identify putative structural changes or dynamic modes. This was shown for the histidine transporter HisQMP2, where we combined normal mode analysis to model protein flexibility with the rotamer library analysis to screen for possible conformational changes in comparison to experimental inter spin distance data. The most prominent agreement with one mode led to a working hypothesis of a conformational change and provides the basis for validation in future experiments. Due to the inherent synergy effects, we applied a combined experimental and simulation approach for the EPR-based distance determination in the globular DNA-binding protein LexA to probe conformation and dynamics of the N-terminal DNA-binding domains with respect to the C-terminal domains within the LexA homodimer. While the C-terminal dimerization domains exhibit a well-defined conformation that proved to be independent of DNA-binding, large-scale changes in conformation and dynamics were detected for the N-terminal domains. They were only found in a defined conformation when bound to DNA while in its absence a large rotational freedom of the entire N-terminal domains contributed to the conformational ensemble. Combined with a biochemical characterization of the autocatalytic cleavage of LexA, our data explains how LexA induces the SOS response after DNA damage or under latent antibiotic stress. We further studied the membrane photoreceptor-transducer complex NpSRII/NpHtrII that governs the light-dependent swimming behavior in Natronomonas pharaonis by a two-component signaling system. This system comprises extraordinary features of sensitivity, signal amplification, integration and transducer cooperativity, yet the molecular details of these features are poorly understood, as is signal propagation itself. By combining time-resolved cw EPR spectroscopy of NpSRII/NpHtrII variants spin labeled in the HAMP1 domain with time-resolved optical absorbance spectroscopy to report on the receptor signaling state, we found a tight kinetic coupling of receptor and transducer during the relaxation back to the ground state and hence a prolonged activation period, that with ~500 - ~700 ms is sufficiently long to cause phosphorylation bursts of the cognate kinase CheA. This explains signal amplification already on the level of the NpSRII/NpHtrII dimers. We further determined the transient difference spectra from the time-resolved EPR data that show local differences in dynamics and steric restrictions upon light-activation. Comparing these experimentally observed differences to predictions confirms the assumed two-state structural model and shows this transition between the two states for a single HAMP domain in a light-dependent manner. Additionally, our approach integrates a dynamic view into the model, since the two states are shown to exhibit different local dynamics in a fashion described previously as a competing model for signaling by dynamic differences based on biochemical studies. Here we show unification of the two models into one congruent description encompassing a transition between the two previously suggested states by concerted structural and dynamic changes. In an independent analysis using all-atom and coarse grained molecular dynamics of the NpSRII/NpHtrII complex in the minimal unit that can exert kinase control, the trimer of receptor-transducer dimers, we revealed a distinct dynamical pattern encoded in the primary sequence of the coiled-coil heptad-repeats. Upon receptor activation, these segments alter their dynamics in a concerted fashion with regions such as HAMP1 and the adaptation region becoming more compact, while HAMP2 and the tip become more dynamic, leading to dynamic and to limited structural changes at the CheA-kinase binding sites. Together with an extensive validation against experimental data, these findings suggest the altered dynamics as the mechanism for signal propagation along the extended coiled-coil structure of NpHtrII. This working model, that explains the current body of experimental data, allows for further refinement by all-atom molecular dynamics and provides a basis to devise future experiments for validation. The presented studies outline the versatile methodology of combined experimental and simulation approaches to analyze the conformation and dynamics of biomacromolecules including membrane protein complexes.

Musiktheorie ist eine singuläre Erscheinung: Keine andere künstlerische Disziplin hat eine derartige Theorie ausprägen können. Die Wandlungen, die nicht nur die Gegenstände der Musiktheorie und ihre theoretische Beschreibung, sondern auch den Theoriebegriff als solchen erfasst haben, haben doch eine grundlegende Tatsache unangetastet gelassen: Die Musiktheorie ist eine Theorie rationaler Strukturen und Verhältnisse, seien sie nun tonsystematisch oder werkbezogen, systematisch oder historisch, mathematisch, kosmologisch, physikalisch oder pragmatisch begründet. Nur als solche konnte sie historische Kontinuität ausbilden. Dass Klang als solcher in einer Theorie dieses Zuschnitts zuerst einmal systematisch ausgeschlossen wird, ist kein Zufall und auch kein behebbares Versäumnis, sondern konstitutiv. Klang wird, wie man aristotelisch sagen könnte, einer Theorie der musikalischen Formen zur Materie, zu dem, was nicht strukturell beschrieben werden kann. Damit wird Klang sozusagen negativ bestimmt als das, was sich der Theorie entzieht – nicht dem theoretischen Zugriff schlechthin, aber diesem speziellen. Indem sich die Musiktheorie dem Klang in seinen verschiedenen Dimensionen zuwendet, wird sie sich in einen anderen Typus Theorie verwandeln müssen bzw. mit anderen Theorietypen in Dialog treten. Aus einer Theorie musikalischer Rationalität wird ein ganzes Ensemble von Theorien unterschiedlicher Rationalitätsweisen, deren Zusammenspiel immer wieder neu austariert werden muss. / Music theory is a singular phenomenon: no other artistic field has been able to develop a theory of this type. Through the centuries, its objects and their theoretical examination and also the concept of theory itself have undergone major changes, while one thing has remained untouched: music theory is a theory of rational structures and relationships, regardless if they are located in the tonal system or the work, sought after in systematic or historical analyses, and founded in mathematics, cosmology, physics or in musical practice. This is what has guaranteed its historical coherence. It is no accident that sound as sound is systematically excluded from a theory of this kind, and this exclusion cannot simply be undone because it is constitutive for this kind of theory. For a theory of musical forms, sound becomes matter in the Aristotelian sense; it turns into something that cannot be described structurally. In this way, sound is negatively determined as that which eludes theory – not theory as such but this particular one. In turning to sound in its various dimensions, music theorists will have to adapt music theory to other types of theory. A theory of musical rationality will turn into an ensemble of theories whose interplay will constantly have to be rebalanced.

In dieser Dissertation werden Daten aus drei Jahren vom vollständig fertiggestellten IceCube-Detektor benutzt um nach Neutrinos zu suchen, die in Dunkle-Materie-Annihilationen in fünf nahegelegen Zwerggalaxien, der M31 Galaxie und dem Virgo Galaxienhaufen produziert wurden. Um die Messung durchzuführen, wurde zunächst eine Ereignis-Selektion angewandt, die es ermöglicht, die von aus der Atmosphäre stammenden Teilchen dominierte Rate der Ereignisse von zirka 100 Hz auf 0.5 mHz zu reduzieren. Danach wird eine Maximum-Likelihood-Schätzer eingesetzt um zu bestimmen ob es ein Überschuss von Neutrinos aus der Richtung der jeweiligen Quellen gibt, der mit einen Energie-Spektrum übereinstimmt das mann für Dunkle-Materie-Annihilationen erwartet. Für die M31 Galaxie und den Virgo Galaxienhaufen wurde zusätzlich zu dieser Suche nach einer Punktquelle auch eine Suche für ein erweitertes Signal durchgeführt. In allen untersuchten Fällen ist das Ergebnis der Analyse vereinbar mit einer Messung der Hintergrund-Hypothese, und daraus wurden Limits für den über die Geschwindigkeit gemittelten Wirkungsquerschnitt für Dunkle-Materie-Annihilation für verschiedene Endprodukte bestimmt. Für hohe Dunkle-Materie-Massen gibt es ein Überschuss von Neutrinos aus drei der Zwerggalaxien. Dieser Überschuss hat einen globalen p-Wert von 4.9% und ist damit nicht statistisch signifikant. Die Suche für ein erweitertes Signal von der M31 Galaxie und dem Virgo Galaxienhaufen ergab keinen Überschuss. Die Limits auf den über die Geschwindigkeit gemittelten Wirkungsquerschnitt für Dunkle-Materie-Annihilation haben sich im Vergleich zu vorherigen IceCube-Analysen signifikant verbessert, um bis zu einer Größenordnung. Diese ist teilweise auf Grund Verbesserungen für diese Analyse besonders: eine verbesserte Ereignis-Selektion, und für die Analyse ist eine Maximum-Likelihood-Schätzer eingesetzt statt eine Analyse in ein Suchfenster. / In this thesis, three years worth of data from the completed IceCube detector is used to search for neutrinos produced in dark matter annihilations in five nearby dwarf galaxies, the M31 galaxy and the Virgo cluster. To do this, an event selection which was developed for this analysis is applied to the data sample to reduce the atmospheric background rate from approximately 100 Hz to less than 0.5 mHz. Then, an unbinned maximum likelihood method is used to determine whether there is an excess of neutrinos from the direction of the considered galaxies or galaxy cluster that has an energy spectrum that matches the spectrum expected from dark matter annihilations. For the M31 galaxy and the Virgo cluster an extended signal with a two-dimensional Gaussian shape and width up to 5 degrees is also considered. In all cases, the results of the analysis are compatible with the background-only hypothesis and limits are set on the velocity-averaged dark matter annihilation cross section for different annihilation channels. For high dark matter masses there is an excess of neutrinos from three of the five dwarf galaxies. This excess has a global p-value of 4.9%, so it is not statistically significant. The search for an extended emission from the direction of the M31 galaxy and the Virgo cluster also did not result in an excess: in both cases the global p-value is larger than 50%. The limits on the velocity-averaged dark matter annihilation cross section have improved significantly (up to an order of magnitude) with respect to the previous IceCube analysis considering these same targets. This is partially due to improvements to this analysis specifically: an improved event selection was used to select the final data sample and an unbinned maximum likelihood method was used for the final analysis instead of a binned analysis method.

Erste Anzeichen für die Existenz von Dunkler Materie wurden 1933 entdeckt. Der Astrophysiker Fritz Zwicky beobachtete die Geschwindigkeitsverteilung im Coma Cluster und fand dabei heraus, dass 400 mal mehr Materie im Galaxie Haufen sein muss, damit dieser gravitativ gebunden sein kann oder der Galaxie Haufen würde sich aufösen. Trotz erheblicher Bemühungen über die letzten 80 Jahre ist nicht viel über Dunkle Materie bekannt. Das einzige was man weiÿ ist, dass Dunkle Materie gravitativ aber nicht elektromagnetisch wechselwirkt und Dunkle Materie stellt den gröÿten Bestandteil der Materie im Universum da. Doch derzeitige Experimente die nach Dunkler Materie suchen, sowohl direkte Suchen als auch indirekte, beginnen sensitiv genug zu werden um interessante Parameterbereiche von Dunkle Materie Kandidaten zu untersuchen wie das leichteste Super-symmetrische Teilchen, was bedeutet, dass die Entdeckung von Dunkler Materie in der nahen Zukunft sein könnte. In dieser Arbeit wird eine Signalsummierung von H.E.S.S. Zwerg Galaxien Daten durchgeführt und obere Ausschlussgrenzen berechnet. Weiterhin wird die Leistung einer Dunklen Materie Suche im galaktischen Zentrum durch CTA präsentiert für verschiedene mögliche Teleskop Anordnungen und verschiedene Annihilation Kanäle. Die Ergebnisse werden zeigen, dass CTA in der Lage sein wird geschwindigkeitsgemittelte Annihilations Wirkungsquerschnitte von 3 * 10^-26 cm^3s^1 und geringer, der geschwindigkeitsgemittelte Annihilations Wirkungsquerschnitt der für schwach wechselwirkende Dunkle Materie erwartet wird, in 100 h zu erreichen. Diese Beobachtungszeit kann innerhalb von ein bis zwei Jahren erreicht werden. / First indications for the existence of Dark Matter appeared in 1933. The astrophysicist Fritz Zwicky observed the velocity dispersion of the Coma Cluster and found out that 400 times the visible mass must be contained in the galaxy cluster or the cluster could not be gravitationally bound and would disperse.Despite extensive efforts over the last 80 years not much is known about Dark Matter. The facts known are that Dark Matter interacts via gravitation, does not interact electromagneticly and is the main constituent of matter. But current experiment searching for Dark Matter directly and indirectly begin to reach sensitivities that can probe interesting parameter spaces for Dark Matter candidates like the lightest supersymmetric particle, meaning the first Dark Matter detections could happen in the near future.In this thesis a dwarf stacking analysis for Dark Matter signal search using H.E.S.S. data is performed and a upper limit is calculated. Furthermore the prospect for a Dark Matter search with CTA in the galactic center region of the Milky Way is presented for different candidate arrays and different annihilation channels. The results will show that CTA will be able to reach velocity annihilation below 3 *10^-26 cm^3s^-1, the velocity annihilation crosssection expected for a weakly interacting Dark Matter particle, within 100 h of observation which can reasonably be acquired within one to two years.

Neben ihrer Bedeutung in industriellen Anwendungen dienen Kolloide als Modellsysteme in Experimenten und in der Theorie, um die Struktur und Dynamik von kondensierter Materie zu untersuchen. Kürzlich wurde experimentell gezeigt, dass eine kleine Anisotropie ausreicht, um die viskoelastische Antwort im Vergleich zu harten Kugeln drastisch zu ändern. Die mikroskopischen Ursachen hierfür sind bisher nicht verstanden. In dieser Arbeit werden daher Nichtgleichgewichts-Brownsche-Dynamik-Simulationen (NEBD) von harten kolloidalen Dumbbells in oszillatorischen Scherfeldern entwickelt und eingesetzt, um diese Resultate mit Verbindung zu Rheologie- und Neutronenstreuexperimenten zu erklären. Weiterhin wird die Bedeutung der Anisotropie für Struktur und Dynamik von solchen Suspensionen im Gleichgewicht mit Hilfe von "Linear-Response"-Theorie und Brownsche-Dynamik-Simulationen analysiert. Im linearen Limit zeigt die Scherviskosität bei hohen Packungsdichten einen dramatischen Anstieg jenseits eines kritischen Anisotropieparameters. Dies weist darauf hin, dass schon bei den kleinen Anisotropien kollektive Rotations-Translations-Kopplungen für langsame Zeitskalen verantwortlich sind. Weiterhin wird ein Nichtgleichgewichtsübergang mittels NEBD-Simulationen von Suspensionen harter Dumbbells im PC unter oszillatorischer Scherung ersichtlich. Es wird gezeigt, dass der kontinuierliche Übergang nur für sehr kleine Aspektverhältnisse erhalten bleibt. Oberhalb eines bestimmten Aspektverhältnisses wird der Übergang durch einen ungeordneten Zustand vermittelt. Außerdem wird ein Sliding-Layer Zustand mit kollektiver Ordnung der Teilchenausrichtung bei hohen Scheramplituden beobachtet. Somit zeigt diese Arbeit, dass die NEBD-Simulationen Phänomene in Rheologie- und Streuexperimenten erklären. Angesichts dieser Experimente wird gezeigt, dass der Orientierungsfreiheitsgrad einen starken Einfluss auf den strukturellen Übergang bei steigenden Amplituden hat. / Besides being important for industrial applications, colloidal suspensions have long served as model systems for investigating the structure and dynamics of condensed matter. Recently, it has been demonstrated experimentally that apparently a small particle anisotropy is sufficient to dramatically change the viscoelastic response under external shearing fields, of which the microscopic mechanisms are not yet sufficiently understood. In the present work, NEBD simulations of colloidal hard dumbbells in oscillatory shear fields are developed and employed to elucidate the novel findings in close connection with comprehensive rheology and SANS experiments. Furthermore, by utilising BD simulations and linear response theory, the impact of anisotropy on structure and dynamics of such suspensions in equilibrium is analysed. In the linear response limit, the shear viscosity exhibits a dramatic increase at high packing fractions beyond a critical anisotropy of the particles. This indicates that newly occurring, collective rotational-translational couplings must be made responsible for slow time scales appearing in the PC. Moreover, a non-equilibrium transition emerging at moderate aspect ratios is revealed by NEBD of plastic crystalline suspensions under oscillatory shear. This transition behaviour is systematically studied. It is demonstrated that the continuous nature of the transition is retained for very low aspect ratios only. Above a certain aspect ratio, the transition is mediated by an intermediate disordered state. Furthermore, a partially oriented sliding layer state featuring a finite collective order in the particles'' orientations is observed at high strains. Hence, this thesis demonstrates that the NEBD simulations explain novel phenomena in rheology and scattering experiments. In the light of these experiments, it is shown that the orientational degree of freedom has a vigorous impact on the structural transition under increasing oscillatory shear.

In dieser Arbeit wird mit Hilfe von Daten, die mit dem High Energy Stereocopic System (H.E.S.S.) in Namibia aufgenommen wurden, indirekt nach dunkler Materie im Halo der Milchstraße gesucht / An indirect search for the presence of dark matter particles in the halo of the Milky Way with data that were recorded with the High Energy Stereoscopic System (H.E.S.S.) is discussed in this work

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