Unlocking the Axion-Dilaton in 5D Supergravity

We revisit supersymmetric solutions to five dimensional ungauged N=1 supergravity with dynamic hypermultiplets. In particular we focus on a truncation to the axion-dilaton contained in the universal hypermultiplet. The relevant solutions are fibrations over a four-dimensional Kahler base with a holomorphic axion-dilaton. We focus on solutions with additional symmetries and classify Killing vectors which preserve the additional structure imposed by supersymmetry; in particular we extend the existing classification of solutions with a space-like U(1) isometry to the case where the Killing vector is rotational. We elaborate on general geometrical aspects which we illustrate in some simple examples. We especially discuss solutions describing the backreaction of M2-branes, which for example play a role in the black hole deconstruction proposal for microstate geometries.Comment: 48 pages + appendices, 5 figure

Lorenz, G\"{o}del and Penrose: New perspectives on determinism and causality in fundamental physics

Despite being known for his pioneering work on chaotic unpredictability, the key discovery at the core of meteorologist Ed Lorenz's work is the link between space-time calculus and state-space fractal geometry. Indeed, properties of Lorenz's fractal invariant set relate space-time calculus to deep areas of mathematics such as G\"{o}del's Incompleteness Theorem. These properties, combined with some recent developments in theoretical and observational cosmology, motivate what is referred to as the `cosmological invariant set postulate': that the universe $U$ can be considered a deterministic dynamical system evolving on a causal measure-zero fractal invariant set $I_U$ in its state space. Symbolic representations of $I_U$ are constructed explicitly based on permutation representations of quaternions. The resulting `invariant set theory' provides some new perspectives on determinism and causality in fundamental physics. For example, whilst the cosmological invariant set appears to have a rich enough structure to allow a description of quantum probability, its measure-zero character ensures it is sparse enough to prevent invariant set theory being constrained by the Bell inequality (consistent with a partial violation of the so-called measurement independence postulate). The primacy of geometry as embodied in the proposed theory extends the principles underpinning general relativity. As a result, the physical basis for contemporary programmes which apply standard field quantisation to some putative gravitational lagrangian is questioned. Consistent with Penrose's suggestion of a deterministic but non-computable theory of fundamental physics, a `gravitational theory of the quantum' is proposed based on the geometry of $I_U$, with potential observational consequences for the dark universe.Comment: This manuscript has been accepted for publication in Contemporary Physics and is based on the author's 9th Dennis Sciama Lecture, given in Oxford and Triest

Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions

Non peer reviewe

Enhanced SPH modeling of free-surface flows with large deformations

The subject of the present thesis is the development of a numerical solver to study the violent interaction of marine flows with rigid structures. Among the many numerical models available, the Smoothed Particle Hydrodynamics (SPH) has been chosen as it proved appropriate in dealing with violent free-surface flows. Due to its Lagrangian and meshless character it can naturally handle breaking waves and fragmentation that generally are not easily treated by standard methods. On the other hand, some consolidated features of mesh-based methods, such as the solid boundary treatment, still remain unsolved issues in the SPH context. In the present work a great part of the research activity has been devoted to tackle some of the bottlenecks of the method. Firstly, an enhanced SPH model, called delta-SPH, has been proposed. In this model, a proper numerical diffusive term has been added in the continuity equation in order to remove the spurious numerical noise in the pressure field which typically affects the weakly-compressible SPH models. Then, particular attention has been paid to the development of suitable techniques for the enforcement of the boundary conditions. As for the free-surface, a specific algorithm has been designed to detect free-surface particles and to define a related level-set function with two main targets: to allow the imposition of peculiar conditions on the free-surface and to analyse and visualize more easily the simulation outcome (especially in 3D cases). Concerning the solid boundary treatment, much effort has been spent to devise new techniques for handling generic body geometries with an adequate accuracy in both 2D and 3D problems. Two different techniques have been described: in the first one the standard ghost fluid method has been extended in order to treat complex solid geometries. Both free-slip and no-slip boundary conditions have been implemented, the latter being a quite complex matter in the SPH context. The proposed boundary treatment proved to be robust and accurate in evaluating local and global loads, though it is not easy to extend to generic 3D surfaces. The second technique has been adopted for these cases. Such a technique has been developed in the context of Riemann-SPH methods and in the present work is reformulated in the context of the standard SPH scheme. The method proved to be robust in treating complex 3D solid surfaces though less accurate than the former. Finally, an algorithm to correctly initialize the SPH simulation in the case of generic geometries has been described. It forces a resettlement of the fluid particles to achieve a regular and uniform spacing even in complex configurations. This pre-processing procedure avoids the generation of spurious currents due to local defects in the particle distribution at the beginning of the simulation. The delta-SPH model has been validated against several problems concerning fluid-structure interactions. Firstly, the capability of the solver in dealing with water impacts has been tested by simulating a jet impinging on a flat plate and a dam-break flow against a vertical wall. In this cases, the accuracy in the prediction of local loads and of the pressure field have been the main focus. Then, the viscous flow around a cylinder, in both steady and unsteady conditions, has been simulated comparing the results with reference solutions. Finally, the generation and propagation of 2D gravity waves has been simulated. Several regimes of propagation have been tested and the results compared against a potential flow solver. The developed numerical solver has been applied to several cases of free-surface flows striking rigid structures and to the problem of the generation and evolution of ship generated waves. In the former case, the robustness of the solver has been challenged by simulating 2D and 3D water impacts against complex solid surfaces. The numerical outcome have been compared with analytical solutions, experimental data and other numerical results and the limits of the model have been discussed. As for the ship generated waves, the problem has been firstly studied within the 2D+t approximation, focusing on the occurrence and features of the breaking bow waves. Then, a dedicated 3D SPH parallel solver has been developed to tackle the simulation of the entire ship in constant forward motion. This simulation is quite demanding in terms of complexities of the boundary geometry and computational resources required. The wave pattern obtained has been compared against experimental data and results from other numerical methods, showing in both the cases a fair and promising agreement

Metalloproteins and protein-protein complexes investigated by CW and pulsed EPR spectroscopy

One of the central research topics in the field of biophysical chemistry is the structure and function of membrane proteins involved in energy transduction. Both, the aerobic and the anaerobic respiration include electron transfer and proton translocation across the mitochondrial and bacterial membranes. These electron transfer processes lead to changes in oxidation states of cofactors some of which are paramagnetic. Therefore, EPR spectroscopy is the method of choice to obtain electronic and structural information directly related to the function of the respiratory chain proteins. In this work, multifrequency continuous wave (CW) and pulsed EPR spectroscopy has been used to characterize the molybdenum active site of polysulfide reductase (Psr) from the anaerobic bacterium Wolinella succinogenes and the protein-protein complex between cytochrome c oxidase (CcO) and cytochrome c from the aerobic bacterium Paracoccus denitrificans. Molybdenum in Psr-Psr is an enzyme essential for the sulfur respiration of Wolinella succinogenes. Biochemical studies suggested that the active site of this enzyme contains a mononuclear Mo center, which catalyzes the reduction of the substrate polysulfide to sulfide. Until now there is no crystal structure available for Psr. Consequently, current characterizations of this enzyme have to rely on biochemical and spectroscopic investigations. Within the present work, CW and modern pulsed EPR techniques were applied to investigate its catalytically active site. In the first part of this thesis, different redox agents have been used to generate paramagnetic states of Psr. Multifrequency CW-EPR spectroscopy was applied to identify the Mo(V) states. Using simulations of the experimental spectra, three spectroscopically distinct states have been identified based on the Mo hyperfine- and g-tensor values. Comparison of their EPR parameters with those of related enzymes indicated five or six sulfur ligands at the Mo center depending on the state. The state generated by addition of polysulfide is suggested to be the catalytically active form, in which the Mo is coordinated by a sulfur of the polysulfide chain as the sixth ligand. 33S (I = 3/2) labeled polysulfide was prepared to probe the proximity of the polysulfide to the molybdenum center via its hyperfine coupling. 1D-ESEEM and 2D122 HYSCORE spectroscopy was used to detect these hyperfine and quadrupole interactions, which are too small to be observed in conventional CW EPR spectra. To date there has been only one pulsed-EPR study involving a 33S nucleus [Finazzo et.al. 2003]. The reasons are that this nucleus has a high nuclear spin of I = 3/2 and a large nuclear quadrupole moment in addition to the low Larmor frequency. All these make the detection of sulfur and the extraction of structural information demanding. However, analysis of the 2D-data led to a Mo(V) 33S distance in a range of about 2 to 2.5 Å. Mo-S distances found in molybdenum enzymes of the same family are in a range of 1.8 to 2.8 Å suggesting that the 33S is indeed the sixth ligand of the Mo(V) center and demonstrating that polysulfide is the actual substrate for this enzyme. Thus HYSCORE experiments have been proved to be a powerful technique to gain further insight into the active site structures of molybdenum enzymes and the trafficking of substrate atoms during catalysis. Density functional theory (DFT) calculations together with quantitative numerical simulations of the 2D-data will help to obtain more structural details about the molybdenum binding site in Psr. CcO:cytochrome c complex Protein-protein complex formation is an important step in energy conversion biological processes such as respiration and photosynthesis. These protein-protein complexes are involved in long range electron transfer reactions and are known to be of transient nature. Within the bacterial and mitochondrial respiratory electron transport chains such a complex is formed between CcO and cytochrome c. Upon complex formation cytochrome c donates the electrons required for the CcO catalyzed reduction of dioxygen to water. Here, the protein-protein complex formation between CcO and cytochrome c from Paracoccus denitrificans was investigated by pulsed EPR spectroscopy. The idea was to use the relaxation enhancement due to the distance and orientation dependent magnetic dipole-dipole interaction between the paramagnetic centers in the different CcO constructs and cytochromes. Two-pulse electron spin echo experiments were carried out on mixtures of the CuA containing soluble subunit II or the full size CcO with the physiological partner cytochrome c552 or horse heart cytochrome c. Significantly enhanced relaxation of CuA due to specific protein-protein complex formation has been observed in all four cases. In contrast the non-binding cytochrome c1 showed only a very weak relaxation enhancement due to unspecific protein-protein interactions. The echo decays of the slowly relaxing observer spin (CuA of CcO) measured in the absence and presence of the fast relaxing spin (Fe(III) of cytochrome c) permitted the extraction of the pure dipolar relaxation contributions for the different complexes. Measurements at different temperatures proved the dipolar nature of the relaxation enhancement. Furthermore, it was demonstrated experimentally that this approach also works for the full-size CcO, which contains four paramagnetic metal centers, in complex with cytochrome c. Quantitative simulations of the data suggest a broad distribution in distances (2 - 4 nm) and orientations between the CuA and Fe(III) in the complex between CcO and cytochrome c. High-field EPR spectroscopy will be useful to further analyze and prove these complex structures. Within the present work, it has been shown that pulsed relaxation enhancement experiments can be used to investigate the distance and relative orientation between paramagnetic metal centers. Furthermore, it has been demonstrated on a qualitative level, that this method can be used complimentary to other biophysical approaches to study transient electron transfer protein-protein complexes. Finally, within this work it has been proven that this method can be applied also to biological systems where more than two paramagnetic centers are present. This is particularly interesting for supercomplexes between membrane proteins.Eines der zentralen Forschungsziele in der biophysikalischen Chemie ist die Aufklärung der Struktur und Funktion von Membranproteinen, die in Energieübertragungswegen eine Rolle spielen. Sowohl die aerobe als auch die anaerobe Atmung beinhalten Elektronentransfer und Protonentranslokation durch die mitochondrialen und bakteriellen Membranen. Die Elektronentransferprozesse führen zu Änderungen im Oxidationszustand der beteiligten Kofaktoren, wodurch paramagnetische Spezies entstehen können. Aus diesem Grund ist die elektronenparamagnetische Resonanzspektroskopie (EPR-Spektroskopie) die Methode der Wahl, um Informationen über die elektronische und molekulare Struktur der paramagnetischen Intermediate zu erhalten. Diese strukturellen Informationen sind wiederum direkt verknüpft mit Erkenntnissen über die Funktion der Proteine der Atmungskette. In dieser Arbeit wurden Multifrequenz-Continuous-Wave- (CW) und Puls-EPR-Spektroskopie verwendet, um die Molybdänbindungsstelle in Polysulfidreduktase (Psr) aus dem anaeroben Bakterium Wolinella succinogenes sowie den Protein-Protein-Komplex zwischen Cytochrom c-Oxidase (CcO) und Cytochrom c aus dem aeroben Bakterium Paracoccus denitrificans zu charakterisieren. Molybdän in Psr-Psr ist ein essentielles Enzym für die Schwefelatmung von Wolinella succinogenes. Biochemische Studien deuten darauf hin, dass das aktive Zentrum dieses Enzyms ein mononukleares Molybdänzentrum enthält, das die Reduktion des Polysulfidsubstrats zu Sulfid katalysiert. Da keine Kristallstruktur von Psr existiert, müssen biochemische und spektroskopische Methoden angewandt werden, um strukturelle Informationen über dieses Enzym zu gewinnen. In der vorliegenden Arbeit wurden daher CW- und moderne Puls-EPR-Techniken verwendet, um das katalytisch aktive Zentrum zu untersuchen. Im ersten Teil dieser Dissertation wurden verschiedene Reduktionsmittel eingesetzt, um paramagnetische Zustände von Psr zu generieren. Anschließend wurde Multifrequenz-EPR-Spektroskopie zur Identifikation der Mo(V)-Spezies verwendet. Mit Hilfe von Simulationen der experimentellen Spektren konnten – basierend auf Molybdän-Hyperfeinkopplungs- und g-Tensorwerten – drei verschiedene Zustände identifiziert werden. Auf Grund eines Vergleichs dieser EPR-Parameter mit denen verwandter und gut charakterisierter Enzyme konnte gefolgert werden, dass je nach Zustand fünf oder sechs Schwefelliganden an das Molybdänzentrum koordiniert sind. Derjenige Zustand, der durch Zugabe von Polysulfid entsteht, wurde als katalytisch aktive Form vorgeschlagen. In diesem aktiven Zustand sollte als sechster Ligand ein Schwefelatom der Polysulfidkette an das Molybdän gebunden sein. Um die postulierte Nähe des Polysulfids zum Molybdänzentrum über Hyperfeinwechselwirkungen nachzuweisen, wurde 33S-markiertes Polysulfid synthetisiert und als Substrat eingesetzt. Im Anschluss daran wurden 1D-ESEEM- und 2D-HYSCORE-Spektroskopie zur Detektion der 33SHyperfein- und 33S-Quadrupolwechselwirkungen verwendet, da diese Wechselwirkungen zu klein waren, um in konventionellen CW-EPR-Spektren beobachtet werden zu können. Bis heute existiert nur eine einzige Puls-EPR-Studie, die 33S-Wechselwirkungen behandelt, da der 33S-Kern einen Kernspin I = 3/2, ein großes Kernquadrupolmoment und eine niedrige Larmorfrequenz aufweist. All diese Eigenschaften machen es schwer, 33S zu detektieren und aus den 33S-Spektren strukturelle Informationen zu gewinnen. In dieser Arbeit war es jedoch mittels Analyse der 2D-Daten möglich, den Mo(V)-33S-Abstand auf einen Bereich von 2 bis 2.5 Å einzugrenzen. Bekannte Mo-S-Abstände für Molybdänenzyme der gleichen Familie liegen zwischen 1.8 und 2.8 Å, was den Schluss nahe legt, dass 33S aus Polysulfid tatsächlich der sechste Ligand des Mo(V)-Zentrums. Damit konnte demonstriert werden, dass Polysulfid das Substrat von Psr ist. Die präsentierte Untersuchung unterstreicht, dass HYSCORE-Experimente eine wirkungsvolle Methode darstellen, um detaillierte Einblicke in die Strukturen von aktiven Zentren von Molybdänenzymen und den Reaktionsweg von Substratatomen während der Katalyse zu gewinnen. Dichtefunktionaltheorie-Rechnungen (DFT-Rechnungen) und quantitative numerische Simulationen der 2D-Daten können in diesem Zusammenhang helfen, weitere strukturelle Details über die Molybdänbindungsstelle in Psr aus den experimentellen Daten zu extrahieren. CcO:Cytochrom c-Komplex Die Bildung von Protein-Protein-Komplexen ist ein wichtiger Schritt in biologischen Prozessen der Energieumwandlung wie z.B. der Atmung oder der Photosynthese. Solche relativ kurzlebigen Protein-Protein-Komplexe sind an langreichweitigen Elektronentransferreaktionen beteiligt. In den Elektronentransportketten der bakteriellen und mitochondrialen Atmung findet die Bildung eines Komplexes zwischen CcO und Cytochrom c statt. Nach der Komplexbildung werden die Elektronen, die CcO zur Reduktion von von O2 zu H2O benötigt, von Cytochrom c auf CcO übertragen. In dieser Arbeit wurde die Komplexbildung zwischen CcO und Cytochrom c aus Paracoccus Idenitrificans mit Hilfe gepulster EPR-Spektroskopie untersucht. Hierbei sollte der Einfluss der abstands- und orientierungsabhängigen Elektronenspin-Dipol-Dipol- Wechselwirkung zwischen verschiedenen paramagnetischen Zentren auf die Elektronenspin-Relaxation (‚relaxation enhancement’) ausgenutzt werden, um verschiedene CcO-Cytochrom-Komplexe zu charakterisieren. Daher wurden Zweipuls-Elektronenspinecho-Experimente auf Mischungen aus der löslichen Untereinheit II von CcO, die das CuA-Zentrum enthält, bzw. der kompletten CcO mit Cytochrom c552, dem physiologischen Partner, oder Cytochrom c aus Pferdeherzen angewandt. In allen vier Fällen konnte eine deutlich verstärkte Relaxation des CuA, die durch die Bildung spezifischer Protein-Protein-Komplexe verursacht wurde, beobachtet werden. Im Gegensatz dazu zeigte sich in Experimenten mit dem nichtbindenden Cytochrom c1 nur eine sehr geringe Verstärkung der Relaxation auf Grund von unspezifischen Protein-Protein-Wechselwirkungen. Ein Vergleich der Echozerfälle des langsam relaxierenden Beobachter-Spins (CuA in CcO) in An- bzw. Abwesenheit des schnell relaxierenden Elektronenspins (Fe(III) im Cytochrom) erlaubte es, die rein dipolaren Relaxationsbeiträge für die verschiedenen Komplexe zu separieren und getrennt zu untersuchen. Durch temperaturabhängige Messungen war es möglich, den dipolaren Charakter der beobachteten Verstärkung der Relaxation zu beweisen. Schließlich wurde in dieser Arbeit gezeigt, dass die verwendete experimentelle Herangehensweise auch für den CcO-Cytochrom c-Komplex mit der kompletten CcO, die insgesamt vier paramagnetische Zentren enthält, funktioniert. Quantitative Simulationen der erhaltenen Daten für die verschiedenen Komplexe ergaben eine breite Abstands- (2-4 nm) und Orientierungsverteilung für die relative Anordnung der CuA- und Fe(III)-Zentren. Um die Strukturen der Komplexe noch detaillierter zu analysieren und die bisherigen Ergebnisse zu untermauern, werden Hochfeld-EPR-Experimente durchgeführt werden. Zusammengefasst konnte in der vorliegenden Arbeit gezeigt werden, dass der Einfluss dipolarer Relaxation auf die Ergebnisse gepulste EPR-Experimente dazu verwendet werden kann, Abstände zwischen und relative Orientierungen von paramagnetischen Metallzentren zu untersuchen. Weiterhin wurde auf einem qualitativen Niveau demonstriert, dass diese – zu anderen biophysikalischen Techniken komplementäre –Methode geeignet ist, um kurzlebige Elektronentransfer-Protein-Protein-Komplexe zu studieren. Schließlich konnte in dieser Arbeit experimentell belegt werden, dass die beschriebene Methode auf biologische Systeme mit mehr als zwei paramagnetischen Zentren angewandt werden kann. Dieses Resultat ist insbesondere von Interesse für zukünftige Charakterisierungen von Membranprotein-Superkomplexen

Online trigger processing for the NA62 rare kaon decay experiment

The work presented in this thesis covers almost all the aspects of the common Trigger and Data Acquisition of the NA62 experiment that has as main goal the measurement the Branching Ratio of the ultra-rare K+ -> pi+ nu nubar decay, very useful to obtain a stringent test of the Standard Model. This PhD work began with the development and the testing of the firmware of common boards of the NA62 TDAQ system: TDCB and TEL62. The TDCB is a daughter-board of the TEL62 and measures the detector hit times. The TEL62 processes and stores these detector data in a buffer memory; at the arrival of a L0 trigger request, it extracts the data within a programmable time window around the trigger time to send them to the PC farm. The TEL62s of some detectors also take care of producing the L0 trigger primitives that are merged to generate L0 trigger requests. In this thesis is described the significant contribution given to the developing, the testing and the commissioning of the TDCB and TEL62 firmware. Since the 2012 Technical Run to the 2015 Run the system was tested, and evolved to be compatible with the detector input rate and the beam at growing intensity up to nominal. After three main versions the system composed by TDCB and TEL62 manages to cope with the design rate. Once the work on the Data Acquisition system was concluded, I focuses on the Trigger system and the analysis of the L0 and L1 triggers. The goal of this work was to study the detector response and the trigger conditions required to obtain the needed rejection factor with the minimum amount of signal loss. Starting from 13 MHz of event rate, the L0 trigger must provide a factor 13 of rejection to reach the design L0 output rate of 1 MHz; the L1 trigger should provide a rejection of a factor 10 to achieve the goal of 100 KHz of L1 event output rate. The starting L0 and L1 scheme analysed failed to reach the output rate request by a factor 5. This gap could be filled only by using the STRAW spectrometer at the L1. For this reason in the last part of this work the development of a L1 STRAW algorithm is described, starting from a Monte Carlo simulation and validating with the use of real data samples used for the L0 and L1 analysis. The results reached by the STRAW algorithm plus other improvements allows to achieve the required L1 rejection factor