Title: Study of Diradicals by Explicitly Correlated Multireference Coupled Cluster Methods Author: Matej Švaňa Department: Department of Physical and Macromelecular Chemistry Supervisor: Mgr. Jiří Pittner, Dr. rer. nat., J. Heyrovský Institute of Physical Chemistry Abstract: Total energies of cyclopropane, trimethylene, and propylidene were calculated with conventional post-HF CCSD(T), BWCCSD(T), MkCCSD(T) methods and their explicitly correlated alternatives. Main aims of the the- sis were to compare the basis set convergence of total energies and relative energies between cyclopropane and trimethylene/propylidene, both at the conventional and the explicitly correlated levels. It was shown that use of explicit correlation accelerates the convergence of the total energy by one or- der of basis set quality, resulting in considerable savings in computational times. Also, the MkCCSD(T)-F12/QZ and the BWCCSD(T)-F12/QZ calcula- tions belong to the most sophisticated approaches employed for estimation of the relative energies of cyclopropane and trimethylene/propylidene to date. Keywords: explicitly correlated, coupled cluster, multi-reference, cyclopropane isomerisation, trimethylene, propylidene 1

Considering the late in-vessel phase of an unlikely core melt down scenario in a light water reactor (LWR) with the formation of a corium pool in the lower head of the re-actor pressure vessel (RPV) the possible failure modes of the RPV and the time to failure have to be investigated to assess the possible loadings on the containment. In this work, an integral model was developed to describe the processes in the lower plenum of the RPV. Two principal model domains have to be distinguished: The temperature field within the melt and RPV is calculated with a thermodynamic model, while a mechanical model is used for the structural analysis of the vessel wall. In the introducing chapters a description is given of the considered accident scenario and the relevant analytical, experimental, and numerical investigations are discussed which were performed worldwide during the last three decades. Following, the occur-ring physical phenomena are analysed and the scaling differences are evaluated between the FOREVER-experiments and a prototypical scenario. The thermodynamic and the mechanical model can be coupled recursively to take into account the mutual influence. This approach not only allows to consider the tem-perature dependence of the material parameters and the thermally induced stress in the mechanical model, it also takes into account the response of the temperature field itself upon the changing vessel geometry. New approaches are applied in this work for the simulation of creep and damage. Using a creep data base, the application of single creep laws could be avoided which is especially advantageous if large temperature, stress, and strain ranges have to be covered. Based on experimental investigations, the creep data base has been de-veloped for an RPV-steel and has been validated against creep tests with different scalings and geometries. It can be stated, that the coupled model is able to exactly describe and predict the vessel deformation in the scaled integral FOREVER-tests. There are uncertainties concerning the time to failure which are related to inexactly known material parame-ters and boundary conditions. The main results of this work can be summarised as follows: Due to the thermody-namic behaviour of the large melt pool with internal heat sources, the upper third of the lower RPV head is exposed to the highest thermo-mechanical loads. This region is called hot focus. Contrary to that, the pole part of the lower head has a higher strength and therefore relocates almost vertically downwards under the combined thermal, weight and internal pressure load of the RPV. On the one hand, it will be possible by external flooding to retain the corium within the RPV even at increased pressures and even in reactors with high power (as e.g. KONVOI). On the other hand, there is no chance for melt retention in the considered scenario if neither internal nor external flooding of the RPV can be achieved. Two patents have been derived from the gained insights. Both are related to pas-sively working devices for accident mitigation: The first one is a support of the RPV lower head pole part. It reduces the maximum mechanical load in the highly stressed area of the hot focus. In this way, it can prevent failure or at least extend the time to failure of the vessel. The second device implements a passive accident mitigation measure by making use of the downward movement of the lower head. Through this, a valve or a flap can be opened to flood the reactor pit with water from a storage res-ervoir located at a higher position in the reactor building. With regard to future plant designs it can be stated - differing from former presump-tions - that an In-Vessel-Retention (IVR) of a molten core is possible within the reac-tor pressure vessel even for reactors with higher power.

Es wurde ein Modell zur realistischen Beschreibung der Kühlmittelvermischung innerhalb des Reaktordruckbehälters von Druckwasserreaktoren in den gekoppelten Programmkomplex DYN3D/ATHLET implementiert. Diese Modell basiert auf dem Prinzip der linearen Superposition Dirac-Impuls-ähnlicher Störungen und kann für die Modellierung der Vermischung von Kühlmittel unterschiedlicher Temperatur und/oder unterschiedlicher Borsäurekonzentration eingesetzt werden. Der um das Vermischungsmodell erweiterte Programmkomplex DYN3D/ATHLET wurde für Analyse von Borverdünnungsstörfällen und Frischdampflecks angewandt. Für den Fall "Start der ersten Hauptkühlmittelpumpe bei Vorhandensein eines minderborierten Pfropfens im kalten Strang" zeigten die Ergebnisse der durchgeführten Parameterstudie, dass es selbst bei Annahme des maximal möglichen Pfropfenvolumens nicht zu einer Schädigung des Brennstoffes kommt. Mit den Analysen zu einem generischen Frischdampfleckszenario wurde die Anwendbarkeit des Programmkomplexes DYN3D/ATHLET auf die zweite Störfallklasse, in der die Kühlmittelvermischung eine wichtige Rollen spielt, demonstriert. Im Rahmen der Arbeiten zum Projekt wurde außerdem gezeigt, dass der Einfluss der turbulenten Schwankungen des Geschwindigkeitsfeldes innerhalb des Reaktordruckbehälters auf neutronenkinetische Parameter im Nominalbetrieb und unter Störfallbedingungen nicht zu vernachlässigen ist. A model for the realistic description of the coolant mixing inside the pressure vessel of pressurized water reactors was implemented into the coupled code complex DYN3D/ATHLET. This model is based on the linear superposition Dirac-pulse-like perturbations. The model can be applied to the mixing of coolant of different temperature and/or boron concentration. The coupled code complex DYN3D/ATHLET with the newly implemented model was applied to the analysis of boron dilution and steam line break accidents. The results of a parameter study for the case "Start-up of the first main coolant pump with a slug of lower borated water in the cold leg" have shown, that even under the conditions of the maximum slug volume there is no fuel damage. The applicability to the second class of accidents, where the coolant mixing has to be considered, was demonstrated by the analysis of a generic main steam line break scenario. Further it was shown, that the influence of turbulent fluctuations of the velocity inside the reactor pressure vessel during nominal and accident conditions on neutron-kinetic parameters cannot be neglected.

Das Vorhaben bestand in der Validierung des gekoppelten neutronenkinetisch-thermohydraulischen Programmkomplexes ATHLET/DYN3D für Siedewasserreaktoren durch Teilnahme an dem OECD/NRC Benchmark zum Turbinenschnellschluss. Das von der OECD und der amerikanischen NRC definierte Benchmark basiert auf einem Experiment mit Schließens des Turbinenschnellschlussventils, das 1977 im Rahmen einer Serie von 3 Experimenten im Kernkraftwerk Peach Bottom 2 durchgeführt wurde. Im Experiment erzeugte das Schließen des Ventils eine Druckwelle, die sich unter Abschwächung bis in den Reaktorkern ausbreitete. Die durch den Druckanstieg bewirkte Kondensation von Dampf im Reaktorkern führte zu einem positiven Reaktivitätseintrag. Der folgende Anstieg der Reaktorleistung wurde durch die Rückkopplung und das Einfahren der Regelstäbe begrenzt. Im Rahmen des Benchmarks konnten die Rechenprogramme durch Vergleiche mit den Messergebnissen und den Ergebnissen der anderen Teilnehmer an dem Benchmark validiert werden. Das Benchmark wurde in 3 Phasen oder Exercises eingeteilt. Die Phase I diente der Überprüfung des thermohydraulischen Modells für das System bei vorgegebener Leistungsfreisetzung im Kern. In der Phase II wurden 3-dimensionale Berechnungen des Reaktorkerns für vorgegebene thermohydraulische Randbedingungen durchgeführt. Die gekoppelten Rechnungen für das ausgewählte Experiment und für 4 extreme Szenarien erfolgten in der Phase III. Im Rahmen des Projekts nahm FZR an Phase II und Phase III des Benchmarks teil. Die Rechnungen für Phase II erfolgten mit dem Kernmodell DYN3D unter Berücksichtigung der Heterogenitätsfaktoren und mit 764 thermohydraulischen Kanälen (1 Kanal/Brennelement). Der ATHLET-Eingabedatensatz für die Reaktoranlage wurde von der Gesellschaft für Anlagen- und Reaktorsicherheit (GRS) übernommen und für die Rechnungen zu Phase III, die mit der parallelen Kopplung von ATHLET mit DYN3D erfolgten, geringfügig modifiziert. Für räumlich gemittelte Parameter wurde eine gute Übereinstimmung mit den Messergebnissen und den Resultaten anderer Codes erzielt. Der Einfluss der Modellunterschiede wurde mit Hilfe von Variantenrechnungen zu Phase II untersucht. So können Unterschiede in der Leistungs- und Voidverteilung in einzelnen Brennelementen auf die unterschiedliche neutronenkinetische und thermohydraulische Modellierung des Reaktorkerns zurückgeführt werden. Vergleiche zwischen ATHLET/DYN3D (parallele Kopplung) und ATHLET/QUABOX-CUBBOX (interne Kopplung) zeigen für räumlich gemittelte Parameter nur geringe Unterschiede. Abweichungen in den lokalen Parametern können im wesentlichen mit der unterschiedlichen Modellierung des Reaktorkerns erklärt werden (geringere Anzahl von modellierten Kühlkanälen, keine Berücksichtigung der Heterogenitätsfaktoren und ein anderes Siedemodell in der Rechnung mit ATHLET/QUABOX-CUBBOX). Die Rechnungen für die extremen Szenarien von Phase III zeigen die Anwendbarkeit des gekoppelten Programms ATHLET/DYN3D für die Bedingungen bei Störfällen, die weit über das Experiment hinausgehen.

Bentonite is regarded as an ideal geomaterial for the engineering barrier system of a deep geological repository (DGR) where nuclear wastes are disposed, as it has several desirable properties for sealing the nuclear wastes, including low permeability, low diffusion coefficient, high adsorption capacity and proper swelling ability. Nevertheless, gas migration in saturated bentonite may undermine the sealing ability of the geomaterial. Previous experimental studies showed that the gas migration process is accompanied by complex hydromechanical (HM) behaviors, such as gas breakthrough phenomenon, development of preferential pathways, build-up of water pressure and total stress, nearly saturated state after gas injection test, localized consolidation, water exchange between clay matrix and developed fractures and self-sealing process. These experimentally observed behaviors should be properly modelled for conducting a reliable performance assessment for the geomaterial over the lifespan of DGR. In this thesis, two different coupled HM frameworks, i.e., one based on double porosity (DP) concept, referred to as coupled HM-DP framework, and the other on phase field (PF) method, referred to as coupled HM-PF framework, are proposed to simulate the gas migration process in saturated bentonite. For the coupled HM-DP framework, the saturated bentonite is assumed as a superposition of a MAcro-Continuum (MAC) and a MIcro-Continuum (MIC). Two-phase flow is only allowed in the MAC, whereas the MIC is impermeable to both water and gas. Nevertheless, the water can transfer between the MIC and the MAC under the water pressure gap. The first coupled HM model in this framework is based on a double effective stress concept. Mechanical behaviors of the MAC and the MIC are respectively governed by Bishop-type effective stress and Terzaghi’s effective stress. The model can well simulate the evolutions of both gas pressure and gas outflow rate, the water exchange between clay matrix and developed pathways, the high degree of saturation and the consolidation of clay matrix. To account for the development of preferential pathways, the damaging effect has been introduced in the framework. In this improved model, Bishop-type effective stress for the MAC is replaced by the independent stress state variables, i.e., net normal stress and suction, since using the net normal stress is beneficial to simulating tensile failure under high gas pressure. Numerical results showed that the damage-enhanced model can well describe the effect of the development of preferential pathways on the build-up of water pressure and total stress. In addition, the proposed hysteretic models for intrinsic and relative permeabilities make the coupled HM framework more flexible to reproduce the experimental results. To explicitly simulate the development of preferential pathways, a coupled HM-PF framework is developed by using Coussy’s thermodynamic theory and the microforce balance law. The coupled HM-PF framework is implemented in the standard Finite Element Method (FEM). To avoid the pore pressure oscillation and enhance the computational efficiency, a stabilized mixed finite element, in which linear shape functions are selected for interpolating all primary variables, is adopted to discretize the whole domain. In the developed framework, swelling pressure (initial stress) is accounted for by introducing a modified strain tensor that is the sum of the strain tensor due to deformation and the strain tensor calculated from the initial stress. The numerical results showed that the developed coupled HM-PF framework can capture some important behaviors, such as the discrete pathways, localized gas flow, built-up of water pressure and total stress under constant volume condition and nearly saturated state in clay matrix. A spatially autocorrelated random field is introduced into the framework to describe the heterogeneous distribution of HM properties in bentonite. The heterogeneity is beneficial to simulating the fracture branching and the complex fracture trajectory. Numerical results showed that some factors, such as Gaussian random field, coefficient of variation, boundary condition and injection rate, have significant influences on the fracture trajectory. At the end of the thesis, the obtained numerical results are synthesized and analyzed. Based on the analysis, the pros and cons of the developed numerical models are discussed. Corresponding to the limitations, some recommendations are proposed for future studies.

Protein-protein interaction dominates all major biology processes in living cells. Recent studies suggestthat the surface expression and activity of G protein-coupled receptors (GPCRs), which are the largestfamily of receptors in human cells, can be modulated by receptor activity–modifying proteins (RAMPs). Computational tools are essential to complement experimental approaches for the understanding ofmolecular activity of living cells and molecular dynamics simulations are well suited to providemolecular details of proteins function and structure. The classical atom-level molecular modeling ofbiological systems is limited to small systems and short time scales. Therefore, its application iscomplicated for systems such as protein-protein interaction in cell-surface membrane. For this reason, coarse-grained (CG) models have become widely used and they represent an importantstep in the study of large biomolecular systems. CG models are computationally more effective becausethey simplify the complexity of the protein structure allowing simulations to have longer timescales. The aim of this degree project was to determine if the applications of coarse-grained molecularsimulations were suitable for the understanding of the dynamics and structural basis of the GPCRRAMP interactions in a membrane environment. Results indicate that the study of protein-proteininteractions using CG needs further improvement with a more accurate parameterization that will allowthe study of complex systems.

Important considerations of a photovoltaic (PV) source are achieving a high voltage and drawing currents with very little ripple component from it. Furthermore, the output from such a source is variable depending on irradiation and temperature. In this research, literature review of prior methods employed to boost the output voltage of a PV source is examined and their limitations identified. This research then proposes a multi-phase tapped-coupled inductor boost DC-DC converter that can achieve high voltage boost ratios, without adversely compromising performance, to be used as an interface to a PV source. The proposed converter achieves minimal current and voltage ripple both at the input and output. The suitability of the proposed converter topology for variable input voltage and variable power operation is demonstrated in this dissertation. The proposed converter is also shown to have good performance at high power levels, making it very suitable for high power applications. Detailed analysis of the proposed converter is done. Advantages of the proposed converter are explained analytically and confirmed through simulations and experimentally. Regulation of the converter output voltage is also explained and implemented using a digital controller. The simulation and experimental results confirm that the proposed converter is suitable for high power as well as variable power, variable voltage applications where high voltage boost ratios are required. / Dissertation (MEng)--University of Pretoria, 2013. / gm2014 / Electrical, Electronic and Computer Engineering / Unrestricted

Höhere Drehzahlen, neue Anwendungen in elektrischen Fahrzeugen und der damit verbundene Leichtbau führen zu stärkeren Schwingungsphänomenen in elektrischen Drehfeldmaschinen. Besondere Bedeutung kommt dabei lateralen Rotorschwingungen zu, die sich akustisch bemerkbar machen und im Extremfall sogar zum Versagen des gesamten Systems führen können. In diesem Beitrag wird ein neuartiges Modell vorgestellt, welches rotordynamische Phänomene beliebiger Drehfeldmaschinen in transienten Fahrzuständen unter Berücksichtigung der vollen elektromagnetischen Kopplung abbilden kann. Im vorliegenden Beitrag wird eine FEM-Validierung des vorgeschlagenen Modells präsentiert. Danach wird ein Szenario vorgestellt, bei dem magnetisch angefachte Lateralschwingungen aufklingen. / Higher Speeds, new applications in electric vehicles and the need for lightweight structures lead to increasing occurrence of vibration phenomena in rotating field electrical machines. Lateral rotor oscillations take a particular role in this context, as they produce noise and may cause the entire system to fail in an extreme case. In this contribution, a novel modelling approach is presented, which allows for the fully coupled simulation of transient rotordynamics in all kinds of rotating field machines. This paper includes a FEM-validation of the proposed model. After that a scenario where self-excited lateral oscillations occur is presented.

Flies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis all have the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be reasonably rigid, with an S 2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis were used to construct two models for each receptor: Drome-AKHR, Sarcr-AKHR, and Bacdo-AKHR. It is proposed that these two models represent the active and inactive state of the receptor. The models based on the crystal structure of the β-2 adrenergic receptor were found to bind Phote-HrTH with a predicted binding free energy of –107 kJ mol–1 for Drome-AKHR, –102 kJ mol–1 for Sarcr-AKHR and –102 kJ mol–1 for Bacdo-AKHR. Under molecular dynamics simulation, in a POPC membrane, the β-2AR receptor-like complexes transformed to rhodopsin-like. The identification and characterisation of the ligand-binding site of each receptor provide novel information on ligand-receptor interactions, which could lead to the development of species-specific control substances to use discriminately against these pest flies.

Proton fluxes through plasma membranes are essential for regulating intracellular and extracellular pH and mediating co-transport of metabolites and ions. Although conventional electrical measurements are highly sensitive and precise for proton current detection, they provide limited specificity and spatial information. My thesis focuses on developing optical approaches to visualize proton fluxes from ion channels and transporters. It has been demonstrated that channel-mediated acid extrusion causes proton depletion at the inner surface of the plasma membrane. Yet, proton dynamics at the extracellular microenvironment are still unclear. In Chapter II, we developed an optical approach to directly measure pH change in this nanodomain by covalently attaching small-molecule, fluorescent proton sensors to the cell’s glycocalyx using glyco-engineering and copper free ‘click’ chemistry. The extracellularly facing sensors enable real-time detection of proton accumulation and depletion at the plasma membrane, providing an indirect readout of channel and transporter activity that correlated with whole-cell proton current. Moreover, the proton wavefront emanating from one cell was readily visible as it crossed over nearby cells. The transport of monocarboxylates, such as lactate and pyruvate is critical for energy metabolism and is mainly mediated by proton-coupled monocarboxylate transporters (MCT1-MCT4). Although pH electrodes and intracellular fluorescent pH sensors have been widely used for measuring the transport of proton-coupled MCTs, they are unable to monitor the subcellular activities and may underestimate the transport rate due to cell’s volume and intracellular buffering. In Chapter III, we used the Chapter II approach to visualize proton-coupled transport by MCT1-transfected HEK293T cells and observed proton depletion followed by a recovery upon extracellular perfusion of L-lactate or pyruvate. In addition, we identified a putative MCT, CG11665/Hrm that is essential for autophagy during cell death in Drosophila. The results demonstrate that Hrm is a bona fide proton-coupled monocarboxylate transporter that transports pyruvate faster than lactate. Although the approach developed in Chapter II enables visualization of proton fluxes from ion channels and transporters, it’s not applicable in some cell types which cannot incorporate unnatural sialic acid precursors into their glycocalyx, such as INS-1 cells and cardiomyocytes. To address this, in Chapter IV we developed a pH-sensitive, fluorescent WGA conjugate, WGA-pHRho that binds to endogenous glycocalyx. Compared to the results in Chapter II and III, cell surface-attached WGA-pHRho has similar fluorescent signals in response to proton fluxes from proton channel Hv1, omega mutant Shaker-IR R362H and MCT1. With WGA-pHRho, we were able to label the plasma membrane of INS-cells and cardiomyocytes and visualized the transport activity of MCT1 in these cells. Taken together, these findings provide news insights into proton dynamics at the extracellular environment and provide new optical tools to visualize proton fluxes from ion channels and transporters. Moreover, the modularity of the approaches makes them adaptable to study any transport events at the plasma membrane in cells, tissues, and organisms.