The free energy landscape of a protein-like chain is constructed from exhaustive simulation studies using a combination of discontinuous molecular dynamics and parallel tempering methods. The protein model is a repeating sequence of four kinds of monomers, in which hydrogen bond attraction, electrostatic repulsion, and covalent bond vibrations are modeled by step, shoulder and square-well potentials, respectively. These protein-like chains exhibit a helical structure in their folded states. The model allows a natural definition of a configuration by considering which beads are bonded. In the absence of a solvent, the relative free energy of dominant structures is determined from the relative populations, and the probabilities predicted from the calculated free energies are found to be in excellent agreement with the observed probabilities at different temperatures. The free energy landscape of the protein-like chain is analyzed and confirmed to have funnel-like characteristics, confirmed by the fact that the probability of observing the most common configuration approaches unity at low enough temperatures for chains with fewer than 30 beads. The effect on the free energy landscape of an explicit square-well solvent, where the beads that can form intra-chain bonds can also form (weaker) bonds with solvent molecules while other beads are insoluble, is also examined. Simulations for chains of 15, 20 and 25 beads show that at low temperatures, the most likely structures are collapsed helical structures. The temperature at which collapsed helical structures become dominant is higher than in the absence of a solvent. Finally, the dynamics of the protein-like chain immersed in an implicit hard sphere solvent is studied using a simple model in which the implicit solvent interacts on a fast time scale with the chain beads and provides sufficient friction so that the motion of monomers is governed by the Smoluchowski equation. Using a Markovian model of the kinetics of transitions between conformations, the equilibration process from an ensemble of initially extended configurations to mainly folded configurations is investigated at low effective temperatures for a number of different chain lengths. It was observed that folding profiles appear to be single exponentials and independent of temperature at low temperatures.

The free energy landscape of a protein-like chain is constructed from exhaustive simulation studies using a combination of discontinuous molecular dynamics and parallel tempering methods. The protein model is a repeating sequence of four kinds of monomers, in which hydrogen bond attraction, electrostatic repulsion, and covalent bond vibrations are modeled by step, shoulder and square-well potentials, respectively. These protein-like chains exhibit a helical structure in their folded states. The model allows a natural definition of a configuration by considering which beads are bonded. In the absence of a solvent, the relative free energy of dominant structures is determined from the relative populations, and the probabilities predicted from the calculated free energies are found to be in excellent agreement with the observed probabilities at different temperatures. The free energy landscape of the protein-like chain is analyzed and confirmed to have funnel-like characteristics, confirmed by the fact that the probability of observing the most common configuration approaches unity at low enough temperatures for chains with fewer than 30 beads. The effect on the free energy landscape of an explicit square-well solvent, where the beads that can form intra-chain bonds can also form (weaker) bonds with solvent molecules while other beads are insoluble, is also examined. Simulations for chains of 15, 20 and 25 beads show that at low temperatures, the most likely structures are collapsed helical structures. The temperature at which collapsed helical structures become dominant is higher than in the absence of a solvent. Finally, the dynamics of the protein-like chain immersed in an implicit hard sphere solvent is studied using a simple model in which the implicit solvent interacts on a fast time scale with the chain beads and provides sufficient friction so that the motion of monomers is governed by the Smoluchowski equation. Using a Markovian model of the kinetics of transitions between conformations, the equilibration process from an ensemble of initially extended configurations to mainly folded configurations is investigated at low effective temperatures for a number of different chain lengths. It was observed that folding profiles appear to be single exponentials and independent of temperature at low temperatures.

The electrical properties, in particular the U–I characteristics, current and voltage signal shapes within the pulse, are important parameters for the understanding of the processes taking place in the pulsed glow discharge (PGD). The electrical properties are also closely related to the analytical performance of the PGD such as sputtering rates, crater shapes and emission yields. Moreover, the dependence of the U–I plots on the density of the discharge gas can be used to estimate the gas temperature. This result is relevant for the analysis of thermally fragile samples. Nevertheless, there is a lack of PGD studies where the current and voltage signals are considered in detail. Therefore, this article is dedicated to the electrical properties of PGD. The influence of the PGD parameters (duty cycle and pulse duration) on the electrical properties is examined. The results highlight the optimum parameters for particular analytical applications. The question, whether direct current (dc) and radio frequency (rf) discharges behave similarly is also discussed and all experiments are performed for both modes. The comparative studies reveal strong similarities between dc and rf pulsed discharges. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

In dieser Dissertation werden algorithmische Verbesserungen und Varianten für Simulationen der zwei-Flavor Gitter QCD mit dynamischen Fermionen studiert. Der O(a)-verbesserte Dirac-Wilson-Operator wird im Schrödinger Funktional mit einem Update des Hybrid Monte Carlo (HMC)-Typs verwendet. Sowohl der Hermitische als auch der nicht-Hermitische Operator werden betrachtet. Für den Hermitischen Dirac-Wilson-Operator untersuchen wir die Vorteile des symmetrischen gegenüber dem asymmetrischen Gerade-Ungerade-Präkonditionierens, wie man von einem mehr Zeitskalen-Integrator profitieren kann, sowie die Auswirkungen der kleinsten Eigenwerte auf die Stabilität des HMC Algorithmus. Im Fall des nicht-Hermitischen Operators leiten wir eine (semi)-analytische Schranke für das Spektrum her und zeigen eine Methode, um Informationen über den spektralen Rand zu gewinnen, indem wir komplexe Eigenwerte mit dem Lanczos-Algorithmus abschätzen. Diese spektralen Ränder erlauben es, Vorzüge des symmetrischen Gerade-Ungerade-Präkonditionierens oder den Effekt des Sheikholeslami-Wohlert-Terms für das Spektrum des nicht-Hermitischen Operators zu zeigen. Unter Verwendung der Informationen des spektralen Randes konstruieren wir angepasste, komplexe, skalierte und verschobene Tschebyschow Polynome zur Approximation des inversen Dirac-Wilson-Operators. Basierend auf diesen Polynomen entwickeln wir eine neue HMC-Variante, genannt nicht-Hermitischer polynomialer Hybrid Monte Carlo (NPHMC). Sie erlaubt, vom Importance Sampling unter Kompensation mit einem Gewichtungsfaktor abzuweichen. Zudem wird eine Erweiterung durch Anwendung des Hasenbusch-Tricks abgeleitet. Erste Größen der Leistungsfähigkeit, die die Abhängingkeit von den Eingabeparametern als auch einen Vergleich mit unserem Standard-HMC zeigen, werden präsentiert. Im Vergleich der beiden ein-Pseudofermion-Varianten ist der neue NPHMC etwas besser; eine eindeutige Aussage im Fall der zwei-Pseudofermion-Variante ist noch nicht möglich. / In this thesis algorithmic improvements and variants for two-flavor lattice QCD simulations with dynamical fermions are studied using the O(a)-improved Dirac-Wilson operator in the Schrödinger functional setup and employing a hybrid Monte Carlo-type (HMC) update. Both, the Hermitian and the Non-Hermitian operator are considered. For the Hermitian Dirac-Wilson operator we investigate the advantages of symmetric over asymmetric even-odd preconditioning, how to gain from multiple time scale integration as well as how the smallest eigenvalues affect the stability of the HMC algorithm. In case of the non-Hermitian operator we first derive (semi-)analytical bounds on the spectrum before demonstrating a method to obtain information on the spectral boundary by estimating complex eigenvalues with the Lanzcos algorithm. These spectral boundaries allow to visualize the advantage of symmetric even-odd preconditioning or the effect of the Sheikholeslami-Wohlert term on the spectrum of the non-Hermitian Dirac-Wilson operator. Taking advantage of the information of the spectral boundary we design best-suited, complex, scaled and translated Chebyshev polynomials to approximate the inverse Dirac-Wilson operator. Based on these polynomials we derive a new HMC variant, named non-Hermitian polynomial Hybrid Monte Carlo (NPHMC), which allows to deviate from importance sampling by compensation with a reweighting factor. Furthermore an extension employing the Hasenbusch-trick is derived. First performance figures showing the dependence on the input parameters as well as a comparison to our standard HMC are given. Comparing both algorithms with one pseudo-fermion, we find the new NPHMC to be slightly superior, whereas a clear statement for the two pseudo-fermion variants is yet not possible.

The electrical properties, in particular the U–I characteristics, current and voltage signal shapes within the pulse, are important parameters for the understanding of the processes taking place in the pulsed glow discharge (PGD). The electrical properties are also closely related to the analytical performance of the PGD such as sputtering rates, crater shapes and emission yields. Moreover, the dependence of the U–I plots on the density of the discharge gas can be used to estimate the gas temperature. This result is relevant for the analysis of thermally fragile samples. Nevertheless, there is a lack of PGD studies where the current and voltage signals are considered in detail. Therefore, this article is dedicated to the electrical properties of PGD. The influence of the PGD parameters (duty cycle and pulse duration) on the electrical properties is examined. The results highlight the optimum parameters for particular analytical applications. The question, whether direct current (dc) and radio frequency (rf) discharges behave similarly is also discussed and all experiments are performed for both modes. The comparative studies reveal strong similarities between dc and rf pulsed discharges. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Ziel dieser Arbeit war es, ein enantiomerenspezifisches Analysenverfahren für die Bestimmung von Hexabromcyclododecan (HBCD) in Biota-Proben zu entwickeln und die bei erhöhten Temperaturen auftretende Isomerisierung der HBCD-Stereoisomere zu untersuchen. Als erstes wurden die sechs HBCD-Enantiomere isoliert, mittels Einkristallstrukturanalyse, NMR- und IR-Spektroskopie charakterisiert und erstmals die spezifischen Drehwinkel der reinen Enantiomere mit den absoluten Konfigurationen und der Elutionsreihenfolge auf einer chiralen beta-PM-Cyclodextrin-Phase korreliert. Die Untersuchungen der HBCD-Enantiomere in Biota-Proben wurden mit einem HPLC-Tandem-MS-System unter Verwendung einer Kombination aus einer C18- und einer chiralen beta-PM-Cyclodextrin-Phase durchgeführt. Das entwickelte Analysenverfahren wurde validiert und ein Messunsicherheitsbudget erstellt. Die mittlere Wiederfindung für die internen Standards lag im Bereich von 96 - 104 % und die Nachweisgrenzen lagen zwischen 6 und 21 pg/g. Mit Hilfe dieses Analysenverfahrens wurden sowohl maritime als auch Süßwasser Biota-Proben von verschiedenen Probenahmepunkten in Europa untersucht. Die ermittelten Enantiomeren-Verhältnisse, die in allen Fällen vom (±)-alpha-HBCD dominiert wurden, zeigten signifikante Abweichungen von den razemischen Zusammensetzungen. Auffällig hierbei war, dass eine bevorzugte Anreicherung der zuerst eluierenden HBCD-Enantiomere ((-)-alpha-, (-)-beta- und (+)-gamma-HBCD) stattfand. Im Ergebnis der Untersuchungen zur thermisch induzierten intramolekularen Isomerisierung der HBCD-Stereoisomere konnten die verschiedenen Isomerisierungsreaktionen eindeutig aufgeklärt und die jeweiligen Geschwindigkeitskonstanten bei einer Temperatur von 160 °C ermittelt werden. Ergänzend wurde die Isomerisierung mit Hilfe der statistischen Thermodynamik unter Verwendung eines neuen Ansatzes für die klassische Hybrid Monte-Carlo-Simulation untersucht. / The major objectives of this thesis were the development of an analytical procedure for the enantio-specific determination of hexabromocyclododecane (HBCD) in biota samples and the investigation of the interconversion of the individual HBCD isomers at elevated temperatures. The six HBCD enantiomers were isolated, characterised by X-ray diffractometry, NMR- and IR-spectroscopy and the sense of rotation was correlated for the first time with the absolute configurations of the HBCD enantiomers as well as their order of elution on a chiral beta-PM-cyclodextrine-phase. Trace quantification of the individual HBCD enantiomers was achieved by means of high performance liquid chromatography coupled to tandem mass spectrometry equipped with a combination of a C18- and a chiral analytical column. Validation data and an uncertainty budget were determined. The mean recoveries of the different enantiomeric internal standards ranged from 96 to 104 % and the limits of detection are in the range of 6 to 21 pg/g. The analytical procedure was successfully applied to marine and freshwater biota samples from different European sites. The enantiomeric pattern of the six HBCD enantiomers, with (±)-alpha-HBCD as the dominant diastereomer, was determined for all biota samples and showed in most cases a significant deviation from the technical racemate. In these cases a preferential enrichment of the first eluted enantiomers ((-)-alpha-, (-)-beta- and (+)-gamma-HBCD) could be observed. The unambiguous elucidation of the individual isomerisation reactions as well as the quantification of all respective rate constants for the interconversion of the HBCD stereoisomers at 160 °C was done. A mechanistic explanation for the differences of the rate constants which govern the composition of HBCD diastereomers at equilibrium was given. Additionally, the interconversion was investigated by means of statistical thermodynamics using a new approach to classical hybrid Monte-Carlo simulations.

Fundamental understanding of the behaviour of nuclear fuel has been of great importance. Enhancing this knowledge not only by means of experimental observations, but also via multi-scale modelling is of current interest. The overall goal of this thesis is to understand the impact of atomic interactions on the nuclear fuel material properties. Two major topics are tackled in this thesis. The first topic deals with non-stoichiometry in uranium dioxide (UO2) to be addressed by empirical potential (EP) studies. The second fundamental question to be answered is the effect of the atomic fraction of americium (Am), neptunium (Np) containing uranium (U) and plutonium (Pu) mixed oxide (MOX) on the material properties.UO2 has been the reference fuel for the current fleet of nuclear reactors (Gen-II and Gen-III); it is also considered today by the Gen-IV International Forum for the first cores of the future generation of nuclear reactors on the roadmap towards minor actinide (MA) based fuel technology. The physical properties of UO2 highly depend on material stoichiometry. In particular, oxidation towards hyper stoichiometric UO2 – UO2+x – might be encountered at various stages of the nuclear fuel cycle if oxidative conditions are met; the impact of physical property changes upon stoichiometry should therefore be properly assessed to ensure safe and reliable operations. These physical properties are intimately linked to the arrangement of atomic defects in the crystalline structure. The first paper evaluates the evolution of defect concentration with environment parameters – oxygen partial pressure and temperature by means of a point defect model, with reaction energies being derived from EP based atomic scale simulations. Ultimately, results from the point defect model are discussed, and compared to experimental measurements of stoichiometry dependence on oxygen partial pressure and temperature. Such investigations will allow for future discussions about the solubility of different fission products and dopants in the UO2 matrix at EP level.While the first paper answers the central question regarding the dominating defects in non-stoichiometry in UO2, the focus of the second paper was on the EP prediction of the material properties, notably the lattice parameter of Am, Np containing U and Pu MOX as a function of atomic fractions.The configurational space of a complex U1-y-y’-y’’PuyAmy’Npy’’O2 system, was assessed via Metropolis-Monte Carlo techniques. From the predicted configuration, the relaxed lattice parameter of Am, Np bearing MOX fuel was investigated and compared with available literature data. As a result, a linear behaviour of the lattice parameter as a function of Am, Np content was observed, as expected for an ideal solid solution. These results will allow to support and increase current knowledge on Gen-IV fuel properties, such as melting temperature, for which preliminary results are presented in this thesis, and possibly thermal conductivity in the future. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished