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The subject of this thesis is the experimental investigation of the neutron-capture cross sections of the neutron-rich, short-lived boron isotopes 13B and 14B, as they are thought to influence the rapid neutron-capture process (r process) nucleosynthesis in a neutrino-driven wind scenario.
The 13;14B(n,g)14;15B reactions were studied in inverse kinematics via Coulomb dissociation at the LAND/R3B setup (Reactions with Relativistic Radioactive Beams). A radioactive beam of 14;15B was produced via in-flight fragmentation and directed onto a lead-target at about 500 AMeV. The neutron breakup of the projectile within the electromagnetic field of the target nucleus was investigated in a kinematically complete measurement. All outgoing reaction products were detected and analyzed in order to reconstruct the excitation energy.
The differential Coulomb dissociation cross sections as a function of the excitation energy were obtained and first experimental constraints on the photoabsorption and the neutron-capture cross sections were deduced. The results were compared to theoretical approximations of the cross sections in question. The Coulomb dissociation cross section of 15B into 14B(g.s.) + n was determined to be s(15B;14B(g:s:)+n) CD = 81(8stat)(10syst) mb ; while the Coulomb dissociation cross section of 14B into a neutron and 13B in its ground state was found to be s(14B;13B(g:s:)+n) CD = 281(25stat)(43syst) mb: Furthermore, new information on the nuclear structure of 14B were achieved, as the spectral shape of the differential Coulomb dissociation cross section indicates a halolike structure of the nucleus.
Additionally, the Coulomb dissociation of 11Be was investigated and compared to previous measurements in order to verify the present analysis. The corresponding Coulomb dissociation cross section of 11Be into 10Be(g.s.) + n was found to be 450(40stat)(54syst ) mb, which is in good agreement with the results of Palit et al.
A multiple filter test for the detection of rate changes in renewal processes with varying variance
(2014)
The thesis provides novel procedures in the statistical field of change point detection in time series.
Motivated by a variety of neuronal spike train patterns, a broad stochastic point process model is introduced. This model features points in time (change points), where the associated event rate changes. For purposes of change point detection, filtered derivative processes (MOSUM) are studied. Functional limit theorems for the filtered derivative processes are derived. These results are used to support novel procedures for change point detection; in particular, multiple filters (bandwidths) are applied simultaneously in oder to detect change points in different time scales.
This work is concerned with two topics at the intersection of convex algebraic geometry and optimization.
We develop a new method for the optimization of polynomials over polytopes. From the point of view of convex algebraic geometry the most common method for the approximation of polynomial optimization problems is to solve semidefinite programming relaxations coming from the application of Positivstellensätze. In optimization, non-linear programming problems are often solved using branch and bound methods. We propose a fused method that uses Positivstellensatz-relaxations as lower bounding methods in a branch and bound scheme. By deriving a new error bound for Handelman's Positivstellensatz, we show convergence of the resulting branch and bound method. Through the application of Positivstellensätze, semidefinite programming has gained importance in polynomial optimization in recent years. While it arises to be a powerful tool, the underlying geometry of the feasibility regions (spectrahedra) is not yet well understood. In this work, we study polyhedral and spectrahedral containment problems, in particular we classify their complexity and introduce sufficient criteria to certify the containment of one spectrahedron in another one.
The ab-initio molecular dynamics framework has been the cornerstone of computational solid state physics in the last few decades. Although it is already a mature field it is still rapidly developing to accommodate the growth in solid state research as well as to efficiently utilize the increase in computing power. Starting from the first principles, the ab-initio molecular dynamics provides essential information about structural and electronic properties of matter under various external conditions. In this thesis we use the ab-initio molecular dynamics to study the behavior of BaFe2As2 and CaFe2As2 under the application of external pressure. BaFe2As2 and CaFe2As2 belong to the family of iron based superconductors which are a novel and promising superconducting materials. The application of pressure is one of two key methods by which electronic and structural properties of iron based superconductors can be modified, the other one being doping (or chemical pressure). In particular, it has been noted that pressure conditions have an important effect, but their exact role is not fully understood. To better understand the effect of different pressure conditions we have performed a series of ab-initio simulations of pressure application. In order to apply the pressure with arbitrary stress tensor we have developed a method based on the Fast Inertial Relaxation Engine, whereby the unit cell and the atomic positions are evolved according to the metadynamical equations of motion. We have found that the application of hydrostatic and c axis uniaxial pressure induces a phase transition from the magnetically ordered orthorhombic phase to the non-magnetic collapsed tetragonal phase in both BaFe2As2 and CaFe2As2. In the case of BaFe2As2, an intermediate tetragonal non-magnetic tetragonal phase is observed in addition. Application of the uniaxial pressure parallel to the c axis reduces the critical pressure of the phase transition by an order of magnitude, in agreement with the experimental findings. The in-plane pressure application did not result in transition to the non-magnetic tetragonal phase and instead, rotation of the magnetic order direction could be observed. This is discussed in the context of Ginzburg-Landau theory. We have also found that the magnetostructural phase transition is accompanied by a change in the Fermi surface topology, whereby the hole cylinders centered around the Gamma point disappear, restricting the possible Cooper pair scattering channels in the tetragonal phase. Our calculations also permit us to estimate the bulk moduli and the orthorhombic elastic constants of BaFe2As2 and CaFe2As2.
To study the electronic structure in systems with broken translational symmetry, such as doped iron based superconductors, it is necessary to develop a method to unfold the complicated bandstructures arising from the supercell calculations. In this thesis we present the unfolding method based on group theoretical techniques. We achieve the unfolding by employing induced irreducible representations of space groups. The unique feature of our method is that it treats the point group operations on an equal footing with the translations. This permits us to unfold the bandstructures beyond the limit of translation symmetry and also formulate the tight-binding models of reduced dimensionality if certain conditions are met. Inclusion of point group operations in the unfolding formalism allows us to reach important conclusions about the two versus one iron picture in iron based superconductors.
And finally, we present the results of ab-initio structure prediction in the cases of giant volume collapse in MnS2 and alkaline doped picene. In the case of MnS2, a previously unobserved high pressure arsenopyrite structure of MnS2 is predicted and stability regions for the two competing metastable phases under pressure are determined. In the case of alkaline doped picene, crystal structures with different levels of doping were predicted and used to study the role of electronic correlations.
Acceleration of Biomedical Image Processing and Reconstruction with FPGAs
Increasing chip sizes and better programming tools have made it possible to increase the boundaries of application acceleration with reconfigurable computer chips. In this thesis the potential of acceleration with Field Programmable Gate Arrays (FPGAs) is examined for applications that perform biomedical image processing and reconstruction. The dataflow paradigm was used to port the analysis of image data for localization microscopy and for 3D electron tomography from an imperative description towards the FPGA for the first time.
After the primitives of image processing on FPGAs are presented, a general workflow is given for analyzing imperative source code and converting it to a hardware pipeline where every node processes image data in parallel. The theoretical foundation is then used to accelerate both example applications. For localization microscopy, an acceleration of 185 compared to an Intel i5 450 CPU was achieved, and electron tomography could be sped up by a factor of 5 over an Nvidia Tesla C1060 graphics card while maintaining full accuracy in both cases.
Efficient algorithms for object recognition are crucial for the newly robotics and computer vision applications that demand real-time and on-line methods. Some examples are autonomous systems, navigating robots, autonomous driving. In this work, we focus on efficient semantic segmentation, which is the problem of labeling each pixel of an image with a semantic class.
Our aim is to speed-up all of the parts of the semantic segmentation pipeline. We also aim at delivering a labeling solution on a time budget, that can be decided on-the-fly. For this purpose, we analyze all the components of the semantic segmentation pipeline, and identify the computational bottleneck of each of them. The different components of the pipeline are over-segmenting the image with local regions, extracting features and classify the local regions, and the final inference of the image labeling with semantic classes. We focus on each of these steps.
First, we introduce a new superpixel algorithm to over-segment the image. Our superpixel method runs in real-time and can deliver a solution at any time budget. Then, for feature extraction, we focus on the framework that computes descriptors and encodes them, followed by a pooling step. We see that the encoding step is the bottleneck, for computational efficiency and performance. We present a novel assignment-based encoding formulation, that allows for the design of a new, very efficient, encoding. Finally, the image labeling output is obtained modeling the dependencies with a Conditional Random Field (CRF). In semantic image segmentation, the computational cost of instantiating the potentials is much higher than MAP inference. We introduce Active MAP inference to on-the-fly select a subset of potentials to be instantiated in the energy function, leaving the rest as unknown, and to estimate the MAP labeling from such incomplete energy function.
We perform experiments on all proposed methods for the different parts of the semantic segmentation pipeline. We show that our superpixel extraction achieves higher accuracy than state-of-the-art on standard superpixel benchmark, while it runs in real-time. We test our feature encoding on standard image classification and segmentation benchmarks, and we show that our method achieves competitive results with the state-of-the-art, and requires less time and memory. Finally, results for semantic segmentation benchmark show that Active MAP inference achieves similar levels of accuracy but with major efficiency gains.
Drought stress is one of the major abiotic factors diminishing crop productivity world wide. In the course of climate change, regions which already experience dry seasons nowadays will suffer from elongated drought periods and water shortage. These climatic changes will not only have an impact on the regional flora and fauna but also on the people inhabiting these areas. It is therefore of great importance to understand the reactions of plants to drought stress to help breeding and biotechnological approaches for the benefit of new robust cereal cultures growing under low water regimes. In this dissertation four grasses of the genus Panicum, P. bisulcatum (C3), P. laetum, P. miliaceum and P. turgidum (all C4 NAD-ME) were subjected to drought stress. The plants diverse reactions were investigated on a physiological as well as on a molecular level to deepen the understanding of drought stress responses. Drought stress was imposed for a species-specific period until a relative leaf water content (RWC) of ~50 % was reached in each grass. Physiological measurements were conducted on leaves with a RWC of ~50 % investigating chlorophyll a fluorescence parameters with a Plant Efficiency Analyzer (PEA) and gas exchange parameters like the photosynthesis rate and stomatal conductance with a Gas Fluorescence Chamber (GFS-3000). Subsequent molecular analysis were conducted on leaf samples taken (RWC = 50 %) analysing different proteins and the transcriptome of the Panicum species. The physiological measurements revealed a higher photosynthesis rate for the C4 grasses under drought stress with no significant differences between the C4 species. Also the water use efficiency was significantly higher in the C4 species in comparison to the C3 species independent from the water regime supporting results from the literature. The chlorophyll a measurements revealed the strongest adaptation to water shortage in the C4 species P. turgidum followed by the C3 species P. bisulcatum. It has been shown before (GHANNOUM 2009) that the C4 photosynthesis apparatus is more prone to drought stress than the C3 apparatus – despite the higher water use efficiency. Results also suggested that the great adaptation of P. turgidum to drought stress arose from its ability to recover from drought stress (all JIP test parameters showed no significant differences between control and recovery samples). The additional down-regulation of PS II but not of PS I under drought stress also helped the plant to endure times of water shortage and facilitated the recovery when water was available again. Protein analyses on the content of PEPC, OEC and RubisCO (LSU and SSU) revealed no changes. Dehydrin 1 in contrast was strongly up-regulated under drought stress and Summary 108 recovery in all four Panicum species. The stable content of the OEC protein was therefore not the catalyst of rising K peaks measured by chlorophyll a fluorescence and a reduced OEC activity was supposed. Transcriptomic analyses revealed a myriad of differentially regulated tags. Due to unsequenced genomes, tags could only be partially (8 % maximum for P. turgidum) annotated to their specific genes. Diverse methods were therefore used to annotate the most highly regulated tags to their genes and their products. Special emphasis was put on the regulation of five gene products confirming the regulation schemata from the HT-SuperSAGE analyses. Interestingly one protein – the NCED1 – was down-regulated under stress conditions, in contrast to results from the literature. It is therefore of great importance to investigate longer lasting drought to understand the full range of drought stress adaptation. Future genome sequencing projects might also include the Panicum species investigated in this dissertation and important gene candidates with no hits (maybe completely new to the research community) might help breeding and biotechnology approaches to produce more drought resistant crop species.
In the past sixty years, excessive water consumption and dam construction have significantly influenced natural flow regimes and surface freshwater ecosystems throughout China, and thus resulted in serious environmental problems. In order to balance the competing water demands between human and environment and provide knowledge on sustainable water management, assessments on anthropogenic flow alterations and their impacts on aquatic and riparian ecosystems in China are needed.
In this study, the first evaluation on quantitative relationships between anthropogenic flow alterations and ecological responses in eleven river basins and watersheds in China was performed based on the data that could be obtained from published case studies. Quantitative relationships between changes in average annual discharge, seasonal low flow and seasonal high flow and changes in ecological indicators (fish diversity, fish catch and vegetation cover, etc.) were analyzed. The results showed that changes in riparian vegetation cover as well as changes in fish diversity and fish catch were strongly correlated with the changes in flow magnitude (r = 0.77, 0.66), especially with changes in average annual river discharge. In addition, more than half of the variations in vegetation cover could be explained by changes in average annual river discharge (r² = 0.63) and roughly 50 % changes in fish catch in arid and semi-arid region and 60% changes of fish catch in humid region could be related to alterations in average annual river discharge (r² = 0.53, 0.58).
In a supplementary analysis of this study, the first estimation on quantitative relationships between decreases in native fish species richness and anthropogenic flow alterations in 34 river basins and sub-basins in China was conducted. Linear relationships between losses of native fish species and five ecologically relevant flow indicators were analyzed by single and multiple regression models. For the single regression analysis, significant linear relationships were detected for the indicators of long-term average annual discharge (ILTA) and statistical low flow Q90 (IQ90). For the multiple regressions, no indicator other than ILTA has significant relationships with changes in number of fish species mainly due to collinearity. Two conclusions emerged from the analysis: 1) losses of fish species were positively correlated with changes in ILTA in China and 2) indicator of ILTA was dominant over other flow indicators included in this research for the given dataset. These results provide a guideline for the sustainable water resources management in rivers with high risk of fish extinction in China.
The human endothelin receptors, ETA and ETB, are two members of the G-protein coupled receptors family (GPCRs) and they are key players in cardiovascular regulation. The characterization of their functionality in vitro has been limited by the possibility to obtain high quality samples using conventional expression systems. The Cell-Free expression system is an alternative technique for the production of membrane protein as well as GPCRs and can overcome some of the limitations that are commonly encountered using an in vivo approach. Cell-Free expression protocols for the two receptors ETA and ETB have been optimized by implementing post- and co-translational association to lipid bilayers. The efficiency of the reconstitution or association to liposomes and nanodiscs has systematically been studied and the ligand binding properties of the two receptors have been analyzed using a set of different complementary techniques. In several different conditions a high affinity binding of the peptide ligand ET-1 to both endothelin receptors could be obtained and the highest activity values were detected in sample prepared using a co-translational approach in presence of nanodiscs. Furthermore, the characteristic differential binding pattern of selected agonists and antagonists to the two receptors was confirmed. In samples obtained from several Cell-Free expression conditions, two intrinsic properties of the functionally folded ETB receptor, such as the proteolytic processing based on conformational recognition as well as the formation of SDS-resistant complexes with the peptide ligand ET-1, were detected. ETA and ETB are able to induce in vivo the activation of hetrotrimeric G proteins upon stimulation with an agonist, leading to the dissociation of the heterotrimeric complex and the exchange of GDP to GTP in the Galpha subunit. The Cell-Free expression system was chosen for the production of two G alpha subunit, Galpha s and Galpha q. Soluble expression of the two proteins was achieved and the production of active Galpha s was confirmed using fluorescent as well as radioactive assays. In conclusion, the obtained results document a new process for the production of ligand binding competent endothelin receptors, as well as Galpha proteins, using a Cell-Free expression system. The combination of this expression system and the nanodiscs technology appears to be a promising tool for the further characterization of membrane proteins as well as GPCRs.
During the last decade of the 20th century, the field of mass spectrometry has seen a revolutionary change in its application and scope. The introduction of soft ionization methods for the analysis of biological molecules has expanded the area of mass spectrometry from its early roots in the analysis of inorganic and organic species into the fields of biology and medicine.
Today, the use of the mass spectrometry is extended to a wide range of applications in biotechnology and pharmaceutical industry, in geological, environmental and clinical research. In biochemistry, the principles of mass spectrometry are, however, broadly applicable in accurate molecular weight determination, reaction monitoring, amino acid sequencing, oligonucleotide sequencing and protein structure.
In order to carry out their biological activities, proteins interact most often to each other and form transient or stable complexes. In addition, some proteins specifically interact also with other proteins or with non-protein molecules, such as DNA, RNA or metabolites, these interactions being critical for their function. Hence, defining the composition of protein complexes, as well as understanding how protein complexes are assembled and regulated yield invaluable insights into protein function. Coupled with an isolation technique to purify a specific protein complex of interest, mass spectrometry can rapidly and reliably identify the components of complexes. In addition, quantitative MS techniques offer the possibility of studying dynamically regulated interactions....
The Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes high fever, rash, and recurrent arthritis in humans. The majority of symptoms disappear after about one week. However, arthritis can last for months or even years (in about 30% of cases), which makes people unable to work during this period. The virus is endemic in Sub-Saharan Africa, the Indian Ocean islands, India, and Southeast Asia. It has additionally caused several large outbreaks in the last few years, affecting millions of people. The mortality rate is very low (0.1%), but the infection rates are high (sometimes 30%) and the number of asymptomatic cases is rare (about 15%). The first CHIKV outbreak in a country with a moderate climate was detected in Italy in 2007. Furthermore, the virus has spread to the Caribbean in late 2013. Due to climate change, globalization, and vector switching, the virus will most likely continue to cause new worldwide outbreaks. Additionally, more temperate regions of the world like Europe or the USA, which have recently reported their first cases, will likely become targets. Alarmingly, there is no specific treatment or vaccination against CHIKV available so far.
The cell entry process of CHIKV is also not understood in detail, and was thusly the focus of study for this project. The E2 envelope protein is responsible for cell attachment and entry. It consists of the domain C, located close to the viral membrane, domain A, in the center of the protein, and domain B, at the distal end, prominently exposed on the viral surface.
In this work, the important role of cell surface glycosaminoglycans (GAGs) for CHIKV cell attachment was uncovered. GAGs consist of long linear chains of heavily sulfated disaccharide units and can be covalently linked to membrane associated proteins. They play an important role in different cell signaling pathways. So far, solely cell culture passage has revealed an increased GAG-dependency of CHIKV due to mutations in E2 domain A, which was associated with virus attenuation in vivo. However, in this work it could be shown that cell surface GAGs promote CHIKV entry using non-cell culture adapted CHIKV envelope (Env) proteins. Transduction and infection of cell surface GAG-deficient pgsA-745 cells with CHIKV Env pseudotyped vector particles (VPs) and with wild-type CHIKV revealed decreased transduction and replication rates. Furthermore, cell entry and transduction rates of GAG-containing cells were also dose-dependently decreased in the presence of soluble GAGs. In contrast, transduction of pgsA-745 cells with CHIKV Env pseudotyped VPs was enhanced by the addition of soluble GAGs. This data suggests a mechanism by which GAGs activate CHIKV particles for subsequent binding to a cellular receptor. However, at least one GAG-independent entry pathway might exist, as CHIKV entry could not be totally inhibited by soluble GAGs and entry into pgsA-745 was, albeit at a lower rate, still possible. Further binding experiments using recombinant CHIKV E2 domains A, B, and C suggest that domain B is responsible for the GAG binding, domain A possibly for receptor binding, and domain C is not involved in cell binding. These results are in line with the geometry of CHIKV Env on the viral surface. They altogether reveal that GAG binding promotes viral cell entry and that the E2 domain B plays a central role for this mechanism.
As no vaccine against CHIKV has been approved so far, another goal of this project was to test new vaccination approaches. It has been published that a single linear epitope of E2 is the target of the majority of early neutralizing antibodies against CHIKV in patients. Artificial E2-derived proteins were created, expressed in E.coli, and successfully purified. They consisted of 5 repeats of the mentioned linear epitope (L), the surface exposed regions of domain A linked by glycine-serine linkers (sA), the whole domain B plus a part of the β-ribbon connector (B+), or a combination of these 3 modules. Vaccination experiments revealed that B+ was necessary and sufficient to induce a neutralizing immune response in mice, with the protein sAB+ yielding the best results. sAB+, as a protein vaccine, efficiently and significantly reduced viral titers in mice upon CHIKV challenge, which was not the case for recombinant Modified Vaccinia virus Ankara (MVA; MVA-CHIKV-sAB+), as a vaccine platform expressing the same protein. These experiments show that a small rationally designed CHIKV Env derived protein might, after optimization of some vaccination parameters, be sufficient as a safe, easy-to-produce, and cheap CHIKV vaccine.
Epigallocatechin-3-gallate (EGCG) is a catechin found in green tea and was, in this work, found to inhibit the CHIKV life cycle at the entry state in in vitro experiments using CHIKV Env VPs and wild-type virus. EGCG was recently published to inhibit attachment of several viruses to cell surface GAGs, which is in line with the role for GAGs in CHIKV entry revealed in this work. EGCG might serve as a lead compound for the development of a small molecule treatment against CHIKV.
Heme-copper oxidases (HCOs) are the terminal enzymes of the aerobic respiratory chain in the inner mitochondrial membrane or the plasma membrane in many prokaryotes. These multi-subunit membrane protein complexes catalyze the reduction of oxygen to water, coupling this exothermic reaction to the establishment of an electrochemical proton gradient across the membrane in which they are embedded. The energy stored in the electrochemical proton gradient is used e.g. by the FOF1-ATP synthase to generate ATP from ADP and inorganic phosphate. The superfamily of HCOs is phylogenetically classified into three major families: A, B and C. The A-family HCOs, represented by the well-studied aa3-type cytochrome c oxidases (aa3-CcOs), are found in mitochondria and many bacteria. The B-family of HCOs contains a number of bacterial and archaeal oxidases. The C-family comprises only the cbb3-type cytochrome c oxidase (cbb3-CcO) and is most distantly related to the mitochondrial respiratory oxidases.
In this thesis, a novel 257 kHz chopper device was numerically developed, technically designed and experimentally commissioned; a 4-solenoid, low-energy ion beam transport line was numerically investigated, installed and experimentally commissioned; and a novel massless beam-separation system was numerically developed.
The chopper combines a pulsed electric field with a static magnetic field in an ExB or Wien-filter type field configuration. Chopped beam pulses with a 257 kHz repetition rate and rise times of 110 ns were experimentally achieved using a 14 keV helium beam.
Due to the achieved results, the complete LEBT line for the future Frankfurt Neutron Source FRANZ is ready to deliver a dc or a pulsed beam. At the same time, the LEBT section represents an attractive test stand for the study of low-energy ion beams. It combines magnetic lenses, which allow space-charge compensated beam transport, and a chopper system capable of producing short beam pulses in the hundred nanosecond range. Since these beam pulses are transported onwards, their longitudinal and transverse properties can be analyzed. The pulse duration and time of flight are well below the rise time for the space-charge compensation through residual gas ionization. This opens the possibility for dedicated investigations of the transport of short, low-energy beam pulses including longitudinal and transverse space-charge effects and of relevant issues like the dynamics of space-charge compensation and electron effects in short pulses.
During this study clumped isotope analysis of carbonates was established at the Goethe University of Frankfurt, Germany. Therefore, preparation protocols and analytical parameters were elaborated to obtain precise and accurate Δ47 data. Briefly, analyte CO2 was cleaned cryogenically using glass extraction lines to remove traces of water that enable re-equilibration of C–O bonds in the gases. Furthermore, analyte CO2 was passed through a gas chromatograph (GC) to clean it from contaminants that produce isobaric interferences with m/z 47. Initially, phosphoric acid digestions of carbonates was conducted at 25 °C in McCrea-type reaction vessels. Afterwards samples were reacted at 90 °C using a common acid bath. Mass spectrometric analyses were performed using a MAT 253 equipped with a dual inlet system. Δ47 values were directly projected to the absolute scale using CO2 gases equilibrated at distinct temperatures.
In cooperation with Stefano Bernasconi and his research group at ETH Zurich we studied the non-linearity that occurs for the measurement of m/z 47. This effect results from secondary electrons created by the m/z 44 beam. These electrons cause a negative background on the m/z 47 collector. A correction procedure was proposed that relies on the determination of the negative background on the m/z 47 Faraday cup. This approach might reduce time-consuming analyses of heated gases which were used so far to account for the observed non-linearity. However, the suggested correction of the negative background on the m/z 47 cup is only applicable if the slit width of the m/z 44 beam is significantly wider than that of the m/z 47 beam.
This thesis, furthermore, presents a comparison of the different phosphoric acid digestion techniques which are commonly used for carbonate clumped isotope analysis. For calcitic and aragonitic material digested at 25 °C in McCrea-type vessels we observed that the sample size has an effect on Δ47 data: higher mean Δ47 values and a larger scatter of data were received for samples <7 mg than for larger aliquots. For carbonate samples digested at 90 °C in a common acid bath no sample size effect was determined. We assume that secondary re-equilibration of CO2 with water preferentially occurs at 25 °C producing the observed differences. However, a sample size effect can be avoided if reaction temperature is increased to 90 °C.
In order to make carbonate Δ47 data obtained from acid digestions at 90 °C comparable to Δ47 data received from reactions at 25 °C the difference of the acid fractionation factores (Δ47*25-90) between both temperatures has to be known. For the determination of the Δ47*25-90 value we have considered Δ47 data made at 25 °C from samples >7 mg only. For calicte and aragonite we obtained differences in fractionation factores of 0.075‰ and 0.066‰, respectively. These Δ47*25-90 values are coincident with the theoretical prediction of 0.069‰ proposed for calcite (Guo et al., 2009).
Moreover, this dissertation comprises a calibration study of the clumped isotope thermometer based on various natural calcites that grew between 9 and 38 °C. The samples include a brachiopod shell, a bivalve shell, an eggshell of an ostrich and foraminifera tests which formed from distinct biomineralizing processes. Furthermore we included an authigenic carbonate crystallized from biological-induced precipitation. The following linear relationship between 1/T2 and Δ47 was determined (with Δ47 in ‰ and T in K):
Δ47 = 0.0327 (± 0.0026) x 106 / T2 + 0.3030 (± 0.0308) (R2 = 0.9915)
This equation differs from the pioneering Ghosh et al. (2006a) calibration. However, our regression line is statistically indistinguishable from that of Henkes et al. (2013) which is based on aragonitic mollusks and calcitic brachiopod shells. Both studies have in common that calibration data were, at first, directly referenced to the absolute scale. In addition, both datasets rely on similar digestion techniques. Furthermore, the two calibrations are conform with the theoretical prediction of Guo et al. (2009).
The calcite calibration of the clumped isotope paleothermometer received in this study was applied to Δ47 data measured for Silurian brachiopods shells from Gotland/Sweden. Prior to isotopic analysis the fossils were intensively investigated for their preservation state (CL, SEM, trace elements). The lowest T(Δ47) values of ca. 28 to 33 °C were estimated from ultrastructurally well-preserved regions of some shells. For these samples also the lowest δ18Ow values of Silurian seawater were determined. These estimates of ca. −1‰ confirm the assumption that the δ18O value of the Silurian ocean was buffered to (0 ± 1)‰.
Nevertheless, most studied shells were characterized by a patchwork of pristine and altered shell portions resulting in elevated T(Δ47) values which plot mostly between 40 and 60 °C. Our results indicate that the clumped isotopic composition of the shells were altered at low water-rock ratios, not affecting the δ18O values. Δ47 and δ18O data of associated diagenetic phases (sparitic and micritic phases of the inner fillings of the fossils) provide evidence that the sparitic cements grew during several diagenetic events which occurred at different temperatures in fluid-buffered systems. We, furthermore, conclude that the micritic phases lithified at a very early diagenetic stage with the δ18O values being most probably close to a Silurian seawater composition
The work presented in this thesis is devoted to two classes of mathematical population genetics models, namely the Kingman-coalescent and the Beta-coalescents. Chapters 2, 3 and 4 of the thesis include results concerned with the first model, whereas Chapter 5 presents contributions to the second class of models.
Cognitive flexibility and cognitive stability : neural and behavioral correlates in men and mice
(2014)
The ability to flexibly adjust behavior according to a changing environment is crucial to ensure a species' survival. However, the successful pursuit of goals also requires the stable maintenance of behavior in the face of potential distractors. Thus, cognitive flexibility and cognitive stability are important processes for the cognitive control of behavior. There is a large body of behavioral and neuroimaging research concerning cognitive control in general, but also specifically on cognitive flexibility and cognitive stability, albeit most often assessed in separate task paradigms. Nevertheless, whether cognitive flexibility and cognitive stability depend upon separate or shared neuronal bases is still a matter of debate. Complementing empirical research, computational models have become an important strategy in neuroscientific research, as they have the potential of providing mechanistic explanations of empirical observations, for example by allowing for the direct manipulation of molecular parameters in simulated neural networks. The computational model underlying the so-called Dual-State Theory contains specific hypotheses with respect to cognitive flexibility and cognitive stability. The neural networks simulated by this model exhibit multiple stable firing states, i.e., the neural network can maintain a high firing state also without continuing external input due to a network architecture consisting of recurrently connected neurons. Transitions between such network states, also called attractor states, can be induced by external input, and represent working memory contents or active task rules. Simulations showed that the stability of these attractor states, and thus of task rule representations, depend on the dopamine state of the system and can consequently vary between persons. The Dual-State Theory predicts an antagonistic relationship between cognitive flexibility and cognitive stability, as robust attractor states would facilitate the inhibition of distractors, but impair efficient task switching, while rather unstable attractor states would promote efficient transitions between representations but would also come at the cost of increased distractibility.
Based on the Dual-State Theory, a task paradigm was designed allowing for the simultaneous assessment of cognitive flexibility, in the sense of rule-based task switching, and cognitive stability, in the sense of inhibiting irrelevant distractors. Furthermore, a behavioral measure was developed to assess the individual attractor state stability, named spontaneous switching rate (SSR). In the first study of this work, this paradigm was tested in a sample of healthy human subjects using functional magnetic resonance imaging (fMRI). An overlapping fronto-parietal network was activated for both cognitive flexibility and cognitive stability. Furthermore, behavioral as well as neuroimaging results are in favor of an antagonistic relationship between cognitive flexibility and cognitive stability. A specific prefrontal region, the inferior frontal junction (IFJ), was implied to potentially contain the relevant neural networks mediating the transitions between attractor states, i.e., task rule representations, as its activity was modulated by the SSR such that persons with rather unstable attractor states activated it less during task switching while showing better performance. Most importantly, functional connectivity of the IFJ was antagonistically modulated by the SSR: more flexible persons connected it less to another prefrontal area during task switching, while showing higher functional connectivity during distractor inhibition.
In a second study, a larger human sample was assessed and further hypotheses derived from the Dual-State Theory on variability of neural processing were tested: we hypothesized that persons with high brain signal variability should have less stable network states and thus benefit on tasks requiring cognitive flexibility but suffer from it when the task requires a higher degree of cognitive stability. Furthermore, recent fMRI-research on brain signal variability revealed beneficial effects of higher brain signal variability on cognitive performance in general. Using a novel customized analysis pipeline to measure trial-to-trial fMRI-signal variability, we indeed found differential effects of brain signal variability: higher levels of brain signal variability were found to be beneficial for effectiveness, i.e., performance in terms of error rates, for both cognitive flexibility and stability. However, brain signal variability impaired the efficiency in terms of response times of inhibiting distractors, i.e., cognitive stability.
Due to further predictions of the Dual-State Theory concerning schizophrenia and the dopaminergic system, it was considered valuable to pursue a translational approach and thus allowing for the employment of animal models of psychiatric diseases. Consequently, in a first step the human paradigm was translated for a murine population using an innovative touchscreen approach. Results showed analogous behavioral effects in wildtype mice as before in healthy humans: the antagonistic relation between cognitive flexibility and cognitive stability was replicated and also for mice, a behavioral measure for the individual attractor stability was established and validated, named the individual spontaneous switching score.
To conclude, we established a novel paradigm assessing both cognitive flexibility and stability simultaneously showing an antagonistic relationship between these two cognitive functions on the behavioral level in two different species, which supports predictions from the Dual-State Theory. This was further underlined by evidence on the activation, functional connectivity and signal variability level in the human brain.
Construction and commissioning of a setup to study ageing phenomena in high rate gas detectors
(2014)
In high-rate heavy-ion experiments, gaseous detectors encounter big challenges in terms of degradation of their performance due to a phenomenon dubbed ageing. In this thesis, a setup for high precision ageing studies has been constructed and commissioned at the GSI detector laboratory. The main objective is the study of ageing phenomena evoked by materials used to build gaseous detectors for the Compressed Baryonic Matter (CBM) experiment at the future Facility for Antiproton and Ion Research (FAIR).
The precision of the measurement, e.g., of the gain of a gaseous detector, is a key element in ageing studies: it allows to perform the measurement at realistic rates in an acceptable time span. It is well known the accelerating ageing employing high intensity sources might produce misleading results. The primary objective is to build an apparatus which allows very accurate measurements and is thus sensitive to minute degradations in detector performance. The construction and commissioning of the
setup has been carried out in two steps. During the first step of this work, a simpler setup which already existed in the detector laboratory of GSI had been utilised to define all conditions related to ageing studies. The outcome of these studies defined the properties and characteristics that must be met to build and operate a new, sophisticated and precise setup. The already existing setup consisted of two identical Multi Wire Proportional Chambers (MWPCs), a gas mixing station, an 55Fe source, an x-ray generator, an outgassing box and stainless steel tubing. In a first step, the gain and electric field configuration of the MWPCs were simulated by a combination of a gas simulation (Magboltz) and electric field simulation program (Garfield). The performance and operating conditions of the chambers have been thoroughly characterised before utilising them in first preparatory ageing test. The main diagnostic parameter in ageing studies is the detector gain, thus it is mandatory for precise ageing studies to minimise the systematic and statistical variation of the pressure and temperature corrected gain. To achieve the required accuracy, several improvements of the chamber design and the gas system have been implemented. In addition, the temperature measurement has been optimised. During the preparatory tests, several ageing studies have been carried out. The ageing effect of seven materials and gases have been carried out during these tests: RTV-3145, Ar/CO2 gas, Durostone flushed with Ar/Isobutane gas, Vetronit G11, Vetronit G11 contaminated with Micro 3000 and Gerband 705. The results of these studies went into the design of the new sophisticated ageing setup. For example some tests revealed that there was, even after cleaning, a certain level of contamination with "ageing agents" in the existing setup, which made it imperative to ensure a very high level cleanness of all components during the construction of the setup. The curing period of some testing samples like glues or the gas flow rate were found to be very important factors that must be taken into account to obtain comparable results. Very important changes in the chamber design have been made, i.e., the aluminium-Kapton cathodes used in MWPCs have been replaced with multi-wire planes and the fibreglass housing of the chamber has been changed to metal. The second step started with building the new setup which was designed based on the findings from the first step. The new ageing setup consists of three MWPCs, two moving platforms, an 55Fe source, a copper-anode x-ray generator, two outgassing boxes, both flexible and rigid stainless steel tubes. Before fabrication of the chambers, simulations of their electric field and the gain have been done using Magboltz and Garfield programs. After that, the chambers were installed and tested. A 0.3% peak-to-peak residual variation of the corrected gain has been achieved. Finally, the complete setup has been operated with full functionality in no-ageing conditions during one week. This test revealed very stable gain in all three chambers. After that two materials (Gerban 705 and RTV-3145) have been inserted in the two outgassing boxes and tested. They revealed an ageing rate of about 0.3%/mC/cm and 3%/mC/cm respectively. The final test proves the stability and accuracy of the ageing measurements carried out with the ageing setup at the detector laboratory at GSI which is ready to conduct the envisaged systematic ageing studies.
Der Radiofrequenzquadrupol (RFQ) wird typischerweise als erstes beschleunigendes Element in Beschleunigeranlagen eingesetzt. Das elektrische Quadrupolfeld ermöglicht die gleichzeitige Fokussierung und Beschleunigung des Ionenstrahls. Zudem ist der RFQ in der Lage den Gleichstromstrahl von der Ionenquelle zu Teilchenpaketen (Bunche) zu formen, die von den nachfolgenden Driftröhrenbeschleunigern benötigt werden. Ziel der vorliegenden Arbeit war die Untersuchung zur Realisierbarkeit eines 325 MHz 4-rod RFQ Beschleunigers. Die Frequenz von 325 MHz stellt eine ungewöhnlich hohe Betriebsfrequenz für die 4-rod Struktur dar und wird z.B. für den Protonenlinac des FAIR Projektes benötigt. Ein Problem hierbei war, dass durch die bauartbedingten unsymmetrischen Elektrodenaufhängung und der hohen Frequenz ein, das Quadrupolfeld überlagerndes, Dipolfeld erzeugt wird. Dieses störende Feld kann z.B. zu einem Versatz der Strahlachse führen. Hierzu wurde die 4-rod Struktur in Simulationen grundlegend auf Einflüsse von verschiedenen Parametern auf die Resonanzfrequenz und das Dipolfeld untersucht. Es wurden Lösungsstrategien erarbeitet das Diopolfeld zu kompensieren und auf einen Prototypen angewendet. Zudem wurde das Verhalten höherer Schwingungsmoden dieser Struktur simuliert. In diesem Rahmen wurden auch Simulationen zu Randfeldern zwischen den 4-rod Elektroden und der Tankwand untersucht, um nachteilige Effekte für die Strahlqualität auszuschließen. Basierend auf den Simulationsergebnissen wurde ein Prototyp angefertigt. Dieser Prototyp wurde zur Demonstration der Betriebseigenschaften mit Leistungen bis 40 kW getestet. Hierbei wurde die Elektrodenspannung mittels Gammaspektroskopie bestimmt und daraus die Shuntimpedanz berechnet. Diese Werte wurden mit anderen Methoden der Shuntimpedanzbes- timmung verglichen. Außerdem wurden alternative RFQ Resonatorkonzepte ebenfalls auf ihre Realisierbarkeit für den Protonenlinac untersucht. Die Einflüsse verschiedener Parameter auf die Betriebsfrequenz, die Möglichkeiten des Frequenztunings und der Einstellung der longitudinalen Spannungsverteilung gefertigter Modelle wurden in einer Diskussion gegenübergestellt.
The PANDA experiment at FAIR will perform world class physics studies using high-intensity cooled antiproton beams with momenta between 1.5 and 15 GeV/c. A rich physics program requires very good particle identification (PID). Charged hadron PID for the barrel section of the target spectrometer has to cover the angular range of 22-140° and separate pions from kaons for momenta up to 3.5 GeV/c with a separation power of at least 3 standard deviations. The system that will provide it has to be thin and operate in a strong magnetic field. A ring imaging Cherenkov detector using the DIRC principle meets those requirements. The design of the PANDA Barrel DIRC is based on the successful BABAR DIRC counter with several important changes to improve the performance and optimize the costs. The design options are being studied in detailed Monte Carlo simulation, and implemented in increasingly complex system prototypes and tested in particle beams. Before building the full system prototypes the radiator bars and lenses are measured on the test benches. The performance of the DIRC prototype was quantified in terms of the single photon Cherenkov angle resolution and the photon yield. Results for two full system prototypes will be presented. The prototype in 2011 aimed at investigating the full size expansion volume. It was found that the resolution for this configuration is at the level of in good agreement with ray tracing simulation results. A more complex prototype, tested in 2012, provided the first experience with a compact fused silica prism expansion volume, a wide radiator plate, and several advanced lens options for the focusing system. The performance of the baseline configuration of the prototype with a standard lens and an air gap met the requirements for the PANDA PID for most of the polar angle range but failed at polar angles around 90° due to photon loss at the air gap. Measurements with a prototype high-refractive index compound lens without an air gap at a polar angle of 128° beam angle showed a good resolution of σΘC = 11.8 ± 0.7 mrad and a high photon yield of Nph = 26.1 ± 0.4. Even at polar angles close to 90° the photon yield with this lens exceeded 15 detected photons per particle, meeting the PANDA Barrel DIRC PID requirements for the entire phase space and demonstrating that the compact focusing DIRC is a very promising option for PANDA.