Automated Motion of a Radiation Source for Testing Micromegas Detectors & Modeling QGP Flow Coefficients Using a Particle Transport Model

This thesis consists of two independent parts. In the first section, an automated system for moving a radiation source for testing micromegas detectors was designed, assembled, and programmed. Micromegas amplify the signal from incident radiation through the ionization of the gas filling the detectors. They are reliable and maintain high accuracy under high incident particle flux conditions, but remain vulnerable to ion backflow, which reduces tracking accuracy. To characterize ion backflow, the current drawn by the detector's drift mesh can be measured. However, due to the current's picoamp scale it is very sensitive to noise and drift, which necessitates a time-consuming process of repeated, alternating measurements with a radiation source present and a control with none present. The work presented here automates the motion of the radiation source using code that is easily integrable into existing data-collection programs, in order to facilitate the measurement of ion backflow in micromegas. In the second section, a particle transport model is used to examine flow coefficients of quark-gluon plasma. These coefficients describe the modes of flow of the medium produced in collisions of relativistic nuclei. Studies using AMPT, a particle transport model, have shown that lower-order flow coefficients can be produced due to differential particle escape from the medium. This project uses a simplified particle transport model to investigate whether the escape mechanism can contribute to the quadrangular (fourth-order) flow coefficient

The historical development of West Germany’s new left from a politico-theoretical perspective with particular emphasis on the Marxistische Gruppe and Maoist K-Gruppen

There is a gap in the existing literature as to why the New Left in West Germany entered a phase of rapid decline by the end of the 1970s. The overarching aim of this thesis is to offer a politico-theoretical explanation for the historical development of the New Left and why the ‘red decade’ between 1967 and 1976/7 ended so abruptly. Within this context, the thesis will focus on the Maoist K-Gruppen and particular emphasis will be placed on the Marxistische Gruppe, which defied the general decline of West Germany’s New Left and developed into its largest organisation during the 1980s. Furthermore, the Red Cells movement will be analysed from which both currents emerged in the wake of the student movement. Key works of the Marxistische Gruppe will be analysed with particular emphasis on politico-theoretical aspects. The analysis of the group’s theoretical work will provide a better understanding of the New Left’s historical developments against the background of the changing political environment. This thesis will conclude with reflections on developments of the radical left after the collapse of the New Left in 1989/91 and how the red decade’s legacy is still prominent in the work of the Gegenstandpunkt publishing house (the Marxistische Gruppe’s ideological successor). In conclusion, this thesis will reveal that the influence of politico-theoretical aspects on the historical development of the New Left has been given too little consideration and that the New Left’s fate cannot be adequately explained by external factors, but demands the consideration of the very development of theories and the practical conclusions organisations reached regarding their social, economic and cultural circumstances. This work will be the first to provide an insight into the potential of such a theoretical explanation for an understanding of the specific developments of the post-1968 West German New Left

Rationality and distribution in the socialist economy

The thesis provides a philosophically grounded account of a socialist planned economy. While I do not primarily consider a positive case for socialism, I address two major objections to it and thus argue that the possibility of socialism as an alternative form of economic organisation has been dismissed too quickly. Furthermore, I provide an account of the precise form a socialist economy should take, outlining general principles of planning and distribution. Based on a welfarist interpretation of Marx, I show that distribution of consumer goods should be facilitated by an equal distribution of tokens. These tokens can be redeemed for consumer products or substituted for additional leisure time. The rates at which tokens can be redeemed for consumer products should correspond to market clearing prices. Welfare-oriented socialism is also defended against a deontological objection to socialism by Robert Nozick, who claims that socialism leads to injustice because it violates private property rights. The thesis also considers Ludwig von Mises’s calculation argument against socialism, which claims that socialism leads to the abolition of economic rationality. I show how this objection can be overcome by using optimal planning techniques which are responsive to consumer demand as signalled by the market clearing rates of consumer products. The resulting model of socialism is tested using a computer simulation. The simulation also demonstrates that a novel system of valuation based on opportunity cost leads to a better adaptation of production in response to environmental constraints when compared to the labour values of classical political economy

SNP-specific extraction of haplotype-resolved targeted genomic regions

The availability of genotyping platforms for comprehensive genetic analysis of complex traits has resulted in a plethora of studies reporting the association of specific single-nucleotide polymorphisms (SNPs) with common diseases or drug responses. However, detailed genetic analysis of these associated regions that would correlate particular polymorphisms to phenotypes has lagged. This is primarily due to the lack of technologies that provide additional sequence information about genomic regions surrounding specific SNPs, preferably in haploid form. Enrichment methods for resequencing should have the specificity to provide DNA linked to SNPs of interest with sufficient quality to be used in a cost-effective and high-throughput manner. We describe a simple, automated method of targeting specific sequences of genomic DNA that can directly be used in downstream applications. The method isolates haploid chromosomal regions flanking targeted SNPs by hybridizing and enzymatically elongating oligonucleotides with biotinylated nucleotides based on their selective binding to unique sequence elements that differentiate one allele from any other differing sequence. The targeted genomic region is captured by streptavidin-coated magnetic particles and analyzed by standard genotyping, sequencing or microarray analysis. We applied this technology to determine contiguous molecular haplotypes across a ∼150 kb genomic region of the major histocompatibility complex

The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

Abstract Background The ability to capture and sequence large contiguous DNA fragments represents a significant advancement towards the comprehensive characterization of complex genomic regions. While emerging sequencing platforms are capable of producing several kilobases-long reads, the fragment sizes generated by current DNA target enrichment technologies remain a limiting factor, producing DNA fragments generally shorter than 1 kbp. The DNA enrichment methodology described herein, Region-Specific Extraction (RSE), produces DNA segments in excess of 20 kbp in length. Coupling this enrichment method to appropriate sequencing platforms will significantly enhance the ability to generate complete and accurate sequence characterization of any genomic region without the need for reference-based assembly. Results RSE is a long-range DNA target capture methodology that relies on the specific hybridization of short (20-25 base) oligonucleotide primers to selected sequence motifs within the DNA target region. These capture primers are then enzymatically extended on the 3’-end, incorporating biotinylated nucleotides into the DNA. Streptavidin-coated beads are subsequently used to pull-down the original, long DNA template molecules via the newly synthesized, biotinylated DNA that is bound to them. We demonstrate the accuracy, simplicity and utility of the RSE method by capturing and sequencing a 4 Mbp stretch of the major histocompatibility complex (MHC). Our results show an average depth of coverage of 164X for the entire MHC. This depth of coverage contributes significantly to a 99.94 % total coverage of the targeted region and to an accuracy that is over 99.99 %. Conclusions RSE represents a cost-effective target enrichment method capable of producing sequencing templates in excess of 20 kbp in length. The utility of our method has been proven to generate superior coverage across the MHC as compared to other commercially available methodologies, with the added advantage of producing longer sequencing templates amenable to DNA sequencing on recently developed platforms. Although our demonstration of the method does not utilize these DNA sequencing platforms directly, our results indicate that the capture of long DNA fragments produce superior coverage of the targeted region

A QM/MM approach for the study of monolayer-protected gold clusters

We report the development and implementation of hybrid methods that combine quantum mechanics (QM) with molecular mechanics (MM) to theoretically characterize thiolated gold clusters. We use, as training systems, structures such as Au25(SCH2-R)18 and Au38(SCH2-R)24, which can be readily compared with recent crystallographic data. We envision that such an approach will lead to an accurate description of key structural and electronic signatures at a fraction of the cost of a full quantum chemical treatment. As an example, we demonstrate that calculations of the 1H and 13C NMR shielding constants with our proposed QM/MM model maintain the qualitative features of a full DFT calculation, with an order-of-magnitude increase in computational efficiency.Comment: Journal of Materials Science, 201

The soybean GmSNAP18 gene underlies two types of resistance to soybean cyst nematode

Two types of resistant soybean (Glycine max (L.) Merr.) sources are widely used against soybean cyst nematode (SCN, Heterodera glycines Ichinohe). These include Peking-type soybean, whose resistance requires both the rhg1-a and Rhg4 alleles, and PI 88788-type soybean, whose resistance requires only the rhg1-b allele. Multiple copy number of PI 88788-type GmSNAP18, GmAAT, and GmWI12 in one genomic segment simultaneously contribute to rhg1-b resistance. Using an integrated set of genetic and genomic approaches, we demonstrate that the rhg1-a Peking-type GmSNAP18 is sufficient for resistance to SCN in combination with Rhg4. The two SNAPs (soluble NSF attachment proteins) differ by only five amino acids. Our findings suggest that Peking-type GmSNAP18 is performing a different role in SCN resistance than PI 88788-type GmSNAP18. As such, this is an example of a pathogen resistance gene that has evolved to underlie two types of resistance, yet ensure the same function within a single plant species

Global Mapping of Transposon Location

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential