| 1. |
- Dharamshi, Jennah E., 1989-
(författare)
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Expanding the Chlamydiae tree : Insights into genome diversity and evolution
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles.Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions. Anaerobic metabolism is found across modern eukaryotes, and syntrophic hydrogen exchange is central in many hypotheses for eukaryotic evolution, but its origin is unknown. Chlamydial and eukaryotic homologs were the closest relatives in several of these gene phylogenies, providing evidence for a chlamydial contribution of these genes during eukaryotic evolution.Gene-tree aware ancestral-state-reconstruction revealed a fermentative, mobile, facultatively anaerobic Chlamydiae ancestor, which was capable of endosymbiosis. Examination of Chlamydiae gene content evolution indicated complex dynamics, with a central role of horizontal gene transfer in major evolutionary transitions, related to energy metabolism and aerobiosis. Furthermore, chlamydiae have evolved through genome expansion in addition to gene loss, counter to many other obligate endosymbionts.Sponge microbiome-associated chlamydiae were found in high relative abundance in some sponge species. Genome-resolved metagenomics identified diverse, yet co-associating chlamydial lineages, with distinctive genetic repertoires, including unexpected degradative and biosynthetic potential. Biosynthetic gene clusters were found across Chlamydiae, suggestive of secondary metabolite production and host-defence roles. Surveying environmental prevalence indicated wider associations between chlamydiae and marine invertebrates.Finally, a wide-scale assessment of chlamydiae genetic contributions to eukaryotic evolution was performed. Over 100 distinct Chlamydiae-eukaryotic clades were identified in phylogenies across shared protein families. Although patterns are complex and direction of transfers often unclear, our results indicate larger avenues of chlamydial gene exchange with both plastid-bearing eukaryotes, and the last eukaryotic common ancestor. In summary, in this thesis, cultivation-independent methods and evolutionary-driven investigations were used to expand the Chlamydiae tree, and to provide new insights into genomic diversity and evolution of the phylum.
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| 2. |
- Paptchikhine, Alexander
(författare)
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Asymmetric Hydrogenations using N, P - Ligated Iridium Complexes
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The research described in this thesis focuses on the catalytic asymmetric hydrogenation of prochiral olefins using N, P – chelated iridium catalysts. This catalytic system is tolerant to a wide range of substrates and performs better than the well-known ruthenium- and rhodium-catalytic systems for substrates devoid of coordinating groups in proximity of the olefin. Low catalytic loadings (often <1 %) and the high atom efficiency of this reaction make it a synthetically useful method of chiral molecule synthesis. The primary aim of this thesis was to develop new catalysts that rapidly and efficiently hydrogenate a broad range of alkenes asymmetrically. Papers I and II describe the synthesis and evaluation of new, highly efficient, chiral N, P – ligated iridium complexes. These catalysts were obtained in relatively few steps, while leaving open possibilities to modify and fine-tune their structure. Their versatility is ideally suited to both industrial uses and to equip any catalyst box. Paper III deals with a common problem of defluorination of vinylic fluorides during the hydrogenation. The catalyst designed in that work performs well for several substrates giving very low defluorination rates making it a good starting point for further improvements to cover a broader scope of vinyl fluorides. The structures of the catalysts from papers I and III also offers an easy approach to attach the catalyst ligands to a solid support. Paper IV explores hydrogenation of vinyl boronates, which gives synthetically interesting borane compounds with high enantioselectivities. Taking into account the rich chemistry of organic boranes, these compounds are very important. Paper V deals with hydrogenation of diphenylvinylphosphine oxides and vinyl phosphonates, another important classes of substrates that give chiral phosphorous containing compounds of interest in many fields of chemistry: such as medicinal chemistry and organocatalysis. In papers VI and VII we explore the Birch reaction as a source of prochiral olefins. By combining asymmetric hydrogenation with it, we obtain a powerful method to create chiral compounds with excellent enantioselectivities that are next to impossible to make by other routes. The products of the asymmetric hydrogenation are further modified by other well-known transformation to create other induced stereogenic centres.
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| 3. |
- Pietrow, Alexander G. M., 1991-
(författare)
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Physical properties of chromospheric features : Plage, peacock jets, and calibrating it all
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The chromosphere is a complex and dynamic layer of the solar atmosphere, largely dominated by the local magnetic field configuration. It acts as an important interface between the photosphere below it and the hot corona above. However, studying this layer is not straightforward, as it is largely transparent in optical wavelengths. On top of that most of its observable radiation is formed in conditions far from thermodynamic equilibrium, and thus only partially sensitive to local plasma conditions. Observations of the active features found in the chromosphere such as plage, fibrils, and jets, are therefore more difficult to interpret than emission from active features in the photosphere.This thesis focuses on plage and peacock-jets, two types of chromospheric features. Additionally, I study the quiet solar atmosphere for calibration purposes. In all three cases, I utilize high-resolution spectral and spectro-polarimetric data from the Swedish 1-m Solar Telescope (SST) in order to constrain the physical parameters of these regions and to create high-resolution reference profiles of the quiet regions.In the first paper, the magnetic field vector of a plage region is inferred using STiC, a spectro-polarimetric inversion code, which is achieved after applying several methods to improve the signal-to-noise ratio.In the second paper, a peacock jet near an X9.3-class flare is studied. The expanding flare ribbon moves under the jet and inhibits new material from being accelerated upwards. This coupled with back-lighting from the heavily broadened line profile of the flare ribbon that can be approximated as quasi-continuum, allowed us to estimate its density and mass by using a cloud model. The third paper is an observational study of the center-to-limb variations of ten spectral lines commonly used for solar diagnostics.
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| 4. |
- Siemers, Alexander, 1970-
(författare)
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Contributions to Modelling and Visualisation of Multibody Systems Simulations with Detailed Contact Analysis
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The steadily increasing performance of modern computer systems is having a large influence on simulation technologies. It enables increasingly detailed simulations of larger and more comprehensive simulation models. Increasingly large amounts of numerical data are produced by these simulations.This thesis presents several contributions in the field of mechanical system simulation and visualisation. The work described in the thesis is of practical relevance and results have been tested and implemented in tools that are used daily in the industry i.e., the BEAST (BEAring Simulation Tool) tool box. BEAST is a multibody system (MBS) simulation software with special focus on detailed contact calculations. Our work is primarily focusing on these types of systems.focusing on these types of systems. Research in the field of simulation modelling typically focuses on one or several specific topics around the modelling and simulation work process. The work presented here is novel in the sense that it provides a complete analysis and tool chain for the whole work process for simulation modelling and analysis of multibody systems with detailed contact models. The focus is on detecting and dealing with possible problems and bottlenecks in the work process, with respect to multibody systems with detailed contact models.The following primary research questions have been formulated:How to utilise object-oriented techniques for modelling of multibody systems with special reference tocontact modelling?How to integrate visualisation with the modelling and simulation process of multibody systems withdetailed contacts.How to reuse and combine existing simulation models to simulate large mechanical systems consistingof several sub-systems by means of co-simulation modelling?Unique in this work is the focus on detailed contact models. Most modelling approaches for multibody systems focus on modelling of bodies and boundary conditions of such bodies, e.g., springs, dampers, and possibly simple contacts. Here an object oriented modelling approach for multibody simulation and modelling is presented that, in comparison to common approaches, puts emphasis on integrated contact modelling and visualisation. The visualisation techniques are commonly used to verify the system model visually and to analyse simulation results. Data visualisation covers a broad spectrum within research and development. The focus is often on detailed solutions covering a fraction of the whole visualisation process. The novel visualisation aspect of the work presented here is that it presents techniques covering the entire visualisation process integrated with modeling and simulation. This includes a novel data structure for efficient storage and visualisation of multidimensional transient surface related data from detailed contact calculations.Different mechanical system simulation models typically focus on different parts (sub-systems) of a system. To fully understand a complete mechanical system it is often necessary to investigate several or all parts simultaneously. One solution for a more complete system analysis is to couple different simulation models into one coherent simulation. Part of this work is concerned with such co-simulation modelling. Co-simulation modelling typically focuses on data handling, connection modelling, and numerical stability. This work puts all emphasis on ease of use, i.e., making mechanical system co-simulation modelling applicable for a larger group of people. A novel meta-model based approach for mechanical system co-simulation modelling is presented. The meta-modelling process has been defined and tools and techniques been created to fully support the complete process. A component integrator and modelling environment are presented that support automated interface detection, interface alignment with automated three-dimensional coordinate translations, and three dimensional visual co-simulation modelling. The integrated simulator is based on a general framework for mechanical system co-simulations that guarantees numerical stability.
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