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Coming theses from other universities

Please note that the date and time given on these pages is the time of electronic publication, and not the date of the public defense. To find the time and venue of the public defense, please follow the link to DiVA of the thesis in question.
  • Baltic Sea from Space : The use of ocean colour data to improve our understanding of ecological drivers across the Baltic Sea basin – algorithm development, validation and ecological applications

    Author: Dmytro Kyryliuk
    Publication date: 2019-09-04 09:00

    Coastal areas are the most densely populated areas in the world and thus are under immense anthropogenic pressure. To ensure their function and ecological role, coastal areas require continuous monitoring and management. The rapidly emerging field of satellite remote sensing provides a unique opportunity to monitor both land and oceans from Space. This thesis explores recent developments in ocean colour remote sensing, tests several image processing algorithms, evaluates and maps water quality indicators – both on local and Baltic Sea-wide scale – as well as provides essential monitoring data to complement already existing ship-based monitoring and modelling techniques. The overall aim of the thesis is to broaden our understanding and applicability of ocean colour remote sensing for improved modelling and management of the Baltic Sea and its coastal areas.

    The thesis deals with four independent research topics. In paper I the spatial distribution of Total Suspended Matter (TSM) during the summer season is evaluated using the European Space Agency’s (ESA) MEdium Resolution Imaging Spectrometer (MERIS). The TSM distribution and concentration is retrieved quantitatively from MERIS data for the HELCOM-defined Baltic Sea sub-basins for the summer seasons 2009, 2010, 2011, and summarized in a 3-year summer composite image. Manuscript II deals with the correspondence between satellite, in situ and modelled data in Bråviken bay, NW Baltic proper, which is optically dominated by Coloured Dissolved Organic Matter (CDOM). Chlorophyll-a (CHL-a) and Secchi depth data are analyzed along a horizontal transects reaching from the inner coastal bay out into the open sea. The study addresses the scarcity of in situ monitoring data in comparison to satellite and modelled data. Further, an empirical relationship is established between modelled total nitrogen and CHL-a derived from satellite, potentially allowing to infer information on the distribution of total nitrogen from satellite data. Paper III evaluates the performance of MERIS’s successor – the Ocean and Land Colour Instrument (OLCI) launched on board Sentinel-3A (S3A) satellite. The water quality products derived from S3A OLCI using the Case-2 Regional CoastColour Processor are evaluated via several dedicated validation campaigns (2016-2018) in the NW Baltic proper. In manuscript IV, the in-water relationship between particle scatter at 440 nm and Inorganic Suspended Particulate Matter (ISPM) is used to develop a novel algorithm to derive ISPM from satellite-derived scatter. This algorithm was applied to OLCI data and tested on an independent dataset. The algorithm allows to map the distribution of ISPM across the Baltic Sea basin and to assess the influence of coastal processes.

    The key outcome of this thesis are reliable water-quality products generated on a Baltic Sea-wide scale, using state-of-the-art Ocean Colour data. Specifically, the thesis highlights the benefits of using remote sensing to improve our understanding of coastal and dynamical processes, as well as Baltic Sea ecology on a wider scale, which simply is not possible by any other scientific means. 

  • Structure and Biogenesis of Membrane Proteins

    Author: Mama Ndi
    Publication date: 2019-09-03 09:00

    Membrane proteins make up about one-third of the cellular proteome. The diverse roles that membrane proteins have in cells include major life-sustaining processes, making them major drug targets. The respiratory chain comprises a series of complexes of membrane proteins residing in the inner mitochondrial membrane, which serve as major drivers of ATP synthesis. Assembly of the respiratory chain complexes (RCC) requires coordinated synthesis of nuclear and mitochondrial subunits. Cbp3-Cbp6 complex binds to the mitoribosome as translational activator for cytochrome b synthesis and binds the nascent polypeptide to facilitate its hemylation. Cbp3 consists of an N-terminal domain specific to mitochondrial homologues and a conserved C-terminal ubiquinol-cytochrome c chaperone domain. In this thesis I present the first crystal structure of the C-terminal domain from a bacterial homologue that has enabled us to identify the interaction sites of yeast Cbp3 with Cbp6 and cytochrome b using site-specific photo-crosslinking. Our finding suggests that Cbp3 contacts the mitoribosome via the N-terminal domain in a manner that positions the substrate binding site close to the tunnel exit. In the second project, we have analyzed the effects of disease causing cytochrome b mutations, on bc1 complex assembly. We found that complex III assembly is blocked at either intermediate 0 or I due to impaired insertion of bL or bH heme respectively, which indicates that assembly processes are involved in disease development. We then focused on NADH; a product of alpha-ketoglutarate dehydrogenase complex (KGDH) catalyzed citric acid cycle reaction and one of the substrates that supply electron to the respiratory chain. Kgd4 is a novel subunit of this enzyme complex and two functional variants (Kgd4S and Kgd4L) of unknown origins exist in yeast. We report in our work that Kgd4L originates from a UUG alternative start site, 90 nucleotides upstream and in frame of the annotated start codon. The sequence context upstream of UUG determines the efficiency of recognition of this alternative start codon. Finally, Na+/H+ antiporters are present in all species and are involved in regulation of intracellular pH, cell volume and sodium concentration. ATP formed during oxidative phosphorylation serves as energy source for Na+/K+ ATPase to generate Na+ gradient across the inner mitochondrial membrane, which drives local Na+/H+ antiporters. We show that K305 is involved in proton transport and responsible for the electrogenicity of NapA, while human NHA2 shows electroneutral antiporter activity.

  • Experimental investigations of model catalytic surface reactions on metal and metal oxide surfaces

    Author: Kess Marks
    Publication date: 2019-09-03 09:00

    In the development of renewable energies catalysis plays an important role, for example in the production of H2 gas that drives fuel cells, or in the decomposition of annoying by-products of renewable energy production. Most catalysts and catalytic processes currently used in the industry have their roots in macroscopic empirical investigations and trial and error-based optimization. In order to be able to design novel catalytic processes more efficiently, detailed understanding of the catalyst-reactant interaction and the dynamics of the microscopic reaction steps is needed. The present thesis aims to contribute to the fundamental understanding of catalyst reactant systems by means of experiments using model systems in Ultra High Vacuum. For this purpose, several surface science techniques were employed such as vibrational sum-frequency generation (SFG), X-ray photoelectron spectroscopy (XPS), temperature programmed desorption (TPD) and femtochemistry.

    In the present thesis the results of three different projects are presented. The first concerns the adsorption and decomposition of naphthalene on Ni(111). Using scanning tunnelling microscopy (STM) and density functional theory (DFT) we identify the adsorption energy and geometry of the naphthalene molecule. Using SFG and TPD we investigate the temperature dependent breakdown of the naphthalene molecule and identify geometrical changes of the adsorbate as an intermediate step in the decomposition reaction. Additionally, we observe poisoning of the surface due to graphene growth using both STM and XPS and explore the possible effect of co-adsorption with oxygen on the reaction pathway and the poisoning of the catalyst.

    The second section concerns the adsorption and decomposition of ethanol and methanol on cuprous oxide (Cu2O). Using mainly XPS and SFG we show that ethanol adsorbs dissociatively on Cu2O(100) and (111) and that methanol adsorbs dissociatively on the (100) but molecularly on the (111) surface. Furthermore, we identify intermediate surface species and products of the temperature dependent dehydrogenation of both alcohols and show that the (111) surface is the more effective catalyst for decomposition.

    The third section explores the physics of non-thermal excitation methods and discusses CO oxidation on ruthenium (0001) induced by an optical laser and by X-rays from a free electron laser. Based on these femtochemistry experiments we discuss in particular the energy transfer both for direct excitation and for substrate mediated excitations. We show that we were able to control the branching ratios of competing mechanisms and understand the role of non-thermal electrons in the mechanisms of optical laser excitation. Furthermore, we show that it is possible to induce CO oxidation by direct X-ray core hole excitation and can rationalize the relaxation process that leads to CO oxidation.

  • Sustainable building ventilation solutions with heat recovery from waste heat

    Author: Behrouz Nourozi
    Publication date: 2019-08-30 17:49

    The energy used by building sector accounts for approximately 40% of the total energy usage. In residential buildings, 30-60% of this energy is used for space heating which is mainly wasted by transmission heat losses. A share of 20-30% is lost by the discarded residential wastewater and the rest is devoted to ventilation heat loss.


    The main objective of this work was to evaluate the thermal potential of residential wastewater for improving the performance of mechanical ventilation with heat recovery (MVHR) systems during the coldest periods of year. The recovered heat from wastewater was used to preheat the incoming cold outdoor air to the MVHR in order to avoid frost formation on the heat exchanger surface.


    Dynamic simulations using TRNSYS were used to evaluate the performance of the suggested air preheating systems as well as the impact of air preheating on the entire system. Temperature control systems were suggested based on the identified frost thresholds in order to optimally use the limited thermal capacity of wastewater and maintain high temperature efficiency of MVHR. Two configurations of air preheating systems with temperature stratified and unstratified tanks were designed and compared. A life cycle cost analysis further investigated the cost effectiveness of the studied systems.


    The results obtained by this research work indicated that residential wastewater had the sufficient thermal potential to reduce the defrosting need of MVHR systems (equipped with a plate heat exchanger) in central Swedish cities to 25%. For colder regions in northern Sweden, the defrosting time was decreased by 50%. The temperature control systems could assure MVHR temperature efficiencies of more than 80% for most of the heating season while frosting period was minimized. LCC analysis revealed that wastewater air preheating systems equipped with temperature stratified and unstratified storage tanks could pay off their costs in 17 and 8 years, respectively.

  • Groundwater resources in hard rock coastal terrains : Insights into heterogeneity and spatial variability

    Author: Robert Earon
    Publication date: 2019-08-30 13:24

    Challenges regarding water security in hard rock coastal regions with limited soil cover are: a seasonal absence of recharge during times of peak residency, heterogeneity and variability of the fracture network, close proximity to saline water sources and spatially inconsistent storage and extraction. In areas where it is not feasible to connect residents to municipal water systems, a better understanding of the resilience of reservoirs is needed. The purpose of this study is to investigate and describe the spatial nature of hydraulic data in these types of terrains and present several novel GIS-based groundwater tools with the intent of increasing local water security and aiding in sustainable water resources management. Methods used in this study include groundwater balance modelling and conceptual groundwater storage modelling, as well as a combination of parametric and non-parametric statistical methods such as ANOVA, PCA, correlation and semivariogram analyses. Specific capacity estimates from the Geological Survey of Sweden’s well archive grouped by age or rock type showed very little autocorrelation and in assumed homogeneous geological regions showed statistically significant differences when arbitrarily grouped along a lineament. Estimates of kinematic porosity based on surface fracture data were found have statistically significant correlations with the well data. A GIS-based multivariate prediction tool for assessing Groundwater Resources Potential (GRP) was found to have statistically significant correlations with well data. The GRP method was then combined with a conceptual groundwater storage model and was subsequently found to have statistically significant correlations with chloride concentrations in well quality tests. The storage model was found to have a spatially-dependent sensitivity, meaning that different assumptions within the model had varying effects on the model depending on the geological settings. Incorporating the storage model into a spatial groundwater balance model was then compared with groundwater level time series data over a period of two years, where it was found to have a good explanative capacity and RMSE values of the storage ratio (0.06 to 0.34). Additionally, a soil depth model was developed, tested and found to produce promising results in regions with frequent rock outcrops, where up to 86% of estimates were within 2 m of actual soil depths. Conclusions from this study illustrate the need for a spatial approach to groundwater resources in these types of terrains, and demonstrate a strong potential of several new tools for quantity, capacity and vulnerability estimates to increase water security in a changing climate.

  • Experiments on Heat Transfer During Diesel Combustion Using Optical Methods

    Author: Christian Binder
    Publication date: 2019-08-30 11:33

    Transportation is a crucial part of modern societies. This includes their economies. Trade and the transportation of goods have a great influence on prosperity. Nevertheless, the transportation sector with road transport in particular is heavily dependent on fossil fuels and emits a significant amount of greenhouse gases. One approach to mitigate the negative environmental impact of road transport is to increase the efficiency of its most common propulsion system, that is the internal combustion engine. Due to its dominant role in the road freight transportation sector, this thesis directs its attention to heavy-duty diesel engines. In-cylinder heat losses are one of the main factors that reduce engine efficiency. Therefore, the objective of this thesis is to gain a better understanding of the processes that influence in-cylinder heat losses by resolving them in time and space using optical methods. In diesel engines, most of the in-cylinder heat losses are transferred to the piston. As a result, this thesis focuses specifically on that component.

    In this research project, the task to determine in-cylinder heat losses to the piston in heavy-duty diesel engines is divided into two parts. The most important part consists of fast surface temperature measurements on the piston using phosphor thermometry. The heat transfer coefficient inside the piston cooling gallery defines an additional steady-state boundary condition.

    The work presented in this thesis includes therefore efforts to improve in-cylinder surface temperature measurements and an assessment of their accuracy and precision. Furthermore, it comprises of experimental results from measurements on steel pistons and a piston with an insulating thermal barrier coating. Results reveal spatial differences of the heat transfer during diesel combustion. Measurements at the impingement point indicate a strong influence of flame impingement on local heat transfer. A correlation is detected between heat transfer and cycle-to-cycle variations of flame impingement.

    The thesis also reports efforts to determine the heat transfer coefficient inside the piston cooling gallery. Using an infrared camera a method is presented to spatially resolve convective heat transfer inside this cooling channel.

  • Endosymbiosis of Frankia cluster-2

    Author: Fede Berckx
    Publication date: 2019-08-29 16:54

    Actinobacteria of the genus Frankia engage in root endosymbiosis with actinorhizal plants belonging to the Fagales, Cucurbitales and Rosales. The genus Frankia consists of four different clades. Strains belonging to cluster-1, -2, and -3 exhibit host-specificity which plants they can nodulate, while cluster-4 strains do not engage in symbiosis. Cluster-2 is the earliest divergent clade, and most of its members could not be cultured thus far, with the exception of Frankia coriariae BMG5.1 and BMG5.30. Unlike other nodule symbioses where ammonia is the nitrogen source exported to the host, it has been shown in nodules of Datisca glomerata that an assimilated nitrogen metabolite, namely arginine, is exported to the host. In the study on bacterial transcription patterns during symbiosis presented here, it is suggested that in nodules of Ceanothus thyrsiflorus an assimilated nitrogen source, most likely asparagine, is delivered by Frankia cluster-2. Analysis of the carbon metabolism indicates that citrate could be the carboxylate delivered from the host to the bacteria. Analysis of the tricarboxylic acid cycle indicates that the glyoxylate shunt is missing in genomes of Frankia cluster-2. During symbiosis the pathway mostly works linear between input of carbon skeletons and the output of assimilated nitrogen metabolites. This feature could explain why Frankia cluster-2 strains have a low saprotrophic potential.

    Analysis of genomes of Frankia cluster-2 have shown that murC is present in two gene copies within the genome of cluster-2 and cluster-3 strains, but only present as one copy in cluster-1 and cluster-4. MurC plays a key role in biosynthesis of peptidoglycan, a polymer that makes up a thick layer as part of cell wall of Gram-positive bacteria. Phylogenetic analysis show one of the two copies encodes a protein highly similar to MurC protein of other actinobacteria, and therefore is considered the ancestral copy, murC1. The other copy, murC2, can be found in all Frankia clusters and encodes a protein showing more similarity to MurC from cyanobacteria and plants. This similarity could be explained through either horizontal gene transfer, which is not unlikely as Frankia can be found intracellularly in its host plants. The other possible scenario is that a gene duplication event was followed by convergent evolution, leading to similarity between MurC2 and the MurC proteins of cyanobacteria and plants. This would allow for plasticity in the structure of the peptidoglycan layer of the cell wall.

    The features of nitrogen and carbon metabolism, as well as the phylogeny of MurC, indicate Frankia cluster-2 has undergone several adaptations to intracellular endosymbiosis.

  • Exploitation of interactions with the neonatal Fc receptor to manipulate biological half-lives for therapeutic applications

    Author: Shengze Yu
    Publication date: 2019-08-29 14:31

    Protein engineering provides powerful tools to create useful proteins with desired properties. In this thesis, rational design principles have been used for development of fusion proteins that can interact with the neonatal Fc receptor (FcRn) for potential medical applications. 

    FcRn is widely expressed in the human body. The natural ligands of FcRn are immunoglobulin G (IgG) and serum albumin (SA). FcRn can bind to both proteins in a pH dependent manner and endow them with an unusually long half-life in vivo. Protein building blocks interacting directly or indirectly with FcRn may potentially be used to either piggy-back on the FcRn-system for extension of the in vivo half-life or to saturate the system to decrease the in vivo half-life of the natural ligands. In this thesis, I have explored an FcRn binding affibody molecule (ZFcRn) and/or an albumin binding domain (ABD) for these purposes. 

    In study I and II, the prolactin receptor was found to often be expressed in glioblastoma multiforme tumors from patients as well as in glioblastoma multiforme cells lines. We investigated a novel antagonist of the prolactin receptor in vitro and found that it could block signaling through the receptor as well as cellular invasiveness. An antagonist of prolactin receptor could thus potentially become a drug for treatment of glioblastoma multiforme. However, the antagonist will likely have a short plasma half-life due to its small molecular size, which limits its usability. Therefore, it was expressed as a fusion to ABD, which interacts indirectly with FcRn. The produced fusion protein was found to be able to block signaling through the prolactin receptor in vitro and also had a prolonged plasma half-life in vivo

    The goal of study III was to investigate the properties of human growth hormone (hGH) when it was expressed as a protein fusion with ZFcRn, interacting directly with FcRn, and/or ABD. The fusion proteins, ZFcRn-hGH, ABD-hGH, and ZFcRn-ABD-hGH could be recombinantly expressed and successfully purified to homogeneity. They had the expected binding abilities to FcRn, SA and hGH receptor. They were all found to be able to induce signaling over the plasma membrane in a model cell line. 

    Patients suffering from many autoimmune diseases produce particular IgG molecules, which are responsible for the disease symptoms. A potential treatment could be to increase the catabolism of these IgGs to relieve disease symptoms. In study IV, an FcRn interacting affibody molecule was investigated for IgG depletion by blocking the IgG/FcRn interaction. In vitro, we first found that the affibody molecule shares a common binding site with IgG on FcRn, which indicates that the affibody should be able to block IgG from binding to FcRn. In vivo, we injected large amounts of the affibody molecules in different formats in mice and found up to 39% reduction of total endogenous IgG. In a clinical setting, reduction of total IgG level would also reduce the disease causing IgGs, and potentially ameliorate the symptoms of IgG-driven autoimmune diseases. 

    Taken together, I have in this thesis explored application of FcRn interacting molecules for extension of biological half-lives of therapeutically relevant proteins and reduction of total IgG level by FcRn blocking. 

  • Supernova surroundings on circumstellar and galactic scales

    Author: Anders Nyholm
    Publication date: 2019-08-29 09:00

    Some stars cease to be in a bright and destructive display called a supernova. This thesis explores what we can learn about supernovae (SNe) by studying their immediate surroundings, and what the SNe can teach us about their environments. The work presented is mostly based on the rich harvest of observations from 2009-2017 by the Palomar Transient Factory (PTF) and its successor, the intermediate PTF (iPTF). The PTF/iPTF was an untargeted sky survey at Palomar Observatory, aimed at finding and following up astronomical transients, such as SNe. During its existence, a massive star typically loses several solar masses of material. If much mass is lost in the decades or centuries before the SN, this material around the star (the circumstellar medium, CSM) will be quickly swept up by the ejecta of the eventual SN. This interaction can contribute strongly to the luminosity of the SN and make the light curve of an interacting SN carry signs of the progenitor star mass loss history. SNe with a hydrogen-rich CSM are called SNe Type IIn. A SN of this type, iPTF13z, found and followed by iPTF, had a slowly declining lightcurve with at least 5 major rebrightenings ("bumps") indicating rich structure in the CSM. Archival images clearly shows a precursor outburst about 210 days before the SN discovery, demonstrating the iPTF13z progenitor to be restless before its demise. Type IIn supernovae are heterogeneous, but only limited statistics has been done on samples. From PTF/iPTF, a sample of 42 SNe Type IIn was therefore selected, with photometry allowing their light curve rise times, decline rates and peak luminosities to be measured. It was shown that more luminous events are generally more long-lasting, but no strong correlation was found between rise times and peak luminosities. Two clusters of risetimes (around 20 and 50 days, respectively) were identified. The less long-lasting SNe Type IIn dominate the sample, suggesting that stars with a less extended dense CSM might be more common among SN Type IIn progenitors. Thermonuclear SNe (SNe Type Ia) are useful as standardisable candles, but no secure identification has yet been made of the progenitor system of a SN Type Ia. Using a late-time spectrum from the Nordic Optical Telescope of the nearby thermonuclear SN 2014J, a search for material ablated from a possible non-compact companion gave the upper limit of about 0.0085 solar masses of hydrogen-rich ablated gas. One likely explanation is that the SN 2014J progenitor system was a binary white dwarf. Supernovae are also useful tracers of the star formation history in their host galaxies, with SNe Type Ia tracing earlier epochs of star formation and exploding massive stars tracing more recent. For active galactic nuclei (AGN, the luminous centres of galaxies harbouring accreting supermassive black holes) SNe allows the so-called unification model to be tested. The unification model assumes that the main distinction between the two types of AGN is the viewing angle towards the central black hole, and that other properties (e.g. star formation history) of the host galaxies should be the same for the two AGN types. Matching 2190 SNe from PTF/iPTF to about 89000 AGN with spectra from the Sloan Digital Sky Survey, a significantly higher number of SNe in the hosts of AGN type 2 was found, challenging the unification model.

  • Probing the early Universe with B-mode polarization : The Spider instrument, optical modelling and non-Gaussianity

    Author: Adriaan Judocus Duivenvoorden
    Publication date: 2019-08-28 09:00

    One of the main goals of modern observational cosmology is to constrain or detect a stochastic background of primordial gravitational waves. The existence of such a background is a generic prediction of the inflationary paradigm: the leading explanation for the universe's initial perturbations. A detection of the gravitational wave signal would provide strong evidence for the paradigm and would amount to an indirect probe of an energy scale far beyond that of conventional physics. Several dedicated experiments search for the signal by performing highly accurate measurements of a unique probe of the primordial gravitational wave background: the B-mode signature in the polarization of the cosmic microwave background (CMB) radiation. A part of this thesis is devoted to one of these experiments: the balloon-borne Spider instrument. The analysis of the first dataset, obtained in two (95 and 150 GHz) frequency bands during a January 2015 Antarctic flight, is described, along with details on the characterisation of systematic signal and the calibration of the instrument. The case of systematic signal due to poorly understood optical properties is treated in more detail. In the context of upcoming experiments, a study of systematic optical effects is presented as well as a numerically efficient method to consistently propagate such effects through an analysis pipeline. This is achieved by a `beam convolution' algorithm capable of simulating the contribution from the entire sky, weighted by the optical response, to the instrument's time-ordered data. It is described how the algorithm can be employed to forecast the performance of upcoming CMB experiments. In the final part of the thesis, an additional use of upcoming B-mode data is described. Constraints on the non-Gaussian correlation between the large-angular-scale B-mode field and the CMB temperature or E-mode anisotropies on small angular scales constitute a rigorous consistency check of the inflationary paradigm. An efficient statistical estimation procedure, a generalised bispectrum estimator, is derived and the constraining power of upcoming CMB data is explored.