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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.
  • Theoretical spectroscopic investigation of hybrid halide perovskite solar cell materials

    Author: Cody Sterling
    Publication date: 2020-12-01 12:38

    Perovskite solar cells have recently become a very promising candidate in the search for an effective solar cell material. Over the past 10 years, their power conversion efficiency has increased to over 25% and there is a wide range of different potential chemical makeups that provide a range of materials to investigate. However, there are still questions about the specific role of all the different chemical components in the material. This thesis aims to investigate the effect of material composition and structure on the electronic structure of the system. Two largely separate investigations are presented: first a study on the differences between MAPI (CH3NH3PbI3) and MAPB (CH3NH3PbBr3) and how differences in local structure can affect the N 1s X-ray absorption spectrum. Various geometric parameters are found to affect the shape of the spectrum and these are explained via specific orbital changes. Second, charge transfer between the MA+ ion and the inorganic PbI3 lattice inside MAPI is investigated, and this is paired with an explanation of hybridization of states between MAPI and its Pb-less precursor MAI (CH3NH3I).

  • Reconstructing the Primordial Seeds of Cosmic Structures in Galaxy Surveys

    Author: Adam Johansson Andrews
    Publication date: 2020-12-01 12:37

    One of the most outstanding questions in modern cosmology concerns the physical processes governing the primordial universe and the origin of cosmic structure. These primordial signals appear in a variety of cosmic large-scale structure probes, e.g., in the higher-order statistics of the density field and as a scale-dependent factor in the two-point correlations of the galaxy field. The detection and measurement of such a non-Gaussian primordial signal would generate insights into the shape of the potential of the inflaton field, the hypothetical particle driving cosmic inflation. In the coming years, the next generation of galaxy surveys will commence operation, with the scientific goal of constraining the nonlinearity parameter fnl to the uncertainty required to identify viable inflationary models. However, achieving this goal requires novel statistical data analysis techniques to correctly account for stochastic and systematic uncertainties when measuring these subtle signals from observations.

    In this licentiate thesis, I present a new approach to measuring primordial non-Gaussianity in galaxy redshift surveys, and demonstrate the proof of concept. State-of-the-art approaches use only a limited set of summary statistics of the density field and cannot account for the full information content of the three-dimensional cosmic structure. To address this problem, I propose a method based on the forward modelling of the initial density field in a Bayesian hierarchical framework. The presented method performs a full-scale Bayesian uncertainty quantification of the posterior distribution of fnl using a Hamiltonian Markov Chain Monte Carlo approach. The method accounts for the gravitational formation of the three-dimensional cosmic structure and thus utilizes the full information content of the three-dimensional dark matter density and velocity field available in the data to constrain primordial non-Gaussianity. In this fashion, the method naturally and fully self-consistently accounts for all stochastic uncertainties and systematic effects associated with selection effects, galaxy biasing, and survey geometries. Notably, multiple probes of primordial non-Gaussianity are jointly incorporated: the 3-point correlation, mass distributions of galaxies, and the scale-dependent bias effect, where this final effect is included into a novel bias model I presented in this work. I apply my method to mock data based on the SDSS-III/BOSS survey, outline tests, and present preliminary results. In addition, I present a variety of scientifically valuable data products, e.g., density field reconstructions and novel maps of primordial curvature fluctuations. Finally, future work is discussed, involving different ways of how to extend the model and additional test data sets on which to apply the method.

  • Linear response theory: from black hole thermalization to Weyl semimetals

    Author: Jorge Larana-Aragon
    Publication date: 2020-12-01 12:33

    Linear response theory is an incredibly powerful calculation tool. We apply this framework in quantum field theory to a variety of models originated from distinct areas in theoretical physics and for different reasons. In the context of black hole holography, we consider a quench model where we investigate effective thermalization as well as the boundary signal of the so called evanescent modes which indicate the presence of a black hole like object in the bulk. The problem of quantum thermalization plays a central role within the holographic duality between thermal states in the boundary field theory and black hole like objects in the bulk. However, quantum thermalization is also an interesting question in itself from a fundamental point of view and with that motivation we continue to explore this phenomenon further. Inspired by recent progress in understanding how operators in quantum field theories thermalize, which occurs even when considering integrable models, we investigate the so called operator thermalization hypothesis. We focus on gauge theories at finite temperature with a large number of fields which present a phase transition between the low-temperature and high-temperature regimes. In particular, these theories are the so called vector model and the adjoint matrix model. Last, within the common background of linear response theory we investigate transport properties in a family of Weyl semimetal systems. Concretely, we develop a general analytic method to compute the magneto-optical conductivity of these systems in the presence of an external magnetic field aligned with the tilt of the spectrum.

  • Novelty in social-ecological systems: understanding the past to plan the future

    Author: Yosr Ammar
    Publication date: 2020-11-25 10:54

    Human activities are shaping the Earth system and creating novel properties in the intertwined Social-Ecological Systems (SES). Although novelty is acknowledged in SES theories, the concept of novelty is not well understood, and little mathematical formalization and empirical foundations have been made. Building on the theoretical frameworks of Complex Adaptive Systems (CAS) and concepts of novelty in ecology, this licentiate thesis suggests a first attempt to quantify novelty in a marine ecosystem, in a SES context. Here, I focus on the past emergence of novelty in a marine SES to better understand when and where novelty has emerged and which drivers affect this emergence. Novelty emerges in a CAS when it has moved beyond its historical range of variation. The historical state depends on the temporal and spatial scale as well as the context of the study. Building on the characteristics of CAS, novelty is multidimensional, emerges on a continuum, can be nonlinear, and follows baseline specific trajectories. It has been quantified as the degree of dissimilarity of a system relative to a specific baseline. I used the case of the Baltic Sea SES, where long-term data exists, and many ecological, political, and economic changes have been recorded. Here, I focus on structural changes of the system rather than interactions and feedbacks. Paper 1 focuses on the ecological novelty in the Baltic Sea and contributes as the first study that quantifies novelty in marine ecosystems and across different trophic levels. Results reveal that over the 35-year study-period (1980-2015), novelty has emerged following the pattern of change, but at a slower pace. It has emerged in complex temporal and spatial pattern of the tested abiotic and biotic components. Both abiotic and biotic novelty showed a higher rate of novelty in confined northern basins than in the Central Baltic Sea, which indicated that some areas are more susceptible to the rise of novelty than others. Temperature and salinity were identified as the main abiotic drivers of biotic novelty in the Baltic Sea. Paper 2 contributes as the first study to quantify socio-economic novelty in a marine SES. Socio-economic novelty in the Baltic Sea showed a change in the contribution to novelty from factors linked to local and regional management levels, i.e., fishing gears and commercial groups, to trades which are linked to international level. A high increase in imports and exports in recent years marked the fastest increase in novelty over the period studied. In the latter, novelty in terms of economic value of fishery products was higher than their novelty in quantity. Sweden, Denmark, and Poland have been the countries contributing most to the emergence of novelty in the studied period. This paper illustrates that understanding socio-economic novelty together with ecological novelty, may provide a better understanding of the complexity of marine SES. Although not all the characteristics of CAS could be captured by the methodological approach used in Paper 1 and 2, many have been identified and considered. However, this highlights the need for more methods that can capture different characteristics of CAS, such as interactions and feedbacks, and more knowledge on the emergence of novelty in SES. Understanding how novelty emerges, its processes in different SES components and across-scales, may reduce the risk of missing opportunities for biodiversity conservation, and of unintended management outcomes for long-term sustainability.

  • Brain morphology and behaviour in the guppy (Poecilia reticulata) : Effects of plasticity and mosaic brain evolution

    Author: Stephanie Fong
    Publication date: 2020-11-24 08:00

    Understanding how brains have evolved and subsequently culminated in the huge variation in brain morphology among contemporary vertebrate species has fascinated researchers for many decades. It has been recognized that brain morphology is both genetically and environmentally determined. Adaptations to ecological challenges, for one, has been proposed to be a major force in brain diversification processes. Considering the large energetic costs of neural tissue, it is believed that brain evolution is a highly complex process, involving a delicate balance between the corresponding costs and benefits. 

    Using the guppy (Poecilia reticulata) as the model organism, I first examined the conditions under which diversity in brain morphology is generated. This was done by investigating factors known to exert an influence on brain plasticity, namely environmental and cognitive effects (Paper I). Existing studies generally indicate that the provision of environmental enrichment lead to the enlargement of specific brain structures. While plastic alterations in brain morphology was found to respond to environmental complexity in my study, successful performance in two cognitive tasks did not produce any significant changes. 

    I next assessed the feasibility of the mosaic brain evolution hypothesis by artificially selecting for an increase and decrease in the relative size of the telencephalon (Paper II). Telencephalon size was shown to respond rapidly to divergent selection pressures, with no substantial changes in any of the other brain regions. A comparison with wild fish revealed that fish from the unselected control treatment had telencephalon sizes most similar to that of wild populations, whereas both up-selected and down-selected fish had considerably larger and smaller telencephalon, respectively. 

    I tested fish from the artificial selection lines in a test battery to determine if known differences in telencephalon size affects boldness (Paper III). Individuals were subjected to an emergence test, an open field test and a novel object test. I found no differences in boldness levels across selection treatments, but distinct sex differences were noted whereby males were more active and bolder. 

    The cognitive benefits associated with a larger telencephalon were examined in males in a test of self-control (Paper IV). Guppies from the up-selected lines attained a steeper learning curve and made more correct detours compared to their down-selected conspecifics. 

    In conclusion, I provide experimental evidence for the mosaic brain evolution hypothesis by showing that a specific brain region (telencephalon) can evolve rapidly and independently under directed selection. Future tests on other cognitive benefits as well as implicated costs, together with underlying neuronal changes would help to further unravel the factors governing brain evolution.

  • Localic Categories of Models and Categorical Aspects of Intuitionistic Ramified Type Theory

    Author: Johan Lindberg
    Publication date: 2020-11-23 08:00

    This thesis contains three papers, all in the general area of categorical logic, together with an introductory part with some minor results and proofs of known results which does not appear to be (easily) available in the literature.

    In Papers I and II we investigate the formal system Intuitionistic Ramified Type Theory (IRTT), introduced by Erik Palmgren, as an approach to predicative topos theory. In Paper I we construct and study the category of "local sets" in IRTT, including an extension with inductive definitions. We there also give a model of IRTT in univalent type theory using h-sets. In Paper II we adapt triposes and hyperdoctrines to the ramified setting. These give a categorical semantics for certain formal languages ramified in the same way as IRTT.

    Paper III, which is part of a joint project with Henrik Forssell, concerns logical aspects of the localic groupoid/category representations of Grothendieck toposes that originate from the work of Joyal and Tierney. Working constructively, we give explicit logical descriptions of locales and localic categories used for representing classifying toposes of geometric theories. Aspects of these descriptions are related to work by Coquand, Sambin et al in formal topology, and we show how parts of their work can be captured and extended in our framework.

  • Fungal disease dynamics, genetic variation and biodiversity-yield relationships : — a study along a gradient of coffee management in southwestern Ethiopia

    Author: Beyene Zewdie Hailu
    Publication date: 2020-11-23 08:00

    Intensification of agricultural systems is a major threat to the associated biodiversity and could also affect the dynamics of pests and pathogens. One such system that is currently under an intensification trajectory is the production of Arabica coffee. In this thesis, I studied the relationships between fungal diseases and their natural enemies, the genetic variation in coffee, coffee yield and associated biodiversity along a coffee management gradient in southwestern Ethiopia.

    The specific goals of this thesis were to investigate variation in fungal diseases on coffee and their natural enemies along a gradient of management (I, II), how genetic variation in coffee among sites relate to variation in incidence of the fungal diseases (III), and to investigate the trade-offs in biodiversity-yield relationships along the gradient of coffee management (IV). To answer these questions, I selected 60 sites along a gradient of management that ranged from coffee naturally growing in only little disturbed forests to intensively managed plantations. I used both observational studies and molecular approaches.

    In paper I, I examined if the severity of the four major fungal diseases on coffee varied along the gradient and assessed the main drivers of variation in disease severity. I found that two of the fungal diseases were more severe in the intensively managed coffee sites, while the other two were more severe in the less intensively managed sites. Altitude was the main driver for the diseases, but related in a different way to the different diseases. In paper II, I examined the temporal dynamics in coffee leaf rust-hyperparasite interaction, the biocontrol potential of the hyperparasite and environmental drivers for the two species for three consecutive years during the dry and wet seasons. I found that the rust was more common during the dry season and in managed sites while the hyperparasite was common during the wet season and in sites that were less managed. My results also revealed that higher hyperparasite incidence during the wet season resulted in a lower growth rate of the rust during the subsequent dry season. In paper III, I investigated if genetic composition and diversity of coffee sites relate to the incidence of the fungal diseases assessed. I found that genetic composition of the coffee stands was linked to the incidence of the four fungal diseases, but genetic diversity among the coffee sites did not relate to the incidence of the diseases. In paper IV, I examined biodiversity-yield trade-offs and shape of the relationships between biodiversity and yield along the gradient of management. I found a steep, concave shape initial decline in biodiversity values as coffee yield increased to a certain level, after which a further increase in yield did not have much effect on biodiversity values.

    In conclusion, I found different drivers for the different diseases and for the parasite-hyperparasite interaction. It is difficult to achieve a single management approach that can suit the different pathogen species investigated. High genetic diversity among coffee sites did not reduce disease pressure. While the more complex, less managed sites provide high biodiversity values, and could potentially serve as habitats for natural pest control and in situ conservation for coffee genetic diversity, the yield gap compared to more intensively managed sites was very high. To optimize coffee management and conservation of biodiversity in these landscapes, there is a need to develop strategies whereby the smallholder farmers who depend on coffee and the forest as the main source of livelihood can benefit through for example coffee certification schemes that can pay premium prices for biodiversity-friendly coffee management.

  • 231Pa, 230Th and 232Th as tracers of deep water circulation and particle transport : Insights from the Mediterranean Sea and the Arctic Ocean

    Author: Sandra Gdaniec
    Publication date: 2020-11-18 08:00

    The naturally occurring U and Th-series radionuclides have shown to have a considerable importance for the understanding of biogeochemical processes on Earth and in the ocean. In this thesis, the isotopes 230-thorium (230Th), 232-thorium (232Th) and 231-protactinium (231Pa) are used as tracers of the transport and scavenging of marine particles and water circulation. Pa and Th are particle reactive elements, which makes the production, transport and distribution of Pa and Th key factors for our understanding of the origin, fate and distribution of marine particles in the oceans. 

    This thesis explores the distribution of 231Pa, 230Th and 232Th in two different ocean continental margin environments. In particular, the relative influence of water circulation and particles on the 231Pa, 230Th and 232Th distributions in the Arctic Ocean and Mediterranean Sea was investigated. 231Pa, 230Th and 232Th were analyzed in particles and seawater collected in the Mediterranean Sea during the MedSeA-GA04-S cruise along the GEOTRACES section GA04S and in the Arctic Ocean during the PS94 GN04 ARK-XXIX/3 along the GEOTRACES section GN04.

    One of the important findings of this thesis was the low fractionation between 231Pa and 230Th in the Mediterranean Sea, contrasting what is observed in the open ocean. Additionally, the observed depth profiles of Pa-Th allowed the identification of deep water convection and ventilation in the Western and Eastern Basins, respectively. Moreover, the particle settling speed was reevaluated to ~500 – 1000 m/y.

    In the Arctic Ocean, scavenging onto particles derived from hydrothermal activity was producing relatively low F-factors (FTh/Pa ~ 10), while higher values were observed in deep waters (FTh/Pa ~ 20). Additionally, the hydrothermal particles in the Nansen interior produce lower FTh/Pa values compared to FTh/Pa observed at the Nansen continental margin. Application of a boundary scavenging model revealed the importance of 230Th scavenging at the continental margin along the Nansen Basin, hereafter the Nansen margin, and advocate for the advection of 231Pa into the Atlantic Ocean. As the ocean margin was included in this model, a particle settling speed of 600 m/y was obtained at the Nansen margin.

    Moreover, this thesis includes an inter-comparison of dissolved and particulate 231Pa, 230Th and 232Th measurements between four laboratories of the GEOTRACES community. This comparison was conducted to provide detailed descriptions of various chemical procedures used for Pa-Th analysis and to provide a measure of consistency between the laboratories. Results demonstrated that participating labs can determine concentrations of dissolved 230Th and 231Pa in deep water (below 500 m depth) that are internally consistent within 4 % of the mean values. Analysis of particulate 231Pa, 230Th and 232Th allowed the highlighting of an incomplete Pa dissolution problem with our initial leaching procedure, a problem solved by measuring aliquots of particulate samples at two labs. However, in the present work, consistent particulate 231Pa concentrations as low as ~ 0.002 fg/kg were obtained. Overall, it suggests an improvement of the results consistency compared to the previous GEOTRACES intercalibration exercise.

  • Role of lactobacilli in Helicobacter pylori pathogenesis and host cell responses

    Author: Hanna Gebreegziabher Gebremariam
    Publication date: 2020-11-18 08:00

    Helicobacter pylori is well adapted to the harsh environment of the human stomach, allowing it to persistently colonize the gastric mucosa of at least 50% of the global population for decades. Long-term colonization induces chronic inflammation that can eventually lead to development of peptic ulcer and gastric cancer. The interaction between host, bacterial and environmental factors are crucial for the pathogenesis of H. pylori. In contrast, Lactobacillus species are members of the human microbiota and act as a first line of defense against pathogens. However, the underlying mechanisms behind lactobacilli-mediated pathogen inhibition still need further investigation.

    This thesis focuses on understanding the interplay between commensal and pathogenic bacteria with the human host. In Paper I, we investigated the effect of different Lactobacillus strains on the initial attachment of H. pylori to gastric epithelial cells and found that certain Lactobacillus strains can prevent the adhesion of the pathogen by decreasing the expression of SabA. In Paper II, the anti-inflammatory activity of Lactobacillus strains against H. pylori-induced production of proinflammatory cytokines was explored. We demonstrated the ability of L. gasseri Kx110A1 to reduce the level of TNF and IL-6 in human macrophages through suppression of ADAM17, a metalloproteinase responsible for releasing transmembrane proteins. Lactobacilli-mediated inhibition of these cytokines was not H. pylori-specific, suggesting a general anti-inflammatory property of L. gasseri Kx110A1. In Paper III, we characterized the role of sortase-dependent proteins in L. gasseri Kx110A1. We showed that the deletion of sortase A in lactobacilli resulted in the reduction of auto-aggregation and attachment to host gastric epithelial cells. Moreover, sortase A mutant lactobacilli were not effective in preventing H. pylori initial adherence. Finally, in Paper IV, we showed that lactate can affect the expression of H. pylori adherence genes and the production of bacterial-induced proinflammatory cytokines.

  • Data-Efficient Reinforcement and Transfer Learning in Robotics

    Author: Xi Chen
    Publication date: 2020-11-17 10:41

    In the past few years, deep reinforcement learning (RL) has shown great potential in learning action selection policies for solving different tasks.Despite its impressive success in games, several challenges remain, such as designing appropriate reward functions, collecting large amounts of interactive data, and dealing with unseen cases, which make it difficult to apply RL algorithms to real-world robotics tasks. The ability of data-efficient learning and rapid adaptation to novel cases is essential for an RL agent to solve real-world problems.

    In this thesis, we discuss algorithms to address the challenges in RL by reusing past experiences gained while learning other tasks to improve the efficiency of learning new tasks.Instead of learning directly from the target task, which is complicated and sometimes unavailable during training, we propose first learning from relevant tasks that contain valuable information about the target environment, and reuse the obtained solutions in solving the target task.We follow two approaches to achieve knowledge sharing between tasks. In the first approach, we model the problem as a transfer learning problem and learn to minimize the distance between the representations found based on the training and the target data, such that the learned solution can be applied to the target task using a small amount of data from the target environment.In the second approach, we formulate it as a meta-learning problem and obtain a model that is explicitly trained for rapid adaptation using a small amount of data. At test time, we can learn quickly on top of the trained model in a few iterations when facing a new task.

    We demonstrate the effectiveness of the proposed frameworks by evaluating the methods on a number of real and simulated robotic tasks, including robot navigation, motion control, and manipulation. We show how these methods can be applied to challenging tasks with high-dimensional state/action spaces, limited data, sparse rewards, and requiring diverse skills.

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