| 1. |
- Ahmed, Taha, 1984-
(författare)
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Nanostructured ZnO and metal chalcogenide films for solar photocatalysis
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The increasing demand for clean energy and safe water resources has driven the development of efficient and sustainable technologies. Among these technologies, photocatalysis using semiconducting materials has emerged as a promising solution for both solar hydrogen generation and water purification. Low-dimensional ZnO, including nanorods, nanoparticles, and quantum confined particles (so called quantum dots), has demonstrated excellent photocatalytic properties due to their large surface area, high electron mobility, and tunable band gap.The work in this thesis aims to investigate the potential of low-dimensional ZnO alone and in combination with CdS and Fe2O3 for solar hydrogen generation and photocatalytic water purification. The thesis includes a comprehensive analysis of the synthesis, characterization, and optimization of low-dimensional ZnO-based photocatalyst systems for solar hydrogen generation and photocatalytic water purification. Additionally, the thesis will evaluate the performance of the ZnO-based photocatalysts under different experimental conditions, either as photoelectrodes or as distributed particle systems for water purification. The work includes detailed size control of ZnO by itself in dimensions below 10 nm using a hydrothermal method, to provide an increased total surface area and introduce quantum confinement effects that increase the band gap to enable degradation of chemical bonds in a model pollutant in a distributed system for water purification. The work also includes a relatively detailed study of the phonon–phonon and electron–phonon coupling as a function of dimension from 10 nm to 150 nm for ZnO using non-resonant and resonant Raman spectroscopy. Ultimately, the thesis aims to provide insight into the potential of low-dimensional ZnO alone and in combination with other inorganic materials for solar hydrogen generation and photocatalytic water purification and pave the way for the development of efficient and sustainable technologies for clean energy and safe water resources.
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| 2. |
- Ayala, Ana I.
(författare)
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Modelling impact climate-related change on the thermal responses of lakes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In response to climate-related changes, lakes worldwide have experienced warmer surface water temperatures, shorter ice cover periods and changes in lake stratification. As these aspects of lake dynamics exert substantial control over nutrient availability, oxygenation and biogeochemical cycling, predicting changes in lake water temperature and stratification dynamics can improve our understanding of the consequences of warming on lake ecosystems. This thesis investigates the long-term and short-term (extreme event) effects of climate change on lake thermal dynamics using 1D hydrodynamic lake models.Long-term lake water temperature simulations showed that water temperatures and thermal stratification metrics were projected to clearly shift toward lake thermal conditions that are consistent with a warmer climate at the end of the 21st century, i.e. warmer surface and bottom temperatures and a stronger and longer duration of summer thermal stratification as a result of an earlier onset of stratification and later fall overturn. The simulated lake thermal structure was controlled by energy exchange between the lake surface and the atmosphere (surface heat fluxes) and wind stress. The individual surface heat flux components were projected to change substantially under future climate scenarios. However, the combined changes showed compensating effects, leading to a small overall change in total surface heat flux, that was still sufficient to lead to important changes in whole-lake temperature. On a seasonal scale, spring heating and autumnal cooling were projected to decrease, while only small changes were projected in winter and summer. An extended analysis during summer using 47 lakes showed that while all lakes gained heat during summer under all scenarios, differences in the amount of heat gained during historical and future conditions were small. Additionally, hydrodynamic lake models performed well in reproducing the magnitude and direction of changes in lake temperature and stratification metrics during storms and heatwaves. However, the lake model performance decreased in accuracy compared to non-extreme condition, which should be taken into account. 1D hydrodynamic lake models have been shown to be powerful tools to predict long-term and short-term climate-related changes in lake thermal dynamics, making an in-depth analysis of the surface heat fluxes possible.
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| 3. |
- Baykal, Yunus
(författare)
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Source and age of late Quaternary loess deposits in Europe
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Atmospheric mineral dust is a fundamental component of the Earth’s climate system, with dust both responding to and driving climate change. This close link between dust and climate is recorded in archives of past dust activity, which show that abrupt 101-3 yr shifts in temperature during the last glacial period were accompanied with fluctuations in dust activity. However, the precise mechanism behind this close coupling of dust and climate and the specific role dust plays in modulating rapid climate change remains unclear. Terrestrial wind-blown dust deposits (loess) in Europe serve as source proximal archives of past dust activity. Loess formation chronologies across this region generally indicate greatly enhanced dust deposition during the last glacial cold phases of MIS 4 and, most notably, MIS 2. However, currently chronological precision is not sufficient to constrain more abrupt changes in dust activity and their potential links to climate change. More fundamentally, uncertainties over the sources of loess in Europe limit understanding of the causes of this last glacial dust deposition variability. The four chapters that comprise this thesis address these uncertainties through detailed analysis of the age and sources of loess in the Northern European Plain and English Channel region. Overall, the results demonstrate that abrupt changes in dust deposition during the late last glacial were a function of changes in ice sheet driven sediment supply. Eurasian and Alpine Ice Sheet derived meltwater pulses periodically greatly enhanced sediment availability and dust emission along their drainage routes, as reflected by abrupt dust deposition variability recorded in European loess deposits. Upon discharge into the North Atlantic, these meltwater pulses are also believed to have interacted with ocean circulation, potentially driving abrupt climate fluctuations during the last glacial. This provides a mechanism linking changes in dust, climate and ocean circulation on millennial timescales via ice sheet dynamics and provides the first coherent explanation of the close coupling of millennial scale variation in climate and dust during the Quaternary. Moreover, these findings suggest that meltwater pulses not only affected last glacial climate by changing ocean circulation but also through their impact on the high latitude dust cycle.
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| 4. |
- Bengtsson, Rhodel
(författare)
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Creep aspects of softwood from the cell-wall level to structures
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis addresses the intricate mechanical behaviour of natural materials, with a particular focus on wood. Despite millennia of use, understanding the mechanical behaviour of wood materials remains challenging due to their complex microstructures. For instance, they exhibit variations in properties among samples, nonlinear behaviour under elevated loads, and are sensitive to alterations in moisture content.Wood and related natural biobased materials hold immense potential due to their renewability, cost-effectiveness, eco-friendliness, and ease of use in sustainable construction. Wood boasts remarkable stiffness and strength along its primary axis, surpassing many man-made materials in strength-to-weight ratios. However, its anisotropic and heterogeneous nature gives rise to challenges, necessitating the consideration of multiple parameters for accurate characterization to be used in design.Wood is intrinsically heterogeneous, leading to considerable variations in local stresses and deformations during loading. To address these microstructural effects on macroscopically measurable phenomena, mathematical homogenization methods, established since the 1970s, have found applications in material mechanics, including both fibre composites and wood.In recent years, there has been a growing focus on the viscoelastic behaviour of composites and timber structures, given their increased long-term use in load-carrying applications. While numerous investigations have explored the relationship between the microstructure of wood and its elastic properties, few studies have explored the connection between microstructure and viscoelastic properties.The thesis focuses on the static and, more notably, on the time-dependent mechanical properties of wood, bridging the gap from cell-wall creep to structures. It includes experiments and numerical work, culminating in the development of a material model suitable for orthotropic materials like wood. The multiscale model establishes a link between microstructural parameters and macroscopic properties, potentially applicable to various softwood species. Given the lack of shear creep data in the literature, the thesis introduces straightforward methods to characterize shear creep properties, addressing a significant knowledge gap.Furthermore, the thesis progresses from material-level experiments to higher length scales, demonstrating how the results can be applied to larger wooden structures, such as the tower for a counter-rotating axis tilted turbine. While these results require further validation in the absence of experimental data for wooden wind turbine structures, they offer useful insights into simulating creep behaviour in such applications.In conclusion, this thesis highlights the multifaceted nature of a natural material like wood, its mechanical challenges, and the promising research avenues for comprehensive understanding and practical use. The outcome provides contributions to the efficient utilization of wood in load-carrying structures and underlines the importance of ongoing research in this field.
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| 5. |
- Benz, Caroline
(författare)
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Diving into short linear motifs : Large-scale identification of endogenous and host-pathogen protein-protein interactions and further characterized by deep mutational scanning
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Short linear motifs (SLiMs) are protein-protein interaction sites that play an essential role in distinct cellular processes. Those interactions are challenging to capture by common high-throughput methods. Therefore, we established an improved version of Proteomic Peptide Phage Display (ProP-PD) as a dedicated method to identify SLiM-based interactions. ProP-PD libraries were created for the discovery of endogenous and host-pathogen protein-protein interactions. The M13 bacteriophage libraries present 16 amino acid long peptides from the intrinsically disordered regions (IDRs) of the human (HD2) proteome or the proteomes of RNA viruses (RiboVD). Through benchmarking of the approach using 35 well-known SLiMs binding domains and the HD2 library, we defined parameters for assigning confidence levels to the results. The selections against the HD2 library revealed >2000 SLiMs-based interaction pairs. Regarding host-pathogen interactions, we focused on interactions mediated by coronavirus proteins, exploring how human proteins bind to viral peptides and how viral proteins bind to human SLiMs. By screening more than 130 human bait proteins against the RiboVD, we revealed several host proteins potentially being targeted by SARS-CoV-2 proteins. Viral hijacking of human G3BP1/2 by the N-protein from SARS-CoV-2 impacted stress granule formation, and inhibition of the interaction was found to have an antiviral effect. Using SARS-CoV-2 proteins in selections with our HD2 library, we found that viral proteins may bind host SLiMs. Selected interactions were validated via affinity measurements revealing a wide range of affinities. Finally, we uncovered that a peptide binding to the NSP9 has an antiviral effect. It is not always possible to establish binding determinants directly from ProP-PD derived peptides. Therefore, we developed a deep mutational scanning (DMS) by phage display protocol. To test the approach, we designed libraries in which all amino acid positions of binding peptides were individually mutated, and the effect on binding was investigated through peptide phage selection. The approach was validated against well-studied interactions and applied to SLiM-based interactions between human proteins and SARS-CoV-2 proteins. Based on the DMS by phage display data we could create a higher affinity binder for NSP9 with increased antiviral effects. The research presented in this thesis has established a platform for large-scale interaction screening through phage display. The results contribute to a deeper understanding of the SLiMs binding and function and also pinpoint novel potential targets for the development of antiviral agents.
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| 6. |
- Blasi Romero, Anna
(författare)
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Bioactive nanocellulose materials for the treatment of chronic wounds
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Chronic wounds represent a burden for the healthcare system and significantly affect the quality of life of the patients. There is currently a lack of efficient treatments but new, improved therapeutic approaches are under development. Suggested innovative wound care therapies consist on the topical administration of bioactive compounds aimed at restoring the balance in the wound environment and promoting the healing. However, their effectiveness is limited due to the highly oxidative and proteolytic environment in the chronic wound. In the work presented in this thesis, a series of bioactive nanocellulose-based materials were developed with the aim of addressing some of the present demands in chronic wound care. Wood-derived cellulose nanofibrils (CNFs) were functionalized with selected bioactive molecules expected to endow CNFs with the ability to modulate the chronic wound environment. Different chemical approaches were explored to combine CNFs with the following biomolecules: the amino acid cysteine, the peptide oligoproline and the host defense peptide KR-12. Materials were characterized in terms of chemical structure, degree of substitution and bioactivity.The immobilization of cysteine onto CNFs (cys-CNF) provided the material with radical oxygen species (ROS) scavenging properties and the ability to inhibit protease activity, properties that were related to the presence of free thiol groups on the nanofibers. Storage conditions in an inert atmosphere or in the form of aerogel were proposed to assure the long-term activity of the cys-CNF material. Investigations on the use of the ROS-sensitive oligoproline to crosslink CNFs provided optimized protocols to maximize peptide substitution and the degree of crosslinking. The oligoproline-CNF materials were sensitive to ROS-mediated cleavage and provided a protective effect to cells exposed to oxidative conditions. Moreover, the feasibility of preparing ROS-responsive drug delivery hydrogels based on the oligoproline-CNF was demonstrated, with indications that tuning the length of the oligoproline peptide could be exploited to tailor the release rate of small proteins. CNF materials with antibacterial properties and the ability to modulate the response of pro-inflammatory macrophages were obtained by immobilizing KR-12 derivatives onto CNFs. This study highlighted the importance in the selection of the conjugation chemistry to preserve the activity of the peptide once immobilized. To conclude, this work has contributed with valuable strategies to develop bioactive CNF-based materials with the potential of paving the way for advanced solutions in the field of chronic wound care.
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| 7. |
- Bohm, Katja
(författare)
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Provenance of the pre-Quaternary aeolian dust deposits of East Asia
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Atmospheric mineral dust is a key component in the climate system, but its effect on and response to climate changes are poorly understood, especially over long timescales. This thesis investigates the sources of late Paleogene and Neogene dust deposits that formed under warmer-than-present global climates in the northern Chinese Loess Plateau (CLP) region in mid-latitude East Asia. Provenance research on wind-blown (aeolian) dust is one of the few available methods to constrain past wind directions, dust sources and transport pathways, which is crucial for understanding regional paleoclimate and its changes during global climate transitions.Aeolian dust deposits from three sites are analysed here: the late Paleogene (35–27 Ma) Ulantatal dust sequence, the late Neogene (7–2.6 Ma) Baode Red Clay, and a c. 4 Ma sample from the Nihewan Red Clay. A joint single-grain analysis of detrital zircon (DZ) U-Pb geochronology and detrital rutile (DR) trace element analysis was applied to trace provenance. This thesis is the first use of DR geochemistry as a provenance indicator for CLP dust, and the thesis therefore summarizes the tectonic history of potential primary source regions and presents DR data from 14 potential secondary/sedimentary dust source regions, for comparison to dust deposits.The results highlight the importance of multimineral single-grain analysis, as some provenance signals were not evident from DZ data alone. Fundamentally, the results demonstrate the long-term stability of overall atmospheric circulation in Central-East Asia, with modern-type atmospheric components existing since the late Paleogene. Dust was mostly transported by Siberian High pressure system (SH) -induced northwesterly winds, and planetary mid-latitude circulation -driven westerly winds from primary source regions of the Central Asian Orogenic Belt and Northern Tibetan Plateau, respectively. The results also show provenance changes at the Eocene-Oligocene, Miocene-Pliocene, and Pliocene-Pleistocene boundaries, indicating a long-term link between the Central-East Asian dust cycle and global cooling events. This thesis further argues that overall, both the dust provenance, and possibly the formation of northern CLP region dust deposits since the latest Eocene in general, were controlled by the Northern Hemisphere glaciations via the SH and northwesterly winds. The results shed light on the long-term environmental history of Central-East Asia and demonstrate the link between the regional dust cycle and global cooling. The findings of this thesis provide important constraints to guide future modelling work on dust-climate interactions under warmer-than-present global climates in Central-East Asia, one of the most populated regions on Earth.
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| 8. |
- Bollmark, Gunnar
(författare)
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Order in Strongly Correlated Quasi-One-Dimensional Systems : Solving Higher-Dimensional Systems Combining Matrix-Product-State Methods and Mean-Field Theory
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Since their discovery the understanding of unconventional superconductors (USCs) has posed a great challenge in condensed matter physics. One central problem, both of theory and experiment, lies in determining the microscopic origin of electron pairing in such systems. Partly, the difficulty lies in numerically simulating systems hypothesized to represent USCs. In particular, it remains an open question whether the ground state of the two-dimensional Hubbard model realizes an USC. This system epitomizes the combined difficulty of finding both whether electrons form pairs and whether they condense into an USCs phase.Conversely, the one-dimensional (1D) Hubbard ladder is readily solved numerically using matrix-product state (MPS) methods. Doped away from a half-filled lattice repulsively mediated electron pairing is realized in the system. However, quantum fluctuations hinder ordering in such systems even at zero temperature viz. continuous symmetries cannot be spontaneously broken. Instead, quasi-one-dimensional (Q1D) systems featuring arrays of one-dimensional (1D) chains weakly coupled into a higher-dimensional system can be studied. While pairing is resolved in each 1D system using MPS the condensation of such pairs into a superconductor may be treated using mean-field (MF) theory. The subject of this thesis is the development of the MPS+MF framework: An algorithm utilizing MPS and MF theory capable of solving Q1D systems.Developing new methods requires comparison with known solutions to learn of their potential inaccuracies. Thus, development is split into three steps: i) Simulation of bosons to test the basic approach, ii) simulation of attractive fermions, iii) simulation of an USC composed of repulsive Hubbard ladders. The first two targets admit comparison to quantum Monte Carlo simulations and, for some parameters, analytical methods. The MPS+MF framework is found to simulate the critical temperature of condensation with a fixed ratio to the true critical temperature, independent of Q1D coupling. Additionally, the framework is found capable of resolving competition of insulating and USC phases.Utilizing the possibility of evolving states in time using MPS numerics, MPS+MF is extended to perform self-consistent time evolution. We find that this method allows the detection of superconductivity out of equilibrium and, in particular, dynamically induced superconductivity.
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| 9. |
- Breznik, Eva
(författare)
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Image Processing and Analysis Methods for Biomedical Applications
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- With new technologies and developments medical images can be acquired more quickly and at a larger scale than ever before. However, increased amount of data induces an overhead in the human labour needed for its inspection and analysis. To support clinicians in decision making and enable swifter examinations, computerized methods can be utilized to automate the more time-consuming tasks. For such use, methods need be highly accurate, fast, reliable and interpretable. In this thesis we develop and improve methods for image segmentation, retrieval and statistical analysis, with applications in imaging-based diagnostic pipelines. Individual objects often need to first be extracted/segmented from the image before they can be analysed further. We propose methodological improvements for deep learning-based segmentation methods using distance maps, with the focus on fully-supervised 3D patch-based training and training on 2D slices under point supervision. We show that using a directly interpretable distance prior helps to improve segmentation accuracy and training stability.For histological data in particular, we propose and extensively evaluate a contrastive learning and bag of words-based pipeline for cross-modal image retrieval. The method is able to recover correct matches from the database across modalities and small transformations with improved accuracy compared to the competitors. In addition, we examine a number of methods for multiplicity correction on statistical analyses of correlation using medical images. Evaluation strategies are discussed and anatomy-observing extensions to the methods are developed as a way of directly decreasing the multiplicity issue in an interpretable manner, providing improvements in error control. The methods presented in this thesis were developed with clinical applications in mind and provide a strong base for further developments and future use in medical practice.
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| 10. |
- Brodmerkel, Maxim N.
(författare)
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Theoretical and Biochemical : Advancing Protein Structure Investigations with Complementing Computations
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Life as we know it today would not exist without proteins. The functions of proteins for us and other organisms are linked to their three-dimensional structures. As such, protein structure investigations are a crucial contribution for understanding proteins and the molecular basis of life. Some methods probe the structure of proteins in the gas phase, which brings various advantages as well as complications. Amongst them is mass spectrometry, a powerful method that provides a multitude of information on gaseous protein structures. Whilst mass spectrometry shines in obtaining data of the higher-order structures, atomistic details are out of reach. Molecular dynamics simulations on the other hand allow the interrogation of proteins in high-resolution, which makes it an ideal method for their structural research, be it in or out of solution.This thesis aims to advance the understanding of protein structures and the methods for their study utilising classic molecular dynamics simulations. The research presented in this thesis can be divided into two themes, comprising the rehydration of vacuum-exposed structures and the interrogation of the induced unfolding process of proteins. Out of their native environment, proteins undergo structural changes when exposed to vacuum. Investigating the ability to revert those potential vacuum-induced structural changes by means of computational rehydration provided detailed information on the underlying protein dynamics and how much of the structure revert back to their solution norm. We have further shown through rehydration simulations that applying an external electric field for dipole-orientation purposes does not induce irreversible changes to the protein structures. Our investigations on the induced unfolding of protein structures allowed a detailed look into the process of unfolding, accurately pinpointing areas within the proteins that unfolded first. The details provided by our simulations enabled us to describe potential mechanisms of the unfolding processes of different proteins on an atomistic level. The obtained results thus provide a potent theoretical basis for current and future experiments, where it will be very interesting to see MD compared with or complemented to experiments.
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