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1.	Amvrosiadi, Nino (author) The value of experimental data and modelling for exploration of hydrological functioning: The case of a till hillslope 2017 Doctoral thesis (other academic/artistic)abstract Successfully modeling one system response (e.g. hydrograph or solute transport) sometimes gives the false sense of well-characterizing the modeled system. This is partly because of the well-known equifinality issue; during the calibration process multiple parameter combinations can produce similarly good results. One step forward towards a better-defined system is using measured (at relevant scale) values for the model parameters, as well as using multiple conditions to constrain the model.But when not enough, or relevant, field measurements are available, virtual experiments (VE’s) can be used as a supplementary method to model calibration. The advantage of VE’s over model calibration is that they can also be used to explore assumptions both on the system hydrological processes, and on the model structure.One goal of this study was to utilize both field measurements and models for better characterization of the S-transect hillslope, located in Västrabäcken catchment, Northern Sweden. This included (a) characteristics in space: system vertical boundaries, hydraulic parameters, pore water velocity distribution, spatial correlation of flowpaths, soil water retention properties; (b) characteristic of system’s dynamic behavior: storage – discharge relationship, transit time distribution, turnover time; and (c) outputs’ sensitivity to external forcing, and to small scale structure assumptions. The second goal was to comment on the value of field measurements and virtual experiments for extracting information about the studied system.An intensely monitored study hillslope was chosen for this work. Although the hillslope has already been the subject of multiple field and modelling studies, there are still open questions regarding the characteristics listed above. The models used were the Vertical Equilibrium Model (VEM), and the Multiple Interacting Pathways (MIPs) model.It was found that the hillslope was well connected; from the near-stream areas up to the water divide the storage – discharge relationship could be described as an exponential function. Also, the dynamic storage (which controls the hydrograph dynamics) was much smaller comparing to the total hillslope storage. The unsaturated soil storage was found to be more sensitive to water table positions than vertical flux magnitude. The dynamic condition of external forcing (precipitation and evapotranspiration) affected the transit time distribution (TTD) shape. And, opposite to expectations, TTD was not sensitive to micro-scale structural assumptions tested here.
2.	Aagaard, Sunniva Margrethe Due (author) Reticulate Evolution in Diphasiastrum (Lycopodiaceae) 2009 Doctoral thesis (other academic/artistic)abstract In this thesis relationships and the occurrence of reticulate evolutionary events in the club moss genus Diphasiastrum are investigated. Diphasiastrum is initially established as a monophyletic group within Lycopodiaceae using non recombinant chloroplast sequence data. Support is obtained for eight distinct parental lineages in Diphasiastrum, and relationships among the putative parent taxa in the hypothesized hybrid complexes; D. alpinum, D. complanatum, D. digitatum, D. multispicatum, D. sitchense, D. tristachyum and D. veitchii are presented. Feulgen DNA image densitometry data and sequence data obtained from three nuclear regions, RPB2, LEAFY and LAMB4, were used to infer the origins of three different taxa confirmed to be allopolyploid; D. zanclophyllum from South Africa, D. wightianum from Malaysia and an undescribed taxon from China. The two Asian polyploids have originated from two different hybrid combinations, D. multispicatum x D. veitchii and D. tristachyum x D. veitchii. Diphasiastrum zanclophyllum originates from a cross between D. digitatum and an unidentified diploid taxon. The occurrence of three homoploid hybrid combinations commonly recognized in Europe, D. alpinum x D. complanatum, D. alpinum x D. tristachyum and D. complanatum x D. tristachyum, are verified using the same three nuclear regions. Two of the three hybrid combinations are also shown to have originated from reciprocal crosses. Admixture analyses performed on an extended, dataset similarly identified predominately F1 hybrids and backcrosses. The observations and common recognition of hybrid species in the included populations are hence most likely due to frequent observations of neohybrids in hybrid zones. Reticulate patterns are, however, prominent in the presented dataset. Hence future studies addressing evolutionary and ecological questions in Diphasiastrum should emphasize the impact of gene flow between parent lineages rather than speciation as the result of hybridization.
3.	Abbas, Qaisar, 1975- (author) Weak Boundary and Interface Procedures for Wave and Flow Problems 2011 Doctoral thesis (other academic/artistic)abstract In this thesis, we have analyzed the accuracy and stability aspects of weak boundary and interface conditions (WBCs) for high order finite difference methods on Summations-By-Parts (SBP) form. The numerical technique has been applied to wave propagation and flow problems.The advantage of WBCs over strong boundary conditions is that stability of the numerical scheme can be proven. The boundary procedures in the advection-diffusion equation for a boundary layer problem is analyzed. By performing Navier-Stokes calculations, it is shown that most of the conclusions from the model problem carries over to the fully nonlinear case.The work was complemented to include the new idea of using WBCs on multiple grid points in a region, where the data is known, instead of at a single point. It was shown that we can achieve high accuracy, an increased rate of convergence to steady-state and non-reflecting boundary conditions by using this approach.Using the SBP technique and WBCs, we have worked out how to construct conservative and energy stable hybrid schemes for shocks using two different approaches. In the first method, we combine a high order finite difference scheme with a second order MUSCL scheme. In the second method, a procedure to locally change the order of accuracy of the finite difference schemes is developed. The main purpose is to obtain a higher order accurate scheme in smooth regions and a low order non-oscillatory scheme in the vicinity of shocks.Furthermore, we have analyzed the energy stability of the MUSCL scheme, by reformulating the scheme in the framework of SBP and artificial dissipation operators. It was found that many of the standard slope limiters in the MUSCL scheme do not lead to a negative semi-definite dissipation matrix, as required to get pointwise stability.Finally, high order simulations of shock diffracting over a convex wall with two facets were performed. The numerical study is done for a range of Reynolds numbers. By monitoring the velocities at the solid wall, it was shown that the computations were resolved in the boundary layer. Schlieren images from the computational results were obtained which displayed new interesting flow features.
4.	Abdurakhmanov, Eldar, 1977- (author) Discovery and evaluation of direct acting antivirals against hepatitis C virus 2015 Doctoral thesis (other academic/artistic)abstract Until recently, the standard therapy for hepatitis C treatment has been interferon and ribavirin. Such treatment has only 50% efficacy and is not well tolerated. The emergence of new drugs has increased the treatment efficacy to 90%. Despite such an achievement, the success is limited since the virus mutates rapidly, causing the emergence of drug resistant forms. In addition, most new drugs were developed to treat genotype 1 infections. Thus, development of new potent antivirals is needed and drug discovery against hepatitis C is continued.In this thesis, a FRET-based protease assay was used to evaluate new pyrazinone based NS3 protease inhibitors that are structurally different to the newly approved and currently developing drugs. Several compounds in this series showed good potencies in the nanomolar range against NS3 proteases from genotype 1, 3, and the drug resistance variant R155K. We assume that these compounds can be further developed into drug candidates that possess activity against above mentioned enzyme variants.By using SPR technology, we analyzed interaction mechanisms and characteristics of allosteric inhibitors targeting NS5B polymerases from genotypes 1 and 3. The compounds exhibited different binding mechanisms and displayed a low affinity against NS5B from genotype 3.In order to evaluate the activity and inhibitors of the NS5B polymerase, we established an SPR based assay, which enables the monitoring of polymerization and its inhibition in real time. This assay can readily be implemented for the discovery of inhibitors targeting HCV.An SPR based fragment screening approach has also been established. A screen of a fragment library has been performed in order to identify novel scaffolds that can be used as a starting point for development of new allosteric inhibitors against NS5B polymerase. Selected fragments will be further elaborated to generate a new potent allosteric drug candidate.Alternative approaches have successfully been developed and implemented to the discovery of potential lead compounds targeting two important HCV drug targets.
5.	Abenius, Erik, 1971- (author) Direct and Inverse Methods for Waveguides and Scattering Problems in the Time Domain 2005 Doctoral thesis (other academic/artistic)abstract Numerical simulation is an important tool in understanding the electromagnetic field and how it interacts with the environment. Different topics for time-domain finite-difference (FDTD) and finite-element (FETD) methods for Maxwell's equations are treated in this thesis. Subcell models are of vital importance for the efficient modeling of small objects that are not resolved by the grid. A novel model for thin sheets using shell elements is proposed. This approach has the advantage of taking into account discontinuities in the normal component of the electric field, unlike previous models based on impedance boundary conditions (IBCs). Several results are presented to illustrate the capabilities of the shell element approach. Waveguides are of fundamental importance in many microwave applications, for example in antenna feeds. The key issues of excitation and truncation of waveguides are addressed. A complex frequency shifted form of the uniaxial perfectly matched layer (UPML) absorbing boundary condition (ABC) in FETD is developed. Prism elements are used to promote automatic grid generation and enhance the performance. Results are presented where reflection errors below -70dB are obtained for different types of waveguides, including inhomogeneous cases. Excitation and analysis via the scattering parameters are achieved using waveguide modes computed by a general frequency-domain mode solver for the vector Helmholtz equation. Huygens surfaces are used in both FDTD and FETD for excitation in waveguide ports. Inverse problems have received an increased interest due to the availability of powerful computers. An important application is non-destructive evaluation of material. A time-domain, minimization approach is presented where exact gradients are computed using the adjoint problem. The approach is applied to a general form of Maxwell's equations including dispersive media and UPML. Successful reconstruction examples are presented both using synthetic and experimental measurement data. Parameter reduction of complex geometries using simplified models is an interesting topic that leads to an inverse problem. Gradients for subcell parameters are derived and a successful reconstruction example is presented for a combined dielectric sheet and slot geometry.
6.	Abrahamson, Alexandra, 1978- (author) Gill EROD Activity in Fish : A Biomarker for Waterborne Ah-receptor Agonists 2007 Doctoral thesis (other academic/artistic)abstract Induction of the cytochrome P450(CYP)1A protein and the connected increase in 7-ethoxyresorufin O-deethylase (EROD) activity are common biomarkers in fish. Enhanced activity of this protein signals exposure to Ah-receptor agonists such as chlorinated dioxins, co-planar polychlorinated biphenyls (PCBs) and certain polycyclic aromatic hydrocarbons (PAHs). The EROD biomarker is commonly analyzed in liver microsomes. However, the gill is directly exposed to waterborne pollutants, and in this thesis the gill filament EROD assay was therefore evaluated as a monitoring tool for waterborne CYP1A inducers in fish. Originally developed in rainbow trout (Oncorhynchus mykiss), the assay was here applied in various limnic and marine species. Following exposure to low waterborne concentrations of the readily metabolized CYP1A inducers benzo(a)pyrene (BaP) and indigo, a strong EROD induction was observed in the gill but not in the liver. This likely reflected metabolic clearance of the inducers in gill and other extrahepatic tissues. The high sensitivity of the gill was confirmed in studies of fish caged in waters in urban and rural areas in Sweden where the gill consistently showed a more pronounced EROD induction compared with the liver and the kidney. Fish caged in the reference waters showed surprisingly strong gill EROD induction and CYP1A immunostaining. Consequently, there may be CYP1A inducers present in the aquatic environment that are not yet identified. The assay was further applied in Atlantic cod (Gadus morhua) as a biomarker of exposure to crude oil and produced water (PW) from oil fields in the North Sea. The assay was finally adapted to detect inhibiting compounds, and an imidazole, a triazole and a plant flavonoid turned out to be potent gill EROD inhibitors. The overall conclusion from the studies of this thesis is that the gill filament EROD assay is a practical and sensitive biomarker of exposure to waterborne CYP1A inducers in various fish species. The induction of gill EROD activity in fish also at the reference sites in the field studies calls for further studies on background contamination in Swedish waters.
7.	Abrahamsson, Johan, 1977- (author) Kinetic Energy Storage and Magnetic Bearings : for Vehicular Applications 2014 Doctoral thesis (other academic/artistic)abstract One of the main challenges in order to make electric cars competitive with gas-powered cars is in the improvement of the electric power system. Although many of the energy sources currently used in electric vehicles have sufficientlyhigh specific energy, their applicability is limited due to low specific power. It would therefore be advantageous to create a driveline with the main energy storage separated from a smaller energy buffer, designed to have high power capabilities and to withstand frequent and deep discharge cycles. It has been found that rotating kinetic energy storage in flywheels is very well suited for this type of application.A composite shell, comprising an inner part made of glassfiber and an outer part made of carbonfiber, was analyzed analytically and numerically, designed, and constructed. The shell was fitted onto a metallic rotor using shrinkfitting. The cost of the shell, and the complexity of assembly, was reduced by winding the glass- and carbonfiber consecutively on a mandrel, and curing the complete assembly simultaneously. Thereby, the shell obtained an internal segmentation, without the need for fitting several concentric parts onto each other. The radial stress inside the composite shell was kept compressive thanks to a novel approach of using the permanent magnets of the integrated electric machine to provide radial mechanical load during rotation.Two thrust bearing units (one upper and one lower) comprising one segmented unit with the permanent magnets in a cylindrical Halbach configuration and one non-segmented unit in a up/down configuration were optimized, constructed and tested. Each thrust bearing unit generated 1040 N of repelling force, and a positive axial stiffness of 169 N/mm at the nominal airgap of 5 mm. Two radial active magnetic bearings (one upper and one lower) were optimized, constructed and tested. By parameterizing the shape of the actuators, a numerical optimization of force over resistive loss from the bias currentcould be performed. The optimized shape of the electromagnets was produced by watercutting sheets of laminated steel. A maximum current stiffness of120 N/A at a bias current of 1.5 A was achieved.
8.	Abrahamsson, Maria, 1975- (author) Tuning of the Excited State Properties of Ruthenium(II)-Polypyridyl Complexes 2006 Doctoral thesis (other academic/artistic)abstract Processes where a molecule absorbs visible light and then converts the solar energy into chemical energy are important in many biological systems, such as photosynthesis and also in many technical applications e.g. photovoltaics. This thesis describes a part of a multidisciplinary project, aiming at a functional mimic of the natural photosynthesis, with the overall goal of production of a renewable fuel from sun and water. More specific, the thesis is focused on design and photophysical characterization of new photosensitizers, i.e. light absorbers that should be capable of transferring electrons to an acceptor and be suitable building blocks for supramolecular rod-like donor-photosensitizer-acceptor arrays. The excited state lifetime, the excited state energy and the geometry are important properties for a photosensitizer. The work presented here describes a new strategy to obtain longer excited state lifetimes of the geometrically favorable Ru(II)-bistridentate type complexes, without a concomitant substantial decrease in excited state energy. The basic idea is that a more octahedral coordination around the Ru will lead to longer excited state lifetimes. In the first generation of new photosensitizers a 50-fold increase of the excited state lifetime was observed, going from 0.25 ns for the model complex to 15 ns for the best photosensitizer. The second generation goes another step forward, to an excited state lifetime of 810 ns. Furthermore, the third generation of new photosensitizers show excited state lifetimes in the 0.45 - 5.5 microsecond region at room temperature, a significant improvement. In addition, the third generation of photosensitizers are suitable for further symmetric attachment of electron donor and acceptor motifs, and it is shown that the favorable properties are maintained upon the attachment of anchoring groups. The reactivity of the excited state towards light-induced reactions is proved and the photostability is sufficient so the new design strategy has proven successful.
9.	Abril, Claudia, 1985- (author) Seismicity and crustal structure in Iceland 2018 Doctoral thesis (other academic/artistic)abstract The main goal of this Ph.D. thesis is to improve locations of earthquake hypocenters and to resolve heterogeneous crustal structure and its effects on travel times. The data and case studies are drawn from the Icelandic national SIL network and the temporary NICE project deploy-ment in the Tjörnes Fracture Zone. Iceland presents complex tectonics and active volcanism, consequences of its position astride the Mid-Atlantic Ridge between the European and North American plates and on top of a melting anomaly in the mantle below. Studies focused on characterizing the seismicity and the crustal structure are prerequisites for further seismologi-cal studies in Iceland, e.g., on seismic sources, the evolution of volcanic systems, activity on seismic faults and seismic hazard, among others.Different methods have been explored. First, we estimated empirically travel-time functions of seismic waves and their uncertainties for 65 stations in the Icelandic permanent network (SIL) using arrival times. The estimated travel-time functions and uncertainties were used to relocate the complete catalog applying a nested-search algorithm to this non-linear problem. The clearest changes in locations compared to the SIL solutions were obtained in the peripheral areas of the network, in particular in the Tjörnes Fracture Zone (North Iceland) and on the Reykjanes Peninsula (South Iceland).Relocations with empirical travel times were used complementary with constrained earth-quake relocation and the collapsing methods of Li et al. [2016] to study the seismicity in the Hengill area (South Iceland). Patterns in the seismicity in the ﬁnal locations reproduce lin-eations previously found in relative relocations in the area. The brittle-ductile transition was estimated, obtaining a smaller depth in the northern part of the region, dominated by volcanic processes, compared with the south, controlled by tectonic processes. Furthermore, the Hengill ﬁssure swarm that hosts two large geothermal power plants, was found to have deeper penetrat-ing earthquakes than adjacent volcanic areas, presumably because it is more effectively cooled.Local earthquake tomography was used to solve simultaneously for earthquake location and velocity structure in the Tjörnes Fracture Zone, using data from the temporary network installed during the North ICeland Experiment, and data from the permanent SIL network. 3-D velocity models for P- and S-waves were obtained for the area and used to relocate the complete SIL catalog. The results demonstrate signiﬁcant structures associated with the different branches of this complex transform region, e.g. low velocities along the Husavík-Flatey Fault (HFF), penetrating to about 10 km depth. Low Vp/Vs ratios were also mapped at depth along the HFF indicating presence of highly compressible ﬂuids in the middle crust. In general, the seismicity pattern was shifted towards the surface from SIL locations and clariﬁed in its lateral distribution. This highlighted a zone of concentrated deformation in the Tjörnes Microplate, which intersections with the two main strands of the overall zone coincide with changes in their geometry and character.
10.	Abtahi, Sayyed Mohammad (author) Airborne Gravity Gradient, Magnetic and VLF datasets : Case studies of modelling, inversion and interpretation 2016 Doctoral thesis (other academic/artistic)abstract Northern Sweden is one of the largest hosts for mineral resources in Europe and always has been an interesting area for researchers from various disciplines of Earth sciences. This dissertation is a comprehensive summary of three case study papers on airborne VLF, gravity gradient and magnetic data in the area.In the first paper, tensor VLF data is extracted from an old data set which contains only the total and the vertical magnetic components. The anomalous part of the horizontal magnetic field components is computed by a Hilbert transform of the vertical magnetic field. The normal part of the horizontal magnetic field component is computed as a function of total, vertical and anomalous part of horizontal magnetic fields. The electric field is also calculated for TE mode and impedance tensor and apparent resistivity are computed. In addition tippers are calculated for two transmitters and inverted by a 3D inversion algorithm. Comparison of the estimated model and geology map of bedrock shows that lower resistivity zones are correlated with mineralizations.The second paper deals with the internal consistency of airborne gravity gradient data. The six components of the data are estimated from a common potential function. It is shown that the data is adequately consistent but at shorter land clearances the difference between the estimated data and the original data is larger. The technique is also used for computing the Bouguer anomaly from terrain corrected FTG data. Finally the data is inverted in 3D, which shows that the estimated density model in shallow depth is dominated by short wave length features.Inversion of TMI data is the topic of the third paper where a new type of reference model for 3D inversion of magnetic data is proposed by vertically extending the estimated magnetization of a 2D terrain magnetization model. The final estimated 3D result is compared with the magnetization model where no reference model is used. The comparison shows that using the reference model helps the high magnetization zones in the estimated model at shallow depths to be better correlated with measured high remanent magnetization from rock samples. The high magnetization zones are also correlated with gabbros and volcanic metasediments.
11.	Acharya, Sandipta, 1972- (author) Some Aspects of Physicochemical Properties of DNA and RNA 2006 Doctoral thesis (other academic/artistic)abstract This thesis is based on nine research publications (I – IX) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, pKa values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. Papers I – II showed that the ionization of 2'-OH group is nucleobase-dependant. Paper III showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. Papers IV – VI show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. Paper VII showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. Paper VIII showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. Paper IX showed that the pKa values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.
12.	Adamaki, Angeliki, 1983- (author) Seismicity Analyses Using Dense Network Data : Catalogue Statistics and Possible Foreshocks Investigated Using Empirical and Synthetic Data 2017 Doctoral thesis (other academic/artistic)abstract Precursors related to seismicity patterns are probably the most promising phenomena for short-term earthquake forecasting, although it remains unclear if such forecasting is possible. Foreshock activity has often been recorded but its possible use as indicator of coming larger events is still debated due to the limited number of unambiguously observed foreshocks. Seismicity data which is inadequate in volume or character might be one of the reasons foreshocks cannot easily be identified. One method used to investigate the possible presence of generic seismicity behavior preceding larger events is the aggregation of seismicity series. Sequences preceding mainshocks chosen from empirical data are superimposed, revealing an increasing average seismicity rate prior to the mainshocks. Such an increase could result from the tendency of seismicity to cluster in space and time, thus the observed patterns could be of limited predictive value. Randomized tests using the empirical catalogues imply that the observed increasing rate is statistically significant compared to an increase due to simple clustering, indicating the existence of genuine foreshocks, somehow mechanically related to their mainshocks. If network sensitivity increases, the identification of foreshocks as such may improve. The possibility of improved identification of foreshock sequences is tested using synthetic data, produced with specific assumptions about the earthquake process. Complications related to background activity and aftershock production are investigated numerically, in generalized cases and in data-based scenarios. Catalogues including smaller, and thereby more, earthquakes can probably contribute to better understanding the earthquake processes and to the future of earthquake forecasting. An important aspect in such seismicity studies is the correct estimation of the empirical catalogue properties, including the magnitude of completeness (Mc) and the b-value. The potential influence of errors in the reported magnitudes in an earthquake catalogue on the estimation of Mc and b-value is investigated using synthetic magnitude catalogues, contaminated with Gaussian error. The effectiveness of different algorithms for Mc and b-value estimation are discussed. The sample size and the error level seem to affect the estimation of b-value, with implications for the reliability of the assessment of the future rate of large events and thus of seismic hazard.
13.	Adams, Christopher, 1978- (author) Secondary and Higher Order Structural Characterization of Peptides and Proteins by Mass Spectrometry 2007 Doctoral thesis (other academic/artistic)abstract The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. Fragment ion abundances are a quantifiable tool providing chiral recognition (RChiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding.The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.
14.	Adlmann, Franz Alois (author) Opportunities and challenges of surface scattering at next generation neutron sources 2018 Doctoral thesis (other academic/artistic)abstract Complex fluids and soft matter are ubiquitously found in the world and all contacts in life are made over surfaces. To describe the mechanical behavior of such substances, rheological methods are used. Flow instabilities are a big challenge in rheology since they will be reflected in the macroscopic variables probed, like e. g. the viscosity. Many such discontinuities may actually originate at the surface. Investigating the properties of liquids in contact with the surface under mechanical load is the main course of the thesis. Neutron reflectometry and GISANS are perfect tools in this context to access the solid liquid interfaces, since they can penetrate many engineering materials and show a comparably large scattering potential at deuterated samples. In this thesis shear was applied on a model solution and neutron scattering techniques were used to investigate the structure under load. The focus was set on the development of the measurement methods themselves to enable new scientific insights in the future. First, by stroboscopic measurements the flux limitations are overcome for oscillatory rheology. By reintegration in the post processing it is shown that kinetic measurements with neutrons are possible with a time resolution below one millisecond. Second, the transformation of grazing incidence data from the laboratory system into q-space is strongly non-linear resulting in a need for re-binning. In this thesis a universal tool has been developed for this purpose. Finally, there is an ongoing discussion on depth sensitive neutron scattering experiments from solid-liquid boundaries. By using emission densities we show that such experiments face severe limitations due to the low absorption cross section of the neutron.
15.	Agervald, Åsa (author) Maturation and Regulation of Cyanobacterial Hydrogenases 2009 Doctoral thesis (other academic/artistic)abstract Accelerated global warming plus an increasing need for energy is an equation not easily solved, thus new forms of sustainable energy production are urgently requested. In this context hydrogen production based on a cyanobacterial system offers an environmentally friendly alternative for energy capture and conversion. Cyanobacteria can produce hydrogen gas from sun light and water through the combination of photosystems and hydrogenases, and are suitable to cultivate in large scale. In the present thesis the maturation process of [NiFe]-hydrogenases is investigated with special focus on transcription of the accessory genes encoding proteins needed for assembly of the large and possibly also for the small hydrogenase subunit. The cyanobacteria used are two N2-fixing, filamentous, heterocystous strains; Nostoc sp. strain PCC 7120 and Nostoc punctiforme PCC 73102. For a biotechnological exploration of hydrogen production tools for regulatory purposes are important. The transcription factor CalA (cyanobacterial AbrB like) (Alr0946 in the genome) in Nostoc sp. strain PCC 7120 was found to be involved in hydrogen metabolism by regulating the transcription of the maturation protein HypC. Further the bidirectional hydrogenase activity was down-regulated in the presence of elevated levels of CalA, a result important to take into account when optimizing cyanobacteria for hydrogen production. CalA regulates at least 25 proteins in Nostoc sp. strain PCC 7120 and one of the down-regulated proteins was superoxide dismutase, FeSOD. The characterization of FeSOD shows that it has a specific and important function in the oxidative stress tolerance of Nostoc sp. stain PCC 7120. Since CalA is involved in regulation of both the hydrogen metabolism as well as stress responses these findings indicate that Alr0946 is an important transcription factor in Nostoc sp. strain PCC 7120 active on a global level in the cell. This thesis adds more knowledge concerning maturation and regulation of cyanobacterial hydrogenases which might be useful for future large scale hydrogen.
16.	Aguirre Rivera, Javier, 1989- (author) Tracking single molecules in uncharted territory : A single-molecule method to study kinetics in live bacteria 2020 Doctoral thesis (other academic/artistic)abstract The synthesis of proteins, also known as translation, is a fundamental process in every living organism. The steps in the translation of genetic information to functional proteins have been meticulously studied, mostly using in vitro techniques, yielding a detailed model of their mechanisms. However, the use of minimal cell-free systems allows for the possibility to miss interactions from absent components or that reactions are affected by the buffer composition. The work presented in this thesis opens a way to study the kinetics of complex molecular processes, like protein synthesis, directly inside live bacterial cells in real time. We developed and optimized a method to deliver dye-labeled macromolecules inside live cells and generate a kinetic model of the particle’s interactions based on its diffusion inside the cell.This method facilitated the study of translation elongation and initiation directly in live cells. Our measurements of reaction times of tRNA in the ribosome, agree with previous reports from in vitro techniques. We further applied the method to examine the effects of three aminoglycoside antibiotics and erythromycin directly in live cells. The aminoglycoside antibiotics slowed-down protein synthesis 2- to 4-fold, while the number of elongation cycles per initiation event decreased significantly. In the case of erythromycin, cells showed a 4-fold slower protein synthesis. Additionally, we measured the kinetics of sequence-specific effects of erythromycin: translational arrest, and peptidyl-tRNA drop-off; these in vivo measurements revealed a complex mechanism of action of the drug, in agreement with models suggested by previous experiments. Additionally, we applied the method to measure the effects, on the kinetics of protein synthesis, caused by modifications in the C-terminal tail of the S13 ribosomal protein. Our measurements showed that specific mutations led to different changes in the occupancy and dwell-time of labeled-tRNA in the ribosome.To summarize, the present work will guide the reader through the development of a method to study the kinetics of protein synthesis directly in live bacterial cells, as well as its application to characterize the effects of different antibiotics within the complex environment of a living organism.
17.	Agåker, Marcus, 1976- (author) Double Excitations in Helium Atoms and Lithium Compounds 2006 Doctoral thesis (other academic/artistic)abstract This thesis addresses the investigation of doubly excited 2l´nl states in helium atoms and double core excitations in solid lithium compounds.Measurements on He are made in field free environments and under the influence of electric and magnetic fields, using synchrotron based inelastic photon scattering. Cross sections for scattering to singly excited final states are directly determined and compared to theoretical results and are found to be in excellent agreement. Radiative and spin-orbit effects are quantified and are shown to play an important role in the overall characterization of highly excited He states below the N =2 threshold. A dramatic electric field dependence is also observed in the flourecence yield already for relatively weak fields. This signal increase, induced by electric as well as magnetic fields, is interpreted in terms of mixing with states of higher fluorescence branching ratios.Double core excitations at the lithium site in solid lithium compounds are investigated using resonant inelastic x-ray scattering (RIXS). The lithium halides LiF, LiCl, LiBr and LiI are studied as well as the molecular compounds Li2O, Li2CO3 and LiBF4. States with one, as well as both, of the excited electrons localized at the site of the bare lithium nucleus are identified, and transitions which involve additional band excitations are observed. A strong influence of the chemical surrounding is found, and it is discussed in terms of the ionic character of the chemical bond.
18.	Ahani, Ghafour (author) Optimal Scheduling for Timely Information in Communication Systems 2021 Doctoral thesis (other academic/artistic)abstract The explosive growth of data in information society poses significant challenges in the timely delivery of information in the context of communication networks. Hence, optimal utilization of scarce network resources is crucial. This dissertation contributes to several aspects related to the timely delivery of information, including scheduling of data flows between sources and destinations in a network, scheduling of content caching in a base station of mobile networks, and scheduling of information collection. Two important metrics, namely, delivery deadline and information freshness, are accounted for. Mathematical models and tailored solution approaches are developed via tools from optimization.Five research papers are included in the dissertation. Paper I studies a flow routing and scheduling problem with delivery deadline. This type of problem arises in many applications such as data exchange in scientific projects or data replication in data centers where large amounts of data need to be timely distributed across the globe. Papers II, III, and IV investigate content caching along time in a base station. Content caching at the network’s edge has recently been considered a costefficient way of providing users with their requested information. In Paper II, the schedule for updating the cache is optimized with respect to the content requests of users and the popularity of contents over time. Paper III, as an extension of Paper II, addresses the question of how to keep the cache information fresh, as all contents can not be updated due to the limited capacity of the backhaul link. The freshness of information is quantified via the notion of age of information (AoI). Paper IV investigates joint optimization of content caching as well as recommendation; the latter contributes to satisfying content requests in case of a cache miss. Paper V studies optimal scheduling of information collection from a set of sensor nodes via an unmanned aerial vehicle. The objective is to keep the overall AoI as small as possible.In these studies, analysis of problem complexity is provided, and timeefficient solution algorithms based on column generation, Lagrangian decomposition, and graph labeling are developed. The algorithms also yield a bound of global optimum, that can be used to assess the performance of any given solution. The effectiveness of the algorithms in obtaining nearoptimal solutions is demonstrated via extensive simulations.
19.	Ahlberg, Martina, 1980- (author) Critical Phenomena and Exchange Coupling in Magnetic Heterostructures 2012 Doctoral thesis (other academic/artistic)abstract The continuous phase transition in thin magnetic films and superlattices has been studied using the magneto-optical Kerr effect (MOKE) and polarized neutron scattering (PNR). It has been shown that the critical behavior of amorphous thin films belonging to the 2D XY universality class can be described within the same theory as crystalline sample. This means that quenched disorder only serves as a marginal perturbation in systems with this symmetry. The connection between interlayer exchange coupling and the observed critical behavior in Fe/V superlattices was explored. The results prove that the origin of unusually high values of the exponent β can be traced to a position dependence of the magnetization at elevated temperatures. The magnetization of the outermost layers within the superlattice shows a more pronounced decrease at lower temperatures, compared to the inner layers, which in turn have a more abrupt decrease in the vicinity of the critical temperature. This translates to a high exponent, especially when the layers are probed by a technique where more weight is given to the layers close to the surface, e.g.MOKE. The interlayer exchange coupling as a function of spacer thickness and temperature was also studied in its own right. The data was compared to the literature, and a dependence on the thickness of the magnetic layers was concluded. The phase transition in amorphous FeZr/CoZr multilayers, where the magnetization emanates from ferromagnetic proximity effects, was investigated. Even though the determined exponents of the zero-field magnetization, the susceptibility and the critical isotherm did not correspond to any universality class, scaling plots displayed an excellent data collapse. Samples consisting of Fe δ-layers (0.3-1.4 monolayers) embedded in Pd were studied using element-specific resonant x-ray magnetic scattering. The magnetization of the two constituents showed distinctly different temperature dependences.
20.	Ahlberg, Patrik, 1985- (author) Graphene Implementation Study in Semiconductor Processing 2016 Doctoral thesis (other academic/artistic)abstract Graphene, with its two-dimensional nature and unique properties, has for over a decade captured enormous interests in both industry and academia. This work tries to answer the question of what would happen to graphene when it is subjected to various processing conditions and how this would affect the graphene functionality. The focus is placed on its ability to withstand different thin-film deposition environments with regard to the implementation of graphene in two application areas: as a diffusion barrier and in electronic devices.With single-layer graphene films grown in-house by means of chemical vapor deposition (CVD), four techniques among the well-established thin-film deposition methods are studied in detail: atomic layer deposition (ALD), evaporation, sputter-deposition and spray-deposition. And in this order, these methods span a large range of kinetic impact energies from low to high. Graphene is known to have a threshold displacement energy of 22 eV above which carbon atoms are ejected from the lattice. Thus, ALD and evaporation work with energies below this threshold, while sputtering and spraying may involve energies above. The quality of the graphene films undergone the various depositions is mainly evaluated using Raman spectroscopy.Spray deposition of liquid alloy Ga-In-Sn is shown to require a stack of at least 4 layers of graphene in order to act as an effective barrier to the Ga diffusion after the harsh spray-processing. Sputter-deposition is found to benefit from low substrate temperature and high chamber pressure (thereby low kinetic impact energy) so as to avoid damaging the graphene. Reactive sputtering should be avoided. Evaporation is non-invasiveness with low kinetic impact energy and graphene can be subjected to repeated evaporation and removal steps without losing its integrity. With ALD, the effects on graphene are of different nature and they are investigated in the field-effect-transistor (FET) configuration. The ALD process for deposition of Al2O3 films is found to remove undesired dopants from the prior processing and the Al2O3 films are shown to protect the graphene channel from doping by oxygen. When the substrate is turned hydrophobic by chemical treatment prior to graphene transfer-deposition, a unipolar transistor behavior is obtained.
21.	Ahlgren, Joakim, 1972- (author) Organic Phosphorus Compounds in Aquatic Sediments : Analysis, Abundance and Effects 2006 Doctoral thesis (other academic/artistic)abstract Phosphorus (P) is often the limiting nutrient in lacustrine and brackish eco-systems, and enhanced input of P into an aquatic system might therefore negatively impact the environment. Because modern waste water manage-ment have reduced external P input to surface waters, internal P loading from the sediment has become one of the main P sources to aquatic ecosys-tems, in which relatively unknown organic P compounds seem to be more active in P recycling than previously thought. This thesis focus is on improving analysis methods for organic P com-pounds in lacustrine and brackish sediments, as well as determining which of these compounds might be degraded, mobilized and subsequently recycled to the water column and on what temporal scale this occur. In both lacustrine and brackish environments, the most labile P compound was pyrophosphate, followed by different phosphate diesters. Phosphate monoesters were the least labile organic P compounds and degraded the slowest with sediment depth. In regulated lakes, it was shown that pyrophosphate and polyphos-phate compound groups were most related to lake trophic status, thus indi-cating their involvement in P cycling. This thesis also indicates faster P turn-over in sediment from the brackish environment compared to sediment from the lacustrine environment. A comparison of organic P extraction procedures showed that pre-extraction with EDTA, and NaOH as main extractant, was most efficient for total P extraction. Using buffered sodium dithionite (BD) as a pre-extractant and NaOH as main extractant was most efficient for extracting the presuma-bly most labile organic P compound groups, pyrophosphate and polyphos-phate. Furthermore, it was determined that organic P compounds associated with humic substances were more recalcitrant than other P compounds, that the BD step used in traditional P fractionation might extract phosphate monoesters, and that NMR is a statistically valid method for quantification of organic P compounds in sediment extracts.
22.	Ahlinder, Linnea, 1987- (author) Raman Spectroscopy and Hyperspectral Analysis of Living Cells Exposed to Nanoparticles 2015 Doctoral thesis (other academic/artistic)abstract Nanoparticles, i.e. particles with at least one dimension smaller than 100 nm, are present in large quantities in ambient air and can also be found in an increasing amount of consumer products. It is known that many nanomaterials have physicochemical properties that differ from physicochemical properties of the same material in bulk size. It is therefore important to characterize nanoparticles and to evaluate their toxicity. To understand mechanisms behind nanotoxicity, it is important to study the uptake of nanoparticles, and how they are accumulated. For these purposes model studies of cellular uptake are useful. In this thesis metal oxide and carbon-based nanoparticles have been studied in living cells using Raman spectroscopy. Raman spectroscopy is a method that facilitates a non-destructive analysis without using any fluorescent labels, or any other specific sample preparation. It is possible to collect Raman images, i.e. images where each pixel corresponds to a Raman spectrum, and to use the spectral information to detect nanoparticles, and to identify organelles in cells. In this thesis the question whether or not nanoparticles can enter the cell nucleus of lung epithelial cells has been addressed using hyperspectral analysis. It is shown that titanium dioxide nanoparticles and iron oxide nanoparticles are taken up by cells, and also in the cell nucleus. In contrast, graphene oxide nanoparticles are mainly found attached on the outside of the cell membrane and very few nanoparticles are found in the cell, and none have been detected in the nucleus. It is concluded that graphene oxide nanoparticles are not cytotoxic. However, a comparison of Raman spectra of biomolecules in cells exposed to graphene oxide, unexposed cells and apoptotic cells, shows that the graphene oxide nanoparticles do affect lipid and protein structures. In this thesis, several multivariate data analysis methods have been used to analyze Raman spectra and Raman images. In addition, super-resolution algorithms, which originally have been developed to improve the resolution in photographic images, were optimized and applied to Raman images of cells exposed to submicron polystyrene particles in living cells.
23.	Ahmad, Mohd Riduan, 1980- (author) Interaction of Lightning Flashes with Wireless Communication Networks : Special Attention to Narrow Bipolar Pulses 2014 Doctoral thesis (other academic/artistic)abstract In this thesis, the features of electric field signatures of narrow bipolar pulses (NBPs) generated by cloud flashes are investigated and their effects on wireless communication systems are studied. A handful amount of NBPs (14.5%) have been observed to occur as part of cloud-to-ground flashes in South Malaysia. Occurrence of NBPs in Sweden has been reported for the first time in this thesis. The electric field waveform characteristics of NBPs as part of cloud-to-ground flashes were similar to isolated NBPs found in Sweden and South Malaysia and also to those isolated NBPs reported by previous studies from various geographical areas. This is a strong indication that their breakdown mechanisms are similar at any latitudes regardless of geographical areas.A comparative study on the occurrence of NBPs and other forms of lightning flashes across various geographical areas ranging from northern regions to the tropics is presented. As the latitude decreased from Uppsala, Sweden (59.8°N) to South Malaysia (1.5°N), the percentage of NBP emissions relative to the total number of lightning flashes increased significantly from 0.13% to 12%. Occurrences of positive NBPs were more common than negative NBPs at all observed latitudes. However, as latitudes decreased, the negative NBP emissions increased significantly from 20% (Sweden) to 45% (South Malaysia). Factors involving mixed-phase region elevations and vertical extents of thundercloud tops are invoked to explain the observed results. These factors are fundamentally latitude dependent.In this thesis, the interaction between microwave radiations emitted by cloud-to-ground and cloud flashes events and bits transmission in wireless communication networks are also presented. To the best of our knowledge, this is the first time such effects are investigated in the literature. Narrow bipolar pulses were found to be the strongest source of interference that interfered with the bits transmission.
24.	Ahmad, Noor Azlinda, 1978- (author) Broadband and HF Radiation from Cloud Flashes and Narrow Bipolar Pulses 2011 Doctoral thesis (other academic/artistic)abstract Remote measurement of electric field generated by lightning has played a major role in understanding the lightning phenomenon. Even though other measurements such as photographic and channel base current have contributed to this research field, due to practical reasons remote measurements of electric field is considered as the most useful tool in lightning research. This thesis discusses the remotely measured radiation field component of electric field generated by cloud flashes (ICs) and narrow bipolar pulses (NBPs). The associated HF radiation of these events at 3 MHz and 30 MHz are also discussed. To understand the initiation process of these discharges, a comparative study of the initial pulse of cloud flashes against the initial pulse of cloud to ground flashes was conducted. The result suggests that both discharges might have been initiated by similar physical processes inside the thunderclouds. Comparing the features of initial pulse of cloud and ground flashes with that of pulses that appeared in the later stages of cloud flashes suggests that the initiation process involved in both flashes are not very much different from the initiation of cloud flashes at the later stage. The average spectral amplitudes of electric field of full duration cloud flashes (180 ms) showed f -1 frequency dependence within the interval of 10 kHz to approximately 10 MHz. This is in contrast to the standard f -2 decrement (or even steeper ) at high frequency region for other lightning processes such as return strokes. It was suggested that small pulses which repeatedly appeared at the later stage of cloud flashes might have contributed to enhance the spectral amplitude at higher frequencies. Electric fields generated by Narrow Bipolar Pulses (NBPs), which are considered as one of the strongest sources of HF radiation, were measured in the tropics of Malaysia and Sri Lanka. Their features were also studied and show a good agreement with previously published observations of NBPs from other geographical regions. Thorough analyses and observations of these pulses found previously unreported sharp, fine peaks embedded in the rising and decaying edge of the electric field change of NBPs. Therefore it was suggested that these fine peaks are mostly responsible for the intense HF radiation at 30 MHz.
25.	Ahmadi, Omid, 1980- (author) Application of the Seismic Reflection Method in Mineral Exploration and Crustal Imaging : Contributions to Hardrock Seismic Imaging 2015 Doctoral thesis (other academic/artistic)abstract The seismic reflection method has been used extensively in mineral exploration and for imaging crustal structures within hardrock environments. In this research the seismic reflection method has been used and studied to address problems associated with hardrock settings. Papers I and II, address delineating and imaging a sulfide ore body and its surrounding rocks and structures in Garpenberg, central Sweden, at an active mine. 3D ray-tracing and finite-difference modeling were performed and the results suggest that although the detection of the ore body by the seismic reflection method is possible in the area, the presence of backfilled stopes in the mine makes seismic imaging of it difficult. In paper III the deeper structures of the Pärvie fault system in northern Sweden were revealed down to about 8 km through 2D seismic reflection profiling. The resulting images were interpreted using microearthquake data as a constraint. Based on the interpretation, some locations were suggested for future scientific deep drilling into the fault system. In paper IV, the seismic signature of complex geological structures of the Cue-Weld Range area in Western Australia was studied using a portion of a deep 2D seismic reflection profile. The pronounced reflections on the seismic images were correlated to their corresponding rock units on an available surface geological map of the study area. 3D constant velocity ray-tracing was performed to constrain the interpretation. Furthermore, the proposed structural model was tested using a 2D acoustic finite-difference seismic modeling method. Based on this study, a new 3D structural model was proposed for the subsurface of the area. These studies have investigated the capability of the seismic reflection method for imaging crustal structures within challenging hardrock and complex geological settings and show some its potential, but also its limitations.
26.	Ahmadova, Nigar (author) Studies of the two redox active tyrosines in Photosystem II 2017 Doctoral thesis (other academic/artistic)abstract Photosystem II is a unique enzyme which catalyzes light induced water oxidation. This process is driven by highly oxidizing ensemble of four Chl molecules, PD1, PD2, ChlD1 and ChlD2 called, P680. Excitation of one of the Chls in P680 leads to the primary charge separation, P680+Pheo-. Pheo- transfers electrons sequentially to the primary quinone acceptor QA and the secondary quinone acceptor QB. P680+ in turn extracts electrons from Mn4CaO5 cluster, a site for the water oxidation. There are two redox active tyrosines, TyrZ and TyrD, found in PSII. They are symmetrically located on the D1 and D2 central proteins. Only TyrZ acts as intermediate electron carrier between P680 and Mn4CaO5 cluster, while TyrD does not participate in the linear electron flow and stays oxidized under light conditions. Both tyrosines are involved in PCET.The reduced TyrD undergoes biphasic oxidation with the fast (msec-sec time range) and the slow (tens of seconds time range) kinetic phases. We assign these phases to two populations of PSII centers with proximal or distal water positions. We also suggest that the TyrD oxidation and stability is regulated by the new small lumenal protein subunit, PsbTn. The possible involvement of PsbTn protein in the proton translocation mechanism from TyrD is suggested.To assess the possible localization of primary cation in P680 the formation of the triplet state of P680 and the oxidation of TyrZ and TyrD were followed under visible and far-red light. We proposed that far-red light induces the cation formation on ChlD1.Transmembrane interaction between QB and TyrZ has been studied. The different oxidation yield of TyrZ, measured as a S1 split EPR signal was correlated to the conformational change of protein induced by the QB presence at the QB-site. The change is transferred via H-bonds to the corresponding His-residues via helix D of the D1 protein.
27.	Ahmed, Taha, 1984- (author) Nanostructured ZnO and metal chalcogenide films for solar photocatalysis 2023 Doctoral thesis (other academic/artistic)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.
28.	Aihara, Aya, 1989- (author) Aeroacoustic Prediction for Vertical Axis Wind Turbines 2021 Doctoral thesis (other academic/artistic)abstract This thesis investigates the aerodynamic and aeroacoustic prediction of vertical axis wind turbines, using computational fluid dynamics simulations. Noise pollution from wind turbines is one of the disadvantages of wind energy, calling for strategies to reduce noise levels. Yet for vertical axis wind turbines in particular, there is insufficient knowledge of how to identify sound sources and mitigate the sound level. The aim of this study is to predict aerodynamic noise, using large eddy simulation and acoustic analogy, so as to better understand the mechanism of sound generation for vertical axis wind turbines. First, the prediction method is validated for a static single blade in stall. This model is able to capture the dominant frequency, but it does not well reproduce the broadband characteristics. Next, the aerodynamic behavior of the 12 kW H-rotor vertical axis wind turbine is studied, whereby the focus is on the importance of properly modeling the strut influence for an accurate prediction of the blade forces. To achieve this, the flow field is solved for three different tip speed ratios. The results show that the struts significantly affect on the force distribution along the blade. The reduction of the blade force is observed to occur not only at the attachment points of the struts, but also over a large area of the blade section in the downwind side where the blade interacts with the wake created in the upwind. Finally, the noise radiated from the vertical axis wind turbine operating at high tip speed ratio is predicted. Measurements are conducted to validate the prediction, with the experimental data representing the broadband noise characteristics dominant at around 800 Hz. The prediction reproduces the sound pressure level observed at a radial distance of 1.4 rotor diameter, with a few decibels difference. However, these discrepancies become more pronounced at double distance, which can be considered to arise due to the effect of the ground reflection being ignored. The simulation furthermore indicates, that the main sound sources are emitted when the blade rotates in the downwind. It is suggested that future work should properly consider the atmospheric turbulence for more accurate predictions.
29.	Aiso, Toshiharu, 1983- (author) Workpiece steels protecting cutting tools from wear : A study of the effects of alloying elements on material transfer and coating damage mechanisms 2016 Doctoral thesis (other academic/artistic)abstract The vision of this thesis is to improve the machinability of workpiece steels. Workpiece material frequently transfers to the cutting tools during machining, and the transfer layers then forming on the tools may give both good and bad effects on machining performance and tool life. The objective of this work is to understand the effects of alloying element additions to workpiece steels on material transfer and the roles of the formed transfer layers on friction characteristics and wear of tools.To isolate and study the influence of the individual alloying elements, model steels are specifically designed. These steels include one reference with C as the only alloying element and others alloyed also with single additions or combined additions of 1 mass% Si, Mn, Cr and Al. The experiments are performed using both a sliding test, simulating the material transfer in milling, and a turning test.In a sliding contact, the mode of transfer is strongly dependent on the normal load and sliding speed. Material transfer initiates extremely fast, in less than 0.025 s, and characteristic transfer layers develop during the first few seconds. The different steel compositions result in the formation of different types of oxides in the transfer layers. At the workpiece/tool interface where the conditions involve high temperature, high pressure and low oxygen supply, easily oxidized alloying elements in the steel are preferentially transferred, enriched and form a stable oxide on the tool surface. The degree of enrichment of the alloying elements in the oxides is strongly related to their tendencies to become oxidized.The difference in melting temperature of the oxides, and thus the tendency to soften during sliding, explains the difference in the resulting friction coefficient. The widest differences in friction coefficients are found between the Si and Al additions. A Si containing oxide shows the lowest friction and an Al containing oxide the highest.The damage mechanism of coated tools is chiefly influenced by the form and shear strength of the transferred material. Absence of transfer layer or non-continuous transferred material leads to continuous wear of the coating. Contrastingly, continuous transfer layers protect it from wear. However, transfer layers with very high shear strength result in high friction heat and a large amount of steel transfer. This leads to rapid coating cracking or adhesive wear.
30.	Ajawatanawong, Pravech, 1974- (author) Mine the Gaps : Evolution of Eukaryotic Protein Indels and their Application for Testing Deep Phylogeny 2014 Doctoral thesis (other academic/artistic)abstract Insertions/deletions (indels) are potentially powerful evolutionary markers, but little is known about their evolution and few tools exist to effectively study them. To address this, I developed SeqFIRE, a tool for automated identification and extraction of indels from protein multiple sequence alignments. The program also extracts conserved alignment blocks, thus covering all major steps in preparing multiple sequence alignments for phylogenetic analysis.I then used SeqFIRE to build an indel database, using 299 single copy proteins from a broad taxonomic sampling of mainly multicellular eukaryotes. A total of 4,707 indels were extracted, of which 901 are simple (one genetic event) and 3,806 are complex (multiple events). The most abundant indels are single amino acid simple indels. Indel frequency decreases exponentially with length and shows a linear relationship with host protein size. Singleton indels reveal a strong bias towards insertions (2.31 x deletions on average). These analyses also identify 43 indels marking major clades in Plantae and Fungi (clade defining indels or CDIs), but none for Metazoa.In order to study the 3806 complex indels they were first classified by number of states. Analysis of the 2-state complex and simple indels combined (“bi-state indels”) confirms that insertions are over 2.5 times as frequent as deletions. Three-quarters of the complex indels had three-nine states (“slightly complex indels”). A tree-assisted search method was developed allowing me to identify 1,010 potential CDIs supporting all examined major branches of Plantae and Fungi.Forty-two proteins were also found to host complex indel CDIs for the deepest branches of Metazoa. After expanding the taxon set for these proteins, I identified a total of 49 non-bilaterian specific CDIs. Parsimony analysis of these indels places Ctenophora as sister taxon to all other Metazoa including Porifera. Six CDIs were also found placing Placozoa as sister to Bilateria. I conclude that slightly complex indels are a rich source of CDIs, and my tree-assisted search strategy could be automated and implemented in the program SeqFIRE to facilitate their discovery. This will have important implications for mining the phylogenomic content of the vast resource of protist genome data soon to become available.
31.	Ajaxon, Ingrid, 1983- (author) Can Bone Void Fillers Carry Load? : Behaviour of Calcium Phosphate Cements Under Different Loading Scenarios 2017 Doctoral thesis (other academic/artistic)abstract Calcium phosphate cements (CPCs) are used as bone void fillers and as complements to hardware in fracture fixation. The aim of this thesis was to investigate the possibilities and limitations of the CPCs’ mechanical properties, and find out if these ceramic bone cements can carry application-specific loads, alone or as part of a construct. Recently developed experimental brushite and apatite cements were found to have a significantly higher strength in compression, tension and flexion compared to the commercially available CPCs chronOS™ Inject and Norian® SRS®. By using a high-resolution measurement technique the elastic moduli of the CPCs were determined and found to be at least twice as high compared to earlier measurements, and closer to cortical bone than trabecular bone. Using the same method, Poisson's ratio for pure CPCs was determined for the first time. A non-destructive porosity measurement method for wet brushite cements was developed, and subsequently used to study the porosity increase during in vitro degradation. The compressive strength of the experimental brushite cement was still higher than that of trabecular bone after 25 weeks of degradation, showing that the cement can carry high loads over a time span sufficiently long for a fracture to heal. This thesis also presents the first ever fatigue results for acidic CPCs, and confirms the importance of testing the materials under cyclic loading as the cements may fail at stress levels much lower than the material’s quasi-static compressive strength. A decrease in fatigue life was found for brushite cements containing higher amounts of monetite. Increasing porosity and testing in a physiological buffer solution (PBS), rather than air, also decreased the fatigue life. However, the experimental brushite cement had a high probability of surviving loads found in the spine when tested in PBS, which has previously never been accomplished for acidic CPCs. In conclusion, available brushite cements may be able to carry the load alone in scenarios where the cortical shell is intact, the loading is mainly compressive, and the expected maximum stress is below 10 MPa. Under such circumstances this CPC may be the preferred choice over less biocompatible and non-degradable materials.
32.	Akansel, Serkan, 1983- (author) Magnetization Dynamics in Ferromagnetic Thin Films : Evaluation of Different Contributions to Damping in Co2FeAl and FeCo Film Structures 2018 Doctoral thesis (other academic/artistic)abstract Static and dynamic magnetic properties of Co2FeAl and Fe65Co35 alloys have been investigated. Co2FeAl films were deposited at different temperatures and the deposition parameters were optimized with respect to structural and magnetic properties. As a result, a film with B2 crystalline phase was obtained without any post-annealing process. A lowest magnetic damping parameter of was obtained for the film deposited at 573K. This obtained low value is comparable to the lowest values reported in research literature. After optimizing the deposition parameters of this alloy, different seed layers and capping layers were added adjacent to the Co2FeAl layer and the effect of these layers on the magnetic relaxation was investigated. In addition to adding nonmagnetic layers to Co2FeAl, the dependence of the magnetic damping parameter with respect to the thickness of Co2FeAl was investigated by depositing films with different thicknesses. A temperature dependent study of the magnetic damping parameter was also performed and the measured damping parameters were compared with theoretically calculated intrinsic Gilbert damping parameters. Different extrinsic contributions to the magnetic damping, such as two magnon scattering, spin pumping, eddy-current damping and radiative damping, were identified and subtracted from the experimentally obtained damping parameter. Hence, it was possible to obtain the intrinsic damping parameter, that is called the Gilbert damping parameter.In the second part of the thesis, Fe65Co35 alloys were investigated in terms of static and dynamic magnetic properties. Fe65Co35 films were deposited without and with different seed layers in order to first understand the effect of the seed layer on static magnetic properties of the films, such as the coercivity of the films. Then the films with seed layers yielding the lowest coercivity were investigated in terms of dynamic magnetic properties. Fe65Co35 films with different rhenium dopant concentrations and with ruthenium as the seed and capping layer were also investigated. The purpose of this study was to increase the damping parameter of the films and an increase of about ~230% was obtained by adding the dopant to the structure. This study was performed at different temperatures and after subtraction of the extrinsic contributions to the damping, the experimental values were compared with theoretically calculated values of the Gilbert damping parameter. During the thesis work, magnetic looper and superconducting quantum interference device magnetometers set-ups were used for static magnetic measurements and cavity, broadband in-plane and broadband out-of-plane ferromagnetic resonance set-ups were used for dynamic measurements.
33.	Akhtar, Sultan (author) Transmission Electron Microscopy of Graphene and Hydrated Biomaterial Nanostructures : Novel Techniques and Analysis 2012 Doctoral thesis (other academic/artistic)abstract Transmission Electron Microscopy (TEM) on light element materials and soft matters is problematic due to electron irradiation damage and low contrast. In this doctoral thesis techniques were developed to address some of those issues and successfully characterize these materials at high resolution. These techniques were demonstrated on graphene flakes, DNA/magnetic beads and a number of water containing biomaterials. The details of these studies are given below.A TEM based method was presented for thickness characterization of graphene flakes. For the thickness characterization, the dynamical theory of electron diffraction is used to obtain an analytical expression for the intensity of the transmitted electron beam as a function of thickness. From JEMS simulations (experiments) the absorption constant λ in a low symmetry orientation was found to be ~ 208 nm (225 ± 9 nm). When compared to standard techniques for thickness determination of graphene/graphite, the method has the advantage of being relatively simple, fast and requiring only the acquisition of bright-field (BF) images. Using the proposed method, it is possible to measure the thickness change due to one monolayer of graphene if the flake has uniform thickness over a larger area.A real-space TEM study on magnetic bead-DNA coil interaction was conducted and a statistical analysis of the number of beads attached to the DNA-coils was performed. The average number of beads per DNA coil was calculated around 6 and slightly above 2 for samples with 40 nm and 130 nm beads, respectively. These results are in good agreement with magnetic measurements. In addition, the TEM analysis supported an earlier hypothesis that 40 nm beads are preferably attached interior of the DNA-coils while 130 nm beads closer to the exterior of the coils.A focused ion-beam in-situ lift-out technique for hydrated biological specimens was developed for cryo-TEM. The technique was demonstrated on frozen Aspergillus niger spores which were frozen with liquid nitrogen to preserve their cellular structures. A thin lamella was prepared, lifted out and welded to a TEM grid. Once the lamella was thinned to electron transparency, the grid was cryogenically transferred to the TEM using a cryo-transfer bath. The structure of the cells was revealed by BF imaging. Also, a series of energy filtered images was acquired and C, N and Mn elemental maps were produced. Furthermore, 3 Å lattice fringes of the underlying Al support were successfully resolved by high resolution imaging, confirming that the technique has the potential to extract structural information down to the atomic scale. The experimental protocol is ready now to be employed on a large variety of samples e.g. soft/hard matter interfaces.
34.	Akiyama, Reiko, 1981- (author) Life History and Tolerance and Resistance against Herbivores in Natural Populations of Arabidopsis thaliana 2011 Doctoral thesis (other academic/artistic)abstract In this thesis, I combined observational studies with field and greenhouse experiments to examine selection on life history traits and variation in tolerance and resistance against herbivores in natural populations of the annual herb Arabidopsis thaliana in its native range. I investigated (1) phenotypic selection on flowering time and plant size, (2) the effects of timing of germination on plant fitness, (3) the effect of leaf damage on seed production, and (4) correlations between resistance against a specialist and a generalist insect herbivore. In all three study populations, flowering time was negatively related to plant fitness, but in only one of the populations, significant selection on flowering time was detected when controlling for size prior to the flowering season. The results show that correlations between flowering time and plant fecundity may be confounded by variation in plant size prior to the reproductive season. A field experiment detected conflicting selection on germination time: Early germination was associated with low seedling survival, but also with large leaf rosette before winter and high survival and fecundity among established plants. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination, and that the optimal timing of germination should vary in space and time as a function of the relative strength of selection acting during different life-history stages. Experimental leaf damage demonstrated that tolerance to damage was lowest among vegetative plants early in the season, and highest among flowering plants later in the season. Given similar damage levels, leaf herbivores feeding on plants before flowering should thus exert stronger selection on defence traits than those feeding on plants during flowering. Resistance against larval feeding by the specialist Plutella xylostella was negatively correlated with resistance against larval feeding by the generalist Mamestra brassicae and with resistance against oviposition by P. xylostella when variation in resistance was examined within and among two Swedish and two Italian A. thaliana populations. The results suggest that negative correlations between resistance against different herbivores and different life-history stages of herbivores may contribute to the maintenance of genetic variation in resistance.
35.	Aktekin, Burak (author) The Electrochemistry of LiNi0.5-xMn1.5+xO4-δ in Li-ion Batteries : Structure, Side-reactions and Cross-talk 2019 Doctoral thesis (other academic/artistic)abstract The use of Li-ion batteries in portable electronic products is today widespread and on-going research is extensively dedicated to improve their performance and energy density for use in electric vehicles. The largest contribution to the overall cell weight comes from the positive electrode material, and improvements regarding this component thereby render a high potential for the development of these types of batteries. A promising candidate is LiNi0.5Mn1.5O4 (LMNO), which offers both high power capability and energy density. However, the instability of conventional electrolytes at the high operating potential (~4.7 V vs. Li+/Li) associated with this electrode material currently prevents its use in commercial applications.This thesis work aims to investigate practical approaches which have the potential of overcoming issues related to fast degradation of LNMO-based batteries. This, in turn, necessitates a comprehensive understanding of degradation mechanisms. First, the effect of a well-known electrolyte additive, fluoroethylene carbonate is investigated in LNMO-Li4Ti5O12 (LTO) cells with a focus on the positive electrode. Relatively poor cycling performance is found with 5 wt% additive while 1 wt% additive does not show a significant difference as compared to additive-free electrolytes. Second, a more fundamental study is performed to understand the effect of capacity fading mechanisms contributing to overall cell failure in high-voltage based full-cells. Electrochemical characterization of LNMO-LTO cells in different configurations show how important the electrode interactions (cross-talk) can be for the overall cell behaviour. Unexpectedly fast capacity fading at elevated temperatures is found to originate from a high sensitivity of LTO to cross-talk.Third, in situ studies of LNMO are conducted with neutron diffraction and electron microscopy. These show that the oxygen release is not directly related to cation disordering. Moreover, microstructural changes upon heating are observed. These findings suggest new sample preparation strategies, which allow the control of cation disorder without oxygen loss. Following this guidance, ordered and disordered samples with the same oxygen content are prepared. The negative effect of ordering on electrochemical performance is investigated and changes in bulk electronic structure following cycling are found in ordered samples, accompanied by thick surface films on surface and rock-salt phase domains near surface.
36.	Akula, Srinivas (author) The mast cell transcriptome and the evolution of granule proteins and Fc receptors 2019 Doctoral thesis (other academic/artistic)abstract Protection against disease-causing pathogens, known as immunity, involves numerous cells organs, tissues and their products. To able to understand the biology of immune cells (hematopoietic cells) and their role in an immune system, we have used several different methods, including transcriptome analyses, bioinformatics, production of recombinant proteins and analyses of some of them, focusing on the granule proteases by substrate phage display.Hematopoietic cells express surface receptors interacting with the constant region of immunoglobulins (Igs) known as Fc receptors (FcRs). These receptors play major roles in the immune system, including enhancing phagocytosis, activating antibody dependent cellular cytotoxicity and cell activation. A detailed bioinformatics analysis of FcRs reveals that the poly-Ig receptors (PIGR), FcR-like molecules and common signalling γ chain all appeared very early with the appearance of the bony fishes, and thereby represent the first major evolutionary step in FcR evolution. The FcμR, FcαμR, FcγR and FcεR receptors most likely appeared in reptiles or early mammals, representing the second major step in FcR evolution.Cells of several of the hematopoietic cell lineages contain large numbers of cytoplasmic granules, and serine proteases constitute the major protein content of these granules. In mammals, these proteases are encoded from four different loci: the chymase, the met-ase, the granzyme (A/K) and the mast cell tryptase loci. The granzyme (A/K) locus was the first to appear and came with the cartilaginous fishes. This locus is also the most conserved of the three. The second most conserved locus is the met-ase locus, which is found in bony fishes. The chymase locus appeared relatively late, and we find the first traces in frogs, indicating it appeared in early tetrapods.To study the early events in the diversification of these hematopoietic serine proteases we have analyzed key characteristics of a protease expressed by an NK-like cell in the channel catfish, catfish granzyme–like I. We have used phage display and further validated the results using a panel of recombinant substrates. This protease showed a strict preference for Met at the P1 (cleavage) position, which indicates met-ase specificity. From the screening of potential in vivo substrates, we found an interesting potential target caspase 6, which indicates that caspase-dependent apoptosis mechanisms have been conserved from fishes to mammals.A larger quantitative transcriptome analysis of purified mouse peritoneal mast cells, cultured mast cells (BMMCs), and mast cells isolated from mouse ear and lung tissue identified the major tissue specific transcripts in these mast cells as the granule proteases. Mast cell specific receptors and processing enzymes were expressed at approximately 2 orders of magnitude lower levels. The levels of a few proteases were quite different at various anatomical sites between in vivo and cultured BMMCs. These studies have given us a new insights into mast cells in different tissues, as well as key evolutionary aspects concerning the origins of a number of granule proteases and FcRs.
37.	Al-Adili, Ali (author) Measurements of the 234U(n,f) Reaction with a Frisch-Grid Ionization Chamber up to En=5 MeV 2013 Doctoral thesis (other academic/artistic)abstract This study on the neutron-induced fission of 234U was carried out at the 7 MV Van de Graaff accelerator of IRMM in Belgium. A Twin Frisch-Grid Ionization Chamber (TFGIC) was used to study 234U(n,f) between En = 0.2 and 5.0 MeV. The reaction is important for fission modelling of the second-chance fission in 235U(n,f). The fission fragment (FF) angular-, energy and mass distributions were determined using the 2E-method highlighting especially the region of the vibrational resonance at En = 0.77 MeV.The experiment used both conventional analogue and modern digital acquisition systems in parallel. Several advantages were found in the digital case, especially a successful pile-up correction. The shielding limitations of the Frisch-grid, called "grid-inefficiency", result in an angular-dependent energy signal. The correction of this effect has been a long-standing debate and a solution was recently proposed using the Ramo-Shockley theorem. Theoretical predictions from the latter were tested and verified in this work using two different grids. Also the neutron-emission corrections as a function of excitation energy were investigated. Neutron corrections are crucial for the determination of FF masses. Recent theoretical considerations attribute the enhancement of neutron emission to the heavier fragments exclusively, contrary to the average increase assumed earlier. Both methods were compared and the impact of the neutron multiplicities was assessed. The effects found are significant and highlight the importance of further experimental and theoretical investigation.In this work, the strong angular anisotropy of 234U(n,f ) was confirmed. In addition, and quite surprisingly, the mass distribution was found to be angular-dependent and correlated to the vibrational resonances. The anisotropy found in the mass distribution was consistent with an anisotropy in the total kinetic energy (TKE), also correlated to the resonances. The experimental data were parametrized assuming fission modes based on the Multi-Modal Random Neck-Rupture model. The resonance showed an increased yield from the Standard-1 fission mode and a consistent increased TKE. The discovered correlation between the vibrational resonances and the angular-dependent mass distributions for the asymmetric fission modes may imply different outer fission-barrier heights for the two standard modes.
38.	Al-Ramadan, Khalid, 1976- (author) Impact of Diagenetic Alterations on Reservoir Quality and Heterogeneity of Paralic and Shallow Marine Sandstones : Links to Depositional Facies and Sequence Stratigraphy 2006 Doctoral thesis (other academic/artistic)abstract This thesis constrains the distribution of diagenetic alterations and their impact on reservoir-quality and heterogeneity evolution pathways in relation to depositional environments and sequence stratigraphy (systems tracts and key sequence stratigraphic surfaces) of four selected paralic and shallow marine siliciclastic successions. Typical eogenetic alterations encountered include the dissolution and kaolinitization of framework silicates, which are closely associated to shoreface facies of forced regressive systems tract (FRWST), lowstand systems tract (LST), upper part of the highstand systems tract (HST), and below the sequence boundary (SB). These alterations are attributed to incursion of meteoric water owing to rapid and considerable fall in the relative sea level. Extensive carbonate cementation is most evident below marine and maximum flooding surfaces (MFS), whereas dissolution of carbonate cement and detrital dolomite occur in LST, HST and below SB. Parameters controlling the patterns and texture (microcrystalline vs. poikilotopic) of calcite cement have been constrained within sequence stratigraphic framework of the sandstones. Coarse crystalline to poikilotopic calcite textures of meteoric water origin are thus closely linked to the FRWST, LST and upper part of the HST sandstones and occur mainly as stratabound concretions, whereas microcrystalline calcite, which was precipitated from marine porewaters, occurs as continuously cemented layers in the transgressive systems tract (TST) and lower part of the HST sandstones.Eogenetic alterations impose, in turn, profound control on the distribution pattern of mesogenetic alterations, and hence on reservoir quality evolution (destruction vs. preservation) pathways of sandstones. Eogenetic infiltrated clays, which occur in the tidal estuarine TST and HST sandstones, have helped preserving porosity in deeply buried sandstone reservoirs (≈ 5 km) through inhibition of extensive cementation by quartz overgrowths. Other essential findings of this thesis include deciphering the control on the formation of authigenic illite and chlorite by ultra-thin (≤ 1 µm thick), grain-coating clay mineral substrate.
39.	Al-Smadi, Derar, 1983- (author) Carboligation using the aldol reaction : A comparison of stereoselectivity and methods 2018 Doctoral thesis (other academic/artistic)abstract The research summarized in this thesis focuses on synthesizing aldehyde and aldol compounds as substrates and products for the enzyme D-fructose-6-aldolase (FSA). Aldolases are important enzymes for the formation of carbon-carbon bonds in nature. In biological systems, aldol reactions, both cleavage and formation play central roles in sugar metabolism. Aldolases exhibit high degrees of stereoselectivity and can steer the product configurations to a given enantiomeric and diastereomeric form. To become truly useful synthetic tools, the substrate scope of these enzymes needs to become broadened.In the first project, phenylacetaldehyde derivatives were synthesized for the use as test substrates for E. coli FSA. Different methods were discussed to prepare phenylacetaldehyde derivatives, the addition of a one carbon unit to benzaldehyde derivatives using a homologation reaction was successful and was proven efficient and non-sensitive to the moisture. The analogues were prepared through two steps with 75-80 % yields for both meta- and para-substituted compounds.The second project focuses on synthesizing aldol compound using FSA enzymes, both wild type and mutated variants selected from library screening, the assay has been successfully used to identify a hit with 10-fold improvement in an R134V/S166G variant. This enzyme produces one out of four possible stereoisomers.The third project focuses on the synthesis of a range of aldol compounds using two different approaches reductive cross-coupling of aldehydes by SmI2 or by organocatalysts using cinchonine. Phenylacetaldehydes were reacted with hydroxy-, dihydroxyacetone and hydroxyacetophenone in presence of cinchonine, the reaction was successful with hydroxyacetophenone in moderate yields and 60-99 % de ratio. On the other hand, the aldehydes reacting with methyl- and phenylglyoxal in the presence of SmI2 resulted in moderate yields and without stereoselectivity.
40.	Alavioon, Ghazal, 1986- (author) Haploid selection in animals : Exploring the fitness consequences and underlying mechanisms 2018 Doctoral thesis (other academic/artistic)abstract A consequence of sexual reproduction in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid gametic phases. While our focus in evolutionary biology is on selection during the diploid phase, we know relatively little about selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals, where gene expression and hence selection have long been thought to be absent in haploid cells like gametes and particularly sperm. During my PhD, I tested the idea of selection during the haploid gametic phase using zebrafish Danio rario as a study species. I combined a large-scale selection experiment over three generations with fitness assays and next-generation sequencing to assess the importance of haploid selection. We measured offspring fitness in all three generations. In addition, we compared gene expression in brain and testes of F1 and F3 adult male from each treatment by RNA sequencing. We found that offspring sired by longer-lived sperm showed higher survival rate and higher early- and late-life reproductive fitness compared to offspring sired by shorter-lived sperm. We also found differentially expressed genes between the two treatments with functions in metabolic and developmental pathways. These findings suggest that the observed fitness differences to be caused by small expression changes in many basic genes. We also tested for a genetic underpinning of the selected sperm phenotypes and identified allelic differences across the entire genome. Finally, we investigated the additive genetic component and parental effect of different sperm phenotypes. We found generally low additive genetic variation and high parental effects on sperm performance traits. In conclusion, this thesis provides evidence that the phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness throughout life and provides a clear link between sperm phenotype and offspring fitness and between sperm phenotype and sperm genotype.
41.	Alfimov, Vasily, 1978- (author) Accelerator Mass Spectrometry of 36Cl and 129I : Analytical Aspects and Applications 2004 Doctoral thesis (other academic/artistic)abstract Two long-lived halogen radionuclides (36Cl, T1/2 = 301 kyr, and 129I, T1/2 = 15.7 Myr) have been studied by means of Accelerator Mass Spectrometry (AMS) at the Uppsala Tandem Laboratory. The 36Cl measurements in natural samples using a medium-sized tandem accelerator (~1 MeV/amu) have been considered. A gas-filled magnetic spectrometer (GFM) was proposed for the separation of 36Cl from its isobar, 36S. Semi-empirical Monte-Carlo ion optical calculations were conducted to define optimal conditions for separating 36Cl and 36S. A 180° GFM was constructed and installed at the dedicated AMS beam line. 129I has been measured in waters from the Arctic and North Atlantic Oceans. Most of the 129I currently present in the Earth's surface environment can be traced back to liquid and gaseous releases from the nuclear reprocessing facilities at Sellafield (UK) and La Hague (France). The anthropogenic 129I inventory in the central Arctic Ocean was found to increase proportionally to the integrated 129I releases from these reprocessing facilities. The interaction and origin of water masses in the region have been clearly distinguished with the help of 129I labeling. Predictions based on a compartment model calculation showed that the Atlantic Ocean and deep Arctic Ocean are the major sinks for the reprocessed 129I. The variability in 129I concentration measured in seawater along a transect from the Baltic Sea to the North Atlantic suggests strong enrichment in the Skagerrak–Kattegat basin. The 129I inventory in the Baltic and Bothnian Seas is equal to ~0.3% of the total liquid releases from the reprocessing facilities. A lake sediment core sampled in northeastern Ireland was analyzed for 129I to study the history of the Sellafield releases, in particular the nuclear accident of 1957. High 129I concentration was observed corresponding to 1990 and later, while no indication of the accident was found. The results of this thesis research clearly demonstrate the uniqueness and future potential of 129I as a tracer of processes in both marine and continental archives.
42.	Alfredsson, Ylvi, 1973- (author) Electronic and Structural Properties of Thin Films of Phthalocyanines and Titanium Dioxide 2005 Doctoral thesis (other academic/artistic)abstract This thesis is based on experimental studies in chemical physics. Titanium dioxide (TiO2) and phthalocyanine’s (Pc’s), interesting in many future perspectives, have been deposited as thin films and studied as follows. Information has been obtained on e.g. molecular orientation, crystal structure, depth profile of the chemical composition, electrochemical properties and electronic structure. This has been achieved by means of a combination of techniques: X-ray photoelectron spectroscopy (XPS), near edge x-ray absorption fine structure (NEXAFS), density functional theory calculations (DFT), UV-visible absorption spectroscopy (UVVIS) and cyclic voltammetry (CV).Metal-free phthalcyanine (H2Pc) has been shown to form films with different crystal structure and molecular orientation depending on deposition method, evaporation/sublimation or powder deposition, on commercial conducting glass (fluorine doped tin oxide, FTO), which is used e.g. in solar cells and organic light emitting devices (OLEDs). The unoccupied molecular orbitals are divided in x, y and z space coordinates of the molecule and also divided in inequivalent nitrogen components.The electronic structure is also studied for a sublimated titanyl phthalocyanine (TiOPc) film and related to the metal-free phthalocyanine. The ligand field around the titanium atom in TiOPc is compared with that of TiO2 to delineate the unoccupied levels recorded by means of x-ray absorption spectroscopy.Nanostructured TiO2 films were manufactured by screen printing/doctor blading on FTO. Such films were additionally covered with lutetium diphthalocyanine (LuPc2) by means of surface assembly from solution. LuPc2-, LuPc2+ and LuPc2H were identified and the stability of the electrochromic reactions in this system was monitored.Chemical vapor deposition (CVD) has been used to grow nanometer sized anatase TiO2 crystals on pre-oxidized Si (111) without formation of interfacial carbon and with an interface layer of the size of 15- 25Å. The interface layer was found to be amorphous TiSixOy with graded stoichiometry.
43.	Alghamdi, Fayiq, 1985- (author) Dimensions of Professionalism : A Study of Computer Science Teaching in Saudi Arabia 2020 Doctoral thesis (other academic/artistic)abstract In Saudi Arabia, new computing education programs have been introduced in alignment with the Saudi Vision 2030, which is a plan launched in 2017 to reduce Saudi Arabia's reliance on oil, diversify its economy, and develop its health, education, recreation, infrastructure and tourism. Computer science is a rapidly changing area, which places high demands on teachers in the subject to develop both their subject and pedagogical competence. This thesis explores computer science teachers’ perspectives on professional development from three viewpoints—the Saudi Teaching Competencies Standard, engagement in teachers’ awards and self-directed learning. The thesis examines the efforts of computer science teachers as they develop new pedagogies during their teaching careers as a result of the new regulations. The main question is ‘How do Saudi Arabian computer science teachers develop their teaching professionalism?’ Conclusions draw on the outcomes of four sub-studies. A mixed-methods approach consisting of interviews and questionnaires was used to collect data. The participants comprised 389 computer science teachers from different Saudi Arabian cities with different demographics and different teaching experience. The analysis drew on a theoretical framework that integrates elements of the Theory of Reasoned Action, the Theory of Planned Behaviour and the Adult Learning Theory. A model for pedagogical change was developed and used to understand how and why computer science teachers change their educational pedagogy. The model explains the teachers’ shift in pedagogy and answers the question of how and why computer science teachers adopt a new pedagogical strategy. The studies show that both internal and external factors motivate the study participants to engage in competency development. In the Saudi model, the Saudi Teaching Competencies Standard and awards are external factors as they include a preparatory period of intensive skills development. Teachers' experience from this informs the picture of Saudi teachers' training that is presented in the dissertation. Indeed, the trial participants stated that they mainly used self-directed learning for their competence development, drawing on internal motivation. One reason for this was that they felt that many of the skills development programs offered lacked timeliness and relevance. The studies on which the dissertation is based have been conducted in Saudi Arabia, but the results also provide insights into general challenges associated with regulating teachers' competence and the design of in-service training for teachers. The results clearly point out the importance of teachers' participation in the development of the profession in order for changes to be accepted and incorporated into their profession. Behavior change theories can be used to understand and predict how new regulations and pedagogical strategies will be received, and if they are likely to be accepted or rejected by teachers. These theories, therefore, constitute a useful tool in regulating teaching and the teaching profession.
44.	Alhassan, Erwin, 1984- (author) Nuclear data uncertainty quantification and data assimilation for a lead-cooled fast reactor : Using integral experiments for improved accuracy 2015 Doctoral thesis (other academic/artistic)abstract For the successful deployment of advanced nuclear systems and optimization of current reactor designs, high quality nuclear data are required. Before nuclear data can be used in applications they must first be evaluated, tested and validated against a set of integral experiments, and then converted into formats usable for applications. The evaluation process in the past was usually done by using differential experimental data which was then complemented with nuclear model calculations. This trend is fast changing due to the increase in computational power and tremendous improvements in nuclear reaction models over the last decade. Since these models have uncertain inputs, they are normally calibrated using experimental data. However, these experiments are themselves not exact. Therefore, the calculated quantities of model codes such as cross sections and angular distributions contain uncertainties. Since nuclear data are used in reactor transport codes as input for simulations, the output of transport codes contain uncertainties due to these data as well. Quantifying these uncertainties is important for setting safety margins; for providing confidence in the interpretation of results; and for deciding where additional efforts are needed to reduce these uncertainties. Also, regulatory bodies are now moving away from conservative evaluations to best estimate calculations that are accompanied by uncertainty evaluations.In this work, the Total Monte Carlo (TMC) method was applied to study the impact of nuclear data uncertainties from basic physics to macroscopic reactor parameters for the European Lead Cooled Training Reactor (ELECTRA). As part of the work, nuclear data uncertainties of actinides in the fuel, lead isotopes within the coolant, and some structural materials have been investigated. In the case of the lead coolant it was observed that the uncertainty in the keff and the coolant void worth (except in the case of 204Pb), were large, with the most significant contribution coming from 208Pb. New 208Pb and 206Pb random nuclear data libraries with realistic central values have been produced as part of this work. Also, a correlation based sensitivity method was used in this work, to determine parameter - cross section correlations for different isotopes and energy groups.Furthermore, an accept/reject method and a method of assigning file weights based on the likelihood function are proposed for uncertainty reduction using criticality benchmark experiments within the TMC method. It was observed from the study that a significant reduction in nuclear data uncertainty was obtained for some isotopes for ELECTRA after incorporating integral benchmark information. As a further objective of this thesis, a method for selecting benchmark for code validation for specific reactor applications was developed and applied to the ELECTRA reactor. Finally, a method for combining differential experiments and integral benchmark data for nuclear data adjustments is proposed and applied for the adjustment of neutron induced 208Pb nuclear data in the fast energy region.
45.	Ali, Hasan, 1985- (author) Towards atomically resolved magnetic measurements in the transmission electron microscope : A study of structure and magnetic moments in thin films 2020 Doctoral thesis (other academic/artistic)abstract The magnetic properties of thin metallic films are significantly different from the bulk properties due to the presence of interfaces. The properties shown by such thin films are influenced by the atomic level structure of the films and the interfaces. Transmission electron microscope (TEM) has the potential to analyse the structure and the magnetic properties of such systems with atomic resolution. In this work, the TEM is employed to characterize the structure of the Fe/V and Fe/Ni multilayers and the technique of electron magnetic circular dichroism (EMCD) is developed to obtain the quantitative magnetic measurements with high spatial resolution.From TEM analysis of short period Fe/V multilayers, a coherent superlattice structure is found. In short period Fe/Ni multilayer samples with different repeat frequency, only the TEM technique could verify the existence of the multilayer structure in the thinnest layers. The methods of scanning TEM imaging and electron energy loss spectroscopy (EELS) results were used and refined to determine interdiffusion at the interfaces. The confirmation of the multilayer structure helped to explain the saturation magnetization of these samples.Electron magnetic circular dichroism (EMCD) has the potential to quantitatively measure the magnetic moments of the materials with atomic resolution, but the technique presents several challenges. First, the EMCD measurements need to acquire two EELS spectra at two different scattering angles. These spectra are mostly acquired one after the other which makes it difficult to guaranty the identical experimental conditions and the spatial registration between the two acquisitions. We have developed a technique to simultaneously acquire the two angle-resolved EELS spectra in a single acquisition. This not only ensures the accuracy of the measurements but also improves the signal to noise ratio as compared to the previously used methods. The second important question is the effect of crystal orientations on the measured EMCD signals, considering the fact that the crystal orientation of a real crystal does not remain the same in the measured area. We developed the methodology to simultaneously acquire the EMCD signals and the local crystal orientations with high precision and experimentally showed that the crystal tilt significantly changes the magnetic signal. The third challenge is to obtain EMCD measurements with atomic resolution which is hampered by the need of high beam convergence angles. We further developed the simultaneous acquisition technique to obtain the quantitative EMCD measurements with beam convergence angles corresponding to atomic size electron probes.
46.	Ali, Muhammad, 1990- (author) Identification of SLiMs: Mapping and characterizing motif-based protein interactions 2020 Doctoral thesis (other academic/artistic)abstract During the last twenty years it has become evident that about 35-40% of amino acids in the proteome are in regions that have evolved to remain unstructured. These intrinsically disordered regions contain short linear motifs (SLiMs), which serve as docking sites for protein-protein interactions. SLiMs often mediate low-to-medium affinity interactions that are transient in their nature. The characteristics of SLiM-based interactions make them difficult to be captured using conventional approaches like affinity-purification coupled to mass spectrometry or yeast-two-hybrid. We therefore used and developed a dedicated method for large-scale screening of SLiM-based interactions termed proteomic peptide phage display (ProP-PD).Using ProP-PD, We identified large sets of ligands, for the binding pocket of shank1 PDZ domain, containing C-terminal or internal binding motifs and established the consensus motifs to be xTxL/F-COOH and xTxFx respectively. We further validated interactions using biophysical affinity determinations and pulldown experiments. Using X-ray crystallization, we uncovered that shank1 PDZ binds to internal xTxFx motifs using a binding mode similar to that for C-terminal peptides.Adding a level of complexity, we explored interactions of the multiple binding pocket containing FERM domains from four closely related proteins: ezrin, radixin, moesin and merlin. We found hundreds of FERM ligands, which contained binding motifs of at least four different classes. By combining docking simulations with experiments, we established ligands binding to different pockets, and uncovered a complex interplay between distinct pockets.We further developed an optimized version of a phage library that displays intrinsically disordered regions of the human proteome. We benchmarked the library using a set of protein domains and reported better recovery of known SLiM-based interactions. Furthermore, we highlighted the functional aspects of identified SLiMs, in the case of nuclear localization signals, found for binding to importin-subunit alpha-3. Finally, we validated predicted binding of SLiMs in the Sars-CoV-2 host receptor ACE2, which illustrates the importance of fundamental knowledge for SLiMs and their binding partners.This work, taken together, contributes with method development for expansion of motifs based interactomes and provide insights into the plastic yet selective nature of peptide binding proteins.
47.	Alipour, Mehdi (author) Rethinking Dynamic Instruction Scheduling and Retirement for Efficient Microarchitectures 2020 Doctoral thesis (other academic/artistic)abstract Out-of-order execution is one of the main micro-architectural techniques used to improve the performance of both single- and multi-threaded processors. The application of such a processor varies from mobile devices to server computers. This technique achieves higher performance by finding independent instructions and hiding execution latency and uses the cycles which otherwise would be wasted or caused a CPU stall. To accomplish this, it uses scheduling resources including the ROB, IQ, LSQ and physical registers, to store and prioritize instructions.The pipeline of an out-of-order processor has three macro-stages: the front-end, the scheduler, and the back-end. The front-end fetches instructions, places them in the out-of-order resources, and analyzes them to prepare for their execution. The scheduler identifies which instructions are ready for execution and prioritizes them for scheduling. The back-end updates the processor state with the results of the oldest completed instructions, deallocates the resources and commits the instructions in the program order to maintain correct execution.Since out-of-order execution needs to be able to choose any available instructions for execution, its scheduling resources must have complex circuits for identifying and prioritizing instructions, which makes them very expansive, therefore, limited. Due to their cost, the scheduling resources are constrained in size. This limited size leads to two stall points respectively at the front-end and the back-end of the pipeline. The front-end can stall due to fully allocated resources and therefore no more new instructions can be placed in the scheduler. The back-end can stall due to the unfinished execution of an instruction at the head of the ROB which prevents other resources from being deallocated, preventing new instructions from being inserted into the pipeline.To address these two stalls, this thesis focuses on reducing the time instructions occupy the scheduling resources. Our front-end technique tackles IQ pressure while our back-end approach considers the rest of the resources. To reduce front-end stalls we reduce the pressure on the IQ for both storing (depth) and issuing (width) instructions by bypassing them to cheaper storage structures. To reduce back-end stalls, we explore how we can retire instructions earlier, and out-of-order, to reduce the pressure on the out-of-order resource.
48.	Allalou, Amin, 1981- (author) Methods for 2D and 3D Quantitative Microscopy of Biological Samples 2011 Doctoral thesis (other academic/artistic)abstract New microscopy techniques are continuously developed, resulting in more rapid acquisition of large amounts of data. Manual analysis of such data is extremely time-consuming and many features are difficult to quantify without the aid of a computer. But with automated image analysis biologists can extract quantitative measurements and increases throughput significantly, which becomes particularly important in high-throughput screening (HTS). This thesis addresses automation of traditional analysis of cell data as well as automation of both image capture and analysis in zebrafish high-throughput screening. It is common in microscopy images to stain the nuclei in the cells, and to label the DNA and proteins in different ways. Padlock-probing and proximity ligation are highly specific detection methods that produce point-like signals within the cells. Accurate signal detection and segmentation is often a key step in analysis of these types of images. Cells in a sample will always show some degree of variation in DNA and protein expression and to quantify these variations each cell has to be analyzed individually. This thesis presents development and evaluation of single cell analysis on a range of different types of image data. In addition, we present a novel method for signal detection in three dimensions. HTS systems often use a combination of microscopy and image analysis to analyze cell-based samples. However, many diseases and biological pathways can be better studied in whole animals, particularly those that involve organ systems and multi-cellular interactions. The zebrafish is a widely-used vertebrate model of human organ function and development. Our collaborators have developed a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae. This thesis presents improvements to the system, including accurate positioning of the fish which incorporates methods for detecting regions of interest, making the system fully automatic. Furthermore, the thesis describes a novel high-throughput tomography system for screening live zebrafish in both fluorescence and bright field microscopy. This 3D imaging approach combined with automatic quantification of morphological changes enables previously intractable high-throughput screening of vertebrate model organisms.
49.	Allard, Erik, 1976- (author) Metabolic Studies with Liquid Separation Coupled to Mass Spectrometry 2009 Doctoral thesis (other academic/artistic)abstract Metabolism is the sum of all chemical processes with the purpose to maintain life, as well as enable reproduction, in a living organism. Through the study of metabolism, increased understanding of pharmacological mechanisms and diseases can be achieved. This thesis describes several ways of doing so, including targeted analysis of selected metabolites and investigations of systematic metabolic differences between selected groups through pattern recognition. A method for exploring metabolic patterns in urine samples after intake of coffee or tea was developed. The methodology was later used with the aim to find biomarkers for prostate cancer and urinary bladder cancer. Furthermore, a fully automated quantitative method was developed for concentration measurements of the double prodrug ximelagatran and its metabolites in pig liver. The method was then used to study the roll of active transporters in pig liver cells. Moreover, a fundamental study was conducted to investigate how monitoring of small, doubly charged analytes can improve the limit of detection and precision in a quantitative method. The techniques used for the experiments were liquid separation coupled to electrospray mass spectrometry. Extra efforts were made to make the separation and the ionization as compatible as possible to each other for increased quality of the collected data.
50.	Alm, Oscar, 1977- (author) Heterogeneous Photolytic Synthesis of Nanoparticles 2007 Doctoral thesis (other academic/artistic)abstract Nanoparticles of iron, cobalt and tungsten oxide were synthesised by photolytic laser assisted chemical vapour deposition (LCVD). An excimer laser (operating at 193 nm) was used as an excitation source. The LCVD process, was monitored in situ by optical emission spectroscopy (OES). The synthesised particles were further analysed using transmission electron spectroscopy (TEM), X-ray diffraction (XRD), high resolution scanning electron microscopy (HRSEM), X-ray fluorescence spectroscopy (XRF), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy.Iron and cobalt single crystalline nanoparticles were synthesized using ferrocene and cobaltocene precursors. The diameter of the particles could be tailored by the experimental parameters (e.g., partial pressure and laser power) and were in the range 1 - 50 nm in diameter. In both cases, the particles were covered by a carbon shell, typically 7 nm thick. A thin graphitic layer was observed at the interface metal-carbon. Amorphous carbon was deposited on top of the graphitic carbon. Particle temperature, reaching the boiling point of the respective metal, was observed by OES of the thermal emission during the laser-induced particle formation process (and subsequent heating). Both bcc and fcc Fe phases were formed, both hcp and fcc for the Co phases. Size dependent magnetic properties were observed using superconducting quantum interference device (SQUID) measurements, where super-paramagnetic magnetic domains dominated for d < 10 nm. The iron particles were further processed, whereby the amorphous shell was removed by refluxing in nitric acid. In a subsequent step, the graphitic surface was functionalized by attaching an octyl ester, rendering the particles hydrophobic.Tungsten oxides were synthesized from combinations of WF6/H2/O2 as precursors. No particles could be deposited if H2 was removed from the gas-mixture. The as-deposited oxide nanoparticle film was amorphous. A monoclinic WO3 particle film could be achieved by annealing the amorphous oxide. Above 400°C, the oxide particles increased in size from ca. 20 nm to 60 nm through coalescence. The gas-sensing properties of the tungsten oxide were tested by conductance measurements using H2S as analyte. The sensitivity of the amorphous oxide nanoparticle film was found to be superior to that of a crystalline oxide nanoparticle film.

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University: Uppsala University (2043); Högskolan Dalarna (8); University of Gävle (7); Royal Institute of Technology (5); Linköping University (5); RISE (4); show more...; Södertörn University (3); Mälardalen University (2); Kristianstad University College (1); Stockholm University (1); Lund University (1); Chalmers University of Technology (1); Linnaeus University (1); Karlstad University (1); Swedish National Defence College (1); show less...

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