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1.	Amvrosiadi, Nino (författare) The value of experimental data and modelling for exploration of hydrological functioning: The case of a till hillslope 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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 (författare) Reticulate Evolution in Diphasiastrum (Lycopodiaceae) 2009 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Weak Boundary and Interface Procedures for Wave and Flow Problems 2011 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Discovery and evaluation of direct acting antivirals against hepatitis C virus 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Direct and Inverse Methods for Waveguides and Scattering Problems in the Time Domain 2005 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Gill EROD Activity in Fish : A Biomarker for Waterborne Ah-receptor Agonists 2007 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Kinetic Energy Storage and Magnetic Bearings : for Vehicular Applications 2014 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Tuning of the Excited State Properties of Ruthenium(II)-Polypyridyl Complexes 2006 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Seismicity and crustal structure in Iceland 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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 (författare) Airborne Gravity Gradient, Magnetic and VLF datasets : Case studies of modelling, inversion and interpretation 2016 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Some Aspects of Physicochemical Properties of DNA and RNA 2006 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Seismicity Analyses Using Dense Network Data : Catalogue Statistics and Possible Foreshocks Investigated Using Empirical and Synthetic Data 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Secondary and Higher Order Structural Characterization of Peptides and Proteins by Mass Spectrometry 2007 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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 (författare) Opportunities and challenges of surface scattering at next generation neutron sources 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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 (författare) Maturation and Regulation of Cyanobacterial Hydrogenases 2009 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Tracking single molecules in uncharted territory : A single-molecule method to study kinetics in live bacteria 2020 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Double Excitations in Helium Atoms and Lithium Compounds 2006 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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 (författare) Optimal Scheduling for Timely Information in Communication Systems 2021 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Critical Phenomena and Exchange Coupling in Magnetic Heterostructures 2012 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Graphene Implementation Study in Semiconductor Processing 2016 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Organic Phosphorus Compounds in Aquatic Sediments : Analysis, Abundance and Effects 2006 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Raman Spectroscopy and Hyperspectral Analysis of Living Cells Exposed to Nanoparticles 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Interaction of Lightning Flashes with Wireless Communication Networks : Special Attention to Narrow Bipolar Pulses 2014 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Broadband and HF Radiation from Cloud Flashes and Narrow Bipolar Pulses 2011 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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- (författare) Application of the Seismic Reflection Method in Mineral Exploration and Crustal Imaging : Contributions to Hardrock Seismic Imaging 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.

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