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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.	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.
3.	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.
4.	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.
5.	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.
6.	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.
7.	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.
8.	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.
9.	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.
10.	Ahmadova, Nigar (författare) Studies of the two redox active tyrosines in Photosystem II 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
11.	Aiso, Toshiharu, 1983- (författare) Workpiece steels protecting cutting tools from wear : A study of the effects of alloying elements on material transfer and coating damage mechanisms 2016 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
12.	Ajaxon, Ingrid, 1983- (författare) Can Bone Void Fillers Carry Load? : Behaviour of Calcium Phosphate Cements Under Different Loading Scenarios 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
13.	Akansel, Serkan, 1983- (författare) Magnetization Dynamics in Ferromagnetic Thin Films : Evaluation of Different Contributions to Damping in Co2FeAl and FeCo Film Structures 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
14.	Aktekin, Burak (författare) The Electrochemistry of LiNi0.5-xMn1.5+xO4-δ in Li-ion Batteries : Structure, Side-reactions and Cross-talk 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
15.	Akula, Srinivas (författare) The mast cell transcriptome and the evolution of granule proteins and Fc receptors 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
16.	Al-Smadi, Derar, 1983- (författare) Carboligation using the aldol reaction : A comparison of stereoselectivity and methods 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
17.	Alavioon, Ghazal, 1986- (författare) Haploid selection in animals : Exploring the fitness consequences and underlying mechanisms 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
18.	Alhassan, Erwin, 1984- (författare) Nuclear data uncertainty quantification and data assimilation for a lead-cooled fast reactor : Using integral experiments for improved accuracy 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
19.	Almquist, Martin, 1988- (författare) Efficient Simulation of Wave Phenomena 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Wave phenomena appear in many fields of science such as acoustics, geophysics, and quantum mechanics. They can often be described by partial differential equations (PDEs). As PDEs typically are too difficult to solve by hand, the only option is to compute approximate solutions by implementing numerical methods on computers. Ideally, the numerical methods should produce accurate solutions at low computational cost. For wave propagation problems, high-order finite difference methods are known to be computationally cheap, but historically it has been difficult to construct stable methods. Thus, they have not been guaranteed to produce reasonable results.In this thesis we consider finite difference methods on summation-by-parts (SBP) form. To impose boundary and interface conditions we use the simultaneous approximation term (SAT) method. The SBP-SAT technique is designed such that the numerical solution mimics the energy estimates satisfied by the true solution. Hence, SBP-SAT schemes are energy-stable by construction and guaranteed to converge to the true solution of well-posed linear PDE. The SBP-SAT framework provides a means to derive high-order methods without jeopardizing stability. Thus, they overcome most of the drawbacks historically associated with finite difference methods.This thesis consists of three parts. The first part is devoted to improving existing SBP-SAT methods. In Papers I and II, we derive schemes with improved accuracy compared to standard schemes. In Paper III, we present an embedded boundary method that makes it easier to cope with complex geometries. The second part of the thesis shows how to apply the SBP-SAT method to wave propagation problems in acoustics (Paper IV) and quantum mechanics (Papers V and VI). The third part of the thesis, consisting of Paper VII, presents an efficient, fully explicit time-integration scheme well suited for locally refined meshes.
20.	Alves, Ricardo (författare) Leveraging Existing Microarchitectural Structures to Improve First-Level Caching Efficiency 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Low-latency data access is essential for performance. To achieve this, processors use fast first-level caches combined with out-of-order execution, to decrease and hide memory access latency respectively. While these approaches are effective for performance, they cost significant energy, leading to the development of many techniques that require designers to trade-off performance and efficiency.Way-prediction and filter caches are two of the most common strategies for improving first-level cache energy efficiency while still minimizing latency. They both have compromises as way-prediction trades off some latency for better energy efficiency, while filter caches trade off some energy efficiency for lower latency. However, these strategies are not mutually exclusive. By borrowing elements from both, and taking into account SRAM memory layout limitations, we proposed a novel MRU-L0 cache that mitigates many of their shortcomings while preserving their benefits. Moreover, while first-level caches are tightly integrated into the cpu pipeline, existing work on these techniques largely ignores the impact they have on instruction scheduling. We show that the variable hit latency introduced by way-misspredictions causes instruction replays of load dependent instruction chains, which hurts performance and efficiency. We study this effect and propose a variable latency cache-hit instruction scheduler, that identifies potential misschedulings, reduces instruction replays, reduces negative performance impact, and further improves cache energy efficiency.Modern pipelines also employ sophisticated execution strategies to hide memory latency and improve performance. While their primary use is for performance and correctness, they require intermediate storage that can be used as a cache as well. In this work we demonstrate how the store-buffer, paired with the memory dependency predictor, can be used to efficiently cache dirty data; and how the physical register file, paired with a value predictor, can be used to efficiently cache clean data. These strategies not only improve both performance and energy, but do so with no additional storage and minimal additional complexity, since they recycle existing cpu structures to detect reuse, memory ordering violations, and misspeculations.
21.	Amlinger, Lina (författare) The type I-E CRISPR-Cas system : Biology and applications of an adaptive immune system in bacteria 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract CRISPR-Cas systems are adaptive immune systems in bacteria and archaea, consisting of a clustered regularly interspaced short palindromic repeats (CRISPR) array and CRISPR associated (Cas) proteins. In this work, the type I-E CRISPR-Cas system of Escherichia coli was studied.CRISPR-Cas immunity is divided into three stages. In the first stage, adaptation, Cas1 and Cas2 store memory of invaders in the CRISPR array as short intervening sequences, called spacers. During the expression stage, the array is transcribed, and subsequently processed into small CRISPR RNAs (crRNA), each consisting of one spacer and one repeat. The crRNAs are bound by the Cascade multi-protein complex. During the interference step, Cascade searches for DNA molecules complementary to the crRNA spacer. When a match is found, the target DNA is degraded by the recruited Cas3 nuclease.Host factors required for integration of new spacers into the CRISPR array were first investigated. Deleting recD, involved in DNA repair, abolished memory formation by reducing the concentration of the Cas1-Cas2 expression plasmid, leading to decreased amounts of Cas1 to levels likely insufficient for spacer integration. Deletion of RecD has an indirect effect on adaptation. To facilitate detection of adaptation, a sensitive fluorescent reporter was developed where an out-of-frame yfp reporter gene is moved into frame when a new spacer is integrated, enabling fluorescent detection of adaptation. Integration can be detected in single cells by a variety of fluorescence-based methods. A second aspect of this thesis aimed at investigating spacer elements affecting target interference. Spacers with predicted secondary structures in the crRNA impaired the ability of the CRISPR-Cas system to prevent transformation of targeted plasmids. Lastly, in absence of Cas3, Cascade was successfully used to inhibit transcription of specific genes by preventing RNA polymerase access to the promoter.The CRISPR-Cas field has seen rapid development since the first demonstration of immunity almost ten years ago. However, much research remains to fully understand these interesting adaptive immune systems and the research presented here increases our understanding of the type I-E CRISPR-Cas system.
22.	Andersson, Andreas, 1981- (författare) Air-sea exchange of O2 and CO2 : Processes controlling the transfer efficiency 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract World oceans cover more than 70% of the earth surface and constitutes a major sink of atmospheric CO2. Two of the most important gases in the marine carbon cycling are O2 and CO2 and hence accurate descriptions of the air-sea gas exchange of these gases are crucial. Still there is a lack of knowledge of the relative importance of processes controlling the efficiency of the air-sea gas transfer. This is especially true for Arctic and high latitude seas were studies on air-sea gas exchange are few. By studying processes causing water-side turbulence, using gases of different solubility and various measurement techniques, more knowledge on the governing processes can be obtained.Here we present the very first air-sea fluxes of O2 using atmospheric eddy covariance measurements and investigate the dependence between the gas transfer velocity of O2 and turbulence generated by the mean wind. The instrument was found to suffer from the limited precision and time response, causing significant corrections on the O2 flux. After correcting for this, the O2 fluxes displays an anti-correlation with the air-sea fluxes of CO2 in agreement with the measured air-sea gradient of O2. The transfer velocities for O2 indicates a stronger wind dependence than other commonly used parameterizations of the transfer velocity for CO2 and O2, this especially for wind speeds > 5 m s-1 where the typical onset of wave breaking occur.During two winter months eddy covariance measurements were taken over a high Arctic fjord. The data revealed a significant enhancement of the gas transfer velocity for CO2 from water-side convection, generated by cooling of surface waters. The dependence between water-side convection and gas transfer velocity were found for winds as high as 9 m s-1, but were strongest for wind speeds< 7 m s-1. The data also showed on enhanced air-sea gas transfer of CO2 when conditions were unstable very close to neutral. This enhanced transfer were associated to increased contribution to the CO2 flux from downdraft of air with higher concentrations of CO2. The combined effect of water-side convection and turbulence generated by wind results in a very effective transfer, thus the air-sea gas exchange at these latitudes may be significantly underestimated.
23.	Andersson, Magnus, 1977- (författare) 3D Structure and Emplacement of the Alnö Alkaline and Carbonatite Complex, Sweden : Integrated Geophysical and Physical Property Investigations 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Carbonatites are carbonate-rich magmatic rocks that are rare and of great relevance for our understanding of crustal and mantle processes. Although found on all continents and in settings ranging from Archaean to present-day, their deeper plumbing system is still poorly understood. Therefore, the main goal of this thesis is to broaden the existing knowledge of carbonatite systems, often limited to surface geological observations, by providing depth constraints using a number of geophysical methods and petrophysical measurements. The Alnö alkaline and carbonatite complex in central Sweden was chosen for this purpose. Data from three reflection seismic lines, ground gravity and magnetic measurements are presented. These data are complemented by a series of petrophysical measurements, including ultrasonic velocities, density, magnetic bulk susceptibility, anisotropy of magnetic susceptibility (AMS), and magnetic remanence, to aid in the interpretation of the geophysical data. The reflection seismic data indicate a solidified saucer-shaped fossil magma chamber at about 3 km depth. Caldera-style volcanism, constrained by surface geological observations, provides a plausible scenario to explain the emplacement of the complex, suggesting that carbonatite magmas have been stored, transported and erupted in a similar manner to known emplacement mechanisms for silicic calderas, although these are compositionally different. The AMS data from most of the carbonatite sheets in Alnö show a strong degree of anisotropy and oblate-shaped susceptibility ellipsoids. A set of syn- and post-emplacement processes that may control the AMS signature is evaluated based on the dataset. Overprinting of the primary flow patterns by processes related to sheet closure at the terminal stage of magma transport may explain the AMS observations. A complementary study using 3D inversion of ground gravity and aeromagnetic data was then carried out to better delineate the 3D internal architecture of the complex. Resulting models indicate a depth extent of the complex to about 3-4 km, consistent with the interpretation of the reflection seismic data. The modelling results of a ring-shaped magnetic anomaly observed in the Klingefjärden bay adjacent to Alnö Island further suggest that the complex may extend laterally about 3 km towards the north.
24.	Andersson, Marie, 1974- (författare) Cellular transport and secretion of the cyanobacterial neurotoxin BMAA into milk and egg : Implications for developmental neurotoxicity 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract The cyanobacterial amino acid β-N-methylamino-L-alanine (BMAA) is a neurotoxin implicated in the etiology of neurodegenerative diseases. Cyanobacteria are cosmopolitan organisms present in various environments. BMAA can cause long-term neurodegenerative alterations in rats exposed during the neonatal period, a period that corresponds to the last trimester and the first few years of life in humans. As BMAA has been reported to be bioaccumulated in the aquatic food chain and detected in mussels, crayfish and fish used for human consumption, the main aim of this thesis has been to investigate the final step in the mammalian food-chain, i.e. the transfer of BMAA into breast milk.Autoradiographic imaging and mass spectrometry analysis showed an enantiomer-selective uptake of BMAA and that the neurotoxin was transferred from lactating mice and rat, via the milk, to the brain of the nursed pups. The results show that transport of BMAA may be disproportional to dose. In addition, BMAA was found present both as free amino acid and tightly associated to proteins in rat brains. Surprisingly, however, no association to milk proteins was found. In vitro studies of murine (HC11) and human (MCF7) mammary epithelial cells suggest that BMAA can pass the human mammary epithelium into milk. Additional transport studies on human intestinal, glioblastoma and neuroblastoma cells showed that L-BMAA was consistently favored over D-BMAA and that the transport was mediated by several amino acid transporters. We also demonstrated that egg-laying quail transfer BMAA to its offspring by deposition in the eggs, particularly in the yolk but also in the albumen. Furthermore, comparative analysis of carboxyl- and methyl-labeled [14C]-BMAA suggested that BMAA was not metabolized to a large degree.Altogether, the results indicate that BMAA can be transferred from mothers, via the milk, to the brain of nursed human infants. Determinations of BMAA in mothers’ milk and cows’ milk are therefore warranted. We also propose that birds’ eggs could be an additional source of BMAA exposure in humans. It might therefore be of concern that mussels are increasingly used as feed in commercial egg production.
25.	Andersson, Martin (författare) Extent and limitations of functional redundancy among bacterial communities towards dissolved organic matter 2017 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract One of the key processes in the carbon cycle on our planet is the degradation of dissolved organic matter (DOM) in aquatic environments. The use of organic matter by bacteria links energy from DOM to higher trophic levels of the ecosystem when bacteria are consumed by other organisms. This is referred to as the microbial loop. In this thesis I examined if the communities were functionally redundant in their ability to utilize organic matter, or if variation in bacterial composition and richness is of importance. To test this overarching question several experiments were conducted that include methods such as illumina sequencing of the 16S rRNA gene for taxonomic identification of bacterial communities, flow cytometry to follow the growth of communities and spectroscopic measurement to describe the composition of the organic matter pool. Initially we demonstrated how to optimally sterilize organic matter for experimental studies in order to preserve its natural complexity. In further experiments we found that bacterial communities are redundant in their utilization of organic matter and can maintain optimal performance towards a range of organic matter pools. Related to this we found that pre-adaptation to organic matter played a small role as communities performed equally well regardless of their environmental history. We saw a small effect of richness and composition of bacterial communities on the efficiency of organic matter use, but conclude that this is of minor importance relative to abiotic factors. Still, we also show that organic matter can put strong selection pressure on bacterial communities with regards to richness and composition. Additionally we found that the supply rate of a carbon compound greatly influenced the energy utilization of the compound, i.e. a higher growth rate can be maintained if substrate is delivered in pulses relative to a continuous flow. Finally we conclude that the variation in bacterial communities is unlikely to have a major influence on carbon cycling in boreal lakes, but to enable a finer understanding, the genetics underlying the carbon utilization needs to be further explored.

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