Matemaattis-luonnontieteellinen tiedekunta

 

Recent Submissions

  • Cole, Elizabeth (Helsingin yliopisto, 2017)
    The universe is populated with magnetically active stars. This magnetic activity is thought to be generated by dynamos operating in turbulent stellar convection zones, a process by which kinetic energy is converted into magnetic energy. The solar dynamo is but one dynamo type possible for stars. Rapidly rotating late-type stars are observed to have large spots, activity cycles, flip-flops, and active longitudes, all indicating a different dynamo mechanism may be responsible. Numerical simulations provide a tool for better understanding some of the mechanisms responsible for these dynamos. In this thesis, direct numerical simulations in spherical wedges are used to study dynamo mechanisms in the stellar convection zone. These spherical wedges are used to investigate the dependence of the resulting magnetic field on input parameters such as the density stratification and rotation rate. Mean-field models are used to evaluate the assumption that the wedges can be used to approximate full spheres. As rotation increases, differential rotation decreases in the models, in agreement with observations where more rapidly rotating stars have smaller estimates for differential rotation. As density stratification approaches more realistic values, a lat- itudinal dynamo wave with equatorward propagation is found. The impact of the domain size in the azimuthal direction on the results is explored. When the domain size is increased to 2pi in the azimuthal direction, a non-axisymmetric m = 1 mode is excited. This non-axisymmetry is reminiscent of the field configurations of rapidly rotating late-type stars. The azimuthal dynamo wave rotates nearly independently of latitude and depth, and its rotation rate is slower than that of the mean rotation of the model. This azimuthal dynamo can provide a possible explanation for the observed rotational difference of spots from the mean rotation observed on stars. The wedges use the perfect conductor boundary conditions at the latitudinal boundary to compensate for the omission of polar regions due to the time step becoming prohibitively small there. Simple mean-field models with only a latitudinal extent and perfectly conducting boundaries do not oscillate when the model is extended to the poles. Thus oscillations near the polar region may be an artifact of the boundary condition. However, when the alpha effect from mean-field dynamo theory and magnetic diffusivity are concentrated towards lower latitudes, oscillatory solutions with equatorward migration are found. When sufficient shear is added, oscillatory solutions are again found, and the Parker-Yoshimura rule for latitudinal dynamo wave propagation is obeyed. It is concluded that numerical simulations where the alpha effect and diffusivity are found to be stronger at lower latitudes and simulations with sufficient shear are considered good approximations of full spheres. These numerical simulations are put into context with stellar observations. Two young solar analogs are selected, V352 Canis Majoris and LQ Hydrae. V352 CMa is considered an active star, while LQ Hya is classified as a super-active star. The continuous period search method is applied to the low-amplitude light curves of V352 CMa. Stable active longitudes with rotation periods of 7.157 days are found. This is faster than the mean rotation of 7.24 days. Such active longitudes may be due to the underlying magnetic structure with azimuthal dynamo waves competing with differential rotation. LQ Hya rotates even more rapidly with a rotation period of only 1.600 days. A carrier period is selected of 1.605 days using the D2 statistical analysis. Primary and secondary light curve minima are found with the carrier fit analysis. No stable active longitudes are found, instead, there is only a short period spanning a few years where an active longitude may exist, but the rotation period is poorly defined. Several possible flip-flop events are identified. The azimuthal dynamo waves in numerical simulations with comparable rotation rates have a similar chaotic nature. The Doppler Imaging technique is applied to LQ Hya to examine the latitudinal spot structure. Spots at high and low latitudes are in agreement with the bimodal structure of the D2 statistic used in the carrier fit analysis. Temperature maps of LQ Hya spanning four years show an increase and a decrease in spot coverage, but no cycle can be found. Because LQ Hya is a rapidly rotating star, differential rotation is estimated to be very small. The azimuthal dynamo wave presents a new possible explanation for the jumps and trends of the spots in observations of this star.
  • Holopainen, Jani (Helsingin yliopisto, 2017)
    Bone is a fibrous nanocomposite material with a complex hierarchical system of different macro-, micro- and nanostructures. The structure elegantly supports the bone cell functions and facilitates bone remodeling by cellular activity. Injuries and diseases, e.g. osteoporosis, can cause bone fractures and loss that need to be treated with orthopedic implants. The global orthopedic market was estimated at $30 500 000 000 in 2012 and predicted to grow rapidly. A substantial amount of this goes to revision surgery due to implant failures. This not only causes unnecessary costs and work but reduces the quality of life for patients. The key for improving the performance of current implants lies in optimizing both the surface chemistry and structure from macro- to nanoscale. At best bone defects can be treated with bone scaffolds that induce formation of new bone via cellular functions and are degraded by the body thus evading the need for implant removal surgery. However, combining the favorable mechanical, structural and chemical properties poses challenges for the design and preparation methods used for bone implants and scaffolds. The aim of this work was to investigate the preparation of thin film and fibrous biomaterials for bone implants and scaffolds. New processes were developed for various biomaterials and their properties were thoroughly characterized. A method to convert CaCO3 nanostructures to nanocrystalline hydroxyapatite (HA) by treatment in phosphate solution was used to prepare HA thin films and fibers from atomic layer deposited (ALD) and electrospun CaCO3, respectively. HA fibers were also fabricated conventionally by annealing electrospun composite fibers that incorporated Ca and P precursors. Biocomposite fibers of HA nanoparticles and polylactic acid (nHA/PLA) were directly electrospun. These different nanofibers are highly interesting for bone scaffolds owing to their high surface area and the structural similarity to the fibrous nanostructure found in bone. However, conventional electrospinning is limited by its modest production rate. A needleless twisted wire electrospinning (NTWE) setup was developed to increase the production rate and was studied for the preparation of HA fibers for the bone scaffolds. Solution blow spinning (SBS) and electroblowing (EB) of HA were studied as other upscaling alternatives. Promising results were obtained in cell culture studies with the different materials. The electrospun materials could find use in fibrous bone scaffolds. The HA fibers were found out to be very interesting from a biological standpoint, but the fragility of the fibers limits their usability as such and therefore methods to incorporate bioceramic fibers into more rigid support structures should be developed. The method to prepare nanocrystalline HA by the conversion of CaCO3 proved to be highly conformal as evidenced by its ability to preserve the original shape of the ALD films and electrospun fibers. NTWE and EB were shown to be capable of producing high quality nanofibers and to provide a viable upscaling route to conventional electrospinning. In contrast, the quality of the SBS fibers needs improvement. Further work would be required to conclude if EB and NTWE are upscalable to industrial scale production levels.
  • Luoma, Samrit (Helsingin yliopisto, 2016)
    This thesis clarifies the potential impacts of climate change and sea-level rise under future climate scenarios on groundwater recharge and surface leakage, and consequently on the groundwater vulnerability of a shallow, unconfined, low-lying coastal sedimentary aquifer in southern Finland. The study utilised multiple approaches, including field investigations, well monitoring, three-dimensional (3D) geological modelling, 3D groundwater flow modelling, multivariate statistical approaches (principal component analysis (PCA) and hierarchical cluster analysis (HCA)), the stable isotopes δ2H and δ18O, conventional hydrogeochemistry and groundwater intrinsic vulnerability assessment methods. The UZF1 model was coupled with the 3D groundwater MODFLOW model to simulate flow from the unsaturated zone through the aquifer. The well-calibrated groundwater flow model was used to simulate and predict the potential impacts of climate change on groundwater recharge under future climate and sea-level rise scenarios. The results indicate changes in the groundwater recharge patterns during the years 2071 2100, with recharge occurring earlier in winter and early spring. Because the aquifer is located in a cold snow-dominated region, the seasonal impacts of climate change on groundwater recharge were more significant, with land surface overflow resulting in flooding during the winter and early spring and drought during the summer. Rising sea levels would cause some parts of the aquifer to be submerged under the sea, compromising groundwater quality due to the intrusion of seawater. This, together with increased groundwater recharge, would raise the groundwater level and consequently contribute to more surface leakage. The groundwater geochemistry of the coastal aquifer in Hanko is very similar to that of inland shallow aquifers generally in Finland, where the groundwater is mainly of the Ca HCO3 type, with low dissolved element concentrations, low pH and alkalinity, and low Ca and Mg concentrations due to rapid percolation or the short residence time. The stable isotopes δ2H and δ18O clearly suggest that the Hanko aquifer recharges directly from meteoric water (snowmelt and rainfall), with minor or insignificant contributions from the Baltic Sea and surface water. However, the geochemistry of the groundwater suggests sulphate reduction in the mixed zone between freshwater and seawater, indicating that local seawater intrusion may temporarily take place, although the contribution of seawater was found to be very low. Further inland, the influence of surface water could be observed from higher levels of KMnO4 consumption in wells near the lake above the aquifer. The findings also demonstrated that the use of stable isotopes δ2H and δ18O alone to identify seawater aquifer interaction is not sufficient to determine the rate of water exchange. The high temporal variation in groundwater chemistry directly corresponded to groundwater recharge. With an increase in groundwater recharge, KMnO4 consumption, EC, alkalinity and Ca concentrations also increased in most wells, while Fe, Al, Mn and SO4 were occasionally increased during the spring after snowmelt under specific geological conditions. Based on the future climate scenarios, precipitation in the Hanko area is expected to increase and the Baltic Sea level to rise. This could cause increased recharge of the aquifer from surface water, but also some seawater intrusion due to the sea-level rise and storm surges, as well as increased groundwater abstraction. An increase in the concentrations of some dissolved elements and changes in groundwater geochemistry along the coastline can be expected in the future. Thus, in coastal aquifers with low hydraulic gradients, the hydrogeochemistry should be used to confirm the intrusion of seawater. The PCA and HCA multivariate statistical approaches are useful tools to extract the main components that are able to identify the vulnerable areas of the aquifer impacted by natural or human activities, either on regional or site-specific scales. The integration of PCA and HCA with conventional classification of groundwater types, as well as with the hydrogeochemical data, provided an understanding of the complex groundwater flow systems, supporting aquifer vulnerability assessment and groundwater management in the future. The degree of groundwater vulnerability in the Hanko aquifer has been greatly impacted by seasonal variations in groundwater recharge during the year, and will also vary depending on climate change variability in the long term. The potential for high groundwater vulnerability to contamination from sources on the ground surface occurs during the period with a high groundwater recharge rate after snowmelt, while high vulnerability to seawater intrusion could occur when there is a low groundwater recharge rate in the dry season. This thesis study highlighted the importance of the integration of groundwater vulnerability assessment methods for shallow, unconfined, low-lying coastal aquifers from a comparison of three intrinsic vulnerability mapping methods: the AVI, a modified version of SINTACS and the GALDIT method. The modified SINTACS could be used as a guideline for groundwater vulnerability assessment of glacial and deglacial deposits in inland aquifers, and in combination with GALDIT, it could provide a useful tool for assessing groundwater vulnerability to both contamination from sources on the ground surface and to seawater intrusion for shallow, unconfined, low-lying coastal aquifers under future climate change.
  • Sukselainen, Leena (Helsingin yliopisto, 2016)
    Pliopithecoidea is an extinct and diverse superfamily of primitive catarrhine primates with no known descendants. They first appear in the fossil record in the late early Miocene China, ca. 18 17 million years ago (Ma). They were widely distributed throughout Eurasia between ca. 17 and 7 Ma and were among the first primates to be discovered and described. Despite their wide distribution, pliopithecoids are rarely found together with the contemporaneous and equally widely distributed hominoid primates. The latest known occurrence of pliopithecoids is also from China where they co-existed with hominoids in the late Miocene ca 6.9 6.2 Ma. Continuing climatic deterioration and dispersal of cercopithecoid primates from Africa may have contributed to their demise. The main objective of this study is to produce new information on pliopithecoids, their environments, as well as on environmental conditions in Eurasia during the Miocene (23 5.3 Ma), with a special focus on the middle Miocene Inner Mongolian locality of Damiao. These goals are approached first by inspecting the differences between pliopithecoid localities and other contemporaneous localities with particular focus on the rare localities of co-occurring pliopithecoid and hominoid primates. To do this we used both traditional ecological diversity analysis as well as direct ecometric method based on hypsodonty in mammalian herbivores. A closer examination of the Inner Mongolian pliopithecoid locality, Damiao, will follow, using small mammal taphonomy, faunal similarity, ecometrics, and stable isotope analyses. The aim is to understand the presence of humid-favouring pliopithecoid primates in central Asia after the middle Miocene climatic optimum (MMCO; ca. 17 15 Ma). The reason this is interesting is because it seems to contradict the general trend of strengthening climatic zonality and increasing aridity from the early Miocene onwards. The results show that pliopithecoids inhabited more humid environments than other contemporary primate groups, suggesting an inability to adapt to changing environmental conditions. The conservative nature of pliopithecoid adaptations seems to have restricted the co-occurrence of pliopithecoids and hominoids, and has been therefore rarely documented. The study also suggests that direct ecometric analysis gives a better separation of the ecological preferences of these primates than do analyses of taxonomically based community structure. The results in Damiao support previous inferences concerning the presence of locally humid environments within the increasingly arid surroundings that characterized Central Asia. Environments within the DM01 locality may have been more humid and possibly more forested and wooded, as suggested by hypsodonty, estimated mean annual precipitation (MAP), local sedimentology and large mammal fossils. We compared our results with the adjacent fossil-rich middle Miocene Tunggur localities. However, the small mammal fauna and isotope data are consistent with a mosaic of forest and grassland environment for all Damiao localities. Based on our results, Tunggur may have been too seasonal or not sufficiently humid for pliopithecoids. This idea is supported by the higher mean hypsodonty and lower predicted MAP estimates, as well as slightly higher δ13C values. We suggest that DM01, the driest known Asian pliopithecoid locality, may have been a more humid refugium within a generally drier regional context. The bone material in Damiao was mainly accumulated by predators and deposited in a fluvial setting. Some reworking by fluvial process took place in DM01 and DM02. DM16 represents the distal part of the floodplain; DM01 portrays a channel-fill; and DM02 is a result of an episodic flood discharge to the floodplain. We also show that systematic excavation for small mammals is possible, and allows for the reduction of some of the damage collecting always causes.
  • Kangas, Juho-Kustaa (Helsingin yliopisto, 2016)
    Graphical models are a framework for representing joint distributions over random variables. By capturing the structure of conditional independencies between the variables, a graphical model can express the distribution in a concise factored form that is often efficient to store and reason about. As constructing graphical models by hand is often infeasible, a lot of work has been devoted to learning them automatically from observational data. Of particular interest is the so-called structure learning problem, of finding a graph that encodes the structure of probabilistic dependencies. Once the learner has decided what constitutes a good fit to the data, the task of finding optimal structures typically involves solving an NP-hard problem of combinatorial optimization. While first algorithms for structure learning thus resorted to local search, there has been a growing interest in solving the problem to a global optimum. Indeed, during the past decade multiple exact algorithms have been proposed that are guaranteed to find optimal structures for the family of Bayesian networks, while first steps have been taken for the family of decomposable graphical models. This thesis presents combinatorial algorithms and analytical results with applications in the structure learning problem. For decomposable models, we present exact algorithms for the so-called full Bayesian approach, which involves not only finding individual structures of good fit but also computing posterior expectations of graph features, either by exact computation or via Monte Carlo methods. For Bayesian networks, we study the empirical hardness of the structure learning problem, with the aim of being able to predict the running time of various structure learning algorithms on a given problem instance. As a result, we obtain a hybrid algorithm that effectively combines the best-case performance of multiple existing techniques. Lastly, we study two combinatorial problems of wider interest with relevance in structure learning. First, we present algorithms for counting linear extensions of partially ordered sets, which is required to correct bias in MCMC methods for sampling Bayesian network structures. Second, we give results in the extremal combinatorics of connected vertex sets, whose number bounds the running time of certain algorithms for structure learning and various other problems.
  • Väänänen, Riikka (Helsingin yliopisto, 2016)
    Atmospheric aerosols have an impact on the global radiation budget, and thus on climate, they reduce the air quality and visibility, and have multiple harmful health effects. The climatic significance of aerosols result from their ability to scatter and absorb solar radiation, and, if being large enough, mediate the cloud albedo and lifetime by acting as cloud condensation nuclei (CCN). The climatic effect, however, has a notable uncertainty. Particles can be either directly emitted to atmosphere or they can form there from precursor vapors. The latter is called new particle formation (NPF). Globally, NPF has been estimated to be responsible for even half of CCN sized tropospheric particles. The understanding of the NPF mechanisms and the spatial and temporal variation of NPF in many scales is necessary to correctly represent aerosols in climate models. In this work, we quantified the importance of biogenic organic vapours and anthropogenic sulfuric emissions in the NPF in northern boreal environment. Aerosol number size distribution data from three measurement sites were used to calculate the average continuous increase in aerosol particle diameter and number concentration when air masses travelled over land. A 14-year-long time series of aerosol and gas measurements were used to determine the effect of reduced Kola Peninsula SO2 emissions on aerosol population at Eastern Finnish Lapland. Secondly, this thesis describes in-situ aerosol measurements conducted with a light aircraft within the lowest 4 km of the troposphere. The data were used to determine the vertical and horizontal extent and variability of the NPF events in the surroundings of the Hyytiälä SMEAR II station. The airborne and ground level measurements were compared to find out the representativeness of the on ground measurements in the lowest parts of the atmosphere, in the planetary boundary layer. The results showed that the Aitken mode particles grew, on average, at the apparent rate of around 1 nm h−1 when they travelled over the northern boreal environment during the growing season. The average calculated growth rates during the NPF events were 3 6 times higher than this apparent average growth rate. The result implied that the condensation has a significant role in the particle growth even when NPF is not explicit. Also, the NPF events inside the planetary boundary layer were found to occur in area over a hundred kilometers. However, within this area, a notable variation in nucleation mode particles was observed.
  • Holding, Ashley John (Helsingin yliopisto, 2016)
    In this thesis, the synthesis and application of tetraalkylphosphonium-based ionic liquids towards the dissolution of cellulose (and lignocellulose) is explored. Ionic liquids were synthesised from trialkylphosphines by quaternisation with alkyl halides or dimethylcarbonate and subsequent anion exchange reactions. The ionic liquids were used to dissolve lignin, and were found only to dissolve cellulose upon addition of a polar aprotic molecular solvent, such as DMSO (dimethylsulfoxide). The cellulose dissolution capabilities of a range of these phosphonium ionic liquids in combination with DMSO was studied. It was found that these organic electrolyte solutions were very effective solvents for cellulose, with a high molar dissolution capacity. At the greatest extent, only one mole of ionic liquid per glucose units in cellulose is needed to dissolve cellulose. The role of the cation and anion in the dissolution process is explored, with the aid of solvent parametisation techniques and NMR studies. Other solvents, including GVL (gamma-valerolactone), were explored as greener replacements for DMSO. For the shorter chain phosphonium ionic liquids with DMSO and GVL, upper critical solution temperature behaviour was observed and explored in more detail. In these solutions, cellulose is only soluble at high temperatures, and reforms at low temperatures to form a gel with a spherical micro-particle morphology. The phase behaviour of hydrophobic phosphonium ionic liquids, DMSO, and water was studied and applied to the recovery of the ionic liquid after cellulose dissolution in the electrolyte solutions. Ternary phase diagrams of three of the hydrophobic ionic liquids in combination with DMSO and water were constructed. Finally, phosphonium ionic liquid and deuterated DMSO electrolytes were studied and successfully used for the NMR analysis of high molecular weight cellulose materials. Future work in this area is expected to focus further on the theoretical understanding of cellulose dissolution in phosphonium ionic liquid-based organic electrolyte solutions - with expanded NMR measurements, and other experimental techniques, in tandem with molecular dynamics modelling. Additionally, it is expected that techniques for the solution-state NMR of cellulose will be applied at extended range of analytes, including but not limited to, whole biomass, modified and unmodified nano-celluloses, and high molecular weight cellulose derivatives. The thermo-responsive behaviour (UCST-type) phase-separation of cellulose will continue to be explored especially in its application to new materials, included fibres and shaped spherical particles.
  • Seitola, Teija (Helsingin yliopisto, 2016)
    The ability of climate models to simulate the climate variability is of great importance when considering the reliability of, for instance, multi-annual or longer-term predictions. The aim of this thesis is to study the 20th century low-frequency variability patterns in the Earth system and how these patterns are represented by the current modelling systems. Another, equally important objective is to enable efficient spatio-temporal analysis of high-dimensional climate data sets. Decadal scale variability and predictability, from the point of view of the Nordic region, is also summarised in this study. The work is based on the near-surface temperature of two 20th century reanalyses, obtained from the NOAA/OAR/ESRL and ECMWF, and historical climate model simulations from the coupled model intercomparison project5 (CMIP5) data archive. In addition, a millennial Earth system model simulation is analysed. The analysis relies on a powerful dimensionality reduction method, called random projection (RP), which is introduced as a preprocessing for high-dimensional climate data sets to enhance or enable the analysis. The spectral decomposition of the data sets is based on randomised multi-channel singular spectrum analysis (RMSSA), which is one of the main achievements of this thesis. It is shown that dimensionality reduction obtained by RP preserves the main spatial and temporal patterns with high accuracy. In addition, RMSSA is shown to provide an efficient tool for identifying different variability modes in high-dimensional climate data sets. This study shows that the 20th century variability patterns in the two reanalysis data sets are very similar. It is also shown that none of the studied climate models can closely reproduce all the variability modes identified in the reanalyses, although many aspects are simulated well. Taking into account the rapidly accumulating amount of data and increasing dimensionality of data sets, RP is a promising method for dimensionality reduction. The results of the model evaluation can be useful in model development due better understanding of the deficiencies in representing the low-frequency modes. In addition to near-surface temperature, it would be a natural extension to include more variables in the analysis, especially because RP allows efficient data compression.
  • Tenkanen, Tommi (Helsingin yliopisto, 2016)
    Cosmic inflation, an era of rapid expansion in the early universe, and dark matter, an unknown non-baryonic matter component exceeding the amount of the usual baryonic matter by a factor of five, are known to play an important role in describing the physics of the early universe and in explaining the contents of the universe we observe today. Yet the reason for the occurrence of inflation and for the production of dark matter, or their properties, are not known. In this thesis we study the observational consequences of a class of particle physics models related to inflation and dark matter which are challenging to test by direct experiments, such as particle colliders, but which can be tested by cosmological and astrophysical observations. In particular, we concentrate on observational properties of self-interacting Higgs portal dark matter. Whenever a model contains scalar fields which are light and energetically subdominant during cosmic inflation, so-called spectator fields , they acquire large fluctuations which may leave observable imprints on the Cosmic Microwave Background radiation. Carefully investigating the spectator field dynamics during cosmic inflation, we solve for typical initial conditions for post-inflationary dynamics and calculate the dark matter yield originating from non-thermal decay of spectator condensates. As a result, we find a novel connection between the energy scale of inflation and the dark matter abundance. We also study alternative thermal histories of hidden sector dark matter and demonstrate how the usual dark matter production mechanisms may not be sufficient to correctly describe the evolution of dark matter relic density from its generation to the present day. We show that even if the coupling between the hidden and visible sectors is almost negligible, the scenario has observable consequences. Especially a positive observation of primordial tensor perturbations would immensely affect not only models of inflation but also very weakly coupled dark matter models, ruling out large portions of the otherwise viable parameter space. The derived bounds are generic to most weakly coupled portal models with light scalar fields, and qualitatively similar results are also expected to arise in other portal type extensions of the Standard Model of particle physics.
  • Pfau-Kempf, Yann (Helsingin yliopisto, 2016)
    The Sun is the source of the solar wind, a continuous stream of electrically charged particles and magnetic fields pervading the Solar system. Its interaction with the magnetic field of the Earth, in and around the region called the magnetosphere, controls the flow of matter and energy in near-Earth space. A fundamental understanding of the physical processes at play is crucial for the building of forecasting and warning systems, as the influence of the solar wind during space storms can harm life and technology in space and on the ground. These effects, collectively known as space weather, are one of the biggest albeit least understood natural threats to society. The research effort needed includes the development of observational methods as well as theories and models, to first describe and later predict the mechanisms and consequences of space weather. This doctoral thesis, comprising an introduction and four peer-reviewed articles, presents the hybrid-Vlasov model Vlasiator developed at the Finnish Meteorological Institute. Based on a detailed description of proton physics in space plasmas, Vlasiator allows to simulate both local contexts and the Earth's magnetosphere on global scales. This unprecedented capability is only accessible by harnessing the power of modern supercomputers. The aim of this work is threefold. The current version of Vlasiator is documented considering physical and computational aspects, the correctness of the simulations is demonstrated by comparing to analytical theories and spacecraft observations, and new scientific results gained with this model are presented.
  • Koskelo, Jaakko (Helsingin yliopisto, 2016)
    The response of materials to electromagnetic radiation is important for two reasons: it is crucial for many applications and can also be used to study the microscopic and electronic structure that determine other properties of materials. Calculations on the quantum-mechanical state of the electrons, the electronic structure, are useful for interpreting the results of experiments where materials are probed by electromagnetic radiation. This thesis consists of three studies where electronic-structure calculations have been employed in investigating materials and their response to electromagnetic radiation. In the first paper, x-ray Compton-profile difference between solid and liquid phases of ionic liquid [mmim]Cl is calculated. The structural changes that affect this Compton-profile difference are analyzed. In the second paper, the dopant configuration and band structure of an intermediate-band solar-cell material Fe-doped CuGaS2 is studied, along with optical absorption spectra. In the third paper, excitons in layered materials are investigated using a hexagonal boron nitride as an example material, and the connection between bulk and monolayer excitons is discussed. These studies provide a view on the possibilities of electronic-structure calculations for understanding the spectroscopic properties of materials from atomic and electronic level.
  • Vehkala, Minna (Helsingin yliopisto, 2016)
    This thesis introduces statistical analysis methods for two types of bacterial data: metabolic data produced by phenotype microarray technology, and genomic data produced by sequencing technologies. As both technologies produce vast amounts of data, as well as have special features, there is a need for bioinformatics tools that adequately process and analyze the information produced. Similar to all biomolecular data analyses, the interplay between biological components poses an additional challenge to the method development. A specific complication, regarding the metabolic data, is the lack of larger quantities of replicates due to the high expenses of performing the experiments. In terms of the sequence data, genome-wide analysis tools are desired, since such methods have not yet been widely developed for bacteria, even though they exist for eukaryotic genetics. The thesis briefly reviews the current methods, and introduces new approaches tackling the above mentioned problems.
  • Niinikoski, Paula (Helsingin yliopisto, 2016)
    Access to clean water is a growing global concern, and understanding all the different processes affecting the quantity and quality of both surface and groundwater is crucial to meeting this increasing demand for water. Information on the carbon contents of surface water systems is also essential for understanding the carbon balance of the entire atmosphere. Whether surface waters serve as a source or a sink of carbon can have an effect on atmospheric changes in CO2 at a global scale. Better knowledge of the carbon cycle in rivers is, therefore, an important part of preparing for changes due to the increase in the CO2 concentration of the atmosphere. In addition, studying the carbon contents of river water increases our understanding of the vulnerability of catchments, and helps to enhance the quality of drinking water. Stable isotopes are natural tracers. The stable isotopic composition of oxygen and hydrogen in water can be used to monitor the travel times and routes of surface and groundwater by utilising the fractionation effects caused by temperature on precipitation, and evaporation on surface water. The isotopic composition of dissolved inorganic carbon in the river water can be used to investigate the origin of carbon, which provides implications for the organic and inorganic processes transferring carbon into the water. In this study, stable isotopes are utilized together with multiple chemical analyses and modelling methods to further understand the processes that control the hydrosphere. The two main aims are: 1) to establish the conditions under which the stable isotopic composition of hydrogen and oxygen in water can be used to determine mean residence times (MRT), and 2) to better understand the processes controlling the dissolved carbon contents in artificial and natural water systems, in order to use this understanding to help maintain and improve the quality of the water. The study sites included two rivers, the Vantaanjoki and the Kokemäenjoki River, in southern and southwestern Finland, respectively, and a managed aquifer recharge (MAR) site at Virttaankangas in southwestern Finland. The mean residence time of water was determined for both rivers and the MAR site using the isotopic composition of oxygen in water. The results suggested that isotope based MRT determination is applicable in simple systems with known water sources. This was the case for the Vantaanjoki River, where the water mainly comes from two distinct sources: base flow and surface flow during spring flooding. The mean residence time of the snow cover, and the water in the flooding event, could be determined by the isotope method. The base flow component was too old to be dated by this method. At the Virttaankangas MAR site, the two known components were local groundwater and infiltrated water, the latter being suitable for MRT determination. The carbon budget of the Vantaanjoki River showed signs of both base flow influence and photosynthesis and decay taking place in the river channel. Human induced changes played a minor role in the inorganic carbon balance. Decay of organic material could also be perceived at Virttaankangas MAR site, where the organic matter in the infiltrated water is microbially decomposed into inorganic form. This process could be monitored by combining the isotopic technique with geochemical modelling. The beginning of the decomposition was delayed compared to most MAR sites, which may be due to an uncommonly high pH of the water in the aquifer, caused by calcite dissolution. These results confirm that there are many applications for isotopic methods. The annual isotope signal in precipitation is a good tool for determining the MRT, especially in two component systems. The isotopic composition of DIC, together with that of oxygen and hydrogen, can be applied to study surface flow base flow interaction in river catchments. Oxidative decomposition of DOC in MAR can be monitored using δ13CDIC together with geochemical modelling in cases where there are other sources contributing to the DIC.
  • Honkanen, Mika (Helsingin yliopisto, 2016)
    There are several definitions of the regional policy. In regional policy research one must make a disctinction between regional policy as a discipline, regional policy practices and regional policy planning. Although regional policy is controlled by the legislation and the laws are passed by the Parliament there has been only little research on regional policy from this point of view. The research material consists of the speeches given by the Members of Parliament in plenary sessions during four major regional law generations in 1966, 1975, 1988 and 1993. In terms of time the research covers the Finnish national regional policy prior to the EU membership. In addition to the voters of their region the MPs represent parties. The support of the parties varies according to the constituency. The differences in the regional policy activity of the parties observed in the source literature are confirmed in the Parliament debates. Regional policy was the most important issue for the Centre Party during the entire research period. Among other parties only the Social Democratic Party was continuously active, whereas the activity of the other parties varied every year. None of the parliamentary debates on the Regional Policy Act achieved a joint view on the direction of the regional development. The importance of uniformity and effectiveness varied in the debates, but the aim was always to achieve them both simultaneously. Uniformity was continuously justified by fairness and impartial treatment, but within time the reasons for the effectiveness focused increasingly on taking care of the international competitiveness. Regional policy gradually expanded from northern and eastern Finland throughout the country and at the same time the confrontation between different parts of the country decreased, but remained between urban and rural areas, particularly between the capital region and the rest of Finland. The definition of the position of the metropolitan area as a fertile part of the country´s regional politics did not succeed. In the Finnish Parliament the Helsinki metropolitan area was identified as a political partner, but not as a part of province. It was better understood as a specific type of region, a metropolis. In addition, the City of Helsinki had its own constituency. Although the prevailing theories of regions were known to researchers and officials, the MPs did not argue based on them. This is partly explained by the parliament as the ven-ue. MPs did not want to use language that was not familiar to all members of the parlia-ment. Sometimes they appealed to the individual researchers and their views, so it was rather through persuasion of other representatives of authority, than the theory-based reasoning. The connection between the political academic research and the political deci-sion-maker remained unnecessarily distant, although the theory of regions clearly affect-ed the shape of the regional policy.
  • Chen, Wen (Helsingin yliopisto, 2016)
    Human exhaled breath contains hundreds of volatile compounds. Breath analysis is a method of seeking biomarkers among these volatiles, which could potentially serve as non-invasive medical indicators in disease diagnosis. With the development of analytical techniques more disease-related breath volatiles are being discovered. Exhaled hydrogen cyanide (HCN) and ammonia (NH3) have been studied previously. Both of them are potential biomarkers in clinical practice. Breath HCN has been proposed as a biomarker of Pseudomonas aeruginosa colonization in cystic fibrosis patients, since high levels of HCN are detected in the headspace of P. aeruginosa in vitro. Breath NH3 has been suggested as an indicator for monitoring hemodialysis (HD) adequacy in end-stage renal disease (ESRD) patients, since breath NH3 is strongly correlated to blood urea. To validate breath HCN and NH3 tests for clinical application, one has to understand the biochemical mechanisms of breath HCN and NH3 production in the human body. In some earlier studies, it was assumed that the oral cavity is a major production site for both breath HCN and NH3. However, the biochemical pathways of oral HCN and NH3 production have not been extensively studied. In this thesis, we investigated the correlation between salivary HCN and breath HCN in healthy subjects and confirmed that saliva is the main source for breath HCN. Additionally, we observed that oral anaerobes, including the genus of Porphyromonas, Prevotella and Fusobacterium, produce low levels of HCN in vitro. This implies that oral bacteria probably contribute to breath HCN generation. To explore the mechanism of breath NH3 production, we first conducted experiments on healthy subjects and found that salivary urea is the main source of breath NH3. We extended our study to ESRD patients during their HD treatment to investigate the connection between blood urea and breath NH3. Through the observation of strong correlations between blood urea, salivary urea, salivary ammonia and breath NH3, we were able to suggest a biochemical pathway for breath NH3 production. Blood urea is diffused into saliva through salivary glands. Salivary urea is subsequently hydrolysed into ammonia by urease activity. Finally, salivary ammonia evaporates into the gas phase and becomes breath NH3.