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  • Hirvonen, Sami-Pekka (Helsingin yliopisto, 2015)
    Poly(benzimidazobenzophenanthroline) (BBL), which may be doped into a p- and n-type semiconductor, has been chemically modified to enhance its processability. In its pristine form BBL is processable only in some concentrated acids and nitromethane/Lewis acid solutions. The corrosiveness of these solvents and moisture sensitivity of the solutions severely limits the possibilities for the use of BBL as an electroactive material in organoelectronic devices and limit the possibilities for its post synthetic chemical modification. In this work processable BBL derivatives have been prepared using two different approaches i) preparation of block-copolymers by attachment of water soluble polymers on BBL functional chain ends ii) attaching bulky side groups on one of the monomers and using that as a starting material in the polymerization reaction. Short BBLs of DP 10 or 20 were prepared with functional chain ends and monofunctional poly(ethylene oxide) (PEO) or poly(N-isopropylacrylamide) of several different molecular weights were attached at the chain ends. Elemental analysis showed that the extent of chain end substitution varied quite a lot when PEO was used. It was also shown that thermogravimetric analysis (TGA) was not suitable to determine the fraction of PEO in BBL-PEO block-copolymers. However, the extent of chain end substitution using PNIPAM was evaluated using TGA. BBL-PEOs could be processed into aqueous dispersions at concentrations ≥ 1.5 mg/ml by means of ultrasonication, and these dispersions were proven to be colloidally very stable. The dispersions could be used to spin- or drop cast films. At higher concentrations BBL-PEO dispersions were shown to form gels. The reason for the gelling is the packing of the polymer into nano-wire structures which then aggregate into 3D-network. SEM- and cryo-TEM imaging confirmed the existence of wire-type structures. Wire structures and gelation were also observed for aqueous dispersions of pristine BBL. BBL-PNIPAM block-copolymers were found to be indispersible in water with PNIPAM fractions lower than 35 mass %. However, they gelled upon ultrasonication. With higher PNIPAM fractions the polymers were dispersible and did not form gels in any of the studied concentrations. Dispersibility in water and the colloidal stability of BBL-PEOs and BBL-PNIPAMs was attributed to electrostatic stabilization as the particles showed negative zeta-potentials. Dispersible BBL-PNIPAMs were more stable due the high amount of dissociative groups originating from the partial degradation of the amide moieties during the coupling to BBL. One of the monomers used to prepare BBL, 1,4,5,8-naphthalenetetracarboxylic acid 1,8-monoanhydride, was successfully mono- and dibrominated. The bromine was then used as a functional group and replaced either directly with 2-ethyl-1-hexylamine or substituted with azide and reacted with 1-hexyne. The modified monomers were used in preparation of BBL. BBLs bearing either 2-ethyl-1-hexylamine or 4-butyl-1,2,3-triazole groups were found to be sparingly soluble in dimethylsulphoxide and N-methyl-2-pyrrolidone.
  • Salmi, Emma (Helsingin yliopisto, 2015)
    Corrosion is a major global challenge with both economical and technological impacts. The total world-wide costs of corrosion have been evaluated to rise to over 2 000 000 million euros annually. While several methods exist for corrosion protection, atomic layer deposited (ALD) coatings have an advantage in applications where thin, fully conformal, highly precise and well-defined coatings both in composition and thickness are needed. In this work the corrosion protection properties of ALD Al2O3 and Ta2O5 based coatings on low alloy steel were studied. The aim was to increase the general understanding on factors affecting the protective properties and failure mechanisms of the ALD coatings. The protective performance of ALD coatings on steel was improved by focusing on three topics: substrate pre-treatment, optimisation of the ALD coating architecture, and combination of the optimised ALD coatings with layers deposited by other methods. The substrate surface was found to significantly influence the ALD coating performance. Improved protective properties were found on steel samples that were mechanically polished to a lower surface roughness, and efficiently cleaned with H2-Ar plasma in addition to the traditional degreasing with an organic solvent. The smoother surface finish was concluded to be beneficial due to decreased defect formation after the coating deposition upon detachment of loose particles or mechanically fragile sites. The H2-Ar plasma removed organic residues from the steel surface, therefore improving the quality of the first layers of the ALD coating. The performance of the ALD coatings themselves was found to improve when Al2O3 and Ta2O5 were combined to produce Al2O3-Ta2O5 nanolaminate and AlxTayOz mixture coatings. In these coatings Al2O3 provided sealing properties and Ta2O5 the chemical stability, therefore resulting in coatings with better long-term performance than could be achieved with either material alone. Optimisation of the Al2O3-Ta2O5 nanolaminate and AlxTayOz mixture coating architectures further enhanced the protective properties. To further improve the coating-steel interface and to widen the application areas for the ALD based protective coatings, the optimised ALD coating processes were combined with layers deposited with other methods. Firstly, thin filtered cathodic arc sublayers were used to separate the ALD process from the steel surface. This enabled a more precise control of the coating-steel interface and led to improved durability of the ALD coatings. Secondly, pinhole defects in physical vapour and plasma-enhanced chemical vapour deposited hard coatings were sealed with ALD to afford coatings with both good corrosion protection performance and resistance against mechanical wear.
  • Ridderstad, Marianna (Helsingin yliopisto, 2015)
    Studies of ancient monuments and buildings have shown that many of them were astronomically oriented. The examination of the orientations of the structures constructed by past cultures can thus reveal previously unknown details of their astronomical knowledge, calendric practices and religious beliefs. In this thesis, the orientations of two types of structures from prehistoric and early historical Finland were investigated: the Giants Churches (GCs), which are large Neolithic (ca. 1800-3000 BCE) stone enclosures situated mainly on the ancient coast of Ostrobothnia, and the medieval stone churches of Finland (ca. 1300-1550 CE). The results of the studies showed that the axes and gates of the GCs pointed towards the directions of certain solar and lunar events, possibly even indicating the existence of a lunar or lunisolar seasonal pointer calendric system of the type that has been previously suggested for European Neolithic monuments. The small GCs were oriented differently from the large ones, and especially the very largest GCs had orientations towards some of the main solar events of the year. The studies also revealed that the GCs were positioned to face open views towards the eastern and south-eastern horizon, and that the cairns around them were often symmetrically placed with respect to each other and the enclosures of the GCs. The orientations of the stone churches were found to have been mainly towards the sunrises of the equinoxes as given by the various possible definitions of the equinox in medieval times. Part of the orientation distribution could also be related to the sunrises of the Easter Day, and some individual churches may have been targeted towards the sunrises of the feast days of their patron saints. Comparison of the monument orientations from the two very different periods of time and cultures, the Neolithic GC culture and the medieval Finland showed that while there were many similarities in the orientations themselves, the interpretations made of the orientations and their possible related belief systems necessarily have differences. Also, the uncertainties in the interpretations of the orientations of a distant illiterate culture, in this case the Neolithic GC culture, persist. The concrete use of pre-Christian myths in rituals at the time when the medieval Christian churches were at use illustrates the complexity of the situation of the vernacular religion in Finland in historical times. This complexity naturally has an effect on the interpretations made on how the medieval Finnish parish members may have interpreted the observed orientations of the stone churches. Thus, also the interpretations made of the meanings of the orientations in a literate culture relatively close in time, where one has written sources preserved, may bear uncertainties due to the complex situation of the vernacular religious practices and beliefs. The complexity of the religious situation and the related interpretations of the church orientations in medieval Finland indicate the existence of limitations on how the orientations of the Neolithic structures, which are much more distant in time and culture, can and should be interpreted.
  • Al-Hunaiti, Afnan (Helsingin yliopisto, 2015)
    The catalytic oxidation by using transition metal complexes offers attractive opportunities for industrial applications following environmentally benign manufacturing processes. However, the number of such catalytic methods has substantially decreased. In this thesis, we developed and utilized three iron based catalysts (FeIII/thymine-1-acetic acid, FeIII/Phenanthroline, and FeII/Nmethylimidazole) and one organic catalysts (1,2-Di(1-naphthyl)-1,2-ethanediamine (NEDA)). The iron/THA catalyst (iron/thymine-1-acetic acid) is efficiently capable of oxidizing both primary and secondary aliphatic alcohols into their corresponding carbonyl compounds, acids and ketones. The system can also oxidize alkanes with different steric and electronic environment. We also presented a new method for the oxidation of benzylic and aliphatic primary and secondary alcohols using iron-based catalyst, which is [Fe(phen)2Cl2]NO3 (iron/Phenanthroline), with hydrogen peroxide as a terminal oxidant. The easily accessible catalyst (iron/N-methylimidazole) was developed to form dehydrogenative coupling reaction between benzaldehydes and styrenes. The CH activation to produce α,β unsaturated ketones has been also developed. The organic (metal-free) catalyst (1,2-Di(1-naphthyl)-1,2-ethanediamine (NEDA)) has shown to be an efficient catalyst for the oxidation of secondary alcohols with t-BuOOH as a terminal oxidant. Under mild reaction conditions, a secondary alcohol is converted into its corresponding ketone.
  • Lusa, Merja (Helsingin yliopisto, 2015)
    129I, 79Se and 135Cs are among the most important radionuclides in the biosphere safety assessments of the disposal of spent nuclear fuel. The sorption, retention and migration of these nuclides in the surface environment is of importance when the radiation doses for humans and other organisms in the future is considered. In this doctoral thesis the abiotic and biotic factors affecting the retention of iodide (I-), selenite (SeO32-) and cesium (Cs+) in a nutrient-poor boreal bog environment were investigated. Batch sorption experiments were used both for the bog layer samples from the surface moss, subsurface peat, gyttja and clay layers of the bog and for bacteria isolated from the bog. The bacteria isolates belonged to four different phyla: Pseudomonas, Rhodococcus, Burkholderia and Paenibacillus commonly found in the various environments. I- and SeO32- retention in the surface moss, peat, gyttja and clay was found to be strongly linked to the microbial activity found in this bog. Sterilization of the surface moss, peat, gyttja and clay samples significantly reduced the retention of both I- and SeO32- and anoxic conditions reduced the sorption of I-. These results supported the hypothesis that viable microbiota (bacteria/fungi) are necessary for the incorporation of I- into the organic matter and for the retention of SeO32- through microbiotically mediated reduction in the acidic bog environment and that I- is oxidized into I2 and/or HIO prior to its incorporation into the organic matter. In the case of SeO32- the removal from the solution phase presumably takes place via reduction of SeO32- into insoluble Se0 (and possible further reduction to Se2-, which reacts with iron). Some proportion of abiotic reduction of SeO32- in association with sulfide oxidation is possible, but the majority of the reduction is assumed to occur microbiotically. This is supported by the observation that SeO32- removal from the solution was at the same level both under oxic and anoxic conditions, but was decreased as samples were sterilized and incubated under oxic conditions. In addition the bacteria isolated from the bog were found to remove both I- and SeO32- from the solution, although the removal was considerably higher for SeO32-. The behaviour of Cs+ was affected by both abiotic and biotic factors (i.e. pH, clay minerals and bacteria) in the acidic nutrient-poor boreal bog investigated in this thesis. Increase in the pH, increased the sorption of Cs+ in all studied bog layers and highest sorption was observed in the bottom layer of the bog. In this layer, clay minerals, especially illite, were found. Sterilization of the samples decreased the sorption of Cs+, but the difference between sterilized and unsterilized samples was not statistically significant. However the bacteria isolated from the bog were found to remove Cs+ from the solution, though the extend of the removal was significantly lower than that observed for SeO32-. In addition implications on the importance of plant uptake and rhizoidosphere effects of Sphagnum moss on the Cs+ retention in the surface layer of the bog were observed.
  • Avchaciov, Konstantin (2015)
    Rapid technological development motivates the research community to find out new processing technologies for producing materials with unique properties. Production of new materials or improving the existing ones requires development of new methods, which sometimes involves processing under far-from-equilibrium conditions. Usually underlying physical processes, taking place during such processing, are not well known. Understanding them is the key to the enhancement of processing methods. This thesis covers only a tiny part of a huge number of problems existing in the material science. The studies done here could be useful for solving the problem of metallic glass brittleness and for further development of the ion beam technology for controlling magnetic properties of thin films. Discussion on the pathway of the self-propagating high-temperature synthesis in multilayer metallic films was also included in the thesis We studied the effect of ion irradiation on Cu64Zr36 metallic glass by means of molecular dynamics (MD). Low-energy ion irradiation of metallic glass produces damage zones, where the local structure of glass differs from the structure of pristine glass. These changes are independent on ion energy and flux due to the possibility of partial recovery during cascade relaxation. However, the size of the damage zones could be controlled by varying the dose of ions. This makes possible the production of either isolated damaged regions or homogeneously damaged glass. We showed that mechanical properties of the glass strongly depend on the local structure. In damage zones, the specific arrangement of the structural units is destroyed. This promotes the formation of many shear transformation zones in the damaged area, when a mechanical load is applied. It results in enhanced plasticity of the irradiated glass. Our research indicates that ion irradiation could be used for the softening of brittle metallic glasses for preventing formation of cracks in them. Atomistic studies of the reaction pathway in the multilayer Ru/Al films were done to interpret the results from X-ray diffraction measurements. The MD simulations covered the first nanoseconds; at this timescale, no information about the reaction pathway could be obtained from the experimental methods. The MD simulations demonstrated simultaneous Ru dissolution into liquid Al and $B2$ RuAl phase nucleation at the Ru/Al interface. Our results agreed well with experimental observations, and, moreover, helped to refine understanding of the X-Ray diffractograms. We also studied structural modifications of Pt/Co/Pt trilayer films, which could explain appearance of the perpendicular magnetic anisotropy (PMA) after irradiation with Ga+ ions. Molecular dynamics and Monte Carlo (MD-MC) simulations were performed to find changes in the long range order and short range order, associated with ion irradiation. The results of our simulations showed that the separated metal layers containing Pt and Co were intermixed and formed the new solid solution. This solution was chemically disordered at the nanosecond time scale. With combined MD-MC simulations, we showed that the transition between chemically ordered and disordered phases was possible. The fractions of the ordered phases grew monotonously with an ion dose due to the ongoing process of ion-beam mixing. However, assuming the correlation between the magnetic properties of the film and the fraction of the chemically ordered CoPt phase in it, this result cannot explain the disappearance of PMA at the high doses. The strain analysis showed that the Co layer exhibited tensile strain in the lateral direction at the moderate doses, where the PMA was detected. We explained the appearance of strains by changing of the thickness of the hcp-Co layer right inside the trilayer Pt/Co/Pt structure, which was possible due to its partial transformation to the fcc structure. Below the critical size of the hcp layer, the strain inside it appears, which, in our opinion, could cause the appearance of PMA at the moderate doses and the disappearance of PMA at the high doses.
  • Koivisto, Juha (Helsingin yliopisto, 2015)
    The growing number of x-ray examinations being routinely performed on patients using cone-beam computed tomography (CBCT) and multi-slice computed tomography (MSCT) devices have led to an emerging risk of and concern about radiation exposure. Typical CBCT absorbed doses range between 1 7 mGy, and thus values less than 1 mGy can be considered as low dose values. To date, most studies concerning effective dose assessment in the maxillofacial region use anthropomorphic phantoms in combination with thermoluminescent dosimeters (TLD). Recently, MOSFET dosimeters have been considered as a possible alternative to TLDs for in vitro dose assessment. The major benefit of MOSFET dosimeters is their real-time dose measurement capabilities. All 20 MOSFET dosimeters were characterized for CBCT photon energy ranges, dose properties, and organ dose measurements using TLD dosimeters (I). The MOSFET dosimeter energy dependencies were evaluated for two photon energy ranges in order to encompass the typical mean photon energies used in dental radiology. Furthermore, the MOSFET dosimeter uncertainty was assessed by repetitive measurements at different doses. The MOSFET angular sensitivity was investigated using dental photon energies and soft tissue equivalent backscatter material. After MOSFET characterization, a dose measurement setup was developed. The setup comprised 20 MOSFET dosimeters that were placed into the allocated grid holes of an anthropomorphic RANDO phantom. The MOSFET dose measurement setup was validated using two different methods: Monte Carlo simulations and TLD dosimeters. The setup was used for organ and effective dose assessments resulting from supine, prone, and oblique phantom positions in the maxillofacial region using a novel cone beam computed tomography (CBCT) device and from two conventional dental CBCTs and one multi-slice computed tomography (MSCT) device. All MOSFET dosimeters demonstrated a statistically insignificant energy dependency when using typical dental photon energies. Furthermore, the MOSFETs demonstrated excellent dose linearity and resulted in similar absorbed organ doses to those attained in the TLD measurements. The required low dose limit was achieved by averaging the values attained using eight MOSFET exposures. The MOSFET dosimeter angular dependency demonstrated a 5% standard deviation from the mean sensitivity value. The MOSFET dose assessment setup demonstrated similar effective doses to those attained using the Monte Carlo simulations and TLD measurements. Effective dose was strongly dependent on the vertical phantom positioning and minor vertical changes resulted in dose increases of up to 16%. The dose measurements acquired using the same FOV on all CBCT and MSCT devices 3 resulted in the following values: Planmed Verity CBCT scanner 247 μSv in supine, 192 μSv in prone, and 134 μSv in oblique position, the ProMax 3D MAX CBCT 168 μSv, i-CAT Next Generation 170 μSv, Philips Brilliance 64 MSCT 781 μSv. The results of this study demonstrate that the mean photon energy dose dependency corrections are not required in typical dental energy ranges. Furthermore, averaging eight MOSFET exposures attained typical TLD low dose values. Due to their variation in angular sensitivity, MOSFET dosimeters should always be calibrated in clinical settings for beam geometry and the angular range of the CBCT exposure. Based on the results of the Monte Carlo simulations and TLD measurements, the MOSFET measurement setup constitutes a feasible method for low dose assessment in CBCT and MSCT devices in the maxillofacial region. When using the same FOV and exposure parameters, the effective doses obtained in the supine position were 29% higher (247 μSv) than those obtained in the prone position (192 μSv). When the prone and oblique positions were compared, the observed effective dose in the oblique position was 30% lower. Thus, optimal patient positioning can reduce the dose and subsequently minimize the radiation risks. In summary, the fast and dependable low- dose measurement setup presented in this thesis provides an effective means of CBCT dose assessment using a variety of exposure parameters, patient positioning, and FOVs. Further, the setup presented in this study can be used to test and develop CBCT devices that would subsequently produce lower effective doses. Since radiologists commonly only have access to the radiation output of different devices, they lack the possibility to assess the actual effective dose. Therefore, the setup developed in this thesis can also be utilized to increase the awareness of the lifetime radiation risks amongst radiologists leading to dose reduction
  • Sahlstedt, Elina (Helsingin yliopisto, 2015)
    Fluid evolution in fractured bedrock at the Olkiluoto site in Finland was investigated by examining the stable oxygen and carbon isotope composition of secondary calcite and sulfur isotope composition of secondary sulfide minerals. The study site, located on the western coast of Finland, is the planned site for the geological disposal of spent nuclear fuel. Therefore, hydrogeochemical conditions in the deep bedrock are of special interest. The aim of this study was to characterize the latest fracture fillings and use the isotope composition of these fillings as a proxy of past geochemical conditions. In addition to traditional stable isotope analyses, sulfur and carbon isotope variations in the samples were analysed in situ using secondary ion mass spectrometry (SIMS). The results demonstrated a high variability in isotopic composition of mineral grains within a few tens of micrometers. The study material consists of drill core sections hosting fracture infills, obtained from water conducting fractures in hydrologically active zones in the bedrock. Fracture filling calcites were grouped into five groups according to calcite morphology, mineral associations and their relative position in the fracture sequence. The latest fracture fillings were identified from the surfaces of open fractures as clear, platy or euhedral fillings (Group 1) which occasionally contained minor amount of silicate inclusions (Group 2). Massive, older calcite fillings were separated into three groups (Groups 3-5) representing high temperature fluid circulation. Group 3 fillings preceded the late-stage calcite fillings and are interpreted to be associated with a Paleozoic (541-252 Ma) thermal event. Group 5 and Group 4 fillings represent the earliest hydrothermal events in the bedrock, likely related to the rapakivi granite and diabase intrusions of Mesoproterozoic (1600-1000 Ma) age. A characteristic feature of the late-stage fillings (Group 1, 2) is small-scale variations in stable isotope compositions, indicating the influence of microbial processes on groundwater conditions. Furthermore, a comparison with the groundwater data showed that the late-stage fillings are generally not in isotopic equilibrium with the current groundwaters. Based on the results obtained in this work, the following characteristics of the paleogroundwaters representing Group 1-2 mineralizations can be identified: Transitions between geochemically distinct environments can be identified in the shallow bedrock, at depths < 100 m. The upper ca. 30 m were characterized by bacterial sulfate reduction (BSR) and depths < 54 m characterized by methanogenetic activity. A narrow zone existed at the depths of ~34-54 m, where BSR was accompanied by minor methanotrophic activity. After the precipitation of calcite in Groups 1-2, the methanic environment in the depth range of ~60-300 m has been replaced by sulfidic conditions. Changes to this environment were most likely associated with the infiltration events related to deglaciation events and glacioisostatic land movements, which have occurred repeatedly during the Quaternary period (< 2.58 Ma).
  • Mäkelä, Minja (Helsingin yliopisto, 2015)
    The focus of this thesis is on observations of star-forming globules that have cometary morphologies and are associated with or located in HII regions. Our study presents a sample of globules at different size-scales and investigates their structure, formation mechanism, and star formation using observations made at infrared (IR) and millimeter (mm)-wave wavelengths. The studied globules offer examples of associated low-mass star formation triggered by the influence of an HII region. Infrared, mm, and radio observations are fundamental in detecting signs of on-going star formation embedded inside dusty, dense globules. The embedded young stellar objects (YSOs) are detected directly in the IR and indirectly via jets and outflows in shocked H2 and mm-wave CO observations. This thesis is a case study of different types of globules. Cometary globules (CGs) represent the classical globules with sizes of ~0.1-1 pc and masses of ~10 M_sun, and the so-called globulettes are an order of magnitude smaller than CGs. We observe on-going low-mass star formation in both types of globules. Compression associated with radiation from the hot central star (via so-called radiation driven implosion, RDI) is suggested as the cause. The star formation in the globulettes may result in low-mass stars and/or possibly in free-floating planetary-mass objects. Five publications are included, two of which discuss two cometary globules, CG 1 and CG 2, in the Gum Nebula. Earlier studies have discovered a pre-main sequence star outside the head of CG 1, and we find second generation star formation in the head of CG 1 which contains an embedded object and a large outflow cavity. Two near-IR (NIR)-excess objects are seen in the direction of CG 1 tail and one in the head of CG 2. Our original goal was to study if the CG formation mechanism is triggered by supernovae shocks or by RDI, but based on the observations, we cannot fully determine between the two. The next two papers discuss mm-wave and NIR observations of small globulettes in the Rosette Nebula. Globulettes have not been studied in the NIR before this. The globulettes are dense and they are irradiated by ultraviolet radiation from the central Rosette cluster which causes bright fluorescent H2 rims in the globulettes in the NIR. The globulettes are observed along with long pillars of gas extending toward the central cluster, so-called elephant trunks. These together form a system that expands at the same velocity from the central cluster. Star formation is on-going in the largest Rosette globulette observed in this study and in the tip of one elephant trunk. The final paper reports NIR observations of two globules on the inner molecular shell of the Rosette Nebula. They have fluorescent H2 rims similar to the globulettes. A NIR-excess object is located in the direction of one globule and the other contains an embedded YSO. The YSO drives an outflow seen in shocked H2. Imaging in the optical and NIR suggest that the outflow is parsec-scaled and interacts with the shell of the Rosette Nebula. The globules we observed are subject to ionizing radiation from OB stars, which photo-erodes the globules and drives the RDI process. Star formation takes place in all globule types we observed, and the second generation star in the head of CG 1 is indicative of triggered star formation. The first detailed NIR and mm-wave observations of the Rosette Nebula globulettes are presented here. Star formation is detected in one globulette and in one of the associated elephant trunks, but we cannot determine if the globulettes can collapse to directly form brown dwarfs or planetary-mass objects. Future observations using ALMA and other high-resolution instruments are needed in determining the physical and chemical structure of the globulettes.
  • Numminen, Elina (Helsingin yliopisto, 2015)
    A central goal in science is to learn from observations about the process that generated the observations. The principles of statistical inference describe a systematic approach for such learning, in which prior information, knowledge about the underlying mechanisms and the observed data can be combined. In practice, lack of mathematical tractability, huge amounts of missing information, and the sensitivity of the conclusions on the assumptions made represent genuine challenges in the theoretically sound statistical framework. Statistical studies on the dynamics of infectious diseases easily face all these problems at once. In the thesis we present case-studies in which the datasets on bacterial diversity, mostly on Streptococcus pneumoniae, described in terms of either genotypes or serotypic strains, are analysed. By utilizing the machinery of modern computational statistics different strategies for inference are formulated, which aim to take the special characteristics of each of the studied problem into account, while overcoming the previously mentioned challenges in computational studies. For instance, an approximate Bayesian computation scheme is formulated for analysing cross-sectional strain prevalence data and an importance sampling scheme for analysing transmission trees with a priori known complex features. The obtained results unravel the mechanisms of seasonality in pneumococcal carriage, consequences of the host population structure and the nature of within-host competition between the bacterial strains.
  • Kempa, Dominik (Helsingin yliopisto, 2015)
    This thesis studies efficient algorithms for constructing the most fundamental data structures used as building blocks in (compressed) full-text indexes. Full-text indexes are data structures that allow efficiently searching for occurrences of a query string in a (much larger) text. We are mostly interested in large-scale indexing, that is, dealing with input instances that cannot be processed entirely in internal memory and thus a much slower, external memory needs to be used. Specifically, we focus on three data structures: the suffix array, the LCP array and the Lempel-Ziv (LZ77) parsing. These are routinely found as components or used as auxiliary data structures in the construction of many modern full-text indexes. The suffix array is a list of all suffixes of a text in lexicographical order. Despite its simplicity, the suffix array is a powerful tool used extensively not only in indexing but also in data compression, string combinatorics or computational biology. The first contribution of this thesis is an improved algorithm for external memory suffix array construction based on constructing suffix arrays for blocks of text and merging them into the full suffix array. In many applications, the suffix array needs to be augmented with the information about the longest common prefix between each two adjacent suffixes in lexicographical order. The array containing such information is called the longest-common-prefix (LCP) array. The second contribution of this thesis is the first algorithm for computing the LCP array in external memory that is not an extension of a suffix-sorting algorithm. When the input text is highly repetitive, the general-purpose text indexes are usually outperformed (particularly in space usage) by specialized indexes. One of the most popular families of such indexes is based on the Lempel-Ziv (LZ77) parsing. LZ77 parsing is the encoding of text that replaces long repeating substrings with references to other occurrences. In addition to indexing, LZ77 is a heavily used tool in data compression. The third contribution of this thesis is a series of new algorithms to compute the LZ77 parsing, both in RAM and in external memory. The algorithms introduced in this thesis significantly improve upon the prior art. For example: (i) our new approach for constructing the LCP array in external memory is faster than the previously best algorithm by a factor of 2-4 and simultaneously reduces the disk space usage by a factor of four; (ii) a parallel version of our improved suffix array construction algorithm is able to handle inputs much larger than considered in the literature so far. In our experiments, computing the suffix array of a 1 TiB file with the new algorithm took a little over a week and required only 7.2 TiB of disk space (including input and output), whereas on the same machine the previously best algorithm would require 3.5 times as much disk space and take about four times longer.
  • Zhou, Luxi (Helsingin yliopisto, 2015)
    Aerosols are common air pollutants that pose serious threats to health. They also impact the Earth’s climate by interacting with solar radiation and altering cloud properties. One important phenomenon associated with the atmospheric aerosol system is new particle formation. This thesis is devoted to study the processes related to new particle formation as well as aerosol precursor gases in the boundary layer, where exchanges between the surface and the atmosphere take place. Model SOSAA, a one-dimensional transport model with detailed chemistry and aerosol microphysics, was constructed, tested and used as the main tool. Variations in the main biogenic volatile organic compounds (BVOCs), OH and H2SO4 across different environment were analysed. The simulated concentrations of main emitted organic compounds in two rural sites agree well with the observations. Due to missing OH reactivity in rural environment, the concentration of OH at Hyytiälä is overestimated. In contrast, the concentration of OH is likely underestimated in an urban environment due to missing production from HONO. H2SO4 production is underestimated at every site studied. New particle formation was studied in two phases: nucleation and growth. Large uncertainties are introduced to nucleation rates when calculating dependencies based on sulphuric acid alone. The oxidation products of monoterpenes by OH are shown not to be a suitable proxy for nucleation at either the urban site in Beijing or the rural site at Hyytiälä in summer. While they mainly contribute to the growth of particles at the rural site in Hyytiälä, the oxidation products of monoterpenes might only have major role in particle growth at Manitou during the evening. The rapid particle growth at Manitou in the daytime is possibly related to the oxidation products of 2-Methyl-3 Buten-2-Ol (MBO) by OH or any compound that has similar concentration and diurnal variation to the oxidation product of MBO by OH. The last model study assessed the climatic impact of aerosols in a hypothetic scenario with high atmospheric methane loading. The impact associated with aerosols and the change in atmospheric composition is shown to be as large as the impact due to methane itself. A NOx mitigation strategy was evaluated by SOSAA as effective to remove methane but the side product of hazardous tropospheric ozone makes the method unfavourable in real life. The process-based model SOSAA developed during this doctoral study is a useful tool for atmospheric research since it provides flexibility in time and space. The results call for further research into the ultimate mechanisms controlling nucleation and particle growth. This thesis also identifies knowledge gaps in the related precursor gases and encourages further studies in fields such as emission inventory of volatile organic compounds, sulphuric acid production, and atmospheric oxidation cycle.
  • Kaasalainen, Touko (Helsingin yliopisto, 2015)
    The number of computed tomography (CT) examinations has increased in recent years due to developments in scanner technology and the increased diagnostic capabilities of CT. Nowadays, CT has become a major contributor to accumulated radiation doses from radiological examinations, accounting for approximately 60% of the overall medical radiation dose in Western countries. Ionizing radiation is generally considered harmful to health, and current knowledge suggests that the risk for stochastic effects increases linearly with radiation dose. Minimizing patient doses in CT requires effective optimization practices, including both technical and clinical approaches. CT optimization aims to reduce patients exposure to radiation without compromising image quality for diagnosis. The aim of this dissertation was to explore the feasibility of using anthropomorphic phantoms and metal-oxide-semiconductor field-effect transistors (MOSFETs) in CT optimization and patient dose measurements, and to study CT optimization in versatile clinical situations. Specifically, this thesis focused on studying the effects of patient centering on the CT scanner isocenter by determining changes in patient dose and image quality. Additionally, as a part of this thesis, we constructed and optimized ultralow-dose CT protocols for craniosynostosis imaging, and explored different optimization methods for reducing radiation exposure to eye lenses. Moreover, fetal radiation doses were assessed in the most typical CT examinations of a pregnant woman which also place the fetus at the highest risk for ionizing radiation-induced health detriments. Anthropomorphic phantoms and MOSFET dosimeters proved feasible in CT optimization even with the use of ultralow-dose levels. Patient vertical off-centering posed a common and serious problem in chest CT, as a majority of the scanned patients were positioned below the isocenter of the CT scanner, which significantly affected both radiation dose and image quality. This exposes the radiosensitive anterior surface tissues, including the breasts and thyroid gland, to greater risk. Special attention should focus on pediatric patients in particular, as they were typically miscentered lower than adults were. The use of constructed ultralow-dose CT protocols with model-based iterative reconstruction can enable craniosynostosis CT imaging with sufficient image quality for diagnosis with an effective dose of less than 20 μSv for the patient. This dose level was approximately 85% lower than the level used in routine CT protocols in the hospital for craniosynostosis, and was comparable to the radiation exposure of a plain-skull radiography examination. The most efficient method for reducing the dose to the eye lens proved to be gantry tilting, which leaves the eye lenses outside the primary radiation beam, thereby reducing the absorbed dose up to 75%. However, measurements with two different anthropomorphic head phantoms showed that patient geometry significantly affects dose-reduction capabilities. If lenses can only partially be cropped outside the primary beam, organ-based tube current modulation or bismuth shields may also be used for reducing the dose to the lenses. Based on the measured absorbed doses in this thesis, the radiation dose to the fetus poses no obstacle to an optimized CT examination with a medically necessary indication. The volumetric CT dose index (CTDIvol) provides a rough estimate of the fetal dose when the uterus is in the primary radiation beam, although the extent of the scan range has a substantial effect on the fetal dose. The results support the conception that when the fetus or uterus is not in the scan range, the fetal dose is affected mainly by the distance from the scan range.
  • Jokinen, Tuija (Helsingin yliopisto, 2015)
    We live in a world full of aerosols and witness their existence constantly. Changes in visibility, road dust and pollen filling the air in the spring time and even dosing some medicines are all related to aerosols. The most important aspect for this thesis is however, the formation of aerosol precursor molecules and clusters and their possible effects on aerosol properties. Different types of aerosols e. g. organic and inorganic, ice and pollen, biogenic and anthropogenic, when acting as cloud condensation nuclei (CCN), can change the optical properties of clouds and thus have different climate effects via changes in precipitation or cloud cover. Also the mechanism how the small cloud seeds are formed can have a major effect on the cloud properties. Clouds reflect and scatter radiation cooling the atmosphere but to this day aerosol effects still form the largest uncertainty in estimates of the climate of the future. Low-volatility compounds in the ambient air are the most important components in both aerosol formation and their growth to sizes that can affect cloud properties such as their reflectivity. The vapours in the atmosphere form around half of the first precursors of aerosol particles via nucleation, still molecular in size. The rest is released directly into the air e.g. by the traffic or from the oceans as sea salt. Neutral molecular size precursor substituents are difficult to detect because they lack electric charge and their concentrations rarely exceed the detection limits of the used measurement instruments. This is one of the reasons why the first steps of nucleation process are still partly unsolved after decades of research. This thesis concentrates first in development of selective methods and ultrasensitive instrumentation for the detection of acidic aerosol precursor molecules and clusters. These compounds include sulphuric acid, which is known to be highly important precursor for new particle formation. This thesis presents the first ambient measurements with the new instrumentation and even though sulphuric acid was detected in relative high concentrations during a particle formation event, no ambient cluster formation was yet observed. The same instrumentation was further used in an ultraclean chamber experiment were sulphuric acid and dimethyl amine formed growing clusters and they were detected from the smallest clusters all the way up to ~2 nm size. These compounds are likely to dominate the new particle formation with low-volatility organic compounds. Tens of thousands of volatile organic compounds (VOC) are emitted in the atmosphere by terrestrial vegetation, marine environments and anthropogenic sources, making the search for the meaningful compounds for new particle formation extremely difficult. In this thesis a new group of extremely low-volatility organic compounds (ELVOC) from terpene oxidation are introduced. They form a large source of secondary organic aerosol (SOA) and might help explaining the former big gap between the measured and the modelled SOA loads in the atmosphere. Formation of these compounds from RO2 radicals via rapid autoxidation process to stable molecules is also studied in details in laboratory experiments. This thesis also utilizes a global modelling framework, where the measurement results are applied. According to this thesis, ELVOC in particular are in crucial role when estimating SOA and CCN formation in the air. All together this thesis is a comprehensive study of both organic and inorganic low-volatility precursor molecules and clusters in the atmosphere, from their origin, formation mechanisms, and measurement techniques to their possible effects on climate now and in the future.
  • Kangasluoma, Juha (Helsingin yliopisto, 2015)
    Atmospheric aerosols exhibit the largest uncertainties in the radiative forcings of the Earth s climate. A large fraction of the uncertainties originates from the aerosol-cloud in-teractions, a process which is not understood completely. Understanding the processes related to aerosol formation and growth will help to narrow down these uncertainties and understand the anthropogenic fraction of the radiative forcings. Atmospheric new particle formation creates a large fraction of the particles present in the atmosphere. To understand the process thoroughly, direct measurements of the par-ticle concentration and chemical composition are needed. This need has pushed the in-strument development forward, allowing measurements which were not possible five years ago: a direct measurement of the concentration and composition of sub-3 nm particles. The purpose of this thesis was to develop methods to calibrate the instruments to reliably measure sub-3 nm particles. We developed an experimental setup to reproducibly generate well-characterized sub-3 nm particles in the laboratory, with the particular aim to characterize particle counters. During the course of the work the particle generation meth-ods were modified to provide test aerosols smaller than 3 nm, of which chemical composi-tion was monitored simultaneously with a mass spectrometer. Together with the modifica-tion of the generators, commercial fine particle counters were shown to be capable of sub-2 nm particle detection Controlling the properties of the generated particles was found to be extremely important in the measurement of sub-3 nm particles. With the various test particles we studied the importance of the particle size, charging state and chemical composition on their detection, as well as the importance of the particle counter working fluid on the de-tection. The chemical composition of the particles was the most important factor determin-ing the smallest detectable size in the sub-3 nm size range. One of the particle counters, the Particle Size Magnifier (PSM) was characterized more in depth at low pressure conditions and various operation temperatures, providing in depth understanding on the instrument operation. The results provided key aspects on how the instrument should be operated in field experiments in order to obtain reliable data. In laboratory conditions the inversion routine of the particle PSM was experimentally verified against a high resolution differential mobility analyzer and an electrometer. The results of this thesis provide basic knowledge on sub-3 nm particle generation and detection. The utilization of several generation techniques and test aerosols of differ-ent chemical composition, the operation of sub-3 nm particle detectors was improved along with a more in-depth understanding on the parameters governing the particle - vapor interactions. The laboratory instrumentation used in this thesis offer tools for chemical (composition) and physical (electrical mobility, charging state) characterization of the sub-3 nm particles. Overall this thesis improved the methods dealing with sub-3 nm particles from their generation to characterization, and to their detection. The methods are directly applicable to other fields of nanomaterial production and characterization, as well as envi-ronmental and industrial nanoparticle monitoring.
  • Soto, Tomás (Helsingin yliopisto, 2015)
    The homogeneous Besov spaces B(s,p,q) and the homogeneous Triebel-Lizorkin spaces F(s,p,q) are two scales of function spaces on the Euclidean space that include the standard and fractional-order Sobolev spaces, and arise naturally in the contexts of e.g. partial differential equations and interpolation theory. In the first article presented in this thesis (joint work with H. Koch, P. Koskela and E. Saksman), we characterize the homeomorphisms of the Euclidean space that induce bounded composition operators on the Besov spaces whose norms are invariant under a scaling change of variable, i.e. where sp equals the dimension of the underlying space, for most indices in the smoothness range 0 < s < 1. We also establish similar results in the setting of certain more general metric measure spaces. In the second article (joint work with M. Bonk and E. Saksman), we present a new characterization of the Triebel-Lizorkin spaces for most indices in the smoothness range 0 < s < 1 in the setting of doubling metric measure spaces, and use the characterization to expand on an earlier result by Koskela, Yang and Zhou concerning the bounded composition operators on the scaling invariant Triebel-Lizorkin spaces. We also establish results concerning general Sobolev-type embeddings and complex interpolation for these function spaces in the generality of doubling metric measure spaces. In the third article, we establish several characterizations of certain larger scales of function spaces on the Euclidean space introduced by Yang and Yuan. One of these characterizations can in particular be applied in the setting of more general metric measure spaces.
  • Hänninen, Timo (Helsingin yliopisto, 2015)
    Controlling integral operators by dyadic model operators, and studying the boundedness of dyadic operators on Lebesgue spaces are central themes in dyadic harmonic analysis. This dissertation consists of an introductory part and five articles contributing to these themes. Many operators of harmonic analysis can be dominated by positive dyadic operators by using Lerner's median oscillation decomposition. In the first and fifth article, we extend this decomposition to Banach space valued functions and non-doubling measures. Dyadic shifts and paraproducts are dyadic model operators for Calderón-Zygmund operators. In the second article, we study the boundedness of these operators on unweighted Lebesgue spaces in an abstract operator-valued setting. We prove that operator-valued dyadic shifts are bounded, and we characterize the boundedness of operator-valued dyadic paraproducts. Furthermore, we extend Hytönen's dyadic representation theorem, which states that every Calderón-Zygmund operator can be represented by dyadic shifts and paraproducts, to the operator-valued setting. In the third article, we characterize the boundedness of linear and bilinear positive dyadic operators from a weighted Lebesgue space to another. We consider the case that the Lebesgue exponent of the range side is strictly less than the Lebesgue exponent of the domain side. We show that, in this range of the exponents, the Sawyer testing condition is insufficient for the boundedness. We introduce a sequential testing condition, of which the Sawyer testing condition can be viewed as an endpoint case, and prove that this testing condition is both sufficient and necessary for the boundedness. No characterization in the bilinear case was available until this article. Furthermore, we show that the sequential testing condition is necessary for the boundedness of any positive linear or bilinear operator, and hence it may be helpful in charactering the boundedness of other operators as well. In the fourth article, we characterize the boundedness of positive dyadic operators from a weighted Lebesgue space to another in an abstract operator-valued setting. The purpose is to understand which kind of testing condition is needed in this setting. We prove that an operator-valued positive dyadic operator is bounded if and only if the operator and its adjoint are each bounded on the class of all functions localized on dyadic cubes and taking values on a unit sphere. Furthermore, we show that the boundedness on unweighted Lebesgue spaces is characterized by an endpoint case of this condition. We work directly with Lebesgue spaces, without using interpolation between endpoint spaces. In the second article, we give new (in our opinion simple) proofs for the key tools that we use: decoupling inequality for martingale differences and a variant of Pythagoras' theorem for Lebesgue spaces.
  • Niinimäki, Teppo (Helsingin yliopisto, 2015)
    Bayesian networks are probabilistic graphical models, which can compactly represent complex probabilistic dependencies between a set of variables. Once learned from data or constructed by some other means, they can both give insight into the modeled domain and be used for probabilistic reasoning tasks, such as prediction of future data points. Learning a Bayesian network consists of two tasks: discovering a graphical dependency structure on variables, and finding the numerical parameters of a conditional distribution for each variable. Structure discovery has attracted considerable interest in the recent decades. Attention has mostly been paid to finding a structure that best fits the data under certain criterion. The optimization approach can lead to noisy and partly arbitrary results due to the uncertainty caused by a small amount of data. The so-called full Bayesian approach addresses this shortcoming by learning the posterior distribution of structures. In practice, the posterior distribution is summarized by constructing a representative sample of structures, or by computing marginal posterior probabilities of individual arcs or other substructures. This thesis presents algorithms for the full Bayesian approach to structure learning in Bayesian networks. Because the existing exact algorithms only scale to small networks of up to about 25 variables, we investigate sampling based, Monte Carlo methods. The state-of-the-art sampling algorithms draw orderings of variables along a Markov chain. We propose several improvements to this algorithm. First, we show that sampling partial orders instead of linear orders can lead to radically improved mixing of the Markov chain and consequently better estimates. Second, we suggest replacing Markov chain Monte Carlo by annealed importance sampling. This can further improve the accuracy of estimates and has also other advantages such as independent samples and easy parallelization. Third, we propose a way to correct the bias that is caused by sampling orderings of variables instead of structures. Fourth, we present an algorithm that can significantly speed up per-sample computations via approximation. In addition, the thesis proposes a new algorithm for so-called local learning of the Bayesian network structure. In local learning the task is to discover the neighborhood of a given target variable. In contrast to previous algorithms that are based on conditional independence tests between variables, our algorithm gives scores to larger substructures. This approach often leads to more accurate results.
  • Franti, Lasse (Helsingin yliopisto, 2015)
    The gauge/gravity duality connects the dynamics of gravity theories in the bulk with the dynamics of field theories on the boundary. In this thesis we introduce two thermalization scenarios and investigate them using a suitable holographic description. We will first study the thermalization of equal-time correlators and entanglement entropy in a hyperscaling violating AdS-Lifshitz-Vaidya metric. This work verifies the agreement between numerical procedures and preceding analytical predictions and generalises the previous studies of thermalization in this kind of situations. In the latter part we will use the duality to describe the quark-qluon plasma created in heavy ion collisions. The anisotropic plasma is modelled by introducing anisotropies into the source on the gravity side and letting them evolve according to the equations of motion. The boundary dynamics is extracted by finding the boundary stress-energy tensor. The results agree with the conventional models. The situations considered here are rather simple but this work demonstrates the applicability of holography in the anisotropic case.
  • Kajos, Maija (Helsingin yliopisto, 2015)
    Vast amount of volatile organic compounds (VOCs) are emitted into the atmosphere from various natural and manmade sources. VOCs have an important role in the atmospheric chemistry. They participate in ozone production in the planetary boundary layer and affect the oxidation capacity of the atmosphere. VOCs also contribute to the formation and growth processes of atmospheric aerosol particles, which, once large enough, can act as a cloud condensation nuclei (CCN) and influence the climate by altering the properties of clouds. Globally, VOC emissions from forest vegetation are dominating over the other sources. The circumpolar boreal forests cover more than 35% of the Earth s total forested area, making it one of the biggest biomes on planet. This thesis focuses on the biogenic VOCs in the boreal forests with regard to their shoot scale emissions to their role in the atmosphere. First, the VOC emissions of two different Larix species, L. cajanderi and L. sibirica, were measured and reported quantitatively for the first time. Larix species are the predominant trees in large parts of the Siberian forests, where the climate is too harsh for other tree species to grow. The emissions of both examined Larix species were dominated by monoterpenes similarly to other tree species with comparable emission potentials. Second, a protocol for proton transfer reaction mass spectrometer (PTR-MS) was developed for calibration and data processing of long-term and stand-alone VOC measurements. The reliability of this protocol was tested by comparing simultaneous VOC measurements of two PTR-MS and two gas chromatograph mass spectrometers (GC-MS). The detection of five compounds was analyzed in depth and strengths and weaknesses of the measurements were highlighted. Third, the increase in biogenic VOC and CCN concentrations was investigated in connection with the global warming. This was done by analyzing long-term data of concentrations and compositions of aerosol particles and their biogenic precursor VOCs in different environments. A negative aerosol-climate feedback, driven by the increase of BVOC emissions due to climate warming, was hypothesized and found.