Browsing by Issue Date

Sort by: Order: Results:

Now showing items 1-20 of 872
  • Mehtälä, Juha (Helsingin yliopisto, 2015)
    Continuous-time Markov processes with a finite state space can be used to model countless real world phenomena. Therefore, researchers often encounter the problem of estimating the transition rates that govern the dynamics of such processes. Ideally, the estimation of transition rates would be based on observed transition times between the states in the model, i.e., on continuous-time observation of the process. However, in many practical applications only the current status of the process can be observed on a pre-defined set of time points (discrete-time observations). The estimation of transition rates is considerably more challenging when based on discrete-time data as compared to continuous observation. The difficulty arises from missing data due to the unknown evolution of the process between the actual observation times. To be able to estimate the rates reliably, additional constraints on how they vary in time will usually be necessary. A real world application considered in this thesis involves the asymptomatic carriage state (colonisation) with the bacterium \textit{Streptococcus pneumoniae} (the pneumococcus). The pneumococcus has over 90 strains and for understanding the dynamics of the pneumococcus among humans it is important to understand within-host competition between these strains. Research questions regarding competition in this thesis are: does colonisation by one serotype protect from acquisition of other serotypes and is clearance affected by concurrent colonisation by other serotypes? A question regarding the implication of competition to pneumococcal dynamics after vaccination is also of interest. In addition, vaccine protection may be heterogeneous across individuals, leading to a question about how well such vaccine protection can be estimated from discrete-time data. When only discrete-time observations are available, the decision when to measure the current status of the process is particularly important. With measurements that are temporally apart from each other, information about the state of the process at one point does not give information about the state at the other points. When measurements are very close to each other, knowing the state at one point bears information about the state at other, temporally close points. This thesis addresses the estimation of transition rates based on repeated observations of the current status of an underlying continuous-time Markov process. Applications to actual data concern the process of pneumococcal colonisation. Optimal study designs are considered for improved future studies of similar type, applications including but not limited to pneumococcal colonisation studies.
  • Loman, Tina (Helsingin yliopisto, 2015)
    Health behaviours are important to prevention and public health. Health behaviours include usually food habits, physical activity, drinking, smoking and sleeping. Improving health behaviours help reduce risks for several major chronic diseases and mortality. Food habits and physical activity play a key role in reducing weight gain and related disease risk. Health behaviours are socially patterned and they vary between socioeconomic groups, and contribute to inequalities in health. In order to reduce socioeconomic differences in health, novel evidence is needed of changes in socioeconomic differences of health behaviours as well as reasons behind the socioeconomic differences. The main aim of this study was to examine socioeconomic differences in food habits, physical activity and weight gain, and their changes over time among middle-aged female and male public sector employees. Specific aims were to examine first changes in occupational class differences in food habits and second in physical inactivity and activity during a follow-up of 5-7 years, considering the effects of covariates. The third specific aim was to examine the association between weight gain and multiple socioeconomic indicators. This study is part of the Helsinki Health Study (HHS). The baseline data were collected by questionnaire surveys in 2000, 2001 and 2002 (n=8 960, response rate 67%). Mail surveys were sent to employees of the City of Helsinki aged 40-60 years. The follow-up survey data were collected in 2007 among the baseline respondents (n=7 332, response rate 83%). For data analysis general linear models, logistic regression analysis and the relative index of inequality were used. In many food habits, there was a hierarchical order according to occupational class, i.e. those in higher occupational classes used more often the studied food item than those in lower classes. In some food habits, there was a reverse hierarchical order and in some food habits there were no socioeconomic differences. Occupational class differences largely remained stable over the follow-up in the food habits. At baseline, there were no occupational class differences in leisure-time physical activity, but over the follow-up physical activity increased among women with the highest occupational class and decreased among men with the lowest occupational class, suggesting the emergence of occupational class differences at follow-up. The covariates (age, marital status, body mass index physical and mental health functioning, employment status) did not substantially affect the observed occupational class differences in leisure-time physical activity at follow-up. Among women and men, socioeconomic differences were observed in at least 5 kg weight gain, and current economic difficulties showed the strongest association with weight gain. Socioeconomic differences largely remained stable over the 5-7 year follow-up in food habits, whereas in leisure-time physical activity differences emerged. There were clear differences in weight gain by economic difficulties. Thus, there is a continuous need for reducing socioeconomic inequalities in the studied health behaviours. Healthy behaviours should be promoted in particular among those in lower occupational classes and those with economic difficulties.
  • Xiong, Jie (Helsingin yliopisto, 2015)
    A general inductive probabilistic framework for clustering and classification is introduced using the principles of Bayesian predictive inference, such that all quantities are jointly modelled and the uncertainty is fully acknowledged through the posterior predictive distribution. Several learning rules have been considered and the theoretical results are extended to acknowledge complex dependencies within the datasets. Multiple probabilistic models have been developed for analysing data from a wide variate of fields of application. State-of-art algorithms are introduced and developed for the model optimization.
  • Karjalainen, Erno (Helsingin yliopisto, 2015)
    This thesis combines anion responsive polymeric ionic liquids (PILs) with thermoresponsive polymers. The polymers have been synthesized with controlled radical polymerization methods. A water-insoluble PIL was used as a macro-chain transfer agent in synthesis of block copolymers with poly(N-isopropyl acrylamide) (PNIPAm). PNIPAm chains of various lengths were grown to the same PIL-block. These polymers show a lower cirical solution temperature (LCST) type behavior, typical to PNIPAm. The PIL block and the PNIPAm block interact strongly, no phase transition can be observed for the block copolymers with short PNIPAm chains. The block copolymers form complex aggregates in water. The hydrophobic PIL-homopolymer can be used to make stable particles in salt free water. Also triblock copolymers with a long central PNIPAm block and short water soluble PIL blocks were synthesized. These polymers also show interactions between the PIL and PNIPAm blocks. This can be seen for example as reduced enthalpy of phase transition for the triblock copolymers compared to the PNIPAm homopolymer. The triblock copolymers form complex aggregates at elevated temperatures. The LCST-type phase transtiton of weakly cationic poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) can be modified with bis(trifluoromethane)sulfonamide (NTf2) ions. The presence of NTf2 induces also an upper critical solution temperature (UCST) type transition for PDMAEMA, if the polymer is charged enough. NTf2 turns PDMAEMA to a stronger base, presumably due to the effective screening of charges. NTf2 induces an UCST-type transition for strong polycations in the presence of an added electrolyte. The phase behavior of the polycation-NTf2 system can be influenced by addition of sodium chloride. Similar transition can also be induced by trifluoromethanesulfonate (OTf), though OTf is needed in much higher concetrations. This allows the use of OTf as the only salt. The NTf2-polycation interactions influence the phase behavior of copolymers of N-isopropyl acrylamide (NIPAm) and strongly cationic (3-acrylamidopropyl) trimethylammonium chloride (AMPTMA). With low AMPTMA content, the copolymers show LCST-type behavior in the presence of NTf2 and a copolymer with high AMPTMA-content shows UCST-type behavior. If NIPAm and AMPTMA are copolymerized in nearly equal amounts, both transitions may coexist.
  • Eskelä, Elina (Helsingin yliopisto, 2015)
    Cities are striving to attract and retain talented workers in order to increase their competitiveness in the new economy, which is highly dependent on innovation and knowledge. Residential satisfaction has been identified as a key determinant of whether a person stays or moves to another location. However, given the tendency to focus on the housing of immigrant groups with a lower socio-economic status, the factors that affect the residential satisfaction of skilled migrants remain understudied. This article-based dissertation in the field of urban geography examines the determinants of residential satisfaction among skilled migrants living in the Helsinki metropolitan area (HMA), Finland. The research setting is intended to maximise the cultural and socio-economic as well as locational diversity within the limits of recognised skilled migrant groups. The analysis focuses on how the interplay between individuals norms and the situational conditions is manifested when immigrants assess a single housing market, the HMA. The study is qualitative in nature and draws on 70 semi-structured interviews with skilled migrants and with experts on migration and housing in the city region. Despite the cultural, socioeconomic and locational heterogeneity of the interviewees, their experiences of housing in the HMA were notably similar: the uppermost assessment was that it is expensive, cramped and uniform. On the other hand, they appreciated the overall safety and functionality of the city region, as well as the natural environment: the predominant influence, for them, is the family life cycle rather than the urban amenities that are often assumed to be highly important for the creative class . The results also show that homeownership is not a simple indicator of the intention to stay in or leave the region, which contradicts earlier findings on ethnic-minority housing. The study underlines the importance of the social environment in creating residential satisfaction among skilled migrants. Whereas earlier studies revealed the essential nature of social networks and personal trajectories in the location decisions of skilled workers, the results of this study indicate that the supply of local, neighbourhood-based social ties is particularly limited in the case of the HMA, and that this has a negative impact on the residential satisfaction of skilled migrants. Furthermore, the structural element of housing seemed to have an effect on local social ties: among international students the extent of such ties varied according to the housing form. Although many skilled migrants are in a good socio-economic position, they are not immune to problems related to finding suitable housing. Housing availability, quality and affordability are therefore significant factors in enhancing residential satisfaction among such groups. Furthermore, as local social ties serve a mediating role with regard to the residential area as well as to society, the formation of such ties would promote the integration of migrants. These aspects of housing should be acknowledged in the strategies of cities wishing to accommodate and retain global talent. Keywords: skilled migrants, housing, residential satisfaction, social ties, Helsinki metropolitan area
  • Juntunen, Marianne (Helsingin yliopisto, 2015)
    Chemistry plays an important role in making the future more sustainable and solving the related global issues. Curricula, national and international educational strategies, research literature and chemical industry are all focusing on sustainable development. We need more environmentally literate chemists, chemistry teachers and students future citizens, who are to solve the numerous environmental challenges that face the whole world. The main aim of this design research study was to find out what are the features of holistic and inquiry-based education for sustainable development in chemistry. At the same time, the aim was to foster students environmental literacy, argumentation skills and positive attitudes towards chemistry. Education for sustainable development in chemistry is related to socio-scientific issues, e.g., life-cycle thinking and green chemistry. Theoretical problem-analysis of the study was used to investigate the approaches that are of key importance to the study presented in this dissertation: sustainable development, green chemistry, the life-cycles of different products, environmental literacy, socio-scientific education, and the pedagogical methods of inquiry-based learning and argumentation. The empirical design phase sought an answer to the main research question: What are the main features of holistic and inquiry-based education for sustainable development in chemistry? The main focus of the research was in teaching life-cycle analysis, which is one of the key elements in the Finnish national curriculum. The design research project constituted of three phases, which were conducted during the years 2010 2014. The first empirical phase was conducted in four chemistry teachers in-service training courses. During these courses, a total of 20 chemistry teachers created new inquiry-based methods for teaching life-cycle analysis in chemistry. This development process was based on theoretical problem analysis. The second empirical phase focused on creating a collaboratively-developed design solution based on the teachers concepts and the effects of this solution. The participants in this second phase were 105 9th grade students, whose environmental literacy, argumentation skills and attitudes towards chemistry learning were evaluated. The third phase was theoretical. It consisted of comparing the gained empirical knowledge to theoretical literature in order to answer the main research question. The methods of data analysis included content analysis of texts, semi-structured interviews and quantitative surveys. The validity of the results of the conducted cyclic design research project is enhanced by theoretical literature analysis, methodological triangulation, researcher triangulation, the testing of the developed teaching concept in authentic environments and the systematic, visualised documentation of the design phases. The design phases resulted in three types of knowledge: 1) new chemistry teaching concepts for sustainability education that use life-cycle thinking and inquiry-based learning methods, and a collaboratively-developed design solution (Article I), 2) knowledge about how inquiry-based learning of life-cycle analysis affects students environmental literacy, argumentation skills and attitudes towards chemistry (Articles II and III) and 3) domain knowledge about holistic and inquiry-based education for sustainable development in chemistry (Article IV). Holistic and inquiry-based education for sustainable development in chemistry includes interdisciplinary and socio-scientific issues. Socio-constructivist and contextual chemistry education is bound to societal actors and co-operational, real-life activities. Learning occurs in social interaction, through argumentation and self-reflection, for example. The students themselves may choose the focus of inquiry, and it may relate to raw materials, consumer products, food substances or water, for example. As the knowledge of chemistry is combined with possibilities for societal action, the importance of chemistry becomes apparent to the students. They gain competence to act towards building a more sustainable future. The improved scientific and ecological argumentation skills reflect their environmental literacy and competence in societal thinking. The holistic and inquiry-based chemistry education presented in this dissertation supports versatile studying and citizenship skills in a new way. It motivates students to study chemistry and guides them to take sustainable development into account. Education for sustainable development is needed at all school levels. The approaches presented in this study may be applied on all levels of education. The results may be used to promote sustainable development in the planning of chemistry education and the education of chemistry teachers. Keywords: chemistry education, sustainable development, green chemistry, teaching concepts, design research
  • Paramonov, Mikhail (Helsingin yliopisto, 2015)
    The research conducted and presented herein concentrates primarily on the life cycle of a cloud condensation nucleus CCN. The primary motivation of the work is the importance of CCN in the global aerosol-cloud-climate system, and focus is placed on the production of CCN, their behaviour in the atmosphere and their properties with respect to CCN activation, as well as the removal pathways. The work presented in this thesis covers measurements performed at 16 locations around the world. The results further corroborated the notion that atmospheric new particle formation NPF is an important and widespread source of CCN in the atmosphere. The number of newly formed CCN from NPF depends on many factors, including, but not limited to, biogenic and anthropogenic emissions, frequency of NPF events, nucleation and growth rates and pre-existing CCN concentrations; method of calculation also affects the estimate of NPF contribution to CCN budgets. Highest relative increase in CCN as a result of NPF was observed at a clean remote location in Northern Finland, where in the summer the number concentration of particles above 50 nm in diameter N50 can increase by as much as 800%. Highest absolute increases in NCCN as a result of NPF (up to 3500 particles cm 3 for N50) were found at a dry savannah location of Botsalano in South Africa. In Hyytiälä Type I nucleation events were found to always, at the very least, double NCCN concentrations. It was found that in many environments around the world a rather similar fraction of aerosols activated into cloud droplets at any given level of supersaturation S, and a simple linear parameterisation is provided for an easy calculation of annual mean CCN concentration NCCN based only on total number concentration NCN and the desired S. At the majority of studied locations hygroscopicity was found to increase with size, with accumulation mode hygroscopicity parameter κ values being significantly larger than Aitken mode κ at some locations. Depending on the focus and desired accuracy, the use of κ values as a function of particle dry size rather than the assumption of a size-independent κ should preferably be considered. The photochemistry, aging processes, atmospheric NPF and other atmospheric processes occurring on a diurnal scale were found to affect the CCN activation and hygroscopic properties of Aitken mode aerosol only. The hygroscopicity of the accumulation mode aerosol is more affected by processes occurring on a time scale of a few days to months, e.g. long range transport and seasonal variation in vegetation activity. Below-cloud scavenging by snow was found to be an inefficient mechanism of CCN removal from the atmosphere compared to, e.g., in-cloud scavenging. Additionally, nucleation and Aitken mode particles are scavenged by snow more efficiently that CCN-sized aerosol. No apparent difference in the scavenging efficiency of snow was observed between a rural and an urban site in Southern Finland. Ambient relative humidity was found to correlate positively with the scavenging efficiency of snow, and a new parameterisation for calculating snow scavenging coefficients based on both particle dry size and relative humidity is presented. A reconsideration of the purpose, the focus and the motivation for the cloud condensation nuclei counter CCNC measurements at the SMEAR II is needed if they are to be continued with reasonable, interesting and exciting output.
  • Kalinowski, Jaroslaw (2015)
    One of the goals of modern quantum chemistry is to simulate actual chemical experiments. In order to study species closer to real life systems and bulk environments there is a need for methodological developments. There are two ways to approach large systems with a given level of accuracy: conceptual changes to quantum chemistry methods or algorithmic developments for current methods. Many scientists believe that the conceptual changes truly increase the size of the systems one can study. With more or less advanced approximations to the method it is possible to increase the efficiency of calculations orders of magnitude. The implementation and algorithms fall down in the priority list, as advanced algorithmic developments are time consuming and usually lead to lower efficiency increases than conceptual changes. In this work it is shown that algorithmic developments cannot be neglected, and that even simple changes help in utilizing the power of modern computers and can also increase the efficiency by orders of magnitude. In this work new algorithmic developments are presented and used for solving various timely chemical problems.
  • Häme (née Häkkinen), Silja (Helsingin yliopisto, 2015)
    Aerosol particles are important atmospheric constituents. They exist in both polluted and remote areas but the sizes and concentrations of these particles vary greatly depending on location. Aerosol particles damage human health via inhalation, reduce visibility with high mass loadings, and among all, contribute to climate change. Particles directly scatter and absorb solar radiation. In addition, particles that are large enough can participate in cloud formation and affect cloud properties by acting as cloud condensation nuclei (CCN). A notable fraction of submicron atmospheric aerosol mass consists of organic compounds, and a large fraction of this material has been formed through condensation of organic vapors onto aerosol particles (secondary organic aerosol, SOA). Most of the global SOA mass is deemed to be biogenic in origin, but recent studies suggest that a significant fraction of it may be controlled by anthropogenic pollution. However, due to poor understanding of this anthropogenic enhancement in biogenic SOA formation, it is not systematically accounted for in current atmospheric models. Due to these kind of uncertainties in global SOA mass burden and lack of detailed knowledge of chemical, physical and optical properties of SOA, estimates of organic aerosol effect on the climate are highly uncertain. To decrease the uncertainty in the climate effects of the organic aerosol, an improved understanding of the formation mechanisms and properties of SOA is needed. In addition, nanoparticle growth to CCN-sizes by condensation of secondary organic matter needs to be accurately described in atmospheric models. In this thesis the formation of SOA is investigated in the presence of both biogenic and anthropogenic compounds. The chemical and physical properties volatility and hygroscopicity of SOA are examined via field and laboratory experiments combined with process modeling. The thesis introduces improvements for the treatment of SOA related to nanoparticle growth in atmospheric models and evaluates their performance. The thesis shows that interactions between atmospheric biogenic and anthropogenic aerosol components can form aerosol material of low-volatility. For instance organic salt formation via chemical reactions between organic acids and inorganic salts can lower aerosol volatility. Particulate-phase processing may also alter aerosol hygroscopic properties. Description of nanoparticle growth by low-volatility secondary organics is important in improving the estimates of particle and CCN numbers. The thesis highlights the significance of biogenic organic matter formed under anthropogenic influence in the nanoparticle growth. This warrants future studies focusing on the formation mechanisms and properties of anthropogenically driven biogenic organic aerosol.
  • Zou, Xiaochen (Helsingin yliopisto, 2015)
    Leaf angle distribution (LAD) is one of the most important parameters used to describe the structure of horizontally homogeneous vegetation canopies, such as field crops. LAD affects how incident photosynthetically active radiation is distributed on plant leaves, thus directly affecting plant productivity. However, the LAD of crops is difficult to quantify; usually it is assumed to be spherical. The purpose of this dissertation is to develop leaf angle estimation methods and study their effect on leaf area index (LAI) and chlorophyll a and b content (Cab) measured from optical observation. The study area was located in Viikki agricultural experimental field, Helsinki, Finland. Six crop species, faba bean, narrow-leafed lupin, turnip rape, oat, barley and wheat, were included in this study. A digital camera was used to take photographs outside the plot to record crop LAD. LAI and Cab were determined for each plot. Airborne imaging spectroscopy data was acquired using an AISA Eagle II imaging spectrometer covering the spectral range in visible and near-infrared (400 1000 nm). A recently developed method for the determination of leaf inclination angle was applied in field crops. This method was previously applied only to small and flat leaves of tree species. The error of LAI determination caused by the assumption of spherical LAD varied between 0 and 1.5 LAI units. The highest correlation between leaf mean tilt angle (MTA) and spectral reflectance was found at a wavelength of 748 nm. MTA was retrieved from imaging spectroscopy data using two algorithms. One method was to retrieve MTA from reflectance at 748 nm using a look-up table. The second method was to estimate MTA using the strong dependence of blue (479 nm) and red (663 nm) on MTA. The two approaches provide a new means to determine crop canopy structure from remote sensing data. LAI and MTA effects on Cab sensitive vegetation indices were examined. Three indices (REIP, TCARI/OSAVI and CTR6) showed strong correlations with Cab and similar performance in model-simulated and empirical datasets. However, only two (TCARI/OSAVI and CTR6) were independent from LAI and MTA. These two indices were considered as robust proxies of crop leaf Cab. Keywords: leaf angle; leaf area index; leaf chlorophyll; digital photograph; imaging spectroscopy; PROSAIL model; vegetation indices
  • Muuronen, Mikko (Helsingin yliopisto, 2015)
    Understanding the electronic structure of a chemical system in detail is essential for describing its chemical reactivity. In the present work, quantum chemical methods are applied in combination with experimental studies to achieve such detailed mechanistic understanding of chemical systems. Understanding the basic theory behind computational methods is of importance when applying them to chemical problems. Therefore, the first part of this work provides an introduction to quantum chemical methods. The results of this work are published in four peer-reviewed publications. In each publication, the understanding of the chemical system has been obtained using a combination of experimental and quantum chemical studies. These include the design of a new-type of Au(III)-catalysts, and understanding mechanistic aspects related to a Au(III) catalytic cycle. We have also focused on understanding how the electronic structure of an alkyne affects the regioselectivity in the Pauson-Khand reaction. A computational model, which provides a qualitative and, to some extent, a quantitative prediction of regiochemical outcomes is presented.
  • Mogensen, Ditte (Helsingin yliopisto, 2015)
    Forests emit biogenic volatile organic compounds (BVOCs) that, together with e.g. sulfuric acid, can operate as aerosol precursor compounds when oxidised. Aerosol particles affect both air visibility, human health and the Earth s radiative budget, thus making the emission inputs and oxidation mechanisms of VOCs absolutely crucial to understand. This thesis discusses the life cycle of compounds in the atmosphere. Specifically, we studied the representations of emission of BVOCs, the atmosphere s oxidation ability along with the sources and sinks of sulfuric acid. The main tool to achieve this was numerical modelling, often compared to field observations. Additionally, we performed computational chemistry simulations in order to calculate transitions in sulfuric acid. The main findings of this thesis can be summarised into the following: (1) Biological understanding of VOC emission processes needs to be enhanced in order to predict VOC concentrations with a high precision. (2) The unexplained fraction of the total OH reactivity in the boreal forest is larger than the known fraction and known secondary organic oxidation products of primary emitted terpenes cannot explain the missing reactivity. (3) OH is the main oxidation agent of organic compounds in the boreal atmosphere. (4) Criegee Intermediates, produced from unsaturated hydrocarbons, can oxidise SO2 effectively in order to provide as an essential source of sulfuric acid in areas with high VOC concentrations. (5) Two-photon electronic excitation did not turn out to be a significant sink of gaseous sulfuric acid in the stratosphere. This thesis closes a large part of the sulfuric acid concentration gap in VOC rich environments. Further, this thesis raises awareness of the fact that we still do not fully comprehend the mechanisms leading to BVOC emissions nor the organic atmospheric chemistry in the boreal forest. Finally, this work encourage to study alternative BVOC emission sources as well as alternative atmospheric oxidants.
  • Sand, Andrea (Helsingin yliopisto, 2015)
    In the face of the world's increasing demand for energy, and the need to find sustainable and environmentally friendly ways of producing that energy, fusion power offers an attractive possibility. However, the harsh operating conditions of future fusion devices poses a significant challenge for materials development and engineering. Tungsten (W) and tungsten alloys are current candidate materials for both structural and plasma-facing components, due to favourable properties such as good thermal conductivity, high heat strength and stability, and resistance to erosion. However, fusion reactor components will be subjected to high neutron loads, and little is currently known of the effects of radiation on the mechanical properties of this intrinsically brittle metal. The extreme conditions in a future fusion reactor cannot be reproduced in existing experimental facilities, rendering simulation an invaluable tool in understanding the radiation damage processes. Multiscale methods are necessary to span the length and time scales involved, from the picosecond and nanometer scale of displacement cascades giving rise to the primary damage, to the evolution of the radiation induced microstructure over the seconds of typical in-situ ion irradiation experiments, and further to the years of a reactor component s life time. In order to implement a multiscale simulation method, information must be distilled and transferred from the smaller scale to the larger. Molecular dynamics (MD) simulations are ideal for studying the primary damage, but individual cascades vary greatly, and simulating high energy impacts in MD requires immense computer capacity. It is therefore not possible to simulate directly the whole variety of cascade outcomes. General laws deduced from the MD data can, however, be used to statistically generate varying cascades in the thousands. In this thesis we use MD simulations to study the primary damage in metals, with focus on tungsten. We identify aspects of the simulation methodology which affect the results, and validate our methods by direct comparison to experiments. Detailed analysis of the primary damage from high-energy cascades shows the formation of novel defects, confirming recent experimental observations. We also show that defect cluster sizes follow a general scaling law, which can be used to statistically generate cascade debris as input for microstructural evolution models, circumventing the need to directly simulate thousands of cascades.
  • Nylén, Tua (Helsingin yliopisto, 2015)
    General patterns and processes of the unique land uplift beaches are still insufficiently understood. Advanced modelling methods and large homogeneous datasets provide novel opportunities to analyse spatio-temporal environmental processes. This doctoral thesis aims at expanding on the knowledge of the beach and adjacent coastal dunes as an ecogeomorphic system. More specifically, the thesis aims at answering: (1) which abiotic, biotic and temporal factors are the main determinants of substrate and vegetation properties, (2) what are the effects of the main drivers on substrate and vegetation properties, (3) how temporal processes interact with main spatial drivers in determining species richness and (4) how these effects differ between functional groups representing different adaptive strategies? Two advanced statistical methods, boosted regression trees and generalised linear mixed models, are utilised to analyse the effects of multiple factors on substrate and vegetation. My results demonstrate that substrate properties vary stronger along regional than local environmental gradients. The main drivers of textural properties are parent material and shore exposure, while organic properties are also determined by the local disturbance regime. Vegetation is mainly controlled by time, disturbance, productivity and biotic interactions. Specialist species richness and distribution are also influenced by habitat patch size and connectivity. The study highlights three mechanisms in shaping the mosaic of vegetation patterns: biotic interactions (i.e. competition and facilitation), the interplay of spatial and temporal processes and functional group (or species-) specific responses to environmental drivers. The doctoral thesis contributes to understanding the components of the ecogeomorphic beach system by identifying the main drivers of substrate and vegetation. Particularly, I demonstrate the variety of ecologic responses and the importance of dominant species in shaping vegetation assemblages. Furthermore, the feasibility of extensive homogeneous datasets and advanced modelling methods are demonstrated in analysing beach processes. Thus, the thesis may serve as one step towards a more in-depth understanding of the complex beach system and provide new methodology for further research. This knowledge is vital to the conservation of beaches that are unique landscapes and considerably contribute to biodiversity but are subject to multiple land use pressures.
  • Nikkonen, Taru (Helsingin yliopisto, 2015)
    In photosynthetic systems, chlorophylls have a vital role in converting the energy of light into chemical energy. The absorption by antenna pigments and subsequent excitation energy transfer to the reaction centre, where charge separation processes take place, result in an electrochemical potential which is utilized in carbohydrate production. The structural properties of the chlorophylls as well as supramolecular interactions, mutual distances and orientations in their natural environment, determine the function of each pigment. The aim of this doctoral thesis was to mimic photosynthetic systems and to develop chlorophyll-based structures and materials for artificial photosynthetic applications. The literature review of this thesis will concentrate on the structural, photophysical, and supramolecular properties of chlorophyll derivatives. Their functions in natural environments and their potential use in artificial light-harvesting assemblies will be thoroughly discussed. The focus of the literature review will be solely on biomimetic systems that are built by the supramolecular approach. In addition to chlorophyll (chlorin) assemblies, supramolecular systems of some important chlorophyll analogues (e.g., porphyrins) are presented. The experimental part of this thesis is based on publications I-IV. Chlorophylls were separated from green algae and modified synthetically to achieve the desired photophysical and structural/supramolecular properties. In the first part of this thesis, the energy transferring antenna structure was designed utilizing a polymer, poly(4-vinylpyridine) (P4VP), to which Zn chlorin pigments were bound noncovalently through metal-ligand axial coordination. The investigation of the assemblies revealed tight coordination both in solution and solid state films. The absorptive and emitting regimes of the solid state Zn chlorin-P4VP assemblies with variable doping levels were determined. In another part of this thesis, a series of covalently linked chlorin dimers were synthesized and their intramolecular folding abilities were investigated using both spectroscopic and theoretical techniques. It was proven that chlorin dimers fold into a C2-symmetric structure via hydrogen bonding when the linker has a suitable length. To be exact, the folding was shown to be favored with 4-10 carbon atom linkers, of which the carbon linker with a 6-atom backbone was the most optimal. As a continuation of the work, the electron donating chlorin dimer was attached to an electron acceptor, fullerene, to give a chlorin dimer−azafulleroid. The experimental spectroscopical studies and theoretical investigations showed that the chlorin dimer−azafulleroid undergoes conformational switching depending on the polarity of the media. In nonpolar media, the hydrogen bonded folded dimer is present, while in polar media the two hydrophopic chlorins wrap around the azafulleroid. The photophysical studies indicated that the lifetime of photoinduced charge separation is longer in the folded conformation having similarities to the natural photosynthetic reaction centre special pair, that is, the self-assembled chlorophyll dimer that performs the primary electron transfer step in photosynthesis. Strong electron donors, such as ferrocene, Fe(η5-C5H5)2, and ruthenocene, Ru(η5-C5H5)2, are often utilized as electron donors in donor-acceptor pairs or conjugated to electron donors to achieve improved charge transfer properties with electron donating moieties. For the first time, metallocene-appended (either [Fe(η5-C5H5)(η5-C5H4)] or [Ru(η5-C5Me5)(η5-C5H4)]) chlorin derivatives were synthesized. The resulting metallocene-chlorins oxidized spontaneously under air to give certain oxidation products depending on the type of metallocene attached to the aromatic chlorin macrocycle. The oxidized metallocene-chlorins were characterized by steady-state and time-resolved absorption and emission spectroscopy.
  • Witos, Joanna (Helsingin yliopisto, 2015)
    This doctoral thesis describes the development of novel miniaturized analytical tools applicable to in situ nanoscale studies for a deeper understanding of biomolecular interactions. Capillary electrophoresis (CE), atomic force microscopy (AFM), quartz crystal microbalance (QCM) measurements, and partial filling affinity capillary electrophoresis (PF-ACE) were utilized to study the separation of lipoproteins and their interactions with extracellular matrix (ECM) components. The major focus of the study was on low and high density lipoprotein particles (LDL and HDL), which are the main vehicles of cholesterol transport in human circulation. Lipoproteins are involved in specific interactions with proteoglycans (PGs) and collagens, structural components of ECM of the arterial wall. The interactions lead to the development and progression of atherosclerosis and diabetes. The first step of the work was to clarify, by AFM, the structural and molecular properties of collagens I and III under physiological conditions. Study was made of the effect of decorin on the fibril formation of collagen, which promotes and enhances the binding of collagen with LDL. Moreover, the immobilized collagen I surface was exposed to in situ glycation, and the adsorption pattern of the glycated collagen was elucidated. In addition to AFM, QCM was used to examine characteristics of the interaction between collagens and apolipoprotein B-100 (apoB-100), the major protein of LDL. Values of the dissociation constant were then estimated by evaluating the differences in strength of the binding process. To avoid strong and unwanted adsorption of lipoprotein particles on the inner wall of the capillary, the effect of five different sugars on the separation of lipoproteins was studied by CE in uncoated capillary at physiological pH 7.4. In addition, the effect of the sugars on the size of the lipoproteins was elucidated by asymmetrical flow field-flow fractionation (AsFlFFF) and dynamic light scattering (DLS) measurements. Molecular dynamics (MD) simulations were employed to discover the influence of sugars on the structures of apolipoprotein E (apoE) of HDL and apoB-100 of LDL. In another attempt to eliminate the adsorption of positive analytes and allow their separation, a polycationic coating was developed and covalently bound to the inner wall of the fused silica capillary. The immobilization of the coating was achieved in a three-step procedure during on-line polymerization. The stability study of the coating in wide pH range 3 8 demonstrated the suitability of the coating for the separation of small proteins and -blockers. Finally, PF-ACE technique was used to evaluate in detail the interactions involved in the binding of the most common isoforms of apoE with the major glycosaminoglycan (GAG) chain of PGs, viz., chondroitin-6-sulfate (C6S). As is well known, PF-ACE enables the evaluation of affinity constants only for single-type interactions, and adsorption energy distribution (AED) calculations were introduced to widen its application. AED allowed characterization of the heterogeneity of interactions and permitted evaluation of differences in the binding process strengths. The key contributions of the work are the promising and reliable tools developed for separation and interaction studies of biological processes occurring in the ECM.
  • Wang, Liang (Helsingin yliopisto, 2015)
    In-network caching aims at improving content delivery and alleviating pressures on network bandwidth by leveraging universally networked caches. This thesis studies the design of cooperative in-network caching strategy from three perspectives: content, topology and cooperation, specifically focuses on the mechanisms of content delivery and cooperation policy and their impacts on the performance of cache networks. The main contributions of this thesis are twofold. From measurement perspective, we show that the conventional metric hit rate is not sufficient in evaluating a caching strategy on non-trivial topologies, therefore we introduce footprint reduction and coupling factor, which contain richer information. We show cooperation policy is the key in balancing various tradeoffs in caching strategy design, and further investigate the performance impact from content per se via different chunking schemes. From design perspective, we first show different caching heuristics and smart routing schemes can significantly improve the caching performance and facilitate content delivery. We then incorporate well-defined fairness metric into design and derive the unique optimal caching solution on the Pareto boundary with bargaining game framework. In addition, our study on the functional relationship between cooperation overhead and neighborhood size indicates collaboration should be constrained in a small neighborhood due to its cost growing exponentially on general network topologies.
  • Özcan-Ketola, Nergiz (Helsingin yliopisto, 2015)
    In this thesis, structural effects on magnetic response properties: magnetically induced ring currents, the ESR g-tensor and hyperfine coupling tensor, and NMR chemical shifts, are investigated computationally with DFT methods, using various exchange-correlation functionals and basis sets. Magnetically induced currents are calculated for thieno-bridged porphyrins with the emphasis on the aromatic character of the systems, the degree of which is investigated for varying molecular modifications. The ESR g-tensor, as well as the hyperfine coupling tensors for Sn and O nuclei in the vicinity of a positively charged oxygen vacancy in solid tin dioxide, are reported with finite cluster methods using different cluster embedding techniques to define the structural environment. The NMR spectral trends for increasing-size nanoflakes of graphenic materials are predicted as functions of the size and boundary geometry of the flakes. Finally, a number of dye molecules are subjected to NMR chemical shift calculations where the intermolecular interaction effects present in liquid solution are studied with dynamic simulation techniques. The magnetically induced currents calculated for thieno-bridged porphyrins show that the changes in the molecular structure such as the direction of the thiophene ring or the substitution by Zn^2+ do not change the aromatic character of the molecule. It is possible to confirm the experimental assignment of the ESR signal with the g-factor around 2.00 to the positively charged vacancy in tin dioxide, whereas the other experimental assignment of a signal at g=1.89 is not supported by our calculations. Distinct characteristic NMR spectral patterns are found for graphene nanoflakes reflecting the effects of increasing size and different boundary geometries on the NMR shifts. Solvent effects on the NMR of dye molecules are found to be location-specific: nuclei from different regions of the systems display distinct response to solvation.
  • Kohonen, Jukka (Helsingin yliopisto, 2015)
    Clustering is a central task in computational statistics. Its aim is to divide observed data into groups of items, based on the similarity of their features. Among various approaches to clustering, Bayesian model-based clustering has recently gained popularity. Many existing works are based on stochastic sampling methods. This work is concerned with exact, exponential-time algorithms for the Bayesian model-based clustering task. In particular, we consider the exact computation of two summary statistics: the number of clusters, and pairwise incidence of items in the same cluster. We present an implemented algorithm for computing these statistics substantially faster than would be achieved by direct enumeration of the possible partitions. The method is practically applicable to data sets of up to approximately 25 items. We apply a variant of the exact inference method into graphical models where a given variable may have up to four parent variables. The parent variables can then have up to 16 value combinations, and the task is to cluster them and find combinations that lead to similar conditional probability tables. Further contributions of this work are related to number theory. We show that a novel combination of addition chains and additive bases provides the optimal arrangement of multiplications, when the task is to use repeated multiplication starting from a given number or entity, but only a certain kind of function of the successive powers is required. This arrangement speeds up the computation of the posterior distribution for the number of clusters. The same arrangement method can be applied to other multiplicative tasks, for example, in matrix multiplication. We also present new algorithmic results related to finding extremal additive bases. Before this work, the extremal additive bases were known up to length 23. We have computed them up to length 24 in the unrestricted case, and up to length 41 in the restricted case.
  • R. Labafzadeh, Sara (Helsingin yliopisto, 2015)
    Worldwide research is focused on the use of renewable and biodegradable raw materials due to the limited existing quantities of fossil supplies and the environmental degradation caused by global warming. Cellulose, derived from natural resources such as wood, annual plants and microbes, represents the most abundant renewable polymeric material on earth. Due to its low cost and functional versatility, cellulose has been a key feedstock for the production of chemicals with various properties and applications over the past century. It has found a wide range of applications in food, printing, cosmetics, pharmacy, therapeutics, paper making and in the textile industry. This partly crystalline polymer has not yet reached its full application potential due to its essential insolubility in most common solvents. Many investigations focus on the development of novel media for efficient and economically feasible functionalization of cellulose. The chemical modification of cellulose overcomes this obstacle and offers considerable opportunities for preparing cellulose-based polymeric materials. The modification could adjust the properties of the macromolecule for different purposes and meet the environmental requirements by using green reagents and recyclable solvent systems. Synthesis of new cellulose-based polymers and their thorough characterization and increasing the usefulness of cellulose by altering its properties have been of growing research interest for the past few years. The objective of this research was to investigate new paths for the preparation of cellulose-based materials with a variety of structural features to obtain advanced materials suitable for different applications. Most of the research has focused purely on the synthesis of cellulose derivatives in new and economically feasible solvent systems, but it also has general relevance for the material properties of the obtained derivatives. Also, the potential application of synthesized cellulose derivatives as barrier films for packaging was investigated. Highly substituted cellulose esters, carbamates and carbonates were prepared using various recyclable reaction solvents. Biomaterials with the potential for use in the packaging sector should provide high mechanical properties, in addition to good barrier properties for oxygen and water vapour. Some derivatives showed good barrier properties being promising for packaging application.