Matemaattis-luonnontieteellinen tiedekunta


Recent Submissions

  • Ciragan, Annika (2017)
    At the present time resistance to every main class of antibiotic has been observed. Therefore, the continuous development of new-generation antibiotics is crucial to combat the rise of antibiotic resistant strains. Identification of potential antibiotic targets and investigation of their structure and function represent a rational approach to developing a better understanding of the essential processes in which they are involved, and may lead to finding a mechanism to inhibit these processes. The first part of this thesis covers structural characterization and functional studies of the potential antibiotic targets TonB protein and the cell shape determining protein MreC. TonB is needed for TonB-dependent uptake of scarce nutrients, such as iron and vitamin B 12. The cell shape determining protein MreC is involved in cell wall synthesis, which is the target of penicillin and its derivatives. In this study, the three dimensional structures of the C-terminal domain of Helicobacter pylori TonB of different lengths and the C-terminal domain of Bacillus subtilis MreC were determined using nuclear magnetic resonance (NMR) spectroscopy. Additionally, interaction studies of MreC with penicillin-binding proteins were done using NMR spectroscopy and a bacterial two-hybrid system. NMR spectroscopy is a versatile tool to investigate protein structure, dynamics and interactions. One of the advantages of NMR is that proteins can be studied in solution under nearly physiological conditions. However, with increasing molecular size (> 25 – 30 kDa), structural investigation by NMR becomes more complex and often requires specific labelling techniques and alternative methodologies for NMR measurements. Segmental isotopic labelling, where only a part of the protein is stable isotopic labelled, is an attractive method to overcome the challenges of studying large proteins by NMR. Segmental isotopic labelling allows, e.g. investigation of individual protein domains in a full-length context. Furthermore, NMR is a powerful tool to study the integrity of a protein. Certain requirements, however, have to be fulfilled: the protein has to be soluble at high concentrations and stable over the whole measurement time. Therefore it is important to optimize protein production in order to obtain soluble, properly folded proteins at high concentrations. In the second part of this study, TonB has been used as a model protein to show traceless intein-mediated segmental isotopic labelling by salt induced protein trans splicing using a halophilic intein. This approach facilitates structural investigations of TonB by NMR. TonB consists of a well-structured C-terminal domain and a flexible proline-rich region, which would severely interfere with spectral quality in a uniformly labelled sample. Furthermore TonB was used as a model protein to show the benefit in protein expression of using tandem SUMO fusion vectors as tools for the expression of more soluble proteins, which tend to be expressed in an insoluble form. Both of these applications are beneficial for structural investigation of proteins by NMR and can be applied to other proteins.
  • Al-Qaisi, Feda'a (2016)
    The conversion of carbon dioxide (CO2), an abundant renewable carbon reagent, into cyclic carbonate is of academic and industrial interest. Cyclic carbonate serve as green solvent and have some outstanding properties such as a high boiling point and low toxicity. Titanium and iron would be attractive metal candidates as benign and efficient alternative to other metal catalysis for CO2 conversion to cyclic carbonate, due combination of low toxicity and high Lewis acidity. In the present work the coupling reactions of carbon dioxide with epoxides to produce five-membered cyclic carbonates (propylene, 1-hexene, cyclohexene, styrene, and epichlorohydrin carbonates) were efficiently catalyzed either by sustainable metal-based catalysts of: (1) titanium alkoxide complexes/tetrabutylammonium salts; (2) Schiff base iron(III) complexes/onium salts; (3) bifunctional imidazole-Schiff base iron(III) complex; and (4) metal-free systems consisting of a simple, preferably primary or secondary, amines and halides with organic or inorganic cations (such as tetrabutylammonium or lithium chloride, bromide or iodide). Reactivity of the four above-mentioned catalytic systems was further studied and compared in the coupling reactions.
  • Mei, Peng (2013)
    In this thesis, the main goal is to study the kinetic dynamics based on Hubbard model in dimensions d>2. We analyse rigorously some basic properties of the dynamics in the following scaling limit. As the coupling constant converges to zero, we rescale the time variable to capture the slow dynamics: we let coupling constant go to zero, time to infinity in such a way that the product of square of the coupling constant and time has a finite limit. The main ingredient of the kinetic limit is that, combining some basic ideas of scattering theory (long time scale) and perturbation theory (small coupling parameter), it automatically selects from the microscopic dynamics some dominating terms. This gives rise to a new description of time evolution (given by quantum Boltzmann equation), whose form can already be postulated from the second order perturbative expansion. The limit equation is expected to capture nontrivial information about the original system. Besides the weak coupling dynamics, we also discuss two complementary results in related Fermion systems.
  • Vuollekoski, Henri (Helsingin yliopisto, 2010)
    Aerosols impact the planet and our daily lives through various effects, perhaps most notably those related to their climatic and health-related consequences. While there are several primary particle sources, secondary new particle formation from precursor vapors is also known to be a frequent, global phenomenon. Nevertheless, the formation mechanism of new particles, as well as the vapors participating in the process, remain a mystery. This thesis consists of studies on new particle formation specifically from the point of view of numerical modeling. A dependence of formation rate of 3 nm particles on the sulphuric acid concentration to the power of 1-2 has been observed. This suggests nucleation mechanism to be of first or second order with respect to the sulphuric acid concentration, in other words the mechanisms based on activation or kinetic collision of clusters. However, model studies have had difficulties in replicating the small exponents observed in nature. The work done in this thesis indicates that the exponents may be lowered by the participation of a co-condensing (and potentially nucleating) low-volatility organic vapor, or by increasing the assumed size of the critical clusters. On the other hand, the presented new and more accurate method for determining the exponent indicates high diurnal variability. Additionally, these studies included several semi-empirical nucleation rate parameterizations as well as a detailed investigation of the analysis used to determine the apparent particle formation rate. Due to their high proportion of the earth's surface area, oceans could potentially prove to be climatically significant sources of secondary particles. In the lack of marine observation data, new particle formation events in a coastal region were parameterized and studied. Since the formation mechanism is believed to be similar, the new parameterization was applied in a marine scenario. The work showed that marine CCN production is feasible in the presence of additional vapors contributing to particle growth. Finally, a new method to estimate concentrations of condensing organics was developed. The algorithm utilizes a Markov chain Monte Carlo method to determine the required combination of vapor concentrations by comparing a measured particle size distribution with one from an aerosol dynamics process model. The evaluation indicated excellent agreement against model data, and initial results with field data appear sound as well.
  • Reijonen, Vappu (2010)
    Einstein's general relativity is a classical theory of gravitation: it is a postulate on the coupling between the four-dimensional, continuos spacetime and the matter fields in the universe, and it yields their dynamical evolution. It is believed that general relativity must be replaced by a quantum theory of gravity at least at extremely high energies of the early universe and at regions of strong curvature of spacetime, cf. black holes. Various attempts to quantize gravity, including conceptually new models such as string theory, have suggested that modification to general relativity might show up even at lower energy scales. On the other hand, also the late time acceleration of the expansion of the universe, known as the dark energy problem, might originate from new gravitational physics. Thus, although there has been no direct experimental evidence contradicting general relativity so far - on the contrary, it has passed a variety of observational tests - it is a question worth asking, why should the effective theory of gravity be of the exact form of general relativity? If general relativity is modified, how do the predictions of the theory change? Furthermore, how far can we go with the changes before we are face with contradictions with the experiments? Along with the changes, could there be new phenomena, which we could measure to find hints of the form of the quantum theory of gravity? This thesis is on a class of modified gravity theories called f(R) models, and in particular on the effects of changing the theory of gravity on stellar solutions. It is discussed how experimental constraints from the measurements in the Solar System restrict the form of f(R) theories. Moreover, it is shown that models, which do not differ from general relativity at the weak field scale of the Solar System, can produce very different predictions for dense stars like neutron stars. Due to the nature of f(R) models, the role of independent connection of the spacetime is emphasized throughout the thesis.
  • Lakkala, Kaisa (Helsingin yliopisto, 2010)
    The Earth's ecosystems are protected from the dangerous part of the solar ultraviolet (UV) radiation by stratospheric ozone, which absorbs most of the harmful UV wavelengths. Severe depletion of stratospheric ozone has been observed in the Antarctic region, and to a lesser extent in the Arctic and midlatitudes. Concern about the effects of increasing UV radiation on human beings and the natural environment has led to ground based monitoring of UV radiation. In order to achieve high-quality UV time series for scientific analyses, proper quality control (QC) and quality assurance (QA) procedures have to be followed. In this work, practices of QC and QA are developed for Brewer spectroradiometers and NILU-UV multifilter radiometers, which measure in the Arctic and Antarctic regions, respectively. These practices are applicable to other UV instruments as well. The spectral features and the effect of different factors affecting UV radiation were studied for the spectral UV time series at Sodankylä. The QA of the Finnish Meteorological Institute's (FMI) two Brewer spectroradiometers included daily maintenance, laboratory characterizations, the calculation of long-term spectral responsivity, data processing and quality assessment. New methods for the cosine correction, the temperature correction and the calculation of long-term changes of spectral responsivity were developed. Reconstructed UV irradiances were used as a QA tool for spectroradiometer data. The actual cosine correction factor was found to vary between 1.08-1.12 and 1.08-1.13. The temperature characterization showed a linear temperature dependence between the instrument's internal temperature and the photon counts per cycle. Both Brewers have participated in international spectroradiometer comparisons and have shown good stability. The differences between the Brewers and the portable reference spectroradiometer QASUME have been within 5% during 2002-2010. The features of the spectral UV radiation time series at Sodankylä were analysed for the time period 1990-2001. No statistically significant long-term changes in UV irradiances were found, and the results were strongly dependent on the time period studied. Ozone was the dominant factor affecting UV radiation during the springtime, whereas clouds played a more important role during the summertime. During this work, the Antarctic NILU-UV multifilter radiometer network was established by the Instituto Nacional de Meteorogía (INM) as a joint Spanish-Argentinian-Finnish cooperation project. As part of this work, the QC/QA practices of the network were developed. They included training of the operators, daily maintenance, regular lamp tests and solar comparisons with the travelling reference instrument. Drifts of up to 35% in the sensitivity of the channels of the NILU-UV multifilter radiometers were found during the first four years of operation. This work emphasized the importance of proper QC/QA, including regular lamp tests, for the multifilter radiometers also. The effect of the drifts were corrected by a method scaling the site NILU-UV channels to those of the travelling reference NILU-UV. After correction, the mean ratios of erythemally-weighted UV dose rates measured during solar comparisons between the reference NILU-UV and the site NILU-UVs were 1.007±0.011 and 1.012±0.012 for Ushuaia and Marambio, respectively, when the solar zenith angle varied up to 80°. Solar comparisons between the NILU-UVs and spectroradiometers showed a ±5% difference near local noon time, which can be seen as proof of successful QC/QA procedures and transfer of irradiance scales. This work also showed that UV measurements made in the Arctic and Antarctic can be comparable with each other.
  • Kivekäs, Niku (Helsingin yliopisto, 2010)
    In order to predict the current state and future development of Earth s climate, detailed information on atmospheric aerosols and aerosol-cloud-interactions is required. Furthermore, these interactions need to be expressed in such a way that they can be represented in large-scale climate models. The largest uncertainties in the estimate of radiative forcing on the present day climate are related to the direct and indirect effects of aerosol. In this work aerosol properties were studied at Pallas and Utö in Finland, and at Mount Waliguan in Western China. Approximately two years of data from each site were analyzed. In addition to this, data from two intensive measurement campaigns at Pallas were used. The measurements at Mount Waliguan were the first long term aerosol particle number concentration and size distribution measurements conducted in this region. They revealed that the number concentration of aerosol particles at Mount Waliguan were much higher than those measured at similar altitudes in other parts of the world. The particles were concentrated in the Aitken size range indicating that they were produced within a couple of days prior to reaching the site, rather than being transported over thousands of kilometers. Aerosol partitioning between cloud droplets and cloud interstitial particles was studied at Pallas during the two measurement campaigns, First Pallas Cloud Experiment (First PaCE) and Second Pallas Cloud Experiment (Second PaCE). The method of using two differential mobility particle sizers (DMPS) to calculate the number concentration of activated particles was found to agree well with direct measurements of cloud droplet. Several parameters important in cloud droplet activation were found to depend strongly on the air mass history. The effects of these parameters partially cancelled out each other. Aerosol number-to-volume concentration ratio was studied at all three sites using data sets with long time-series. The ratio was found to vary more than in earlier studies, but less than either aerosol particle number concentration or volume concentration alone. Both air mass dependency and seasonal pattern were found at Pallas and Utö, but only seasonal pattern at Mount Waliguan. The number-to-volume concentration ratio was found to follow the seasonal temperature pattern well at all three sites. A new parameterization for partitioning between cloud droplets and cloud interstitial particles was developed. The parameterization uses aerosol particle number-to-volume concentration ratio and aerosol particle volume concentration as the only information on the aerosol number and size distribution. The new parameterization is computationally more efficient than the more detailed parameterizations currently in use, but the accuracy of the new parameterization was slightly lower. The new parameterization was also compared to directly observed cloud droplet number concentration data, and a good agreement was found.
  • Raento, Mika (Mika Raento, 2007)
    Ubiquitous computing is about making computers and computerized artefacts a pervasive part of our everyday lifes, bringing more and more activities into the realm of information. The computationalization, informationalization of everyday activities increases not only our reach, efficiency and capabilities but also the amount and kinds of data gathered about us and our activities. In this thesis, I explore how information systems can be constructed so that they handle this personal data in a reasonable manner. The thesis provides two kinds of results: on one hand, tools and methods for both the construction as well as the evaluation of ubiquitous and mobile systems---on the other hand an evaluation of the privacy aspects of a ubiquitous social awareness system. The work emphasises real-world experiments as the most important way to study privacy. Additionally, the state of current information systems as regards data protection is studied. The tools and methods in this thesis consist of three distinct contributions. An algorithm for locationing in cellular networks is proposed that does not require the location information to be revealed beyond the user's terminal. A prototyping platform for the creation of context-aware ubiquitous applications called ContextPhone is described and released as open source. Finally, a set of methodological findings for the use of smartphones in social scientific field research is reported. A central contribution of this thesis are the pragmatic tools that allow other researchers to carry out experiments. The evaluation of the ubiquitous social awareness application ContextContacts covers both the usage of the system in general as well as an analysis of privacy implications. The usage of the system is analyzed in the light of how users make inferences of others based on real-time contextual cues mediated by the system, based on several long-term field studies. The analysis of privacy implications draws together the social psychological theory of self-presentation and research in privacy for ubiquitous computing, deriving a set of design guidelines for such systems. The main findings from these studies can be summarized as follows: The fact that ubiquitous computing systems gather more data about users can be used to not only study the use of such systems in an effort to create better systems but in general to study phenomena previously unstudied, such as the dynamic change of social networks. Systems that let people create new ways of presenting themselves to others can be fun for the users---but the self-presentation requires several thoughtful design decisions that allow the manipulation of the image mediated by the system. Finally, the growing amount of computational resources available to the users can be used to allow them to use the data themselves, rather than just being passive subjects of data gathering.
  • Vänskä, Simopekka (Suomalainen tiedeakatemia, 2006)
    We consider an obstacle scattering problem for linear Beltrami fields. A vector field is a linear Beltrami field if the curl of the field is a constant times itself. We study the obstacles that are of Neumann type, that is, the normal component of the total field vanishes on the boundary of the obstacle. We prove the unique solvability for the corresponding exterior boundary value problem, in other words, the direct obstacle scattering model. For the inverse obstacle scattering problem, we deduce the formulas that are needed to apply the singular sources method. The numerical examples are computed for the direct scattering problem and for the inverse scattering problem.
  • Kytölä, Kalle (Helsingin yliopisto, 2006)
    This thesis consists of an introduction, four research articles and an appendix. The thesis studies relations between two different approaches to continuum limit of models of two dimensional statistical mechanics at criticality. The approach of conformal field theory (CFT) could be thought of as the algebraic classification of some basic objects in these models. It has been succesfully used by physicists since 1980's. The other approach, Schramm-Loewner evolutions (SLEs), is a recently introduced set of mathematical methods to study random curves or interfaces occurring in the continuum limit of the models. The first and second included articles argue on basis of statistical mechanics what would be a plausible relation between SLEs and conformal field theory. The first article studies multiple SLEs, several random curves simultaneously in a domain. The proposed definition is compatible with a natural commutation requirement suggested by Dubédat. The curves of multiple SLE may form different topological configurations, ``pure geometries''. We conjecture a relation between the topological configurations and CFT concepts of conformal blocks and operator product expansions. Example applications of multiple SLEs include crossing probabilities for percolation and Ising model. The second article studies SLE variants that represent models with boundary conditions implemented by primary fields. The most well known of these, SLE(kappa, rho), is shown to be simple in terms of the Coulomb gas formalism of CFT. In the third article the space of local martingales for variants of SLE is shown to carry a representation of Virasoro algebra. Finding this structure is guided by the relation of SLEs and CFTs in general, but the result is established in a straightforward fashion. This article, too, emphasizes multiple SLEs and proposes a possible way of treating pure geometries in terms of Coulomb gas. The fourth article states results of applications of the Virasoro structure to the open questions of SLE reversibility and duality. Proofs of the stated results are provided in the appendix. The objective is an indirect computation of certain polynomial expected values. Provided that these expected values exist, in generic cases they are shown to possess the desired properties, thus giving support for both reversibility and duality.
  • Hännikäinen, Outi-Kristiina (Siirtolaisuusinstituutti, 2010)
    The present study examines how the landscape of the rural immigrant colony of New Finland (Saskatchewan, Canada) has reflected the Finnish origins of the about 350 settlers and their descendants, their changing ideologies, values, sense of collectiveness and the meanings of the Finnish roots. The study also reveals the reasons and power structures behind the ethnic expressions. Researched time period runs from the beginning of the settlement in 1888 to the turn of the millennium. The research concentrates on buildings, cemeteries, personal names and place names which contain strong visual and symbolic messages and are all important constituents of mundane landscapes. For example, the studied personal names are important identity-political indexes telling about the value of the Finnish nationalism, community spirit, dual Finnish-Canadian identities and also the process of assimilation which, for example, had differences between genders. The study is based on empirical field research, and iconographical and textual interpretations supported by classifications and comparative analyses. Several interviews and literature were essential means of understanding the changing political contexts which influenced the Finnish settlement and its multiple landscape representations. Five historical landscape periods were identified in New Finland. During these periods the meanings and representations of Finnish identity changed along with national and international politics and local power structures. For example, during the Second World War Canada discouraged representations of Finnish culture because Finland and Canada were enemies. But Canada s multicultural policy in the 1980s led to several material and symbolic representations indicating the Finnish settlement after a period of assimilation and deinstitutionalization. The study shows how these representations were indications of the politics of a (selective) memory. Especially Finnish language, cultural traditions and the Evangelical-Lutheran values of the pioneers, which have been passed down to new generations, are highly valued part of the Finnish heritage. Also the work of the pioneers and their participation in the building of Saskatchewan is an important collective narrative. The selectiveness of a memory created the landscape of forgetting which includes deliberately forgotten parts of the history. For example, the occasional disputes between the congregations are something that has been ignored. The results show how the different landscape elements can open up a useful perspective to diaspora colonies or other communities also by providing information which otherwise would be indistinguishable. In this case, for example, two cemeteries close together were a sign of religious distributions among the early settlers.
  • Bäcklund, Pia (Helsingin kaupungin tietokeskus, 2007)
    The present study examines citizen participation in local government and municipal democracy. Previous research has shown that the prerequisite for active citizenship lies in the opportunities available for local residents to determine which perspectives and planning needs are relevant. This research looks at whether the conception of knowledge employed in municipal planning allows for this kind of active role for local citizens. Methodologically the study employs an hermeneutic approach. The aim has been to identify various approaches steering the practice of municipal democracy. The theory behind the study comes from the assumption of the intersubjectivity of reality. Construing the rationality of one s own behaviour is seen as a prerequisite for meaningful action. In this context, criteria for the functionality of municipal democracy and the purpose of strengthening citizen participation are defined. The study is divided into two parts. Firstly, the purpose of participation and the opportunities for local residents to contribute is examined theoretically with reference to previous studies. The intention is to provide an overview of the Finnish cross-disciplinary debate on resident participation. This debate is reflected onto the prevailing views on changes in the municipal operating environment and modes of operation. In conclusion, a theoretical model is constructed to explain how the various modes of operation in regional municipalities affect the purpose of resident participation and the utilisation of information received through this participation. The second part of the study discusses the utilisation of this information and knowledge acquired through the participation of local residents and all those involved in political and administrative processes in municipalities. These first-hand reports are analysed using the model constructed earlier in the study. The goal is to understand how political and administrative practice affects opportunities for local residents to participate and contribute. The core of this analysis is based on the pragmatic conception of knowledge employed in municipal administration. The study argues that the normal practice of municipal administration does not support the systematic utilisation of local residents experience. This is caused by two interlinked factors: firstly, knowledge constructed through these practices requires that the knowledge is apolitical; secondly, arising from this there is confusion with regard to when during a planning process does information obtained from the public become relevant; in other words, what are the politics of knowledge? The study suggests that the solution is in the complementary concept of knowledge, which implicitly acknowledges the politics of knowledge. The complementary concept of knowledge would serve the politicisation of issues on the level of interpretations linked with social reality, an indispensable requirement for functional democracy. Keywords: participation, municipal democracy, knowledge base for planning, experiential knowledge
  • Eronen, Jussi Tuomas (Suomen Eläin- ja Kasvitieteellinen Julkaisutoimikunta, 2006)
    The development and changes in the distribution of herbivorous mammal communities during the Neogene is complex. The Eurasian scale environmental patterns reflect the large scale geographical and climatic patterns. The reorganization of these affect the biome distribution throughout the continent. The distribution of mammal taxa was closely associated with the distribution of biomes. In Eurasia the Neogene development of environments was twofold. The early and middle Miocene that seemed to have been advantageous for mammals was followed by drying of environments during the late Neogene. The mid-latitude drying was the main trend, and it is the combined result of the retreat of Paratethys, the uplift of Tibetan Plateau and changes in the ocean currents and temperatures. The common mammals were "driving" the evolution of mammalian communities. During the late Miocene we see the drying affecting more and more regions, and we see changes in the composition of mammalian communities.