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  • Pesonen, Janne (Helsingin yliopisto, 2001)
  • Bućko, Michał (Helsingin yliopisto, 2012)
    Road traffic is at present one of the major sources of environmental pollution in urban areas. Magnetic particles, heavy metals and others compounds generated by traffic can greatly affect ambient air quality and have direct implications for human health. The general aim of this research was to identify and characterize magnetic vehicle-derived particulates using magnetic, geochemical and micro-morphological methods. A combination of three different methods was used to discriminate sources of particular anthropogenic particles. Special emphasis was placed on the application of various collectors (roadside soil, snow, lichens and moss bags) to monitor spatial and temporal distribution of traffic pollution on roadsides. The spatial distribution of magnetic parameters of road dust accumulated in roadside soil, snow, lichens and moss bags indicates that the highest concentration of magnetic particles is in the sampling points situated closest to the road edge. The concentration of magnetic particles decreases with increasing distance from the road indicating vehicle traffic as a major source of emission. Significant differences in horizontal distribution of magnetic susceptibility were observed between soil and snow. Magnetic particles derived from road traffic deposit on soil within a few meters from the road, but on snow up to 60 m from the road. The values of magnetic susceptibility of road dust deposited near busy urban motorway are significantly higher than in the case of low traffic road. These differences are attributed to traffic volume, which is 30 times higher on motorway than on local road. Moss bags placed at the edge of urban parks situated near major roads show higher values of magnetic susceptibility than moss bags from parks located near minor routes. Enhanced concentrations of heavy metals (e.g. Fe, Mn, Zn, Cu, Cr, Ni and Co) were observed in the studied samples. This may be associated with specific sources of vehicle emissions (e.g. exhaust and non-exhaust emissions) and/or grain size of the accumulated particles (large active surface of ultrafine particles). Significant correlations were found between magnetic susceptibility and the concentration of selected heavy metals in the case of moss bags exposed to road traffic. Low-coercivity magnetite was identified as a major magnetic phase in all studied roadside collectors (soil, snow, moss bags and lichens). However, magnetic minerals such as titanomagnetite, ilmenite, pyrite and pyrrhotite were also observed in the studied samples. The identified magnetite particles are mostly pseudo-single-domain (PSD) with a predominant MD fraction (>10 μm). The ultrafine iron oxides (>10 nm) were found in road dust extracted from roadside snow. Large magnetic particles mostly originate from non-exhaust emissions, while ultrafine particles originate from exhaust emissions. The examined road dust contains two types of anthropogenic particles: (1) angular/aggregate particles composed of various elements (diameter ~1-300 µm); (2) spherules (~1-100 µm) mostly composed of iron. The first type of particles originates from non-exhaust emissions such as the abrasion of vehicle components, road surface and winter road maintenance. The spherule-shaped particles are products of combustion processes e.g. combustion of coal in nearby power plants and/or fuel in vehicle engines. This thesis demonstrates that snow is an efficient collector of anthropogenic particles, since it can accumulate and preserve the pollutants for several months (until the late stages of melting). Furthermore, it provides more information about spatial and temporal distribution of traffic-generated magnetic particles than soil. Since the interpretation of data obtained from magnetic measurements of soil is problematic (due to its complexity), this suggests the application of alternative collectors of anthropogenic magnetic particulates (e.g. snow and moss bags). Moss bags and lichens are well suited for magnetic biomonitoring studies, since they effectively accumulate atmospheric pollution and can thus be applied to monitor the spatio-temporal distribution of pollution effects.
  • Välimäki, Niko (Helsingin yliopisto, 2012)
    Recent advancements in the field of compressed data structures create interesting opportunities for interdisciplinary research and applications. Compressed data structures provide essentially a time--space tradeoff for solving a problem; while traditional data structures use extra space in addition to the input, compressed data structures replace the input and require space proportional to the compressed size of the input. The amount of available memory is often fixed, thus, the user might be willing to spend more time if it allows the use of larger inputs. However, despite the potential behind compressed data structures, they have not quite reached the audience of other disciplines. We study how to take advantage of compressed data structures in the fields of bioinformatics, data analysis and information retrieval. We present several novel applications for compressed data structures and include an experimental evaluation of the time--space tradeoffs achieved. More precisely, we propose (i) a space-efficient string mining algorithm to recognise substrings that admit the given frequency constraints, (ii) both theoretical and practical methods for computing approximate overlaps between all string pairs, (iii) a practical path-based graph kernel for predicting the function of unknown enzymatic reactions, and (iv) a compressed XML index that supports efficient XPath queries on both the tree-structure and textual content of XML documents. Problem (i) is motivated by knowledge discovery in databases, where the goal is to extract emerging substrings that discriminate two (or more) databases. Problem (ii) is one of the first phases in a sequence assembly pipeline and requires efficient algorithms due to the new high-throughput sequencing systems. Problem (iii) is motivated by machine learning, where kernels are used to measure the similarity of complex objects. Problem (iv) has its background in information retrieval. The proposed methods achieve theoretical and practical improvements over the earlier state of the art. To raise the overall awareness of compressed data structures, our results have been published in interdisciplinary forums, including conferences and journals from the fields of bioinformatics, data engineering and data mining.
  • Zahabi, Seyedali (Helsingin yliopisto, 2013)
    This thesis investigates different aspects of conformal field theory and string theory and their applications in statistical properties of systems. First, we study the free fermions in planar Ising model and its scaling limit at criticality. On the one hand, we examine the relation between the transfer matrix formalism and discrete holomorphicity. We show that the fermion operators of the Ising model satisfy a complexification of the defining relations of s-holomorphicity, a strong notion of discrete holomorphicity, and examples of fermion correlation functions are shown to reproduce s-holomorphic parafermionic observables. On the other hand, we study the relation between fermionic conformal field theory and Schramm Loewner evolution by focusing on the interfaces and fermionic correlation functions of the Ising model. We demonstrate an explicit, rigorous realization of the CFT/SLE correspondence in the case of Ising model. Second, we develop a statistical framework for bosonic string theory in order to study transport properties of black holes in the context of membrane paradigm. We find that the shear viscosity of a highly excited bosonic string is equal to that of black hole horizon up to a numerical factor.
  • Markkanen, Tommi (Helsingin yliopisto, 2014)
    Cosmic inflation is a phase of accelerating, nearly exponential expansion of the spacetime fabric of the Universe, which is assumed to have taken place almost immediately after the Big Bang. Inflation possesses the appealing property that it provides solutions to deep cosmological problems, such as the flatness and horizon problems, and also gives a natural origin for the formation of the large scale structures we observe today. In this thesis we set out to investigate the role quantum corrections play for some simple models where inflation is driven by a single scalar field. It is essential that here the quantum corrections are calculated via curved space field theory. In this technique one quantizes only the matter fields, the dynamics of which take place on a curved classical background. This approach is rarely used in mainstream cosmology and it has the benefit that it allows the quantum fluctuations to back-react on classical Einsteinian gravity. The curved space quantum corrections are studied first in the effective action formalism via the Schwinger-DeWitt expansion and then by constructing effective equations of motion by using the slow-roll technique. We also focus on consistent renormalization and show how to renormalize the effective equations of motion without any reference to an effective action for an interacting theory in curved spacetime. Due to a potential infrared enhancement in effective equations in quasi-de Sitter space, we also perform a resummation of Feynman diagrams in curved non-static space and observe that it regulates the infrared effects. Concerning implications for actual inflationary models, we focus on chaotic type models and observe the quantum corrections to be insignificant, but nevertheless to have theoretically a non-trivial structure.
  • Vepsäläinen, Mikko (Helsingin yliopisto, 2007)
    When heated to high temperatures, the behavior of matter changes dramatically. The standard model fields go through phase transitions, where the strongly interacting quarks and gluons are liberated from their confinement to hadrons, and the Higgs field condensate melts, restoring the electroweak symmetry. The theoretical framework for describing matter at these extreme conditions is thermal field theory, combining relativistic field theory and quantum statistical mechanics. For static observables the physics is simplified at very high temperatures, and an effective three-dimensional theory can be used instead of the full four-dimensional one via a method called dimensional reduction. In this thesis dimensional reduction is applied to two distinct problems, the pressure of electroweak theory and the screening masses of mesonic operators in quantum chromodynamics (QCD). The introductory part contains a brief review of finite-temperature field theory, dimensional reduction and the central results, while the details of the computations are contained in the original research papers. The electroweak pressure is shown to converge well to a value slightly below the ideal gas result, whereas the pressure of the full standard model is dominated by the QCD pressure with worse convergence properties. For the mesonic screening masses a small positive perturbative correction is found, and the interpretation of dimensional reduction on the fermionic sector is discussed.
  • Tahkokallio, Touko (Helsingin yliopisto, 2008)
    The description of quarks and gluons, using the theory of quantum chromodynamics (QCD), has been known for a long time. Nevertheless, many fundamental questions in QCD remain unanswered. This is mainly due to problems in solving the theory at low energies, where the theory is strongly interacting. AdS/CFT is a duality between a specific string theory and a conformal field theory. Duality provides new tools to solve the conformal field theory in the strong coupling regime. There is also some evidence that using the duality, one can get at least qualitative understanding of how QCD behaves at strong coupling. In this thesis, we try to address some issues related to QCD and heavy ion collisions, applying the duality in various ways.
  • Mykkänen, Anne-Mari (Helsingin yliopisto, 2012)
    In this thesis we use lattice field theory to study different frontier problems in strongly coupled non-Abelian gauge theories, focusing on large-N models and walking technicolor theories. Implementing lattice studies of technicolor theories, we consider the SU(2) gauge theory with two fermions transforming under the adjoint representation, which constitutes one of the candidate theories for technicolor. The early lattice Monte Carlo studies of this model have used an unimproved Wilson fermion formulation. However, large lattice cutoff effects can be expected with the unimproved formulation, and so we present the calculation of the O(a) improved lattice Wilson-clover action. In addition to the adjoint representation fermions, we also determine the improvement coefficients for SU(2) gauge theory with two fundamental representation fermions. In another work, we study the deconfined phase of strongly interacting matter, investigating Casimir scaling and renormalization properties of Polyakov loops in different irreducible representations, in SU(N) gauge theories at finite temperature. We study the approach to the large-N limit by performing lattice simulations of Yang-Mills theories with gauge groups from SU(2) to SU(6), taking the twelve lowest irreducible representations for each gauge group into consideration. We find clear evidence of Casimir scaling and identify the temperature dependence of the renormalized Polyakov loops. The third study I present is related to the long-standing idea of non-Abelian gauge theories having a close relation to some kind of string theory. In the confining regime of SU(N) gauge theories, the flux lines between well separated color sources are expected to be squeezed in a thin, stringlike tube, and the interaction between the sources can be described by an effective string theory. One of the consequences of the effective string description at zero temperature is the presence of the Luescher term - a Casimir effect due to the finiteness of the interquark distance - in the long distance interquark potential. To study the validity of this effective model, we compute the static quark potential in SU(3) and SU(4) Yang-Mills theories through lattice simulations, generalizing an efficient `multilevel' algorithm proposed by Luescher and Weisz to an improved lattice action.
  • Collin, Anssi (Helsingin yliopisto, 2006)
  • Köster, Urs (Helsingin yliopisto, 2009)
    What can the statistical structure of natural images teach us about the human brain? Even though the visual cortex is one of the most studied parts of the brain, surprisingly little is known about how exactly images are processed to leave us with a coherent percept of the world around us, so we can recognize a friend or drive on a crowded street without any effort. By constructing probabilistic models of natural images, the goal of this thesis is to understand the structure of the stimulus that is the raison d etre for the visual system. Following the hypothesis that the optimal processing has to be matched to the structure of that stimulus, we attempt to derive computational principles, features that the visual system should compute, and properties that cells in the visual system should have. Starting from machine learning techniques such as principal component analysis and independent component analysis we construct a variety of sta- tistical models to discover structure in natural images that can be linked to receptive field properties of neurons in primary visual cortex such as simple and complex cells. We show that by representing images with phase invariant, complex cell-like units, a better statistical description of the vi- sual environment is obtained than with linear simple cell units, and that complex cell pooling can be learned by estimating both layers of a two-layer model of natural images. We investigate how a simplified model of the processing in the retina, where adaptation and contrast normalization take place, is connected to the nat- ural stimulus statistics. Analyzing the effect that retinal gain control has on later cortical processing, we propose a novel method to perform gain control in a data-driven way. Finally we show how models like those pre- sented here can be extended to capture whole visual scenes rather than just small image patches. By using a Markov random field approach we can model images of arbitrary size, while still being able to estimate the model parameters from the data.
  • Johansson, Mikael (Helsingin yliopisto, 2007)
    Quantum effects are often of key importance for the function of biological systems at molecular level. Cellular respiration, where energy is extracted from the reduction of molecular oxygen to water, is no exception. In this work, the end station of the electron transport chain in mitochondria, cytochrome c oxidase, is investigated using quantum chemical methodology. Cytochrome c oxidase contains two haems, haem a and haem a3. Haem a3, with its copper companion, CuB, is involved in the final reduction of oxygen into water. This binuclear centre receives the necessary electrons from haem a. Haem a, in turn, receives its electrons from a copper ion pair in the vicinity, called CuA. Density functional theory (DFT) has been used to clarify the charge and spin distributions of haem a, as well as changes in these during redox activity. Upon reduction, the added electron is shown to be evenly distributed over the entire haem structure, important for the accommodation of the prosthetic group within the protein. At the same time, the spin distribution of the open-shell oxidised state is more localised to the central iron. The exact spin density distribution has been disputed in the literature, however, different experiments indicating different distributions of the unpaired electron. The apparent contradiction is shown to be due to the false assumption of a unit amount of unpaired electron density; in fact, the oxidised state has about 1.3 unpaired electrons. The validity of the DFT results have been corroborated by wave function based coupled cluster calculations. Point charges, for use in classical force field based simulations, have been parameterised for the four metal centres, using a newly developed methodology. In the procedure, the subsystem for which point charges are to be obtained, is surrounded by an outer region, with the purpose of stabilising the inner region, both electronically and structurally. Finally, the possibility of vibrational promotion of the electron transfer step between haem a and a3 has been investigated. Calculating the full vibrational spectra, at DFT level, of a combined model of the two haems, revealed several normal modes that do shift electron density between the haems. The magnitude of the shift was found to be moderate, at most. The proposed mechanism could have an assisting role in the electron transfer, which still seems to be dominated by electron tunnelling.
  • Käpyaho, Asko (Helsingin yliopisto, 2007)
    This thesis summarises the results of four original papers concerning U-Pb geochronology and geochemical evolution of Archaean rocks from the Kuhmo terrain and the Nurmes belt, eastern Finland. The study area belongs to a typical Archaean granite-greenstone terrain, composed of metavolcanic and metasedimentary rocks in generally N-S trending greenstone belts as well as a granitoid-gneiss complex with intervening gneissic and migmatised supracrustal and plutonic rocks. U-Pb data on migmatite mesosomes indicate that the crust surrounding the Tipasjärvi-Kuhmo-Suomussalmi greenstone belt is of varying age. The oldest protolith detected for a migmatite mesosome from the granitoid-gneiss complex is 2.94 Ga, whereas the other dated migmatites protoliths have ages of 2.84 2.79 Ga. The latter protoliths are syngenetic with the majority of volcanic rocks in the adjacent Tipasjärvi-Kuhmo-Suomussalmi greenstone belt. This suggests that the genesis of some of the volcanic rocks within the greenstone belt and surrounding migmatite protoliths could be linked. Metamorphic zircon overgrowths with ages of 2.84 2.81 Ga were also obtained. The non-migmatised plutonic rocks in the Kuhmo terrain and in the Nurmes belt record secular geochemical evolution, typical of Archaean cratons. The studied tonalitic rocks have ages of 2.83 2.75 Ga and they have geochemical characteristics similar to low-Al and high-Al TTD (tonalite-trondhjemite-dacite). The granodiorites, diorites, and gabbros with high Mg/Fe and LILE-enriched characteristics were mostly emplaced between 2.74 2.70 Ga and they exhibit geochemical characteristics typical of Archaean sanukitoid suites. The latest identified plutonic episode took place at 2.70 2.68 Ga, when compositionally heterogeneous leucocratic granitoid rocks, with a variable crustal component, were emplaced. U-Pb data on migmatite leucosomes suggest that leucosome generation may have been coeval with this latest plutonic event. On the basis of available U-Pb and Sm-Nd isotopic data it appears that the plutonic rocks of the Kuhmo terrain and the Nurmes belt do not contain any significant input from Palaeoarchaean sources. A characteristic feature of the Nurmes belt is the presence of migmatised paragneisses, locally preserving primary edimentary structures, with sporadic amphibolite intercalations. U-Pb studies on zircons indicate that the precursors of the Nurmes paragneisses were graywackes that were deposited between 2.71 Ga and 2.69 Ga and that they had a prominent 2.75 2.70 Ga source. Nd isotopic and whole-rock geochemical data for the intercalated amphibolites imply MORB sources. U-Pb data on zircons from the plutonic rocks and paragneisses reveal that metamorphic zircon growth took place at 2.72 2.63 Ga. This was the last tectonothermal event related to cratonisation of the Archaean crust of eastern Finland.
  • Würtz, Peter (Helsingin yliopisto, 2008)
    NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of 13C,15N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.
  • Hänninen, Teemu (Helsingin yliopisto, 2006)
    The concept of an atomic decomposition was introduced by Coifman and Rochberg (1980) for weighted Bergman spaces on the unit disk. By the Riemann mapping theorem, functions in every simply connected domain in the complex plane have an atomic decomposition. However, a decomposition resulting from a conformal mapping of the unit disk tends to be very implicit and often lacks a clear connection to the geometry of the domain that it has been mapped into. The lattice of points, where the atoms of the decomposition are evaluated, usually follows the geometry of the original domain, but after mapping the domain into another this connection is easily lost and the layout of points becomes seemingly random. In the first article we construct an atomic decomposition directly on a weighted Bergman space on a class of regulated, simply connected domains. The construction uses the geometric properties of the regulated domain, but does not explicitly involve any conformal Riemann map from the unit disk. It is known that the Bergman projection is not bounded on the space L-infinity of bounded measurable functions. Taskinen (2004) introduced the locally convex spaces LV-infinity consisting of measurable and HV-infinity of analytic functions on the unit disk with the latter being a closed subspace of the former. They have the property that the Bergman projection is continuous from LV-infinity onto HV-infinity and, in some sense, the space HV-infinity is the smallest possible substitute to the space H-infinity of analytic functions. In the second article we extend the above result to a smoothly bounded strictly pseudoconvex domain. Here the related reproducing kernels are usually not known explicitly, and thus the proof of continuity of the Bergman projection is based on generalised Forelli-Rudin estimates instead of integral representations. The minimality of the space LV-infinity is shown by using peaking functions first constructed by Bell (1981). Taskinen (2003) showed that on the unit disk the space HV-infinity admits an atomic decomposition. This result is generalised in the third article by constructing an atomic decomposition for the space HV-infinity on a smoothly bounded strictly pseudoconvex domain. In this case every function can be presented as a linear combination of atoms such that the coefficient sequence belongs to a suitable Köthe co-echelon space.