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  • Cheng, Zhuo (Helsingin yliopisto, 2015)
    Risk management is essential in forest management planning. However, decision making with risk analysis is rarely done in forestry. This study presents an example of the application of conditional value-at-risk (CVaR) as a decision tool and optimizes the management planning problem from a risk perspective. Stochastic programming is used to solve the problem. The model contains four different types of risk using an assumed probability distribution and quantifies these risks, namely, inventory errors, growth model errors, price uncertainty and policy uncertainty. The results suggest that forest owners’ risk tolerance, i.e., their willingness and ability to assume risk determines to the greatest extent the return potential. When the expected first period income is maximized, the subsequent period always experiences a loss that is the greatest of the entire management horizon. The proportion of carbon subsidy in the first period is also the highest. With this model it is possible to hedge some risks or to use it as means to assess the amount of insurance to purchase in order to transfer risks. The use of CVaR in forest management planning can be seen as a useful tool to manage risk and to assist in the decision making process to assess forest owners’ willingness and ability to tolerate risks.
  • Tahvanainen, Janina (2013)
    Olennaiset toimintaedellytykset- oppi liittyy määräävän markkina-aseman väärinkäyttöön. Eräät toimintaedellytykset ovat niin olennaisia, että määräävässä markkina-asemassa oleva toimija ei voi kieltäytyä toimittamasta niitä kilpailijalleen ilman, että se syyllistyisi artiklan 102 (SEUT) rikkomukseen. Tutkielmassani tarkastellaan kyseisen opin soveltamisessa ilmeneviä eroja erityisesti energiasektorilla sekä erityisesti suhteessa aloihin, joilla immateriaalioikeudet ovat merkittävässä roolissa. Näin pystytään pohtimaan opin soveltamista kahdessa täysin erilaisessa markkinaympäristössä. Keskeinen ongelma doktriinin soveltamisessa on sen negatiivinen vaikutus määräävässä markkina-asemassa olevan yrityksen kannustimiin panostaa innovaatioon. Bronner- tapauksen mukaan toimittamasta kieltäytymisen pitäisi poistaa kilpailu kokonaan sellaisen kilpailijan osalta, joka haluaa käyttää toimintaedellytystä. Lisäksi edellytetään, että kieltäytymiselle ei ole objektiivisia perusteita ja että toimintaedellytys on välttämätön, eikä ilman sitä toiminta markkinoilla ole mahdollista. Suhteessa immateriaalioikeuksiin opin soveltaminen on edellyttänyt, että kieltäytyminen estää uuden tuotteen markkinoille tulon. Microsoft- tapauksessa lähestymistapaa muutettiin. Kieltäytymisen ei tarvinnut estää uuden tuotteen markkinoille tuloa vaan opin soveltamiselle riittävää oli, että tekninen kehitys markkinoilla rajoittuu. Tapauksessa määriteltiin myös, että muutaman kilpailijan läsnäolo markkinoilla ei estä opin soveltamista. Pian tämän jälkeen komission ensisijaisia täytäntöönpanotavoitteita koskevassa tiedonannossa teknisen kehityksen rajoittaminen korvattiin kuluttajahaitalla. Tämä edellyttää, että toimittamisesta kieltäytymiseen liittyvät kielteiset vaikutukset ovat suuremmat kuin toimintaedellytyksen käytön sallimisesta aiheutuvat seuraukset. Komission tiedoksiannossa ei tehdä eroa eri immateriaalioikeuksien välillä. Näin ollen opin soveltamista patentteihin ei pidä rajoittaa. Standardisointeihin sisällytettyjen patenttien osalta uusi tuote- vaatimusta ei edes välttämättä ole perusteltua soveltaa, koska asiakkaat saattavat tarvita enemmän yhteensopivia tuotteita kuin uutta tuotetta. Kyseisen edellytyksen soveltaminen olisi hankalaa myös energiasektorilla, jossa tuote on yleensä homogeeninen. Huomioon pitää myös ottaa, että komission tiedoksiannon mukaan käytön sallimisesta aiheutuvien negatiivisten vaikutusten puuttuminen voidaan olettaa, jos toimintaedellytyksen rakentamiseen on käytetty julkisia varoja, toimija on nauttinut yksinoikeuksia tai lainsäädäntö velvoittaa sallimaan kilpailijoiden toimintaedellytyksen käytön. Tällainen tilanne saattaa olla käsillä esimerkiksi vasta liberalisoiduilla markkinoilla. Microsoft-tapaukseen liittyy kuitenkin sellaisia erityispiirteitä, jotka saattavat hankaloittaa siinä käytettyjen edellytysten soveltamista. EU-tuomioistuimet ovat olleet myös vastahakoisia soveltamaan komission tiedoksiantoa. Post Danmark- tapaus kuitenkin antaa aihetta uskoa, että tämä linja olisi muuttumassa.
  • Kulesskiy, Evgeny (Helsingin yliopisto, 2015)
    Syndecans are cell surface heparan sulfate proteoglycans which are present in all tissues and cell types and have distinct temporal and spatial expression patterns. They play important roles in embryonic development of the organism and control relocation and alteration of extracellular matrix components. Syndecans regulate cell migration, adhesion and proliferation and are engaged in tissue injury, inflammation processes, pathogenesis of infectious diseases and tumor biology. This thesis summarizes the results of studies on one of the syndecan family receptors syndecan-3 (also known as N-syndecan). This proteoglycan is abundantly expressed in developing brain. Syndecan-3 acts as a signaling receptor upon binding of its ligand, heparin-binding growth associated molecule (HB-GAM; also known as pleiotrophin), which activates the cortactin c-Src signaling pathway. This leads to rapid neurite extension in neuronal cells, which makes syndecan-3 an interesting transmembrane receptor in neuronal development and regeneration. However, little is known about the signaling mechanism of syndecan-3. Here I show formation of ligand-syndecan-3 signaling complexes at the cell surface using fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET). Ligand binding leads to dimerization of syndecan-3 at the cell surface. The dimerized syndecan-3 colocalizes with actin in the filopodia of cells. Lysine 383 in the juxtamembrane (ERKE) sequence and G392 and G396 from GXXXG canonical motif are shown to be important for the ligand-induced dimerization, whereas the cytosolic domain are not required for the dimerization. In addition to acting as a signaling receptor, syndecan-3 acts as a co-receptor in epidermal growth factor receptor (EGFR) ligand binding. FRET analysis suggests that interactions of syndecan-3 and EGFR depend on a shared ligand such as heparin-binding EGF-like growth factor (HB-EGF). Furthermore, it was shown that syndecan-3 may act as a receptor for other ligands, like glial cell line-derived neurotrophic factor (GDNF). In addition, I have found a new receptor for HB-GAM glypican-2 which may be involved in regulation of HB-GAM signaling by competing with syndecan-3 for ligand binding.
  • Nousiainen, Aura (Helsingin yliopisto, 2015)
    The use of pesticides has allowed the efficient use of agricultural soil and provided humans with greater yields and agri-food security. Unfortunately, many pesticides have also adverse effects to the environment or human health, and may end up where they were not intended: the precious groundwater reserves. The use of atrazine, a herbicide used for controlling broad-leaf weeds, was banned in the EU for this reason in 2004, but is still globally one of the most widely used herbicides today. Although atrazine can be completely mineralized by microbes, in the subsurface, slow or incomplete degradation of atrazine is often observed. The ability of atrazine degradation by microbes can be utilized in bioremediation, a technique in which contaminants are removed by microbial activity. This study was undertaken to elucidate the potential use of genetic tools, such as quantitative PCR (qPCR), radiorespirometry, microautoradiography (MAR), clone libraries and genetic fingerprinting methods, in atrazine contaminated soils, and to apply them in atrazine bioremediation. Collaboration with our Indian partner permitted comparison between atrazine treated, cropped agricultural soils and boreal subsoil contaminated two decades ago with residual atrazine from weed control in municipal areas. Four different bioremediation methods, natural attenuation, bioaugmentation, biostimulation, and their combination, were used to reduce atrazine concentration in soil. Atrazine degradation copy numbers often reflected the atrazine degradation potential, indicating their robustness as monitoring tools in different soils. The most efficient bioremediation treatment was bioaugmentation by atrazine degrading bacterial strains Pseudomonas citronellolis or Arthrobacter aurescens, or by an atrazine degrading bacterial consortium: in the agricultural soil, up to 90% of atrazine was degraded in less than a week, whereas in the boreal subsoil, 76% of atrazine was mineralized. In the clone library constructed from boreal soil, several clones related to taxa which include known atrazine degraders were found. In this soil, biostimulation with additional carbon was an efficient treatment at reduced temperature. In general, the efficiency of atrazine removal in different treatments was bioaugmentation and biostimulation > bioaugmentation > biostimulation > natural attenuation. Previous exposure to atrazine was the most influential factor in atrazine disappearance from soil, as recent exposure always correlated with faster atrazine degradation, and greatly affected the composition of the microbial community, elucidated by LH-PCR. These results serve as an example on how soil origin, exposure history, organic content and use must be taken into account while choosing the best bioremediation method. Knowledge on the presence of genetic degradation potential can be helpful in choosing the treatment method. While bioaugmentation removed 90% of atrazine from soil, its application in field scale may be challenging. Our results show, that biostimulation alone may serve as the treatment method of choice, even in the challenging subsoil surroundings where atrazine concentrations are low.
  • Pesonen, Janne (Helsingin yliopisto, 2001)
  • Chen, Yongchen (2013)
    Soil contamination with oily products poses great healthy and environmental risks to the polluted sites. The remediation difficulty mainly comes from the complexity of hydrocarbons. Different kinds of remediation technologies have been applied for hydrocarbon removal from soil. New technologies especially in situ bioremediation technologies are emerging constantly. Soil assessment is a key step in the remediation processes since it provides information about the contamination level and potential risks. In the present study, hydrocarbon contaminated soil samples were collected from two sites (one site was contaminated by weathered oily sludge waste with some vegetated plots; the other was contaminated with fuel oil with short-chain hydrocarbons). The samples were analyzed for physicochemical properties and hydrocarbon degraders were enumerated. Four degrading strains were isolated from the samples and their 16S rRNA genes were sequenced. The samples and isolates were investigated to check the existence of three catabolic genes involved in petroleum degradation. The objective was to reveal the intrinsic bioremediation potential of contaminated soils by investigating the key remediation “players” i.e. the degrader microorganisms and catabolic genes. The coexistence of abundant degraders and diverse catabolic genes give the soil a good potential for bioremediation. In addition, the relationships between degrader counts, genes detection and soil contamination levels can reveal how the contaminants affect the indigenous microbial community. The differences between vegetated and nonvegetated plots can also suggest if vegetation with legumes has good potential for hydrocarbon bioremediation. According to the results, both sites were moderately contaminated with different hydrocarbon composition. In the landfarming site, the TPH depletion in vegetated fields was higher than the unvegetated bulk soil areas. However, the degrading microorganism counts had no significant differences between vegetated and nonvegetated plots. The hydrocarbon contamination level had no correlation with the degrader counts. In subsurface soils where aeration was quite limited, degrading microorganisms were much lower than those in surface soils. Catabolic genes were detected from the isolated strains but rarely from the contaminated soil samples. The contaminants co-extracted with soil DNA may inhibit the PCR-based gene detection. With more primer sets or primers targeting broader genetic diversity ranges, more detection results can be expected.
  • 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.
  • Inkinen, Ville (2014)
    In June 2012, the Commission introduced the Monitoring and Reporting Regulation (601/2012) by virtue of Article 14(1) of the ETS Directive (2003/87/EC). In recital 2 of the MRR the Commission puts forward an interpretation of the Renewable Energy Directive which marks a major policy change. According to the interpretation, the sustainability criteria for biofuels and bioliquids in Article 17 of the Renewable Energy Directive must be fulfilled as a precondition to the rule in Annex IV of the ETS Directive according to which emissions from the use biomass shall be considered zero. Applying the sustainability criteria in the Renewable Energy Directive results from the interpretation that biomass zero-treatment constitutes ‘financial support’ within the meaning of Article 17(1)(c) of the Renewable Energy Directive. Presently, due to the limited use of biofuels and bioliquids in the Emissions Trading sector, the policy change is of minor significance. However, the Commission is preparing a proposal to introduce sustainability criteria also for solid and gaseous biomass in heating and cooling and electricity. The proposal is expected to be formally tabled in fall 2013. In many Member States, emissions from the use of solid biomass are significant as compared to the current emissions in the whole Emissions Trading sector, and thus the economic consequences can be major. The treatment of emissions from solid biomass is also likely to have major implications for the Member States in fulfilling their binding national targets under the Renewable Energy Directive. Firstly, this study analyses the described interaction between the ETS Directive and the RED. The main finding in this regard is that the interpretation whereby biomass zero-treatment would constitute ‘financial support’ within the meaning of Article 17(1)(c) of the Renewable Energy Directive is highly problematic. Secondly, the competence of the Commission in amending the Annex IV of the ETS Directive is examined. This study posits that the Commission does not have the competence to modify biomass zero-treatment to the extent of imposing a precondition to fulfil the sustainability criteria. Lastly, the upcoming sustainability criteria for solid and gaseous biomass will be briefly discussed. The upcoming criteria will resemble those for biofuels and bioliquids with some alterations. Pivotal with respect to biomass zero-treatment will be the wording of the upcoming provisions. If the norm requiring fulfilling the criteria to be eligible for financial support will be formulated in the same manner as in the Renewable Energy Directive, the interpretation in recital 2 of the Monitoring and Reporting Regulation could have the result that the upcoming extension will apply in the Emissions Trading Scheme automatically.
  • 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.
  • Ylinen, Pekka (Helsingin yliopisto, 2006)
    The aim of the present experimental study was to find out if the applications of coralline hydroxyapatite (HA) can be improved by using bioabsorbable containment or binding substance with particulate HA in mandibular contour augmentation and by using bioabsorbable fibre-reinforced HA blocks in filling bone defects and in anterior lumbar interbody fusion. The use of a separate curved polyglycolide (PGA) containment alone or together with a fast resorbing polyglycolide/polylactide (PGA/PLA) binding substance were compared to the conventional non-contained method in ridge augmentation in sheep. The contained methods decreased HA migration, but the augmentations did not differ significantly. The use of the containment caused a risk for wound dehiscence and infection. Histologically there was a rapid connective tissue ingrowth into the HA graft and it was more abundant with the PGA containment compared to the non-contained augmentation and even additionally rich when the HA particles were bound with PGA/PLA copolymer. However, the bone ingrowth was best in the non-contained augmentation exceeding 10-12 % of the total graft area at 24 weeks. Negligible or no bone ingrowth was seen in the cases where the polymer composite was added to the HA particles and, related to that, foreign-body type cells were seen at the interface between the HA and host bone. The PGA and poly-dl/l-lactide (PDLLA) fibre-reinforced coralline HA blocks were studied in the metaphyseal and in the diaphyseal defects in rabbits. A rapid bone ingrowth was seen inside the both types of implants. Both PGA and PDLLA fibres induced an inflammatory fibrous reaction around themselves but it did not hinder the bone ingrowth. The bone ingrowth pattern was directed according to the loading conditions so that the load-carrying cortical ends of the implants as well as the implants sited in the diaphyseal defects were the most ossified. The fibre-reinforced coralline HA implants were further studied as stand-alone grafts in the lumbar anterior interbody implantation in pigs. The strength of the HA implants proved not to be adequate, the implants fractured in six weeks and the disc space was gradually lost similarly to that of the discectomized spaces. Histologically, small quantities of bone ingrowth was seen in some of the PGA and PDLLA reinforced coralline implants while no bone formation was identified in any of the PDLLA reinforced synthetic porous HA implants. While fragmented, the inner structure of the implants was lost, the bone ingrowth was minimal, and the disc was replaced by the fibrous connective tissue. When evaluated radiologically the grade of ossification was assessed as better than histologically, and, when related to the histologic findings, CT was more dependable than the plain films to show ossification of the implanted disc space. Local kyphosis was a frequent finding along with anterior bone bridging and ligament ossification as a consequence of instability of the implanted segment.
  • 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.
  • Ryynänen, Heikki (Helsingin yliopisto, 2006)
    Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.
  • 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.
  • Pääkkönen, Kimmo (Helsingin yliopisto, 2003)