Väsyttävästi kuormitettujen hitsattujen rakenteiden suunnittelukäytännön kehittäminen

Hitsatuilla rakenteilla väsyminen on keskeinen vauriotekijä. Väsymiskestoiän laskentaan on olemassa useita erilaisia menetelmiä, joista hot spot ﷓menetelmä on hitsattujen rakenteiden yhteydessä yhä yleistyvä ja sangen käyttökelpoinen. Hot spot menetelmässä kestoikälaskenta perustuu rakenteellisen jännityksen vaihteluun ja pieneen joukkoon kokeellisesti määrättyjä Wöhler-käyriä. Rakenteellinen jännitys voidaan määrittää joko prototyypistä mittaamalla, elementtimenetelmällä laskemalla tai parametristen kerrointen avulla. Suunnittelukäytännön kehittämisessä tutkittiin esimerkkirakenteena Rammer RC 22 leikkurimurskainta. Tarkoituksena oli mitata murskaimesta voimasuureita, joita voitaisiin käyttää kuormitustietona laskettaessa jännityksiä elementtimenetelmällä. Myöhempien laskentatulosten verifiointia varten mitattiin lisäksi muutamia hot spot ﷓jännityksiä. Työn kokeellinen puoli keskittyi voimasuuremittauksiin ja niistä saatavien tulosten saattamiseen sopusointuun vapaakappalemallien kanssa. Suoritettiin lukuisia kalibrointimittauksia ja mittausjärjestelyä kehitettiin, kunnes syyt aluksi saatujen mittaustulosten virheellisyyteen selvisivät. Leikkausvoimamittausten osalta tuloksia verifioitiin elementtimenetelmälaskelmin. Työn tuloksena saatiin luotua toimiva pohja voimasuure- ja hot spot ﷓mittauksille. Jatkossa voidaan siirtyä tekemään mittauksia todellisissa työskentelytilanteissa.

Ultralujasta teräksestä valmistetun henkilönostimen teleskooppipuomin kehittäminen

Tässä työssä kehitettiin palo- ja pelastuskäyttöön tarkoitettuun henkilönostimeen teleskooppipuomin profiilit. Profiilien valmistusmateriaalina oli kuumavalssattu, ultraluja säänkestävä rakenneteräs. Työssä kehitettiin standardien ja ohjeiden pohjalta laskentapohja, jolla voidaan tutkia teleskooppipuomin jaksojen tukireaktioita, taivutus- ja vääntömomentteja ja leikkaus ja normaalivoimia. Laskentapohjassa voidaan varioida eri kuormitusten suuntia, teleskooppipuomin sivusuuntaista ulottumaa ja nostokulmaa. Profiilien alustavassa mitoituksessa hyödynnettiin paikallisen lommahduksen huomioon ottavia standardeja ja suunnitteluohjeita. Eri poikkileikkausten ominaisuuksia verrattiin keskenään ja profiili valittiin yhdessä kohdeyrityksen kanssa. Alustavan mitoituksen yhteydessä muodostettiin apuohjelma valitulle poikkileikkaukselle, jolla voitiin tutkia profiilin eri muuttujien vaikutusta mm. paikalliseen lommahdukseen ja jäykkyyteen. Laskentapohjaan sisällytettiin myös optimointirutiini, jolla voitiin minimoida poikkileikkauksen pinta-ala ja tätä kautta profiilin massa. Lopullinen mitoitus suoritettiin elementtimenetelmällä. Mitoituksessa tutkittiin alustavasti mitoitettujen profiilien paikallista lommahdusta lineaarisen stabiilius- ja epälineaarisen analyysin pohjalta. Profiilien jännityksiä tutkittiin tarkemmin mm. varioimalla kuormituksia ja osittelemalla elementtien normaalijännityksiä. Diplomityössä kehitetyllä ja analysoidulla teleskooppipuomilla voitiin keventää jaksojen painoja 15-30 %. Sivusuuntainen ulottuma parani samalla lähes 20 % ja nimelliskuorma kasvoi 25 %.

Ultrakevyen rahtialuksen kansiluukkujen sekä luukkujen siirto- ja varastointijärjestelmän suunnittelu hyödyntäen kevytrakennekonsepteja

Tämän työn tarkoituksena oli tutkia miten rahtialuksen kansiluukut voitaisiin valmistaa mahdollisimman kevyiksi. Katettavan ruuman pinta-ala on n. 10 m x 40 m. Luukkujen suuresta jännevälistä johtuen, rakenteelta vaaditaan suurta jäykkyyttä. Erilaisina vaihtoehtoina tutkittiin vaahtomaista alumiinia, alumiinisia kennorakenteita ja polyuretaanisia sandwich-rakenteita. Työssä vertailtiin myös erilaisia geometrisia ratkaisuja, joilla kansiluukkujen jäykkyyttä pyrittiin lisäämään ja sitä kautta pääsemään pienempään materiaalin tarpeeseen. Geometriaa suunniteltaessa huomioitiin myös vaikutukset ruuman tilavuuteen ja lainsäädännön asettamat reunaehdot. Lainsäädännöstä saatiin esimerkiksi turvakaiteiden minimikorkeus, joka vaikuttaa suoraan ruuman tilavuuteen, kun aluksen korkeimmaksi kohdaksi on valittu laivan keskilinja ja tämä korkeus on annettu suunnittelun lähtötietona. Tietokoneavusteisen lujuuslaskennan avulla eri vaihtoehdoista muodostettiin elementtimallit. Malleja varioimalla ja tuloksia vertailemalla saatiin selville kevyin mahdollinen rakenne ja geometria. Malleista saatiin selville myös luukkujen tukireaktiovoimat, eli voimat, jotka luukut kohdistavat aluksen muihin rakenteisiin. Lisäksi työssä mietittiin erilaisia tapoja ruuman avaamiseen ja avaamistavan vaikutusta kansiluukkujen painoon, geometriaan ja ruuman tilavuuteen.

Flexible multibody dynamics and intelligent control of a hydraulically driven hybrid redundant robot machine

The assembly and maintenance of the International Thermonuclear Experimental Reactor (ITER) vacuum vessel (VV) is highly challenging since the tasks performed by the robot involve welding, material handling, and machine cutting from inside the VV. The VV is made of stainless steel, which has poor machinability and tends to work harden very rapidly, and all the machining operations need to be carried out from inside of the ITER VV. A general industrial robot cannot be used due to its poor stiffness in the heavy duty machining process, and this will cause many problems, such as poor surface quality, tool damage, low accuracy. Therefore, one of the most suitable options should be a light weight mobile robot which is able to move around inside of the VV and perform different machining tasks by replacing different cutting tools. Reducing the mass of the robot manipulators offers many advantages: reduced material costs, reduced power consumption, the possibility of using smaller actuators, and a higher payload-to-robot weight ratio. Offsetting these advantages, the lighter weight robot is more flexible, which makes it more difficult to control. To achieve good machining surface quality, the tracking of the end effector must be accurate, and an accurate model for a more flexible robot must be constructed. This thesis studies the dynamics and control of a 10 degree-of-freedom (DOF) redundant hybrid robot (4-DOF serial mechanism and 6-DOF 6-UPS hexapod parallel mechanisms) hydraulically driven with flexible rods under the influence of machining forces. Firstly, the flexibility of the bodies is described using the floating frame of reference method (FFRF). A finite element model (FEM) provided the Craig-Bampton (CB) modes needed for the FFRF. A dynamic model of the system of six closed loop mechanisms was assembled using the constrained Lagrange equations and the Lagrange multiplier method. Subsequently, the reaction forces between the parallel and serial parts were used to study the dynamics of the serial robot. A PID control based on position predictions was implemented independently to control the hydraulic cylinders of the robot. Secondly, in machining, to achieve greater end effector trajectory tracking accuracy for surface quality, a robust control of the actuators for the flexible link has to be deduced. This thesis investigates the intelligent control of a hydraulically driven parallel robot part based on the dynamic model and two schemes of intelligent control for a hydraulically driven parallel mechanism based on the dynamic model: (1) a fuzzy-PID self-tuning controller composed of the conventional PID control and with fuzzy logic, and (2) adaptive neuro-fuzzy inference system-PID (ANFIS-PID) self-tuning of the gains of the PID controller, which are implemented independently to control each hydraulic cylinder of the parallel mechanism based on rod length predictions. The serial component of the hybrid robot can be analyzed using the equilibrium of reaction forces at the universal joint connections of the hexa-element. To achieve precise positional control of the end effector for maximum precision machining, the hydraulic cylinder should be controlled to hold the hexa-element. Thirdly, a finite element approach of multibody systems using the Special Euclidean group SE(3) framework is presented for a parallel mechanism with flexible piston rods under the influence of machining forces. The flexibility of the bodies is described using the nonlinear interpolation method with an exponential map. The equations of motion take the form of a differential algebraic equation on a Lie group, which is solved using a Lie group time integration scheme. The method relies on the local description of motions, so that it provides a singularity-free formulation, and no parameterization of the nodal variables needs to be introduced. The flexible slider constraint is formulated using a Lie group and used for modeling a flexible rod sliding inside a cylinder. The dynamic model of the system of six closed loop mechanisms was assembled using Hamilton’s principle and the Lagrange multiplier method. A linearized hydraulic control system based on rod length predictions was implemented independently to control the hydraulic cylinders. Consequently, the results of the simulations demonstrating the behavior of the robot machine are presented for each case study. In conclusion, this thesis studies the dynamic analysis of a special hybrid (serialparallel) robot for the above-mentioned special task involving the ITER and investigates different control algorithms that can significantly improve machining performance. These analyses and results provide valuable insight into the design and control of the parallel robot with flexible rods.

The Plastic Capacity of Boiler Supporting Headers

The goal of this thesis was to make a dimensioning tool to determine the plastic capacity of the boiler supporting header. The capacity of the header is traditionally determined by using FE-method during the project phase. By using the dimensioning tool the goal is to ensure the capacity already in the proposal phase. The study began by analyzing the headers of the ongoing projects by using FE-method. For the analytical solution a plain header was analyzed without the effects of branches or lug. The calibration of parameters in the analytical solution was made using these results. In the analytical solution the plastic capacity of the plastic hinges in the header was defined. The stresses caused by the internal pressure as well as the normal and shear forces caused by the external loading reduced the plastic moment. The final capacity was determined by using the principle of virtual work. The weakening effect of the branches was taken into account by using pressure areas. Also the capacity of the punching shear was defined. The results from the FE-analyses and the analytical solution correlate with each other. The results from the analytical solution are conservative but give correct enough results when considering the accuracy of the used method.

Monooxygenase Diversity and Oxygen Activation within Polyketide Antibiotic Biosynthesis

Molecular oxygen (O2) is a key component in cellular respiration and aerobic life. Through the redox potential of O2, the amount of free energy available to organisms that utilize it is greatly increased. Yet, due to the nature of the O2 electron configuration, it is non-reactive to most organic molecules in the ground state. For O2 to react with most organic compounds it must be activated. By activating O2, oxygenases can catalyze reactions involving oxygen incorporation into organic compounds. The oxygen activation mechanisms employed by many oxygenases to have been studied, and they often include transition metals and selected organic compounds. Despite the diversity of mechanisms for O2 activation explored in this thesis, all of the monooxygenases studied in the experimental part activate O2 through a transient carbanion intermediate. One of these enzymes is the small cofactorless monooxygenase SnoaB. Cofactorless monooxygenases are unusual oxygenases that require neither transition metals nor cofactors to activate oxygen. Based on our biochemical characterization and the crystal structure of this enzyme, the mechanism most likely employed by SnoaB relies on a carbanion intermediate to activate oxygen, which is consistent with the proposed substrate-assisted mechanism for this family of enzymes. From the studies conducted on the two-component system AlnT and AlnH, both the functions of the NADH-dependent flavin reductase, AlnH, and the reduced flavin dependent monooxygenase, AlnT, were confirmed. The unusual regiochemistry proposed for AlnT was also confirmed on the basis of the structure of a reaction product. The mechanism of AlnT, as with other flavin-dependent monooxygenases, is likely to involve a caged radical pair consisting of a superoxide anion and a neutral flavin radical formed from an initial carbanion intermediate. In the studies concerning the engineering of the S-adenosyl-L-methionine (SAM) dependent 4-O-methylase DnrK and the homologous atypical 10-hydroxylase RdmB, our data suggest that an initial decarboxylation of the substrate is catalyzed by both of these enzymes, which results in the generation of a carbanion intermediate. This intermediate is not essential for the 4-O-methylation reaction, but it is important for the 10-hydroxylation reaction, since it enables substrate-assisted activation of molecular oxygen involving a single electron transfer to O2 from a carbanion intermediate. The only role for SAM in the hydroxylation reaction is likely to be stabilization of the carbanion through the positive charge of the cofactor. Based on the DnrK variant crystal structure and the characterizations of several DnrK variants, the insertion of a single amino acid in DnrK (S297) is sufficient for gaining a hydroxylation function, which is likely caused by carbanion stabilization through active site solvent restriction. Despite large differences in the three-dimensional structures of the oxygenases and the potential for multiple oxygen activation mechanisms, all the enzymes in my studies rely on carbanion intermediates to activate oxygen from either flavins or their substrates. This thesis provides interesting examples of divergent evolution and the prevalence of carbanion intermediates within polyketide biosynthesis. This mechanism appears to be recurrent in aromatic polyketide biosynthesis and may reflect the acidic nature of these compounds, propensity towards hydrogen bonding and their ability to delocalize π-electrons.

Particle transport method for convection-diffusion-reaction problems

Convective transport, both pure and combined with diffusion and reaction, can be observed in a wide range of physical and industrial applications, such as heat and mass transfer, crystal growth or biomechanics. The numerical approximation of this class of problemscan present substantial difficulties clue to regions of high gradients (steep fronts) of the solution, where generation of spurious oscillations or smearing should be precluded. This work is devoted to the development of an efficient numerical technique to deal with pure linear convection and convection-dominated problems in the frame-work of convection-diffusion-reaction systems. The particle transport method, developed in this study, is based on using rneshless numerical particles which carry out the solution along the characteristics defining the convective transport. The resolution of steep fronts of the solution is controlled by a special spacial adaptivity procedure. The serni-Lagrangian particle transport method uses an Eulerian fixed grid to represent the solution. In the case of convection-diffusion-reaction problems, the method is combined with diffusion and reaction solvers within an operator splitting approach. To transfer the solution from the particle set onto the grid, a fast monotone projection technique is designed. Our numerical results confirm that the method has a spacial accuracy of the second order and can be faster than typical grid-based methods of the same order; for pure linear convection problems the method demonstrates optimal linear complexity. The method works on structured and unstructured meshes, demonstrating a high-resolution property in the regions of steep fronts of the solution. Moreover, the particle transport method can be successfully used for the numerical simulation of the real-life problems in, for example, chemical engineering.

A Bridge Builder or a Raconteur? How Japan Manoeuvres the Global Development Discourse within the TICAD Process

Japan has been a major actor in the field of development cooperation for five decades, even holding the title of largest donor of Official Development Assistance (ODA) during the 1990s. Financial flows, however, are subject to pre-existing paradigms that dictate both donor and recipient behaviour. In this respect Japan has been left wanting for more recognition. The dominance of the so called ‘Washington Consensus’ embodied in the International Monetary Fund (IMF) and the World Bank has long circumvented any indigenous approaches to development problems. The Tokyo International Conference on African Development (TICAD) is a development cooperation conference that Japan has hosted since 1993 every five years. As the main organizer of the conference Japan has opted for the leading position of African development. This has come in the wake of success in the Asian region where Japan has called attention to its role in the so called ‘Asian Miracle’ of fast growing economies. These aspirations have enabled Japan to try asserting itself as a major player in directing the course of global development discourse using historical narratives from both Asia and Africa. Over the years TICAD has evolved into a continuous process with ministerial and follow-up meetings in between conferences. Each conference has produced a declaration that stipulates the way the participants approach the question of African development. Although a multilateral framework, Japan has over the years made its presence more and more felt within the process. This research examines the way Japan approaches the paradigms of international development cooperation and tries to direct them in the context of the TICAD process. Supplementing these questions are inquiries concerning Japan’s foreign policy aspirations. The research shows that Japan has utilized the conference platform to contest other development actors and especially the dominant forces of the IMF and the World Bank in development discourse debate. Japan’s dominance of the process is evident in the narratives found in the conference documents. Relative success has come about by remaining consistent as shown by the acceptance of items from the TICAD agenda in other forums, such as the G8. But the emergence of new players such as China has changed the playing field, as they are engaging other developing countries from a more equal level.

„Und frei erklär' ich alle meine Knechte“ : Höflichkeit als Ausdruck sozialer Utopie in Schillers Drama Wilhelm Tell.

My dissertation is an interdisciplinary study of the relationship between the Swiss peasants and nobles in Friedrich Schiller’s play Wilhelm Tell (1804). Changes to this relationship are of particular interest. Communication in the play is examined via a micro-analysis based on Penelope Brown’s and Stephen C. Levinson’s theoretical framework Politeness: Some universals in language usage. (1978, 1987). Brown and Levinson distinguish between positivepoliteness and negative-politeness strategies and their distinction is useful for my argument, since they claim that the use of positive-politeness strategies reflects the speaker’s intention to minimize the distance between the interlocutors (Brown and Levinson 1987: 103). Negative-politeness strategies, by contrast, result in social distancing (Brown and Levinson 1987: 130). In accordance with Brown’s and Levinson’s theory, it can be argued that the distribution of positive-politeness and negative-politeness strategies reflects changes in the distance between the fictional interlocutors as representatives of their social classes in Wilhelm Tell. The analysis of the communication in the play highlights that existing conflicts within the social groups are resolved and replaced with solidarity (cf. ‘Claim ’common ground’ and ‘Claim in-group membership with H’) before the peasants and noblemen appear on stage simultaneously in III, 3. In the scene in question, Geßler forces Tell to shoot the apple off his son’s head. Although both nobles and peasants are present, they do not communicate with each other. Thus, communication between the social classes occurs for the first time in IV, 2. This scene is crucial with regard to the changes in the relationship between the social classes in the play. The younger generation, with Rudenz as a representative of the nobility and Melchthal as a representative of the peasants, break with the prevailing conventions and initiate a new type of cooperation based on mutual helping and equality in the right and the duty to protect the country from the violent oppressors representing Habsburg (cf. ‘Convey that S and H are cooperators’, ‘Claim reflexivity’ and ‘Claim reciprocity’). The linguistic analysis reveals the crucial role of the Swiss nobility in the development of the social utopia, as well as the non-contribution of Wilhelm Tell. In fact, Tell never communicates with the Swiss noblemen. The role of the nobility and the role of Wilhelm Tell are further investigated in a comparison between Schiller’s Wilhelm Tell and four of Schiller’s historical sources. These sources, which contain earlier, non-dramatic versions of the establishment of the Swiss Confederation, are the following: Kronica von der loblichen Eydtgnoschaft compiled by Petermann Etterlin (1507), Gemeiner loblicher Eydgnoschafft Stetten Landen vnd Völckeren Chronik wirdiger thaaten beschreybung (1548) written by Johann Stumpf, Chronicon Helveticum of Aegidius Tschudi (the publication of Iselin from 1734 and 1736) and Johannes von Müller’s Geschichten schweizerischer Eidgenossenschaft (1786). Thecomparison sheds light on the fact that both Tschudi and von Müller emphasize unity among the Swiss and cooperation in their attempt to defeat the enemy. However, Schiller has reinforced the role of the nobility in the cooperation. In addition, the comparison between Schiller’s play and the historical sources reveals profound differences with regard to the role of Wilhelm Tell. In all of Schiller’s sources, Tell is present at Rütli, whereas he is absent from Rütli in Schiller’s play. In the play in general, Tell is conspicuously separated from the other peasants. Explanations of my linguistic results, which correspond to the above mentioned differences between the roles of the figures in Wilhelm Tell and the depictions in Schiller’s sources, are found by comparing the path of Schiller’s Swiss towards an egalitarian perspective with the kind of social evolution depicted by the German philosopher Johann Benjamin Erhard in his essay Über das Recht des Volks zu einer Revolution (1795). Aiming at considering Schiller’s social utopia within the larger cultural framework of the German response to the French Revolution, the comparison suggests that both authors depict the need for social change in terms of a change in social hierarchies (Erhard 1970: 95-96, cf. Foi 2005: 225). Erhard’s essay thus helps explain the political intention of Schiller’s play to keep the ideals of the French Revolution as crucial aims but profoundly change the means towards freedom and equality. In his attempt to claim the political resistance of the nobles and peasants as just, however, Schiller sacrificed the figure of Wilhelm Tell. Guilty of the murder of Geßler, Tell was no longer suitable for the righteous revolution imagined by Schiller (cf. Bloch 2008: 215 and Schulz 2005: 228). This explains Tell’s absence in the Rütli scene, his isolation in the plot, as well as his non-contribution to the social utopia. Together, the linguistic analysis and contextualisation of Schiller’s play support my hypothesis that Wilhelm Tell describes a process of change in the relationship between peasants and nobles. The interdisciplinary approach to the topic proved to be fruitful for all areas of the research involved.

Dual light barrier method for six degrees of freedom tool center point calibration of an industrial robot

Tool center point calibration is a known problem in industrial robotics. The major focus of academic research is to enhance the accuracy and repeatability of next generation robots. However, operators of currently available robots are working within the limits of the robot´s repeatability and require calibration methods suitable for these basic applications. This study was conducted in association with Stresstech Oy, which provides solutions for manufacturing quality control. Their sensor, based on the Barkhausen noise effect, requires accurate positioning. The accuracy requirement admits a tool center point calibration problem if measurements are executed with an industrial robot. Multiple possibilities are available in the market for automatic tool center point calibration. Manufacturers provide customized calibrators to most robot types and tools. With the handmade sensors and multiple robot types that Stresstech uses, this would require great deal of labor. This thesis introduces a calibration method that is suitable for all robots which have two digital input ports free. It functions with the traditional method of using a light barrier to detect the tool in the robot coordinate system. However, this method utilizes two parallel light barriers to simultaneously measure and detect the center axis of the tool. Rotations about two axes are defined with the center axis. The last rotation about the Z-axis is calculated for tools that have different width of X- and Y-axes. The results indicate that this method is suitable for calibrating the geometric tool center point of a Barkhausen noise sensor. In the repeatability tests, a standard deviation inside robot repeatability was acquired. The Barkhausen noise signal was also evaluated after recalibration and the results indicate correct calibration. However, future studies should be conducted using a more accurate manipulator, since the method employs the robot itself as a measuring device.

Functionalisation of spruce O-acetyl-galactoglucomannans for barrier and composite applications

The increasing use of energy, food, and materials by the growing population in the world is leading to the situation where alternative solutions from renewable carbon resources are sought after. The growing use of plastics depends on the raw-oil production while oil refining are politically governed and required for the polymer manufacturing is not sustainable in terms of carbon footprint. The amount of packaging is also increasing. Packaging is not only utilising cardboard and paper, but also plastics. The synthetic petroleum-derived plastics and inner-coatings in food packaging can be substituted with polymeric material from the renewable resources. The trees in Finnish forests constitute a huge resource, which ought to be utilised more effectively than it is today. One underutilised component of the forests is the wood-derived hemicelluloses, although Spruce Oacetyl-galactoglucomannans (GGMs) have previously shown high potential for material applications and can be recovered in large scale. Hemicelluloses are hydrophilic in their native state, which restrains the use of them for food packaging as non-dry item. To cope with this challenge, we intended to make GGMs more hydrophobic or amphiphilic by chemical grafting and consequently with the focus of using them for barrier applications. Methods of esterification with anhydrides and cationic etherification with a trimethyl ammonium moiety were established. A method of controlled synthesis to obtain the desired properties by the means of altering temperature, reaction time, the quantity of the reagent, and even the solvent for purification of the products was developed. Numerous analytical tools, such as NMR, FTIR, SEC-MALLS/RI, MALDI-TOF-MS, RP-HPLC and polyelectrolyte titration were used to evaluate the products from different perspectives and to acquire parallel proofs of their chemical structure. Modified GGMs with different degree of substitution and the correlating level of hydrophobicity was applied as coatings on cartonboard and on nanofibrillated cellulose-GGM films to exhibit barrier functionality. The water dispersibility in processing was maintained with GGM esters with low DS. The use of chemically functionalised GGM was evaluated for the use as barriers against water, oxygen and grease for the food packaging purposes. The results show undoubtedly that GGM derivatives exhibit high potential to function as a barrier material in food packaging.

Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Detection, Identification and Molecular Variation of Human Enteroviruses

Picornaviruses are the most common human viruses and the identification of the picornaviruses is nowadays based on molecular techniques, for example, reverse transcriptase polymerase chain reaction (RT-PCR). One aim of this thesis was to improve the identification of picornaviruses, especially rhino- and enteroviruses, with a real-time assay format and, also, to improve the differentiation of the viruses with genus-specific locked nucleic acid (LNA) probes. Another aim was to identify and study the causative agent of the enterovirus epidemics that appeared in Finland during seasons 2008-2010. In this thesis, the first version of picornavirus qRT-PCR with a melting curve analysis was used in a study of rhinovirus transmission within families with a rhinovirus positive index child where rhinovirus infection was monitored in all family members. In conclusion, rhinoviruses spread effectively within families causing mostly symptomatic infections in children and asymptomatic infections in adults. To improve the differentiation between rhino- and enterovirus the picornavirus qRT-PCR was modified with LNA-incorporated probes. The LNA probes were validated with picornavirus prototypes and different clinical specimen types. The LNA probe-based picornavirus qRT-PCR was able to differentiate all rhino- and enteroviruses correctly, which makes it suitable for diagnostic use. Moreover, in this thesis enterovirus outbreaks were studied with a well-observed method to create a strain-specific qRT-PCR from the typing region VP1 protein. In a hand-foot-and-mouth-disease (HFMD) outbreak in 2008, the causative agent was identified as CV-A6 and when the molecular evolution of the new HFMD CV-A6 strain was studied it was found that CV-A6 was the emerging agent for HFMD and onychomadesis. Furthermore, unusual E-30 meningitis epidemics that apeared during seasons 2009 and 2010 were studied with strain-specific qRT-PCR. The E-30 affected mostly adolescents and was probably spread in sports teams.

Information Content of Bank Credit Rating Changes: Evidence from Europe

This thesis examines the short-term impact of credit rating announcements on daily stock returns of 41 European banks indexed in STOXX Europe 600 Banks. The time period of this study is 2002–2015 and the ratings represent long-term issuer ratings provided by S&P, Moody’s and Fitch. Bank ratings are significant for a bank’s operation costs so it is interesting to investigate how investors react to changes in creditworthiness. The study objective is achieved by conducting an event study. The event study is extended with a cross-sectional linear regression to investigate other potential determinants surrounding rating changes. The research hypotheses and the motivation for additional tests are derived from prior research. The main hypotheses are formed to explore whether rating changes have an effect on stock returns, when this possible reaction occurs and whether it is asymmetric between upgrades and downgrades. The findings provide evidence that rating announcements have an impact on stock returns in the context of European banks. The results also support the existence of an asymmetry in capital market reaction to rating upgrades and downgrades. The rating downgrades are associated with statistically significant negative abnormal returns on the event day although the reaction is rather modest. No statistically significant reaction is found associated with the rating upgrades on the event day. These results hold true with both rating changes and rating watches. No anticipation is observed in the case of rating changes but there is a statistically significant cumulative negative (positive) price reaction occurring before the event day for negative (positive) watch announcements. The regression provides evidence that the stock price reaction is stronger for rating downgrades occurring within below investment grade class compared with investment grade class. This is intuitive as investors are more concerned about their investments in lower-rated companies. Besides, the price reaction of larger banks is more mitigated compared with smaller banks in the case of rating downgrades. The reason for this may be that larger banks are usually more widely followed by the public. However, the study results may also provide evidence of the existence of the so-called “too big to fail” subsidy that dampens the negative returns of larger banks.