Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Construction Plan Image Service for Mobile Devices

The forthcoming media revolution of exchanging paper documents to digital media in construction engineering requires new tools to be developed. The basis of this bachelor’s thesis was to explore the preliminary possibilities of exporting imagery from a Building Information Modelling –software to a mobile phone on a construction yard. This was done by producing a Web Service which uses the design software’s Application Programming Interface to interact with a structures model in order to produce the requested imagery. While mobile phones were found lacking as client devices, because of limited processing power and small displays, the implementation showed that the Tekla Structures API can be used to automatically produce various types of imagery. Web Services can be used to transfer this data to the client. Before further development the needs of the contractor, benefits for the building master and inspector and the full potential of the BIM-software need to be mapped out with surveys.

Animal Lovers, Bridge-Builders, and Supervising Watchdogs: Framing and Civil Society Construction by Japanese Pro-Animal Organizations in the Kansai and Tokyo Areas

Unlike their counterparts in Europe and America, the citizen organizations acting for the well-being of animals in Japan have not received scholarly attention. In this research, I explore the activities of twelve Japanese pro-animal organizations in Tokyo and Kansai area from the perspective of social movement and civil society studies. The concept of a ‘pro-animal organization’ is used to refer generally to the collectives promoting animal well-being. By using the collective action frame analysis and the three core framing tasks – diagnostic, prognostic, and motivational – as the primarily analytical tools, I explore the grievances, tactics, motivational means, constructions of agency and identity as well as framing of civil society articulated in the newsletters and the interviews of the twelve organizations I interviewed in Japan in 2010. As the frame construction is always done in relation to the social and political context, I study how the organizations construct their roles as civil society actors in relation to other actors, such as the state, and the idea of citizen activism. The deficiencies in the animal welfare law and lack of knowledge among the public are identified as the main grievances. The primary tactic to overcome these problems was to educate and inform the citizens and authorities, because most organizations lack the channels to influence politically. The audiences were mostly portrayed as either ignorant bystanders or potential adherents. In order to motivate people to join their cause and to enforce the motivation within the organization, the organizations emphasized their uniqueness, proved their efficiency, claimed credit and celebrated even small improvements. The organizations tended to create three different roles for citizen pro-organizations in civil society: reactive, apolitical and emphatic animal lovers concentrating on saving individual animals, proactive, educative bridge-builders seeking to establish equal collaborative relations with authorities, and corrective, supervising watchdogs demanding change in delinquencies offending animal rights. Based on the results of this research, I suggest that by studying how and why the different relations between civil society and the governing actors of the state are constructed, a more versatile approach to citizens’ activism in its context can be achieved.

Segregation of powder mixtures in silos with particular reference to dry mineral-based construction materials

Segregering eller segregation är ett fenomen som kan förekomma inom olika områden av samhället. Inom samhällsvetenskaperna kan segregering definieras som det rumsliga åtskiljandet av befolkningsgrupper på urval av ras eller etniskt ursprung, kön, social härkomst, religion, ålder, yrke, osv. Segregering av befolkningsgrupper sker ofta mer eller mindre frivilligt och är motsatsen till integration. Inom partikelteknologi definieras segregering oftast som det rumsliga åtskiljandet av beståndsdelarna i en blandning av olika partiklar. Segregering sker då på urval av bl.a. partiklarnas storlek, densitet, form, elektrostatiska eller mekaniska egenskaper, och kan beskrivas som motsatsen till blandning. Segregeringsmekanismer används för att förklara hur och varför en partikelblandning segregerar samt vad slutresultatet i form av den rumsliga fördelningen av partiklarna blir till följd av att blandningen utsetts för en viss behandling. I denna avhandling har segregering av partikelblandningar och speciellt torra mineralbaserade byggmaterial (t.ex. murbruk) till följd av lagring i siloer studerats. Vid industriell produktion av mineralbaserade byggmaterial används siloer för korttidslagring av slutprodukterna precis innan förpackning. Segregering leder till kraftiga variationer i sammansättningen för partikelströmmen ut ur silon, vilket gör att slutprodukterna inte uppfyller kvalitetskraven och kan därmed inte säljas till kunder. Detta leder till arbetsam och dyr bearbetning (återcirkulation) av produkterna med påföljder för produktionsekonomin samt hållbara utvecklingen. I avhandlingen identifierades de väsentligaste segregeringsmekanismerna för torra mineralbaserade byggmaterial i siloer. Dessutom klargjordes effekterna av materialegenskaper, processbetingelser och siloparametrar. Slutligen behandlas möjliga åtgärder för minskning av partikelsegregering i siloer samt tillämpning av matematiska metoder för simulering av partikelflöden med hjälp av datorer.

The Dark Side of International Business? Stakeholder Approach to Human Trafficking in Finnish Construction and Service Sectors

Human trafficking is not a new phenomenon. It has existed in various forms for ages around the world. Some researchers have even compared it to slavery, calling it the modern form of slavery in the 21st century. This study is particularly interested in the role of work-related human trafficking in Finnish business. In order for something to be called work-related human trafficking, the concepts of forced labour and human trafficking have to overlap. From the economic point of view, human trafficking is governed by the laws of supply and demand. In many countries the global pressure on cutting costs has created two trends: the increased supply of migrant workers and the deregulation of labour markets. These competitive pressures can have an adverse impact on the conditions of employment and, in the worst cases, can lead to forced labour and trafficking. In fact, trafficking has become one of the most profitable illicit industries worldwide, generating tremendous profits due to its low costs and huge profits. Therefore, it is important to investigate the phenomenon from the business point of view. This study is a qualitative research conducted by using theme interviews as a research approach. Altogether 13 interviews have been conducted and some secondary data has been used in order to find out what the role of human trafficking is in Finnish business. The special sectors investigated are the Finnish construction and service sectors. The theory framework used in this study follows the stakeholder approach. The relevant stakeholder groups for this study are: ‘institutions and authorities’, ‘law enforcement’, ‘management’ and ‘employees – potential victims’ of trafficking. With the help of these stakeholder groups, a holistic picture of the phenomenon is formed. It can be concluded that the role of human trafficking is complicated but it does exist in Finnish business. It appears in low-cost business sectors where the demand for cheap labour is high. Thus, often the victims are foreigners who do not know the culture or the Finnish conditions of employment. Especially smaller Finnish companies are at risk of getting involved in human trafficking or related exploitation cases since monitoring is much more scarce in these firms than in larger companies. The risk of human trafficking and exploitation is also higher at the bottom of the complicated subcontracting chains or when using foreign recruitment agencies. Thus, the study believes that active and intensive collaboration between the company’s different stakeholder groups is needed in order to prevent work-related human trafficking from flourishing in Finland.

Future trends of Finnish cement based construction

The construction material sector, as a capital intensive industry, is highly vulnerable to rapid fluctuations in the economic cycles. In Finland this was witnessed especially during the late 2000s, as in 2007 and 2008 the demand for several construction materials exceeded their supply and right after this, in 2009 the demand collapsed fast as a result of an international recession. These factors brought about the need to study the future trends of the market place of the commissioning company, Finnsementti Oy. As reliable short term market forecasts for the sector are difficult to compose, the study concentrates primarily in examining and identifying the trends that are likely to affect the Finnish cement industry, and as an extension, the concrete industry in a frame of 10 to 15 years. The study’s scope comprehends also the examination of the domestic construction sector, as it represents the end user industry of both cement and concrete. These motives for the study produce the research problem, which is to conduct a trend analysis for cement based building in the Finnish market area in the 2020s. The theoretical frame for composing a trend analysis in the case of this study is twofold. This is due to the fact that both, the macro and micro environments of the examined industries are studied. The main methods used are the PESTE-model (macro) and Porter’s five forces model (micro). The study applies a qualitative approach and the data is gathered by interviewing a group of experts from the cement, concrete and construction industries. The result of the paper is an overall trend analysis for the Finnish cement based building sector, which is based on ‘sub trend analyses’ concerning four identified sub-sectors of the Finnish construction industry. The results are a combination of findings from these sub-sectors and the analyzed data that deals with the studied sector’s macro and micro environment. The conclusions provide an overall picture of the examined sectors’ potential future as a whole and by defined sub-sectors of the construction industry. The recognition of future trends in different areas of the construction industry can be applied as a means for an industry actor’s decision making and in estimating the types of construction that are likely to grow or decline. Finally, based on the analyzed data and conclusions, the commissioning company is provided with a brief SWOT analysis, that provides additional tools for decision making and planning processes regarding the future.

Applications and Benefits of Adaptive Pulsed GMAW

In ship and offshore terminal construction, welded cross sections are thick and the number of welds very high. Consequently, there are two aspects of great importance; cost and heat input. Reduction in the welding operation time decreases the costs of the work force and avoids excessive heat, preventing distortion and other weld defects. The need to increase productivity while using a single wire in the GMAW process has led to the use of a high current and voltage to improve the melting rate. Unfortunately, this also increases the heat input. Innovative GMAW processes, mostly implemented for sheet plate sections, have shown significant reduction in heat input (Q), low distortion and increase in welding speed. The aim of this study is to investigate adaptive pulsed GMAW processes and assess relevant applications in the high power range, considering possible benefits when welding thicker sections and high yield strength steel. The study experimentally tests the usability of adaptive welding processes and evaluates their effects on weld properties, penetration and shapes of the weld bead.The study first briefly reviews adaptive GMAW to evaluate different approaches and their applications and to identify benefits in adaptive pulsed. Experiments are then performed using Synergic Pulsed GMAW, WiseFusionTM and Synergic GMAW processes to weld a T-joint in a horizontal position (PB). The air gap between the parts ranges from 0 to 2.5 mm. The base materials are structural steel grade S355MC and filler material G3Si1. The experiment investigates heat input, mechanical properties and microstructure of the welded joint. Analysis of the literature reveals that different approaches have been suggested using advanced digital power sources with accurate waveform, current, voltage, and feedback control. In addition, studies have clearly indicated the efficiency of lower energy welding processes. Interest in the high power range is growing and a number of different approaches have been suggested. The welding experiments in this study reveal a significant reduction of heat input and a weld microstructure with the presence of acicular ferrite (AF) beneficial for resistance to crack propagation. The WiseFusion bead had higher dilution, due to the weld bead shape, and low defects. Adaptive pulse GMAW processes can be a favoured choice when welding structures with many welded joints. The total heat reduction mitigates residual stresses and the bead shape allows a higher amperage limit. The stability of the arc during the process is virtually spatter free and allows an increase in welding speed.

Surface transformation hardening of carbon steel with high power fiber laser

This study investigated the surface hardening of steels via experimental tests using a multi-kilowatt fiber laser as the laser source. The influence of laser power and laser power density on the hardening effect was investigated. The microhardness analysis of various laser hardened steels was done. A thermodynamic model was developed to evaluate the thermal process of the surface treatment of a wide thin steel plate with a Gaussian laser beam. The effect of laser linear oscillation hardening (LLOS) of steel was examined. An as-rolled ferritic-pearlitic steel and a tempered martensitic steel with 0.37 wt% C content were hardened under various laser power levels and laser power densities. The optimum power density that produced the maximum hardness was found to be dependent on the laser power. The effect of laser power density on the produced hardness was revealed. The surface hardness, hardened depth and required laser power density were compared between the samples. Fiber laser was briefly compared with high power diode laser in hardening medium-carbon steel. Microhardness (HV0.01) test was done on seven different laser hardened steels, including rolled steel, quenched and tempered steel, soft annealed alloyed steel and conventionally through-hardened steel consisting of different carbon and alloy contents. The surface hardness and hardened depth were compared among the samples. The effect of grain size on surface hardness of ferritic-pearlitic steel and pearlitic-cementite steel was evaluated. In-grain indentation was done to measure the hardness of pearlitic and cementite structures. The macrohardness of the base material was found to be related to the microhardness of the softer phase structure. The measured microhardness values were compared with the conventional macrohardness (HV5) results. A thermodynamic model was developed to calculate the temperature cycle, Ac1 and Ac3 boundaries, homogenization time and cooling rate. The equations were numerically solved with an error of less than 10-8. The temperature distributions for various thicknesses were compared under different laser traverse speed. The lag of the was verified by experiments done on six different steels. The calculated thermal cycle and hardened depth were compared with measured data. Correction coefficients were applied to the model for AISI 4340 steel. AISI 4340 steel was hardened by laser linear oscillation hardening (LLOS). Equations were derived to calculate the overlapped width of adjacent tracks and the number of overlapped scans in the center of the scanned track. The effect of oscillation frequency on the hardened depth was investigated by microscopic evaluation and hardness measurement. The homogeneity of hardness and hardened depth with different processing parameters were investigated. The hardness profiles were compared with the results obtained with conventional single-track hardening. LLOS was proved to be well suitable for surface hardening in a relatively large rectangular area with considerable depth of hardening. Compared with conventional single-track scanning, LLOS produced notably smaller hardened depths while at 40 and 100 Hz LLOS resulted in higher hardness within a depth of about 0.6 mm.

A Steel Company Entering the Market Area of St. Petersburg

Tutkimuksen tavoitteena on selvittää tarkoituksenmukaisin etabloitumismenetelmä teräsyhtiön kansainvälistymisessä Pietarin markkinoille. Vaikka kansainvälistymistä onkin tutkittu paljon, kyseisen kontekstin erityispiirteisiin on aiemmissa tutkimuksissa kiinnitetty vain vähän huomiota. Kansainvälistymisteorioista työhön valittiin John Dunningin eklektinen paradigma sekä Uppsala-malli. Etabloitumismenetelmän valintaa puolestaan tarkastellaan eri vaihtoehtojen kautta, jotka kattavat viennin, suorat ulkomaan investoinnit, sopimusjärjestelyt sekä yhteisyrityksen. Valintaa selitetään taustalla vaikuttavien tekijöiden sekä kansainvälistymisprosessin kautta. Kohteena olevan markkina-alueen potentiaalin, ongelmien sekä yrityksen kilpailuetujen arvioinnin jälkeen ehdotetaan optimaalista ratkaisua. Omat haasteensa operaatiomuodon valintaan luovat potentiaalinen mutta haastava kohdemarkkina-alue sekä yrityksen sisäiset tekijät. Kontekstiin parhaiten sopivaksi etabloitumismenetelmäksi esitetään aloittamista välittömällä viennillä asiakkaiden etsimiseksi ja suhteiden luomiseksi. Kun asiakkuuksia alueella on riittävästi, myyntikonttorin perustaminen Pietarin lähelle nähdään tarkoituksenmukaisena paikallisen läsnäolon lisäämiseksi. Empiirinen data kattaa kahdeksan asiantuntijahaastattelua, jotka yhdessä muun lähdeaineiston kanssa rakentavat perustan empiirisille tuloksille. Tutkimuksen tulokset tarjoavat yritykselle perustellun ratkaisuehdotuksen siitä, kuinka Pietarin markkinoille tulisi etabloitua.

Feasibility studies of the weldability of structural steels used in the offshore environment

The rising demand for oil and gas has made it very necessary for the oil and gas industries to explore the offshore. There is a huge resources which is available in the offshore. The search for oil and gas is faced with greater challenges because of the nature of the marine environment as it poses difficult and harsh conditions for the construction of offshore structures. The major problem of the construction of offshore structure is the ability to produce a sound weld that gives the whole structure the structural integrity needed to withstand the harsh environmental conditions. This research work presents the performance of typical offshore steels with improved weldability. The ability of reducing the carbon content of thermo-mechanically rolled steels down to 0.08% makes it possible to achieve good weldability, toughness and strength for high strength steels used in offshore applications. Importantly, the ideal welding procedure should be strictly followed as recommended. The fabrication process is as important as the welding procedure in achieving a sound weld which is free of weld defects such as hydrogen induced cracking, lamellar tearing and solidification cracking. This research work also considers the corrosion as it affects offshore structure and necessary measures to mitigate the problem caused by corrosion.

Scaling up stepwise feature introduction to construction of large software systems

Developing software is a difficult and error-prone activity. Furthermore, the complexity of modern computer applications is significant. Hence,an organised approach to software construction is crucial. Stepwise Feature Introduction – created by R.-J. Back – is a development paradigm, in which software is constructed by adding functionality in small increments. The resulting code has an organised, layered structure and can be easily reused. Moreover, the interaction with the users of the software and the correctness concerns are essential elements of the development process, contributing to high quality and functionality of the final product. The paradigm of Stepwise Feature Introduction has been successfully applied in an academic environment, to a number of small-scale developments. The thesis examines the paradigm and its suitability to construction of large and complex software systems by focusing on the development of two software systems of significant complexity. Throughout the thesis we propose a number of improvements and modifications that should be applied to the paradigm when developing or reengineering large and complex software systems. The discussion in the thesis covers various aspects of software development that relate to Stepwise Feature Introduction. More specifically, we evaluate the paradigm based on the common practices of object-oriented programming and design and agile development methodologies. We also outline the strategy to testing systems built with the paradigm of Stepwise Feature Introduction.

Identification of Some Additional Loss Components in High-Power Low-Voltage Permanent Magnet Generators

Permanent magnet generators (PMG) represent the cutting edge technology in modern wind mills. The efficiency remains high (over 90%) at partial loads. To improve the machine efficiency even further, every aspect of machine losses has to be analyzed. Additional losses are often given as a certain percentage without providing any detailed information about the actual calculation process; meanwhile, there are many design-dependent losses that have an effect on the total amount of additional losses and that have to be taken into consideration. Additional losses are most often eddy current losses in different parts of the machine. These losses are usually difficult to calculate in the design process. In this doctoral thesis, some additional losses are identified and modeled. Further, suggestions on how to minimize the losses are given. Iron losses can differ significantly between the measured no-load values and the loss values under load. In addition, with embedded magnet rotors, the quadrature-axis armature reaction adds losses to the stator iron by manipulating the harmonic content of the flux. It was, therefore, re-evaluated that in salient pole machines, to minimize the losses and the loss difference between the no-load and load operation, the flux density has to be kept below 1.5 T in the stator yoke, which is the traditional guideline for machine designers. Eddy current losses may occur in the end-winding area and in the support structure of the machine, that is, in the finger plate and the clamping ring. With construction steel, these losses account for 0.08% of the input power of the machine. These losses can be reduced almost to zero by using nonmagnetic stainless steel. In addition, the machine housing may be subjected to eddy current losses if the flux density exceeds 1.5 T in the stator yoke. Winding losses can rise rapidly when high frequencies and 10–15 mm high conductors are used. In general, minimizing the winding losses is simple. For example, it can be done by dividing the conductor into transposed subconductors. However, this comes with the expense of an increase in the DC resistance. In the doctoral thesis, a new method is presented to minimize the winding losses by applying a litz wire with noninsulated strands. The construction is the same as in a normal litz wire but the insulation between the subconductors has been left out. The idea is that the connection is kept weak to prevent harmful eddy currents from flowing. Moreover, the analytical solution for calculating the AC resistance factor of the litz-wire is supplemented by including an end-winding resistance in the analytical solution. A simple measurement device is developed to measure the AC resistance in the windings. In the case of a litz-wire with originally noninsulated strands, vacuum pressure impregnation (VPI) is used to insulate the subconductors. In one of the two cases studied, the VPI affected the AC resistance factor, but in the other case, it did not have any effect. However, more research is needed to determine the effect of the VPI on litz-wire with noninsulated strands. An empirical model is developed to calculate the AC resistance factor of a single-layer formwound winding. The model includes the end-winding length and the number of strands and turns. The end winding includes the circulating current (eddy currents that are traveling through the whole winding between parallel strands) and the main current. The end-winding length also affects the total AC resistance factor.