Minimization of the experimental workload for the prediction of pollutants propagation in rivers. Mathematical modelling and knowledge re-use

The present thesis in focused on the minimization of experimental efforts for the prediction of pollutant propagation in rivers by mathematical modelling and knowledge re-use. Mathematical modelling is based on the well known advection-dispersion equation, while the knowledge re-use approach employs the methods of case based reasoning, graphical analysis and text mining. The thesis contribution to the pollutant transport research field consists of: (1) analytical and numerical models for pollutant transport prediction; (2) two novel techniques which enable the use of variable parameters along rivers in analytical models; (3) models for the estimation of pollutant transport characteristic parameters (velocity, dispersion coefficient and nutrient transformation rates) as functions of water flow, channel characteristics and/or seasonality; (4) the graphical analysis method to be used for the identification of pollution sources along rivers; (5) a case based reasoning tool for the identification of crucial information related to the pollutant transport modelling; (6) and the application of a software tool for the reuse of information during pollutants transport modelling research. These support tools are applicable in the water quality research field and in practice as well, as they can be involved in multiple activities. The models are capable of predicting pollutant propagation along rivers in case of both ordinary pollution and accidents. They can also be applied for other similar rivers in modelling of pollutant transport in rivers with low availability of experimental data concerning concentration. This is because models for parameter estimation developed in the present thesis enable the calculation of transport characteristic parameters as functions of river hydraulic parameters and/or seasonality. The similarity between rivers is assessed using case based reasoning tools, and additional necessary information can be identified by using the software for the information reuse. Such systems represent support for users and open up possibilities for new modelling methods, monitoring facilities and for better river water quality management tools. They are useful also for the estimation of environmental impact of possible technological changes and can be applied in the pre-design stage or/and in the practical use of processes as well.

Some advances in mathematical models for preference relations

Preference relations, and their modeling, have played a crucial role in both social sciences and applied mathematics. A special category of preference relations is represented by cardinal preference relations, which are nothing other than relations which can also take into account the degree of relation. Preference relations play a pivotal role in most of multi criteria decision making methods and in the operational research. This thesis aims at showing some recent advances in their methodology. Actually, there are a number of open issues in this field and the contributions presented in this thesis can be grouped accordingly. The first issue regards the estimation of a weight vector given a preference relation. A new and efficient algorithm for estimating the priority vector of a reciprocal relation, i.e. a special type of preference relation, is going to be presented. The same section contains the proof that twenty methods already proposed in literature lead to unsatisfactory results as they employ a conflicting constraint in their optimization model. The second area of interest concerns consistency evaluation and it is possibly the kernel of the thesis. This thesis contains the proofs that some indices are equivalent and that therefore, some seemingly different formulae, end up leading to the very same result. Moreover, some numerical simulations are presented. The section ends with some consideration of a new method for fairly evaluating consistency. The third matter regards incomplete relations and how to estimate missing comparisons. This section reports a numerical study of the methods already proposed in literature and analyzes their behavior in different situations. The fourth, and last, topic, proposes a way to deal with group decision making by means of connecting preference relations with social network analysis.

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.

A quantitative view on fuzzy numbers

Since its introduction, fuzzy set theory has become a useful tool in the mathematical modelling of problems in Operations Research and many other fields. The number of applications is growing continuously. In this thesis we investigate a special type of fuzzy set, namely fuzzy numbers. Fuzzy numbers (which will be considered in the thesis as possibility distributions) have been widely used in quantitative analysis in recent decades. In this work two measures of interactivity are defined for fuzzy numbers, the possibilistic correlation and correlation ratio. We focus on both the theoretical and practical applications of these new indices. The approach is based on the level-sets of the fuzzy numbers and on the concept of the joint distribution of marginal possibility distributions. The measures possess similar properties to the corresponding probabilistic correlation and correlation ratio. The connections to real life decision making problems are emphasized focusing on the financial applications. We extend the definitions of possibilistic mean value, variance, covariance and correlation to quasi fuzzy numbers and prove necessary and sufficient conditions for the finiteness of possibilistic mean value and variance. The connection between the concepts of probabilistic and possibilistic correlation is investigated using an exponential distribution. The use of fuzzy numbers in practical applications is demonstrated by the Fuzzy Pay-Off method. This model for real option valuation is based on findings from earlier real option valuation models. We illustrate the use of number of different types of fuzzy numbers and mean value concepts with the method and provide a real life application.

Luminescent Lanthanide Reporters: New Concepts for Use in Bioanalytical Applications

Lanthanides represent the chemical elements from lanthanum to lutetium. They intrinsically exhibit some very exciting photophysical properties, which can be further enhanced by incorporating the lanthanide ion into organic or inorganic sensitizing structures. A very popular approach is to conjugate the lanthanide ion to an organic chromophore structure forming lanthanide chelates. Another approach, which has quickly gained interest, is to incorporate the lanthanide ions into nanoparticle structures, thus attaining improved specific activity and binding capacity. The lanthanide-based reporters usually express strong luminescence emission, multiple narrow emission lines covering a wide wavelength range, and exceptionally long excited state lifetimes enabling timeresolved detection. Because of these properties, the lanthanide-based reporters have found widespread applications in various fields of life. This study focuses on the field of bioanalytical applications. The aim of the study was to demonstrate the utility of different lanthanide-based reporters in homogeneous Förster resonance energy transfer (FRET)-based bioaffinity assays. Several different model assays were constructed. One was a competitive bioaffinity assay that utilized energy transfer from lanthanide chelate donors to fluorescent protein acceptors. In addition to the conventional FRET phenomenon, a recently discovered non-overlapping FRET (nFRET) phenomenon was demonstrated for the first time for fluorescent proteins. The lack of spectral overlap in the nFRET mechanism provides sensitivity and versatility to energy transfer-based assays. The distance and temperature dependence of these phenomena were further studied in a DNA-hybridization assay. The distance dependence of nFRET deviated from that of FRET, and unlike FRET, nFRET demonstrated clear temperature dependence. Based on these results, a possible excitation mechanism operating in nFRET was proposed. In the study, two enzyme activity assays for caspase-3 were also constructed. One of these was a fluorescence quenching-based enzyme activity assay that utilized novel inorganic particulate reporters called upconverting phosphors (UCPs) as donors. The use of UCPs enabled the construction of a simple, rather inexpensive, and easily automated assay format that had a high throughput rate. The other enzyme activity assay took advantage of another novel reporter class, the lanthanidebinding peptides (LBPs). In this assay, energy was transferred from a LBP to a green fluorescent protein (GFP). Using the LBPs it was possible to avoid the rather laborious, often poorly repeatable, and randomly positioned chemical labeling. In most of the constructed assays, time-resolved detection was used to eliminate the interfering background signal caused by autofluorescence. The improved signal-to-background ratios resulted in increased assay sensitivity, often unobtainable in homogeneous assay formats using conventional organic fluorophores. The anti-Stokes luminescence of the UCPs, however, enabled the elimination of autofluorescence even without time-gating, thus simplifying the instrument setup. Together, the studied reporters and assay formats pave the way for increasingly sensitive, simple, and easily automated bioanalytical applications.

Mathematical modeling of laboratory scale three-phase fixed bed reactors

Detta arbete fokuserar på modellering av katalytiska gas-vätskereaktioner som genomförs i kontinuerliga packade bäddar. Katalyserade gas-vätskereaktioner hör till de mest typiska reaktionerna i kemisk industri; därför behandlas här packade bäddreaktorer som ett av de populäraste alternativen, då kontinuerlig drift eftersträvas. Tack vare en stor katalysatormängd per volym har de en kompakt struktur, separering av katalysatorn behövs inte och genom en professionell design kan den mest fördelaktiga strömningsbilden upprätthållas i reaktorn. Packade bäddreaktorer är attraktiva p.g.a. lägre investerings- och driftskostnader. Även om packade bäddar används intensivt i industri, är det mycket utmanande att modellera. Detta beror på att tre faser samexisterar och systemets geometri är komplicerad. Existensen av flera reaktioner gör den matematiska modelleringen även mera krävande. Många förenklingar blir därmed nödvändiga. Modellerna involverar typiskt flera parametrar som skall justeras på basis av experimentella data. I detta arbete studerades fem olika reaktionssystem. Systemen hade studerats experimentellt i vårt laboratorium med målet att nå en hög produktivitet och selektivitet genom ett optimalt val av katalysatorer och driftsbetingelser. Hydrering av citral, dekarboxylering av fettsyror, direkt syntes av väteperoxid samt hydrering av sockermonomererna glukos och arabinos användes som exempelsystem. Även om dessa system hade mycket gemensamt, hade de också unika egenskaper och krävde därför en skräddarsydd matematisk behandling. Citralhydrering var ett system med en dominerande huvudreaktion som producerar citronellal och citronellol som huvudprodukter. Produkterna används som en citrondoftande komponent i parfymer, tvålar och tvättmedel samt som plattform-kemikalier. Dekarboxylering av stearinsyra var ett specialfall, för vilket en reaktionsväg för produktion av långkedjade kolväten utgående från fettsyror söktes. En synnerligen hög produktselektivitet var karakteristisk för detta system. Även processuppskalning modellerades för dekarboxylerings-reaktionen. Direkt syntes av väteperoxid hade som målsättning att framta en förenklad process att producera väteperoxid genom att låta upplöst väte och syre reagera direkt i ett lämpligt lösningsmedel på en aktiv fast katalysator. I detta system förekommer tre bireaktioner, vilka ger vatten som oönskad produkt. Alla dessa tre reaktioner modellerades matematiskt med hjälp av dynamiska massbalanser. Målet med hydrering av glukos och arabinos är att framställa produkter med en hög förädlingsgrad, nämligen sockeralkoholer, genom katalytisk hydrering. För dessa två system löstes ämnesmängd- och energibalanserna simultant för att evaluera effekter inne i porösa katalysatorpartiklar. Impulsbalanser som bestämmer strömningsbetingelser inne i en kemisk reaktor, ersattes i alla modelleringsstudier med semi-empiriska korrelationsuttryck för vätskans volymandel och tryckförlust och med axiell dispersionsmodell för beskrivning av omblandningseffekter. Genom att justera modellens parametrar kunde reaktorns beteende beskrivas väl. Alla experiment var genomförda i laboratorieskala. En stor mängd av kopplade effekter samexisterade: reaktionskinetik inklusive adsorption, katalysatordeaktivering, mass- och värmeöverföring samt strömningsrelaterade effekter. En del av dessa effekter kunde studeras separat (t.ex. dispersionseffekter och bireaktioner). Inverkan av vissa fenomen kunde ibland minimeras genom en noggrann planering av experimenten. På detta sätt kunde förenklingar i modellerna bättre motiveras. Alla system som studerades var industriellt relevanta. Utveckling av nya, förenklade produktionsteknologier för existerande kemiska komponenter eller nya komponenter är ett gigantiskt uppdrag. Studierna som presenterades här fokuserade på en av den teknisk-vetenskapliga utfärdens första etapper.

Spontaneous Focusing on Quantitative Relations and the Development of Rational Number Conceptual Knowledge

The aim of the present set of studies was to explore primary school children’s Spontaneous Focusing On quantitative Relations (SFOR) and its role in the development of rational number conceptual knowledge. The specific goals were to determine if it was possible to identify a spontaneous quantitative focusing tendency that indexes children’s tendency to recognize and utilize quantitative relations in non-explicitly mathematical situations and to determine if this tendency has an impact on the development of rational number conceptual knowledge in late primary school. To this end, we report on six original empirical studies that measure SFOR in children ages five to thirteen years and the development of rational number conceptual knowledge in ten- to thirteen-year-olds. SFOR measures were developed to determine if there are substantial differences in SFOR that are not explained by the ability to use quantitative relations. A measure of children’s conceptual knowledge of the magnitude representations of rational numbers and the density of rational numbers is utilized to capture the process of conceptual change with rational numbers in late primary school students. Finally, SFOR tendency was examined in relation to the development of rational number conceptual knowledge in these students. Study I concerned the first attempts to measure individual differences in children’s spontaneous recognition and use of quantitative relations in 86 Finnish children from the ages of five to seven years. Results revealed that there were substantial inter-individual differences in the spontaneous recognition and use of quantitative relations in these tasks. This was particularly true for the oldest group of participants, who were in grade one (roughly seven years old). However, the study did not control for ability to solve the tasks using quantitative relations, so it was not clear if these differences were due to ability or SFOR. Study II more deeply investigated the nature of the two tasks reported in Study I, through the use of a stimulated-recall procedure examining children’s verbalizations of how they interpreted the tasks. Results reveal that participants were able to verbalize reasoning about their quantitative relational responses, but not their responses based on exact number. Furthermore, participants’ non-mathematical responses revealed a variety of other aspects, beyond quantitative relations and exact number, which participants focused on in completing the tasks. These results suggest that exact number may be more easily perceived than quantitative relations. As well, these tasks were revealed to contain both mathematical and non-mathematical aspects which were interpreted by the participants as relevant. Study III investigated individual differences in SFOR 84 children, ages five to nine, from the US and is the first to report on the connection between SFOR and other mathematical abilities. The cross-sectional data revealed that there were individual differences in SFOR. Importantly, these differences were not entirely explained by the ability to solve the tasks using quantitative relations, suggesting that SFOR is partially independent from the ability to use quantitative relations. In other words, the lack of use of quantitative relations on the SFOR tasks was not solely due to participants being unable to solve the tasks using quantitative relations, but due to a lack of the spontaneous attention to the quantitative relations in the tasks. Furthermore, SFOR tendency was found to be related to arithmetic fluency among these participants. This is the first evidence to suggest that SFOR may be a partially distinct aspect of children’s existing mathematical competences. Study IV presented a follow-up study of the first graders who participated in Studies I and II, examining SFOR tendency as a predictor of their conceptual knowledge of fraction magnitudes in fourth grade. Results revealed that first graders’ SFOR tendency was a unique predictor of fraction conceptual knowledge in fourth grade, even after controlling for general mathematical skills. These results are the first to suggest that SFOR tendency may play a role in the development of rational number conceptual knowledge. Study V presents a longitudinal study of the development of 263 Finnish students’ rational number conceptual knowledge over a one year period. During this time participants completed a measure of conceptual knowledge of the magnitude representations and the density of rational numbers at three time points. First, a Latent Profile Analysis indicated that a four-class model, differentiating between those participants with high magnitude comparison and density knowledge, was the most appropriate. A Latent Transition Analysis reveal that few students display sustained conceptual change with density concepts, though conceptual change with magnitude representations is present in this group. Overall, this study indicated that there were severe deficiencies in conceptual knowledge of rational numbers, especially concepts of density. The longitudinal Study VI presented a synthesis of the previous studies in order to specifically detail the role of SFOR tendency in the development of rational number conceptual knowledge. Thus, the same participants from Study V completed a measure of SFOR, along with the rational number test, including a fourth time point. Results reveal that SFOR tendency was a predictor of rational number conceptual knowledge after two school years, even after taking into consideration prior rational number knowledge (through the use of residualized SFOR scores), arithmetic fluency, and non-verbal intelligence. Furthermore, those participants with higher-than-expected SFOR scores improved significantly more on magnitude representation and density concepts over the four time points. These results indicate that SFOR tendency is a strong predictor of rational number conceptual development in late primary school children. The results of the six studies reveal that within children’s existing mathematical competences there can be identified a spontaneous quantitative focusing tendency named spontaneous focusing on quantitative relations. Furthermore, this tendency is found to play a role in the development of rational number conceptual knowledge in primary school children. Results suggest that conceptual change with the magnitude representations and density of rational numbers is rare among this group of students. However, those children who are more likely to notice and use quantitative relations in situations that are not explicitly mathematical seem to have an advantage in the development of rational number conceptual knowledge. It may be that these students gain quantitative more and qualitatively better self-initiated deliberate practice with quantitative relations in everyday situations due to an increased SFOR tendency. This suggests that it may be important to promote this type of mathematical activity in teaching rational numbers. Furthermore, these results suggest that there may be a series of spontaneous quantitative focusing tendencies that have an impact on mathematical development throughout the learning trajectory.

Container logistic innovations in forest-energy sector: Markets, future service concepts and technical improvements

The report presents the results of the commercialization project called the Container logistic services for forest bioenergy. The project promotes new business that is emerging around overall container logistic services in the bioenergy sector. The results assess the European markets of the container logistics for biomass, enablers for new business creation and required service bundles for the concept. We also demonstrate the customer value of the container logistic services for different market segments. The concept analysis is based on concept mapping, quality function deployment process (QFD) and business network analysis. The business network analysis assesses key shareholders and their mutual connections. The performance of the roadside chipping chain is analysed by the logistic cost simulation, RFID system demonstration and freezing tests. The EU has set the renewable energy target to 20 % in 2020 of which Biomass could account for two-thirds. In the Europe, the production of wood fuels was 132.9 million solid-m3 in 2012 and production of wood chips and particles was 69.0 million solidm3. The wood-based chips and particle flows are suitable for container transportation providing market of 180.6 million loose- m3 which mean 4.5 million container loads per year. The intermodal logistics of trucks and trains are promising for the composite containers because the biomass does not freeze onto the inner surfaces in the unloading situations. The overall service concept includes several packages: container rental, container maintenance, terminal services, RFID-tracking service, and simulation and ERP-integration service. The container rental and maintenance would provide transportation entrepreneurs a way to increase the capacity without high investment costs. The RFID-concept would lead to better work planning improving profitability throughout the logistic chain and simulation supports fuel supply optimization.