Mechanistic population Models in Biology: Model Derivation and Application

In general, models of ecological systems can be broadly categorized as ’top-down’ or ’bottom-up’ models, based on the hierarchical level that the model processes are formulated on. The structure of a top-down, also known as phenomenological, population model can be interpreted in terms of population characteristics, but it typically lacks an interpretation on a more basic level. In contrast, bottom-up, also known as mechanistic, population models are derived from assumptions and processes on a more basic level, which allows interpretation of the model parameters in terms of individual behavior. Both approaches, phenomenological and mechanistic modelling, can have their advantages and disadvantages in different situations. However, mechanistically derived models might be better at capturing the properties of the system at hand, and thus give more accurate predictions. In particular, when models are used for evolutionary studies, mechanistic models are more appropriate, since natural selection takes place on the individual level, and in mechanistic models the direct connection between model parameters and individual properties has already been established. The purpose of this thesis is twofold. Firstly, a systematical way to derive mechanistic discrete-time population models is presented. The derivation is based on combining explicitly modelled, continuous processes on the individual level within a reproductive period with a discrete-time maturation process between reproductive periods. Secondly, as an example of how evolutionary studies can be carried out in mechanistic models, the evolution of the timing of reproduction is investigated. Thus, these two lines of research, derivation of mechanistic population models and evolutionary studies, are complementary to each other.

Statistical Analysis and Numerics of Heat Exchanger Models

The identifiability of the parameters of a heat exchanger model without phase change was studied in this Master’s thesis using synthetically made data. A fast, two-step Markov chain Monte Carlo method (MCMC) was tested with a couple of case studies and a heat exchanger model. The two-step MCMC-method worked well and decreased the computation time compared to the traditional MCMC-method. The effect of measurement accuracy of certain control variables to the identifiability of parameters was also studied. The accuracy used did not seem to have a remarkable effect to the identifiability of parameters. The use of the posterior distribution of parameters in different heat exchanger geometries was studied. It would be computationally most efficient to use the same posterior distribution among different geometries in the optimisation of heat exchanger networks. According to the results, this was possible in the case when the frontal surface areas were the same among different geometries. In the other cases the same posterior distribution can be used for optimisation too, but that will give a wider predictive distribution as a result. For condensing surface heat exchangers the numerical stability of the simulation model was studied. As a result, a stable algorithm was developed.

Models in country scale carbon accounting of forest soils

Selective papers of the workshop on "Development of models and forest soil surveys for monitoring of soil carbon", Koli, Finland, April 5-9 2006.

Regime Switching Models for Electricity Time Series that Capture Fat Tailed Distributions

In the power market, electricity prices play an important role at the economic level. The behavior of a price trend usually known as a structural break may change over time in terms of its mean value, its volatility, or it may change for a period of time before reverting back to its original behavior or switching to another style of behavior, and the latter is typically termed a regime shift or regime switch. Our task in this thesis is to develop an electricity price time series model that captures fat tailed distributions which can explain this behavior and analyze it for better understanding. For NordPool data used, the obtained Markov Regime-Switching model operates on two regimes: regular and non-regular. Three criteria have been considered price difference criterion, capacity/flow difference criterion and spikes in Finland criterion. The suitability of GARCH modeling to simulate multi-regime modeling is also studied.

A comparison of electricity spot prices simulation using ARMA-GARCH and mean-reverting models

The aim of this work is to compare two families of mathematical models for their respective capability to capture the statistical properties of real electricity spot market time series. The first model family is ARMA-GARCH models and the second model family is mean-reverting Ornstein-Uhlenbeck models. These two models have been applied to two price series of Nordic Nord Pool spot market for electricity namely to the System prices and to the DenmarkW prices. The parameters of both models were calibrated from the real time series. After carrying out simulation with optimal models from both families we conclude that neither ARMA-GARCH models, nor conventional mean-reverting Ornstein-Uhlenbeck models, even when calibrated optimally with real electricity spot market price or return series, capture the statistical characteristics of the real series. But in the case of less spiky behavior (System prices), the mean-reverting Ornstein-Uhlenbeck model could be seen to partially succeeded in this task.

Numerical Investigation of Flow Past a Circular Cylinder and in a Staggered Tube Bundle Using Various Turbulence Models

Transitional flow past a three-dimensional circular cylinder is a widely studied phenomenon since this problem is of interest with respect to many technical applications. In the present work, the numerical simulation of flow past a circular cylinder, performed by using a commercial CFD code (ANSYS Fluent 12.1) with large eddy simulation (LES) and RANS (κ - ε and Shear-Stress Transport (SST) κ - ω! model) approaches. The turbulent flow for ReD = 1000 & 3900 is simulated to investigate the force coefficient, Strouhal number, flow separation angle, pressure distribution on cylinder and the complex three dimensional vortex shedding of the cylinder wake region. The numerical results extracted from these simulations have good agreement with the experimental data (Zdravkovich, 1997). Moreover, grid refinement and time-step influence have been examined. Numerical calculations of turbulent cross-flow in a staggered tube bundle continues to attract interest due to its importance in the engineering application as well as the fact that this complex flow represents a challenging problem for CFD. In the present work a time dependent simulation using κ – ε, κ - ω! and SST models are performed in two dimensional for a subcritical flow through a staggered tube bundle. The predicted turbulence statistics (mean and r.m.s velocities) have good agreement with the experimental data (S. Balabani, 1996). Turbulent quantities such as turbulent kinetic energy and dissipation rate are predicted using RANS models and compared with each other. The sensitivity of grid and time-step size have been analyzed. Model constants sensitivity study have been carried out by adopting κ – ε model. It has been observed that model constants are very sensitive to turbulence statistics and turbulent quantities.

Stellar population synthesis: the effect of improved Asymptotic Giant Branch models and of interstellar dust on mass-to-light–color relations

Teoreettisen populaatiosynteesin avulla voidaan mallintaa tähtijoukkojen ja galaksien fotometrisiä ominaisuuksia yhdistämällä yksittäisten tähtien tuottama säteily, joka saadaan teoreettisista tähtien kehitysmalleista. Valitsemalla sopiva massajakauma syntyville tähdille voidaan muodostaa yksinkertainen tähtipopulaatio, joka koostuu saman ikäisistä ja kemialliselta koostumukseltaan yhtenäisistä tähdistä. Monimutkaisempia tähtipopulaatioita voidaan muodostaa konvoloimalla yksinkertaisten tähtipopulaatioiden luminositeetti jonkin valitun tähtienmuodostushistorian kanssa sekä yhdistämällä näin muodostettuja populaatioita. Tässä työssä tarkastellaan asymptoottisen jättiläishaaran (AGB) tähtien uusien, tarkentuneiden evoluutiomallien vaikutusta populaatiosynteesin tuloksiin niin yksinkertaisten tähtipopulaatioiden kuin galaksien mallinnukseen soveltuvien monimutkaisempien tähtipopulaatioiden kohdalla. Työn päätarkoitus on tuottaa uudistuneisiin malleihin perustuvat populaation massa-luminositeetti -suhteen ja värin väliset relaatiot (MLC-relaatiot). MLC-relaatioita voidaan käyttää populaation massan määrittämiseen sen fotometristen ominaisuuksien (väri, luminositeetti) perusteella. Lisäksi tutkitaan tähtienvälisen pölyn vaikutusta yksinkertaisen spiraaligalaksimallin MLC-relaatioihin. Työssä käytetyt tähtien kehitysmallit perustuvat julkaisuun Marigo et al. (Astronomy & Astrophysics 482, 2008). Havaitaan, että AGB-tähtien vaikutus populaation integroituun luminositeettiin on pieni näkyvillä aallonpituuksilla, mutta merkittävä lähi-infrapuna-alueella. Vaikutus MLC-relaatioihin on vastaavasti merkittävä tarkkailtaessa luminositeettia lähi-infrapunassa sekä käytettäessä värejä, joissa yhdistetään optisia ja lähi-infrapunan kaistoja. Todetaan, että MLC-relaatioiden käyttö lähi-infrapunassa edellyttää tarkentuneen AGB-vaiheen sisällyttämistä populaatiosynteesin malleihin. Tähtienvälisen pölyn vaikutus MLC-relaatioihin todetaan riippuvan käytetystä kaistasta ja väristä, mutta vaikutuksen havaitaan olevan suurin optisen ja lähi-infrapunan väriyhdistelmillä.

Analysis of electricity distribution network operation business models and capitalization of control room functions with DMS

Electricity distribution network operation (NO) models are challenged as they are expected to continue to undergo changes during the coming decades in the fairly developed and regulated Nordic electricity market. Network asset managers are to adapt to competitive technoeconomical business models regarding the operation of increasingly intelligent distribution networks. Factors driving the changes for new business models within network operation include: increased investments in distributed automation (DA), regulative frameworks for annual profit limits and quality through outage cost, increasing end-customer demands, climatic changes and increasing use of data system tools, such as Distribution Management System (DMS). The doctoral thesis addresses the questions a) whether there exist conditions and qualifications for competitive markets within electricity distribution network operation and b) if so, identification of limitations and required business mechanisms. This doctoral thesis aims to provide an analytical business framework, primarily for electric utilities, for evaluation and development purposes of dedicated network operation models to meet future market dynamics within network operation. In the thesis, the generic build-up of a business model has been addressed through the use of the strategicbusiness hierarchy levels of mission, vision and strategy for definition of the strategic direction of the business followed by the planning, management and process execution levels of enterprisestrategy execution. Research questions within electricity distribution network operation are addressed at the specified hierarchy levels. The results of the research represent interdisciplinary findings in the areas of electrical engineering and production economics. The main scientific contributions include further development of the extended transaction cost economics (TCE) for government decisions within electricity networks and validation of the usability of the methodology for the electricity distribution industry. Moreover, DMS benefit evaluations in the thesis based on the outage cost calculations propose theoretical maximum benefits of DMS applications equalling roughly 25% of the annual outage costs and 10% of the respective operative costs in the case electric utility. Hence, the annual measurable theoretical benefits from the use of DMS applications are considerable. The theoretical results in the thesis are generally validated by surveys and questionnaires.

Viral and cellular modulation of virus-induced apoptosis in experimental infection models

The aim of this study was to investigate herpes simplex virus type 1 (HSV-1)- and measles virus (MV)-induced cell death. HSV-1 with deletion in genes encoding infected cell protein (ICP)4 and protein kinase Us3 (d120) induced apoptosis and cathepsin activation in epithelial (HEp-2) and monocytic (U937) cells. Inhibition of cathepsin activity decreased the amount of d120-induced apoptosis indicating that d120-induced apoptosis could be cathepsin-mediated. Also, HSV-1 infection increased caspase activation suggesting that d120-induced apoptosis is probably caspase-mediated. Cystatin treatment decreased the activity of cathepsins and the replication of HSV-1 indicating that cathepsins contribute to HSV-1 infection. Interestingly, d120 induced also necroptosis in monocytic cells. This is the first report on necroptosis in HSV-1- infected cells. MV induced apoptosis in uninfected bystander T lymphocytes, probably via interaction of MV-infected monocytes with uninfected lymphocytes. The expression of death receptor Fas was clearly increased on the surface of lymphocytes. The number of apoptotic cells and the activation of cathepsins and caspases were increased in MVinfected U937 cells suggesting that MV-induced apoptosis could be cathepsin- and caspase-mediated. Cystatin treatment inhibited cathepsin activities but not MV-induced apoptosis. Besides HSV-1-induced apoptosis, innate immune responses were studied in HSV-1-infection. HSV-1 viruses with either ICP4 and Us3, or Us3 deletion only, increased the expression of Toll-like receptor (TLR)3 and stimulated its downstream pathways leading to increased expression of type I interferon gene and to functional interferons. These findings suggest that besides controlling apoptosis, HSV-1 ICP4 and Us3 genes are involved in the control of TLR3 response in infected cell.

The Use of Radiostereometric Analysis in Fractures of the Distal Radius: From Phantom Models to Clinical Application

Radiostereometric analysis (RSA) is a highly accurate method for the measurement of in vivo micromotion of orthopaedic implants. Validation of the RSA method is a prerequisite for performing clinical RSA studies. Only a limited number of studies have utilised the RSA method in the evaluation of migration and inducible micromotion during fracture healing. Volar plate fixation of distal radial fractures has increased in popularity. There is still very little prospective randomised evidence supporting the use of these implants over other treatments. The aim of this study was to investigate the precision, accuracy, and feasibility of using RSA in the evaluation of healing in distal radius fractures treated with a volar fixed-angle plate. A physical phantom model was used to validate the RSA method for simple distal radius fractures. A computer simulation model was then used to validate the RSA method for more complex interfragmentary motion in intra-articular fractures. A separate pre-clinical investigation was performed in order to evaluate the possibility of using novel resorbable markers for RSA. Based on the validation studies, a prospective RSA cohort study of fifteen patients with plated AO type-C distal radius fractures with a 1-year follow-up was performed. RSA was shown to be highly accurate and precise in the measurement of fracture micromotion using both physical and computer simulated models of distal radius fractures. Resorbable RSA markers demonstrated potential for use in RSA. The RSA method was found to have a high clinical precision. The fractures underwent significant translational and rotational migration during the first two weeks after surgery, but not thereafter. Maximal grip caused significant translational and rotational interfragmentary micromotion. This inducible micromotion was detectable up to eighteen weeks, even after the achievement of radiographic union. The application of RSA in the measurement of fracture fragment migration and inducible interfragmentary micromotion in AO type-C distal radius fractures is feasible but technically demanding. RSA may be a unique tool in defining the progress of fracture union.