Monte Carlo -reaktorifysiikkalaskennan ja laskennallisen virtausmekaniikan kytkentä kuulakekoreaktorissa

Monte Carlo -reaktorifysiikkakoodit nykyisin käytettävissä olevilla laskentatehoilla tarjoavat mielenkiintoisen tavan reaktorifysiikan ongelmien ratkaisuun. Neljännen sukupolven ydinreaktoreissa käytettävät uudet rakenteet ja materiaalit ovat haasteellisia nykyisiin reaktoreihin suunnitelluille laskentaohjelmille. Tässä työssä Monte Carlo -reaktorifysiikkakoodi ja CFD-koodi yhdistetään kytkettyyn laskentaan kuulakekoreaktorissa, joka on yksi korkealämpötilareaktorityyppi. Työssä käytetty lähestymistapa on uutta maailmankin mittapuussa ajateltuna.

Optimization and Applications of Large-Scale Biomedical Event Networks

The overwhelming amount and unprecedented speed of publication in the biomedical domain make it difficult for life science researchers to acquire and maintain a broad view of the field and gather all information that would be relevant for their research. As a response to this problem, the BioNLP (Biomedical Natural Language Processing) community of researches has emerged and strives to assist life science researchers by developing modern natural language processing (NLP), information extraction (IE) and information retrieval (IR) methods that can be applied at large-scale, to scan the whole publicly available biomedical literature and extract and aggregate the information found within, while automatically normalizing the variability of natural language statements. Among different tasks, biomedical event extraction has received much attention within BioNLP community recently. Biomedical event extraction constitutes the identification of biological processes and interactions described in biomedical literature, and their representation as a set of recursive event structures. The 2009–2013 series of BioNLP Shared Tasks on Event Extraction have given raise to a number of event extraction systems, several of which have been applied at a large scale (the full set of PubMed abstracts and PubMed Central Open Access full text articles), leading to creation of massive biomedical event databases, each of which containing millions of events. Sinece top-ranking event extraction systems are based on machine-learning approach and are trained on the narrow-domain, carefully selected Shared Task training data, their performance drops when being faced with the topically highly varied PubMed and PubMed Central documents. Specifically, false-positive predictions by these systems lead to generation of incorrect biomolecular events which are spotted by the end-users. This thesis proposes a novel post-processing approach, utilizing a combination of supervised and unsupervised learning techniques, that can automatically identify and filter out a considerable proportion of incorrect events from large-scale event databases, thus increasing the general credibility of those databases. The second part of this thesis is dedicated to a system we developed for hypothesis generation from large-scale event databases, which is able to discover novel biomolecular interactions among genes/gene-products. We cast the hypothesis generation problem as a supervised network topology prediction, i.e predicting new edges in the network, as well as types and directions for these edges, utilizing a set of features that can be extracted from large biomedical event networks. Routine machine learning evaluation results, as well as manual evaluation results suggest that the problem is indeed learnable. This work won the Best Paper Award in The 5th International Symposium on Languages in Biology and Medicine (LBM 2013).

Photodamage to Oxygen Evolving Complex - An Initial Event in Photoinhibition of Photosystem II.

Photosystem II (PSII) of oxygenic photosynthesis is susceptible to photoinhibition. Photoinhibition is defined as light induced damage resulting in turnover of the D1 protein subunit of the reaction center of PSII. Both visible and ultraviolet (UV) light cause photoinhibition. Photoinhibition induced by UV light damages the oxygen evolving complex (OEC) via absorption of UV photons by the Mn ion(s) of OEC. Under visible light, most of the earlier hypotheses assume that photoinhibition occurs when the rate of photon absorption by PSII antenna exceeds the use of the absorbed energy in photosynthesis. However, photoinhibition occurs at all light intensities with the same efficiency per photon. The aim of my thesis work was to build a model of photoinhibition that fits the experimental features of photoinhibition. I studied the role of electron transfer reactions of PSII in photoinhibition and found that changing the electron transfer rate had only minor influence on photoinhibition if light intensity was kept constant. Furthermore, quenching of antenna excitations protected less efficiently than it would protect if antenna chlorophylls were the only photoreceptors of photoinhibition. To identify photoreceptors of photoinhibition, I measured the action spectrum of photoinhibition. The action spectrum showed resemblance to the absorption spectra of Mn model compounds suggesting that the Mn cluster of OEC acts as a photoreceptor of photoinhibition under visible light, too. The role of Mn in photoinhibition was further supported by experiments showing that during photoinhibition OEC is damaged before electron transfer activity at the acceptor side of PSII is lost. Mn enzymes were found to be photosensitive under visible and UV light indicating that Mn-containing compounds, including OEC, are capable of functioning as photosensitizers both in visible and UV light. The experimental results above led to the Mn hypothesis of the mechanism of continuous-light-induced photoinhibition. According to the Mn hypothesis, excitation of Mn of OEC results in inhibition of electron donation from OEC to the oxidized primary donor P680+ both under UV and visible light. P680 is oxidized by photons absorbed by chlorophyll, and if not reduced by OEC, P680+ may cause harmful oxidation of other PSII components. Photoinhibition was also induced with intense laser pulses and it was found that the photoinhibitory efficiency increased in proportion to the square of pulse intensity suggesting that laser-pulse-induced photoinhibition is a two-photon reaction. I further developed the Mn hypothesis suggesting that the initial event in photoinhibition under both continuous and pulsed light is the same: Mn excitation that leads to the inhibition of electron donation from OEC to P680+. Under laser-pulse-illumination, another Mn-mediated inhibitory photoreaction occurs within the duration of the same pulse, whereas under continuous light, secondary damage is chlorophyll mediated. A mathematical model based on the Mn hypothesis was found to explain photoinhibition under continuous light, under flash illumination and under the combination of these two.

Upgrading of thethird generation of the Remote Diagnostic Systems for ABB Marine Propulsion Systems

Remote diagnostics has become very popular in marine industry. Diagnostic systems are improved all the time and the newest monitoring systems are constantly taken into operation. Most vessels are, however, rigged up by outmoded facilities, which should be updated. In this work the principles of operating of such a remote diagnostic system as the ABB's third generation remote diagnostic system (RDS) and the newest Propulsion Condition Management System (PCMS) are studied. As a result of the thesis the ways of upgrading the old systems of RDS are presented. Specifically, the work focuses on the establishment of the connection between Advant controller AC-110 from the old system and PCMS server, and in other words how to get Modbus data by OPC server.

Investment Determinants and Future Shape of Russia's Power Generation

The reformation of power sector is still in the process of development. The present day situation in Russian electricity power market ischaracterized as transitional period: competitive electricity market is forming, new companies are being created and the power of government regulation is decreasing. The main aim of the reformation is to attract much-needed private investments to the power sector. The electricity consumption increases very rapidly and power sector has to cope with high demand. The goal of this master's thesis is to analyze the nowadays situation in Russian power sector, such as generation structure, condition of electricity networks, electricity price formation for end-users, shape of fuel sector and investments risks and attraction.The final result of this work is creation of scenario of Russian power sector future shape and analysis of the present day situation.