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.

Design of traction transmission and suspension systems for an omni-directional mobile robot

This project aims to design and manufacture a mobile robot with two Universal Robot UR10 mainly used indoors. In order to obtain omni-directional maneuverability, the mobile robot is constructed with Mecanum wheels. The Mecanum wheel can move in any direction with a series of rollers attached to itself. These rollers are angled at 45º about the hub’s circumference. This type of wheels can be used in both driving and steering with their any-direction property. This paper is focused on the design of traction system and suspension system, and the velocity control of Mecanum wheels in the close-loop control system. The mechanical design includes selection of bearing housing, couplers which are act as connection between shafts, motor parts, and other needed components. The 3D design software SolidWorks is utilized to assemble all the components in order to get correct tolerance. The driving shaft is designed based on assembled structure via the software as well. The design of suspension system is to compensate the assembly error of Mecanum wheels to guarantee the stability of the robot. The control system of motor drivers is realized through the Robot Operating System (ROS) on Ubuntu Linux. The purpose of inverse kinematics is to obtain the relationship among the movements of all Mecanum wheels. Via programming and interacting with the computer, the robot could move with required speed and direction.

The Dynamic Relationship between Finnish Stock Market and Commodities

Since different stock markets have become more integrated during 2000s, investors need new asset classes in order to gain diversification benefits. Commodities have become popular to invest in and thus it is important to examine whether the investors should use commodities as a part for portfolio diversification. This master’s thesis examines the dynamic relationship between Finnish stock market and commodities. The methodology is based on Vector Autoregressive models (VAR). The long-run relationship between Finnish stock market and commodities is examined with Johansen cointegration while short-run relationship is examined with VAR models and Granger causality test. In addition, impulse response test and forecast error variance decomposition are employed to strengthen the results of short-run relationship. The dynamic relationships might change under different market conditions. Thus, the sample period is divided into two sub-samples in order to reveal whether the dynamic relationship varies under different market conditions. The results show that Finnish stock market has stable long-run relationship with industrial metals, indicating that there would not be diversification benefits among the industrial metals. The long-run relationship between Finnish stock market and energy commodities is not as stable as the long-run relationship between Finnish stock market and industrial metals. Long-run relationship was found in the full sample period and first sub-sample which indicate less room for diversification. However, the long-run relationship disappeared in the second sub-sample which indicates diversification benefits. Long-run relationship between Finnish stock market and agricultural commodities was not found in the full sample period which indicates diversification benefits between the variables. However, long-run relationship was found from both sub-samples. The best diversification benefits would be achieved if investor invested in precious metals. No long-run relationship was found from either sample. In the full sample period OMX Helsinki had short-run relationship with most of the energy commodities and industrial metals and the causality was mostly running from equities to commodities. During the first sub period the number of short-run relationships and causality shrunk but during the crisis period the number of short-run relationships and causality increased. The most notable result found was unidirectional causality from gold to OMX Helsinki during the crisis period.

The functional fit between collaborative software and work systems:Qualification of work system needs to software functionality

The study develops an approach that tries to validate software functionality to work systems needs in SMEs. The formulated approach is constructed by using a SAAS based software i.e., work collaboration service (WCS), and SMEs as the elements of study. Where the WCS’s functionality is qualified to the collaboration needs that exist in operational and project work within SMEs. For this research constructivist approach and case study method is selected because the nature of the current study requires an in depth study of the work collaboration service as well as a detailed study of the work systems within different enterprises. Four different companies are selected in which fourteen interviews are conducted to gather data pertaining. The work systems method and framework are used as a central part of the approach to collect, analyze and interpret the enterprises work systems model and the underlying collaboration needs on operational and project work. On the other hand, the functional model of the WCS and its functionality is determined from functional model analysis, software testing, documentation and meetings with the service vendor. The enterprise work system model and the WCS model are compared to reveal how work progression differs between the two and make visible unaddressed stages of work progression. The WCS functionality is compared to work systems collaboration needs to ascertain if the service will suffice the needs of the project and operational work under study. The unaddressed needs provide opportunities to improve the functionality of the service for better conformity to the needs of enterprise and work. The results revealed that the functional models actually differed in how operational and project work progressed within the stages. WCS shared similar stages of work progression apart from the stages of identification and acceptance, and progress and completion stages were only partially addressed. Conclusion is that the identified unaddressed needs such as, single point of reference, SLA and OLA inclusion etc., should be implemented or improved within the WCS at appropriate stages of work to gain better compliance of the service to the needs of the enterprise an work itself. The developed approach can hence be used to carry out similar analysis for the conformance of pre-built software functionality to work system needs with SMEs.

Cascade hydropower capacity increase profitability analysis with optimisation modelling

The electricity market and climate are both undergoing a change. The changes impact hydropower and provoke an interest for hydropower capacity increases. In this thesis a new methodology was developed utilising short-term hydropower optimisation and planning software for better capacity increase profitability analysis accuracy. In the methodology income increases are calculated in month long periods while varying average discharge and electricity price volatility. The monthly incomes are used for constructing year scenarios, and from different types of year scenarios a long-term profitability analysis can be made. Average price development is included utilising a multiplier. The method was applied on Oulujoki hydropower plants. It was found that the capacity additions that were analysed for Oulujoki were not profitable. However, the methodology was found versatile and useful. The result showed that short periods of peaking prices play major role in the profitability of capacity increases. Adding more discharge capacity to hydropower plants that initially bypassed water more often showed the best improvements both in income and power generation profile flexibility.

Sähkösalkun tuotteistaminen ja salkunhallinnan menestyksen seuranta

Sähkömarkkinoiden vapautumisen ja pörssimuotoisen kaupankäynnin myötäyhä useampi toimija on siirtynyt perinteisistä kiinteähintaisista sopimuksista salkkumuotoiseen sähkönhankintaan. Aktiivisen salkunhallinnan myötä kanava markkinoille pysyy jatkuvasti avoimena ja ostopäätös voidaan jakaa pidemmälle ajanjaksolle, jolloin riippuvaisuus vain yhden hetken hintatasosta pienenee. Sähkön hankintahinnan suojaamiseen käytettävien finanssituotteiden määrä pörssissä ja OTC-markkinalla on kasvanut viime vuosina merkittävästi. Tämän seurauksena myös käytettävien instrumenttien valinta ja perustelu asiakkaalle vaatii entistä tarkempaa huomiota. Työssä käsiteltävän tuotteistuksen tavoitteena oli luoda salkunhallinnan perustapauksille yksinkertaiset rungot, joita voidaan täydentää erilaisillalisäominaisuuksilla. Tuotteistuksella pyritään myös selkeyttämään asiakkaalle muodostuvaa mielikuvaa tarjolla olevista vaihtoehdoista sekä edesauttamaan markkinointia. Diplomityön toisena tavoitteena oli kehittää salkunhallinnan menestyksen seurantaa varten mittarit, joiden avulla sekä asiakas että salkunhoitaja pystyvät seuraamaan salkunhallinnan onnistumista. Mittarit toteutettiin Excel-ympäristössä ja testattavat salkut koostuivat pääasiassa lopullisista tuotteistettaviksi valituista salkuista. Työn pohjalta on määrä toteuttaa olemassa olevan internet-pohjaisen salkunhallintapalvelun osaksi sovellus, joka mahdollistaa salkunhallinnan menestyksen jatkuvan seurannan.