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 the sensorless pressure control system for a centrifugal pump

This thesis investigates the pressure-based control of a variable-speed-driven pump system in the case of existing output pressure measurement and in the case of sensorless system, where the actual output pressure value is calculated with the steady state estimator.

Relay protection in active distribution networks

Increasingly growing share of distributed generation in the whole electrical power system’s generating system is currently a worldwide tendency, driven by several factors, encircling mainly difficulties in refinement of megalopolises’ distribution networks and its maintenance; widening environmental concerns adding to both energy efficiency approaches and installation of renewable sources based generation, inherently distributed; increased power quality and reliability needs; progress in IT field, making implementable harmonization of needs and interests of different-energy-type generators and consumers. At this stage, the volume, formed by system-interconnected distributed generation facilities, have reached the level of causing broad impact toward system operation under emergency and post-emergency conditions in several EU countries, thus previously implementable approach of their preliminary tripping in case of a fault, preventing generating equipment damage and disoperation of relay protection and automation, is not applicable any more. Adding to the preceding, withstand capability and transient electromechanical stability of generating technologies, interconnecting in proximity of load nodes, enhanced significantly since the moment Low Voltage Ride-Through regulations, followed by techniques, were introduced in Grid Codes. Both aspects leads to relay protection and auto-reclosing operation in presence of distributed generation generally connected after grid planning and construction phases. This paper proposes solutions to the emerging need to ensure correct operation of the equipment in question with least possible grid refinements, distinctively for every type of distributed generation technology achieved its technical maturity to date and network’s protection. New generating technologies are equivalented from the perspective of representation in calculation of initial steady-state short-circuit current used to dimension current-sensing relay protection, and widely adopted short-circuit calculation practices, as IEC 60909 and VDE 0102. The phenomenon of unintentional islanding, influencing auto-reclosing, is addressed, and protection schemes used to eliminate an sustained island are listed and characterized by reliability and implementation related factors, whereas also forming a crucial aspect of realization of the proposed protection operation relieving measures.

Dynamic Modelling of Circulating Fluidized Bed Plant with Gas Turbine Repowering

Increasing amount of renewable energy source based electricity production has set high load control requirements for power grid balance markets. The essential grid balance between electricity consumption and generation is currently hard to achieve economically with new-generation solutions. Therefore conventional combustion power generation will be examined in this thesis as a solution to the foregoing issue. Circulating fluidized bed (CFB) technology is known to have sufficient scale to acts as a large grid balancing unit. Although the load change rate of the CFB unit is known to be moderately high, supplementary repowering solution will be evaluated in this thesis for load change maximization. The repowering heat duty is delivered to the CFB feed water preheating section by smaller gas turbine (GT) unit. Consequently, steam extraction preheating may be decreased and large amount of the gas turbine exhaust heat may be utilized in the CFB process to reach maximum plant electrical efficiency. Earlier study of the repowering has focused on the efficiency improvements and retrofitting to maximize plant electrical output. This study however presents the CFB load change improvement possibilities achieved with supplementary GT heat. The repowering study is prefaced with literature and theory review for both of the processes to maximize accuracy of the research. Both dynamic and steady-state simulations accomplished with APROS simulation tool will be used to evaluate repowering effects to the CFB unit operation. Eventually, a conceptual level analysis is completed to compare repowered plant performance to the state-of-the-art CFB performance. Based on the performed simulations, considerably good improvements to the CFB process parameters are achieved with repowering. Consequently, the results show possibilities to higher ramp rate values achieved with repowered CFB technology. This enables better plant suitability to the grid balance markets.

Modelling the exothermic heat and the demand of cooling in paper and pulp industry biological wastewater treatment

This master thesis presents a study on the requisite cooling of an activated sludge process in paper and pulp industry. The energy consumption of paper and pulp industry and it’s wastewater treatment plant in particular is relatively high. It is therefore useful to understand the wastewater treatment process of such industries. The activated sludge process is a biological mechanism which degrades carbonaceous compounds that are present in waste. The modified activated sludge model constructed here aims to imitate the bio-kinetics of an activated sludge process. However, due to the complicated non-linear behavior of the biological process, modelling this system is laborious and intriguing. We attempt to find a system solution first using steady-state modelling of Activated Sludge Model number 1 (ASM1), approached by Euler’s method and an ordinary differential equation solver. Furthermore, an enthalpy study of paper and pulp industry’s vital pollutants was carried out and applied to revise the temperature shift over a period of time to formulate the operation of cooling water. This finding will lead to a forecast of the plant process execution in a cost-effective manner and management of effluent efficiency. The final stage of the thesis was achieved by optimizing the steady state of ASM1.