Subshifts with Simple Cellular Automata

A subshift is a set of in nite one- or two-way sequences over a xed nite set, de ned by a set of forbidden patterns. In this thesis, we study subshifts in the topological setting, where the natural morphisms between them are ones de ned by a (spatially uniform) local rule. Endomorphisms of subshifts are called cellular automata, and we call the set of cellular automata on a subshift its endomorphism monoid. It is known that the set of all sequences (the full shift) allows cellular automata with complex dynamical and computational properties. We are interested in subshifts that do not support such cellular automata. In particular, we study countable subshifts, minimal subshifts and subshifts with additional universal algebraic structure that cellular automata need to respect, and investigate certain criteria of `simplicity' of the endomorphism monoid, for each of them. In the case of countable subshifts, we concentrate on countable so c shifts, that is, countable subshifts de ned by a nite state automaton. We develop some general tools for studying cellular automata on such subshifts, and show that nilpotency and periodicity of cellular automata are decidable properties, and positive expansivity is impossible. Nevertheless, we also prove various undecidability results, by simulating counter machines with cellular automata. We prove that minimal subshifts generated by primitive Pisot substitutions only support virtually cyclic automorphism groups, and give an example of a Toeplitz subshift whose automorphism group is not nitely generated. In the algebraic setting, we study the centralizers of CA, and group and lattice homomorphic CA. In particular, we obtain results about centralizers of symbol permutations and bipermutive CA, and their connections with group structures.

A simple culture system for time-lapse video recording of bovine embryos

Selostus: Yksinkertainen viljelymenetelmä naudan alkioiden aikaviivenauhoitusta varten

A simple device for sampling of volumetric forest soil cores

Summary

Fluorescence in situ hybridization of potato somatohaploids and their somatic hybrid donors using two Solanum brevidens specific sequences

Selostus: Perunan somaattisten hybridien ja niiden somatohaploidien fluoresenssi in situ -hybridisaatio Solanum brevidens -lajin spesifisten sekvenssien avulla

Reduced simple ratio better than NDVI for estimating LAI in Finnish pine and spruce stands

Abstract

Hybrid LC Filter for Power Electronic Drives: Theory and Implementation

Power electronic converter drives use, for the sake of high efficiency, pulse-width modulation that results in sequences of high-voltage high-frequency steep-edged pulses. Such a signal contains a set of high harmonics not required for control purposes. Harmonics cause reflections in the cable between the motor and the inverter leading to faster winding insulation ageing. Bearing failures and problems with electromagnetic compatibility may also result. Electrical du/dt filters provide an effective solution to problems caused by pulse-width modulation, thereby increasing the performance and service life of the electrical machines. It is shown that RLC filters effectively decrease the reflection phenomena in the cable. Improved (simple, but effective) solutions are found for both differential- and common-mode signals; these solutions use a galvanic connection between the RLC filter star point and the converter DC link. Foil chokes and film capacitors are among the most widely used components in high-power applications. In actual applications they can be placed in different parts of the cabinet. This fact complicates the arrangement of the cabinet and decreases the reliability of the system. In addition, the inductances of connection wires may prevent filtration at high frequencies. This thesis introduces a new hybrid LC filter that uses a natural capacitance between the turns of the foil choke based on integration of an auxiliary layer into it. The main idea of the hybrid LC filter results from the fact that both the foil choke and the film capacitors have the same roll structure. Moreover, the capacitance between the turns (“intra capacitance”) of the foil inductors is the reason for the deterioration of their properties at high frequencies. It is shown that the proposed filter has a natural cancellation of the intra capacitance. A hybrid LC filter may contain two or more foil layers isolated from each other and coiled on a core. The core material can be iron or even air as in the filter considered in this work. One of the foils, called the main foil, can be placed between the inverter and the motor cable. Other ones, called auxiliary foils, may be connected in star to create differential-mode noise paths, and then coupled to the DC link midpoint to guarantee a traveling path, especially for the common-mode currents. This way, there is a remarkable capacitance between the main foil and the auxiliary foil. Investigations showed that such a system can be described by a simple equivalent LC filter in a wide range of frequencies. Because of its simple hybrid construction, the proposed LC filter can be a cost-effective and competitive solution for modern power drives. In the thesis, the application field of the proposed filter is considered and determined. The basics of hybrid LC filter design are developed further. High-frequency behaviour of the proposed filter is analysed by simulations. Finally, the thesis presents experimental data proving that the hybrid LC filter can be used for du/dt of PWM pulses and reduction of common-mode currents.

Development of simple and efficient synthetic strategies for production of fine chemicals of pharmaceutical relevance : metal-mediated allylation combined with applied catalysis

Den snart 200 år gamla vetenskapsgrenen organisk synteskemi har starkt bidragit till moderna samhällens välfärd. Ett av flaggskeppen för den organiska synteskemin är utvecklingen och produktionen av nya läkemedel och speciellt de aktiva substanserna däri. Därmed är det viktigt att utveckla nya syntesmetoder, som kan tillämpas vid framställningen av farmaceutiskt relevanta målstrukturer. I detta sammanhang är den ultimata målsättningen dock inte endast en lyckad syntes av målmolekylen, utan det är allt viktigare att utveckla syntesrutter som uppfyller kriterierna för den hållbara utvecklingen. Ett av de centralaste verktygen som en organisk kemist har till förfogande i detta sammanhang är katalys, eller mera specifikt möjligheten att tillämpa olika katalytiska reaktioner vid framställning av komplexa målstrukturer. De motsvarande industriella processerna karakteriseras av hög effektivitet och minimerad avfallsproduktion, vilket naturligtvis gynnar den kemiska industrin samtidigt som de negativa miljöeffekterna minskas avsevärt. I denna doktorsavhandling har nya syntesrutter för produktion av finkemikalier med farmaceutisk relevans utvecklats genom att kombinera förhållandevis enkla transformationer till nya reaktionssekvenser. Alla reaktionssekvenser som diskuteras i denna avhandling påbörjades med en metallförmedlad allylering av utvalda aldehyder eller aldiminer. De erhållna produkterna innehållende en kol-koldubbelbindning med en närliggande hydroxyl- eller aminogrupp modifierades sedan vidare genom att tillämpa välkända katalytiska reaktioner. Alla syntetiserade molekyler som presenteras i denna avhandling karakteriseras som finkemikalier med hög potential vid farmaceutiska tillämpningar. Utöver detta tillämpades en mängd olika katalytiska reaktioner framgångsrikt vid syntes av dessa molekyler, vilket i sin tur förstärker betydelsen för de katalytiska verktygen i organiska kemins verktygslåda.

Automatic recognition of fish from video sequences

The problem of automatic recognition of the fish from the video sequences is discussed in this Master’s Thesis. This is a very urgent issue for many organizations engaged in fish farming in Finland and Russia because the process of automation control and counting of individual species is turning point in the industry. The difficulties and the specific features of the problem have been identified in order to find a solution and propose some recommendations for the components of the automated fish recognition system. Methods such as background subtraction, Kalman filtering and Viola-Jones method were implemented during this work for detection, tracking and estimation of fish parameters. Both the results of the experiments and the choice of the appropriate methods strongly depend on the quality and the type of a video which is used as an input data. Practical experiments have demonstrated that not all methods can produce good results for real data, whereas on synthetic data they operate satisfactorily.

Metal-Ion-Binding Oligonucleotides: High-Affinity Probes for Nucleic Acid Sequences

Small non-coding RNAs have numerous biological functions in cell and are divided into different classes such as: microRNA, snoRNA, snRNA and siRNA. MicroRNA (miRNA) is the most studied non-coding RNA to date and is found in plants, animals and some viruses. miRNA with short sequences is involved in suppressing translation of target genes by binding to their mRNA post-transcriptionally and silencing it. Their function besides silencing of the viral gene, can be oncogenic and therefore the cause of cancer. Hence, their roles are highlighted in human diseases, which increases the interest in using them as biomarkers and drug targets. One of the major problems to overcome is recognition of miRNA. Owing to a stable hairpin structure, chain invasion by conventional Watson-Crick base-pairing is difficult. One way to enhance the hybridization is exploitation of metal-ion mediated base-pairing, i. e. oligonucleotide probes that tightly bind a metal ions and are able to form a coordinative bonds between modified and natural nucleobases. This kind of metallo basepairs containing short modified oligonucleotides can also be useful for recognition of other RNA sequences containing hairpin-like structural motives, such as the TAR sequence of HIV. In addition, metal-ion-binding oligonucleotides will undoubtedly find applications in DNA-based nanotechnology. In this study, the 3,5-dimethylpyrazol-1-yl substituted purine derivatives were successfully incorporated within oligonucleotides, into either a terminal or non-terminal position. Among all of the modified oligonucleotides studied, a 2-(3,5-dimethylpyrazol-1-yl)-6-oxopurine base containing oligonucleotide was observed to bind most efficiently to their unmodified complementary sequences in the presence of both Cu2+ or Zn2+. The oligonucleotide incorporating 2,6-bis(3,5-dimethylpyrazol-1-yl)purine base also markedly increased the stability of duplexes in the presence of Cu2+ without losing the selectivity.

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.