21 resultados para chromatin assembly and disassembly
em Doria (National Library of Finland DSpace Services) - National Library of Finland, Finland
Resumo:
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.
Resumo:
The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.
Resumo:
It is necessary to use highly specialized robots in ITER (International Thermonuclear Experimental Reactor) both in the manufacturing and maintenance of the reactor due to a demanding environment. The sectors of the ITER vacuum vessel (VV) require more stringent tolerances than normally expected for the size of the structure involved. VV consists of nine sectors that are to be welded together. The vacuum vessel has a toroidal chamber structure. The task of the designed robot is to carry the welding apparatus along a path with a stringent tolerance during the assembly operation. In addition to the initial vacuum vessel assembly, after a limited running period, sectors need to be replaced for repair. Mechanisms with closed-loop kinematic chains are used in the design of robots in this work. One version is a purely parallel manipulator and another is a hybrid manipulator where the parallel and serial structures are combined. Traditional industrial robots that generally have the links actuated in series are inherently not very rigid and have poor dynamic performance in high speed and high dynamic loading conditions. Compared with open chain manipulators, parallel manipulators have high stiffness, high accuracy and a high force/torque capacity in a reduced workspace. Parallel manipulators have a mechanical architecture where all of the links are connected to the base and to the end-effector of the robot. The purpose of this thesis is to develop special parallel robots for the assembly, machining and repairing of the VV of the ITER. The process of the assembly and machining of the vacuum vessel needs a special robot. By studying the structure of the vacuum vessel, two novel parallel robots were designed and built; they have six and ten degrees of freedom driven by hydraulic cylinders and electrical servo motors. Kinematic models for the proposed robots were defined and two prototypes built. Experiments for machine cutting and laser welding with the 6-DOF robot were carried out. It was demonstrated that the parallel robots are capable of holding all necessary machining tools and welding end-effectors in all positions accurately and stably inside the vacuum vessel sector. The kinematic models appeared to be complex especially in the case of the 10-DOF robot because of its redundant structure. Multibody dynamics simulations were carried out, ensuring sufficient stiffness during the robot motion. The entire design and testing processes of the robots appeared to be complex tasks due to the high specialization of the manufacturing technology needed in the ITER reactor, while the results demonstrate the applicability of the proposed solutions quite well. The results offer not only devices but also a methodology for the assembly and repair of ITER by means of parallel robots.
Resumo:
Suunniteltiin ja rakennettiin suoraa vääntömomenttisäätöä soveltava taajuudenmuuttajakäyttö oikosulkumoottorin ohjaukseen korvaamaan passiivinen jarrukäyttö. Laite on kuntoutuslaite, jolla tehdään lihasvoiman mittauksia ja voimaharjoituksia. Selvitettiin kaupallisten moottoreiden ja taajuudenmuuttajien suoritusominaisuuksia ja tämän perusteella valittiin käyttöön sopivat laitteet. Työssä esitetään kaksi oikosulkumoottorin ohjaustapaa: vektorisäätö ja suora vääntömomenttisäätö. Merkittävin osa tästä työstä käsittelee - tarkan turvallisuussuunnitelman lisäksi - kuntoutuslaitteen prototyypin komponentteja, kokoamista ja suoritustestien tuloksia.
Resumo:
Aim of this thesis was to design and manufacture a microdistillation column. The literature review part of this thesis covers stainless steels, material processing and basics about engineering design and distillation. The main focus, however, is on the experimental part. Experimental part is divided into five distinct sections: First part is where the device is introduced and separated into three parts. Secondly the device is designed part by part. It consists mostly of detail problem solving, since the first drawings had already been drawn and the critical dimensions decided. Third part is the manufacture, which was not fully completed since the final assembly was left out of this thesis. Fourth part is the test welding for the device, and its analysis. Finally some ideas for further studies are presented. The main goal of this thesis was accomplished. The device only lacks some final assembly but otherwise it is complete. One thing that became clear during the process was how difficult it is to produce small and precise steel parts with conventional manufacturing methods. Internal stresses within steel plates and thermal distortions can easily ruin small steel structures. Designing appropriate welding jigs is an important task for even simple devices. Laser material processing is a promising tool for this kind of steel processing because of the flexibility, good cutting quality and also precise and low heat input when welding. Next step in this project is the final assembly and the actual distillation tests. The tests will be carried out at Helsinki University of Technology.
Resumo:
The nucleus is a membrane enclosed organelle containing most of the genetic information of the cell in the form of chromatin. The nucleus, which can be divided into many sub-organelles such as the nucleoli, the Cajal bodies and the nuclear lamina, is the site for several essential cellular functions such as the DNA replication and its regulation and most of the RNA synthesis and processing. The nucleus is often affected in disease: the size and the shape of the nucleus, the chromatin distribution and the size of the nucleoli have remained the basis for the grading of several cancers. The maintenance of the vertebrate body shape depends on the skeleton. Similarly, in a smaller context, the shape of the cell and the nucleus are mainly regulated by the cytoskeletal and nucleoskeletal elements. The nuclear matrix, which by definition is a detergent, DNase and salt resistant proteinaceous nuclear structure, has been suggested to form the nucleoskeleton responsible for the nuclear integrity. Nuclear mitotic apparatus protein, NuMA, a component of the nuclear matrix, is better known for its mitotic spindle organizing function. NuMA is one of the nuclear matrix proteins suggested to participate in the maintenance of the nuclear integrity during interphase but its interphase function has not been solved to date. This thesis study concentrated on the role of NuMA and the nuclear matrix as structural and functional components of the interphase nucleus. The first two studies clarified the essential role of caspase-3 in the disintegration of the nuclear structures during apoptosis. The second study also showed NuMA and chromatin to co-elute from cells in significant amounts and the apoptotic cleavage of NuMA was clarified to have an important role in the dissociation of NuMA from the chromatin. The third study concentrated on the interphase function of NuMA showing NuMA depletion to result in cell cycle arrest and the cytoplasmic relocalization of NuMA interaction partner GAS41. We suggest that the relocalization of the transcription factor GAS41 may mediate the cell cycle arrest. Thus, this study has given new aspects in the interactions of NuMA, chromatin and the nuclear matrix.
Resumo:
The assembly and maintenance of the International Thermonuclear Experimental Reactor (ITER) vacuum vessel (VV) is highly challenging since the tasks performed by the robot involve welding, material handling, and machine cutting from inside the VV. The VV is made of stainless steel, which has poor machinability and tends to work harden very rapidly, and all the machining operations need to be carried out from inside of the ITER VV. A general industrial robot cannot be used due to its poor stiffness in the heavy duty machining process, and this will cause many problems, such as poor surface quality, tool damage, low accuracy. Therefore, one of the most suitable options should be a light weight mobile robot which is able to move around inside of the VV and perform different machining tasks by replacing different cutting tools. Reducing the mass of the robot manipulators offers many advantages: reduced material costs, reduced power consumption, the possibility of using smaller actuators, and a higher payload-to-robot weight ratio. Offsetting these advantages, the lighter weight robot is more flexible, which makes it more difficult to control. To achieve good machining surface quality, the tracking of the end effector must be accurate, and an accurate model for a more flexible robot must be constructed. This thesis studies the dynamics and control of a 10 degree-of-freedom (DOF) redundant hybrid robot (4-DOF serial mechanism and 6-DOF 6-UPS hexapod parallel mechanisms) hydraulically driven with flexible rods under the influence of machining forces. Firstly, the flexibility of the bodies is described using the floating frame of reference method (FFRF). A finite element model (FEM) provided the Craig-Bampton (CB) modes needed for the FFRF. A dynamic model of the system of six closed loop mechanisms was assembled using the constrained Lagrange equations and the Lagrange multiplier method. Subsequently, the reaction forces between the parallel and serial parts were used to study the dynamics of the serial robot. A PID control based on position predictions was implemented independently to control the hydraulic cylinders of the robot. Secondly, in machining, to achieve greater end effector trajectory tracking accuracy for surface quality, a robust control of the actuators for the flexible link has to be deduced. This thesis investigates the intelligent control of a hydraulically driven parallel robot part based on the dynamic model and two schemes of intelligent control for a hydraulically driven parallel mechanism based on the dynamic model: (1) a fuzzy-PID self-tuning controller composed of the conventional PID control and with fuzzy logic, and (2) adaptive neuro-fuzzy inference system-PID (ANFIS-PID) self-tuning of the gains of the PID controller, which are implemented independently to control each hydraulic cylinder of the parallel mechanism based on rod length predictions. The serial component of the hybrid robot can be analyzed using the equilibrium of reaction forces at the universal joint connections of the hexa-element. To achieve precise positional control of the end effector for maximum precision machining, the hydraulic cylinder should be controlled to hold the hexa-element. Thirdly, a finite element approach of multibody systems using the Special Euclidean group SE(3) framework is presented for a parallel mechanism with flexible piston rods under the influence of machining forces. The flexibility of the bodies is described using the nonlinear interpolation method with an exponential map. The equations of motion take the form of a differential algebraic equation on a Lie group, which is solved using a Lie group time integration scheme. The method relies on the local description of motions, so that it provides a singularity-free formulation, and no parameterization of the nodal variables needs to be introduced. The flexible slider constraint is formulated using a Lie group and used for modeling a flexible rod sliding inside a cylinder. The dynamic model of the system of six closed loop mechanisms was assembled using Hamilton’s principle and the Lagrange multiplier method. A linearized hydraulic control system based on rod length predictions was implemented independently to control the hydraulic cylinders. Consequently, the results of the simulations demonstrating the behavior of the robot machine are presented for each case study. In conclusion, this thesis studies the dynamic analysis of a special hybrid (serialparallel) robot for the above-mentioned special task involving the ITER and investigates different control algorithms that can significantly improve machining performance. These analyses and results provide valuable insight into the design and control of the parallel robot with flexible rods.
Resumo:
For advanced devices in the application fields of data storage, solar cell and biosensing, one of the major challenges to achieve high efficiency is the fabrication of nanopatterned metal oxide surfaces. Such surfaces often require both precise structure at the nanometer scale and controllable patterned structure at the macro scale. Nowadays, the dominating candidates to fabricate nanopatterned surfaces are the lithographic technique and block-copolymer masks, most of which are unfortunately costly and inefficient. An alternative bottom-up approach, which involves organic/inorganic self-assembly and dip-coating deposition, has been studied intensively in recent years and has proven to be an effective technique for the fabrication of nanoperforated metal oxide thin films. The overall objective of this work was to optimize the synthesis conditions of nanoperforated TiO2 (NP-TiO2) thin films, especially to be compatible with mixed metal oxide systems. Another goal was to develop fabrication and processing of NP-TiO2 thin films towards largescale production and seek new applications for solar cells and biosensing. Besides the traditional dip-coating and drop-casting methods, inkjet printing was used to prepare thin films of metal oxides, with the advantage of depositing the ink onto target areas, further enabling cost-effective fabrication of micro-patterned nanoperforated metal oxide thin films. The films were characterized by water contact angle determination, Atomic Force Microscopy, Scanning Electron Microscopy, X-ray Photoelectron Spectroscopy and Grazing Incidence XRay Diffraction. In this study, well-ordered zinc titanate nanoperforated thin films with different Zn/Ti ratios were produced successfully with zinc precursor content up to 50 mol%, and the dominating phase was Zn2Ti3O8. NP-TiO2 structures were also obtained by a cost-efficient means, namely inkjet printing, at both ambient temperature and 60 °C. To further explore new biosensing applications of nanoperforated oxide thin films, inkjet printing was used for the fabrication of both continuous and patterned polymeric films onto NP-TiO2 and perfluorinated phosphate functionalized NP-TiO2 substrates, respectively. The NP-TiO2 films can be also functionalized with a fluoroalkylsilane, resulting in hydrophobic surfaces on both titania and silica. The surface energy contrast in the nanoperforations can be tuned by irradiating the films with UV light, which provides ideal model systems for wettability studies.
Resumo:
Teklab is a manufacturer of electrical workstations. One major client group for the workstations is schools.Recently Teklab has started to concentrate on offering laboratory packages instead of single workstations. Laboratory packages include e.g. workstations, furniture, assembly and maintenance program. Teklab is looking for ideas to create more value for the laboratory package. One possibility is to design an educationalintroduction package to electric laboratories. In this thesis basic research isdone by studying the teaching methods in use today. Also modern education technology is presented. The thesis analyses different technologies for the laboratory introduction package. The technologies are analysed e.g. by applicability and feasibility. As a result of the work, the introduction has been done using an interactive presentation system. The presentation uses a software program and wireless student handsets designed by Dolphin Interactive. As a part of the work, also the recreation of the Teklab devices' instruction manuals has been started. For the future work, a digital learning object is under work, and a laboratory test is planned.
Resumo:
Tässä diplomityössä suunniteltiin parametrisesti modulaarinen koneen runko. Pyrkimyksenä oli suunnitella kokonaiskustannuksiltaan alhaisempi runkosarja jo olemassa oleviin suurnopeuskompressoreihin. Raportissa kerrotaan ensin modulaaristen tuoterakenteiden suunnittelusta ja käytettävästä suunnitteluohjelmistosta (SolidWorks). Sen jälkeen keskitytään suurnopeuskompressorin runkosarjan suunnitteluun esimerkkitapauksena. Aluksi keskitytään selvittämään rungolle asetettuja vaatimuksia ja ideoimaan erilaisia runkokonsepteja. Työ etenee ideoiden vertailun kautta modulaaristen konseptien luomiseen ja kahden moduulin moduulikohtaiseen suunnitteluun. Suunnitteluprosessissa käytetään rakenteen käyttäytymisen arviointiin äärellisten elementtien menetelmää (FEM). Työssä kehitettiin alkuperäisiin runkorakenteisiin verrattuna 10 % kustannuksiltaan edullisempi runkorakenneratkaisu, jonka purettavuus lisäksi alentaa rakenteen kuljetus- ja varastointikustannuksia.
Resumo:
Paperikoneen telalle integroitujen mekaanisten käyttölaitteiden valmistuksen siirtoprojektin yhteydessä on raportoitu huomattavan paljon valmistuksen aikaisia poikkeamia. Poikkeamien juurisyyn hahmottamiseksi tehtiin kvantitatiivinen analyysi raportoiduista poikkeamista ja kvalitatiivinen analyysi kokoonpanon nykytilasta. Kokoonpanotyöstä suuri osa on tällä hetkellä arvoa jalostamatonta työtä. Tutkimuksessa havaittiin valmistusprosessissa kaikkia kokoonpanon poikkeamien perustyyppejä ja näitä poikkeamia olivat aiheuttaneet kaikki mahdolliset aiheuttajat. Etenkin hankittavien osien laatua tulisi käsitellä poikkeamien aiheuttamien kokonaiskustannusten kautta. Kokoonpanon tarvitsema tieto on olemassa täsmällisessä muodossa, mutta sen luoksepäästävyys on huono. Prosessin kuvauksella, hiljaisen tiedon kirjaamisella ja täsmällisen tiedon julkistamisella voidaan parantaa tuotannon laatua tuotetuntemuksen parantuessa. Käyttökohteen tunteminen parantaa vaatimusten ymmärtämistä. Tutkimuksessa havaittujen poikkeamien analysoinnin perusteella erityistä huomiota tulisi kiinnittää tarkastusvaiheiden olemassa oloon, sijoitukseen ja niiden laatuun. Suuri osa poikkeamista oli edennyt kokoonpanoon jonkin tarkastusvaiheen läpi. Tarkastusvaiheiden laatutason tulee parantua, jotta moninkertaisesta tarkastuksesta voidaan luopua.
Resumo:
Osien hyvä valmistettavuus on aina asettanut haasteita suunnittelulle. Yritysten verkostoituminen lisää haasteellisuutta, kun tuotteiden suunnittelu tehdään erillään kokoonpanosta ja osavalmistus tapahtuu alihankintana. Tällöin on ensiarvoisen tärkeää, että suunnittelulla on tarvittavat perustiedot eri valmistusmenetelmistä, jotta suunniteltujen osien valmistus ja kokoonpano luonnistuu ongelmitta. Työn alun kirjallisuusosiossa käsitellään suunnittelun teoriaa, joka toimii perustana hyvälle osasuunnittelulle. Teorian lisäksi työssä käsitellään eri työmenetelmiä koskevat rajoitukset ja mahdollisuudet. Oikein suunniteltu osa on työstömenetelmien kannalta hyvin valmistettavissa, työ voidaan tehdä taloudellisilla työmenetelmillä ja kokoonpanossa osat sopivat yhteen ilman sovitustyötä. Käytännön osuudessa on käsitelty The Switch Drive Systems Oy:n tuotteiden valmistettavuuden kehityskohteita, joilla tuotteiden valmistettavuutta voidaan parantaa. Kehityskohteiden perusteella on laadittu valmistusmenetelmäkohtainen suunnittelun ohjeistus, jonka avulla kehitetään The Switchin suunnittelua vastaamaan paremmin laitetoimittajien tarpeisiin. Näiden ohjeistuksien avulla voidaan kehittää suunnittelutyötä siten, että osien valmistettavuus sekä laatu paranevat ja kokoonpano nopeutuu.
Resumo:
Palonrajoittimet ovat tuotteita, jotka estävät tulen ja savun leviämisen palo-osastosta toiseen ja mahdollistavat ihmisten turvallisen ulospääsyn palotilanteessa. Tämän diplomityön tavoitteena oli vähentää suorakulmaisten palonrajoittimien valmistuskustannuksia niiden valmistettavuutta kehittämällä. Työn teoriaosassa käsitellään valmistettavuutta ja kokoonpantavuutta kehittäviä menetelmiä DFM:ää (Design for Manufacturability) ja DFA:ta (Design for Assembly) sekä palonrajoittimien ja ohutlevytuotteiden erityispiirteitä. Käytännön osuudessa esitellään tutkimusta varten valmistetut kolme kehitettävää palonrajoitinta, joita vertaillaan myös kilpaileviin tuotteisiin. Tuotteista analysoidaan osamääriä, materiaalikustannuksia ja työaikoja. Palonrajoittimien ongelmakohtia olivat muun muassa liittäminen ja kokoonpantavuus. Työssä esitetään keinoja palonrajoitinten valmistusystävälliseen suunnitteluun ja uusi moduloitu tuoteperhemalli, jolla vähennetään varsinkin valmistuksesta aiheutuvia kiinteitä kustannuksia. Lisäksi työssä esitetään alustava runkoratkaisumalli uudelle tuoteperheelle.
Resumo:
Tutkimuksen tarkoituksena oli löytää menetelmiä tuotteen kokoonpantavuuden kehittämiseen ja parantaa sitä DFMA-ajattelun sekä Lean–filosofian avulla. Työn teoreettisessa osuudessa tarkasteltiin läpimenoajan käsitettä ja käytettävissä olevien resurssien merkitystä. Lisäksi tarkastelun kohteena oli DFMA:n hyödyntäminen kokoonpanon nopeuttamisessa sekä Lean–filosofian hyödyntäminen tuotantoprosessin kehittämiseksi. Empiirinen osuus kohdentui Outotec Turula Oy:n anodivalimon kokoonpanossa ilmenneisiin ongelmiin ja niiden poistamiseen. Tutkimuksella saatiin selvitettyä resurssien ja osaamisen merkitys valmistusprosessin kehittämisen turvaamisessa. DFMA:n ja Lean:in avulla on mahdollista löytää toimintatapoja, joiden avulla anodivalimon kokoonpanon läpimenoaikaa on mahdollista lyhentää.
Resumo:
Tämän diplomityön tavoitteena oli tutkia ja selvittää kuormakoneen takarunkorakenteen silloitushitsauksen robotisointia. Työ päätettiin rajata koskemaan vain tiettyä moduulia takarungosta. Työssä kartoitettiin tarvittava laitteisto, selvitettiin runkomoduulin silloitusajat sekä arvioitiin investoinnin kannattavuutta. Silloituksen suorittavan järjestelmän vaatimuksena oli, että sen tulee asettaa osat paikoilleen hitsauskiinnittimeen ja tehdä tarvittavat silloitushitsaukset automaattisesti. Sopivaksi laitteistoksi osoittautui taloudellisuuden ja toiminnallisuuden näkökulmasta yhdestä kappaleenkäsittely- sekä hitsausrobotista muodostuva järjestelmä. Kappaleenkäsittelijän ohjauksessa käytetään konenäköä sekä osien paikannuksessa että laadunvarmistuksessa. Robotit liikkuvat yhteisellä lineaariradalla, jonka rinnalla on kappaleenkäsittelylaitteistoja hitsauskiinnittimineen. Robotisoinnin käyttöönotolla yhden takarungon moduulien kokoonpanoon ja silloitukseen käytettävä aika pienenee alle puoleen manuaaliseen työhön verrattuna. Näin saavutetaan merkittäviä kustannussäästöjä. Lisäksi hitsauskiinnittimet voivat olla verrattain yksinkertaisia manuaalityöhön verrattuna, jolloin myös säästetään työkaluinvestoinneissa. Robotisointiprojektin jatkotoimenpiteitä ovat laajamittaiset tuotantosimulaatiot layoutin, laitteiston sekä työkiertojen tarkaksi määrittämiseksi. Lisäksi itse tuotetta on muokattava paremmin robottisilloitukseen sopivaksi.