DnaSP v5: A software for comprehensive analysis of DNA polymorphism data

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

High Molecular Weight Methacrylate Sealing of a Bridge Deck, HR-2031, Construction Report, 1988

The Iowa Department of Transportation used a high molecular weight methacrylate (HMWM) resin to seal a 3,340 ft. x 64 ft. bridge deck in October 1986. The sealing was necessary to prevent deicing salt brine from entering a substantial number of transverse cracks that coincided with the epoxy coated top steel and unprotected bottom steel. HMWM resin is a three component product composed of a monomer, a curnene hydroperoxide initiator and a cobalt naphthenate promoter. The HMWM was applied with a dual spray bar system and flat-fan nozzles. Initiated monomer delivered through one spray bar was mixed in the air with promoted monomer from the other spray bar. The application rate averaged 0.956 gallons per 100 square feet for the tined textured driving lanes. Dry sand was broadcast on the surface at an average coverage of 0.58 lbs. per square yard to maintain friction. Coring showed that the H.MWM resin penetrated the cracks more than two inches deep. Testing of the treated deck yielded Friction Numbers averaging 33 with a treaded tire compared to 36 prior to treatment. An inspection soon after treatment found five leaky cracks in one of the 15 spans. One inspection during a steady rain showed no leakage, but leakage from numerous cracks occurred during a subsequent rain. A second HMWM application was made on two spans to determine if a double application would prevent leakage. This evaluation has not been completed.

Biomechanical concept and clinical outcome of dual mobility cups

La luxation d'une prothèse totale de la hanche est une complication majeure en termes de morbidité pour le patient et des coûts pour le système de santé. Cette complication est retrouvée entre 2 à 3% selon les séries (1-3) pour des prothèses primaires, et beaucoup plus élevée suite à des révisions. Pour remédier à ce problème, des systèmes de prothèses contraintes sont une option, cependant associés à des descellements fréquents entre 10 à 26 % selon les séries (4-6). Ces échecs étant en partie expliqués par une usure rapide des surfaces de frottements due aux fortes contraintes, mais également par les contraintes cupule-os occasionnant des descellements mécaniques (7). Par conséquent, pour augmenter la stabilité, tout en évitant les contraintes sur le couple de frottement, Bousquet développe, en 1976, une prothèse totale de hanche « à double mobilité ». Ce système consiste à combiner deux articulations apparentes, premièrement une tête métallique dans un insert de polyéthylène, articulé lui- même dans la concavité d'une cupule métallique fixée au bassin. En tant que tel, ce système biomécanique réduirait en théorie le risque de luxation. Dès lors, on aperçoit depuis environ 15 ans une augmentation progressive de l'utilisation de ce type d'implants que ce soit comme implant primaire ou secondaire, chez des patients jeunes ou âgés. Cependant, des études in vitro, ont montré que des grandes surfaces de friction sont associées à une augmentation de l'usure du polyéthylène (8). En revanche, les données sur la cinématique et l'usure, in vivo, de ce type d'implant étaient jusqu'alors limitées. Depuis quelques années, un certain nombre d'études cliniques avec un follow up significatif ont été publiées. CONCLUSIONS ET PERSPECTIVES FUTURES La prothèse totale de hanche à double mobilité, développée par Bousquet dans les années 1970, est un concept novateur dans l'arthroplastie totale de hanche. Depuis sa première conception, de nombreuses améliorations ont été adoptées. Cependant, ses effets à long terme sur la survie de l'implant doivent encore être effectué. Certes, des études ont montré un net effet sur la réduction du taux de luxation des prothèses primaires, lors de révision ou après résection tumorale. Toutefois, compte tenu des données limitées à long terme sur le taux d'usure et le descellement aseptique, il convient d'utiliser ce type d'implant avec prudence, en particulier lors d'arthroplastie primaire chez des patients jeunes.

Analysis of Industrial Granular Flow Applications by Using Advanced Collision Models

Granular flow phenomena are frequently encountered in the design of process and industrial plants in the traditional fields of the chemical, nuclear and oil industries as well as in other activities such as food and materials handling. Multi-phase flow is one important branch of the granular flow. Granular materials have unusual kinds of behavior compared to normal materials, either solids or fluids. Although some of the characteristics are still not well-known yet, one thing is confirmed: the particle-particle interaction plays a key role in the dynamics of granular materials, especially for dense granular materials. At the beginning of this thesis, detailed illustration of developing two models for describing the interaction based on the results of finite-element simulation, dimension analysis and numerical simulation is presented. The first model is used to describing the normal collision of viscoelastic particles. Based on some existent models, more parameters are added to this model, which make the model predict the experimental results more accurately. The second model is used for oblique collision, which include the effects from tangential velocity, angular velocity and surface friction based on Coulomb's law. The theoretical predictions of this model are in agreement with those by finite-element simulation. I n the latter chapters of this thesis, the models are used to predict industrial granular flow and the agreement between the simulations and experiments also shows the validation of the new model. The first case presents the simulation of granular flow passing over a circular obstacle. The simulations successfully predict the existence of a parabolic steady layer and show how the characteristics of the particles, such as coefficients of restitution and surface friction affect the separation results. The second case is a spinning container filled with granular material. Employing the previous models, the simulation could also reproduce experimentally observed phenomena, such as a depression in the center of a high frequency rotation. The third application is about gas-solid mixed flow in a vertically vibrated device. Gas phase motion is added to coherence with the particle motion. The governing equations of the gas phase are solved by using the Large eddy simulation (LES) and particle motion is predicted by using the Lagrangian method. The simulation predicted some pattern formation reported by experiment.

Volcanic debris avalanche deposits of the upper Maronne valley (Cantal Volcano, France): evidence for contrasted formation and transport mechanisms

The deposits of two volcanic debris avalanches (VDA I and II) that occur in the upper Maronne valley, northwest sector of Cantal Volcano, France, were studied to establish their mechanisms of formation, transport and deposition. These two volcanic debris avalanches that clearly differ with regard to their structures, textures and extensions, exemplify the wide spectrum of events associated with large-scale sector collapse. VDA I is voluminous (similar to1 km(3) in the upper Maronne valley) and widespread. The deposits comprise two distinct facies: the block facies that forms the intermediate and upper part of the unit and the mixed facies that crops out essentially at the base of the unit. The block facies consists of more or less brecciated lava, block-and-ash-flow breccia and pumice-flow tuff megablocks set in breccias resulting from block disaggregation. Mixing and differential movements are almost absent in this part of the VDA. The mixed facies consists of breccias rich in fine particles that originate from block disagregation, as well as being picked up from the substratum during movement. Mixing and differential movements are predominant in this zone. Analysis of fractures on lava megablocks suggests that shear stress during the initial sliding is the principal cause of fracture. These data strongly indicate that VDA I is purely gravitational and argue for a model in which the initial sliding mass transforms into a flow due to differential in situ fragmentation caused by the shear stress. VDA II is restricted to low-topography areas. Its volume, in the studied area, is about 0.3 km(3). The deposits consist of brecciated, rounded blocks and megablocks set in a fine-grained matrix composed essentially of volcanic glass. This unit is stratified, with a massive layer that contains all the megablocks at the base and in the intermediate part, and in the upper part a normally graded layer that contains only blocks <1 m in size. The different lithologies present are totally mixed. These observations suggest that VDA II may be of the Bezymianny-type and that it underwent a flow transformation from a turbulent to a stratified flow consisting of a basal hyperconcentrated laminar body overlain by a dilute layer. (C) 2000 Elsevier Science B.V. All rights reserved.

Modeling and Synthesis of Tracking Control for the Belt Drive System

Usingof belt for high precision applications has become appropriate because of the rapid development in motor and drive technology as well as the implementation of timing belts in servo systems. Belt drive systems provide highspeed and acceleration, accurate and repeatable motion with high efficiency, long stroke lengths and low cost. Modeling of a linear belt-drive system and designing its position control are examined in this work. Friction phenomena and position dependent elasticity of the belt are analyzed. Computer simulated results show that the developed model is adequate. The PID control for accurate tracking control and accurate position control is designed and applied to the real test setup. Both the simulation and the experimental results demonstrate that the designed controller meets the specified performance specifications.

Superjumborullien rullauksen hallinta

UPM-Kymmene Oyj:n Jämsänkosken PK6:n ongelmana ovat olleet ajoittaiset pohjakatkot suurilla rullilla. Diplomityön tavoitteena oli parantaa superjumborullien rullauksen hallintaa Jagenbergin rakentamalla VariTop keskiörullaimella. Kirjallisuusosassa selvitettiin rullanmuodostumista ja erilaisia rullausteorioita. Samalla käytiin läpi paperin rullautuvuuteen vaikuttavia tekijöitä, rullausperäisten vikojen muodostumisen syitä sekä pehmeän rullaussylinterin etuja verrattuna kovaan sylinteriin. Kokeellisessa osassa suoritettiin koeajoja tuotannon pituusleikkurilla. Näistä kokeista saatujen tulosten perusteella leikkurin ajoreseptit päivitettiin vastaamaanoptimaalisinta rullarakennetta. Pehmeän rullaussylinterin etuja verrattuna kovaan rullaussylinteriin selvitettiin koeajoissa Voithin koeleikkurilla Saksan Krefeldissä. Tuloksista selvisi, että samalla ajoreseptillä rullattaessa pehmeä sylinteri antoi valmiille rullalle suuremman kovuuden. Myös paperissa olevien profiilivirheiden vaikutukset lievenivät käytettäessä pehmeää rullaussylinteriä. Istukoiden luistamisesta johtuvaa hylsyjen sisäpinnan jauhautumista on ilmennyt suurilla jumborullilla. Tämä johtuu todennäköisimmin kasvaneesta rasituksesta hylsyn sisäpinnalla, mikä on seurausta rullien kasvusta. Ratkaisuina tälle ongelmalle on mahdollinen istukan pidentäminen sekä välyksen pienentäminen istukan ja hylsyn välissä. Myös hylsyjen toimintaa testattiin rullauksessa jahuomattiin niiden täyttävän toimittajien antamat laatuarvot. Lepo- ja liikekitkalla tiedetään olevan suuri merkitys rullausperäisten vikojenmuodostumiseen. Eri lajeista lähetettiin paperinäytteitä UPM-Kymmene Oyj:n Lappeenrannan tutkimuskeskukseen kitkojen määrittämiseksi. Tulosten perusteella havaittiin luettelolajilla lepo- ja liikekitkassa merkittävä ero. Standardi SC lajilla ero oli selvästi pienempi kuin luettelolajilla. Tämä saattaa olla yksi syy luettelolajeilla ilmeneviin pohjaongelmiin.

Development of a Testing Method for Convertibility of Paperboard

Työssä tutkittiin muovattujen kartonkivuokien sekä muovattujen kartonkinäytteiden rinnastettavuutta. Puristusvaiheen prosessiolosuhteiden miellettiin vaikuttavan eniten multidimensionaliseen muodonmuutokseen. Multidimensionaalista muodonmuutosta simuloitiin uudella muovaamiseen soveltuvalla muovauslaitteella. Kirjallisuusosassa keskeisiä teemoja ovat kartongin muovaus sekä kuitupohjaisen materiaalin reologinen käyttäytyminen. Kirjallisuusosassa esitellään lisäksi yksi tekninen sovellus, jonka avulla kyetään ennustamaan kuitumateriaalin muovautuvuutta sekä mittaamaan tapahtunutta muodonmuutosta. Prosessiparametrien teoreettista vaikutustakuituihin tarkastellaan myös kirjallisuusosassa. Kokeellisessa osassa toteutettiin kartonkivuokien valmistus puristamalla. Vastaavilla prosessiparametreilla muovattiin myös pienemmät testinäytteet. Perinteiset yksidimensionaliset deformaatiomittaukset toteutettiin lujuusominaisuuksien laboratoriomäärityksinä. Myös kitka, joka toimii tärkeänä muuttujana prässäysprosessissa, mitattiin laboratorio-olosuhteissa. Tämän työn tulokset osoittavat uuden kehitetyn muovausmenetelmän toimivuuden. Asema-voima kuvaajat ovat selkeitä sekä helposti luettavia. Tuloksissa havaittiin materiaalin muovauspotentiaalin sekä asema-voima kuvaajan välillä vallitseva yhteys. Erittäin merkittävä huomio oli myös, että muovipäällystetyllä kartongilla oli yhteys päällystämättömän kartongin asema-voima kuvaajaan. Tämä tulos osoittaa, että muovipäällystetyn kartongin muovautuvuutta voi olla mahdollista ennustaa pohjakartongin muovautuvuustulosten perusteella. Perinteiset yksidimensionaliset laboratoriomittaukset eivät kykene antamaan riittävää informaatiota muovautuvuuden ennustamiseen. Tästä näkökulmasta on tärkeää että kartongin multidimensionalista muotoutuvuutta voidaankin tutkia kehitetyllä muovausmenetelmällä.

Terässiilojen mitoitusohjelman kehittäminen

Siiloja käytetään jauhemaisten ja rakeisten aineiden varastointiin ja annosteluun maataloudessa sekä mm. lasi-, laasti- ja tasoiteteollisuudessa. Tällaiset laitokset toimitetaan usein kokonaistoimituksina, joissa tavanomaisten teräsrakenteiden kustannusvaikutus voi olla jopa 30 % koko toimituksen arvosta. Niinpä osaltaan siilojen tehokkaalla mitoituksella ja erilaisiarakenneratkaisuja vertailemalla voidaan alentaa toimitusten kokonaiskustannuksia. Tässä diplomityössä perehdyttiin siilojen rakenteisiin ja niiden lujuustekniseen mitoitukseen etenkin tuentaratkaisujen osalta. Mitoituksen osalta työssä perehdyttiin pääasiassa uusiin Eurooppalaisiin standardeihin SFS-EN 1991-4 ja SFS-EN 1993-4-1. Niiden mukaan määritetään mitoituskuormat sekä tehdään lujuustekninen mitoitus. Työn tuloksena laadittiin Microsoft Excel -pohjainen mitoitusohjelma, jolla voidaan nopeasti mitoittaa siilojen olennaisimmat teräsrakenteet. Ohjelmalla voidaan määrittää mitoitus koskien siilon lieriön ja kartion seinämiä sekä tuentaratkaisuja. Ohjelma nopeuttaa erityisesti tarjousvaiheen suunnittelua ja antaa pohjan varsinaiselle siilojen yksityiskohtaiselle mitoittamiselle ja suunnittelulle.

SIMULATION OF AMB SUPPORTED ROTOR DURING DROP ON RETAINER BEARINGS

The active magnetic bearings present a new technology which has many advantages compared to traditional bearing designs. Active magnetic bearings, however, require retainer bearings order to prevent damages in the event of a component, power or a control loop failure. In the dropdown situation, when the rotor drops from the magnetic bearings to the retainer bearings, the design parameters of the retainer bearings have a significant influence on the behaviour of the rotor. In this study, the dynamics of an active magnetic bearings supported electric motor during rotor drop on retainer bearings is studied using a multibody simulation approach. Various design parameters of retainer bearings are studied using a simulation model while results are compared with those found in literature. The retainer bearings are modelled using a detailed ball bearing model, which accounts damping and stiffness properties, oil film and friction between races and rolling elements. The model of the ball bearings includes inertia description of rollingelements. The model of the magnetic bearing system contains unbalances of the rotor and stiffness and damping properties of support. In this study, a computationally efficient contact model between the rotor and the retainer bearings is proposed. In addition, this work introduces information for the design of physicalprototype and its retainer bearings.

Dynamic Simulations of Rotors during Drop on Retainer Bearings

The active magnetic bearings have recently been intensively developed because of noncontact support having several advantages compared to conventional bearings. Due to improved materials, strategies of control, and electrical components, the performance and reliability of the active magnetic bearings are improving. However, additional bearings, retainer bearings, still have a vital role in the applications of the active magnetic bearings. The most crucial moment when the retainer bearings are needed is when the rotor drops from the active magnetic bearings on the retainer bearings due to component or power failure. Without appropriate knowledge of the retainer bearings, there is a chance that an active magnetic bearing supported rotor system will be fatal in a drop-down situation. This study introduces a detailed simulation model of a rotor system in order to describe a rotor drop-down situation on the retainer bearings. The introduced simulation model couples a finite element model with component mode synthesis and detailed bearing models. In this study, electrical components and electromechanical forces are not in the focus. The research looks at the theoretical background of the finite element method with component mode synthesis that can be used in the dynamic analysis of flexible rotors. The retainer bearings are described by using two ball bearing models, which include damping and stiffness properties, oil film, inertia of rolling elements and friction between races and rolling elements. Thefirst bearing model assumes that the cage of the bearing is ideal and that the cage holds the balls in their predefined positions precisely. The second bearing model is an extension of the first model and describes the behavior of the cageless bearing. In the bearing model, each ball is described by using two degrees of freedom. The models introduced in this study are verified with a corresponding actual structure. By using verified bearing models, the effects of the parameters of the rotor system onits dynamics during emergency stops are examined. As shown in this study, the misalignment of the retainer bearings has a significant influence on the behavior of the rotor system in a drop-down situation. In this study, a stability map of the rotor system as a function of rotational speed of the rotor and the misalignment of the retainer bearings is presented. In addition, the effects of parameters of the simulation procedure and the rotor system on the dynamics of system are studied.

Numerical and ExperimentalModelling of Gas Flow and Heat Transfer in the Air Gap of An Electric Machine

This work deals with the cooling of high-speed electric machines, such as motors and generators, through an air gap. It consists of numerical and experimental modelling of gas flow and heat transfer in an annular channel. Velocity and temperature profiles are modelled in the air gap of a high-speed testmachine. Local and mean heat transfer coefficients and total friction coefficients are attained for a smooth rotor-stator combination at a large velocity range. The aim is to solve the heat transfer numerically and experimentally. The FINFLO software, developed at Helsinki University of Technology, has been used in the flow solution, and the commercial IGG and Field view programs for the grid generation and post processing. The annular channel is discretized as a sector mesh. Calculation is performed with constant mass flow rate on six rotational speeds. The effect of turbulence is calculated using three turbulence models. The friction coefficient and velocity factor are attained via total friction power. The first part of experimental section consists of finding the proper sensors and calibrating them in a straight pipe. After preliminary tests, a RdF-sensor is glued on the walls of stator and rotor surfaces. Telemetry is needed to be able to measure the heat transfer coefficients at the rotor. The mean heat transfer coefficients are measured in a test machine on four cooling air mass flow rates at a wide Couette Reynolds number range. The calculated values concerning the friction and heat transfer coefficients are compared with measured and semi-empirical data. Heat is transferred from the hotter stator and rotor surfaces to the coolerair flow in the air gap, not from the rotor to the stator via the air gap, althought the stator temperature is lower than the rotor temperature. The calculatedfriction coefficients fits well with the semi-empirical equations and precedingmeasurements. On constant mass flow rate the rotor heat transfer coefficient attains a saturation point at a higher rotational speed, while the heat transfer coefficient of the stator grows uniformly. The magnitudes of the heat transfer coefficients are almost constant with different turbulence models. The calibrationof sensors in a straight pipe is only an advisory step in the selection process. Telemetry is tested in the pipe conditions and compared to the same measurements with a plain sensor. The magnitudes of the measured data and the data from the semi-empirical equation are higher for the heat transfer coefficients than thenumerical data considered on the velocity range. Friction and heat transfer coefficients are presented in a large velocity range in the report. The goals are reached acceptably using numerical and experimental research. The next challenge is to achieve results for grooved stator-rotor combinations. The work contains also results for an air gap with a grooved stator with 36 slots. The velocity field by the numerical method does not match in every respect the estimated flow mode. The absence of secondary Taylor vortices is evident when using time averagednumerical simulation.

Dynamic analysis of belt-drives using the absolute nodal coordinate formulation

Belt-drive systems have been and still are the most commonly used power transmission form in various applications of different scale and use. The peculiar features of the dynamics of the belt-drives include highly nonlinear deformation,large rigid body motion, a dynamical contact through a dry friction interface between the belt and pulleys with sticking and slipping zones, cyclic tension of the belt during the operation and creeping of the belt against the pulleys. The life of the belt-drive is critically related on these features, and therefore, amodel which can be used to study the correlations between the initial values and the responses of the belt-drives is a valuable source of information for the development process of the belt-drives. Traditionally, the finite element models of the belt-drives consist of a large number of elements thatmay lead to computational inefficiency. In this research, the beneficial features of the absolute nodal coordinate formulation are utilized in the modeling of the belt-drives in order to fulfill the following requirements for the successful and efficient analysis of the belt-drive systems: the exact modeling of the rigid body inertia during an arbitrary rigid body motion, the consideration of theeffect of the shear deformation, the exact description of the highly nonlinear deformations and a simple and realistic description of the contact. The use of distributed contact forces and high order beam and plate elements based on the absolute nodal coordinate formulation are applied to the modeling of the belt-drives in two- and three-dimensional cases. According to the numerical results, a realistic behavior of the belt-drives can be obtained with a significantly smaller number of elements and degrees of freedom in comparison to the previously published finite element models of belt-drives. The results of theexamples demonstrate the functionality and suitability of the absolute nodal coordinate formulation for the computationally efficient and realistic modeling ofbelt-drives. This study also introduces an approach to avoid the problems related to the use of the continuum mechanics approach in the definition of elastic forces on the absolute nodal coordinate formulation. This approach is applied to a new computationally efficient two-dimensional shear deformable beam element based on the absolute nodal coordinate formulation. The proposed beam element uses a linear displacement field neglecting higher-order terms and a reduced number of nodal coordinates, which leads to fewer degrees of freedom in a finite element.

Dynamic drag modeling of submerged aquatic vegetation canopy flows

Vegetation has a profound effect on flow and sediment transport processes in natural rivers, by increasing both skin friction and form drag. The increase in drag introduces a drag discontinuity between the in-canopy flow and the flow above, which leads to the development of an inflection point in the velocity profile, resembling a free shear layer. Therefore, drag acts as the primary driver for the entire canopy system. Most current numerical hydraulic models which incorporate vegetation rely either on simple, static plant forms, or canopy-scaled drag terms. However, it is suggested that these are insufficient as vegetation canopies represent complex, dynamic, porous blockages within the flow, which are subject to spatially and temporally dynamic drag forces. Here we present a dynamic drag methodology within a CFD framework. Preliminary results for a benchmark cylinder case highlight the accuracy of the method, and suggest its applicability to more complex cases.

Expresiones para la determinación del factor de fricción en ríos de fuerte pendiente

Con base en una selección de 145 datos pertenecientes a ríos de montaña de fuerte pendiente (³ 1%) se han desarrollado cinco expresiones para determinar el factor de fricción de Darcy-Weisbach. La primera expresión se fundamenta en la aplicación para flujo turbulento rugoso en lámina libre de la ley semilogarítmica de Prandtl-Kárman, que es función de la sumersión relativa (relación entre el calado medio y la rugosidad equivalente). La segunda y tercera corresponden a correciones de la primera para flujo macrorrugoso, propuestas por Thompson y Campbell (1979) y Aguirre-Pe y Fuentes (1990) respectivamente. La cuarta ecuación consiste una en potencia de la sumersión relativa, mientras que la quinta corrige la fórmula anterior incorporando una potencia de la pendiente, tal y como propugnan Meunier (1989) y Rickenmann (1990). Las expresiones derivadas presentan un ajuste significativo, si se tienen en cuenta las limitaciones hidrométricas existentes en ríos de material grueso y fuerte pendiente. Destaca el mayor ajuste conseguido con las ecuaciones con las ecuaciones del tipo potencial frente a las del tipo semilogarítmico. Se ha encontrado, asimismo, una capacidad de predicción ligeramente superior en aquellas expresiones que incluyen modificaciones respecto a la ecuación original, ecuaciones del tipo segundo, tercero y quinto anteriormente indicado.