Gas turbines for military applications, when operating in harsh environments like deserts often encounter unexpected operation faults. Such performance deterioration of the gas turbine decreases the mission readiness of the Air Force and simultaneously increases the maintenance costs. Some of the major factors responsible for the reduced performance are ingestion of debris during take off and landing, distorted intake flows during low altitude maneuvers, and hot gas ingestion during artillery firing. The focus of this thesis is to study ingestion of debris; specifically sand. The region of interest being the internal cooling ribbed duct of the turbine blade. The presence of serpentine passages and strong localized cross flow components makes this region prone to deposition, erosion, and corrosion (DEC) by sand particles. A Lagrangian particle tracking technique was implemented in a generalized coordinate multi-block Navier-Stokes solver in a distributed parallel framework. The developed algorithm was validated by comparing the computed particle statistics for 28 microns lycopodium, 50 microns glass, and 70 microns copper with available data [2] for a turbulent channel flow at Ret=180. Computations were performed for a particle-laden turbulent flow through a stationary ribbed square duct (rib pitch / rib height = 10, rib height / hydraulic diameter = 0.1) using an Eulerian-Lagrangian framework. Particle sizes of 10, 50, and 100 microns with response times (normalized by friction velocity and hydraulic diameter) of 0.06875, 1.71875, and 6.875 respectively are considered. The calculations are performed for a nominal bulk Reynolds number of 20,000 under fully developed conditions. The carrier phase was solved using Large Eddy Simulation (LES) with Dynamic Smagorinsky Model [1]. Due to low volume fraction of the particles, one-way fluid-particle coupling was assumed. It is found that at any given instant in time about 40% of the total number of 10 micron particles are concentrated in the vicinity (within 0.05 Dh) of the duct surfaces, compared to 26% of the 50 and 100 micron particles. The 10 micron particles are more sensitive to the flow features and are prone to preferential concentration more so than the larger particles. At the side walls of the duct, the 10 micron particles exhibit a high potential to erode the region in the vicinity of the rib due to secondary flow impingement. The larger particles are more prone to eroding the area between the ribs and towards the center of the duct. At the ribbed walls, while the 10 micron particles exhibit a fairly uniform propensity for erosion, the 100 micron particles show a much higher tendency to erode the surface in the vicinity of the reattachment region. The rib face facing the flow is by far the most susceptible to erosion and deposition for all particle sizes. While the top of the rib does not exhibit a large propensity to be eroded, the back of the rib is as susceptible as the other duct surfaces because of particles which are entrained into the recirculation zone behind the rib. / Master of Science

Three-dimensional particle tracking is a valuable tool in microfluidics for obtaining information about a system. General Defocus Particle Tracking (GDPT) is a straightforward method of 3D particle tracking that only requires a single-camera plane, making it applicable to existing equipment in a laboratory.  This project's aim was to evaluate the open-source module DefocusTracker which uses GDPT. DefocusTracker was used to track particles that were levitated in a microchip using ultrasonic standing waves.  The effects of different calibration methods used and the evaluation of the acoustic energy density over an active part of a piezo on an microchip device were investigated. Different procedures to generate a depth model from the calibration images showed that the choice of step length affects the accuracy of the depth model. A depth model created from the middle part of the field of view provides more accurate results compared to one made from the edge. Levitation experiments demonstrate that higher applied voltages result in a stronger acoustic energy density field over the field of view. The acoustic energy density field and pressure amplitude field show variations across the active piezo on the device, potentially due to a non-uniform thickness of the fluid layer and variations in energy delivery from the piezo. Overall, GDPT proves to be a useful method for evaluating unknown aspects of a microfluidic system under the influence of ultrasonic standing waves. / Tredimensionell partikelspårning är ett värdefullt verktyg inom mikrofluidik för att få ut information om ett system. Generell ur-fokus partikel spårning (GDPT) är en okomplicerad metod för 3D-partikelspårning som endast kräver ett plan med en kamera. Detta gör den tillämpningsbar på befintliga utrustningar i ett laboratorium.  Syftet med detta projekt var att utvärdera den öppna modulen DefocusTracker som använder sig av GDPT. DefocusTracker användes för att spåra partiklar som leviterades i ett mikrochip med hjälp av stående ultraljudsvågor.  Effekterna av olika kalibreringsmetoder och utvärderingen av den akustiska energitätheten över en aktiv del av en piezo på ett mikrochip undersöktes. Olika metoder för att generera en djup modell från kalibreringsbilderna visade att valet av steglängd påverkar djup modellens noggrannhet. En djup modell som skapats från mitten av synfältet ger mer användbara resultat jämfört med en som skapats från kanten. Levitationsexperiment visar att högre använda spänningar resulterar i ett starkare akustiskt energitäthetsfält över synfältet. Fältet för den akustiska energitätheten och tryckamplituden visar variationer över den aktiva piezon på enheten, vilket kan bero på en ojämn tjocklek på vätskelagret och variationer i energitillförseln från piezon.  Allmänt visar sig GDPT vara en användbar metod för att utvärdera okända aspekter av ett mikrofluidiskt system under påverkan av stående ultraljudsvågor.

Der eukaryotische Zellzyklus ist auf allen Ebenen der Genexpres- sion reguliert. Sowohl breit angelegte genetische Screens als auch funktionale Studien zu den beteiligten Proteinen haben unser Ver- ständnis dieses fundamentalen Prozesses geprägt. In dieser Arbeit behandle ich räumliche Aspekte der post-transkriptionalen Regulation des Zellzyklus, die mit lichtmikroskopischen Einzelzell- und Einzel- molekülmethoden experimentell zugänglich werden. Insbesondere untersuchte ich die subzelluläre Lokalisierung der messenger RNA von CLB2, einem zentralen Regulator der Mitose im eukaryotischen Modellorganismus Saccharomyces cerevisiae (Bierhefe). Frühere Studien zeigten, dass diese RNA sich im Laufe des vegetativen Zellwachstums in der entstehenden Tochterzelle, der Knospe, anreichert. Mithilfe modernster Fluoreszenzmikroskopie charakterisierte ich die Bewe- gung und Verteilung einzelner CLB2 messenger RNA-Moleküle auf Zeitskalen von Millisekunden bis hin zur Generationszeit dieser He- fen. Ich zeigte, dass sich mit Hilfe von Multifokusmikroskopie unter Verwendung optimierter Fluoreszenzmarker und der Entwicklung objektiver Analysemethoden die Bewegung einzelner RNA-Moleküle zwischen Mutterzelle und Knospe nachvollziehen lässt. Dazu präsen- tiere ich eine Methode um die beobachteten Trajektorien der messenger RNA mathematischen Analysen der Systembiologie zugänglich zu machen. Weiterhin gab die Beobachtung der Verteilung einzelner CLB2 messenger RNA Moleküle über den Zellzyklus hinweg mittels einer neuartigen Lichtblattmikroskopie (Lattice Light Sheet Microscopy) Hinweise auf eine bisher unbekannte Dynamik in der Lokalisierung dieser messenger RNA. Die hier entwickelten Methoden ermöglichen eine quantitative Untersuchung räumlicher Aspekte der posttranskrip- tionalen Zellzyklusregulation. / The eukaryotic cell cycle is regulated on all levels of gene expression. Genetic screens and functional studies of the involved proteins have shaped our understanding of this fundamental process. In this thesis I use single cell and single molecule light microscopy methods to investigate spatial aspects of post-transcriptional cell cycle regulation. I investigated the subcellular localization of CLB2 mRNA, a central regulator of mitosis in the eukaryotic model organism Saccharomyces cerevisiae (baker’s yeast). Previous studies have shown that that this messenger RNA is enriched in the emerging daughter cell, the bud, during vegetative growth. Using pre-commercial fluorescence micro- scopes I characterized the dynamics and partitioning of single CLB2 mRNA on time scales from milliseconds to the generation time of this yeast. I demonstrate that using aberration corrected multifocus mi- croscopy, optimized fluorescent markers, and here developed objective analysis methods, the translocation of single mRNA molecules be- tween mother and bud can be observed. In addition, I report a method to make these trajectories available for the mathematical approaches of Systems Biology. Further, the observation of single CLB2 mRNA partitioning throughout the cell cycle with the use of lattice light sheet microscopy suggested a previously unknown localization behavior of the transcript. The methods developed here enable a quantitative analysis of spatial aspects of post-transcriptional cell cycle regulation.

Over the last few decades, the use of light to control and manipulate microscopic particles has become widespread. These methods are enabling new areas of research to flourish across the physical and biological sciences. This thesis describes investigations into both optical trapping and the closely related field of optical sorting. It documents the development of a variety of new techniques. The thesis begins with a short review of optical trapping and existing methods for sorting mixtures of microscopic particles. The first half of this chapter highlights some of the reasons behind optical trapping's rapid growth in popularity. By reviewing an array of methods for sorting particles and discussing the relative merits of each, the case for optical sorting is established. The second chapter describes research into using a spatial light modulator to create three-dimensional optically trapped colloidal structures using the time-sharing technique. Limiting factors inherent in the technology are discussed in detail. The third chapter reviews a sophisticated particle-tracking software package that has proved to be a considerable success. It was developed explicitly with colloidal microscopy in mind and experimental plots produced by the software are used throughout the thesis. Experimental studies have been performed into the behaviour of microscopic particles moving under the influence of two classes of propagation-invariant beams: Mathieu beams and Bessel beams. The Bessel beam studies have been complimented by a theoretical model and have led ultimately to a new method for the static optical sorting of both solid particles and biological cells, with particular emphasis on human blood. The fifth and final chapter describes how re-configurable optical devices can be implemented to spatially separate different colloidal species. A new method for creating arbitrary optical landscapes using an acousto-optic modulator is reported. This new technique is then used to optically sort four particle species simultaneously - the first experimental demonstration of polydisperse optical fractionation. Additionally, experiments are reported that demonstrate controlled, static optical sorting using a spatial light modulator.

<p>When protection zones for wells are delineated, it is important to acquire good knowledge about possible travel time from different points in the catchment area to the well. Often, simple analytical methods are used for estimating travel times and the assumption is made that the hydraulic conductivity is relatively homogenous within the aquifer. Nevertheless, many aquifers are strongly heterogeneous which may lead to differences between estimates and actual travel times. As a part of the process to develop improved methods for delineating protection zones for groundwater supply wells, a tracer experiment was performed in a glaciofluvial esker formation in Järlåsa. On the basis of the experiment, a numerical flow model was created for the test site.</p><p>The purpose of this master’s thesis was to apply the flow model to an aquifer where the hydraulic conductivity shows great variability and should be described by a stochastic distribution. The purpose was also to determine the statistical properties of the hydraulic conductivity and to simulate the transport times and their variation from different locations in the aquifer to the pumping well.</p><p>The hydraulic conductivity was estimated from grain size distributions in soil samples that were taken at various locations within the test site. The analysis of the hydraulic conductivity showed a large variation and confirmed the hypothesis that the aquifer is heterogeneous. Using the statistics, a large number of stochastic conductivity fields were created and flow simulation was performed for each realization. From the simulation result, frequency distributions of the transport times were produced describing the probability for the transit time for a water particle between a certain location in the aquifer and the pumping well. A comparison with the tracer experiment shows higher simulated transport times implying the need for improved model calibration. The conclusion is that the method used in this project is suitable for glaciofluvial esker aquifers. When protection zones are delineated, stochastic modeling can be used to express the zone boundaries in statistical terms.</p> / <p>När skyddsområden för grundvattentäkter skapas är det viktigt att ha god kännedom om vattnets transporttider från olika delar i tillrinningsområdet till uttagsplatsen av grundvattnet. Metoderna för att bestämma dessa tider är ofta enkla och vanligen görs antagandet att områdets hydrauliska konduktivitet är relativt homogen. Många akviferer är dock kraftigt heterogena och de verkliga transporttiderna kan då skilja sig från de uppskattade. Som ett led i metodutvecklingen för bättre avgränsning av skyddsområden genomfördes ett spårämnesförsök i en isälvsavlagring i Järlåsa. Med utgångspunkt från försöket har en numerisk flödesmodell konstruerats över försöksområdet.</p><p>Syftet med examensarbetet var att tillämpa flödesmodellen i en akvifer där den hydrauliska konduktiviteten visar sådana variationer att den beskrivs bäst av en stokastisk fördelning. Vidare var syftet att bestämma den hydrauliska konduktivitetens statistiska egenskaper och att simulera transporttiderna och deras variation från olika punkter i akviferen till pumpbrunnen.</p><p>Den hydrauliska konduktiviteten uppskattades utifrån kornstorleksfördelningar i jordprover som togs på en mängd platser i försöksområdet. Analysen av den hydrauliska konduktiviteten visar stora variationer i området vilket bekräftar att akviferen är heterogen.</p><p>Utifrån konduktivitetens statistik genererades ett stort antal stokastiska konduktivitetsfält och transporttiderna beräknades för varje realisering. Resultatet från simuleringarna gav frekvensfördelningar för transporttiderna som beskriver sannolikheten för hur lång uppehållstid en vattenpartikel har i marken mellan en startpunkt och pumpbrunnen. Jämfört med spårämnesförsöket blev de simulerade transporttiderna något större vilket tyder på att flödesmodellen kräver en bättre kalibrering mot fältmätningar. Slutsatsen är att metodiken är lämplig för att studera vattnets transporttider i isälvsavlagringen och när ett skyddsområde skapas för den här typen av akvifer kan stokastisk modellering användas för att beskriva skyddszoner i form av statistiska termer.</p>

The knowledge of the behavior of non-spherical particles suspended in turbulent flows covers a wide range of applications in engineering and science. Dispersed two-phase flows and turbulence are the most challenging subjects in engineering, and when combined it gives rise to more complexities as the result of the inherent stochastic nature of the turbulence of the carrier-phase together with the random distribution of the dispersed phase. Moreover, for anisotropic particles the coupling between the translation and rotation of particle increases the complication. Because of the practical importance of prolate particleladen turbulent flows, the plenty of numerical and experimental works have been conducted to study such suspensions. Numerical approaches have given valuable insight of turbulent suspension flows, although the computation has been only carried out at the macro scale and models, not including flow distortion around the particle, comprise the detail of the flow in the order of a particle size. In addition, the model of the forces imposed on the particle by the fluid and mass point treatment are strictly valid for infinitely small particle having size less than all scales of the fluid turbulence. Fully resolved solution at the scale of the dispersed phase in turbulent flows for high Reynolds number has been recently performed but is still a challenge. On the other hand, the presence of particle as the dispersed phase makes experimental measurements much more complicated than those with single phase as a result of particles interference. The area of considerable difficulty with this type of experiments is the measurement of the fluid-phase velocity remarkably close to the particle surface. Generally, experimental researches have been concentrated on measuring the mean velocity and Reynolds stresses of the carrier-phase, and the mean velocity, fluctuations, orientation and accumulation of the non-spherical particles. Higher-order quantities, including Lagrangian particle velocity correlations, the carrier-phase turbulence modulation, and two-particle and particlefluid velocity correlations are also of interest. It has been found that the rotational and translational movements of the fibershaped particle depend on the nature of carrier-phase field and fiber characteristics such as aspect ratio, fiber Stokes number, fiber Reynolds number, and the ratio of fiber to flow length scale. With the development of PIV (Particle Image Velocimetry) and PTV (Particle Tracking Velocimetry) techniques, it has been appeared that combined PIV/PTV will be the best available choice for the experimental study of dispersed two-phase flows. The purpose of combined PIV/PTV measurement of two-phase systems is simultaneous measurements of fluid and suspended objects, where the PIV measurement of the fluid phase are combined with PTV measurement of the dispersed phase. The objective of this doctoral thesis is to study the behavior of rod-like particles suspended in wall-bounded turbulent flow through simultaneous PIV/PTV measurements of the velocity of the flow field and particle motion. As a representative of rod-like particles, I have employed cellulose acetate fibers with the length to diameter ratio (aspect ratio) larger than one. Here, It has been considered only dilute suspensions with no flocculation; thus fiber-fiber interaction is negligible. The measurements have been conducted within the parallel planes (2D view) illuminated by laser in the streamwise direction in thin film suspension flowing on the water table setup at Linné FLOW Centre, KTH Mechanics Lab. It is shown that this setup is a well-behaved experimental model of half channel flows often used in Direct Numerical Simulation (DNS) investigations. Therefore, the experimental results are comparable to their DNS counterpart where it is convenient. A single camera PIV technique has been used to measure flowing suspension. Therefore, it has been needed to preprocess images using a spatial median filter to separate images of two phases, tracer particles as representative of fluid and fibers suspended. The well-known PIV processing algorithms have been applied to the phase of fluid. I have also introduced a novel algorithm to recognize and match fibers in consecutive images to track fibers and estimate their velocity. It is not feasible to study all relevant aspects of particle-laden turbulent flows in a single study. In this study, I present the statistics of the rotational and translational motion of fiber-like particles and the surrounding fluid velocity. To the author’s knowledge, remarkably little experimental work has been published to date on simultaneous measurement of fiber motion and turbulence field in a turbulent fiber suspension flow to reveal dynamics of fibers in this regime. Therefore, the results of this work will be profitable in better understanding of such multiphase flows. The statistical analysis of the translational motion of fibers shows that the size of fiber is a significant factor for the dynamical behavior of the fiber near the wall. It has been observed that, in the region near the wall, the probability of presence of the long fibers is high in both the high-speed and low-speed streaks of flow, and the mean velocity of fibers almost conforms to the mean velocity of flow; whereas the short fibers are mostly present in the low-speed areas, and the fiber mean velocity obey the dominant flow velocity in these areas. In the far-wall regions, the translation of fibers is practically unaffected by the aspect ratio, whereas it depends crucially on the wall-normal distance. Moreover, it was found that in the case of long fibers near the wall, the low speed fibers mostly are orientated in streamwise direction. On the other hand, there is no preferential orientation for fast long fibers. Although wall-normal velocities were not measured in this study, it is hypothesized that this behavior is a result of fibers being affected by the sweep and ejection events known to occur in wall-bounded turbulent flow. The fast fibers are in sweep environment and comes from the upper layer. The low speed fibers are into ejection areas in the vicinity of the wall, and the wall has a stabilizing effect on them. The short fibers are still oriented mostly in streamwise direction for a certain range of low velocity. Furthermore, since a considerable change of the fiber behavior is observed in a certain ratio of the fiber length to the fiber distance from the solid wall, it is supposed that this ratio is also a prominent parameter for the behavior of fiber near the wall. The results presented are in terms of viscous wall units wherever are denoted by superscript “+”.

Foamyviren (FV) gehören zur Familie der Retroviridae, werden aber aufgrund besonderer Eigenschaften in eine eigene Unterfamilie, die Spumaretrovirinae, eingeordnet. FV besitzen vor allem in vitro einen sehr breiten Tropismus, so dass bisher keine Zelllinie bekannt war, die nicht durch FV infiziert werden konnte. Obwohl diese Besonderheit darauf schließen lässt, dass ein sehr ubiquitäres Molekül auf der Wirtszelloberfläche für die FV-Bindung verwendet wird, ist der Rezeptor für die Virus-Aufnahme noch nicht bekannt. Dass FV einen pH-abhängigen Aufnahmemechanismus verwenden, lässt eine endozytotische Aufnahme vermuten. Dennoch sind die frühen Replikationsschritte, die zur Fusion der viralen und Wirtszellmembran führen, nur unzureichend charakterisiert. Deswegen wurden in der vorliegenden Arbeit funktionelle autofluoreszierende FV hergestellt, um die Bindung und Aufnahmemechanismen foamyviraler Partikel in Wirtszellen mit fluoreszenzmikroskopischen Analysen zu untersuchen. Mit diesen Methoden konnten erstmalig vier Zelllinien identifiziert werden, die nicht mit FV infizierbar sind, und damit mögliche Kandidaten für die Identifizierung des unbekannten FV Rezeptors darstellen. Des Weiteren wurden die fluoreszierenden FV erfolgreich eingesetzt, um die Fusionsereignisse zwischen viraler und zellulärer Membran in Echtzeit in lebenden Zellen zu untersuchen. Die durchgeführte „Single Virus Tracking“-Analyse zeigte, dass PFV (Prototype FV) Env-tragende Partikel sowohl an der Plasmamembran als auch in vermeintlichen Endosomen fusionieren können, wohingegen SFV (Simian FV) Env-tragende Partikel die Fusion wahrscheinlich nur in Endosomen auslösen können. Hinweis zur Nutzung der Filmdateien: Öffnen mit QuickTimePlayer bzw. ImageJ

In biology, many different kinds of microscopy are used to study cells. There are many different kinds of transmission microscopy, where light is passed through the cells, that can be used without staining or other treatments that can harm the cells. There is also fluorescence microscopy, where fluorescent proteins or dyes are placed in the cells or in parts of the cells, so that they emit light of a specific wavelength when they are illuminated with light of a different wavelength. Many fluorescence microscopes can take images on many different depths in a sample and thereby build a three-dimensional image of the sample. Fluorescence microscopy can also be used to study particles, for example viruses, inside cells. Modern microscopes often have digital cameras or other equipment to take images or record time-lapse video. When biologists perform experiments on cells, they often record image sequences or sequences of three-dimensional volumes to see how the cells behave when they are subjected to different drugs, culture substrates, or other external factors. Previously, the analysis of recorded data has often been done manually, but that is very time-consuming and the results often become subjective and hard to reproduce. Therefore there is a great need for technology for automated analysis of image sequences with cells and particles inside cells. Such technology is needed especially in biological research and drug development. But the technology could also be used clinically, for example to tailor a cancer treatment to an individual patient by evaluating different treatments on cells from a biopsy. This thesis presents algorithms to find cells and particles in images, and to calculate tracks that show how they have moved during an experiment. We have developed a complete system that can find and track cells in all commonly used imaging modalities. We selected and extended a number of existing segmentation algorithms, and thereby created a complete tool to find cell outlines. To link the segmented objects into tracks, we developed a new track linking algorithm. The algorithm adds tracks one by one using dynamic programming, and has many advantages over prior algorithms. Among other things, it is fast, it calculates tracks which are optimal for the entire image sequence, and it can handle situations where multiple cells have been segmented incorrectly as one object. To make it possible to use information about the velocities of the objects in the linking, we developed a method where the positions of the objects are preprocessed using a filter before the linking is performed. This is important for tracking of some particles inside cells and for tracking of cell nuclei in some embryos.       We have developed an open source software which contains all tools that are necessary to analyze image sequences with cells or particles. It has tools for segmentation and tracking of objects, optimization of settings, manual correction, and analysis of outlines and tracks. We developed the software together with biologists who used it in their research. The software has already been used for data analysis in a number of biology publications. Our system has also achieved outstanding performance in three international objective comparisons of systems for tracking of cells. / Inom biologi används många olika typer av mikroskopi för att studera celler. Det finns många typer av genomlysningsmikroskopi, där ljus passerar genom cellerna, som kan användas utan färgning eller andra åtgärder som riskerar att skada cellerna. Det finns också fluorescensmikroskopi där fluorescerande proteiner eller färger förs in i cellerna eller i delar av cellerna, så att de emitterar ljus av en viss våglängd då de belyses med ljus av en annan våglängd. Många fluorescensmikroskop kan ta bilder på flera olika djup i ett prov och på så sätt bygga upp en tre-dimensionell bild av provet. Fluorescensmikroskopi kan även användas för att studera partiklar, som exempelvis virus, inuti celler. Moderna mikroskop har ofta digitala kameror eller liknande utrustning för att ta bilder och spela in bildsekvenser. När biologer gör experiment på celler spelar de ofta in bildsekvenser eller sekvenser av tre-dimensionella volymer för att se hur cellerna beter sig när de utsätts för olika läkemedel, odlingssubstrat, eller andra yttre faktorer. Tidigare har analysen av inspelad data ofta gjorts manuellt, men detta är mycket tidskrävande och resultaten blir ofta subjektiva och svåra att reproducera. Därför finns det ett stort behov av teknik för automatiserad analys av bildsekvenser med celler och partiklar inuti celler. Sådan teknik behövs framförallt inom biologisk forskning och utveckling av läkemedel. Men tekniken skulle också kunna användas kliniskt, exempelvis för att skräddarsy en cancerbehandling till en enskild patient genom att utvärdera olika behandlingar på celler från en biopsi. I denna avhandling presenteras algoritmer för att hitta celler och partiklar i bilder, och för att beräkna trajektorier som visar hur de har förflyttat sig under ett experiment. Vi har utvecklat ett komplett system som kan hitta och följa celler i alla vanligt förekommande typer av mikroskopi. Vi valde ut och vidareutvecklade ett antal existerande segmenteringsalgoritmer, och skapade på så sätt ett heltäckande verktyg för att hitta cellkonturer. För att länka ihop de segmenterade objekten till trajektorier utvecklade vi en ny länkningsalgoritm. Algoritmen lägger till trajektorier en och en med hjälp av dynamisk programmering, och har många fördelar jämfört med tidigare algoritmer. Bland annat är den snabb, den beräknar trajektorier som är optimala över hela bildsekvensen, och den kan hantera fall då flera celler felaktigt segmenterats som ett objekt. För att kunna använda information om objektens hastighet vid länkningen utvecklade vi en metod där objektens positioner förbehandlas med hjälp av ett filter innan länkningen utförs. Detta är betydelsefullt för följning av vissa partiklar inuti celler och för följning av cellkärnor i vissa embryon. Vi har utvecklat en mjukvara med öppen källkod, som innehåller alla verktyg som krävs för att analysera bildsekvenser med celler eller partiklar. Den har verktyg för segmentering och följning av objekt, optimering av inställningar, manuell korrektion, och analys av konturer och trajektorier. Vi utvecklade mjukvaran i samarbete med biologer som använde den i sin forskning. Mjukvaran har redan använts för dataanalys i ett antal biologiska publikationer. Vårt system har även uppnått enastående resultat i tre internationella objektiva jämförelser av system för följning av celler. / <p>QC 20161125</p>

Injection in the LHC is a delicate moment, since the LHC collimation system cannot offer adequate protection during beam transfer. For this reason, a complex chain of injection protection devices has been put in place. Among them, the SPS scrapers are the multi-turn cleaning system installed in the SPS aimed at halo removal immediately before injection in the LHC. The upgrade in luminosity of the LHC foresees beams brighter than those currently available in machine, posing serious problems to the performance of the existing injection protection systems. In particular, the integrity of beam-intercepting devices is challenged by unprecedented beam parameters, leading to interactions potentially destructive. In this context, a new design of scrapers has been proposed, aimed at improved robustness and performance. This thesis compares the two scraping systems, i.e. the existing one and the one proposed for upgrade. Unlike any other collimation system for regular halo cleaning, both are "fast" systems, characterised by the variation of the relative distance between the beam and the absorbing medium during cleaning, which enhances the challenge on energy deposition values. Assets/liabilities of the two systems are highlighted by means of numerical simulations and discussed, with particular emphasis on energy deposition in the absorbing medium, time evolution of the beam current during scraping and losses in the machine. Advantages of the system proposed for upgrade over the existing one are highlighted. The analysis of the existing system takes into account present operational conditions and addresses the sensitivity to settings previously not considered, updating and extending past studies. The work carried out on the upgraded system represents the first extensive characterisation of a multi-turn cleaning system based on a magnetic bump. Results have been obtained with the Fluka-SixTrack coupling, developed during this PhD activity from its initial version to being a state-of-art tracking tool for cleaning studies in circular machines. Relevant contributions to the development involve the handling of time-varying impact conditions. An extensive benchmark against a test of the scraper blades with beam has been carried out, to verify the reliability of results. Effcts induced in the tested blades confirm the high values of energy deposition predicted by the simulation. Moreover, the comparison with the time profile of the beam intensity measured during scraping allowed the reconstruction of the actual settings of the blades during the test. Finally, the good agreement of the quantitative benchmark against readouts of beam loss monitors finally proves the quality of the analyses and the maturity of the coupling.

The author developed a computational framework for the study of the correlation between airway morphology and aerosol deposition based on a population of human subjects. The major improvement on the previous framework, which consists of a geometric airway model, a computational fluid dynamics (CFD) model, and a particle tracking algorithm, lies in automatic geometry construction and mesh generation of airways, which is essential for a population-based study. The new geometric model overcomes the shortcomings of both centerline (CL)-based cylindrical models, which are based on the skeleton and average branch diameters of airways called one-dimensional (1-D) trees, and computed tomography (CT)-based models. CL-based models are efficient in terms of pre- and post-processing, but fail to represent trifurcations and local morphology. In contrast, in spite of the accuracy of CT-based models, it is time-consuming to build these models manually, and non-trivial to match 1-D trees and three-dimensional (3-D) geometry. The new model, also known as a hybrid CL-CT-based model, is able to construct a physiologically-consistent laryngeal geometry, represent trifurcations, fit cylindrical branches to CT data, and create the optimal CFD mesh in an automatic fashion. The hybrid airway geometries constructed for 8 healthy and 16 severe asthmatic (SA) subjects agreed well with their CT-based counterparts. Furthermore, the prediction of aerosol deposition in a healthy subject by the hybrid model agreed well with that by the CT-based model. To demonstrate the potential application of the hybrid model to investigating the correlation between skeleton structure and aerosol deposition, the author applied the large eddy simulation (LES)-based CFD model that accounts for the turbulent laryngeal jet to three hybrid models of SA subjects. The correlation between diseased branch and aerosol deposition was significant in one of the three SA subjects. However, whether skeleton structure contributes to airway abnormality requires further investigation.