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1
Rassou, Sébastien. "Accélération d'électrons par onde de sillage laser : Développement d’un modèle analytique étendu au cas d’un plasma magnétisé dans le régime du Blowout." Thesis, Université Paris-Saclay (ComUE), 2015. http://www.theses.fr/2015SACLS066/document.
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Une impulsion laser intense se propageant dans un plasma sous-dense (ne< 10¹⁸ W.cm⁻²) et de durée très courte (τ₀< 100 fs), , on atteint le régime de la bulle. Les champs électriques dans ces bulles, de l’ordre de 100 GV/m, peuvent accélérer un faisceau d’électrons jusqu’au GeV sur des distances de l’ordre du centimètre. Dans ce régime, les électrons expulsés par la force pondéromotrice du laser forment une fine et dense couche à la surface d'une cavité d'ions restés immobiles. Les propriétés de ce régime sont examinées par l’intermédiaire d’un modèle analytique, que nous avons développé en nous inspirant du travail de W. Lu et S. Yi. En nous plaçant dans ce régime prometteur, nous avons étudié les mécanismes d’injection et de piégeage dans l'onde de sillage. Dans l’injection optique, les polarisations parallèles ou circulaires positives conduisent respectivement à une injection mettant en jeu du chauffage stochastique, ou à l’injection froide. Un paramètre de similarité est introduit, celui-ci permet de déterminer la méthode d’injection la plus appropriée pour maximiser la charge injectée. Enfin, le modèle analytique présenté en première partie est étendu afin d’étudier l’onde de sillage dans le régime de la bulle lorsqu’un champ magnétique longitudinal initial est appliqué au plasma. Lorsque le plasma est magnétisé deux phénomènes remarquables se manifestent, d'une part une ouverture apparaît à l'arrière de la bulle et d'autre part un mécanisme d'amplification du champ magnétique longitudinale est induit par la variation du flux magnétique. Les prédictions de notre modèle analytique sont confrontées aux résultats de simulations PIC 3D issues du code CALDER-Circ. La conséquence immédiate de la déformation de l'onde de sillage est la réduction, voire la suppression de l'auto-injection. L’application d’un champ magnétique longitudinal, combinée à un choix judicieux des paramètres laser-plasma, permet de réduire la dispersion en énergie des faisceaux d’électrons produits après injection optique<br>An intense laser pulse propagating in an under dense plasma (ne< 10¹⁸ W.cm⁻²) and short(τ₀< 100 fs), the bubble regime is reached. Within the bubble the electric field can exceed 100 GV/m and a trapped electron beam is accelerated to GeV energy with few centimetres of plasma.In this regime, the electrons expelled by the laser ponderomotive force are brought back and form a dense sheath layer. First, an analytic model was derived using W. Lu and S. Yi formalisms in order to investigate the properties of the wakefield in the blowout regime. In a second part, the trapping and injection mechanisms into the wakefield were studied. When the optical injection scheme is used, electrons may undergo stochastic heating or cold injection depending on the lasers’ polarisations. A similarity parameter was introduced to find out the most appropriate method to maximise the trapped charge. In a third part, our analytic model is extended to investigate the influence of an initially applied longitudinal magnetic field on the laser wakefield in the bubble regime. When the plasma is magnetized two remarkable phenomena occur. Firstly the bubble is opened at its rear, and secondly the longitudinal magnetic field is amplified - at the rear of the bubble - due to the azimuthal current induced by the variation of the magnetic flux. The predictions of our analytic model were shown to be in agreement with 3D PIC simulation results obtained with Calder-Circ. In most situations the wake shape is altered and self-injection can be reduced or even cancelled by the applied magnetic field. However, the application of a longitudinal magnetic field, combined with a careful choice of laser-plasma parameters, reduces the energy spread of the electron beam produced after optical injection
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Lindemann, Dirk, Kristin Stirnnagel, Daniel Lüftenegger, et al. "Analysis of Prototype Foamy Virus particle-host cell interaction with autofluorescent retroviral particles." BMC, 2010. https://tud.qucosa.de/id/qucosa%3A28868.
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Background
The foamy virus (FV) replication cycle displays several unique features, which set them apart from orthoretroviruses. First, like other B/D type orthoretroviruses, FV capsids preassemble at the centrosome, but more similar to hepadnaviruses, FV budding is strictly dependent on cognate viral glycoprotein coexpression. Second, the unusually broad host range of FV is thought to be due to use of a very common entry receptor present on host cell plasma membranes, because all cell lines tested in vitro so far are permissive.
Results
In order to take advantage of modern fluorescent microscopy techniques to study FV replication, we have created FV Gag proteins bearing a variety of protein tags and evaluated these for their ability to support various steps of FV replication. Addition of even small N-terminal HA-tags to FV Gag severely impaired FV particle release. For example, release was completely abrogated by an N-terminal autofluorescent protein (AFP) fusion, despite apparently normal intracellular capsid assembly. In contrast, C-terminal Gag-tags had only minor effects on particle assembly, egress and particle morphogenesis. The infectivity of C-terminal capsid-tagged FV vector particles was reduced up to 100-fold in comparison to wild type; however, infectivity was rescued by coexpression of wild type Gag and assembly of mixed particles. Specific dose-dependent binding of fluorescent FV particles to target cells was demonstrated in an Env-dependent manner, but not binding to target cell-extracted- or synthetic- lipids. Screening of target cells of various origins resulted in the identification of two cell lines, a human erythroid precursor- and a zebrafish- cell line, resistant to FV Env-mediated FV- and HIV-vector transduction.
Conclusions
We have established functional, autofluorescent foamy viral particles as a valuable new tool to study FV - host cell interactions using modern fluorescent imaging techniques. Furthermore, we succeeded for the first time in identifying two cell lines resistant to Prototype Foamy Virus Env-mediated gene transfer. Interestingly, both cell lines still displayed FV Env-dependent attachment of fluorescent retroviral particles, implying a post-binding block potentially due to lack of putative FV entry cofactors. These cell lines might ultimately lead to the identification of the currently unknown ubiquitous cellular entry receptor(s) of FVs.
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Lindemann, Dirk, Kristin Stirnnagel, Daniel Lüftenegger, et al. "Analysis of Prototype Foamy Virus particle-host cell interaction with autofluorescent retroviral particles." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-176566.
Full textAbstract:
Background
The foamy virus (FV) replication cycle displays several unique features, which set them apart from orthoretroviruses. First, like other B/D type orthoretroviruses, FV capsids preassemble at the centrosome, but more similar to hepadnaviruses, FV budding is strictly dependent on cognate viral glycoprotein coexpression. Second, the unusually broad host range of FV is thought to be due to use of a very common entry receptor present on host cell plasma membranes, because all cell lines tested in vitro so far are permissive.
Results
In order to take advantage of modern fluorescent microscopy techniques to study FV replication, we have created FV Gag proteins bearing a variety of protein tags and evaluated these for their ability to support various steps of FV replication. Addition of even small N-terminal HA-tags to FV Gag severely impaired FV particle release. For example, release was completely abrogated by an N-terminal autofluorescent protein (AFP) fusion, despite apparently normal intracellular capsid assembly. In contrast, C-terminal Gag-tags had only minor effects on particle assembly, egress and particle morphogenesis. The infectivity of C-terminal capsid-tagged FV vector particles was reduced up to 100-fold in comparison to wild type; however, infectivity was rescued by coexpression of wild type Gag and assembly of mixed particles. Specific dose-dependent binding of fluorescent FV particles to target cells was demonstrated in an Env-dependent manner, but not binding to target cell-extracted- or synthetic- lipids. Screening of target cells of various origins resulted in the identification of two cell lines, a human erythroid precursor- and a zebrafish- cell line, resistant to FV Env-mediated FV- and HIV-vector transduction.
Conclusions
We have established functional, autofluorescent foamy viral particles as a valuable new tool to study FV - host cell interactions using modern fluorescent imaging techniques. Furthermore, we succeeded for the first time in identifying two cell lines resistant to Prototype Foamy Virus Env-mediated gene transfer. Interestingly, both cell lines still displayed FV Env-dependent attachment of fluorescent retroviral particles, implying a post-binding block potentially due to lack of putative FV entry cofactors. These cell lines might ultimately lead to the identification of the currently unknown ubiquitous cellular entry receptor(s) of FVs.
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Mack, Stuart Anderson. "Experimental and computational study of the behaviour of free-cells in discharging silos." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/experimental-and-computational-study-of-the-behaviour-of-freecells-in-discharging-silos(1f0b6130-7c2c-4a96-ad56-54ff71af2e98).html.
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This study aims to deduce an appropriate shape and density for an electronic free-cell that could be placed into a silo so that position and other desired physical parameters could be recorded. To determine how density and shape affects the trajectory and displacement of free cells, the trajectory and displacement of cylindrical, cuboid and triangular prism free-cells of equivalent volume was investigated in a discharging quasi 3D silo slice. The free-cells were placed at twelve different starting positions spread evenly over one half of the 3D slice. Tests were conducted using a monosized batch of spherical particles with a diameter of approximately 5 mm. Tests were also conducted in a binary mixture consisting of particles of different sizes (5 mm/4 mm) and the same density (1.28 g/cm3) and a binary mixture consisting of particles of different size (6 mm/5 mm) and different densities (1.16 g/cm3/1.28 g/cm3).The rotation of the free cells was also briefly discussed.Computer simulations were conducted using the Discrete Element Method (DEM). The simulation employed the spring-slider-dashpot contact model to represent the normal and tangential force components and the modified Euler integration scheme was applied to calculate the particle velocities and positions at each time step. One trial of each of the metal and plastic, cylindrical, cuboid and triangular prism free cells was compared with the average of three experimental trials. The trajectory and displacement of a representative particle positioned at the same starting position as the free cell was also obtained from DEM simulation and compared with the path and displacement of each of the free cells to determine which free cell followed the particle most closely and hence to determine a suitable free cell that would move with the rest of the grains. Spherical particles are idealised particles. Therefore tests were also conducted with a small number of polyhedral particles, to deduce their flow rate and the critical orifice width at which blockages were likely to form. Simulations were also conducted to test the feasibility of the DEM in modelling the behaviour of these polyhedral particles.Results indicate that for a free cell to move along the same trajectory and have the same displacement and velocity as an equivalent particle in the batch it should have a similar density to the majority of the other particles. A cylindrical free cell of similar density to the particles was found to follow the path of the representative particle more closely than the cuboid or triangular prism. Polyhedral particles were found to have a greater flow rate than spherical particles of equivalent volume.
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Stamm, Matthew T. "Particle Dynamics and Particle-Cell Interaction in Microfluidic Systems." Diss., The University of Arizona, 2013. http://hdl.handle.net/10150/308886.
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Particle-laden flow in a microchannel resulting in aggregation of microparticles was investigated to determine the dependence of the cluster growth rate on the following parameters: suspension void fraction, shear strain rate, and channel-height to particle-diameter ratio. The growth rate of an average cluster was found to increase linearly with suspension void fraction, and to obey a power-law relationships with shear strain rate as S^0.9 and channel-height to particle-diameter ratio as (h/d)^-3.5. Ceramic liposomal nanoparticles and silica microparticles were functionalized with antibodies that act as targeting ligands. The bio-functionality and physical integrity of the cerasomes were characterized. Surface functionalization allows cerasomes to deliver drugs with selectivity and specificity that is not possible using standard liposomes. The functionalized particle-target cell binding process was characterized using BT-20 breast cancer cells. Two microfluidic systems were used; one with both species in suspension, the other with cells immobilized inside a microchannel and particle suspension as the mobile phase. Effects of incubation time, particle concentration, and shear strain rate on particle-cell binding were investigated. With both species in suspension, the particle-cell binding process was found to be reasonably well-described by a first-order model. Particle desorption and cellular loss of binding affinity in time were found to be negligible; cell-particle-cell interaction was identified as the limiting mechanism in particle-cell binding. Findings suggest that separation of a bound particle from a cell may be detrimental to cellular binding affinity. Cell-particle-cell interactions were prevented by immobilizing cells inside a microchannel. The initial stage of particle-cell binding was investigated and was again found to be reasonably well-described by a first-order model. For both systems, the time constant was found to be inversely proportional to particle concentration. The second system revealed the time constant to obey a power-law relationship with shear strain rate as τ∝S^.37±.06. Under appropriate scaling, the behavior displayed in both systems is well-described by the same exponential curve. Identification of the appropriate scaling parameters allows for extrapolation and requires only two empirical values. This could provide a major head-start in any dosage optimization studies.
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Pachler, Klaus, Thomas Frank, and Klaus Bernert. "Simulation of Unsteady Gas-Particle Flows including Two-way and Four-way Coupling on a MIMD Computer Architectur." Universitätsbibliothek Chemnitz, 2002. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-200200352.
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The transport or the separation of solid particles or droplets suspended in a fluid flow is a common task in mechanical and process engineering. To improve machinery and physical processes (e.g. for coal combustion, reduction of NO_x and soot) an optimization of complex phenomena by simulation applying the fundamental conservation equations is required. Fluid-particle flows are characterized by the ratio of density of the two phases gamma=rho_P/rho_F, by the Stokes number St=tau_P/tau_F and by the loading in terms of void and mass fraction.
Those numbers (Stokes number, gamma) define the flow regime and which relevant forces are acting on the particle. Dependent on the geometrical configuration the particle-wall interaction might have a heavy impact on the mean flow structure. The occurrence of particle-particle collisions becomes also more and more important with the increase of the local void fraction of the particulate phase. With increase of the particle loading the interaction with the fluid phase can not been neglected and 2-way or even 4-way coupling between the continous and disperse phases has to be taken into account.
For dilute to moderate dense particle flows the Euler-Lagrange method is capable to resolve the main flow mechanism. An accurate computation needs unfortunately a high number of numerical particles (1,...,10^7) to get the reliable statistics for the underlying modelling correlations. Due to the fact that a Lagrangian algorithm cannot be vectorized for complex meshes the only way to finish those simulations in a reasonable time is the parallization applying the message passing paradigma.
Frank et al. describes the basic ideas for a parallel Eulererian-Lagrangian solver, which uses multigrid for acceleration of the flow equations. The performance figures are quite good, though only steady problems are tackled. The presented paper is aimed to the numerical prediction of time-dependend fluid-particle flows using the simultanous particle tracking approach based on the Eulerian-Lagrangian and the particle-source-in-cell (PSI-Cell) approach. It is shown in the paper that for the unsteady flow prediction efficiency and load balancing of the parallel numerical simulation is an even more pronounced problem in comparison with the steady flow calculations, because the time steps for the time integration along one particle trajectory are very small per one time step of fluid flow integration and so the floating point workload on a single processor node is usualy rather low.
Much time is spent for communication and waiting time of the processors, because for cold flow particle convection not very extensive calculations are necessary. One remedy might be a highspeed switch like Myrinet or Dolphin PCI/SCI (500 MByte/s), which could balance the relative high floating point performance of INTEL PIII processors and the weak capacity of the Fast-Ethernet communication network (100 Mbit/s) of the Chemnitz Linux Cluster (CLIC) used for the presented calculations. Corresponding to the discussed examples calculation times and parallel performance will be presented. Another point is the communication of many small packages, which should be summed up to bigger messages, because each message requires a startup time independently of its size. Summarising the potential of such a parallel algorithm, it will be shown that a Beowulf-type cluster computer is a highly competitve alternative to the classical main frame computer for the investigated Eulerian-Lagrangian simultanous particle tracking approach.
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Ljung, Patric. "Visualization of Particle In Cell Simulations." Thesis, Linköping University, Department of Science and Technology, 2000. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2340.
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<p>A numerical simulation case involving space plasma and the evolution of instabilities that generates very fast electrons, i.e. approximately at half of the speed of light, is used as a test bed for scientific visualisation techniques. A visualisation system was developed to provide interactive real-time animation and visualisation of the simulation results. The work focuses on two themes and the integration of them. The first theme is the storage and management of the large data sets produced. The second theme deals with how the Visualisation System and Visual Objects are tailored to efficiently visualise the data at hand. </p><p>The integration of the themes has resulted in an interactive real-time animation and visualisation system which constitutes a very powerful tool for analysis and understanding of the plasma physics processes. The visualisations contained in this work have spawned many new possible research projects and provided insight into previously not fully understood plasma physics phenomena.</p>
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Tatomirescu, Emilian-Dragos. "Accélération laser-plasma à ultra haute intensité - modélisation numérique." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0013/document.
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Avec les dernières augmentations de l'intensité maximale de laser réalisable grâce à de courtes impulsions à haute puissance (gamme femtoseconde) un intérêt a surgi dans les sources de plasma laser potentiels. Les lasers sont utilisés en radiographie proton, allumage rapide, hadronthérapie, la production de radioisotopes et de laboratoire astrophysique. Au cours de l'interaction laser-cible, les ions sont accélérés par des processus physiques différents, en fonction de la zone de la cible. Tous ces mécanismes ont un point commun: les ions sont accélérés par des champs électriques intenses, qui se produisent en raison de la séparation de forte charge induite par l'interaction de l'impulsion laser avec la cible, directement ou indirectement. Deux principales sources distinctes pour le déplacement de charge peuvent être mis en évidence. Le premier est le gradient de charge provoquée par l'action directe de la force ponderomotive de laser sur les électrons dans la surface avant de la cible, qui est la prémisse pour le processus d'accélération des radiations de pression (RPA). Une deuxième source peut être identifiée comme provenant du rayonnement laser qui est transformée en énergie cinétique d'une population d'électrons relativistes chaud (~ quelques MeV). Les électrons chauds se déplacent et font recirculer à travers la cible et forment un nuage d'électrons relativistes à la sortie de la cible dans le vide. Ce nuage, qui se prolonge pour plusieurs longueurs de Debye, crée un champ électrique extrêmement intense longitudinal, la plupart du temps dirigé le long de la surface normale, ce qui, par conséquent, est la cause de l'accélération d'ions efficace, qui conduit à l'accélération cible normale gaine (TNSA) processus . Le mécanisme TNSA permet d'utiliser des géométries différentes cibles afin de parvenir à une meilleure focalisation des faisceaux de particules de l'ordre de plusieurs dizaines de microns, avec des densités d'énergie élevées. Les électrons chauds sont produits par l'irradiation d'une feuille solide avec une impulsion laser intense; ces électrons sont transportés à travers la cible, la formation d'un champ électrostatique fort, normal à la surface cible. Protons et les ions chargés positivement de la surface arrière de la cible sont accélérés par ce domaine jusqu'à ce que la charge de l'électron est compensée. La densité d'électrons chauds et la température dans le vide arrière dépendent des propriétés géométriques et de composition cibles tels que la courbure de la cible, les structures de mise au point d'impulsion et de microstructure pour l'accélération de protons améliorée. Au cours de ma première année, j'ai étudié les effets de la géométrie de la cible sur le proton et l'ion énergie et la distribution angulaire afin d'optimiser les faisceaux de particules laser accéléré au moyen de deux dimensions (2D) particule-in-cell (PIC) simulations de l'interaction de l'ultra-court impulsions laser avec plusieurs cibles microstructurées. Également au cours de cette année, je l'ai étudié la théorie derrière les modèles utilisés<br>With the latest increases in maximum laser intensity achievable through short pulses at high power (femtosecond range) an interest has arisen in potential laser plasma sources. Lasers are used in proton radiography, rapid ignition, hadrontherapy, production of radioisotopes and astrophysical laboratory. During the laser-target interaction, the ions are accelerated by different physical processes, depending on the area of the target. All these mechanisms have one thing in common: the ions are accelerated by intense electric fields, which occur due to the separation of high charge induced by the interaction of the laser pulse with the target, directly or indirectly. Two main distinct sources for charge displacement can be identified. The first is the charge gradient caused by the direct action of the laser ponderomotive force on the electrons in the front surface of the target, which is the premise for the pressure ramping acceleration (RPA) process. A second source can be identified as coming from the laser radiation which is transformed into kinetic energy of a hot relativistic electron population (~ a few MeV). The hot electrons move and recirculate through the target and form a cloud of relativistic electrons at the exit of the target in a vacuum. This cloud, which extends for several lengths of Debye, creates an extremely intense longitudinal electric field, mostly directed along the normal surface, which is therefore the cause of effective ion acceleration, which leads to the normal target sheath acceleration (TNSA) process. The TNSA mechanism makes it possible to use different target geometries in order to obtain a better focusing of the beams of particles on the order of several tens of microns, with high energy densities. Hot electrons are produced by irradiating a solid sheet with an intense laser pulse; these electrons are transported through the target, forming a strong electrostatic field, normal to the target surface. Protons and positively charged ions from the back surface of the target are accelerated by this domain until the charge of the electron is compensated. The density of hot electrons and the temperature in the back vacuum depend on the target geometric and compositional properties such as target curvature, pulse and microstructure tuning structures for enhanced proton acceleration. In my first year I studied the effects of target geometry on the proton and energy ion and angular distribution in order to optimize the accelerated laser particle beams by means of two-dimensional (2D) particle -in-cell (PIC) simulations of the interaction of ultra-short laser pulses with several microstructured targets. Also during this year, I studied the theory behind the models used
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Przebinda, Viktor. "Vertical optimization of particle in cell simulation." Diss., Connect to online resource, 2005. http://wwwlib.umi.com/cr/colorado/fullcit?p1425790.
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Edwards, Essex. "A high-order accurate particle-in-cell method." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/26106.
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We propose the use of high-order accurate interpolation and approximation schemes alongside high-order accurate time integration methods to enable high-order accurate Particle-in-Cell methods. The key insight is to view the unstructured set of particles as the underlying representation of the continuous fields;
the grid used to evaluate integro-differential coupling terms is purely auxiliary. We also include a novel regularization term to avoid the accumulation of noise in the particle samples without harming the convergence rate. We include numerical examples for several model problems: advection-diffusion, shallow water, and incompressible Navier-Stokes in vorticity formulation. The implementation demonstrates fourth-order convergence, shows very low numerical dissipation, and is competitive with high-order accurate Eulerian schemes.
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Birch, Paul C. "Particle-in-cell simulations of the lunar wake." Thesis, University of Warwick, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.392768.
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Lindmark, Sofia. "Cell Tracking in Microscopy Images Using a Rao-Blackwellized Particle Filter." Thesis, Uppsala universitet, Avdelningen för visuell information och interaktion, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-236769.
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Analysing migrating cells in microscopy time-lapse images has already helped the understanding of many biological processes and may be of importance in the development of new medical treatments. Today’s biological experiments tend to produce a huge amount of dynamic image data and tracking the individual cells by hand has become a bottleneck for the further analysis work. A number of cell tracking methods have therefore been developed over the past decades, but still many of the techniques have a limited performance. The aim of this Master Project is to develop a particle filter algorithm that automatically detects and tracks a large number of individual cells in an image sequence. The solution is based on a Rao-Blackwellized particle filter for multiple object tracking. The report also covers a review of existing automatic cell tracking techniques, a review of well-known filter techniques for single target tracking and how these techniques have been developed to handle multiple target tracking. The designed algorithm has been tested on real microscopy image data of neutrophils with 400 to 500 cells in each frame. The designed algorithm works well in areas of the images where no cells touch and can in these situations also correct for some segmentation mistakes. In areas where cells touch, the algorithm works well if the segmentation is correct, but often makes mistakes when it is not. A target effectiveness of 77 percent and a track purity of 80 percent are then achieved.
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Larsgård, Nils Magnus. "Parallelizing Particle-In-Cell Codes with OpenMP and MPI." Thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2007. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-8722.
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<p>Today's supercomputers often consists of clusters of SMP nodes. Both OpenMP and MPI are programming paradigms that can be used for parallelization of codes for such architectures. OpenMP uses shared memory, and hence is viewed as a simpler programming paradigm than MPI that is primarily a distributed memory paradigm. However, the Open MP applications may not scale beyond one SMP node. On the other hand, if we only use MPI, we might introduce overhead in intra-node communication. In this thesis we explore the trade-offs between using OpenMP, MPI and a mix of both paradigms for the same application. In particular, we look at a physics simulation and parallalize it with both OpenMP and MPI for large-scale simulations on modern supercomputers. A parallel SOR solver with OpenMP and MPI is implemented and the effects of such hybrid code are measured. We also utilize the FFTW-library that includes both system-optimized serial implementations and a parallel OpenMP FFT implementation. These solvers are used to make our existing Particle-In-Cell codes be more scalable and compatible with current programming paradigms and supercomputer architectures. We demonstrate that the overhead from communications in OpenMP loops on an SMP node is significant and increases with the number of CPUs participating in execution of the loop compared to equivalent MPI implementations. To analyze this result, we also present a simple model on how to estimate the overhead from communication in OpenMP loops. Our results are both surprising and should be of great interest to a large class of parallel applications.</p>
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Druma, Calin. "A particle in cell formulation for extrusion of fluoropolymers." Ohio : Ohio University, 2003. http://www.ohiolink.edu/etd/view.cgi?ohiou1178048890.
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Popoola, O. M. "A reconfigurable computer for particle-in-cell plasma simulations." Thesis, University of Sussex, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418534.
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Peng, Zhizi. "Modeling of Particle and Biological Cell Transport in Microchannels." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1324660368.
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Slator, Paddy. "Characterising cell membrane heterogeneity through analysis of particle trajectories." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/79961/.
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Single particle tracking (SPT) trajectories are fundamentally stochastic, which makes the extraction of robust biological conclusions difficult. This is especially the case when trying to detect heterogeneous movement of molecules in the plasma membrane. This heterogeneity could be due to a number of biophysical processes such as: receptor clustering, traversing lipid microdomains or cytoskeletal barriers. Working in a Bayesian framework, we developed multiple hidden Markov models for heterogeneity, such as confinement in a harmonic potential well, switching between diffusion coefficients, and diffusion in a fenced environment (or "hop" diffusion). We implement these models using a Markov chain Monte Carlo (MCMC) methodology, developing algorithms that infer model parameters and hidden states from single trajectories. We also calculate model selection statistics, to determine the most likely model given the trajectory. For LFA-1 receptors diffusing on T cells we show that 12-26% of trajectories display clear switching between diffusive states, depending on treatment. We also demonstrated that allowing for measurement noise is essential, as otherwise false detection of heterogeneity may be observed. Analysis of the motion of GM1 lipids bound to the cholera toxin B subunit (CTxB) in model membranes confirmed transient confinement. On this dataset we also demonstrated a clear signature in the confinement shape for individual tagging molecules, and showed that confinement events are not exponentially distributed. Finally, we developed an algorithm which detects hopping diffusion, validating on simulated data. Rather than methods which rely on generic properties of Brownian motions, our approach allows us to test which biophysical model best fits a trajectory. Using a model-based approach we can also extract biophysical parameters, segment trajectories into different motion states, and hence analyse particle motion in high detail. With the continuing improvement in spatial and temporal resolution of trajectories, these methods will be important for biological interpretation of SPT experiments.
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Relich, Peter Kristopher II. "Single Particle Tracking| Analysis Techniques for Live Cell Nanoscopy." Thesis, The University of New Mexico, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10251887.
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<p> Single molecule experiments are a set of experiments designed specifically to study the properties of individual molecules. It has only been in the last three decades where single molecule experiments have been applied to the life sciences; where they have been successfully implemented in systems biology for probing the behaviors of sub-cellular mechanisms. The advent and growth of super-resolution techniques in single molecule experiments has made the fundamental behaviors of light and the associated nano-probes a necessary concern amongst life scientists wishing to advance the state of human knowledge in biology. This dissertation disseminates some of the practices learned in experimental live cell microscopy. The topic of single particle tracking is addressed here in a format that is designed for the physicist who embarks upon single molecule studies. Specifically, the focus is on the necessary procedures to generate single particle tracking analysis techniques that can be implemented to answer biological questions. These analysis techniques range from designing and testing a particle tracking algorithm to inferring model parameters once an image has been processed. The intellectual contributions of the author include the techniques in diffusion estimation, localization filtering, and trajectory associations for tracking which will all be discussed in detail in later chapters. The author of this thesis has also contributed to the software development of automated gain calibration, live cell particle simulations, and various single particle tracking packages. Future work includes further evaluation of this laboratory's single particle tracking software, entropy based approaches towards hypothesis validations, and the uncertainty quantification of gain calibration.</p><p>
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Tomalik, Edyta. "Image-based Microscale Particle Velocimetry in Live Cell Microscopy." Thesis, Blekinge Tekniska Högskola, Institutionen för programvaruteknik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:bth-2564.
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Background: Nowadays, one of the medical problem is rolling cell adhesion. Rolling cell adhesion is a complex process that requires the analysis of the challenging environment such as body fluid and is the process responsible for recruiting the cell to specific organs. In order to explore the rolling cell adhesion, mathematical model is proposed. Different image processing methods are created, such as optical flow - Lucas Kanade algorithm, and other type of methods related to mechanical fluid, namely PIV (Particle Image Velocimetry). Aim: The aim of this master thesis is the identification of challenges while using PIV in live cell images and propose the algorithm, which may analyze the rolling cell adhesion problem. Methods: In order to understand properly the rolling cell adhesion problem from biological site, literature review combined with the expert consultation is performed. According to gather information, mathematical model is proposed. Particle Image Velocimetry is explained according to literature review, where at the beginning the expert recommends some books as a primary research. As a result of this research, PIV challenges are identified and generally PIV idea is explained. Then two experiments are performed. The first experiment evaluates detection algorithms and the second one, analyses track algorithm vs. PIV. In order to evaluate the mentioned algorithms, some evaluation method are selected and some criteria are defined. Unfortunately the found methods are not perfect, therefore a new method related to performance evaluation using time series is proposed. Thesis result: The result of this thesis is a proposition of the algorithm, which can be used in the rolling cell adhesion. The algorithm is formed according to the detailed exploration of the rolling cell adhesion and analysis of the selected algorithms related to the image analysis during the theoretical research and experiments.
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Twala, Busisiwe V. "Preparation of a self-contained NADH co-factor recycling particle system." Master's thesis, University of Cape Town, 2010. http://hdl.handle.net/11427/4343.
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Includes abstract.<br>Includes bibliographical references (leaves 101-116).<br>Oxidoreductases are interesting enzymes with potential applications in a number of different industries such as the textile, food and feed, chemical and biomedical industries. Oxidoreductases require the use of co-factors. These small molecules are relatively expensive and are required in stoichiometric amounts for their enzymatic reaction; this negatively impacts the economic viability of their potential applications. Several methods have been developed to counteract this problem, the most preferred of which is the enzymatic co-factor recycling method. A few methods for the co-immobilisation of enzymes and co-factors have been developed. These systems are of interest as they offer the advantages of recycling the enzymes together with the co-factor, thereby enabling re-use. The immobilisation of enzymes also provides a platform for improving their stability, activity, specificity and selectivity. Since glucose dehydrogenase (GDH) and NADH oxidase, are industrially relevant co-factor recycling enzymes for NAD(P)H and NAD+ respectively, characterisation of their immobilisation is of interest. The current work describes the use of the proprietary particle technology, termed ReSyn™, for the construction of a self-contained co-factor recycling system. The research included the optimisation of immobilisation for the individual enzymes, followed by the co-immobilisation with subsequent co-factor entrapment. The immobilised enzymes displayed improved thermal and pH stability compared to the non-immobilised enzymes. Immobilised GDH also displayed increased activity over the acidic range when compared to free GDH. The system was shown to be capable of recycling NADH/NAD+ up to at least 142 times with a specific activity of 10.18 U.mg¯1. The system was recovered and recycled with a 77% activity efficiency indicating recovery of the system and reusability. Preparation of a functional self-contained co-factor recycling system was demonstrated consisting of the biological components NADH oxidase and glucose dehydrogenase, immobilised on a polyethylenimine support with entrapped cofactor. This serves as proof-of-principle for the construction of derivative systems that could be used for the development of applications such as efficient biosynthesis, novel biosensors, diagnostic and therapeutic systems.
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Martinez, Bertrand. "Effets radiatifs et quantiques dans l'interaction laser-matière ultra-relativiste." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0442/document.
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L'avènement d'une nouvelle génération de lasers ultra-relativistes (d'éclairement supérieur à 10^22 W/cm2), tels le laser APOLLON sur le plateau de Saclay, donnera lieu à un régime d'interaction laser-matière sans précédent, couplant physique des plasmas relativistes et effets électrodynamiques quantiques. Sources de particules et de rayonnements aux propriétés énergétiques et spatio-temporelles inédites, ces lasers serviront, entre autres applications, à la mise au point de nouveaux concepts d'accélérateurs et de diagnostics radiographiques, au chauffage de plasmas denses, comme à la reproduction de configurations astrophysiques en laboratoire. En prévision des futures expériences, les codes particle-in-cell (PIC), qui constituent les outils de référence pour la simulation de l'interaction laser-plasma, doivent être enrichis des processus radiatifs et quantiques propres à ce nouveau régime d'interaction. C'est le cas du code CALDER développé au CEA/DAM, qui modélise désormais l'émission de photons énergétiques et la conversion de ceux-ci en paires électron-positron ; autant d'effets susceptibles d'affecter le bilan d'énergie de l'interaction laser-cible et, plus précisément, le rendement du laser en particules et rayonnements énergétiques. L'objet de ce stage théorique est d'étudier, à l'aide du code CALDER, l'influence de ces processus dans un certain nombre de scénarios physiques en champ extrême (accélération électronique et ionique dans un plasma surcritique, production de rayonnement, génération de choc non-collisionnel…)<br>Forthcoming multi-petawatt laser systems, such as the French Apollon and European Extreme Light Infrastructure facilities, are expected to deliver on-target laser intensities exceeding 10^22 W/cm^2. A novel regime of laser-matter interaction will ensue, where ultra-relativistic plasma effects are coupled with copious generation of high-energy photons and electron-positron pairs. This will pave the way for many transdisciplinary applications in fundamental and applied research, including the development of unprecedentedly intense, compact particle and radiation sources, the experimental investigation of relativistic astrophysical scenarios and tests of quantum electrodynamics theory.In recent years, most theoretical studies performed in this research field have focused on the impact of synchrotron photon emission and Breit-Wheeler pair generation, both directly induced by the laser field and believed to be dominant at intensities >10^22 W/cm^2. At the lower intensities (≲10^21 Wcm^(-2)) currently attainable, by contrast, photon and pair production mainly originate from, respectively, Bremsstrahlung and Bethe-Heitler/Trident processes, all triggered by atomic Coulomb fields. The conditions for a transition between these two regimes have, as yet, hardly been investigated, particularly by means of integrated kinetic numerical simulations. The purpose of this PhD is precisely to study the aforementioned processes under various physical scenarios involving extreme laser-plasma interactions. This work is carried out using the particle-in-cell CALDER code developed at CEA/DAM which, over the past few years, had been enriched with modules describing the synchrotron and Breit-Wheeler processes.Our first study aimed at extending the simulation capabilities of CALDER to the whole range of photon and positron generation mechanisms arising during relativistic laser-plasma interactions. To this purpose, we have implemented modules for the Coulomb-field-mediated Bremsstrahlung, Bethe-Heitler and Trident processes. Refined Bremsstrahlung and Bethe-Heitler cross sections have been obtained which account for electronic shielding effects in arbitrarily ionized plasmas. Following validation tests of the Monte Carlo numerical method, we have examined the competition between Bremsstrahlung/Bethe-Heitler and Trident pair generations by relativistic electrons propagating through micrometer copper foils. Our self-consistent simulations qualitatively agree with a 0-D theoretical model, yet they show that the deceleration of the fast electrons due to target expansion significantly impacts pair production.We then address the competition between Bremsstrahlung and synchrotron emission from copper foils irradiated at 10^22 Wcm^(-2). We show that the maximum radiation yield (into >10 keV photons) is achieved through synchrotron emission in relativistically transparent targets of a few 10 nm thick. The efficiency of Bremsstrahlung increases with the target thickness, and takes over synchrotron for >2μm thicknesses. The spectral properties of the two radiation processes are analyzed in detail and correlated with the ultrafast target dynamics.Finally, we investigate the potential of nanowire-array targets to enhance the synchrotron yield of a 10^22 Wcm^(-2) femtosecond laser pulse. Several radiation mechanisms are identified depending on the target parameters and as a function of time. A simulation scan allows us to identify the optimal target geometry in terms of nanowire width and interspacing, yielding a ∼10% radiation efficiency. In this configuration, the laser-driven nanowire array rapidly expands to form a quasi-uniform, relativistically transparent plasma. Furthermore, we demonstrate that uniform sub-solid targets can achieve synchrotron yields as high as in nanowire arrays, but that the latter enable a strong emission level to be sustained over a broader range of average plasma density
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Pitsillides, Costas M. 1973. "Selective cell targeting with light-absorbing particles." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/89257.
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Vanderburgh, Richard N. "One-Dimensional Kinetic Particle-In-Cell Simulations of Various Plasma Distributions." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1610313011646245.
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Armiger, Travis J. "Force Propagation in Mammalian Cell Systems and the Relevance of the Mechanically Integrated Cell." Research Showcase @ CMU, 2018. http://repository.cmu.edu/dissertations/1143.
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Mammalian cells are known to respond to both extra- and intra- cellular forces as well as the physical properties of the surrounding tissue. There is increasing evidence to support the fundamental role of force, applied to or generated within cells, in maintaining proper tissue function. The mechanical integration from the exterior of a cell to the interior of the nucleus is crucial for cellular sensing of, and response to, the physical environment. Further, misregulation of this mechanosensitive ability can lead to the development or propagation of many diseases such as cancers, cardiovascular diseases, and tissue fibrosis. In this thesis, we investigate the role of various proteins in regulating the mechanical properties of mammalian cells. We also develop techniques to examine the propagation of forces through cells and multicell systems with the aim of elucidating critical biophysical factors involved in regulating cell function. The idea that the genome can be regulated through changes in forces applied to cells or changes in the propagation of forces through a cell, (i.e. mechanotransduction) is becoming widely accepted. The complex interplay between biochemical and biophysical mechanisms that ultimately control mechanotransduction are beginning to be uncovered; however, a true understanding of this remarkable cellular process has not yet been achieved. By investigating multiple factors which impact mechanosensitivity (such as protein expression, cell-cell and cell-environment connections, cell generated contractions, and physical connections through the cellular interior), we aim to further the understanding of potential pathways of mechanotransduction. Through novel studies and technological advances, the field of cellular biomechanics will continue to grow as we hope to uncover the physical mechanisms that regulate cell function or lead to disease.
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Burger, Marieta. "Production and immunogenicity of chimaeric human papillomavirus-like particle vaccines." Master's thesis, University of Cape Town, 2010. http://hdl.handle.net/11427/12377.
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Includes bibliographical references (leaves 129-146).<br>Human papillomavirus (HPV) infection, specifically with oncogenic types, has been implicated in effectively all cervical cancer cases. Cervical cancer is a global health burden, especially in the developing world. Up to 18 types of HPV are considered oncogenic, of which HPV -16 and -18 cause 70% of cervical cancer cases worldwide. Two vaccines are available on the market:
Gardasil(R), targeted against HPV -16, -18; -6 and -11, and Cervarix(TM), against -16 and -18. Both vaccines are based on the L1 capsid proteins of the types they are targeted to and are efficient, pro- phylactic, typespecific vaccines. However, two problems remain: they do not protect against nonvaccine types, that may cause a significant proportion of cancers specifically in African and HIV- positive populations, and they cannot be used to treat existing infections. We designed eight different chimaeric vaccines.
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Almaghrabi, Mohammednoor Naher. "Flotation of coarse particles in a modified flotation column cell." Thesis, University of Nottingham, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240560.
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Drouin, Mathieu. "Vers la simulation particulaire réaliste de l'interaction laser-plasma surcritique : conception d'un schéma implicite avec amortissement ajustable et fonctions de forme d'ordre élevé." Phd thesis, École normale supérieure de Cachan - ENS Cachan, 2009. http://tel.archives-ouvertes.fr/tel-00442715.
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Le caractère éminemment cinétique et hors équilibre de l'interaction laser-plasma et du transport électronique nécessite de résoudre le système complet des équations de Vlasov-Maxwell. Cette thèse se concentre sur les méthodes PIC (‘‘Particle-In-Cell''), et vise à en accroître le régime de fonctionnement. Tout d'abord, nous présentons l'analyse de stabilité linéaire d'un algorithme PIC explicite incluant l'effet de la discrétisation spatio-temporelle. Cette analyse met en exergue l'instabilité d'aliasing, que nous relions au problème, plus général, du chauffage numérique dans les codes PIC en régime surcritique. Nous montrons l'influence bénéfique de la montée en ordre du facteur de forme pour réduire ce chauffage, permettant ainsi d'atteindre des régimes de densité jusque là inaccessibles. Les codes PIC implicites ne sont pas soumis aux mêmes contraintes de stabilité que leurs équivalents explicites. En particulier nous ne sommes plus tenus de résoudre les modes haute fréquence électroniques. Une telle propriété est particulièrement précieuse lorsqu'on modélise l'interaction entre un laser à ultra-haute intensité et un plasma fortement sur-critique. Nous présentons ici l'extension relativiste de la méthode implicite dite directe, en y incluant un paramètre d'amortissement ajustable et des facteurs de forme d'ordre élevé. Ce formalisme a été implémenté dans le code ELIXIRS, 2D en espace et 3D en vitesse. Ce code est validé sur de nombreux problèmes de physique des plasmas, allant de l'expansion d'un plasma à une ou deux températures électroniques, à l'interaction laser-plasma à haut-flux, en passant par les instabilités ‘‘deux faisceaux'' et de filamentation en régime relativiste. Nous montrons notamment la capacité du code à capturer les principales caractéristiques de l'interaction laser-plasma, malgré une discrétisation spatio-temporelle dégradée, autorisant ainsi des gains substantiels en temps de calcul.
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Gasparin, Pedraza Laia. "Particle in Cell Simulations of Electrostatic Waves in Saturn's Magnetosphere." Thesis, KTH, Rymd- och plasmafysik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-103415.
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The characteristics of electrostatic waves are investigated using PIC simulations of a four component plasma: cool and hot electrons, cool ions and an electron beam. The velocities are de ned by Maxwellian distributions. The system is one dimensional and simulates a collisionless, unmagnetized plasma. Langmuir waves, electron acoustic waves, beam-driven waves and ion acoustic waves are excited in the simulations. The results are analysed using the dispersion relation and compared with previous investigations and analytical results.
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Sáez, Pous Xavier. "Particle-in-cell algorithms for plasma simulations on heterogeneous architectures." Doctoral thesis, Universitat Politècnica de Catalunya, 2016. http://hdl.handle.net/10803/381258.
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During the last two decades, High-Performance Computing (HPC) has grown rapidly in performance by improving single-core processors at the cost of a similar growth in power consumption. The single-core processor improvement has led many scientists to exploit mainly the process level parallelism in their codes. However, the performance of HPC systems is becoming increasingly limited by power consumption and power density, which have become a primary concern for the design of new computer systems. As a result, new supercomputers are designed based on the power efficiency provided by new homogeneous and heterogeneous architectures.
The growth in computational power has introduced a new approach to science, Computational Physics. Its impact on the study of nuclear fusion and plasma physics has been very significant. This is because the experiments are difficult and expensive to perform whereas computer simulations of plasma are an efficient way to progress. Particle-In-Cell (PIC) is one of the most used methods to simulate plasma. The improvement in the processing power has enabled an increase in the size and complexity of the PIC simulations. Most PIC codes have been designed with a strong emphasis on the physics and have traditionally included only process level parallelism. This approach has not taken advantage of multiprocessor platforms. Therefore, these codes exploit inefficiently the new computing platforms and, as a consequence, they are still limited to using simplified models.
The aim of this thesis is to incorporate in a PIC code the latest technologies available in computer science in order to take advantage of the upcoming multiprocessor supercomputers. This will enable an improvement in the simulations, either by introducing more physics in the code or by incorporating more detail to the simulations.
This thesis analyses a PIC code named EUTERPE on different computing platforms. EUTERPE is a production code used to simulate fusion plasma instabilities in fusion reactors. It has been implemented for traditional HPC clusters and it has been parallelized prior to this work using only Message Passing Interface (MPI). Our study of its scalability has reached up to tens of thousands of processors, which is several orders of magnitude higher than the scalability achieved when this thesis was initiated.
This thesis also describes the strategies adopted for porting a PIC code to a multi-core architecture, such as introducing thread level parallelism, distributing the work among different computing devices, and developing a new thread-safe solver. These strategies have been evaluated by applying them to the EUTERPE code. With respect to heterogeneous architectures, it has been possible to port this kind of plasma physics codes by rewriting part of the code or by using a programming model called OmpSs. This programming model is specially designed to make this computing power easily available to scientists without requiring expert knowledge on computing.
Last but not least, this thesis should not be seen as the end of a way, but rather as the beginning of a work to extend the physics simulated in fusion codes through exploiting available HPC resources.<br>Durant les darreres dues dècades, la Computació d'Alt Rendiment (HPC) ha crescut ràpidament en el rendiment mitjançant la millora dels processadors d'un sol nucli a costa d'un creixement similar en el consum d'energia. La millora en els processadors d'un sol nucli ha portat a molts científics a explotar tot el paral·lelisme a nivell de procés en els seus codis. No obstant això, el rendiment dels sistemes HPC està cada cop més limitat pel consum d'energia i la densitat de potència, que s'han convertit en una de les principals preocupacions en el disseny dels nous sistemes informàtics. Com a resultat, els nous supercomputadors estan dissenyats sobre la base de l'eficiència energètica proporcionada per les noves arquitectures homogènies i heterogènies. El creixement de la potència de càlcul ha introduït un nou enfocament a la ciència, la Física Computacional. El seu impacte en l'estudi de la fusió nuclear i la física del plasma ha estat molt significatiu. Això és perquè els experiments són difícils i costosos de realitzar mentre que les simulacions del plasma amb computadors són una manera eficaç de progressar. Particle-In-Cell (PIC) és un dels mètodes més utilitzats per simular el plasma. La millora en la potència de processament ha permès un augment en la grandària i la complexitat de les simulacions PIC. La majoria dels codis PIC s'han dissenyat amb un fort èmfasi en la física i tradicionalment han inclòs només paral·lelisme a nivell de procés. Aquest enfocament no ha aprofitat les plataformes multiprocessador. Per tant, aquests codis exploten ineficientment les noves plataformes de computació i, com a conseqüència, encara estan limitats a tractar amb models simplificats. L'objectiu d'aquesta tesi és incorporar en un codi PIC les últimes tecnologies disponibles en informàtica per tal d'aprofitar els propers supercomputadors multiprocessador. Això permetrà una millora en les simulacions, ja sigui mitjançant la introducció de més física en el codi o mitjançant la incorporació de més detall en les simulacions. Aquesta tesi analitza un codi PIC anomenat EUTERPE en diferents plataformes de computació. EUTERPE és un codi de producció utilitzat per simular les inestabilitats del plasma en els reactors de fusió. S'ha implementat per clústers HPC tradicionals i s'ha paral·lelitzat prèviament a aquest treball usant només la Interfície de Pas de Missatges (MPI). El nostre estudi de la seva escalabilitat ha arribat fins a desenes de milers de processadors, que és diversos ordres de magnitud més gran que l'escalabilitat que s'havia assolit quan es va iniciar aquesta tesi. Aquesta tesi també descriu les estratègies adoptades per portar un codi PIC a una arquitectura multi-nucli, com ara la introducció de paral·lelisme a nivell de thread, la distribució de la feina entre diferents dispositius de computació i el desenvolupament d'un nou solver thread-safe. Aquestes estratègies han estat avaluades amb la seva aplicació al codi EUTERPE. Pel que fa a les arquitectures heterogènies, ha estat possible portar aquest tipus de codis de la física del plasma reescrivint part del codi o mitjançant l'ús d'un model de programació anomenat OmpSs. Aquest model de programació està especialment dissenyat per posar aquesta potència de càlcul a l'abast dels científics sense necessitat de coneixements d'experts en computació. Finalment, però no menys important, aquesta tesi no ha de ser vista com el final d'un camí, sinó més aviat com l'inici d'un treball per estendre la física simulada en els codis de fusió nuclear mitjançant l'explotació dels recursos disponibles de HPC.
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Fuenmayor, Garcés Javier. "Enhancement of virus-like particle production in HEK293 cell cultures." Doctoral thesis, Universitat Autònoma de Barcelona, 2018. http://hdl.handle.net/10803/650410.
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Les virus-like particles (VLP) tenen un gran potencial com a candidats pel
desenvolupament de vacunes. En aquest treball, s’han aplicat diverses estratègies per la
millora de la producció de VLPs (basades en la poliproteïna Gag del VIH-1) en HEK293
mitjançant la transfecció transitòria i l’expressió estable. Aquest candidat té aplicacions
potencials en el desenvolupament d’una vacuna terapèutica contra la SIDA. Tres capítols
del treball descriuen estratègies basades en la transfecció transitòria, mentre que l’últim
capítol consisteix en la generació d’una línea HEK293 estable per la producció de VLPs de
VIH-1.
En el primer capítol, es va dur a terme la combinació de l’estratègia extended gene
expression (EGE) amb la complementació del medi amb additius químics. L’EGE (basada en
la repetició de diversos recanvis de medi i retransfeccions) ha reportat una millora en la
producció de VLPs de 12 cops mentre que la complementació química del medi amb
potenciadors de l’expressió gènica comporta una millora de 4 cops. La combinació de l’EGE
amb additius químics va resultar en una millora de 1.5 cops en la producció de VLPs de VIH-
1 comparat amb l’EGE sola. Com alternativa a l’ús d’additius químics, es va provar
l’expressió de shRNA que produeixin el mateix efecte sobre les cèl·lules. Aquesta estratègia
innovadora va millorar la producció de VLP en 2.3 cops sense cap detriment sobre la
viabilitat cel·lular. Finalment, la combinació dels shRNA amb l’EGE va comportar una millora
en la producció de VLPs de 1.3 cops, comparat amb el protocol tradicional d’EGE.
En el segon capítol de la tesi, es va dur a terme l’escalat a nivell de reactor d’EGE,
obtenint una producció de VLP comparable a l’erlenmeyer. El bioreactor va permetre
l’assoliment de densitats cel·lulars i creixements específics molts més alts. Degut al major
creixement en el bioreactor, el percentatge final de cèl·lules GFP positives era
considerablement menor que a l’erlenmeyer, la qual cosa podria ser millorada ampliant el
nombre de retransfeccions realitzades al cultiu cel·lular. L’anàlisi per quantificació de
nanopartícules va revelar un ratio de VLPs respecte a partícules totals més alt en el cas de
l’erlenmeyer que en el reactor; possiblement degut a les altes densitat cel·lulars del
bioreactor. La metodologia d’EGE va poder ser escala satisfactòriament a nivell de reactor
per primer cop, mantenint les produccions de GagGFP.
En el tercer capítol, es va realitzar l’optimització de les concentracions de DNA i PEI
usades a la transfecció transitòria per a tres línies HEK293 diferents i tres plasmidis
d’expressió. Les concentracions de DNA i PEI optimitzades per a les nou combinacions van ser molt similar per tots el casos; el que ens indica que l’eficiència de transfecció depèn de
la quantitat concreta de DNA i PEI emprada. A més, dues de les tres línies reconeixen
orígens de replicació específics. Els orígens de replicació estan inclosos a les seqüències dels
vectors per tal de provar la seva capacitat d’augmentar la producció de VLPs. El sistema
HEK293E/OriP va ser l’escollit perquè permet una millora de la producció de VLPs de VIH-1
de 3 cops, mantenint les mateixes densitats i viabilitats cel·lulars comparat amb un plasmidi
control.
En l’últim capítol d’aquest treball, es va dur a terme la generació d’una línea estable
de HEK293 per l’expressió de VLPs. Després d’un procés de selecció basat en la producció,
es van seleccionen cinc clons per l’adaptació a suspensió i a medis lliures de sèrum. El clon
10H9 va presentar un temps de duplicació i una densitat cel·lular màxima semblant a la
resta de clons i va assolir una la màxima productivitat específica; per tant, va ser
seleccionat com a productor de VLPs.<br>Virus-like particles (VLP) have a high potential as candidates for vaccine
development. In this work, several strategies are tested for VLP production enhancement in
HEK293 cells by transient gene expression (TGE) and stable gene expression (SGE). The VLP
of interest is based on HIV-1 Gag polyprotein which has potential applications in
therapeutic AIDS vaccine development. Three chapters present strategies based on TGE
while the last chapter consist of the generation of a stable HEK293 cell line for the
production of HIV-1 VLPs.
In the first chapter, the combination of extended gene expression (EGE) strategy
with chemical additives supplementation was tested. EGE (based on repeated medium
exchanges and retransfections) improves VLP production titers in 12-fold while chemical
media supplementation leads to a 4-fold enhancement of VLP titers, despite their effect on
cell viability. The combination of EGE protocol with chemical additives resulted in a 1.5-fold
improvement in production compared with the EGE protocol alone (4.45x1010 VLPs/mL
compared with 2.89x1010 VLPs/mL). As an alternative, the expression of shRNAs that could
provide the same effects was also tested. This novel strategy enhanced VLP production by
2.3 fold without any detrimental effect on cell viability. Finally, the combination of shRNA
with EGE resulted in more than 1.3-fold improvement compared with the EGE protocol
traditionally used.
In the second chapter, the scalability of EGE at bioreactor level was tested and the
VLP production was compared to the results obtained in shake flasks. Cell viability was
comparable between the two systems tested; however, the bioreactor enabled to reach
much higher cell densities and specific growth rates than shake flasks. Due to this increased
cell growth in the bioreactor, the final percentage of GFP-positive cells was considerably
lower than in the shake flasks, which could be improved by performing further
retransfections of the cell culture. GagGFP VLP titers were similar in both shake flasks and
bioreactor. Nanoparticle tracking analysis revealed that the ratio of VLPs/total particles
(VLPs and microvesicles) was higher in the shake flasks than in the bioreactor, possibly due
to higher cell densities achieved in the bioreactor. EGE methodology was successfully
carried out in a bioreactor system for the first time while maintaining GagGFP production
titers.
In the third chapter, DNA and PEI concentration optimization was carried out for
three different HEK293 cell lines (HEK293SF-3F6, T and 6E) and three different expression plasmids (pSV40, p(-), and pOriP)). The concentration of DNA and PEI was optimized for the
nine combinations and the obtained resulted are very similar in all cases (DNA: 2.34 ± 0.18
μg/mL; and PEI: 5.81 ± 0.18 μg/mL), revealing that transfection efficiency was not
dependent on the cell line or vector type. Furthermore, two of the cell lines tested
recognize specific origins of replication: HEK293T/SV40 and HEK293E/oriP. Origins of
replication were included in the vector sequences to test their capacity to increase
production titers. HEK293T/SV40 resulted in a decrease of cell density and productivity of
2.3 fold compared to a control plasmid. On the other hand, HEK293E/OriP platform enabled
a 3-fold improvement in HIV-1 VLP production keeping the same cell densities and
viabilities compared to a control plasmid.
In the last chapter of this work, the generation of a stable HEK293 cell line expressing Gag
VLPs was attempted through a random site integration strategy. After a screening process
based on GagGFP production, five clones were selected for adaptation to suspension and
serum-free conditions. 10H9 clone presents similar duplication time and maximum cell
density than the other clones. Furthermore, 10H9 showed highest GagGFP productivity and
also highest specific productivity and was hence the selected GagGFP producer HEK293
clone.
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Rollié, Sascha [Verfasser]. "Heteroaggregation processes in colloidal particle and cell systems / Sascha Rollié." Aachen : Shaker, 2010. http://d-nb.info/1104048000/34.
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Monnier, Nilah. "Bayesian Inference Approaches for Particle Trajectory Analysis in Cell Biology." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11020.
Full textAbstract:
Despite the importance of single particle motion in biological systems, systematic inference approaches to analyze particle trajectories and evaluate competing motion models are lacking. An automated approach for robust evaluation of motion models that does not require manual intervention is highly desirable to enable analysis of datasets from high-throughput imaging technologies that contain hundreds or thousands of trajectories of biological particles, such as membrane receptors, vesicles, chromosomes or kinetochores, mRNA particles, or whole cells in developing embryos. Bayesian inference is a general theoretical framework for performing such model comparisons that has proven successful in handling noise and experimental limitations in other biological applications. The inherent Bayesian penalty on model complexity, which avoids overfitting, is particularly important for particle trajectory analysis given the highly stochastic nature of particle diffusion. This thesis presents two complementary approaches for analyzing particle motion using Bayesian inference. The first method, MSD-Bayes, discriminates a wide range of motion models--including diffusion, directed motion, anomalous and confined diffusion--based on mean- square displacement analysis of a set of particle trajectories, while the second method, HMM-Bayes, identifies dynamic switching between diffusive and directed motion along individual trajectories using hidden Markov models. These approaches are validated on biological particle trajectory datasets from a wide range of experimental systems, demonstrating their broad applicability to research in cell biology.
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Récamier, Vincent. "Single particle imaging in the cell nucleus : a quantitative approach." Phd thesis, Université René Descartes - Paris V, 2013. http://tel.archives-ouvertes.fr/tel-00998389.
Full textAbstract:
The cell nucleus is a chemical reactor. Nuclear components interact with each other to express genes, duplicate the chromosomes for cell division, and protect DNA from alteration. These reactions are regulated along the cell cycle and in response to stress. One of the fundamental nuclear processes, transcription, enables the production of a messenger RNA from a template DNA sequence. While mandatory for the cell, transcription nevertheless may involve a very small number of molecules. Indeed, a single gene would have only few copies in the genome. During my PhD, I studied nuclear processes in human cells nuclei at the single molecule level with novel imaging techniques. I developed new statistical tools to quantify nuclear components movement that revealed a dynamic nuclear architecture. Since the 90s, simple methods have been developed for the observation of single molecules in the cell. These experiments can be conducted in an ordinary inverted microscope. We used these methods to monitor nuclear molecules called transcription factors (TF) that regulate transcription. From TF dynamics, we concluded that nuclear exploration by transcription factors is regulated by their chemical interactions with partners. The organization of the components of the nucleus guide transcription factors in their search of a gene. As an example of this organization, we then studied chromatin, the de-condensed form of nuclear DNA, proving that it displays the characteristics of a self-organized fractal structure. This structure changes in response to cellular fate and stress. In yeast, we showed that the interminglement of chromatin constrained DNA locus movement in a reptation regime. All these results show the interdependence of the structure of the nucleus and of its chemical reactions. With combination of realistic modeling and high resolution microscopy, we have enlightened the specificity of the nucleus as a chemical reactor. This thesis has also enabled the development of accurate methods for the statistical analysis of single molecule data.
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Dowds, Brendan J. P. "Particle-in-cell simulations of streamer initiation and plasma generation." Thesis, University of Glasgow, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.398637.
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Creusot, Remi Jerome. "Particle-mediated DNA immunisation : CD+T cell priming and cooperation." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399172.
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Fox, Justin M. 1981. "Parallelization of particle-in-cell simulation modeling Hall-effect thrusters." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/28905.
Full textAbstract:
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2005.<br>Includes bibliographical references (p. 136-139).<br>MIT's fully kinetic particle-in-cell Hall thruster simulation is adapted for use on parallel clusters of computers. Significant computational savings are thus realized with a predicted linear speed up efficiency for certain large-scale simulations. The MIT PIC code is further enhanced and updated with the accuracy of the potential solver, in particular, investigated in detail. With parallelization complete, the simulation is used for two novel investigations. The first examines the effect of the Hall parameter profile on simulation results. It is concluded that a constant Hall parameter throughout the entire simulation region does not fully capture the correct physics. In fact, it is found empirically that a Hall parameter structure which is instead peaked in the region of the acceleration chamber obtains much better agreement with experiment. These changes are incorporated into the evolving MIT PIC simulation. The second investigation involves the simulation of a high power, central-cathode thruster currently under development. This thruster presents a unique opportunity to study the efficiency of parallelization on a large scale, high power thruster. Through use of this thruster, we also gain the ability to explicitly simulate the cathode since the thruster was designed with an axial cathode configuration.<br>by Justin M. Fox.<br>S.M.
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Fife, John Michael. "Two-dimensional hybrid particle-in-cell modeling of Hall thrusters." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/11568.
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Kafafy, Raed. "Immersed Finite Element Particle-In-Cell Simulations of Ion Propulsion." Diss., Virginia Tech, 2005. http://hdl.handle.net/10919/29057.
Full textAbstract:
A new particle-in-cell algorithm was developed for plasma simulations involving complex
boundary conditions. The new algorithm is based on the three-dimensional
immersed finite element method which is developed in this thesis, and a modified
legacy particle-in-cell code. The model also applies a new meshing technique that
separates the field solution mesh from the particle pushing mesh in order to increase
the computational eciency of the model.
The new simulation model is used in two applications of great importance to the
development of ion propulsion technology: the ion optics performance and the interaction
between spacecraft and the ion thruster. The first application is ion optics
simulations. Simulations are performed to investigate ion optics plasma flow for a
whole subscale NEXT ion optics. The operating conditions modeled cover the entire
cross-over to perveance limit range. The results of the ion optics simulations
demonstrated good agreement with the available experimental data. The second
application is ion thruster plume simulations. Simulations are performed to investigate
ion thruster plume - spacecraft interactions for the Dawn spacecraft. Plume
induced contaminations on the solar array are studied for a variety of ion thruster
configurations including multiple thruster firings.<br>Ph. D.
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Godar, Trenton J. "Testing of Two Novel Semi-Implicit Particle-In-Cell Techniques." Wright State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=wright1402492857.
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Orlowski, Gregory M. "Cathosis: Cathepsins in Particle-induced Inflammatory Cell Death: A Dissertation." eScholarship@UMMS, 2005. http://escholarship.umassmed.edu/gsbs_diss/770.
Full textAbstract:
Sterile particles underlie the pathogenesis of numerous inflammatory diseases. These diseases can often become chronic and debilitating. Moreover, they are common, and include silicosis (silica), asbestosis (asbestos), gout (monosodium urate), atherosclerosis (cholesterol crystals), and Alzeihmer’s disease (amyloid Aβ). Central to the pathology of these diseases is a repeating cycle of particle-induced cell death and inflammation. Macrophages are the key cellular mediators thought to drive this process, as they are especially sensitive to particle-induced cell death and they are also the dominant producers of the cytokine responsible for much of this inflammation, IL-1β. In response to cytokines or microbial cues, IL-1β is synthesized in an inactive form (pro-IL-1β) and requires an additional signal to be secreted as an active cytokine. Although a multimolecular complex, called the NLRP3 inflammasome, controls the activation/secretion of IL-1β (and has been thought to also control cell death) in response to particles in vitro, the in vivo inflammatory response to particles occurs independently of inflammasomes. Therefore, I sought to better understand the mechanisms governing IL-1β production and cell death in response to particles, focusing specifically on the role of lysosomal cathepsin proteases. Inhibitor studies have suggested that one of these proteases, cathepsin B, plays a role in promoting inflammasome activation subsequent to particle-induced lysosomal damage, however genetic models of cathepsin B deficiency have argued otherwise. Through the use of inhibitors, state-of-the-art biochemical tools, and multi-cathepsin-deficient genetic models, I found that multiple redundant cathepsins promote pro-IL-1β synthesis as well as particle-induced NLRP3 activation and cell death. Importantly, I also found that particle-induced cell death does not depend on inflammasomes, suggesting that this may be why inflammasomes do not contribute to particle-induced inflammation in vivo. Therefore, my observations suggest that cathepsins may be multifaceted therapeutic targets involved in the two key pathological aspects of particle-induced inflammatory disease, IL-1β production and cell death.
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Orlowski, Gregory M. "Cathosis: Cathepsins in Particle-induced Inflammatory Cell Death: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/770.
Full textAbstract:
Sterile particles underlie the pathogenesis of numerous inflammatory diseases. These diseases can often become chronic and debilitating. Moreover, they are common, and include silicosis (silica), asbestosis (asbestos), gout (monosodium urate), atherosclerosis (cholesterol crystals), and Alzeihmer’s disease (amyloid Aβ). Central to the pathology of these diseases is a repeating cycle of particle-induced cell death and inflammation. Macrophages are the key cellular mediators thought to drive this process, as they are especially sensitive to particle-induced cell death and they are also the dominant producers of the cytokine responsible for much of this inflammation, IL-1β. In response to cytokines or microbial cues, IL-1β is synthesized in an inactive form (pro-IL-1β) and requires an additional signal to be secreted as an active cytokine. Although a multimolecular complex, called the NLRP3 inflammasome, controls the activation/secretion of IL-1β (and has been thought to also control cell death) in response to particles in vitro, the in vivo inflammatory response to particles occurs independently of inflammasomes. Therefore, I sought to better understand the mechanisms governing IL-1β production and cell death in response to particles, focusing specifically on the role of lysosomal cathepsin proteases. Inhibitor studies have suggested that one of these proteases, cathepsin B, plays a role in promoting inflammasome activation subsequent to particle-induced lysosomal damage, however genetic models of cathepsin B deficiency have argued otherwise. Through the use of inhibitors, state-of-the-art biochemical tools, and multi-cathepsin-deficient genetic models, I found that multiple redundant cathepsins promote pro-IL-1β synthesis as well as particle-induced NLRP3 activation and cell death. Importantly, I also found that particle-induced cell death does not depend on inflammasomes, suggesting that this may be why inflammasomes do not contribute to particle-induced inflammation in vivo. Therefore, my observations suggest that cathepsins may be multifaceted therapeutic targets involved in the two key pathological aspects of particle-induced inflammatory disease, IL-1β production and cell death.
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Doche, Antoine. "Particle acceleration with beam driven wakefield." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLX023/document.
Full textAbstract:
Les accélérateurs par onde de sillage plasma produites par faisceaux de particules (PWFA) ou par faisceaux laser (LWFA) appartiennent à un nouveau type d’accélérateurs de particules particulièrement prometteur. Ils permettent d’exploiter des champs accélérateurs jusqu’à cent Gigaélectronvolt par mètre alors que les dispositifs conventionnels se limitent à cent Megaélectronvolt par mètre. Dans le schéma d’accélération par onde de sillage plasma, ou par onde de sillage laser, un faisceau de particules ou une impulsion laser se propage dans un plasma et créé une structure accélératrice dans son sillage : c’est une onde de densité électronique à laquelle sont associés des champs électromagnétiques dans le plasma. L’un des principaux résultats de cette thèse a été la démonstration de l’accélération par onde de sillage plasma d’un paquet distinct de positrons. Dans le schéma utilisé, un plasma de Lithium était créé dans un four, et une onde plasma était excitée par un premier paquet de positrons (le drive ou faisceau excitateur) et l’énergie était extraite par un second faisceau (le trailing ou faisceau témoin). Un champ accélérateur de 1,36 GeV/m a ainsi été obtenu durant l’expérience, pour une charge accélérée typique de 40 pC. Nous montrons également ici la possibilité d’utiliser différents régimes d’accélération qui semblent très prometteurs. Par ailleurs, l’accélération de particule par sillage laser permet quant à elle, en partant d’une impulsion laser femtoseconde de produire un faisceau d’électron quasi-monoénergétique d’énergie typique de l’ordre de 200 MeV. Nous présentons les résultats d’une campagne expérimentale d’association de ce schéma d’accélération par sillage laser avec un schéma d’accélération par sillage plasma. Au cours de cette expérience un faisceau d’électrons créé par laser est refocalisé lors d’une interaction dans un second plasma. Une étude des phénomènes associés à cette plateforme hybride LWFA-PWFA est également présentée. Enfin, le schéma hybride LWFA-PWFA est prometteur pour optimiser l’émission de rayonnement X par les électrons du faisceau de particule crée dans l’étage LWFA de la plateforme. Nous présentons dans un dernier temps la première réalisation expérimentale d’un tel schéma et ses résultats prometteurs<br>Plasma wakefield accelerators (PWFA) or laser wakefield accelerators (LWFA) are new technologies of particle accelerators that are particularly promising, as they can provide accelerating fields of hundreds of Gigaelectronvolts per meter while conventional facilities are limited to hundreds of Megaelectronvolts per meter. In the Plasma Wakefield Acceleration scheme (PWFA) and the Laser Wakefield Acceleration scheme (LWFA), a bunch of particles or a laser pulse propagates in a gas, creating an accelerating structure in its wake: an electron density wake associated to electromagnetic fields in the plasma. The main achievement of this thesis is the very first demonstration and experimental study in 2016 of the Plasma Wakefield Acceleration of a distinct positron bunch. In the scheme considered in the experiment, a lithium plasma was created in an oven, and a plasma density wave was excited inside it by a first bunch of positrons (the drive bunch) while the energy deposited in the plasma was extracted by a second bunch (the trailing bunch). An accelerating field of 1.36 GeV/m was reached during the experiment, for a typical accelerated charge of 40 pC. In the present manuscript is also reported the feasibility of several regimes of acceleration, which opens promising prospects for plasma wakefield accelerator staging and future colliders. Furthermore, this thesis also reports the progresses made regarding a new scheme: the use of a LWFA-produced electron beam to drive plasma waves in a gas jet. In this second experimental study, an electron beam created by laser-plasma interaction is refocused by particle bunch-plasma interaction in a second gas jet. A study of the physical phenomena associated to this hybrid LWFA-PWFA platform is reported. Last, the hybrid LWFA-PWFA scheme is also promising in order to enhance the X-ray emission by the LWFA electron beam produced in the first stage of the platform. In the last chapter of this thesis is reported the first experimental realization of this last scheme, and its promising results are discussed
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Hosseini, Amin Seyed Majid. "A particle-based model for computing fluid flows and cell dynamics." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/42186.
Full textAbstract:
The connection between certain human diseases and changes in the mechanical properties of living cells is well established, e.g. in the cases of malaria and cancer. However, the mechanism for the mechanical modifications, which tend to facilitate the pathogenesis of such diseases, is not always clear. For instance, the overall loss of deformability of malaria-infected red blood cells (RBCs) corresponds to a 10-fold increase in the rigidity of the cell membrane. On the other hand, micropipette aspiration has only measured a 3-fold increase in the elastic modulus.
In this thesis, a particle-based model is developed to explore the interplay between the underlying microstructures and the behavior of the cell as a whole. The research consists of three related projects. The first project deals with the long-standing problem of Smoothed Particle Hydrodynamics (SPH) method with open boundaries and solid walls. We propose a "rotational pressure-correction scheme" with a consistent pressure boundary condition that leads to a large improvement in accuracy of calculated pressure and the drag coefficient on solid obstacles. The second and third projects concern developing a 2D and then 3D particle-based model for RBCs to explore the parasite-driven changes in malaria-infected RBCs. In our models the cell membrane is replaced by a set of discrete particles connected by linear or nonlinear springs. In addition, a linear bending elasticity is implemented using the deviation of the local curvature from the innate curvature of the biconcave shape of a resting RBC. The cytoplasm and the external liquid are modelled as homogeneous Newtonian fluids, and discretized by particles as in standard SPH solution of the Navier-Stokes equations. The malaria parasite is modelled as an aggregate of particles constrained to rigid-body motion. We argue that the discrepancy in the estimated elastic modulus of the membrane is caused by the presence of the rigid parasite particles inside infected cells, and have carried out numerical simulations to demonstrate this mechanism. Our three-dimensional simulation of RBC stretching tests by optical tweezers accurately demonstrates the compensating effects between the existence of malaria parasites and the elevated stiffness of the membrane on the overall deformability of infected RBC.
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Coetzee, Corné J. "The modelling of granular flow using the particle-in-cell method /." Link to the online version, 2004. http://hdl.handle.net/10019.1/1334.
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Lawrence-Douglas, Alistair. "Ionisation effects for laser-plasma interactions by particle-in-cell code." Thesis, University of Warwick, 2013. http://wrap.warwick.ac.uk/57465/.
Full textAbstract:
The particle-in-cell code EPOCH was extended to include field and collisional ionisation for use in simulating initially neutral or partially-ionised targets in laser-plasma inter- actions. The means by which particles ionise in the the field of an intense laser was described and physical models were included to determine the instantaneous ionisa- tion rate at particles within the simulation domain for multiphoton, tunnelling, barrier- suppression and electron-impact ionisation. The algorithms used to implement these models were presented and demonstrated to produce the correct ionisation statistics. A scheme allowing for modelling small amounts of ionisation for an arbitrarily low number of superparticles was also presented for comparison and it was shown that for sufficient simulation time the two schemes converge. The three major mechanisms of ionisation in laser-plasma interactions were described as being ionisation-induced defocussing, fast shuttering and ionisation injection. Simulations for these three effects were presented and shown to be in good agreement with theory and experiment. For fast-shuttering, plasma mirrors were simulated using the pulse profile for the Astra Gemini laser at the Central Laser Facility. Rapid switch-on and the theoretical maximum for contrast ratio was observed. For ionisation injection, simulations for laser wakefield acceleration in a helium gas were performed and the accelerated electron population was shown to be greatly increased through use of a 1% nitrogen dopant consistent with the experimental results of McGuffey et al. A study of the laser filamentation instability due to SRS backscatter at the relativistically corrected quarter critical surface (RCQCS) was per- formed in collaboration with C.S. Brady and T.D. Arber at the University of Warwick [1]. It was found that for hydrogen and plastic the instability was unaffected by the in- clusion of ionisation. Further study with argon revealed a attening of the RCQCS and it was demonstrated that for a material with multiple ionisation levels ionising strongly near the self-focussed intensities at the RCQCS, rapid ionisation caused an inversion of the RCQCS that suppressed the filamentation instability.
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Coetzee, Corne J. "The modelling of granular flow using the particle-in-cell method." Thesis, Stellenbosch : University of Stellenbosch, 2004. http://hdl.handle.net/10019.1/1334.
Full textAbstract:
Thesis (PhD (Mechanical and Mechatronic Engineering))--University of Stellenbosch, 2004.<br>Granular flow occurs in a broad spectrum of industrial applications that
range from separation and mixing in the pharmaceutical industry, to grinding
and crushing, blasting, stockpile construction, flow in and from hoppers,
silos, bins, and conveyer belts, agriculture, mining and earthmoving.
Two totally different approaches of modelling granular flow are the Discrete
Element Method (DEM) and continuum methods such as Finite Element
Methods (FEM). Continuum methods can be divided into nonpolar or
classic continuum methods and polar continuum methods. Large displacements
are usually present during granular flow which, without remeshing,
cannot be solved with standard finite element methods due to severe mesh
distortion. The Particle-in-Cell (PIC) method, which is a so-called meshless
method, eliminates this problem since all the state variables are traced by
material points moving through a fixed mesh.
The main goal of this research was to model the flow of noncohesive
granular material in front of flat bulldozer blades and into excavator buckets
using a continuum method. A PIC code was developed to model these processes
under plane strain conditions. A contact model was used to model
Coulomb friction between the material and the bucket/blade. Analytical
solutions, published numerical and experimental results were used to validate
the contact model and to demonstrate the code’s ability to model large
displacements and deformations.
The ability of both DEM and PIC to predict the forces acting on the blade
and bucket and the material flow patterns were demonstrated. Shear bands
that develop during the flow of material were investigated. As part of the
PIC analyses, a comparison between classic continuum and polar continuum
(Cosserat) results were made. This includes mesh size and orientation
dependency, flow patterns and the forces acting on the blade and the
bucket.
It is concluded that the interaction of buckets and blades with granular
materials can successfully be modelled with PIC. In the cases conducted
here, the nonpolar continuum was more accurate than the polar continuum,
but the polar continuum results were less dependent on the mesh
size. The next step would be to apply this technology to solve industrial
problems.
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Payne, Joshua Estes. "Implementation and performance evaluation of a GPU particle-in-cell code." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/76970.
Full textAbstract:
Thesis (S.M. and S.B.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering; and, (S.B.)--Massachusetts Institute of Technology, Dept. of Physics, 2012.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 105-107).<br>In this thesis, I designed and implemented a particle-in-cell (PIC) code on a graphical processing unit (GPU) using NVIDA's Compute Unified Architecture (CUDA). The massively parallel nature of computing on a GPU nessecitated the development of new methods for various steps of the PIC method. I investigated different algorithms and data structures used in the past for GPU PIC codes, as well as developed some of new ones. The results of this research and development were used to implement an efficient multi-GPU version of the 3D3v PIC code SCEPTIC3D. The performance of the SCEPTIC3DGPU code was evaluated and compared to that of the CPU version on two different systems. For test cases with a moderate number of particles per cell, the GPU version of the code was 71x faster than the system with a newer processor, and 160x faster than the older system. These results indicate that SCEPTIC3DCPU can run problems on a modest workstation that previously would have required a large cluster.<br>by Joshua Estes Payne.<br>S.B.<br>S.M.and S.B.
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Beidler, Penh Koetwongjun 1974. "Two dimensional particle-in-cell simulation model for Hall type thrusters." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/9726.
Full textAbstract:
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 1998.<br>Includes bibliographical references (p. 79-80).<br>In this master's thesis, a two-dimensional model of a Hall type thruster, was developed, to include secondary electron emission at the wall, ion recombination at the wall, diffuse reflection for neutrals bouncing off of the wall, wall potential calculation based on the collected wall charge and a steady state non-uniform magnetic field found in Hall thruster configurations. The model used a non-collisional, two dimensional in regular space and three dimensional in phase space, particle-in-cell (PIC) formulation for simulation of the plasma, while a separate model accounted for particle collisions, using Argon-electron elastic, excitation and ionization cross-sections. The collision model used an electron-neutral collision frequency on the same order as the electron plasma frequency, which made the neutral density to be on the order of 1025m- 3 Such a large neutral density implied that ion-neutral interactions, typically neglected in Hall thrusters, must also be taken into account. However, in this simulation they were neglected. Proceeding forward, the simulation size was 50x20 Debye lengths. Cell size was half of the plasma Debye length, in both dimensions. Time step was based on the condition that the electron gyroradius be ten times the Debye length, for a given electron temperature of 10 eV and maximum magnetic field of 0.8 Tesla, which made the electron density to be on the order of 10-2 0m - 3 . Neutral particle injection rate assumed a particle temperature of 1000K. Electron injection rate from the cathode equaled the electron collection rate at the anode. Ion and neutral mass were set to 1000 times that of the electron mass, in an attempt to accelerate plasma phenomena. Simulation of the model proceeded for 50000 iterations or 7.11 x 10- 9 seconds, which was equivalent to three ion passes through the simulation. Results analysis consisted of studying simulation output at different points in time. It was concluded that the simulation here does not simulate an actual Hall thruster, but introduces some computer models for it.<br>by Penh Koetwongjun Beidler.<br>S.M.
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RUSSELL, ALEX. "Modeling Ultrashort Pulse Laser Damage with the Particle in Cell Method." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1552154386797503.
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Vanthieghem, Arno. "Theoretical and numerical studies of relativistic collisionless shock waves." Thesis, Sorbonne université, 2019. http://www.theses.fr/2019SORUS398.
Full textAbstract:
Les ondes de choc relativistes et sans collisions jouent un rôle majeur dans la physique des objets astrophysiques extrêmes, tels que les sursauts gamma, les blazars ou les nébuleuses de vent de pulsar, au sein desquels elles contribuent à la production de distributions non thermiques de particules et rayonnement. Ces ondes de choc résultent de l'interaction, par l'entremise d'une turbulence électromagnétique engendrée par des micro-instabilités, entre un faisceau de particules accélérées par processus de Fermi et le plasma ambiant. La modélisation de leur dynamique constitue un problème complexe, dont le traitement requiert de combiner analyse théorique et simulations numériques de type particle-in-cell (PIC). Après un résumé des concepts et des outils numériques nécessaires à la modélisation du problème, nous étudions l'évolution non-linéaire de l'instabilité de filamentation de courant qui domine la physique du précurseur de tels chocs. Dans un second temps, nous développons un modèle complet de la micro-physique de ces chocs, basé sur la définition d'un référentiel privilégié dans lequel la turbulence est quasi magnétostatique. Ce référentiel nous permet de caractériser le chauffage et le ralentissement du plasma de fond ainsi que la dynamique du faisceau. Pour terminer, nous explorons l'effet d'un éjecta neutronique sur l'évolution du choc avant dans un sursaut gamma. Pour chaque étude, nos prédictions théoriques sont étayées par des simulations PIC de haute résolution<br>Collisionless relativistic shock waves play a major role in extreme astrophysical objects such as gamma-ray bursts, blazars and pulsars wind nebulae, in which they are held responsible for producing nonthermal particle and radiation distributions. Without an external magnetic field, these shocks stem from the interaction, mediated by microinstabilities, of a beam of Fermi-accelerated particles with the ambient plasma. There results an electromagnetic turbulence that scatters both the beam and plasma particles. While the background plasma is mainly slowed down and heated, a fraction of its particles are accelerated to suprathermal energies, thus sustaining the shock wave. Understanding the highly nonlinear physics of such structures requires combining analytical models and large-scale particle-in-cell (PIC) numerical simulations. After a short review of the concepts and numerical techniques used to address the topic, we first examine the evolution of the current filamentation instability, which prevails in the precursor region of initially unmagnetized shocks. We then develop a comprehensive microphysical model of such shocks. To this purpose, we introduce the notion of a preferential frame, in which the microturbulence is quasi-magnetostatic, thus allowing the description of the particle scattering to be greatly simplified. Finally, we analyze the influence of a neutron ejecta propagating upstream of a gamma-ray burst shock. For each study, our model predictions are substantiated by state-of-the-art PIC simulations. particules