Relevant bibliographies by topics / Single Particle Tracking (SPT

Academic literature on the topic 'Single Particle Tracking (SPT'

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Published: 7 July 2024

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Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Journal articles on the topic "Single Particle Tracking (SPT":

1

Hou, Shangguo, Courtney Johnson, and Kevin Welsher. "Real-Time 3D Single Particle Tracking: Towards Active Feedback Single Molecule Spectroscopy in Live Cells." Molecules 24, no. 15 (August 2, 2019): 2826. http://dx.doi.org/10.3390/molecules24152826.

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Single molecule fluorescence spectroscopy has been largely implemented using methods which require tethering of molecules to a substrate in order to make high temporal resolution measurements. However, the act of tethering a molecule requires that the molecule be removed from its environment. This is especially perturbative when measuring biomolecules such as enzymes, which may rely on the non-equilibrium and crowded cellular environment for normal function. A method which may be able to un-tether single molecule fluorescence spectroscopy is real-time 3D single particle tracking (RT-3D-SPT). RT-3D-SPT uses active feedback to effectively lock-on to freely diffusing particles so they can be measured continuously with up to photon-limited temporal resolution over large axial ranges. This review gives an overview of the various active feedback 3D single particle tracking methods, highlighting specialized detection and excitation schemes which enable high-speed real-time tracking. Furthermore, the combination of these active feedback methods with simultaneous live-cell imaging is discussed. Finally, the successes in real-time 3D single molecule tracking (RT-3D-SMT) thus far and the roadmap going forward for this promising family of techniques are discussed.
2

Speckner, Konstantin, and Matthias Weiss. "Single-Particle Tracking Reveals Anti-Persistent Subdiffusion in Cell Extracts." Entropy 23, no. 7 (July 13, 2021): 892. http://dx.doi.org/10.3390/e23070892.

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Single-particle tracking (SPT) has become a powerful tool to quantify transport phenomena in complex media with unprecedented detail. Based on the reconstruction of individual trajectories, a wealth of informative measures become available for each particle, allowing for a detailed comparison with theoretical predictions. While SPT has been used frequently to explore diffusive transport in artificial fluids and inside living cells, intermediate systems, i.e., biochemically active cell extracts, have been studied only sparsely. Extracts derived from the eggs of the clawfrog Xenopus laevis, for example, are known for their ability to support and mimic vital processes of cells, emphasizing the need to explore also the transport phenomena of nano-sized particles in such extracts. Here, we have performed extensive SPT on beads with 20 nm radius in native and chemically treated Xenopus extracts. By analyzing a variety of distinct measures, we show that these beads feature an anti-persistent subdiffusion that is consistent with fractional Brownian motion. Chemical treatments did not grossly alter this finding, suggesting that the high degree of macromolecular crowding in Xenopus extracts equips the fluid with a viscoelastic modulus, hence enforcing particles to perform random walks with a significant anti-persistent memory kernel.
3

Travers, Théo, Vincent G. Colin, Matthieu Loumaigne, Régis Barillé, and Denis Gindre. "Single-Particle Tracking with Scanning Non-Linear Microscopy." Nanomaterials 10, no. 8 (August 3, 2020): 1519. http://dx.doi.org/10.3390/nano10081519.

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This study describes the adaptation of non-linear microscopy for single-particle tracking (SPT), a method commonly used in biology with single-photon fluorescence. Imaging moving objects with non-linear microscopy raises difficulties due to the scanning process of the acquisitions. The interest of the study is based on the balance between all the experimental parameters (objective, resolution, frame rate) which need to be optimized to record long trajectories with the best accuracy and frame rate. To evaluate the performance of the setup for SPT, several basic estimation methods are used and adapted to the new detection process. The covariance-based estimator (CVE) seems to be the best way to evaluate the diffusion coefficient from trajectories using the specific factors of motion blur and localization error.
4

Rose, Katie A., Daeyeon Lee, and Russell J. Composto. "pH-Mediated nanoparticle dynamics in hydrogel nanocomposites." Soft Matter 17, no. 10 (2021): 2765–74. http://dx.doi.org/10.1039/d0sm02213f.

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The effect of static silica particles on the dynamics of quantum dot (QD) nanoparticles grafted with a poly(ethylene glycol) (PEG) brush in hydrogel nanocomposites is investigated using single particle tracking (SPT).
5

Zhong, Yaning, and Gufeng Wang. "Three-Dimensional Single Particle Tracking and Its Applications in Confined Environments." Annual Review of Analytical Chemistry 13, no. 1 (June 12, 2020): 381–403. http://dx.doi.org/10.1146/annurev-anchem-091819-100409.

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Single particle tracking (SPT) has proven to be a powerful technique in studying molecular dynamics in complicated systems. We review its recent development, including three-dimensional (3D) SPT and its applications in probing nanostructures and molecule-surface interactions that are important to analytical chemical processes. Several frequently used 3D SPT techniques are introduced. Especially of interest are those based on point spread function engineering, which are simple in instrumentation and can be easily adapted and used in analytical labs. Corresponding data analysis methods are briefly discussed. We present several important case studies, with a focus on probing mass transport and molecule-surface interactions in confined environments. The presented studies demonstrate the great potential of 3D SPT for understanding fundamental phenomena in confined space, which will enable us to predict basic principles involved in chemical recognition, separation, and analysis, and to optimize mass transport and responses by structural design and optimization.
6

Clarke, David T., and Marisa L. Martin-Fernandez. "A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor." Methods and Protocols 2, no. 1 (January 30, 2019): 12. http://dx.doi.org/10.3390/mps2010012.

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Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
7

Reina, Francesco, John M. A. Wigg, Mariia Dmitrieva, Joël Lefebvre, Jens Rittscher, and Christian Eggeling. "TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data." F1000Research 10 (August 20, 2021): 838. http://dx.doi.org/10.12688/f1000research.54788.1.

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Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox – 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
8

Reina, Francesco, John M. A. Wigg, Mariia Dmitrieva, Bela Vogler, Joël Lefebvre, Jens Rittscher, and Christian Eggeling. "TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data." F1000Research 10 (January 31, 2022): 838. http://dx.doi.org/10.12688/f1000research.54788.2.

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Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox – 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
9

Shin, Kyujin, Yo Song, Yeongchang Goh, and Kang Lee. "Two-Dimensional and Three-Dimensional Single Particle Tracking of Upconverting Nanoparticles in Living Cells." International Journal of Molecular Sciences 20, no. 6 (March 21, 2019): 1424. http://dx.doi.org/10.3390/ijms20061424.

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Lanthanide-doped upconversion nanoparticles (UCNPs) are inorganic nanomaterials in which the lanthanide cations embedded in the host matrix can convert incident near-infrared light to visible or ultraviolet light. These particles are often used for long-term and real-time imaging because they are extremely stable even when subjected to continuous irradiation for a long time. It is now possible to image their movement at the single particle level with a scale of a few nanometers and track their trajectories as a function of time with a scale of a few microseconds. Such UCNP-based single-particle tracking (SPT) technology provides information about the intracellular structures and dynamics in living cells. Thus far, most imaging techniques have been built on fluorescence microscopic techniques (epifluorescence, total internal reflection, etc.). However, two-dimensional (2D) images obtained using these techniques are limited in only being able to visualize those on the focal planes of the objective lens. On the contrary, if three-dimensional (3D) structures and dynamics are known, deeper insights into the biology of the thick cells and tissues can be obtained. In this review, we introduce the status of the fluorescence imaging techniques, discuss the mathematical description of SPT, and outline the past few studies using UCNPs as imaging probes or biologically functionalized carriers.
10

Parrish, Emmabeth, Katie A. Rose, Matteo Cargnello, Christopher B. Murray, Daeyeon Lee, and Russell J. Composto. "Nanoparticle diffusion during gelation of tetra poly(ethylene glycol) provides insight into nanoscale structural evolution." Soft Matter 16, no. 9 (2020): 2256–65. http://dx.doi.org/10.1039/c9sm02192b.

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Single particle tracking (SPT) of PEG grafted nanoparticles (NPs) was used to examine the gelation of tetra poly(ethylene glycol) (TPEG) succinimidyl glutarate (TPEG-SG) and amine (TPEG-A) terminated 4-armed stars.
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Journal articles Dissertations / Theses

Dissertations / Theses on the topic "Single Particle Tracking (SPT":

1

Robson, Alex J. "Single particle tracking as a tool to investigate the dynamics of integrated membrane complexes in vivo." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:7769f80c-a56d-4513-9123-1d65ef8c9911.

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The last decade has seen substantial advances in single-molecule tracking methods with nano-metre level precision. A powerful tool in single-molecule tracking is fluorescence imaging. One particular application, total internal reflection microscopy, can capture biological processes at high contrast video rate imaging at the single-particle level. This thesis presents methodologically novel methods in analysing single particle tracking data. Presented here is an application of a Bayesian statistical approach that can discriminate between the different diffusive modes that appear with the presence of membrane architecture. This algorithm is denoted BARD; a Bayesian Analysis to Ranking Diffusion. These algorithms are applied to a total internal fluorescence microscopy based experimental data of a novel membrane probe in Escherichia coli. This probe is a plasmid expressed, non-native membrane integrating trans-membrane helix and thus acts as an ideal protein based probe under no specific native control. Two experiments were performed using a combination of varying helix probe size and growth temperature experiments effectively altering the transition temperature of the membrane. These data are suggestive of a passive partitioning of the helix protein into mobile and immobile domains that emerge from the underlying phase behaviour of the membrane.
2

Mawoussi, Kodjo. "Effet de l'encombrement des protéines sur la diffusion des lipides et des protéines membranaires." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066541/document.

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La diffusion latérale des lipides et des protéines transmembranaires est essentielle pour les fonctions biologiques. Dans le contexte cellulaire, la fraction surfacique des protéines membranaires est élevée, atteignant environ de 50 à 70% selon le type de membrane. La diffusion se fait donc dans un milieu très encombré. Le but de ce travail est d'étudier in vitro l'effet de l'encombrement des protéines sur la diffusion des protéines et des lipides. Jusqu'à présent, les mesures de diffusion latérale ont généralement été réalisées à faible densité de protéines, et l'effet de l'encombrement des inclusions membranaires ou des protéines membranaires a été peu étudié expérimentalement. Nous avons utilisé une méthode de suivi de particules uniques (SPT) pour suivre les trajectoires de la pompe à protons Bactériorhodopsine (BR) et de lipides marqués avec des quantum dots au bas de vésicules unilamellaires géantes (GUVs) en fonction de la fraction de surface totale (Ф) de BR reconstituée dans la membrane constituée par ailleurs de 1,2-Dioleoyl-sn-glycéro-3-phosphocholine (DOPC)
Lateral diffusion of lipids and transmembrane proteins is essential for biological functions. In the cellular context, the surface fraction of membrane proteins is high, reaching approximately 50 to 70% depending on the membrane type. Therefore, diffusion occurs in a very crowded environment. The aim of this work is to study in vitro the effect of protein crowding on their own diffusion and on those of the surrounding lipids. So far, lateral diffusion measurements generally have been carried out at low protein density, and the effect of proteins crowding has not been much studied experimentally. We used a single particle tracking (SPT) method to track the trajectories of the Bacterorhodopsin (BR) proton pump and of lipids labeled with quantum dots at the bottom of giant unilamellar vesicles (GUVs) as a function of the total surface fraction (Ф) of BR reconstituted in 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane
3

Mereghetti, Alessio. "Performance evaluation of the SPS scraping system in view of the high luminosity LHC." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/performance-evaluation-of-the-sps-scraping-system-in-view-of-the-high-luminosity-lhc(600579c0-0877-415d-bf8d-32896497b5ff).html.

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Injection in the LHC is a delicate moment, since the LHC collimation system cannot offer adequate protection during beam transfer. For this reason, a complex chain of injection protection devices has been put in place. Among them, the SPS scrapers are the multi-turn cleaning system installed in the SPS aimed at halo removal immediately before injection in the LHC. The upgrade in luminosity of the LHC foresees beams brighter than those currently available in machine, posing serious problems to the performance of the existing injection protection systems. In particular, the integrity of beam-intercepting devices is challenged by unprecedented beam parameters, leading to interactions potentially destructive. In this context, a new design of scrapers has been proposed, aimed at improved robustness and performance. This thesis compares the two scraping systems, i.e. the existing one and the one proposed for upgrade. Unlike any other collimation system for regular halo cleaning, both are "fast" systems, characterised by the variation of the relative distance between the beam and the absorbing medium during cleaning, which enhances the challenge on energy deposition values. Assets/liabilities of the two systems are highlighted by means of numerical simulations and discussed, with particular emphasis on energy deposition in the absorbing medium, time evolution of the beam current during scraping and losses in the machine. Advantages of the system proposed for upgrade over the existing one are highlighted. The analysis of the existing system takes into account present operational conditions and addresses the sensitivity to settings previously not considered, updating and extending past studies. The work carried out on the upgraded system represents the first extensive characterisation of a multi-turn cleaning system based on a magnetic bump. Results have been obtained with the Fluka-SixTrack coupling, developed during this PhD activity from its initial version to being a state-of-art tracking tool for cleaning studies in circular machines. Relevant contributions to the development involve the handling of time-varying impact conditions. An extensive benchmark against a test of the scraper blades with beam has been carried out, to verify the reliability of results. Effcts induced in the tested blades confirm the high values of energy deposition predicted by the simulation. Moreover, the comparison with the time profile of the beam intensity measured during scraping allowed the reconstruction of the actual settings of the blades during the test. Finally, the good agreement of the quantitative benchmark against readouts of beam loss monitors finally proves the quality of the analyses and the maturity of the coupling.
4

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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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.

5

Sanamrad, Arash. "Biological Insights from Single-Particle Tracking in Living Cells." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-229342.

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Single-particle tracking is a technique that allows for quantitative analysis of the localization and movement of particles. In this technique, trajectories are constructed by determining and connecting the positions of individual particles from consecutive images. Recent advances have made it possible to track hundreds of particles in an individual cell by labeling the particles of interest with photoactivatable or photoconvertible fluorescent proteins and tracking one or a few at a time. Single-particle tracking can be used to study the diffusion of particles. Here, we use intracellular single-particle tracking and trajectory simulations to study the diffusion of the fluorescent protein mEos2 in living Escherichia coli cells. Our data are consistent with a simple model in which mEos2 diffuses normally at 13 µm2 s−1 in the E. coli cytoplasm. Our approach can be used to study the diffusion of intracellular particles that can be labeled with mEos2 and are present at high copy numbers. Single-particle tracking can also be used to determine whether an individual particle is bound or free if the free particle diffuses significantly faster than its binding targets and remains bound or free for a long time. Here, we use single-particle tracking in living E. coli cells to determine the fractions of free ribosomal subunits, classify individual subunits as free or mRNA-bound, and quantify the degree of exclusion of bound and free subunits separately. We show that, unlike bound subunits, free subunits are not excluded from the nucleoid. This finding strongly suggests that translation of nascent mRNAs can start throughout the nucleoid, which reconciles the spatial separation of DNA and ribosomes with co-transcriptional translation. We also show that, after translation inhibition, free subunit precursors are partially excluded from the compacted nucleoid. This finding indicates that it is active translation that normally allows ribosomal subunits to assemble on nascent mRNAs throughout the nucleoid and that the effects of translation inhibitors are enhanced by the limited access of ribosomal subunits to nascent mRNAs in the compacted nucleoid.
6

Guerrier, Mark Paul. "The development and evaluation of phosphorescent particle tracking." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324887.

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Woringer, Maxime. "Tools to analyze single-particle tracking data in mammalian cells." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS419.

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Ce travail présente des outils pour analyser la régulation de la transcription dans les cellules eucaryotes, en particulier pour le suivi de facteurs de transcription (TF) individuels dans les cellules de mammifères. Un noyau de cellule eucaryote est complexe et contient de nombreuses molécules (ADN, ARN, protéines, ATP, etc). Ces molécules interagissent avec des TF et influencent la transcription. Certaines de ces interactions peuvent être étudiées par des techniques de biochimie. La plupart, en particulier les interactions faibles, non covalentes, sont invisibles par ces méthodes. La microscopie de cellules vivantes et le suivi de molécules uniques (SPT en anglais) sont de plus en plus utilisées pour étudier ces phénomènes. L'inférence des paramètres biophysiques d'un facteur de transcription, par exemple son coefficient de diffusion, son nombre de sous-populations ou son temps de résidence sur l'ADN sont cruciaux pour comprendre sa dynamique et son influence sur la transcription. Des outils validés et précis sont donc nécessaires pour analyser les données de SPT. Pour être utile, un outil de SPT doit être non seulement validé, mais aussi accessible à des non-programmeurs. Ils doivent aussi tenir compte des biais expérimentaux présents dans les données. Nous proposons un outil d'analyse de SPT, qui se fonde sur l'estimation du propagateur de la diffusion. Ce outil a été validé et est accessible par une interface web. Nous avons montré qu'il donne des résultats proches de l'état de l'art. Il a été testé dans deux cadres : (1) l'étude de la diffusion augmentée par la catalyse enzymatique in vitro et (2) l'analyse de la dynamique du TF c-Myc dans des cellules de mammifères
This work aims at providing tools to dissect the regulation of transcription in eukaryotic cells, with a focus on single-particle tracking of transcription factors in mammalian cells. The nucleus of an eukeryotic cell is an extremely complex medium, that contains a high concentration of macromolecules (DNA, RNA, proteins) and other small molecules (ATP, etc). How these molecules interact with transcription factors, and thus influence transcription rates is an area of intense investigations. Although some of these interactions can be captured by regular biochemistry, many of them, including weak, non-covalent interactions remain undetected by these methods. Live-cell imaging and single-particle tracking (SPT) techniques are increasingly used to characterize such effects. The inference of biophysical parameters of a given transcription factor (TF), such as its diffusion constant, the number of subpopulations or its residence time on DNA, are crucial to understanding how TF dynamics and transcription intertwine. Accurate and validated SPT analysis tools are needed. To be used by the community, SPT tools should not only be carefully validated, but also be easily accessible to non-programmers. They should also be designed to take into account known biases of the imaging techniques. In this work, we first propose a tool, accessible through a web interface, based on the modeling of the diffusion propagator. We validate it extensively and show that it exhibits state-of-the art performance. We apply this tool to two experimental settings: (1) the study of catalysis-enhanced diffusion in-vitro and (2) the analysis of the dynamics of the c-Myc transcription factor in mammalian cells
8

Piette, Nathalie. "Micropatterning subcellulaire pour étudier la connectivité neuronale." Electronic Thesis or Diss., Bordeaux, 2024. http://www.theses.fr/2024BORD0034.

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L'impression protéique a initialement été utilisée pour reproduire et comprendre l’influence de la matrice extracellulaire sur les cellules et certains de leurs composants. Au cours de la dernière décennie, l'impression subcellulaire s’est développée, permettant d’étudier les interactions protéiques et leur rôle dans les voies de signalisation ainsi que dans la formation de synapses, immunologiques ou neuronales.La connexion synaptique est médiée par les protéines d’adhésion synaptique présentes de chaque côté de la synapse. En raison de la complexité de l’environnement synaptique mais également du manque de modèle in vitro permettant d’étudier la connexion synaptique dans un environnement biomimétique et contrôlé, les rôles exacts de ces protéines dans la synaptogénèse restent encore incertains. L’impression protéique subcellulaire est une solution potentielle pour combler ce manque. Pour cela, nous avons développé deux modèles biomimétiques basés sur l’impression protéique : un premier, utilisant des cellules hétérologues, permettant d’obtenir des informations sur la cinétique d’interaction des couples protéiques et ainsi de lier cela à leur fonction potentielle. Et un deuxième, utilisant des neurones primaires hippocampique, permettant de former des synapses artificielles pour étudier la nano-organisation de la synapse au cours du développement.Le système d’impression protéique PRIMO, commercialisé par Alvéole, qui co-finance cette thèse, est peu utilisé par les neuroscientifiques. En plus des objectifs biologiques, l'objectif industriel de cette thèse est de développer des méthodologies et des preuves de concept afin de démontrer les avantages et la faisabilité de la technologie PRIMO en neuroscience.En couplant notre premier modèle avec des techniques d’imagerie sur cellules vivantes (sptPALM et FRAP), nous avons pu différencier des cinétiques d’interaction entre différents couples de protéines d’adhésion synaptique mais également pour des interactions avec des protéines d’échafaudage. Une interaction labile pour SynCAM1, qui est connue pour son rôle dans la morphologie synaptique. Une forte et stable interaction pour Neuroligine1- Neurexine1β, due à la dimérisation de Neuroligine1, qui est indispensable pour la fonctionnalité de la synapse.Avec le second modèle, nous avons démontré, en présence de LRRTM2, la formation spécifique de synapses artificielles. Ces hémi-synapses présentent des caractéristiques morphologiques et fonctionnelles proches de synapses natives, avec la présence de vésicules et d’une activité calcique spontanée. Cependant, nous n’avons pas réussi à former de postsynapses artificielles avec Neurexine1β. Basés sur nos observations et une analyse bibliographique, nous avons formulé l’hypothèse que la postsynapse pourrait être le compartiment initiateur de la synaptogenèse.En conclusion, cette étude démontre : (1) que l’impression subcellulaire est un excellent modèle pour étudier la connectivité synaptique et l’adhésion de manière générale, aussi bien d’un point de vue fonctionnel qu’organisationnel. (2) Que les modèles d’hémi-synapses utilisant l’impression protéique sont plus spécifiques que les anciens modèles. (3) Que le système PRIMO ouvre de nombreuses perspectives en neurosciences via ses capacités d’impressions quantitatives
Micropatterning was initially employed to replicate and understand the influence of the extracellular matrix on cells and some of their components. Over the past decade, subcellular printing has emerged, enabling the study of protein interactions and their role in signaling pathways as well as in the formation of synaptic, immunological, or neuronal pathways.The synaptic connection is mediated by synaptic adhesion proteins present on each side of the synapse. Due to the complexity of the synaptic environment and the lack of in vitro models to study synaptic connection in a biomimetic and controlled environment, the exact roles of these proteins in synaptogenesis remain uncertain. Subcellular protein printing presents a potential solution to address this gap. For this purpose, we have developed two biomimetic models based on protein printing: a first one using heterologous cells, providing insights into the interaction kinetics of protein pairs and linking them to their potential function. And a second one using primary neurons, allowing the formation of artificial synapses to study synaptic nano-organization during development.The protein printing system PRIMO, commercialized by Alvéole, which is co-funding this thesis, is underutilized by neuroscientists. Besides these biological objectives, the industrial aim of this thesis is to develop methodologies and proofs of concept to demonstrate the advantages and feasibility of the PRIMO technology in neuroscience.By coupling our first model, based on heterologous cells, with live-cell imaging techniques (sptPALM and FRAP), we differentiated interaction kinetics among various synaptic adhesion protein pairs and also for interactions with scaffold proteins. A labile interaction was observed for SynCAM1, known for its role in synaptic morphology. A strong and stable interaction was evident for Neuroligin1/Neurexine1β due to Neuroligin1's dimerization, which is essential for synaptic functionality.With the second model using primary hippocampal neurons, we demonstrated, in the presence of LRRTM2, the specific formation of artificial synapses. These hemi-synapses exhibited morphological and functional characteristics close to native synapses, including the presence of vesicles and spontaneous calcium activity. However, we were unable to form artificial postsynapses with Neurexine1β. Based on our observations and bibliographic analysis, we hypothesize that the postsynapse could be the initiating compartment for synaptogenesis.In conclusion, this study demonstrates: (1) that subcellular printing is an excellent model to study synaptic connectivity and adhesion from both a functional and organizational perspective. (2) That models of hemi-synapses using micropatterning are more specific than previous models. (3) That the PRIMO system opens numerous perspectives in neuroscience through its quantitative printing capabilities
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Naeem, Asad. "Single and multiple target tracking via hybrid mean shift/particle filter algorithms." Thesis, University of Nottingham, 2010. http://eprints.nottingham.ac.uk/12699/.

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This thesis is concerned with single and multiple target visual tracking algorithms and their application in the real world. While they are both powerful and general, one of the main challenges of tracking using particle filter-based algorithms is to manage the particle spread. Too wide a spread leads to dispersal of particles onto clutter, but limited spread may lead to difficulty when fast-moving objects and/or high-speed camera motion throw trackers away from their target(s). This thesis addresses the particle spread management problem. Three novel tracking algorithms are presented, each of which combines particle filtering and Kernel Mean Shift methods to produce more robust and accurate tracking. The first single target tracking algorithm, the Structured Octal Kernel Filter (SOK), combines Mean Shift (Comaniciu et al 2003) and Condensation (Isard and Blake 1998a). The spread of the particle set is handled by structurally placing the particles around the object, using eight particles arranged to cover the maximum area. Mean Shift is then applied to each particle to seek the global maxima. In effect, SOK uses intelligent switching between Mean Shift and particle filtering based on a confidence level. Though effective, it requires a threshold to be set and performs a somewhat inflexible search. The second single target tracking algorithm, the Kernel Annealed Mean Shift tracker (KAMS), uses an annealed particle filter (Deutscher et al 2000), but introduces a Mean Shift step to control particle spread. As a result, higher accuracy and robustness are achieved using fewer particles and annealing levels. Finally, KAMS is extended to create a multi-object tracking algorithm (MKAMS) by introducing an interaction filter to handle object collisions and occlusions. All three algorithms are compared experimentally with existing single/multiple object tracking algorithms. The evaluation procedure compares competing algorithms' robustness, accuracy and computational cost using both numerical measures and a novel application of McNemar's statistic. Results are presented on a wide variety of artificial and real image sequences.
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Zelman-Femiak, Monika [Verfasser], and Gregory [Akademischer Betreuer] Harms. "Single Particle Tracking ; Membrane Receptor Dynamics / Monika Zelman-Femiak. Betreuer: Gregory Harms." Würzburg : Universitätsbibliothek der Universität Würzburg, 2012. http://d-nb.info/1026414768/34.

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Books on the topic "Single Particle Tracking (SPT":

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Braüchle, Christoph, Don C. Lamb, and Michaelis Jens. Single particle tracking and single molecule energy transfer. Weinheim: Wiley-VCH, 2010.

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Walter, Nils G. Single molecule tools: Super-resolution, particle tracking, multiparameter and force based methods. San Diego, CA: Academic Press/Elsevier, 2010.

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Bräuchle, Christoph, Don C. Lamb, and Jens Michaelis, eds. Single Particle Tracking and Single Molecule Energy Transfer. Wiley, 2009. http://dx.doi.org/10.1002/9783527628360.

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Michaelis, Jens, Christoph Bräuchle, Don Carroll Lamb, and Christoph Bräuchle. Single Particle Tracking and Single Molecule Energy Transfer. Wiley & Sons, Limited, John, 2009.

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Recent Advances in Single-Particle Tracking: Experiment and Analysis. MDPI, 2022. http://dx.doi.org/10.3390/books978-3-0365-3486-2.

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Single Molecule Tools, Part B:Super-Resolution, Particle Tracking, Multiparameter, and Force Based Methods. Elsevier, 2010. http://dx.doi.org/10.1016/c2009-0-62452-1.

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Furst, Eric M., and Todd M. Squires. Light scattering microrheology. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199655205.003.0005.

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The fundamentals and best practices of passive microrheology using dynamic light scattering and diffusing wave spectroscopy are discussed. The principles of light scattering are introduced and applied in both the single and multiple scattering regimes, including derivations of the light and field autocorrelation functions. Applications to high-frequency microrheology and polymer dynamics are presented, including inertial corrections. Methods to treat gels and other non-ergodic samples, including multi-speckle and optical mixing designs are discussed. Dynamic light scattering (DLS) is a well established method for measuring the motion of colloids, proteins and macromolecules. Light scattering has several advantages for microrheology, especially given the availability of commercial instruments, the relatively large sample volumes that average over many probes, and the sensitivity of the measurement to small particle displacements, which can extend the range of length and timescales probed beyond those typically accessed by the methods of multiple particle tracking and bulk rheology.

Book chapters on the topic "Single Particle Tracking (SPT":

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Récamier, Vincent. "Intra-Nuclear Single-Particle Tracking (I-SPT) to Reveal the Functional Architecture of Chromosomes." In Methods in Molecular Biology, 265–74. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3631-1_18.

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Saxton, Michael J. "Single Particle Tracking." In Fundamental Concepts in Biophysics, 1–33. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-397-4_6.

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Sanamrad, Arash, and Johan Elf. "Single-Particle Tracking." In Encyclopedia of Biophysics, 2355–58. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_487.

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Deschout, Hendrik, and Kevin Braeckmans. "Single Particle Tracking." In Encyclopedia of Biophysics, 2326–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_821.

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Yildiz, Ahmet. "Single-Molecule Fluorescent Particle Tracking." In Handbook of Single-Molecule Biophysics, 1–18. New York, NY: Springer US, 2009. http://dx.doi.org/10.1007/978-0-387-76497-9_1.

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Wasim, Laabiah, and Bebhinn Treanor. "Single-Particle Tracking of Cell Surface Proteins." In Methods in Molecular Biology, 183–92. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7474-0_13.

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Tinevez, Jean-Yves, and Sébastien Herbert. "The NEMO Dots Assembly: Single-Particle Tracking and Analysis." In Bioimage Data Analysis Workflows, 67–96. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-22386-1_4.

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Costello, Deirdre A., and Susan Daniel. "Single Particle Tracking Assay to Study Coronavirus Membrane Fusion." In Coronaviruses, 183–94. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2438-7_16.

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Zhang, Xiaowei, Wei Li, and Zongqiang Cui. "Single-Particle Tracking of Virus Entry in Live Cells." In Subcellular Biochemistry, 153–68. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-40086-5_5.

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Chen, Kuangcai, Xiaodong Cheng, and Ning Fang. "Instrumental Design for Five-Dimensional Single-Particle Rotational Tracking." In Biomotors and their Nanobiotechnology Applications, 257–63. Boca Raton: CRC Press, 2023. http://dx.doi.org/10.1201/9780429203367-24.

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Conference papers on the topic "Single Particle Tracking (SPT":

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Cardwell, Nicholas D., and Pavlos P. Vlachos. "A Multi-Parametric Particle Pairing Algorithm for Particle Tracking Velocimetry in Single and Multiphase Flows." In ASME-JSME-KSME 2011 Joint Fluids Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/ajk2011-31023.

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The measurement of turbulent flows becomes problematic when considering a dispersed multiphase flow, which typically requires special techniques focusing on the simultaneous resolution of both the carrier and discrete phases present in the flowfield. The method presented in this paper, a multi-parametric particle pairing algorithm for particle tracking velocimetry (MP3-PTV), provides a powerful and flexible technique for the measurement of multiphase flows. Combined with a traditional Particle Image Velocimetry (PIV) system, the MP3-PTV employs a variable pair-matching algorithm which utilizes displacement preconditioning in combination with estimated particle size and intensity to match particle pairs between successive images. To improve the method’s efficiency, a new particle identification and segmentation routine was also developed. Validation of the new method was performed on two artificial data sets: a traditional single-phase flow published by the Visualization Society of Japan (VSJ) and an in-house generated multiphase flow having a bi-modal distribution of particles diameters. On the VSJ data set, the newly presented segmentation routine delivered a two-fold increase in identifying particles compared to other published methods. For the simulated multiphase flow data set, measurement efficiency of the dispersed phase improved from 9% to 41% for MP3-PTV as compared to traditional hybrid PTV.
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Lee, Yerim, Kai Tao, Carey Phelps, Tao Huang, Barmak Mostofian, Daniel Zuckerman, and Xiaolin Nan. "Probing the spatiotemporal dynamics of Ras-associated membrane nanodomains with high-throughput single particle tracking via photoactivated localization microscopy (spt-PALM)." In High-Speed Biomedical Imaging and Spectroscopy V, edited by Keisuke Goda and Kevin K. Tsia. SPIE, 2020. http://dx.doi.org/10.1117/12.2547699.

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Hu, Y. Thomas, HsinChen Chung, and Maxey Jason. "What is More Important for Proppant Transport, Viscosity or Elasticity?" In SPE Hydraulic Fracturing Technology Conference. SPE, 2015. http://dx.doi.org/10.2118/spe-173339-ms.

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Abstract The contributions of viscosity and elasticity to inhibiting proppant settling in gelled fracturing fluids are quantified and decoupled in this study. The settling velocity of a single particle under orthogonal shear flow was measured in a transparent Couette flow cell using automatic particle tracking, and the local flow field was mapped using particle tracking velocimetry. The settling behavior is correlated with the rheological properties of the fluids. In carboxymethyl hydroxypropyl guar (CMHPG) crosslinked with borate, particle settling slows as the orthogonal shear rate increases, with settling essentially stopping at sufficiently high shear rates. The authors propose that there are two primary mechanisms for the enhanced particle suspending under the orthogonal shear—shear thickening and elastic lifting. The relative importance of the two factors depends on the shear rate and fluid relaxation time. Specifically, the ratio of the elastic and viscous contribution to particle suspension is γe/v=0.5cλN1(γ˙)η(γ˙), where c is a constant, λ is the stress relaxation time, N1(γ˙)) is the first normal stress difference that depends on the shear rate γ˙, and η(η(γ˙)) is the viscosity. For the crosslinked CMHPG gel examined in this work, it is determined that γe/v=0.26γ˙2, indicating that the viscosity is more important at γ⋅<2s−1, whereas the elasticity becomes dominant at γ˙<2 s−1 for proppant suspending. For the uncrosslinked CMHPG, γe/v=0.0035γ˙1.3 , indicating that the elastic contribution becomes more important than the viscous contribution only at shear rates > 80 s−1. The understanding of the relative importance of viscosity and elasticity can provide guidance for chemists to develop better fracturing fluids and for engineers to model proppant transport
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Braun, S., C. Höfler, R. Koch, and H. J. Bauer. "Modeling Fuel Injection in Gas Turbines Using the Meshless Smoothed Particle Hydrodynamics Method." In ASME Turbo Expo 2013: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/gt2013-94027.

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For predicting primary atomization a numerical code has been developed based on the Lagrangian Smoothed Particle Hydrodynamics (SPH) method. The advantage of this approach is the inherent interface advection. In contrast to commonly used grid based methods such as the Volume of Fluid (VoF) or Level Set method there is no need for costly and approximative interface tracking or reconstruction techniques which are required to avoid interface diffusion. It has been demonstrated by various test cases that the SPH method is capable to correctly predict single — as well as multiphase flows including the effect of surface tension. The goal of this work is to further develop the methodology with the intention to simulate primary atomization within airblast atomizers of jet engines. The authors present two test cases relevant for the simulation of primary atomization. The shear-driven deformation of a fuel droplet in a gaseous flow has been investigated and compared to data from literature. Moreover, the liquid film disintegration at the trailing edge of a planar prefilming airblast atomizer has been studied. The geometry has been derived from an existing test rig, where extensive experimental data have been acquired. Resulting droplet sizes and shear-off frequencies for different geometrical setups have been analyzed and compared to the experiment. The results reveal the promising performance of this new method for predicting primary atomization.
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Puduppakkam, Karthik V., Abhijit U. Modak, Chitralkumar V. Naik, Joaquin Camacho, Hai Wang, and Ellen Meeks. "A Soot Chemistry Model That Captures Fuel Effects." In ASME Turbo Expo 2014: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/gt2014-27123.

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A detailed chemistry model is necessary to simulate the effects of variations in fuel composition on soot emissions. In this work, we have developed a detailed chemistry model for the soot formation and oxidation chemistry, with a focus on the surface kinetics of the soot-particle. The model has been compared to a unique set of soot particle-size data measured in flames for several single-component fuels. Fuel components used in the experiments represent the chemical classes found in jet, gasoline, and diesel fuels, including n-heptane (representative of n-alkanes) and toluene (aromatic). Measurements were taken in burner-stabilized stagnation-flame (BSSF) experiments, which can be simulated well using the 1-dimensional BSSF flame model in CHEMKIN-PRO. Soot volume fraction and particle size distributions are modeled using the sectional method option for Particle Tracking, within CHEMKIN-PRO software. The well-characterized flow of the BSSF experiments allows the modeling to focus on the kinetics. Validated detailed reaction mechanisms for fuel combustion and PAH production, combined with the new soot surface-kinetics mechanism, were used in the simulations. Simulation results were compared to measurements for both particle size distributions and total soot volume fraction. Observed effects of fuel, temperature, pressure, equivalence ratio and residence time on the soot size distribution shape and soot quantity were reproduced by the model. The chemistry in the soot surface model includes particle nucleation, growth through the HACA (hydrogen-abstraction/carbon-addition) and PAH-condensation (polycyclic aromatic hydrocarbons) pathways, as well as soot-oxidation pathways. In addition to soot chemistry, the physics of particle coagulation and aggregation were included in the model. The results demonstrate the ability of well-validated chemistry to predict both dramatic and subtle effects related to soot mass and soot particle size.
6

Chang, Ai-Tang, Yi-Ren Chang, Sien Chi, and Long Hsu. "The single particle tracking system." In SPIE NanoScience + Engineering, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2010. http://dx.doi.org/10.1117/12.860934.

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Su, Di, Ronghui Ma, and Liang Zhu. "Multiscale Simulation of Nanoparticle Transport and Deposition in Fiber Matrix During a Nanofluid Filtration Process." In ASME 2009 Heat Transfer Summer Conference collocated with the InterPACK09 and 3rd Energy Sustainability Conferences. ASMEDC, 2009. http://dx.doi.org/10.1115/ht2009-88621.

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A multiscale model is developed to simulate filtration process for the fabrication of composite material with nanoparticle additives. The model consists of two components. One is a particle trajectory tracking model (PTTM) which can predict the deposition rate of nanoparticle on the fiber matrix in a single pore structure, and the other one is a macroscale transport model of fluid flow in porous fiber structures. The flow of the fluid in the porous media with a free moving surface is solved by using the meshless SPH method. The integrated model is used to predict the local deposition rate coefficient and the distribution of the nanoparticle concentration in the carrier fluid and on the fiber surface. We envision this as the first step of a systematic study towards to an advanced understanding of the process as well as the optimization of the operational parameters for achieving homogeneous material properties of the materials.
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Hoefler, C., S. Braun, R. Koch, and H. J. Bauer. "Modeling Spray Formation in Gas Turbines: A New Meshless Approach." In ASME Turbo Expo 2012: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/gt2012-68489.

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A new meshless Lagrangian particle code has been developed in order to tackle the challenging numerical modeling of primary atomization. In doing so the correct treatment and representation of the interfacial physics are crucial prerequisites. Grid based codes using interface tracking or interface capturing techniques, such as the Volume of Fluid or Level Set method, exhibit some difficulties regarding mass conservation, curvature capturing and interface diffusion. The objective of this work is to overcome these shortcomings of common state-of-the-art grid based FVM approaches. Our multi-dimensional meshless particle code is based on the Smoothed Particle Hydrodynamics method [1] [2]. Various test cases have been conducted, by which the capability of accurately capturing the physics of single and multiphase flows is verified and the future potential of this approach is demonstrated. Compressible as well as incompresssible fluids can be modeled. Surface tension effects are taken into account by two different models, one of them being more suitable for free surface flows and the other for simulating multiphase flows. Solid walls as well as periodic boundary conditions offer a broad variety of numerically modeling technical applications. In a first step, single phase calculations of shear driven liquid flows have been carried out. Furthermore, the disintegration of a gravity driven liquid jet emerging from a generic nozzle has been investigated in free surface simulations. The typical formation of a meniscus due to surface tension is observed. Spray formation is qualitatively in good agreement compared to experiments. Surface tension effects have been taken into account via the cohesive force model. Finally, the results of a two-phase simulation with a fluid density ratio of 1000, which is similar to a fuel-air fluid system as in airblast atomizers, are presented. The surface minimization and pressure jump across the droplet interface due to surface tension can be predicted accurately. The test cases conducted so far demonstrate the accuracy of the existing code and underline the promising potential of this new method for successfully predicting primary atomization.
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Sokolov, Igor, Ariel Lubelski, and Joseph Klafter. "Nonergodicity mimicking inhomogeneity in single particle tracking." In 3rd International ICST Conference on Performance Evaluation Methodologies and Tools. ICST, 2008. http://dx.doi.org/10.4108/icst.valuetools.2008.50.

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So, Peter T. C., Timothy Ragan, Enrico Gratton, Jenny Carerro, and Edward Voss. "Two-photon single particle tracking in 3D." In BiOS '97, Part of Photonics West, edited by Daniel L. Farkas and Bruce J. Tromberg. SPIE, 1997. http://dx.doi.org/10.1117/12.274323.

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Reports on the topic "Single Particle Tracking (SPT":

1

Gu, Yan. Principles and biophysical applications of single particle super-localization and rotational tracking. Office of Scientific and Technical Information (OSTI), January 2013. http://dx.doi.org/10.2172/1116711.

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Chen, Kuangcai. Development and applications of single particle orientation and rotational tracking in dynamic systems. Office of Scientific and Technical Information (OSTI), February 2016. http://dx.doi.org/10.2172/1342544.

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Sun, Wei. Developing new optical imaging techniques for single particle and molecule tracking in live cells. Office of Scientific and Technical Information (OSTI), January 2010. http://dx.doi.org/10.2172/1037983.

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Noll, Daniel, and Giulio Stancari. Field calculations, single-particle tracking, and beam dynamics with space charge in the electron lens for the Fermilab Integrable Optics Test Accelerator. Office of Scientific and Technical Information (OSTI), November 2015. http://dx.doi.org/10.2172/1230044.

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