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Cabello-Aguilar, Simon. "Lecture de macromolécules par translocation au travers d'un nanopore unique." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20242.
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La translocation de macromolécules au travers d'un nanopore unique est utilisée dans un but de détection et d'identification. Au cours de ces travaux de thèse, un dispositif expérimental, permettant la mesure du courant ionique dans les nanopores de façon optimisée, a été mis en place. Nous avons développé des programmes qui permettent le filtrage du courant mesuré et l'analyse des signaux de translocation. Nous avons fabriqué des nanopores uniques de haut rapport d'aspect avec, un diamètre ajusté au nanomètre près, et à l'état de surface contrôlé, grâce à la combinaison de techniques d'attaque de trace et de dépôt de couches atomiques. A l'aide du dispositif expérimental fabriqué nous avons effectué des mesures de courant ionique dans les nanopores à différentes échelles (autour de 100 nm et en dessous de 10 nm), en utilisant des systèmes différents (solides et hybrides) en présence de macromolécules ou pas. L'interprétation et l'analyse des signaux de courant résultant nous ont permis de mettre en évidence l'importance (i) de l'état de surface du nanopore aussi bien pour le transport des ions au travers du pore que pour leur entrée (ii) et des interactions des ions organisés autour des molécules en translocation avec les ions organisés dans le pore particulièrement lorsque son diamètre est faible (< 10 nm). L'étude de la translocation des polynucléotides au travers d'un nanopore hybride nous a permis de montrer qu'une protéine complexe peut préserver ses propriétés biologiques dans un nanopore solide si son diamètre est proche du diamètre extérieur de la protéine et son état de surface est semblable au milieu dans lequel évolue la protéineThe translocation of macromolecules through a single nanopore is used for purposes of detection and identification. During this thesis, an experimental set-up for ionic current recording in nanopores has been created. We have developed programs that allow filtering of the measured current and signal analysis. We have made high aspect ratio single nanopores with a diameter adjusted at the nanometer scale, and a controlled surface state by using a combination of track-etching and atomic layer deposition techniques. Using the experimental device created we performed measurements of ionic current through the nanopores at different scales (around 100 nm and below 10 nm), using different systems (solid and hybrid) and in the presence of macromolecules or not. The interpretation and analysis of translocation signals allowed us to highlight the importance of (i) the surface state of the nanopore for both the transport of ions through the pore and their entry (ii) and the interactions of the ions organized around the translocating molecule with the ions organized in the nanopore (in particular when the pore diameter is below 10 nm). The study of the translocation of polynucleotides through a hybrid nanopore showed that a complex protein can preserve its biological properties in a solid nanopore if its diameter is close to the outer diameter of the protein and its surface state is similar to the biological environment of the protein
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Lepoitevin, Mathilde P. "Conception d'un nanopore unique pour mimer un canal biologique et pour la détection de bio-macromolécules." Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT226/document.
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Un nanopore artificiel est une ouverture de taille nanométrique faite dans un film mince synthétique (polymère ou inorganique). Un nanopore unique peut être considéré comme l’élément simple constitutif d’une membrane. Les récentes avancées dans ce domaine ont ouvert des opportunités pour développer des outils pour la détection de molécules cibles à faible concentration (fmol L-1), en temps réel. Les nanopores artificiels s’inspirent des canaux biologiques situés dans la membrane cellulaire. Ces derniers permettent le transport d’ions ou de molécules entre les milieux intra- et extra-cellulaires, grâce à leurs fortes sélectivités ou leurs propriétés d’ouverture/fermeture. Comparé à leurs homologues biologiques, les limitations des nanopores solides sont leurs manques de sélectivité et de réponse aux stimuli extérieurs. Toutefois, les nanopores solides ont l’avantage d’être beaucoup plus résistant, robuste et facile à manipuler que les pores biologiques. Ainsi la fonctionnalisation de leur surface, avec des systèmes plus ou moins complexes, permettrait d’améliorer à la fois leurs propriétés de transport sélectif, leurs capacités de détection de biomolécules ou encore d’étudier plus précisément les mécanismes fondamentaux du transport des macromolécules en milieu confiné.Dans cette thèse, nous avons conçu dans un premier temps des nanopores bi-fonctionnels, répondant au pH, et à l’attache d’un ligand. Pour fabriquer ces nanopores bi-fonctionnels, nous avons utilisé un système biotine-avidine fixé dans des nanopores polymères. Nous avons démontré qu’il est possible de moduler l’ouverture et la fermeture du nanopore avec le pH de façon réversible. De plus, il est possible de détecter des protéines biotinylées et des anticorps par l’analyse des rectifications de courant. Le principal défaut de cette stratégie est son irréversibilité. En utilisant une stratégie similaire combinée avec des polyélectrolytes, nous avons obtenu des fonctionnalisations réversibles. Ils permettent de moduler la sélectivité ionique du pore et les propriétés de conduction en fonction du pH et de ligand. Dans un second temps, nous nous sommes intéressés aux questions fondamentales de la translocation de polynucléotide, plus précisément de l’analyse de l’influence de l’état de surface du nanopore (hydrophobicité, charge), dans les conditions où la distance de Debye devient équivalente au diamètre du nanopore. Nous avons démontré que si le nanopore présente la même charge que la PolyAdénosine et la PolyCytosine, la vitesse de passage de la molécule augmente et la barrière globale d’énergie d’entrée du nanopore diminue par rapport au nanopore non-chargé hydrophobe. Ensuite, en modifiant la surface d’un nanopore en PET, nous avons montré qu’il est possible de détecter des brins simples et doubles d’ADN très courts (10 à 40 bases). Enfin, nous avons tenté une fonctionnalisation de nanopores pour éviter l’adsorption non spécifique des protéines afin d’étudier la translocation de longs fibrilles d’amyloïdes de lysozyme. Cet objectif n’a pas été complètement atteint compte tenu des résultats qui ne permettent pas d’affirmer quand au passage des molécules à travers le pore.Dans cette thèse nous nous sommes attachés à montrer l’intérêt et la nécessité de fonctionnaliser les pores, aussi bien pour obtenir des nanopores biomimétiques stimuli-répondants (pH et ligand) ou anti-bioadhérants que pour des études fondamentales de transport. Il est également facile de transposer cette technique à des membranes multipores. Il est donc possible de concevoir des membranes optimisées pour des applications de séparation ionique, de capture de molécules cibles ou plus généralement de filtrationArtificial nanopores are nanometer sized aperture made in synthetic thin films (polymer or inorganic). A single nanopore can be considered as a constitutive element from membranes. Recent advances in this field are bringing new tools for real time detection of target molecules at low concentration (fmol L-1). Biological channels inside the cell membrane are used as models to design solid-state nanopores. They allow ions or molecules transport through intra- and extra-cellular side, thanks to their high selectivity and their gating properties. Compared to their biological counterparts, limitations of the synthetic nanopores are their lack of selectivity and unresponsiveness towards external stimuli. However, the solid state presents several advantages compared to the biological ones, such as nanopores robustness, the control of the number of pores and a long lifetime (several days or weeks). Thus their surface functionalization would increase their selective transport properties, their abilities to detect biomolecules or to study more in details their fundamental mechanisms.In this thesis, we design first bi-functional nanopores, pH- and ligand-gated. To do it, we used biotin-avidin system grafted inside a polymeric nanopore. We demonstrated that it is possible to reversibly gate the nanopore with pH modulation. Moreover, we are able to detect protein labeled with biotin and antibodies by analyzing the current rectification. The major drawback comes from the irreversibility of its covalent bonds. By using a similar concept combined with polyelectrolytes, we obtain a reversible functionalization. Depending on the ligand, the ionic selectivity and the conduction properties can be modulated. Next, we focused on fundamental questions regarding polynucleotides translocation, and more precisely on the influence of the surface state of the nanopore (hydrophobicity, charge) when the Debye distance is similar to the pore diameter. We show that if the nanopore has the same charge as the polyAdenosine or polyCytosine, the translocation time decreases, and the energy barrier of entrance decreases compared to an uncharged hydrophobic nanopore. Then, by modifying the surface of the nanopore made in PET film, we are able to detect short single and double strand of DNA (10 to 40 bases). Finally, we tried to functionalize PET nanopores to avoid unspecific adsorption of proteins and to study the translocation of long fibrils of amyloids from lysozyme. This goal has not been entirely reach since we cannot claim that the fibrils translocate through the pore.In this thesis we show the interest and the need to functionalize the nanopores, to obtain biomimetic stimuli-responsive (pH and ligand), to avoid unspecific adsorption or to study transport properties with the nanopore. It is easy to upscale those techniques to multipores membranes. Thus it is possible to design membranes to enhance their ionic separation, target molecule detection or more generally filtration applications
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Vlassarev, Dimitar. "DNA Characterization with Solid-State Nanopores and Combined Carbon Nanotube across Solid-State Nanopore Sensors." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10310.
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A DNA molecule passing through a nanopore in a liner and sequential fashion allows for unprecedented interrogation of the polymer. Adding transverse electrodes that are comparable in size and sensitive to the DNA molecule, can further the attempts to rapidly sequence DNA. Carbon nanotubes are comparable in size and interact strongly with the DNA molecule. This makes them an excellent choice for integration with nanopores. Only the section of the carbon nanotube in immediate proximity to the nanopore should be sensitive to the DNA molecules. Atomic layer deposition of metal-oxides passivates the sections of the carbon nanotube that are not to interact with the DNA molecule. The coating also protects the thin film interconnects leading to the carbon nanotube. Hafnium oxide is superior to aluminum oxide in chemical resistance and electrical insulation but leads to a high failure rate of the carbon nanotube across nanopore devices. Aluminum oxide, combined with gold thin film interconnects to the carbon nanotube, produced the first functioning devices in electrolyte. These devices had concurrently functioning ionic (current across the nanopore) and transverse (current through the carbon nanotube) channels. No concurrent DNA translocation signal was recorded on the ionic and nanotube current traces. Analyzing the translocation events recorded on the ionic channel indicated that double-stranded DNA (dsDNA) passed through the carbon nanotube articulated nanopore an order of magnitude slower than it would have through a comparable unarticulated nanopore. The slower translocation observed is a necessary condition for sequencing. Investigating dsDNA translocation under various experimental conditions led to the discovery of a new interaction between the molecule and small nanopores. A dsDNA molecule is trapped when the electric field near the nanopore attracts and immobilizes a non-end segment of the molecule at the nanopore orifice without inducing folded translocation. In this work, the expression “trapped dsDNA” will exclusively refer to the immobilization of a dsDNA molecule at the orifice of the nanopore. The ionic current through the nanopore decreases when the dsDNA molecule is trapped by the nanopore. By contrast, a translocating dsDNA molecule under the same conditions causes an ionic current increase. Finite element modeling results predict this behavior for the conditions of the experiment.Physics
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Manara, Richard. "Free energy calculations of DNA translocation through protein nanopores and nanopore design for DNA sequencing." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/374791/.
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DNA sequencing has vastly opened up the world of molecular biology, leading to new areas of interest, especially in medical research. Unfortunately the methods of DNA sequencing have only ever seen gradual improvements, as Sanger sequencing is still very much the norm despite its high cost and slow speed. Nanopores present an exciting opportunity for DNA sequencing, however, despite the concept being presented in 1996 several problems have prevented the creation of a publicly available sequencing device. The two main focuses of research into nanopores so far have been improving the resolution between bases and the slowing down of DNA translocation through the pore so modern ammeters can read the sequence accurately. The simulation work presented in this thesis largely focuses on the energetics associated with DNA translocation. This is performed in several parts; an investigation into the probability of pore entry, study into the free energy of translocation for two proteins in addition to solvent contribution to this free energy, finally a theoretical project was undertaken to investigate bottom up nanopore design.
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Ahmadi, Amir. "Wafer-scale processing of arrays of nanopore devices." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47533.
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Nanopore-based single-molecule analysis of biomolecules such as DNA and proteins is a subject of strong scientific and technological interest. In recent years, solid state nanopores have been demonstrated to possess a number of advantages over biological (e.g., ion channel protein) pores due to the relative ease of tuning the pore dimensions, pore geometry, and surface chemistry. However, solid state fabrication methods have been limited in their scalability, automation, and reproducibility.
In this work, a wafer-scale fabrication method is first demonstrated for reproducibly fabricating large arrays of solid-state nanopores. The method couples the high-resolution processes of electron beam lithography (EBL) and atomic layer deposition (ALD). Arrays of nanopores (825 per wafer) are successfully fabricated across a series of 4' wafers, with tunable pore sizes from 50 nm to sub-20 nm. The nanopores are fabricated in silicon nitride films with thicknesses varying from 10 nm to 50 nm. ALD of aluminum oxide is used to tune the nanopore size in the above range. By careful optimization of all the processing steps, a device survival rate of 96% is achieved on a wafer with 50 nm silicon nitride films on 60- 80 micron windows. Furthermore, a significant device survival rate of 88% was obtained for 20 nm silicon nitride films on order 100 micron windows. In order to develop a deeper understanding of nanopore fabrication-structure relationships, a modeling study was conducted to examine the physics of EBL, in particular: to investigate the effects of beam blur, dose, shot pattern, and secondary electrons on internal pore structure. Under the operating conditions used in pore production, the pores were expected to taper to a substantially smaller size than their apparent size in SEM. This finding was supported by preliminary conductance readings from nanopores.
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Edmonds, Christopher Michael. "Computational investigations of biopolymer translocation through nanopore devices." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50260.
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Nanopores (1 – 10 nm diameter) constructed in solid-state membranes, have shown promise as next-generation biopolymer analysis devices offering both high resolution and high throughput. One promising application of nanopores is in the analysis of nucleic acids, such as DNA. This involves translocation experiments in which DNA is placed in an ionic solution and is forced through a nanopore with the aid of an applied electric field. The modulation of ionic current through the pore during DNA translocation can then be correlated to various properties of the biopolymer such as the length.
To optimally design and operate nanopore devices, it would be advantageous to develop an accurate computer simulation methodology to predict the physics of the translocation process. Hence, I have developed a physically accurate, computationally efficient simulation methodology to predict and analyze the physics of biopolymer translocation through solid-state (silicon nitride) nanopores. The overall theme of this thesis is to use this simulation methodology to thoroughly investigate important issues in the physics underlying translocation experiments and thereby determine the effects of key structural and operation parameters, such as nanopore dimensions, applied voltage, hydrodynamic interactions, solvent viscosity, and the polymer chain length. The results from these simulation studies can assist in not only proper nanopore design, but also help determine the proper experimental environments and parameters for nanopore operation.
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Tasserit, Christophe. "Transport d'ions et d'objets dans des nanopores." Phd thesis, Ecole Polytechnique X, 2011. http://pastel.archives-ouvertes.fr/pastel-00589602.
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Il existe différentes techniques de manipulation et de détection de molécules uniques. Parmi elles, la mesure du courant ionique traversant un pore nanométrique unique est la plus ancienne. Le travail effectué dans cette thèse utilise cette technique et s'articule autour de deux objectifs. Tout d'abord, l'utilisation d'un nanopore unique obtenu par attaque de trace permet d'imiter les expériences déjà faites dans la littérature avec d'autres types de pores. Certains phénomènes, tels que la rectification par exemple, ont pu être observés, mais d'autres comme la translocation n'ont pu l'être. Ensuite, une étude du bruit de conductance électrique démontre l'existence d'un phénomène qui n'avait jusqu'alors pas été soulevé dans la littérature. En effet, ce bruit ne peut pas être imputé aux fluctuations des caractéristiques de la géométrie du pore ou de sa paroi, mais plutôt à des effets coopératifs sur la mobilité des ions dans un milieu confiné.
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Fazi, Davide. "Progetto di un nodo sensore a nanocorrenti basato su microcontrollore." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13141/.
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Le prestazioni e la densità di integrazione dei circuiti integrati hanno avuto una incredibile crescita negli ultimi decenni.
Questo incredibile sviluppo ha portato ad una enorme crescita delle applicazioni dei circuiti elettronici, fino ad arrivare a pensare di poter rendere “smart” e connesso ad Internet ogni oggetto di uso comune, grazie alla cosiddetta “Internet of Things”.
In questo panorama trovano dunque sempre maggior spazio i sensori, indispensabili al fine di monitorare i parametri d’interesse negli oggetti da controllare.
Un altro aspetto molto importante è quello di ridurre il consumo dei dispositivi. Gli oggetti da connettere ad internet nella maggior parte dei casi saranno infatti da alimentare a batteria.
Lo scopo di questo elaborato è quello di sviluppare un nodo sensore con annesso un datalogger mediante l’utilizzo di un microcontrollore. L’obiettivo principale è di ridurne il consumo al minimo, con correnti di standby dell’ordine delle decine di nA, così da poter alimentare tale circuito per un periodo di diversi anni con la batteria più piccola possibile.
Il circuito sarà non solo progettato ma anche realizzato su PCB, al fine di poterne collaudare il funzionamento reale e di poterlo confrontare con quello previsto.
Un dispositivo di questo tipo, oltre ad essere un utile caso di studio per mostrare i valori minimi di consumo verso i quali sia possibile spingersi, potrebbe trovare applicazione in situazioni in cui si renda necessario monitorare determinati parametri in condizioni tali da rendere difficoltosa la sostituzione della batteria e quindi anche il monitoraggio real-time che richiederebbe necessariamente un maggior consumo.
Il progetto si compone di un microcontrollore che, oltre a gestire la lettura di un sensore, si occupa di implementare la funzione di datalogger. Un altro componente fondamentale è un timer, avente lo scopo di gestire il periodo di attività del µC.
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Kipnusu, Wycliffe Kiprop. "Effects of Nanoscale Confinement on the Structure and Dynamics of Glass-forming Systems." Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-183530.
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Structure and dynamics of nanoconfined glass-forming oligomers and diblock coplymers (BPCs) are investigated by a combination of infrared transition moment orientational analysis (IR-TMOA), positron annihilation lifetime spectroscopy (PALS), grazing incidence small angle X-ray scattering (GISAXS), atomic force microscopy (AFM), scanning electron microscopy (SEM) and broadband dielectric spectroscopy (BDS). The oligomers probed are the van der Waals type, tris(2-ethyhexyl)phosphate (TEHP) and the self-associating molecules of 2-ethyl-1-hexanol (2E1H). Symmetric and asymmetric poly(styrene-b-1,4-isoprene) P(S-b-I) are studied for the case of BCPs. The samples are confined either in one-dimensional (1D) in form of thin films or in 2D (nanopores) geometrical constraints. The molecular order of TEHP in nanopores as studied by IR-TMOA shows that about 7% of the molecules are preferentially oriented perpendicular to the long axis of the pores due to their interaction with the pore walls. PALS results reveal that 2E1H confined in nanopores exhibit larger free volume with respect to the bulk. In thin films (1D), P(S-b-I) having volume fraction of isoprene blocks f(PI)= 0.55 exhibits randomly oriented lamellae and their thicknesses are directly proportional to the film thickness d(film). For f(PI) = 0.73, perpendicular cylinders with respect to the substrate are observed for d(film)>50 nm but they lie along the substrate plane when d(film) < 50 nm. In AAO pores (2D) with average pore diameter d(pore) of 150 nm, straight nanorods are formed which change to helical structures in 18 nm pores. Molecular dynamics of 2E1H and TEHP constrained in nanopores (2D), is influenced by the interplay between confinement and surface effects. Confinement effects show up as an increase in the structural relaxation rate with decreasing pore sizes at the vicinity of the glass transition temperature. This is attributed to the reduced packing density of the molecules in pores as quantified by PALS results for 2E1H. Whereas the orientation and morphologies of the domains in P(S-b-I) and the chain dynamics of isoprene chains are influenced by the finite--size and dimensionality of confinement, the segmental motion, related to the dynamic glass transition (DGT) of both styrene and isoprene blocks remains unaffected-in its relaxation time-within experimental accuracy. Effects of nanoscale confinement on the molecular dynamics therefore depend on a number of factors: the type of molecules (polymers, low molecular liquids), interfacial interactions and the dimensionality of the constraining geometries.
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Raghupathy, Bala Praveen Chakkravarthy. "Spray freeze-drying of zirconia nanopowder." Thesis, Loughborough University, 2007. https://dspace.lboro.ac.uk/2134/34738.
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Industrial exploitation of ceramic nanopowders is inhibited by their poor flowability and strong tendency to agglomerate. To achieve good flowability and die-filling characteristics, controlled agglomeration is required whilst the strength of the agglomerates is minimised so that they crush into primary particles when die pressed. Yttria stabilised zirconia nanopowders with a primary particle size of ~16 nm were obtained through different drying routes from an aqueous suspension and characterised in terms of flowability and agglomerate strength.
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Szalay, Tamas. "Improved Analysis of Nanopore Sequence Data and Scanning Nanopore Techniques." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493548.
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The field of nanopore research has been driven by the need to inexpensively and rapidly sequence DNA. In order to help realize this goal, this thesis describes the PoreSeq algorithm that identifies and corrects errors in real-world nanopore sequencing data and improves the accuracy of \textit{de novo} genome assembly with increasing coverage depth. The approach relies on modeling the possible sources of uncertainty that occur as DNA advances through the nanopore and then using this model to find the sequence that best explains multiple reads of the same region of DNA. PoreSeq increases nanopore sequencing read accuracy of M13 bacteriophage DNA from 85\% to 99\% at 100X coverage. We also use the algorithm to assemble \textit{E. coli} with 30X coverage and the $\lambda$ genome at a range of coverages from 3X to 50X. Additionally, we classify sequence variants at an order of magnitude lower coverage than is possible with existing methods.
This thesis also reports preliminary progress towards controlling the motion of DNA using two nanopores instead of one. The speed at which the DNA travels through the nanopore needs to be carefully controlled to facilitate the detection of individual bases. A second nanopore in close proximity to the first could be used to slow or stop the motion of the DNA in order to enable a more accurate readout.
The fabrication process for a new pyramidal nanopore geometry was developed in order to facilitate the positioning of the nanopores. This thesis demonstrates that two of them can be placed close enough to interact with a single molecule of DNA, which is a prerequisite for being able to use the driving force of the pores to exert fine control over the motion of the DNA.
Another strategy for reading the DNA is to trap it completely with one pore and to move the second nanopore instead. To that end, this thesis also shows that a single strand of immobilized DNA can be captured in a scanning nanopore and examined for a full hour, with data from many scans at many different voltages obtained in order to detect a bound protein placed partway along the molecule.Engineering and Applied Sciences - Applied Physics
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Roman, Jean. "Détection et analyse électrique de nanoparticules grâce à un nanopore solide et intégration microfluidique." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLE020/document.
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L'analyse électrique par nanopore est une technique relativement nouvelle permettant l'analyse de nanoparticules et de composés chimiques à l'échelle de la molécule unique. On utilise un trou nanométrique fait dans une membrane isolante délimitant deux électrolytes. On peut ainsi mesurer la résistance électrique de ce nanopore au cours du temps. Quand une particule d'intérêt s'approche du pore, la résistance électrique de celui-ci augmente de manière transitoire et on obtient ainsi une signature électrique liée à cette particule. Les applications de cette technique vont de la détection de virus jusqu'au séquençage de l'ADN ou d'autres polymères. Les nanopores solides sont une voie de développement de cette technique, démontrant une plus grande adaptabilité et robustesse que les nanopores protéiques, dont le développement est néanmoins plus avancé à ce jour. Cette thèse discute de l'intégration dans un dispositif microfluidique des puces contenant un nanopore solide ainsi que des traitement de surface nécessaires à la bonne utilisation de ces derniersNanopore-based electrical analysis is a relatively new technique for the analysis of nanoparticles and chemical compounds at the single molecule scale. A nanometric pore is placed in an ultra-thin insulating membrane. We can then measure the electrical resistance of the pore. When a particle goes near the pore, this resistance increases transiently, thus yielding information on the passing nanoparticle. The applications of such a technique range from virus detection to DNA or other polymers sequencing. Solid-state nanopores are a growing competitor to the more developed proteic nanopores showing better adaptability and robustness. This thesis discuss the microfluidic integration of solid-state nanopores as well as the surface enhancement to permit their use
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Muthukumar, Murugappan. "Macromolecular translocation through nanopores." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-184573.
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Valiullin, Rustem, Jörg Kärger, and Peter Monson. "Adsorption hysteresis in nanopores." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-196715.
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Muthukumar, Murugappan. "Macromolecular translocation through nanopores." Diffusion fundamentals 16 (2011) 6, S. 1, 2011. https://ul.qucosa.de/id/qucosa%3A13734.
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Berrigan, John Daniel. "Nanopowder nickel aluminate for benzothiophene adsorption from dodecane." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26580.
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Thesis (M. S.)--Materials Science and Engineering, Georgia Institute of Technology, 2009.Committee Chair: Carter, W.B.; Committee Member: Cochran, Joseph; Committee Member: Venugopal, Ganesh. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Chavis, Amy. "Cluster Enhanced Nanopore Spectrometry." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4290.
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Nanopore sensing is a label-free method used to characterize water-soluble molecules. Recent work describes how Au25(SG)18 clusters improve the single molecule nanopore spectrometry (SMNS) technique when analyzing polyethylene glycol (PEG). This thesis will further study and optimize the enhancement effect resulting from a cluster’s presence. Additionally, a model describing the interaction between a cluster and PEG is developed to assist in understanding this mechanism of enhancement. This thesis will also discuss expanding the SMNS method to detect peptides, using Au25(SG)18 for enhancement, and adjusting solution conditions to improve the sensitivity of the SMNS system for peptide detection. Finally, a model describing the relationship between nanopore current blockades and molecular weight is developed to demonstrate the feasibility of using SMNS as a viable analytical technique for characterizing a wide variety of water-soluble molecules.
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Reimann, Peter, Andreas Meyer, Thomas Töws, and Sebastian Getfert. "Modeling DNA-translocation through nanopores." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-179409.
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HajHossein, Talasaz AmirAli. "Bioactivated nanopores for molecular analysis /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Zorkot, Mira. "Current fluctuations in ionic nanopores." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:0a8def87-04ee-4f5f-8619-92000d70b7f2.
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From electrical current to ecological and biological systems, fluctuations are characterised based on the frequency dependence of the power spectral density. Surprisingly - given the diversity of the systems considered - the power spectra of many systems reveal an inverse power- law dependence on the frequency f in certain regimes. This ubiquitous phenomenon famously known as '1/f noise' has triggered an abundance of investigations aimed at understanding its mechanism. Recently, '1/f noise' has also been observed in the ionic electric current through biological ion channels, nanometre-scale membrane pores and solid-state nanopores. Identifying and understanding the source of 1/f noise in nanopores emerges as a crucial prerequisite to design nanopore systems for their use in technological devices, such as nanopore- based DNA sequencers. At the same time, the current power spectrum in nanopores contains a wealth of information which, if extracted, would help towards a detailed characterisation of the nanopore's microscopic properties. To analyse the mechanism behind the occurrence of 1/f in nanopores, we study nanopores using Langevin-dynamics simulations and analytical methods. Ions move through the pore driven by an applied electric field, and the induced current is recorded. The power spectral density calculated from this data indicates the existence of a power law frequency dependence in an extended frequency regime. To verify a series of conclusions drawn from experimental investigations, we systematically vary all parameters characterising the system, including the geometry, the electric field, the ion density and the flexibility of the pore wall. Furthermore, we derive an analytical expression for the current power spectral density and compare it to the results from the Langevin-dynamics simulations. Finally, we evaluate the role of hydrodynamic interactions and find that it does not induce any major changes in the current power spectral density. Our studies allow us to uncover the mechanism that leads to the power law behaviour: interactions among the ionic components.
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Tumati, Raghu. "Solid-State Nanopore Characterization and Low noise Transimpedance Amplifier for Nanopore-Based Gene Sequencer." Fogler Library, University of Maine, 2008. http://www.library.umaine.edu/theses/pdf/TumatiR2008.pdf.
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Fennouri, Aziz. "Analyse de molécules individuelles de glucides bioactifs confinées dans des nanopores." Thesis, Evry-Val d'Essonne, 2013. http://www.theses.fr/2013EVRY0037/document.
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Les glycosaminoglycanes (GAGs), des polysaccharides bio-actifs exprimés à la surface des cellules et dans la matrice extracellulaire, sont à l’origine d’un grand nombre de processus physiologiques et pathologiques tels le développement embryonnaire, la croissance cellulaire, l’homéostasie, etc. Parmi les biopolymères, ils offrent le plus grand potentiel d’information grâce à la variété de combinaisons et de modifications régio-sélectives des monosaccharides les constituant. Leur analyse structurale représente ainsi l’un des défis des glycosciences les plus difficiles à relever. De nouvelles approches basées sur la détection à l’échelle de la molécule unique permettent l’observation directe et la nano-manipulation de biomolécules. Principalement utilisées pour les acides nucléiques ou les protéines, ces approches ont rarement été appliquées à l’étude des polysaccharides. Nous présentons ici la détection à l'échelle de la molécule unique d’oligo-glycosaminoglycanes individuels confinés dans un nanopore protéique d’aérolysine et d’α-hémolysine. Nos résultats montrent la capacité de cette technique à discriminer les oligosaccharides d’acide hyaluronique selon leur degré de polymérisation, d’après la durée et la fréquence des blocages de courants. La preuve de la translocation a été montrée par spectrométrie de masse. Cette approche nous a permis de suivre la dépolymérisation enzymatique de l’acide hyaluronique et de déterminer ses paramètres cinétiques. D’autres oligosaccharides (l'héparine, le dermatane sulfate et le dextrane sulfate) ont été étudiés, présentant des signatures caractéristiques différentes, mettant en évidence des différences de structures et/ou conformationsGlycosaminoglycans (GAGs) are bio-active polysaccharide expressed at the cell surface and in the extra-cellular matrix, which mediate cell-cell and cell-matrix interactions at the origin of a variety of physiological and pathological activities such as in embryonic development, cell growth, homeostasis, etc. Among all biopolymers, they offer the largest potential of information owing the incomparable variety of combinations and region-selective modifications of their building monosaccharides. The structural analysis of such complex carbohydrates is recognized as one of the most challenging task of glycosciences. New approaches based on single-molecule detection are currently arousing great interest in biology as it allows the direct observation and nano-manipulation of bio-molecules. Mainly applied to nucleic acids and proteins, these approaches have been not often used for the study of carbohydrates. We report here the detection of individual glycosaminoglycan oligosaccharides confined in aerolysin and α-hemolysin proteic nanopores. Our results show the capability of this new approach to discriminate hyaluronic acid (HA) oligosaccharides according to their polymerization degree based on the analysis of duration and frequency of the current blockades. This feature prompted us to apply this approach to the enzyme monitoring of the hyaluronidase-catalyzed depolymerization of HA and the determination of its kinetic parameters. Translocation has also been proved by mass spectrometry. Other oligosaccharides like heparin, dermatan sulfate and dextran sulfate, have also been studied, showing different characteristic “fingerprints”, due to structure and/or conformation differences
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Butler, Thomas. "Nanopore analysis of nucleic acids /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9674.
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Rostiashvili, Vakhtang G., Johan L. Dubbeldam, Andrey Milchev, and Thomas A. Vilgis. "Polymer translocation through a nanopore." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-183221.
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Gibb, Thomas. "Nanopore sensing using multiphase microfluidics." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/30836.
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This thesis describes a new approach to the investigation of the contents of microfluidic droplets at the single molecule level. Glass nanopores with diameters below 25nm, formed by pipette pulling, are inserted into a microfluidic channel with a height and width of 100 μm. Subsequently, a segmented flow of buffered KCl droplets in an FC-40 carrier oil is flowed through the device and analysed via changes in the measured electrical signal upon application of a voltage between the nanopipettes. Initially, the thesis focuses on the optimisation of droplet generation and pipette performance. A T-junction geometry and a novel method of droplet generation using an integrated pipette are both trialled as methods for droplet production in the device. In addition, atomic layer deposition (ALD) is investigated as an approach to optimise the size of the glass nanopore for the detection of single molecules. Subsequently, droplets in the segmented flow are examined with the device. Optical studies are undertaken to study the viability of droplets in the device and the preservation of their 'isolated microreactor' status. The length and frequency of droplets is then measured electrically and compared to an optical control, the excellent agreement between the two methods confirming the validity of the electrical approach. Attention then turns to the measurement of the bulk properties of the droplet with the determination of the KCl concentration within individual droplets. Finally, single molecules of 10 kbp double stranded DNA are translocated from within the droplet into the nanopipette, illustrating the device's potential for the analysis of droplet contents and the control of their contents at the single molecule level.
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Laohakunakorn, Nadanai. "Electrokinetic phenomena in nanopore transport." Thesis, University of Cambridge, 2015. https://www.repository.cam.ac.uk/handle/1810/252690.
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Nanopores are apertures of nanometric dimensions in an insulating matrix. They are routinely used to sense and measure properties of single molecules such as DNA. This sensing technique relies on the process of translocation, whereby a molecule in aqueous solution moves through the pore under an applied electric field. The presence of the molecule modulates the ionic current through the pore, from which information can be obtained regarding the molecule's properties. Whereas the electrical properties of the nanopore are relatively well known, much less work has been done regarding their fluidic properties. In this thesis I investigate the effects of fluid flow within the nanopore system. In particular, the charged nature of the DNA and pore walls results in electrically-driven flows called electroosmosis. Using a setup which combines the nanopore with an optical trap to measure forces with piconewton sensitivity, we elucidate the electroosmotic coupling between multiple DNA molecules inside the confined environment of the pore. Outside the pore, these flows produce a nanofluidic jet, since the pore behaves like a small electroosmotic pump. We show that this jet is well-described by the low Reynolds number limit of the classical Landau-Squire solution of the Navier-Stokes equations. The properties of this jet vary in a complex way with changing conditions: the jet reverses direction as a function of salt concentration, and exhibits asymmetry with respect to voltage reversal. Using a combination of simulations and analytic modelling, we are able to account for all of these effects. The result of this work is a more complete understanding of the fluidic properties of the nanopore. These effects govern the translocation process, and thus have consequences for better control of single molecule sensing. Additionally, the phenomena we have uncovered could potentially be harnessed in novel microfluidic applications, whose technological implications range from lab-on-a-chip devices to personalised medicine.
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Cressiot, Benjamin. "Transport de protéines natives, partiellement et complètement dépliées à travers des nanopores protéiques et artificiels." Thesis, Evry-Val d'Essonne, 2012. http://www.theses.fr/2012EVRY0016.
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Nous étudions le transport de protéines natives, partiellement ou complètement dépliées à travers des nanopores protéiques ou solides à l’échelle de la molécule unique en utilisant une détection électrique. Le système modèle que nous avons choisi est la protéine MalE sauvage ou mutante, en particulier la protéine MalE 219 qui se déplie à de plus faibles concentrations d’agent dénaturant que la protéine sauvage. Nous montrons que la translocation de protéines partiellement dépliées à travers un canal protéique, l’hémolysine du staphylocoque doré, dépend des conformations individuelles que nous pouvons distinguer. Les molécules dépliées passent rapidement dans les nanopores. Nous mesurons directement leur fraction en fonction de la concentration en agent dénaturant. La technique est très sensible aux mutations affectant le repliement.. Nous avons également étudié le transport de protéines à travers des nanopores solides dans différents cas. Nous comparons d’abord le transport de protéines natives et de protéines complètement dépliées à travers un nanopore de grand diamètre puis nous étudions la translocation de protéines dépliées à travers un nanopore étroit de diamètre inférieur à la taille de la protéine. Nous observons différents régimes de translocation quand nous varions le champ électrique appliqué que nous interprétons à l’aide d’un modèle théorique simpleWe study the transport of native, partially or completely unfolded proteins through protein or solid-state nanopores at the single molecule level using an electrical detection. The model system that we use is the wild-type MalE or mutant protein, in particular MalE219, which unfolds at lower concentration of denaturing agent than the wild type. We show that the translocation of partially unfolded proteins through the Hemolysin protein channel, a toxin from Staphylococcus aureus, depends on of individual conformations that we can distinguish. The unfolded proteins pass rapidly through the nanopores. We directly measure their proportion as a function of the concentration of denaturing agent. The technique is very sensitive to the mutations affecting the folding properties. We also study the transport of proteins through solid-state nanopores in different situations. We first compare the transport of native and fully unfolded proteins through a nanopore of large diameter. We then study the tranlocation of unfolded proteins through a narrow pore, whose diameter is smaller than the protein size. We observe different regimes of translocation by varying the applied electric field, which we interpret using a simple theoretical model
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Pambos, Oliver James. "Single molecule detection with hybrid nanopores." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709288.
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Lu, Zhengmao. "Evaporation from nanopores : probing interfacial transport." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118723.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2018.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 82-87).
Evaporation, a commonly found phenomenon in nature, is widely used in thermal management, water purification, and steam generation as it takes advantage of the enthalpy of vaporization. Despite being extensively studied for decades, the fundamental understanding of evaporation, which is necessary for making full use of evaporation, remains limited up to date. It is in general difficult to experimentally characterize the interfacial heat and mass transfer during evaporation. In this thesis, we designed and microfabricated an ultrathin nanoporous membrane as an experimental platform to overcome some critical challenges including: (1) realizing accurate and yet non-invasive interface temperature measurement; (2) decoupling the interfacial transport resistance from the thermofluidic resistance in the liquid phase and the diffusion resistance in the vapor phase; and (3) mitigating the blockage risk of the liquid-vapor interface due to nonevaporative contaminants. Our nano device consisted of an ultrathin free-standing membrane (~200 nm thick) containing an array of nanopores (pore diameter ~100 nm). A gold layer deposited on the membrane served as an electric heater to induce evaporation as well as a resistive temperature detector to closely monitor the interface temperature. This configuration minimizes the thermofluidic resistance in the liquid and mitigates the contamination risk. We characterized evaporation from this nano device in air as well as pure vapor. We demonstrated interfacial heat fluxes of ~~500 W/cm² for evaporation in air, where we elucidated that the Maxwell- Stefan equation governed the overall transport instead of Fick's law, especially in the high flux regime. In vapor, we achieved kinetically limited evaporation with an interfacial heat transfer coefficient up to 54 kW/cm² K. We utilized the kinetic theory with the Boltzmann transport equation to model the evaporative transport. With both experiments and modeling, we demonstrated that the kinetic limit of evaporation is determined by the pressure ratio between the vapor in the far field and that generated by the interface. The improved fundamental understanding of evaporation that we gained indicates the significant promise of utilizing an ultrathin nanoporous design to achieve high heat fluxes for evaporation in thermal management, desalination, steam generation, and beyond.
by Zhengmao Lu.
Ph. D.
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Ayub, Mariam. "Metallic nanopores for single molecule biosensing." Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/9124.
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This thesis describes a novel approach to the fabrication and characterisation of metallic nanopores and their application for the detection of single DNA molecules. Metallic nanopores with apparent diameters below 20 nm are produced using electrochemical deposition and real-time ionic current feedback. Beginning with large nanopores (diameter 100-200 nm) milled into gold silicon nitride membranes using a focused ion beam, platinum metal is electrodeposited onto the gold surface, thus reducing the effective pore diameter. By simultaneously observing the ion current feedback, the shrinking of the nanopore can be monitored and terminated at any pre-defined value of the pore conductance in a precisely controlled and reproducible way. The ion transport properties of the metallic nanopore system are investigated by characterising the pore conductance at varying potentials across the nanopore and concentrations of electrolyte. The results are compared to conventional bare silicon nitride nanopore systems. Chemical modification at the nanopore surface is also studied using thiolisation to reduce the capacitive charging effects observed with metallic nanopores. Further to this, impedance measurements are carried out to study the resistive behaviour exhibited in these systems. An equivalent circuit model is proposed to validate the results obtained from the experimental studies. To evaluate the suitability of these nanopores for applications in single-molecule biosensing, translocation experiments using λ-DNA are performed. DNA molecules are electrokinetically driven through the nanopore under an applied electric field, hence as the DNA translocates through the pore, current blockade events are detected. Each event is the result of a single molecular interaction of DNA with the nanopore and is characterised by its dwell time and amplitude. Characterisation studies and noise analysis towards the applicability of metallic nanopores as single molecule detectors are also studied and compared to current bare silicon nitride pore systems.
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Piguet, Fabien. "Etude théorique et expérimentale de la translocation de macromolécules à travers un nanopore." Thesis, Cergy-Pontoise, 2014. http://www.theses.fr/2014CERG0728/document.
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La translocation, le passage d'une macromolécule à travers un pore inséré dans une membrane, est impliquée dans de nombreux processus biologiques. On peut citer comme exemple le transport d'ARN ou de protéines entre les composants de la cellule, et l'infection d'une cellule par le passage d'un ADN viral à travers la membrane cellulaire. Aujourd'hui la translocation est aussi la base d'applications technologiques, comme le fait d'utiliser les pores en tant que détecteurs pour le séquençage rapide de molécules ou en tant que filtre moléculaire. La compréhension du processus de translocation est importante à la fois d'un point de vue fondamental et pour la fabrication de nouveaux dispositifs de translocation à usage spécifique. Dans cette thèse, nous réalisons des expériences et des simulations informatiques pour étudier certains des effets les plus importants mis en jeu lors de la translocation.Nous utilisons des simulations informatiques avec un modèle à ``gros grain'' pour étudier qualitativement l'influence d'une interaction attractive entre les parois du pore et un polymère en train de transloquer. Nous montrons que la position de l'interaction influence la fréquence d'entrée et le temps de résidence du polymère dans le pore. La fréquence d'entrée est plus grande lorsque l'entrée du pore est attractive. Le comportement du temps de résidence avec la longueur du polymère est qualitativement et quantitativement affecté par la position de l'interaction dans le pore. Cependant, quelle que soit la position de l'interaction, nous observons que le temps de translocation augmente linéairement avec la longueur du polymère lorsque le polymère est plus long que le pore. Cette observation est qualitativement en accord avec des données expérimentales publiées.Lorsque la translocation est lente, la corrélation entre les mouvements des monomères confinés dans le pore peut jouer un rôle important. Cet effet n'a pas été pris en compte jusqu'à présent. Nous développons un nouveau modèle pour la translocation de polymères, inspiré par le processus d'exclusion asymétrique (ASEP process), qui permet d'étudier spécifiquement cet effet. Nous montrons que les mouvements corrélés des monomères confinés dans le pore génèrent un comportement du temps de résidence avec la longueur du polymère qui est qualitativement similaire à ce qui est habituellement interprété comme la présence d'une barrière d'énergie libre dans le processus de translocation, même lorsqu'une telle barrière n'existe pas. Notre modèle réduit fortement le temps de simulation comparé aux simulations de dynamique moléculaire traditionnelles (quelques secondes contre quelques mois pour un système similaire). Cette accélération provient de l'idéalisation des portions du polymère à l'extérieur du pore. Une telle idéalisation est également présente dans les modèles largement utlisés de type Fokker-Planck, mais dans notre cas le comportement de la partie de la chaîne confinée dans le pore est mieux modélisé.Enfin nous réalisons des expériences pour tester l'existence d'un flot électro-osmotique (EOF) à travers le nanopore d'alpha-hémolysine de staphylococcus aureus. Malgré de nombreux travaux ces dernières années, la question de l'EOF à travers l'un des nanopores biologiques les plus utlisés fait toujours débat. Nous montrons qu'un EOF existe à travers l'alpha-hémolysine et qu'il contrôle la fréquence d'entrée et le temps de résidence de molécules neutres (beta-cyclodextrines) dans le nanopore. La force de l'EOF dépend du type de cation en solution. En particulier nous montrons que l'EOF est plus fort en présence de LiCl que de KClTranslocation, the passage of a macromolecule through a pore inserted in a membrane, is involved in many biological processes. Examples include the transport of RNA or proteins between cell components, and the infection of a cell by the passage of a viral DNA through the cell membrane. Today translocation is also the basis of technological applications, such as using pores as sensors for fast molecule sequencing or molecular sieves. The comprehension of the translocation process is important both from a fundamental point of view and for the design of new translocation setups for specific uses.In this thesis both experiments and computer simulations are used to investigate some of the most important effects at work during translocation.Coarse-grained computer simulations are used to study qualitatively the influence of an attractive interaction between the pore walls and a translocating polymer. The location of the interaction is shown to influence both the entry frequency and residence time of the polymer in the pore. The entry frequency is greater when the pore entry is attractive. The behaviour of the residence time with the polymer length is qualitatively and quantitatively affected by the location of the interaction within the pore. Nevertheless, regardless of the location of the interaction, a linear increase of the residence time with polymer length occurs when the polymer becomes longer than the pore. This observation is in qualitative agreement with published experimental data.In the case of slow translocation the correlation between the movements of the monomers confined in the pore may be important. This effect has not been considered previously. A new model of polymer translocation, inspired by the asymmetric exclusion process (ASEP), is developped which enables to specifically investigate this effect. The correlated movements of the monomers confined in the pore are shown to give rise to a behaviour of the residence time with polymer length which is qualitatively similar to what is usually interpreted as the presence of a free-energy barrier in the translocation process, even when such barrier is absent. Our model greatly reduces the simulation time compared to traditional molecular dynamics simulations (several seconds versus several months for similar systems). This speed up comes from the idealization of the portions of the polymer outside the pore. Such idealization is also present in the widely used Fokker-Planck models, but in our case the behaviour of the portion of the chain confined in the pore is better modelled.Finally, experiments are performed to probe the existence of an electro-osmotic flow (EOF) through the nanopore of alpha-hemolysin, from staphylococcus aureus. Despite numerous works during past years, the question of EOF through one of the most commonly used biological nanopores is still under debate. An EOF is shown to exist through alpha-hemolysin and to control the entry frequency and residence time of neutral molecules (beta-cyclodextrins) in the nanopore. The strength of the EOF depends on the type of cations in solution. In particular EOF is shown to be stronger in LiCl solution than in KCl solution
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Wang, Yijun. "High elastic modulus nanopowder reinforced resin composites for dental applications." College Park, Md. : University of Maryland, 2007. http://hdl.handle.net/1903/7406.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2007.Thesis research directed by: Material Science and Engineering. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Bell, Nicholas Andrew William. "DNA origami nanopores and single molecule transport through nanocapillaries." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648810.
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Faye, Ibrahima. "Polymères en étoile de cyclodextrine amphiphiles et leurs interactions avec une membrane lipidique modèle." Thesis, Université Paris-Saclay (ComUE), 2015. http://www.theses.fr/2015SACLE002/document.
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Ce projet traite de la synthèse de copolymères en étoile amphiphiles à coeur -cyclodextrine et de leurs possibles interactions avec une membrane lipidique modèle en tant que nanopores artificiels. Dans un premier temps, la synthèse d’un amorceur multifonctionnel, per(2-O-méthyl-3,6-di-O-hydroxypropyl)--CD, a été réalisée et sa caractérisation par RMN 1H, 13C et spectrométrie de masse (ESI-MS) confirme sa structure. La polymérisation d’oxyde de butylène amorcée par ce dérivé de -cyclodextrine, en présence de base phosphazène, a alors été réalisée dans un deuxième temps et nous a permis de synthétiser des polymères en étoile à 14 branches hydrophobes, caractérisés par RMN (1H, 13C, DOSY) et chromatographie d’exclusion stérique. Ces derniers polymères hydrophobes sont couplés à leur tour à des chaînes polymères hydrophiles, poly(éthylène glycol) par méthode convergente (substitution nucléophile, chimie clic), ou polyglycidol par méthode divergente, et la caractérisation de l’architecture des copolymères résultants a été réalisée (RMN, CES). Enfin, parmi les différentes applications potentielles, l’aptitude de ces copolymères en étoile à former des nanopores artificiels a été testée par électrophysiologieThe aim of this work is the synthesis of amphiphilic star copolymers based on -cyclodextrin and their possible interactions with model lipid bilayers, such as artificial nanopores. In a first step, the synthesis of multifunctional initiator, per(2-O-methyl-3,6-di-O-hydroxypropyl)--CD, was performed and its characterization by 1H, 13C NMR and ESI-mass spectrometry confirms itsstructure. The polymerization of butylene oxide initiated by -CD derivative, in presence of phosphazene base, was then performed and allowed us to synthesize hydrophobic 14-arm star polymers, characterizedby NMR (1H, 13C, DOSY) and size exclusion chromatography. Hydrophilic macromolecular chains (polyethylene glycol, polyglycidol) are coupled to those latter hydrophobic polymers, using ‘grafting onto’ and ‘grafting from’ methods, and the characterization of the resulting copolymer architecture was performed (NMR, SEC). Finally, among the different potential applications, the ability of the star copolymers to form artificial nanoporeswas evaluated by patch-clamp technique
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Dubbeldam, Johan, Andrey Milchev, Vakhtang Rostiashvili, and Thomas Vilgis. "Driven polymer translocation through a nanopore." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-193311.
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Peng, Hongbo. "Towards hybridization-assisted nanopore DNA sequencing." View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318349.
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Angevine, Christopher. "Nanopore thermodynamics via infrared laser heating." VCU Scholars Compass, 2017. https://scholarscompass.vcu.edu/etd/5200.
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Single molecule nanopore spectroscopy is a label-free method for characterizing a wide variety of water-soluble molecules. Recently there have been efforts to expand nanopore sensing to new areas of study. Forensic investigators require an easy to deploy method to identify an unknown number of contributors in a solution. Currently there is no easily available method to distinguish between a single or multiple contributor solution of DNA before being processed by more advanced analytical techniques which has led to wasted time and resources increasing the backlog of samples waiting to be processed. In this work we present a new nanopore technique capable of distinguishing between single and multiple contributors with an easy to deploy infrared heating laser. Previous cluster-nanopore enhancement interaction studies, produced by this group, have found that polymers in the presence of a gold-nanopore complex spend longer periods of time inside the pore. This is of great interest to the nanopore sensing community because longer residence times enable more accurate statistics on single polymers. In order to understand why x some polymers see large enhancements in the residence times (i.e. 20x) while other polymers see much less enhancement (i.e. 3x) a more complete picture of the free energy components is required. By using a IR heating laser, we construct an Eyring transition graph to extract the enthalpic and entropic energy components to find entropy plays a more important role than previously thought when a polymer interacts with a the nanopore. For nanoconfined polymers, entropy plays an important role on how a polymer will interact with the cluster-nanopore structure which in turn may lead to an increase or decrease of the residence time enhancement factor. This work shows with the addition of an infrared laser heater to a nanopore system a new tool has been added to the field. The IR laser coupled to a nanopore system allows for precise adjustments to residence times of events and extracts the free energy components without the need to physically modify the nanopore.
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Trivedi, Dhruti Mayur. "Fabrication and characterization of silicon nitride nanopores." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/7288.
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The fabrication of synthetic nanopores with dimensional and electrical properties similar to organic alpha-hemolysin (α-HL) nanopores is required for the development of a novel genotyping device. This thesis details the development of synthetic nanopores with diameters below 5 nm fabricated by sputtering a free standing silicon nitride membrane using a tightly focused electron beam. Nanometer control is achieved with sputtering rates of 0.5 – 0.75 nm/s. This technique is further extended to fabricate a proof-of-concept array of 44 sub-5 nm nanopores in a single membrane to enable the detection of unamplified genomic DNA with acceptable signal-to-noise.
As-drilled inorganic nanopores have inferior electrical characteristics compared to α-HL. Careful study, however, revealed electrical noise sources that could be effectively reduced by chemical pretreatment of the pores and surface coating with poly-di-methyl-siloxane (PDMS). The chemical pretreatment targeted 1/f noise, while the PDMS reduced dielectric noise with an overall reduction in RMS current noise by a factor of 10. This resulted in processed nanopores with extremely favorable noise characteristics. These low noise silicon nitride nanopores were used to demonstrate single-molecule DNA translocation and probe capture with exceptional signal-to-noise ratios ranging from 40 – 150.
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Davenport, Matthew W. "Synthetic Nanopores| Biological Analogues and Nanofluidic Devices." Thesis, University of California, Irvine, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3565849.
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Nanoscopic pores in biological systems – cells, for example – are responsible for regulating the transport of ionic and molecular species between physiologically distinct compartments maintained by thin plasma membranes. These biological pores are proteinaceous structures: long, contorted chains of chemical building blocks called amino acids. Protein pores have evolved to span a staggering range of shapes, sizes and chemical properties, each crucial to a pore's unique functionality.
Protein pores have extremely well-defined jobs. For instance, pores called ion channels only transport ions. Within this family, there are pores designated to selectively transport specific ions, such as sodium channels for sodium, chloride channels for chloride and so on. Further subdivisions exist within each type of ion channel, resulting in a pantheon of specialized proteins pores.
Specificity and selectivity are bestowed upon a pore through its unique incorporation and arrangement of its amino acids, which in turn have their own unique chemical and physical properties. With hundreds of task-specific pores, deciphering the precise relationship between form and function in these protein channels is a critical, but daunting task. In this thesis, we examine an alternative for probing the fundamental mechanisms responsible for transport on the nanoscale.
Solid-state membranes offer well-defined structural surrogates to directly address the science underlying pore functionality. Numerous protein pores rely on electronic interactions, size exclusion principles and hydrophobic effects to fulfill their duties, regardless of their amino acid sequence. Substituting an engineered and well-characterized pore, we strive to achieve and, thus, understand the hallmarks of biological pore function: analyte recognition and selective transport.
While we restrict our study to only two readily available membrane materials – one a polymer and the other a ceramic – nanofabrication techniques give us access to a virtually limitless combination of pore shapes and sizes. Exploiting this, we investigate the role of pore geometry in mediating the electrostatic and steric interactions responsible for transport on the nanoscale. Through targeted chemical modifications of our homogenous pores, we easily tailor their surface properties to investigate the role of hydrophobic effects in confined environments. Unbound by the physiological limitations of protein structures (such as sensitivity to electrolyte composition and fragility to external forces), our report concludes with the fusion of fabrication and modification considerations to design robust components for nanofluidic circuitry and nanoscopic biosensors.
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Cazade, Pierre-André, Jalal Dweik, Benoit Coasne, Francois Henn, and John Palmeri. "Dynamics of electrolyte solutions confined in nanopores." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-189425.
Full text
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Ruthven, Douglas M. "The technological impact of diffusion in nanopores." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-196355.
Full textAbstract:
The impact of nanopore diffusion on the performance of adsorption separation processes is reviewed. Zeolite membrane processes and kinetically selective cyclic adsorption processes depend for their selectivity on differences in intracrystalline diffusion rates so these processes are designed to operate under conditions of intracrystalline diffusion control. In contrast, the performance of equilibrium based adsorption separation processes is adversely affected by diffusional resistance so in such processes the minimization of all resistances to mass transfer is a major design objective. Zeolite catalyzed reactions constitute a further important class of processes in which intrusion of diffusional resistance can be either advantageous or disadvantageous. Such effects are illustrated by considering in detail the conversion of methanol to light olefins (MTO) over SAPO34. Within the chemical process industries diffusion is important over a wide range of length scales. In this paper we focus only on diffusion at the nanometer scale since diffusional phenomena on this scale are critically important in adsorption separation
processes as well as in many heterogeneous catalytic systems. Indeed membrane separations and molecular sieving adsorption processes (kinetic separations) are driven by differences in nanoscale diffusivities. For such processes the conditions of operation must therefore be
selected so as to maximize the influence of nanoscale diffusion. This is true also for certain catalytic processes in which product selectivity can sometimes be improved by operating under conditions of diffusion control. More commonly, in equilibrium controlled adsorptive separations
and in catalytic systems where activity rather than selectivity is the important feature, process performance is adversely affected by nanoscale diffusion, and in such systems it is obviously desirable to design the process in such a way as to minimize the intrusion of diffusional resistances. Some examples of both classes of process are discussed
below.
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Ding, Shu Gu Li-Qun. "Aptamer encoded nanopores as single molecule sensors." Diss., Columbia, Mo. : University of Missouri--Columbia, 2008. http://hdl.handle.net/10355/5767.
Full textAbstract:
The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on September 21, 2009). Thesis advisor: Liqun Gu Includes bibliographical references.
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Briggs, Kyle. "Solid-State Nanopores: Fabrication, Application, and Analysis." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/38541.
Full textAbstract:
The work presented in this thesis is divided loosely into three main areas of interest: development of a novel method of solid-state nanopore fabrication; applications of this method to some of the open problems in the field; and analysis of nanopore data.
The first of these occupies the majority of the research presented in this thesis, covering research dedicated to the development and characterization of a novel method of solid-state nanopore fabrication which achieves nanometer scale control over matter using simple and low cost circuitry. Termed controlled breakdown (CBD), this technique is in the process of revolutionizing the field of nanopore research, and in the few short years I have been part of its development it has seen adoption in nanopore labs across the globe, both academic and industrial.
Due to the simple nature of CBD, this technique also enables novel applications of nanopores in device architectures that were inaccessible to the expensive and inflexible methods used previously. The second part of this thesis takes advantage of the unique opportunities presented by CBD to develop a device architecture comprising two nanopores in series. This nanodevice tackles one of the main problems standing between nanopores and the promise of cheap genomic analysis: control of the motion and conformation of the polymer both prior to and during translocation through the pore.
Finally, because the field of nanopore research is still relatively young, very few tools are available which provide high-quality analysis of nanopore data. The last part of this thesis is dedicated to a thorough discussion of the complexities involved in analysing nanopore signals, as well as the development of several tools which directly address this knowledge gap.
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Ruthven, Douglas M. "The technological impact of diffusion in nanopores." Diffusion fundamentals 2 (2005) 77, S. 1-23, 2005. https://ul.qucosa.de/id/qucosa%3A14412.
Full textAbstract:
The impact of nanopore diffusion on the performance of adsorption separation processes is reviewed. Zeolite membrane processes and kinetically selective cyclic adsorption processes depend for their selectivity on differences in intracrystalline diffusion rates so these processes are designed to operate under conditions of intracrystalline diffusion control. In contrast, the performance of equilibrium based adsorption separation processes is adversely affected by diffusional resistance so in such processes the minimization of all resistances to mass transfer is a major design objective. Zeolite catalyzed reactions constitute a further important class of processes in which intrusion of diffusional resistance can be either advantageous or disadvantageous. Such effects are illustrated by considering in detail the conversion of methanol to light olefins (MTO) over SAPO34. Within the chemical process industries diffusion is important over a wide range of length scales. In this paper we focus only on diffusion at the nanometer scale since diffusional phenomena on this scale are critically important in adsorption separation
processes as well as in many heterogeneous catalytic systems. Indeed membrane separations and molecular sieving adsorption processes (kinetic separations) are driven by differences in nanoscale diffusivities. For such processes the conditions of operation must therefore be
selected so as to maximize the influence of nanoscale diffusion. This is true also for certain catalytic processes in which product selectivity can sometimes be improved by operating under conditions of diffusion control. More commonly, in equilibrium controlled adsorptive separations
and in catalytic systems where activity rather than selectivity is the important feature, process performance is adversely affected by nanoscale diffusion, and in such systems it is obviously desirable to design the process in such a way as to minimize the intrusion of diffusional resistances. Some examples of both classes of process are discussed
below.
45
Cazade, Pierre-André, Jalal Dweik, Benoit Coasne, Francois Henn, and John Palmeri. "Dynamics of electrolyte solutions confined in nanopores." Diffusion fundamentals 11 (2009) 20, S. 1, 2009. https://ul.qucosa.de/id/qucosa%3A13959.
Full text
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Hiratsuka, Tatsumasa. "Kinetic Nature of Capillary Condensation in Nanopores." 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225638.
Full text
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Mörsdorf, Alexander. "Metal-assisted etching of nanopores in silicon." Thesis, KTH, Skolan för informations- och kommunikationsteknik (ICT), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-177359.
Full textAbstract:
Nanoporous membranes are an interesting approach to manufacture a variety of devices for different applications. For example in biomedicine the separation of molecules or cells or the sequence-based analysis of single-stranded DNA are of great interest. Based on silicon membranes, a promising method to achieve pores with a high aspect ratio is metal-assisted etching, where noble metal particles serve as catalysts for the oxidation of the underneath Si, which is subsequently removed by hydrofluoric acid. This thesis project deals with developing a method, based on wet chemical etching of nanopores into a silicon membrane, utilizing noble metal particles as catalysts. The main goal was to investigate if it is possible to achieve straight channels perpendicular to the substrate surface with approximately the same diameter as the particle size. Therefore, the etching behaviour of gold, silver and platinum nanoparticles with different diameters on various substrates and etching solutions has been investigated. First the optimal substrate and etching solution for defined pore growth were determined using gold nanoparticles. Long-time measurements have been conducted showing a saturation of the etch speed and square aperture growth after a few hours. Next the etching reaction was enhanced with adding HCl and applying a voltage and it was found that the particle concentration has an influence on the orientation of the pores. After showing only erratic movement in the beginning, erect pores with a maximum aspect ratio of ~ 20 could be manufactured using CTAB coated particles. After that silver particles have been investigated. Initially, the optimal compositions for synthesis and etching solution were determined. Then the behaviour for long-time immersion was investigated, implicating that the pores grow fast and constantly within the first hour. In the end, highly straight pores with aspect ratios of ~ 1000 were etched. But due to the high particle concentration, the surface was badly affected by strong etching, as well. For both noble metals, diluting the etching solution and thus slowing down the etching reaction resulted in more oriented pore growth. For the platinum particles, however, no promising results could be achieved, because platinum seems to be a too strong catalyst for the etching reaction.
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Shim, Ji Wook. "Single-molecule investigation and nanopore-integrated biochip." Diss., Columbia, Mo. : University of Missouri-Columbia, 2008. http://hdl.handle.net/10355/6673.
Full textAbstract:
Thesis (Ph. D.)--University of Missouri-Columbia, 2008.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on June 19, 2009) Includes bibliographical references.
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Thibaud, Jean-Marc. "Nanocomposites zéolithe/polymère à fonctionallité multiple (NANOPOZE)." Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT240/document.
Full textAbstract:
Synthèses et structures cristallines de nanocomposites polymère/zéolithe obtenus à haute pression. Les nanocomposites polymère/zéolithe forment une classe de matériaux constitués par une chaine de polymère à l’intérieur d’une zéolithe (matériau poreux dont la matrice est principalement formée par des tétraèdres SiO4). Le confinement élevé dans les micropores du matériau stabilise le polymère réactif et améliore les propriétés physiques (électrique, optique,...) tout en permettant leurs exploitations. L’insertion du monomère dans la zéolithe a lieu à haute pression en utilisant une cellule à enclumes de diamant et la polymérisation (suivie par spectroscopie infrarouge) est induite par la pression pour former le polymère confiné dans les pores. Aucune aide externe supplémentaire ou catalyseur n’est nécessaire. Quelques études précédentes ont montré la faisabilité de synthétiser des nanocomposites polymère/zéolithe à partir d’une zéolithe à porosité 3D. Ici on s’intéresse aux zéolithes hôtes à porosité 1D qui, contrairement aux pores tridimensionnels, peuvent induire la formation de chaines polymères linéaires disposant de propriétés directionnelles.Dans cette étude on a travaillé sur la synthèse de polyacétylène/TON et de polycarbonyle/TON, les chaines polymères s’adaptent étroitement avec les pores unidimensionnels de 5.7x4.6 Å de la TON (Theta-1, ZSM-22).La caractérisation par diffraction des rayons X a permis l’affinement de la structure des nanocomposites par méthode de Rietveld et la localisation du polymère grâce aux cartes de différence Fourier, ce qui permet de quantifier le nombre de chaines par maille. Il y en a quatre dans le cas du polyacétylène et une pour le polycarbonyle. Des calculs DFT ont été réalisés dans le cas de la TON, le polyacétylène/TON et le polycarbonyle/TON pour prévoir les propriétés physiques : modification d’un état isolant en semi-conducteur ou métalliqueSynthesis of linear polymer/zeolite nanocomposites under high pressurePolymer/zeolite nanocomposites form a class of materials constituted by polymer chains inside the pores of the zeolite (porous materials with a framework principally built up of SiO4 tetrahedra). Confinement in the microporous material allows reactive polymers to be stabilized, opening the way for the exploitation of their electrical and optical properties. The insertion of monomers in the zeolite takes place in a diamond anvil cell under high pressure, which induces polymerization (monitored by infrared spectroscopy) without any external assistance, avoiding the use of unwanted catalysts. The use of a zeolite host with unidirectional porosity, unlike previously investigated three-dimensional pore systems zeolites, can induce the formation of linear polymers with useful directional properties. In this work, we studied the synthesis of polyacetylene/TON and polycarbonyl/TON composites, as the linear polymers fit in the unidirectional 5.7x4.6 Å micropores of TON (Theta-1, ZSM-22).Characterization by X-ray diffraction allowed us to perform structure refinements of nanocomposites by the Rietveld method and to locate the polymer using difference Fourier maps, which also provide information on the number of chains by unit cell. There are 4 in the case of polyacetylene and 1 for polycarbonyl. DFT calculations were performed for TON, polyacetylene/TON and polycarbonyl/TON to predict their physical properties: transition from an insulating to a semi-conducting or metallic state
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Santiago, Garcia Eric, and Aspåker Hannes Salomonsson. "Temporal Convolutional Networks for Nanopore DNA Sequencing." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-295625.
Full textAbstract:
Nanopore DNA sequencing is a novel method forsequencing DNA where an electronic signal is modulated bynucleotides passing through nanosized pores embedded in a mem-brane. While current state-of-the-art solutions employ recurrentneural networks to analyse the signal, temporal convolutionalnetworks have recently been shown to match or outperformrecurrent networks in signal processing tasks. In this project, weinvestigate the performance of temporal convolutional networkson a simplified version of the sequencing task, where thegoal is to predict the nucleotides passing through the pore ateach instance in time, without reconstructing the correspondingDNA sequence. The impact of several network parameters onpredictive performance is analysed to determine an optimalarchitecture. While the implemented networks are shown tobe proficient at predicting nucleotides within the pore, thecurrent implementation is unlikely to outperform state-of-the-art solutions without further improvement.En nyligen utvecklad metod för att sekvensera DNA innefattar att en elektrisk signal moduleras genom att nukleotider passerar genom porer i nanostorlek. I kommersiella lösningar analyseras denna signal med hjälp av maskininlärning via Recurrent Neural Networks, men en variant av neruala nätverk som kallas Temporal Convolution Networks har nyligen har visat sig ha bättre prestanda jämfört med Recurrent Networks för olika typer av signalbehandlingsproblem. Målet med detta projekt är att undersöka användbarheten av Temporal Convolutional Networks för en förenklad version av DNA-sekvensering, där uppdraget endast är att identifera de nukleotider som passerar genom poren vid varje given tidpunkt, istället för att rekonstruera en komplett DNA-sekvens. För att kunna bestämma en optimal arkitektur på nätverket så undersöks effekten av flera olika parametrar. De implementerade nätverken visas ha god förmåga att klassificera nukleotider, men är troligtvis i behov av ytterligare förbättringar för att kunna konkurrera med nuvarande kommersiella lösningar.
Kandidatexjobb i elektroteknik 2020, KTH, Stockholm