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Andrinopoulos, Lampros. "Including van der Waals interactions in first-principles electronic structure calculations." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/22152.
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Dispersion (van der Waals or vdW) interactions are long-range, non-local in nature, and can be important for understanding and predicting structure and energetics in many systems. Examples of such systems include weakly bound dimers, molecules on surfaces and molecular crystals. Because of the inherent non-locality of these interactions, they are not accounted for by traditional local and semi-local exchange and correlation functionals in density functional theory (DFT). In this thesis, two different approaches to including dispersion interactions in DFT were investigated and implemented. The first approach is based on a recently developed method [Silvestrelli, PRL 100, 053002 (2008)] that maps the DFT ground-state electron density onto a set of maximally-localized Wannier functions (MLWFs). These MLWFs act as fragments of electron density that are used in a pairwise summation of the vdW contribution to the total energy. This contribution is added to the total DFT ground-state energy in a post-processing fashion. The method, as originally proposed, has a number of shortcomings that hamper its predictive power. To overcome these problems, we developed and implemented a number of improvements to it and demonstrated that these modifications give rise to calculated binding energies and equilibrium geometries that are in closer agreement to results of quantum-chemical coupled-cluster calculations. The second approach, known as the vdW density functional (vdW-DF) method, incorporates a non-local vdW term directly into the exchange and correlation functional. Following a recent efficient implementation [Guillermo Román-Pérez and José M. Soler, PRL 103, 096102 (2009)] we coded this approach and a number of vdW functionals (vdW-DF, vdW-DF2, optB88, optPBE) in the ONETEP linear-scaling DFT package, enabling treatment of very large systems that were previously too computationally demanding for such methods. We applied the vdW-DF method to a system of interest for applications in photovoltaics, namely fullerene (C60) molecular crystals, and investigated the effect of including vdW interactions on the relative stability of different crystal structures.
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Lee, Hee-Seung. "The structure, spectroscopy and dynamics of Small Van Der Waals Complexes /." The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486572165276376.
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SCHMIDT, PER MARTIN. "Structure et dynamique des complexes de van der waals benzene-argon." Paris 11, 1992. http://www.theses.fr/1992PA112315.
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La presente these a pour objet une etude systematique de l'effet de la solvatation progressive du benzene (bz) par un nombre croissant d'atomes d'argon (ar) (n9). Dans ce but les agregats heterogenes bz-ar#n, formes dans un jet supersonique, sont etudies separement par la technique d'ionisation biphotonique resonnante a deux couleurs associee a la spectrometrie de masse a temps de vol. Cette etude a permis, d'autre part, de caracteriser les changements de la structure electronique du benzene induits par les complexations successives et, d'autre part, d'identifier deux types d'isomeres, les uns avec les argons d'un seul cote du plan moleculaire (n|0), les autres avec les deux cotes occupes (n-m|m). Des modelisations par simulation monte carlo ont fourni une image plus precise de ces structures, et ont notamment permis de mettre en evidence, dans les complexes n|0, l'existence de deux arrangements possibles de l'agregat d'argon au-dessus du benzene. L'ensemble de ces modelisations et des resultats d'une etude spectroscopique plus poussee, ont permis de caracteriser les proprietes thermodynamiques des differents complexes et de mettre en evidence une transition structurale des isomeres n|0 et n-m|m vers des structures de type ponte lorsque la taille des complexes augmente (n4). Finalement, ce travail a mis en evidence un processus de redistribution d'energie vibrationnelle intracluster a l'etat s#1, responsable de l'observation de deux comportements d'ionisation differents
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Watkins, Jason Derrick. "X-ray structures of P22 c2 repressor-DNA complexes the mechansism of direct and indirect readout /." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26709.
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Thesis (Ph.D)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.Committee Chair: Loren D. Williams; Committee Member: Donald Doyle; Committee Member: Nicholas V. Hud; Committee Member: Roger Wartell; Committee Member: Stephen Harvey. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Economides, George. "Investigations of open-shell open-shell Van der Waals complexes." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:e27330e0-2eaa-4181-af30-70e8b7a3a692.
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The question posed in this work is how one would model and predict the rotational spectrum of open-shell open-shell van der Waals complexes. There are two secondary questions that arise: the nature of radical-radical interactions in such systems and the modelling of the large amplitude motion of the constituent molecules. Four different systems were studied in this work, each providing part of the answer to the main question. Starting with the large amplitude motion, there are two theoretical approaches that may be adopted: to either model the whole complex as a semi-rigid molecule, or to perform quantum dynamical calculations. We recorded and analysed the rotational spectrum (using Fourier transform microwave spectroscopy) of the molecule of tertiary butyl acetate (TBAc) which exhibits a high degree of internal rotation; and of the weakly-bound complex between a neon atom and a nitrogen dioxide molecule (Ne-NO2). We used the semi-rigid approach for TBAc and the quantum dynamical approach for Ne-NO2. We also explored the compatibility of these two approaches. Moreover, we were able to predict and analyse the fine and hyperfine structure of the Ne-NO2 spectrum using spherical tensor operator algebra and the results of our dynamics calculations. To explore the nature of the interactions in an radical-radical van der Waals complex we calculated the PESs of the possible states that the complex may be formed in, when an oxygen and a nitrogen monoxide molecule meet on a plane using a number of high level ab initio methods. Finally, our conclusions were tested and applied when we performed the angular quantum dynamics to predict the rotational spectrum of the complex between an oxygen and a nitrogen dioxide molecule, and account for the effect of nuclear spin statistics in that system.
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Constantinescu, Gabriel Cristian. "Large-scale density functional theory study of van-der-Waals heterostructures." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274876.
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Research on two-dimensional (2D) materials currently occupies a sizeable fraction of the materials science community, which has led to the development of a comprehensive body of knowledge on such layered structures. However, the goal of this thesis is to deepen the understanding of the comparatively unknown heterostructures composed of different stacked layers. First, we utilise linear-scaling density functional theory (LS-DFT) to simulate intricate interfaces between the most promising layered materials, such as transition metal dichalcogenides (TMDC) or black phosphorus (BP) and hexagonal boron nitride (hBN). We show that hBN can protect BP from external influences, while also preventing the band-gap reduction in BP stacks, and enabling the use of BP heterostructures as tunnelling field effect transistors. Moreover, our simulations of the electronic structure of TMDC interfaces have reproduced photoemission spectroscopy observations, and have also provided an explanation for the coexistence of commensurate and incommensurate phases within the same crystal. Secondly, we have developed new functionality to be used in the future study of 2D heterostructures, in the form of a linear-response phonon formalism for LS-DFT. As part of its implementation, we have solved multiple implementation and theoretical issues through the use of novel algorithms.
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Walters, Alan. "Spectroscopy and structure of jet cooled aromatics and van der Waals complexes." Thesis, University of Nottingham, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.280097.
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Skouteris, Dimitris. "Structure and dynamics of weakly bound complexes." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301422.
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Duval-Été, Marie-Christine. "Structure électronique et mouvements moléculaires dans les complexes de Van der Waals du mercure." Paris 11, 1988. http://www.theses.fr/1988PA112191.
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The work reported here concerns the vibrational and electronic structures of mercury van der Waals complexes in their excited states. The deactivation paths are shown to depend on the electronic and vibrational states optically excited. The spectroscopic study of several systems, mercury-atom: Hg-Ar and mercury-molecule: N₂ , Hg-CH₄ , Hg-NH₃ and Hg-H₂ 0 leads to the determination of their van der Waals potentials. In the case of the mercury-argon complex a model is proposed which accounts for the structures of the first electronic excited states correlated with the 6³p levels of mercury. The binding energy can be related simply to the average orientation of the 6p mercury orbital with respect to the internuclear axis. The molecular movements of the complex, stretching and bending ones, are studied for the Hg-N ₂ system. Their efficiency upon the deactivation mechanisms is clearly shown, especially the part of the bending vibration in the complex photo dissociation. We provide through the simulation of the various spectra, fluorescence excitation, emission and fragment Hg (6³P0) excitation, a wealth of consistent information about potentials in the ground and excited states. The optical excitation of mercury-ammonia and mercury-water complexes allows the direct observation and the spectroscopic characterization of the well known collisional complexes. The insight into their electronic states, molecular movements and decay modes, helps to interpret their formation and emissions in collision experiments. For the more bound complexes observed in the excited state, we propose a bonding-back bonding mechanism between the excited metal and the molecule to describe the interaction. It is of the same nature to which takes place between ligands and metallic surfaces and producing catalytic phenomena. Thus the deepest bound complexes can be considered as catalytic or precatalytic systemsCe travail porte sur l'étude de la structure électronique et vibrationnelle de complexes de van der Waals du mercure. Il met en évidence l'influence de la nature électronique et vibrationnelle du niveau optiquement excité sur les voies de désactivation. L'étude spectroscopique des différents systèmes, mercure-atome : Hg-Ar et mercure-molécule : Hg-N₂ , Hg-CH₄ , Hg-NH₃ et Hg-H₂ 0, conduit à la détermination des potentiels d'interaction van der Waals. Dans le cas du complexe mercure-argon on a pu montrer, par un modèle simple, que pour les premiers états électroniques excités, états corrélés aux niveaux 6³P du mercure, le facteur essentiel décrivant l'interaction van der Waals est l'orientation moyenne de l'orbitale 6³p du mercure par rapport à l'axe internucléaire du complexe. L'étude des états excités supérieurs corrélés à l'état de Rydberg 7³s₁ du mercure a révélé une structure en double puits. L'argon peut occuper deux positions d'équilibre, situé à l'intérieur du nuage électronique de l'orbitale 7s du mercure, le complexe a les caractéristiques de l'ion Hg+-Ar, situé à l'extérieur de ce nuage il forme une molécule de van der Waals très peu liée. Les mouvements moléculaires du complexe : Allongement et torsion et leur influence sur les mécanismes de désactivation, sont plus spécialement étudiés avec le système Hg-N₂. La modélisation des spectres expérimentaux: Excitation de fluorescence, émission, excitation du fragment Hg (6 ³P0), conduit à une description des potentiels d'interaction de l'état fondamental et des états excités atteints. Les mouvements de torsion du complexe peuvent être décrits comme une rotation bloquée de l'azote. Observant une dépendance de la dissociation du complexe avec le niveau vibrationnel excité, on a pu mettre en évidence le rôle du moment angulaire de vibration sur la dissociation du complexe induisant la relaxation intra multiplet du mercure vers le niveau ³P0. Enfin, l'excitation optique des complexes de van der Waals mercure-ammoniac et mercure-eau permet l'observation directe et la caractérisation spectroscopique des complexes collisionnels dont les émissions ont été observées précédemment. Donnant une image précise de la structure électronique, des mouvements moléculaires et des processus de désactivation de ces complexes, cette étude contribue à la compréhension de leur formation et des émissions caractéristiques leur étant liées. Un mécanisme de double échange de charge entre le mercure et la molécule est proposé pour rendre compte des énergies de liaison des complexes les plus liés à l'état excité. Il est de même nature que ceux ayant lieu entre ligands et surfaces métalliques, aussi les complexes très liés peuvent-ils être considérés comme des systèmes catalytiques ou pré-catalytiques
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Hay, Henri. "Étude de la structure et des propriétés des polymorphes de SiO2 et B2O3 par méthodes ab initio." Electronic Thesis or Diss., Paris 6, 2016. http://www.theses.fr/2016PA066318.
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Au cours de cette thèse nous avons utilisé la théorie de la fonctionnelle de la densité et les calculs Monte Carlo quantiques pour analyser l'impact des effets de van der Waals sur la structure, l'énergie, et les propriétés des polymorphes de SiO2 et B2O3. Nous avons mis en évidence un phénomène de compensation d'erreur, lié à l'utilisation de fonctionnelle d'échange et corrélation incluant les effets de van der Waals, dans les polymorphes basse densité de SiO2 entre une sur-évaluation des longueurs Si-O et une sous-estimation des angles Si-O-Si. Nous avons effectué des calculs Monte-Carlo quantiques afin de prédire la structure et l'énergie d'un nouveau polymorphe de B2O3 avec une grande précision, ce qui nous a permis d'évaluer les performances de différentes fonctionnelles d'échange et corrélation sur B2O3. Nous avons ensuite utilisé la théorie de la fonctionnelle de la densité pour prédire la structure et l'énergie de 25 nouveaux polymorphes de B2O3 , ainsi que leurs propriétés mécaniques et électroniques. Cette étude permet de proposer une explication à l'anomalie de cristallisation de B2O3, et réconcilie le comportement de B2O3 avec celui des autres oxydes formateurs de réseaux. Elle souligne la possibilité de créer des borates cristallins aux propriétés mécaniques remarquables, et confirme qu'il existe lien entre polymorphisme de basse énergie et facilité de vitrificationDuring this PhD I use density functional theory and quantum Monte Carlo to evaluate the importance of van der Waals effects on the structures, the energies, and the properties of SiO2 and B2O3 polymorphs. I show that exchange-correlation functionals including dispersion effects lead to an error cancellation between an overestimation of the Si-O distances and an underestimation of the Si-O-Si angles in low densities SiO2 polymorphs. By using quantum Monte Carlo calculations, I have predicted with high accuracy the relative energy of a new B2O3 polymorph, which allowed me to evaluate the performances of different exchange-correlation functionals on this material. I then use the best functional possible to compute the mechanical and electronic properties of 25 predicted B2O3 polymorphs. Some of the predicted polymorphs exhibit intriguing mechanical properties, such as negative linear compressibility, auxeticity and anisotropy. These calculations allow me to make a hypothesis explaining the crystallization anomaly in B2O3. They underline a seemingly universal link between low energy polymorphism and ease of vitrification
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Duval-Eté, Marie-Christine. "Structure électronique et mouvements moléculaires dans les complexes de Van der Waals du mercure." Grenoble 2 : ANRT, 1988. http://catalogue.bnf.fr/ark:/12148/cb376134263.
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Jasinski, Jakub. "Contrôle des propriétés excitoniques dans les structures à base de dichalcogénures de métaux de transition." Electronic Thesis or Diss., Université de Toulouse (2023-....), 2024. http://www.theses.fr/2024TLSES204.
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Ces dernières années, les dichalcogénures de métaux de transition (TMDs) atomiquement minces ont émergé comme des matériaux semi-conducteurs prometteurs. Leurs propriétés uniques découlent de leur structure de bandes électroniques résultant de la brisure de symétrie d'inversion et du fort couplage spin-orbite, ainsi que de la présence d'excitons fortement liés. Cela leur confère des degrés de liberté supplémentaires pour les porteurs de charge et les excitons, ce qui est prometteur à la fois pour l'étude des phénomènes physiques fondamentaux et pour les applications dans les dispositifs optoélectroniques. La nature van der Waals des liaisons inter-couches des TMDs et d'autres matériaux stratifiés émergents permet la fabrication de structures complexes multicouches, ajoutant une complexité et des opportunités supplémentaires pour obtenir des propriétés optoélectroniques souhaitées. Malgré une recherche intensive, de nombreux mystères concernant les phénomènes physiques fondamentaux régissant les propriétés de ces structures restent à élucider. Le besoin continu d'explorer les caractéristiques intrigantes des TMDs a motivé la réalisation de cette thèse. Ici, je présente des études sur plusieurs structures à base de TMDs, dont l'objectif principal était d'examiner la possibilité de contrôler les propriétés excitoniques par des facteurs intrinsèques et extrinsèques. Dans le cas de la monocouche de MoS2 déposée sur un substrat structuré, je démontre l'effet inattendu de la contrainte anisotrope sur la structure fine et les propriétés de polarisation de l'état excitonique chargé. Dans la monocouche de WSe2, je montre l'importance du mécanisme de couplage de type Dexter sur la polarisation de vallée, et qu'il est possible d'ajuster largement le degré de polarisation de vallée en fonction de l'énergie d'excitation choisie. De même, dans une hétérostructure WSe2/pérovskite 2D, je révèle l'injection de spin réussie du TMD dans la pérovskite 2D et la formation d'un état excitonique inter-couche, dont les propriétés sont étroitement liées à celles de la monocouche WSe2 constituante. Enfin, j'explore le paysage excitonique d'une bicouche naturelle de MoSe2 et la possibilité de moduler les états excitoniques via l'application d'un champ électrique, ce qui a révélé la formation de nouveaux états excitoniques et leurs interactions complexes. Dans l'ensemble, les résultats présentés dans cette thèse constituent une étape importante vers la compréhension des propriétés fondamentales des TMDs et des structures à base de TMDsIn recent years, atomically thin transition metal dichalcogenides (TMDs) have emerged as promising semiconducting materials. Their unique properties stem from their electronic band structure emerging from the broken inversion symmetry and strong spin-orbit coupling, as well the presence of strongly bound excitons. This endows them with additional degrees of freedom for charge carriers and excitons, which are promising for both studies of fundamental physical phenomena and applications in opto-electronic devices. Van der Waals nature of the interlayer bonding of TMDs and other emerging layered materials allows for fabrication of complex multi-layered structures, which add additional complexity and opportunity for achieving desired opto-electronic properties. Despite intense research, many mysteries regarding the fundamental physical phenomena governing properties of such structures remain to be solved. The ongoing need for investigation of the intriguing characteristics of TMDs motivated the realization of this thesis. Here I present studies of several TMD-based structures, the focus of which was the possibility of controlling the excitonic properties via both intrinsic and extrinsic factors. In monolayer MoS2 deposited on patterned substrate I demonstrate the unexpected effect of anisotropic strain on the fine structure and polarization properties of the charged exciton state. In monolayer WSe2 I show the importance of the Dexter-like coupling mechanism on the valley polarization and that it can be used for broad tunability of the degree of valley polarization by the choice of excitation energy. In WSe2/2D-perovskite heterostructure I reveal the succesful spin injection from TMD into the 2D-perovskite and the formation of an interlayer exciton state, whose properties are closely related to that of the constituent WSe2 monolayer. Finally I explore the excitonic landscape of a natural bilayer of MoSe2 and the tunability of the excitonic states via application of electric field, which revealed formation of new excitonic states and their complex interactions. Overall, the results presented in this thesis constitute an important step towards understanding of fundamental properties of TMDs and TMD-based structures
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Di, Felice Daniela. "Electronic structure and transport in the graphene/MoS₂ heterostructure for the conception of a field effect transistor." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS267/document.
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L'isolement du graphène, une monocouche de graphite composée d'un plan d’atomes de carbone, a démontré qu'il est possible de séparer un seul plan d'épaisseur atomique, que l'on appelle matériau bidimensionnel (2D), à partir des solides de Van de Waals (vdW). Grâce à leur stabilité, différents matériaux 2D peuvent être empilés pour former les hétérostructures de vdW. L'interaction vdW à l'interface étant suffisamment faible, les propriétés spécifiques de chaque matériau demeurent globalement inchangées dans l’empilement. En utilisant une démarche théorique et computationnelle basée sur la théorie de la fonctionnelle de la densité (DFT) et le formalisme de Keldysh-Green, nous avons étudié l'hétérostructure graphène/MoS₂ . Le principal intérêt des propriétés spécifiques du graphène et du MoS₂ pour la conception d'un transistor à effet de champ réside dans la mobilité du graphène, à la base d'un transistor haute performance et dans le gap électronique du MoS₂, à la base de la commutation du dispositif. Tout d'abord, nous avons étudié les effets de la rotation entre les deux couches sur les propriétés électroniques à l'interface, en démontrant que les propriétés électroniques globales ne sont pas affectées par l'orientation. En revanche, les images STM (microscope à effet tunnel) sont différentes pour chaque orientation, en raison d'un changement de densité de charge locale. Dans un deuxième temps, nous avons utilisé l’interface graphène/MoS₂ en tant que modèle très simple de Transistor à Effet de Champ. Nous avons analysé le rôle des hétérostructures de vdW sur la performance du transistor, en ajoutant des couches alternées de graphène et MoS₂ sur l'interface graphène/MoS₂. Il a ainsi été démontré que la forme de la DOS au bord du gap est le paramètre le plus important pour la vitesse de commutation du transistor, alors que si l’on ajoute des couches, il n’y aura pas d’amélioration du comportement du transistor, en raison de l'indépendance des interfaces dans les hétérostructures de vdW. Cependant, cela démontre que, dans le cadre de la DFT, on peut étudier les propriétés de transport des hétérostructures de vdW plus complexes en séparant chaque interface et en réduisant le temps de calcul. Les matériaux 2D sont également étudiés ici en tant que pointe pour STM et AFM (microscope à force atomique) : une pointe de graphène testée sur MoS₂ avec défauts a été comparée aux résultats correspondants pour une pointe en cuivre. La résolution atomique a été obtenue et grâce à l'interaction de vdW entre la pointe et l’échantillon, il est possible d’éviter les effets de contact responsables du transfert d'atomes entre la pointe et l'échantillon. En outre, l'analyse des défauts est très utile du fait de la présence de nouveaux pics dans le gap du MoS₂ : ils peuvent ainsi être utilisés pour récupérer un pic de courant et donner des perspectives pour améliorer la performance des transistorsThe isolation of graphene, a single stable layer of graphite, composed by a plane of carbon atoms, demonstrated the possibility to separate a single layer of atomic thickness, called bidimensional (2D) material, from the van der Waals (vdW) solids. Thanks to their stability, 2D materials can be used to form vdW heterostructures, a vertical stack of different 2D crystals maintained together by the vdW forces. In principle, due to the weakness of the vdW interaction, each layer keeps its own global electronic properties. Using a theoretical and computational approach based on the Density Functional Theory (DFT) and Keldish-Green formalism, we have studied graphene/MoS₂ heterostructure. In this work, we are interested in the specific electronic properties of graphene and MoS₂ for the conception of field effect transistor: the high mobility of graphene as a basis for high performance transistor and the gap of MoS₂ able to switch the device. First, the graphene/MoS₂ interface is electronically characterized by analyzing the effects of different orientations between the layers on the electronic properties. We demonstrated that the global electronic properties as bandstructure and Density of State (DOS) are not affected by the orientation, whereas, by mean of Scanning Tunneling Microscope (STM) images, we found that different orientations leads to different local DOS. In the second part, graphene/MoS₂ is used as a very simple and efficient model for Field Effect Transistor. The role of the vdW heterostructure in the transistor operation is analyzed by stacking additional and alternate graphene and MoS₂ layers on the simple graphene/MoS₂ interface. We demonstrated that the shape of the DOS at the gap band edge is the fundamental parameter in the switch velocity of the transistor, whereas the additional layers do not improve the transistor behavior, because of the independence of the interfaces in the vdW heterostructures. However, this demonstrates the possibility to study, in the framework of DFT, the transport properties of more complex vdW heterostructures, separating the single interfaces and reducing drastically the calculation time. The 2D materials are also studied in the role of a tip for STM and Atomic Force Microscopy (AFM). A graphene-like tip, tested on defected MoS₂, is compared with a standard copper tip, and it is found to provide atomic resolution in STM images. In addition, due to vdW interaction with the sample, this tip avoids the contact effect responsible for the transfer of atoms between the tip and the sample. Furthermore, the analysis of defects can be very useful since they induce new peaks in the gap of MoS₂: hence, they can be used to get a peak of current representing an interesting perspective to improve the transistor operation
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Ward, P. Daniel. "Rotational Structure of Extremely Floppy van der Waals Complexes: Adiabatic Separation of Angular and Radial Motion." DigitalCommons@USU, 2000. https://digitalcommons.usu.edu/etd/7026.
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The adiabatic or Born-Oppenheimer approximation is often used in molecular calculations to simplify the solution to the Schrodinger equation. The basis of the approximation is the large difference in the relative motions of the nuclei and electrons in the molecule-the electrons are able to respond almost instantly to the movements of the nuclei. Thus, the nuclei may be regarded as being fixed in a certain position and the Schrodinger equation can then be solved using the potential obtained by solving the electronic problem at fixed nuclear configuration.
A similar argument can be used to decouple the angular and radial motions of many van der Waals complexes because, like nuclei in molecules, the radial motions in many van der Waals complexes are strongly localized. Fixing the radial separation between the atoms and molecules in the complex to a particular value results in a Schrodinger equation that is much simpler to solve because it is only dependent on angles. van der Waals complexes containing helium atoms, however, present a dilemma because the extremely weak interactions present also lead to large amplitude radial as well as angular motions. Because the basis of the adiabatic approximation is a large difference in time scale between the angular and radial motions, the validity of the adiabatic approximation for helium complexes is uncertain.
In this thesis, the adiabatic separation of angular and radial motion is shown to be accurate for extremely floppy complexes of helium by demonstrating its use on the van der Waals molecule He-HCN. A major application of this method is expected to be the quick calculation of approximate wave functions for Diffusion Monte Carlo studies of the rotation of impurity molecules inside ultra-cold droplets of helium. The method presented here is significantly faster than other methods (e.g., Variational Monte Carlo) that have been used to calculate approximate wave functions for Diffusion Monte Carlo.
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Hay, Henri. "Étude de la structure et des propriétés des polymorphes de SiO2 et B2O3 par méthodes ab initio." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066318/document.
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Au cours de cette thèse nous avons utilisé la théorie de la fonctionnelle de la densité et les calculs Monte Carlo quantiques pour analyser l'impact des effets de van der Waals sur la structure, l'énergie, et les propriétés des polymorphes de SiO2 et B2O3. Nous avons mis en évidence un phénomène de compensation d'erreur, lié à l'utilisation de fonctionnelle d'échange et corrélation incluant les effets de van der Waals, dans les polymorphes basse densité de SiO2 entre une sur-évaluation des longueurs Si-O et une sous-estimation des angles Si-O-Si. Nous avons effectué des calculs Monte-Carlo quantiques afin de prédire la structure et l'énergie d'un nouveau polymorphe de B2O3 avec une grande précision, ce qui nous a permis d'évaluer les performances de différentes fonctionnelles d'échange et corrélation sur B2O3. Nous avons ensuite utilisé la théorie de la fonctionnelle de la densité pour prédire la structure et l'énergie de 25 nouveaux polymorphes de B2O3 , ainsi que leurs propriétés mécaniques et électroniques. Cette étude permet de proposer une explication à l'anomalie de cristallisation de B2O3, et réconcilie le comportement de B2O3 avec celui des autres oxydes formateurs de réseaux. Elle souligne la possibilité de créer des borates cristallins aux propriétés mécaniques remarquables, et confirme qu'il existe lien entre polymorphisme de basse énergie et facilité de vitrificationDuring this PhD I use density functional theory and quantum Monte Carlo to evaluate the importance of van der Waals effects on the structures, the energies, and the properties of SiO2 and B2O3 polymorphs. I show that exchange-correlation functionals including dispersion effects lead to an error cancellation between an overestimation of the Si-O distances and an underestimation of the Si-O-Si angles in low densities SiO2 polymorphs. By using quantum Monte Carlo calculations, I have predicted with high accuracy the relative energy of a new B2O3 polymorph, which allowed me to evaluate the performances of different exchange-correlation functionals on this material. I then use the best functional possible to compute the mechanical and electronic properties of 25 predicted B2O3 polymorphs. Some of the predicted polymorphs exhibit intriguing mechanical properties, such as negative linear compressibility, auxeticity and anisotropy. These calculations allow me to make a hypothesis explaining the crystallization anomaly in B2O3. They underline a seemingly universal link between low energy polymorphism and ease of vitrification
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Karam, Jean-Christophe. "Collision d'un atome métastable de gaz rare sur une surface nono ou micro-structurée et optique atomique." Paris 13, 2005. http://www.theses.fr/2005PA132029.
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Dans ce travail on a montré l'occurrence de transitions exothermiques et endothermiques entre les niveaux métastables 3P2 et 3P0 dans la collision d'atomes de gaz rare avec une surface solide. Le développement d'une source d'atomes métastables utilisant le processus d'échange de métastabilité au sein d'un jet supersonique a permis ensuite d'observer la diffraction par un réseau de nanofentes, puis, dans une expérience de collision sur un réseau micrométrique en Cuivre en présence d'un champ magnétique externe, d'observer des transitions Zeeman au sein du niveau 3P2. Le calcul, à partir des données spectroscopiques, de l'interaction de van der Waals entre un atome d'argon métastable dans l'état 3P2 et une surface conductrice plane a révélé outre une partie scalaire, une partie quadrupolaire modifiant l'énergie des sous niveaux au voisinage de la surface. Un modèle d'évolution soudaine prédit alors une probabilité de transition dont l'ordre de grandeur est en accord avec l'expérience.
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Jouvet, Christophe. "Étude de la réactivité chimique et de la relaxation électronique dans les complexes de Van der Waals du mercure." Paris 11, 1985. http://www.theses.fr/1985PA112064.
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Le sujet de ce travail est l’étude de la dissociation des états électroniques excités des complexes de Van der Waals. L’excitation optique d’un complexe de Van der Waals permet d’accéder directement au complexe collisionnel. L’étude du complexe mercure azote met en évidence le rôle de la rotation dans la transition de structure fine Hg (³P₁) → Hg (³P₀) induite par collision. La réactivité des états excités du complexe a été étudiée. L’excitation du complexe Hg-Cl₂ au voisinage de la transition ³P₁ - ¹S₀ permet de mettre en évidence le complexe ionique intervenant dans la réaction Hg* + Cl₂ → HgCl* + Cl. Dans l’étude de la réaction Hg* + H₂ → HgH + H dans le complexe Hg-H₂ il a été observé une différence de réactivité des états électroniques du complexeIn this work, the dissociation of the electronic excited state of Van der Waals complexes have been studied. The excitation of the Van der Waals complex allows the direct observation of the collisional complex. The study of the Hg-N₂ complex has shown that rotations play a major role to induce the fine structure transition: Hg (³P₁) + N₂ → Hg (³P₀) +N₂. The chemical reaction within the complex has been studied. In the excitation of the Hg-Cl₂ complex near the Hg (³P₁ - ¹S₀) transition we have observed the Hg⁺ + Cl₂⁻ ionic intermediate of the reaction Hg* + Cl₂ → Hg*Cl + Cl. For the reaction Hg(³P₁) + H₂ → Hg H + H studied in the HgH₂ complex the difference of reactivity between the electronic states of the complex have been observed
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Fujiwara, Takashige. "Structure and Excited-State Dynamics of 9,9′-Bianthryl and its van der Waals Clusters Studied by Rotational Coherence Spectroscopy." 京都大学 (Kyoto University), 2000. http://hdl.handle.net/2433/151661.
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Bonetti, Daniel Rodrigo Ferraz. "Aumento da eficiência do cálculo da energia de van der Waals em algoritmos genéticos para predição de estruturas de proteínas." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-20052010-110415/.
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As proteínas são moléculas presentes nos seres vivos e essenciais para a vida deles. Para entender a função de uma proteína, devese conhecer sua estrutura tridimensional (o posicionamento correto de todos os seus átomos no espaço). A partir da estrutura de uma proteína vital de um organismo causador de uma doença é possível desenvolver fármacos para o tratamento da doença. Para encontrar a estrutura de uma proteína, métodos biofísicos, como Cristalografia de Raio-X e Ressonância Nuclear Magnética têm sido empregados. No entanto, o uso desses métodos tem restrições práticas que impedem a determinação de várias estruturas de proteínas. Para contornar essas limitações, métodos computacionais para o problema de predição da estrutura da proteína (PSP, Protein Structure Prediction) têm sido investigados. Várias classes de métodos computacionais têm sido desenvolvidas para o problema de PSP. Entre elas, as abordagens ab initio são muito importantes, pois não utilizam nenhuma informação prévia de outras estruturas de proteínas para fazer o PSP, apenas a sequência de aminoácidos da proteína e o gráfico de Ramachandran são empregados. O PSP ab initio é um problema combinatorial que envolve relativamente grandes instâncias na prática, por exemplo, as proteínas em geral têm centenas ou milhares de variáveis para determinar. Para vencer esse entrave, metaheurísticas como os Algoritmos Genéticos (AGs) têm sido investigados. As soluções geradas por um AG são avaliadas pelo cálculo da energia potencial da proteína. Entre elas, o cálculo da interação da energia de van der Waals é custoso computacionalmente tornando o processo evolutivo do AG muito lento mesmo para proteínas pequenas. Este trabalho investiga técnicas para reduzir significativamente o tempo de execução desse cálculo. Basicamente, foram propostas modificações de técnicas de paralelização utilizando MPI e OpenMP para os algoritmos resultantes. Os resultados mostram que o cálculo pode ser 1.500 vezes mais rápido para proteínas gigantes quando aplicadas as técnicas investigadas neste trabalhoProteins are molecules present in the living organism and essential for their life. To understand the function of a protein, its threedimensional structure (the correct positions of all its atoms in the space) should be known. From the structure of a vital protein of an organism that causes a human disease, it is possible to develop medicines for treatment of the disease. To find a protein structure, biophysical methods, as Crystallography of X-Ray and Magnetic Nuclear Resonance, have been employed. However, the use of those methods have practical restrictions that impede the determination of several protein structures. Aiming to overcome such limitation, computational methods for the problem of protein structure prediction (PSP) has been investigated. Several classes of computational methods have been developed for PSP. Among them, ab initio approaches are very important since they use no previous information from other protein structure, only the sequence of amino acids of the protein and the Ramachandran graph are employed. The ab initio PSP is a combinatorial problem that involves relatively large instances in practice, i. e. proteins in general have hundreds or thousands of variables to be determined. To deal with such problem, metaheuristics as Genetic Algorithms (GAs) have been investigated. The solutions generated by a GA are evaluated by the calculus of the potencial energies of the protein. Among them, the calculation of the interaction of van der Waals energy is computationally intense making the evolutionary process of a GA very slow even for non-large proteins. This work investigated techniques to significantly reduce the running time for that calculus. Basically, we proposed modifications parallelization of the resultant algorithm using MPI and OpenMP techniques. The results show that such calculus can be 1.500 times faster when applying the techniques investigated in this work for large proteins
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Kowalczyk, Philippe. "Super-réseaux GeTe/Sb2Te3 pour les mémoires iPCM : croissance PVD par épitaxie van der Waals et étude de leur structure." Thesis, Université Grenoble Alpes (ComUE), 2018. http://www.theses.fr/2018GREAT109/document.
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Afin de faire face à la demande croissante de mémoires de plus en plus performantes dans les systèmes informatiques, de nouvelles technologies se sont développées. Parmi elles, les mémoires résistives à changement de phase (ou PCM pour Phase-Change Memory) ont des propriétés et une maturité suffisante pour développer les nouvelles mémoires SCM (pour Storage Class Memory) comme en témoigne la récente commercialisation des produits Optane par la firme INTEL®. Néanmoins, la consommation énergétique des PCM lors de leur programmation reste élevée, ce qui limite leurs performances. L’intégration de super-réseaux (GeTe)2/(Sb2Te3)m dans des mémoires dites iPCM (pour interfacial Phase-Change Memory) est une des voies les plus prometteuse pour permettre une diminution significative des courants de programmation. Cependant, le mécanisme de transition des iPCM et la structure du matériau dans ses deux états de résistances sont encore méconnus. Dans ce contexte, l’objectif de cette thèse est d’élaborer des super-réseaux (GeTe)2/(Sb2Te3)m (m=1,2,4 et 8) cristallins, de déterminer leur structure puis de les intégrer dans des dispositifs mémoires. La pulvérisation cathodique alternée des matériaux GeTe et Sb2Te3 dans un équipement industriel de dépôt est utilisée pour effectuer l’épitaxie van der Waals de ces super-réseaux. Une optimisation du procédé par l’ajout d’une cible de Te en co-pulvérisation avec la cible de Sb2Te3 montre l’obtention de super-réseaux stœchiométriques présentant la périodicité souhaitée, ainsi qu’une orientation des plans cristallins (0 0 l) parallèle à la surface du substrat. Une description de l’ordre atomique local des super-réseaux ainsi optimisés est ensuite menée par l’étude d’images HAADF-STEM couplée à des simulations. Celle-ci révèle un phénomène d’inter-diffusion entre les couches de GeTe et de Sb2Te3 déposées aboutissant à la formation locale de GexSbyTez rhomboédriques, des mesures quantitatives de l’occupation des plans atomiques en Ge/Sb confirment aussi le phénomène. De plus, un modèle de structure à longue distance de ces super-réseaux considérant un empilement aléatoire de blocs cristallins permet la simulation des courbes de diffraction obtenues expérimentalement. Enfin, les premières intégrations des super-réseaux (GeTe)2/(Sb2Te3)m dans des dispositifs mémoires mettent en évidence une réduction importante des courants de programmation jusqu’à 4 fois inférieurs à une PCM et avec une endurance dépassant les 10 millions cyclesIn order to satisfy the demand for more and more efficient memory in computer systems, new technologies have been developed. Among the latter resistive phase-change memories (PCM) exhibit capacities and sufficient maturity to achieve the so-called new SCM (for Storage Class Memory) devices as evidenced by the recent commercialization of Optane products by INTEL®. Nevertheless, PCM still require strong electrical consumption limiting their performance. Integration of (GeTe)2/(Sb2Te3)m superlattices in so-called iPCM (for interfacial Phase Change Memory) was shown to permit a significant decrease in programming currents. However, the switching mechanism of this memory and the structure of the material in its two resistance states are still under debate. The aim of this thesis is therefore to deposit crystalline (GeTe)2/(Sb2Te3)m (m=1,2,4 et 8) superlattices, to determine their structure and to integrate them into memory devices. GeTe and Sb2Te3 materials are alternately deposited by means of sputtering in an industrial deposition tool to perform van der Waals epitaxy of these superlattices. Stoichiometric superlattices with the desired periodicity and with an orientation of the (0 0 l) crystalline planes parallel to the surface of the substrate are obtained by innovative co-sputtering of Sb2Te3 and Te targets during Sb2Te3 deposition. A description of the local atomic order of superlattices is then carried out by studying HAADF-STEM images coupled to simulations. Intermixing between GeTe and Sb2Te3 deposited layers is thus revealed, leading to the local formation of rhombohedral GexSbyTez. Quantitative measurements of the Ge/Sb atomic plans occupation in further confirm the phenomenon. A long-range order structural model of superlattices by means of random stacking of crystalline blocks allows the simulation of experimental diffraction curves. Finally, the first integrations of (GeTe)2/(Sb2Te3)m (with m=1,2,4 et 8) superlattices in devices demonstrate a programming current up to 4 times lower than a PCM reference with an endurance exceeding 10 millions cycles
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Al, Mohammad Ahmad. "Structure et morphologie des surfaces d'Al2O3α et des films minces WO3 : application à leurs interactions avec Au." Aix-Marseille 3, 2001. http://www.theses.fr/2001AIX30011.
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Ce travail concerne l'étude des surfaces d'oxydes (la préparation, la structure, la morphologie) et de leur interaction avec un dépôt métallique (la granulométrie et la réactivité). Les surfaces d'oxyde qui ont été utilisées sont des surfaces l'alumine et d'oxyde de tungstène. Après avoir préparé et caractérisé les surfaces substrats du point de vue cristallographique par RHEED, AFM, et AES, nous avons étudiée la croissance d'un dépôt d'or sur ces différentes surfaces utilisées comme substrats. Nous avons étudié l'influence de la structure atomique d'une surface sur la croissance de l'or et caractérisé l'interaction entre cette surface et les atomes d'or. Pour ceci nous avons examiné des dépôts d'or de différentes épaisseurs, obtenus à différentes températures sur des surfaces (1012) et (0001) d'AI2O3 stœchiométriques ou réduites. Nous avons mis en évidence des différences dans les mécanismes de croissance de l'or sur ces surfaces: sur les surface stœchiométriques la croissance s'effectue atome par atome et par coalescence des particules. Sur les surfaces réduites la croissance ne se fait qu'atome par atome. Des expériences de croissance nous avons déduit les énergies d'adsorption des atomes d'or sur ces surfaces. .This work concerns the study of the oxyde surfaces (preparation, structure, morphology) and their interaction with metallic deposit (granulometry and reactivity). The oxide surfaces which were used are the alumina surfaces and tungsten oxide. We prepared and characterized the crystallographic structure of the substrate surfaces by RHEED, AFM, and AES techniques. We studied the growth of gold deposit on these various surfaces. We studied the influence of the surface atomic structure on the gold deposit growth and investigated the interactions between the surface and the gold atoms. For that we examined gold deposits of various thicknesses, deposited at various temperatures on stoichiometric or reduced surfaces (1012 ) and (0001) of alumina. .
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Dennis, Christopher Roger. "High resolution spectroscopy of open shell clusters." Thesis, University of Oxford, 1997. http://ora.ox.ac.uk/objects/uuid:43ac8ad5-724a-4a23-a03f-3eb78e6f4e72.
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The microwave spectrum of the open-shell van der Waals complex NO-HF has been recorded in the region 6-20GHz using a pulsed nozzle Fourier transform microwave spectrometer. This is the first observation of the microwave spectrum of a open-shell van der Waals complex between two molecules. The spectrum exhibits a rich hyperfine structure with the observation of intermolecular hyperfine interactions in an isolated system providing a sensitive probe of electron transfer in the complex. The spectrum consists of four fine structure transitions 5/2(e)-3/2(e), 3/2(e)-1/2(e), 5/2(f)-3/2(f), 3/2(f)-1/2(f) which have been fitted to a semi-rigid Hamiltonian developed to include the effects of the orbital and spin angular momenta of the unpaired electron on NO. A new treatment to account for the intermolecular hyperfine interaction was developed. The structure of the complex has been determined and is significantly bent with an angle of between 37 degrees and 49 degrees between the NO internuclear axis and the a-axis of the complex. The Renner-Teller parameter, epsilon 2, is very large and negative having the value of -10 449.32(4)GHz indicating that configuration with the unpaired electron in the plane of the complex is more stable. The analysis of the hyperfine interactions of the hydrogen and fluorine nuclei uses two constants for each nucleus, one for the spatial relationship between the magnetic moments of the unpaired electron and the nuclear magnetic moment and a Fermi-contact term. The Fermi-contact term for hydrogen is the first strong evidence of intermolecular charge transfer in an isolated van der Waals molecule.
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Sant, Roberto. "Exploration par rayonnement synchrotron X de la croissance et de la structure de dichalcogénures 2D." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAY075.
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Les dichalcogenures de métaux de transition bidimensionnels (2D) suscitent un grand intérêt pour des applications variées, principalement en optoelectronique. Toutefois, la faible compréhension des mécanismes liés à leur épitaxie, de leur microstructure et de la nature de leur interaction avec le substrat représentent encore des problèmes ouverts. Nous avons exploré un certain nombre de croissances épitaxiales des dichalcogenures 2D préparés par épitaxie à jets moléculaires sur des substrats différents. Nous en avons examiné la structure atomique et essayé d’en modifier certains in situ. Plusieurs systèmes et processus ont été étudiés: (i) des tellurures de métaux de transition, ZrTe2, MoTe2 et TiTe2, épitaxiés sur un substrat de InAs(111), (ii) l’intercalation d’espèces atomique alcalines entre une monocouche de MoS2 et son substrat d’Au(111), (iii) la croissance et le traitement thermique sous atmosphère de H2S d’une monocouche de PtSe2 sur Pt(111). Notre travail s’appuie sur des approches à la fois phénoménologiques et quantitatives de diffraction de rayons X de surface, souvent complétées par ses analyses effectuées à l’aide d’autres techniques (STM, TEM, XPS et ARPES). Les principaux résultats sont que: (i) une phase orthorhombique et une onde de densité de charge sont stabilisées à température ambiante dans les couches de MoTe2 et TiTe2 par un effet de déformation induite par l’épitaxie; (ii) l’intercalation de césium (Cs) au-dessous du MoS2 induit un découplage structurel mais aussi électronique de la monocouche de son substrat; (iii) la sulfurisation de PtSe2 à chaud en conditions contrôlées permet de substituer des atomes de Se par des atomes de S dans la couche supérieure du dichalcogenure, formant ainsi un alliage ordonné de SPtSe, structure de type JanusTwo-dimensional transition metal dichalcogenides (TMDCs) are promising materials for a variety of applications, especially in optoelectronics. However, the lack of understanding of their epitaxy - i.e. growth mechanism, microscopic structure, nature of the 2D layer-substrate interaction, etc. - is still a crucial issue to address. In this PhD thesis we explored a series of epitaxial growths of monolayer and thin film TMDCs grown by molecular beam epitaxy (MBE) on a variety of substrates. We studied their atomic structures and we attempted the modifications of some of them with various in situ methods. Several systems and processes have been investigated: (i) transition metal ditellurides, ZrTe2 , MoTe2 and TiTe2 on InAs(111) substrate, (ii) the intercalation of alkali metal species between single layer MoS2 and its Au(111) substrate, (iii) the growth and the thermal treatments in H2S atmosphere of monolayer PtSe2 on Pt(111). Our work relies on both phenomenological and quantitative methods based on surface X-ray diffraction, often complemented by parallel analysis performed with other probes, e.g. STM, TEM, XPS, ARPES. Most notably, we found that: (i) a metastable orthorhombic phase and a charge density wave phase can be stabilized at room temperature in MoTe2 and TiTe2 owing to the epitaxial strain in the materials; (ii) the intercalation of Cs atoms under MoS2 induces structural and electronic decoupling of the 2D MoS2 layer from its Au(111) substrate; (iii) the sulfurization of PtSe2 promotes the Se-by-S substitution in one (or both) of its two chalcogen layers, leading either to the full conversion of the selenide into a sulfide or even to an ordered Janus alloy
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Augustus, Adebayo Samuel. "Attractive steric interactions." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391708.
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Chevereau, Élodie. "Synthèse et caractérisation physico-chimique d'un matériau membranaire à structure contrôlée : étude expérimentale de la sélectivité." Lorient, 2011. http://www.theses.fr/2011LORIS249.
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L’objectif de ce travail était de synthétiser des membranes inorganiques type mordénite en vue d’une application en nanofiltration ou en ultrafiltration à bas-seuil de coupure. Cette étude repose sur l’interprétation des mécanismes de transport régissant la rétention d’ions monovalents et divalents au travers d’une membrane minérale à structure contrôlée. La démarche qui a été mise en place nous a conduit, dans un premier temps, à s’assurer de la nature des produits synthétisés et à identifier leurs propriétés de surface, morphologique, et électrique. Nous avons choisi de déterminer les paramètres spécifiques des mordénites synthétisées (tels que le rayon de pore, la surface spécifique, et la charge de surface) à partir des poudres utilisées pour préparer les membranes associées. Parallèlement à ces caractérisations physico-chimiques, des essais de filtration ont été réalisés sur des pilotes de laboratoire afin d’étudier la sélectivité d’une membrane mordénite vis-à-vis des sels monovalents et divalents. Pour cela, un protocole expérimental a été mis en place. Nous avons réussi à observer la rétention d’ions monovalents de petites tailles après modification des propriétés de surface de la mordénite. Le passage facilité ainsi que la rétention spécifique d’ions mono- et divalents ont également été observés dans certaines conditions opératoires. Ainsi, les résultats obtenus lors des essais de filtration en solutions pures et en mélanges nous ont conduit à formuler plusieurs hypothèses concernant les interactions membrane-solutés : la membrane se comporte comme une surface dont la polarité peut être modifiée suite à un traitement alcalin, la polarisabilité des ions hydratés diminue avec leurs enthalpies d’hydratation, les interactions entre la surface traitée et ces ions dépendent des forces de Van der WaalsThe aim of this work was to synthesize mordenite membrane for an application in nanofiltration or in low cut-off ultrafiltration and to understand the transport mechanisms governing the retention of monovalent and divalent ions through a controlled structure mineral membrane. The approach what has been implemented has led us, at first, to ascertain the nature of synthesized products and identify their surface, morphological and electrical properties. We chose to determine the specific parameters of the synthesized mordenite (such as pore radius, surface area and surface charge) from the powders used to prepare the related membrane. In addition to these physical and chemical characterizations, filtration tests were carried out on pilot unit in order to study the mordenite membrane selectivity toward monovalent and divalent salt-water solution. For this, an experimental protocol was defined. We managed to observe the retention of small monovalent ions after changing the surface properties of mordenite. The preferential transport and the specific retention of mono- and divalent ions were also observed under certain operating conditions. Thus, the results obtained during the filtration tests in single and mixed solutions led us to make several hypotheses about solute-membrane interactions: the membrane behaves as a surface whose the polarity can be changed after an alkaline treatment, the polarizability of hydrated ions decreases with their enthalpies of hydration, the interaction between the treated surface and theses ions depend on the Van der Waals forces
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Bonetti, Daniel Rodrigo Ferraz. "Algoritmos de estimação de distribuição para predição ab initio de estruturas de proteínas." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-03082015-193613/.
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As proteínas são moléculas que desempenham funções essenciais para a vida. Para entender a função de uma proteína é preciso conhecer sua estrutura tridimensional. No entanto, encontrar a estrutura da proteína pode ser um processo caro e demorado, exigindo profissionais altamente qualificados. Neste sentido, métodos computacionais têm sido investigados buscando predizer a estrutura de uma proteína a partir de uma sequência de aminoácidos. Em geral, tais métodos computacionais utilizam conhecimentos de estruturas de proteínas já determinadas por métodos experimentais, para tentar predizer proteínas com estrutura desconhecida. Embora métodos computacionais como, por exemplo, o Rosetta, I-Tasser e Quark tenham apresentado sucesso em suas predições, são apenas capazes de produzir estruturas significativamente semelhantes às já determinadas experimentalmente. Com isso, por utilizarem conhecimento a priori de outras estruturas pode haver certa tendência em suas predições. Buscando elaborar um algoritmo eficiente para Predição de Estruturas de Proteínas livre de tendência foi desenvolvido um Algoritmo de Estimação de Distribuição (EDA) específico para esse problema, com modelagens full-atom e algoritmos ab initio. O fato do algoritmo proposto ser ab initio é mais interessante para aplicação envolvendo proteínas com baixa similaridade, com relação às estruturas já conhecidas. Três tipos de modelos probabilísticos foram desenvolvidos: univariado, bivariado e hierárquico. O univariado trata o aspecto de multi-modalidade de uma variável, o bivariado trata os ângulos diedrais (Φ Ψ) de um mesmo aminoácido como variáveis correlacionadas. O hierárquico divide o problema em subproblemas e tenta tratá-los separadamente. Os resultados desta pesquisa mostraram que é possível obter melhores resultados quando considerado a relação bivariada (Φ Ψ). O hierárquico também mostrou melhorias nos resultados obtidos, principalmente para proteínas com mais de 50 resíduos. Além disso, foi realiza uma comparação com algumas heurísticas da literatura, como: Busca Aleatória, Monte Carlo, Algoritmo Genético e Evolução Diferencial. Os resultados mostraram que mesmo uma metaheurística pouco eficiente, como a Busca Aleatória, pode encontrar a solução correta, porém utilizando muito conhecimento a priori (predição que pode ser tendenciosa). Por outro lado, o algoritmo proposto neste trabalho foi capaz de obter a estrutura da proteína esperada sem utilizar conhecimento a priori, caracterizando uma predição puramente ab initio (livre de tendência).Proteins are molecules that perform critical roles in the living organism and they are essential for their lifes. To understand the function of a protein, its 3D structure should be known. However, to find the protein structure is an expensive and a time-consuming task, requiring highly skilled professionals. Aiming to overcome such a limitation, computational methods for Protein Structure Prediction (PSP) have been investigated, in order to predict the protein structure from its amino acid sequence. Most of computational methods require knowledge from already determined structures from experimental methods in order to predict an unknown protein. Although computational methods such as Rosetta, I-Tasser and Quark have showed success in their predictions, they are only capable to predict quite similar structures to already known proteins obtained experimentally. The use of such a prior knowledge in the predictions of Rosetta, I-Tasser and Quark may lead to biased predictions. In order to develop a computational algorithm for PSP free of bias, we developed an Estimation of Distribution Algorithm applied to PSP with full-atom and ab initio model. A computational algorithm with ab initio model is mainly interesting when dealing with proteins with low similarity with the known proteins. In this work, we developed an Estimation of Distribution Algorithm with three probabilistic models: univariate, bivariate and hierarchical. The univariate deals with multi-modality of the distribution of the data of a single variable. The bivariate treats the dihedral angles (Proteins are molecules that perform critical roles in the living organism and they are essential for their lifes. To understand the function of a protein, its 3D structure should be known. However, to find the protein structure is an expensive and a time-consuming task, requiring highly skilled professionals. Aiming to overcome such a limitation, computational methods for Protein Structure Prediction (PSP) have been investigated, in order to predict the protein structure from its amino acid sequence. Most of computational methods require knowledge from already determined structures from experimental methods in order to predict an unknown protein. Although computational methods such as Rosetta, I-Tasser and Quark have showed success in their predictions, they are only capable to predict quite similar structures to already known proteins obtained experimentally. The use of such a prior knowledge in the predictions of Rosetta, I-Tasser and Quark may lead to biased predictions. In order to develop a computational algorithm for PSP free of bias, we developed an Estimation of Distribution Algorithm applied to PSP with full-atom and ab initio model. A computational algorithm with ab initio model is mainly interesting when dealing with proteins with low similarity with the known proteins. In this work, we developed an Estimation of Distribution Algorithm with three probabilistic models: univariate, bivariate and hierarchical. The univariate deals with multi-modality of the distribution of the data of a single variable. The bivariate treats the dihedral angles (Φ Ψ) within an amino acid as correlated variables. The hierarchical approach splits the original problem into subproblems and attempts to treat these problems in a separated manner. The experiments show that, indeed, it is possible to achieve better results when modeling the correlation (Φ Ψ). The hierarchical model also showed that is possible to improve the quality of results, mainly for proteins above 50 residues. Besides, we compared our proposed techniques among other metaheuristics from literatures such as: Random Walk, Monte Carlo, Genetic Algorithm and Differential Evolution. The results show that even a less efficient metaheuristic such as Random Walk managed to find the correct structure, however using many prior knowledge (prediction that may be biased). On the other hand, our proposed EDA for PSP was able to find the correct structure with no prior knowledge at all, so we can call this prediction as pure ab initio (biased-free).
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Shtogun, Yaroslav. "Properties of Carbon Nanotubes Under External Factors: Adsorption, Mechanical Deformations, Defects, and External Electric Fields." Scholar Commons, 2010. https://scholarcommons.usf.edu/etd/1771.
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Carbon nanotubes have unique electronic, optical, mechanical, and transport properties which make them an important element of nanoscience and nanotechnology. However, successful application and integration of carbon nanotubes into new nanodevices requires fundamental understanding of their property changes under the influence of many external factors. This dissertation presents qualitative and quantitative theoretical understanding of property changes, while carbon nanotubes are exposed to the deformations, defects, external electric fields, and adsorption. Adsorption mechanisms due to Van der Waals dispersion forces are analyzed first for the interactions of graphitic materials and biological molecules with carbon nanotubes. In particular, the calculations are performed for the carbon nanotubes and graphene nanoribbons, DNA bases, and their radicals on the surface of carbon nanotubes in terms of binding energies, structural changes, and electronic properties alterations. The results have shown the importance of many-body effects and discrete nature of system, which are commonly neglected in many calculations for Van der Waals forces in the nanotube interactions with other materials at nanoscale.
Then, the effect of the simultaneous application of two external factors, such as radial deformation and different defects (a Stone Wales, nitrogen impurity, and mono-vacancy) on properties of carbon nanotubes is studied. The results reveal significant changes in mechanical, electrical, and magnetic characteristics of nanotubes. The complicated interplay between radial deformation and different kinds of defects leads to the appearance of magnetism in carbon nanotubes which does not exist in perfect ones. Moreover, the combined effect of radial deformation and external electric fields on their electronic properties is shown for the first time. As a result, metal-semiconductor or semiconductor-metal transitions occur and are strongly correlated with the strength and direction of external electric field and the degree of radial deformations.
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Vexiau, Romain. "Dynamique et contrôle optique des molécules froides." Phd thesis, Université Paris Sud - Paris XI, 2012. http://tel.archives-ouvertes.fr/tel-00783399.
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Le travail théorique présenté dans cette thèse concerne la formation de molécules ultra-froides bialcalines et le contrôle de leurs degrés de liberté externes et internes. Cette étude est motivée par les nombreuses expériences en cours visant à l'obtention d'un gaz quantique dégénéré de molécules dans leur état fondamental absolu. Le schéma de formation étudié repose sur le processus de transfert adiabatique stimulé (STIRAP) réalisé en présence d'un potentiel optique de piégeage (réseau optique) des atomes et des molécules.Nous avons déterminé les paramètres du réseau optique (intensité et fréquence du champ laser) qui permettent de piéger efficacement des dimères d'alcalins en évaluant la polarisabilité dynamique acquise par les molécules soumises à un champ externe. Ces calculs reposent en particulier sur la connaissance détaillée de la structure électronique des molécules. Nous avons identifié des plages de longueur d'ondes dites " magiques " où la polarisabilité est la même pour chaque niveau peuplé au cours du transfert adiabatique, permettant ainsi un transfert optimal. Ce formalisme nous a également permis d'obtenir les coefficients Van der Waals de l'interaction à longue portée nécessaires pour étudier les taux de collisions entre molécules.Nous avons réalisé une étude plus détaillée de la molécule RbCs. En étudiant précisément la probabilité de transition de la molécule vers un niveau excité, nous avons proposé un schéma STIRAP pour transférer des molécules de RbCs, initialement dans un niveau vibrationnel excité, vers leur état rovibrationnel fondamental.Ces travaux ont montré l'importance de la connaissance précise de la structure hyperfine de l'état électronique moléculaire excité pour réaliser un gaz dégénéré de molécules dans un état quantique bien défini. Un modèle asymptotique nous a permis d'obtenir une première estimation de la structure hyperfine des courbes d'énergies potentielles des premiers états moléculaires excités des molécules Cs2 et RbCs.
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Zehnacker-Rentien, Anne. "Structure et dynamique de complexes aromatiques formés en jet supersonique." Paris 11, 1988. http://www.theses.fr/1988PA112125.
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Étude spectroscopique de complexes de Van der Waals formés à partir d'un dérivé monosubstitué du benzène (anisole, aniline, benzonitrile) et du benzène. Étude théorique de la conformation au moyen du modelé de Buckingham. Calcul des énergies de liaison à l'état fondamental
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Ben, Jabra Zouhour. "Study of new heterostructures : silicene on graphene." Electronic Thesis or Diss., Aix-Marseille, 2021. http://www.theses.fr/2021AIXM0583.
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Le but de ce travail est la croissance du silicène sur Gr. J'ai décrit le substrat en fonction des conditions d’élaboration par CVD. Lorsque la proportion de H2 est faible il est possible d’obtenir du Gr homogène sur couche tampon (BL) sur SiC. Le STM et LEED montrent la superposition de la maille du Gr et de la reconstruction de la BL représentatif du Gr épitaxié. Lorsque la proportion de H2 est élevée la couche de Gr obtenue est totalement hydrogénée. Ceci est un résultat nouveau car aucun procédé d’intercalation d’hydrogène n’avait permis jusqu’à présent d’hydrogéner totalement les échantillons de (6x6)Gr épitaxié sur BL. Pour des proportions intermédiaires de H2/Ar, la coexistence de (6x6)Gr et H-Gr est observée. En fonction de la proportion de H2 dans le mélange gazeux, soit la surface du SiC reste passivée pendant toute la croissance du Gr et on obtient du H-Gr, soit le H2 désorbe partiellement, ou totalement et on obtient soit la coexistence des deux structures soit du (6x6)Gr pleine plaque. J’ai étudié la croissance par MBE de Si-ene sur (6x6)Gr. J’ai démontré qu'il est possible de former des flaques de Si-ene pour des épaisseurs de dépôt <0.5MC. Nous observons la présence de zones planes d’une épaisseur de 0.2-0.3nm correspondant à une monocouche de Si-ene, entourées d’îlots dendritiques 3D de Si. Les spectres Raman mettent en évidence un pic allant jusqu’à 563cm-1 ce qui est la valeur la plus proche du Si-ene FS jamais obtenue. Ces démontrent la formation de Si-ene quasi-FS. Ce travail contribue à une meilleure compréhension du mécanisme de croissance CVD du Gr et à l’avancement des recherches dans le domaine de la croissance épitaxiale des matériaux 2DThe topic of this thesis deals with the study of the growth and properties of silicene (Si-ene) on graphene (Gr) on 6H-SiC(0001) with the final goal of forming free-standing (FS) Si-ene on an insulating or semiconductor substrate. I have described the substrate as a function of the CVD processing conditions. When the proportion of H2 is low it is possible to obtain homogeneous Gr on buffer layer (BL) on SiC. The STM and LEED show the superposition of the Gr mesh and the BL reconstruction representative of the epitaxial Gr. When the proportion of H2 is high, the resulting Gr layer is fully hydrogenated. This is a new result as no hydrogen intercalation process has been able to fully hydrogenate (6x6)Gr samples epitaxial on BL until now. For intermediate proportions of H2/Ar, the coexistence of (6x6)Gr and H-Gr is observed. Depending on the proportion of H2 in the gas mixture, either the SiC surface remains passivated during the entire Gr growth and H-Gr is obtained, or the H2 partially or totally desorbs and either both structures coexist or full plate (6x6)Gr is obtained. I have studied the MBE growth of Si-ene on (6x6)Gr. I have shown that it is possible to form Si-ene puddles for deposit thicknesses <0.5MC. We observe the presence of flat areas of 0.2-0.3nm thickness corresponding to a Si-ene monolayer, surrounded by 3D dendritic islands of Si. The Raman spectra show a peak up to 563cm-1 which is the closest value to Si-ene FS ever obtained. This demonstrates the formation of quasi-FS Si-ene. This work contributes to a better understanding of the CVD growth mechanism of Gr and to the advancement of research in the field of epitaxial growth of 2D materials
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Karam, Jean-Christophe. "Collision d'un atome métastable de gaz rare sur une surface nano ou micro-structurée et optique atomique." Phd thesis, Université Paris-Nord - Paris XIII, 2005. http://tel.archives-ouvertes.fr/tel-00383051.
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Dans cette thèse, on a montré l'occurrence de transitions exothermiques et endothermiques entre les niveaux métastables 3P_2 et 3P_0 dans la collision d'atomes de gaz rare avec une surface solide. Le développement d'une source d'atomes métastables utilisant le processus d'échange de métastabilité au sein d'un jet supersonique a permis ensuite d'observer la diffraction par un réseau de nanofentes, puis, dans une expérience de collision sur un réseau micrométrique en Cuivre en présence d'un champ magnétique externe, d'observer des transitions Zeeman au sein du niveau 3P_2. Le calcul, à partir des données spectroscopiques, de l'interaction de van der Waals entre un atome d'argon métastable dans l'état 3P_2 et une surface conductrice plane a révélé outre une partie scalaire, une partie quadrupolaire modifiant l'énergie des sous niveaux au voisinage de la surface. Un modèle d'évolution soudaine prédit alors une probabilité de transition dont l'ordre de grandeur est en accord avec l'expérience.
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Giunchi, Andrea <1993>. "Computing the structural and vibrational properties of polymorphic organic molecular crystals through van der Waals corrected density functional theory and the electronic properties of organic thin films through microelectrostatic calculations." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2021. http://amsdottorato.unibo.it/9829/1/tesi_Andrea_Giunchi_21.pdf.
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The present Thesis reports on the various research projects to which I have contributed during my PhD period, working with several research groups, and whose results have been communicated in a number of scientific publications.
The main focus of my research activity was to learn, test, exploit and extend the recently developed vdW-DFT (van der Waals corrected Density Functional Theory) methods for computing the structural, vibrational and electronic properties of ordered molecular crystals from first principles. A secondary, and more recent, research activity has been the analysis with microelectrostatic methods of Molecular Dynamics (MD) simulations of disordered molecular systems.
While only very unreliable methods based on empirical models were practically usable until a few years ago, accurate calculations of the crystal energy are now possible, thanks to very fast modern computers and to the excellent performance of the best vdW-DFT methods. Accurate energies are particularly important for describing organic molecular solids, since they often exhibit several alternative crystal structures (polymorphs), with very different packing arrangements but very small energy differences. Standard DFT methods do not describe the long-range electron correlations which give rise to the vdW interactions. Although weak, these interactions are extremely sensitive to the packing arrangement, and neglecting them used to be a problem. The calculations of reliable crystal structures and vibrational frequencies has been made possible only recently, thanks to development of some good representations of the vdW contribution to the energy (known as “vdW corrections”).
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Marcon, Paul. "Calcul ab-initio des propriétés physiques d'hétérostructures associant des matériaux ferromagnétiques à anisotropie magnétique perpendiculaire et des dichalcogénures de métaux de transition." Electronic Thesis or Diss., Toulouse 3, 2023. http://www.theses.fr/2023TOU30273.
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La possibilité de synthétiser des hétérostructures formées de matériaux 2D offre des perspectives majeures pour l'amélioration des composants spintroniques actuels ou la réalisation de nouveaux dispositifs. Le contrôle et la bonne compréhension des propriétés physiques de ces systèmes constituent de fait un enjeu technologique majeur. Au cours de cette thèse, nous avons étudié, à l'aide de calculs ab initio basés sur la théorie de la fonctionnelle de la densité (DFT), des hétérostructures formées de monocouches de dichalcogénures de métaux de transition (TMDCs) et de cristaux ferromagnétiques présentant une anisotropie magnétique perpendiculaire. Trois objectifs principaux ont été définis : (i) comprendre comment utiliser la proximité magnétique pour lever la dégénérescence des vallées et quantifier l'effet Zeeman des vallées ; (ii) évaluer la possibilité d'injecter un gaz d'électrons polarisé en spin dans des vallées spécifiques du feuillet de TMDC ; (iii) examiner l'impact de la proximité sur le couplage spin-orbite dans le feuillet de TMDC et sur les phénomènes Rashba et Dresselhaus dans ces systèmes. Nous avons d'abord étudié des multicouches possédant une électrode constituée d'un métal et d'une barrière isolante non 2D. Dans le système Fe/MgO/MoS2, nous avons calculé qu'un transfert d'électrons spontané s'opère de la couche de Fe vers le monofeuillet de MoS2, donnant lieu à la formation d'un gaz d'électrons non polarisé en spin. Nous avons établi un modèle expliquant la compétition entre les effets spin-orbite de type Rashba et Dresselhaus et les effets de proximité magnétique sur les bandes de valence de MoS2 : Ce modèle nous a permis de montrer que les effets de proximité sont prédominants pour une faible épaisseur de MgO (<0.42 nm), et tendent à disparaître au profit des effets spin-orbite pour à plus forte épaisseur (> 1.06 nm). Nous avons prédit qu'il est possible d'obtenir des effets spin-orbites plus forts en remplaçant l'électrode de Fe par une électrode non-magnétique de V. Afin d'augmenter les effets de proximité magnétique, nous avons finalement décider d'étudier des hétérostructures [Co1Ni2]n/h-BN/WSe2, dans lesquelles [Co1Ni2]n est un super réseau à anisotropie magnétique perpendiculaire et h-BN un isolant bidimensionnel. Pour ce système, nous prédisons qu'il serait possible d'avoir une polarisation en spin des vallées aux points K et K'. Finalement, nous avons étudié les propriétés particulières de l'hétérostructure de van der Waals Graphène/CrI3/WSe2,dans laquelle l'électrode magnétique est également remplacée par des matériaux 2DThe ability to synthesize heterostructures made up of 2D materials provides significant opportunities for improving current spintronic components or developing new devices. Thus, the control and deep understanding of the physical properties of these systems become a critical technological challenge. During this thesis, we examined heterostructures composed of transition metal dichalcogenide (TMDC) monolayers and ferromagnetic crystals exhibiting perpendicular magnetic anisotropy, using ab initio calculations based on density functional theory (DFT). We focus on three main goals: (i) understanding how to use magnetic proximity to lift valley degeneracy and quantify the valley Zeeman effect; (ii) assessing the possibility of injecting spin-polarized electron gas into specific valleys of the TMDC sheet; (iii) investigating the impact of proximity on spin-orbit coupling in the TMDC sheet and on the Rashba and Dresselhaus phenomena in these systems. We first studied multilayers with an electrode made up of a metal and a non-2D insulating barrier. In the Fe/MgO/MoS2 system, we computed that a spontaneous electron transfer occurs from the Fe layer to the MoS2 monolayer, leading to the formation of a non-spin-polarized electron gas. We established a model explaining the competition between Rashba and Dresselhaus-type spin-orbit effects and magnetic proximity effect on the MoS2 valence bands: This model allowed us to show that proximity effect predominate for thin MgO (<0.42 nm) and tend to disappear in favor of spin-orbit effects for thicker layers (> 1.06 nm). We predicted that stronger spin-orbit effects can be achieved by replacing the Fe electrode with a non-magnetic V electrode. To boost the magnetic proximity effects, we finally decided to study [Co1Ni2]n/h-BN/WSe2 heterostructures, in which [Co1Ni2]n is a superlattice with perpendicular magnetic anisotropy, and h-BN is a two-dimensional insulator. For this system, we predict that it could be possible to have a spin polarization of the valleys at the K and K' points. Ultimately, we explored the unique properties of the van der Waals heterostructure Graphene/CrI3/WSe2, where the magnetic electrode is also replaced by 2D materials
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Chrayteh, Mhamad. "Caractérisation physico-chimique de composés organiques volatils biogéniques et de leurs hydrates." Electronic Thesis or Diss., Université de Lille (2018-2021), 2018. http://www.theses.fr/2018LILUR054.
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Notre étude a porté sur les propriétés physico-chimiques de molécules d’intérêt atmosphérique en phase gazeuse, en particulier le processus de microsolvatation, qui pourrait permettre de mieux comprendre ce qui conduit à la formation d’aérosols organiques secondaires. Nous avons étudié le mécanisme d’hydratation de plusieurs produits d’oxydation des monoterpènes, dont font partie le myrténal et le périllaldéhyde, qui sont deux aldéhydes insaturés de structures proches, avec la verbénone et la fenchone, qui sont deux cétones. Les structures de nombreux édifices (jusqu’à 3 molécules d’eau liées aux molécules) ont été optimisées par calculs de chimie quantique aux niveaux MP2 / 6- 311++G(d,p) et B3LYP-D3BJ / def2-TZVP. La cohésion des hydrates se fait grâce à des liaisons hydrogène et à des interactions de Van der Waals. Nous avons pu mettre enévidence l’existence de beaucoup d’entre eux par spectroscopie mircoonde en jet supersonique dans la gamme de fréquences 2 - 20 GHz et déterminer leur structure expérimentale.Pour le myrténal, nous avons enregistré et analysé le spectre de rotation pure, ainsi que ceux des isotopologues en abondance naturelle (13C et 18O). Avec l’appui des calculs de chimie quantique, nous avons déterminé sa structure moléculaire en phase gazeuse. Concernant les hydrates du myrténal, nous avons analysé le spectre de 2 mono-, 2 di- et un trihydrate, alors que pour le périllaldéhyde 4 mono- et 2 dihydrates sont caractérisés. Avec les cétones, nous avons analysé le spectre de 2 mono-, 2 di- et 1 trihydrate de la verbénone, alors que pour la microhydratation de la fenchone, nous avons caractérisé 2 mono-, 2 di- et 3 trihydrates. Afin de confirmer la structure des complexes, nous avons utilisé de l’eau enrichie en oxygène 18, ce qui nous a permis grâce aux constantes de rotation des isotopomères de calculer la structure des hydrates détectés en déterminant la position des atomes d’oxygène par le calcul de leurs coordonnées de substitution, ainsi qu’une structure effective limitée à l’arrangement des molécules d’eau autour du substratOur study deal on the physicochemical properties of molecules of atmospheric interest in the gas phase, in particular the microsolvation process, which could be useful to better understand what leads to the formation of secondary organic aerosols. We studied the mechanism of hydration of several oxidation products of monoterpenes, which include myrtenal and perillaldehyde, which are two unsaturated aldehydes of close structures, with the verbenone and the fenchone, which are two ketones. The structures of many conformers (up to 3 molecules of water bound to molecules) have been optimized by quantum chemistry calculations at MP2 / 6-311++G(d,p) and B3LYP-D3BJ / def2-TZVP levels of theory. The hydrates cohesion is done thanks to hydrogen bonds and Van der Waals interactions. We were able to evidence of the existence of many of them by supersonic jet mircowave spectroscopy in the range of frequencies 2 - 20 GHz and determine their experimental structure. For the myrtenal, we recorded and analyzed the pure rotation spectra, as well as those of isotopologists in natural abundance (13C and 18O ). With the support of quantum chemistry calculations, we have determined its molecular structure in the gas phase. Regarding the hydrates of myrtenal, we analyzed the spectra of 2 mono-, 2 di- and a trihydrate, while for perillaldehyde 4 mono- and 2 dihydrates are characterized. With ketones, we analyzed the spectra of 2 mono-, 2 di- and 1 trihydrate of verbenone, while for the microhydration of fenchone, we characterized2 mono-, 2 di- and 3 trihydrates. In order to confirm the structure of the complexes, we used water enriched with oxygen 18, which allowed us through the constants of rotation of the isotopomers to calculate the structure of the detected hydrates by determining the position of the oxygen atoms by calculating their substitution coordinates, as well an effective structure limited to the arrangement of water molecules around the substrate
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Bezzi, Luca. "Materiali 2D van der Waals." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2020.
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Dalla scoperta del grafene, molte ricerche sono state condotte sui cosiddetti “materiali 2D”. Questo elaborato si focalizza sulle proprietà strutturali, elettroniche, ottiche ed eccitoniche di due materiali bidimensionali, ossia il grafene il disolfuro di molibdeno (MoS2-1H), quest’ultimo un importante semiconduttore. Le proprietà di questi materiali sono diverse rispetto alla loro controparte massiva (bulk) grafite e MoS2-2H, e un loro confronto è stato preso in considerazione. Come metodo di indagine sono state scelte simulazioni quanto- meccaniche ab initio dei sistemi in esame, un approccio che, negli ultimi decenni, sta avendo un impatto sempre più importante sulla fisica, sulla chimica dello stato solido e sulla scienza dei materiali, promuovendo non solo una comprensione più profonda, ma anche la possibilità di contribuire in modo significativo alla progettazione di materiali per nuove tecnologie. Questo importante passo avanti è stato possibile grazie a: (i) una descrizione migliorata ed efficiente degli effetti elettronici a molti corpi (many-body) nella teoria del funzionale della densità (DFT), nonché lo sviluppo di metodi post-DFT per lo studio di proprietà specifiche; (ii) un’accurata implementazione di questi metodi in software altamente efficienti, stabili e versatili, capaci di sfruttare il potenziale delle architetture informatiche moderne. Tra i possibili software ab initio basati su DFT, abbiamo scelto il pacchetto di simulazione di Vienna ab initio VASP, considerato un gold standard per questo tipo di indagini. I risultati ottenuti per le varie proprietà di bulk e di superficie (bidimensionale) dei materiali scelti sono in ottimo accordo con dati ottenuti in precedenza, sia a livello teorico, sia sperimentale. Questo elaborato getta quindi le basi per futuri studi nel campo dei materiali 2D per comprendere, analizzare, ingegnerizzare nuovi materiali con proprietà desiderabili e per sviluppare nuove applicazioni degli stessi.
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Boddison-Chouinard, Justin. "Fabricating van der Waals Heterostructures." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/38511.
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The isolation of single layer graphene in 2004 by Geim and Novoselov introduced a
method that researchers could extend to other van der Waals materials. Interesting and new properties arise when we reduce a crystal to two dimensions where they are often different from their bulk counterpart. Due to the van der Waals bonding between layers, these single sheets of crystal can be combined and stacked with diferent sheets to create novel materials.
With the goal to study the interesting physics associated to these stacks, the focus of this work is on the fabrication and characterization of van der Waals heterostructures.
In this work, we first present a brief history of 2D materials, the fabrication of heterostructures, and the various tools used to characterize these materials. We then give a description of the custom-built instrument that was used to assemble various 2D heterostructures followed by the findings associated with the optimization of the cleanliness of the stack's interface and surface. Finally, we discuss the results related to the twisting of adjacent layers of stacked MoS2 and its relation to the interlayer coupling between said layers.
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Ma, Yingfang. "Electronic Structure, Optical Properties and Long-Range-Interaction Driven Mesoscale Assembly." Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1497049273517057.
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Tiller, Andrew R. "Spectra of Van der Waals complexes." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333415.
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Mauro, Diego. "Electronic properties of Van der Waals heterostructures." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/10565/.
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L’interazione spin-orbita (SOI) nel grafene è attualmente oggetto di intensa ricerca grazie alla recente scoperta di una nuova classe di materiali chiamati isolanti topologici.
Questi materiali, la cui esistenza è strettamente legata alla presenza di una forte SOI, sono caratterizzati dall’interessante proprietà di avere un bulk isolante ed allo stesso tempo superfici conduttrici. La scoperta teorica degli isolanti topologici la si deve ad un lavoro nato con l’intento di studiare l’influenza dell’interazione spin-orbita sulle proprietà del grafene. Poichè questa interazione nel grafene è però intrinsecamente troppo piccola, non è mai stato possibile effettuare verifiche sperimentali. Per questa ragione, vari lavori di ricerca hanno recentemente proposto tecniche volte ad aumentare questa interazione. Sebbene alcuni di questi studi abbiano mostrato un effettivo aumento dell’interazione spin-orbita rispetto al piccolo valore intrinseco, sfortunatamente hanno anche evidenziato una consistente riduzione della qualità del grafene.
L’obbiettivo che ci si pone in questa tesi è di determinare se sia possibile aumentare l’interazione spin-orbita nel grafene preservandone allo stesso tempo le qualità. La soluzione proposta in questo lavoro si basa sull’utilizzo di due materiali semiconduttori, diselenio di tungsteno WSe2 e solfuro di molibdeno MoS2, utilizzati da substrato su cui sopra verrà posizionato il grafene formando così un’eterostruttura -nota anche di “van der Waal” (vdW)-.
Il motivo di questa scelta è dovuto al fatto che questi materiali, appartenenti alla famiglia dei metalli di transizione dicalcogenuri (TMDS), mostrano una struttura reticolare simile a quella del grafene, rendendoli ideali per formare eterostrutture e ancora più importante, presentano una SOI estremamente grande. Sostanzialmente l’idea è quindi di sfruttare questa grande interazione spin-orbita del substrato per indurla nel grafene aumentandone così il suo piccolo valore intrinseco.
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Klein, Andreas. "Energietransferprozesse in matrixisolierten van-der-Waals-Komplexen." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=962344761.
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Odeyemi, Tinuade A. "Numerical Modelling of van der Waals Fluids." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/22661.
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Many problems in fluid mechanics and material sciences deal with liquid-vapour flows. In these flows, the ideal gas assumption is not accurate and the van der Waals equation of state is usually used. This equation of state is non-convex and causes the solution domain to have two hyperbolic regions separated by an elliptic region. Therefore, the governing equations of these flows have a mixed elliptic-hyperbolic nature.
Numerical oscillations usually appear with standard finite-difference space discretization schemes, and they persist when the order of accuracy of the semi-discrete scheme is increased. In this study, we propose to use a Chebyshev pseudospectral method for solving the governing equations. A comparison of the results of this method with very high-order (up to tenth-order accurate) finite difference schemes is presented, which shows that the proposed method leads to a lower level of numerical oscillations than other high-order finite difference schemes, and also does not exhibit fast-traveling packages of short waves which are usually observed in high-order finite difference methods. The proposed method can thus successfully capture various complex regimes of waves and phase transitions in both elliptic and hyperbolic regimes
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Marsden, Alexander J. "Van der Waals epitaxy in graphene heterostructures." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/77193/.
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Graphene — a two-dimensional sheet of carbon atoms — has surged into recent interest with its host of remarkable properties and its ultimate thinness. However, graphene combined with other materials is starting to attract more attention. These heterostructures can be important for production routes, incorporating graphene into existing technologies, or for modifying its intrinsic properties. This thesis aims to examine the role of van der Waals epitaxy within these heterostructures. First, the graphene-copper interaction during chemical vapour deposition of graphene is investigated. Graphene is found to grow with a mismatch epitaxy of 8 relative to the [001] direction of the Cu(100) surface, despite a mismatch in symmetry and lattice parameter between two. Further, the electronic structure of both graphene and copper is unchanged by the interaction. This highlights the weak interaction between the two, owing to its van der Waals nature. Functionalised graphene is another important heterostructure, and is intensively studied for both graphene production routes and for altering graphene’s properties. Here, it is the change to the homogeneous graphene surface that makes it interesting for van der Waals epitaxy. The effect of functionalisation of graphene with atomic oxygen and nitrogen is presented next. In both cases, only small amounts of functionalisation ( 5 at%) is sufficient to significantly deteriorate the -band structure of the graphene through localisation. For small amounts of nitrogen functionalisation, and greater amounts of oxygen functionalisation, extended topological defects are formed in the graphene lattice. Unlike epoxide oxygen groups, these disruptions to the pristine graphene are found to be irreversible by annealing. Next, the interaction between graphene and the organic semiconducting molecule vanadyl-phthalocyanine (VOPc) is presented. As a result of the van der Waals nature of the graphene surface, VOPc molecules can form crystals microns in size when deposited onto a substrate with an elevated temperature of 155 C; at ambient temperatures, the crystals are only tens of nanometres across. In contrast, the functionalised graphene oxide surface prevents large crystal growth, even at elevated temperatures, because surface functionalities inhibit molecule diffusion. This highlights the importance of graphene as a substrate for molecular crystal growth, even when the growth is not epitaxial. Finally, the supramolecular assembly of trimesic acid (TMA) and terephthalic acid (TPA) is presented. Despite their chemical similarity they display different behaviour as they transition from monolayers to three-dimensional structures: for TMA, the epitaxial chicken wire structure seen at a monolayer templates up through the layers as molecules stack, until a thickness of 20 nm, when random in-plane orientations appear; on the other hand, TPA forms a brickwork structure at the monolayer, which quickly transitions to fibre-like crystals with a bulk structure for the thin films. However, the TPA orientation is still determined by the epitaxy with the graphene substrate, although this is significantly weaker than for TMA.
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Connelly, James Patrick. "Microwave studies of Van der Waals complexes." Thesis, University of Oxford, 1993. http://ora.ox.ac.uk/objects/uuid:3865eb1d-d288-44c9-8d42-84f7ff2c0608.
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This thesis describes the commissioning and development of a pulsed supersonic nozzle, Fourier-transform microwave spectrometer and its application to the study of several weakly bound van der Waals complexes. A pulsed supersonic expansion, Fourier-transform microwave spectrometer based on the Flygare design with a number of modifications has been constructed with an operating range of 6-18 GHz. A homodyne detection circuit mixing signals to modulus values between dc and 1 MHz is used, requiring two measurements to determine absolute transition frequencies. Transition frequencies are measured from the power spectrum by determining the first derivative zero crossing point in a least squares fitting procedure. Semiautomation of many of the spectrometer operations has been achieved allowing unattended data collection over scans of up to 300 MHz. The microwave spectrum of Ar2-OCS and Ar2-OC34S has been observed and analysed using conventional Watson S reduction hamiltonian parameters. Effective structural parameters are derived and used in a harmonic force field analysis, based on the centrifugal distortion constants, to compare the trimer interations with a model based on the sum of dimer interactions. A series of complexes containing the nitrogen molecule undergoing tunnelling motions have been studied. Hyperfine matrix elements for the first order nuclear quadrupole interaction are derived for the coupled identical nuclei case appropriate to the rapid tunnelling motions observed. The microwave spectrum of N2-OCS is described. Tunnelling and nuclear spin statistical effects for two symmetry states are observed arising from the interchange of nitrogen nuclei. Rotational and quadrupole constants are derived; an accidental near degeneracy of two rotational levels allows the off-diagonal quadrupole coupling constant to be determined from second order effects. A tunnelling hamiltonian fitting the quadrupole coupling constants to an angular potential has been used to calculate the tunnelling frequency and barrier to N2 rotation. The microwave spectrum of N2-O3 and a preliminary spectrum of N2-SO3 have been observed. Rotation-inversion motions of the O3 and SO2 moieties must be considered in addition to the N2 tunnelling to fit the spectrum. Tunnelling frequencies for the O3/SO2 and geared motions with the N2 are derived as well as structural parameters. Modifications for production of refractory molecules and complexes by laser ablation have been made. A modified nozzle employing rods of material is used with the ablation process taking place in the nozzle throat. Modifications to obtain an expansion along the axis of the microwave cavity employ a hemispherical Fabry-Perot cavity configuration. The system has been tested on a number of diatomic molecules including PbS and CuCl.
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Wright, Nicholas J. "Bound states of Van der Waals trimers." Thesis, Durham University, 1998. http://etheses.dur.ac.uk/5048/.
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A method for calculating the energy levels and wave functions of floppy tri- atomic systems such as rare-gas trimers has been developed. It is based upon a potential-optimized discrete variable representation and takes into account the wide-amplitude vibrations that occur in such systems. The quadrature error that occurs in DVR calculations is analysed and a method of correction implemented. The diagonalisation procedure is based upon a combination of successive diagonalisation and truncation and a Lanczos diagonaliser. Using this method the wave functions of the Ar(_3) Van der Waals trimer have been calculated. The wave functions for the low-lying states show very regular behaviour. Above the barrier to linearity, most of the wave functions are irregular but some have simple nodal patterns that suggest localization along periodic orbits. In addition to the "horseshoe" states previously described for H(^+)(_3), localized features corresponding to symmetric and antisym metric stretching vibrations around a linear configuration have been identified. The different localized modes can be combined to form more complex states in a manner analogous to normal modes. A preliminary study of the rotational states of Ar(_3) has also been performed. The rotational constants for the low lying states of Ar(_3) reflect the increasing average size of Ar(_3) with increasing vibrational excitation. The rotational constants are obtained from two methods, expectation values and energy level differences. The results for the levels above the barrier to isomerisation reveal that the simple models used for obtaining the rotational constants are no longer valid and indicate that a more sophisticated treatment is necessary.
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Bryan, Robert. "Theoretical studies of Van der Waals clusters." Thesis, Durham University, 1997. http://etheses.dur.ac.uk/4712/.
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The vibrational energy levels of various rare gas trimers, Ar(_3), Ne(_3), He(_3), Ar(_2)Ne and Ne(_2)Ar, have been calculated using a coupled channel approach. We have compared results obtained with previous calculations. The existence of Efi-mov states in He(_3) has been investigated, and no evidence of their existence has been found. The affect of the Eckart conditions on embedding axis into a rotating-vibrating system has been investigated for several rare gas systems. A wide range of rare gas trimers have been studied, Ar(_3), He(_2)Ar, Ar(_2)He, Ar(_2)Ne and Ne(_2)Ar. For each trimer the full range of molecular motion is investigated. The low energy minima for the Ar(_n)N(_2) and Ne(_n)N(_2) systems have been found using simulated annealing search, and a gradient based minimisation technique, of a pairwise potential energy surface. Clusters with n ≥ 12 have been studied, and first solvation shells for both systems have been proposed. For each value of n, for n = 1 - 12, the first few low energy minima of the potential energy surface have been found. From these studies, we have gained a detailed understanding of the interplay of forces that determine the low energy structures for these systems. The affect of three-body interactions on the low energy minima both rare gas-N(_2) systems has been studied. In both system, rare gas-rare gas and rare gas- threebody interactions have been taken into account. This study has shown that the three-body forces have a small affect on the low energy structures of each system.
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Tulegenov, Akyl S. "SIMPER method for van der Waals complexes." Thesis, University of Nottingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.431329.
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McDowell, Sean Alistair Courtney. "Theoretical studies of Van der Waals molecules." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259733.
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Le, Sueur Catherine Ruth. "Induction effects in Van der Waals complexes." Thesis, University of Cambridge, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385523.
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Willberg, Dean Michael Zewail Ahmed H. "Picosecond spectroscopy of van der Waals clusters /." Diss., Pasadena, Calif. : California Institute of Technology, 1994. http://resolver.caltech.edu/CaltechETD:etd-04042008-110156.
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Sukhomlinov, Sergey. "Development of effective interatomic potentials for computer simulation of oxides." Thesis, Lille 1, 2012. http://www.theses.fr/2012LIL10092/document.
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Le modèle de potentiels effectifs d'interactions interatomiques (champ de forces) pour la modélisation d'oxydes a été développé avec l'utilisation de calculs ab initio basés sur la théorie de la fonctionnelle de la densité. Le champ de forces décrit l'énergie potentielle totale du système par la somme de l'énergie électrostatique, celle de dispersion, et l'énergie d'interactions à courte portée. L'énergie électrostatique a été décrite par le modèle d'équilibration des tranferts de charge (SQE) basé sur l'approche d'égalisation du potentiel chimique (CPE). Le calcul de coefficients de dispersion, qui déterminent les interactions de dispersion, a été réalisé avec l'utilisation de fonctions Wannier maximalement localisées (MLWF). Dans les oxydes la position des centres des MLWF près d'atomes permet de calculer les coefficients de dispersion pour chaque atome. Les calculs de ces coefficients ont montré que leur valeur dépend du nombre d'atomes et du rayon de la première sphère de coordination. Le développement de potentiels d'interactions à courte portée a été réalisé avec l'utilisation de la méthode "force-matching", ce qui a permis de choisir la forme analytique des potentiels. Les paramètres des composants du champ de force ont été obtenus sur la base de calculs de chimie quantique de systèmes isolés et périodiques de structures de silicates. Les paramètres du modèle SQE on été calibrés en utilisant le potentiel électrostatique comme la grandeur de référence. Le champ de forces complet a été testé par simulation de polymorphes cristallins de la silice par la méthode de la dynamique moléculaire. Les résultats des calculs ont permis de choisir le meilleur modèle. Le champ de forces sélectionné reproduit bien les caractéristiques structurelles de α-quartz et α-cristobalite. Le calcul de spectres vibrationnels des systèmes montre que le champ de forces sous-estime les constantes de forces Si-O, ce qui conduit à un déplacement de spectres vibrationnels vers les basses fréquences par rapport aux spectres expérimentaux. Des voies visant l'amélioration de la performance du champ de forces sont proposéesThe effective interatomic potential model (force field) for the atomistic modeling of oxide materials was developed with the extensive use of ab initio density functional calculations. The force field represents the total potential energy of system as a sum of the long-range electrostatic, dispersion, and short-range energy contributions. The long-range energy electrostatic energy was described with the use of split-charge equilibration (SQE) model based on the chemical potential equalization (CPE) approach. The electrostatic potential was used as the reference quantity for the calibration of parameters of the SQE model. The computation of dispersion coefficients, which determine the magnitude of the dispersion interactions, was carried out with the use of maximally localized Wannier functions (MLWF). The position of MLWF centers close to the nuclei in oxides permits the computation of the dispersion coefficients in an atom-wise manner. The values of the dispersion coefficients were found to be affected by the coordination number and the radius of the first coordination sphere of atom. The short-range (SR) interaction potentials were designed with the use of force-matching method, which has allowed a judicious choice of the functional form of the SR potentials. The parametrization of the force field components was performed on the basis of extensive quantum-chemical calculations of isolated and periodic silicate systems. The complete force field was tested in the molecular dynamics simulations of crystalline silica polymorphs. Results of the calculations allowed to choose the best model. The selected force field well reproduces structural characteristics of the α-quartz and α-cristobalite polymorphs. The calculation of the vibrational spectra of the systems has shown that the model underestimates the Si-O force constants that leads to a downward shift of the vibrational spectra in comparison with the experimental data. A number of ways aimed at improving the force field's performance are suggested