Tesi: "Atomic and molecular modeling"

1

Tuesday, Andrew J. "Modeling Atomic Defects in a Two-Dimensional Lennard-Jones Lattice Using Molecular Dynamics Simulations". University of Akron / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=akron1334579948.

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2

Ruscio, Jory Zmuda. "Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution". Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/27219.

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While experiments provide valuable information about biological molecules, current technology cannot yet monitor atomic fluctuations at relevant time scales. Theoretical computational simulations are able to model the appropriate interactions at atomic resolution. Computational techniques have become widely used for identifying interactions in biological systems. Such methods have proven quite accurate in their ability to reproduce experimental data and also in screening and predicting pertinent activities. Molecular modeling employs theoretical and computational techniques to elucidate biologically relevant information from macromolecular structures. Three biological systems, the nucleosome core particle, myoglobin and glycosyl hydrolase family 1 beta-glucosidases will be examined with molecular modeling methods. Results of our analyses provide information about DNA flexibility and packaging, internal migration of ligands in a small protein, and substrate specificity of an enzyme system.
Ph. D.

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3

Hooshmand, Mohammad Shahriar. "Atomic-scale modeling of twinning in titanium and other HCP alloys". The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1566143337320934.

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4

Tang, Ming. "Atomic-scale biophysics modelling of type I collagen in the extracellular matrix". Thesis, Queensland University of Technology, 2019. https://eprints.qut.edu.au/124650/1/Ming_Tang_Thesis.pdf.

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This thesis explores the biophysics of collagen in the extracellular matrix under external stimuli, by performing cutting edge MD simulations. The obtained results provide significant insights into the design and manufacturing of artificial biomaterials for surgical tissue treatments, of collagen for regenerative medicine applications, and of gold nanoparticles for biomedical applications. The probed biophysical properties consist of the structural properties and the mechanical properties, where the mechanical properties of collagen are regulated by its structure at different levels of hierarchies.

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5

Marsh, R. J. "Kinematic modelling of non reactive and reactive collisions". Thesis, University of Sussex, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270740.

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6

Gao, D. "Modeling of adsorption and atomic force microscopy imaging of molecules on insulating surfaces". Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1468925/.

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The study of atoms and molecules on bulk insulating surfaces is of critical importance to many fields of surface science including lubrication, and molecular electronics. I studied these systems by using a variety of theoretical methods to predict adsorption geometry, diffusion pathways, and film structure, and to interpret noncontact atomic force microscopy (NCAFM) data. I began by using molecular dynamics (MD) simulations to predict that Pd atoms deposited onto MgO(100) exhibit some transient mobility. They were initially able to move across the surface, but were eventually captured at an adsorption site when enough energy had been dissipated. Similarly, deposited molecules may also be able move around and find nucleation sites such as step edges or kinks before becoming stabilized on surface terraces at low temperature. I then moved on to study the properties of single molecules on oxide surfaces. I combined my theoretical calculations with experimental data to compare adsorption sites and geometries of Co-Salen molecules on NaCl(100) and NiO(100). I used density functional theory calculations (DFT) to show that minor differences in commensurability between the molecule and the surface can qualitatively change adsorption. Both surfaces are bulk insulators with simple cubic crystal structures, however, a much higher adsorption energy and distortion of the molecule on NiO(100) produced a signiﬁcant vertical dipole moment. Single molecules adsorbed onto insulators can be directly imaged with chemical resolution using metal coated NCAFM tips. However, accurate interpretation of the results is needed. I studied metallic tips using DFT calculations and developed a point dipole model to represent the Cr coated tips used experimentally. I then fit the position and magnitude of the point dipole in this model directly to experimental scan-lines and was able to produce virtual AFM (VAFM) images and scan-lines that were in quantitative agreement with experiment. This method simultaneously reduced the complexity of interpretation of experimental data and the computational cost of producing VAFM images. Finally, I studied larger systems using a hybrid quantum mechanics/molecular mechanics (QM/MM) and parametrized classical force fields using genetic algorithm (GA) methods. This allowed me to study CDB, a large organic molecule, on KCl(100). Static DFT calculations and classical MD simulations using these force fields showed that adsorbed CDB molecules are mobile at room temperature and stabilized at step edges due to increased adsorption energy. These results provide insight into the processes and mechanisms that govern deposition, adsorption, and diffusion of atoms and molecules on insulating surfaces and can help guide the design of functional molecules and films.

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7

Mead, Robert Nielle. "Molecular dynamics modelling of the amorphous calcium silicate and titania silicate atomic-scale structure". Thesis, University of Kent, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443767.

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8

Lerebourg, Christophe Jean-Yves Joel. "Development and modelling of a point source integrating cavity absorption meter (PSICAM)". Thesis, University of Plymouth, 2003. http://hdl.handle.net/10026.1/1712.

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The absorption coefficient is a fundamental parameter in understanding the underwater light field, for solving the Radiative Tranfer Equation and understanding/interpreting remotely sensed data from the ocean. Measuring the absorption coefficient is particularly complicated in coastal areas where the optical properties of the water body are the result of a complex mixture of dissolved and particulate components, but mainly because of the interfering effect that scattering has upon the measurements. A great variety of in situ instruments and laboratory techniques have been developed to measure total absorption or the absorption by the various fractions that constitute the total absorption. They are, however, all affected by scattering and empirical corrections need to be applied. Among the instruments to measure absorption, a promising one appeared to be one based on an integrating cavity. Kirk (1995, 1997) outlined the principle and theory of an absorption meter based on an integrating sphere: a Point Source Integrating Cavity Absorption Meter (PSICAM). He argued that owing to its design, a PSICAM would be insensitive to scattering. A novel Monte Carlo code was written to simulate the behaviour of a PSICAM of various cavity radiuses. The results of the simulations carried out with this code showed that such an absorption meter should indeed be unaffected by scattering even with high levels of scatterers. One important disadvantage deduced from numerical modelling for a PSICAM is its sensitivity to the reflectivity of the integrating cavity. Several prototype PSICAMs of increasing quality were built and tested with scattering-free standard solutions. A major difficulty in the development of the prototype was found to be the calibration of the integrating sphere reflectivity. A final laboratory instrument made of a Spectralon sphere was built and tested with artificial and natural water samples containing different levels of scattering particles and compared with existing in situ and laboratory techniques: the ac-9 transmissometer and the filter paper technique for particulate absorption as well as measurement of Coloured Dissolved Organic Matter. Compared with the ac-9 transmissometer, the PSICAM showed remarkable agreement even for water with very high content of Suspended Particulate Matter. Very good correlations were obtained when compared with traditional CDOM measurement. In some cases, significant discrepancies occurred with filter paper measurements of particulate absorption. From laboratory to in situ experiments the PSICAM proved to be a reliable instrument assuming that the instrument was regularly and carefully calibrated. Finally, the PSICAM was deployed during a cruise around the Antarctic Peninsula where total and dissolved absorption measurements were carried out together with chlorophyll absorption measurements after extraction in acetone.

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9

Mallett, Michael John Disney. "An analytical and computer modelling study of atomic motion in fluids constrained by barriers". Thesis, University of Kent, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358039.

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10

Lawrence, A. J. "Modeling the Optical Response to a Near-Field Probe Tip from a Generalized Multilayer Thin Film". PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2328.

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The contrast mechanism in Kerr imaging is the apparent angle through which the plane of polarization is rotated upon reflection from a magnetic surface. This can be calculated for a well characterized surface given the polarization state of the incident light. As in traditional optical microscopy, the spatial resolution is limited by diffraction to roughly half the wavelength of the illumination light. The diffraction limit can be circumvented through the use of near-field scanning optical microscopy, in which the illumination source is an evanescent field at the tip of a tapered optical fiber. A novel probe design for near-field optical imaging in reflection mode will be proposed, and experimental work on the development of a near-field Kerr microscope performed up to this point will be presented. The complication in merging these two techniques arises from the complex polarization profile of the evanescent field. This profile can be characterized for a given probe geometry with the use of electromagnetic field modeling software, allowing for subsequent modeling of the polarization profile of the optical response. An algorithm for predicting the optical response to a near-field probe tip from a generalized multilayer thin-film is presented.

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11

Aubailly, Simon. "From coarse-grained to atomistic molecular modeling : how structure and dynamics shape intra-molecular communication and functional sites in proteins". Thesis, Orléans, 2017. http://www.theses.fr/2017ORLE2002/document.

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Dans cette thèse, nous nous sommes intéressés à la relation subtile qui existe entre lesstructures complexes des protéines et leurs fonctions encore plus raffinées que ces dernièreseffectuent. Basés sur deux descriptions différentes des protéines, à l’échelle de acide-aminé età l’echelle atomique, un de nos objectifs était de connecter des indicateurs structuraux calculésà partir de la topologie des protéines à des sites fonctionnels tels que les sites catalyiquesdans les enzymes. Un autre pan de la recherche de cette thèse était d’utiliser nos outils baséssur la structure et de mettre au point de nouvelles simulations numériques pour étudier lesdéterminants basiques structuraux et dynamiques de la communication intramoléculaire dansles protéines. Une première découverte fut de montrer comment l’analyse des modes normauxet la théorie des reseaux complexes conduisent à la prédiction des sites catalytiques dans lesenzymes. De plus, nous avons travaillé sur un groupe relativement peu connu de modes nor-maux qui ont la particularité d’être localisés à deux endroits très eloignés dans la structure desprotéines. Ces modes bilocalisés ont permis de réaliser des transferts d’énergie à des distancesconsidérables (plus de 70 Å). Finalement, des expériences de refroidissement effectuées sur unsystème protéine-eau décrit à l’échelle atomique ont dévoilé que le refroidissement induit unelocalisation spontanée d’énergie, indiquant certaines déformations des anneaux du benzenecomme possible centres de stockage de l’énergie dans les protéines
In this thesis we have focused on the elusive relation that exists in proteins between theircomplex structures and the even more complex and sophisticated functions that they perform.Based on two different descriptions of proteins, at residue and atomistic scale, one of ouraims was to connect structural indicators computed from the topology of protein scaffoldsto hot spots in proteins such as catalytic sites in enzymes. Another goal of this thesis wasto employ our structure-based tools and set up original simulation scheme to investigate thebasic structural and dynamical determinants of intramolecular communication in proteins.As a first important finding, we have shown how normal mode analysis and specific graph-theoretical approaches lead to the prediction of catalytic sites in enzymes. Moreover, wehave concentrated our attention on an overlooked class of normal modes, that are stronglylocalized at two widely separated locations in protein scaffolds. These bilocalized modesturned out to efficiently mediate energy transfer even across considerable distances (morethan 70 Å). Finally, cooling experiments performed on a protein-water system described atatomic level have unveiled complex cooling-induced spontaneous energy localization patterns,pointing to specific deformation modes of benzene rings as potential energy-storage centers

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12

Silaghi, Marius-Christian. "Ab initio Molecular Modelling of the Dealumination and Desilication Mechanisms of Relevant Zeolite Frameworks". Thesis, Lyon, École normale supérieure, 2014. http://www.theses.fr/2014ENSL0930/document.

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Les zéolites, aluminosilicates cristallisés microporeux, sont largement utilisés en raffinage, en pétrochimie et en conversion de la biomasse. En raison du faible diamètre des micropores, limitations diffusionnelles et effets de confinement peuvent favoriser la formation de sous-Produits non désirés. L'introduction de mésopores par désalumination et/ou désilication ("zéolites hiérarchisées") peut diminuer ces phénomènes. Cependant, les mécanismes ces réactions restent méconnus à l'échelle moléculaire. Par calculs quantiques périodiques, au niveau de la théorie de la fonctionnelle de la densité (DFT) et selon une approche hybride QM/QM, nous avons pu mettre en évidence l'importance de l'attaque de la molécule d'eau sur l'atome d'aluminium, qui se fait en anti par rapport au site acide de Brønsted. Des structures d'Al penta ou tetra coordinées ont aussi été suggérées expérimentalement comme précurseurs de la désalumination. Malgré une forte hétérogénéité structurale des sites T, l'élucidation des chemins réactionnels et les énergies d’activation des étapes d’hydrolyse des liaisons Al-O (70-100 kJ/mol) dans les systèmes zéolitiques investigués (MOR, FAU, MFI, CHA) nous a permis d'établir des corrélations du type Brønsted-Evans-Polanyi. Ces corrélations permettent d'estimer et prédire des énergies d'activation par le biais de la thermodynamique, donne ainsi une prédiction aisée des sites T sensibles à la désalumination. Un autre facteur clé pour la compréhension de la désalumination est l'effet de confinement sur l'espèce aluminique extra-Réseau générée (EFAL), exercé par les cavités. Finalement nous avons pu montrer que le chemin réactionnel de désalumination et désilication, consécutif ou simultané, , est thermodynamiquement plus favorable qu'une simple désalumination ce qui est en accord avec les propositions mécanistiques de la littérature sur la genèse de mésopores par démétallation
Zeolites are crystalline microporous aluminosilicates widely used in refining, petrochemistry and biomass conversion. However, diffusion limitation and confinement effect can promote the formation of undesired products. The introduction of mesopores by dealumination and/or desilication ("hierarchical zeolites") is a possible solution widely used experimentally. Nevertheless, the mechanisms of these demetallation reactions are poorly described at the molecular scale. We determine the mechanisms of the formation of extraframework Al species (EFAL) for zeotypes MOR, FAU, MFI and CHA occurring during the dealumination process, possibly associated with desilication. First-Principles periodic density functional theory (DFT) and hybrid QM/QM calculations have been employed in order to analyze full reaction paths leading to extraframework species and to quantify the activation energies of the determining steps. It has been demonstrated that the initiation of an Al-O(H) bond break takes place via water adsorption on the Al atom in anti-Position to the Brønsted acid site, via a penta- or tetra-Coordinated Al species. Such species are shown to be at the initiation of the Al dislodgement from the zeolitic framework. Despite a strong structural heterogeneity of T sites, we determined Brønsted-Evans-Polanyi (BEP) relationships for the entire dealumination pathway. Moreover, it is shown that not only the initiation and propagation mechanisms are primordial for the understanding of an Al extraction, but also the confinement effect on EFAL species within the zeolites cavities. Finally, from the energy profile of combined dealumination/desilication pathways, we show that it is thermodynamically favoured to extract extraframework Si species (EFSI) in the course of dealumination

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13

Asiri, Yazeed. "Ab Initio and Semi-Empirical Calculations of Cyanoligated Rhodium Dimer Complexs". Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etd/3177.

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Molecular modeling, using both ab initio and semi-empirical methods has been undertaken for a series of dirhodium complexes in order to improve the understanding of the nature of the chemical bonding in this class of homogeneous catalysts. These complexes, with carboxylamidate and carboxylate ligands, are extremely functional metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. The X-ray crystallography shows anomalies in the bond angles that have potential impact on understanding the catalysis. To resolve these issues, minimum energy structures of several examples (e.g. Rh2(NHCOCH3)4, Rh2(NHCOCH3)4NC, Rh2(CO2CH3)4, Rh2(CO2CH3)4NC, Rh2(CHO2)4, and Rh2(CHO2)4NC) were calculated using Hatree-Fock and Density Functional Theory/B3LYP with the LANL2DZ ECP (Rh), and cc-pVDZ (all other atoms) basis sets.

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Amarante, Adriano Moraes. "Desenvolvimento da microscopia de força química usando modelagem molecular". Universidade Federal de São Carlos, 2013. https://repositorio.ufscar.br/handle/ufscar/1169.

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Made available in DSpace on 2016-06-02T19:19:55Z (GMT). No. of bitstreams: 1 AMARANTE_Adriano_2013.pdf: 11925080 bytes, checksum: 6de5e4ba7ae233d30b78c7f1d927740a (MD5) Previous issue date: 2013-03-19
Universidade Federal de Sao Carlos
In this work was developed a prototype of a new nanobiosensor with molecular specificity through a study of theoretical models of Chemical Force Microscope. For the sensing were used molecular modeling techniques as well as experimental models of the functionalized Atomic Force Microscope tip with the Acetil co-A Carboxylase (ACC) attached. Specific and non-specific inhibitors were used to evaluate substrate-enzyme interactions. The nanobiosensor investigates specific enzymatic inhibition characteristics of the ACC enzyme through the herbicide Diclofop by reversing this process applying a force in a determined direction. The force is theoretically calculated by using molecular dynamic techniques associated to the adhesion force experimentally obtained. Theoretical and experimental questions involving nanobiosensors of AFM tips still obscure until now, such as, the number of functional enzymes attached on the AFM tip, the number of the active sites available to interact after immobilization process, the consequences of the enzyme immobilization as well as the substrate and theoretical adhesion between AFM tip and substrate were analyzed here.
Este trabalho teve como objetivo principal desenvolver o protótipo de um novo nanobiossensor de alta especificidade por intermédio do estudo e desenvolvimento de modelos teóricos específicos para a Microscopia de Força Química (MFQ). Para o sensoriamento foram utilizadas técnicas de Modelagem Molecular Computacional (MMC) e resultados experimentais de MFQ, do qual a ponta do Microscópio de Força Atômica (AFM, do inglês Atomic Force Microscopy) foi funcionalizada com enzimas Acetil-coA Carboxilase (ACC). O nanobiossensor foi utilizado para detectar especificamente substratos de herbicidas específicos e não-específicos. O nanobiossensor explora as características de inibição enzimática específica da enzima ACC pelo herbicida Diclofop revertendo esse processo aplicando-se uma força numa determinada direção. Essa força foi calculada teoricamente por intermédio de cálculos de técnicas de Dinâmica Molecular e associada à força de adesão experimental. Os resultados experimentais validaram os modelos teóricos de forma inequívoca. Questões teóricas e experimentais envolvendo nanobiossensores de ponta de AFM não respondidas até o momento (número de enzimas úteis na ponta do AFM que podem interagir com o substrato, o número de sítios ativos disponíveis, consequências da imobilização das enzimas e do substrato, força de adesão teórica entre a ponta do AFM e o substrato de herbicidas, etc.) foram solucionadas neste trabalho.

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15

Bailly, Rémy. "Application de la dynamique moléculaire à plusieurs échelles au complexe hélicase : pontine/reptine". Thesis, Bordeaux, 2016. http://www.theses.fr/2016BORD0415/document.

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Pontine et Reptine constituent de nouvelles cibles thérapeutiques encore très méconnues à ce jour. Outre leur activité ATPase, les complexes multimériques de Pontine et Reptine ont été décrits comme des hélicases capables d’ouvrir les acides nucléiques. La modélisation moléculaire constitue un outil puissant pour l’étude des systèmes protéiques et c’est pourquoi une approche par docking et dynamique a été envisagée. Au vue de la taille d’un complexe à douze sous-unités, les simulations prenant en compte tous les atomes se sont avérées trop coûteuses en termes de puissance de calcul. Une approche mésoscopique,appelée gros-grains, a donc été utilisée pour réduire le nombre de particules à traiter. Legain de temps de calcul offert par ce modèle nous a permis d’étudier les complexes de Pontine et Reptine en présence de partenaires de type ligands, l’ATP et l’ADP, et de type acide nucléique. Par le biais d’un retour au niveau atomique, une ouverture de la double hélice d’ADN a pu être observée ainsi qu’une orientation préférentielle des brins. Des hypothèses mécanistiques de l'activité hélicase du complexe ont alors pu être formulées sur la base de ces résultats
Pontin/Reptin complexes offer new therapeutic opportunities despite the fact they are still notwell known. In addition to their ATPase activity, multimeric complexes of Pontin/Reptin were reported as hélicases able to unwind nucleic acids. Molecular modeling techniques are a powerful tool to study proteins, both a docking and molecular dynamics were applied.Considering the size of a twelve sub-units complex, simulations taking into account all atoms were too expensive in terms of computational costs. A mesoscopic approach, called coarse grain,was used to reduce the number of particles. The calculation time saved with this model allowed the study of Pontin/Reptin complexes in the presence of diverse partners like small ligands (ATP or ADP) and/or nucleic acids. Reverse transformation from coarse-grain to the atomic level led to a DNA double helix opening along to the single strands rearrangement.Several mechanistic hypotheses for the complex helicase activity were formulated from these results

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16

Wang, Zhao. "Propriétés Electro-mécaniques des Nanotubes de Carbone". Phd thesis, Université de Franche-Comté, 2008. http://tel.archives-ouvertes.fr/tel-00352725.

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Le but de cette thèse était de modéliser la réponse mécanique de nanotubes de carbone à des champs électriques. Nous avons commencé par utiliser le potentiel AIREBO dans des simulations de dynamique moléculaire afin d'étudier l'élasticité non-linéaire et la limite de déformation en torsion de divers nanotubes, en fonction de leur longueur, rayon et chiralité. Nous trouvons notamment que le module d'Young effectif des tubes décroît d'autant plus vite que la chiralité est faible. D'autre part, nous montrons que la limite de l'énergie stockable par atome lors de la torsion d'un tube est d'autant plus grande que le diamètre est petit.

Nous modélisons ensuite, de façon atomistique, la distribution surfacique de charge électrique sur des nanotubes de carbone possédant une charge nette. Nous retrouvons notamment l'effet de pointe classique avec un très bon accord quantitatif avec des résultats expérimentaux obtenus par microscopie à force électrostatique.

Par combinaison des méthodes utilisées dans les études précédentes, nous simulons la déflection de nanotubes semi-conducteurs et métalliques par un champ électrique extérieur, dans une configuration de type interrupteur moléculaire. L'effet des caractéristiques géométriques des tubes et du champ sur cette déflection ont été systématiquement étudiés.

En outre, nous avons vu que des simulations de dynamique moléculaire avec le potentiel AIREBO permettent de retrouver quantitativement les énergies expérimentales d'adsorption du benzène, du naphtalène et d'anthracène sur le graphite. Ce type de simulation nous permet d'avancer sur la voie de la compréhension de la sélectivité de l'adsorption de certaines molécules surfactantes à plusieurs cycles benzéniques sur des nanotubes de chiralité donnée.

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Harczuk, Ignat. "Atomic decomposition of molecular properties". Doctoral thesis, KTH, Teoretisk kemi och biologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-187168.

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In this thesis, new methodology of computing properties aimed for multipleapplications is developed. We use quantum mechanics to compute propertiesof molecules, and having these properties as a basis, we set up equations basedon a classical reasoning. These approximations are shown to be quite good inmany cases, and makes it possible to calculate linear and non-linear propertiesof large systems.The calculated molecular properties are decomposed into atomic propertiesusing the LoProp algorithm, which is a method only dependent on the overlapmatrix. This enables the expression of the molecular properties in the two-site atomic basis, giving atomic, and bond-centric force-fields in terms of themolecular multi-pole moments and polarizabilities. Since the original LoProptransformation was formulated for static fields, theory is developed which makesit possible to extract the frequency-dependent atomic properties as well. Fromthe second-order perturbation of the electron density with respect to an externalfield, LoProp is formulated to encompass the first order hyperpolarizability.The original Applequist formulation is extended into a quadratic formula-tion, which produces the second-order shift in the induced dipole moments of thepoint-dipoles from the hyperpolarizability. This enables the calculation of a to-tal hyperpolarizability in systems consisting of interacting atoms and molecules.The first polarizability α and the first hyperpolarizability β obtained via theLoProp transformation are used to calculate this response with respect to anexternal field using the quadratic Applequist equations.In the last part, the implemented analytical response LoProp procedureand the quadratic Applequist formalism is applied to various model systems.The polarizable force-field that is obtained from the decomposition of the staticmolecular polarizability α is tested by studying the one-photon absorption spec-trum of the green fluorescent protein. From the frequency dispersion of thepolarizability α(ω), the effect of field perturbations is evaluated in classicaland QM/MM applications. Using the dynamical polarizabilities, the Rayleigh-scattering of aerosol clusters consisting of water and cis–pinonic acid moleculesis studied. The LoProp hyperpolarizability in combination with the quadraticApplequist equations is used to test the validity of the model on sample wa-ter clusters of varying sizes. Using the modified point-dipole model developedby Thole, the hyper-Rayleigh scattering intensity of a model collagen triple-helix is calculated. The atomic dispersion coefficients are calculated from thedecomposition of the real molecular polarizability at imaginary frequencies. Fi-nally, using LoProp and a capping procedure we demonstrate how the QM/MMmethodology can be used to compute x-ray photoelectron spectra of a polymer.
I denna avhandling utvecklas ny metodik för beräkningar av egenskaper medolika tillämpningar. Vi använder kvantmekanik för att beräkna egenskaper hosmolekyler, och använder sedan dessa egenskaper som bas i klassiska ekvationer.Dessa approximationer visas vara bra i flera sammanhang, vilket gör det direktmöjligt att beräkna linjära och icke-linjära egenskaper i större system.De beräknade molekylära egenskaperna delas upp i atomära bidrag genomLoProp transformationen, en metod endast beroende av den atomära överlapps-matrisen. Detta ger möjligheten att representera en molekyls egenskaper i entvåatomsbasis, vilket ger atomära, och bindningscentrerade kraftfält tagna frånde molekylära multipoler och polarisabiliteter.Eftersom att den originella LoProp transformationen var formulerad medstatiska fält, så utvecklas och implementeras i denna avhandling LoProp meto-den ytterligare för frekvensberoende egenskaper. Genom den andra ordnin-gens störning med avseende på externa fält, så formuleras LoProp så att di-rekt bestämning av första ordningens hyperpolariserbarhet för atomära po-sitioner blir möjlig. De ursprungliga Applequist ekvationerna skrivs om tillen kvadratisk representation för att göra det möjligt att beräkna den andraordningens induktion av dipolmomenten för punktdipoler med hjälp av denförsta hyperpolariserbarheten. Detta gör det möjligt att beräkna den totalahyperpolariserbarheten för större system. Här används den statiska polariser-barheten och hyperpolariserbarheten framtagna via LoProp transformationenför att beräkna ett systems egenskaper då det utsätts av ett externt elektrisktfält via Applequists ekvationer till andra ordningen.Tillämpningar presenteras av den implementerade LoProp metodiken medden utvecklade andra ordnings Applequist ekvationer för olika system. Detpolariserbara kraftfältet som fås av lokalisering av α testas genom studier avabsorptionsspektrat för det gröna fluorescerande proteinet. Via beräkningar avden lokala frekvensavhängande polariserbarheten α(ω), testas effekten av de ex-terna störningar på klassiska och blandade kvant-klassiska egenskaper. Genomden linjära frekvensberoende polariserbarheten så studeras även Rayleigh sprid-ning av atmosfärs partiklar. Via LoProp transformationen av hyperpolariser-barheten i kombination med de kvadratiska Applequist ekvationerna så un-dersöks modellens rimlighet för vattenkluster av varierande storlek. Genom attanvända Tholes exponentiella dämpningsschema så beräknas hyper-Rayleighspridningen för kollagen. Den atomära dispersionskoefficienten beräknas via delokala bidragen till den imaginära delen av den linjära polariserbarheten. Slutli-gen visar vi hur LoProp tekniken tillsammans med en s.k. inkapslingsmetod kananvändas i QM/MM beräkningar av Röntgenfotoelektron spektra av polymerer.

QC 20160517

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18

Campbell, Ewen K. "Atomic polarisation in molecular photodissociation". Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:d1fd3e32-62be-4154-880f-431ec6045baa.

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1) species show a preference for the MJ = ±1 sub-levels. For these bands the electronic alignment is very similar to that observed in the dissociation of OCS, indicating a similar mechanism, at least in the exit channel, is responsible for the polarisation in both systems.

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19

Arora, Bindiya. "Modeling of atomic systems for atomic clocks and quantum information". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 159 p, 2009. http://proquest.umi.com/pqdweb?did=1654501311&sid=2&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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20

Lee, Michael Vernon. "Development of Chemomechanical Functionalization and Nanografting on Silicon Surfaces". BYU ScholarsArchive, 2007. https://scholarsarchive.byu.edu/etd/1435.

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Progress in chemomechanical functionalization was made by investigating the binding of molecules and surface coverage on the silicon surface, demonstrating functionalization of silicon with gases by chemomechanical means, analyzing atomic force microscopy probe tip wear in atomic force microscopy (AFM) chemomechanical nanografting, combining chemomechanical functionalization and nanografting to pattern silicon with an atomic force microscope, and extending chemomechanical nanografting to silicon dioxide. Molecular mechanics of alkenes and alkynes bound to Si(001)-2x1 as a model of chemomechanically functionalized surfaces indicated that complete coverage is energetically favorable and becomes more favorable for longer chain species. Scribing a silicon surface in the presence of ethylene and acetylene demonstrated chemomechanical functionalization with gaseous reagents, which simplifies sample cleanup and adds a range of reagents to those possible for chemomechanical functionalization. Thermal desorption spectroscopy was performed on chemomechanically functionalized samples and demonstrated the similarity in binding of molecules to the scribed silicon surface and to the common Si(001)-2x1 and Si(111)-7x7 surfaces. The wearing of atomic force microscope probe tips during chemomechanical functionalization was investigated by correlating change over time and force with widths of created lines to illustrate the detrimental effect of tip wear on mechanically-driven nanopatterning methods. In order to have a starting surface more stable than hydrogen-terminated silicon, silicon reacted with 1-octene was used as a starting surface for AFM chemomechanical functionalization, producing chemomechanical nanografting. Chemomechanical nanografting was then demonstrated on silicon dioxide using silane molecules; the initial passivating layer reduced the tip friction on the surface to allow only partial nanografting of the silane molecules. These studies broadened the scope and understanding of chemomechanical functionalization and nanografting.

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21

Dullweber, Andreas. "Simulation of atomic and molecular complexes". Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624109.

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22

Fletcher, James. "Studies of atomic and molecular cations". Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1420899/.

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Atomic and molecular cations have the potential to strongly influence a number of industrial, atmospheric and interstellar environments in which they are expected to be present. As a result, information on the generation and reactivity of positively charged species is invaluable when attempting to model and understand the physical and chemical processes taking place in such surroundings. This thesis reports a number of experimental investigations of the formation and reactivity of atomic and molecular cations. Firstly, a detailed study of the electron ionisation of sulphur dioxide (SO2) is presented. Relative precursor-specific partial ionisation cross sections for the fragment ions formed following electron ionisation of sulphur dioxide have been measured using time-of-flight mass spectrometry coupled with ion coincidence detection. These data quantify, for the first time, the formation of all fragment ions, relative to the formation of SO2+, via single, double and triple electron ionization of SO2. Secondly, the investigations of the bimolecular reactivity of a number of doubly (I2+ and N22+) and triply charged (I3+, Xe3+, CS23+) reactants are presented. A crossed-beam mass spectrometer was used to identify ion-molecule reaction products. The doubly and triply charged (I2+ and I3+/Xe3+) reactants are shown to participate in processes involving substantial rearrangement of chemical bonds. This reactivity can be encapsulated using a simple electrostatic model and energetic arguments. Furthermore, the same model has been updated to account for the results observed following the reactions of atomic trications. A different mass spectrometer, equipped with a position-sensitive coincidence ion detector, was then used to explore the dynamics of reactions involving first a molecular dication (N22+) with various low-mass organic molecules and then atomic (Xe3+) and molecular trications (CS23+). Product ion velocities determined using this technique can be used to explore the reaction energetics and angular scattering distributions for individual ion-molecule reaction channels. In turn, the interpretation of these data allow the identification of reaction mechanisms. The range of reactions exhibited in all of these studies is surprisingly diverse, clearly indicating a complex chemistry for collision systems involving dicationic and tricationic reactants.

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23

Bailey, Stephen Malcolm William. "Relativistic atomic photoionization". Thesis, Queen's University Belfast, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387976.

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24

Cisneros, Armas David Alejandro. "Molecular assemblies observed by atomic force microscopy". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1182777560689-53566.

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We use time-lapse AFM to visualize collagen fibrils self-assembly. A solution of acid-solubilized collagen was injected into the AFM fluid cell and fibril formation was observed in vitro. Single fibrils continuously grew and fused with each other until the supporting surface was completely covered by a nanoscopically well-defined collagen matrix. Laterally, the fibrils grew in steps of ~4 nm suggesting a two-step mechanism. In a first step, collagen molecules associated together. In the second step, these molecules rearranged into a structure called a microfibril. High-resolution AFM topographs revealed substructural details of the D-band architecture. These substructures correlated well with those revealed from positively stained collagen fibers imaged by transmission electron microscopy. Secondly, a covalent assembly approach to prepare membrane protein for AFM imaging that avoids crystallization was proposed. High-resolution AFM topographs can reveal structural details of single membrane proteins but, as a prerequisite, the proteins must be adsorbed to atomically flat mica and densely packed in a membrane to restrict their lateral mobility. Atomically flat gold, engineered proteins, and chemically modified lipids were combined to rapidly assemble immobile and fully oriented samples. The resulting AFM topographs of single membrane proteins were used to create averaged structures with a resolution approaching that of 2D crystals. Finally, the contribution of specific amino acid residues to the stability of membrane proteins was studied. Two structurally similar proteins sharing only 30% sequence identity were compared. Single-molecule atomic force microscopy and spectroscopy was used to detect molecular interactions stabilizing halorhodopsin (HR) and bacteriorhodopsin (BR). Their unfolding pathways and polypeptide regions that established stable segments were compared. Both proteins unfolded exactly via the same intermediates. This 3 Molecular Assemblies observed by AFM observation implies that these stabilizing regions result from comprehensive contacts of all amino acids within them and that different amino acid compositions can establish structurally indistinguishable energetic barriers. However, one additional unfolding barrier located in a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides into two stable segments.

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25

Zolotaryuk, Yaroslav. "Nonlinear dynamics of molecular and atomic chains". Thesis, Heriot-Watt University, 1998. http://hdl.handle.net/10399/638.

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26

Hussein, M. I. A. "Photoelectron spectroscopy of atomic and molecular oxygen". Thesis, University of Reading, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356131.

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27

Sochi, T. "Atomic and molecular aspects of astronomical spectra". Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1369696/.

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In the first section of this thesis, we present the atomic part of our investigation. A C2+ atomic target was prepared and used to generate theoretical data required in the investigation of recombination lines that arise from collisions between electrons and ions in thin plasma found in planetary nebulae and other astrophysical objects. The R-matrix method of electron scattering theory was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states were generated in the intermediate-coupling approximation by R-matrix and Autostructure codes and compared to experimental data. The comparison revealed very good agreement. These theoretical data were then used to generate dielectronic recombination data for C+ which include transition lines, oscillator strengths, radiative transition probabilities, as well as emissivity and dielectronic recombination coefficients. The data were cast in the form of a line list, called SS1, containing 6187 optically-allowed transitions which include many C II lines observed in astronomical spectra. The data were validated by comparison to C+ recombination data obtained from a number of sources in the literature. This line list was used to analyze the spectra from a number of astronomical objects, mainly planetary nebulae, and identify their electron temperature where the observational data were obtained from the literature. The electron temperature investigation was also extended to include free electron energy analysis which uses observational and theoretical data of FF and FB transitions to investigate the long-standing problem of discrepancy between the results of recombination and forbidden lines analysis and its possible connection to the electron distribution (Maxwellian or non-Maxwellian). In the course of this investigation two elaborate methods, one for finding and analyzing resonances (K-matrix method) and the other for analyzing and identifying electron temperature from astronomical spectra (least squares minimization), were employed. A computer program for atomic transition analysis was also developed and used as the main tool for obtaining the line list and analyzing the observational spectra. In the second section of the thesis we present the results of our molecular investigation; the generation of a comprehensive, calculated line list of frequencies and transition probabilities for the singly deuterated isotopologue of H3+, H2D+. The line list, which is the most comprehensive one of its kind in existence, contains over 22 million rotational-vibrational transitions occurring between more than 33 thousand energy levels and covers frequencies up to 18500 cm-1. All energy levels with rotational quantum number, J, up to 20 are considered, making the line list useful for temperatures up to at least 3000 K. About 15% of these levels are fully assigned with approximate rotational and vibrational quantum numbers. The list is calculated using a previously proposed, highly accurate, ab initio model implemented in a high-accuracy computer code based on a two-stage discrete variable representation (DVR) approach. Various consistency checks were carried out to test and validate the results. All these checks confirmed the accuracy of the list. A temperature-dependent partition function, valid over a more extended temperature range than those previously published, and cooling function are presented. Temperature-dependent synthetic spectra for the temperatures T=100, 500, 1000 and 2000 K in the frequency range 0-10000 cm-1 were also generated and presented graphically.

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28

Quadrini, Fabio. "Atomic angular momentum polarization in molecular photodissociation". Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670158.

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29

Undurti, Sainadh. "`Attoclock' experiments on atomic and molecular hydrogen". Thesis, Griffith University, 2018. http://hdl.handle.net/10072/381373.

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The current thesis aims at benchmarking strong- eld physics with the help of precision measurements performed on the simplest atomic (H) and molecular (H2) systems. The importance of H in validating strong- eld models is demonstrated through the rst set of experimental data. It aims at calibrating the absolute Carrier-envelope phase (CEP) of few-cycle laser pulses using H against complete ab initio solution of the three dimensional time-dependent Schr odinger equation (3D-TDSE). Subsequent set of measurements with noble gases against widely used strong- eld models based on single-active electron (SAE) approximation, is shown to reveal a systematic o set of 0:25 radians in tagging CEP, questioning the validity of such models. The second experimental study forms the main result of this thesis, that attempts to resolve the ongoing debate on tunnelling times (tunnelling delays in the context of strong- eld physics). We address this by employing the `attoclock' technique with 6 fs pulses on H and validating the results against full numerical solutions of ab initio 3D-TDSE. The validated numerical codes are then used to arti cially screen the parent ion-electron interaction, concluding that the tunnelling time 1.8 as. The nal experimental results presented in this dissertation are the alignmentdependent attoclock measurements using both few-cycle (7 fs) and multi-cycle (28 fs) pulses on H2. The measured attoclock observable for various molecular orientations (in laser polarisation frame) shows a strong modulation with a periodicity of . Initial ab initio simulations for few-cycle pulses under the frozen-nuclei and SAE approximations, fail to explain these observations. Further experimental studies with H2/D2 (50:50 mixed gases) show no signi cant relative di erences among the attoclock observables, suggesting a prominent role of the electron-electron correlations at play. The ongoing study is believed to have far reaching implications in applications such as studying molecular dissociation processes and tomography.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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30

Seiser, Bernhard Josef. "Topologically close-packed phase prediction in Ni-based superalloys : phenomenological structure maps and bond-order potential theory". Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:4298ebde-4b32-4dcc-b294-649493f9146c.

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Single crystal nickel-based superalloys are used in modern gas turbines because of their remarkable resistance to creep deformation at elevated temperatures, which is ensured by the addition of significant amounts of refractory elements. Too high concentrations of refractory elements can lead to the formation of topologically-close packed (TCP) phases during exposure to conditions of high temperature and stress which result in the degradation of the creep properties. The traditional methods for predicting the occurrence of TCP phases in Ni-based superalloys have been based on the PHACOMP and newPHACOMP methodologies which are well-known to fail with respect to new generations of alloys. In this work a novel two-dimensional structure map (Nbar, deltaV/V) for TCP phases where Nbar is the valence-electron count and deltaV/V is a compositional dependent size factor. This map is found to separate the experimental data on the TCP phases of binary, ternary and multi-component TCP phases into well-defined regions corresponding to different structure types such as A15, sigma, chi, delta, P, R, mu, and Laves. In particular, increasing size factor separates the A15, sigma and chi phases from the delta, P, R, mu phases. The structure map is then also used in conjunction with CALPHAD computations of sigma phase stability to show that the predictive power of newPHACOMP for the seven component Ni–Co–Cr–Ta–W–Re–Al system is indeed poor. In order to gain a microscopic understanding of the observed structural trends, namely the differences between the two groups of TCP structures with increasing deltaV/V and the trend from A15 to sigma to chi with increasing Nbar, the electronic structure is coarse-grained from density functional theory (DFT) to tight-binding to bond-order potentials (BOPs). First, DFT is used to calculate the structural energy differences across the elemental 4d and 5d transition metal series and the heats of formation of the binary alloys Mo-Re, Mo-Ru, Nb-Re, and Nb-Ru. These calculations show that the valence electron concentration stabilizes A15, sigma and chi but destablizes mu and Laves phases. The latter are shown to be stabilized instead by relative size difference. Second, a simple canonical TB model and in combination with the structural energy difference theorem is found to qualitatively reproduce the energy differences predicted by the elemental DFT calculations. The structural energy difference theorem rationalizes the importance of the size factor for the stability of the mu and Laves binary phases as observed in the structure map and DFT heats of formation. Finally, analytic BOP theory, is employed to identify the structural origins of the energetic differences between TCP structure-types that lead to the trends found within the two-dimensional structure map.

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31

McAlinden, Mary Trea. "Atomic collisions involving positrons". Thesis, Queen's University Belfast, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317480.

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32

Smeu, Manuel. "Quantum transport modeling of atomic nanostructures on silicon". Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=107818.

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Surface effects can adversely influence the performance of a nanoelectronic device,but may also lead to new functionality. The focus of this thesis is to theoreticallystudy the role of surfaces in nanoelectronics. Our theoretical analysis is from atomicfirst principles achieved by combining density functional theory with the Keldyshnonequilibrium Green's function approach. This technique allows for all atoms in asystem to be treated on an equal footing without any phenomenological parameters.The first part of the thesis considers conduction through a molecule with no substrateto illustrate the sort of system typically modeled in transport calculations. Two Auelectrodes are bridged by a substituted benzenediamine molecule (R = CH3, NH2,OH) where an H atom is removed to form a radical that may behave as a spin filter,depending on the R group. Next is considered a π–stacked line of ethylbenzenemolecules on the Si(100) surface, where the Si atoms are explicitly included in thecalculation. Although the molecules conduct electrons at certain energies, a channeloccurs through the substrate, which can dominate the conductance. The use ofsubstituent groups to modulate the electron transport properties of such wires is alsoinvestigated, showing that the conductance of the molecular wire could be tuned todominate over the substrate. Finally, the conductance of the Si(111)–7 × 7 metallicsurface is studied. Inspired by experiments suggesting that atomic steps reduce thesurface conductance, the atomic structure and transport properties of such steps areexamined, revealing that dimer atom buckling along the step edges is the primaryculprit since it leads to an opening of a local band gap at the step.
Les effets de surface peuvent affecter la performance d'un dispositif nanoélectronique, mais peuvent aussi conduire à de nouvelles fonctionnalités. L'objectif de cette thèse est d'effectuer une étude théorique sur le rôle des surfaces en nanoélectronique. Notre analyse, de type premiers principes atomiques, est effectuée en combinant la théorie de la fonctionnelle de la densité avec les fonctions de Green hors-équilibre. Cette technique permet de traiter tous les atomes de manière égale sans utiliser de paramètres phénoménologiques. La première partie de cette thèse considère la conduction à travers une molécule sans substrat, afin d'illustrer le genre de systèmes typiquement modélisés dans les calculs de transport. Deux électrodes en Au sont mises en contactavec une molécule benzènediamine substituée (R = CH3, NH2, OH), où un atome H est retiré pour former un radical qui peut se comporter comme un filtre de spin, dépendant du groupe R. Ensuite, nous nous concentrons sur une ligne formée d'éthylbenzènes empilées–π sur la surface de Si(100), où les atomes de silicium sont explicitement inclus dans le calcul. Quoique les molécules permettent le transport d'électronsà certaines énergies, un canal se forme à travers le substrat qui peut dominer la conductance. Nous étudions aussi comment certains substituants peuvent moduler les propriétés de transport électronique de ces fils moléculaires. Nous trouvons que la conductance du fil moléculaire peut être modifiée pour dominer l'effet du substrat.Enfin, la conductance de la surface métallique Si(111)–7 × 7 est analysée. Dans lebut d'expliquer théoriquement les expériences suggérant que les marches atomiques réduisent la conductance de la surface, la structure atomique et les propriétés de transport de ces marches ont été examinées. Les résultats révèlent que c'est la déformation atomique des dimères le long des marches qui cause ce phénomène, en raison de la formation d'une bande interdite localisée proche de la marche.

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Mikaberidze, Alexey. "Atomic and molecular clusters in intense laser pulses". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-71087.

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We have investigated processes of ionization, energy absorption and subsequent explosion of atomic and molecular clusters under intense laser illumination using numerical as well as analytical methods. In particular, we focused on the response of composite clusters, those consisting of different atomic elements, to intense light pulses. Another major theme is the effect of the molecular structure of clusters on their Coulomb explosion. The action of intense laser pulses on clusters leads to fundamental, irreversible changes: they turn almost instantaneously into nanoplasmas and subsequently disintegrate into separate ions and electrons. Due to this radical transformation, remarkable new features arise. Transient cluster nanoplasmas are capable of absorbing enormous amounts of laser energy. In some cases more than 90 % of incident laser energy is absorbed by a gas of clusters with a density much smaller than that of a solid. After the efficient absorption, the energy is transformed into production of energetic ions, electrons, photons, and even neutrons. Composite clusters show especially interesting behavior when they interact with intense laser pulses. Nanoplasmas formed in composite clusters may absorb even more laser energy, than those formed in homogeneous clusters, as we demonstrate in this work. One of the most important results of this thesis is the identification of a novel type of plasma resonance. This resonance is enabled by an unusual ellipsoidal shape of the nanoplasma created during the ionization process in a helium droplet doped with just a few xenon atoms. In contrast to the conventional plasma resonance, which requires significant ion motion, here, the resonant energy absorption occurs at a remarkably fast rate, within a few laser cycles. Therefore, this resonance is not only the most efficient (like the conventional resonance), but also, perhaps, the fastest way to transfer laser energy to clusters. Recently, dedicated experimental studies of this effect were performed at the Max Planck Institute in Heidelberg. Their preliminary results confirm our prediction of a strong, avalanche-like ionization of the helium droplet with a small xenon cluster inside. A conventional plasma resonance, which relies on the cluster explosion, also exhibits interesting new properties when it occurs in a composite xenon-helium cluster with a core-shell geometry. We have revealed an intriguing double plasma resonance in this system. This was the first theoretical study of the influence of the helium embedding on the laser- driven nanoplasma dynamics. Our results demonstrate the important role of the interaction between xenon and helium parts of the cluster. Understanding this interaction is necessary in order to correctly interpret the experimental results. We have elucidated several important properties of Coulomb explosion in atomic and molecular clusters. Specifically, it was found that the kinetic energy distribution of ions after the Coulomb explosion of an atomic cluster is quite similar to the initial potential energy distribution of ions and is only weakly influenced by ion overtake effects, as was believed before. For the case of molecular hydrogen clusters, we have shown that the alignment of molecules inside the cluster affects its Coulomb explosion. Investigation of the dynamical processes in composite and molecular clusters induced by intense laser pulses is a step towards understanding them in more complex nano-objects, such as biomolecules or viruses. This is of great interest in the context of x-ray diffractive imaging of biomolecules with atomic resolution, which is one of the main goals of new x-ray free electron laser facilities.

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Sponseller, Daniel Ray. "Molecular Dynamics Study of Polymers and Atomic Clusters". Thesis, George Mason University, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10685723.

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This dissertation contains investigations based on Molecular Dynamics (MD) of a variety of systems, from small atomic clusters to polymers in solution and in their condensed phases. The overall research is divided in three parts. First, I tested a new thermostat in the literature on the thermal equilibration of a small cluster of Lennard-Jones (LJ) atoms. The proposed thermostat is a Hamiltonian thermostat based on a logarithmic oscillator with the outstanding property that the mean value of its kinetic energy is constant independent of the mass and energy. I inspected several weak-coupling interaction models between the LJ cluster and the logarithmic oscillator in 3D. In all cases I show that this coupling gives rise to a kinetic motion of the cluster center of mass without transferring kinetic energy to the interatomic vibrations. This is a failure of the published thermostat because the temperature of the cluster is mainly due to vibrations in small atomic clusters This logarithmic oscillator cannot be used to thermostat any atomic or molecular system, small or large.

The second part of the dissertation is the investigation of the inherent structure of the polymer polyethylene glycol (PEG) solvated in three different solvents: water, water with 4% ethanol, and ethyl acetate. PEG with molecular weight of 2000 Da (PEG₂₀₀₀) is a polymer with many applications from industrial manufacturing to medicine that in bulk is a paste. However, its structure in very dilute solutions deserved a thorough study, important for the onset of aggregation with other polymer chains. I introduced a modification to the GROMOS 54A7 force field parameters for modeling PEG₂₀₀₀ and ethyl acetate. Both force fields are new and have now been incorporated into the database of known residues in the molecular dynamics package Gromacs. This research required numerous high performance computing MD simulations in the ARGO cluster of GMU for systems with about 100,000 solvent molecules. My findings show that PEG₂₀₀₀ in water acquires a ball-like structure without encapsulating solvent molecules. In addition, no hydrogen bonds were formed. In water with 4% ethanol, PEG₂₀₀₀ acquires also a ball-like structure but the polymer ends fluctuate folding outward and onward, although the general shape is still a compact ball-like structure.

In contrast, PEG₂₀₀₀ in ethyl acetate is quite elongated, as a very flexible spaghetti that forms kinks that unfold to give rise to folds and kinks in other positions along the polymer length. The behavior resembles an ideal polymer in a &thetas; solvent. A Principal Component Analysis (PCA) of the minima composing the inherent structure evidences the presence of two distinct groups of ball-like structures of PEG₂₀₀₀ in water and water with 4% ethanol. These groups give a definite signature to the solvated structure of PEG₂₀₀₀ in these two solvents. In contrast, PCA reveals several groups of avoided states for PEG₂₀₀₀ in ethyl acetate that disqualify the possibility of being an ideal polymer in a &thetas; solvent.

The third part of the dissertation is a work in progress, where I investigate the condensed phase of PEG₂₀₀₀ and study the interface between the condensed phase and the three different solvents under study. With a strategy of combining NPT MD simulations at different temperatures and pressures, PEG₂₀₀₀ condensed phase displays the experimental density within a 1% discrepancy at 300 K and 1 atm. This is a very encouraging result on this ongoing project.

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35

Johansson, Pia. "Ultrafast Spectroscopy of Atomic and Molecular Quantum Dynamics". Doctoral thesis, Stockholm : Department of Physics, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1252.

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36

Fulton, Ray. "Atomic and molecular manipulation in pulsed optical fields". Thesis, Heriot-Watt University, 2006. http://hdl.handle.net/10399/125.

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37

Braga, J. P. "Adiabatic and non-adiabatic atomic and molecular collisions". Thesis, University of Sussex, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.375146.

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38

Wang, Liang-Guo. "Studies of Rydberg atomic xenon and molecular hydrogen /". The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487323583622812.

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39

Dahlberg, Martin. "Molecular Modeling of Cardiolipin /". Stockholm : Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-37613.

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Diss. (sammanfattning) Stockholm : Stockholms universitet, 2010.
At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Submitted. Härtill 4 uppsatser.

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40

Lovrić, Josip. "Molecular modeling of aerosols". Thesis, Lille 1, 2017. http://www.theses.fr/2017LIL10080/document.

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Cette thèse est une étude, au niveau moléculaire, par des méthodes de simulation numérique, des propriétés des aérosols organiques, notamment des aérosols marins, et de leur interaction avec des espèces présentes dans l’atmosphère. L’organisation de la matière organique au sein de ces aérosols joue un rôle fondamental pour leurs propriétés optiques, chimiques et leur rôle comme noyau de condensation pour les nuages.Dans une première partie, on présente contexte atmosphérique et les méthodes de dynamique moléculaire classique et les méthodes mixtes quantique/classique utilisées pour simuler ces aérosols. Ensuite, on décrit l’application de ces méthodes à trois cas.Tout d’abord, on a étudié, par dynamique moléculaire classique (logiciel Gromacs), l’organisation, notamment l’orientation, de molécules d’acide palmitique absorbées sur une surface de sel (NaCl) en fonction du taux de couverture en acide gras et de la température. On présente aussi une étude détaillée de l’influence de l’humidité sur l’organisation de ce film organique à la surface du sel, mettant en évidence l’existence d’îlots d’acide gras monocouches structurés. Dans une seconde étude, la réactivité de NO2 avec cet aérosol marin est traitée par une approche mixte quantique/classique (logiciel CP2K), avec prise en compte de l’impact de l’humidité sur cette réactivité.Enfin, la dernière étude concerne une étude par dynamique moléculaire de phases condensées organiques (n-butanol) et de leur interaction avec des molécules d’eau. Cette étude théorique, complémentaire d’expériences de jets moléculaires, a pour but de mieux comprendre le rôle fondamental que jouent ces interactions pour les propriétés des aérosols et des nuages
In this thesis numerical methods are used to study the properties, described at the molecular level, of organic aerosols, especially marine aerosols, and their interaction with species in the atmosphere. The organisation of the organic matter in these aerosols plays a key role for their optical, chemical properties, and their ability to act as a cloud condensation nuclei.The first part reviews atmospheric context and the methods (classical molecular dynamics and hybrid quantum/classical approaches) used in this thesis. Then applications to three cases are detailed.Firstly, the organization, more particularly the orientation, of palmitic acid molecules adsorbed on a salt (NaCl) surface as a function of the fatty acid coverage and temperature has been studied using classical molecular dynamics (Gromacs package). The impact of the humidity on the structuration of this organic coating has been described in details, showing the existence of structured fatty acid island-like monolayers on NaCl surface.In a second study, the reactivity of NO2 with these heterogeneous marine aerosols has been investigated by a hybrid quantum/classical method (CP2K package), with taking into account the effect of the humidity.The last study is a classical molecular dynamics of n-butanol crystal, water accommodation at these surfaces and simulation of water jet collision with n-butanol surface. These simulations, complementary to experiments, were performed to better understand the fundamental role of the water-organic matter interaction on the properties of the aerosols and clouds

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41

Plimmer, Mark David. "Laser spectroscopy of atomic systems". Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329991.

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42

Thomas, Malcolm. "Electron scattering by atomic oxygen". Thesis, Queen's University Belfast, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337031.

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43

Harris, M. "Collisional effects in atomic spectra". Thesis, University of Newcastle Upon Tyne, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.352727.

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44

Docker, M. P. "Molecular photodissociation dynamics". Thesis, University of Nottingham, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378987.

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45

Seda, Kin. "Collisional depolarization of the atomic Cs 6s²S_1/2-10s²S_3/2,9d²D_5/2 transition with argon buffer gas". Connect to this document online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=miami1119285688.

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Thesis (Master of Science)--Miami University, Dept. of Physics, 2005.
Title from first page of PDF document. Document formatted into pages; contains [1], ???, ??? p. : ill. Includes bibliographical references (p. Xx-Xx).

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46

Messina, Luca. "Multiscale modeling of atomic transport phenomena in ferritic steels". Doctoral thesis, KTH, Reaktorfysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-177525.

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Defect-driven transport of impurities plays a key role in the microstructure evolution of alloys, and has a great impact on the mechanical properties at the macroscopic scale. This phenomenon is greatly enhanced in irradiated materials because of the large amount of radiation-induced crystal defects (vacancies and interstitials). For instance, the formation of nanosized solute clusters in neutron-irradiated reactor pressure vessel (RPV) ferritic steels has been shown to hinder dislocation motion and induce hardening and embrittlement. In Swedish RPV steels, this mechanical-property degradation is enhanced by the high content of manganese and nickel impurities. It has been suggested that the formation of Mn-Ni-rich clusters (which contain also Cu, Si, and P) might be the outcome of a dynamic process, where crystal defects act both as nucleation sites and solute carriers. Solute transport by point defects is therefore a crucial mechanism to understand the origin and the dynamics of the clustering process. The first part of this work aims at modeling solute transport by point defects in dilute iron alloys, to identify the intrinsic diffusion mechanisms for a wide range of impurities. Transport and diffusion coefficients are obtained by combining accurate ab initio calculations of defect transition rates with an exact mean-field model. The results show that solute drag by single vacancies is a common phenomenon occurring at RPV temperature (about 300 °C) for all impurities found in the solute clusters, and that transport of phosphorus and manganese atoms is dominated by interstitial-type defects. These transport tendencies confirm that point defects can indeed carry impurities towards nucleated solute clusters. Moreover, the obtained flux-coupling tendencies can also explain the observed radiation-induced solute enrichment on grain boundaries and dislocations. In the second part of this work, the acquired knowledge about solute-transport mechanisms is transferred to kinetic Monte Carlo (KMC) models, with the aim of simulating the RPV microstructure evolution. Firstly, the needed parameters in terms of solute-defect cluster stability and mobility are calculated by means of dedicated KMC simulations. Secondly, an innovative approach to the prediction of transition rates in complex multicomponent alloys is introduced. This approach relies on a neural network based on ab initio-computed migration barriers. Finally, the evolution of the Swedish RPV steels is simulated in a "gray-alloy" fashion, where impurities are introduced indirectly as a modification of the defect-cluster mobilities. The latter simulations are compared to the experimental characterization of the Swedish RPV surveillance samples, and confirm the possibility that solute clusters might form on small interstitial clusters. In conclusion, this work identifies from a solid theoretical perspective the atomic-transport phenomena underlying the formation of embrittling nanofeatures in RPV steels. In addition, it prepares the ground for the development of predictive KMC tools that can simulate the microstructure evolution of a wide variety of irradiated alloys. This is of great interest not only for reactor pressure vessels, but also for many other materials in extreme environments.

QC 20151123

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47

Itckovich, Aleksei A., e Boris Bokstein. "Computer modeling of atomic clusters formation in grain boundaries". Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-198246.

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48

Itckovich, Aleksei A., e Boris Bokstein. "Computer modeling of atomic clusters formation in grain boundaries". Diffusion fundamentals 24 (2015) 25, S. 1-2, 2005. https://ul.qucosa.de/id/qucosa%3A14536.

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49

Zhao, Zengxiu. "Atomic and molecular dynamics in ultrashort intense laaser fields /". Search for this dissertation online, 2005. http://wwwlib.umi.com/cr/ksu/main.

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50

Heijkenskjöld, Filip. "Experimental Techniques for Studies in Atomic & Molecular Physics". Doctoral thesis, Uppsala University, Department of Physics and Materials Science, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9295.

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This thesis is based on a selection of six different experimental techniques used for studies in atomic and molecular physics. The techniques analysed in the thesis are compared to find similarities in strategies and ways to avoid sources of error.

Paper 1 deals with collision based spectroscopy with 60 keV Xe6+ ions on sodium and argon gas targets. Information on energy of Rydberg states in Xe5+ is unveiled by optical spectroscopy in the wavelength range from vacuum ultraviolet (VUV) to visible. In paper 2, the fast ion-beam laser spectroscopy (FIBLAS) is adapted for measuring hyperfine structure of barium isotopes in an isotopically pure ion-beam. This techniques involves changing the isotope during the measurement to minimize sources of error in measurement and enhance the signal from lesser abundant isotopes. The FIBLAS technique is used in paper 3 to study samarium ions. The ions are optically pumped and the recorded optical nutation is used to measure transition probabilities. This technique eludes the difficulties inherent in relative intensity measurements of all the radiative transitions from an excited state. In Paper 4, optical emission spectroscopy is used in the VUV region to study noble gas mixture discharges. The source of the emission bands near the resonance lines of krypton and xenon are found to be heteronuclear dimers. In paper 5, radiation from a pulsed argon plasma with admixture of nitrogen is studied with time resolved spectroscopy in the VUV and ultraviolet wavelength ranges to investigate the mechanism of energy transport. A metastable state of atomic argon is found to be an important source of energy to many radiative processes. In Paper 6, photoelectron spectroscopy (PES) on thiophene, on 3-bromothiophene and on 3,4-dibromothiophene using time-of-flight photoelectron-photoelectron coincidence technique and conventional PES to investigate the onset of double ionisation compared to the onset of single ionisation in molecules.

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Tesi sul tema "Atomic and molecular modeling"

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