Dissertations / Theses: 'Ab-initio molecular dynamics simulation'

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Cassone, Giuseppe. "Ab initio molecular dynamics simulations of H-bonded systems under an electric field." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066061/document.

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Malgré le mécanisme de base du transport protonique (PT) dans l'eau ait été proposé en 1806, à ce jour il n'existe pas de théorie complète qui décrive la protolyse. Ce phénomène est à la base du fonctionnement des batteries à hydrogène et de nombreux processus biologiques. Grâce à la technique de dynamique moléculaire Car-Parrinello (CPMD) et à l'aide de l'application d'un champ electrique (EF), une partie de cette thèse a été consacrée à l'étude du PT dans deux phase de la glace: la phase Ih et sa contrepartie ferroélectrique, la glace XI. Certains mécanismes ont été révélés: le rôle joué par les oxygènes lorsque se produit le PT et la contribution du (dés)ordre afin d'assister ce processus [1,2]. Le phénomène du PT est aussi à la base de nombreaux convertisseurs d'énergie constitués par le méthanol tels que le Direct Methanol Fuel Cells et les membranes Nafion. Afin de révéler la nature intime du PT dans le méthanol liquide, une série de simulations CPMD ont été menées sous l'effet d'un EF extérieur. De cette façon il a été possible de comparer le rôle joué par les liasons hydrogène afin d'assister le PT [3]. De plus, quand les intensités du champ sont plus élevées que celles qui donnent lieu au PT, certaines réactions chimiques ont été observées dans le même échantillon "numérique" du méthanol. En exploitant des paramètres typique de la "Théorie de la fonctionnelle de la densité conceptuelle", il a été possible de clarifier les conditions qui donnent lieu à ces réactions chimiques. Enfin, afin de quantifier la contribution du EF à la formation de méthane et de formaldéhyde dans le système, des simulations de métadynamique en conjonction à ceux ab initio ont été menées Although the basic mechanism of the proton transfer (PT) phenomenon in water has been envisaged in 1806, nowadays does not exist a detailed theoretical framework that envelop the protolysis process. This phenomenon is at the base of the operation of hydrogen batteries, as well as of many biological processes. Via the Car-Parrinello Molecular Dynamics (CPMD) technique and by means of the application of an electric field (EF), part of this thesis has been devoted to the detailed study of PT in two ice phases: ice Ih and its ferroelectric counterpart, ice XI. Several previously unknown mechanisms have been shown. As an example, the role played by the oxygens when a PT occurs and the contribution due to (dis)order in assisting this process [1,2]. The PT phenomenon is also at the base of the functioning of some methanol-based energy converters such as Nafion membranes. To the aim of disclosing the intimate nature of PT in liquid methanol, a series of CPMD simulations have been carried out by applying an external EF; the role played by the H-bond network have been also compared with the similar PT mechanism in water [3]. At field strengths higher than those leading to PT, several chemical reactions have been observed in this sample. By exploiting the conceptual Density Functional Theory framework, it has been possible to clarify the circumstances under which a given chemical reaction occurs. Moreover, in order to disclose the role played by the EF in assisting chemical reactions, the mechanism leading to the formation of formaldehyde and methane in the sample has been studied with metadynamics approaches in conjuction with the ab initio ones

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Cassone, Giuseppe. "Ab initio molecular dynamics simulations of H-bonded systems under an electric field." Electronic Thesis or Diss., Paris 6, 2016. http://www.theses.fr/2016PA066061.

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Abstract:

Malgré le mécanisme de base du transport protonique (PT) dans l'eau ait été proposé en 1806, à ce jour il n'existe pas de théorie complète qui décrive la protolyse. Ce phénomène est à la base du fonctionnement des batteries à hydrogène et de nombreux processus biologiques. Grâce à la technique de dynamique moléculaire Car-Parrinello (CPMD) et à l'aide de l'application d'un champ electrique (EF), une partie de cette thèse a été consacrée à l'étude du PT dans deux phase de la glace: la phase Ih et sa contrepartie ferroélectrique, la glace XI. Certains mécanismes ont été révélés: le rôle joué par les oxygènes lorsque se produit le PT et la contribution du (dés)ordre afin d'assister ce processus [1,2]. Le phénomène du PT est aussi à la base de nombreaux convertisseurs d'énergie constitués par le méthanol tels que le Direct Methanol Fuel Cells et les membranes Nafion. Afin de révéler la nature intime du PT dans le méthanol liquide, une série de simulations CPMD ont été menées sous l'effet d'un EF extérieur. De cette façon il a été possible de comparer le rôle joué par les liasons hydrogène afin d'assister le PT [3]. De plus, quand les intensités du champ sont plus élevées que celles qui donnent lieu au PT, certaines réactions chimiques ont été observées dans le même échantillon "numérique" du méthanol. En exploitant des paramètres typique de la "Théorie de la fonctionnelle de la densité conceptuelle", il a été possible de clarifier les conditions qui donnent lieu à ces réactions chimiques. Enfin, afin de quantifier la contribution du EF à la formation de méthane et de formaldéhyde dans le système, des simulations de métadynamique en conjonction à ceux ab initio ont été menées Although the basic mechanism of the proton transfer (PT) phenomenon in water has been envisaged in 1806, nowadays does not exist a detailed theoretical framework that envelop the protolysis process. This phenomenon is at the base of the operation of hydrogen batteries, as well as of many biological processes. Via the Car-Parrinello Molecular Dynamics (CPMD) technique and by means of the application of an electric field (EF), part of this thesis has been devoted to the detailed study of PT in two ice phases: ice Ih and its ferroelectric counterpart, ice XI. Several previously unknown mechanisms have been shown. As an example, the role played by the oxygens when a PT occurs and the contribution due to (dis)order in assisting this process [1,2]. The PT phenomenon is also at the base of the functioning of some methanol-based energy converters such as Nafion membranes. To the aim of disclosing the intimate nature of PT in liquid methanol, a series of CPMD simulations have been carried out by applying an external EF; the role played by the H-bond network have been also compared with the similar PT mechanism in water [3]. At field strengths higher than those leading to PT, several chemical reactions have been observed in this sample. By exploiting the conceptual Density Functional Theory framework, it has been possible to clarify the circumstances under which a given chemical reaction occurs. Moreover, in order to disclose the role played by the EF in assisting chemical reactions, the mechanism leading to the formation of formaldehyde and methane in the sample has been studied with metadynamics approaches in conjuction with the ab initio ones

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Sulpizi, Marialore. "Ab initio studies of targets for pharmaceutical intervention." Doctoral thesis, SISSA, 2001. http://hdl.handle.net/20.500.11767/4280.

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In this thesis we further explore the capability of first principle methods to provide insights on drug/target interactions in different contexts. In the first part of this work, we address the issue whether OFT methods can be used as a potential tool for drug-screening. First principle calculations are particularly interesting for screening the energetics of drug/target interactions, as they do not involve the painstaking procedure of developing each set of new parameters for each novel drug. In this context, we use ab initio_ methods as a novel tool to determine a scoring function in a series of prodrug I target (herpes simplex type 1 thyimidine kinase) complexes for gene-therapy based anticancer approaches. This work, accompanied by experimental data provided by Prof. Folkers' Lab (ETH, Zurich) provides a new, very simple, ab initiobased approach to the construction of scoring functions for drug-screening. In the second part of the thesis we investigate the capability of OFT to describe non trivial interactions which are encountered in several inhibitor/enzyme complexes of pharmaceutical interest. Clearly, the description of these non-trivial phenomena might require the use of electronic structure methods. Here we present an example of cation-n interaction found in the human immunodeficiency virus reverse transcriptase (HIV-1 RT), one of the major targets for anti-AIDS therapy(Furman et al., 2000)). Furthermore, we provide a description of the hydroxyl-n interactions in the active site of μ-glutathione S-transferase(Xiao et al., 1996) (μ-GST), whose differential expression has been implicated in the development of cancers as well as their resistance to chemotherapeutic drugs ((Mccallum et al., 2000) and reference therein). Finally we present a classic problem treated by quantum-chemical methods: the simulation of an enzymatic reaction. We focus on a class of cysteine proteases, the caspases. These enzymes are extremely important targets for pharmaceutical intervention in therapies against Alzheimer's and other neurodegenerative processes, yet very few inhibitors have been so far designed. Since an important class of inhibitors is the given by the transition state analogs, it is of importance to fully understand the · enzymatic reaction, that is the hydrolysis of peptides. Because of the crucial importance of temperature and environment(Karplus, 2000; Glennon and Warshel, 1998; Varnai and Warshel, 2000; Villa et al., 2000) effects for enzymatic catalysis, we use here a hybrid Car-Parrinello Molecular dynamics I Molecular mechanics approach recently developed in the Lab of Prof. U. Roethlisberger (Laio et al., 2001 ). This technique allows to evaluate the intermolecular interactions at the active site from electronic structure calculations as the simulation proceeds(Car and Parrinello, 1985). Steric and electrostatic effects of the protein scaffold on the quantum region are included using classical MD approach on the rest of the system. The free energy of the process is calculated using a thermodynamic integration approach(Ciccotti et al., 1989; Carloni et al., 2000; Piana et al., 2001). This thesis is organized as follows. The first chapter provides a description of the used computational techniques. The following chapter describes the systems investigated here and summarizes our findings. The subsequent three chapters are devoted to a - detailed description of my thesis work. In a final chapter we draw some conclusions and provide a perspective for possible future applications, which could follow this work.

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Chen, Chi-Yuan. "Ab Initio Molecular Dynamics Simulation of Proton Transfer in Imidazole: An Atom-Centered Density Matrix Propagation (ADMP) Approach." Cincinnati, Ohio : University of Cincinnati, 2006. http://www.ohiolink.edu/etd/view.cgi?acc%5Fnum=ucin1141281810.

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Thesis (M.S.)--University of Cincinnati, 2006. Title from electronic thesis title page (viewed Apr. 24, 2006). Includes abstract. Keywords: ADMP, proton, ONIOM, imidazole. Includes bibliographical references.

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Rimsza, Jessica M. "Reactions and Interfacial Behaviors of the Water–Amorphous Silica System from Classical and Ab Initio Molecular Dynamics Simulations." Thesis, University of North Texas, 2016. https://digital.library.unt.edu/ark:/67531/metadc849660/.

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Due to the wide application of silica based systems ranging from microelectronics to nuclear waste disposal, detailed knowledge of water-silica interactions plays an important role in understanding fundamental processes, such as glass corrosion and the long term reliability of devices. In this dissertation, atomistic computer simulation methods have been used to explore and identify the mechanisms of water-silica reactions and the detailed processes that control the properties of the water-silica interfaces due to their ability to provide atomic level details of the structure and reaction pathways. The main challenges of the amorphous nature of the silica based systems and nano-porosity of the structures were overcome by a combination of simulation methodologies based on classical molecular dynamics (MD) simulations with Reactive Force Field (ReaxFF) and density functional theory (DFT) based ab initio MD simulations. Through the development of nanoporous amorphous silica structure models, the interactions between water and the complex unhydroxylated internal surfaces identified the unusual stability of strained siloxane bonds in high energy ring structure defects, as well as the hydroxylation reaction kinetics, which suggests the difficulty in using DFT methods to simulate Si-O bond breakage with reasonable efficiency. Another important problem addressed is the development of silica gel structures and their interfaces, which is considered to control the long term residual dissolution rate in borosilicate glasses. Through application of the ReaxFF classical MD potential, silica gel structures which mimic the development of interfacial layers during silica dissolution were created A structural model, consisting of dense silica, silica gel, and bulk water, and the related interfaces was generated, to represent the dissolution gel structure. High temperature evolution of the silica-gel-water (SGW) structure was performed through classical MD simulation of the system, and growth of the gel into the water region occurred, as well as the formation of intermediate range structural features of dense silica. Additionally, hydroxylated silica monomers (SiO4H4) and longer polymerized silica chains were formed in the water region, indicating that glass dissolution is occurring, even at short time frames. The creation of the SGW model provides a framework for a method of identifying how interfacial structures which develop at glass-water interfaces can be incorporated into atomistic models for additional analysis of the dissolution of silicates in water.

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Iglesias, Fernández Javier. "Elucidating catalytic mechanisms of glycoside hydrolases and transferases by means of ab initio molecular dynamics simulations." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/283551.

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Carbohydrates play a central role in transport and storage of energy and as molecular building blocks. Additionally, glycoconjugates, specifically glycoproteins and glycolipids, are important components of cell surfaces and the extracellular environment that mediate cellular and molecular interactions. Defects in glycosylation are associated with human diseases while the ability of glycans to modulate immune responses leads to them playing a critical role in susceptibility and resistance to pathogens. This huge amount of glycan structures requires the existence of a diverse group of degrading and remodelling enzymes: glycoside hydrolases (GHs) and glycoside transferases (GTs). GHs and GTs are highly specific enzymes responsible of the hydrolysis (GHs) and formation (GTs) of glycosidic bonds in carbohydrates. They are responsible for the modification of polysaccharides and glycoconjugates involved in numerous biological processes such as pathogenesis mechanisms, cell-cell recognition and polysaccharide degradation for biofuel processing. Knowledge of their enzymatic mechanism at a molecular level is crucial to understand how carbohydrates are assembled/degraded in organisms, as well as in developing new drugs. The detailed characterization of the transition state of the chemical reaction in which they participate, for instance, is key for the development of TS-analog inhibitors, which are known to be very efficient. In recent years, our group has investigated the implications of the conformational changes on the substrate during catalysis in several GHs and has related these changes with the conformations that can be sampled by a single sugar unit (e.g. glucose). This was analyzed by adapting sugar puckering coordinates as collective variables in ab initio metadynamics simulations. These studies are having a significant impact not only in the theoretical community but also in biochemistry and biophysics, because of the possibility to predict substrate catalytic itineraries for GHs. In this thesis, we extend these analyses to other sugar molecules to verify the proposed catalytic itineraries and also to GH inhibitors and sugar oxocarbenium ions to gain insights into transition state mimicry. Unlike GHs, known to operate by means of a double displacement mechanism, the reaction mechanism of retaining GTs is controversial. Both a two-step mechanism (by analogy to retaining glycoside hydrolases) and a one-step mechanism have been proposed and studied by means of quantum mechanics / molecular mechanics (QM/MM) simulations. Here, we applied this methodology to elucidate the catalytic mechanism of an engineered glycoside hydrolase and a glycoside transferase, giving support for a front-face single displacement mechanism. Los azúcares presentan una gran variabilidad estructural que es aprovechada por los diferentes organismos para realizar una multitud de procesos biológicos, que incluyen el almacenamiento de energía, el reconocimiento y la señalización celular. Las glicosil hidrolasas y glicosil transferasas son las enzimas responsables de la hidrólisis y síntesis, respectivamente, de estos biopolímeros y por lo tanto están presentes en una gran variedad de procesos celulares. Las técnicas de modelado molecular permiten analizar estos procesos biológicos, como por ejemplo la reacción de formación de un enlace entre azúcares, a un nivel atomístico. De esta forma, se pueden describir los cambios conformacionales que se producen en el sustrato al unirse a la enzima, identificar el estado de transición de la reacción química y determinar otros aspectos fundamentales de la catálisis enzimática.

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Walbrühl, Martin. "Diffusion in the liquid Co binder of cemented carbides: Ab initio molecular dynamics and DICTRA simulations." Thesis, KTH, Materialvetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-140880.

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A fundamental quantum mechanical modelling approach is used for calculating liquid diffusion parameters in cemented carbides. Up to now, no detailed description of diffusion for alloying elements in a liquid Co matrix is available. Neither are experimental measurements found in the literature for the self- or impurity diffusion in the liquid Co system. State of the art application is the description of gradient formation in cemented carbide systems using DICTRA. In this work it is assumed that diffusion during sintering of cemented carbides takes place mainly in the liquid Co binder phase. With this assumption one can calculate the diffusion coefficient for different alloying elements like W, Ti, N and C in a liquid Co matrix phase. The mean square displacement (MSD) of the diffusing atoms is used to obtain the diffusion coefficients which could be simulated by Ab initio Molecular Dynamics (AIMD). By fitting the computed temperature dependence with the Arrhenius relation one can determine the frequency factor and the activation energy which allows to give a quantitative description of the diffusion. Three methods will be used for validating the data from this work. Available estimated literature values based on calculations (scaling laws, a modified Sutherland equation and classical molecular dynamics) will be used to compare the results in a first instance. The general agreement for diffusion in liquid metals will be done by comparison with experimental data for the liquid Fe system. In a last step, the diffusion values obtained by this work will be used to create a kinetic database for DICTRA. The gradient simulations will be compared with experimentally measured gradients. The AIMD simulations are performed for binary diffusion systems to investigate the diffusion between the liquid Co matrix and one type of alloying element. In a second approach the diffusion for a multicomponent systems with Co, W, Ti and C has been performed. The results from the present AIMD simulations could be shown to be in good agreement with the literature. Only two DICTRA simulations could be performed within the timeframe of this work. Both are predicting a ~3 times bigger gradient zone whereas the initial choice of the labyrinth factor λ = f could be identified as a possible source of disagreement. A labyrinth factor of λ = f2 with the calculated mobility values from the AIMD calculations should give improved results. Although the results from those simulations are not available to this date. The two approaches of the diffusion simulations in the binary and multicomponent system are giving matching results. The non-metallic elements C and N are diffusing two times faster than the fastest metallic element Co. The diffusivity of Ti is slightly lower than Co and W could be identified as the element with the slowest diffusion within the liquid Co matrix. Further investigations of the liquid structure could indicate the tendency to form bonds between C and W and between C and Ti. This gives slowed down diffusion of C in the multicomponent system compared to the diffusion in the binary Co-C system.

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Ilhan, Mehmet Ali [Verfasser], Eckhard [Akademischer Betreuer] Spohr, and Georg [Akademischer Betreuer] Jansen. "Ab Initio Molecular Dynamics Simulation of Proton Transfer in Narrow Ionomer Pores / Mehmet Ali Ilhan. Gutachter: Georg Jansen. Betreuer: Eckhard Spohr." Duisburg, 2015. http://d-nb.info/1067055231/34.

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Cheenicode, Kabeer Fairoja [Verfasser]. "Ab initio Molecular Dynamics Simulations of the Structural Response of Solids to Ultrashort Laser and XUV Pulses / Fairoja Cheenicode Kabeer." Kassel : Universitätsbibliothek Kassel, 2015. http://d-nb.info/1069693669/34.

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Pham, Thanh Tung. "Multiscale modelling and simulation of slip boundary conditions at fluid-solid interfaces." Phd thesis, Université Paris-Est, 2013. http://tel.archives-ouvertes.fr/tel-00980155.

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In most applications concerning a fluid flowing over a solid surface, the no-slip velocity condition was widely used because it is simple and produces the results in agreement with experiments. However, this dynamical boundary condition is not appropriate when the flow under consideration is at a micro or nano length scale.In order to model this effect at the macroscopic scale, the Navier boundary conditions have been introduced, with the slip length as a parameter. When the fluid is a gas, this length is related to the tangential momentum accommodation coefficient (TMAC) and the mean free path, according to the Maxwell model. The aim of this work is to systematically address this model using a multi-scale approach and to extend it by incorporating both the morphology and the anisotropy of a surface. The thesis consists of five chapters. In Chapter 1, the basics of the kinetic theory of gases, the Boltzmann equation and related solutions (Navier-Stokes-Fourier, Burnett, Grad, Direct Simulation Monte Carlo ...) are briefly presented. The models of gas-wall interaction and slip models introduced in the fluid mechanics are also recalled. The chapter ends with a description of the computational method used for the molecular dynamics simulations performed in this work. Chapter 2 is dedicated to the development of a simple technique to simulate the pressure driven flows. The principle is to rely on the atomistic formulas of the stress tensor (Irving Kirkwood, Method of Plane, Virial Stress) and to modify the periodic conditions by maintaining the difference between the kinetic energy of the ingoing and outgoing particles of the simulation domain. Several types of channels are studied with this technique. The results (temperature, velocity ...) are discussed and compared. Chapter 3 deals with the study of the gas-wall interaction potential by the ab-initio method. The code CRYSTAL 09 is used to obtain the potential between an atom of argon (Ar) and a surface of platinum (Pt) <111> as a function of distance. Then the gas-wall potential is decomposed into binary potential and approached by an analytic function. This function is then implemented in a MD code to simulate the gas-wall collisions and determine the TMAC coefficient. In Chapter 4, the effect of morphology is studied. The multi-body Quantum Sutton Chen (QSC) potential is used for Pt <100> solid and the binary potential proposed in the previous chapter for the Ar-Pt couple is employed. The QSC potential is needed to reproduce the surface effects that affect the final results. Different surfaces are treated : smooth, nanostructured surface and, random surface obtained by Chemical vapor deposition (CVD). The TMAC is determined using a generalized approach, i.e. depending on the angle of incident flux of gas atoms on the surface. The surface anisotropy and the scattering kernel are also examined. In Chapter 5, we propose a model of anisotropic slip for fluids based on accommodation tensor. The model is obtained by the analytical approximate calculations developed in the framework of the kinetic theory. We thus generalize Maxwell's equation by showing that the slip length tensor is directly related to the accommodation tensor. The model is in good agreement with the MD results. Thanks to our MD simulations, we develop a suitable technique for reproducing the anisotropy of the accommodation tensor. The thesis ends with a conclusion section in which we suggest some perspectives for a continuation of this work

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SOSSO, GABRIELE CESARE. "A neural network potential for the phase change material gete: large scale molecular dynamics simulations with close to ab initio accuracy." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2013. http://hdl.handle.net/10281/40098.

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Phase change materials based on chalcogenide alloys are attracting an increasing interest worldwide due to their ability to undergo reversible and fast transitions between the amorphous and crystalline phases upon heating. This property is exploited in rewritable optical media (CD, DVD, Blu-Ray Discs) and electronic nonvolatile memories of new concept, the Phase Change Memories (PCM). The strong optical and electronic contrast between the crystal and the amorphous allows discriminating between the two phases that correspond to the two bits of binary information zero and one. The material of choice for applications is the ternary compound Ge2Sb2Te5 (GST). However, the related binary alloy GeTe has also been thoroughly investigated because of its higher crystallization temperature and better data retention at high temperature with respect to GST. PCM devices, born thanks to the work of Ovshinsky in the late 1960s, offer extremely fast programming, extended cycling endurance, good reliability and inexpensive, easy integration. A PCM is essentially a resistor of a thin film of the chalcogenide alloy with a low field resistance that changes by several orders of magnitude across the phase change. In memory operations, cell read out is performed at low bias. Programming the memory requires instead a relatively large current to heat up the chalcogenide and induce the phase change, either the melting of the crystal and subsequent amorphization (RESET) or the recrystallization of the amorphous (SET). In the last few years, atomistic simulations based on density functional theory (DFT) have provided useful insights into the properties of phase change materials. However, several key issues such as the thermal conductivity at the nanoscale or the origin of the fast crystallization, just to name a few, are presently beyond the reach of ab initio simulations due to the high computational cost. In fact, first principles simulations can deal at most with 10^2 atoms on the timescale of 10^2 ps, while many properties like thermal conductivity or direct simulations of the crystallization process require at least 10^3 atoms on the timescale of 10^3 ps. The development of reliable classical interatomic potentials is a possible route to overcome the limitations in system size and time scale of ab initio molecular dynamics. However, traditional approaches based on the fitting of simple functional forms for the interatomic potentials are very challenging due to the complexity of the chemical bonding in the crystalline and amorphous phases revealed by the ab initio simulations. A possible solution has been proposed recently by Behler and Parrinello, who developed highdimensional interatomic potentials with close to ab initio accuracy employing artificial neural networks (NN). In this thesis work, we developed a classical interatomic potential for the bulk phases of GeTe employing this NN technique. The potential was validated by comparing results on the structural and dynamical properties of liquid, amorphous, and crystalline GeTe derived from NN-based simulations with the ab initio data obtained here and in previous works [10]. The NN potential displays an accuracy close to that of the underlying DFT framework at a much reduced computational load that scales linearly with the size of the system. It allows us to simulate several thousands of atoms for tens of ns, which is well beyond present-day capabilities of DFT MD. The development of a reliable interatomic potential with close to DFT accuracy is thus a breakthrough in the modeling of phase change materials. To date, we employed our NNP in order to investigate three issues: 1. the thermal conductivity of the amorphous phase 2. the viscosity and atomic mobility in the supercooled liquid and overheated amorphous phases 3. the dynamics of homogeneous crystallization of the liquid and amorphous phases Thermal conductivity is a key property for the PCM operation, as the phase changes corresponding to the memory writing/erasing processes strongly depend upon heat dissipation and transport. Moreover, thermal cross-talks among the different bits is a crucial reliability issue in PCM. Although experimental data on thermal conductivity are available for few materials in this class it is unclear whether the value measured in the bulk phase could also describe the behavior of the material in nanoscaled devices (10-20 nm) which might be smaller than the phonon mean free path. This is particularly relevant for PCM architectures based on nanostructures employing nanowires, colloidal nanoparticles, thin bridges and nanotubes. In fact, amorphous materials can also display propagating phonons with mean free path as long as 0.5 μm. This has been demonstrated for amorphous Si where propagating modes with long mean free path contribute to half of the total thermal conductivity. It is therefore of great technological relevance to assess whether similar propagating modes with long mean free path might be present in amorphous phase change materials as well. Atomistic simulations can provide crucial insights into the thermal transport properties of phase change materials suitable to aid a reliable modelling of the device operation. However, the calculation of the thermal conductivity in an amorphous system requires very long simulations (on the ns scale) of large models (thousands of atoms) that are presently beyond the reach of fully DFT simulations. The use of NN potentials allowed us to compute the mean free path of phonons in a-GeTe and to assess that ballistic transport is inhibited by disorder even at the nanoscale. The key property that makes some chalcogenide alloys suitable for applications in PCM is the high speed of the transformation which leads to full crystallization on the time scale of 10-100 ns upon Joule heating. What makes some compounds alloys so special in this respect and so different from most amorphous semiconductors is, however, still a matter of debate. The driving force for crystallization of the supercooled liquid is actually the free energy difference between the crystal and the supercooled liquid. However, the crystallization is controlled both by the driving force and by the atomic mobility. The driving force vanishes at melting and increases upon cooling. A large atomic mobility at high supercooling can thus boost the crystallization speed. These conditions can actually be met by fragile liquids. In fact, supercooled liquids are classified as fragile or strong on the basis of the temperature dependence of their viscosity [16]. An ideal strong liquid shows an Arrhenius behavior of the viscosity η from the melting temperature Tm down to the glass transition temperature Tg. On the contrary, in a fragile liquid η is very low down to a crossover temperature T∗, below which a steep rise of the viscosity (and thus a steep decrease in the mobility) is observed. If T∗ is sufficiently far from the melting temperature (Tm), high supercooling and large atomic mobility can be met at the same time. The question is thus whether phase change materials are fragile liquids or not. Due to the high crystallization speed it is unfortunately not possible to measure η below Tm experimentally. We have thus addressed this problem by MD simulations and we have demonstrated that indeed GeTe is a very fragile liquid (fragility index ∼ 100). Moreover a breakdown of the Stokes-Einstein relation between the viscosity and the diffusion coefficient is found, which further increase the atomic mobility down to temperatures very close to Tg. Hysteretic effects in the heating of the amorphous phase above Tg have been addressed as well. Finally, we have performed direct simulations of the homogeneous crystallization of the supercooled liquid and amorphous phases with 4000-atom models and simulation times of several ns. Although similar simulations have been previously performed by fully DFT simulations, the limitations in size (about 200 atoms) and time scale (500 ps) prevented a reliable estimate of the size of the critical nucleus and of the crystallization speed, which are instead accessible by our large scale simulations. This thesis is organised as follows: in the introductory chapter 1 I provide essential information about phase change materials and phase change memories. Chapter 2 is dedicated to theory and methods, while chapters 3,4,5 and 6 are devoted to the results on the thermal conductivity of the amorphous phase of GeTe, on the properties of its supercooled liquid phase and on the homogeneous crystallization from the melt and the overheated amorphous phase.

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Asthana, Abhishek. "Model Development and Application of Molecular Simulations for the Study of Proton Transport in Bulk Water and for the Prediction of Dipole Moments of Organic Compounds." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3389.

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The present work demonstrates the application of molecular simulations (MD) in two different areas: proton transport in bulk water and estimation of the dipole moment of polar organic compounds. In both areas, relatively few successful and robust methodologies exist. In the first part, a new polarizable water model is developed for MD simulations of the proton transport process. The model was parametrized from a combination of quantum chemical calculations and experimental water properties. The model was implemented in MD simulation studies of liquid water at room temperature, as well as with excess protons. For pure water the model gave good agreement with experimental properties. The proton transport rate for a single excess proton also gave a good match with the experimental value. The water model was further extended to include chloride ions. At 0.2 M concentration the resulting density and structure agreed well with experiment, and the proton transport rate was found to be slightly reduced. The model was further extended to include multiple excess protons. For the second part of the project, an open source ab initio MD program, SIESTA, was used to perform simulations of several organic compounds which potentially have multiple stable conformations, to determine their average dipole moments. A series of methods was developed. The most robust method involved modifications to the SIESTA code and statistical analysis of the resulting configurations, in order to more accurately predict the average dipole moment. The resulting dipole moments were in good agreement with the experimental values for cases in which experimental values were reliable. Based on this study, a general method to estimate the average dipole moment of any compound is proposed.

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Peters, Laurens Dirk Marga [Verfasser], and Christian [Akademischer Betreuer] Ochsenfeld. "Development and application of efficient ab initio molecular dynamics simulations of ground and excited states / Laurens Dirk Marga Peters ; Betreuer: Christian Ochsenfeld." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/1209472821/34.

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Kuonen, Oliver Dominik. "De novo design, molecular dynamics simulations and ab initio calculations as tools to investigate biological systems : a critical application of the Molecular Modeling approach in ligand design /." Zürich : ETH, 1997. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=12370.

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21

Amira, Sami. "Classical and Car-Parrinello Molecular Dynamics Simulations of Polyvalent Metal Ions in Water." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5742.

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22

Naseem-Khan, Sehr. "Development of a polarizable ab initio force field : From separability of intermolecular interactions to condensed phase properties." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS564.

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Grâce aux récents progrès de l’informatique, il devient alors possible d’utiliser des champs de forces polarisables sophistiqués tel que SIBFA. En effet, le potentiel intermoléculaire SIBFA et ses gradients sont désormais implémentés dans le code Tinker-HP. La calibration initiale de SIBFA est basée sur la méthode RVS, une méthode de décomposition de l’énergie seulement accessible au niveau Hartree-Fock. Ainsi, les objectifs de ce travail sont double : i) choisir une nouvelle méthode référence de décomposition de l’énergie afin d’obtenir les paramètres de SIBFA au niveau corrélé ; ii) réaliser des simulations de dynamiques moléculaires. La première partie de cette thèse est dédiée à l’étude ab initio de la séparabilité de l’interaction intermoléculaire prédit par les méthodes de décomposition de l’énergie dites variationnelles et perturbationnelles. Nous avons fait des améliorations de l’énergie d’induction au sein de la méthode SAPT(DFT) et nous avons proposé une nouvelle définition du transfert de charge. La seconde partie de cette thèse est dédiée au développement du potentiel polarisable de l’eau de SIBFA, et à notre stratégie pour calculer les propriétés en phase condensée. L’étude ab initio de la séparabilité de l’énergie totale intermoléculaire SAPT(DFT) a mené à une séparabilité totale des contributions du potentiel SIBFA au niveau post Hatree-Fock. Cette thèse marque un réel progrès pour le potentiel SIBFA qui finalise son approche bottom-up : à partir de calculs ab initio en phase gaz vers des simulations de dynamiques moléculaires et des prédictions précises des propriétés en phase condensée Thanks to the recent progresses of computer sciences de-multiplying the available computational resources, the possibility of using sophisticated polarizable force fields such as SIBFA becomes a reality. Indeed, the SIBFA intermolecular potential and its gradients are now implemented in the Tinker-HP package. The original calibration of SIBFA was based on the RVS method, an energy decomposition analysis only available at the Hartree–Fock level of theory. Therefore, the goals of this work are double : i) choosing a new energy decomposition analysis reference scheme in order to upgrade the SIBFA parameters at the correlated level of theory ; ii) performing molecular dynamics. The first part of this thesis is dedicated to the study of the separability of the ab initio intermolecular interaction energy predicted by both variational and perturbational Energy Decomposition Analysis methods. We have made improvements for the induction energy term within the SAPT(DFT) method, and we have proposed a new charge transfer definition. The second part of this thesis is dedicated to the development of the SIBFA polarizable water model and to our definition of a strategy to compute condensed phase properties. The ab initio study of the separability of the total SAPT(DFT) intermolecular interaction energy has led the SIBFA potential to achieve both full separability of its components and high accuracy at the post Hartree-Fock level. This thesis marks a turning-point for the SIBFA potential, finalizing its global bottom-up strategy going from gas phase ab initio computations towards molecular dynamics simulations and accurate condensed phase properties predictions

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Baroni, Axelle. "Etude structurale de B2O3 à l'aide de simulations de dynamique moléculaire incluant des potentiels polarisables." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066265/document.

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Le trioxyde de bore, B2O3, est l'archétype du système formateur de verre avec une unité structurale de base trigonale sous conditions ambiantes. Cette propriété confère à ce système un arrangement particulier à moyenne portée: les unités trigonales s'organisent en phase vitreuses en unités superstructurales appelées anneaux de boroxol. A l'aide de simulations de dynamique moléculaire incluant des potentiels polarisables paramétrés sur des simulations ab-initio, nous avons étudié les transformations structurales de B2O3 dans les phases vitreuse, liquide et cristalline. Nous avons suivi le changement de coordinence des atomes de bore sous une augmentation de pression et la disparition des anneaux, présents sous conditions ambiantes, sous haute pression et haute température. Les résultats obtenus par nos potentiels sont en bon accord avec des mesures expérimentales de diffraction de neutrons et de diffraction des rayons-X. Il font partis des meilleurs potentiels existant dans la littérature à ce jour pour décrire la structure de B2O3 Boron trioxyde, B2O3, is the archetype of network-forming system with trigonal basic structural units under ambient conditions. In the glass under ambient conditions, it has been established that these triangles are packed in superstructural units called boroxol rings. Using molecular dynamics simulations including polarisable potentials we studied structural transformations of B2O3 in glassy, liquid and cristalline phases. We followed the boron coordination change as a function of pressure and the disapperance of boroxol rings at high pressure and high temperature. Results obtained using our potentials are in good agreement with experimental data: neutron diffraction and X-ray diffraction. They belong to best potentials in literature to describe correctly B2O3 structure

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Guymon, Clint Gordon. "MPSA Effects on Copper Electrodeposition: Understanding Molecular Behavior at the Electrochemical Interface." BYU ScholarsArchive, 2005. https://scholarsarchive.byu.edu/etd/333.

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In this work the structure of the electrochemical metal-liquid interface is determined through use of quantum mechanics, molecular simulation, and experiment. Herein are profiled the molecular dynamics details and results of solid-liquid interfaces at flat non-specific solid surfaces and copper metal electrodes. Ab initio quantum-mechanical calculations are reported and define the interatomic potentials in the simulations. Some of the quantum-mechanical calculations involve small copper clusters interacting with 3-mercaptopropanesulfonic acid (MPSA), sodium, chloride, bisulfate and cuprous ions. In connection with these I develop the electrode charge dynamics (ECD) routine to treat the charge mobility in a metal. ECD bridges the gap between small-scale metal-cluster ab initio calculations and large-scale simulations of metal surfaces of arbitrary geometry. As water is the most abundant surface species in aqueous systems, water determines much of the interfacial dynamics. In contrast to prior simulation work, simulations in this work show the presence of a dense 2D ice-like rhombus structure of water on the surface that is relatively impervious to perturbation by typical electrode charges. I also find that chloride ions are adsorbed at both positive and negative electrode potentials, in agreement with experimental findings. Including internal modes of vibration in the water model enhances the ion contact adsorption at the solid surface. In superconformal filling of copper chip interconnects, organic additives are used to bottom-up fill high-aspect ratio trenches or vias. I use molecular dynamics and rotating-disk-electrode experiments to provide insight into the function of MPSA, one such additive. It is concluded that the thiol head group of MPSA inhibits copper deposition by preferentially occupying the active surface sites. The sulfonate head group participates in binding the copper ions and facilitating their transfer to the surface. Chloride ions reduce the work function of the copper electrode, reduce the binding energy of MPSA to the copper surface, and attenuate the binding of copper ions to the sulfonate head group of MPSA.

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Patel, Sonal. "Determination of Phase Equilibria and the Critical Point Using Two-Phase Molecular Dynamics Simulations with Monte Carlo Sampling." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3587.

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The two-phase MD technique employed in this work determines the liquid and vapor phase densities from a histogram of molecular densities within phase clusters in the simulation cell using a new Monte Carlo (MC) sampling method. These equilibrium densities are then fitted in conjunction with known critical-point scaling laws to obtain the critical temperature, and the critical density. This MC post-processing method was found to be more easily implemented in code, and it is efficient and easily applied to complex, structured molecules. This method has been successfully applied and benchmarked for a simple Lennard-Jones (LJ) fluid and a structured molecule, propane. Various degrees of internal flexibility in the propane models showed little effect on the coexisting densities far from critical point, but internal flexibility (angle bending and bond vibrations) seemed to affect the saturated liquid densities in the near-critical region, changing the critical temperature by approximately 20 K. Shorter cutoffs were also found to affect the phase dome and the location of the critical point. The developed MD+MC method was then used to test the efficacy of two all-atom, site-site pair potential models (with and without point charges) developed solely from the energy landscape obtained from high-level ab initio pair interactions for the first time. Both models produced equivalent phase domes and critical loci. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here. Lastly, the transferability of the ab initio potential model was evaluated by applying it to 1-pentanol. An attempt has been made to separate the errors due to transferability of the potential model from errors due to the use of a true-pair potential. The results suggested a good level of transferability for the site-site model. The lack of multi-body effects appears to be dominant weakness in using the generalized ab initio potential model for determination of the phase dome and critical properties of larger alcohols.

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26

Rasim, Karsten. "Conductivité protonique et structures locales par simulations ab initio d'oxydes utilisés comme électrolyte dans les piles à combustible." Phd thesis, Université de Nantes, 2011. http://tel.archives-ouvertes.fr/tel-00983483.

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Cette thèse porte sur une étude de matériaux oxydes fortement désordonnés de type Brownmillerite et présentant diverses substitutions. Les aspects les plus étudiés sont la conductivité protonique des phases hydratées ainsi que les propriétés structurales des composés anhydres. L'étude repose majoritairement sur des calculs de type DFT (réalisés de manière statique à 0 K et à température élevée en utilisant la dynamique moléculaire ab initio). Elle est complétée de mesures XANES (spectroscopie d'absorption des rayons X) qui ont permi de confirmer certains résultats issus des calculs DFT. Ces approches combinées ont fourni des informations cruciales sur la préférence de coordination chimique de plusieurs substituants, sur la mobilité des protons dans divers composés en fonction de leur contenu cationique ainsi que sur les propriétés vibrationnelles. Le matériau Ba2 In2(1 − x)Ti2xO5+x (BITx) a été le centre d'intérêt de cette thèse, au vu des performances prometteuses dans des piles à combustible de type PC-SOFC. Dans une optique de comparaison et de rationalisation, des composés de formulation voisine Sr2In2(1 − x)Ti 2xO5+x (SITx), Ba2In2(1 − x)Zr2xO5+x (BIZx) et Ba2In2(1 − x)Y2xO5 (BIYx) ont également été étudiés pour préciser le rôle des différents substituants sur le comportement de la conductivité protonique (e.g. les effets de piégeage, la force des liaisons hydrogène, la distinction entre plusieurs arrangements protoniques etc...). Tous ces aspects ont été obtenus grâce à la dynamique moléculaire qui intègre naturellement les effets de température et d'entropie.

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27

Morelon, Nhan Duc. "Dynamique moléculaire du composé d'inclusion TANO-heptane : une étude combinée : simulation numérique/diffusion quasiélastique incohérente des neutrons." Université Joseph Fourier (Grenoble), 1999. http://www.theses.fr/1999GRE10015.

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Les composes d'inclusion du tano sont des complexes moleculaires constitues de deux especes chimiques. Les molecules de tano forment une matrice ayant une structure en canaux, dans laquelle sont incluses une grande variete de molecules lineaires (alcanes, polymeres, etc). La complexite et la variete du desordre dynamique rencontre dans ces cristaux plastiques nous a amener a completer les etudes experimentales anterieures par des simulations de dynamique moleculaire. Apres un resume des principales caracteristiques des composes d'inclusion du tano (descriptions des phases basse et haute temperature du tano-heptane, transitions de phase) et un rappel detaille des resultats obtenus precedemment par diffusion quasielastique des neutrons par bee etal, les methodes de simulation utilisees par la suite sont exposees de maniere synthetique. Nous introduisons aussi dans cette partie les fonctions utilisees en diffusion neutronique et leurs liens avec les resultats issus des simulations. Nous decrivons ensuite en detail les procedures utilisees pour mettre au point le potentiel d'interaction empirique a partir des donnees experimentales disponibles et des resultats de calculs ab initio. Cette phase, dite de parametrisation, determine de facon cruciale la qualite des simulations de dynamique moleculaire. Un premier test du potentiel empirique est realise en comparant les structures moleculaires calculees aux resultats experimentaux et ab initio. La description et l'analyse approfondie des simulations de dynamique moleculaire de la phase haute temperature du tano-heptane est ensuite detaillee. Les trajectoires atomiques simulees nous ont permis de calculer les spectres de diffusion quasielastique incoherente et ainsi d'effectuer une comparaison directe de nos simulations aux etudes experimentales. Des etudes experimentales de diffusion quasielastique sous pression concluent notre travail et montrent finalement que les composes d'inclusion du tano sont encore loin d'etre parfaitement compris.

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28

Stepaniuk, Daria. "Molecular dynamic simulation of structural- electronic characteristics and spectral properties of dyes and solutions based on them for DSSC." Electronic Thesis or Diss., Université de Lille (2022-....), 2023. http://www.theses.fr/2023ULILR014.

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L'objectif de cette thèse est d'une part d'analyser les propriétés électroniques de plusieurs modèles de colorants potentiellement utilisables dans les cellules solaires et d'autre part de caractériser l'effet du solvant sur la structure locale du colorant D205 en solution et à l'interface du TiO2. Ces recherches ont été réalisées à l'aide de calculs de chimie quantique et de simulation de dynamique moléculaire (MD).Dans le premier chapitre de la thèse, nous avons essayé de résoudre deux problèmes importants pour décrire et prédire les propriétés spectrales des colorants pour les DSSCs. Les géométries optimisées du colorant D205 dans l'état fondamental S0 et l'état excité S1, ont été réalisées en utilisant respectivement les méthodes DFT et TDDFT. les fonctions B3LYP and CAM-B3LYP (or M06-2X) ont été utilisées dans ce travail avec la base 6-31++G(d,p). Nous avons montré que ce niveau de calcul peut être recommandée pour la prédiction des spectres d'absorption de ces colorants. Nous avons également proposé un algorithme pour prédire de nouvelles structures moléculaires avec des paramètres spectraux électroniques améliorés et avons prédit la structure de trois nouveaux colorants pour les DSSC.Dans la deuxième partie de la thèse, nous avons analysé l'effet de la composition du mélange de colorants D205/Acétonitrile/BmimBF4. Le D205 est un colorant organique utilisé dans les cellules solaires. Pour réaliser cette analyse, nous avons effectué des calculs de chimie quantique afin de paramétrer la partie intramoléculaire du champ de force du colorant D205. Les charges décrivant l'état fondamental et l'état excité du colorant D205 ont également été déterminées tandis que les paramètres de Lennard-Jones ont été tirés de la bibliothèque OPLS(AA). Les fonctions de distribution radiales des plus proches voisins ont été utilisées pour caractériser l'environnement autour des parties donneur, accepteur, pont et chaîne butyle du colorant D205 dans les états fondamental et excité.Dans la troisième partie de cette thèse, des simulations conjointes de dynamique moléculaire (MD) et des calculs de théorie fonctionnelle de la densité (DFT) ont été utilisés pour étudier la structure et la dynamique d'un colorant indoline D205 ancré à l'interface solide˗liquide de petites nanoparticules de TiO2 anatase en mélange avec des solvants tels que l'acétornitrile, et des liquides ioniques à base de 1-butyl-3-méthylimidazolium avec des anions hexapluorophate et trifluorométhanesulfonate. Des calculs DFT ont été effectués pour estimer la géométrie d'équilibre d'une petite nanoparticule d'anatase Ti30O62H4 et pour déduire les paramètres d'interaction pour la liaison bidentate d'un colorant D205 avec le TiO2. L'effet de différents solvants sur la conformation du colorant D205 ancré dans l'anatase a été analysé par des simulations MD, démontrant qu'une représentation explicite du solvant est vitale pour reproduire les spectres optiques d'un colorant D205 The objective of this thesis is on the one hand to analyze the electronic properties of several dye models that can potentially be used in solar cells and on the other hand to characterize the effect of the solvent on the local structure of the dye D205 in solution and at the TiO2 interface. These investigations were carried out using quantum chemistry and molecular dynamics (MD) simulation calculations.In the first chapter of the thesis we tried to solve two problems important for describing and predicting the spectral properties of dyes for DSSCs. It was shown that the Time-Dependent DFT (TDDFT) approximation with a combination of B3LYP and CAM-B3LYP (or M06-2X) functionals with the 6-31++G(d,p) basis set can be recommended for the prediction of dye absorption spectra. We also proposed an algorithm to predict new molecular structures with improved electron spectral parameters and predicted the structure of three new dyes for DSSC.In the second part of the thesis we analyzed the effect of the composition of the D205/Acetonitrile/BmimBF4 dye mixture. D205 is an organic dye used in solar cells. To perform this analysis, we performed quantum chemical calculations to parameterize the intramolecular part of the D205 dye force field. The charges describing the ground state and excited state of the D205 dye were also determined while the Lennard-Jones parameters were taken from the OPLS(AA) library. Radial nearest neighbor distribution functions were used to characterize the environment around the donor, acceptor, bridge and butyl chain moieties of the D205 dye in the ground and excited states.In the third part of this thesis joint molecular dynamics (MD) simulations and density functional theory (DFT) calculations were used to study the structure and dynamics of an indoline dye D205 anchored at the solid˗liquid interface of small TiO2 anatase nanoparticles in admixture with solvents such as acetornitrile , and 1-butyl-3-methylimidazolium-based ionic liquids with hexapluorophate and trifluoromethanesulfonate anions. DFT calculations were performed to estimate the equilibrium geometry of a small Ti30O62H4 anatase nanoparticle and to deduce the interaction parameters for the bidentate bonding of a D205 dye with TiO2. The effect of different solvents on the conformation of the anatase-anchored D205 dye was analyzed by MD simulations, demonstrating that an explicit solvent representation is vital to reproduce the optical spectra of a D205 dye

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Blaise, Philippe. "Dynamique moléculaire quantique : méthodes numériques et étude physique de la structure, de la thermodynamique, de la stabilité et de la fragmentation des agrégats métalliques de sodium." Université Joseph Fourier (Grenoble), 1998. http://www.theses.fr/1998GRE10110.

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Le but de cette these est l'etude des agregats metalliques de sodium par la simulation numerique. Nous avons developpe deux codes de calculs de dynamique moleculaire ab initio en fonctionnelle de densite. Le premier se fonde sur le modele semi-classique de thomas-fermi etendu. La resolution est en espace reel et utilise la methode car-parrinello. Son cout est en o(n), et nous avons mis au point un pseudopotentiel qui accelere le calcul. Au sacrifice des effets de couche, nous pouvons etudier un vaste ensemble d'agregats. Nous montrons alors qu'avec un minimum d'ajustements, les agregats de sodium suivent une energetique goutte liquide. Nous avons etudie les modes vibratoires de compression et de surface, ainsi que la repartition de la charge. Nous montrons que l'energie de surface des agregats est tres sensible a la temperature, et que leur point de fusion est plus bas que celui du solide. Nous avons extrait des barrieres de fission grace a une methode de contrainte. Le deuxieme code est base sur le modele quantique de kohn-sham. La resolution est en espace reel, et son cur est le couplage de l'algorithme du point fixe de broyden pour l'auto-coherence avec l'algorithme iteratif de lanczos-davidson pour le probleme propre. Cette methode possede un cout beaucoup plus eleve. Dans un premier temps, nous avons optimise les structures de plus basse energie des petits agregats et calcule leur energetique. L'accord avec des travaux anterieurs est excellent. Puis nous avons etudie la dynamique des agregats tres charges. Nous montrons que la fission peut etre extremement sensible aux conditions initiales. Nous avons mis en evidence pour la premiere fois, que les systemes de grande fissilite multifragmentaient avec l'emission preferentielle de monomeres sur des echelles de temps inferieures a la pico-seconde. Ces resultats ont pu etre obtenus grace au developpement d'une methode originale de maillage adaptatif dont la geometrie suit celle du systeme lors de la fragmentation.

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30

Mohamed, Fawzi Roberto. "Advanced methods in Ab-initio molecular dynamics /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16893.

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Marzari, Nicola. "Ab-initio molecular dynamics for metallic systems." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285270.

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32

Shaltaf, Riad. "Adsorption And Growth On Si(001) Surface." Phd thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/12604904/index.pdf.

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The (001) surface of silicon has been the topic of our study in this thesis. The clean surface, an-adatom or submonolayer adsorption on the surface, the monolayer adsorption and its stability conditions as well as growth simulation on the surface were investigated using the state of the art techniques. We have used ab initio density functional calculations based on norm-conserving pseudopotentials to investigate the Mg adsorption on the Si(001) surface for 1/4, 1/2 and 1 monolayer (ML) coverages. For both 1/4 and 1/2 ML coverages it has been found that the most favorable site for the Mg adsorption is the cave site between two dimer rows consistent with recent experiments. For the 1 ML coverage (2 Mg atoms per 2X1 unit cell) we have found that the most preferable configuration is when both Mg atoms on 2X1 reconstruction occupy the two shallow sites. We have found that the minimum energy configurations for 1/4 ML coverage is a 2X2 reconstruction while for the 1/2 and 1 ML coverages they are 2X1. Same method was also used to investigate the surface stress and energetics of the clean-, Sb-adsorbed-, and Sb-interdiffused-Si(001) surface. It is found that interdiffusion of Sb into deeper layers of Si(001) leads to a more isotropic surface stress but corresponds to a higher total energy configuration. As a result of competition between stress relief and energy gain, the surface with all the Sb atoms adsorbed on top of Si(001) surface layer is predicted to have a less ordered geometry and roughness in z-direction. We have repeated the similar calculations on the Ge(001) surface for comparison. Finally using empirical molecular dynamics method, we have investigated the crystalline growth of silicon on Si(001) as a function of substrate temperature and incident particle energy. Our results show that the increase of substrate temperature enhances the crystallinity in the film grown on the Si(001) surface, on the other hand, the crystalline growth can be enhanced at low temperature by using higher incidence energy.

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Seriani, Nicola. "First-principles simulations of the oxidation of methane and CO on platinum oxide surfaces and thin films." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2006. http://nbn-resolving.de/urn:nbn:de:swb:14-1163174398225-14223.

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The catalytic oxidation activity of platinum particles in automobile catalysts is thought to originate from the presence of highly reactive superficial oxide phases which form under oxygen-rich reaction conditions. The thermodynamic stability of platinum oxide surfaces and thin films was studied, as well as their reactivities towards oxidation of carbon compounds by means of first-principles atomistic thermodynamics calculations and molecular dynamics simulations based on density functional theory. On the Pt(111) surface the most stable superficial oxide phase is found to be a thin layer of alpha-PtO2, which appears not to be reactive towards either methane dissociation or carbon monoxide oxidation. A PtO-like structure is most stable on the Pt(100) surface at oxygen coverages of one monolayer, while the formation of a coherent and stress-free Pt3O4 film is favoured at higher coverages. Bulk Pt3O4 is found to be thermodynamically stable in a region around 900 K at atmospheric pressure. The computed net driving force for the dissociation of methane on the Pt3O4(100) surface is much larger than on all other metallic and oxide surfaces investigated. Moreover, the enthalpy barrier for the adsorption of CO molecules on oxygen atoms of this surface is as low as 0.34 eV, and desorption of CO2 is observed to occur without any appreciable energy barrier in molecular dynamics simulations. These results, combined, indicate a high catalytic oxidation activity of Pt3O4 phases that can be relevant in the contexts of Pt-based automobile catalysts and gas sensors.

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Watson, Stuart. "Structural relaxation at defects by Ab initio molecular dynamics." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320648.

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Walker, Brent Graham. "Ab initio molecular dynamics studies of liquid metal surfaces." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615985.

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Laino, Teodoro. "Multigrid QM/MM approaches in ab initio molecular dynamics." Doctoral thesis, Scuola Normale Superiore, 2006. http://hdl.handle.net/11384/85799.

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37

Dubosq, Clement. "Simulation de fluorure et d'hydroxyde dans des agrégats d'eau : Vers la dynamique sur l'état excité en solution." Thesis, Normandie, 2017. http://www.theses.fr/2017NORMC218/document.

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Nous étudions la dynamique d’anions hydroxyde et fluorure micro-solvatés dans un agrégat d’eau après photo-excitation. Du fait du coût numérique important des calculs ab-initio et de la faible transférabilité des potentiels modèles de la littérature, nous avons développé un nouveau modèle transférable permettant de décrire l’interaction d’un soluté quelconque avec une molécule d’eau. Nous avons également effectué une étude des propriétés statiques de F^-(H2O)n=1−7 et OH−(H2O)n=1−7 qui sert de référence pour la paramétrisation du modèle et fournit une base à l’interprétation des calculs de dynamique. De cette étude, nous avons déduit le nombre de molécules d’eau nécessaires pour stabiliser le premier état excité de F− et OH−. Nous avons aussi déterminé l’impact de la base sur la description des états excités. Enfin, nous avons mis en évidence un motif géométrique favorable à la recombinaison géminée. L’étude de trajectoires sur le premier état singulet excité pour F^-(H2O)3,5 et OH^-(H2O)3,5 montre des différences de comportement entre le fluorure et l’hydroxyde. Pour F^−, l’électron est très diffus et se transfère en une centaine de femtosecondes à l’eau. Dans le cas de OH^−, à cause du dipôle du radical OH qui maintient l’électron, le transfert de charge ne s’effectue que lorsque le radical OH tourne vers l’agrégat d’eau. Cette différence de comportement entre OH^−et F^−offre une piste pour la compréhension du phénomène de recombinaison géminée rapide observé pour OH^−. Nous avons également étudié le spectre d’énergie de détachement vertical de l’électron pour des agrégats d’eau négativement chargés qui constituent l’un des produits finaux de la dynamique des anions photo-excités. Ces résultats ont été discutés et comparés à l’expérience. Nous avons ainsi pu faire correspondre des structures géométriques aux pics des spectres mesurés expérimentalement. Nous discutons aussi du rôle de l’énergie interne des agrégats sur l’allure des spectres via son impact sur l’évaporation de molécules d’eau We study the dynamics of micro-solvated hydroxide and fluoride anions in water clusters after photoexcitation. Because ab-initio calculations are numerically expensive and model potentials from literature lack of transferability, we developed a transferable model, which allows us to describe the interaction between any solute and a water molecule. We have studied the statics properties of F^−(H2O)n=1−7 and OH^−(H2O)n=1−7. The results from this study serve as a basis for the parametrization of the model and for the interpretation of dynamics simulation. From this study, we deduced the number of water molecules needed to stabilize an excited state for F^−and OH^−. We investogated the impact of the basis on the description of the excited states At last, we highlight a favorable motif for geminate recombination. Study of trajectories on the first excited singlet states of F^−(H2O)3,5 and OH^−(H2O)3,5 shows differences in the dynamics between OH^−and F^− For F^−, the excess electron is very diffuse and transferred quickly to the water For OH−, because of the OH dipole, the excess electron remains bound to the neutral . OH, until charge transfer takes place when OH rotate to the water cluster. This difference provides a way to understand the fast geminate recombination process observed for OH^−. We also studied vertical detachment spectra of the electron for negatively charged water clusters which are the final products of the anions dynamics on the first excited state. These results are compared to experience from literature. We associate isomers to the experimentally observed peaks. We discuss the effect of internal energy on the shape of the spectra through water molecules evaporation

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Au, Yat-yin. "Ab initio calculations : an extension of Sankey's method /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21482706.

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Jeloaica, Léonard. "Etude ab initio des mécanismes réactionnels dans la phase initiale du dépôt par par couches atomiques des oxydes à moyenne et forte permittivité sur silicium." Toulouse 3, 2006. http://www.theses.fr/2006TOU30077.

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L'objectif de ce travail est d'apporter un éclairage nouveau à la compréhension des mécanismes physico-chimiques qui contrôlent la croissance des trois oxydes d'Aluminium, de Zirconium, de Hafnium. Ces matériaux sont considérés comme les meilleurs candidats pour remplacer la silice en tant qu'oxyde de grille dans le futur composant MOS. La précision et la fiabilité de la méthode DFT associé à la fonctionnelle B3LYP, ont été testées à l'aide des résultats expérimentaux et des méthodes ab initio les plus précis telles que CCSD(T) et CISD(T), en utilisant différents ensembles des fonctions de bases. Nos résultats montrent que et la méthode hybride DFT peut prédire de façon précise les propriétés statistiques et dynamiques de la famille d'organométalliques (AlxCyHzOt) et des systèmes moléculaires à base de métaux de transition (Zr/HfxClyOzHt). Les premières études systématiques des surfaces d'énergie potentielle de TMA ont été présentes et les caractéristiques des rotors constitués des groups méthyles ont été rapportées avec une grande précision. Les mécanismes réactionnels, à plusieurs étapes, entre les molécules précurseurs de trois oxydes et les molécules d'eau résiduelle phase gazeuse ont été étudies en détail. Les mouvements internes fortement anharmoniques, des espèces moléculaires présentes touts au long du processus d'hydrolyse ont été déterminés. Les effets qualitatifs sur les cinétiques des réactions ont été discutés. La forte exothermicité de la réaction TMA/H2O a été démontrée, alors que la réaction avec les tétrachlorures de Zirconium et Hafnium ont montré un caractère plutôt endothermique. Nous avons aussi étudié les mécanismes réactionnels de la vapeur d'eau avec d'espèces moléculaires chimisorbés en surface. Les réactions interviennent dans les cycles initiales d'ALD sur en substrat de Si(001)-2x1 légèrement oxydé. Les mécanismes que nous proposons sont qualitativement proches des mécanismes d'hydrolyse discutés dans la phase gaz euse : confirmation de la forte réactivité exothermique avec les hydroxyméthyliques d'Aluminium, endothermicité des réactions avec hydroxychlorures de Zirconium et Hafnium. Les composés avec le Zirconium et le Hafnium ont des comportements similaires. Enfin, les effets de coopérativité, à la fois au niveau des molécules de vapeur d'eau, qu'au niveau des complexes en surface, sur les réactions ont été mis en évidence et discutés. Ils montrent des comportements tout à fait intéressants dans le cas des hydroxychlorures des Zirconium et Hafnium. Par contre, ces effets sont de moindre importance dans les cas de l'oxyde d'aluminium, qui est actuellement considéré comme le matériau le plus compatible avec la croissance par ALD This work attempts to bring a new light on the understanding of some critical aspects of the physicochemical processes that control Alumina, Zirconia and Hafnia ALD growth, yet not sufficiently understood. These materials are addressed as potentially best candidates to replace gate dielectric SiO2 in the near future electronic applications. Most accurate ab initio correlated methods, like couple-cluster CCSD(T) and CISD(T), with different basis sets functions, as well as the available experimental data have been used for testing by a systematic study the accuracy and the reliability of DFT B3LYP functional. Our results have claimed this hybrid-DFT method to be chosen in predicting of high accurate static and dynamic properties throughout the family of organometallic-like (AlxCyHzOt) and transition metal-based (Zr/HfxClyOzHt) molecular systems. First systematic study of torsional potential surfaces of TMA has been performed and the related features of the hindered rotors of the methyl groups revealed with high accuracy. Laying on these accurate results we have also proposed least-squared fit methods to determine frequency scaling factors subject to different thermodynamic properties and/or thermal conditions. Many-step reaction mechanisms of ALD gas phase precursors of each of the three oxides with residual water, or regime of low pressure H2OÓALD pulses, have been studied in detail. Strong anharmonic internal movements of molecular species throughout the hydrolysis reactions have been observed and qualitatively discussed in relation with their possible effects on the reactions' kinetics. TMA/H2O reactions have been validated as strongly exothermic, while Hafnium and Zirconium tetrachlorides have founded to react endothermically with single H2O molecule. We have also studied in detail reaction mechanisms of the related on-surface ALD-complexes with water vapors. Our theoretical investigations address to the initial stage of ALD growth, more s pecifically on SiO2/Si(001)-2x1 like surfaces. The proposed many-step mechanisms, similar to those discussed for the gas phase, confirmed again the strong reactivity of H2O molecule with on-surface Aluminum hydroxymethylides, and responds strong endothemically as for the hydroxylation of Zirconium and Hafnium on-surface hydroxychlorides. The last two proved a very similar surface chemistry. Finally the cooperative effects of H2O molecules have been considered in our models of reactions, and have revealed dramatic influences on the reactivity Zirconium- and Hafnium hydroxychlorides surfaces. Our results proved the importance of both cooperative interactions of on-surface complexes and H2O molecules in the case of the Zirconia and HafniaÓALD growth, while for Aluminum oxide, presently considered ideal for ALD growth, these effects seem of secondary importance

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Eliah, Dawod Ibrahim. "Structural integrity of highly ionized peptides." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-387886.

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In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

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Luo, Ye. "Ab initio molecular dynamics of water by quantum Monte Carlo." Doctoral thesis, SISSA, 2014. http://hdl.handle.net/20.500.11767/3896.

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The chapter 2, we deal with the challenge b). It focuses on the variational Monte Carlo (VMC) and the wavefunction optimization methods based on VMC. The performance of different methods are displayed through the op- timization of the Jastrow factor in our test case Beryllium dimer and the efficiency is improving surprisingly during the evolution of these methods. In chapter 3, we focus on the challenge a). It describes the wavefunc- tion ansatz used by our simulation. In this thesis, we introduce the atomic hybrid orbitals which significantly increase the compactness of our wavefunc- tion without hurting accuracy. This chapter also explain how to optimize the determinant in a way that the number of variational parameters scales only linearly with the system size. This further helps the efficiency of the wavefunction optimization. In chapters 4 and 5, the issue c) is explained in detail. In chapter 4, a second order Langevin dynamics (SLD) scheme is devised particularly for QMC and this thesis improves this scheme by developing a better integration method. Here, we also highlight the remarkable power of the force covari- ance matrix which can be defined only in QMC and is capable of accelerating the slow modes of a dynamics. In chapter 5, this SLD for QMC is validated through intensive benchmarking on the calculation of the vibrational frequen- cies of water and other small molecules. It is shown that many systematic biases in our MD scheme and QMC evaluation can be controlled so that we are confident to push forward this ab initio molecular dynamics for applica- tions on large systems. Finally in chapter 6, we perform the simulation of liquid water with all the preparation done in the previous chapters. The results are encouraging since we’ve closed the discrepancy of the peak positions of RDFs between experi- ments and ab initio simulations. The power of QMC is also demonstrated by the fact that the shapes of our RDFs are much less structured than previous DFT-based ab initio simulations even if the two water molecule interaction is dealt with the same level of accuracy as the DFT/BLYP calculation. In this chapter, we have also studied the features of hydrogen bonds in our simulation of liquid water. All our results indicate that it is important to consider the quantum nature of the ions for a faithful description of liquid water. This will be left for future studies, possible in principle even within the QMC approach.

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Kochman, Michal. "Ab initio simulations of reactions occurring in molecular crystals." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8906.

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Although the solid state may not usually be thought of as an environment suitable for chemical reactions under mild conditions, a growing number of organic compounds are known to undergo interesting and, in many cases, practically useful chemistry in the molecular crystal phase. Of particular interest are photochemical reactions occurring in molecular crystals, which possess a number of characteristic features that make them attractive to study using the methods of theoretical chemistry. Firstly, molecular packing and steric effects strongly influence the mechanistic course of reactions in the crystal phase, which in some cases enables clean and controllable chemistry, including synthetic reactions as well as reversibly switchable isomerisations accompanied by a change of the macroscopic properties of the crystal, such as shape and colour. Secondly, in part due to their fast (subpicosecond) timescales and relatively low conversion rates (of the order of a few per cent), many of these reactions present challenges to experimental techniques, which computer simulation methods are uniquely positioned to overcome. Finally, these systems lend themselves well to simulation using a hybrid combination of two ab initio electronic structure methods, one of which is used to describe the electronic excitation of a reactive molecule while the other is applied to the surrounding bulk lattice. This thesis describes the computational modelling of two such reactions: the syn-anti photoisomerisation of 7-(2-pyridyl)indole and the reversible cis-enol⇄trans-keto photoisomerisation of N-salicylidene-2-chloroaniline. The solid-state mechanisms and rates of both reactions are computed using the TD-DFT/DFT hybrid method, in the latter case validating a previously postulated reaction mechanism. Furthermore, the thermal (ground-state) tautomerisation reaction in the photochromic and non-photochromic polymorphs of N-salicylidene-2-chloroaniline is investigated through calculations at the DFT level of theory. The results of these calculations indicate that both polymorphs are thermochromic, but tautomeric equilibrium in the non-photochromic polymorph is more sensitive to temperature than in the photochromic polymorph. Additionally, a critical assessment is presented of the accuracy of the various emphab initio methods employed throughout this work.

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區逸賢 and Yat-yin Au. "Ab initio calculations: an extension of Sankey's method." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31222195.

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Li, Ming, and 李銘. "Some AB initio studies of positron annihilation in semiconductors." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B31238919.

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Li, Ming. "Some AB initio studies of positron annihilation in semiconductors /." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20128496.

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Li, Hongfei. "Density functional simulations of defect behavior in oxides for applications in MOSFET and resistive memory." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274924.

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Defects in the functional oxides play an important role in electronic devices like metal oxide semiconductor field effect transistors (MOSFETs) and resistive random-access memories (ReRAMs). The continuous scaling of CMOS has brought the Si MOSFET to its physical technology limit and the replacement of Si channel with Ge channel is required. However, the performance of Ge MOSFETs suffers from Ge/oxide interface quality and reliability problems, which originates from the charge traps and defect states in the oxide or at the Ge/oxide interface. The sub-oxide layers composed of GeII states at the Ge/GeO2 interface seems unavoidable with normal passivation methods like hydrogen treatment, which has poor electrical properties and is related to the reliability problem. On the other hand, ReRAM works by formation and rupture of O vacancy conducting filaments, while how this process happens in atomic scale remains unclear. In this thesis, density functional theory is applied to investigate the defect behaviours in oxides to address existing issues in these electronic devices. In chapter 3, the amorphous atomic structure of doped GeO2 and Ge/GeO2 interface networks are investigated to explain the improved MOSFET reliability observed in experiments. The reliability improvement has been attributed to the passivation of valence alternation pair (VAP) type O deficiency defects by doped rare earth metals. In chapter 4, the oxidation mechanism of GeO2 is investigated by transition state simulation of the intrinsic defect diffusion in the network. It is proposed that GeO2 is oxidized from the Ge substrate through lattice O interstitial diffusion, which is different from SiO2 which is oxidized by O2 molecule diffusion. This new mechanism fully explains the strange isotope tracer experimental results in the literature. In chapter 5, the Fermi level pinning effect is explored for metal semiconductor electrical contacts in Ge MOSFETs. It is found that germanides show much weaker Fermi level pinning than normal metal on top of Ge, which is well explained by the interfacial dangling bond states. These results are important to tune Schottky barrier heights (SBHs) for n-type contacts on Ge for use on Ge high mobility substrates in future CMOS devices. In chapter 6, we investigate the surface and subsurface O vacancy defects in three kinds of stable TiO2 surfaces. The low formation energy under O poor conditions and the +2 charge state being the most stable O vacancy are beneficial to the formation and rupture of conducting filament in ReRAM, which makes TiO2 a good candidate for ReRAM materials. In chapter 7, we investigate hydrogen behaviour in amorphous ZnO. It is found that hydrogen exists as hydrogen pairs trapped at oxygen vacancies and forms Zn-H bonds. This is different from that in c-ZnO, where H acts as shallow donors. The O vacancy/2H complex defect has got defect states in the lower gap region, which is proposed to be the origin of the negative bias light induced stress instability.

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Spura, Thomas [Verfasser]. "Ab initio path integral molecular dynamics : theory and applications / Thomas Spura." Paderborn : Universitätsbibliothek, 2015. http://d-nb.info/1078666504/34.

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Tocci, G. "Realistic modelling of water/solid interfaces from ab initio molecular dynamics." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1457448/.

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Water/solid interfaces are of utmost importance to a number of technological processes. Theoretical studies, based on ab initio approaches are suitable to unveil processes occurring at water/solid interfaces and can therefore be instrumental to delineate guidelines to improve the efficiency of these processes. In this thesis we study several systems of current interest using ab initio methods based on density functional theory (DFT). By going often beyond the use of standard DFT methods and approximations we have provided insights into processes occurring at water/solid interfaces under ambient conditions and in non stoichiometric conditions. Specifically, we will investigate the interactions between water and ZnO, an important metal-oxide especially used in industry to produce methanol. One of the most mportant results of this study is that proton hopping is dramatically enhanced under wet conditions compared to ideal ultra-high vacuum conditions. Also, we will compute the friction between liquid water in contact with 2-D layered materials, and delineate the guidelines on how to alter the friction coe cient in membranes used for desalination or osmotic power harvesting. Finally, in collaboration with Geoff Thornton's group we have investigated the role of defects on the surface chemistry of the rutile TiO2(110), which is the model oxide surface used in photocatalysis applications. On the whole, in this work we have used ab initio methods to reduce the gap between the ultra-high vacuum-style studies of adsorption on perfect defect-free surfaces and the complex behaviour of liquid/solid interfaces under technologically relevant conditions.

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Gambino, Davide. "Titanium vacancy diffusion in TiN via non-equilibrium ab initio molecular dynamics." Thesis, Linköpings universitet, Teoretisk Fysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-129555.

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Transition metal nitrides (TMNs) refractory ceramic materials are widely employed as wear-resistant protective coatings in industrial machining as well as diffusion barriers inhibiting migration of metal impurities from the interconnects to the semiconducting region of electronic devices. TiN is the prototype of this class of materials and the most studied among TMNs. However, also for this system, a complete picture of the migration processes occurring at the atomic scale is still lacking. In this work I investigate the stability of Ti vacancy configurations and corresponding migration rates in TiN by means of density functional theory (DFT) calculations and ab-initio molecular dynamics simulations (AIMD). DFT calculations show that Ti vacancies tend to stay isolated because of repulsive interaction which decreases as the inverse of the distance between the vacancies.The equilibrium jump rate of single Ti vacancies in TiN is extrapolated temperature as a function of temperature from the results of non-equilibrium AIMD simulations accelerated by a bias force field according to the color diffusion algorithm. For each force field and, the jump occurrence times are fitted with the two parameters Gamma distribution in order to obtain the non equilibrium jump rate with the corresponding uncertainty. Extrapolated equilibrium values show an Arrhenius-like behavior, with activation energy Ea= (3.78 ± 0.28)eV and attempt frequency A = 4.45 (x3.6±1) x 1014 s-1.

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Koči, Love. "Studies of Material Properties using Ab Initio and Classical Molecular Dynamics." Doctoral thesis, Uppsala universitet, Kondenserade materiens teori (Fysik IV), 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8626.

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In this thesis, material properties have been examined under extreme conditions in computer-based calculations. The research on iron (Fe), nickel (Ni), and ferropericlase (Mg1-xFexO) are not only important for our understanding of the Earth, but also for an improved knowledge of these materials per se. An embedded-atom model for Fe demonstrated to reproduce properties such as structure factors, densities and diffusion constants, and was employed to evaluate temperature gradients at Earth core conditions. A similar interaction together with a two-temperature method was applied for the analysis of shock-induced melting of Ni. For Mg1-xFexO, the magnetic transition pressure was shown to increase with iron content. Furthermore, the C44 softening with pressure and iron composition supports the experimentally observed phase transition for Mg0.8Fe0.2O at 35 GPa. The properties of high density helium (He) is of great interest as the gas is one of the most abundant elements in the solar system. Furthermore, He and neon (Ne) are often used as pressure media in diamond anvil cells. The melting of He showed a possible fcc-bcc-liquid transition starting at T=340 K, P=22 GPa with a Buckingham potential, whereas the bcc phase was not seen with the Aziz form. For Ne, Monte Carlo calculations at ambient pressure showed very accurate results when extrapolating the melting temperatures to an infinite cluster limit. At high pressure, a one-phase ab initio melting curve showed a match with one-phase L-J potential results, which could imply a correspondence between ab initio/classical one-phase/two-phase calculations. In the search for hard materials, ab initio calculations for four TiO2 phases were compared. Just as imposed by experiment, the cotunnite phase was found to be very hard. The anomalous elastic behavior of the superconducting group-V metals V, Nb, Ta was found to be related to shrinking nesting vectors and the electronic topological transition (ETT).

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