Kinetic Monte Carlo(KMC) algorithm are used to simulate the evolution of Au cluster on the Au substrate . The morphology of the thin film and detailed diffusion mechanism can be demonstrated in this study. Molecular dynamics simulation (MD) is used to determine the energy barrier(activation energy) of an Au atom adsorbed on the clean surface of the substrate. Then, the thin cluster evolution process, surface reaction and surface diffusion of the Au atoms is modeled by KMC method. The morphologies of the clusters at different temperatures with different number of atoms are also investigated. The simulation results are compared with literature on experimental results to demonstrate the diffusion mechanism, which is difficultly observed in experiments. A three-dimensional KMC simulation model is used in this study. The results are compared with those from experiments in order to identity the reliability of this KMC model and to modify this model. Nudged Elastic band simulation is used to determine the adsorption energy barrier of an Au atom on a clean Au substrate surface. From the KMC result a surface diffusion of Au migration process is proposed. The effect of the substrate temperature, and the number of atoms duration on the morphology of the Au cluster is obtained. The simulation results show a pyramid structure is built and collapsed from the corner and edge atoms fellow suit and then the atoms of top layers do so as well. Then results indicate that it is possible to to produce nano-gold (metal)-pyramid from Au cluster s by 1, melting clusters in short period and then quenching them, or 2. Depositing Au atoms at lower temperature as well as 500 K with controlled rate.

Cette thèse aborde l'étude du vieillissement thermique du système Fe-Cr. Nous avons étudié le mécanisme de diffusion de la lacune dans le cadre de la théorie de la fonctionnelle de la densité (Density Functional Theory - DFT) et examiné la capacité d'un potentiel empirique de la classe EAM (Embedded Atom Method) à reproduire les résultats DFT. Nous avons montré que l'énergie de migration de la lacune dépend fortement de l'environnement atomique du point de col où les interactions chrome-chrome et chrome-lacune déterminent en partie l’énergie de point de col. Nous avons proposé trois approches pour la paramétrisation d'un modèle Monte Carlo Cinétique (MCC) atomique : l’une entièrement basée sur le potentiel EAM, les autres partiellement basées sur nos calculs DFT. Les simulations par MCC du vieillissement thermique des alliages Fe-20% at. Cr et Fe-25% at. Cr à 773 K montrent la formation de précipités riches en chrome dont la croissance avec le temps suit une loi de puissance avec un exposant 1/3, en accord avec la théorie de Lifshitz-Slyozov-Wagner. La paramétrisation des simulations par MCC entièrement basée sur le potentiel EAM prédit une taille moyenne des précipités supérieure à celle observée expérimentalement, alors que cette dernière est sous-estimée par les paramétrisations partiellement basées sur nos calculs DFT. Ce désaccord semble avoir une origine cinétique plutôt que thermodynamique. La composition de la phase riche en chrome varie au cours de la séparation de phase, indiquant ainsi que la démixtion se produit par nucléation non-classique ou par décomposition spinodale. Des précipités interconnectés sont plus susceptibles de se former dans le système Fe-25% at. Cr plutôt que dans l’alliage Fe-20% at. Cr suggérant ainsi que, lorsque la concentration en soluté augmente, le mécanisme de démixtion se rapproche de la décomposition spinodale. / In this thesis, we address the study of the microstrucutre evolution of the Fe-Cr system under thermal ageing. The vacancy diffusion mechanism was investigated in the framework of the density functional theory (DFT) and the capability of a recently developed embedded atom method (EAM) empirical cohesive model to reproduce the DFT results was examined. We have shown that the vacancy migration energy strongly depends on the saddle point atomic environment where the chromium-chromium and the chromium-vacancy interactions partially determine the saddle point energy. We proposed three approaches for the parameterisation of an atomistic kinetic Monte Carlo (AKMC) model: one fully based on the EAM potential, the others partially based on our DFT calculations. The AKMC simulations of the thermal ageing of the Fe-20 at.%Cr and Fe-25 at.%Cr alloys at 773 K show the formation of chromium-rich precipitates whose growth with time follows a power law with exponent 1/3. This is consistent with the Lifshitz-Slyozov-Wagner theory of coarsening. The AKMC parameterisation fully based on the EAM potential predicts a mean precipitate size higher than the experimentally observed one, whereas the parameterisations partially based on our DFT calculations underestimate it. This disagreement seems to have a kinetic rather than thermodynamic origin. The composition of the precipitating phase varies during the phase separation thus indicating that the unmixing is driven by either a non-classical nucleation or a spinodal decomposition. Interconnected precipitates are more likely to form in the Fe-25 at.%Cr alloy than in the Fe-20 at.%Cr thus suggesting that, as the solute concentration increases, the spinodal decomposition is more likely to occur.

With advancements in computer technology and processing power, the ability to examine chemical systems using theory continues to be more practicable. Using ab initio methods, such as density functional theory, we are now able to routinely simulate hundreds of atoms. This system size allows us to directly simulate surfaces and nano-materials that are industrially relevant. With the expansion of accessible systems comes the opportunity to develop new computational methods to extract their chemical properties. Of particular interest is bridging the time scale gap between simulation and experiment. The evolution of a system chemical in time can be directly simulated using classical dynamics, however, molecules vibrate on the order of femtoseconds and interesting transitions tend to happen on much longer time scales: milliseconds to seconds. In condensed phase chemical systems these interesting transitions are hindered by energy barriers so state to state dynamics are dominated by rare evens. Luckily, rare event transitions tend to happen through mountain passes in the potential energy landscape. Within harmonic transition state theory, the transition states between minima can be characterized by saddle points. Finding saddle points is a challenging problem which has not been satisfactorily solved; nevertheless, there are algorithms currently being used despite their deficiency. In particular, my work strives to improve the efficiency and stability of the nudged elastic band method and compare its performance to similar algorithms on a variety of test systems. In addition, I present a method to predict how energy-based chemical properties change with respect to the chemical composition of the system. This is achieved by taking a derivative of the property with respect to the atomic numbers of the atoms present in the system. The accuracy and predictive quality of these derivatives are assessed for both model and industrially relevant systems. With this information, we can follow these derivatives to optimize a desired property in the space of chemical composition. This method is a step toward using theory to rationally design compounds with desirable properties. / text

Irradiation induces a high concentration of defects in the structural materials of nuclear reactors, which are typically of body-centered cubic Iron (BCC Fe) and its alloys. The primary effect of irradiation is hardening which is caused by the blocking of dislocations with defects and defect clusters like point defects, self-interstitial loops, and voids. The dislocation-defect interactions are atomistic in nature due to the very small length and time scales involved, i.e., of the order of nanometers and picoseconds. To predict the effect of dislocation-defect interactions on the macroscopic mechanical and plastic behavior of the material, it is critically important to develop robust coupling schemes by which accurate atomic level physics of the rate-limiting kinetic processes can be informed into a coarse-grained model such as crystal plasticity. In this thesis we will develop an atomistically informed constitutive model. Relevant atomistic processes are identified from molecular dynamics simulations. The respective unit process studies are conducted using atomistic reaction pathway sampling methods like Nudged Elastic Band method. Stress-dependent activation energies and activation volumes are computed for various rate-liming unit processes like thermally activated dislocation motion via kinkpair nucleation, dislocation pinning due to self interstitial atom, etc. Constitutive laws are developed based on transition state theory, that informs the atomistically determined activation parameters into a coarse-grained crystal plasticity model. The macroscopic deformation behavior predicted by the crystal plasticity model is validated with experimental results and the characteristic features explained in the light of atomistic knowledge of the constituting kinetics. We also investigate on unique irradiation induced defects such as stacking fault tetrahedra, that are formed under non-irradiated condition. This thesis also includes our work on materials with internal interfaces that can resist irradiation induced damage. Overall, the research presented in this thesis involves the implementation and development of novel computational paradigm that encompasses computational approaches of various length and time scales towards robust predictions of the mechanical behavior of irradiated materials.

The minimum energy paths and transition states for the first two pyrolysis reactions of the tannin building blocks gallic acid and (+)-catechin were calculated by combining density functional theory with the climbing-image nudged elastic band method. For both investigated, the combined pyrolysis reaction was found to be endothermic across the full investigated temperature range and exergonic for temperatures of 1000 K and above when evaluated with the quantum chemical 'gold standard' approach CCSD(T). In the case of gallic acid, the dehydrogenation of pyrogallol was identified as the rate-determining pyrolysis step, whereas the catechol split-off was determined to be the rate-determining step of (+)-catechin pyrolysis. Additionally, simulated Raman spectra were able to explain the presence of subtle shoulder peaks in the spectrum of the binder Carbores®P. Another series of spectra assisted the identification of an ellagic acid pyrolysis product.

No description available.

The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2 + 2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for adsorption with the cyclooctyne group in the on-top position is found and traced back to minimal structural deformation of the adsorbate and surface with the help of energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures, a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories for the doubly bonded structures are obtained in agreement with calculations using the nudged elastic band approach. However, our findings disagree with the experimental observations of selective adsorption by the cyclooctyne moiety, which is critically discussed.

No description available.

Hydrocarbons, in particular polycyclic aromatic hydrocarbons (PAHs), have been long discussed to be carriers of interstellar infrared (IR) emission and ultraviolet (UV) absorption features. Yet, their origin in dense phases of the interstellar medium (ISM), such as molecular clouds, remains unclear. In this work, growth mechanisms based on ion-molecule reactions between cationic PAHs/hydrocarbons and methyne (CH) were investigated. The reaction type and the precursor were derived and selected from known chemical and physical properties of the ISM. These chemical reactions were characterised by calculating branching ratios (based on cross sections) and capture rate coefficients, minimum reaction paths, reaction enthalpies, thermal equilibrium constants, and microcanonic isomerisation and radiative deactivation rate coefficients. In order to cope with the variety of reaction parameters, a hierarchic workflow scheme was set up. First, the reaction potential energy surface was sampled by molecular dynamics simulations. Then, minimum energy paths of the most probable reaction channels were investigated. Finally, molecular and kinetic properties of stationary points were calculated. The quantum chemical level of theory was increased at each step from DFTB (tight-binding density-functional), to DFT, and finally to post-Hartree-Fock methods. Results on CH based hydrocarbon growth showed the transition from non-cyclic hydrocarbons to cyclic and aromatic structures and from cyclic to polycyclic aromatic hydrocarbons. Additionally, the reactive collisions between hydrocarbons and CH were found to produce sufficient energy for isomerisation and fragmentation processes even at ultra low temperatures. In all, the results indicate that methyne might be a proper precursor for the formation of large interstellar PAHs. / Kohlenwasserstoffe, insbesondere polyzyklische Kohlenwasserstoffe (engl. PAHs), werden seit einigen Jahren als Mitverursacher interstellar IR-Emissions- und UV-Absorptionsbanden angesehen und diskutiert. Dabei ist die Herkunft dieser Moleküle in den dichten Phasen des interstellaren Mediums (ISM) aber noch nicht aufgeklärt. In dieser Arbeit wurden daher die Bildungsmechanismen, welche auf Ion-Molekül-Reaktionen zwischen kationischen PAHs und Kohlenwasserstoffen und dem Molekül CH beruhen, untersucht. Sowohl der Reaktionstyp als auch der Präkursor wurden anhand von bekannten physikalischen und chemischen Eigenschaften des ISM abgeleitet und ausgewählt. Die Analyse der chemischen Reaktionen basierte auf Berechnungen zur Produktzusammensetzung und Einfangsratenkoeffizienten (welche wiederum aus berechneten Reaktionsquerschnitten hervorgingen) Minimumenergiepfade (MEP), Reaktionsenthalpien, thermische Gleichgewichtskonstanten und mikrokanonische Isomerisierungs- und Strahlungsdeaktivierungs-Ratenkoeffizienten. Um der Vielzahl an Reaktionsparameter gerecht zu werden, wurden die Berechnungsmethoden entsprechend eines hierarischen Fließschemas kombiniert. Hierzu wurden zuerst durch Molekulardynamik-Simulationen die Reaktionspotentialenergieflächen abgerastert. Auf der nächsten Stufe wurden statistisch bedeutsame Reaktionskanäle bezüglich ihrer Minimumenergiepfade untersucht. Den Abschluss bildete die Berechnung molekularer und kinetischer Charakteristika stationärer Punkte auf einem MEP. Entsprechend dieses Schemas wurde die quantenchemische Genauigkeit auf jeder Stufe von approximativer DFT über DFT zu post-Hartree-Fock verändert. Die Ergebnisse des CH-basierten Kohlenwasserstoffwachstums zeigten einen Übergang von nichtzyklischen zu zyklischen and aromatischen Strukturen, sowie von zyklischen zu polyzyklischen Kohlenwasserstoffen. Außerdem zeigte sich, dass reaktive Kollisionen zwischen Kohlenwasserstoffen und CH auch bei Tiefsttemperaturen immer ausreichend Energie für Isomerisierungs- und Fragmentationsprozesse liefert. Die Ergebnisse dieser Arbeit lassen den Schluss zu, dass CH ein geeigneter Präkursor für die Bildung großer interstellarer PAH ist.

Hydrocarbons, in particular polycyclic aromatic hydrocarbons (PAHs), have been long discussed to be carriers of interstellar infrared (IR) emission and ultraviolet (UV) absorption features. Yet, their origin in dense phases of the interstellar medium (ISM), such as molecular clouds, remains unclear. In this work, growth mechanisms based on ion-molecule reactions between cationic PAHs/hydrocarbons and methyne (CH) were investigated. The reaction type and the precursor were derived and selected from known chemical and physical properties of the ISM. These chemical reactions were characterised by calculating branching ratios (based on cross sections) and capture rate coefficients, minimum reaction paths, reaction enthalpies, thermal equilibrium constants, and microcanonic isomerisation and radiative deactivation rate coefficients. In order to cope with the variety of reaction parameters, a hierarchic workflow scheme was set up. First, the reaction potential energy surface was sampled by molecular dynamics simulations. Then, minimum energy paths of the most probable reaction channels were investigated. Finally, molecular and kinetic properties of stationary points were calculated. The quantum chemical level of theory was increased at each step from DFTB (tight-binding density-functional), to DFT, and finally to post-Hartree-Fock methods. Results on CH based hydrocarbon growth showed the transition from non-cyclic hydrocarbons to cyclic and aromatic structures and from cyclic to polycyclic aromatic hydrocarbons. Additionally, the reactive collisions between hydrocarbons and CH were found to produce sufficient energy for isomerisation and fragmentation processes even at ultra low temperatures. In all, the results indicate that methyne might be a proper precursor for the formation of large interstellar PAHs. / Kohlenwasserstoffe, insbesondere polyzyklische Kohlenwasserstoffe (engl. PAHs), werden seit einigen Jahren als Mitverursacher interstellar IR-Emissions- und UV-Absorptionsbanden angesehen und diskutiert. Dabei ist die Herkunft dieser Moleküle in den dichten Phasen des interstellaren Mediums (ISM) aber noch nicht aufgeklärt. In dieser Arbeit wurden daher die Bildungsmechanismen, welche auf Ion-Molekül-Reaktionen zwischen kationischen PAHs und Kohlenwasserstoffen und dem Molekül CH beruhen, untersucht. Sowohl der Reaktionstyp als auch der Präkursor wurden anhand von bekannten physikalischen und chemischen Eigenschaften des ISM abgeleitet und ausgewählt. Die Analyse der chemischen Reaktionen basierte auf Berechnungen zur Produktzusammensetzung und Einfangsratenkoeffizienten (welche wiederum aus berechneten Reaktionsquerschnitten hervorgingen) Minimumenergiepfade (MEP), Reaktionsenthalpien, thermische Gleichgewichtskonstanten und mikrokanonische Isomerisierungs- und Strahlungsdeaktivierungs-Ratenkoeffizienten. Um der Vielzahl an Reaktionsparameter gerecht zu werden, wurden die Berechnungsmethoden entsprechend eines hierarischen Fließschemas kombiniert. Hierzu wurden zuerst durch Molekulardynamik-Simulationen die Reaktionspotentialenergieflächen abgerastert. Auf der nächsten Stufe wurden statistisch bedeutsame Reaktionskanäle bezüglich ihrer Minimumenergiepfade untersucht. Den Abschluss bildete die Berechnung molekularer und kinetischer Charakteristika stationärer Punkte auf einem MEP. Entsprechend dieses Schemas wurde die quantenchemische Genauigkeit auf jeder Stufe von approximativer DFT über DFT zu post-Hartree-Fock verändert. Die Ergebnisse des CH-basierten Kohlenwasserstoffwachstums zeigten einen Übergang von nichtzyklischen zu zyklischen and aromatischen Strukturen, sowie von zyklischen zu polyzyklischen Kohlenwasserstoffen. Außerdem zeigte sich, dass reaktive Kollisionen zwischen Kohlenwasserstoffen und CH auch bei Tiefsttemperaturen immer ausreichend Energie für Isomerisierungs- und Fragmentationsprozesse liefert. Die Ergebnisse dieser Arbeit lassen den Schluss zu, dass CH ein geeigneter Präkursor für die Bildung großer interstellarer PAH ist.