Substrate orientation effects on nanoelectrode lithography : ReaxFF molecular dynamics and experimental study

The crystallographic orientation of the substrate is an essential parameter in the kinetic mechanism for the oxidation process. Hence, the choice of substrate surface orientation is crucial in nanofabrication industries. In the present work, we have studied qualitatively the influence of substrate orientation in nanoelectrode lithography using ReaxFF reactive molecular dynamics simulation. We have investigated the oxidation processes on (100), (110) and (111) orientation surfaces of silicon at different electric field intensities. The simulation results show the thickness of the oxide film and the initial oxygen diffusion rate follow an order of (100) > (110) > (111) at lower electric field intensities. It also confirms that surfaces with higher surface energy are more reactive at lower electric field intensity. Crossovers occurred at a higher electric field intensity (7 V nm -1) under which the thickness of the oxide film yields an order of T(110) > T(100) > T(111). These types of anomalous characteristics have previously been observed for thermal oxidation of silicon surfaces. Experimental results show different orders for the (100) and (111) substrate, while (110) remains the largest for the oxide thickness. A good correlation has been found between the oxide growth and the orientation-dependent parameters where the oxide growth is proportional to the areal density of the surfaces. The oxide growth also follows the relative order of the activation energies, which could be another controlling factor for the oxide growth. Less activation energy of the surface allows more oxide growth and vice versa. However, the differences between simulation and experimental results probably relate to the empirical potential as well as different time and spatial scales of the process

Etude des processus de corrosion du nickel par dynamique moléculaire avec un potentiel réactif ReaxFF

La compréhension des processus de corrosion est un élément majeur de l étude de la durabilité des matériaux en environnements agressifs. C est dans ce cadre que ce travail de thèse se situe. L objectif est d apporter un nouvel éclairage sur les processus de corrosion du nickel en milieu aqueux en utilisant la simulation par dynamique moléculaire avec un champ de force réactif ReaxFF .Nous nous sommes particulièrement intéressé aux réactions entres les molécules d eau et les surfaces monocristallines de nickel. Ces résultats ont montré aucune dissociation de l eau sur les surfaces. Par ailleurs, une adsorption des molécules en bicouche a été constatée, traduisant la polarisation mutuelle entre l eau et le nickel, ce que confirme le calcul de charges. La surface du métal s est chargée positivement alors que la première couche d eau se charge négativement, reproduisant la double couche électrique. L introduction d un champ électrique extérieur a conditionné la réaction entre l eau et le nickel. La présence du champ a permis d observer les différentes étapes d oxydation du nickel : l adsorption des molécules d eau puis leurs dissociations en OH- et H3O+. La dissolution des atomes de nickel à la surface puis la pénétration de O dans Ni. Ces processus d oxydation sont répétés au cours du temps pour obtenir le film d oxyde. L épaisseur du film d oxyde dépend linéairement de l intensité du champ électrique. La cinétique d oxydation est améliorée pour la surface (110) par rapport aux autres surfaces étudiées. L étude de l oxydation d un bicristal de nickel a montré des processus identique. Par ailleurs, nous avons constaté que les premiers germes d oxydation se sont produits au niveau des joints de grains et se sont propagés sur toute la surface. L ensemble de ces résultats est en bon accord avec les observations expérimentalesUnderstanding of corrosion processes is important for the study of the durability of materials in aggressive environment. The objective is to provide new lights on the corrosion processes of nickel in aqueous condition with molecular dynamics simulation using a reactive force field "ReaxFF."We are particularly interested by the reaction between water molecules and mono-crystalline surfaces of nickel. No dissociation of water was showed on the surfaces. Moreover, an adsorption of molecules in bilayer was observed, reflecting the mutual polarization between water and nickel, which confirms the charge calculation. The metal surface is positively charged and the first water layer charged negatively, reproducing the electrical double layer. The introduction of an external electric field has conditioned the reaction between water and nickel. The presence of the field permits to observe the different stages of nickel corrosion: adsorption of water molecules, their dissociation into OH- and H3O+, the dissolution of the nickel atoms on the surface and the penetration of O in Ni. These oxidation processes are repeated over time to obtain the oxide film. The thickness of the oxide film depends linearly on the electric field intensity. The oxidation kinetics is improved to the surface (110) compared with other orientations studied. All these results are in good agreement with experimental observationsDIJON-BU Doc.électronique (212319901) / SudocSudocFranceF

ReaxFF molecular dynamics simulation study of nanoelectrode lithography oxidation process on silicon (100) surface

The nanoelectrode lithography has been strengthened in recent years as one of the most promising methods due to its high reproducibility, low cost and ability to manufacture nano-sized structures. In this work, the mechanism and the parametric influence in nanoelectrode lithography have been studied qualitatively in atomic scale using ReaxFF MD simulation. This approach was originally developed by van Duin and co-workers to investigate hydrocarbon chemistry. We have investigated the water adsorption and dissociation processes on Si (100) surface as well as the characteristics (structure, chemical composition, morphology, charge distribution, etc.) of the oxide growth. The simulation results show two forms of adsorption of water molecules: molecular adsorption and dissociative adsorption. After breaking the adsorbed hydroxyls, the oxygen atoms insert into the substrate to form the Si−O−Si bonds so as to make the surface oxidized. The influence of the electric field intensity (1.5 – 7 V/nm) and the relative humidity (20 – 90%) on the oxidation process have also been discussed. Nevertheless, the results obtained from the simulations have been compared qualitatively with the experimental results and they show in good agreements. Variable charge molecular dynamics allowed us to characterize the nanoelectrode lithography process from an atomistic point of view

Dynamical evolutions of ℓ-boson stars in spherical symmetry

In previous work, we have found new static, spherically symmetric boson star solutions which generalize the standard boson stars (BSs) by allowing a particular superposition of scalar fields in which each of the fields is characterized by a fixed value of its non-vanishing angular momentum number. We call such solutions 'boson stars'. Here, we perform a series of fully non-linear dynamical simulations of perturbed BSs in order to study their stability, and the final fate of unstable configurations. We show that for each value of, the configuration of maximum mass separates the parameter space into stable and unstable regions. Stable configurations, when perturbed, oscillate around the unperturbed solution and very slowly return to a stationary configuration. Unstable configurations, in contrast, can have three different final states: collapse to a black hole, migration to the stable branch, or explosion (dissipation) to infinity. Just as it happens with BSs, migration to the stable branch or dissipation to infinity depends on the sign of the total binding energy of the star: bound unstable stars collapse to black holes or migrate to the stable branch, whereas unbound unstable stars either collapse to a black hole or explode to infinity. Thus, the parameter allows us to construct a new set of stable configurations. All our simulations are performed in spherical symmetry, leaving a more detailed stability analysis including non-spherical perturbations for future work.Fil: Alcubierre, Miguel. Universidad Nacional Autónoma de México. Instituto de Ciencias Nucleares; MéxicoFil: Barranco, Juan. Universidad de Guanajuato; MéxicoFil: Bernal, Argelia. Universidad de Guanajuato; MéxicoFil: Degollado, Juan Carlos. Universidad Nacional Autónoma de México; MéxicoFil: Diez Tejedor, Alberto. Universidad de Guanajuato; MéxicoFil: Megevand Politano, Miguel Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Núñez, Darío. Universidad Nacional Autónoma de México. Instituto de Ciencias Nucleares; MéxicoFil: Sarbach, Olivier. Universidad Michoacana de San Nicolás de Hidalgo; Méxic

ℓ-boson stars

We present new, fully nonlinear numerical solutions to the static, spherically symmetric Einstein-Klein-Gordon system for a collection of an arbitrary odd number N of complex scalar fields with an internal symmetry and no self-interactions. These solutions, which we dub -boson stars, are parametrized by an angular momentum number ℓ =(N - 1)/2, an excitation number n, and a continuous parameter representing the amplitude of the fields. They are regular at every point and possess a finite total mass. For ℓ = 0the standard spherically symmetric boson stars are recovered. We determine their generalizations for ℓ ≤ 0, and show that they give rise to a large class of new static configurations which might have a much larger compactness ratio than stars.Fil: Alcubierre, Miguel. Universidad Nacional Autónoma de México. Instituto de Ciencias Nucleares; MéxicoFil: Barranco, Juan. Universidad de Guanajuato; MéxicoFil: Bernal, Argelia. Universidad de Guanajuato; MéxicoFil: Degollado, Juan Carlos. Universidad Nacional Autónoma de México; MéxicoFil: Diez Tejedor, Alberto. Universidad de Guanajuato; MéxicoFil: Megevand Politano, Miguel Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Núñez, Darío. Universidad Nacional Autónoma de México. Instituto de Ciencias Nucleares; MéxicoFil: Sarbach, Olivier. Universidad Michoacana de San Nicolás de Hidalgo; Méxic

Energetics of hydrogen impurities in aluminum and their effect on mechanical properties

The effects of hydrogen impurities in the bulk and on the surface of aluminum are theoretically investigated. Within the framework of density functional theory, we have obtained the dependence on H concentration of the stacking fault energy, the cleavage energy, the Al/H surface energy and the Al/H/Al interface formation energy. The results indicate a strong dependence of the slip energy barrier in the $[\bar 211]$ direction the cleavage energy in the [111] direction and the Al/H/Al interface formation energy, on H concentration and on tension. The dependence of the Al/H surface energy on H coverage is less pronounced, while the optimal H coverage is $\leq 0.25$ monolayer. The calculated activation energy for diffusion between high symmetry sites in the bulk and on the surface is practically the same, 0.167 eV. From these results, we draw conclusions about the possible effect of H impurities on mechanical properties, and in particular on their role in embrittlement of Al.Comment: 9 pages, 5 figure

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p

Molecular dynamics simulations of nanometric metallic multilayers: Reactivity of the Ni-Al system

International audienceThe reactivity of a layered Ni-Al-Ni system is studied by means of molecular dynamics simulations, using an embedded-atom method type potential. The system, made of an fcc-Al layer embedded in fcc-Ni, is initially thermalized at the fixed temperature of 600 K. The early interdiffusion of Ni and Al at interfaces is followed by the massive diffusion of Ni in the Al layer and by the spontaneous phase formation of B2-NiAl. The solid-state reaction is associated with a rapid system heating, which further enhances the diffusion processes. For longer times, the system may partly lose some its B2-NiAl microstructure in favor of the formation of L12-Ni3Al. This stage is controlled by the diffusion of Al in the Ni-rich phase, and a layer-by-layer development of the new phase is observed

Apport de la dynamique moléculaire et de techniques expérimentales à une échelle locale pour l'étude de surfaces d'aluminium déformées et/ou oxydées

Durant toute leur durée de vie, les matériaux métalliques sont soumis à de nombreuses agressions liées à l environnement extérieur ou à leur mode d utilisation. Ainsi, lors d un processus de corrosion, les métaux et alliages peuvent perdre leur intégrité (piqûration, écaillage ) et leurs propriétés (mécaniques, physiques, chimiques ) risques d être altérées. Cette évolution relève de mécanismes complexes se produisant à des échelles allant de l atome au micromètre (champs de contraintes, diffusion préférentielle ). Il apparaît donc nécessaire de développer des techniques expérimentales ou numériques aux échelles pertinentes - qui dépendent de la microstructure et des mécanismes mis en jeu - pour une compréhension des phénomènes observés macroscopiquement. C est dans cet objectif que nous avons mené ce travail au cours duquel nous avons développé deux approches différentes : la première traitant de la formation de rugosité à la surface d échantillons d aluminium ; la seconde étant axée sur la caractérisation de l oxydation de substrats d'aluminium monocristallin et polycristallin sous différentes conditions (température, pression, contrainte). Cette confrontation des résultats numériques (par dynamique moléculaire) et expérimentaux (notamment par spectroscopie d impédance électrochimique locale) n est pas menée dans un but quantitatif mais plutôt pour obtenir des éléments complémentaires. De plus, elle vise à fournir, à partir de l approche numérique, une vision des mécanismes atomiques des phénomènes qui sont visualisés expérimentalement.During their lifetime, metallic materials are subject to numerous attacks related to the external environment or to their use. Thus, during a corrosion process, metals and alloys can lose their integrity (pitting, spellation...) and their properties (mechanical, physical, chemical...). This development comes from complex mechanisms occurring at scales ranging from the atom to the micrometer (strain field, preferential diffusion...). Therefore, it is necessary to develop experimental or numerical methods at relevant scales - which depend on the microstructure and the mechanisms involved - to understand the phenomena observed at the macroscopic scale. To this end, two different approaches have been developed in this work : firstly, the formation of roughness at the surface of aluminum samples has been studied; secondly, characterizations of the oxidation of monocrystalline and polycrystalline aluminum substrates under different conditions (temperature, pressure, strain) have been performed. This comparison between numerical (by molecular dynamics) and experimental (especially by electrochemical impedance spectroscopy at local scale) approaches is not realized in a quantitative way but rather in order to obtain complementary point of views. In addition, it aims to provide, from the numerical approach, a vision of the atomic mechanisms of the phenomena which are observed experimentally.DIJON-BU Sciences Economie (212312102) / SudocSudocFranceF