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International audience; The physics of Fe-C surface interactions is of fundamental importance to phenomena such as corrosion, catalysis, synthesis of graphene, new steels, etc. To better understand this question, we perform an extensive characterization of the energy landscape for carbon diffusion from bulk to surfaces for bcc iron at low C concentration. C diffusion mechanisms over the three main Fe-surfaces - (100), (110) and (111) - are studied computationally using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo algorithm. Migration and adsorption energies on surfaces as well as absorption energies into the subsurfaces are predicted and then compared to density functional theory (DFT) and experiment. The energy landscape along C-diffusion pathways from bulk to surface is constructed allowing a more extensive characterization of the diffusion pathways between surface and subsurface. In particular, effective migration energies from (100), (110) and (111) surfaces, to the bulk octahedral site are found to be around similar to 1.6 eV, similar to 1.2 eV and similar to 13 eV respectively suggesting that C insertion into the bulk cannot take place in pure crystalline Fe, irrespective of the exposed surface.

The energetics of the catalytic oxidation of CO on a complex metal oxide are investigated for the first time via density functional theory calculations. The catalyst, Co-doped SrTiO3, is modelled using periodically repeated slabs based on the SrTiO3(100) surface. The comparison of the energy profiles obtained for the pure host and the Co-doped material reveals the actual pathway followed by the reaction, and shows that Co doping enhances the catalytic properties of SrTiO3 by reducing the energy cost for the formation of oxygen vacancies.

The effects of hole injection in amorphous-IGZO is analyzed by means of first-principles calculations. The injection of holes in the valence band tail states leads to their capture as a polaron, with high self-trapping energies (from 0.44 to 1.15 eV). Once formed, they mediate the formation of peroxides and remain localized close to the hole injection source due to the presence of a large diffusion energy barrier (of at least 0.6eV). Their diffusion mechanism can be mediated by the presence of hydrogen. The capture of these holes is correlated with the low off-current observed for a-IGZO transistors, as well as, with the difficulty to obtain a p-type conductivity. The results further support the formation of peroxides as being the root cause of Negative bias illumination stress (NBIS). The strong self-trapping substantially reduces the injection of holes from the contact and limits the creation of peroxides from a direct hole injection. In presence of light, the concentration of holes substantially rises and mediates the creation of peroxides, responsible for NBIS., Comment: 8 pages, 8 figures, to be published in Journal of Applied Physics

Human rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We study here a mathematical model for the structural transition between the native particle of human rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e. a sequence of metastable states with decreasing energy connected by minimum energy paths. We explore several transition pathways and discuss their implications for the RNA exit process.

The Fischer-Tropsch reaction is initiated by direct CO dissociation for Iron catalyst even though a H-assisted mechanism may be easier on other metals. In the gas phase, the CO dissociation is only favorable for Fe-clusters composed by more than 11 atoms. We show here the remarkable effect of the support TiO 2 (1 1 0), making this dissociation exothermic for Fe 4 and Fe 5 clusters. The main factor for the CO activation is the electron transfer to the reducible support. The role of the TiO 2 (1 1 0) support is to transform the neutral cluster into a positively charged one for which CO dissociation is easier.

Identification of radiation-induced radicals in relatively simple molecules is a prerequisite for the understanding of reaction pathways of the radiation chemistry of complex systems. Sucrose presents an additional practical interest as a versatile radiation dosimetric system. In this work, we present a periodic density functional theory study aimed to identify the fourth stable radical species in this carbohydrate. The proposed model is a fragment suspended in the lattice by hydrogen bonds with an unpaired electron at the original C5’ carbon of the fructose unit. It requires a double scission of the ring accompanied by substantial chemical and geometric reorganization.

Atomic layer deposition (ALD) has been recognized as a promising method to deposit conformal and uniform thin film of copper for future electronic devices. However, many aspects of the reaction mechanism and the surface chemistry of copper ALD remain unclear. In this paper, we employ plane wave density functional theory (DFT) to study the transmetalation ALD reaction of copper dimethylamino-2-propoxide [Cu(dmap)2] and diethylzinc [Et2Zn] that was realized experimentally by Lee et al. [ Angew. Chem., Int. Ed. 2009, 48, 4536−4539]. We find that the Cu(dmap)2 molecule adsorbs and dissociates through the scission of one or two Cu–O bonds into surface-bound dmap and Cu(dmap) fragments during the copper pulse. As Et2Zn adsorbs on the surface covered with Cu(dmap) and dmap fragments, butane formation and desorption was found to be facilitated by the surrounding ligands, which leads to one reaction mechanism, while the migration of ethyl groups to the surface leads to another reaction mechanism. During both reaction mechanisms, ligand diffusion and reordering are generally endothermic processes, which may result in residual ligands blocking the surface sites at the end of the Et2Zn pulse, and in residual Zn being reduced and incorporated as an impurity. We also find that the nearby ligands play a cooperative role in lowering the activation energy for formation and desorption of byproducts, which explains the advantage of using organometallic precursors and reducing agents in Cu ALD. The ALD growth rate estimated for the mechanism is consistent with the experimental value of 0.2 Å/cycle. The proposed reaction mechanisms provide insight into ALD processes for copper and other transition metals.

The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple “for-loop” construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Results of ab initio density-functional theory calculations of the migration energies of oxygen vacancies and interstitials in stoichiometric ${\text{UO}}_{2}$ are reported. The diffusion of oxygen vacancies in ${\text{UO}}_{2}$ is found to be highly anisotropic, and the [1 0 0] direction is energetically favored. The atomic relaxations play an important role in reducing the migration barriers. Within the generalized gradient approximation (GGA), we find that the migration energies of the preferred vacancies and interstitials paths are, respectively, 1.18 and 1.09 eV. With the inclusion of the Hubbard $U$ parameter to account for the $5f$ electron correlations in $\text{GGA}+U$, the vacancy migration energy is lowered to 1.01 eV while the interstitial migration energy increases slightly to 1.13 eV. We find, however, that the correlation effects have a drastic influence on the mechanism of interstitial migration through the stabilization of Willis-type clusters. Indeed, in contrast to GGA, in $\text{GGA}+U$ there is an inversion of the migration path with the so-called ``saddle-point'' position being lower in energy than the usual starting position. Thus while the migration barriers are nearly the same in GGA and $\text{GGA}+U$, the mechanisms are completely different. Our results clearly indicate that both vacancies and interstitials contribute almost equally to the diffusion of oxygen in ${\text{UO}}_{2}$.

We applied density functional theory based on ultrasoft pseudopotentials to study the structural properties of Ir-4 clusters both in the gas phase and adsorbed on a MgO(100) surface. To resolve the discrepancy between experimental data which suggest a tetrahedral structure for Ir-4 and theoretical results which show a strong preference for the square isomer, we investigated the effect of several adsorbates on the equilibrium atomic structure of the clusters. Calculated binding energies of a single H, C, or O atom, as well as one CO or OH molecule, to three stable Ir-4 isomers indicate that C or CO adsorption significantly influences the relative stability of Ir-4 isomers. For MgO(100)-supported Ir-4, atomic carbon is able to change the isomer preference from the square to the tetrahedral geometry.