CO adsorption on metal surfaces: a hybrid functional study with plane wave basis set

We present a detailed study of the adsorption of CO on Cu, Rh, and Pt (111) surfaces in top and hollow sites. The study has been performed using the local density approximation, the gradient corrected functional PBE, and the hybrid Hartree-Fock density functionals PBE0 and HSE03 within the framework of generalized Kohn-Sham density functional theory using a plane-wave basis set. As expected, the LDA and GGA functionals show a tendency to favor the hollow sites, at variance with experimental findings that give the top site as the most stable adsorption site. The PBE0 and HSE03 functionals reduce this tendency. In fact, they predict the correct adsorption site for Cu and Rh but fail for Pt. But even in this case, the hybrid functional destabilizes the hollow site by 50 meV compared to the PBE functional. The results of the total energy calculations are presented along with an analysis of the projected density of states.Comment: 32 pages, 6 tables, 3 figures. (Re)Submitted to Phys. Rev. B; LDA results added in the tables; minor changes in the tex

DBCChecker: A Bigraph-Based Tool for Checking Security Properties of Container Compositions

Despite their widespread application in modern systems, container composition is often complex and error-prone. In this work, we present DBCChecker, a tool aiming to verify security properties of systems obtained by composition of containers. From the configuration of a container-based system and an abstract description of the interface behaviour of each container, the tool builds a formal model of the overall system, which can be verified in ProVerif (an automatic symbolic protocol verifier), to check that the overall system satisfies the required properties. The system can be described in a specification language capable to express at once the interfaces and connections of containers and the relevant behavioural aspects of their interfaces, called JSON Bigraph Format (JBF), and inspired by previous formal models, based on bigraphs, for containerized architectures

Quantitative evaluation of orofacial motor function in mice: The pasta gnawing test, a voluntary and stress-free behavior test

AbstractBackgroundEvaluation of motor deficits in rodents is mostly restricted to limb motor tests that are often high stressors for the animals.New methodTo test rodents for orofacial motor impairments in a stress-free environment, we established the pasta gnawing test by measuring the biting noise of mice that eat a piece of spaghetti. Two parameters were evaluated, the biting speed and the biting peaks per biting episode. To evaluate the power of this test compared to commonly used limb motor and muscle strength tests, three mouse models of Parkinson’s disease, amyotrophic lateral sclerosis and Niemann-Pick disease were tested in the pasta gnawing test, RotaRod and wire suspension test.ResultsOur results show that the pasta gnawing test reliably displays orofacial motor deficits.Comparison with existing methodsThe test is especially useful as additional motor test in early onset disease models, since it shows first deficits later than the RotaRod or wire suspension test. The test depends on a voluntary eating behavior of the animal with only a short-time food deprivation and should thus be stress-free.ConclusionsThe pasta gnawing test represents a valuable tool to analyze orofacial motor deficits in different early onset disease models

Dynamic instance generation for few-shot handwritten document layout segmentation (short paper)

Historical handwritten document analysis is an important activity to retrieve information about our past. Given that this type of process is slow and time-consuming, the humanities community is searching for new techniques that could aid them in this activity. Document layout analysis is a branch of machine learning that aims to extract semantic informations from digitised documents. Here we propose a new framework for handwritten document layout analysis that differentiates from the current state-of-the-art by the fact that it features few-shot learning, thus allowing for good results with little manually labelled data and the dynamic instance generation process. Our results were obtained using the DIVA - HisDB dataset

Assessing the Performance of Recent Density Functionals for Bulk Solids

We assess the performance of recent density functionals for the exchange-correlation energy of a nonmolecular solid, by applying accurate calculations with the GAUSSIAN, BAND, and VASP codes to a test set of 24 solid metals and non-metals. The functionals tested are the modified Perdew-Burke-Ernzerhof generalized gradient approximation (PBEsol GGA), the second-order GGA (SOGGA), and the Armiento-Mattsson 2005 (AM05) GGA. For completeness, we also test more-standard functionals: the local density approximation, the original PBE GGA, and the Tao-Perdew-Staroverov-Scuseria (TPSS) meta-GGA. We find that the recent density functionals for solids reach a high accuracy for bulk properties (lattice constant and bulk modulus). For the cohesive energy, PBE is better than PBEsol overall, as expected, but PBEsol is actually better for the alkali metals and alkali halides. For fair comparison of calculated and experimental results, we consider the zero-point phonon and finite-temperature effects ignored by many workers. We show how Gaussian basis sets and inaccurate experimental reference data may affect the rating of the quality of the functionals. The results show that PBEsol and AM05 perform somewhat differently from each other for alkali metal, alkaline earth metal and alkali halide crystals (where the maximum value of the reduced density gradient is about 2), but perform very similarly for most of the other solids (where it is often about 1). Our explanation for this is consistent with the importance of exchange-correlation nonlocality in regions of core-valence overlap.Comment: 32 pages, single pdf fil

"Narrow" Graphene Nanoribbons Made Easier by Partial Hydrogenation

It is a challenge to synthesize graphene nanoribbons (GNRs) with narrow widths and smooth edges in large scale. Our first principles study on the hydrogenation of GNRs shows that the hydrogenation starts from the edges of GNRs and proceeds gradually toward the middle of the GNRs so as to maximize the number of carbon-carbon $\pi$-$\pi$ bonds. Furthermore, the partially hydrogenated wide GNRs have similar electronic and magnetic properties as those of narrow GNRs. Therefore, it is not necessary to directly produce narrow GNRs for realistic applications because partial hydrogenation could make wide GNRs "narrower"

Transport properties of copper phthalocyanine based organic electronic devices

Ambipolar charge carrier transport in Copper phthalocyanine (CuPc) is studied experimentally in field-effect transistors and metal-insulator-semiconductor diodes at various temperatures. The electronic structure and the transport properties of CuPc attached to leads are calculated using density functional theory and scattering theory at the non-equilibrium Green's function level. We discuss, in particular, the electronic structure of CuPc molecules attached to gold chains in different geometries to mimic the different experimental setups. The combined experimental and theoretical analysis explains the dependence of the mobilityand the transmission coefficient on the charge carrier type (electrons or holes) and on the contact geometry. We demonstrate the correspondence between our experimental results on thick films and our theoretical studies of single molecule contacts. Preliminary results for fluorinated CuPc are discussed.Comment: 18 pages, 16 figures; to be published in Eur. Phys. J. Special Topic

Global hybrids from the semiclassical atom theory satisfying the local density linear response

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 106, 186406, (2011)] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetical and structural testings, including thermochemistry and geometry, transition metal complexes, non-covalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20\% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semi-empirical dispersion corrections are also provided.Comment: 12 pages, 4 figure

Random-phase approximation and its applications in computational chemistry and materials science

The random-phase approximation (RPA) as an approach for computing the electronic correlation energy is reviewed. After a brief account of its basic concept and historical development, the paper is devoted to the theoretical formulations of RPA, and its applications to realistic systems. With several illustrating applications, we discuss the implications of RPA for computational chemistry and materials science. The computational cost of RPA is also addressed which is critical for its widespread use in future applications. In addition, current correction schemes going beyond RPA and directions of further development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012