Rings sliding on a honeycomb network: Adsorption contours, interactions, and assembly of benzene on Cu(111)

Using a van der Waals density functional (vdW-DF) [Phys. Rev. Lett. 92, 246401 (2004)], we perform ab initio calculations for the adsorption energy of benzene (Bz) on Cu(111) as a function of lateral position and height. We find that the vdW-DF inclusion of nonlocal correlations (responsible for dispersive interactions) changes the relative stability of eight binding-position options and increases the binding energy by over an order of magnitude, achieving good agreement with experiment. The admolecules can move almost freely along a honeycomb web of "corridors" passing between fcc and hcp hollow sites via bridge sites. Our diffusion barriers (for dilute and two condensed adsorbate phases) are consistent with experimental observations. Further vdW-DF calculations suggest that the more compact (hexagonal) Bz-overlayer phase, with lattice constant a = 6.74 \AA, is due to direct Bz-Bz vdW attraction, which extends to ~8 \AA. We attribute the second, sparser hexagonal Bz phase, with a = 10.24 \AA, to indirect electronic interactions mediated by the metallic surface state on Cu(111). To support this claim, we use a formal Harris-functional approach to evaluate nonperturbationally the asymptotic form of this indirect interaction. Thus, we can account well for benzene self-organization on Cu(111).Comment: 13 pages, 7 figures, 3 tables, submitted for publication Accepted for publication in Phys. Rev. B. This version contains improved notation (with corresponding relabeling of figures), very small corrections to some tabulated values, and corrections concerning lattice lengths and subsequent discussion of commensurability of unit-cell dimension

Response of the Shockley surface state to an external electrical field: A density-functional theory study of Cu(111)

The response of the Cu(111) Shockley surface state to an external electrical field is characterized by combining a density-functional theory calculation for a slab geometry with an analysis of the Kohn-Sham wavefunctions. Our analysis is facilitated by a decoupling of the Kohn-Sham states via a rotation in Hilbert space. We find that the surface state displays isotropic dispersion, quadratic until the Fermi wave vector but with a significant quartic contribution beyond. We calculate the shift in energetic position and effective mass of the surface state for an electrical field perpendicular to the Cu(111) surface; the response is linear over a broad range of field strengths. We find that charge transfer occurs beyond the outermost copper atoms and that accumulation of electrons is responsible for a quarter of the screening of the electrical field. This allows us to provide well-converged determinations of the field-induced changes in the surface state for a moderate number of layers in the slab geometry.Comment: 11 pages, 6 figures, 4 tables; accepted for publication by Phys. Rev. B; changes from v1 in response to referee comments, esp. to Sections I and V.B (inc. Table 4), with many added references, but no change in results or conclusion

Reduced-gradient analysis of van der Waals complexes

acceptedVersio

Graphene Nanogap for Gate Tunable Quantum Coherent Single Molecule Electronics

We present atomistic calculations of quantum coherent electron transport through fulleropyrrolidine terminated molecules bridging a graphene nanogap. We predict that three difficult problems in molecular electronics with single molecules may be solved by utilizing graphene contacts: (1) a back gate modulating the Fermi level in the graphene leads facilitate control of the device conductance in a transistor effect with high on/off current ratio; (2) the size mismatch between leads and molecule is avoided, in contrast to the traditional metal contacts; (3) as a consequence, distinct features in charge flow patterns throughout the device are directly detectable by scanning techniques. We show that moderate graphene edge disorder is unimportant for the transistor function.Comment: 8 pages, 6 figure

Spin Signature of Nonlocal Correlation Binding in Metal-Organic Frameworks

We develop a proper nonempirical spin-density formalism for the van der Waals density functional (vdW-DF) method. We show that this generalization, termed svdW-DF, is firmly rooted in the single-particle nature of exchange and we test it on a range of spin systems. We investigate in detail the role of spin in the nonlocal correlation driven adsorption of H-2 and CO2 in the linear magnets Mn-MOF74, Fe-MOF74, Co-MOF74, and Ni-MOF74. In all cases, we find that spin plays a significant role during the adsorption process despite the general weakness of the molecular-magnetic responses. The case of CO2 adsorption in Ni-MOF74 is particularly interesting, as the inclusion of spin effects results in an increased attraction, opposite to what the diamagnetic nature of CO2 would suggest. We explain this counterintuitive result, tracking the behavior to a coincidental hybridization of the O p states with the Ni d states in the down-spin channel. More generally, by providing insight on nonlocal correlation in concert with spin effects, our nonempirical svdW-DF method opens the door for a deeper understanding of weak nonlocal magnetic interactions

Understanding adhesion at as-deposited interfaces from ab initio thermodynamics of deposition growth: thin-film alumina on titanium carbide

We investigate the chemical composition and adhesion of chemical vapour deposited thin-film alumina on TiC using and extending a recently proposed nonequilibrium method of ab initio thermodynamics of deposition growth (AIT-DG) [Rohrer J and Hyldgaard P 2010 Phys. Rev. B 82 045415]. A previous study of this system [Rohrer J, Ruberto C and Hyldgaard P 2010 J. Phys.: Condens. Matter 22 015004] found that use of equilibrium thermodynamics leads to predictions of a non-binding TiC/alumina interface, despite the industrial use as a wear-resistant coating. This discrepancy between equilibrium theory and experiment is resolved by the AIT-DG method which predicts interfaces with strong adhesion. The AIT-DG method combines density functional theory calculations, rate-equation modelling of the pressure evolution of the deposition environment and thermochemical data. The AIT-DG method was previously used to predict prevalent terminations of growing or as-deposited surfaces of binary materials. Here we extent the method to predict surface and interface compositions of growing or as-deposited thin films on a substrate and find that inclusion of the nonequilibrium deposition environment has important implications for the nature of buried interfaces.Comment: 8 pages, 6 figures, submitted to J. Phys.: Condens. Matte

Theory of Polar Corrections to Donor Binding

We calculate the optical phonon correction to the binding energy of electrons to donors in cubic materials. Previous theories calculated the Rydberg energy reduced by the effective mass and the static dielectric function. They omitted an important energy term from the long-range polarization of the ionized donor, which vanishes for the neutral donor. They also omitted the donor-phonon interaction. Including these terms yields a new formula for the donor binding energy

Insights from the shell proteome : Biomineralization to adaptation

Acknowledgments This work was supported by funding from the CACHE (Calcium in a Changing Environment) initial training network (ITN) under the European Union Seventh Framework Programme, reference grant agreement number 605051. We acknowledge E. Dufour (UMR 7209, MNHN) for shell sample preparation. We thank G. Bolbach and L. Matheron (IBPS-FR3631, Paris) for proteomic analysis and discussionsPeer reviewedPublisher PD

van der Waals density functionals built upon the electron-gas tradition: Facing the challenge of competing interactions

The theoretical description of sparse matter attracts much interest, in particular for those ground-state properties that can be described by density functional theory (DFT). One proposed approach, the van der Waals density functional (vdW-DF) method, rests on strong physical foundations and offers simple yet accurate and robust functionals. A very recent functional within this method called vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412] stands out in its attempt to use an exchange energy derived from the same plasmon-based theory from which the nonlocal correlation energy was derived. Encouraged by its good performance for solids, layered materials, and aromatic molecules, we apply it to several systems that are characterized by competing interactions. These include the ferroelectric response in PbTiO$_3$, the adsorption of small molecules within metal-organic frameworks (MOFs), the graphite/diamond phase transition, and the adsorption of an aromatic-molecule on the Ag(111) surface. Our results indicate that vdW-DF-cx is overall well suited to tackle these challenging systems. In addition to being a competitive density functional for sparse matter, the vdW-DF-cx construction presents a more robust general purpose functional that could be applied to a range of materials problems with a variety of competing interactions

Genetic relationships among species of Contracaecum railliet & Henry, 1912 and Phocascaris Höst, 1932 (Nematoda: Anisakidae) from pinnipeds inferred from mitochondrial cox2 sequences, and congruence with allozyme data

The genetic relationships among 11 taxa, belonging to the genus Contracaecum (C. osculatum A, C. osculatum B, C. osculatum (s.s.), C. osculatum D, C. osculatum E, C. osculatum baicalensis, C. mirounga, C. radiatum, C. ogmorhini (s.s.), C. margolisi) and Phocascaris IPhocascaris cystophorae), parasites as adults of seals, were inferred from sequence analysis (519 bp) of the mitochbndrial cytochrome c oxidase subunit II (mtDNA cox2) gene. Phylogenetic analyses obtained from Parsimony (MP) and Neighbour-Joining (NJ) K2P distance values generated similar topologies, each well supported at major nodes. All analyses delineated two main clades: the first encompassing the parasites of the phocid seals, i.e. the C. osculatum species complex, C. osculatum baicalensis, C. mirounga and C. radiatum, with the latter two species forming a separate subclade; the second including the parasites of otarids, i.e. C. ogmorhini (s.s.) and C. margolisi. An overall high congruence between mtDNA inferred tree topologies and those produced from nuclear data sets (20 allozyme loci) was observed. Comparison of the phylogenetic hypothesis here produced for Contracaecum spp. plus Phocascaris with those currently available for their definitive hosts (pinnipeds) suggests parallelism between hosts and parasite phylogenetic tree topologies.Fil: Mattiucci, Simonetta. Università di Roma; ItaliaFil: Paoletti, M.. Università di Roma; Italia. Università degli Studi della Tuscia; ItaliaFil: Webb, S.C.. Cawthron Institute; Nueva ZelandaFil: Sardella, Norma Haydee. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Departamento de Biología. Laboratorio de Parasitología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; ArgentinaFil: Timi, Juan Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Berland, B.. University of Bergen; NoruegaFil: Nascetti, G.. Università degli Studi della Tuscia; Itali