Structure and binding in crystals of cage-like molecules: hexamine and platonic hydrocarbons

In this paper, we show that first-principle calculations using a van der Waals density functional (vdW-DF), [Phys. Rev. Lett. $\mathbf{92}$, 246401 (2004)] permits determination of molecular crystal structure. We study the crystal structures of hexamine and the platonic hydrocarbons (cubane and dodecahedrane). The calculated lattice parameters and cohesion energy agree well with experiments. Further, we examine the asymptotic accounts of the van der Waals forces by comparing full vdW-DF with asymptotic atom-based pair potentials extracted from vdW-DF. The character of the binding differ in the two cases, with vdW-DF giving a significant enhancement at intermediate and relevant binding separations. We analyze consequences of this result for methods such as DFT-D, and question DFT-D's transferability over the full range of separations

Conservation of phase space properties using exponential integrators on the cubic Schrödinger equation

The cubic nonlinear Schrödinger (NLS) equation with periodic boundary conditions is solvable using Inverse Spectral Theory. The nonlinear spectrum of the associated Lax pair reveals topological properties of the NLS phase space that are difficult to assess by other means. In this paper we use the invariance of the nonlinear spectrum to examine the long time behavior of exponential and multisymplectic integrators as compared with the most commonly used split step approach. The initial condition used is a perturbation of the unstable plane wave solution, which is difficult to numerically resolve. Our findings indicate that the exponential integrators from the viewpoint of efficiency and speed have an edge over split step, while a lower order multisymplectic is not as accurate and too slow to compete. © 2006 Elsevier Inc. All rights reserved

Effect of ovarian superstimulation on COC collection and maturation in alpacas

The objective of the present study was to compare the ovarian follicular response, cumulus-oocyte complex (COC) collection rate, and maturational status of COC collected from alpacas subsequent to treatment with two different superstimulatory protocols. Alpacas (n = 7 per group) were treated with: (1) 200 mg of FSH im divided bid for 3 d, plus a single i.v. dose of 1000 IU hCG 24 h after the last FSH treatment, or (2) 1200 IU of eCG as a single i.m. dose, plus a single i.v. dose of 1000 IU of hCG on day 3 after eCG treatment (day 0 = start of superstimulatory treatment). At 20-24 h post-hCG treatment, the ovaries were surgically exposed and COC were collected by needle aspiration of all follicles ≥6 mm. The FSH and eCG treatment groups did not differ with respect to the number of follicles ≥6 mm at the time of COC collection (20.0 ± 7.5 versus 27.0 ± 3.3; P = 0.5), the number of COC collected (26.2 ± 8.4 versus 23.3 ± 3.7; P = 0.7), or the collection rate per follicle aspirated (89% versus 87%; P = 0.7). No differences were detected between FSH- and eCG-treated alpacas in the number of expanded COC collected per alpaca (11.5 ± 2.9 versus 8.8 ± 2.8; P = 0.54), the number of expanded COC in metaphase II (8.5 ± 1.9 versus 6.0 ± 2.1; P = 0.1), or the number of compact COC with ≥3 layers of cumulus cells (12.5 ± 4.3 versus 14.3 ± 2.6; P = 0.72). A greater proportion (P < 0.05) of compact COC collected after FSH treatment matured in vitro to the metaphase II stage than after eCG treatment. Eight expanded alpaca COC were fertilized in vitro with llama sperm, three of which were fixed and stained 18 h after exposure to sperm and five were cultured in vitro. Two of the three stained oocytes were in the pronuclear stage, and all five of the cultured oocytes developed to the two-cell and morula stages at 2 and 7 days, respectively, after in vitro fertilization. In summary, FSH and eCG treatments were equally effective for ovarian superstimulation and oocyte collection. Cumulus-oocyte complexes were collected from more than 80% of follicles aspirated during laparotomy. Nearly one third of the COC collected after superstimulation were in metaphase II, and more than 70% of the remaining COC progressed to metaphase II after in vitro maturation for 26 h, bringing the mean number of oocytes available for in vitro fertilization to 16 per alpaca. Preliminary results support the hypothesis that alpaca oocytes obtained after superstimulation in the absence of progesterone are developmentally competent since morulae developed from all five COC fertilized and cultured in vitro

Evaluation of New Density Functional with Account of van der Waals Forces by Use of Experimental H2 Physisorption Data on Cu(111)

Detailed experimental data for physisorption potential-energy curves of H2 on low-indexed faces of Cu challenge theory. Recently, density-functional theory has been developed to also account for nonlocal correlation effects, including van der Waals forces. We show that one functional, denoted vdW-DF2, gives a potential-energy curve promisingly close to the experiment-derived physisorptionenergy curve. The comparison also gives indications for further improvements of the functionals

Protein Inhibitors of Calcium Salt Crystal Growth in Saliva, Bile and Pancreatic Juice

The control of the formation of crystals in biological fluids is one of the most exciting field of research involving both organic and biochemical areas. Many organisms have evolved mechanisms which minimize or avoid the effects of nucleation and crystal growth formation. One of the most important mechanism is the interaction of specific proteins, called inhibitors, with crystals which alters their habits and leads to their elimination. This article, focused on saliva, pancreatic juice and bile, reviews our present knowledge on the structure-function relationships existing between these proteins and their ability to inhibit the growth of different calcium salt crystals

Benchmarking van der Waals Density Functionals with Experimental Data: Potential Energy Curves for H2 Molecules on Cu(111), (100), and (110) Surfaces

Detailed physisorption data from experiment for the H_2 molecule on low-index Cu surfaces challenge theory. Recently, density-functional theory (DFT) has been developed to account for nonlocal correlation effects, including van der Waals (dispersion) forces. We show that the functional vdW-DF2 gives a potential-energy curve, potential-well energy levels, and difference in lateral corrugation promisingly close to the results obtained by resonant elastic backscattering-diffraction experiments. The backscattering barrier is found selective for choice of exchange-functional approximation. Further, the DFT-D3 and TS-vdW corrections to traditional DFT formulations are also benchmarked, and deviations are analyzed.Comment: 15 pages, 9 figure

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

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

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

Impact of Locally Suppressed Wave sources on helioseismic travel times

Wave travel-time shifts in the vicinity of sunspots are typically interpreted as arising predominantly from magnetic fields, flows, and local changes in sound speed. We show here that the suppression of granulation related wave sources in a sunspot can also contribute significantly to these travel-time shifts, and in some cases, an asymmetry between in and outgoing wave travel times. The tight connection between the physical interpretation of travel times and source-distribution homogeneity is confirmed. Statistically significant travel-time shifts are recovered upon numerically simulating wave propagation in the presence of a localized decrease in source strength. We also demonstrate that these time shifts are relatively sensitive to the modal damping rates; thus we are only able to place bounds on the magnitude of this effect. We see a systematic reduction of 10-15 seconds in $p$-mode mean travel times at short distances ($\sim 6.2$ Mm) that could be misinterpreted as arising from a shallow (thickness of 1.5 Mm) increase ($\sim$ 4%) in the sound speed. At larger travel distances ($\sim 24$ Mm) a 6-13 s difference between the ingoing and outgoing wave travel times is observed; this could mistakenly be interpreted as being caused by flows.Comment: Revised version. Submitted to Ap