Dynamical properties of Au from tight-binding molecular-dynamics simulations

We studied the dynamical properties of Au using our previously developed tight-binding method. Phonon-dispersion and density-of-states curves at T=0 K were determined by computing the dynamical-matrix using a supercell approach. In addition, we performed molecular-dynamics simulations at various temperatures to obtain the temperature dependence of the lattice constant and of the atomic mean-square-displacement, as well as the phonon density-of-states and phonon-dispersion curves at finite temperature. We further tested the transferability of the model to different atomic environments by simulating liquid gold. Whenever possible we compared these results to experimental values.Comment: 7 pages, 9 encapsulated Postscript figures, submitted to Physical Review

Tight-binding study of high-pressure phase transitions in titanium: alpha to omega and beyond

We use a tight-binding total energy method, with parameters determined from a fit to first-principles calculations, to examine the newly discovered gamma phase of titanium. Our parameters were adjusted to accurately describe the alpha Ti-omega Ti phase transition, which is misplaced by density functional calculations. We find a transition from omega Ti to gamma Ti at 102 GPa, in good agreement with the experimental value of 116 GPa. Our results suggest that current density functional calculations will not reproduce the omega Ti-gamma Ti phase transition, but will instead predict a transition from omega Ti to the bcc beta Ti phase.Comment: 3 encapsulated Postscript figures, submitted to Phyical Review Letter

Long-Distance Wind-Dispersal of Spores in a Fungal Plant Pathogen: Estimation of Anisotropic Dispersal Kernels from an Extensive Field Experiment

Given its biological significance, determining the dispersal kernel (i.e., the distribution of dispersal distances) of spore-producing pathogens is essential. Here, we report two field experiments designed to measure disease gradients caused by sexually- and asexually-produced spores of the wind-dispersed banana plant fungus Mycosphaerella fijiensis. Gradients were measured during a single generation and over 272 traps installed up to 1000 m along eight directions radiating from a traceable source of inoculum composed of fungicide-resistant strains. We adjusted several kernels differing in the shape of their tail and tested for two types of anisotropy. Contrasting dispersal kernels were observed between the two types of spores. For sexual spores (ascospores), we characterized both a steep gradient in the first few metres in all directions and rare long-distance dispersal (LDD) events up to 1000 m from the source in two directions. A heavy-tailed kernel best fitted the disease gradient. Although ascospores distributed evenly in all directions, average dispersal distance was greater in two different directions without obvious correlation with wind patterns. For asexual spores (conidia), few dispersal events occurred outside of the source plot. A gradient up to 12.5 m from the source was observed in one direction only. Accordingly, a thin-tailed kernel best fitted the disease gradient, and anisotropy in both density and distance was correlated with averaged daily wind gust. We discuss the validity of our results as well as their implications in terms of disease diffusion and management strategy

Stacking-fault energies for Ag, Cu, and Ni from empirical tight-binding potentials

The intrinsic stacking-fault energies and free energies for Ag, Cu, and Ni are derived from molecular-dynamics simulations using the empirical tight-binding potentials of Cleri and Rosato [Phys. Rev. B 48, 22 (1993)]. While the results show significant deviations from experimental data, the general trend between the elements remains correct. This allows to use the potentials for qualitative comparisons between metals with high and low stacking-fault energies. Moreover, the effect of stacking faults on the local vibrational properties near the fault is examined. It turns out that the stacking fault has the strongest effect on modes in the center of the transverse peak and its effect is localized in a region of approximately eight monolayers around the defect.Comment: 5 pages, 2 figures, accepted for publication in Phys. Rev.

Pressure Dependence of the Elastic Moduli in Aluminum Rich Al-Li Compounds

I have carried out numerical first principles calculations of the pressure dependence of the elastic moduli for several ordered structures in the Aluminum-Lithium system, specifically FCC Al, FCC and BCC Li, L1_2 Al_3Li, and an ordered FCC Al_7Li supercell. The calculations were performed using the full potential linear augmented plane wave method (LAPW) to calculate the total energy as a function of strain, after which the data was fit to a polynomial function of the strain to determine the modulus. A procedure for estimating the errors in this process is also given. The predicted equilibrium lattice parameters are slightly smaller than found experimentally, consistent with other LDA calculations. The computed elastic moduli are within approximately 10% of the experimentally measured moduli, provided the calculations are carried out at the experimental lattice constant. The LDA equilibrium shear modulus C11-C12 increases from 59.3 GPa in Al, to 76.0 GPa in Al_7Li, to 106.2 GPa in Al_3Li. The modulus C_44 increases from 38.4 GPa in Al to 46.1 GPa in Al_7Li, then falls to 40.7 GPa in Al_3Li. All of the calculated elastic moduli increase with pressure with the exception of BCC Li, which becomes elastically unstable at about 2 GPa, where C_11-C_12 vanishes.Comment: 17 pages (REVTEX) + 7 postscript figure

Molecular Biomarkers of Neovascular Age-Related Macular Degeneration With Incomplete Response to Anti-Vascular Endothelial Growth Factor Treatment.

The standard treatment for neovascular age-related macular degeneration (nAMD) consists of intravitreal anti-vascular endothelial growth factors (VEGF). However, for some patients, even maximal anti-VEGF treatment does not entirely suppress exudative activity. The goal of this study was to identify molecular biomarkers in nAMD with incomplete response to anti-VEGF treatment. Aqueous humor (AH) samples were collected from three groups of patients: 17 patients with nAMD responding incompletely to anti-VEGF (18 eyes), 17 patients affected by nAMD with normal treatment response (21 eyes), and 16 control patients without any retinopathy (16 eyes). Proteomic and multiplex analyses were performed on these samples. Proteomic analyses showed that nAMD patients with incomplete anti-VEGF response displayed an increased inflammatory response, complement activation, cytolysis, protein-lipid complex, and vasculature development pathways. Multiplex analyses revealed a significant increase of soluble vascular cell adhesion molecule-1 (sVCAM-1) [ p = 0.001], interleukin-6 (IL-6) [ p = 0.009], bioactive interleukin-12 (IL-12p40) [ p = 0.03], plasminogen activator inhibitor type 1 (PAI-1) [ p = 0.004], and hepatocyte growth factor (HGF) [ p = 0.004] levels in incomplete responders in comparison to normal responders. Interestingly, the same biomarkers showed a high intercorrelation with r2 values between 0.58 and 0.94. In addition, we confirmed by AlphaLISA the increase of sVCAM-1 [ p < 0.0001] and IL-6 [ p = 0.043] in the incomplete responder group. Incomplete responders in nAMD are associated with activated angiogenic and inflammatory pathways. The residual exudative activity of nAMD despite maximal anti-VEGF treatment may be related to both angiogenic and inflammatory responses requiring specific adjuvant therapy. Data are available via ProteomeXchange with identifier PXD02247

An Empirical Charge Transfer Potential with Correct Dissociation Limits

The empirical valence bond (EVB) method [J. Chem. Phys. 52, 1262 (1970)] has always embodied charge transfer processes. The mechanism of that behavior is examined here and recast for use as a new empirical potential energy surface for large-scale simulations. A two-state model is explored. The main features of the model are: (1) Explicit decomposition of the total system electron density is invoked; (2) The charge is defined through the density decomposition into constituent contributions; (3) The charge transfer behavior is controlled through the resonance energy matrix elements which cannot be ignored; and (4) A reference-state approach, similar in spirit to the EVB method, is used to define the resonance state energy contributions in terms of "knowable" quantities. With equal validity, the new potential energy can be expressed as a nonthermal ensemble average with a nonlinear but analytical charge dependence in the occupation number. Dissociation to neutral species for a gas-phase process is preserved. A variant of constrained search density functional theory is advocated as the preferred way to define an energy for a given charge.Comment: Submitted to J. Chem. Phys. 11/12/03. 14 pages, 8 figure

First-principles equation of state and phase stability for the Ni-Al system under high pressures

The equation of state (EOS) of alloys at high pressures is generalized with the cluster expansion method. It is shown that this provides a more accurate description. The low temperature EOSs of Ni-Al alloys on FCC and BCC lattices are obtained with density functional calculations, and the results are in good agreement with experiments. The merits of the generalized EOS model are confirmed by comparison with the mixing model. In addition, the FCC phase diagram of the Ni-Al system is calculated by cluster variation method (CVM) with both spin-polarized and non-spin-polarized effective cluster interactions (ECI). The influence of magnetic energy on the phase stability is analyzed. A long-standing discrepancy between ab initio formation enthalpies and experimental data is addressed by defining a better reference state. This aids both evaluation of an ab initio phase diagram and understanding the thermodynamic behaviors of alloys and compounds. For the first time the high-pressure behavior of order-disorder transition is investigated by ab initio calculations. It is found that order-disorder temperatures follow the Simon melting equation. This may be instructive for experimental and theoretical research on the effect of an order-disorder transition on shock Hugoniots.Comment: 27 pages, 12 figure

Immersed nano-sized Al dispersoids in an Al matrix; effects on the structural and mechanical properties by Molecular Dynamics simulations

We used molecular dynamics simulations based on a potential model in analogy to the Tight Binding scheme in the Second Moment Approximation to simulate the effects of aluminum icosahedral grains (dispersoids) on the structure and the mechanical properties of an aluminum matrix. First we validated our model by calculating several thermodynamic properties referring to the bulk Al case and we found good agreement with available experimental and theoretical data. Afterwards, we simulated Al systems containing Al clusters of various sizes. We found that the structure of the Al matrix is affected by the presence of the dispersoids resulting in well ordered domains of different symmetries that were identified using suitable Voronoi analysis. In addition, we found that the increase of the grain size has negative effect on the mechanical properties of the nanocomposite as manifested by the lowering of the calculated bulk moduli. The obtained results are in line with available experimental data.Comment: 15 pages, 8 figures. Submitted to J. Phys: Condens. Matte