Linear density response function in the projector-augmented wave method: Applications to solids, surfaces, and interfaces

We present an implementation of the linear density response function within the projector-augmented wave (PAW) method with applications to the linear optical and dielectric properties of both solids, surfaces, and interfaces. The response function is represented in plane waves while the single-particle eigenstates can be expanded on a real space grid or in atomic orbital basis for increased efficiency. The exchange-correlation kernel is treated at the level of the adiabatic local density approximation (ALDA) and crystal local field effects are included. The calculated static and dynamical dielectric functions of Si, C, SiC, AlP and GaAs compare well with previous calculations. While optical properties of semiconductors, in particular excitonic effects, are generally not well described by ALDA, we obtain excellent agreement with experiments for the surface loss function of the Mg(0001) surface with plasmon energies deviating by less than 0.2 eV. Finally, we apply the method to study the influence of substrates on the plasmon excitations in graphene. On SiC(0001), the long wavelength $\pi$ plasmons are significantly damped although their energies remain almost unaltered. On Al(111) the $\pi$ plasmon is completely quenched due to the coupling to the metal surface plasmon.Comment: 11 pages, 8 figures, articl

Density functional study of the adsorption and van der Waals binding of aromatic and conjugated compounds on the basal plane of MoS2

Accurate calculations of adsorption energies of cyclic molecules are of key importance in investigations of, e.g., hydrodesulfurization (HDS) catalysis. The present density functional theory (DFT) study of a set of important reactants, products, and inhibitors in HDS catalysis demonstrates that van der Waals interactions are essential for binding energies on MoS2 surfaces and that DFT with a recently developed exchange-correlation functional (vdW-DF) accurately calculates the van der Waals energy. Values are calculated for the adsorption energies of butadiene, thiophene, benzothiophene, pyridine, quinoline, benzene, and naphthalene on the basal plane of MoS2, showing good agreement with available experimental data, and the equilibrium geometry is found as flat at a separation of about 3.5 \uc5 for all studied molecules. This adsorption is found to be due to mainly van der Waals interactions. Furthermore, the manifold of adsorption-energy values allows trend analyses to be made, and they are found to have a linear correlation with the number of main atoms. \ua9 2009 American Institute of Physics

Efficient first principles simulation of electron scattering factors for transmission electron microscopy

Electron microscopy is a powerful tool for studying the properties of materials down to their atomic structure. In many cases, the quantitative interpretation of images requires simulations based on atomistic structure models. These typically use the independent atom approximation that neglects bonding effects, which may, however, be measurable and of physical interest. Since all electrons and the nuclear cores contribute to the scattering potential, simulations that go beyond this approximation have relied on computationally highly demanding all-electron calculations. Here, we describe a new method to generate ab initio electrostatic potentials when describing the core electrons by projector functions. Combined with an interface to quantitative image simulations, this implementation enables an easy and fast means to model electron microscopy images. We compare simulated transmission electron microscopy images and diffraction patterns to experimental data, showing an accuracy equivalent to earlier all-electron calculations at a much lower computational cost.Comment: 10 pages, 5 figures, 2 table

A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi

<p>Abstract</p> <p>Background</p> <p>Many secondary metabolites produced by filamentous fungi have potent biological activities, to which the producer organism must be resistant. An example of pharmaceutical interest is mycophenolic acid (MPA), an immunosuppressant molecule produced by several <it>Penicillium </it>species. The target of MPA is inosine-5'-monophosphate dehydrogenase (IMPDH), which catalyses the rate limiting step in the synthesis of guanine nucleotides. The recent discovery of the MPA biosynthetic gene cluster from <it>Penicillium brevicompactum </it>revealed an extra copy of the IMPDH-encoding gene (<it>mpaF</it>) embedded within the cluster. This finding suggests that the key component of MPA self resistance is likely based on the IMPDH encoded by <it>mpaF</it>.</p> <p>Results</p> <p>In accordance with our hypothesis, heterologous expression of <it>mpaF </it>dramatically increased MPA resistance in a model fungus, <it>Aspergillus nidulans</it>, which does not produce MPA. The growth of an <it>A. nidulans </it>strain expressing <it>mpaF </it>was only marginally affected by MPA at concentrations as high as 200 μg/ml. To further substantiate the role of <it>mpaF </it>in MPA resistance, we searched for <it>mpaF </it>orthologs in six MPA producer/non-producer strains from <it>Penicillium </it>subgenus <it>Penicillium</it>. All six strains were found to hold two copies of IMPDH. A cladistic analysis based on the corresponding cDNA sequences revealed a novel group constituting <it>mpaF </it>homologs. Interestingly, a conserved tyrosine residue in the original class of IMPDHs is replaced by a phenylalanine residue in the new IMPDH class.</p> <p>Conclusions</p> <p>We identified a novel variant of the IMPDH-encoding gene in six different strains from <it>Penicillium </it>subgenus <it>Penicillium</it>. The novel IMPDH variant from MPA producer <it>P. brevicompactum </it>was shown to confer a high degree of MPA resistance when expressed in a non-producer fungus. Our study provides a basis for understanding the molecular mechanism of MPA resistance and has relevance for biotechnological and pharmaceutical applications.</p

Lack of cardioprotection from subcutaneously and preischemic administered Liraglutide in a closed chest porcine ischemia reperfusion model

<p>Abstract</p> <p>Background</p> <p>Glucagon-like peptide 1 (GLP1) analogues are promising new treatment options for patients with type 2 diabetes, but may have both potentially beneficial and harmful cardiovascular effects. This may also be the case for the analogues of GLP1 for clinical use. The present study examined the effect of treatment with Liraglutide, a long-acting GLP1 analogue, on myocardial ischemia and reperfusion in a porcine model.</p> <p>Methods</p> <p>Danish Landrace Pigs (70–80 kg) were randomly assigned to Liraglutide (10 μg/kg) or control treatment given daily for three days before ischemia-reperfusion. Ischemia was induced by balloon occlusion of the left anterior descending artery for 40 minutes followed by 2.5 hours of reperfusion. The primary outcome parameter was infarct size in relation to the ischemic region at risk. Secondary endpoints were the hemodynamic parameters mean pulmonary pressure, cardiac output, pulmonary capillary wedge pressure as measured by a Swan-Ganz catheter as well as arterial pressure and heart rate.</p> <p>Results</p> <p>The infarct size in relation to ischemic risk region in the control versus the Liraglutide group did not differ significantly: 0.46 ± 0.14 and 0.54 ± 0.12) (mean and standard deviation (SD), p = 0.21). Heart rate was significantly higher in the Liraglutide group during the experiment, while the other hemodynamic parameters did not differ significantly.</p> <p>Conclusion</p> <p>Liraglutide has a neutral effect on myocardial infarct size in a porcine ischemia-reperfusion model.</p

Ab initio van der Waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations using van der Waals (vdW) density-functional theory, i.e. using the new exchange-correlation functionals optPBE-vdW and vdW-DF2. Inclusion of the more isotropic vdW interactions counteracts highly directional hydrogen-bonds, which are enhanced by standard functionals. This brings about a softening of the microscopic structure of water, as seen from the broadening of angular distribution functions and, in particular, from the much lower and broader first peak in the oxygen-oxygen pair-correlation function (PCF), indicating loss of structure in the outer solvation shells. In combination with softer non-local correlation terms, as in the new parameterization of vdW-DF, inclusion of vdW interactions is shown to shift the balance of resulting structures from open tetrahedral to more close-packed. The resulting O-O PCF shows some resemblance with experiment for high-density water (A. K. Soper and M. A. Ricci, Phys. Rev. Lett., 84:2881, 2000), but not directly with experiment for ambient water. However, an O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from experiment on low-density liquid water reproduces near-quantitatively the experimental O-O PCF for ambient water, indicating consistency with a two-liquid model with fluctuations between high- and low-density regions

Adaptive evolution of drug targets in producer and non-producer organisms

Mycophenolic acid (MPA) is an immunosuppressive drug produced by several fungi in Penicillium subgenus Penicillium. This toxic metabolite is an inhibitor of IMP dehydrogenase (IMPDH). The MPA biosynthetic cluster of P. brevicompactum contains a gene encoding a B-type IMPDH, IMPDH-B, which confers MPA-resistance. Surprisingly, all members of subgenus Penicillium contain genes encoding IMPDHs of both the A and B type, regardless of their ability to produce MPA. Duplication of the IMPDH gene occurred prior to and independent of the acquisition of the MPA biosynthetic cluster. Both P. brevicompactum IMPDHs are MPA-resistant while the IMPDHs from a nonproducer are MPA-sensitive. Resistance comes with a catalytic cost: while P. brevicompactum IMPDH-B is >1000-fold more resistant to MPA than a typical eukaryotic IMPDH, its value of k(cat)/K(m) is 0.5% of “normal”. Curiously, IMPDH-B of Penicillium chrysogenum, which does not produce MPA, is also a very poor enzyme. The MPA binding site is completely conserved among sensitive and resistant IMPDHs. Mutational analysis shows that the C-terminal segment is a major structural determinant of resistance. These observations suggest that the duplication of the IMPDH gene in Pencillium subgenus Penicillium was permissive for MPA production and that MPA production created a selective pressure on IMPDH evolution. Perhaps MPA production rescued IMPDH-B from deleterious genetic drift