Showing papers by "Vienna University of Technology published in 1999"

From ultrasoft pseudopotentials to the projector augmented-wave method

Abstract: The formal relationship between ultrasoft (US) Vanderbilt-type pseudopotentials and Bl\"ochl's projector augmented wave (PAW) method is derived. It is shown that the total energy functional for US pseudopotentials can be obtained by linearization of two terms in a slightly modified PAW total energy functional. The Hamilton operator, the forces, and the stress tensor are derived for this modified PAW functional. A simple way to implement the PAW method in existing plane-wave codes supporting US pseudopotentials is pointed out. In addition, critical tests are presented to compare the accuracy and efficiency of the PAW and the US pseudopotential method with relaxed core all electron methods. These tests include small molecules $({\mathrm{H}}_{2}{,\mathrm{}\mathrm{H}}_{2}{\mathrm{O},\mathrm{}\mathrm{Li}}_{2}{,\mathrm{}\mathrm{N}}_{2}{,\mathrm{}\mathrm{F}}_{2}{,\mathrm{}\mathrm{BF}}_{3}{,\mathrm{}\mathrm{SiF}}_{4})$ and several bulk systems (diamond, Si, V, Li, Ca, ${\mathrm{CaF}}_{2},$ Fe, Co, Ni). Particular attention is paid to the bulk properties and magnetic energies of Fe, Co, and Ni.

Scaling issues in snow hydrology

Abstract: The concept of scale can be used to quantify characteristic lengths of (a) a natural process (such as the correlation length of the spatial snow water equivalent (SWE) variability); (b) a measurement (such as the size of a snow density sample or the footprint of a satellite sensor), and (c) a model (such as the grid size of a distributed snow model). The different types of scales are denoted as process scale, measurement scale and model scale, respectively. Interpolations, extrapolations, aggregations, and disaggregations are viewed as a change in model scale and/or measurement scale. In a first step we examine, in a linear stochastic analysis, the effect of measurement scale and model scale on the data and the model predictions. It is shown that the ratio of the measurement scale and the process scale, and the ratio of the model scale and the process scale are the driving parameters for the scale effects. These scale effects generally cause biases in the variances and spatial correlation lengths of satellite images, field measurements, and simulation results of snow models. It is shown, by example, how these biases can be identified and corrected by regularization methods, At the core of these analyses is the variogram. For the case of snow cover patterns, it is shown that it may be difficult to infer the true snow cover variability from the variograms, particularly when they span many orders of magnitude. In a second step we examine distributed snow models which are a non-linear deterministic approach to changing the scale. Unlike in the linear case, in these models a change of scale may also bias the mean over a catchment of snow-related variables such as SWE There are a number of fundamental scaling issues with distributed models which include subgrid variability, the question of an optimum element size, and parameter identifiability. We give methods for estimating subgrid variability. We suggest that, in general, an optimum element size may not exist and that the model element scale may in practice be dictated by data availability and the required resolution of the predictions. The scale effects in distributed non-linear models can be related to the linear stochastic case which allows us to generalize the applicability of regularization methods. While most of the paper focuses on physical snow processes, similar conclusions apply and similar methods are applicable to chemical and biological processes.

A comparison of structural CSP decomposition methods

Abstract: We compare tractable classes of constraint satisfaction problems (CSPs). We first give a uniform presentation of the major structural CSP decomposition methods. We then introduce a new class of tractable CSPs based on the concept of hypertree decomposition recently developed in Database Theory. We introduce a framework for comparing parametric decomposition-based methods according to tractability criteria and compare the most relevant methods. We show that the method of hypertree decomposition dominates the others in the case of general (nonbinary) CSPs.

Hypertree decompositions and tractable queries

Abstract: 1 A preliminary version of this paper appeared in the ‘‘Proceedings of the Eighteenth ACM Symposium on Principles of Database Systems (PODS’99),’’ pp. 21–32, Philadelphia, May 1999. Research supported by FWF (Austrian Science Funds) under the Project Z29-INF. Part of the work of Francesco Scarcello has been carried out while visiting the Technische Universitat Wien. Part of the work of Nicola Leone has been carried out while he was with the Technische Universitat Wien. Georg Gottlob

Ab initio calculation of the lattice dynamics and phase diagram of boron nitride

Abstract: We present a detailed study of the lattice dynamics and of the phase stability of cubic zincblende (c-BN) and hexagonal (h-BN) boron nitrides. The phonon-dispersion relations at different densities are calculated using a first-principles force-constant method. The calculated eigenfrequencies and phonon Gr\"uneisen parameters are in good agreement with experimental findings. From the electronic and vibrational energies as a function of volume we calculate the phase $(p,T)$ diagram of boron nitride in a quasiharmonic approximation. At low temperature c-BN is the stable modification; the c-BN/h-BN coexistence line intersects the temperature axis at 1440 K. In experiments this temperature lies between 1200 and 1800 K. Anharmonic corrections improve the agreement between the calculation and experiment for high pressure and temperature.

Using transparent props for interaction with the virtual table

Abstract: The Virtual Table presents stereoscopic graphics to a user in a workbench-like setting This paper reports on a user interface and new interaction techniques for the Virtual Table based on transparent props—a tracked hand-held pen and a pad These props, but in particular the pad, are augmented with 3D graphics from the Virtual Table’s display This configuration creates a very powerful and flexible interface for two-handed interaction that can be applied to other back-projected stereographic displays as well: the pad can serve as a palette for tools and controls as well as a window-like see-through interface, a plane-shaped and throughthe-plane tool, supporting a variety of new interaction techniques

Polymorphism in silica studied in the local density and generalized-gradient approximations

Abstract: The crystal structures of a large number of silica polytypes (- and -quartz, - and -cristobalite, -tridymite, keatite, coesite and stishovite) have been studied using density functional theory, both in the local density approximation and including generalized-gradient corrections to the exchange-correlation functional. All crystal structures have been optimized by minimizing the total energy with respect to all lattice parameters and to the atomic coordinates within the unit cell (up to 40 structural parameters in the case of coesite). The transitions in quartz and cristobalite have been studied in detail, including different variants proposed for the structure of -cristobalite. The tetragonal (I2d) and simple cubic (P213) structures are found to be energetically almost degenerate near the equilibrium volume. On volume expansion both structures converge towards the idealized highly symmetric Fd3m structure. A similar continuous transition from a more compact orthorhombic (C2221) to a highly symmetric hexagonal (P63/mmc) variant is also proposed for -tridymite. For coesite two monoclinic variants (with C2/c and P21/c space-group symmetries, respectively) have been examined and found to be energetically degenerate to within 1 meV per SiO2 unit. It is shown that within the local density approximation (LDA) the equilibrium atomic volume of all polytypes is predicted with an accuracy better than one per cent. The LDA also leads to excellent structural predictions and to accurate values of the bulk modulus. Corrections in the framework of the generalized-gradient approximation (GGA) lead to substantially larger equilibrium volumes, although at fixed volume the LDA and GGA lead to identical crystal structures. The increased volume also leads to less accurate structural parameters. However, we find that gradient corrections are essential for achieving accurate structural energy differences between the tetrahedrally coordinated phases found at larger atomic volumes (all polytypes except stishovite) and the octahedrally coordinated high-pressure polymorphs (stishovite and post-stishovite phases).

Electronic structure of 3d-transition-metal oxides: on-site Coulomb repulsion versus covalency

Abstract: We have performed photoemission and inverse photoemission experiments on a series of 3d-transition-metal oxides with formal ionic configuration from to . The photoemission core-level spectra are analysed in terms of a simple cluster model leading to estimates for the charge-transfer energy , the Coulomb correlation energy , and the hybridization strength V. It is found that the ratio of the correlation energy to the hybridization energy significantly decreases from the late to the early transition metal oxides. This trend is attributed mostly to the increasing number of empty d states in the early transition metals which enhances the effective metal-ligand hybridization. We also compare the experimental valence band spectra with densities of states (DOS) from band-structure calculations. The rather good agreement between the theoretical DOS and the measured single-particle excitation spectra of the early 3d-transition-metal oxides as opposed to the failure of the one-electron description for most of the late transition metal oxides supports the results of the cluster model analysis.

Cohesive, structural, and electronic properties of fe-si compounds

Abstract: Phase stability, structural, and electronic properties of iron silicides in the ${\mathrm{Fe}}_{3}\mathrm{Si},$ FeSi, and ${\mathrm{FeSi}}_{2}$ compositions are investigated by first-principle density-functional calculations based on ultrasoft pseudopotentials and all-electron methods. Structural stabilization versus spin-polarization effects are discussed at the ${\mathrm{Fe}}_{3}\mathrm{Si}$ composition, while for \ensuremath{\epsilon}-FeSi and $\ensuremath{\beta}\ensuremath{-}{\mathrm{FeSi}}_{2}$ we investigate their structural properties and the corresponding semiconducting band properties. All the computed results are analyzed and compared to available experimental data. The stability of the bulk phases, the lattice parameters, the cohesive energies and magnetic properties are found to be in good agreement with experiment when using the generalized gradient approximations for the exchange-correlation functional. Density-functional calculations are unable to account for the small bulk modulus of $\ensuremath{\epsilon}\ensuremath{-}\mathrm{FeSi}$ despite that the computed lattice constant and internal atomic positions coincide with the experimental results. Both full-potential and ultrasoft-pseudopotential methods confirm for $\ensuremath{\beta}\ensuremath{-}{\mathrm{FeSi}}_{2}$ the indirect nature of the fundamental gap, which is attributed to a transition between Y to 0.6\ifmmode\times\else\texttimes\fi{}\ensuremath{\Lambda} being 30% smaller than the experimental gap. Ultrasoft pseudopotential calculations of Fe-Si magnetic phases and of various nonequilibrium metallic phases at the FeSi and ${\mathrm{FeSi}}_{2}$ composition are presented. These calculations provide ab initio information concerning the stabilization of metallic pseudomorphic phases via high pressures or epitaxy.

Light Propagation in Field-Ionizing Media: Extreme Nonlinear Optics

Abstract: A novel equation for light propagation in underdense field-ionizing media is derived by extending concepts of nonlinear optics into the strong-field domain. The equation is first order in the propagation coordinate and is valid for arbitrarily short pulse durations. Solutions of the first-order wave equation are found to be in excellent agreement with solutions of the scalar wave equation. Furthermore, the polarization response of a field-ionizing medium is derived from semiclassical considerations. The polarization reveals, in agreement with experiments, a previously unrecognized contribution that is shown to significantly affect the absorption loss in the presence of ionization.

Entropy of the QCD Plasma

Abstract: Self-consistent approximations in terms of fully dressed propagators provide a simple expression for the entropy of an ultrarelativistic plasma, which isolates the contribution of the elementary excitations as a leading contribution. Further approximations, whose validity is checked on a soluble model involving a scalar field, allow us to calculate the entropy of the QCD plasma. We obtain an accurate description of lattice data for purely gluonic QCD, down to temperatures of about twice the transition temperature.

Expression of two major chitinase genes of Trichoderma atroviride (T. harzianum P1) is triggered by different regulatory signals.

Abstract: Regulation of the expression of the two major chitinase genes, ech42 (encoding the CHIT42 endochitinase) and nag1 (encoding the CHIT73 N-acetyl-β-d-glucosaminidase), of the chitinolytic system of the mycoparasitic biocontrol fungus Trichoderma atroviride (= Trichoderma harzianum P1) was investigated by using a reporter system based on the Aspergillus niger glucose oxidase. Strains harboring fusions of the ech42 or nag1 5′ upstream noncoding sequences with the A. niger goxA gene displayed a glucose oxidase activity pattern that was consistent under various conditions with expression of the native ech42 and nag1 genes, as assayed by Northern analysis. The expression product of goxA in the mutants was completely secreted into the medium, detectable on Western blots, and quantifiable by enzyme-linked immunosorbent assay. nag1 gene expression was triggered during growth on fungal (Botrytis cinerea) cell walls and on the chitin degradation product N-acetylglucosamine. N-Acetylglucosamine, di-N-acetylchitobiose, or tri-N-acetylchitotriose also induced nag1 gene expression when added to mycelia pregrown on different carbon sources. ech42 expression was also observed during growth on fungal cell walls but, in contrast, was not triggered by addition of chitooligomers to pregrown mycelia. Significant ech42 expression was observed after prolonged carbon starvation, independent of the use of glucose or glycerol as a carbon source, suggesting that relief of carbon catabolite repression was not involved in induction during starvation. In addition, ech42 gene transcription was triggered by physiological stress, such as low temperature, high osmotic pressure, or the addition of ethanol. Four copies of a putative stress response element (CCCCT) were found in the ech42 promoter.

First-principles calculations to describe zirconia pseudopolymorphs

Abstract: The structural and electronic properties of four different polytypes of zirconia $({\mathrm{ZrO}}_{2})$ are studied using ab initio total-energy calculations. The calculations are performed in the framework of density-functional theory (DFT) and pseudopotential theory. We compare results obtained within the LDA (local-density approximation) and including generalized gradient corrections (GGC's) in the Perdew-Wang and Perdew-Becke formalisms. Within this approach, we are able to predict the correct monoclinic ground state at low pressure and temperature. We show that GGC's are necessary to correctly describe the high-pressure orthorhombic structure of zirconia. The tetragonal-to-cubic phase transition was studied assuming a martensitic-displacive mechanism following the approach of Jansen [Phys. Rev. B 43, 7267 (1991)].

Scientific Communication--A Vanity Fair?

Abstract: Success in science is rewarded with attention. Citation represents a fee paid through transfer of some of the attention earned by the citing author to the cited author. An economy of attention links the collectively most rewarding allocation of attention with the maximum value of the attention its holder can earn. In terms of the resulting collective efficiency it attains, the intelligence of science as a whole surpasses that which individual scientists can attain in isolation.

A state‐space approach to estimate and test multifactor cox‐ingersoll‐ross models of the term structure

Abstract: The objective of this paper is to estimate and test multifactor versions of the Cox-Ingersoll-Ross (CIR) model of the nominal term structure of interest rates. The proposed state-space approach integrates time series and cross-sectional aspects of the CIR model, is consistent with the underlying economic model, and can use information from all available points of the term structure. We recover estimates of the underlying factors that are consistent with the assumptions about the stochastic processes and compare them with factors obtained from standard factor analysis. We perform thorough diagnostic checking and thereby provide new evidence regarding conclusions about the adequacy of the CIR model. We present empirical results for U.S. Treasury market data. Although the specification of multifactor CIR models is sufficiently flexible for the shape of the term structure, we find strong evidence against the adequacy of the CIR model.

The GATA factor AreA is essential for chromatin remodelling in a eukaryotic bidirectional promoter

Abstract: The linked niiA and niaD genes of Aspergillus nidulans are transcribed divergently. The expression of these genes is subject to a dual control system. They are induced by nitrate and repressed by ammonium. AreA mediates derepression in the absence of ammonium and NirA supposedly mediates nitrate induction. Out of 10 GATA sites, a central cluster (sites 5–8) is responsible for ∼80% of the transcriptional activity of the promoter on both genes. We show occupancy in vivo of site 5 by the AreA protein, even under conditions of repression. Sites 5–8 are situated in a pre‐set nucleosome‐free region. Under conditions of expression, a drastic nucleosomal rearrangement takes place and the positioning of at least five nucleosomes flanking the central region is lost. Remodelling is strictly dependent on the presence of an active areA gene product, and independent from the NirA‐specific and essential transcription factor. Thus, nucleosome remodelling is independent from the transcriptional activation of the niiA–niaD promoter. The results presented cast doubts on the role of NirA as the unique transducer of the nitrate induction signal. We demonstrate, for the first time in vivo , that a GATA factor is involved directly in chromatin remodelling.

A molecular emission detector on a chip employing a direct current microplasma

Abstract: An optical emission detector is presented realized on a glass chip. The device employs a direct current helium plasma for molecular fragmentation and excitation. The plasma was generated in a chamber of 50 nL volume at a typical operating pressure of 130 Torr. The plasma stability and the current/voltage/pressure behavior were investigated. Comparison with the theoretical behavior of downscaled plasma devices shows that the properties of the microplasma do not fundamentally differ from those of larger plasmas. Using the plasma as an excitation source, methane could be detected with a detection limit of 3 × 10-12 g/s (600 ppm), by observing the emission of the CH radical. The lifetime of the present device was limited to ∼2 h by sputtering of the cathode material. When lifetime is increased, the device looks to be a promising detector for on-chip integration with gas chromatography.

Linking Sediment Biofilms, Hydrodynamics, and River Bed Clogging: Evidence from a Large River.

Abstract: We investigated possible effects of the hydrodynamics at the water/sediment interface on river bed biofilms within the reservoir Freudenau (Vienna, Austria) of the Danube River during the period 1996/97. Two study sites (OBB and SSF) that differed in the magnitude of surface/subsurface water exchange were selected and intersite comparisons revealed higher organic matter, bacterial cell numbers, and esterase activity in SSF with lower horizontal outflow. Concentrations of colloidal carbohydrates and uronic acids were unaffected by hydrodynamics. The relative contribution of uronic acids to bulk colloidal carbohydrates was higher in the low-flow site SSF. The distribution patterns of this relative contribution generally matched the subsurface flow pattern. Shortly after impoundment in March 1996 and along with decreased surface flow velocity, maximal biofilm carbohydrate exopolymers concurred with minimal esterase activity in OBB. We hypothesize that this inverse relationship is due to increased diffusional resistance within the exopolymer biofilm matrix that reduces mass transfer and hydrolytic activity. These results, to our knowledge, are the first evidence for microbial participation in the clogging of a large river bed. Biofilm-associated organic carbon increased significantly by a factor of ∼3.3 to 4.4 with progressive clogging as determined by the sediment leakage coefficient, which increased ∼3.8 times. Concomitantly, with ongoing clogging, esterase activity exhibited increasingly higher values at the interface relatively to deeper sediment layers, which translates into steeper depth gradients. Furthermore, minimal inflow from the surface water into the river bed along with steepest esterase gradients concurred with a senescent benthic algal bloom. This suggests an important role for algae in clogging. Either algae obstruct voids mechanically, or their exudates fuel heterotrophic bacteria that in turn are involved in clogging processes. However, our data do not allow unequivocal differentiation between biogenic and physical clogging mechanisms.