Quantum fluid-dynamics from density functional theory

A partial differential eigenvalue equation for the density displacement fields associated with electronic excitations is derived in the framework of density functional theory. Our quantum fluid-dynamical approach is based on a variational principle and the Kohn-Sham ground-state energy functional, using only the occupied Kohn-Sham orbitals. It allows for an intuitive interpretation of electronic excitations in terms of intrinsic local currents that obey a continuity equation. We demonstrate the capabilities of this non-empirical approach by calculating the photoabsorption spectra of small sodium clusters. The quantitative agreement between theoretical and experimental spectra shows that even for the smallest clusters, the resonances observed experimentally at low temperatures can be interpreted in terms of density vibrations.Comment: RevTeX file with 2 figures. Update on April 17 2001: Typos corrected, references updated, larger axes labels on Fig. 1. Accepted for publication in Phys. Rev.

Proximity Effect, Andreev Reflections, and Charge Transport in Mesoscopic Superconducting-Semiconducting Heterostructures

In the quasi-twodimensional (Q2D) electron gas of an InAs channel between an AlSb substrate and superconducting Niobium layers the proximity effect induces a pair potential so that a Q2D mesoscopic superconducting-normal-superconducting (SNS) junction forms in the channel. The pair potential is calculated with quasiclassical Green's functions in the clean limit. For such a junction alternating Josephson currents and current-voltage characteristics (CVCs) are computed, using the non-equilibrium quasiparticle wavefunctions which solve the time-dependent Bogoliubov-de Gennes Equations. The CVCs exhibit features found experimentally by the Kroemer group: A steep rise of the current at small voltages ("foot") changes at a "corner current" to a much slower increase of current with higher voltages, and the zero-bias differential resistance increases with temperature. Phase-coherent multiple Andreev reflections and the associated Cooper pair transfers are the physical mechanisms responsible for the oscillating Josephson currents and the CVCs. Additional experimental findings not reproduced by the theory require model improvements, especially a consideration of the external current leads which should give rise to hybrid quasiparticle/collective mode excitations.Comment: 8 pages, 4 figures (consisting of 5 .ps-files), added referenc

Collectivity in the optical response of small metal clusters

The question whether the linear absorption spectra of metal clusters can be interpreted as density oscillations (collective ``plasmons'') or can only be understood as transitions between distinct molecular states is still a matter of debate for clusters with only a few electrons. We calculate the photoabsorption spectra of Na2 and Na5+ comparing two different methods: quantum fluid-dynamics and time-dependent density functional theory. The changes in the electronic structure associated with particular excitations are visualized in ``snapshots'' via transition densities. Our analysis shows that even for the smallest clusters, the observed excitations can be interpreted as intuitively understandable density oscillations. For Na5+, the importance of self-interaction corrections to the adiabatic local density approximation is demonstrated.Comment: 6 pages, 3 figures. To appear in special issue of Applied Physics B, "Optical properties of Nanoparticles

In Silico Genome-Scale Reconstruction and Validation of the Staphylococcus aureus Metabolic Network

A genome-scale metabolic model of the Gram-positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information. The model comprises 774 metabolic processes representing approximately 23% of all protein-coding regions. The model was extensively validated against experimental observations and it correctly predicted main physiological properties of the wild-type strain, such as aerobic and anaerobic respiration and fermentation. Due to the frequent involvement of S. aureus in hospital-acquired bacterial infections combined with its increasing antibiotic resistance, we also investigated the clinically relevant phenotype of small colony variants and found that the model predictions agreed with recent findings of proteome analyses. This indicates that the model is useful in assisting future experiments to elucidate the interrelationship of bacterial metabolism and resistance. To help directing future studies for novel chemotherapeutic targets, we conducted a large-scale in silico gene deletion study that identified 158 essential intracellular reactions. A more detailed analysis showed that the biosynthesis of glycans and lipids is rather rigid with respect to circumventing gene deletions, which should make these areas particularly interesting for antibiotic development. The combination of this stoichiometric model with transcriptomic and proteomic data should allow a new quality in the analysis of clinically relevant organisms and a more rationalized system-level search for novel drug targets.

Piecewise linearity in the GWGW approximation for accurate quasiparticle energy predictions

We identify the deviation from the straight line error (DSLE) -- i.e., the spurious non-linearity of the total energy as a function of fractional particle number -- as the main source for the discrepancy between experimental vertical ionization energies and theoretical quasiparticle energies, as obtained from the $GW$ and $GW$+SOSEX approximations to many-body perturbation theory (MBPT). For self-consistent calculations, we show that $GW$ suffers from a small DSLE. Conversely, for perturbative $G_0W_0$ and $G_0W_0$+SOSEX calculations the DSLE depends on the starting point. We exploit this starting-point dependence to reduce (or completely eliminate) the DSLE. We find that the agreement with experiment increases as the DSLE reduces. DSLE-minimized schemes, thus, emerge as promising avenues for future developments in MBPT

On the challenge to improve the density response with unusual gradient approximations

Certain excitations, especially ones of long-range charge transfer character, are poorly described by time-dependent density functional theory (TDDFT) when typical (semi-)local functionals are used. A proper description of these excitations would require an exchange-correlation response differing substantially from the usual (semi-)local one. It has recently been shown that functionals of the generalized gradient approximation (GGA) type can yield unusual potentials, mimicking features of the exact exchange derivative discontinuity and showing divergences on orbital nodal surfaces. We here investigate whether these unusual potential properties translate into beneficial response properties. Using the Sternheimer formalism we closely investigate the response obtained with the 2013 exchange approximation by Armiento and K\"ummel (AK13) and the 1988 exchange approximation by Becke (B88), both of which show divergences on orbital nodal planes. Numerical calculations for Na2 as well as analytical and numerical calculations for the hydrogen atom show that the response of AK13 behaves qualitatively different from usual semi local functionals. However, the AK13 functional leads to fundamental instabilities in the asymptotic region that prevent its practical application in TDDFT. Our findings may help the development of future improved functionals, and corroborate that the frequency-dependent Sternheimer formalism is excellently suited for running and analyzing TDDFT calculations

Static Electric Dipole Polarizabilities of Na Clusters

The static electric dipole polarizability of $\mathrm{Na_N}$ clusters with even N has been calculated in a collective, axially averaged and a three-dimensional, finite-field approach for $2\le N \le 20$, including the ionic structure of the clusters. The validity of a collective model for the static response of small systems is demonstrated. Our density functional calculations verify the trends and fine structure seen in a recent experiment. A pseudopotential that reproduces the experimental bulk bond length and atomic energy levels leads to a substantial increase in the calculated polarizabilities, in better agreement with experiment. We relate remaining differences in the magnitude of the theoretical and experimental polarizabilities to the finite temperature present in the experiments.Comment: 7 pages, 3 figures, accepted for publication in the European Physical Journal