Advanced capabilities for materials modelling with Quantum ESPRESSO.

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

The LVV Auger line shape of sulfur on copper studied by Auger photoelectron coincidence spectroscopy.

We have studied the line shapes of Cu(0 0 1)-p (2 × 2)S L2VV and L3VV Auger decay by means of Auger photoelectron coincidence spectroscopy. Measuring the LVV Auger spectrum in coincidence with S 2p1/2 and 2p3/2 photoelectrons respectively, we have been able to separate the two overlapping Auger spectra and determine their intrinsic line shapes. The two Auger transitions, though shifted in energy, display an identical line shape whose main features can be qualitatively understood considering a single particle approximation but are better described within a Cini-Sawatzky (CS) approach. Comparison between the experimental and the CS calculated spectra confirms that a substantial part of the Auger lines (∼20%) can be ascribed to decay events accompanied by the excitation of one additional electron-hole pair in the valence band. For the first time, the locality of the Auger process combined with the surface sensitivity of the APECS technique and its ability to separate overlapping structures are used to study Auger transitions taking place at the the surface states of a S/noble-metal interface.

Enhanced atom mobility on the surface of a metastable film.

A remarkable enhancement of atomic diffusion is highlighted by scanning tunneling microscopy performed on ultrathin metastable body-centered tetragonal Co films grown on Fe(001). The films follow a nearly perfect layer-by-layer growth mode with a saturation island density strongly dependent on the layer on which the nucleation occurs, indicating a lowering of the diffusion barrier. Density functional theory calculations reveal that this phenomenon is driven by the increasing capability of the film to accommodate large deformations as the thickness approaches the limit at which a structural transition occurs. These results disclose the possibility of tuning surface diffusion dynamics and controlling cluster nucleation and self-organization.

Spin-dependent on-site electron correlations and localization in itinerant ferromagnets.

Spin selectivity in angle-resolved Auger photoelectron coincidence spectroscopy (AR-APECS) is used to probe electron correlation in ferromagnetic thin films. In particular, exploiting the AR-APECS capability to discriminate Auger electron emission events characterized by valence hole pairs created either in the high or in the low total spin state, a strong correlation effect in the Fe M(2,3)VV Auger line shape (measured in coincidence with the Fe 3p photoelectrons) of Fe/Cu(001) thin films is detected and ascribed to interactions within the majority spin subband. Such an assignment follows from a close comparison of the experimental AR-APECS line shapes with the predictions of a model based on spin polarized density functional theory and the Cini-Sawatzky approach.

Spin polarized metastable helium de-excitation processes on metal surfaces.

Spin polarized de-excitation of a metastable helium atom interacting with metal surfaces is treated within density functional theory. The method is based on a self-consistent calculation of the spin dependent electronic properties of the system, such as the surface density of states and the localized surface states, to compute the transition rate. On the high work function Ag(100) and Ag(111) surfaces, the helium 2s electron is delocalized in the metal and hence the transition rate is weakly spin dependent. The existence of a Shockley surface state in Ag(111) determines a neutralization rate that is about 59% larger than that from Ag(100). On a low work function metal, namely Na(100), the rate is of smaller magnitude than those on silver because the 2s triplet resonance is found to be more occupied. Consequently, emitted electrons can display a strong spin dependence also for a paramagnetic surface.

Unusually large magnetic anisotropy in electrochemically deposited Co-rich Co-Pt films.

Co-rich Co-Pt films grown by electrodeposition from an amino-nitrite/citrate/glycine electrolyte onto Au(111) substrates apparently grow with a hexagonal structure, with its c-axis directed perpendicular to the surface. The films exhibit a perpendicular magnetic anisotropy (MCA) of the same order of magnitude as the shape anisotropy. Experimental estimates of the MCA result in a higher anisotropy than that reported for bulk materials of the same composition, but similar to values measured in films grown by vacuum methods at relatively high temperature, which partly consist of a high anisotropy, metastable orthorhombic Pmm2 phase. Comparison of valence band X-ray photoelectron spectroscopy measurements on electrodeposited films with density functional theory simulations of the electronic structure of the various reported Co(3)Pt structures support the notion that the films may consist of a mixture of the hexagonal and the Pmm2 structure.

Dynamics of electron distributions probed by helium scattering.

Helium atom scattering (HAS) is the most important tool for surface science investigations. The analysis of helium scattering off a solid surface allows for a detailed analysis of its structural and dynamical properties. In this work we show how the dynamics of electron distributions at a metal surface can be investigated by HAS in the adiabatic approximation. First we examine the anticorrugating effect, namely the property of the He-surface potential of those metal systems in which the classical turning points of He beams are farther away from the surface layer at the bridge than at top sites. Anticorrugation for the system He/Cu(111) is examined in detail by a density functional theory (DFT) calculation and compared with the corrugating behaviour of He/Al(111). To explain such an effect the charge polarization of the system is crucial. Second we consider theoretically a surprising restricted diffusion result in the normal direction for Na adatoms on Cu(001) at coverages larger than 0.04 ML, obtained by measurements with spin polarized (3)He beams. From DFT calculations for this system a model for the description of the He-surface interaction based on the effective medium theory, which accounts for the observed phenomenon, is discussed. We show that the surface charge distribution probed by HAS is altered by the local concentration of the diffusing adatoms which is fluctuating with time and producing variations in the apparent height of the adatom measured by HAS. Our calculations demonstrate that such electronic dynamical rearrangements can be probed by the (3)He spin echo technique, which could be extended to other studies of surface electronic properties.

Evidence for dual modulation of pepsinogen secretion using isoproterenol, carbachol, CCK-8, forskolin, 8 bromo-cAMP, and A23187 probes.

The cellular mechanisms by which pepsinogen (PNG) secretion is controlled are not understood. The aim of this study was to explore whether modulation of PNG secretion is mediated by cAMP or calcium-calmodulin (C-C). PNG secretion in isolated rabbit gastric fundic glands (IGG) was tested, using agents believed to act via cAMP or C-C. IGG were stimulated for 30 minutes with histamine (H) 10(-5) M, isoproterenol (I) 10(-5) M, carbachol (C) 10(-5) M, cholecystokinin-octapeptide (CCK-8) 10(-7) M, forskolin (F) 10(-5) M, 8 bromo-cAMP (8B) 10(-3) M, and A23187 (A) 10(-6) M. PNG levels were determined by spectrophotometric assay of hemoglobin digestion products. PNG amounts secreted were (mean per cent above basal levels of total IGG PNG units +/- SEM): H, -0.02 +/- 0.30%; I, 3.5 +/- 0.9%; C, 5.1 +/- 2.2%; CCK-8, 5.3 +/- 1.5%; F, 10.6 +/- 3.8%; 8B, 13.8 +/- 4.5%; A, 2.1 +/- 1.1%. All secretagogues except H stimulated PNG release significantly above basal levels (p less than 0.05). A primary histaminergic mechanism for pepsinogen secretion is unlikely. Since two other adenylate cyclase activators, isoproterenol and forskolin and the 3':5'-cyclic adenosine monophosphate analog 8-bromo cAMP stimulated pepsinogen secretion, cAMP-dependence is probable. Since carbachol, CCK-8, and A23187, which are believed to act via calcium-calmodulin, also stimulated pepsinogen secretion, this system, too, presumably plays a substantial role. Thus the data support a dual 3':5'-cyclic adenosine monophosphate/calcium-calmodulin modulation of pepsinogen secretion.

Paradoxical effect of trifluoperazine, a calmodulin antagonist, on pepsinogen secretion.

Pepsinogen secretion (PS) is modulated at the intracellular level by both cAMP and calcium ion. Cholecystokinin octapeptide (CCK-8), a potent stimulus for PS, is believed to act through calcium. The most extensively studied pathway for calcium-mediated modulation involves the formation of calcium/calmodulin complexes, leading to activation of calmodulin. We have therefore examined the hypothesis that an inhibitor of calmodulin might inhibit PS stimulated by CCK-8. The phenothiazine derivative trifluoperazine (TFP) was chosen as a calmodulin antagonist. We measured in vitro secretion of pepsinogen by isolated gastric glands as a function of TFP concentration 10(-6) M-5 X 10(-4) M), in the presence and absence of a maximal concentration of CCK-8 (10(-7) M). Cellular viability was determined by measurement of release of the enzyme lactate dehydrogenase (LDH) into the medium. TFP did not significantly inhibit PS stimulation by CCK-8 at any concentration (P greater than 0.05). At 10(-4) M, TFP actually augmented PS stimulation by CCK-8 (P less than 0.05). TFP alone significantly stimulated PS (P less than 0.05) at 5 X 10(-5) M and above. TFP did not raise cAMP levels at any concentration tested (P less than 0.05), in contrast to the adenylate cyclase activator forskolin, 10(-5) M, which caused a 6- to 37-fold increase (P less than 0.05). TFP, 2 X 10(-4) did not increase LDH levels significantly (P less than 0.05). Thus a calmodulin inhibitor, TFP, paradoxically stimulates PS. This stimulatory effect of TFP is not cAMP-dependent and is not accompanied by a nonspecific release of LDH into the medium.(ABSTRACT TRUNCATED AT 250 WORDS)

Vasoactive intestinal peptide augmentation of cholecystokinin-8-stimulated pepsinogen secretion: evidence for dual modulation of chief cell function.

Pepsinogen (PPG) secretion from chief cells (CC) is dually modulated by adenosine 3':5'-monophosphate (cAMP) and calcium second messenger systems. Vasoactive intestinal peptide (VIP) stimulates cellular function by elevating intracellular levels of cAMP. In contrast, cholecystokinin-8 (CCK-8) acts by producing a rise in intracellular calcium concentration. Consequently, it was the purpose of this study to test whether VIP (acting through cAMP-mediated systems) could augment CCK-8 (acting through calcium-dependent systems)-stimulated PPG secretion. Collagenase dispersed rabbit isolated gastric glands (IGG) were incubated alone (unstimulated) or with secretagogues for 30 min. VIP in graded doses of 10(-11) to 10(-7) M was used alone or in combination with CCK-8 (10(-9) M). PPG levels were determined using an assay based on pepsin hydrolysis of [14C]methemoglobin. Results are expressed as percentage of total pepsinogen (within the IGG) secreted above unstimulated levels. VIP alone (10(-11) to 10(-7)) or CCK-8 alone (10(-9)) did not significantly stimulate PPG secretion (P greater than 0.05). The combination of CCK-8 (10(-9) M) plus VIP (10(-7) M) significantly stimulated PPG secretion above unstimulated levels (P less than 0.05). Thus, the combination of VIP and CCK-8 produced greater PPG secretion than either secretagogue alone. These data support the hypothesis that secretagogues acting through either cAMP or calcium-mediated systems contribute to the regulation of PPG secretion from CC and that the two second messenger systems act in concert achieving at least additive effects.

Forskolin (cyclic adenosine monophosphate)-dependent protein phosphorylation in isolated gastric glands.

Improved management of peptic ulcer disease requires elucidation of cellular processes underlying gastric secretion. The intracellular execution of regulatory commands to secretory cells involves protein phosphorylation. We studied cyclic adenosine monophosphate (cAMP)-dependent phosphorylation in isolated gastric glands (IGGs) using forskolin, which directly stimulates adenylate cyclase. Forskolin stimulated secretion by both parietal and chief cells. In a separate set of studies, IGGs were incubated for 45, 90, and 105 minutes in modified Ham's F-10 medium containing orthophosphate labeled with phosphorus 32. The forskolin (10(-4) M) was added to some IGG preparations at 90 minutes. The reaction was terminated with sodium dodecyl sulfate and boiling. The proteins were resolved on sodium dodecyl sulfate-polyacrylamide gels, stained with Coomassie blue, and autoradiographed. Incorporation of phosphorus 32 increased progressively at 45, 90, and 105 minutes. Forskolin enhanced phosphorylated bands around 92 kilodaltons. These results are consistent with the major role of cAMP in the regulation of gastric cellular function. The study of cAMP-stimulated phosphorylation may be an important tool in the elucidation of intracellular regulatory mechanisms of gastric secretion. Modulation of these mechanisms may be the ideal therapeutic modality for treatment of acid-secretory disorders.

The effects of cholecystokinin on parietal cell secretion in isolated gastric glands.

Cholecystokinin (CCK), a peptide hormone found in both gut and brain, shares amino acid homologies with gastrin and has previously been shown to stimulate gastric acid secretion in whole animal experiments. To investigate possible direct effects of CCK apart from extrinsic neural and hormonal influences, we have investigated the effects of the sulfated octapeptide of CCK (CCK-8) in rabbit isolated gastric glands using 14C-aminopyrine accumulation and intrinsic factor (IF) secretion as markers of parietal cell function. CCK-8 stimulated a significant increase (p less than 0.05) in IF secretion and 14C-aminopyrine accumulation. IF secretion was dose dependent for CCK concentrations from 10(-10)M to 10(-6)M. The combination of CCK (10(-6)M) and histamine (5 X 10(-5)M) elicited IF secretion greater than that of either agent alone. These results are similar to those observed for pentagastrin (10(-7)M), suggesting that the effects of CCK on parietal cell secretion may be due at least in part to a direct receptor-mediated parietal cell response to this agent.