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.

Band engineering and magnetic doping of epitaxial graphene on SiC (0001).

Using calculations from first principles we show how specific interface modifications can lead to a fine-tuning of the doping and band alignment in epitaxial graphene on SiC. Upon different choices of dopants, we demonstrate that one can achieve a variation of the valence band offset between the graphene Dirac point and the valence band edge of SiC up to 1.5 eV. Finally, via appropriate magnetic doping one can induce a half-metallic behavior in the first graphene monolayer. These results clearly establish the potential for graphene utilization in innovative electronic and spintronic devices.

Simulation of the electromechanical behavior of multiwall carbon nanotubes.

The enormous potential of carbon nanotubes (CNTs) as primary components in electronic devices and NEMS necessitates the understanding and predicting of the effects of mechanical deformation on electron transport in CNTs. In principle, detailed atomic/electronic calculations can provide both the deformed configuration and the resulting electrical transport behavior of the CNT. However, the computational expense of these simulations limits the size of the CNTs that can be studied with this technique, and a direct analysis of CNTs of the dimension used in nanoelectronic devices seems prohibitive at the present. Here a computationally effective mixed finite element (FE)/tight-binding (TB) approach able to simulate the electromechanical behavior of CNT devices is presented. The TB code is carefully designed to realize orders-of-magnitude reduction in computational time in calculating deformation-induced changes in electrical transport properties of the nanotubes. The FE-TB computational approach is validated in a simulation of laboratory experiments on a multiwall CNT and then used to demonstrate the role of the multiwall structure in providing robustness to conductivity in the event of imposed mechanical deformations.

Onset of ferrielectricity and the hidden nature of nanoscale polarization in ferroelectric thin films.

Using calculations from first principles and the concept of layer polarization, we have elucidated the nanoscale organization and local polarization in ferroelectric thin films between metallic contacts. The profile of the local polarization for different film thicknesses unveils a peculiar spatial pattern of atomic layers with uncompensated dipoles in what was originally thought to be a ferroelectric domain. This effectively ferrielectric behavior is induced by the dominant roles of the interfaces at such reduced dimensionality and can be interpreted using a simple classical model where the latter are explicitly taken into account.

Carbon nanotube-metal cluster composites: a new road to chemical sensors?

Novel carbon nanotube-metal cluster structures are proposed as prototype systems for molecular recognition at the nanoscale. Ab initio calculations show that already the bare nanotube cluster system displays some specificity because the adsorption of ammonia on a carbon nanotube-Al cluster system is easily detected electrically, while diborane adsorption does not provide an electrical signature. Since there are well-established procedures for attaching molecular receptors to metal clusters, these results provide a "proof-of-principle" for the development of novel, high-specificity molecular sensors.

First-principles theory of correlated transport through nanojunctions.

We report the inclusion of electron-electron correlation in the calculation of transport properties within an ab initio scheme. A key step is the reformulation of Landauer's approach in terms of an effective transmittance for the interacting electron system. We apply this framework to analyze the effect of short-range interactions on Pt atomic wires and discuss the coherent and incoherent correction to the mean-field approach.

Mn interstitial diffusion in (ga,mn)as.

We present a combined theoretical and experimental study of the ferromagnetic semiconductor (Ga,Mn)As which explains the remarkably large changes observed on low-temperature annealing. Careful control of the annealing conditions allows us to obtain samples with ferromagnetic transition temperatures up to 159 K. Ab initio calculations, in situ Auger spectroscopy, and resistivity measurements during annealing show that the observed changes are due to out diffusion of Mn interstitials towards the surface, governed by an energy barrier of 0.7-0.8 eV. Electric fields induced by Mn acceptors have a significant effect on the diffusion.

Dynamic conductance of carbon nanotubes

The dynamic conductance of carbon nanotubes was investigated using the nonequilibrium Green's function formalism within the context of a tight-binding model. Specifically, we have studied the ac response of tubes of different helicities, both with and without defects, and an electronic heterojunction. Because of the induced displacement currents, the dynamic conductance of the nanotubes differs significantly from the dc conductance displaying both capacitive and inductive responses. The important role of photon-assisted transport through nanotubes is revealed and its implications for experiments discussed.

The relationship between chromosomal origins of replication and the nuclear matrix during the cell cycle.

A cytological investigation into the dynamic behaviour of the origins of replication with respect to the nuclear matrix has been carried out on Xenopus laevis cultured cells. In order to preferentially label origins or 'non-origin' regions along DNA fibres, 5-fluoro-2'-deoxyuridine (FUdR)-treated cells were pulsed with [3H]deoxyadenosine in early or late S phase. Samples were then allowed to proceed through the cell cycle for increasing times. The DNA loops were induced in situ to completely uncoil around the nuclear matrix. The autoradiographic analysis shows that, under the experimental conditions used, 'non-origin' regions behave as expected from previous studies, i.e., they associate with the nuclear matrix only when they become part of a replication fork, whereas active origins of replication remain associated with the matrix throughout the cell cycle.

Silver positivity of the NORs during embryonic development of Xenopus laevis.

Transcriptional activity of ribosomal RNA (rRNA) genes is detectable around blastula-gastrula transition during the embryonic development of amphibians and other non-mammalian systems. The silver staining reaction, known to selectively stain transcriptionally active nucleolus organizer regions (NORs) both in interphase and metaphase chromosomes allowed us to follow the activation of the NORs during the embryonic development of Xenopus laevis.

Replication of ribosomal DNA in Xenopus laevis.

The study of the localization of the replication origins of rDNA in Xenopus laevis has been approached by two different methods. 1. The DNA of X. laevis larvae was fractionated by CsCl gradient centrifugation in bulk and ribosomal DNA and examined in the electron microscope. In bulk DNA, clusters of microbubbles, which are related with the origins of replication, appear to be spaced along the DNA molecules at intervals comparable with the size of the 'average' replicon of X. laevis. In ribosomal DNA, the distance between adjacent clusters is much shorter and corresponds to the size of the rDNA repeating unit. When ribosomal DNA was submitted to digestion with restriction enzymes (Eco RI and HindIII) the microbubbles are observed in the non-transcribed spacer-containing fragment. 2. Cultured cells of X. laevis were synchronized by mitotic selection and incubated with 5-fluoro-2-deoxyuridine for a time longer than the G1 phase. This treatment synchronizes the replicons and allows them to start replicating very slowly. It was thus possible to obtain a preferential labelling of the regions containing the origins. The analysis by gel electrophoresis of the Eco Ri-digested rDNA showed that the radioactivity was preferentially incorporated in the fragments which contain the non-transcribed spacer. The results of these two approaches indicate that the rRNA gene cluster consists of multiple units of replication, possibly one per gene unit. Furthermore they show that the origins of replication are localized into the non-transcribed spacer.

Selective in vitro transcription by purified yeast RNA polymerase II on cloned 2 micron DNA.

The in vitro transcription properties of purified yeast RNA polymerase II have been analyzed on prokaryotic plasmids (pBR322 and pBR313) and chimaeric plasmids bearing yeast 2 micron sequences (BTYP 1, BTYH 2 and BTYH 3). Conditions for selective transcription of the 2 micron DNA sequences in chimaeric plasmids have been determined. pBR322 and pBR313 are not transcribed by the purified RNA polymerase II when not bearing eukaryotic inserts. We show that the agarose gel electrophoretic analysis of ternary transcription complexes allows the localization of nascent RNA chains. The RNA produced has been visualized by electron microscopy (nascent RNA hybridization loops) and by gel electrophoretic analysis. All the observed properties are shared by RNA polymerase II purified by a conventional method (1) and by a rapid alternative procedure described herein. The peculiar properties of a partially purified form of RNA polymerase II are reported.

Electron microscopic analysis of replicating DNA of sea urchin embryos.

DNA was extracted from Paracentrotus lividus embryos at the third S phase afer fertilization and analyzed with the electron microscope. The most relevant structures observed in this actively replicating DNA are clusters of short, closely spaced microbubbles (about 0.1 micron long on the average), partially or entirely single-stranded molecules and few linear forks. Unexpectedly, no long eye forms were observed. The analysis of DNA purified from gastrulae and from adult somatic tissues has revealed the same structures, although at a low frequency. A quantitative analysis has been carried out to determine the size distribution and spacing of microbubbles. A number of control experiments have been performed to characterize these structures better. Various possiblities are discussed to account for the presence of the observed forms and the absence of larger eyes.

Differently sized rDNA repeating units of Xenopus laevis are arranged as internally homogeneous clusters along the nucleolar organizer.

The organization of differently sized genes coding for rRNA in Xenophus laevis has been investigated by partial EcoRI or HindIII digestion. The electrophoretic patterns obtained revealed that most adjacent repeating units are equally sized. This conclusion is in agreement with a previous suggestion that the nucleolar organizer is made up of internally homogeneous blocks of rRNA genes.