Mn-doped cubic BN as an atomiclike memory device: A density functional study

We investigate the electronic properties of Mn(B) substitutional doping in cubic boron nitride (BN), for different charge states, using density functional theory (DFT) calculations. We show that the neutral Mn has a nonmagnetic ground state (S=0). Upon charge injection, it is unambiguously shown that the Mn(B)(-) has a high-spin configuration with a strong, localized magnetic moment of 5 mu(Bohr). We developed a simple model, parameterized by the DFT results, that allows us to interpret the rules played by the crystal-field and exchange-correlation splitting in the magnetization process.

Systematic investigation of a family of gradient-dependent functionals for solids

Eleven density functionals are compared with regard to their performance for the lattice constants of solids. We consider standard functionals, such as the local-density approximation and the Perdew-Burke-Ernzerhof (PBE) generalized-gradient approximation (GGA), as well as variations of PBE GGA, such as PBEsol and similar functionals, PBE-type functionals employing a tighter Lieb-Oxford bound, and combinations thereof. On a test set of 60 solids, we perform a system-by-system analysis for selected functionals and a full statistical analysis for all of them. The impact of restoring the gradient expansion and of tightening the Lieb-Oxford bound is discussed, and confronted with previous results obtained from other codes, functionals or test sets. No functional is uniformly good for all investigated systems, but surprisingly, and pleasingly, the simplest possible modifications to PBE turn out to have the most beneficial effect on its performance. The atomization energy of molecules was also considered and on a testing set of six molecules, we found that the PBE functional is clearly the best, the others leading to strong overbinding.

Unraveling effects of disorder on the electronic structure of SiO(2) from first principles

We present a first-principles systematic study of the electronic structure of SiO(2) including the crystalline polymorphs alpha quartz and beta cristobalite, and different types of disorder leading to the amorphous phase. We start from calculations within density functional theory and proceed to more sophisticated quasiparticle calculations according to the GW scheme. Our results show that different origins of disorder have also different impact on atomic and electronic-density fluctuations, which affect the electronic structure and, in particular, the size of the mobility gap in each case.

Edge effects in bilayer graphene nanoribbons: Ab initio total-energy density functional theory calculations

We show that the ground state of zigzag bilayer graphene nanoribbons is nonmagnetic. It also possesses a finite gap, which has a nonmonotonic dependence with the width as a consequence of the competition between bulk and strongly attractive edge interactions. All results were obtained using ab initio total-energy density functional theory calculations with the inclusion of parametrized van der Waals interactions.

Defect-induced effects on carrier migration through one-dimensional poly(para-phenylenevinylene) chains

Defects in one-dimensional (1D) systems can be intrinsically distinct from its three-dimensional counterparts, and polymer films are good candidates for showing both extremes that are difficult to individuate in the experimental data. We study theoretically the impact of simple hydrogen and oxygen defects on the electron transport properties of one-dimensional poly(para-phenylenevinylene) chains through a multiscale technique, starting from classical structural simulations for crystalline films to extensive ab initio calculations within density functional theory for the defects in single crystalline-constrained chains. The most disruptive effect on carrier transport comes from conjugation breaking imposed by the overcoordination of a carbon atom in the vinyl group independently from the chemical nature of the defect. The particular case of the [C=O] (keto-defect) shows in addition unexpected electron-hole separation, suggesting that the experimentally detected photoluminescence bleaching and photoconductivity enhancement could be due to exciton dissociation caused by the 1D characteristics of the defect.

Character of magnetic excitations in a quasi-one-dimensional antiferromagnet near the quantum critical points: Impact on magnetoacoustic properties

We report results of magnetoacoustic studies in the quantum spin-chain magnet NiCl(2)-4SC(NH(2))(2) (DTN) having a field-induced ordered antiferromagnetic (AF) phase. In the vicinity of the quantum critical points (QCPs) the acoustic c(33) mode manifests a pronounced softening accompanied by energy dissipation of the sound wave. The acoustic anomalies are traced up to T > T(N), where the thermodynamic properties are determined by fermionic magnetic excitations, the ""hallmark"" of one-dimensional (1D) spin chains. On the other hand, as established in earlier studies, the AF phase in DTN is governed by bosonic magnetic excitations. Our results suggest the presence of a crossover from a 1D fermionic to a three-dimensional bosonic character of the magnetic excitations in DTN in the vicinity of the QCPs.

Approximation to density functional theory for the calculation of band gaps of semiconductors

The local-density approximation (LDA) together with the half occupation (transitionstate) is notoriously successful in the calculation of atomic ionization potentials. When it comes to extended systems, such as a semiconductor infinite system, it has been very difficult to find a way to half ionize because the hole tends to be infinitely extended (a Bloch wave). The answer to this problem lies in the LDA formalism itself. One proves that the half occupation is equivalent to introducing the hole self-energy (electrostatic and exchange correlation) into the Schrodinger equation. The argument then becomes simple: The eigenvalue minus the self-energy has to be minimized because the atom has a minimal energy. Then one simply proves that the hole is localized, not infinitely extended, because it must have maximal self-energy. Then one also arrives at an equation similar to the self- interaction correction equation, but corrected for the removal of just 1/2 electron. Applied to the calculation of band gaps and effective masses, we use the self- energy calculated in atoms and attain a precision similar to that of GW, but with the great advantage that it requires no more computational effort than standard LDA.

Ground-state functional for quantum spin chains with bond defects

We have developed a nonlocal functional of the exchange interaction for the ground-state energy of quantum spin chains described by the Heisenberg Hamiltonian. An alternating chain is used to obtain the correlation energy and a local unit-cell approximation is defined in the context of the density-functional theory. The agreement with our exact numerical data, for small chains, is significantly better than a previous formulation, even for chains with several ferromagnetic or antiferromagnetic bond defects. The results can be particularly relevant in the study of finite spin-1/2 Heisenberg chains, with exchange couplings changing, magnitude, or even sign, from bond-to-bond.

Spin gaps and spin-flip energies in density-functional theory

Energy gaps are crucial aspects of the electronic structure of finite and extended systems. Whereas much is known about how to define and calculate charge gaps in density-functional theory (DFT), and about the relation between these gaps and derivative discontinuities of the exchange-correlation functional, much less is known about spin gaps. In this paper we give density-functional definitions of spin-conserving gaps, spin-flip gaps and the spin stiffness in terms of many-body energies and in terms of single-particle (Kohn-Sham) energies. Our definitions are as analogous as possible to those commonly made in the charge case, but important differences between spin and charge gaps emerge already on the single-particle level because unlike the fundamental charge gap spin gaps involve excited-state energies. Kohn-Sham and many-body spin gaps are predicted to differ, and the difference is related to derivative discontinuities that are similar to, but distinct from, those usually considered in the case of charge gaps. Both ensemble DFT and time-dependent DFT (TDDFT) can be used to calculate these spin discontinuities from a suitable functional. We illustrate our findings by evaluating our definitions for the Lithium atom, for which we calculate spin gaps and spin discontinuities by making use of near-exact Kohn-Sham eigenvalues and, independently, from the single-pole approximation to TDDFT. The many-body corrections to the Kohn-Sham spin gaps are found to be negative, i.e., single-particle calculations tend to overestimate spin gaps while they underestimate charge gaps.

Density-functional description of superconducting and magnetic proximity effects across a tunneling barrier

A density-functional formalism for superconductivity and magnetism is presented. The resulting relations unify previously derived Kohn-Sham equations for superconductors and for noncollinear magnetism. The formalism, which discriminates Cooper-pair singlets from triplets, is applied to two quantum liquids coupled by tunneling through a barrier. An exact expression is derived, relating the eigenstates and eigenvalues of the Kohn-Sham equations, unperturbed by tunneling, on one side of the barrier to the proximity-induced ordering potential on the other.

Density functional theory investigation of 3d, 4d, and 5d 13-atom metal clusters

The knowledge of the atomic structure of clusters composed by few atoms is a basic prerequisite to obtain insights into the mechanisms that determine their chemical and physical properties as a function of diameter, shape, surface termination, as well as to understand the mechanism of bulk formation. Due to the wide use of metal systems in our modern life, the accurate determination of the properties of 3d, 4d, and 5d metal clusters poses a huge problem for nanoscience. In this work, we report a density functional theory study of the atomic structure, binding energies, effective coordination numbers, average bond lengths, and magnetic properties of the 3d, 4d, and 5d metal (30 elements) clusters containing 13 atoms, M(13). First, a set of lowest-energy local minimum structures (as supported by vibrational analysis) were obtained by combining high-temperature first- principles molecular-dynamics simulation, structure crossover, and the selection of five well-known M(13) structures. Several new lower energy configurations were identified, e. g., Pd(13), W(13), Pt(13), etc., and previous known structures were confirmed by our calculations. Furthermore, the following trends were identified: (i) compact icosahedral-like forms at the beginning of each metal series, more opened structures such as hexagonal bilayerlike and double simple-cubic layers at the middle of each metal series, and structures with an increasing effective coordination number occur for large d states occupation. (ii) For Au(13), we found that spin-orbit coupling favors the three-dimensional (3D) structures, i.e., a 3D structure is about 0.10 eV lower in energy than the lowest energy known two-dimensional configuration. (iii) The magnetic exchange interactions play an important role for particular systems such as Fe, Cr, and Mn. (iv) The analysis of the binding energy and average bond lengths show a paraboliclike shape as a function of the occupation of the d states and hence, most of the properties can be explained by the chemistry picture of occupation of the bonding and antibonding states.

Density functional theory and ab initio molecular dynamics study of NO adsorption on Pd(111) and Pt(111) surfaces

The origin of the unique geometry for nitric oxide (NO) adsorption on Pd(111) and Pt(111) surfaces as well as the effect of temperature were studied by density functional theory calculations and ab initio molecular dynamics at finite temperature. We found that at low coverage, the adsorption geometry is determined by electronic interactions, depending sensitively on the adsorption sites and coverages, and the effect of temperature on geometries is significant. At coverage of 0.25 monolayer (ML), adsorbed NO at hollow sites prefer an upright configuration, while NO adsorbed at top sites prefer a tilting configuration. With increase in the coverage up to 0.50 ML, the enhanced steric repulsion lead to the tilting of hollow NO. We found that the tilting was enhanced by the thermal effects. At coverage of 0.75 ML with p(2 x 2)-3NO(fcc+hcp+top) structure, we found that there was no preferential orientation for tilted top NO. The interplay of the orbital hybridization, thermal effects, steric repulsion, and their effects on the adsorption geometries were highlighted at the end.

Functional microarray analysis suggests repressed cell-cell signaling and cell survival-related modules inhibit progression of head and neck squamous cell carcinoma

Background: Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph node metastasis (N+) and recurrent head and neck squamous cell carcinoma (HNSCC) may increase our understanding of the complex biology of this disease. Methods: Tumor samples were obtained from untreated HNSCC patients undergoing surgery. Patients were classified according to pathologic lymph node status (positive or negative) or tumor recurrence (recurrent or non-recurrent tumor) after treatment (surgery with neck dissection followed by radiotherapy). Using microarray gene expression, we screened tumor samples according to modules comprised by genes in the same pathway or functional category. Results: The most frequent alterations were the repression of modules in negative lymph node (N0) and in non-recurrent tumors rather than induction of modules in N+ or in recurrent tumors. N0 tumors showed repression of modules that contain cell survival genes and in non-recurrent tumors cell-cell signaling and extracellular region modules were repressed. Conclusions: The repression of modules that contain cell survival genes in N0 tumors reinforces the important role that apoptosis plays in the regulation of metastasis. In addition, because tumor samples used here were not microdissected, tumor gene expression data are represented together with the stroma, which may reveal signaling between the microenvironment and tumor cells. For instance, in non-recurrent tumors, extracellular region module was repressed, indicating that the stroma and tumor cells may have fewer interactions, which disable metastasis development. Finally, the genes highlighted in our analysis can be implicated in more than one pathway or characteristic, suggesting that therapeutic approaches to prevent tumor progression should target more than one gene or pathway, specially apoptosis and interactions between tumor cells and the stroma.

Late Entry into HIV Care: Estimated Impact on AIDS Mortality Rates in Brazil, 2003-2006

Background: Worldwide, a high proportion of HIV-infected individuals enter into HIV care late. Here, our objective was to estimate the impact that late entry into HIV care has had on AIDS mortality rates in Brazil. Methodology/Principal Findings: We analyzed data from information systems regarding HIV-infected adults who sought treatment at public health care facilities in Brazil from 2003 to 2006. We initially estimated the prevalence of late entry into HIV care, as well as the probability of death in the first 12 months, the percentage of the risk of death attributable to late entry, and the number of avoidable deaths. We subsequently adjusted the annual AIDS mortality rate by excluding such deaths. Of the 115,369 patients evaluated, 50,358 (43.6%) had entered HIV care late, and 18,002 died in the first 12 months, representing a 16.5% probability of death in the first 12 months (95% CI: 16.3-16.7). By comparing patients who entered HIV care late with those who gained timely access, we found that the risk ratio for death was 49.5 (95% CI: 45.1-54.2). The percentage of the risk of death attributable to late entry was 95.5%, translating to 17,189 potentially avoidable deaths. Averting those deaths would have lowered the 2003-2006 AIDS mortality rate by 39.5%. Including asymptomatic patients with CD4(+) T cell counts >200 and <= 350 cells/mm(3) in the group who entered HIV care late increased this proportion by 1.8%. Conclusions/Significance: In Brazil, antiretroviral drugs reduced AIDS mortality by 43%. Timely entry would reduce that rate by a similar proportion, as well as resulting in a 45.2% increase in the effectiveness of the program for HIV care. The World Health Organization recommendation that asymptomatic patients with CD4(+) T cell counts <= 350 cells/mm(3) be treated would not have a significant impact on this scenario.

The impact of measurement errors in the identification of regulatory networks

Background: There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise. Results: This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data. Conclusions: Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.