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.

LIPSCHITZ CLASSIFICATION OF FUNCTIONS ON A HOLDER TRIANGLE

The problem of semialgebraic Lipschitz classification of quasihomogeneous polynomials on a Holder triangle is studied. For this problem, the ""moduli"" are described completely in certain combinatorial terms.

The Lobel-Komlos-Sos conjecture for trees of diameter 5 and for certain caterpillars

Loebl, Komlos, and Sos conjectured that if at least half the vertices of a graph G have degree at least some k is an element of N, then every tree with at most k edges is a subgraph of G. We prove the conjecture for all trees of diameter at most 5 and for a class of caterpillars. Our result implies a bound on the Ramsey number r( T, T') of trees T, T' from the above classes.

Spectroscopic, structural, and functional characterization of the alternative low-spin state of horse heart cytochrome c

The alternative low-spin states of Fe3+ and Fe2+ cytochrome c induced by SDS or AOT/hexane reverse micelles exhibited the heme group in a less rhombic symmetry and were characterized by electron paramagnetic resonance, UV-visible, CD, magnetic CD, fluorescence, and Raman resonance. Consistent with the replacement of Met 80 by another strong field ligand at the sixth heme iron coordination position, Fe3+ ALSScytc exhibited 1-nm Soret band blue shift and e enhancement accompanied by disappearance of the 695-nm charge transfer band. The Raman resonance, CD, and magnetic CD spectra of Fe3+ and Fe2+ ALSScytc exhibited significant changes suggestive of alterations in the heme iron microenvironment and conformation and should not be assigned to unfold because the Trp(59) fluorescence remained quenched by the neighboring heme group. ALSScytc was obtained with His(33) and His(26) carboxyethoxylated horse cytochrome c and with tuna cytochrome c (His(33) replaced by Asn) pointing out Lys(79) as the probable heme iron ligand. Fe3+ ALSScytc retained the capacity to cleave tert-butylhydroperoxide and to be reduced by dithiothreitol and diphenylacetaldehyde but not by ascorbate. Compatible with a more open heme crevice, ALSScytc exhibited a redox potential similar to 200 mV lower than the wild-type protein (1220 mV) and was more susceptible to the attack of free radicals.

Structure, stability, depolarized light scattering, and vibrational spectra of fullerenols from all-electron density-functional-theory calculations

We have investigated the stability, electronic properties, Rayleigh (elastic), and Raman (inelastic) depolarization ratios, infrared and Raman absorption vibrational spectra of fullerenols [C(60)(OH)(n)] with different degrees of hydroxylation by using all-electron density-functional-theory (DFT) methods. Stable arrangements of these molecules were found by means of full geometry optimizations using Becke's three-parameter exchange functional with the Lee, Yang, and Parr correlation functional. This DFT level has been combined with the 6-31G(d,p) Gaussian-type basis set, as a compromise between accuracy and capability to treat highly hydroxylated fullerenes, e.g., C(60)(OH)(36). Thus, the molecular properties of fullerenols were systematically analyzed for structures with n=1, 2, 3, 4, 8, 10, 16, 18, 24, 32, and 36. From the electronic structure analysis of these molecules, we have evidenced an important effect related to the weak chemical reactivity of a possible C(60)(OH)(24) isomer. To investigate Raman scattering and the vibrational spectra of the different fullerenols, frequency calculations are carried out within the harmonic approximation. In this case a systematic study is only performed for n=1-4, 8, 10, 16, 18, and 24. Our results give good agreements with the expected changes in the spectral absorptions due to the hydroxylation of fullerenes.

Bulk structures of PtO and PtO(2) from density functional calculations

Platinum plays an important role in catalysis and electrochemistry, and it is known that the direct interaction of oxygen with Pt surfaces can lead to the formation of platinum oxides (PtO(x)), which can affect the reactivity. To contribute to the atomistic understanding of the atomic structure of PtO(x), we report a density functional theory study of the atomic structure of bulk PtO(x) (1 <= x <= 2). From our calculations, we identified a lowest-energy structure (GeS type, space group Pnma) for PtO, which is 0.181 eV lower in energy than the structure suggested by W. J. Moore and L. Pauling [J. Am. Chem. Soc. 63, 1392 (1941)] (PtS type). Furthermore, two atomic structures were identified for PtO(2), which are almost degenerate in energy with the lowest-energy structure reported so far for PtO(2) (CaCl(2) type). Based on our results and analysis, we suggest that Pt and O atoms tend to form octahedron motifs in PtO(x) even at lower O composition by the formation of Pt-Pt bonds.

Understanding the Influences of Spatial Patterns on N Availability Within the Brazilian Amazon Forest

Nitrogen variations at different spatial scales and integrated across functional groups were addressed for lowland tropical forests in the Brazilian Amazon as follows: (1) how does N availability vary across the region over different spatial scales (regional x landscape scale); ( 2) how are these variations in N availability integrated across plant functional groups ( legume 9 non-legume trees). Leaf N, P, and Ca concentrations as well the leaf N isotope ratios (delta(15)N) from a large set of legume and non-legume tree species were measured. Legumes had higher foliar N/Ca ratios than non-legumes, consistent with the high energetic costs in plant growth associated with higher foliar P/Ca ratios found in legumes than in non-legumes. At the regional level, foliar delta(15)N decreased with increasing rainfall. At the landscape level, N availability was higher in the forests on clayey soils on the plateau than in forests on sandier soils. The isotope as well as the non-isotope data relationships here documented, explain to a large extent the variation in delta(15)N signatures across gradients of rainfall and soil. Although at the regional level, the precipitation regime is a major determinant of differences in N availability, at the landscape level, under the same precipitation regime, soil type seems to be a major factor influencing the availability of N in the Brazilian Amazon forest.

BORON UPTAKE AND DISTRIBUTION IN FIELD GROWN CITRUS TREES

In low fertility tropical soils, boron (B) deficiency impairs fruit production. However, little information is available on the efficiency of nutrient application and use by trees. Therefore, this work verified the effects of soil and foliar applications of boron in a commercial citrus orchard. An experiment was conducted with fertigated 4-year-old `Valencia` sweet orange trees on `Swingle` citrumelo rootstock. Boron (isotopically-enriched 10B) was supplied to trees once or twice in the growing season, either dripped in the soil or sprayed on the leaves. Trees were sampled at different periods and separated into different parts for total B contents and 10B/11B isotope ratios analyses. Soil B applied via fertigation was more efficient than foliar application for the organs grown after the B fertilization. Recovery of labeled B by fruits was 21% for fertigation and 7% for foliar application. Residual effects of nutrient application in the grove were observed in the year after labeled fertilizer application, which greater proportions derived from the soil supply.

Laser-induced breakdown spectroscopy and chemometrics for classification of toys relying on toxic elements

Quality control of toys for avoiding children exposure to potentially toxic elements is of utmost relevance and it is a common requirement in national and/or international norms for health and safety reasons. Laser-induced breakdown spectroscopy (LIBS) was recently evaluated at authors` laboratory for direct analysis of plastic toys and one of the main difficulties for the determination of Cd. Cr and Pb was the variety of mixtures and types of polymers. As most norms rely on migration (lixiviation) protocols, chemometric classification models from LIBS spectra were tested for sampling toys that present potential risk of Cd, Cr and Pb contamination. The classification models were generated from the emission spectra of 51 polymeric toys and by using Partial Least Squares - Discriminant Analysis (PLS-DA), Soft Independent Modeling of Class Analogy (SIMCA) and K-Nearest Neighbor (KNN). The classification models and validations were carried out with 40 and 11 test samples, respectively. Best results were obtained when KNN was used, with corrected predictions varying from 95% for Cd to 100% for Cr and Pb. (C) 2011 Elsevier B.V. All rights reserved.

Kernel machines for epilepsy diagnosis via EEG signal classification: A comparative study

Objective: We carry out a systematic assessment on a suite of kernel-based learning machines while coping with the task of epilepsy diagnosis through automatic electroencephalogram (EEG) signal classification. Methods and materials: The kernel machines investigated include the standard support vector machine (SVM), the least squares SVM, the Lagrangian SVM, the smooth SVM, the proximal SVM, and the relevance vector machine. An extensive series of experiments was conducted on publicly available data, whose clinical EEG recordings were obtained from five normal subjects and five epileptic patients. The performance levels delivered by the different kernel machines are contrasted in terms of the criteria of predictive accuracy, sensitivity to the kernel function/parameter value, and sensitivity to the type of features extracted from the signal. For this purpose, 26 values for the kernel parameter (radius) of two well-known kernel functions (namely. Gaussian and exponential radial basis functions) were considered as well as 21 types of features extracted from the EEG signal, including statistical values derived from the discrete wavelet transform, Lyapunov exponents, and combinations thereof. Results: We first quantitatively assess the impact of the choice of the wavelet basis on the quality of the features extracted. Four wavelet basis functions were considered in this study. Then, we provide the average accuracy (i.e., cross-validation error) values delivered by 252 kernel machine configurations; in particular, 40%/35% of the best-calibrated models of the standard and least squares SVMs reached 100% accuracy rate for the two kernel functions considered. Moreover, we show the sensitivity profiles exhibited by a large sample of the configurations whereby one can visually inspect their levels of sensitiveness to the type of feature and to the kernel function/parameter value. Conclusions: Overall, the results evidence that all kernel machines are competitive in terms of accuracy, with the standard and least squares SVMs prevailing more consistently. Moreover, the choice of the kernel function and parameter value as well as the choice of the feature extractor are critical decisions to be taken, albeit the choice of the wavelet family seems not to be so relevant. Also, the statistical values calculated over the Lyapunov exponents were good sources of signal representation, but not as informative as their wavelet counterparts. Finally, a typical sensitivity profile has emerged among all types of machines, involving some regions of stability separated by zones of sharp variation, with some kernel parameter values clearly associated with better accuracy rates (zones of optimality). (C) 2011 Elsevier B.V. All rights reserved.