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.

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.

New genes of Xanthomonas citri subsp citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

Background: Citrus canker is a disease caused by the phytopathogens Xanthomonas citri subsp. citri, Xanthomonas fuscans subsp. aurantifolli and Xanthomonas alfalfae subsp. citrumelonis. The first of the three species, which causes citrus bacterial canker type A, is the most widely spread and severe, attacking all citrus species. In Brazil, this species is the most important, being found in practically all areas where citrus canker has been detected. Like most phytobacterioses, there is no efficient way to control citrus canker. Considering the importance of the disease worldwide, investigation is needed to accurately detect which genes are related to the pathogen-host adaptation process and which are associated with pathogenesis. Results: Through transposon insertion mutagenesis, 10,000 mutants of Xanthomonas citri subsp. citri strain 306 (Xcc) were obtained, and 3,300 were inoculated in Rangpur lime (Citrus limonia) leaves. Their ability to cause citrus canker was analyzed every 3 days until 21 days after inoculation; a set of 44 mutants showed altered virulence, with 8 presenting a complete loss of causing citrus canker symptoms. Sequencing of the insertion site in all 44 mutants revealed that 35 different ORFs were hit, since some ORFs were hit in more than one mutant, with mutants for the same ORF presenting the same phenotype. An analysis of these ORFs showed that some encoded genes were previously known as related to pathogenicity in phytobacteria and, more interestingly, revealed new genes never implicated with Xanthomonas pathogenicity before, including hypothetical ORFs. Among the 8 mutants with no canker symptoms are the hrpB4 and hrpX genes, two genes that belong to type III secretion system (TTSS), two hypothetical ORFS and, surprisingly, the htrA gene, a gene reported as involved with the virulence process in animal-pathogenic bacteria but not described as involved in phytobacteria virulence. Nucleic acid hybridization using labeled cDNA probes showed that some of the mutated genes are differentially expressed when the bacterium is grown in citrus leaves. Finally, comparative genomic analysis revealed that 5 mutated ORFs are in new putative pathogenicity islands. Conclusion: The identification of these new genes related with Xcc infection and virulence is a great step towards the understanding of plant-pathogen interactions and could allow the development of strategies to control citrus canker.

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.

Functional specialization of Eucalyptus fine roots: contrasting potential uptake rates for nitrogen, potassium and calcium tracers at varying soil depths

1. Little is known about the role of deep roots in the nutrition of forest trees and their ability to provide a safety-net service taking up nutrients leached from the topsoil. 2. To address this issue, we studied the potential uptake of N, K and Ca by Eucalyptus grandis trees (6 years of age - 25 m mean height), in Brazil, as a function of soil depth, texture and water content. We injected NO(3)(-)- (15)N, Rb(+) (analogue of K(+)) and Sr(2+) (analogue of Ca(2+)) tracers simultaneously in a solution through plastic tubes at 10, 50, 150 and 300 cm in depth in a sandy and a clayey Ferralsol soil. A complete randomized design was set up with three replicates of paired trees per injection depth and soil type. Recently expanded leaves were sampled at various times after tracer injection in the summer, and the experiment was repeated in the winter. Soil water contents were continuously monitored at the different depths in the two soils. 3. Determination of foliar Rb and Sr concentrations and (15)N atom % made it possible to estimate the relative uptake potential (RUP) of tracer injections from the four soil depths and the specific RUP (SRUP), defined as RUP, per unit of fine root length density in the corresponding soil layer. 4. The highest tracer uptake rates were found in the topsoil, but contrasting RUP distributions were observed for the three tracers. Whilst the RUP was higher for NO(3)(-)- (15)N than for Rb(+) and Sr(2+) in the upper 50 cm of soil, the highest SRUP values for Sr(2+) and Rb(+) were found at a depth of 300 cm in the sandy soil, as well as in the clayey soil when gravitational solutions reached that depth. 5. Our results suggest that the fine roots of E. grandis trees exhibit contrasting potential uptake rates with depth depending on the nutrient. This functional specialization of roots might contribute to the high growth rates of E. grandis trees, efficiently providing the large amounts of nutrients required throughout the development of these fast-growing plantations.

Cardiac and peripheral adjustments induced by early exercise training intervention were associated with autonomic improvement in infarcted rats: role in functional capacity and mortality

Aims To test the effects of early exercise training (ET) on left ventricular (LV) and autonomic functions, haemodynamics, tissues blood flows (BFs), maximal oxygen consumption (VO(2) max), and mortality after myocardial infarction (MI) in rats. Methods and results Male Wistar rats were divided into: control (C), sedentary-infarcted (SI), and trained-infarcted (TI). One week after MI, TI group underwent an ET protocol (90 days, 50-70% VO2 max). Left ventricular function was evaluated noninvasively and invasively. Baroreflex sensitivity, heart rate variability, and pulse interval were measured. Cardiac output (CO) and regional BFs were determined using coloured microspheres. Infarcted area was reduced in TI (19 +/- 6%) compared with SI (34 +/- 5%) after ET. Exercise training improved the LV and autonomic functions, the CO and regional BF changes induced by MI, as well as increased SERCA2 expression and mRNA vascular endothelial growth factor levels. These changes brought about by ET resulted in mortality rate reduction in the TI (13%) group compared with the SI (54%) group. Conclusion Early aerobic ET reduced cardiac and peripheral dysfunctions and preserved cardiovascular autonomic control after MI in trained rats. Consequently, these ET-induced changes resulted in improved functional capacity and survival after MI.

Endothelial nitric oxide synthase polymorphisms and adaptation of parasympathetic modulation to exercise training

SILVA, B. M., F. J. NEVES, M. V. NEGRÃO, C. R. ALVES, R. G. DIAS, G. B. ALVES, A. C. PEREIRA, M. Urbana A. RONDON, J. E. KRIEGER, C. E. NEGRÃO, and A. C. DA NOBREGA. Endothelial Nitric Oxide Synthase Polymorphisms and Adaptation of Parasympathetic Modulation to Exercise Training. Med. Sci. Sports Exerc., Vol. 43, No. 9, pp. 1611-1618, 2011. Purpose: There is a large interindividual variation in the parasympathetic adaptation induced by aerobic exercise training, which may be partially attributed to genetic polymorphisms. Therefore, we investigated the association among three polymorphisms in the endothelial nitric oxide gene (-786T>C, 4b4a, and 894G>T), analyzed individually and as haplotypes, and the parasympathetic adaptation induced by exercise training. Methods: Eighty healthy males, age 20-35 yr, were genotyped by polymerase chain reaction-restriction fragment length polymorphism analysis, and haplotypes were inferred using the software PHASE 2.1. Autonomic modulation (i.e., HR variability and spontaneous baroreflex sensitivity) and peak oxygen consumption ((V) over dotO(2peak)) were measured before and after training (running, moderate to severe intensity, three times per week, 60 min.day(-1), during 18 wk). Results: Training increased (V) over dotO(2peak) (P < 0.05) and decreased mean arterial pressure (P < 0.05) in the whole sample. Subjects with the -786C polymorphic allele had a significant reduction in baroreflex sensitivity after training (change: wild type (-786TT) = 2% +/- 89% vs polymorphic (-786TC/CC) = -28% +/- 60%, median +/- quartile range, P = 0.03), and parasympathetic modulation was marginally reduced in subjects with the 894T polymorphic allele (change: wild type (894GG) = 8% +/- 67% vs polymorphic (894GT/TT) = -18% +/- 59%, median +/- quartile range, P = 0.06). Furthermore, parasympathetic modulation percent change was different between the haplotypes containing wild-type alleles(-786T/4b/894G) and polymorphic alleles at positions -786 and 894 (-786C/4b/894T) (-6% +/- 56% vs -41% +/- 50%, median T quartile range, P = 0.04). Conclusions: The polymorphic allele at position -786 and the haplotype containing polymorphic alleles at positions -786 and 894 in the endothelial nitric oxide gene were associated with decreased parasympathetic modulation after exercise training.

On the functional integration between postural and supra-postural tasks on the basis of contextual cues and task constraint

In order to evaluate the effects of uncertainty about direction of mechanical perturbation and supra-postural task constraint on postural control young adults had their upright stance perturbed while holding a tray in a horizontal position Stance was perturbed by moving forward or backward a supporting platform contrasting situations of certainty versus uncertainty of direction of displacement Increased constraint on postural stability was Imposed by a supra-postural task of equilibrating a cylinder on the tray Performance was assessed through EMG of anterior leg muscles angular displacement of the main Joints involved in the postural reactions and displacement of the tray Results showed that both certainty on the direction of perturbation and Increased supra-postural task constraint led to decreased angular displacement of the knee and the hip Furthermore combination of certainty and high supra-postural task constraint produced shorter latency of muscular activation Such postural responses were paralleled by decreased displacement of the tray Thesi results suggest a functional integration between the tasks with central set priming reactive postural responses from contextual cues and Increased stability demand (C) 2010 Elsevier B V All rights reserved

The cultural adaptation and validation of the ""Burn Specific Health Scale-Revised"" (BSHS-R): Version for Brazilian burn victims

Background: The Burns Specific Health Scale-Revised (BSHS-R) is of easy application, can be self-administered, and it is considered a good scale to evaluate various important life aspects of burn victims. Objectives: To translate and culturally adapt the BSHS-R into the Brazilian-Portuguese language and to evaluate the internal consistency and convergent validity of the translated BSHS-R. Methods: The cultural adaptation of the BSHS-R included translation and back-translation, discussions with professionals and patients to ensure conceptual equivalence, semantic evaluation, and pre-test of the instrument. The Final Brazilian-Portuguese Version (FBPV) of the BSHS-R was tested on a group of 115 burn patients for internal consistency and validity of construct (using the Rosenberg Self-Esteem Scale (RSES) and the Beck Depression Inventory (BDI)). Results: All values of Cronbach`s alpha were greater than. 8, demonstrating that the internal consistency of the FBPV was very high. Self-esteem was highly correlated with affect and body image (r = .59, p < .001), and with interpersonal relationships (T = .51, p < .001). Correlations between the domains of the FBPV and the BDI were all negative but larger in magnitude than the correlations with RSES. Depression was highly correlated with affect and body image (r = -77, p < .001), and with interpersonal relationships (r = -67, p < .001). Conclusions: The results showed that the adapted version of the BSHS-R into Brazilian-Portuguese fulfills the validity and reliability criteria required from an instrument of health status assessment for burn patients. (C) 2008 Elsevier Ltd and ISBI. All rights reserved.

Upper limb assessment in tetraplegia: clinical, functional and kinematic correlations

The aim of this study was to correlate clinical and functional evaluations with kinematic variables of upper limp reach-to-grasp movement in patients with tetraplegia. Twenty chronic patients were selected to perform reach-to-grasp kinematic assessment using a target placed at a distance equal to the arm`s length. Kinematic variables (hand peak velocity, movement time, percent time-to-maximal velocity, index of curvature, number of peaks, and joint range of motion) were correlated to clinical (Standard Neurological Classification of Spinal Cord Injury-American Spinal Injury Association) and functional [Functional Independence Measure (FIM) and Spinal Cord Independence Measure II (SCIM II)) evaluation scores. Twenty control participants were also selected to obtain normal reference parameters. There was a positive correlation between total motor index and FIM (r=0.6089; P=0.0044) and SCIM II (r=0.5229; P=0.018). Both functional scores showed positive correlation with each other (r=0.8283; P<0.0001). A correlation was also observed between the right and left motor indices, the motor AM, and the SCIM II in most of the reach-to-grasp kinematic variables studied (hand peak velocity, movement time, index of curvature, and number of peaks). In contrast, for the joint range of motion (shoulder, elbow, and wrist), only the wrist in the horizontal plane showed correlation with clinical variables. This study shows that muscle strength assessed by the American Spinal Injury Association motor index influences the reach-to-grasp kinematic variables of patients with tetraplegia. However, the functional assessments did not present the same influence.