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.

Energy spectra for quantum wires and two-dimensional electron gases in magnetic fields with Rashba and Dresselhaus spin-orbit interactions

We introduce an analytical approximation scheme to diagonalize parabolically confined two-dimensional (2D) electron systems with both the Rashba and Dresselhaus spin-orbit interactions. The starting point of our perturbative expansion is a zeroth-order Hamiltonian for an electron confined in a quantum wire with an effective spin-orbit induced magnetic field along the wire, obtained by properly rotating the usual spin-orbit Hamiltonian. We find that the spin-orbit-related transverse coupling terms can be recast into two parts W and V, which couple crossing and noncrossing adjacent transverse modes, respectively. Interestingly, the zeroth-order Hamiltonian together with W can be solved exactly, as it maps onto the Jaynes-Cummings model of quantum optics. We treat the V coupling by performing a Schrieffer-Wolff transformation. This allows us to obtain an effective Hamiltonian to third order in the coupling strength k(R)l of V, which can be straightforwardly diagonalized via an additional unitary transformation. We also apply our approach to other types of effective parabolic confinement, e. g., 2D electrons in a perpendicular magnetic field. To demonstrate the usefulness of our approximate eigensolutions, we obtain analytical expressions for the nth Landau-level g(n) factors in the presence of both Rashba and Dresselhaus couplings. For small values of the bulk g factors, we find that spin-orbit effects cancel out entirely for particular values of the spin-orbit couplings. By solving simple transcendental equations we also obtain the band minima of a Rashba-coupled quantum wire as a function of an external magnetic field. These can be used to describe Shubnikov-de Haas oscillations. This procedure makes it easier to extract the strength of the spin-orbit interaction in these systems via proper fitting of the data.

Universal zero-bias conductance for the single-electron transistor

The thermal dependence of the zero-bias conductance for the single electron transistor is the target of two independent renormalization-group approaches, both based on the spin-degenerate Anderson impurity model. The first approach, an analytical derivation, maps the Kondo-regime conductance onto the universal conductance function for the particle-hole symmetric model. Linear, the mapping is parametrized by the Kondo temperature and the charge in the Kondo cloud. The second approach, a numerical renormalization-group computation of the conductance as a function the temperature and applied gate voltages offers a comprehensive view of zero-bias charge transport through the device. The first approach is exact in the Kondo regime; the second, essentially exact throughout the parametric space of the model. For illustrative purposes, conductance curves resulting from the two approaches are compared.

The role of electron localization in the atomic structure of transition-metal 13-atom clusters: the example of Co(13), Rh(13), and Hf(13)

The crystalline structure of transition-metals (TM) has been widely known for several decades, however, our knowledge on the atomic structure of TM clusters is still far from satisfactory, which compromises an atomistic understanding of the reactivity of TM clusters. For example, almost all density functional theory (DFT) calculations for TM clusters have been based on local (local density approximation-LDA) and semilocal (generalized gradient approximation-GGA) exchange-correlation functionals, however, it is well known that plain DFT fails to correct the self-interaction error, which affects the properties of several systems. To improve our basic understanding of the atomic and electronic properties of TM clusters, we report a DFT study within two nonlocal functionals, namely, the hybrid HSE (Heyd, Scuseria, and Ernzerhof) and GGA + U functionals, of the structural and electronic properties of the Co(13), Rh(13), and Hf(13) clusters. For Co(13) and Rh(13), we found that improved exchange-correlation functionals decrease the stability of open structures such as the hexagonal bilayer (HBL) and double simple-cubic (DSC) compared with the compact icosahedron (ICO) structure, however, DFT-GGA, DFT-GGA + U, and DFT-HSE yield very similar results for Hf(13). Thus, our results suggest that the DSC structure obtained by several plain DFT calculations for Rh(13) can be improved by the use of improved functionals. Using the sd hybridization analysis, we found that a strong hybridization favors compact structures, and hence, a correct description of the sd hybridization is crucial for the relative energy stability. For example, the sd hybridization decreases for HBL and DSC and increases for ICO in the case of Co(13) and Rh(13), while for Hf(13), the sd hybridization decreases for all configurations, and hence, it does not affect the relative stability among open and compact configurations.

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.

Electron theoretical investigation of the stability of the B2-TiFe compound

The metastable phase diagram of the BCC-based ordering equilibria in the Ti-Fe system has been calculated using a truncated cluster expansion, through the combination of FP-LAPW and cluster variation method (CVM) in the irregular tetrahedron cluster approximation. The results are compared with phenomenological CVM assessments of the system and suggest that the value for the experimental formation enthalpy of the B2-TiFe compound should be significantly more negative than the currently assessed value. (C) 2008 Elsevier B.V. All rights reserved.

Thoracic aorta calcification detected by electron beam tomography predicts all-cause mortality

Background: The presence of coronary artery calcium (CAC) is an independent marker of increased risk of cardiovascular disease (CVD) events and mortality. However, the predictive value of thoracic aorta calcification (TAC), which can be additionally identified without further scanning during assessment of CAC, is unknown. Methods: We followed a cohort of 8401 asymptomatic individuals (mean age: 53 +/- 10 years, 69% men) undergoing cardiac risk factor evaluation and TAC and CAC testing with electron beam computed tomography. Multivariable Cox proportional hazards models were developed to predict all-cause mortality based on the presence of TAC. Results: During a median follow-up period of 5 years, 124 (1.5%) deaths were observed. Overall survival was 96.9% and 98.9% for those with and without detectable TAC, respectively (p < 0.0001). Compared to those with no TAC, the hazard ratio for mortality in the presence of TAC was 3.25 (95% CI: 2.28-4.65, p < 0.0001) in unadjusted analysis. After adjusting for age, gender, hypertension, dyslipidemia, diabetes mellitus, smoking and family history of premature coronary artery disease, and presence of CAC the relationship remained robust (HR 1.61, 95% CI: 1.10-2.27, p = 0.015). Likelihood ratio chi(2) statistics demonstrated that the addition of TAC contributed significantly in predicting mortality to traditional risk factors alone (chi(2) = 13.62, p = 0.002) as well as risk factors + CAC (chi(2) = 5.84, p = 0.02) models. Conclusion: In conclusion, the presence of TAC was associated with all-cause mortality in our study; this relationship was independent of conventional CVD risk factors as well as the presence of CAC. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

Molecular orbital calculations of two-electron states for P-donor solid-state spin qubits

We theoretically study the Hilbert space structure of two neighboring P-donor electrons in silicon-based quantum computer architectures. To use electron spins as qubits, a crucial condition is the isolation of the electron spins from their environment, including the electronic orbital degrees of freedom. We provide detailed electronic structure calculations of both the single donor electron wave function and the two-electron pair wave function. We adopted a molecular orbital method for the two-electron problem, forming a basis with the calculated single donor electron orbitals. Our two-electron basis contains many singlet and triplet orbital excited states, in addition to the two simple ground state singlet and triplet orbitals usually used in the Heitler-London approximation to describe the two-electron donor pair wave function. We determined the excitation spectrum of the two-donor system, and study its dependence on strain, lattice position, and interdonor separation. This allows us to determine how isolated the ground state singlet and triplet orbitals are from the rest of the excited state Hilbert space. In addition to calculating the energy spectrum, we are also able to evaluate the exchange coupling between the two donor electrons, and the double occupancy probability that both electrons will reside on the same P donor. These two quantities are very important for logical operations in solid-state quantum computing devices, as a large exchange coupling achieves faster gating times, while the magnitude of the double occupancy probability can affect the error rate.

A practical method for identifying intermetallic phase particles in aluminium alloys by electron probe microanalysis

Aluminium alloys that contain Si, Mg, Fe, Mn and/or Cu usually contain one or more types of intermetallic phases that are not readily distinguishable in the microstructure by conventional microscopy methods. It has thus been a challenge to develop a method that will unambiguously identify them. A practical approach has been developed that is based on an inherent linear relationship revealed for the overall distribution of any two elements in a precipitate/matrix geometry and the first-order approximation of electron probe microanalysis (EPMA) results. Application of this approach to a direct chill cast 6082 alloy is demonstrated, and its major limitations are discussed.

Intramolecular electron transfer in a bacterial sulfite dehydrogenase

Sulfite dehydrogenase (SDH) from Starkeya novella, a sulfite-oxidizing molybdenum-containing enzyme, has a novel tightly bound αβ-heterodimeric structure in which the Mo cofactor and the c-type heme are located on different subunits. Flash photolysis studies of intramolecular electron transfer (IET) in SDH show that the process is first-order, independent of solution viscosity, and not inhibited by sulfate, which strongly indicates that IET in SDH proceeds directly through the protein medium and does not involve substantial movement of the two subunits relative to each other. The IET results for SDH contrast with those for chicken and human sulfite oxidase (SO) in which the molybdenum domain is linked to a b-type heme domain through a flexible loop, and IET shows a remarkable dependence on sulfate concentration and viscosity that has been ascribed to interdomain docking. The results for SDH provide additional support for the interdomain docking hypothesis in animal SO and clearly demonstrate that dependence of IET on viscosity and sulfate is not an inherent property of all sulfite-oxidizing molybdenum enzymes.

Electron transfer complex between nitrous oxide reductase and cytochrome c552 from Pseudomonas nautica: kinetic, nuclear magnetic resonance, and docking studies

Biochemistry. 2008 Oct 14;47(41):10852-62. doi: 10.1021/bi801375q

Mediated catalysis of Paracoccus pantotrophus cytochrome c peroxidase by P. pantotrophus pseudoazurin: kinetics of intermolecular electron transfer

J Biol Inorg Chem (2007) 12:691–698 DOI 10.1007/s00775-007-0219-9

Approximation algorithms for two-state anti-ferromagnetic spin systems on bounded degree graphs

In a seminal paper [10], Weitz gave a deterministic fully polynomial approximation scheme for counting exponentially weighted independent sets (which is the same as approximating the partition function of the hard-core model from statistical physics) in graphs of degree at most d, up to the critical activity for the uniqueness of the Gibbs measure on the innite d-regular tree. ore recently Sly [8] (see also [1]) showed that this is optimal in the sense that if here is an FPRAS for the hard-core partition function on graphs of maximum egree d for activities larger than the critical activity on the innite d-regular ree then NP = RP. In this paper we extend Weitz's approach to derive a deterministic fully polynomial approximation scheme for the partition function of general two-state anti-ferromagnetic spin systems on graphs of maximum degree d, up to the corresponding critical point on the d-regular tree. The main ingredient of our result is a proof that for two-state anti-ferromagnetic spin systems on the d-regular tree, weak spatial mixing implies strong spatial mixing. his in turn uses a message-decay argument which extends a similar approach proposed recently for the hard-core model by Restrepo et al [7] to the case of general two-state anti-ferromagnetic spin systems.

Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy.

Cryo-electron microscopy of vitreous sections (CEMOVIS) has recently been shown to provide images of biological specimens with unprecedented quality and resolution. Cutting the sections remains however the major difficulty. Here, we examine the parameters influencing the quality of the sections and analyse the resulting artefacts. They are in particular: knife marks, compression, crevasses, and chatter. We propose a model taking into account the interplay between viscous flow and fracture. We confirm that crevasses are formed on only one side of the section, and define conditions by which they can be avoided. Chatter is an effect of irregular compression due to friction of the section of the knife edge and conditions to prevent this are also explored. In absence of crevasses and chatter, the bulk of the section is compressed approximately homogeneously. Within this approximation, it is possible to correct for compression by a simple linear transformation for the bulk of the section. A research program is proposed to test and refine our understanding of the sectioning process.

Oxidative stress is increased in critically ill patients according to antioxidant vitamins intake, independent of severity: a cohort study

Introduction. Critically ill patients suffer from oxidative stress caused by reactive oxygen species (ROS) and reactive nitrogen species (RNS). Although ROS/RNS are constantly produced under normal circumstances, critical illness can drastically increase their production. These patients have reduced plasma and intracellular levels of antioxidants and free electron scavengers or cofactors, and decreased activity of the enzymatic system involved in ROS detoxification. The pro-oxidant/antioxidant balance is of functional relevance during critical illness because it is involved in the pathogenesis of multiple organ failure. In this study the objective was to evaluate the relation between oxidative stress in critically ill patients and antioxidant vitamin intake and severity of illness. Methods. Spectrophotometry was used to measure in plasma the total antioxidant capacity and levels of lipid peroxide, carbonyl group, total protein, bilirubin and uric acid at two time points: at intensive care unit (ICU) admission and on day seven. Daily diet records were kept and compliance with recommended dietary allowance (RDA) of antioxidant vitamins (A, C and E) was assessed. Results. Between admission and day seven in the ICU, significant increases in lipid peroxide and carbonyl group were associated with decreased antioxidant capacity and greater deterioration in Sequential Organ Failure Assessment score. There was significantly greater worsening in oxidative stress parameters in patients who received antioxidant vitamins at below 66% of RDA than in those who received antioxidant vitamins at above 66% of RDA. An antioxidant vitamin intake from 66% to 100% of RDA reduced the risk for worsening oxidative stress by 94% (ods ratio 0.06, 95% confidence interval 0.010 to 0.39), regardless of change in severity of illness (Sequential Organ Failure Assessment score). Conclusion. The critical condition of patients admitted to the ICU is associated with worsening oxidative stress. Intake of antioxidant vitamins below 66% of RDA and alteration in endogenous levels of substances with antioxidant capacity are related to redox imbalance in critical ill patients. Therefore, intake of antioxidant vitamins should be carefully monitored so that it is as close as possible to RDA.