Optical absorption and electronic band structure first-principles calculations of alpha-glycine crystals

Light absorption of alpha-glycine crystals grown by slow evaporation at room temperature was measured, indicating a 5.11 +/- 0.02 eV energy band gap. Structural, electronic, and optical absorption properties of alpha-glycine crystals were obtained by first-principles quantum mechanical calculations using density functional theory within the generalized gradient approximation in order to understand this result. To take into account the contribution of core electrons, ultrasoft and norm-conserving pseudopotentials, as well as an all electron approach were considered to compute the electronic density of states and band structure of alpha-glycine crystals. They exhibit three indirect energy band gaps and one direct Gamma-Gamma energy gap around 4.95 eV. The optical absorption related to transitions between the top of the valence band and the bottom of the conduction band involves O 2p valence states and C, O 2p conduction states, with the carboxyl group contributing significantly to the origin of the energy band gap. The calculated optical absorption is highly dependent on the polarization of the incident radiation due to the spatial arrangement of the dipolar glycine molecules; in the case of a polycrystalline sample, the first-principles calculated optical absorption is in good agreement with the measurement when a rigid energy shift is applied.

Accurate band gaps of AlGaN, InGaN, and AlInN alloys calculations based on LDA-1/2 approach

We present parameter-free calculations of electronic properties of InGaN, InAlN, and AlGaN alloys. The calculations are based on a generalized quasichemical approach, to account for disorder and composition effects, and first-principles calculations within the density functional theory with the LDA-1/2 approach, to accurately determine the band gaps. We provide precise results for AlGaN, InGaN, and AlInN band gaps for the entire range of compositions, and their respective bowing parameters. (C) 2011 American Institute of Physics. [doi:10.1063/1.3576570]

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.

Characterisation of the effect of a simulated hydrocarbon spill on diazotrophs in mangrove sediment mesocosm

An analysis of the effect of an oil spill on mangrove sediments was carried out by contamination of mesocosms derived from two different mangroves, one with a history of contamination and one pristine. The association between N(2) fixers and hydrocarbon degradation was assessed using quantitative PCR (qPCR) for the genes rrs and nifH, nifH clone library sequencing and total petroleum hydrocarbon (TPH) quantification using gas chromatography. TPH showed that the microbial communities of both mangroves were able to degrade the hydrocarbons added; however, whereas the majority of oil added to the mesocosm derived from the polluted mangrove was degraded in the 75 days of the experiment, there was only partially degradation in the mesocosm derived from the pristine mangrove. qPCR showed that the addition of oil led to an increase in rrs gene copy numbers in both mesocosms, having almost no effect on the nifH copy numbers in the pristine mangrove. Sequencing of nifH clones indicated that the changes promoted by the oil in the polluted mangrove were greater than those observed in the pristine mesocosm. The main effect observed in the polluted mesocosm was the selection of a single phylotype which is probably adapted to the presence of petroleum. These results, together with previous reports, give hints about the relationship between N(2) fixation and hydrocarbon degradation in natural ecosystems.

Annealing effects on microstructure and coercive field of ferritic-martensitic ODS Eurofer steel

Oxide dispersion strengthened reduced-activation ferritic-martensitic steels are promising candidates for applications in future fusion power plants. Samples of a reduced activation ferritic-martensitic 9 wt.%Cr-oxide dispersion strengthened Eurofer steel were cold rolled to 80% reduction in thickness and annealed in vacuum for 1 h from 200 to 1350 degrees C to evaluate its thermal stability. Vickers microhardness testing and electron backscatter diffraction (EBSD) were used to characterize the microstructure. The microstructural changes were also followed by magnetic measurements, in particular the corresponding variation of the coercive field (H(c)), as a function of the annealing treatment. Results show that magnetic measurements were sensitive to detect the changes, in particular the martensitic transformation, in samples annealed above 850 degrees C (austenitic regime). (C) 2010 Elsevier B.V. All rights reserved.

Annealing behavior of ferritic-martensitic 9%Cr-ODS-Eurofer steel

Oxide dispersion strengthened ferritic-martensitic steels are potential candidates for applications in future fusion power plants. High creep resistance, good oxidation resistance, reduced neutron activation and microstructural long-term stability at temperatures of about 650-700 degrees C are required in this context. In order to evaluate its thermal stability in the ferritic phase field, samples of the reduced activation ferritic-martensitic 9%Cr-ODS-Eurofer steel were cold rolled to 50% and 80% reductions and further annealed in vacuum from 300 to 800 degrees C for 1 h. The characterization in the annealed state was performed by scanning electron microscopy in the backscattered electron mode, high-resolution electron backscatter diffraction and transmission electron microscopy. Results show that the fine dispersion of Y-based particles (about 10 nm in size) is effective to prevent recrystallization. The low recrystallized volume fraction (<0.1) is associated to the nuclei found at prior grain boundaries and around large M(23)C(6) particles. Static recovery was found to be the predominant softening mechanism of this steel in the investigated temperature range. (c) 2010 Elsevier B.V. All rights reserved.

ANNEALING EFFECTS ON THE MICROSTRUCTURE OF FERRITIC-MARTENSITIC ODS-EUROFER STEEL

Oxide dispersion strengthened (ODS) ferritic/martensitic (FM) steels are promising candidates for structural applications in future fusion power reactors. In order to evaluate the thermal stability of 80% cold-rolled ODS-EUROFER, samples were annealed for 1 h at temperatures up to about 0.9 T(m), where T(m) is the absolute melting point. The characterization of the annealed samples was performed using transmission electron microscopy and electron backscatter diffraction. Results show that static recovery is the main softening mechanism of this steel when annealed below 800 degrees C. The volume fraction of recrystallized grains is quite small (below 0.10). Above 900 degrees C, martensitic transformation takes place causing pronounced hardening. Large M(23)C(6) particles are found at the grain boundaries after tempering at 750 degrees C for 2 h.

Thin titanium oxide films deposited by e-beam evaporation with additional rapid thermal oxidation and annealing for ISFET applications

Titanium oxide (TiO(2)) has been extensively applied in the medical area due to its proved biocompatibility with human cells [1]. This work presents the characterization of titanium oxide thin films as a potential dielectric to be applied in ion sensitive field-effect transistors. The films were obtained by rapid thermal oxidation and annealing (at 300, 600, 960 and 1200 degrees C) of thin titanium films of different thicknesses (5 nm, 10 nm and 20 nm) deposited by e-beam evaporation on silicon wafers. These films were analyzed as-deposited and after annealing in forming gas for 25 min by Ellipsometry, Fourier Transform Infrared Spectroscopy (FTIR), Raman Spectroscopy (RAMAN), Atomic Force Microscopy (AFM), Rutherford Backscattering Spectroscopy (RBS) and Ti-K edge X-ray Absorption Near Edge Structure (XANES). Thin film thickness, roughness, surface grain sizes, refractive indexes and oxygen concentration depend on the oxidation and annealing temperature. Structural characterization showed mainly presence of the crystalline rutile phase, however, other oxides such Ti(2)O(3), an interfacial SiO(2) layer between the dielectric and the substrate and the anatase crystalline phase of TiO(2) films were also identified. Electrical characteristics were obtained by means of I-V and C-V measured curves of Al/Si/TiO(x)/Al capacitors. These curves showed that the films had high dielectric constants between 12 and 33, interface charge density of about 10(10)/cm(2) and leakage current density between 1 and 10(-4) A/cm(2). Field-effect transistors were fabricated in order to analyze I(D) x V(DS) and log I(D) x Bias curves. Early voltage value of -1629 V, R(OUT) value of 215 M Omega and slope of 100 mV/dec were determined for the 20 nm TiO(x) film thermally treated at 960 degrees C. (C) 2009 Elsevier B.V. All rights reserved.

Identification by computer-simulated RFLP of phytoplasmas associated with eggplant giant calyx representative of two subgroups, a lineage of 16SrIII-J and the new subgroup 16SrIII-U

Symptoms resembling giant calyx, a graft-transmissible disease, were observed on 1-5% of eggplant (aubergine; Solanum melongena L.) plants in production fields in Sao Paulo state, Brazil. Phytoplasmas were detected in 1 2 of 1 2 samples from symptomatic plants that were analysed by a nested PCR assay employing 16S rRNA gene primers R16mF2/R16mR1 followed by R16F2n/R16R2. RFLP analysis of the resulting rRNA gene products (1.2 kb) indicated that all plants contained similar phytoplasmas, each closely resembling strains previously classified as members of RFLP group 16SrIII (X-disease group). Virtual RFLP and phylogenetic analyses of sequences derived from PCR products identified phytoplasmas infecting eggplant crops grown in Piracicaba as a lineage of the subgroup 16SrIII-J, whereas phytoplasmas detected in plants grown in Braganca Paulista were tentatively classified as members of a novel subgroup 16SrIII-U. These findings confirm eggplant as a new host of group 16SrIII-J phytoplasmas and extend the known diversity of strains belonging to this group in Brazil.

Viability of Lactobacillus acidophilus in synbiotic guava mousses and its survival under in vitro simulated gastrointestinal conditions

The effects of refrigeration, freezing and substitution of milk fat by inulin and whey protein concentrate (WPC) on Lactobacillus acidophilus La-5 viability and resistance to gastric and enteric simulated conditions in synbiotic guava mousses effects were investigated. Refrigerated mousses supplemented with WPC presented the best probiotic viability. ranging from 7.77 to 6.24 log cfu/g during 28 days of storage. The highest probiotic populations, above 7.45 log cfu/g, were observed for all frozen mousses during 112 days of storage. Decreased L acidophilus survival during the in vitro gastrointestinal simulation was observed both for refrigerated and frozen mousses. Nonetheless, for the refrigerated mousses, the addition of inulin enhanced the probiotic survival during the in vitro assays in the first week of storage. L acidophilus survival in simulated gastrointestinal fluids was also improved through freezing. The frozen storage may be used to provide increased shelf-life for synbiotic guava mousses. Even though the protective effect of inulin and WPC on the probiotic microorganism tested was shown to be more specific for the refrigerated products, the partial replacement of milk fat by these ingredients may also help, as it improves the nutritional value of mousses in both storage conditions. (C) 2009 Elsevier B.V. All rights reserved.

Non-Equilibrium Reaction Rates in the Macroscopic Chemistry Method for DSMC Calculations

The Direct Simulation Monte Carlo (DSMC) method is used to simulate the flow of rarefied gases. In the Macroscopic Chemistry Method (MCM) for DSMC, chemical reaction rates calculated from local macroscopic flow properties are enforced in each cell. Unlike the standard total collision energy (TCE) chemistry model for DSMC, the new method is not restricted to an Arrhenius form of the reaction rate coefficient, nor is it restricted to a collision cross-section which yields a simple power-law viscosity. For reaction rates of interest in aerospace applications, chemically reacting collisions are generally infrequent events and, as such, local equilibrium conditions are established before a significant number of chemical reactions occur. Hence, the reaction rates which have been used in MCM have been calculated from the reaction rate data which are expected to be correct only for conditions of thermal equilibrium. Here we consider artificially high reaction rates so that the fraction of reacting collisions is not small and propose a simple method of estimating the rates of chemical reactions which can be used in the Macroscopic Chemistry Method in both equilibrium and non-equilibrium conditions. Two tests are presented: (1) The dissociation rates under conditions of thermal non-equilibrium are determined from a zero-dimensional Monte-Carlo sampling procedure which simulates ‘intra-modal’ non-equilibrium; that is, equilibrium distributions in each of the translational, rotational and vibrational modes but with different temperatures for each mode; (2) The 2-D hypersonic flow of molecular oxygen over a vertical plate at Mach 30 is calculated. In both cases the new method produces results in close agreement with those given by the standard TCE model in the same highly nonequilibrium conditions. We conclude that the general method of estimating the non-equilibrium reaction rate is a simple means by which information contained within non-equilibrium distribution functions predicted by the DSMC method can be included in the Macroscopic Chemistry Method.

Annealing of ion implanted gallium nitride

In this paper, we examine Si and Te ion implant damage removal in GaN as a function of implantation dose, and implantation and annealing temperature. Transmission electron microscopy shows that amorphous layers, which can result from high-dose implantation, recrystallize between 800 and 1100 °C to very defective polycrystalline material. Lower-dose implants (down to 5 × 1013 cm – 2), which are not amorphous but defective after implantation, also anneal poorly up to 1100 °C, leaving a coarse network of extended defects. Despite such disorder, a high fraction of Te is found to be substitutional in GaN both following implantation and after annealing. Furthermore, although elevated-temperature implants result in less disorder after implantation, this damage is also impossible to anneal out completely by 1100 °C. The implications of this study are that considerably higher annealing temperatures will be needed to remove damage for optimum electrical properties. ©1998 American Institute of Physics.

The solution structure of a copper(II) compound of a new cyclic octapeptide by EPR spectroscopy and force field calculations

A new cyclic octapeptide, cyclo(Ile-Ser-(Gly)Thz-Ile-Thr-(Gly)Thz) (PatN), related to patellamide A, has been synthesized and reacted with copper(II) and base to form mono- and dinuclear complexes. The coordination environments around copper(TI) have been characterized by EPR spectroscopy. The solution structure of the thermodynamically most stable product, a purple dicopper(TI) compound, has been examined by simulating weakly dipole-dipole coupled EPR spectra based upon structural parameters obtained from force field (MM and MD) calculations. The MM-EPR method produces a saddle-shaped structure for [Cu-2(PatN)(OH2)(6)] that is similar to the known solution structure of patellamide A and the known solid-state structure of [Cu-2(AscidH(2))CO3(OH2)(2)]. Compared with the latter, [Cu-2(PatN)] has no carbonate bridge and a significantly flatter topology. The MM-EPR approach to solution-structure determination for paramagnetic metallopeptides may find wide applications to other metallopeptides and metalloproteins.

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.