Ab initio electronic properties of dual phosphorus monolayers in silicon

In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated.     

Crystal structure and ab initio calculations of CaZrO3

Calcium zirconate (CaZrO₃), because of its high melting point, low thermal expansion coefficient, high strength and excellent corrosion resistance against alkali oxides, is a good candidate for a novel refractory material. CaZrO₃ is mostly synthesized by the reaction in the solid state but the material obtained in such a way often suffers low bulk density, high porosity and other defects which lower its potential application value. To overcome these obstacles a novel synthesis method by an electric arc melting technique was proposed. The crystal structure of melted CaZrO₃ was compared with a conventionally synthesized material. According to X-ray measurements the obtained material has an orthorhombic perovskite-like structure. Its stoichiometry was confirmed by the scanning electron microscope and EDS analysis. The material is almost poreless with its density close to theoretical. The estimated crystal structure parameters were used to calculate the electronic structure of CaZrO₃ using the full potential linear augmented plane wave (FLAPW) method. It has been found that CaZrO₃ is an insulator with the energy band gap of 4.1 eV. The Ca-O bond is typically ionic while Zr-O bond is of a significant covalent character.     

First-principles, UV Raman, X-ray diffraction and TEM study of the structure and lattice dynamics of the diamond-lonsdaleite system

We report the results of the study of the polycrystalline powder of the diamond-lonsdaleite system by X-ray diffractometry, transmission electron microscopy and UV Raman spectroscopy. The measured data of structural parameters are in good agreement with ab initio calculations. We show that the Raman spectrum is proportional to the phonon density of states of the diamond-lonsdaleite system.     

Study of the oxygen vacancy influence on magnetic properties of Fe- and Co-doped SnO2 diluted alloys

Transition-metal (TM)-doped diluted magnetic oxides (DMOs) have attracted attention from both experimental and theoretical points of view due to their potential use in spintronics towards new nanostructured devices and new technologies. In the present work, we study the magnetic properties of Sn_0.96TM_0.04O₂ and Sn_0.96TM_0.04O_1.98(V_O)_0.02, where TM = Fe and Co, focusing in particular in the role played by the presence of O vacancies nearby the TM. The calculated total energy as a function of the total magnetic moment per cell shows a magnetic metastability, corresponding to a ground state, respectively, with 2 and 1 μ_B/cell, for Fe and Co. Two metastable states, with 0 and 4 μ_B/cell were found for Fe, and a single value, 3 μ_B/cell, for Co. The spin-crossover energies (E_S) were calculated. The values are E_S^0/2 = 107 meV and E_S^4/2 = 25 meV for Fe. For Co, E_S^3/1 = 36 meV. By creating O vacancies close to the TM site, we show that the metastablity and E_S change. For iron, a new state appears, and the state with zero magnetic moment disappears. The ground state is 4 μ_B/cell instead of 2 μ_B/cell, and the energy E_S^2/4 is 30 meV. For cobalt, the ground state is then found with 3 μ_B/cell and the metastable state with 1 μ_B/cell. The spin-crossover energy E_S^1/3 is 21 meV. Our results suggest that these materials may be used in devices for spintronic applications that require different magnetization states.     

Influence of tert-amine groups on the solubility of polymers in CO2

There is a need to develop new, non-fluorous polymers that are highly soluble in CO₂. Experimental evidence indicates that tertiary amine and pyridine groups may exhibit favorable Lewis acid-Lewis base type interactions with CO₂. It is therefore reasonable to assume that incorporation of tertiary amines into the side chain or backbone of non-fluorous polymers may impart a degree of CO₂-solubility to the polymer. We present experimental results for eight different tert-amine-containing polymers. Of these polymers, only propyl dimethylamine-functionalized poly(dimethylsiloxane) is soluble in CO₂ at temperatures and pressures accessible in our experiments, but even this polymer is less soluble than non-functionalized poly(dimethylsiloxane) at the same chain length. We have performed ab initio calculations on tertiary amine-containing moieties representative of some of the polymers examined experimentally. Our calculations confirm that amine-CO₂ interactions are indeed energetically favorable. However, we also find that the moiety self-interactions are typically more favorable than the CO₂-moiety interactions. This indicates that the lack of solubility of amine-containing polymers in CO₂ is a direct result of strong polymer-polymer interactions.     

Towards a Molecular Understanding of the Biosynthesis of Amaryllidaceae Alkaloids in Support of Their Expanding Medical Use

The alkaloids characteristically produced by the subfamily Amaryllidoideae of the Amaryllidaceae, bulbous plant species that include well know genera such as Narcissus (daffodils) and Galanthus (snowdrops), are a source of new pharmaceutical compounds. Presently, only the Amaryllidaceae alkaloid galanthamine, an acetylcholinesterase inhibitor used to treat symptoms of Alzheimer’s disease, is produced commercially as a drug from cultivated plants. However, several Amaryllidaceae alkaloids have shown great promise as anti-cancer drugs, but their further clinical development is restricted by their limited commercial availability. Amaryllidaceae species have a long history of cultivation and breeding as ornamental bulbs, and phytochemical research has focussed on the diversity in alkaloid content and composition. In contrast to the available pharmacological and phytochemical data, ecological, physiological and molecular aspects of the Amaryllidaceae and their alkaloids are much less explored and the identity of the alkaloid biosynthetic genes is presently unknown. An improved molecular understanding of Amaryllidaceae alkaloid biosynthesis would greatly benefit the rational design of breeding programs to produce cultivars optimised for the production of pharmaceutical compounds and enable biotechnology based approaches.     

Solvation of hydrocarbon radicals in sub-CW and SCW: An ab initio MD study

Solvation of methyl radicals in subcritical and supercritical water was investigated with the ab initio MD simulation to increase the understanding of the thermal cracking of hydrocarbons under the severe hydrothermal environments. The calculation results show that water clusters around the radical could be formed with the following prerequisites: the bulk density of water is close to liquid phase, and the state point of water on its phase diagram is far away from the critical point and from the vapor-liquid equilibrium boundary. The occurrence of water clusters superimposes a negative influence on the originally depressed diffusivity of the radical under the dense hydrothermal environments, and the interference from the immediately adjacent water molecules with the frontier orbitals of the radical results in randomly reduced activity of the radical. Regardless of whether there are water clusters around the radical or not, in subcritical and supercritical water the bimolecular reactions participating via hydrocarbon radicals should be partially suppressed by the reduced diffusivity and lower activity of the radical.     

Ab initio study on the Li deintercalation in ternary lithium nitridocuprate Li2.5Cu0.5N

Using the first-principles method within the density functional theory and the generalized gradient approximation, the properties of lithium deintercalation were studied in the ternary lithium transition metal nitride Li_2.5Cu_0.5N. The lithium deintercalation formation energies per lithium atom were found to be between −2.72 and −4.08 eV for various amounts of Li extraction. The changes in the crystal volume, the electronic structures and the changes in charge densities of the Li_xCu_0.5N due to Li extractions are also presented. This study demonstrates that the extraction of lithium ions from the [Li₂N] layer is easier than that from the [Li_0.5Cu_0.5] layer. The change in unit cell volume was less than 5% for extractions of less than 30% of the Li ions in the unit cell. However, for a higher percentage of Li extractions, the system could shrink much more remarkably. The sequence of Li deintercalation, which was based on the calculated formation energies and the ratio of volume change, also gave some insight into the amorphization phenomenon after the first charge.     

First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum

The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state.     

Effects of a buried cysteine-to-serine mutation on yeast triosephosphate isomerase structure and stability

All the members of the triosephosphate isomerase (TIM) family possess a cystein residue (Cys126) located near the catalytically essential Glu165. The evolutionarily conserved Cys126, however, does not seem to play a significant role in the catalytic activity. On the other hand, substitution of this residue by other amino acid residues destabilizes the dimeric enzyme, especially when Cys is replaced by Ser. In trying to assess the origin of this destabilization we have determined the crystal structure of Saccharomyces cerevisiae TIM (ScTIM) at 1.86 Å resolution in the presence of PGA, which is only bound to one subunit. Comparisons of the wild type and mutant structures reveal that a change in the orientation of the Ser hydroxyl group, with respect to the Cys sulfhydryl group, leads to penetration of water molecules and apparent destabilization of residues 132–138. The latter results were confirmed by means of Molecular Dynamics, which showed that this region, in the mutated enzyme, collapses at about 70 ns.     

In situ wet-cell TEM observation of gold nanoparticle motion in an aqueous solution

In situ wet-cell transmission electron microscopy (TEM) technology enables direct observation of nanomaterials in a fully hydrated environment with high spatial and temporal resolution, which can be used to address a wide range of scientific problems. In this paper, the motions of approximately 5-nm sized gold nanoparticles in an aqueous solution are studied using the wet-cell TEM technology. It is observed that gold nanoparticles can be either in a single particle or cluster forms, and dynamic displacement and rotation motions are observed for both forms in the solution. Under electron beam irradiation, nanoparticles in some clusters gradually fused together; sometimes they also showed dramatic growth behavior. Mechanisms for the motion and growth of the particles/clusters are discussed.     

Polymorphisms of the Ovine BMPR-IB,BMP-15 and FSHR and Their Associations with Litter Size in Two Chinese Indigenous Sheep Breeds

The Small Tailed Han sheep and Hu sheep are two prolific local sheep in China. In this study, the polymorphisms of BMPR-IB (Bone morphogenetic protein receptor IB), BMP-15 (Bone morphogenetic protein 15) and FSHR (follicle stimulating hormone receptor) were investigated to check whether they are associated with litter size in Small Tailed Han sheep and Hu sheep. Consequently, three polymorphisms, FecB mutation in BMPR-IB (c.746A>G), FecG mutation in BMP-15 (c.718C>T) and the mutation (g. 47C>T) in FSHR were found in the above two sheep breeds with a total number of 1630 individuals. The single marker association analysis showed that the three mutations were significantly associated with litter size. The ewes with genotype FecB^B/FecB^B and FecB^B/FecB⁺ had 0.78 and 0.58 more lambs (p < 0.01) than those with genotype FecB⁺/FecB⁺, respectively. The heterozygous Han and Hu ewes with FecX^G/FecX⁺ genotype showed 0.30 (p = 0.05) more lambs than those with the FecX⁺/FecX⁺ genotype. For FSHR gene, the ewes with genotype CC had 0.52 (p < 0.01) and 0.75 (p < 0.01) more lambs than those with genotypes TC and TT, respectively. Combined effect analyses indicated an extremely significant interaction (p < 0.01) between the random combinations of BMPR-IB, BMP-15 and FSHR genes on litter size. In addition, the Han and Hu ewes with BB/G+/CC genotype harbor the highest litter size among ewes analyzed in current study. In conclusion, BMPR-IB, BMP-15 and FSHR polymorphisms could be used as genetic markers in multi-gene pyramiding for improving litter size in sheep husbandry.     

Integrated -Omics: A Powerful Approach to Understanding the Heterogeneous Lignification of Fibre Crops

Lignin and cellulose represent the two main components of plant secondary walls and the most abundant polymers on Earth. Quantitatively one of the principal products of the phenylpropanoid pathway, lignin confers high mechanical strength and hydrophobicity to plant walls, thus enabling erect growth and high-pressure water transport in the vessels. Lignin is characterized by a high natural heterogeneity in its composition and abundance in plant secondary cell walls, even in the different tissues of the same plant. A typical example is the stem of fibre crops, which shows a lignified core enveloped by a cellulosic, lignin-poor cortex. Despite the great value of fibre crops for humanity, however, still little is known on the mechanisms controlling their cell wall biogenesis, and particularly, what regulates their spatially-defined lignification pattern. Given the chemical complexity and the heterogeneous composition of fibre crops’ secondary walls, only the use of multidisciplinary approaches can convey an integrated picture and provide exhaustive information covering different levels of biological complexity. The present review highlights the importance of combining high throughput -omics approaches to get a complete understanding of the factors regulating the lignification heterogeneity typical of fibre crops.     

Influence of argon plasma on the deposition of Al2O3 film onto the PET surfaces by atomic layer deposition

In this paper, polyethyleneterephthalate (PET) films with and without plasma pretreatment were modified by atomic layer deposition (ALD) and plasma-assisted atomic layer deposition (PA-ALD). It demonstrates that the Al₂O₃ films are successfully deposited onto the surface of PET films. The cracks formed on the deposited Al₂O₃ films in the ALD, plasma pretreated ALD, and PA-ALD were attributed to the energetic ion bombardment in plasmas. The surface wettability in terms of water contact angle shows that the deposited Al₂O₃ layer can enhance the wetting property of modified PET surface. Further characterizations of the Al₂O₃ films suggest that the elevated density of hydroxyl -OH group improve the initial growth of ALD deposition. Chemical composition of the Al₂O₃-coated PET film was characterized by X-ray photoelectron spectroscopy, which shows that the content of C 1s reduces with the growing of O 1s in the Al₂O₃-coated PET films, and the introduction of plasma in the ALD process helps the normal growth of Al₂O₃ on PET in PA-ALD.     

Effects of inflorescence stem structure and cell wall components on the mechanical strength of inflorescence stem in herbaceous peony

Herbaceous peony (Paeonia lactiflora Pall.) is a traditional famous flower, but its poor inflorescence stem quality seriously constrains the development of the cut flower. Mechanical strength is an important characteristic of stems, which not only affects plant lodging, but also plays an important role in stem bend or break. In this paper, the mechanical strength, morphological indices and microstructure of P. lactiflora development inflorescence stems were measured and observed. The results showed that the mechanical strength of inflorescence stems gradually increased, and that the diameter of inflorescence stem was a direct indicator in estimating mechanical strength. Simultaneously, with the development of inflorescence stem, the number of vascular bundles increased, the vascular bundle was arranged more densely, the sclerenchyma cell wall thickened, and the proportion of vascular bundle and pith also increased. On this basis, cellulose and lignin contents were determined, PlCesA3, PlCesA6 and PlCCoAOMT were isolated and their expression patterns were examined including PlPAL. The results showed that cellulose was not strictly correlated with the mechanical strength of inflorescence stem, and lignin had a significant impact on it. In addition, PlCesA3 and PlCesA6 were not key members in cellulose synthesis of P. lactiflora and their functions were also different, but PlPAL and PlCCoAOMT regulated the lignin synthesis of P. lactiflora. These data indicated that PlPAL and PlCCoAOMT could be applied to improve the mechanical strength of P. lactiflora inflorescence stem in genetic engineering.     

Exploring the Nature of Silicon-Noble Gas Bonds in H3SiNgNSi and HSiNgNSi Compounds (Ng = Xe,Rn)

Ab initio and density functional theory-based computations are performed to investigate the structure and stability of H₃SiNgNSi and HSiNgNSi compounds (Ng = Xe, Rn). They are thermochemically unstable with respect to the dissociation channel producing Ng and H₃SiNSi or HSiNSi. However, they are kinetically stable with respect to this dissociation channel having activation free energy barriers of 19.3 and 23.3 kcal/mol for H₃SiXeNSi and H₃SiRnNSi, respectively, and 9.2 and 12.8 kcal/mol for HSiXeNSi and HSiRnNSi, respectively. The rest of the possible dissociation channels are endergonic in nature at room temperature for Rn analogues. However, one three-body dissociation channel for H₃SiXeNSi and one two-body and one three-body dissociation channels for HSiXeNSi are slightly exergonic in nature at room temperature. They become endergonic at slightly lower temperature. The nature of bonding between Ng and Si/N is analyzed by natural bond order, electron density and energy decomposition analyses. Natural population analysis indicates that they could be best represented as (H₃SiNg)⁺(NSi)⁻ and (HSiNg)⁺(NSi)⁻. Energy decomposition analysis further reveals that the contribution from the orbital term (ΔE_orb) is dominant (ca. 67%–75%) towards the total attraction energy associated with the Si-Ng bond, whereas the electrostatic term (ΔE_elstat) contributes the maximum (ca. 66%–68%) for the same in the Ng–N bond, implying the covalent nature of the former bond and the ionic nature of the latter.     

Molecular dynamics simulation of cis-1,4-polybutadiene. 2. Chain motion and origin of the fast process

Molecular dynamics (MD) simulations of cis-1,4-polybutadiene in bulk amorphous state were performed to elucidate the origin of a fast relaxation process observed by quasielastic neutron scattering (QENS) measurements. The details of the torsional motion for each dihedral angle were investigated with the torsional auto- and cross-correlation functions for several temperatures in this study. Temperature dependence of the correlation between the torsional autocorrelation and cross-correlation functions is also evaluated. The origin of the fast process of cis-1,4-polybutadiene is found to be mainly the cooperative conformational transitions of two dihedral angles located at both sides of the CH₂-CH₂ bond when the bond is in the trans conformation. The cooperative conformational transitions exhibit even below the glass transition temperature of cis-1,4-polybutadiene. The cooperative motion appears at about 50 K below the glass transition temperature, corresponding to the Vogel-Fulcher temperature.     

Differential Proteomic Analysis of the Pancreas of Diabetic db/db Mice Reveals the Proteins Involved in the Development of Complications of Diabetes Mellitus

Type 2 diabetes mellitus is characterized by hyperglycemia and insulin-resistance. Diabetes results from pancreatic inability to secrete the insulin needed to overcome this resistance. We analyzed the protein profile from the pancreas of ten-week old diabetic db/db and wild type mice through proteomics. Pancreatic proteins were separated in two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and significant changes in db/db mice respect to wild type mice were observed in 27 proteins. Twenty five proteins were identified by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) and their interactions were analyzed using search tool for the retrieval of interacting genes/proteins (STRING) and database for annotation, visualization and integrated discovery (DAVID). Some of these proteins were Pancreatic α-amylase, Cytochrome b5, Lithostathine-1, Lithostathine-2, Chymotrypsinogen B, Peroxiredoxin-4, Aspartyl aminopeptidase, Endoplasmin, and others, which are involved in the metabolism of carbohydrates and proteins, as well as in oxidative stress, and inflammation. Remarkably, these are mostly endoplasmic reticulum proteins related to peptidase activity, i.e., they are involved in proteolysis, glucose catabolism and in the tumor necrosis factor-mediated signaling pathway. These results suggest mechanisms for insulin resistance, and the chronic inflammatory state observed in diabetes.     

Ab initio study of interfacial correlations in polymer electrolyte membranes for fuel cells at low hydration

Polymer electrolyte membranes (PEMs) are the critical components of polymer electrolyte fuel cells (PEFCs). Proper operation of current PEMs hinges on sufficient amounts of water as the medium for proton conduction. Membrane dehydration, thus, causes failure of the fuel cell. For the design of advanced PEMs it is of foremost interest, whether high-proton mobility could be attained at low hydration and elevated temperature (>100 °C). Under such conditions structural correlations and interfacial proton transport at acid-functionalized hydrated polymer aggregates are vital for membrane operation. We consider a minimally hydrated, densely packed array of proton-binding surface groups as a model of microscopic interfacial elements in PEMs. Terminating carbon atoms of these surface groups are fixed at the positions of a regular hexagonal array. We explore the role of density, chemical architecture, and conformational flexibility of surface groups on interfacial correlations and acid dissociation. The transition from highly ordered to clustered conformations occurs at the same critical density of surface groups for all systems. For longer polymeric sidechains, the formation energy at the most stable conformation decreases slightly, while the range of 2D correlations extends to markedly reduced densities of surface groups.