Crack mechanical failure in lithium niobate crystal under ion irradiation; novel simulation by extended finite elements

Swift heavy ion irradiation (ions with mass heavier than 15 and energy exceeding MeV/amu) transfer their energy mainly to the electronic system with small momentum transfer per collision. Therefore, they produce linear regions (columnar nano-tracks) around the straight ion trajectory, with marked modifications with respect to the virgin material, e.g., phase transition, amorphization, compaction, changes in physical or chemical properties. In the case of crystalline materials the most distinctive feature of swift heavy ion irradiation is the production of amorphous tracks embedded in the crystal. Lithium niobate is a relevant optical material that presents birefringence due to its anysotropic trigonal structure. The amorphous phase is certainly isotropic. In addition, its refractive index exhibits high contrast with those of the crystalline phase. This allows one to fabricate waveguides by swift ion irradiation with important technological relevance. From the mechanical point of view, the inclusion of an amorphous nano-track (with a density 15% lower than that of the crystal) leads to the generation of important stress/strain fields around the track. Eventually these fields are the origin of crack formation with fatal consequences for the integrity of the samples and the viability of the method for nano-track formation. For certain crystal cuts (X and Y), these fields are clearly anisotropic due to the crystal anisotropy. We have used finite element methods to calculate the stress/strain fields that appear around the ion-generated amorphous nano-tracks for a variety of ion energies and doses. A very remarkable feature for X cut-samples is that the maximum shear stress appears on preferential planes that form +/-45º with respect to the crystallographic planes. This leads to the generation of oriented surface cracks when the dose increases. The growth of the cracks along the anisotropic crystal has been studied by means of novel extended finite element methods, which include cracks as discontinuities. In this way we can study how the length and depth of a crack evolves as function of the ion dose. In this work we will show how the simulations compare with experiments and their application in materials modification by ion irradiation.

An extended electron beam for auroral studies

An electrically floating metallic bare tether in a low Earth orbit would be highly negative with respect to the ambient plasma over most of its length, and would be bombarded by ambient ions. This would liberate secondary electrons, which, after acceleration through the same voltage, would form a magnetically guided two-sided planar e-beam. Upon impact on the atmospheric E-layer, at about 120-140 Km altitude auroral effects (ionization and light emission) can be expected. This paper examines in a preliminary way the feasibility of using this effect as an upper atmospheric probe. It is concluded that significant perturbations can be produced along the illuminated planar sheet of the atmosphere, with ionization rates of several thousand cm-3 sec1. Observation of the induced optical emission is made difficult by the narrowness and high moving speed of the illuminated zone, but it is shown that vertical resolution of single spectral lines is possible, as is wider spectral coverage with no vertical resolution.

Interband absorption of photons by extended states in intermediate band solar cells

This paper considers sub-bandgap photon absorption in an InAs/GaAs quantum dot matrix. Absorption coefficients are calculated for transitions from the extended states in the valence band to confined states in the conduction band. This completes a previous body of work in which transitions between bound states were calculated. The calculations are based on the empirical k·p Hamiltonian considering the quantum dots as parallelepipeds. The extended states may be only partially extended?in one or two dimensions?or extended in all three dimensions. It is found that extended-to-bound transitions are, in general, weaker than bound-to-bound transitions, and that the former are weaker when the initial state is extended in more coordinates. This study is of direct application to the research of intermediate band solar cells and other semiconductor devices based on light absorption in semiconductors nanostructured with quantum dots.

Oxygen extended sooting index of FAME blends with aviation kerosene

The use of biofuels in the aviation sector has economic and environmental benefits. Among the options for the production of renewable jet fuels, hydroprocessed esters and fatty acids (HEFA) have received predominant attention in comparison with fatty acid methyl esters (FAME), which are not approved as additives for jet fuels. However, the presence of oxygen in methyl esters tends to reduce soot emissions and therefore particulate matter emissions. This sooting tendency is quantified in this work with an oxygen-extended sooting index, based on smoke point measurements. Results have shown considerable reduction in the sooting tendency for all biokerosenes (produced by transesterification and eventually distillation) with respect to fossil kerosenes. Among the tested biokerosenes, that made from palm kernel oil was the most effective one, and nondistilled methyl esters (from camelina and linseed oils) showed lower effectiveness than distilled biokerosenes to reduce the sooting tendency. These results may constitute an additional argument for the use of FAME’s as blend components of jet fuels. Other arguments were pointed out in previous publications, but some controversy has aroused over the use of these components. Some of the criticism was based on the fact that the methods used in our previous work are not approved for jet fuels in the standard methods and concluded that the use of FAME in any amount is, thus, inappropriate. However, some of the standard methods are not updated for considering oxygenated components (like the method for obtaining the lower heating value), and others are not precise enough (like the methods for measuring the freezing point), whereas some alternative methods may provide better reproducibility for oxygenated fuels.

Extended phone log-likelihood ratio features and acoustic-based I-vectors for language recognition

This paper presents new techniques with relevant improvements added to the primary system presented by our group to the Albayzin 2012 LRE competition, where the use of any additional corpora for training or optimizing the models was forbidden. In this work, we present the incorporation of an additional phonotactic subsystem based on the use of phone log-likelihood ratio features (PLLR) extracted from different phonotactic recognizers that contributes to improve the accuracy of the system in a 21.4% in terms of Cavg (we also present results for the official metric during the evaluation, Fact). We will present how using these features at the phone state level provides significant improvements, when used together with dimensionality reduction techniques, especially PCA. We have also experimented with applying alternative SDC-like configurations on these PLLR features with additional improvements. Also, we will describe some modifications to the MFCC-based acoustic i-vector system which have also contributed to additional improvements. The final fused system outperformed the baseline in 27.4% in Cavg.

The extended Betz–Lanchester limit

A proposal for an extended formulation of the power coefficient of a wind turbine is presented. This new formulation is a generalization of the Betz–Lanchester expression for the power coefficient as function of the axial deceleration of the wind speed provoked by the wind turbine in operation. The extended power coefficient takes into account the benefits of the power produced and the cost associated to the production of this energy. By the simple model proposed is evidenced that the purely energetic optimum operation condition giving rise to the Betz–Lanchester limit (maximum energy produced) does not coincide with the global optimum operational condition (maximum benefit generated) if cost of energy and degradation of the wind turbine during operation is considered. The new extended power coefficient is a general parameter useful to define global optimum operation conditions for wind turbines, considering not only the energy production but also the maintenance cost and the economic cost associated to the life reduction of the machine.

Membrane-bound state of the colicin E1 channel domain as an extended two-dimensional helical array

Atomic level structures have been determined for the soluble forms of several colicins and toxins, but the structural changes that occur after membrane binding have not been well characterized. Changes occurring in the transition from the soluble to membrane-bound state of the C-terminal 190-residue channel polypeptide of colicin E1 (P190) bound to anionic membranes are described. In the membrane-bound state, the α-helical content increases from 60–64% to 80–90%, with a concomitant increase in the average length of the helical segments from 12 to 16 or 17 residues, close to the length required to span the membrane bilayer in the open channel state. The average distance between helical segments is increased and interhelix interactions are weakened, as shown by a major loss of tertiary structure interactions, decreased efficiency of fluorescence resonance energy transfer from an energy donor on helix V of P190 to an acceptor on helix IX, and decreased resonance energy transfer at higher temperatures, not observed in soluble P190, implying freedom of motion of helical segments. Weaker interactions are also shown by a calorimetric thermal transition of low cooperativity, and the extended nature of the helical array is shown by a 3- to 4-fold increase in the average area subtended per molecule to 4,200 Å2 on the membrane surface. The latter, with analysis of the heat capacity changes, implies the absence of a developed hydrophobic core in the membrane-bound P190. The membrane interfacial layer thus serves to promote formation of a highly helical extended two-dimensional flexible net. The properties of the membrane-bound state of the colicin channel domain (i.e., hydrophobic anchor, lengthened and loosely coupled α-helices, and close association with the membrane interfacial layer) are plausible structural features for the state that is a prerequisite for voltage gating, formation of transmembrane helices, and channel opening.

A peptide that inhibits hydroxyapatite growth is in an extended conformation on the crystal surface

Proteins play an important role in the biological mechanisms controlling hard tissue development, but the details of molecular recognition at inorganic crystal interfaces remain poorly characterized. We have applied a recently developed homonuclear dipolar recoupling solid-state NMR technique, dipolar recoupling with a windowless sequence (DRAWS), to directly probe the conformation of an acidic peptide adsorbed to hydroxyapatite (HAP) crystals. The phosphorylated hexapeptide, DpSpSEEK (N6, where pS denotes phosphorylated serine), was derived from the N terminus of the salivary protein statherin. Constant-composition kinetic characterization demonstrated that, like the native statherin, this peptide inhibits the growth of HAP seed crystals when preadsorbed to the crystal surface. The DRAWS technique was used to measure the internuclear distance between two 13C labels at the carbonyl positions of the adjacent phosphoserine residues. Dipolar dephasing measured at short mixing times yielded a mean separation distance of 3.2 ± 0.1 Å. Data obtained by using longer mixing times suggest a broad distribution of conformations about this average distance. Using a more complex model with discrete α-helical and extended conformations did not yield a better fit to the data and was not consistent with chemical shift analysis. These results suggest that the peptide is predominantly in an extended conformation rather than an α-helical state on the HAP surface. Solid-state NMR approaches can thus be used to determine directly the conformation of biologically relevant peptides on HAP surfaces. A better understanding of peptide and protein conformation on biomineral surfaces may provide design principles useful for the modification of orthopedic and dental implants with coatings and biological growth factors that are designed to enhance biocompatibility with surrounding tissue.

Hippocampal, but not amygdala, activity at encoding correlates with long-term, free recall of nonemotional information

Participation of two medial temporal lobe structures, the hippocampal region and the amygdala, in long-term declarative memory encoding was examined by using positron emission tomography of regional cerebral glucose. Positron emission tomography scanning was performed in eight healthy subjects listening passively to a repeated sequence of unrelated words. Memory for the words was assessed 24 hr later with an incidental free recall test. The percentage of words freely recalled then was correlated with glucose activity during encoding. The results revealed a striking correlation (r = 0.91, P < 0.001) between activity of the left hippocampal region (centered on the dorsal parahippocampal gyrus) and word recall. No correlation was found between activity of either the left or right amygdala and recall. The findings provide evidence for hippocampal involvement in long-term declarative memory encoding and for the view that the amygdala is not involved with declarative memory formation for nonemotional material.

Basolateral amygdala is not critical for cognitive memory of contextual fear conditioning

Evidence that lesions of the basolateral amygdala complex (BLC) impair memory for fear conditioning in rats, measured by lack of “freezing” behavior in the presence of cues previously paired with footshocks, has suggested that the BLC may be a critical locus for the memory of fear conditioning. However, evidence that BLC lesions may impair unlearned as well as conditioned freezing makes it difficult to interpret the findings of studies assessing conditioned fear with freezing. The present study investigated whether such lesions prevent the expression of several measures of memory for contextual fear conditioning in addition to freezing. On day 1, rats with sham lesions or BLC lesions explored a Y maze. The BLC-lesioned rats (BLC rats) displayed a greater exploratory activity. On day 2, each of the rats was placed in the “shock” arm of the maze, and all of the sham and half of the BLC rats received footshocks. A 24-hr retention test assessed the freezing, time spent per arm, entries per arm, and initial entry into the shock arm. As previously reported, shocked BLC rats displayed little freezing. However, the other measures indicated that the shocked BLC rats remembered the fear conditioning. They entered less readily and less often and spent less time in the shock arm than did the control nonshocked BLC rats. Compared with the sham rats, the shocked BLC rats entered more quickly and more often and spent more time in the shock arm. These findings indicate that an intact BLC is not essential for the formation and expression of long-term cognitive/explicit memory of contextual fear conditioning.

The extended environment of mononuclear metal centers in protein structures

The objectives of this and the following paper are to identify commonalities and disparities of the extended environment of mononuclear metal sites centering on Cu, Fe, Mn, and Zn. The extended environment of a metal site within a protein embodies at least three layers: the metal core, the ligand group, and the second shell, which is defined here to consist of all residues distant less than 3.5 Å from some ligand of the metal core. The ligands and second-shell residues can be characterized in terms of polarity, hydrophobicity, secondary structures, solvent accessibility, hydrogen-bonding interactions, and membership in statistically significant residue clusters of different kinds. Findings include the following: (i) Both histidine ligands of type I copper ions exclusively attach the Nδ1 nitrogen of the histidine imidazole ring to the metal, whereas histidine ligands for all mononuclear iron ions and nearly all type II copper ions are ligated via the Nɛ2 nitrogen. By contrast, multinuclear copper centers are coordinated predominantly by histidine Nɛ2, whereas diiron histidine contacts are predominantly Nδ1. Explanations in terms of steric differences between Nδ1 and Nɛ2 are considered. (ii) Except for blue copper (type I), the second-shell composition favors polar residues. (iii) For blue copper, the second shell generally contains multiple methionine residues, which are elements of a statistically significant histidine–cysteine–methionine cluster. Almost half of the second shell of blue copper consists of solvent-accessible residues, putatively facilitating electron transfer. (iv) Mononuclear copper atoms are never found with acidic carboxylate ligands, whereas single Mn2+ ion ligands are predominantly acidic and the second shell tends to be mostly buried. (v) The extended environment of mononuclear Fe sites often is associated with histidine–tyrosine or histidine–acidic clusters.

Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism

I attempt to reconcile apparently conflicting factors and mechanisms that have been proposed to determine the rate constant for two-state folding of small proteins, on the basis of general features of the structures of transition states. Φ-Value analysis implies a transition state for folding that resembles an expanded and distorted native structure, which is built around an extended nucleus. The nucleus is composed predominantly of elements of partly or well-formed native secondary structure that are stabilized by local and long-range tertiary interactions. These long-range interactions give rise to connecting loops, frequently containing the native loops that are poorly structured. I derive an equation that relates differences in the contact order of a protein to changes in the length of linking loops, which, in turn, is directly related to the unfavorable free energy of the loops in the transition state. Kinetic data on loop extension mutants of CI2 and α-spectrin SH3 domain fit the equation qualitatively. The rate of folding depends primarily on the interactions that directly stabilize the nucleus, especially those in native-like secondary structure and those resulting from the entropy loss from the connecting loops, which vary with contact order. This partitioning of energy accounts for the success of some algorithms that predict folding rates, because they use these principles either explicitly or implicitly. The extended nucleus model thus unifies the observations of rate depending on both stability and topology.

Glucocorticoid enhancement of memory storage involves noradrenergic activation in the basolateral amygdala

Evidence indicates that the modulatory effects of the adrenergic stress hormone epinephrine as well as several other neuromodulatory systems on memory storage are mediated by activation of β-adrenergic mechanisms in the amygdala. In view of our recent findings indicating that the amygdala is involved in mediating the effects of glucocorticoids on memory storage, the present study examined whether the glucocorticoid-induced effects on memory storage depend on β-adrenergic activation within the amygdala. Microinfusions (0.5 μg in 0.2 μl) of either propranolol (a nonspecific β-adrenergic antagonist), atenolol (a β1-adrenergic antagonist), or zinterol (a β2-adrenergic antagonist) administered bilaterally into the basolateral nucleus of the amygdala (BLA) of male Sprague–Dawley rats 10 min before training blocked the enhancing effect of posttraining systemic injections of dexamethasone (0.3 mg/kg) on 48-h memory for inhibitory avoidance training. Infusions of these β-adrenergic antagonists into the central nucleus of the amygdala did not block the dexamethasone-induced memory enhancement. Furthermore, atenolol (0.5 μg) blocked the memory-enhancing effects of the specific glucocorticoid receptor (GR or type II) agonist RU 28362 infused concurrently into the BLA immediately posttraining. These results strongly suggest that β-adrenergic activation is an essential step in mediating glucocorticoid effects on memory storage and that the BLA is a locus of interaction for these two systems.

Galactose-extended glycans of antibodies produced by transgenic plants

Plant-specific N-glycosylation can represent an important limitation for the use of recombinant glycoproteins of mammalian origin produced by transgenic plants. Comparison of plant and mammalian N-glycan biosynthesis indicates that β1,4-galactosyltransferase is the most important enzyme that is missing for conversion of typical plant N-glycans into mammalian-like N-glycans. Here, the stable expression of human β1,4-galactosyltransferase in tobacco plants is described. Proteins isolated from transgenic tobacco plants expressing the mammalian enzyme bear N-glycans, of which about 15% exhibit terminal β1,4-galactose residues in addition to the specific plant N-glycan epitopes. The results indicate that the human enzyme is fully functional and localizes correctly in the Golgi apparatus. Despite the fact that through the modified glycosylation machinery numerous proteins have acquired unusual N-glycans with terminal β1,4-galactose residues, no obvious changes in the physiology of the transgenic plants are observed, and the feature is inheritable. The crossing of a tobacco plant expressing human β1,4-galactosyltransferase with a plant expressing the heavy and light chains of a mouse antibody results in the expression of a plantibody that exhibits partially galactosylated N-glycans (30%), which is approximately as abundant as when the same antibody is produced by hybridoma cells. These results are a major step in the in planta engineering of the N-glycosylation of recombinant antibodies.

Crystal structure of the ectodomain of Methuselah, a Drosophila G protein-coupled receptor associated with extended lifespan

The Drosophila mutant methuselah (mth) was identified from a screen for single gene mutations that extended average lifespan. Mth mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage. The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family. Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site. Here we report the 2.3-Å resolution crystal structure of the Mth extracellular region, revealing a folding topology in which three primarily β-structure-containing domains meet to form a shallow interdomain groove containing a solvent-exposed tryptophan that may represent a ligand binding site. The Mth structure is analyzed in relation to predicted Mth homologs and potential ligand binding features.