Alfveacuten continuum deformation by kinetic geodesic effect in rotating tokamak plasmas

Using a quasitoroidal set of coordinates with coaxial circular magnetic surfaces, Vlasov equation is solved for collisionless plasmas in drift approach and a perpendicular dielectric tensor is found for large aspect ratio tokamaks in a low frequency band. Taking into account plasma rotation and charge separation parallel electric field, it is found that an ion geodesic effect deform Alfveacuten wave continuum producing continuum minimum at the rational magnetic surfaces, which depends on the plasma rotation and poloidal mode numbers. In kinetic approach, the ion thermal motion defines the geodesic effect but the mode frequency also depends on electron temperature. A geodesic ion Alfveacuten mode predicted below the continuum minimum has a small Landau damping in plasmas with Maxwell distribution but the plasma rotation may drive instability.

Kinetic ion effect on geodesic acoustic Alfven modes in tokamaks

Using a quasitoroidal set of coordinates with coaxial circular magnetic surfaces, the Vlasov equation is solved for collisionless plasmas, and the dielectric tensor is found for large aspect ratio tokamaks in a low frequency band. Taking into account q-profile and charge separation parallel electric field, it is found that the Alfven wave continuum is deformed by ion geodesic effects producing continuum minimum at the rational magnetic surfaces. Low frequency geodesic ion induced Alfven waves are found below the continuum minimum where collisionless damping has a gap for Maxwell distribution. In kinetic approach, the ion thermal motion defines the geodesic effect but the mode frequency is strongly corrected due to parallel motion of electrons.

Kinetic effect on low frequency Alfven continuum in tokamaks

Using a quasi-toroidal set of coordinates in plasmas with coaxial circular magnetic surfaces, the Vlasov equation is solved, and dielectric tensor is found for large aspect ratio tokamaks in a low frequency band. Taking into account the q-profile and drift effects, Alfven wave continuum deformation by geodesic effects is analyzed. It is shown that the Alfven continuum has a minimum defined by the ion thermal velocity at the rational magnetic surfaces q(s)=-M/N, where M and N are the poloidal and toroidal mode numbers, respectively, and the parallel wave number is zero. Low frequency global Alfven waves are found below the continuum minimum. In hot ion plasmas, the geodesic term changes sign, provoking some deformation of Alfven velocity by a factor (1+q(2))(-1/2), and the continuum minimum disappears. (C) 2008 American Institute of Physics.

On molecular chirality within naturally occurring secondary organic aerosol particles from the central Amazon Basin

In this perspectives article, we reflect upon the existence of chirality in atmospheric aerosol particles. We then show that organic particles collected at a field site in the central Amazon Basin under pristine background conditions during the wet and dry seasons consist of chiral secondary organic material. We show how the chiral response from the aerosol particles can be imaged directly without the need for sample dissolution, solvent extraction, or sample preconcentration. By comparing the chiral-response images with optical images, we show that chiral responses always originate from particles on the filter, but not all aerosol particles produce chiral signals. The intensity of the chiral signal produced by the size resolved particles strongly indicates the presence of chiral secondary organic material in the particle. Finally, we discuss the implications of our findings on chiral atmospheric aerosol particles in terms of climate-related properties and source apportionment.

Theory of near-gap second harmonic generation in centrosymmetric magnetic semiconductors: Europium chalcogenides

Second harmonic generation is strictly forbidden in centrosymmetric materials, within the electric dipole approximation. Recently, it was found that the centrosymmetric magnetic semiconductors EuTe and EuSe can generate near-gap second harmonics, if the system is submitted to an external magnetic field. Here, a theoretical model is presented, which well describes the observed phenomena. The model shows that second harmonic generation becomes efficient when the magnetic dipole oscillations between the band-edge excited states of the system, induced by the excitation light, enter the in-phase regime, which can be achieved by applying a magnetic field to the material.

Connectivity and dynamics of neuronal networks as defined by the shape of individual neurons

Biological neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of neuron shape on the overall connectivity and dynamics of the emerging networks. The current work addresses this issue by considering simplified neuronal shapes consisting of circular regions (soma/axons) with spokes (dendrites). Networks are grown by placing these patterns randomly in the two-dimensional (2D) plane and establishing connections whenever a piece of dendrite falls inside an axon. Several topological and dynamical properties of the resulting graph are measured, including the degree distribution, clustering coefficients, symmetry of connections, size of the largest connected component, as well as three hierarchical measurements of the local topology. By varying the number of processes of the individual basic patterns, we can quantify relationships between the individual neuronal shape and the topological and dynamical features of the networks. Integrate-and-fire dynamics on these networks is also investigated with respect to transient activation from a source node, indicating that long-range connections play an important role in the propagation of avalanches.

Chemical and in vitro study of the potential of 3-(aryl)-2-sulfanylpropenoic acids and their Zn(II) complexes as protective agents against cadmium toxicity

The free H(2)xspa ligands [xspa = pspa, Clpspa, tspa or fspa where p = 3-(phenyl), Clp = 3-(2-chlorophenyl), t = 3-(2-thienyl), f = 3-(2-furyl) and spa = 2-sulfanylpropenoato], their Zn(II) complexes of formula [HQ](2)[Zn(xspa)(2)] (HQ=diisopropylammonium) and the Cd(II) equivalents were prepared and characterized by elemental analysis and by IR, Raman and NMR ((1)H, (13)C) spectroscopy. X-Ray studies of the crystal structures of [HQ](2)[Zn(pspa)(2)], [HQ](2)[Zn(Clpspa)2], [HQ](2)[Zn(tspa)(2)] and [HQ](2)[Zn(fspa)(2)] show that the zinc atom is coordinated to two O atoms and two S atoms of the ligands in a distorted tetrahedral ZnO(2)S(2) environment. In the structures of [HQ](2)[Cd(pspa)(2)] and [HQ](2)[Cd(Clpspa)(2)] the cadmium atom is coordinated to three S atoms and two carboxylato O atoms of the ligands in a distorted trigonal bipyramidal environment. The interchange of ligands between Zn( II) and Cd( II) was studied by (113)Cd NMR spectroscopy. The in vitro protective effect of H(2)xspa and their Zn( II) complexes against Cd toxicity was investigated using the human hepatocarcinoma HepG2 cell line and the pig renal proximal tubule LLC-PK1 cell line. The incorporation of Zn( II) was found to be relevant in the case of H(2)pspa, with an increase observed in the cell viability of the LCC-PK1 cells with respect to the value for the free ligand.

Structure of an Odorant-Binding Protein from the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive ""Lid""

Background: The yellow fever mosquito, Aedes aegypti, is the primary vector for the viruses that cause yellow fever, mostly in tropical regions of Africa and in parts of South America, and human dengue, which infects 100 million people yearly in the tropics and subtropics. A better understanding of the structural biology of olfactory proteins may pave the way for the development of environmentally-friendly mosquito attractants and repellents, which may ultimately contribute to reduction of mosquito biting and disease transmission. Methodology: Previously, we isolated and cloned a major, female-enriched odorant-binding protein (OBP) from the yellow fever mosquito, AaegOBP1, which was later inadvertently renamed AaegOBP39. We prepared recombinant samples of AaegOBP1 by using an expression system that allows proper formation of disulfide bridges and generates functional OBPs, which are indistinguishable from native OBPs. We crystallized AaegOBP1 and determined its three-dimensional structure at 1.85 angstrom resolution by molecular replacement based on the structure of the malaria mosquito OBP, AgamOBP1, the only mosquito OBP structure known to date. Conclusion: The structure of AaegOBP1 (= AaegOBP39) shares the common fold of insect OBPs with six alpha-helices knitted by three disulfide bonds. A long molecule of polyethylene glycol (PEG) was built into the electron-density maps identified in a long tunnel formed by a crystallographic dimer of AaegOBP1. Circular dichroism analysis indicated that delipidated AaegOBP1 undergoes a pH-dependent conformational change, which may lead to release of odorant at low pH (as in the environment in the vicinity of odorant receptors). A C-terminal loop covers the binding cavity and this ""lid"" may be opened by disruption of an array of acid-labile hydrogen bonds thus explaining reduced or no binding affinity at low pH.

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.

The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid

We present here the sequence of the mitochondrial genome of the basidiomycete phytopathogenic hemibiotrophic fungus Moniliophthora perniciosa, causal agent of the Witches` Broom Disease in Theobroma cacao. The DNA is a circular molecule of 109103 base pairs, with 31.9 % GC, and is the largest sequenced so far. This size is due essentially to the presence of numerous non-conserved hypothetical ORFs. It contains the 14 genes coding for proteins involved in the oxidative phosphorylation, the two rRNA genes, one ORF coding for a ribosomal protein (rps3), and a set of 26 tRNA genes that recognize codons for all amino acids. Seven homing endonucleases are located inside introns. Except atp8, all conserved known genes are in the same orientation. Phylogenetic analysis based on the cox genes agrees with the commonly accepted fungal taxonomy. An uncommon feature of this mitochondrial genome is the presence of a region that contains a set of four, relatively small, nested, inverted repeats enclosing two genes coding for polymerases with an invertron-type structure and three conserved hypothetical genes interpreted as the stable integration of a mitochondrial linear plasmid. The integration of this plasmid seems to be a recent evolutionary event that could have implications in fungal biology. This sequence is available under GenBank accession number AY376688. (c) 2008 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

A new species of land planarian of Gigantea Ogren and Kawakatsu, 1990 (Platyhelminthes, Tricladida, Terricola) from Colombia, with taxonomic remarks on the genus

A new species of land planarian from Colombia, Gigantea maupoi sp. nov., is described herein. The penis papilla of the new species is provided with numerous accessory genital organs, or mgo. These mgo are of a unique morphology, consisting of a very strong barrel-shaped circular muscle coat and an underlying longitudinal one, both derived from the subepithelial musculature of the penis papilla. The central mass of each mgo contains secretions and 8-15 canalicula that open to the male atrium on the central region of the organ. Differences in structures constituting the mgo and details of the muscular systems and of the reproductive organs among the 11 Gigantea species from literature and from type material of G. bistriata (Hyman, 1962), G. chiriquii (Hyman, 1962), and G. sandersoni (Prudhoe, 1949) reexamined here show that the genus is heterogeneous.

Birefringence enhancement by using D-shaped microstructured optical fibers

In this study, a detailed numerical investigation is presented, seeking to enhance the birefringence effect by using D-shaped microstructured optical fibers (MOFs). We studied a D-shape core geometry associated with three different air-hole configurations: circular and elliptical, aligned with either the x-direction or the y-direction. Results have shown that ultrahigh birefringence MOFs, with B values of the order of 10(-2) for a wide range of wavelengths, can be obtained. The highest birefringence B was equal 3.97 x 10(-2), a value found for a D-MOF (circular holes) at 1550 nm. To the best of our knowledge, this is the highest theoretical value in the published literature.

Evaluation of passive confinement in CFT columns

This paper presents the experimental results of 32 axially loaded concrete-filled steel tubular columns (CFT). The load was introduced only on the concrete core by means of two high strength steel cylinders placed at the column ends to evaluate the passive confinement provided by the steel tube. The columns were filled with structural concretes with compressive strengths of 30, 60, 80 and 100 MPa. The outer diameter (D) of the column was 114.3 mm, and the length/diameter (L/D) ratios considered were 3, 5, 7 and 10. The wall thicknesses of the tubes (t) were 3.35 mm and 6.0 mm, resulting in diameter/thickness (D/t) ratios of 34 and 19, respectively. The force vs. axial strain curves obtained from the tests showed, in general, a good post-peak behavior of the CFT columns, even for those columns filled with high strength concrete. Three analytical models of confinement for short concrete-filled columns found in the literature were used to predict the axial capacity of the columns tested. To apply these models to slender columns, a correction factor was introduced to penalize the calculated results, giving good agreement with the experimental values. Additional results of 63 CFT columns tested by other researchers were also compared to the predictions of the modified analytical models and presented satisfactory results. (C) 2009 Elsevier Ltd. All rights reserved.

Influence of concrete strength and length/diameter on the axial capacity of CFT columns

This paper presents an experimental analysis of the confinement effects in steel-concrete composite columns regarding two parameters: concrete compressive strength and column slenderness. Sixteen concrete-filled steel tubular columns with circular cross section were tested under axial loading. The tested columns were filled by concrete with compressive strengths of 30, 60. 80, and 100 MPa, and had length/diameter ratios of 3, 5, 7, and 10. The experimental values of the columns` ultimate load were compared to the predictions of 4 code provisions: the Brazilian Code NBR 8800:2008, Eurocode 4 (EN 1994-1-1:2004), AINSI/AISC 360:2005, and CAN/CSA S16-01:2001. According to the results, the load capacity of the composite columns increased with increasing concrete strength and decreased with increasing length/diameter ratio. In general, the code provisions were highly accurate in the prediction of column capacity. Among them, the Brazilian Code was the most conservative, while Eurocode 4 presented the values closest to the experimental results. (C) 2009 Elsevier Ltd. All rights reserved.

Analytical formulae for electromechanical effective properties of 3-1 longitudinally porous piezoelectric materials

A unidirectional fiber composite is considered here, the fibers of which are empty cylindrical holes periodically distributed in a transversely isotropic piezoelectric matrix, The empty-fiber cross-section is circular and the periodicity is the same in two directions at an angle pi/2 or pi/3. Closed-form formulae for all electromechanical effective properties of these 3-1 longitudinally periodic porous piezoelectric materials are presented. The derivation of such expressions is based on the asymptotic homogenization method as a limit of the effective properties of two-phase transversely isotropic parallel fiber-reinforced composites when the fibers properties tend to zero. The plane effective coefficients satisfy the corresponding Schulgasser-Benveniste-Dvorak universal type of relations, A new relation among the antiplane effective constants from the solutions of two antiplane strains and potential local problems is found. This relation is valid for arbitrary shapes of the empty-fiber cross-sections. Based on such a relation, and using recent numerical results for isotropic conductive composites, the antiplane effective properties are computed for different geometrical shapes of the empty-fiber cross-section. Comparisons with other analytical and numerical theories are presented. (c) 2008 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.