Statics and dynamics of domain patterns in hexagonal-orthorhombic ferroelastics

We study the statics and the dynamics of domain patterns in proper hexagonal-orthorhombic ferroelastics; these patterns are of particular interest because they provide a rare physical realization of disclinations in crystals. Both our static and dynamical theories are based entirely on classical, nonlinear elasticity theory; we use the minimal theory consistent with stability, symmetry and ability to explain qualitatively the observed patterns. After scaling, the only parameters of the static theory are a temperature variable and a stiffness variable. For moderate to large stiffness, our static results show nested stars, unnested stars, fans and other nodes, triangular and trapezoidal regions of trapped hexagonal phase, etc observed in electron microscopy of Ta4N and Mg-Cd alloys, and also in lead orthovanadate (which is trigonal-monoclinic); we even find imperfections in some nodes, like those observed. For small stiffness, we find patterns like those observed in the mineral Mg-cordierite. Our dynamical studies of growth and relaxation show the formation of these static patterns, and also transitory structures such as 12-armed bursts, streamers and striations which are also seen experimentally. The major aspects of the growth-relaxation process are quite unlike those in systems with conventional order parameters, for it is inherently nonlocal; for example, the changes from one snapshot to the next are not predictable by inspection.Comment: 9 pages, 3 figures (1 b&w, 2 colour); animations may be viewed at http://huron.physics.utoronto.ca/~curnoe/sim.htm

Structure optimization effects on the electronic properties of Bi2_2Sr2_2CaCu2_2O8_8

We present detailed first-principles calculations for the normal state electronic properties of the high T$_C$ superconductor Bi$_2$Sr$_2$CaCu$_2$O$_8$, by means of the linearized augmented plane wave (LAPW) method within the framework of density functional theory (DFT). As a first step, the body centered tetragonal (BCT) cell has been adopted, and optimized regarding its volume, $c/a$ ratio and internal atomic positions by total energy and force minimizations. The full optimization of the BCT cell leads to small but visible changes in the topology of the Fermi surface, rounding the shape of CuO$_2$ barrels, and causing both the BiO bands, responsible for the pockets near the \textit{\=M} 2D symmetry point, to dip below the Fermi level. We have then studied the influence of the distortions in the BiO plane observed in nature by means of a $\sqrt{2}\times\sqrt{2}$ orthorhombic cell (AD-ORTH) with $Bbmb$ space group. Contrary to what has been observed for the Bi-2201 compound, we find that for Bi-2212 the distortion does not sensibly shift the BiO bands which retain their metallic character. As a severe test for the considered structures we present Raman-active phonon frequencies ($q = 0$) and eigenvectors calculated within the frozen-phonon approximation. Focussing on the totally symmetric A$_{g}$ modes, we observe that for a reliable attribution of the peaks observed in Raman experiments, both $c$- and a-axis vibrations must be taken into account, the latter being activated by the in-plane orthorhombic distortion.Comment: 22 pages, 4 figure

Simulations of cubic-tetragonal ferroelastics

We study domain patterns in cubic-tetragonal ferroelastics by solving numerically equations of motion derived from a Landau model of the phase transition, including dissipative stresses. Our system sizes, of up to 256^3 points, are large enough to reveal many structures observed experimentally. Most patterns found at late stages in the relaxation are multiply banded; all three tetragonal variants appear, but inequivalently. Two of the variants form broad primary bands; the third intrudes into the others to form narrow secondary bands with the hosts. On colliding with walls between the primary variants, the third either terminates or forms a chevron. The multipy banded patterns, with the two domain sizes, the chevrons and the terminations, are seen in the microscopy of zirconia and other cubic-tetragonal ferroelastics. We examine also transient structures obtained much earlier in the relaxation; these show the above features and others also observed in experiment.Comment: 7 pages, 6 colour figures not embedded in text. Major revisions in conten

Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters

BACKGROUND:Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)(4) can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. METHODOLOGY/PRINCIPAL FINDINGS:Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. CONCLUSIONS/SIGNIFICANCE:Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins

Mycobacterium abscessus-Induced Granuloma Formation Is Strictly Dependent on TNF Signaling and Neutrophil Trafficking

Mycobacterium abscessus is considered the most common respiratory pathogen among the rapidly growing non-tuberculous mycobacteria. Infections with M. abscessus are increasingly found in patients with chronic lung diseases, especially cystic fibrosis, and are often refractory to antibiotic therapy. M. abscessus has two morphotypes with distinct effects on host cells and biological responses. The smooth (S) variant is recognized as the initial airway colonizer while the rough (R) is known to be a potent inflammatory inducer associated with invasive disease, but the underlying immunopathological mechanisms of the infection remain unsolved. We conducted a comparative stepwise dissection of the inflammatory response in S and R pathogenesis by monitoring infected transparent zebrafish embryos. Loss of TNFR1 function resulted in increased mortality with both variants, and was associated with unrestricted intramacrophage bacterial growth and decreased bactericidal activity. The use of transgenic zebrafish lines harboring fluorescent macrophages and neutrophils revealed that neutrophils, like macrophages, interact with M. abscessus at the initial infection sites. Impaired TNF signaling disrupted the IL8-dependent neutrophil mobilization, and the defect in neutrophil trafficking led to the formation of aberrant granulomas, extensive mycobacterial cording, unrestricted bacterial growth and subsequent larval death. Our findings emphasize the central role of neutrophils for the establishment and maintenance of the protective M. abscessus granulomas. These results also suggest that the TNF/IL8 inflammatory axis is necessary for protective immunity against M. abscessus and may be of clinical relevance to explain why immunosuppressive TNF therapy leads to the exacerbation of M. abscessus infections