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When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/
The following four features of the high-Tc copper oxides are discussed. (i) They have intergrowth structures consisting of superconductive layers of fixed oxygen concentration and 'inactive' layers of variable oxygen concentration. The intergrowth structure imparts anisotropy, internal electric fields and bond-length mismatch, all of which influence the chemistry, structure and superconductive properties of these materials. (ii) Superconductivity occurs in a narrow compositional range in which the correlation splitting of a sigma *(x2-y2) band and its associated short-range spin fluctuations are retained through a transition from antiferromagnetic semiconductor to normal metal. (iii) The interaction Cu3++O2- to or from Cu2++O- is not biased strongly to the right or to the left. (iv) The width of the conduction band is at the narrow-band limit for a mixed-valent conductor; perturbations that transform mobile charge carriers from itinerant electrons/holes to small polarons suppress the superconductivity. A final assessment is made of the classes of theoretical suggestions that have been put forward to explain the high-Tc phenomenon.
We have discovered a new high- T c oxide superconductor of the Bi-Sr-Ca-Cu-O system without any rare earth element. The oxide BiSrCaCu 2 O x has T c of about 105 K, higher than that of YBa 2 Cu 3 O 7 by more than 10 K. In this oxide, the coexistence of Sr and Ca is necessary to obtain high T c .
The available data on the microwave surface impedance Z/sub s/ of high-T/sub c/ superconductors from more than 30 laboratories around the world are reviewed to show the frequency, temperature, and field dependence of the surface resistance R/sub s/ and the temperature dependence of the field penetration depth lambda . The data are discussed on the basis of a two-fluid model and are compared with results from the classical superconductors Nb and Nb/sub 3/Sn. At temperatures above 0.8 T/sub c/, Z/sub s/ values of classical and high-T/sub c/ superconductors show strong similarities and are in close agreement with the Mattis-Bardeen theory. The comparatively very high R/sub s/ of the cuprates at 4.2 K, however, is indicative of a high density of unpaired charge carriers. The lowest values for R/sub s/ and lambda obtained until now with epitaxially grown YBa/sub 2/Cu/sub 3/O/sub 7- delta / films are 16 mu Omega at 4.2 K and 10 GHz and 140 nm, respectively. Such films are required for high RF field applications. Polycrystalline samples show a strong field dependence of R/sub s/. The highest magnetic surface field without R/sub s/ deterioration achieved so far on single crystals of YBa/sub 2/Cu/sub 3/O/sub 7- delta / is about 100 G.
In solid-state physics two different paradigms are typically applied. The first is a local picture, in which one visualizes the quantum states of electrons in atomic orbitals or at impurity atoms in real space (r-space). The second is the momentum or reciprocal space (k-space) picture, where electrons are viewed as de Broglie waves completely delocalized throughout the material. Understanding these two separate paradigms is essential for a complete understanding of the physics of condensed matter, but rarely has it been as necessary to combine both pictures as it has been to gain insight into the electronic structure of the high-temperature superconductors (HTSCs). In this article, we review recent developments in the understanding of the relationship between the r-space and k-space electronic spectroscopies used to explore high-temperature superconductivity.
The current status of tunneling measurements of the superconducting density of states near the Fermi level of high-T c superconductors is reviewed. A number of the characteristics of the tunneling data that had previously been considered to be "non-ideal" follow quite naturally from conventional tunneling theory, if the effects of the unusually large energy gap, often unusually small tunneling barriers, and gap anisotropy and/or inhomogeneity are correctly accounted for. Despite formidable problems in making these measurements, due to both the very short coherence lengths and materials problems in these superconductors, a consistent body of data is emerging. A consistent picture can be drawn from this data with the aid of the new modelling presented here.
In high-T c superconductors (HTSC) the thermal fluctuation of the vortex lattice (VL) may become large since the vortex lattice is soft due to the strong overlap of the vortex fields and since the temperature T can be high. It was thus argued that the three-dimensional (3D) vortex lattice is thermally entangled and may “melt”. This type of transition and the consequences of melting are not clear as yet since the always present pinning of the vortex cores by material inhomogeneities may cause similar disorder. In HTSC the pinning energy may become comparable with k B T because the coherence length ξ (vortex radius) is small and T may be high. Therefore, thermally activated depinning competes with possible effects of “flux melting”, and the “irreversibility line” in the B-T-plane (B=magnetic field) should better be called “depinning line”. Due to the diffusive character of flux motion the depinning line of a given experiment, a line of constant flux diffusivity D(T, B), depends on the frequency or sweep rate, on the size and shape of the superconductor, and on the field orientation; it is thus not a material property alone. In this review it is argued that theories predicting “new phases of vortex matter” (flux solid, flux liquid, vortex plasma, vortex glass, and hexatic vortex glass) may be improved by replacing the 2D straight-vortex interaction by the correct 3D interaction between all vortex segments. This interaction (a) facilitates vortex crossing and reconnection, (b) reduces the elastic energy of short-wavelength tilt by a very large factor (non-local elasticity), and (c) yields the correct reduction of the tilt energy by the crystal anisotropy. The non-local elasticity of the VL is reviewed and a general solution of the anisotropic London theory for arbitrary vortex arrangements is given. A very useful phenomenological theory of layered superconductors is the Lawrence-Doniach model, which defines a 2D Ginzburg-Landau function in each layer. The point vortices in the layers interact with each other magnetically and, between neighboring layers, by Josephson coupling. At sufficiently large fields their thermal fluctuation is quasi-2D and, at an in general different field, their pinning becomes 2D.
We introduce and study the nodal liquid, a novel zero-temperature quantum phase obtained by quantum-disordering a d-wave superconductor. It has numerous remarkable properties which lead us to suggest it as an explanation of the pseudo-gap state in underdoped high-temperature superconductors. In the absence of impurities, these include power-law magnetic order, a T-linear spin susceptibility, nontrivial thermal conductivity, and two- and one-particle charge gaps, the latter evidenced, e.g. in transport and electron photoemission (which exhibits pronounced fourfold anisotropy inherited from the d-wave quasiparticles). We use a (2+1)-dimensional duality transformation to derive an effective field theory for this phase. The theory is comprised of gapless neutral Dirac particles living at the former d-wave nodes, weakly coupled to the fluctuating gauge field of a dual Ginzburg–Landau theory. The nodal liquid interpolates naturally between the d-wave superconductor and the insulating antiferromagnet, and our effective field theory is powerful enough to permit a detailed analysis of a panoply of interesting phenomena, including charge ordering, antiferromagnetism, and d-wave superconductivity. We also discuss the zero-temperature quantum phase transitions which separate the nodal liquid from various ordered phases.
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A theoretical analysis was performed for an extremely high-Q resonator formed by a sapphire rod sandwiched by a pair of high-T/sub c/ superconductor (HTS) films. A number of these HTS-sapphire-HTS resonators at C-band and Ka-band were designed, fabricated, and tested. At 5.552 GHz, Q/sub 0/ reached 2*10/sup 6/ at 90 K, 3*10/sup 6/ at 80 K and 1.4*10/sup 7/ at 4.2 K with circulating power up to 500 kW. Formulas for calculating the resonant frequency and Q-value derived from the theoretical analysis were verified by experimental data with good agreement. Three different thin-film HTS materials-Tl/sub 2/Ba/sub 2/CaCu/sub 2/O/sub 8/, YBa/sub 2/Cu/sub 3/O/sub 7- delta / and Tl/sub 0.5/Pb/sub 0.5/Sr/sub 2/CaCu/sub 2/O/sub 7/-were tested. The sensitivity of the high Q-value and the parasitic coupling to the case modes are discussed. Applications such as frequency stabilized oscillators, filters, and HTS film characterization are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Partial substitution of Pb for Bi in the Bi-Sr-Ca-Cu-O system has been found to sharply increase the volume fraction of the high- T c phase when both the starting material (coprecipitated oxalate being used in the present study) and the heating process are appropriate. The sharp powder X-ray diffraction pattern obtained from well-grown particles, 5∼10 µm wide and 0.5 µm thick typically, was assigned to an orthorhombic cell with a =0.537 nm, b =2.682 nm, and c =3.726 nm. The electrical resistance dropped to zero at 107 K within the experimental limit of 10 -6 Ω. A large diamagnetic response in the ac susceptibility due to the Meissner effect was seen below 120 K. The dominance of the high- T c phase over the low- T c phase was roughly estimated at 9/1 in volume.
High-grade rocks occur in the Chinese Altai, but the timing of metamorphism is poorly constrained, which hinders our understanding of the thermo-tectonic history of the region. Representative high-grade samples from the sillimanite zone extending from Hanas to Fuyun were selected for zircon U-Pb dating and temperature estimation. LA-ICP-MS analyses of zircon overgrowth rims and recrystallized domains give consistent ages of ∼390 Ma, which is interpreted to record a regional metamorphic event. Temperature (*T*) estimations using the amphibole-plagioclase-quartz (Amp-Pl-Qtz) and garnet-biotite (GB) geothermometers give relatively high temperatures ranging from 650 to 700 °C. The zircon metamorphic rims yield temperature estimates of ∼720 °C by using the Ti-in-zircon thermometer. These data suggest that a high-temperature metamorphic event took place in the Chinese Altai in the Middle Devonian, and may imply a tectonic environment involving an unusually elevated heat flux from a deep-seated source. Our data support possible ridge subduction around 390 Ma that caused upwelling of the hot asthenosphere and triggered the high-*T* metamorphism. This model can also account for coeval volcanic activity with a range of geochemical characteristics, diverse mafic intrusions and extensive hydrothermal mineralization in the Altai orogen.
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Understanding Dirac-like fermions has become an imperative in modern condensed matter sciences: All across the research frontier, from graphene to high T c superconductors to the topological insulators and beyond, various electronic systems exhibit properties that can be well described by the Dirac equation. Such physics is no longer the exclusive domain of quantum field theories and other esoteric mathematical musings; instead, physics of real condensed matter systems is governed by such equations, and important materials science and practical implications hinge on our understanding of Dirac particles in two and three dimensions. Although the physics that gives rise to the massless Dirac fermions in each of the above-mentioned materials is different, the low-energy properties are governed by the same Dirac kinematics. The aim of this article is to review a selected cross-section of this vast field by highlighting the generalities and contrasting the specifics of several physical systems.
Co-decomposition of mixed nitrates of Bi, Pb, Sr, Ca and Cu around 830°C under low oxygen pressure led to the formation of a high- T c superconducting phase of Bi(Pb)-Sr-Ca-Cu-O with T c (zero) at 107.5 K. A sample prepared by a conventional solid state reaction method under low oxygen pressure also showed the superconducting transition at 107.5 K. X-ray powder diffraction and magnetic susceptibility measurements on these samples revealed the high- T c phase without 80 K or semiconducting phase. The reaction under low oxygen pressure has an effect to lower the temperature with broad ranges to render the high- T c phase of the Bi-Sr-Ca-Cu-O.
In order to elucidate the correlations between composition, structure and electrical properties of a high- T c superconductor Ba-Y-Cu-O system, thermogravimetric measurement and chemical analysis of oxygen nonstoichiometry were made at a temperature range of 350 to 1000°C and under the oxygen partial pressure of 10 -4 to 1 atm. Within a stability range of the composition Ba 2 YCu 3 O 7-δ , the oxygen deficiency, δ, was found to vary approximately from zero to 0.9, with associated mean valence of copper ions varying from 2.33 to 1.73. At a possible phase boundary region of tetragonal to orthorhombic crystal structures, no sign of discontinuity in δ was observed, suggesting its phase transition was of higher than a first order.
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Occurrence of high- T c superconductivity with T c near 30 K is observed for the single phase of (La·Ba) 2 CuO 4- y by both magnetic susceptibility and resistivity measurements. This indicates that high- T c superconductivity in La-Ba-Cu oxide is realized in the K 2 NiF 4 -type structure, (La·Ba) 2 CuO 4- y .
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A model for the modulated crystal structure (Matsui et al. : Jpn. J. Appl. Phys. in press) in high- T c superconductor in a Bi-Sr-Ca-Cu-O system is proposed based on the high-resolution electron microscope images. Ideally, it is body-centered orthorhombic with a =0.54, b =5 a =2.7 and c =3.08 nm. The Bi 2 O 2 layers do not form complete sheets, but contain occupational and/or positional fluctuation of Bi-sites to form “Bi-concentrated bands” which extend in the a -direction. Contraction of lattice planes along the b -axis is induced in the Bi-concentrated bands, causing compensating expansion in the remaining Bi-deficient ones.