986 resultados para vortex core structure
Resumo:
The superconducting gap is a basic character of a superconductor. While the cuprates and conventional phonon-mediated superconductors are characterized by distinct d- and s-wave pairing symmetries with nodal and nodeless gap distributions respectively, the superconducting gap distributions in iron-based superconductors are rather diversified. While nodeless gap distributions have been directly observed in Ba1–xKxFe2As2, BaFe2–xCoxAs2, LiFeAs, KxFe2–ySe2, and FeTe1–xSex, the signatures of a nodal superconducting gap have been reported in LaOFeP, LiFeP, FeSe, KFe2As2, BaFe2–xRuxAs2, and BaFe2(As1–xPx)2. Due to the multiplicity of the Fermi surface in these compounds s± and d pairing states can be both nodeless and nodal. A nontrivial orbital structure of the order parameter, in particular the presence of the gap nodes, leads to effects in which the disorder is much richer in dx2–y2-wave superconductors than in conventional materials. In contrast to the s-wave case, the Anderson theorem does not work, and nonmagnetic impurities exhibit a strong pair-breaking influence. In addition, a finite concentration of disorder produces a nonzero density of quasiparticle states at zero energy, which results in a considerable modification of the thermodynamic and transport properties at low temperatures. The influence of order parameter symmetry on the vortex core structure in iron-based pnictide and chalcogenide superconductors has been investigated in the framework of quasiclassical Eilenberger equations. The main results of the thesis are as follows. The vortex core characteristics, such as, cutoff parameter, ξh, and core size, ξ2, determined as the distance at which density of the vortex supercurrent reaches its maximum, are calculated in wide temperature, impurity scattering rate, and magnetic field ranges. The cutoff parameter, ξh(B; T; Г), determines the form factor of the flux-line lattice, which can be obtained in _SR, NMR, and SANS experiments. A comparison among the applied pairing symmetries is done. In contrast to s-wave systems, in dx2–y2-wave superconductors, ξh/ξc2 always increases with the scattering rate Г. Field dependence of the cutoff parameter affects strongly on the second moment of the magnetic field distributions, resulting in a significant difference with nonlocal London theory. It is found that normalized ξ2/ξc2(B/Bc2) dependence is increasing with pair-breaking impurity scattering (interband scattering for s±-wave and intraband impurity scattering for d-wave superconductors). Here, ξc2 is the Ginzburg-Landau coherence length determined from the upper critical field Bc2 = Φ0/2πξ2 c2, where Φ0 is a flux quantum. Two types of ξ2/ξc2 magnetic field dependences are obtained for s± superconductors. It has a minimum at low temperatures and small impurity scattering transforming in monotonously decreasing function at strong scattering and high temperatures. The second kind of this dependence has been also found for d-wave superconductors at intermediate and high temperatures. In contrast, impurity scattering results in decreasing of ξ2/ξc2(B/Bc2) dependence in s++ superconductors. A reasonable agreement between calculated ξh/ξc2 values and those obtained experimentally in nonstoichiometric BaFe2–xCoxAs2 (μSR) and stoichiometric LiFeAs (SANS) was found. The values of ξh/ξc2 are much less than one in case of the first compound and much more than one for the other compound. This is explained by different influence of two factors: the value of impurity scattering rate and pairing symmetry.
Resumo:
We present a numerical method for generating vortex rings in Bose-Einstein condensates confined in axially symmetric traps. The vortex ring is generated using the line-source approximation for the vorticity, i.e., the curl of the superfluid velocity field is different from zero only on a circumference of a given radius located on a plane perpendicular to the symmetry axis and coaxial with it. The particle density is obtained by solving a modified Gross-Pitaevskii equation that incorporates the effect of the velocity field. We discuss the appearance of density profiles, the vortex core structure, and the vortex nucleation energy, i.e., the energy difference between vortical and ground-state configurations. This is used to present a qualitative description of the vortex dynamics.
Resumo:
The quasiclassical approach was applied to the investigation of the vortex properties in the ironbased superconductors. The special attention was paid to manifestation of the nonlocal effects of the vortex core structure. The main results are as follows: (i) The effects of the pairing symmetries (s+ and s₊₊) on the cutoff parameter of field distribution, ξh, in stoichiometric (like LiFeAs) and nonstoichiometric (like doped BaFe₂As₂) iron pnictides have been investigated using Eilenberger quasiclassical equations. Magnetic field, temperature and impurity scattering dependences of ξh have been calculated. Two opposite behavior have been discovered. The ξh /ξc2 ratio is less in s+ symmetry when intraband impurity scattering (Γ₀) is much larger than one and much larger than interband impurity scattering (Γπ), i.e. in nonstoichiometric iron pnictides. Opposite, the value ξh /ξc2 is higher in s+ case and the field dependent curve is shifted upward from the "clean" case (Γ₀ = Γπ = 0) for stoichiometric iron pnictides (Γ₀ = Γπ ≪ 1). (ii) Eilenberger approach to the cutoff parameter, ξh, of the field distribution in the mixed state of high
Resumo:
The polypeptide composition of the U7 small nuclear ribonucleoprotein (snRNP) involved in histone messenger RNA (mRNA) 3' end formation has recently been elucidated. In contrast to spliceosomal snRNPs, which contain a ring-shaped assembly of seven so-called Sm proteins, in the U7 snRNP the Sm proteins D1 and D2 are replaced by U7-specific Sm-like proteins, Lsm10 and Lsm11. This polypeptide composition and the unusual structure of Lsm11, which plays a role in histone RNA processing, represent new themes in the biology of Sm/Lsm proteins. Moreover this structure has important consequences for snRNP assembly that is mediated by two complexes containing the PRMT5 methyltransferase and the SMN (survival of motor neurons) protein, respectively. Finally, the ability to alter this polypeptide composition by a small mutation in U7 snRNA forms the basis for using modified U7 snRNA derivatives to alter specific pre-mRNA splicing events, thereby opening up a new way for antisense gene therapy.
Resumo:
A set of seven Sm proteins assemble on the Sm-binding site of spliceosomal U snRNAs to form the ring-shaped Sm core. The U7 snRNP involved in histone RNA 3' processing contains a structurally similar but biochemically unique Sm core in which two of these proteins, Sm D1 and D2, are replaced by Lsm10 and by another as yet unknown component. Here we characterize this factor, termed Lsm11, as a novel Sm-like protein with apparently two distinct functions. In vitro studies suggest that its long N-terminal part mediates an important step in histone mRNA 3'-end cleavage, most likely by recruiting a zinc finger protein previously identified as a processing factor. In contrast, the C-terminal part, which comprises two Sm motifs interrupted by an unusually long spacer, is sufficient to assemble with U7, but not U1, snRNA. Assembly of this U7-specific Sm core depends on the noncanonical Sm-binding site of U7 snRNA. Moreover, it is facilitated by a specialized SMN complex that contains Lsm10 and Lsm11 but lacks Sm D1/D2. Thus, the U7-specific Lsm11 protein not only specifies the assembly of the U7 Sm core but also fulfills an important role in U7 snRNP-mediated histone mRNA processing.
Resumo:
We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.
Resumo:
Inositol polyphosphate 1-phosphatase, inositol monophosphate phosphatase, and fructose 1,6-bisphosphatase share a sequence motif, Asp-Pro-(Ile or Leu)-Asp-(Gly or Ser)-(Thr or Ser), that has been shown by crystallographic and mutagenesis studies to bind metal ions and participate in catalysis. We compared the six alpha-carbon coordinates of this motif from the crystal structures of these three phosphatases and found that they are superimposable with rms deviations ranging from 0.27 to 0.60 A. Remarkably, when these proteins were aligned by this motif a common core structure emerged, defined by five alpha-helices and 11 beta-strands comprising 155 residues having rms deviations ranging from 1.48 to 2.66 A. We used the superimposed structures to align the sequences within the common core, and a distant relationship was observed suggesting a common ancestor. The common core was used to align the sequences of several other proteins that share significant similarity to inositol monophosphate phosphatase, including proteins encoded by fungal qa-X and qutG, bacterial suhB and cysQ (identical to amtA), and yeast met22 (identical to hal2). Evolutionary comparison of the core sequences indicate that five distinct branches exist within this family. These proteins share metal-dependent/Li(+)-sensitive phosphomonoesterase activity, and each predicted tree branch exhibits unique substrate specificity. Thus, these proteins define an ancient structurally conserved family involved in diverse metabolic pathways including inositol signaling, gluconeogenesis, sulfate assimilation, and possibly quinone metabolism. Furthermore, we suggest that this protein family identifies candidate enzymes to account for both the therapeutic and toxic actions of Li+ as it is used in patients treated for manic depressive disease.
Resumo:
The influence of thermally induced changes in the lipid core structure on the oxidative resistance of discrete, homogeneous low density lipoprotein (LDL) subspecies (d, 1.0297-1.0327 and 1.0327-1.0358 g/ml) has been evaluated. The thermotropic transition of the LDL lipid core at temperatures between 15 degrees C and 37 degrees C, determined by differential scanning calorimetry, exerted significant effects on the kinetics of copper-mediated LDL oxidation expressed in terms of intrinsic antioxidant efficiency (lag time) and diene production rate. Thus, the temperature coefficients of oxidative resistance and maximum oxidation rate showed break points at the core transition temperature. Temperature-induced changes in copper binding were excluded as the molecular basis of such effects, as the saturation of LDL with copper was identical below and above the core transition. At temperatures below the transition, the elevation in lag time indicated a greater resistance to oxidation, reflecting a higher degree of antioxidant protection. This effect can be explained by higher motional constraints and local antioxidant concentrations, the latter resulting from the freezing out of antioxidants from crystalline domains of cholesteryl esters and triglycerides. Below the transition temperature, the conjugated diene production rate was decreased, a finding that correlated positively with the average size of the cooperative units of neutral lipids estimated from the calorimetric transition width. The reduced accessibility and structural hindrance in the cluster organization of the core lipids therefore inhibits peroxidation. Our findings provide evidence for a distinct effect of the dynamic state of the core lipids on the oxidative susceptibility of LDL and are therefore relevant to the atherogenicity of these cholesterol-rich particles.
Resumo:
The performance of supersonic engine inlets and external aerodynamic surfaces can be critically affected by shock wave / boundary layer interactions (SBLIs), whose severe adverse pressure gradients can cause boundary layer separation. Currently such problems are avoided primarily through the use of boundary layer bleed/suction which can be a source of significant performance degradation. This study investigates a novel type of flow control device called micro-vortex generators (µVGs) which may offer similar control benefits without the bleed penalties. µVGs have the ability to alter the near-wall structure of compressible turbulent boundary layers to provide increased mixing of high speed fluid which improves the boundary layer health when subjected to flow disturbance. Due to their small size,µVGs are embedded in the boundary layer which provide reduced drag compared to the traditional vortex generators while they are cost-effective, physically robust and do not require a power source. To examine the potential of µVGs, a detailed experimental and computational study of micro-ramps in a supersonic boundary layer at Mach 3 subjected to an oblique shock was undertaken. The experiments employed a flat plate boundary layer with an impinging oblique shock with downstream total pressure measurements. The moderate Reynolds number of 3,800 based on displacement thickness allowed the computations to use Large Eddy Simulations without the subgrid stress model (LES-nSGS). The LES predictions indicated that the shock changes the structure of the turbulent eddies and the primary vortices generated from the micro-ramp. Furthermore, they generally reproduced the experimentally obtained mean velocity profiles, unlike similarly-resolved RANS computations. The experiments and the LES results indicate that the micro-ramps, whose height is h≈0.5δ, can significantly reduce boundary layer thickness and improve downstream boundary layer health as measured by the incompressible shape factor, H. Regions directly behind the ramp centerline tended to have increased boundary layer thickness indicating the significant three-dimensionality of the flow field. Compared to baseline sizes, smaller micro-ramps yielded improved total pressure recovery. Moving the smaller ramps closer to the shock interaction also reduced the displacement thickness and the separated area. This effect is attributed to decreased wave drag and the closer proximity of the vortex pairs to the wall. In the second part of the study, various types of µVGs are investigated including micro-ramps and micro-vanes. The results showed that vortices generated from µVGs can partially eliminate shock induced flow separation and can continue to entrain high momentum flux for boundary layer recovery downstream. The micro-ramps resulted in thinner downstream displacement thickness in comparison to the micro-vanes. However, the strength of the streamwise vorticity for the micro-ramps decayed faster due to dissipation especially after the shock interaction. In addition, the close spanwise distance between each vortex for the ramp geometry causes the vortex cores to move upwards from the wall due to induced upwash effects. Micro-vanes, on the other hand, yielded an increased spanwise spacing of the streamwise vortices at the point of formation. This resulted in streamwise vortices staying closer to the wall with less circulation decay, and the reduction in overall flow separation is attributed to these effects. Two hybrid concepts, named “thick-vane” and “split-ramp”, were also studied where the former is a vane with side supports and the latter has a uniform spacing along the centerline of the baseline ramp. These geometries behaved similar to the micro-vanes in terms of the streamwise vorticity and the ability to reduce flow separation, but are more physically robust than the thin vanes. Next, Mach number effect on flow past the micro-ramps (h~0.5δ) are examined in a supersonic boundary layer at M=1.4, 2.2 and 3.0, but with no shock waves present. The LES results indicate that micro-ramps have a greater impact at lower Mach number near the device but its influence decays faster than that for the higher Mach number cases. This may be due to the additional dissipation caused by the primary vortices with smaller effective diameter at the lower Mach number such that their coherency is easily lost causing the streamwise vorticity and the turbulent kinetic energy to decay quickly. The normal distance between the vortex core and the wall had similar growth indicating weak correlation with the Mach number; however, the spanwise distance between the two counter-rotating cores further increases with lower Mach number. Finally, various µVGs which include micro-ramp, split-ramp and a new hybrid concept “ramped-vane” are investigated under normal shock conditions at Mach number of 1.3. In particular, the ramped-vane was studied extensively by varying its size, interior spacing of the device and streamwise position respect to the shock. The ramped-vane provided increased vorticity compared to the micro-ramp and the split-ramp. This significantly reduced the separation length downstream of the device centerline where a larger ramped-vane with increased trailing edge gap yielded a fully attached flow at the centerline of separation region. The results from coarse-resolution LES studies show that the larger ramped-vane provided the most reductions in the turbulent kinetic energy and pressure fluctuation compared to other devices downstream of the shock. Additional benefits include negligible drag while the reductions in displacement thickness and shape factor were seen compared to other devices. Increased wall shear stress and pressure recovery were found with the larger ramped-vane in the baseline resolution LES studies which also gave decreased amplitudes of the pressure fluctuations downstream of the shock.
Resumo:
Xanthine phosphoribosyltransferase (XPRT; EC 2.4.2.22) from Escherichia coil is a tetrameric enzyme having 152 residues per subunit. XPRT catalyzes the transfer of the phosphoribosyl group from 5-phospho-alpha-D-ribosyl l-pyrophosphate (PRib-PP) to the 6-oxopurine bases guanine, xanthine, and hypoxanthine to form GMP, XMP, and IMP, respectively. Crystals grown in the absence of substrate or product were used to determine the structure of XPRT at a resolution of 1.8 Angstrom by multiple isomorphous replacement. The core structure of XPRT includes a five-stranded parallel B-sheet surrounded by three or-helices, which is similar to that observed in other known phosphoribosyltransferase (PRTase) structures. The XPRT structure also has several interesting features. A glutamine residue in the purine binding site may be responsible for the altered 6-oxopurine base specificity seen in this enzyme compared to other 6-oxopurine PRTases. Also, we observe both a magnesium ion and a sulfate ion bound at the PRib-PP binding site of XPRT. The sulfate ion interacts with Arg-37 which has a cis-peptide conformation, and the magnesium ion interacts with Asp-89, a highly conserved acidic residue in the PRib-PP binding site motif. The XPRT structure also incorporates a feature which has not been observed in other PRTase structures. The C-terminal 12 residues of XPRT adopt an unusual extended conformation and make interactions with a neighboring subunit. The very last residue, Arg-152, could form part of the active site of a symmetry-related subunit in the XPRT tetramer.
Resumo:
The effect of confinement on the magnetic structure of vortices of dipolar coupled ferromagnetic nanoelements is an issue of current interest, not only for academic reasons, but also for the potential impact in a number of promising applications. Most applications, such as nano-oscillators for wireless data transmission, benefit from the possibility of tailoring the vortex core magnetic pattern. We report a theoretical study of vortex nucleation in pairs of coaxial iron and Permalloy cylinders, with diameters ranging from 21nm to 150nm, and 12nm and 21nm thicknesses, separated by a non-magnetic layer. 12nm thick iron and Permalloy isolated (single) cylinders do not hold a vortex, and 21nm isolated cylinders hold a vortex. Our results indicate that one may tailor the magnetic structure of the vortices, and the relative chirality, by selecting the thickness of the non-magnetic spacer and the values of the cylinders diameters and thicknesses. Also, the dipolar interaction may induce vortex formation in pairs of 12nm thick nanocylinders and inhibit the formation of vortices in pairs of 21nm thick nanocylinders. These new phases are formed according to the value of the distance between the cylinderes. Furthermore, we show that the preparation route may control relative chirality and polarity of the vortex pair. For instance: by saturating a pair of Fe 81nm diameter, 21nm thickness cylinders, along the crystalline anisotropy direction, a pair of 36nm core diameter vortices, with same chirality and polarity is prepared. By saturating along the perpendicular direction, one prepares a 30nm diameter core vortex pair, with opposite chirality and opposite polarity. We also present a theoretical discussion of the impact of vortices on the thermal hysteresis of a pair of interface biased elliptical iron nanoelements, separated by an ultrathin nonmagnetic insulating layer. We have found that iron nanoelements exchange coupled to a noncompensated NiO substrate, display thermal hysteresis at room temperature, well below the iron Curie temperature. The thermal hysteresis consists in different sequences of magnetic states in the heating and cooling branches of a thermal loop, and originates in the thermal reduction of the interface field, and on the rearrangements of the magnetic structure at high temperatures, 5 produce by the strong dipolar coupling. The width of the thermal hysteresis varies from 500 K to 100 K for lateral dimensions of 125 nm x 65 nm and 145 nm x 65 nm. We focus on the thermal effects on two particular states: the antiparallel state, which has, at low temperatures, the interface biased nanoelement with the magnetization aligned with the interface field and the second nanoelement aligned opposite to the interface field; and in the parallel state, which has both nanoelements with the magnetization aligned with the interface field at low temperatures. We show that the dipolar interaction leads to enhanced thermal stability of the antiparallel state, and reduces the thermal stability of the parallel state. These states are the key phases in the application of pairs of ferromagnetic nanoelements, separated by a thin insulating layer, for tunneling magnetic memory cells. We have found that for a pair of 125nm x 65nm nanoelements, separated by 1.1nm, and low temperature interface field strength of 5.88kOe, the low temperature state (T = 100K) consists of a pair of nearly parallel buckle-states. This low temperature phase is kept with minor changes up to T= 249 K when the magnetization is reduced to 50% of the low temperature value due to nucleation of a vortex centered around the middle of the free surface nanoelement. By further increasing the temperature, there is another small change in the magnetization due to vortex motion. Apart from minor changes in the vortex position, the high temperature vortex state remains stable, in the cooling branch, down to low temperatures. We note that wide loop thermal hysteresis may pose limits on the design of tunneling magnetic memory cells
Resumo:
In the present work we study a long superconducting wire with a columnar defect in the presence of an applied magnetic field. The cross section of the cylinder is assumed to be circular. The field is taken uniform and parallel to the cylinder axis. We use the London theory to investigate the vortex lattice inside the wire. Although this theory is valid in the limit of low vortex density, that is, when the nearest neighbor vortex distance is much larger than the coherence length, we can obtain a reasonable qualitative description of lattice properties. We calculate: (1) the vortex lattice structure using the simulated annealing technique; (2) the magnetization curve as a function of the applied field.
Resumo:
A numerical study of the time-dependent Gross-Pitaevskii equation for an axially symmetric trap to obtain insight into the free expansion of vortex states of BEC is presented. As such, the ratio of vortex-core radius to radia rms radius xc/xrms(<1) is found to play an interesting role in the free expansion of condensed vortex states. the larger this ratio, the more prominent is the vortex core and the easier is the possibility of experimental detection of vortex states.
Resumo:
In the present work, a detailed analysis of a Mediterranean TLC occurred in January 2014 has been conducted. The author is not aware of other studies regarding this particular event at the publication of this thesis. In order to outline the cyclone evolution, observational data, including weather-stations data, satellite data, radar data and photographic evidence, were collected at first. After having identified the cyclone path and its general features, the GLOBO, BOLAM and MOLOCH NWP models, developed at ISAC-CNR (Bologna), were used to simulate the phenomenon. Particular attention was paid on the Mediterranean phase as well as on the Atlantic phase, since the cyclone showed a well defined precursor up to 3 days before the minimum formation in the Alboran Sea. The Mediterranean phase has been studied using different combinations of GLOBO, BOLAM and MOLOCH models, so as to evaluate the best model chain to simulate this kind of phenomena. The BOLAM and MOLOCH models showed the best performance, by adjusting the path erroneously deviated in the National Centre for Environmental Prediction (NCEP) and ECMWF operational models. The analysis of the cyclone thermal phase shown the presence of a deep-warm core structure in many cases, thus confirming the tropical-like nature of the system. Furthermore, the results showed high sensitivity to initial conditions in the whole lifetime of the cyclone, while the Sea Surface Temperature (SST) modification leads only to small changes in the Adriatic phase. The Atlantic phase has been studied using GLOBO and BOLAM model and with the aid of the same methodology already developed. After tracing the precursor, in the form of a low-pressure system, from the American East Coast to Spain, the thermal phase analysis was conducted. The parameters obtained showed evidence of a deep-cold core asymmetric structure during the whole Atlantic phase, while the first contact with the Mediterranean Sea caused a sudden transition to a shallow-warm core structure. The examination of Potential Vorticity (PV) 3-dimensional structure revealed the presence of a PV streamer that individually formed over Greenland and eventually interacted with the low-pressure system over the Spanish coast, favouring the first phase of the cyclone baroclinic intensification. Finally, the development of an automated system that tracks and studies the thermal phase of Mediterranean cyclones has been encouraged. This could lead to the forecast of potential tropical transition, against with a minimum computational investment.
Resumo:
A new total synthesis of the marine macrolide (-)-zampanolide (1) and the structurally and stereochemically related non-natural levorotatory enantiomer of (+)-dactylolide (2), that is, ent-2, has been developed. The synthesis features a high-yielding, selective intramolecular Horner-Wadsworth-Emmons (HWE) reaction to close the 20-membered macrolactone ring of 1 and ent-2. The β-keto phosphonate/aldehyde precursor for the ring-closure reaction was obtained by esterification of a ω-diethylphosphono carboxylic acid fragment and a secondary alcohol fragment incorporating the THP ring that is embedded in the macrocyclic core structure of 1 and ent-2. THP ring formation was accomplished through a segment coupling Prins-type cyclization. Employing the same overall strategy, 13-desmethylene-ent-2 as well as the monocyclic desTHP derivatives of 1 and ent-2 were prepared. Synthetic 1 inhibited human cancer cell growth in vitro with nM IC(50) values, while ent-2, which lacks the diene-containing hemiaminal-linked side chain of 1, is 25- to 260-fold less active. 13-Desmethylene-ent-2 as well as the reduced versions of ent-2 and 13-desmethylene-ent-2 all showed similar cellular activity as ent-2 itself. The same activity level was attained by the monocyclic desTHP derivative of 1. Oxidation of the aldehyde functionality of ent-2 gave a carboxylic acid that was converted into the corresponding N-hexyl amide. The latter showed only μM antiproliferative activity, thus being several hundred-fold less potent than 1.