Short Junctions Research Articles

Superconducting phase-dependent force in SNS junctions with mobile scatterers

We calculate the quantum (Casimir-like) superconducting phase-dependent force acting on mobile scatterers in superconductor–normal metal–superconductor (SNS) junctions. Repulsive Casimir forces are predicted in short SNS junctions with nonequilibrium (inverse) Andreev level populations. An anomalous (nonmonotonic) temperature dependence of the quantum force is found in long SNS junctions.

Transport through asymmetric two-lead junctions of Luttinger liquid wires

We calculate the conductance of a system of two spinless Luttinger liquid wires with different interaction strengths g1 , g2 , connected through a short junction, within the scattering state formalism. Following earlier work we formulate the problem in current algebra language, and calculate the scale dependent contribution to the conductance in perturbation theory keeping the leading universal contributions to all orders in the interaction strength. From that we derive a renormalization group (RG) equation for the conductance. The analytical solution of the RG-equation is discussed in dependence on g1 , g2 . The regions of stability of the two fixed points corresponding to conductance G = 0 and G = 1,respectively, are determined.

Comparative full genome analysis of four infectious laryngotracheitis virus (Gallid herpesvirus-1) virulent isolates from the United States

Gallid herpesvirus-1 (GaHV-1), commonly named infectious laryngotracheitis (ILT) virus, causes the respiratory disease in chickens known as ILT. The molecular determinants associated with differences in pathogenicity of GaHV-1 strains are not completely understood, and a comparison of genomic sequences of isolates that belong to different genotypes could help identify genes involved in virulence. Dideoxy sequencing, 454 pyrosequencing and Illumina sequencing-by-synthesis were used to determine the nucleotide sequences of four genotypes of virulent strains from GaHV-1 groups I-VI. Three hundred and twenty-five open reading frames (ORFs) were compared with those of the recently sequenced genome of the Serva vaccine strain. Only four ORFs, ORF C, U(L)37, ICP4 and U(S)2 differed in amino acid (aa) lengths among the newly sequenced genomes. Genome sequence alignments were used to identify two regions (5' terminus and the unique short/repeat short junction) that contained deletions. Seventy-eight synonymous and 118 non-synonymous amino acid substitutions were identified with the examined ORFs. Exclusive to the genome of the Serva vaccine strain, seven non-synonymous mutations were identified in the predicted translation products of the genes encoding glycoproteins gB, gE, gL and gM and three non-structural proteins U(L)28 (DNA packaging protein), U(L)5 (helicase-primase) and the immediate early protein ICP4. Furthermore, our comparative sequence analysis of published and newly sequenced GaHV-1 isolates has provided evidence placing the cleavage/packaging site (a-like sequence) within the inverted repeats instead of its placement at the 3' end of the U(L) region as annotated in the GenBank's entries NC006623 and HQ630064.

Rheological properties of Ca2+-gels of partially methylesterified polygalacturonic acid: Effect of “mixed” patterns of methylesterification

Abstract Subjecting homogalacturonan to a combination of processes which modify the extent of pectin's methylesterification results in the generation of distinct patterns of methylesterification on the polymer. In this study, the influence of these “mixed” patterns of methylesterification on the rheological characteristics of Ca 2+ -gels is extensively examined, using partially methylesterified poly- d -galacturonic acid (mPGA) as a model for homogalacturonan. The uncontrolled pattern of methylesterification induced on mPGA was combined with that resulting from subsequent controlled chemical or enzymatic de-esterification. Afterwards, the produced mPGAs were characterised in terms of degree and pattern of methylesterification. The latter structural feature was quantified as “absolute degree of blockiness” through enzymatic fingerprinting. Characterised mPGAs were used for the preparation of gels with various calcium ion (Ca 2+ ) concentrations. All Ca 2+ -pectin systems formed “true” gels with a strong elastic behaviour, but vary in gel stiffness. The gels’ rheological characteristics not only depend on the extent of mPGA de-esterification, but also on the “mixed” patterns of methylesterification. The experimental results also indicate that extremely short non-cooperative junction zones contribute to the stiffness of Ca 2+ -mPGA gels.

A duplex real-time RT-PCR assay for the simultaneous genogroup-specific detection of noroviruses in both clinical and environmental specimens

Norovirus (NoV) is the major etiological agent causing foodborne and waterborne outbreaks worldwide. We developed a novel duplex real-time quantitative RT-PCR assay designed for the simultaneous detection of and discrimination between NoV genogroups GI and GII, by targeting the short junction region between ORF1 and ORF2, with sensitivity and efficiency comparable to those of each simplex RT-PCR assay. This new duplex assay was evaluated against clinical stool (n = 82) and environmental (groundwater or surface water, n = 60) specimens from South Korea, and the results were compared with those of conventional RT-PCR (cRT-PCR) assays. The duplex assay detected more positive samples than did the cRT-PCR for both clinical (74 vs. 71) and, more strikingly, environmental (24 vs. 10) specimens. No cross-reactivity against specimens containing other enteric viruses such as rotavirus, adenovirus, and poliovirus were observed. These results suggest that this newly developed duplex real-time RT-PCR assay can be used for the sensitive and simultaneous genogroup-specific detection of NoV in both clinical and environmental specimens.

Josephson effect in S/F/S junctions: Spin bandwidth asymmetry versus Stoner exchange

We analyze the dc Josephson effect in a ballistic superconductor/ferromagnet/superconductor junction by means of the Bogoliubov--de Gennes equations in the quasiclassical Andreev approximation. We consider the possibility of ferromagnetism originating from a mass renormalization of carriers of opposite spin, i.e., a spin bandwidth asymmetry. We provide a general formula for Andreev levels that is valid for arbitrary interface transparency, exchange interaction, and bandwidth asymmetry, and we analyze the current-phase relation, free energy, and critical current in the short junction regime. We compare the phase diagrams and the critical current magnitudes of two identical junctions differing only in the mechanism by which the midlayer becomes magnetic. We show that a larger number of $0\ensuremath{-}\ensuremath{\pi}$ transitions caused by a change in junction width or polarization magnitude is expected when ferromagnetism is driven by spin bandwidth asymmetry compared to Stoner magnetism. Moreover, we show that these features can be present also for ferromagnets of the Stoner type having only a partial bandwidth asymmetry.

Radiation of Terahertz Electromagnetic Waves from Build-In Nano Josephson Junctions of Cuprate High-Tc Superconductors

The nano-scale intrinsic Josephson junctions in highly anisotropic cuprate superconductors have potential for generation of terahertz electromagnetic waves. When the thickness of a superconductor sample is much smaller than the wavelength of electromagnetic waves in vacuum, the superconductor renders itself as a cavity. Unlike conventional lasers, the presence of the cavity does not guarantee a coherent emission because of the internal degree of freedom of the superconductivity phase in long junctions. We study the excitation of terahertz wave by solitons in a stack of intrinsic Josephson junctions, especially for relatively short junctions. Coherent emission requires a rectangular configuration of solitons. However such a configuration is unstable against weak fluctuations, contrarily solitons favor a triangular lattice corresponding to an out phase oscillation of electromagnetic waves. To utilize the cavity, we propose to use an array of stacks of short intrinsic Josephson junctions to generate powerful terahertz electromagnetic waves. The cavity synchronizes the plasma oscillation in different stacks and the emission intensity is predicted to be proportional to the number of stacks squared.

Nonlinear microwave response of aluminum weak-link Josephson oscillators

We present the driven response at T=30 mK of 6 GHz superconducting resonators constructed from capacitively-shunted three-dimensional (3D) aluminum nanobridge superconducting quantum interference devices (nanoSQUIDs). We observe flux modulation of the resonant frequency in quantitative agreement with numerical calculation and characteristic of near-ideal short weak-link junctions. Under strong microwave excitation, we observe stable bifurcation in devices with coupled quality factor (Q) ranging from 30–3500. Near this bias point, parametric amplification with >20 dB gain, 40 MHz bandwidth, and near quantum-limited noise performance is observed. Our results indicate that 3D nanobridge junctions are attractive circuit elements to realize quantum bits.

Closed form solutions for the self-resonances in a short Josephson junction

We present a closed form solution for the self-resonances in a short Josephson tunnel junction. This solution is alternative to the well-known textbook result (Barone and Paternó (1982) and Kulik (1965)) [1,2] based on a series expansion. Results are derived for the up-to-date case of a 0 – π junction.

Can the transition from tunneling to hopping in molecular junctions be predicted by theoretical calculation?

The electron transport mechanism changes from tunneling to hopping as molecular length increases. To validate the theoretical simulation after the transition point and clarify influence of electronic structures on the transition, we calculated the conductance of a series of conjugated molecules by density functional theory together with the nonequilibrium Green's function. We found that the highest occupied molecular orbital energy level, transmission spectrum, and the reorganization energy are good indicators for the transition of the electron transport mechanism. The calculated resistances of short junctions (<50 Å, before the transition point) are consistent with the experimental result, following the tunneling mechanism. However, the theoretical predication failed for long molecules, indicating the limitation of the theoretical framework of elastic scattering when the electron transport mechanism changes to hopping.

Collapse of an AB copolymer single chain with alternating blocks of different stiffness

Using the Langevin dynamics, we studied the conformational properties of an AB copolymer single chain built of alternating stiff and flexible blocks having different steady-state affinities to a solvent. Two opposite conditions were simulated, viz., where a solvent is poor for stiff blocks and good for flexible blocks and vice versa. The behavior of the molecules built of equal-length blocks and long stiff blocks linked through short flexible junctions were considered. Upon transition of a chain to the compact state, nanostructures with different morphologies, such as bunches, networks, and others, can form.

Strongly anharmonic current-phase relation in ballistic graphene Josephson junctions

Motivated by a recent experiment directly measuring the current-phase relation (CPR) in graphene under the influence of a superconducting proximity effect, we here study the temperature dependence of the CPR in ballistic graphene SNS Josephson junctions within the the self-consistent tight-binding Bogoliubov-de Gennes (BdG) formalism. By comparing these results with the standard Dirac-BdG method, where rigid boundary conditions are assumed at the SN interfaces, we show on a crucial importance of both proximity effect and depairing by current for the CPR. The proximity effect grows with temperature and reduces the skewness of the CPR towards the harmonic result. In short junctions ($L<\xi$) current depairing is also important and gives rise to a critical phase $\phi_c<\pi/2$ over a wide range of temperatures and doping levels.

Josephson current in ballistic superconductor-graphene systems

We calculate the phase, the temperature and the junction length dependence of the supercurrent for ballistic graphene Josephson-junctions. For low temperatures we find non-sinusoidal dependence of the supercurrent on the superconductor phase difference for both short and long junctions. The skewness, which characterizes the deviation of the current-phase relation from a simple sinusoidal one, shows a linear dependence on the critical current for small currents. We discuss the similarities and differences with respect to the classical theory of Josephson junctions, where the weak link is formed by a diffusive or ballistic metal. The relation to other recent theoretical results on graphene Josephson junctions is pointed out and the possible experimental relevance of our work is considered as well.

Self-resonant modes in Josephson junctions with a phase discontinuity

We extend the theory of self-resonances in short Josephson junctions to the case of a piecewise constant critical current density and a κ discontinuity in the Josephson phase. We calculate the amplitude of the self-resonances as a function of applied magnetic field by using an extension of the approach introduced by Kulik for conventional Josephson junctions (I. O. Kulik, JETP Lett. 2, 84 (1965)). The theory given here agrees with existing experiments on superconducting–insulator–ferromagnet–superconductor 0–π Josephson junctions. The results are relevant to the characterization of all modern 0–π junctions as well as 0–κ junctions with artificially created phase discontinuities: high-temperature grain boundary junctions, junctions with a ferromagnetic barrier, and junctions with current injectors.

Spindle cell oncocytoma with late recurrence and unique neuroimaging characteristics due to recurrent subclinical intratumoral bleeding

Spindle cell oncocytoma (SCO) is a rare sellar-region tumor recently codified in the World Health Organization (WHO) 2007 Classification as a grade I neoplasm. Despite this grading, recurrences have been demonstrated but, to date, extensive recurrent bleeding into these tumors has not been documented. A 70-year-old woman first presented in 1996 with visual difficulties and was found to have a sellar-region mass with heterogeneous neuroimaging features, leading to preoperative diagnosis of craniopharyngioma. Transsphenoidal, gross total resection was achieved despite extensive intraoperative bleeding; pathology showed an unusual spindle cell neoplasm which could not be further classified. She received no further treatment and was lost to our follow-up until 2009, when she again presented with visual deterioration. Neuroimaging demonstrated recurrence of a large sellar-region tumor with heterogeneous signal characteristics, prompting re-resection. Review of her original and recurrent tumor allowed diagnosis of SCO; extensive intratumoral hemorrhage of varying ages and widespread hemosiderin accounted for her complex neuroimaging features. Vimentin, S100, and galectin-3 immunoreactivity was consistent with SCO. EM demonstrated abundant mitochondria, short intercellular junctions, and absence of neurosecretory granules. Thyroid disease was documented clinically. SCOs are sufficiently rare that documentation of unusual features is important. Recurrent bleeding with resultant complex neuroimaging is unique to this case, but appears to overlap with a related sellar-region tumor, pituicytoma. The presence of thyroid disease also links SCO with pituicytoma. The 13-year interval to recurrence is the longest reported to date in SCO; WHO grade I designation may be premature for this neoplasm.

Conductance decay of a surface hydrogen tunneling junction fabricated along a Si(001)-(2×1)-H atomic wire

On a Si(001)-$(2\ifmmode\times\else\texttimes\fi{}1)$-H substrate, electrons tunneling through hydrogen atomic junctions fabricated between two surface dangling-bond (DB) wires are theoretically investigated using the elastic-scattering quantum-chemistry method. The surface states introduced in the Si band gap by removing H atoms from a Si(001)-$(2\ifmmode\times\else\texttimes\fi{}1)$-H surface were calculated and also analyzed using a simple tight-binding model. The two-channel surface conductance of a DB wire results from a combination of through-space and through-lattice electronic couplings between DB states. The conductance of the DB wire-H-junction-DB wire structure decreases exponentially with the length of H junction with an inverse decay rate ranging from 0.20 to $0.23\text{ }{\text{\AA{}}}^{\ensuremath{-}1}$, depending on the energy. When the DB wire-H-junction-DB wire structure is contacted by Au nanoelectrodes, the transmission resonances corresponding to the DB wire states split, demonstrating a coupling of the DB wires through short surface hydrogen atomic junctions. This splitting decreases with the length of H junction between the DB wires with an inverse decay length ranging from 0.22 to $0.44\text{ }{\text{\AA{}}}^{\ensuremath{-}1}$, indicating that such an atomic scale surface tunneling junction is not a very good insulator.

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

During growth under selection, mutant types appear that are rare in unselected populations. Stress-induced mechanisms may cause these structures or selection may favor a series of standard events that modify common preexisting structures. One such mutation is the short junction (SJ) duplication with long repeats separated by short sequence elements: AB*(CD)*(CD)*E (* = a few bases). Another mutation type, described here, is the tandem inversion duplication (TID), where two copies of a parent sequence flank an inverse-order segment: AB(CD)(E'D'C'B')(CD)E. Both duplication types can amplify by unequal exchanges between direct repeats (CD), and both are rare in unselected cultures but common after prolonged selection for amplification. The observed TID junctions are asymmetric (aTIDs) and may arise from a symmetrical precursor (sTID)-ABCDE(E'D'C'B'A')ABCDE-when sequential deletions remove each palindromic junction. Alternatively, one deletion can remove both sTID junctions to generate an SJ duplication. It is proposed that sTID structures form frequently under all growth conditions, but are usually lost due to their instability and fitness cost. Selection for increased copy number helps retain the sTID and favors deletions that remodel junctions, improve fitness, and allow higher amplification. Growth improves with each step in formation of an SJ or aTID amplification, allowing selection to favor completion of the mutation process.

Switching dynamics in a short and a long natural Josephson junction of Bi2Sr2CaCu2O8+δ single crystals

We studied thermally activated and macroscopically quantum-tunneled switching from the zero-voltage state to a first resistive state in stacks of short and long Josephson junctions (JJs) naturally formed in Bi2Sr2CaCu2O8+δ single crystals. In the short (long) JJs the switching corresponds to an escape of a phase particle (a flexible phase line) from a potential well. The effective barrier height in the long JJs is reduced in proportion to the length of the junctions.

English

&nbsp; The current investigation was carried out at Sirw, northern part of Egypt, during 2007 and 2008 seasons. The present study mainly aimed to evaluate the morphological and molecular variation among Egyptian Jasmine and its 10 M5 derived mutants under saline soil conditions. Some mutant lines have the advantage of early maturation nearly one month earlier compared with the original variety Egyptian Jasmine. In addition, other derived mutants significantly surpassed the Egyptian Jasmine in terms of yield and its components. The biomass and grain yield recorded the highest value of expected genetic advance. The values of heritability were high for all yields and yield attributes. Some morphological traits were utilized in order to identify the M5&nbsp;morphology. DNA Markers namely Short Sequence Repeats (SSR) and Intron Splice Junction (ISJ) were used to reveal the molecular variations at molecular level among all entries. A significant level of polymorphism based on morphological and molecular levels was observed. The overall evaluation for the newly developed lines revealed that the best line was in Jasmine Sirw Line No. 3 and followed equally by Jasmine Sirw Line Nos. 8 and 9. &nbsp; Key words:&nbsp;Jasmine rice, induced mutation, DNA markers.

Imaging of Order Parameter InducedπPhase Shifts in Cuprate Superconductors by Low-Temperature Scanning Electron Microscopy

Low-temperature scanning electron microscopy (LTSEM) has been used to image the supercurrent distribution in ramp-type Josephson junctions between Nb and either the electron-doped cuprate Nd_{2-x}Ce_{x}CuO_{4-y} or the hole-doped cuprate YBa_{2}Cu_{3}O_{7}. For zigzag-shaped devices in the short junction limit the critical current is strongly suppressed at zero applied magnetic field. The LTSEM images show that this is due to the Josephson current counterflow in neighboring 0 and pi facets, which is induced by the d_{x;{2}-y;{2}} order parameter in the cuprates. Thus, LTSEM provides imaging of the sign change of the superconducting order parameter, which can also be applied to other types of Josephson junctions.