Y-shaped Junction Research Articles

Scattering-matrix formalism of electron transport through three-terminalquantum structures: formulation and application to Y-junction devices

In this paper we present a formalism for the calculation of electron transportthrough three-terminal junction devices, which have received attentiondue to their recently demonstrated non-linear electrical properties. Theformalism, which is based on the scattering-matrix method, takes quantuminterference effects fully into account. Furthermore, the formalism providesnumerical stability in the calculations as well as large flexibility in themodelling of arbitrary potential profiles due to the common basis approachused in the formulation. The method is used to calculate the transportproperties for Y-shaped three-terminal ballistic junction (TBJ) structures withconfigurations typical of recently performed experiments. Quantum interferenceeffects are shown to strongly influence the transport characteristics of TBJstructures due to complex scattering of the electrons in the cavity-like couplingwindow between the three arms of the device. The theoretical approachpresented in this paper provides a flexible tool for the study of such quantuminterference effects, which may play an important role in the design andfunctionality of future nanoscale devices based on three-terminal junctions.

PII: S0969-2126(01)00700-6

PII: S0969-2126(01)00700-6

Junctions of supersymmetric tubes

We begin by reviewing the noncommutative supersymmetric tubular configurations in the matrix theory. We identify the worldvolume gauge fields, the charges and the moment of RR charges carried by the tube. We also study the fluctuations around many tubes and tube–D0 systems. Based on the supersymmetric tubes, we have constructed more general configurations that approach supersymmetric tubes asymptotically. These include a bend with angle and a junction that connects two tubes to one. The junction may be interpreted as a finite-energy domain wall that interpolates U(1) and U(2) worldvolume gauge theories. We also construct a tube along which the noncommutativity scale changes. Relying upon these basic units of operations, one may build physical configurations corresponding to any shape of Riemann surfaces of arbitrary topology. Variations of the noncommutativity scale are allowed over the Riemann surfaces. Particularly simple such configurations are Y-shaped junctions.

Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric cre recombinase bound to a three-way lox DNA junction

The crystal structure of a novel Cre-Lox synapse was solved using phases from multiple isomorphous replacement and anomalous scattering, and refined to 2.05 Å resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pseudo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombination. The three-way DNA junction was accommodated by a simple kink without significant distortion of the adjoining DNA duplexes. Although the mean angle between DNA arms in the Y and X structures was similar, adjacent Cre trimer subunits rotated 29 ° relative to those in the tetramers. This rotation was accommodated at the protein-protein and DNA-DNA interfaces by interactions that are “quasi-equivalent” to those in the tetramer, analogous to packing differences of chemically identical viral subunits at non-equivalent positions in icosahedral capsids. This structural quasi-equivalence extends to function as Cre can bind to, cleave and perform strand transfer with a three-way Lox substrate. The structure explains the dual recognition of three and four-way junctions by site-specific recombinases as being due to shared structural features between the differently branched substrates and plasticity of the protein-protein interfaces. To our knowledge, this is the first direct demonstration of quasi-equivalence in both the assembly and function of an oligomeric enzyme.

A wavelet formulation of the finite-difference method: full-vector analysis of optical waveguide junctions

We have developed an efficient, large-stencil finite-difference scheme of the time-dependent Maxwell's curl equations based on the wavelet-collocation formulation in the time-domain. The proposed scheme enables, for the first time within a limited computational resource, full-vector analysis of three-dimensional rib waveguides that are typically used in integrated planar optical devices. The formulation takes advantage of compactly-supported interpolating bases to expand and represent the electric and magnetic fields. Moreover, unlike the well-known beam propagation methods, the numerical scheme is based on the first-principle algorithm with no explicit approximation, and thus rigorous and versatile for various types of boundary conditions. We demonstrate the efficiency of the method by first analyzing a straight rib-waveguide and examining the convergence of the results. Then we investigate a Y-shaped junction structure that is electrically too large to analyze with the conventional finite-difference time-domain scheme.

Excess counterion binding and ionic stability of kinked and branched DNA

We compute the excess number of counterions associated with kinked and branched DNA, and the ionic stabilities of these structures as a function of chain length and both sodium and magnesium salt concentration, using numerical counterion condensation theory. The DNA structures are modeled as two or more finite lines of phosphate charges radiating from the kink or junction center. The number of excess counterions around the (40–90°) kinked duplex is very small (at most four). The geometries of large three- and four-way DNA junctions (with >50 base pairs per arm) in solutions containing low to moderate NaCl concentrations, by contrast, accumulate a substantial number of excess sodium ions (>20) but no more than 15 magnesium counterions. The excess number of counterions surrounding the kinked linear chain and the branched DNA structures either remains invariant or increases with chain length, tending to reach a plateau value. Open configurations, such as the planar Y-shaped three-way junction (with three 120° inter-arm angles) and the 90° cross-shaped four-way junction, are ionically more stable than compact geometries, such as pyramidal three-way junctions and X-shaped four-way junctions, over the entire range of salt concentration considered (10 −5–10 −1 M NaCl or MgCl 2). The ionic stabilities of the compact forms increase with increasing salt concentration and become comparable to those of the extended geometries at high salt (especially when magnesium is the supporting salt).

Phenomenal Shrinkage and Expansion of Visual Surfaces: Is Amodal Completion a Factor?

When two figures intersect, two apparently paradoxical size effects take place (Kanizsa, 1979 Organization in Vision chapter 11): (1) the partly occluded figure looks shorter than an identical unoccluded figure, and (2) the modally visible parts of the occluded figure look larger than identical isolated parts. Kanizsa explains such effects as due to amodal completion. Three experiments were carried out by the method of adjustment to test this explanation: two were devoted to the shrinkage effect, and the third one was devoted to the expansion effect. The first experiment exploited the properties of the so-called Helmholtz - Ratoosh law (T-shaped vs Y-shaped junctions) to test whether a figural shrinkage is also present in a pattern in which amodal completion should not occur. The second experiment was aimed at checking whether stereoscopic displacement of the ‘occluded’ figure ‘behind’ or ‘in front of’ the ‘occluding’ one is capable of affecting the amount of shrinkage. In the third experiment the Helmholtz - Ratoosh law was again applied to the expansion. The results of all three experiments converge in showing that the amount of shrinkage of the whole ‘occluded’ figure as well as the ammount of expansion of the ‘modally visible’ parts are not affected by the presence or the absence of amodal completion. We conclude that both the shrinkage and the expansion effects are due to other factors, probably the same factors as those that affect classical optical-geometrical illusions, such as the Oppel - Kundt or the horizontal - vertical illusions.

Migration Behavior of Granule Cell Neurons in Cerebellar Cultures I. A PKH26 Labeling Study in Microexplant and Organotypic Cultures: (mouse cerebellar granule cell/microexplant culture/organotypic explant culture/PKH26/migration).

Granule cells were dissociated from early postnatal mouse cerebella and labeled with a fluorescent dye probe PKH26. Small number of the labeled cells were mixed with cerebellar cortical microexplant cultures or transplanted into cerebellar cortical organotypic explants, and their time-dependent morphological changes during cultures were examined with fluorescence microscopy. Granule cell neurons first extended asymmetrical short bipolar processes in both cultures, and migrated actively in microexplant cultures. After elongation of symmetrically bipolar long and thin neurites, they sprouted short thick processes from cell bodies and migrated perpendicular to neurite bundles that were devoid of glia in microexplant cultures, or migrated vertically inward into the internal granular layer in the organotypic explant. During such migrations, they extended short thick processes in front and thin processes behind the cell body. The latter processes were connected to thin long neurites with T- or Y-shaped junctions in both cultures. Finally, they extended many short thick processes from cell bodies in both cultures. Such behaviors of granule cell neurons in microexplant cultures were, thus, similar to those in organotypic explant cultures despite of the absence of Bergmann glial cells. These migration patterns may be closely related to migration of granule cells in histogenesis of the cerebellar cortex.

Is Amodal Completion Necessary for the Formation of Illusory Figures?

Kanizsa's hypothesis suggests that the creation of an anomalous surface is due to the amodal completion of the inducers. In the present paper a new pattern that is able to disconfirm this explanation is presented. According to the Helmholtz-Ratoosh law amodal completion only occurs when the borders of two adjacent surfaces meet forming T-shaped junctions. When the borders of the two adjacent surfaces have Y-shaped junctions, amodal completion is absent. However, when a pattern inducing an anomalous figure has the latter figural characteristics, in spite of the absence of amodal completion, an illusory figure is still visible. In this paper a set of experimental results (carried out by means of a magnitude estimation procedure as well as the method of constant stimuli) supporting the aforementioned observations is presented.

Ultrastructure of the attachment of Cryptosporidium sporozoites to tissue culture cells.

The attachment of Cryptosporidium sporozoites to Madin-Darby canine kidney (MDCK) cells was examined using transmission electron microscopy. As the anterior end of the sporozoite came into close proximity to the MDCK cell, the host cell membrane evaginated around the sporozoite, forming a parasitophorous vacuole. A dense band formed below the host cell membrane at the site nearest to the conoid. Variably electron-dense material was apparently released from the conoid and a large membrane-bound vacuole was formed in the anterior end of the sporozoite, displacing the typical anterior electron-dense organelles (rhoptries and micronemes). The outer membrane of the sporozoite pellicle then fused with the host cell membrane immediately adjacent to the conoid. The membrane surrounding the anterior vacuole was also fused with the common host-parasite membrane, forming Y-shaped membrane junctions where each limb was a unit membrane. A direct link was thereby established between the anterior vacuole of the sporozoite and the host cell cytoplasm. The anterior vacuole membrane separating the sporozoite and the host cell cytoplasm was the precursor of the feeder organelle.

Ordered transmembrane and extracellular structure in squid photoreceptor microvilli.

Invertebrate retinas contain hexagonal arrays of microvilli that form the honeycomb structure of rhabdome photoreceptors. The largest and most crystalline rhabdomes are found in the squid retina, and we have taken advantage of their unique properties to derive a model for the electron density distribution in microvillar membranes using low angle X-ray diffraction combined with correlation averaging of electron microscope images. The model electron density map, calculated to a resolution of approximately 35 A, shows an unusually high protein content in the membranes. This may be associated with a dense meshwork of membrane junctions between neighboring microvilli as revealed by electron microscope image analysis. Membrane pair contacts are resolved as two or more strands of density crossing the membranes. The microvilli are also linked together by Y-shaped junctions at their three-way contacts. These two sorts of junctions link the membranes into a three-dimensional array and partition them into a mosaic of deformable and rigid domains. This arrangement maintains a remarkable degree of long-range order in squid rhabdomes, and may be responsible for the alignment of rhodopsin molecules. The structural order observed is necessary for these photoreceptors to achieve their high sensitivity to the plane of polarized light. Rhodopsin constitutes about one-half the microvillar protein. The remaining proteins, which can be divided into approximately equal detergent-soluble and insoluble fractions, could account for the composition of the new structures described.

Viscoelastic Flow in Y-Shaped Channel

A two-dimensional steady flow of viscoelastic and Newtonian liquids is investigated in Y-shaped channel. In the present paper a Maxwell model in which the viscosity term is due to Carreau is used for the viscoelastic liquid. It is the purpose of the present work to investigate the effects of elasticity and non-Newtonian viscosity on flow pattern.Numerical results agree qualitatively with experimental observations. With viscoelastic liquids a secondary flow appears upstream of the Y-shaped junction on its acute angle side. The region of secondary flow becomes larger with increasing Reynolds and Weissenberg numbers showing effects of elasticity and non-Newtonian viscosity. Whereas in the Newtonian flow no secondary flow appears at these Reynolds numbers, but when the Reynolds number becomes large a secondary flow appears downstream of the Y-shaped junction on its acute angle side.

Viscoelastic Flow in Y-Shaped Channel

A two-dimensional steady flow of viscoelastic and Newtonian liquids is investigated in Y-shaped channel. In the present paper a Maxwell model in which the viscosity term is due to Carreau is used for the viscoelastic liquid. It is the purpose of the present work to investigate the effects of elasticity and non-Newtonian viscosity on flow pattern.Numerical results agree qualitatively with experimental observations. With viscoelastic liquids a secondary flow appears upstream of the Y-shaped junction on its acute angle side. The region of secondary flow becomes larger with increasing Reynolds and Weissenberg numbers showing effects of elasticity and non-Newtonian viscosity. Whereas in the Newtonian flow no secondary flow appears at these Reynolds numbers, but when the Reynolds number becomes large a secondary flow appears downstream of the Y-shaped junction on its acute angle side.

Viscoelastic Flow in Y-Shaped Channel

A two-dimensional steady flow of viscoelastic and Newtonian liquids is investigated in Y-shaped channel. In the present paper a Maxwell model in which the viscosity term is due to Carreau is used for the viscoelastic liquid. It is the purpose of the present work to investigate the effects of elasticity and non-Newtonian viscosity on flow pattern.Numerical results agree qualitatively with experimental observations. With viscoelastic liquids a secondary flow appears upstream of the Y-shaped junction on its acute angle side. The region of secondary flow becomes larger with increasing Reynolds and Weissenberg numbers showing effects of elasticity and non-Newtonian viscosity. Whereas in the Newtonian flow no secondary flow appears at these Reynolds numbers, but when the Reynolds number becomes large a secondary flow appears downstream of the Y-shaped junction on its acute angle side.

Normal branching, induced branching, and steering of cultured parasympathetic motor neurons

Cultured embryonic parasympathetic motor neurons branch in vitro by a process in which (1) the central, most anterior portion of the growth cone surface becomes quiescent; (2) the two adjacent lateral growth cone regions remain motile; (3) flat portions of the “split” growth cone round into cylindrical branch axons; and (4) the Y-shaped junction of the branch axons regresses slightly toward the soma. Branching of a seemingly identical type can be induced with a needle by manipulating the central anterior portion of a growth cone. The needle may lift the cell surface from the substratum to cause the branching. Growth cones at the ends of such induced branches can, in turn, be induced with the needle to branch so that they form subsidiary branches. Growth cones may be “steered” in desired directions by passing needles under one side or the other and displacing the growth cone surface from the substratum. When this is done, the cone moves in the opposite direction. The results imply that changes in cell-to-substratum contact may contribute to axonal branching or to directional movement over a substratum.

A fine structural and E-PTA study of photoreceptor synaptogenesis in the chick retina.

Photoreceptor synaptogenesis in the embryonic and hatchling chick retina was studied with conventional EM techniques and ethanolic phosphotungstic acid (E-PTA). The photoreceptors line up between 11 and 13 embryonic days with their undifferentiated synaptic bases facing the outer plexiform layer (OPL). E-PTA staining at 11 embryonic days does not reveal any para-membranous specializations of the receptors but numerous stained punctae adhaerentes are observed in the OPL. At 13 embryonic days neurites of presumed bipolar and horizontal neurons are aligned parallel to the bases of the receptors and cytoplasmic protrusions of the receptors project between some of these neurites to form dyad appositions. An osmiophilic undercoating, which is not E-PTA positive at this time, is present on the cytoplasmic face of the receptor membrane in these apposition regions. Between 13 and 15 embryonic days the filopodial protrusions of the receptors continue to elongate further and become aligned with neurites in dyad and triad appositions. The osmiophilic undercoating now extends along the entire inner surface of the receptor pedicle protrusions and becomes E-PTA positive. Between 15 and 17 embryonic days focal aggregations of osmiophilic and E-PTA stained material appear along the membranes of the protrusions and there is some E-PTA staining of the postsynaptic densities and intervening cleft material. Between 17 and 21 embryonic days mature ribbon synapses are observed on the surfaces of the conical-shaped, receptor pedicles where the ribbons and their synaptic vesicles are associated with the dense aggregations (arciform densities), seen earlier as isolated focal aggregations, and the receptor undercoating is restricted to non-synaptic regions. E-PTA staining shows that ribbons are positively stained around their borders only and that they are contiguous with the intensely stained arciform densities. The cleft material and postsynaptic densities of some synapses first stain as V-shaped junctions and later as Y-shaped junctions. These observations suggest that ribbon synaptic junction formation begins with an alignment of pre- and postsynaptic membranes and the presence of the receptor presynaptic membrane undercoating, followed by the appearance of the presynaptic arciform densities and some staining of the cleft material and postsynaptic densities. These events are followed by the appearance of synaptic ribbons which are associated with the presynaptic arciform densities and by a further differentiation of the cleft material and postsynaptic densities.

Geometry and kinetics of the polygonization of sodium chloride

The geometry and kinetics of the domain growth during polygonization of sodium chloride is studied. It is found that the breaking up of ending walls is the dominating process in the initial stages, whilst the Y-shaped junctions dominate the growth process in the final stages. The interaction between growth in subboundaries and the newly formed polygon walls is also considered. In an appendix the interaction of isolated edge dislocations with a wall of edge dislocations is discussed in some detail. The kinetics of the polygonization process was studied by means of isothermal annealing curves. Two different activation energies are found: one for the low temperature range (49 kcal/mol) and one for temperatures above 375°C (30 kcal/mol). The difference between these two activation energies is interpreted as the activation energy for jog formation; its value is 0.6–0.8 eV.