Adjacent Junctions Research Articles

Effect of shot noise on a Coulomb blockaded single Josephson junction

We have investigated how the Coulomb blockade of a mesoscopic Josephson junction in a high-impedance environment is suppressed by shot noise from an adjacent junction. The presented theoretical analysis is an extension of the phase correlation theory for the case of a non-Gaussian noise. Asymmetry of the non-Gaussian noise should result in the shift of the conductance minimum from zero voltage and the ratchet effect (nonzero current at zero voltage), which have been experimentally observed. The analysis demonstrates that a Coulomb blockaded tunnel junction in a high impedance environment can be used as an effective noise detector.

Self-organization of histone-jointed three-dimensional DNA network

A three-dimensional deoxyribonucleic acid (DNA) network was self-organized in a space between two cover slips, which was filled with an aqueous solution of lambda DNA mixed with multivalent cations such as Ca 2+ and histone; the former behaves as a DNA fixation factor on the cover-slip surface and the latter as a junction and pillar construction factor for the network. The geometry and the components of the three-dimensional DNA network thus formed were observed by fluorescence microscopy. It is revealed that (1) the three-dimensional network is based on two-dimensional networks formed on the inner surfaces of the two cover slips, (2) the three-dimensional network is composed of junctions for forming the two-dimensional networks, chains for connecting two adjacent junctions, and pillars connecting the two-dimensional network on one cover-slip surface to the other, and (3) the chains are made of bundles of stretched lambda DNA molecules, and the junctions and the pillars are made of the aggregates of DNA–histone complexes.

Genotyping in 46 patients with tentative diagnosis of Treacher Collins syndrome revealed unexpected phenotypic variation.

To define the range of phenotypic expression in Treacher Collins syndrome (TCS; Franceschetti-Klein syndrome), we performed mutation analysis in the TCOF1 gene in 46 patients with tentative diagnosis of TCS and evaluated the clinical data, including a scoring system. A total of 27 coding exons of TCOF1 and adjacent splice junctions were analysed by direct sequencing. In 36 patients with a clinically unequivocal diagnosis of TCS, we detected 28 pathogenic mutations, including 25 novel alterations. No mutation was identified in the remaining eight patients with unequivocal diagnosis of TCS and 10 further patients, in whom the referring diagnosis of TCS was clinically doubtful. There is no overt genotype-phenotype correlation except that conductive deafness is significantly less frequent in patients with mutations in the 3' part of the open reading frame. Inter- and intrafamilial variation is wide. Some mutation carriers, parents of typically affected patients, are so mildly affected that the diagnosis might be overlooked clinically. This suggests that modifying factors are important for phenotypic expression. Based on these findings, minimal diagnostic criteria were defined: downward slanting palpebral fissures and hypoplasia of the zygomatic arch. The difficulties in genetic counselling, especially diagnosis of family members with a mild phenotype, are described.

MECP2 structural and 3'-UTR variants in schizophrenia, autism and other psychiatric diseases: a possible association with autism.

Mutations in the gene coding for methyl-CpG-binding protein 2 (MECP2) cause Rett syndrome (RTT) and have also been reported in a number of X-linked mental retardation syndromes. Furthermore, putative mutations recently have been described in a few autistic patients and a boy with language disorder and schizophrenia. In this study, DNA samples from individuals with schizophrenia and other psychiatric diseases were scanned in order to explore whether the phenotypic spectrum of mutations in the MECP2 gene can extend beyond the traditional diagnoses of RTT in females and severe neonatal encephalopathy in males. The coding regions, adjacent splicing junctions, and highly conserved segments of the 3'-untranslated region (3'-UTR) were examined in 214 patients, including 106 with schizophrenia, 24 with autism, and 84 patients with other psychiatric diseases by detection of virtually all mutations-single strand conformation polymorphism (SSCP) (DOVAM-S). To our knowledge, this is the first analysis of variants in conserved regions of the 3'-UTR of this gene. A total of 5.2 kb per haploid gene was analyzed (1.5 Mb for 214 patients). A higher frequency of missense and 3'-UTR variants was found in autism. One missense and two 3'-UTR variants were found in 24 patients with autism versus one patient with a missense change in 144 ethnically similar individuals without autism (P = 0.009). These mutations suggest that a possible association between MECP2 mutations and autism may warrant further study.

First variation of anisotropic energies and crystalline mean curvature of partitions

We rigorously derive the notion of crystalline mean curvature of an anisotropic partition with no restriction on the space dimension. Our results cover the case of crystalline networks in two dimensions, polyhedral partitions in three dimensions, and generic anisotropic partitions for smooth anisotropies. The natural equilibrium conditions on the singular set of the partition are derived. We discuss several examples in two dimensions (also for two adjacent triple junctions) and one example in three dimensions when the Wulff shape is the unit cube. In the examples we also analyze the stability of the partitions.

Connectivity and topology of a phase-separating bicontinuous structure in a polymer mixture: Direct measurements of coordination number, inter-junction distances and Euler characteristic

A new set of topological parameters describing connectivity of a phase-separated bicontinuous structure of a polymer mixture in the late stage of spinodal decomposition has been directly measured by use of laser scanning confocal microscopy. A 3D thinning algorithm was used to transform one of the phase-separated domains into a skeletal network that locates at about the center of the domain. Number of channels intersecting at a junction, Nj, and distance between the adjacent junctions, Dj, were obtained from the resulting skeletal network. It was found that the phase-separated domain of the polymer mixture possesses, for the most part, 3 branches at each junction. The Euler characteristic, describing topology of the network, was found to be between ∼−2 to −4, topologically equivalent to a sphere with ∼2 to 3 handles. Time-evolution of the histograms of the coordination number, H(Nj), and distance, H(Dj), clearly demonstrates that the bicontinuous structure grows with self-similarity in topological sense.

Modelling of microstructure formation and interface dynamics

A phase-field model for a general class of binary three-phase metallic alloys is presented which describes both, multi-phase solidification phenomena as well as polycrystalline grain structures. The model serves as a computational tool to simulate the motion and kinetics of multiple phase boundaries and enables the visualization of the diffusion processes and phase transitions in multi-phase alloy systems. A selection of numerical simulation results illustrates the capability of the phase-field model to recover a variety of complex experimental growth structures. In particular, the discretized model is used to simulate the microstructure evolution in eutectic, peritectic and monotectic alloys. Moreover, the temporal development of polycrystalline grain structures with effects such as wetting, grain growth, symmetry properties of adjacent triple junctions in thin film samples and stability criteria at multiple junctions is shown in various simulations.

Na/Ca exchanger and PMCA localization in neurons and astrocytes: functional implications.

Immunocytochemistry reveals that the Na/Ca exchanger (NCX) in neuronal somata and astrocytes is confined to plasma membrane (PM) microdomains that overlie sub-PM (junctional) endoplasmic reticulum (jER). By contrast, the PM Ca(2+) pump (PMCA) is more uniformly distributed in the PM. At presynaptic nerve terminals, the NCX distribution is consistent with that observed in the neuronal somata, but the PMCA is clustered at the active zones. Thus, the PMCA, with high affinity for Ca(2+) (K(d) congruent with 100 nM), may keep active zone Ca(2+) very low and thereby "reprime" the vesicular release mechanism following activity. NCX, with lower affinity for Ca(2+) (K(d) congruent with 1,000 nM), on the other hand, may extrude Ca(2+) that has diffused away from the active zones and been temporarily sequestered in the endoplasmic reticulum. The PL microdomains that contain the NCX also contain Na(+) pump high ouabain affinity alpha2 (astrocytes) or alpha 3 (neurons) subunit isoforms (IC(50) congruent with 5-50 nM ouabain). In contrast, the alpha1 isoform (low ouabain affinity in rodents; IC(50) >10,000 nM), like the PMCA, is more uniformly distributed in these cells. The sub-PM endoplasmic reticulum in neurons (and probably glia and other cell types as well) and the adjacent PM form junctions that resemble cardiac muscle dyads. We suggest that the PM microdomains containing NCX and alpha 2/alpha 3 Na(+) pumps, the underlying jER, and the intervening tiny volume of cytosol (<10(-18) l) form functional units (PLasmERosomes); diffusion of Na(+) and Ca(2+) between these cytosolic compartments and "bulk" cytosol may be markedly restricted. The activity of the Na(+) pumps with alpha 2/alpha 3 subunits may thus regulate NCX activity and jER Ca(2+) content. This view is supported by studies in mice with genetically reduced (by congruent with 50%) alpha 2 Na(+) pumps: evoked Ca(2+) transients were augmented in these cells despite normal cytosolic Na(+) and resting Ca(2+) concentrations ([Na(+)](CYT) and [Ca(2+)](CYT)). We conclude that alpha 2/alpha 3 Na(+) pumps control PLasmERosome (local) [Na(+)](CYT). This, in turn, via NCX, modulates local [Ca(2+)](CYT), jER Ca(2+) storage, Ca(2+) signaling, and cell responses.

Expression of fertilin and CD9 in bovine trophoblast and endometrium during implantation.

The superficial placentation of cattle involves the development of fetal binucleate cells that arise from the chorion and migrate between adjacent cell tight junctions to fuse with maternal epithelium. Thus, the temporal and spatial patterns of expression of the cell migration, adhesion, and fusion molecules fertilin and CD9 were investigated in bovine trophoblast and endometrium. Bovine fertilin alpha and fertilin beta messenger RNA sequences were amplified by reverse transcriptase-polymerase chain reaction in testis (positive control), peri-implantation (Days 18, 19, and 21), and postimplantation (Days 35-40) trophoblast RNA, but not in caruncular endometrium (Day 40). Northern blot analysis indicated that the transcript hybridizing to fertilin alpha in trophoblast RNA was approximately 4.0 kilobases (kb), whereas in testis, 2 transcripts of approximately 3.3 and 3.8 kb were indicated. The transcript hybridizing to the fertilin beta probe was also larger in trophoblast than in testis ( approximately 3.8 vs. 2.4 kb, respectively). In situ hybridization revealed that fertilin beta mRNA was expressed by trophoblast cells, including binucleate cells. Immunohistochemical study of CD9, a member of the transmembrane-4-superfamily which is thought to be involved in sperm-egg fusion, showed that CD9 was present on the apical surface of uterine epithelium and in a subpopulation of binucleate cells of the trophoblast. Immunoprecipitation followed by Western blot analysis showed association between CD9 and integrin alpha3 in endometrium. The results support the hypothesis that fertilin and CD9 are involved in bovine binucleate cell migration and fusion.

Phase-field modeling of multi-phase solidification

A phase-field model for a general class of multi-phase metallic alloys is now proposed which describes both multi-phase solidification phenomena as well as polycrystalline grain structures. The model serves as a computational method to simulate the motion and kinetics of multiple phase boundaries and enables the visualization of the diffusion processes and of the phase transitions in multi-phase systems. Numerical simulations are presented which illustrate the capability of the phase-field model to recover a variety of complex experimental growth structures. In particular, the phase-field model can be used to simulate microstructure evolutions in eutectic, peritectic and monotectic alloys. In addition, polycrystalline grain structures with effects such as wetting, grain growth, symmetry properties of adjacent triple junctions in thin film samples and stability criteria at multiple junctions are described by phase-field simulations.

Magnetic interaction between spatially extended superconducting tunnel junctions

A general description of magnetic interactions between superconducting tunnel junctions is given. The description covers a wide range of possible experimental systems, and we explicitly explore two experimentally relevant limits of coupled junctions. One is the limit of junctions with tunneling distance much smaller than the London penetration depth of the superconductors, the other is the limit where the tunneling distance is much larger than the London penetration depth. The former case has previously been studied in the context of adjacent conventional Josephson junctions, while the latter has been considered through arrays of superconducting weak links based on semiconductor quantum wells with superconducting electrodes. We use the model to make direct interpretations of the published experiments and thereby propose that long-range magnetic interactions are responsible for the reported experimental signatures of coupling between tunnel junctions.

Characterization of crosstalk between CMOS photodiodes

The crosstalk in CMOS photodiodes has been measured, at two wavelengths of 543 and 633 nm, by an experimental structure containing several types of photodiodes with varying dimensions. The role of the design of the junction in reducing crosstalk is studied. The measurements indicate that to reduce crosstalk it is essential to optically shield the gap between junctions and to reverse bias the adjacent junctions. Crosstalk is significantly reduced in double-junction photodiodes, but at the cost of lower quantum efficiency. The results indicate that with properly designed layout, the crosstalk may be small. However, there is a tradeoff between small crosstalk, reduced fill factor and quantum efficiency.

Topological polymer chemistry: systematic classification of nonlinear polymer topologies.

Nonlinear polymer topologies composed of cyclic and branched polymer segments are systematically classified by reference to constitutional isomerism in a series of alkanes (CnH2n+2), monocycloalkanes (CnH2n), and polycycloalkanes (CnH2n-2, CnH2n-4, etc). Thus, the total number of chain ends (termini) and of branch points (junctions) are maintained as invariant parameters, as well as the number of branches at each junction and the connectivity of junction. On the other hand, the distance between two adjacent junctions and that between the junction and terminus are taken as variant parameters. On the basis of the classification of polymer topologies, a novel synthetic strategy by an "electrostatic self-assembly and covalent fixation" technique has been proposed to construct a variety of topologically unique polymer architectures.

Features of Preparing the Butyl Acrylate–Acrylonitrile Copolymer by Radiation-Induced Emulsion Polymerization

Some specific features of the radiation-induced emulsion copolymerization of butyl acrylate and acrylonitrile and radiation-induced crosslinking of the resulting copolymer in the latex form were studied. The effect of polymerization conditions on the polymerization rate and the molecular mass of the polymer was determined. The copolymer was shown to undergo efficient crosslinking in the latex form by the action of γ-radiation. The radiation-chemical yield of crosslinking sites (G) and the average molecular mass (Mc) of chain segments between two adjacent network junctions were determined.

A Monte Carlo study of polymer network dynamics

Junction fluctuations in a polymer network are investigated by using the Monte Carlo method. In our calculation, a modified bond-fluctuation model is adopted. In our model, the kuhnian bond lengths are set to vary between 2 and 4, which is different from the lengths between 2 and √ 10 of the standard model. It is found that the average fluctuations of junctions i and j may be expressed in the form of ΔR i 2 / r 2 0= a (φ−1) +b(φ=3, 4, 5, 6) 〈ΔR iΔR j〉/ r 2 0= a′ (φ−1) +b′(φ=3, 4, 5, 6) where a=0.83, b=−0.076, a′=0.06, b′= 0.0075, and 〈 r 2〉 0 is the mean-square end-to-end distance of two adjacent junction points and φ is the junction functionality. Comparisons with the Cayley tree model are also made. Our method uses real, rather than phantom, chains, and this method can be used to investigate the dynamics of polymer network chains.

EPDM−Carbon Black Interactions and the Reinforcement Mechanisms, As Studied by Low-Resolution1H NMR

Proton, low-resolution T2 NMR relaxation experiments are used to study the adsorption of EPDM to the surface of carbon blacks and the structure of the physical EPDM/carbon black network in cured and uncured compounds. It is shown that a layer of immobilized EPDM is formed at the carbon black surface after mixing. The estimated thickness of the interfacial EPDM is in the range of one to two diameters of the monomer unit (≈1 nm). At temperatures of up to 160 °C, the mobility of EPDM chain units in the interface is strongly hindered and is comparable to that in an unfilled EPDM at temperatures 10−15 deg above Tg. It is suggested that the sites of the interaction between the carbon black and the EPDM cause physical adsorption network junctions in the rubber matrix. The average molar mass of EPDM chains between the adjacent adsorption junctions in bound EPDM rubber is about 1800−2500 g/mol and depends on the content and the type of the filler. The mean end-to-end distance between the adsorption junctions is comparable to the average distance between the adjacent carbon black aggregates. This suggests that the carbon black aggregates are interconnected by EPDM bridging chains, and a continuous EPDM/carbon black physical network is formed in the bound rubber fraction of the compound. The results obtained for uncured filled rubbers provide strong evidence of a “bimodal” structure of the physical network. The two types of EPDM chains and/or chain fragments, which have strongly different densities of EPDM−carbon black adsorption junctions, are present in the elastomer matrix outside of the EPDM−carbon black interface. There is an EPDM fraction that is loosely bound to the carbon black by adsorption interactions. This loosely bound rubber has numerous adsorption network junctions, similar to those of the bound rubber. The other fraction of EPDM, the extractable (unbound) rubber, has a relatively low number of adsorption network junctions and can apparently be extracted from the compound. The fraction of loosely bound EPDM chains, as measured by NMR, increases as the maximum possible EPDM−carbon black contact area per unit volume of the elastomer increases, regardless of the type of carbon black, and is relatively close to the content of the bound rubber. Results of mechanical property tests on the carbon black filled vulcanisates reveal that several factors contribute to the reinforcing effect of the filler. Besides the hydrodynamic effects, the occluded EPDM, the chemical cross-links, and the formation of the physical EPDM−carbon black network, the filler−filler interactions provide a significant contribution to the modulus in the low-strain region, while they are broken at high strains.

MEN1 gene analysis in sporadic adrenocortical neoplasms.

Adrenocortical tumors occur as sporadic tumors, as part of the multiple endocrine neoplasia type 1 (MEN1) syndrome or as part of other hereditary disorders. We recently cloned the MEN1 gene, a tumor-suppressor gene located on chromosome 11q13. Subsequently, we showed that sequential somatic inactivation of both alleles of the MEN1 gene contributes to the development of some sporadic endocrine neoplasms (parathyroid, enteropancreatic neuroendocrine, bronchial carcinoid, and pituitary tumors). We now studied whether somatic inactivation of the MEN1 gene contributes to the pathogenesis of sporadic adrenocortical neoplasms. Seven adrenocortical carcinomas, 2 adrenocortical carcinoma cell lines, and 11 aldosterone-secreting, 8 cortisol-secreting, and 5 nonsecreting benign adrenocortical tumors were studied. Seven tumors (5 of 5 carcinomas, 2 of 21 nonsecreting benign adenomas; P < 0.001) exhibited loss of heterozygosity on 11q13. All 33 tumors and cell lines were screened for mutation throughout the MEN1 open-reading frame and adjacent splice junctions. None exhibited a mutation within the MEN1-coding region. We conclude that somatic MEN1 mutation within the MEN1-coding region does not occur commonly in sporadic adrenocortical tumors, although the majority of adrenocortical carcinomas exhibit 11q13 loss of heterozygosity.

A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme.

Group II introns are ribozymes with a complex tertiary architecture that is of great interest as a model for RNA folding. Domain 5 (D5) is a highly conserved region of the intron that is considered one of the most critical structures in the catalytic core. Despite its central importance, the means by which D5 interacts with other core elements is unclear. To obtain a map of potential interaction sites, dimethyl sulfate was used to footprint regions of the intron that are involved in D5 binding. These studies were complemented by measurements of D5 binding to a series of truncated intron derivatives. In this way, the minimal region of the intron required for strong D5 association was defined and the sites most likely to represent thermodynamically significant positions of tertiary contact were identified. These studies show that ground-state D5 binding is mediated by tertiary contacts to specific regions of D1, including a tetraloop receptor and an adjacent three-way junction. In contrast, D2 and D3 are not found to stabilize D5 association. These data highlight the significance of D1-D5 interactions and will facilitate the identification of specific tertiary contacts between them.

Development and autocalibration of an input-output model of chlorine transport in drinking water distribution systems

Chlorine concentrations within drinking water distribution systems (DWDS) must be maintained between an Environmental Protection Agency enforced minimum and maximum values driven by formation of harmful disinfectant byproducts. The DWDS input-output (I-O) model developed expresses the chlorine concentration at a given pipe junction and time as a weighted average of exponentially decayed values of the concentrations at all adjacent upstream junctions. The upstream junction concentrations are known if they are a chlorine treatment point, or can be calculated in the same manner as the original unknown junction concentration. This is the basis for a recursive procedure with which the I-O model backtracks through the DWDS until all paths from consumption to treatment are found. Since the I-O model finds all paths from treatment to a given measurement, the reaction rate associated with chlorine decay at the pipe wall can be adjusted to improve predicted chlorine concentrations.

Static and dynamic properties of stacked Josephson junctions: Analytic solution

Static and dynamic properties of stacked Josephson junctions are studied theoretically. An approximate analytic solution for a stack with arbitrary junction parameters was obtained. The analytic solution is in good agreement with numerical simulations. Characteristic penetration depths, Swihart velocities, the lower critical field, the first integral, and the free energy for a stack of nonidentical junctions were derived and studied for different parameters of the stack. We show that attractive interaction of fluxons in adjacent junctions exists in the dynamic state of the stack, leading to appearance of the ``in-phase'' state with fluxons on top of each other. In a given external magnetic field the Gibbs free energy has a number of local minima corresponding to particular fluxon distributions (modes) in the stack each representing a quasiequilibrium state. For a stack of $N$ junctions each mode would result in $N$ distinct flux-flow branches in the current-voltage characteristic. Taking into account that different modes with equal total number of fluxons are not identical we conclude that the total possible number of flux-flow branches can be much larger than the number of junctions in the stack.