Circular Junction Research Articles

A robust hybridizable discontinuous Galerkin scheme with harmonic averaging technique for steady state of real-world semiconductor devices

Solving real-world nonlinear semiconductor device problems modeled by the drift-diffusion equations coupled with the Poisson equation (also known as the Poisson-Nernst-Planck equations) necessitates an accurate and efficient numerical scheme which can avoid non-physical oscillations even for problems with extremely sharp doping profiles. In this paper, we propose a flexible and high-order hybridizable discontinuous Galerkin (HDG) scheme with harmonic averaging (HA) technique to tackle these challenges. The proposed HDG-HA scheme combines the robustness of finite volume Scharfetter-Gummel (FVSG) method with the high-order accuracy and hp-flexibility offered by the locally conservative HDG scheme. The coupled Poisson equation and two drift-diffusion equations are simultaneously solved by the Newton method. Indicators based on the gradient of net doping and solution variables are proposed to switch between cells with HA technique and high-order conventional HDG cells, utilizing the flexibility of HDG scheme. Numerical results suggest that the proposed scheme does not exhibit oscillations or convergence issues, even when applied to heavily doped and sharp PN-junctions. Devices with circular junctions and realistic doping profiles are simulated in two dimensions, qualifying this scheme for practical simulation of real-world semiconductor devices.

Dynamic photon heat transport through a Majorana fermion modulated circular mesoscopic Josephson device adjusted by ac magnetic flux

The photonic heat current and conductance of circular mesoscopic Josephson junction device coupled with Majorana fermions under the application of ac magnetic flux have been investigated. This system is equivalent to the situation that the Josephson junction is biased by the dc voltage V and an ac voltage with frequency Ω0. The dc voltage induce the Josephson current with oscillation frequency ω=2eVħ. The time-dependent Landauer-like formula and linear dc photonic heat conductance formula are derived. The application of Majorana fermions suppresses the amplitude, and splits the resonant peaks of heat current. The heat conductance is suppressed with increasing the coupling constants of Majorana fermions. With the coupling of Majorana fermions, the magnitude of heat conductance is enhanced with the increase of ω/Ω0, and it is suppressed due to increasing the magnitude of applied ac flux. The photon-pumping heat current has been evaluated at thermal equilibrium state, to show the suppression and splitting effects resulting from Majorana fermions.

Large amplification of the sensitivity of symmetric-response magnetic tunnel junctions with a high gain flux concentrator

Miniaturized, ultra-sensitive and easily integrable magnetometers are needed for many applications like space exploration or medical survey. In this study, we combine innovative magnetic tunnel junctions having a symmetric resistance-field (R–H) response with a high gain flux concentrator. In our junctions, the magnetization of the free layer (FL) is stabilized in an anti-parallel configuration with respect to that of the reference layer. This configuration is achieved by using a soft exchange pinning of the FL. We precisely adjust the exchange field value with a dusting layer of ruthenium used to weakly decouple the magnetization of the FL from the local moments of the antiferromagnet. In order to improve the junction's sensitivity, we study the influence of the exchange field value and of the shape anisotropy on the even-function R–H response. In particular, we compare circular junctions with elliptic or rectangular junctions of various aspect ratios and orientations. We find that the sensitivity of the junctions increases when reducing the soft-pinning exchange field and by using junctions with an elongated shape in the direction of the applied field. Finally, we were able to further increase the sensitivity by a factor 440 due to a flux concentrator placed around the junction by electrochemical deposition of NiFe. Its design is optimized (elongated shape, 5–7 μm thickness and 10 μm air-gap) in order to obtain this very high gain. The complete sensor system composed of these magnetic tunnel junctions and the flux concentrator allows to reach sensitivities larger than 1000%/mT.

Circular ferroelectric tunnel junctions for the improvement of memory window and endurance

A circular ferroelectric tunnel junction (C-FTJ) is proposed for a larger memory window and better endurance than a conventional planar FTJ (P-FTJ). The electrical characteristics of the proposed C-FTJ are evaluated compared with a conventional P-FTJ by using device simulation. It is confirmed that C-FTJs have more excellent ferroelectric switching than P-FTJs because the electric field becomes more concentrated across the ferroelectric layer. Also, C-FTJs show better endurance because the electric field applied to the interfacial layer is alleviated.

Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles.

To bring new extrachromosomal circular DNA (eccDNA) enrichment technologies closer to the clinic, specifically for screening, early diagnosis, and monitoring of diseases or lifestyle conditions, it is paramount to identify the differential pattern of the genic eccDNA signal between two states. Current studies using short-read sequenced purified eccDNA data are based on absolute numbers of unique eccDNAs per sample or per gene, length distributions, or standard methods for RNA-seq differential analysis. Previous analyses of RNA-seq data found significant transcriptomics difference between sedentary and active life style skeletal muscle (SkM) in young people but very few in old. The first attempt using circulomics data from SkM and blood of aged lifelong sedentary and physically active males found no difference at eccDNA level. To improve the capability of finding differences between circulomics data groups, we designed a computational method to identify Differentially Produced per Gene Circles (DPpGCs) from short-read sequenced purified eccDNA data based on the circular junction, split-read signal, of the eccDNA, and implemented it into a software tool DifCir in Matlab. We employed DifCir to find to the distinctive features of the influence of the physical activity or inactivity in the aged SkM that would have remained undetected by transcriptomics methods. We mapped the data from tissue from SkM and blood from two groups of aged lifelong sedentary and physically active males using Circle_finder and subsequent merging and filtering, to find the number and length distribution of the unique eccDNA. Next, we used DifCir to find up-DPpGCs in the SkM of the sedentary and active groups. We assessed the functional enrichment of the DPpGCs using Disease Gene Network and Gene Set Enrichment Analysis. To find genes that produce eccDNA in a group without comparison with another group, we introduced a method to find Common PpGCs (CPpGCs) and used it to find CPpGCs in the SkM of the sedentary and active group. Finally, we found the eccDNA that carries whole genes. We discovered that the eccDNA in the SkM of the sedentary group is not statistically different from that of physically active aged men in terms of number and length distribution of eccDNA. In contrast, with DifCir we found distinctive gene-associated eccDNA fingerprints. We identified statistically significant up-DPpGCs in the two groups, with the top up-DPpGCs shed by the genes AGBL4, RNF213, DNAH7, MED13, and WWTR1 in the sedentary group, and ZBTB7C, TBCD, ITPR2, and DDX11-AS1 in the active group. The up-DPpGCs in both groups carry mostly gene fragments rather than whole genes. Though the subtle transcriptomics difference, we found RYR1 to be both transcriptionally up-regulated and up-DPpGCs gene in sedentary SkM. DifCir emphasizes the high sensitivity of the circulome compared to the transcriptome to detect the molecular fingerprints of exercise in aged SkM. It allows efficient identification of gene hotspots that excise more eccDNA in a health state or disease compared to a control condition.

Aharonov–Bohm-like effects and Fano resonances in circular DNA molecular junctions

DNA electronics has reattracted great interest in recent years and showed a number of fascinating phenomena. Here, we present a theoretical study of electron transport through a two-terminal circular DNA junction under a perpendicular magnetic field. Our results indicate that this circular DNA exhibits Aharonov–Bohm-like effects and a semiconductor–insulator–semiconductor transition by tuning this magnetic field, with the transmission spectrum nearly oscillating periodically. Interestingly, Fano resonances appear around integer multiples of the magnetic flux quantum accompanied by several vortices of local currents. Moreover, the circular DNA behaves as a nanoscale switch, and this switching effect is robust and could be improved for longer molecular length and weaker molecule–electrode coupling, with the on/off ratio exceeding 104 for long circular DNA. These results may help for designing novel circular DNA-based molecular devices.

Oscillations of photonic heat current through parallel-coupled double circular mesoscopic Josephson junction devices

Oscillations of photonic heat current through parallel-coupled double circular mesoscopic Josephson junction devices

Experimental and numerical investigation of the effect of horseshoe vortex legs on heat characteristics of the downstream region of a circular cylinder-wall junction

The present study was investigated experimentally and numerically the effect of horseshoe vortex (HV) legs on the wall heat transfer in a turbulent boundary layer in the downstream region of a circular cylinder-wall junction. The experiments were carried out at three Reynolds number, ReD = 20,000, 40,000, and 60,000 (based on the cylinder diameter and the free-stream velocity) encompassing the turbulent region, while numerical simulations were performed at ReD=20,000 only. In the studies carried out, the ratio of cylinder diameter to boundary layer thickness at ReD = 20,000, 40,000, and 60,000 at the point where the cylinder is placed is 2.44, 3.20, and 3.37, respectively. A constant–temperature anemometer and copper-constant thermocouples were used for measurements of velocity and turbulent intensity, and temperature, respectively. The results showed that the flat surface in the downstream region of a circular cylinder-wall junction increased the Stanton number up to 43% compared to the flat surface without cylinders. Furthermore, the increase in the Stanton number at the saddle point at the end of the downstream region of the HV legs showed a peak, while the increase at the separation line point at the beginning of the upstream region is found to be minimum. Another finding observed is that the increase in the Stanton number decreases dramatically from the end of the downstream region of the HV leg to the origin of the upstream region.

Circular RNA in Chemonaive Lymph Node Negative Colon Cancer Patients.

Simple SummaryColon cancer (CC) is one of the most common types of cancer. Circular RNAs (circRNAs) appear to play an important role in tumor progression of CC. They are stably expressed in saliva, blood, and exosomes, potentially rendering them promising biomarkers for the diagnosis, prognosis, and treatment of CC. In this study we describe the identification of an extensive catalog of circRNAs in a large cohort of 181 chemonaive, stage I/II primary colon tumors and related circRNA expression to consensus molecular subtypes (CMS), microsatellite instability (MSI) status and clinical outcome. We observed that a high diversity in circRNAs was associated with favorable disease-free survival, and that several circRNAs were associated with MSI and CMS, demonstrating the potential clinical value of circRNAs in CC.Circular RNAs (circRNAs) appear important in tumor progression of colon cancer (CC). We identified an extensive catalog of circRNAs in 181 chemonaive stage I/II colon tumors, who underwent curative surgery between 2007 and 2014. We identified circRNAs from RNAseq data, investigated common biology related to circRNA expression, and studied the association between circRNAs and relapse status, tumor stage, consensus molecular subtypes (CMS), tumor localization and microsatellite instability (MSI). We identified 2606 unique circRNAs. 277 circRNAs (derived from 260 genes) were repeatedly occurring in at least 20 patients of which 153 showed a poor or even negative (R < 0.3) correlation with the expression level of their linear gene. The circular junctions for circSATB2, circFGD6, circKMT2C and circPLEKHM3 were validated by Sanger sequencing. Multiple correspondence analysis showed that circRNAs were often co-expressed and that high diversity in circRNAs was associated with favorable disease-free survival (DFS), which was confirmed by Cox regression analysis (Hazard Ratio (HR) 0.60, 95% CI 0.38–0.97, p = 0.036). Considering individual circRNAs, absence of circMGA was significantly associated with relapse, whereas circSATB2, circNAB1, and circCEP192 were associated with both MSI and CMS. This study represents a showcase of the potential clinical utility of circRNAs for prognostic stratification in patients with stage I–II colon cancer and demonstrated that high diversity in circRNAs is associated with favorable DFS.

DEBKS: A Tool to Detect Differentially Expressed Circular RNAs

Circular RNAs (circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that a circRNA is formed from the host gene by back-splicing (BS). To distinguish the expression difference originating from BS or the host gene, we present differentially expressed back-splicing (DEBKS), a software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying to real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

The fibers of the circular junction of the linea alba in normal adult anatomy.

The linea alba (LA) is known to be useful to surgeons for making surgical incisions. Laparoscopic entry into the peritoneal cavity using the open technique may involve identification of a point just above or below the umbilicus where the peritoneum is fused to the LA. This anatomical site is found through superficial dissection to expose the junction between the umbilical stalk (US) and the LA, where distinct fibers seem to form a unique ligament-like structure in normal adult anatomy. This point, in fact, is part of a circular fibrous structure that exists almost like a ring around the remnant US. It is formed by the fusion of oblique and transverse fibers of the LA with circular fibers from proliferation of an encircling band of compact mesoderm to close a patent umbilical ring. We describe and name this anatomical landmark as junctio circularis alba or the "circular junction of the LA" as encountered in normal adult human anatomy. We believe this is crucial for describing key surgical procedures at this site to aid effective surgical training and reduce iatrogenic complications from laparoscopic port site entries.

Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs.

Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2′–5′ bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences.

The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced by RNase_MRP (ribozyme RNA). We specifically investigated the intronic circRNA of ATXN2L, which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.

Field cooled annular Josephson tunnel junctions

We investigate the physics of planar annular Josephson tunnel junctions quenched through their transition temperature in the presence of an external magnetic field. Experiments carried out with long Nb/Al-AlOx/Nb annular junctions showed that the magnetic flux trapped in the high-quality doubly-connected superconducting electrodes forming the junction generates a persistent current whose associated magnetic field affects the both the static and dynamics properties of the junctions. More specifically, the field trapped in the hole of one electrode combined with a d.c. bias current induces a viscous flow of dense trains of Josephson vortices which manifests itself through the sequential appearance of displaced linear slopes, Fiske step staircases and Eck steps in the junction’s current-voltage characteristic. Furthermore, a field shift is observed in the first lobe of the magnetic diffraction pattern. The effects of the persistent current can be mitigated or even canceled by an external magnetic field perpendicular to the junction plane. The radial field associated with the persistent current can be accurately modeled with the classical phenomenological sine-Gordon model for extended one-dimensional Josephson junctions. Extensive numerical simulations were carried out to disclose the basic flux-flow mechanism responsible for the appearance of the magnetically induced steps and to elucidate the role of geometrical parameters. It was found that the imprint of the field cooling is enhanced in confocal annular junctions which are the natural generalization of the well studied circular annular junctions.

Quantitative study of electronic whispering gallery modes in electrostatic-potential induced circular graphene junctions

Electronic whispering gallery modes (EWGMs) have been recently observed in several circular graphene junctions, pn and pp′, created in scanning tunneling microscopy experiments. By computing the local density of states within the Dirac–Weyl formalism for massless fermions we demonstrate that the EWGMs may really be emerged in any type of the electrostatic-potential induced circular graphene junctions, including uni-junctions (e.g. np- or pp′-junctions) as well as bipolar-junctions (e.g. pnp-heterojunctions). Surprisingly, quantitative analyses show that for all the EWGMs identified (regardless of junction types) the quality (Q) factors seem to be ≤102, very small compared to those in ordinary optical whispering gallery modes microresonators, while the corresponding mode radii may tunably be in nanometer-scale. Our theoretical results are in good agreement with existent experimental data, putting a question to the application potential of the EWGMs identified.

Traffic Modelling of the Circular Junction in the City of Žilina

Traffic Modelling of the Circular Junction in the City of Žilina

Boundary-condition and geometry engineering in electronic hydrodynamics

We analyze the role of boundary geometry in viscous electronic hydrodynamics. We address the twin questions of how boundary geometry impacts flow profiles, and how one can engineer boundary conditions -- in particular the effective slip parameter -- to manipulate the flow in a controlled way. We first propose a micropatterned geometry involving finned barriers, for which we show by an explicit solution that one can obtain effectively no-slip boundary conditions regardless of the detailed microscopic nature of the channel surface. Next we analyse the role of mesoscopic boundary curvature on the effective slip length, in particular its impact on the Gurzhi effect. Finally we investigate a hydrodynamic flow through a circular junction, providing a solution, which suggests an experimental set-up for determining the slip parameter. We find that its transport properties differ qualitatively from the case of ballistic conduction, and thus presents a promising setting for distinguishing the two.

Apicomplexan F‐actin is required for efficient nuclear entry during host cell invasion

The obligate intracellular parasites Toxoplasma gondii and Plasmodium spp. invade host cells by injecting a protein complex into the membrane of the targeted cell that bridges the two cells through the assembly of a ring‐like junction. This circular junction stretches while the parasites apply a traction force to pass through, a step that typically concurs with transient constriction of the parasite body. Here we analyse F‐actin dynamics during host cell invasion. Super‐resolution microscopy and real‐time imaging highlighted an F‐actin pool at the apex of pre‐invading parasite, an F‐actin ring at the junction area during invasion but also networks of perinuclear and posteriorly localised F‐actin. Mutant parasites with dysfunctional acto‐myosin showed significant decrease of junctional and perinuclear F‐actin and are coincidently affected in nuclear passage through the junction. We propose that the F‐actin machinery eases nuclear passage by stabilising the junction and pushing the nucleus through the constriction. Our analysis suggests that the junction opposes resistance to the passage of the parasite's nucleus and provides the first evidence for a dual contribution of actin‐forces during host cell invasion by apicomplexan parasites.

Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.

MotivationIn recent years, multiple circular RNAs (circRNA) biogenesis mechanisms have been discovered. Although each reported mechanism has been experimentally verified in different circRNAs, no single biogenesis mechanism has been proposed that can universally explain the biogenesis of all tens of thousands of discovered circRNAs. Under the hypothesis that human circRNAs can be categorized according to different biogenesis mechanisms, we designed a contextual regression model trained to predict the formation of circular RNA from a random genomic locus on human genome, with potential biogenesis factors of circular RNA as the features of the training data.ResultsAfter achieving high prediction accuracy, we found through the feature extraction technique that the examined human circRNAs can be categorized into seven subgroups, according to the presence of the following sequence features: RNA editing sites, simple repeat sequences, self-chains, RNA binding protein binding sites and CpG islands within the flanking regions of the circular RNA back-spliced junction sites. These results support all of the previously reported biogenesis mechanisms of circRNA and solidify the idea that multiple biogenesis mechanisms co-exist for different subset of human circRNAs. Furthermore, we uncover a potential new links between circRNA biogenesis and flanking CpG island. We have also identified RNA binding proteins putatively correlated with circRNA biogenesis.Availability and implementationScripts and tutorial are available at http://wanglab.ucsd.edu/star/circRNA. This program is under GNU General Public License v3.0.Supplementary information Supplementary data are available at Bioinformatics online.

CircMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs.

Circular RNAs (circRNAs), a class of non-coding RNAs generated from non-canonical back-splicing events, have emerged to play key roles in many biological processes. Though numerous tools have been developed to detect circRNAs from rRNA-depleted RNA-seq data based on back-splicing junction-spanning reads, computational tools to identify critical genomic features regulating circRNA biogenesis are still lacking. In addition, rigorous statistical methods to perform differential expression (DE) analysis of circRNAs remain under-developed. We present circMeta, a unified computational framework for circRNA analyses. circMeta has three primary functional modules: (i) a pipeline for comprehensive genomic feature annotation related to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements such as Alu elements and SINEs, competition score for forming circulation and RNA editing in back-splicing flanking introns; (ii) a two-stage DE approach of circRNAs based on circular junction reads to quantitatively compare circRNA levels and (iii) a Bayesian hierarchical model for DE analysis of circRNAs based on the ratio of circular reads to linear reads in back-splicing sites to study spatial and temporal regulation of circRNA production. Both proposed DE methods without and with considering host genes outperform existing methods by obtaining better control of false discovery rate and comparable statistical power. Moreover, the identified DE circRNAs by the proposed two-stage DE approach display potential biological functions in Gene Ontology and circRNA-miRNA-mRNA networks that are not able to be detected using existing mRNA DE methods. Furthermore, top DE circRNAs have been further validated by RT-qPCR using divergent primers spanning back-splicing junctions. The software circMeta is freely available at https://github.com/lichen-lab/circMeta. Supplementary data are available at Bioinformatics online.