Cilia are microtubule-based organelles protruding from almost all mammalian cells which, when dysfunctional, result in genetic disorders called “ciliopathies”. High-throughput studies have revealed that cilia are composed of thousands of proteins. However, despite many efforts, much remains to be determined regarding the biological functions of this increasingly important complex organelle.We have derived an online tool, from a systematic network-based approach to dissect the cilia/centrosome complex interactome (CCCI). The tool integrates all current available data into a model which provides an “interaction” perspective on ciliary function. We generated a network of interactions between human proteins organized into functionally relevant “communities”, which can be defined as groups of genes that are both highly inter-connected and strongly co-expressed. We then combined sequence and co-expression data in order to identify the transcription factors responsible for regulating genes within their respective communities. Our analyses have discovered communities significantly specialized for delegating specific biological functions such as mRNA processing, protein translation, folding and degradation processes that had never been associated with ciliary proteins until now.CCCI will allow us to clarify the roles of previously unknown ciliary functions, elucidate the molecular mechanisms underlying ciliary-associated phenotypes, and apply our knowledge of the functional roles of relatively uncharacterized molecular entities to disease phenotypes and new clinical applications.The online version of this article (doi:10.1186/1471-2164-15-658) contains supplementary material, which is available to authorized users. Cilia are specialized evolutionarily conserved organelles protruding from the cell surface of most mammalian cells. The cilium consists of a basal body located under the cell surface, from which the organelle is initially assembled, a transition zone that is important for docking of proteins, and the axoneme. In non-mitotic quiescent cells the mother centriole, a centrosomal component, migrates and docks at the apical cell surface, forming the basal body as a result. The ciliary axoneme, which is nucleated and organized by the basal body, is a cytoskeletal structure, formed by a cylinder of nine doublets of microtubules and in some cases, a central pair of microtubules contained within an extension of the plasma membrane .Cilia can be broadly categorized into two subgroups. Motile cilia, protrude from the surface of cells such as tracheal cells, and promote liquid mobility along the surface. On the other hand, primary cilia, appear as individual non-motile sensory organelles, which, for example, can be found in epithelial cells of kidney tubules and neurons. The ciliary membrane contains ion channels, receptors and other signaling proteins that control axoneme bending for motility and/or sense chemical or mechanical stimuli to transduce internal signals . Primarysitus inversus, obesity, ciliary dyskinesia, mental retardation, CNS malformations and cysts in the kidney, liver and pancreas. Some examples of ciliopathies are Bardet-Biedl syndromes (BBS), Oral-facial-digital type 1 (OFD1) syndrome, polycystic kidney diseases (PKD), Joubert syndrome and related disorders, nephronophthisis and Meckel Grouber syndrome [Mutations in 103 proteins that traffic to the basal body and axoneme of cilia have been causally related to human diseases called “ciliopathies”, disorders which present overlapping phenotypes such as retinal degeneration, skeletal defects, syndrome .C. elegans, C. intestinalis, C. reinhardtii, D. melanogaster, P. tetraurelia, M. musculus and H. sapiens have revealed that cilia are composed of thousands of proteins potentially involved in ciliary function and biogenesis [in silico [http://centrosome.cnb.csic.es) the Ciliome Database [http://www.sfu.ca/~leroux/ciliome_home.htm), Ciliaproteome [http://v3.ciliaproteome.org/cgi-bin/index.php), and Cildb [http://cildb.cgm.cnrs-gif.fr/). To date, Cildb is the most comprehensive compilation as it incorporates the largest collection of experiments, including some of those from other databases, in a unified and consistent framework [Model organisms have been extensively used to investigate ciliary functions. High-throughput studies conducted in ogenesis –12. Althn silico , and thon silico  . By analysing the network we detected functionally relevant “communities”, consisting of groups of genes that are both highly inter-connected and strongly co-expressed. Intriguingly, our analysis unveiled communities significantly associated with specific biological functions that had never been associated with ciliary proteins until now.In order to resolve this disparity, the list of interactors for each specific gene may now be visualized in CentrosomeDB . Unfortuhttp://cildb.cgm.cnrs-gif.fr/), a database dedicated to proteins involved with centrioles, centrosomes, basal bodies, cilia and flagella in eukaryotes which collects the results from 32 high-throughput experiments carried out in 10 different species [We collected 3,502 human ciliary genes from Cildb ( species . Since h species ) and, afhttp://string-db.org), a resource that acts as a “one-stop shop” for all information regarding known and predicted functional links between proteins. STRING quantitatively integrates data from various sources, such as genomic context, high-throughput experiments, co-expression and previous knowledge [We obtained interactions among genes from the “Search Tool for the Retrieval of Interacting Genes” (STRING) database  [http://ccci.tigem.it).Among ciliopathy genes, yndrome) , shows thttp://www.syscilia.org). SYSCILIA Gold Standard contains genes considered to be ciliary only if evidence was published for ciliary localization , function in ciliogenesis (including cilium-specific transcription) and involvement in ciliopathies [We then compared the complete gene set  with the SYSCILIA Gold Standard (SCGSv1), a list of 303 known confirmed ciliary components curated by the multinational SYSCILIA consortium (opathies . We founhttp://ccci.tigem.it) containing, on average, 9 genes each . Thirty-nine communities contained at least 5 genes. Figure The centrosome, basal body and cilium are able to regulate their complex behaviors thanks to a set of proteins that perform different but coordinated functions. We questioned whether or not functional modules could be found within the CCCI, as they may reveal how the network is organized. We searched the network for modules, which are defined as “communities”, i.e. group of genes densely interconnected with each other and connected to few genes outside the group, via a clustering algorithm . We idenhttp://ccci.tigem.it). This percentage increases to up to 74% when only communities composed by at least 5 genes are considered. Twelve communities are composed of at least 20 genes, and each of them is enriched for a specific biological process (Table We found with Gene Ontology (GO) analysis that 45 (50%) of these communities were equipped to manage specific biological functions , respectively. All of these results are consistent with previous findings and represent internal controls that support the validity of our approach .Interestingly, four communities  are enriched for processes including mRNA processing, protein synthesis, protein folding and degradation which control the protein expression levels in eukaryotes. Members of community 7 mainly encode mRNA splicing factors, RNA binding proteins, small nuclear ribonucleoproteins (snRNPs), and RNA helicase and protein translation initiation factors; genes encoding structural constituents of ribosomes, translation elongation and termination factors, are components of the community 3. Proteins that promote correct folding of the other proteins, like chaperonin CCT complex subunits and proteins that are involved in ubiquitin-dependent protein catabolic processes, such as ubiquitin, ubiquitin-conjugating enzymes and different 26S proteasome subunits are the main components of communities 11 and 1, respectively.C. elegans [de novo protein synthesis in near proximity to centrosomes via phosphorylation [de novo protein synthesis and centrosome formation, supporting the centrosome’s dependence on components of translational machinery [Functional links between primary cilia and processes that cooperate to control the protein expression levels had never been presented before. Recently, mutations in DDX59, which encodes a member of the DEAD-box-containing the RNA helicase family of proteins, have been associated with Orofaciodigital syndrome , a clini elegans . Interes elegans . These d elegans –36, and achinery .Proteins that are involved in ubiquitin-dependent protein catabolic processes, such as ubiquitin, ubiquitin-conjugating enzymes and different 26S proteasome subunits are the main components of community 1. This non-lysosomal degradation pathway plays a crucial role in biological processes. It not only degrades misfolded and damaged proteins, but also regulates cell-signaling pathways involved in proliferation, adaptation to stress, and regulation of cell size and cell death. Indeed, it has been already shown that, although the ubiquitin proteasome system localizes and can act throughout the cytosol, the catalytic subunit 20S is also localized at the mammalian centrosome  MoreoverThe “proteasome community” is enriched in ciliary components belonging to the SYSCILIA Gold Standard SCGSv1)  and diverse groups of enzymes belonging to the cytochrome P450 and glutathione-S-transferases superfamilies (community 6 and 8).Gene products involved in nucleoside triphosphate GTP/UTP/CTP biosynthetic processes and enzymes mediating the acidification of intracellular organelles, such as subunits of vacuolar ATPase (V-ATPase), are members of two of community 10 and 12, respectively. As far we know these biological processes have never been associated with cilia physiology before and further experiments are needed in order to confirm the role of cilia in these processes.Genes belonging to different communities differ in the frequency in which they interact with each other and the communities with which they interact. Therefore communities vary in the degree to which they are interconnected and associated with one another. In particular, we expect communities with related genes, e.g. involved in related biological process, to be more likely to be interconnected. We explicitly investigated these types of interactions in order to better elucidate community relationships and obtain a general overview of the processes in which the CCCI is involved.We calculated the Interaction Strength (IS) between two communities, which is defined as the number of connections between genes belonging to two different communities, divided by the expected number of connections. If the IS is different from 0, then a connection exists between genes belonging to two different communities. Similarly to the gene-wise network, also the community-wise network can also be mapped out by assigning each node to a community. There is an edge connecting two communities only if the IS is different from 0. We obtained a community-wise network composed of 90 communities represented as nodes and 237 interactions. Using the same approach initially used to find communities of genes, we then grouped the communities with at least 5 genes into sets of highly interconnected communities that we call “super-communities” (SCs), i.e. communities of communities. We obtained 2 SCs  to be abundant in ciliary genes  and 7 communities (18%) in centrosomal genes   < 0.05)  complex, interact with pericentrin to regulate centrosome integrity . These rWe finally explored whether communities were enriched in specific transcription factors (TFs) targets. In order to get the most accurate annotation, we combined sequence and expression data. In particular, to keep as many meaningful gene-gene connections as possible, we considered a gene to be a target of a TF if (i) there was a conserved binding site within the gene (plus a flanking region 10Kb upstream and 5Kb downstream) , 49 and More specifically, we collected a list of TFs and relative targets with at least one binding site within the genomic region of a ciliary gene from the UCSC Genome Browser. We further refined this list by only retaining targets co-expressed with the TF located in the CCCI. Figure We used this list to explore target density for each community. We found 11 communities to be significantly enriched (FDR < 0.05 and at least 5 targets within the community), in 30 out of the 102 tested different TFs. Additional file As expected, we found that some communities contained members of Regulatory factor X (RFX) transcription factors, which are known to play a conserved role in ciliogenesis throughout evolution , 50–52 aWe collected the information from the primary literature and classified the functions and biological roles of the transcription factors that we had identified. Most (54%) of the transcription factors, such as COUP-TF1, AP2REP, GCNF, PAX4, HMX1, HNF1A, LHX3, OCT1, RFX, NFYA, YY1, NKX3, MZF1, GATA1, GATA2 and RUNX1, are involved in developmental processes, and 10 of the 11 communities  are enriched in these developmental TFs. Interestingly, 4 of these, MZF1, GATA1, GATA2 and AML1, are regulators of transcriptional events during hematopoietic development.OFD1, BBS1 and BBS4 both in vivo and in vitro [Communities 2, 4 and 5 host TFs, such as NFAT, AREB6, NF-κB and STAT1, which play a central role in inducible gene transcription during immune response. NF-κB is a TF that is crucial in promoting inflammation through its ability to induce transcription of pro-inflammatory genes . Interesin vitro . Moreovein vitro .Communities 4, 5, 11, 15 and 26 include transcription factors involved in cell cycle control such as CREB1, c-MYC-MAX complex, ELK1, E2F1, ER-alpha, FREAC7, CREBP1, RREB1 and MAZR. They represent about a quarter (30%) of the TFs identified.Communities 4 and 5 also include MYOD, a nuclear protein belonging to the myogenic factors subfamily that regulates muscle cell differentiation and muscle regeneration.http://ccci.tigem.it). The CCCI can be searched by gene of interest and the tool interactively shows information on that gene (e.g. the community to which it belongs to) as well as its interacting genes. It is possible to explore the different communities and their properties.Our resource is publicly available as an online tool  which allows the user to navigate and explore the interactome.We integrated information from different sources to provide a comprehensive view on the genes in the cilia/centrosome complex and the interactions among them. By using a network-based approach, we identified communities of genes more closely interacting and showed that most of these communities are enriched in proteins that carry out specific biological processes. Strikingly, we identified several communities related to mRNA processing, protein synthesis, protein folding and degradation. We also showed that some of the communities contain genes that had been, until now, known to be preeminently expressed in the nucleus. Finally, we identified TF targets in some communities, but the roles of these targets and how they contribute to ciliogenesis need to be elucidated. All the results are freely available through an online tool  were extracted from STRING 9.0 . We starribed in  but discThe final interactome consists of 11,608 interactions between 1,695 ciliary genes plus 1,845 singletons (ciliary genes with no interactions).We investigated the main categories of genes present in the CCCI by using GO . GO termNetwork analysis  and visualization were performed using Cytoscape ver. 2.8.2 . CommuniThe IS between communities was calculated using the statistical framework R by using the approach defined in .http://www.R-project.org).Throughout the study a p-value of 0.05 was considered to be the statistically significant value after false discovery rate correction. All statistical analyses were performed using R ver. 2.12.1 , and 7 were designed to investigate basal body/centriole/MTOC and centrosome proteome . For each gene we counted: (A) the number of experiments in the “ciliary group” in which the gene was present and (B) the number of experiments in the “centrosomal group” in which the gene was present. If (A) was larger than (B) plus one (A > B + 1), the gene localization was set to “ciliary”. Conversely, if (B) was larger than (A) plus one (B > A + 1), the gene localization was set to “centrosomal”. If the difference between (A) and (B) was either 0 or 1, the gene was annotated as “unknown”.http://www.uniprot.org) [The list of nuclear genes was obtained from UniProtKB release 2012_07 (available at rot.org) . We extrThe presence of ciliary, centrosomal and nuclear genes in the communities was calculated in R, using the “fisher.test” and “p.adjust” functions, whilst considering CCCI genes as the background.For the TF analysis we used both sequence (binding motif) and expression (co-expression) data. We obtained the sequence information from the DAVID Bioinformatics Resources 6.7 “UCSC TFBS” table, which is based on the “tfbsConsSites” track of the UCSC Genome Browser. In this table, a gene is considered to be target of a TF if it has a binding site for the TF conserved in the human/mouse/rat alignment (i) within 10Kbp-region of 5′ (upstream) end, (ii) within 3Kbp-region of 3′ (down stream) end, or (iii) with in exon/intron region. Any TF without at least one binding site within the genomic region of a ciliary gene (i.e. present in the CCCI) was removed, resulting in a list of 140 TFs.This list was further filtered by only considering genes/targets that were also significantly co-expressed with the TF according to . To thisThe presence of TF targets in the communities was then assessed using this list, and corrected p-values were calculated in R using the “fisher.test” and “p.adjust” functions, considering CCCI genes as background.Table S2 includes information about the communities of CCCI. (XLSX 284 KB)Additional file 1: Table S1: Includes information about all the genes included in the analysis;


To the general public, the Internet is an acceptable method of obtaining information. It also plays an important role in guiding patients and solving their problems.We investigated the clinical characteristics of an Internet website to provide guidelinesand tips for consultation.In this retrospective observational study, we analyzed the useof a free public Internet perinatal consultation website provided by the Ministry of Healthand Welfare of Korea. We evaluated 2,254 Internet perinatal consultations and assessments of prenatal and obstetrics from August 2006 to December 2009. We evaluated thepatients’ questions based on Williams’ textbook categories and their clinical characteristics.The mean age of patients seeking consultation was 33.9 ± 13.2 years, and paritywas 1.2 ± 0.5. The most commonly asked questions were about drug safety during pregnancy (20.4%), and questions regarding prenatal care (18.7%) and labor pain (15.4%)were the second and third most commonly asked questions, respectively.The Internet can provide good information to patients. Thus, guidelines regarding pregnancy-related questions and answers should be created. Obstetricians coulduse our data to identify question tendencies. Women who wish to become pregnant usuallyseek educational methods such as books and magazinesfor safe fertility and delivery. The Internetis currently a common and acceptable method bywhich patients seek answers to their questions.Based on 33 websites about Internet usage by pregnantwomen, 96.6% of women have Internet accessat home . PregnanIn the present study, we investigated the clinicalcharacteristics of questions on an Internet websiteto provide guidelines and tips for consultation.In this retrospective observational study, we analyzedthe use of a free public Internet perinatalconsultation website provided by the Ministry ofHealth and Welfare of Korea. This website providesinformation on pregnancy, delivery, childcare, and infant health programs and provides amultilingual system for immigrants as well.The website also offers perinatal consultationsand assessments of gynecologic problems free of charge. On average, there were 25,192 logins per day. The service was accessible via a Korean web domain. Fourteen obstetricians conducted the consultations using a private personal computer. Pediatric doctors also consulted with patients about pediatric problems. The consultant had a duty to reply to each patient’s questions. Women asked questions on the site, and an automatic, immediate, repetitive alarm sounded on the consultant’s telephone until a reply was updated on the website. The consultant was required to complete the reply while on duty. Duty days covered all 365 days of the year. All replies were completed within 24 hours.We evaluated 2,254 consultations from August 2006 to December 2009. A total of 122 consultations occurred during the initiation year, whereas 802 consultations were performed in 2009. Two research nurses and one obstetrician evaluated each consultation. We evaluated the questions based on Williams’ textbook categories and patients’ clinical characteristics.Approval for this study was given by the Human Ethics Committee at SCH (Soonchunhyang University) Medical Center . We mention that no personal data is published and the privacy of the users was respected.Results are presented as number and percentage values. Variables were expressed using the number and the percentage. Statistical data were generated with the SPSS version 12 for Windows .The mean age of patients seeking consultation was 33.9 ± 13.2 years, and parity was 1.2 ± 0.5. Most of the consultations were with women  , and theIn Korea, there are almost 80 known websites about pregnancy, delivery, and child care . Our datThe Internet is useful for pregnant women and plays a role in decision-making. In a Web survey of Internet use in 24 countries, most women (97%) used the Internet for pregnancy-related questions . MankataThe preconception period was also a common topic of consultation based on our data. Mankata reported that 5% of those asking questions were husbands, similar to our study 4.7%). Women in other countries were interested in and had many questions regarding pregnancy, but the topics in which they were interested were not the same. Pregnancy-associated questions are common on the Internet, which is a very cost-effective way to obtain information (.7%. WomeThe Internet can provide good information, but that information is sometimes confusing and may be inaccurate. If the website evaluated in this study had an automatic system for differentiating questions based on keywords, trimester, previous related questions, and so forth, the questions could easily be categorized and the evaluation time could be reduced. Thus, such a system should be created for pregnancy-related questions and answers. Culture and health care systems might influence the nature of the most frequent questions. We inferred that Korean women are very anxious about the health of the baby, so they were very eager to obtain information about drug safety and preconception care.


Very few cases of scar sarcoidosis affecting the eyes and bone together have been reported in the last few years.We report a case of a 49-year-old Spanish man with recurrent bilateral granulomatous uveitis and a fistulous nodular lesion in the left pre-tibial region (scar granuloma) on the site of an 8-year-old scar. He presented with bilateral hilar adenopathies and elevation of inflammatory markers and angiotensin-converting enzyme. A histologically confirmed sarcoid of the tibia with a radiologic appearance unusual for long tubular bone involvement was observed. He also had bilateral ophthalmologic involvement.Sarcoidosis is a disease of unknown cause histologically characterized by non-caseating granulomas that can involve any organ or tissue. Osseous sarcoidosis is a relatively rare presentation. However, on the basis of cases reported in the literature, sarcoid lesions on bones are generally asymptomatic. Biologic agents are considered an alternative therapy for sarcoidosis resistant to conventional treatment. Scar sarcoidosis of the tibia is considered a rare disease. It is usually described in old scars 10 years) [0 years .In the last few years, very few cases of scar sarcoidosis affecting the eyes or bone have been described in the literature. The appropriate treatment consists of steroids with gradual dose increases until the condition is controlled, followed by immunosuppressive agents such as methotrexate and azathioprine for control of inflammation . SeveralA 49-year-old Spanish man was referred to our hospital by an ophthalmologist in June 2010 with a symptom of red eyes. A uveitis protocol was implemented. A chest X-ray was ordered. The X-ray showed mediastinal adenopathy, for which the patient was referred to the respiratory medicine department. The results of his respiratory function tests were normal, so a high-resolution computed tomographic (CT) scan of the lungs was ordered. As he had no interstitial disease, he was diagnosed with stage I pulmonary sarcoidosis, and no systemic treatment was prescribed. A sacroiliac X-ray and a magnetic resonance imaging scan showed sclerotic changes that appeared chronic. No bone edema was observed. His human leukocyte antigen B27 test was negative, and his angiotensin-converting enzyme (ACE) level was elevated. His physical examination showed that he was hemodynamically stable and afebrile and that his overall health status was good. His musculoskeletal examination revealed a raised fistulous erythematous lesion with serous bloody secretion. He had no erythema or joint effusion. In an examination of his skin, no erythematous bullous lesions were found on his lower extremities.Toxoplasma, Treponema pallidum, Borrelia, Mycoplasma and Chlamydia). To rule out the possibility of tuberculosis, a Mantoux test (negative) and serial urine cultures with auramine staining (negative) were ordered. His high-resolution CT scan was compatible with stage I sarcoidosis .The patient’s blood examination results showed elevated acute-phase reactants  but no leukocytosis or left shift. His kidney and liver function, electrolytes and clotting were normal. His ACE level was somewhat elevated, and his urine sediment was normal. The results of his serologic tests were negative  that do not generally require treatment. However, soft tissues can be affected, with formation of fistulas on the skin that require curettage and corticosteroid therapy or chloroquine, which generally work very well with cutaneous sarcoidosis. The incidence of these lesions is 1–13%, and bone lesions due to sarcoid granulomas are diagnosed by biopsy .Approximately 38% of all cases of erythema nodosum are related to sarcoidosis in Löfgren syndrome, and they occur with skin lesions such as plaques, nodules and scars –19. WhenIn 50−70% of sarcoidosis cases related to other sites, the eyes are also involved and the eye condition often becomes chronic and recurring –22.ACE values are elevated in 88% of patients with active sarcoidosis, but using these levels to diagnose the disease can be misleading because approximately 10% of results are false positives and about 40% are false negatives. However, measuring the ACE level is useful to monitor disease progression .The cornerstone treatment is based on corticosteroids with gradual dose decreases until the disease is controlled. If the patient’s sarcoidosis is still active, immunosuppressive agents followed by second-line treatments such as methotrexate or azathioprine, as well as biologic agents such as infliximab, can be used for several clinical manifestations, although the evidence for these is based on small studies, so more extensive studies are needed to establish use of these treatments , 14, 23.Four other scar sarcoidosis clinical cases have been reported to date. Scar sarcoidosis was found in all of them. This is an uncommon but specific manifestation of sarcoidosis. One of the patients developed scar sarcoidosis on his right finger . AnotherTo the best of our knowledge, this is the first case of tibia sarcoidosis scar reported in the literature. Sarcoidosis generally responds well to corticosteroid therapy, but it is not self-limiting and often also requires the use of an immunosuppressant to avoid corticosteroids and to achieve remission without recurrence. When the eyes are involved, it is often related to other sarcoidosis symptoms. If the disease is not controlled, these symptoms will not be controlled either. Sarcoidosis is usually treated with methotrexate, cyclosporine, azathioprine or cyclophosphamide. New biologic therapies have also been used, with infliximab producing the best response, although the number of studies on the subject is limited , 27, 28.Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.


Since the tunable ranges for λ and μ in graphene are experimentally reachable, we thus open the possibilities for its device application. The symmetry in spatial distribution is broken by the vertical and the transversal spin-spin correlations due to the effect of spin-orbit coupling, leading to the spatial anisotropy of spin exchange, which distinguish our findings from the case in normal Fermi liquid.Two magnetic impurities on the edge of a zigzag graphene nanoribbon strongly interact with each other via indirect coupling, which can be mediated by conducting carriers. By means of Quantum Monte Carlo (QMC) simulations, we find that the spin-orbit coupling  Fk as well as decay behavior Rγ−Due to the unusual electronic quasi-particles and the flexible carrier concentration46k ↔ −k is forbidden without a spin flip. Due to this scenario, there is spin-current vortex around the single local spin on the helical edge132Se3 Recently, there is a surge of interest in effect of spin-orbit coupling (SOC) on electronic properties, which opens a class of novel time-reversal invariant topological insulators (TI)In this paper, we consider two Anderson impurities on the edge of a zigzag graphene ribbon, and investigated the effect of Kane-Mele SOC and chemical potential on the local spin exchange, which can be achieved by heavy metal doping or electric field. Through Quantum Monte Carlo simulation at finite temperature, we carry out a comprehensive study on the spin and charge coupling strengthes of this impurity pair. For the spin-spin correlation, which measures the RKKY interaction, we found that, the in-plane components of correlations favor ferromagnetism but the out-plane correlation can be tuned from ferromagnetism to antiferromagnetism by the SOC, while such transition is much dependent on the on-site Coulomb interaction of impurity orbital. From recent first-principal and experimental results of enhanced SOC in graphene, we conclude that spin-spin exchange among impurities in graphene is experimentally tunable by SOC. In contrast, the charge fluctuation between two impurities is always suppressed. Meanwhile, in-plane components of correlation will decay with an oscillation behavior when the distance between two impurities is increased, but the out-plane spin and charge correlations will decay smoothly, which is totally different from the Fermi liquid behavior, and leading to the spatial anisotropy of spin exchange.To simulate the model, we construct a model with width of 20 Å zigzag-edge graphene ribbon and along the horizontal direction we adopt periodical condition. As indicated in Kane-Mele investigationHK-M is the Kane-Mele model in a zigzag edge graphene ribbonHK-M = tH + Hso, with tH being the usual nearest-neighbor hopping of tight-binding model in grapheneHso is the SOC term and zσ is the z Pauli matrix. Hso thus has opposite signs for opposite electron spins. The parameters ijν = −jiν = ±1 depend on the orientation of the two nearest neighbor bonds as the electron hops from site i to j: ijν = +1 if the electron makes a left turn to the second bond. It is negative if it makes a right turn. H1 is the part for two impuritiesH2 describes the hybridization between impurities and conducting electronsm is the index of two impurities, in H1 and H2, mε is the energy of the impurity orbital and mU is Coulomb repulsion inhibiting the simultaneous occupancy of the orbital by two electrons and mV is the hybridization strength. In this work, we consider the two identical impurities, so the above parameters in Hamiltonian are m-independent.The QMC simulation is based on two-Anderson-impurity model, the total Hamiltonian reads asτ = 0.1 to suppress the systemic error. The QMC naturally returns the imaginary-time Green's function α = x, y, z directions versus distance asαS (R) directly reflect the RKKY interaction which is mediated by conducting electrons on the helical edge, while charge-charge correlation C(R) indicates the indirect Coulomb repulsion.We use the single-impurity QMC base on discrete-time algorithmμ = 0 and zS highly depend on SOC, which can be reduced in a linearly way and have a wide variation range. When SOC is increased, the value of vertical correlation zS can be changed from positive to negative, it means that a transition from a ferromagnetic (FM) to anti-ferromagnetic (AFM) correlation is achieved when the SOC reaches a critical value. It is interesting to note that, the critical SOC strength for such a transition increases as Coulomb interaction is increased, from the QMC simulations. For example, the critical SOC value is about 100 meV when U is 1 eV, but it is increased to 300 meV when U is is 5 eV. The underlying mechanism can be attributed to the competition of spin and charge fluctuations between two impurities. When they are close to each other, the changing in carriers SOC can directly result in the spin-flip process which reflects in zS, but the increasing Coulomb interaction U can block spin flip, so it is seen that with a larger U in zS but in xSy) at SOC strength λ = 0. But when λ ≠ 0, the SOC effect on both spin correlation is different, leading to non-degenerated zS and xSy)( (μ is in the range of −0.2 t to −0.8 t). But when μ is further reduced, both zS and xSy) and transversal one xSy)((R) have different spatial distribution. xSy)((R) has both the behavior of decaying and oscillating, but zS(R) is always decaying with the increased distance. Similar to zS(R), the charge-charge correlation is also decaying with distance (f1(R), f2(R) and f3(R) are decaying function of distance has the formula as 1/γR.The distance between two impurities is expected to influence the couplings of spin-spin and charge-charge due to the fact that the RKKY interation is sensitive to the distance. We preformed the QMC calculations to address the problem when varying the distance. In distance . These cxSy)((R)/C(R) and zS(R)/C(R). We find that zS(R)/C(R) is a trivial constant, but xSy)((R)/C(R) is an oscillating function of distance, as shown in To more clearly display these correlations, we calculate the ratios U′ in graphene and hybridization. In realistic graphene zigzag nanoribbon, the Coulomb interaction plays a signification role and stabilizes a spin-polarized ground stateRγ− cos 2FRk, here Fk is the Fermi momentum. The decaying factor γ is the function of Hubbard U′: when U′ = 0, γ = 1, and when U′ ≠ 0, 0 < γ < 1 31U′ = 0. The methods used to enhance the graphene's SOC in π bands still dominate near the Fermi energy and Kane-Mele Hamiltonian is also valid and the effect of hybridization can be absorbed in the enhanced SOC through second order approximationFinally, we discuss the model Hamiltonian of In conclusion, we investigate two Anderson impurities on a zigzag graphene nanoribbon by QMC simulation in present work. When the system is under a topological phase transition driven by Kane-Mele SOC, we find that, the spin rotation symmetry in RKKY interaction between two impurities can be partly broken because of the SOC. As the two impurities are close to each other and the Fermi energy is near the Dirac point, the in-plane RKKY interactions favor ferromagnetism but the out-plane component can be tuned from ferromagnetism to anti-ferromagnetism by the SOC. The distance effect on RKKY interaction is also systermatically investigated, the in-plane interaction has both behavior of decaying and oscillation, but the out-plane interaction and charge-charge correlation only has decaying as the distance between them is increased. This behavior is totally different from the conventional Fermi liquid. Our theoretical findings here provide some useful suggestions of the spin-polarized STM measurement to RKKY interactionF.H. conceived the idea and do the QMC calculation, L.K. made the first-principle discussion and collected the data in the Table 1, and F.H. and L.K. wrote the manuscript together. F.H., L.K. and T.F. discussed the results and reviewed the manuscript.


Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which “universal” archaeal 16S rRNA gene primers are impacted by the presence of intron sequences.Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different “universal” 16S rRNA primers employed in environmental microbial community analysis.This article was reviewed by Dr. Eugene Koonin and Dr. W. Ford Doolittle.The online version of this article (doi:10.1186/s13062-015-0065-6) contains supplementary material, which is available to authorized users. Archaea contain 16S rRNA gene introns, which are mobile genetic elements that do not appear to impact the host’s growth or metabolism. 16S rRNA gene introns have been identified in two genera of the order Desulfurococcales (Aeropyrum and Staphylothermus) ).Pyrobaculum spp. contained the majority of known introns and these are found at diverse loci across the 16S rRNA gene . Other genera in the Thermoproteales also contain intron sequences at many of the same loci: Thermoproteus , Caldivirga , and Vulcanisaeta (locus 1391). Desulfurococcales-like introns were identified in six loci .Intron sequences were confined to 13 loci across the 16S rRNA gene Fig. . PyrobacP. oguniense 16S rRNA homing endonuclease (Pog.S1213) promoted the homing of its own intron and guaranteed the co-conversion of both the downstream hairpin-forming intron (Pog.S1205) and the intervening eight nucleotides by cleaving at the intron− locus 1205 [Most 9/13) intron regions contained two or more predicted homing endonuclease genes, which code for either one or two of the canonical LAGLI-DADG motifs . The nucleotide sequences comprising the DNA insertion sites and the BHB motif vary among loci and it is unclear how sequence specificity of the homing endoribonuclease or the splicing ligase contributes to intron propagation and distribution. Several intron loci were identified in both the Crenarchaeota and Aigarchaeota , which suggests that these loci have been sites of intron insertions since the divergence of these two phyla. Based on extant insertion loci, intron sequences radiated throughout the Thermoproteales, specifically in the Pyrobaculum and Thermoproteus spp.Comparison of intron sequences within the same loci identified highly-conserved nucleotide residues near the intron-exon junctions, which represent conserved intron cores , 25. ThePyrobaculum sp. 1860 [P. neutrophilum [P. yellowstonensis strain WP30 [Vulcanisaeta distributa IC-065 clone from Japan [Pyrobaculum and Thermoproteus). Introns found at different 16S rRNA gene loci were too different for phylogenetic comparison (<20 % nt/aa identity).Intron sequences within the same loci were successfully aligned at the nucleotide level and subsequent phylogenetic analysis revealed both intra-locus and geographic separation Fig. . Intron sp. 1860  and P. nrophilum , respectain WP30  that is Pyrobaculum contain the most abundant 16S rRNA introns in the order Thermoproteales and although they predominate in high-temperature, near-neutral to alkaline (pH > 6) geothermal systems, populations of the other Thermoproteales genera  are found with Pyrobaculum in > 65 °C, pH 5 - 7 hot springs [The phylogenetic distribution of intron sequences by geographic location is consistent with the hypothesis that once a homing endonuclease becomes fixed in a genome, selection pressure for the gene significantly decreases resulting in degeneration (mutation) and enforcing the requirement of frequent horizontal transmissions between populations to maintain intron propagation . Populat springs , 48. The springs , these e springs . Very liPrimer sequences designed for archaeal 16S rRNA genes (n = 51) were manually aligned to intron-containing 16S rRNA gene sequences to determine which primers were interrupted by, or spanned intron sequences . All transcribed introns form predictable secondary structure including the characteristic bulge-helix-bulge motif. Many intron sequences encoded homing endonucleases, although other introns were short and/or non-coding sequences. Phylogenetic analysis revealed that intron sequences grouped together by geographic location and then by host taxa. The presence of introns in highly conserved regions of 16S rRNA introns directly interferes with use of “universal” primers often used in environmental gene surveys.Intron sequences were identified by querying (blastn/blastx) the NCBI nr and the DOE-Joint Genome Institute (DOE-JGI) Integrated Microbial Genomes (with Microbiome Samples (IMG/M) databases) with previously identified 16S gene introns  before phylogenetic analysis and/or Weblogo3 analysis . PhylogeReport form: Jay and Inskeep report the distribution of Group I introns in 16S RNA genes from hyperthermophilic archaea, and in particular Thermoproteles, where these introns are most common. The analysis is carefully performed, and there is an important conclusion on the evolution of self-splicing introns, namely that they group by geographic location, i.e. spread primarily horizontally. Also, this analysis is of practical value because the authors carefully assess the effect of introns on the use of universal primers.Authors’ response: We thank the reviewer for these comments.Quality of written English: Acceptable.Report form: This is a perfectly fine and straightforward report and summary of the distribution of introns in the rRNA genes of members of the Thermoproteales. It will provide a basis for future experimental and comparative studies, and raises some interesting questions, such as the means by which introns are transferred between different lineages in a given environment and the structural adaptations of the intron RNA to high temperature, but does not attempt to answer them. It also points out how intron presence might result in failure to amplify specific regions of rRNA genes by PCR. Members of Thermoproteales might thus be underestimated in environmental sampling, and one wonders whether there are abundant major groups that go undetected because they always have such introns. Indeed, is there anything to keep introns from becoming colonized by genes essential for cellular survival, so that pieces of the rRNA gene become permanently separated, and the cells that bear them become undetectable with standard molecular methods?Authors response: We thank the reviewer for these comments, and for the very interesting question regarding possible ‘colonization’ of introns by genes coding for essential function, and subsequent separation of rRNA gene fragments . The question regarding intron colonization by other genes is difficult to answer due to the complexities of intron propagation. As we currently understand 16S rRNA gene introns in the Thermoproteales, a homing endonuclease (gene or transcript) is required for intron insertion into a functional rRNA. Consequently, any disruption to the homing endonuclease would not allow for insertion and propagation of the intron sequence. Any cell that may bear intron fragments by definition will still have a functioning rRNA somewhere in the genome and therefore would be detectable with standard methods.Quality of written English: Acceptable.


A high-quality monolayer graphene with 97% transparency and 350 Ω/□ sheet resistance grown by atmospheric pressure chemical vapor deposition method was transferred onto planar Si cells. An increase in efficiency from 5.38% to 7.85% was observed upon deposition of graphene onto Si cells, which further increases to 8.94% upon SiO2 deposition onto the graphene/Si structure. A large increase in photon conversion efficiency as a result of graphene deposition shows that the electronic interaction and the presence of an electric field at the graphene/Si interface together play an important role in this improvement and additionally lead to a reduction in series resistance due to the conducting nature of graphene.This work presents an experimental and finite difference time domain (FDTD) simulation-based study on the application of graphene as a transparent conducting layer on a planar and untextured crystalline  Graphene has been considered as one of the promising materials for photovoltaic device applications due to its two-dimensional nature with extraordinary optical (transmittance ~98%), electronic , and mechanical properties (Young's modulus 1.0 TPa) . Many atIn silicon solar cell, the power conversion efficiency is limited by many fundamental losses such as incomplete absorption of the solar spectrum, recombination of the photo-generated charge carriers, shading losses, and series resistance losses ,17. AntiIn this paper, we investigate the transparent conducting and surface field properties of graphene layers onto planar and untextured crystalline Si surface by carrying out experimental investigations and finite difference time domain (FDTD) calculations. In addition, the effect of graphene layer on the photovoltaic parameters and spectral responses of planar and untextured Si solar cell has also been investigated.2 (30 sccm) was then introduced into the reaction tube for degassing the air inside. The flow rate of Ar was kept constant (500 sccm) for all the experiments mentioned in this manuscript. The reactor was heated up to 1,030°C in 30 min, and this temperature was kept constant for the next 30 min to anneal the Cu foil. Then, CH4 (3 sccm) was fed into the reactor. After 30 min, the feeding of CH4 was cut off and the reactor was cooled down to room temperature naturally in an Ar and H2 environment. The flow of all the gases was stopped as the temperature reached close to the room temperature.The growth of graphene has been carried out on a 25-μm-thick Cu foil  using an atmospheric pressure chemical vapor deposition (APCVD) system at a temperature of 1,030°C. A split-type furnace with a quartz tube reactor was used for graphene growth. Before loading into the reaction tube, the Cu foil was cleaned in acetic acid followed by acetone, deionized water, and isopropyl alcohol to remove the copper oxide present at the surface. A mixture of Ar (500 sccm) and HMW ~996,000, item no. 182265, 10 mg/ml in anisole) was used for the transfer of graphene onto different substrates like quartz, Si, SiO2-sputtered Si, and solar cells to study graphene quality and its electronic and optical properties. In the first step, the graphene-deposited Cu foil was attached to a glass slide with the help of a scotch tape and then PMMA was spin coated on one side of the Cu foil. The other side of the foil was immersed into 10% HNO3 solution for 2 min to etch out the graphene from that side. Subsequently, the Cu foil was etched using FeCl3 (10% wt./vol.) for 3–4 h. The PMMA coated graphene film was transferred to the desired substrate  on several dips in deionized (DI) water as a cleaning step. In the final step, PMMA was etched out using acetone at 80°C for a duration of 2 h. Some residual PMMA was further removed by annealing in a H2 (500 sccm) and Ar (500 sccm) environment at a temperature of 450°C for 2 h.On successful growth of graphene on Cu foil, polymethyl methacrylate (PMMA)  liquid dopant was used, and the wafers were subjected to elevated temperature in a furnace resulting in the formation of a thin layer of n-doped region (~0.5 μm). The wafers were etched using freon-oxygen (CF4) gas mixture in dry plasma etch machine to remove the junction regions created on the edge. These wafers were then chemically etched to remove the oxides and phosphorous glass formed on their surfaces. The entire backside was metallized with Ag-Al paste. Front contacts on the wafer surface were formed by screen printing the required pattern with a suitable metallic paste on them. The metal paste was dried and sintered in an infrared sintering belt furnace where temperature and belt speed were optimized to achieve a sharp temperature profile. The printed cells were then cut into smaller cells of dimension 10 mm × 10 mm for deposition of graphene. A similar printed cell is kept for comparative studies.In order to study the effect of graphene on photon absorption and carrier collection, we first fabricated Si solar cells with planar and untextured surfaces. A 156-mm monocrystalline silicon wafer was dipped in high-concentration alkali solution at 80°C for 1 to 2 min to remove the roughness of the wafer. A 2 layer was deposited over mc-Si solar cell after the deposition of graphene layer using radio frequency (RF)-magnetron sputtering from a Si target (<111>) with 99.99% purity. The sputtering was carried out for 22 min by introducing Ar (15.8 sccm) and O2 (2.8 sccm) gases at room temperature with an applied RF power of 100 W.A 100-nm-thin film of SiO+ laser for excitation. The scattered light was analyzed with a Renishaw spectrometer having a charged couple device for detection. All the optical measurements were carried out on a Lambda 35 UV/Vis spectrophotometer . The photovoltaic characterization of the solar cell was carried out by measuring the I-V behavior using a 2400 SourceMeter  under simulated AM 1.5 solar illumination at 100 mW/cm2 from a xenon arc lamp in ambient atmosphere.Raman spectroscopic measurements were carried out in backscattering geometry using the 514.5-nm line of Ar4/H2 flow rate. The quality of graphene was analyzed by Raman spectroscopy of the as-deposited graphene on the Cu foil. It is well known that graphene has three most prominent Raman features at ~1,350 cm-1 (D band), ~1,580 cm-1 (G band), and ~2,700 cm-1 (2D band). The D peak is related to the presence of defects  in graphene. The G peak denotes the symmetry-allowed graphite band corresponding to the in-plane vibration of sp2-hybridized carbon atoms, which constitute the graphene sheets. The 2D peak originates from the second-order double resonant Raman scattering from the zone boundary. It is quite established that Raman scattering can be used as a fingerprint for the quality and number of graphene layers. The ratio of the intensity of 2D and G peaks (I2D/IG) and full width at half maximum (FWHM) of the 2D peak are important parameters to evaluate the quality of graphene [-1 and the G peak at 1,580 cm-1, are observed. It is worth noting that the defect-related D  peak decreases with increase in temperature and finally disappears at a temperature of 1,030°C, indicating the improved quality of graphene deposited at higher temperatures. The improved quality of graphene is also confirmed by the I2D/IG ratio and FWHM (2D) plots in Figure I2D/IG ratio increases and FWHM (2D) decreases with increase in temperature.The APCVD conditions have been optimized to synthesize a single-layer graphene by tailoring the growth temperature and CHgraphene ,27. Figu4/H2 flow rate for growing good-quality single-layer graphene, five flow rates of CH4/H2 content were chosen, i.e., 01/10, 03/30, 05/50, 10/100, and 20/200 sccm, while keeping the CH4:H2 flow rate ratio (1:10) constant. The growth temperature was set at the optimized value of 1,030°C with a deposition time of 30 min to ensure complete coverage of graphene. Raman spectra of graphene samples grown at different CH4/H2 flow rates are shown in Figure I2D/IG ratio and FWHM data are shown in Figure -1) and large and symmetrical graphene G  and 2D  peaks. The D peak is negligible in all the cases, indicating a defect-free graphene growth. Furthermore, the FWHM of the 2D peak increases gradually from 30 to 65 cm-2  and FWHM (≈32 cm-1) in graphene grown at 1,030°C and 03/30-sccm CH4/H2 flow rate match well with the previously reported values for monolayer graphene [4 and 30 sccm of H2 flow rates was used for investigating the effect of graphene and G/SiO2 layers on Si solar cell as a transparent conducting and antireflection layer.In order to optimize the CHgraphene ,28-30. B2) graphene transferred onto a SiO2 (300 nm thick)/Si substrate. In order to measure the transmittance values, graphene layer was transferred to a quartz substrate and an average value of transmittance of 97% -coated Si substrate. A comparison of sheet resistance and transmittance of graphene layer used in studies involving G/Si cells is given in Table 3N4 antireflection layer along with a textured surface. It is difficult to deposit/transfer graphene layer on a textured surface. In order to study the transparent conducting properties of graphene layer, it is necessary to remove the Si3N4 layer and texturing of these cells. Therefore, the silicon solar cells with these properties, i.e., with planar Si surface, were fabricated for carrying out these experiments. The procedure followed for fabricating Si (p-n) solar cells with planar top surface (without texturing and AR coating) is described in the ‘Methods’ section. For applying graphene as a transparent conducting and surface field layer on Si solar cells, we chose SiO2 as the antireflection layer. Experimental and simulation studies were performed on the planar Si solar cell to investigate the reflectance properties of monolayer graphene on Si surface. Subsequently, the thickness of SiO2 layer as an antireflection coating for G/Si solar cell was optimized. It was observed that a 100-nm-thick SiO2 layer was sufficient to work as an antireflection layer over the graphene-Si interface. SiO2 (refractive index 1.45) was chosen due to its well-known antireflection properties [Figure operties .2/G overlayers with 100 nm SiO2 thickness were then applied onto the fabricated crystalline Si solar cell having a planar and untextured Si surface  a bare Si solar cell having a planar surface, (ii) graphene on the planar Si solar cell (G/Si), and (iii) 100-nm-thick SiO2 coating on graphene/Si solar cell (SiO2/G/Si). The solar cell performance parameters of open circuit voltage (VOC), short circuit current density (JSC), maximum voltage (VM), maximum current (IM), series resistance (RS), shunt resistance (RSH), fill factor (FF), and the energy conversion efficiency (Eff.) are shown in Table VOC by 20 mV and in JSC by 10.5 mA/cm2. It is important to note that the graphene overlayer on planar Si solar cell (G/Si) has higher conversion efficiency (7.85%) in comparison to the bare Si cell (5.38%) without graphene layer. This conversion efficiency is further increased to 8.94% on introduction of the antireflection SiO2 layer. Improvement in the I-V properties on deposition of graphene onto Si cells may be due to changes in the reflection properties of planar Si cells, improvements in the photovoltaic parameters due to transparent conducting properties of graphene, and the formation of surface electric field layer at the G/Si surface. To separate theses effects, reflectance and junction properties of the G/Si junctions were evaluated.Graphene and SiOe Figure a to expeFigure I-V behavior of graphene/Si (G/n-Si) structure was obtained to study the nature of G/n-Si junction. Figure I-V characteristics of the G/n-Si in dark and light. The forward bias condition was observed with graphene connected to the negative terminal with respect to n-Si. This shows that the interface between the graphene and n-Si behaves like a n+-n junction. The favorable direction of the electric field formed at the interface helps in the reduction of the effective recombination at the front surface and enhances the collection of light-generated free carriers and thus improves the efficiency of solar cell. The n-type or p-type nature of graphene is very sensitive to the synthesis method, adsorbed molecules, nature of the substrate underneath, etc. [n-type) in G/Si cells in the present study acts like an n-type layer.The th, etc. -45. It cJSC and conversion efficiency values as shown in Table n-Si interface and reduction in the associated series resistance. The J-V curve  in G/Si cell (6.2 Ω) in comparison to pristine cell (11.4 Ω). It is important to note that the improvement in efficiency (2.47%) for Si solar cell by using graphene as a surface field layer is larger than or similar to the efficiency improvement (2.38%) obtained by using the n+ doping (thickness ≈ 2 × 1020 cm-3 and 0.07 μm) on the front surface [J-V characteristics are further validated by the incident photon conversion efficiency (IPCE) measurements shown in Figure 2/G layers improve the photon to electron conversion ratio considerably compared to the bare planar Si solar cell. The decrease in the reflectance (∆R) of graphene-deposited Si  is much larger than the decrease in reflectance (∆R) as one goes from Si to G/Si structure. This confirms that the electric field formed at the G/n-Si interface is aiding carrier collection. Thus, the deposition of graphene onto polished n-Si surface is aiding carrier collection or photon absorption in addition to lowering its reflectance. A slight increase in VOC from 573 to 582 mV also indicates the active participation of graphene in the solar cell device. Earlier, a number of studies have reported the effect of graphene quality, number of graphene layers, and adsorbed molecules on the electronic properties of graphene-Si interface. Li et al. reported that the incorporation of graphene introduced a built-in electric field near the interface between the graphene and silicon (n-type) to help in the collection of photo-generated carriers [2 (on going from G/Si to SiO2/G/Si cell), the increase in IPCE is much smaller than the decrease in the reflectance value  is primarily due to the antireflection properties of the 100-nm-thick SiO2 layer. Consequently, the large improvement in JSC and small increase in VOC indicate that graphene behaves like an n+ layer which intrudes a surface field at the interface to enhance the collection of light-generated carriers thereby improving the efficiency of the p-n Si solar cell. Further, a decrease in the series resistance value and a small increase in VOC on deposition of SiO2 layer on the G/Si cell are due to modification in the electronic properties of the G-Si interface during SiO2 deposition process. By modifying the electronic properties of graphene layer, the photovoltaic properties of silicon solar cell can be improved further.A large increase in the short circuit current on graphene deposition onto planar Si solar cell is very interesting on various accounts. As mentioned earlier, there are two important contributions that might result in the enhancement in e Figure b shows avement 2.8% obtainvement 2.8% obtain/Si cell .2 Ω in ccarriers . Attenticarriers ,25,46. Fp-n Si solar cell; (ii) as an antireflection layer, which reduces the reflectance of the planar p-n Si solar cell due to the presence of wrinkles; and (iii) as a surface field layer onto n-type Si due to n+-n nature of the interface, which provides a favorable electric field for reducing the carrier recombination. Due to these effects, an increase in efficiency from 5.38% to 7.85% is observed. Deposition of a layer of SiO2 of an optimized thickness value leads to a further increase in the short circuit current density due to its antireflection properties.The present study is a clear demonstration of the useful combination of the properties of graphene: (i) as a transparent conducting layer, which provides high transmittance (97%) and reduces the series resistance of planar The authors declare that they have no competing interests.2 deposition. SR, SM, SS, and PJ jointly fabricated the p-n Si solar cell. BRM supervised the overall study, analyzed the results, and finalized the manuscript. All authors read and approved the final manuscript.RK carried out all the experiments in this study, analyzed and interpreted the data, and drafted the manuscript. MB was involved in SiORK and MB are PhD students in the Department of Physics, IIT Delhi, India. BRM is a professor (Schlumberger Chair) in the Department of Physics, IIT Delhi, India. SM, SS, and PJ are photovoltaics engineers at BHEL, India.


Carrier mobility and chemical doping level are essential figures of merit for graphene, and large-scale characterization of these properties and their uniformity is a prerequisite for commercialization of graphene for electronics and electrodes. However, existing mapping techniques cannot directly assess these vital parameters in a non-destructive way. By deconvoluting carrier mobility and density from non-contact terahertz spectroscopic measurements of conductance in graphene samples with terahertz-transparent backgates, we are able to present maps of the spatial variation of both quantities over large areas. The demonstrated non-contact approach provides a drastically more efficient alternative to measurements in contacted devices, with potential for aggressive scaling towards wafers/minute. The observed linear relation between conductance and carrier density in chemical vapour deposition graphene indicates dominance by charged scatterers. Unexpectedly, significant variations in mobility rather than doping are the cause of large conductance inhomogeneities, highlighting the importance of statistical approaches when assessing large-area graphene transport properties. Graphene23456781011131416171920232527in-situ electrically gated THz-TDS imaging. In contrast to prior electrically gated THz spectroscopy experiments performed on graphene293031+ boron-doped, nano-crystalline silicon, to ensure a negligible THz response from free carriers injected into the gate-electrode. This allows for isolation of the graphene sheet conductance from non-contact THz-TDS transmission measurements and thus a quantitative extraction of the graphene field-effect mobility.Here we demonstrate quantitative mapping of the field-effect carrier mobility in a large-area monolayer CVD graphene film based on 3N4). The THz response of the poly-Si/Si3N4 stack is found to be negligible with a frequency-independent transmission of 100% ± 1% and a diminishing phase-shift of 2 ° , 50 nm boron-doped poly-crystalline Si (poly-Si), and 165 nm Si nitride 2S2O8. A large-area graphene film is grown on commercially available Cu foil by means of a standard catalytic chemical vapour deposition (CVD) and is subsequently transferred onto the layered substrate, as shown in 3N4/poly-Si/Si were recorded at 21 different gate voltages between 0V and 40V, a selection of which are shown in Vg =24 V THz map. The complex, frequency-dependent sheet conductance 2πf≪1/τ), the Drude-Smith and Drude models, expected for the THz response of pristine graphene, dictates that the real part of THz maps of the CVD graphene on Siσs. The evolution of σs with varying Vg in the series of images in In s as a function of Vg for three distinct areas in the map with highly conducting graphene, less conducting graphene, and no graphene coverage. The measured of σs shows a linear dependence on the applied gate voltage in the range 0V < Vg < 18 V with different slopes throughout the extent of the graphene film, reflecting the local field-effect mobility for hole carriers. This observation is found to be representative throughout the graphene film area. For gate voltages 24 V < Vg < 40 V a plateau with slowly increasing σs is found. This observation indicates that electron-conduction is greatly impaired in this particular graphene film with electron mobilities that are more than an order of magnitude lower than the observed hole mobilities. Application of a gate voltage, Vg, between the poly-Si thin film and the graphene film induces a proportional change in the free carrier density, Δns, in the poly-Si and graphene films, as Vg = 24 V. This minimum represents the charge-neutrality-point (CNP), indicating a constant, and homogeneous presence of residual absorbates with a density of approximately 5 × 1012 cm−2, which p-dopes the entire graphene film. Within the regime of long-range, charged impurity scattering, the added free graphene carriers result in a roughly linear change in the graphene sheet conductance, σs, with the field effect mobility being a proportionality factor. The sheet conductance, σs, of the graphene film is thus described by the relationsCg is the gate capacitance, e is the electronic charge, ε0 is the vacuum permittivity, εSiN = 7.5 is the relative permittivity of Si nitride, t is the thickness of Si nitride gate dielectric, and μFE is the field-effect mobility of the graphene film.where μpoly-Si < 10 cm2/Vs) of our poly-Si thin film relative to the hole mobility of the investigated graphene film, which is approximately two orders of magnitude higher. Because of the choice of a low-mobility, high carrier concentration gate material, the experiments presented here provide a direct and reliable measure of the gate-induced conductance evolution of the graphene film with an insignificant contribution from gate-induced carriers in the substrate. Following |Δσs/ΔVg| in the high density-region well below the CNP. Based on this central result we are able to show a spatially resolved field-effect hole mobility map for the large-area CVD graphene film in Δσs/ΔVg| was found in each pixel by a linear fitting routine to σs vs. Vg from 0 V to +18 V. Similarly, the carrier density due to chemical doping of the graphene film at zero gate bias, can be evaluated across the map from the determined hole mobilities and the sheet conductance at Vg = 0, by utilizing the relation σs= ensμhole. ns (ns is set to 0 in pixels where μhole < 100 cm2/Vs). We note that carrier mobility measured using this technique is affected by the coverage of graphene, because The gate-induced conductance in the gate electrode can be neglected because of the insignificant carrier mobility  from the central region of the graphene film, marked by dashed, black rectangles in μhole = 1174 cm2/Vs and ns(0 V) = 6.2 × 1012 cm−2, and relative standard deviations of std(μhole)/avg(μhole) = 14.0% and std(ns)/avg(ns) = 4.8%.Unexpectedly, We find that the procedure presented here gives far more comprehensive information than the typical convention of relying on a few representative electrical measurements from random or selected areas of a large graphene film. We also note that the features and inhomogeneities in the field effect mobility in We anticipate that quantitative, non-contact mapping of graphene carrier mobility as presented in this work will have a significant technological importance for the advancement of production and implementations of large-area graphene in commercial electronic applications and that it can contribute to the fundamental insight into charge carrier dynamics of the graphene solid-state-system by paving the way for investigations of transport dynamics with unprecedented statistical basis.2 large-area CVD film by in-situ electrically gated THz-TDS measurements. While THz-TDS is non-contact, optical characterization, the frequency range is well below the inverse scattering time of the graphene charge carriers, making the obtained conductance directly comparable the DC value. The technique thus opens up the possibility for assessment of fundamental electrical transport properties such as carrier mobility and chemical doping level on basis of large statistical ensembles, or large-area spatial mapping. Far from the charge-neutrality-point, our measurements show a linear dependence of the THz sheet conductance on carrier density, which is interpreted as a signature of electrical transport limited by long-range, charged impurity scattering, also observed in most DC transport measurements on graphene. Unexpectedly, we find that the mobility varies by up to a factor of 2 on a scale of just few mm, and that significant conductance variations in the investigated CVD graphene are due to mobility rather doping variations, which highlights the importance of techniques that facilitate highly statistical or spatially resolved approaches for assessing transport properties in large-area graphene.In conclusion, we have presented non-contact, quantitative mapping of graphene field effect mobility in a 10 × 10 mm© T-ray™ 4000 fiber-coupled THz time-domain spectrometer relying on photoconductive switches for THz generation and detection, which is detailed elsewhere2 graphene film. Through utilization of the electric field effect in graphene, THz maps are recorded at different carrier densities by applying voltages, Vg, in the range from 0 V to 40 V between poly-Si thin film and graphene film. The full acquisition time for each map is 16 minutes, and Vg is increased in discrete steps of 2 V between each map.The experiments are carried out using a PicometrixSi = 3.4173N4/poly-Si/Si) to that of a reference waveform, 3N4/poly-Si/Si-substrate), and can be related to real and imaginary parts of the sheet conductance asThe sheet conductance of the graphene film was extracted in each pixel of the THz maps based on an approach described previously0 = 377 Ω is the vacuum impedance.where ZHow to cite this article: Buron, J. D. et al. Graphene mobility mapping. Sci. Rep.5, 12305; doi: 10.1038/srep12305 (2015).


Moreover, at low carrier density transport measurements allow probing the density of localized states at edges, thus offering a unique handle on edge physics in graphene devices.Quantum point contacts are cornerstones of mesoscopic physics and central building blocks for quantum electronics. Although the Fermi wavelength in high-quality bulk graphene can be tuned up to hundreds of nanometres, the observation of quantum confinement of Dirac electrons in nanostructured graphene has proven surprisingly challenging. Here we show ballistic transport and quantized conductance of size-confined Dirac fermions in lithographically defined graphene constrictions. At high carrier densities, the observed conductance agrees excellently with the Landauer theory of ballistic transport without any adjustable parameter. Experimental data and simulations for the evolution of the conductance with magnetic field unambiguously confirm the identification of size quantization in the constriction. Close to the charge neutrality point, bias voltage spectroscopy reveals a renormalized Fermi velocity of ∼1.5 × 10 Quantum point contacts are narrow electrical connections of a width comparable to the wavelength of the conducting electrons. Here, the authors create such contacts in graphene by etching constrictions and use them to identify ballistic transport and quantized conductance of size-confined Dirac fermions. The observation of unique transport phenomena in graphene, such as Klein tunnelling35712131416In this work we report on the observation of size quantization and localized trap states in ballistic transport through graphene constrictions approximating quantum point contacts. Away from the Dirac point, the current features evenly spaced, reproducible kinks superposed on a linear background, in agreement with transport simulations. Scattering at the rough constriction edges reduces quantization steps to kinks in both experiment and theory. The kink spacing, and their evolution with magnetic field, allows us to unambiguously identify them as signatures of size quantization. Close to the Dirac point, deviations from ballistic behaviour allow for probing the density of localized trap states.2/Si substrates and use reactive ion etching to pattern narrow constrictions (see Methods) with widths ranging from W≈230 to 850 nm, connecting wide leads  sandwiches on SiOde leads . The grar device . From th V−1 s−1 , resultiW , j>0. In the presence of edge roughness, c0 is reduced to a value below 1 due to limited average transmission, and the higher Fourier components are expected to decay in magnitude and acquire random scattering phases φj≠0. Consequently, the sharp quantization steps turn into periodic modulations as will be shown below. Averaged over these modulations only the zeroth-order term in the expansion (G(0) of a constriction of width W thus features a linear dependenc on kF, or, equivalently, a square-root dependence as a function of back-gate voltage assuming an energy-independent transmission c0 of all modes, in accord with For an ideal constriction xpansion  survivesα for each device (Vg and study both the electron and hole conductance as function of kF (G(kF), the product c0W can be extracted for each device and compared with its width W (c0W extracted from G(0) lie only slightly below the width W, where c0 decreases for decreasing width. This suggests that for the narrower devices reflections, most likely due to device geometry and edge roughness, are playing a more important role. From the data in c0≈0.56 for our smallest constriction. Below we will show that, indeed, reflections at the rough edges of the constriction and not a reduction in active channel width is responsible for the deviation of the experimentally extracted c0W from the SEM width W.By measuring the carrier-density-dependent quantum Hall effect at high magnetic fields4h device . We can on of kF . From th width W  determin width W . The estkF<50 × 106 m−1  the measured conductances systematically deviate from the expected linear behaviour  becomes more apparent when focusing on G around the charge neutrality point (CNP). The conductance as function of n for two different cool-downs of the same graphene constriction  an identical c0W and (ii) almost identical, regularly spaced kink structures  from, for example, localized trap states modifies the relation between n and kF toFor small ehaviour . This deows in n . These oαΔVg will be strongly modified by deviations nT from the linear density of states of ideal Dirac fermions and approaches nT(ΔVg) near the CNP. The trap states do not contribute to transport, yet they contribute to the charging characteristicsG from the nT from experimental conductance data  and the corresponding linear extrapolation to very low values of kF  is probably due to microcracks at the edges of the device.Away from the CNP our data agrees remarkably well with ballistic transport simulations through the device geometry using a modular Green's function approachG(kF), we find reproducible modulations (kinks) in the conductance (G varying in the range of (2−4)e2/h (see arrows in kF), as well as on the constriction width and is strongly influenced by the overall transmission c0 (G of the steps close to 4e2/h for one of our wide samples (W≈310 nm) at elevated conductance values on both the electron and hole sides =G−G(0) provide direct information on the quantized conductance through the constriction (δG(kF) offers an alternative route towards the determination of the constriction width complementary to that from the mean conductance G(0). For example, the pronounced peak of the first harmonic at 230 nm  is more pronounced on the electron side (By subtracting the zeroth-order Fourier component∝triction . One keyron side  than on W (c0W (first term in c0W) from the effective width of the constriction, and proves the relation between the observed Fourier periodicity and the device geometry.Performing such a Fourier analysis for several devices  yields mW  than an E=13.5±2 meV near the CNP (vF=2WΔE/h=(1.5±0.2) × 106 m s−1. This is a clear signature of a substantially renormalized Fermi velocity in nanostructured graphene, possibly enhanced by electron–electron interactionBias voltage spectroscopy measurements yield an estimate for the energy scale of the size quantization steps11 the CNP . With th the CNP  we can eB. The transition from size quantization at zero B-field to Landau quantization at high magnetic fields occurs when the cyclotron radius lC becomes smaller than half the constriction width W. For the Landau level m the transition should occur at lB the magnetic length. This transition line in the B−n plane (see black dashed curve in B=0 T) to the corresponding lowest Landau levels at low temperatures (T=1.7 K) can be easily tracked (T=6 K) the evolution of quantized sub-bands to Landau levels is observed even for higher conductance plateaus  to the Landau levels for large fields (lB<W) remarkably well, further supporting the notion that they are, indeed, a signature of size quantization.Additional clear fingerprints of size quantization appear in the parametric evolution of the conductance steps tracked . At highplateaus . For a cWe have shown ballistic conductance of confined Dirac fermions in high-mobility graphene nanoconstrictions sandwiched by hBN. Away from the Dirac point, we observe a linear increase in conductance as function of Fermi wave vector with a slope proportional to constriction width. Close to the Dirac point, the charging of localized edge states distorts this linear relation. Superimposed on the linear conductance, we observe reproducible, evenly spaced modulations (kinks). Tight-binding simulations for the device reproduce these structures related to size quantization at the constriction. We can unambiguously identify these ‘kinks' as size quantization signatures by both Fourier spectroscopy at zero magnetic field and their evolution with magnetic field, finding good agreement between theory and experiment.6 atmosphere, prior deposition of a ∼10-nm-thick Cr etching mask. Residues of Cr oxide are removed by immersing the samples in a tetramethylammonium hydroxide solution for about 30–35 s. All transport measurements are performed in a four-probe configuration using standard lock-in techniques. Since the distances between the contacted current-carrying electrodes and the voltage probes are small compared with the other length scales of the system, we have an effective two-probe configuration. Importantly, this way we exclude the one-dimensional contact resistances.The hBN–graphene–hBN sandwich structuresWe simulate the experimental device geometry using a third-nearest neighbour tight-binding ansatz. We rescale our device by a factor of four compared with experiment, to arrive at a numerically feasible geometry. We determine the Green's function using the modular recursive Green's function method30How to cite this article: Terrés, B. et al. Size quantization of Dirac fermions in graphene constrictions. Nat. Commun. 7:11528 doi: 10.1038/ncomms11528 (2016).Supplementary Figures 1-15, Supplementary Table 1, Supplementary Notes 1-9 and Supplementary References


Two different polarization configurations are used. In an in-plane configuration, the polarization direction of both incident and scattered light is parallel to the graphene plane. In an out-of-plane configuration, the angle between the polarization vector and the graphene plane is the same as the angle of laser incidence (θ). The normalized Raman intensity of the G-band measured in the out-of-plane configuration, with respect to that in the in-plane configuration, was analyzed as a function of θ. The normalized Raman intensity showed approximately cos2θ-dependence up to θ = 70°, which can be explained by the fact that only the electric field component of the incident and the scattered photon in the out-of-plane configuration projected onto the graphene plane can contribute to the Raman scattering process because of the perfect confinement of the electrons to the graphene plane.Chemical vapor deposition (CVD)-grown single-layer graphene samples, transferred onto a transmission electron microscope (TEM) grid and onto a quartz plate, were studied using polarized Raman spectroscopy with differing angles of laser incidence ( Graphene, an almost perfect two-dimensional crystal, has been intensively investigated for the last decade, since its discovery in 2004 ,2, due t−1, the G-band near 1,585 cm−1, and the 2D-band at approximately 2,675 cm−1. By analyzing both the normalized Raman intensity of the 2D-band with respect to that of the G-band and the line-shape of the 2D-band, the number of graphene layers can be accurately determined [Raman spectroscopy has played an important role in studying graphene ,13. A tytermined .cos2α-dependence in which α is the angle between the CNT axis and the polarization direction of the incident light [Polarizations of the incident laser and the scattered light are important in the Raman scattering on low-dimensional crystals. For a carbon nanotube (CNT), which is a quasi-one-dimensional crystal, the Raman intensities of CNT vibrational modes are maximum when the polarization directions of both the incident and the scattered light are parallel to the CNT direction whereas the Raman scattering is forbidden when the polarization directions of both the incident and the scattered light are perpendicular to the CNT direction . In factnt light . Similarnt light -19.θ, the electric field vector of the incident light can be fully contained in the graphene plane (in-plane configuration) or it can make an angle θ (out-of-plane configuration), depending on the polarization direction of the incident light, as shown in Figure For a two-dimensional crystal, polarized Raman spectroscopy on single-layer graphene revealed strong polarization anisotropy for the Raman intensity of the double-resonant 2D-band, whereas that of the G-band is isotropic, under the normal laser incidence in the backscattering geometry . Polarizout-of-plane configuration, with respect to that in the in-plane configuration, was analyzed as a function of θ. The normalized Raman intensity showed approximately cos2θ-dependence up to θ = 70°.In this work, we investigated polarization anisotropy of the G-band and the 2D-band of single-layer graphene for oblique laser incidence with differing angles of laser incidence for the first time. The normalized Raman intensity of the 2D-band measured in the Single-layer graphene films were grown on 25-μm thick Cu foils  by a commercial plasma-enhanced chemical vapor deposition (CVD) system  at 830°C using methane. Details can be found in ref. .3. Prior to wet-etching, the surface of graphene/Cu was spin-coated with poly-methyl methacrylate (PMMA: 950 A2), followed by baking at 150°C for 3 min. Once Cu foil was dissolved completely, the PMMA/graphene membrane was washed with deionized water and placed on a TEM grid or a quartz substrate. Finally the PMMA film was removed by acetone.For Raman spectroscopy, the synthesized graphene films were transferred either onto transmission electron microscope (TEM) grids or onto quartz substrates by etching the Cu foil in an aqueous solution of FeCl−1.Raman spectra were measured at room temperature by using a 532-nm line from a frequency-doubled Nd:YAG laser  as the excitation light source. Scattered light from the samples was analyzed through a single grating spectrometer  with a focal length of 50 cm  and detected with a liquid-nitrogen-cooled silicon CCD detector . The laser spot size on the sample was approximately 100 μm, and the spectral resolution was approximately 1 cmθ with the graphene plane as the laser incident angle θ. Thus, the in-plane configuration and the out-of-plane configuration can be denoted by (VV) and (HH), respectively. Polarized Raman spectra were measured in both (VV) and (HH) configurations for each laser incident angle θ ranging from −70° to 70°.Two different Raman scattering geometries were used in this work. The backscattering geometry was used for the single-layer graphene on a TEM grid but the forward-scattering geometry for that on a quartz plate. For both scattering geometries, the vertical direction is assigned to the polarization direction of the incident light when its electric field is fully contained in the graphene plane whereas the horizontal direction is assigned to that when its electric field made the same angle Raman spectrum of the CVD-grown graphene sample used in this work is shown in Figure 2α-dependence in which α is the angle between the CNT axis and the polarization direction of the incident light [out-of-plane configuration with respect to that measured in in-plane configuration, 2θ-dependence. Experimental data, shown in Figure θ, agreed quite well with cos2θ-dependence (the black solid line) as expected.Figure nt light . Thus, t2θ-dependence as shown in Figure Figure In order to double-check that the observed polarization anisotropy in Figures out-of-plane configuration with respect to that in the in-plane configuration was analyzed as a function of the laser incident angle θ. The normalized Raman intensity 2θ-dependence up to θ = 70°, which is the direct consequence of the two-dimensional nature of graphene.We investigated polarization anisotropy of the G-band and the 2D-band of single-layer graphene for oblique laser incidence with differing angles of laser incidence for the first time. The normalized Raman intensity of the 2D-band measured in the