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Kiphart D, Harkavyi Y, Balin K, Szade J, Mróz B, Kuświk P, Jurga S, Wiesner M. Investigations of proximity-induced superconductivity in the topological insulator Bi 2Te 3 by microRaman spectroscopy. Sci Rep 2021; 11:22980. [PMID: 34837028 PMCID: PMC8626455 DOI: 10.1038/s41598-021-02475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/01/2021] [Indexed: 11/12/2022] Open
Abstract
We used the topological insulator (TI) Bi2Te3 and a high-temperature superconductor (HTSC) hybrid device for investigations of proximity-induced superconductivity (PS) in the TI. Application of the superconductor YBa2Cu3O7-δ (YBCO) enabled us to access higher temperature and energy scales for this phenomenon. The HTSC in the hybrid device exhibits emergence of a pseudogap state for T > Tc that converts into a superconducting state with a reduced gap for T < Tc. The conversion process has been reflected in Raman spectra collected from the TI. Complementary charge transport experiments revealed emergence of the proximity-induced superconducting gap in the TI and the reduced superconducting gap in the HTSC, but no signature of the pseudogap. This allowed us to conclude that Raman spectroscopy reveals formation of the pseudogap state but cannot distinguish the proximity-induced superconducting state in the TI from the superconducting state in the HTSC characterised by the reduced gap. Results of our experiments have shown that Raman spectroscopy is a complementary technique to classic charge transport experiments and is a powerful tool for investigation of the proximity-induced superconductivity in the Bi2Te3.
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Affiliation(s)
- D Kiphart
- Adam Mickiewicz University, Faculty of Physics, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - Y Harkavyi
- Adam Mickiewicz University, Faculty of Physics, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - K Balin
- A. Chełkowski Institute of Physics and Silesian Center for Education and Interdisciplinary Research, University of Silesia, 75 Pułku Piechoty 1A, 41-500, Chorzow, Poland
| | - J Szade
- A. Chełkowski Institute of Physics and Silesian Center for Education and Interdisciplinary Research, University of Silesia, 75 Pułku Piechoty 1A, 41-500, Chorzow, Poland
| | - B Mróz
- Adam Mickiewicz University, Faculty of Physics, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - P Kuświk
- Institute of Molecular Physics, Polish Academy of Sciences, ul. Smoluchowskiego 17, 60-179, Poznan, Poland
| | - S Jurga
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614, Poznan, Poland
| | - M Wiesner
- Adam Mickiewicz University, Faculty of Physics, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland.
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Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001; 29:102-5. [PMID: 11125061 PMCID: PMC29827 DOI: 10.1093/nar/29.1.102] [Citation(s) in RCA: 357] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).
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Affiliation(s)
- E Huala
- Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA.
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Waugh M, Hraber P, Weller J, Wu Y, Chen G, Inman J, Kiphart D, Sobral B. The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research. Nucleic Acids Res 2000; 28:87-90. [PMID: 10592189 PMCID: PMC102488 DOI: 10.1093/nar/28.1.87] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.
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Affiliation(s)
- M Waugh
- The National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, NM 87505, USA
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Harger C, Chen G, Farmer A, Huang W, Inman J, Kiphart D, Schilkey F, Skupski MP, Weller J. The genome sequence DataBase. Nucleic Acids Res 2000; 28:31-2. [PMID: 10592174 PMCID: PMC102463 DOI: 10.1093/nar/28.1.31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/1999] [Revised: 10/13/1999] [Accepted: 10/13/1999] [Indexed: 11/13/2022] Open
Abstract
The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have occurred in the past year: GSDB stopped accepting data submissions from researchers; ownership of data submitted to GSDB was transferred to GenBank; sequence analysis capabilities were expanded to include Smith-Waterman and Frame Search; and Sequence Viewer became available to Mac users. The content of GSDB remains up-to-date because publicly available data is acquired from the International Nucleotide Sequence Database Collaboration databases (IC) on a nightly basis. This allows GSDB to continue providing researchers with the ability to analyze, query and retrieve nucleotide sequences in the database. GSDB and its related tools are freely accessible from the URL: http://www.ncgr.org
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Affiliation(s)
- C Harger
- National Center for Genome Resources, 1800 Old Pecos Trail, Suite A, Santa Fe, NM 87505, USA.
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Skupski MP, Booker M, Farmer A, Harpold M, Huang W, Inman J, Kiphart D, Kodira C, Root S, Schilkey F, Schwertfeger J, Siepel A, Stamper D, Thayer N, Thompson R, Wortman J, Zhuang JJ, Harger C. The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Res 1999; 27:35-8. [PMID: 9847136 PMCID: PMC148091 DOI: 10.1093/nar/27.1.35] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.
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Affiliation(s)
- M P Skupski
- National Center for Genome Resources, 1800 Old Pecos Trail, Suite A, Santa Fe, NM 87505, USA
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Harger C, Skupski M, Bingham J, Farmer A, Hoisie S, Hraber P, Kiphart D, Krakowski L, McLeod M, Schwertfeger J, Seluja G, Siepel A, Singh G, Stamper D, Steadman P, Thayer N, Thompson R, Wargo P, Waugh M, Zhuang JJ, Schad PA. The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res 1998; 26:21-6. [PMID: 9399793 PMCID: PMC147232 DOI: 10.1093/nar/26.1.21] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In 1997 the primary focus of the Genome Sequence DataBase (GSDB; www. ncgr.org/gsdb ) located at the National Center for Genome Resources was to improve data quality and accessibility. Efforts to increase the quality of data within the database included two major projects; one to identify and remove all vector contamination from sequences in the database and one to create premier sequence sets (including both alignments and discontiguous sequences). Data accessibility was improved during the course of the last year in several ways. First, a graphical database sequence viewer was made available to researchers. Second, an update process was implemented for the web-based query tool, Maestro. Third, a web-based tool, Excerpt, was developed to retrieve selected regions of any sequence in the database. And lastly, a GSDB flatfile that contains annotation unique to GSDB (e.g., sequence analysis and alignment data) was developed. Additionally, the GSDB web site provides a tool for the detection of matrix attachment regions (MARs), which can be used to identify regions of high coding potential. The ultimate goal of this work is to make GSDB a more useful resource for genomic comparison studies and gene level studies by improving data quality and by providing data access capabilities that are consistent with the needs of both types of studies.
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Affiliation(s)
- C Harger
- National Center for Genome Resources, 1800 Old Pecos Trail, Suite A, Santa Fe, NM 87505, USA.
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