Pub Date : 2016-02-01DOI: 10.1007/s00791-016-0269-z
P. Frolkovic, D. Logashenko, Christian Wehner
{"title":"Flux-based level-set method for two-phase flows on unstructured grids","authors":"P. Frolkovic, D. Logashenko, Christian Wehner","doi":"10.1007/s00791-016-0269-z","DOIUrl":"https://doi.org/10.1007/s00791-016-0269-z","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"18 1","pages":"31-52"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-016-0269-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52164316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-02-01DOI: 10.1007/s00791-016-0268-0
P. Frolkovic, M. Lampe, G. Wittum
{"title":"Numerical simulation of contaminant transport in groundwater using software tools of $$r^3t$$r3t","authors":"P. Frolkovic, M. Lampe, G. Wittum","doi":"10.1007/s00791-016-0268-0","DOIUrl":"https://doi.org/10.1007/s00791-016-0268-0","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"28 1","pages":"17-29"},"PeriodicalIF":0.0,"publicationDate":"2016-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-016-0268-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52164181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mono-nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii.
{"title":"Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development.","authors":"Fuli Liu, Zimin Hu, Wenhui Liu, Jingjing Li, Wenjun Wang, Zhourui Liang, Feijiu Wang, Xiutao Sun","doi":"10.1038/srep18947","DOIUrl":"10.1038/srep18947","url":null,"abstract":"<p><p>Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mono-nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii. </p>","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"19 1","pages":"18947"},"PeriodicalIF":4.6,"publicationDate":"2016-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1038/srep18947","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58192498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-12-01DOI: 10.1007/s00791-016-0266-2
Felix Henneke, M. Liebmann
{"title":"A generalized Suzuki–Trotter type method in optimal control of coupled Schrödinger equations","authors":"Felix Henneke, M. Liebmann","doi":"10.1007/s00791-016-0266-2","DOIUrl":"https://doi.org/10.1007/s00791-016-0266-2","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"17 1","pages":"277-293"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-016-0266-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52164001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-12-01DOI: 10.1007/s00791-016-0263-5
Sambasiva Rao Chinnamsetty, Mike Espig, W. Hackbusch
{"title":"Mesh-free canonical tensor products for six-dimensional density matrix: computation of kinetic energy","authors":"Sambasiva Rao Chinnamsetty, Mike Espig, W. Hackbusch","doi":"10.1007/s00791-016-0263-5","DOIUrl":"https://doi.org/10.1007/s00791-016-0263-5","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"17 1","pages":"267-275"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-016-0263-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52163649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-12-01DOI: 10.1007/s00791-016-0265-3
A. Hauser, G. Wittum
{"title":"Adaptive large eddy simulation","authors":"A. Hauser, G. Wittum","doi":"10.1007/s00791-016-0265-3","DOIUrl":"https://doi.org/10.1007/s00791-016-0265-3","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"17 1","pages":"295-304"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-016-0265-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52163860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.1007/S00791-016-0260-8
Peiyao Luo, C. Rodrigo, F. Gaspar, C. Oosterlee
{"title":"Multigrid method for nonlinear poroelasticity equations","authors":"Peiyao Luo, C. Rodrigo, F. Gaspar, C. Oosterlee","doi":"10.1007/S00791-016-0260-8","DOIUrl":"https://doi.org/10.1007/S00791-016-0260-8","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"17 1","pages":"255-265"},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/S00791-016-0260-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52163403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.1007/s00791-016-0261-7
Markus M. Knodel, A. Nägel, S. Reiter, M. Rupp, A. Vogel, P. Targett-Adams, E. Herrmann, G. Wittum
{"title":"Multigrid analysis of spatially resolved hepatitis C virus protein simulations","authors":"Markus M. Knodel, A. Nägel, S. Reiter, M. Rupp, A. Vogel, P. Targett-Adams, E. Herrmann, G. Wittum","doi":"10.1007/s00791-016-0261-7","DOIUrl":"https://doi.org/10.1007/s00791-016-0261-7","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"28 1","pages":"235-253"},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-016-0261-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52163532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-08-01DOI: 10.1007/s00791-015-0259-6
C. V. Hansen, H. Schroll, D. Wüstner
{"title":"Computational modeling of fluorescence loss in photobleaching","authors":"C. V. Hansen, H. Schroll, D. Wüstner","doi":"10.1007/s00791-015-0259-6","DOIUrl":"https://doi.org/10.1007/s00791-015-0259-6","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"40 1","pages":"151-166"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00791-015-0259-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52163373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-08-01DOI: 10.1007/S00791-015-0256-9
T. Schenk, A. Gilg, M. Mühlbauer, R. Rosen, J. C. Wehrstedt
{"title":"Architecture for modeling and simulation of technical systems along their lifecycle","authors":"T. Schenk, A. Gilg, M. Mühlbauer, R. Rosen, J. C. Wehrstedt","doi":"10.1007/S00791-015-0256-9","DOIUrl":"https://doi.org/10.1007/S00791-015-0256-9","url":null,"abstract":"","PeriodicalId":52439,"journal":{"name":"Computing and Visualization in Science","volume":"17 1","pages":"167-183"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/S00791-015-0256-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"52163245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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