Xavier, Crislaine; Cabral-de-Mello, Diogo Cavalcanti; de Moura, Rita Cássia
2014-12-01
Cytogenetic studies of the Neotropical beetle genus Dichotomius (Scarabaeinae, Coleoptera) have shown dynamism for centromeric constitutive heterochromatin sequences. In the present work we studied the chromosomes and isolated repetitive sequences of Dichotomius schiffleri aiming to contribute to the understanding of coleopteran genome/chromosomal organization. Dichotomius schiffleri presented a conserved karyotype and heterochromatin distribution in comparison to other species of the genus with 2n = 18, biarmed chromosomes, and pericentromeric C-positive blocks. Similarly to heterochromatin distributional patterns, the highly and moderately repetitive DNA fraction (C 0 t-1 DNA) was detected in pericentromeric areas, contrasting with the euchromatic mapping of an isolated TE (named DsmarMITE). After structural analyses, the DsmarMITE was classified as a non-autonomous element of the type miniature inverted-repeat transposable element (MITE) with terminal inverted repeats similar to Mariner elements of insects from different orders. The euchromatic distribution for DsmarMITE indicates that it does not play a part in the dynamics of constitutive heterochromatin sequences.
Wang, Yajun; Dong, Qing; Ding, Zhaolan; Gai, Kexin; Han, Xiaoyun; Kaleri, Farah Naz; He, Qun; Wang, Ying
2016-10-01
Catalase-3 (CAT-3) constitutes the main catalase activity in growing hyphae of Neurospora crassa, and its activity increases during exponential growth or is induced under different stress conditions. Although extensive progress has been made to identify catalase regulators, the regulation mechanism of CAT-3 at the chromatin level still remains unclear. Here, we aim at investigating the molecular regulation mechanisms of cat-3 at the chromatin level. We found that CAT-3 protein levels increased in mutants defective in proper global heterochromatin formation. Bioinformatics analysis identified a 5-kb AT-rich sequence adjacent to the cat-3 promoter as a heterochromatin region because of its enrichment of H3K9me3 and HP1. Expression of CAT-3 was induced by H 2 O 2 treatment in wild-type and such change occurred along with the accumulation of histone H3 acetylation at 5-kb heterochromatin boundaries and cat-3 locus, but without alteration of its H3K9me3 repressive modification. Moreover, disruption of 5-kb heterochromatin region results in elevated cat-3 expression, and higher levels of cat-3 expression were promoted by the combination with global heterochromatin defective mutants. Interestingly, the molecular weight and activity bands of CAT-3 protein are different in heterochromatin defective mutants compared with those in wild-type, suggesting that its N-terminal processing and modification may be altered. Our study indicates that the local chromatin structure creates a heterochromatin repressive environment to repress nearby gene expression. Copyright © 2016 Elsevier Inc. All rights reserved.
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Varvara A Khoroshko
Full Text Available Late-replicating domains (intercalary heterochromatin in the Drosophila genome display a number of features suggesting their organization is quite unique. Typically, they are quite large and encompass clusters of functionally unrelated tissue-specific genes. They correspond to the topologically associating domains and conserved microsynteny blocks. Our study aims at exploring further details of molecular organization of intercalary heterochromatin and has uncovered surprising heterogeneity of chromatin composition in these regions. Using the 4HMM model developed in our group earlier, intercalary heterochromatin regions were found to host chromatin fragments with a particular epigenetic profile. Aquamarine chromatin fragments (spanning 0.67% of late-replicating regions are characterized as a class of sequences that appear heterogeneous in terms of their decompactization. These fragments are enriched with enhancer sequences and binding sites for insulator proteins. They likely mark the chromatin state that is related to the binding of cis-regulatory proteins. Malachite chromatin fragments (11% of late-replicating regions appear to function as universal transitional regions between two contrasting chromatin states. Namely, they invariably delimit intercalary heterochromatin regions from the adjacent active chromatin of interbands. Malachite fragments also flank aquamarine fragments embedded in the repressed chromatin of late-replicating regions. Significant enrichment of insulator proteins CP190, SU(HW, and MOD2.2 was observed in malachite chromatin. Neither aquamarine nor malachite chromatin types appear to correlate with the positions of highly conserved non-coding elements (HCNE that are typically replete in intercalary heterochromatin. Malachite chromatin found on the flanks of intercalary heterochromatin regions tends to replicate earlier than the malachite chromatin embedded in intercalary heterochromatin. In other words, there exists a
Genome mapping and characterization of the Anopheles gambiae heterochromatin
Directory of Open Access Journals (Sweden)
Sharakhova Maria V
2010-08-01
Full Text Available Abstract Background Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized. Results To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1 and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin. Conclusions Our results demonstrate that Anopheles polytene chromosomes
Czech Academy of Sciences Publication Activity Database
Evtushenko, E.V.; Levitsky, V.G.; Elisafenko, E.A.; Gunbin, K.V.; Belousov, A.I.; Šafář, Jan; Doležel, Jaroslav; Vershinin, A.V.
2016-01-01
Roč. 17, MAY 4 (2016), s. 337 ISSN 1471-2164 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Tandem repeats * Transposable elements * Subtelomeric heterochromatin Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.729, year: 2016
Acosta, M J; Marchal, J A; Fernández-Espartero, C H; Bullejos, M; Sánchez, A
2008-01-01
The chromosomal distribution of mobile genetic elements is scarcely known in Arvicolinae species, but could be of relevance to understand the origin and complex evolution of the sex chromosome heterochromatin. In this work we cloned two retrotransposon sequences, L1 and SINE-B1, from the genome of Chionomys nivalis and investigated their chromosomal distribution on several arvicoline species. Our results demonstrate first that both retroelements are the most abundant repeated DNA sequences in the genome of these species. L1 elements, in most species, are highly accumulated in the sex chromosomes compared to the autosomes. This favoured L1 insertion could have played an important role in the origin of the enlarged heterochromatic blocks existing in the sex chromosomes of some Microtus species. Also, we propose that L1 accumulation on the X heterochromatin could have been the consequence of different, independent and rapid amplification processes acting in each species. SINE elements, however, were completely lacking from the constitutive heterochromatin, either in autosomes or in the heterochromatic blocks of sex chromosomes. These data could indicate that some SINE elements are incompatible with the formation of heterochromatic complexes and hence are necessarily missing from the constitutive heterochromatin.
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Jiro C Yasuhara
2008-01-01
Full Text Available Constitutive heterochromatin is enriched in repetitive sequences and histone H3-methylated-at-lysine 9. Both components contribute to heterochromatin's ability to silence euchromatic genes. However, heterochromatin also harbors hundreds of expressed genes in organisms such as Drosophila. Recent studies have provided a detailed picture of sequence organization of D. melanogaster heterochromatin, but how histone modifications are associated with heterochromatic sequences at high resolution has not been described. Here, distributions of modified histones in the vicinity of heterochromatic genes of normal embryos and embryos homozygous for a chromosome rearrangement were characterized using chromatin immunoprecipitation and genome tiling arrays. We found that H3-di-methylated-at-lysine 9 (H3K9me2 was depleted at the 5' ends but enriched throughout transcribed regions of heterochromatic genes. The profile was distinct from that of euchromatic genes and suggests that heterochromatic genes are integrated into, rather than insulated from, the H3K9me2-enriched domain. Moreover, the profile was only subtly affected by a Su(var3-9 null mutation, implicating a histone methyltransferase other than SU(VAR3-9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos. On a chromosomal scale, we observed a sharp transition to the H3K9me2 domain, which coincided with increased retrotransposon density in the euchromatin-heterochromatin (eu-het transition zones on the long chromosome arms. Thus, a certain density of retrotransposons, rather than specific boundary elements, may demarcate Drosophila pericentric heterochromatin. We also demonstrate that a chromosome rearrangement that created a new eu-het junction altered H3K9me2 distribution and induced new euchromatic sites of enrichment as far as several megabases away from the breakpoint. Taken together, the findings argue against simple classification of H3K9me as the definitive signature
Caizzi, Ruggiero; Moschetti, Roberta; Piacentini, Lucia; Fanti, Laura; Marsano, Renè Massimiliano; Dimitri, Patrizio
2016-08-01
The term heterochromatin has been long considered synonymous with gene silencing, but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes. Several studies have addressed the epigenetic changes that enable the expression of genes in pericentric heterochromatin, yet little is known about the evolutionary processes through which this has occurred. By combining genome annotation analysis and high-resolution cytology, we have identified and mapped 53 orthologs of D. melanogaster heterochromatic genes in the genomes of two evolutionarily distant species, D. pseudoobscura and D. virilis. Our results show that the orthologs of the D. melanogaster heterochromatic genes are clustered at three main genomic regions in D. virilis and D. pseudoobscura. In D. virilis, the clusters lie in the middle of euchromatin, while those in D. pseudoobscura are located in the proximal portion of the chromosome arms. Some orthologs map to the corresponding Muller C element in D. pseudoobscura and D. virilis, while others localize on the Muller B element, suggesting that chromosomal rearrangements that have been instrumental in the fusion of two separate elements involved the progenitors of genes currently located in D. melanogaster heterochromatin. These results demonstrate an evolutionary repositioning of gene clusters from ancestral locations in euchromatin to the pericentromeric heterochromatin of descendent D. melanogaster chromosomes. Remarkably, in both D. virilis and D. pseudoobscura the gene clusters show a conserved association with the HP1a protein, one of the most highly evolutionarily conserved epigenetic marks. In light of these results, we suggest a new scenario whereby ancestral HP1-like proteins (and possibly other epigenetic marks) may have contributed to the evolutionary repositioning of gene clusters into heterochromatin.
Myster, Steven H; Wang, Fei; Cavallo, Robert; Christian, Whitney; Bhotika, Seema; Anderson, Charles T; Peifer, Mark
2004-01-01
Genomic sequences provide powerful new tools in genetic analysis, making it possible to combine classical genetics with genomics to characterize the genes in a particular chromosome region. These approaches have been applied successfully to the euchromatin, but analysis of the heterochromatin has lagged somewhat behind. We describe a combined genetic and bioinformatics approach to the base of the right arm of the Drosophila melanogaster second chromosome, at the boundary between pericentric h...
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Thibaut Josse
2007-09-01
Full Text Available The study of P-element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE, a repression mechanism by which a transposon or a transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequence or TAS has the capacity to repress in trans in the female germline, a homologous transposon, or transgene located in euchromatin. TSE shows variegation among egg chambers in ovaries when silencing is incomplete. Here, we report that TSE displays an epigenetic transmission through meiosis, which involves an extrachromosomal maternally transmitted factor. We show that this silencing is highly sensitive to mutations affecting both heterochromatin formation (Su(var205 encoding Heterochromatin Protein 1 and Su(var3-7 and the repeat-associated small interfering RNA (or rasiRNA silencing pathway (aubergine, homeless, armitage, and piwi. In contrast, TSE is not sensitive to mutations affecting r2d2, which is involved in the small interfering RNA (or siRNA silencing pathway, nor is it sensitive to a mutation in loquacious, which is involved in the micro RNA (or miRNA silencing pathway. These results, taken together with the recent discovery of TAS homologous small RNAs associated to PIWI proteins, support the proposition that TSE involves a repeat-associated small interfering RNA pathway linked to heterochromatin formation, which was co-opted by the P element to establish repression of its own transposition after its recent invasion of the D. melanogaster genome. Therefore, the study of TSE provides insight into the genetic properties of a germline-specific small RNA silencing pathway.
Development of polygon elements based on the scaled boundary finite element method
International Nuclear Information System (INIS)
Chiong, Irene; Song Chongmin
2010-01-01
We aim to extend the scaled boundary finite element method to construct conforming polygon elements. The development of the polygonal finite element is highly anticipated in computational mechanics as greater flexibility and accuracy can be achieved using these elements. The scaled boundary polygonal finite element will enable new developments in mesh generation, better accuracy from a higher order approximation and better transition elements in finite element meshes. Polygon elements of arbitrary number of edges and order have been developed successfully. The edges of an element are discretised with line elements. The displacement solution of the scaled boundary finite element method is used in the development of shape functions. They are shown to be smooth and continuous within the element, and satisfy compatibility and completeness requirements. Furthermore, eigenvalue decomposition has been used to depict element modes and outcomes indicate the ability of the scaled boundary polygonal element to express rigid body and constant strain modes. Numerical tests are presented; the patch test is passed and constant strain modes verified. Accuracy and convergence of the method are also presented and the performance of the scaled boundary polygonal finite element is verified on Cook's swept panel problem. Results show that the scaled boundary polygonal finite element method outperforms a traditional mesh and accuracy and convergence are achieved from fewer nodes. The proposed method is also shown to be truly flexible, and applies to arbitrary n-gons formed of irregular and non-convex polygons.
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Rocha Marla Piumbini
1998-01-01
Full Text Available We describe the karyotypes of eight bee species of the genus Melipona and compare them in terms of heterochromatin content and location (C-banding technique. All species had 2n = 18 (females and n = 9 (males chromosomes, but a wide variation in heterochromatin content was detected among karyotypes. On the basis of these differences, the species were divided into two functional groups, one of them comprising species with a karyotype having a low heterochromatin content (M. bicolor bicolor, M. quadrifasciata, M. marginata, and M. asilvai, and the other species with a high heterochromatin content (M. seminigra fuscopilosa, M. capixaba, M. scutellaris, and M. captiosa. In the species with high heterochromatin content, heterochromatin occupied practically the entire extent of all chromosomes, with euchromatin being limited to the extremities, a fact that prevented observation of the centromere. In contrast, in the species with karyotypes having a low heterochromatin content, heterochromatin was visualized only in some chromosomes. In the chromosomes in which it was present, heterochromatin was located in the centromere or on the short arm. M. bicolor bicolor had the smallest heterochromatin content with only three chromosome pairs presenting heterochromatin in females. Increased heterochromatin content may be explained by interstitial and pericentromeric growth.
Mixed Element Formulation for the Finite Element-Boundary Integral Method
National Research Council Canada - National Science Library
Meese, J; Kempel, L. C; Schneider, S. W
2006-01-01
A mixed element approach using right hexahedral elements and right prism elements for the finite element-boundary integral method is presented and discussed for the study of planar cavity-backed antennas...
International Nuclear Information System (INIS)
Ozgener, B.
1998-01-01
A boundary integral equation (BIE) is developed for the application of the boundary element method to the multigroup neutron diffusion equations. The developed BIE contains no explicit scattering term; the scattering effects are taken into account by redefining the unknowns. Boundary elements of the linear and constant variety are utilised for validation of the developed boundary integral formulation
Boundary element method for modelling creep behaviour
International Nuclear Information System (INIS)
Zarina Masood; Shah Nor Basri; Abdel Majid Hamouda; Prithvi Raj Arora
2002-01-01
A two dimensional initial strain direct boundary element method is proposed to numerically model the creep behaviour. The boundary of the body is discretized into quadratic element and the domain into quadratic quadrilaterals. The variables are also assumed to have a quadratic variation over the elements. The boundary integral equation is solved for each boundary node and assembled into a matrix. This matrix is solved by Gauss elimination with partial pivoting to obtain the variables on the boundary and in the interior. Due to the time-dependent nature of creep, the solution has to be derived over increments of time. Automatic time incrementation technique and backward Euler method for updating the variables are implemented to assure stability and accuracy of results. A flowchart of the solution strategy is also presented. (Author)
Ring-like distribution of constitutive heterochromatin in bovine senescent cells.
Pichugin, Andrey; Beaujean, Nathalie; Vignon, Xavier; Vassetzky, Yegor
2011-01-01
Cells that reach "Hayflick limit" of proliferation, known as senescent cells, possess a particular type of nuclear architecture. Human senescent cells are characterized by the presence of highly condensed senescent associated heterochromatin foci (SAHF) that can be detected both by immunostaining for histone H3 three-methylated at lysine 9 (H3K9me3) and by DAPI counterstaining. We have studied nuclear architecture in bovine senescent cells using a combination of immunofluorescence and 3D fluorescent in-situ hybridization (FISH). Analysis of heterochromatin distribution in bovine senescent cells using fluorescent in situ hybridization for pericentric chromosomal regions, immunostaining of H3K9me3, centromeric proteins CENP A/B and DNA methylation showed a lower level of heterochromatin condensation as compared to young cells. No SAHF foci were observed. Instead, we observed fibrous ring-like or ribbon-like heterochromatin patterns that were undetectable with DAPI counterstaining. These heterochromatin fibers were associated with nucleoli. Constitutive heterochromatin in bovine senescent cells is organized in ring-like structures.
Ring-like distribution of constitutive heterochromatin in bovine senescent cells.
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Andrey Pichugin
Full Text Available BACKGROUND: Cells that reach "Hayflick limit" of proliferation, known as senescent cells, possess a particular type of nuclear architecture. Human senescent cells are characterized by the presence of highly condensed senescent associated heterochromatin foci (SAHF that can be detected both by immunostaining for histone H3 three-methylated at lysine 9 (H3K9me3 and by DAPI counterstaining. METHODS: We have studied nuclear architecture in bovine senescent cells using a combination of immunofluorescence and 3D fluorescent in-situ hybridization (FISH. RESULTS: Analysis of heterochromatin distribution in bovine senescent cells using fluorescent in situ hybridization for pericentric chromosomal regions, immunostaining of H3K9me3, centromeric proteins CENP A/B and DNA methylation showed a lower level of heterochromatin condensation as compared to young cells. No SAHF foci were observed. Instead, we observed fibrous ring-like or ribbon-like heterochromatin patterns that were undetectable with DAPI counterstaining. These heterochromatin fibers were associated with nucleoli. CONCLUSIONS: Constitutive heterochromatin in bovine senescent cells is organized in ring-like structures.
Stanojcic, Slavica; Gimenez, Sylvie; Permal, Emmanuelle; Cousserans, François; Quesneville, Hadi; Fournier, Philippe; d'Alençon, Emmanuelle
2011-01-01
Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism. PMID:21980354
Eberle, Andrea B.; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Hessle, Viktoria; Silberberg, Gilad; von Euler, Anne; Silverstein, Rebecca A.; Visa, Neus
2015-01-01
RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin. PMID:26389589
Mammalian ChlR1 has a role in heterochromatin organization
International Nuclear Information System (INIS)
Inoue, Akira; Hyle, Judith; Lechner, Mark S.; Lahti, Jill M.
2011-01-01
The ChlR1 DNA helicase, encoded by DDX11 gene, which is responsible for Warsaw breakage syndrome (WABS), has a role in sister-chromatid cohesion. In this study, we show that human ChlR1 deficient cells exhibit abnormal heterochromatin organization. While constitutive heterochromatin is discretely localized at perinuclear and perinucleolar regions in control HeLa cells, ChlR1-depleted cells showed dispersed localization of constitutive heterochromatin accompanied by disrupted centromere clustering. Cells isolated from Ddx11 -/- embryos also exhibited diffuse localization of centromeres and heterochromatin foci. Similar abnormalities were found in HeLa cells depleted of combinations of HP1α and HP1β. Immunofluorescence and chromatin immunoprecipitation showed a decreased level of HP1α at pericentric regions in ChlR1-depleted cells. Trimethyl-histone H3 at lysine 9 (H3K9-me3) was also modestly decreased at pericentric sequences. The abnormality in pericentric heterochromatin was further supported by decreased DNA methylation within major satellite repeats of Ddx11 -/- embryos. Furthermore, micrococcal nuclease (MNase) assay revealed a decreased chromatin density at the telomeres. These data suggest that in addition to a role in sister-chromatid cohesion, ChlR1 is also involved in the proper formation of heterochromatin, which in turn contributes to global nuclear organization and pleiotropic effects. -- Highlights: → New role for ChlR1 (DDX11), a cohesinopathy gene, in heterochromatin organization. → Loss of ChlR1 altered heterochromatin localization and centromere clustering. → Reduced ChlR1 levels also reduced HP1α and H3K9-me3 binding to pericentric DNA. → Decreased DNA methylation was found in pericentric repeats of Ddx11 -/- embryos. → These findings will aid in understanding the pathogenesis of Warsaw breakage syndrome.
The complex variable boundary element method: Applications in determining approximative boundaries
Hromadka, T.V.
1984-01-01
The complex variable boundary element method (CVBEM) is used to determine approximation functions for boundary value problems of the Laplace equation such as occurs in potential theory. By determining an approximative boundary upon which the CVBEM approximator matches the desired constant (level curves) boundary conditions, the CVBEM is found to provide the exact solution throughout the interior of the transformed problem domain. Thus, the acceptability of the CVBEM approximation is determined by the closeness-of-fit of the approximative boundary to the study problem boundary. ?? 1984.
Pairing of heterochromatin in response to cellular stress
International Nuclear Information System (INIS)
Abdel-Halim, H.I.; Mullenders, L.H.F.; Boei, J.J.W.A.
2006-01-01
We previously reported that exposure of human cells to DNA-damaging agents (X-rays and mitomycin C (MMC)) induces pairing of the homologous paracentromeric heterochromatin of chromosome 9 (9q12-13). Here, we show that UV irradiation and also heat shock treatment of human cells lead to similar effects. Since the various agents induce very different types and frequencies of damage to cellular constituents, the data suggest a general stress response as the underlying mechanism. Moreover, local UV irradiation experiments revealed that pairing of heterochromatin is an event that can be triggered without induction of DNA damage in the heterochromatic sequences. The repair deficient xeroderma pigmentosum cells (group F) previously shown to fail pairing after MMC displayed elevated pairing after heat shock treatment but not after UV exposure. Taken together, the present results indicate that pairing of heterochromatin following exposure to DNA-damaging agents is initiated by a general stress response and that the sensing of stress or the maintenance of the paired status of the heterochromatin might be dependent on DNA repair
A Novel Mesh Quality Improvement Method for Boundary Elements
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Hou-lin Liu
2012-01-01
Full Text Available In order to improve the boundary mesh quality while maintaining the essential characteristics of discrete surfaces, a new approach combining optimization-based smoothing and topology optimization is developed. The smoothing objective function is modified, in which two functions denoting boundary and interior quality, respectively, and a weight coefficient controlling boundary quality are taken into account. In addition, the existing smoothing algorithm can improve the mesh quality only by repositioning vertices of the interior mesh. Without destroying boundary conformity, bad elements with all their vertices on the boundary cannot be eliminated. Then, topology optimization is employed, and those elements are converted into other types of elements whose quality can be improved by smoothing. The practical application shows that the worst elements can be eliminated and, with the increase of weight coefficient, the average quality of boundary mesh can also be improved. Results obtained with the combined approach are compared with some common approach. It is clearly shown that it performs better than the existing approach.
Using reciprocity in Boundary Element Calculations
DEFF Research Database (Denmark)
Juhl, Peter Møller; Cutanda Henriquez, Vicente
2010-01-01
The concept of reciprocity is widely used in both theoretical and experimental work. In Boundary Element calculations reciprocity is sometimes employed in the solution of computationally expensive scattering problems, which sometimes can be more efficiently dealt with when formulated...... as the reciprocal radiation problem. The present paper concerns the situation of having a point source (which is reciprocal to a point receiver) at or near a discretized boundary element surface. The accuracy of the original and the reciprocal problem is compared in a test case for which an analytical solution...
Recent advances in boundary element methods
Manolis, GD
2009-01-01
Addresses the needs of the computational mechanics research community in terms of information on boundary integral equation-based methods and techniques applied to a variety of fields. This book collects both original and review articles on contemporary Boundary Element Methods (BEM) as well as on the Mesh Reduction Methods (MRM).
Energy Technology Data Exchange (ETDEWEB)
Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)
2007-01-01
Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in
Boundary Associated Long Noncoding RNA Mediates Long-Range Chromosomal Interactions.
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Ifeoma Jane Nwigwe
Full Text Available CCCTC binding factor (CTCF is involved in organizing chromosomes into mega base-sized, topologically associated domains (TADs along with other factors that define sub-TAD organization. CTCF-Cohesin interactions have been shown to be critical for transcription insulation activity as it stabilizes long-range interactions to promote proper gene expression. Previous studies suggest that heterochromatin boundary activity of CTCF may be independent of Cohesin, and there may be additional mechanisms for defining topological domains. Here, we show that a boundary site we previously identified known as CTCF binding site 5 (CBS5 from the homeotic gene cluster A (HOXA locus exhibits robust promoter activity. This promoter activity from the CBS5 boundary element generates a long noncoding RNA that we designate as boundary associated long noncoding RNA-1 (blncRNA1. Functional characterization of this RNA suggests that the transcript stabilizes long-range interactions at the HOXA locus and promotes proper expression of HOXA genes. Additionally, our functional analysis also shows that this RNA is not needed in the stabilization of CTCF-Cohesin interactions however CTCF-Cohesin interactions are critical in the transcription of blncRNA1. Thus, the CTCF-associated boundary element, CBS5, employs both Cohesin and noncoding RNA to establish and maintain topologically associated domains at the HOXA locus.
PREditOR: a synthetic biology approach to removing heterochromatin from cells.
Molina, Oscar; Carmena, Mar; Maudlin, Isabella E; Earnshaw, William C
2016-12-01
It is widely accepted that heterochromatin is necessary to maintain genomic stability. However, direct experimental evidence supporting this is slim. Previous studies using either enzyme inhibitors, gene knockout or knockdown studies all are subject to the caveat that drugs may have off-target effects and enzymes that modify chromatin proteins to support heterochromatin formation may also have numerous other cellular targets as well. Here, we describe PREditOR (protein reading and editing of residues), a synthetic biology approach that allows us to directly remove heterochromatin from cells without either drugs or global interference with gene function. We find that removal of heterochromatin perturbs mitotic progression and causes a dramatic increase in chromosome segregation defects, possibly as a result of interfering with the normal centromeric localization of the chromosomal passenger complex.
DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing.
Saveliev, Alexander; Everett, Christopher; Sharpe, Tammy; Webster, Zoë; Festenstein, Richard
2003-04-24
Gene repression is crucial to the maintenance of differentiated cell types in multicellular organisms, whereas aberrant silencing can lead to disease. The organization of DNA into chromatin and heterochromatin is implicated in gene silencing. In chromatin, DNA wraps around histones, creating nucleosomes. Further condensation of chromatin, associated with large blocks of repetitive DNA sequences, is known as heterochromatin. Position effect variegation (PEV) occurs when a gene is located abnormally close to heterochromatin, silencing the affected gene in a proportion of cells. Here we show that the relatively short triplet-repeat expansions found in myotonic dystrophy and Friedreich's ataxia confer variegation of expression on a linked transgene in mice. Silencing was correlated with a decrease in promoter accessibility and was enhanced by the classical PEV modifier heterochromatin protein 1 (HP1). Notably, triplet-repeat-associated variegation was not restricted to classical heterochromatic regions but occurred irrespective of chromosomal location. Because the phenomenon described here shares important features with PEV, the mechanisms underlying heterochromatin-mediated silencing might have a role in gene regulation at many sites throughout the mammalian genome and modulate the extent of gene silencing and hence severity in several triplet-repeat diseases.
Periodic Boundary Conditions in the ALEGRA Finite Element Code
International Nuclear Information System (INIS)
Aidun, John B.; Robinson, Allen C.; Weatherby, Joe R.
1999-01-01
This document describes the implementation of periodic boundary conditions in the ALEGRA finite element code. ALEGRA is an arbitrary Lagrangian-Eulerian multi-physics code with both explicit and implicit numerical algorithms. The periodic boundary implementation requires a consistent set of boundary input sets which are used to describe virtual periodic regions. The implementation is noninvasive to the majority of the ALEGRA coding and is based on the distributed memory parallel framework in ALEGRA. The technique involves extending the ghost element concept for interprocessor boundary communications in ALEGRA to additionally support on- and off-processor periodic boundary communications. The user interface, algorithmic details and sample computations are given
The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis
DEFF Research Database (Denmark)
Tuzon, Creighton T; Borgstrøm, Britta; Weilguny, Dietmar
2004-01-01
Telomeres share the ability to silence nearby transcription with heterochromatin, but the requirement of heterochromatin proteins for most telomere functions is unknown. The fission yeast Rik1 protein is required for heterochromatin formation at centromeres and the mating-type locus, as it recrui...... meiosis. However, Rik1 is dispensable for the protective roles of telomeres in preventing chromosome end-fusion. Thus, a Swi6-independent heterochromatin function distinct from that at centromeres and the mating-type locus operates at telomeres during sexual differentiation....
He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric
2012-12-01
Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes ("H-probes") for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin.
He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric
2012-01-01
Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes (“H-probes”) for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin. PMID:22745230
Centromeric heterochromatin: the primordial segregation machine.
Bloom, Kerry S
2014-01-01
Centromeres are specialized domains of heterochromatin that provide the foundation for the kinetochore. Centromeric heterochromatin is characterized by specific histone modifications, a centromere-specific histone H3 variant (CENP-A), and the enrichment of cohesin, condensin, and topoisomerase II. Centromere DNA varies orders of magnitude in size from 125 bp (budding yeast) to several megabases (human). In metaphase, sister kinetochores on the surface of replicated chromosomes face away from each other, where they establish microtubule attachment and bi-orientation. Despite the disparity in centromere size, the distance between separated sister kinetochores is remarkably conserved (approximately 1 μm) throughout phylogeny. The centromere functions as a molecular spring that resists microtubule-based extensional forces in mitosis. This review explores the physical properties of DNA in order to understand how the molecular spring is built and how it contributes to the fidelity of chromosome segregation.
8th International Conference on Boundary Element Methods
Brebbia, C
1986-01-01
The International Conference on Boundary Element Methods in Engineering was started in 1978 with the following objectives: i) To act as a focus for BE research at a time when the technique wasjust emerging as a powerful tool for engineering analysis. ii) To attract new as weIl as established researchers on Boundary Elements, in order to maintain its vitality and originality. iii) To try to relate the Boundary Element Method to other engineering techniques in an effort to help unify the field of engineering analysis, rather than to contribute to its fragmentation. These objectives were achieved during the last 7 conferences and this meeting - the eighth - has continued to be as innovative and dynamic as any ofthe previous conferences. Another important aim ofthe conference is to encourage the participation of researchers from as many different countries as possible and in this regard it is a policy of the organizers to hold the conference in different locations. It is easy to forget when working on scientific ...
Improved design of special boundary elements for T-shaped reinforced concrete walls
Ji, Xiaodong; Liu, Dan; Qian, Jiaru
2017-01-01
This study examines the design provisions of the Chinese GB 50011-2010 code for seismic design of buildings for the special boundary elements of T-shaped reinforced concrete walls and proposes an improved design method. Comparison of the design provisions of the GB 50011-2010 code and those of the American code ACI 318-14 indicates a possible deficiency in the T-shaped wall design provisions in GB 50011-2010. A case study of a typical T-shaped wall designed in accordance with GB 50011-2010 also indicates the insufficient extent of the boundary element at the non-flange end and overly conservative design of the flange end boundary element. Improved designs for special boundary elements of T-shaped walls are developed using a displacement-based method. The proposed design formulas produce a longer boundary element at the non-flange end and a shorter boundary element at the flange end, relative to those of the GB 50011-2010 provisions. Extensive numerical analysis indicates that T-shaped walls designed using the proposed formulas develop inelastic drift of 0.01 for both cases of the flange in compression and in tension.
Essential Boundary Conditions with Straight C1 Finite Elements in Curved Domains
International Nuclear Information System (INIS)
Ferraro, N.M.; Jardin, S.C.; Luo, X.
2010-01-01
The implementation of essential boundary conditions in C1 finite element analysis requires proper treatment of both the boundary conditions on second-order differentials of the solution and the curvature of the domain boundary. A method for the imposition of essential boundary conditions using straight elements (where the elements are not deformed to approximate a curved domain) is described. It is shown that pre-multiplication of the matrix equation by the local rotation matrix at each boundary node is not the optimal transformation. The uniquely optimal transformation is found, which does not take the form of a similarity transformation due to the non-orthogonality of the transformation to curved coordinates.
(Environmental and geophysical modeling, fracture mechanics, and boundary element methods)
Energy Technology Data Exchange (ETDEWEB)
Gray, L.J.
1990-11-09
Technical discussions at the various sites visited centered on application of boundary integral methods for environmental modeling, seismic analysis, and computational fracture mechanics in composite and smart'' materials. The traveler also attended the International Association for Boundary Element Methods Conference at Rome, Italy. While many aspects of boundary element theory and applications were discussed in the papers, the dominant topic was the analysis and application of hypersingular equations. This has been the focus of recent work by the author, and thus the conference was highly relevant to research at ORNL.
Microlocal methods in the analysis of the boundary element method
DEFF Research Database (Denmark)
Pedersen, Michael
1993-01-01
The application of the boundary element method in numerical analysis is based upon the use of boundary integral operators stemming from multiple layer potentials. The regularity properties of these operators are vital in the development of boundary integral equations and error estimates. We show...
Neitzel, H; Kalscheuer, V; Singh, A P; Henschel, S; Sperling, K
2002-01-01
Mobile elements are most abundant in the mammalian genome, comprising at least 40-50% of the DNA. They are differentiated into two most prominent families: the LINE elements, which are preferentially located in the G-bands, and SINES, which are clustered in the R-bands. We report here a novel mammalian non-L1-retroposon, which invaded the genome of Microtus agrestis in a very short time from an evolutionary viewpoint. No relevant sequence homology could be demonstrated to known sequences in the NCBI database. However, cross-hybridizing sequences exist in the genomes of all other Microtus species analyzed, but not in Mus musculus, indicating the recent evolutionary origin of this element. This retroposon is enriched in the entire heterochromatin of the X and Y chromosomes, but is also interspersed in autosomal locations in euchromatic portions of the genome. We show that the retroposon is heavily transcribed from the heterochromatin during female meiosis prerequisite for the subsequent retrotransposition. The estimated rate of retrotransposition is at least 1-2 x 10(-2) per generation, which is hundred-fold higher than that of the majority of invertebrate retroposons and also higher than the transposition rate of a murine L1 element, which was calculated to be 3 x 10(-3) per generation. Copyright 2002 S. Karger AG, Basel
Multidimensional phase change problems by the dual-reciprocity boundary-element method
International Nuclear Information System (INIS)
Jo, J.C.; Shin, W.K.; Choi, C.Y.
1999-01-01
Transient heat transfer problems with phase changes (Stefan problems) occur in many engineering situations, including potential core melting and solidification during pressurized-water-reactor severe accidents, ablation of thermal shields, melting and solidification of alloys, and many others. This article addresses the numerical analysis of nonlinear transient heat transfer with melting or solidification. An effective and simple procedure is presented for the simulation of the motion of the boundary and the transient temperature field during the phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual-reciprocity boundary-element method. The dual-reciprocity boundary-element approach provided in this article is much simpler than the usual boundary-element method in applying a reciprocity principle and an available technique for dealing with the domain integral of the boundary element formulation simultaneously. In this article, attention is focused on two-dimensional melting (ablation)/solidification problems for simplicity. The accuracy and effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of some examples of one-phase ablation/solidification problems with their known semianalytical or numerical solutions where available
Khoroshko, V A; Zykova, T Yu; Popova, O O; Zhimulev, I F
2018-03-01
The precise genomic localization of the borders of 62 intercalary heterochromatin bands in Drosophila polytene chromosomes was determined. A new type of bands containing chromatin of different states was identified. This type is a combination of the gray band and the intercalary heterochromatin band, creating a genetic structure that with a light microscope is identified as a continuous band. The border structure of such bands includes the coding regions of genes with ubiquitous activity.
Boundary element simulation of petroleum reservoirs with hydraulically fractured wells
Pecher, Radek
The boundary element method is applied to solve the linear pressure-diffusion equation of fluid-flow in porous media. The governing parabolic partial differential equation is transformed into the Laplace space to obtain the elliptic modified-Helmholtz equation including the homogeneous initial condition. The free- space Green's functions, satisfying this equation for anisotropic media in two and three dimensions, are combined with the generalized form of the Green's second identity. The resulting boundary integral equation is solved by following the collocation technique and applying the given time-dependent boundary conditions of the Dirichlet or Neumann type. The boundary integrals are approximated by the Gaussian quadrature along each element of the discretized domain boundary. Heterogeneous regions are represented by the sectionally-homogeneous zones of different rock and fluid properties. The final values of the interior pressure and velocity fields and of their time-derivatives are found by numerically inverting the solutions from the Laplace space by using the Stehfest's algorithm. The main extension of the mostly standard BEM-procedure is achieved in the modelling of the production and injection wells represented by internal sources and sinks. They are treated as part of the boundary by means of special single-node and both-sided elements, corresponding to the line and plane sources respectively. The wellbore skin and storage effects are considered for the line and cylindrical sources. Hydraulically fractured wells of infinite conductivity are handled directly according to the specified constraint type, out of the four alternatives. Fractures of finite conductivity are simulated by coupling the finite element model of their 1D-interior with the boundary element model of their 2D- exterior. Variable fracture width, fractures crossing zone boundaries, ``networking'' of fractures, fracture-tip singularity handling, or the 3D-description are additional advanced
Finite element analysis of three dimensional crack growth by the use of a boundary element sub model
DEFF Research Database (Denmark)
Lucht, Tore
2009-01-01
A new automated method to model non-planar three dimensional crack growth is proposed which combines the advantages of both the boundary element method and the finite element method. The proposed method links the two methods by a submodelling strategy in which the solution of a global finite...... element model containing an approximation of the crack is interpolated to a much smaller boundary element model containing a fine discretization of the real crack. The method is validated through several numerical comparisons and by comparison to crack growth measured in a test specimen for an engineering...
Simulation of galvanic corrosion using boundary element method
International Nuclear Information System (INIS)
Zaifol Samsu; Muhamad Daud; Siti Radiah Mohd Kamaruddin; Nur Ubaidah Saidin; Abdul Aziz Mohamed; Mohd Saari Ripin; Rusni Rejab; Mohd Shariff Sattar
2011-01-01
Boundary element method (BEM) is a numerical technique that used for modeling infinite domain as is the case for galvanic corrosion analysis. The use of boundary element analysis system (BEASY) has allowed cathodic protection (CP) interference to be assessed in terms of the normal current density, which is directly proportional to the corrosion rate. This paper was present the analysis of the galvanic corrosion between Aluminium and Carbon Steel in natural sea water. The result of experimental was validated with computer simulation like BEASY program. Finally, it can conclude that the BEASY software is a very helpful tool for future planning before installing any structure, where it gives the possible CP interference on any nearby unprotected metallic structure. (Author)
Rumex acetosa Y chromosomes: constitutive or facultative heterochromatin?
Mosiołek, Magdalena; Pasierbek, Paweł; Malarz, Janusz; Moś, Maria; Joachimiak, Andrzej J
2005-01-01
Condensed Y chromosomes in Rumex acetosa L. root-tip nuclei were studied using 5-azaC treatment and immunohistochemical detection of methylated histones. Although Y chromosomes were decondensed within root meristem in vivo, they became condensed and heteropycnotic in roots cultured in vitro. 5-azacytidine (5-azaC) treatment of cultured roots caused transitional dispersion of their Y chromosome bodies, but 7 days after removal of the drug from the culture medium, Y heterochromatin recondensed and again became visible. The response of Rumex sex chromatin to 5-azaC was compared with that of condensed segments of pericentromeric heterochromatin in Rhoeo spathacea (Sw.) Steam roots. It was shown that Rhoeo chromocentres, composed of AT-rich constitutive heterochromatin, did not undergo decondensation after 5-azaC treatment. The Y-bodies observed within male nuclei of R. acetosa were globally enriched with H3 histone, demethylated at lysine 4 and methylated at lysine 9. This is the first report of histone tail-modification in condensed sex chromatin in plants. Our results suggest that the interphase condensation of Y chromosomes in Rumex is facultative rather than constitutive. Furthermore, the observed response of Y-bodies to 5-azaC may result indirectly from demethylation and the subsequent altered expression of unknown genes controlling tissue-specific Y-inactivation as opposed to the global demethylation of Y-chromosome DNA.
Fu, Shulan; Lv, Zhenling; Guo, Xiang; Zhang, Xiangqi; Han, Fangpu
2013-08-20
Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres. Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-Imperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat-rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny of a monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA (TTTAGGG)n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives. Copyright © 2013. Published by Elsevier Ltd.
Zhang, Weiqi; Li, Jingyi; Suzuki, Keiichiro; Qu, Jing; Wang, Ping; Zhou, Junzhi; Liu, Xiaomeng; Ren, Ruotong; Xu, Xiuling; Ocampo, Alejandro; Yuan, Tingting; Yang, Jiping; Li, Ying; Shi, Liang; Guan, Dee; Pan, Huize; Duan, Shunlei; Ding, Zhichao; Li, Mo; Yi, Fei; Bai, Ruijun; Wang, Yayu; Chen, Chang; Yang, Fuquan; Li, Xiaoyu; Wang, Zimei; Aizawa, Emi; Goebl, April; Soligalla, Rupa Devi; Reddy, Pradeep; Esteban, Concepcion Rodriguez; Tang, Fuchou; Liu, Guang-Hui; Belmonte, Juan Carlos Izpisua
2015-06-05
Werner syndrome (WS) is a premature aging disorder caused by WRN protein deficiency. Here, we report on the generation of a human WS model in human embryonic stem cells (ESCs). Differentiation of WRN-null ESCs to mesenchymal stem cells (MSCs) recapitulates features of premature cellular aging, a global loss of H3K9me3, and changes in heterochromatin architecture. We show that WRN associates with heterochromatin proteins SUV39H1 and HP1α and nuclear lamina-heterochromatin anchoring protein LAP2β. Targeted knock-in of catalytically inactive SUV39H1 in wild-type MSCs recapitulates accelerated cellular senescence, resembling WRN-deficient MSCs. Moreover, decrease in WRN and heterochromatin marks are detected in MSCs from older individuals. Our observations uncover a role for WRN in maintaining heterochromatin stability and highlight heterochromatin disorganization as a potential determinant of human aging. Copyright © 2015, American Association for the Advancement of Science.
Boundary element method for internal axisymmetric flow
Directory of Open Access Journals (Sweden)
Gokhman Alexander
1999-01-01
Full Text Available We present an accurate fast method for the computation of potential internal axisymmetric flow based on the boundary element technique. We prove that the computed velocity field asymptotically satisfies reasonable boundary conditions at infinity for various types of inlet/exit. Computation of internal axisymmetric potential flow is an essential ingredient in the three-dimensional problem of computation of velocity fields in turbomachines. We include the results of a practical application of the method to the computation of flow in turbomachines of Kaplan and Francis types.
RNAi and heterochromatin repress centromeric meiotic recombination
DEFF Research Database (Denmark)
Ellermeier, Chad; Higuchi, Emily C; Phadnis, Naina
2010-01-01
During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes, is essen......During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes....... Surprisingly, one mutant derepressed for recombination in the heterochromatic mating-type region during meiosis and several mutants derepressed for centromeric gene expression during mitotic growth are not derepressed for centromeric recombination during meiosis. These results reveal a complex relation between...... types of repression by heterochromatin. Our results also reveal a previously undemonstrated role for RNAi and heterochromatin in the repression of meiotic centromeric recombination and, potentially, in the prevention of birth defects by maintenance of proper chromosome segregation during meiosis....
Fast multipole acceleration of the MEG/EEG boundary element method
International Nuclear Information System (INIS)
Kybic, Jan; Clerc, Maureen; Faugeras, Olivier; Keriven, Renaud; Papadopoulo, Theo
2005-01-01
The accurate solution of the forward electrostatic problem is an essential first step before solving the inverse problem of magneto- and electroencephalography (MEG/EEG). The symmetric Galerkin boundary element method is accurate but cannot be used for very large problems because of its computational complexity and memory requirements. We describe a fast multipole-based acceleration for the symmetric boundary element method (BEM). It creates a hierarchical structure of the elements and approximates far interactions using spherical harmonics expansions. The accelerated method is shown to be as accurate as the direct method, yet for large problems it is both faster and more economical in terms of memory consumption
Casas-Delucchi, Corella S; van Bemmel, Joke G; Haase, Sebastian; Herce, Henry D; Nowak, Danny; Meilinger, Daniela; Stear, Jeffrey H; Leonhardt, Heinrich; Cardoso, M Cristina
2012-01-01
The replication of the genome is a spatio-temporally highly organized process. Yet, its flexibility throughout development suggests that this process is not genetically regulated. However, the mechanisms and chromatin modifications controlling replication timing are still unclear. We made use of the prominent structure and defined heterochromatic landscape of pericentric regions as an example of late replicating constitutive heterochromatin. We manipulated the major chromatin markers of these regions, namely histone acetylation, DNA and histone methylation, as well as chromatin condensation and determined the effects of these altered chromatin states on replication timing. Here, we show that manipulation of DNA and histone methylation as well as acetylation levels caused large-scale heterochromatin decondensation. Histone demethylation and the concomitant decondensation, however, did not affect replication timing. In contrast, immuno-FISH and time-lapse analyses showed that lowering DNA methylation, as well as increasing histone acetylation, advanced the onset of heterochromatin replication. While dnmt1(-)(/)(-) cells showed increased histone acetylation at chromocenters, histone hyperacetylation did not induce DNA demethylation. Hence, we propose that histone hypoacetylation is required to maintain normal heterochromatin duplication dynamics. We speculate that a high histone acetylation level might increase the firing efficiency of origins and, concomitantly, advances the replication timing of distinct genomic regions.
Directory of Open Access Journals (Sweden)
Miguel Casanova
2013-09-01
Full Text Available The equalization of pericentric heterochromatin from distinct parental origins following fertilization is essential for genome function and development. The recent implication of noncoding transcripts in this process raises questions regarding the connection between RNA and the nuclear organization of distinct chromatin environments. Our study addresses the interrelationship between replication and transcription of the two parental pericentric heterochromatin (PHC domains and their reorganization during early embryonic development. We demonstrate that the replication of PHC is dispensable for its clustering at the late two-cell stage. In contrast, using parthenogenetic embryos, we show that pericentric transcripts are essential for this reorganization independent of the chromatin marks associated with the PHC domains. Finally, our discovery that only reverse pericentric transcripts are required for both the nuclear reorganization of PHC and development beyond the two-cell stage challenges current views on heterochromatin organization.
International Nuclear Information System (INIS)
Choi, C. Y.
1997-01-01
A geometrical inverse heat conduction problem is solved for the infrared scanning cavity detection by the boundary element method using minimal energy technique. By minimizing the kinetic energy of temperature field, boundary element equations are converted to the quadratic programming problem. A hypothetical inner boundary is defined such that the actual cavity is located interior to the domain. Temperatures at hypothetical inner boundary are determined to meet the constraints of measurement error of surface temperature obtained by infrared scanning, and then boundary element analysis is performed for the position of an unknown boundary (cavity). Cavity detection algorithm is provided, and the effects of minimal energy technique on the inverse solution method are investigated by means of numerical analysis
Rumex acetosa Y chromosomes: constitutive or facultative heterochromatin?
Directory of Open Access Journals (Sweden)
Andrzej J. Joachimiak
2011-08-01
Full Text Available Condensed Y chromosomes in Rumex acetosa L. root-tip nuclei were studied using 5-azaC treatment and immunohistochemical detection of methylated histones. Although Y chromosomes were decondensed within root meristem in vivo, they became condensed and heteropycnotic in roots cultured in vitro. 5-azacytidine (5-azaC treatment of cultured roots caused transitional dispersion of their Y chromosome bodies, but 7 days after removal of the drug from the culture medium, Y heterochromatin recondensed and again became visible. The response of Rumex sex chromatin to 5-azaC was compared with that of condensed segments of pericentromeric heterochromatin in Rhoeo spathacea (Sw. Stearn roots. It was shown that Rhoeo chromocentres, composed of AT-rich constitutive heterochromatin, did not undergo decondensation after 5-azaC treatment. The Y-bodies observed within male nuclei of R. acetosa were globally enriched with H3 histone, demethylated at lysine 4 and methylated at lysine 9. This is the first report of histone tail-modification in condensed sex chromatin in plants. Our results suggest that the interphase condensation of Y chromosomes in Rumex is facultative rather than constitutive. Furthermore, the observed response of Y-bodies to 5-azaC may result indirectly from demethylation and the subsequent altered expression of unknown genes controlling tissue-specific Y-inactivation as opposed to the global demethylation of Y-chromosome DNA.
9th International Conference on Boundary Elements
Wendland, W; Kuhn, G
1987-01-01
This book contains the edited versions of most of the papers presented at the 9th International Conference on Boundary Elements held at the University of Stuttgart, Germany from August 31st to September 4th, 1987, which was organized in co-operation with the Computational Mechanics Institute and GAMM (Society for Applied Mathematics and Mechanics). This Conference, as the previous ones, aimed to review the latest developments in technique and theory and point out new advanced future trends. The emphasis of the meeting was on the engineering advances versus mathematical formulations, in an effort to consolidate the basis of many new applications. Recently engineers have proposed different techniques to solve non-linear and time dependent problems and many of these formulations needed a better mathematical understanding. Furthermore, new approximate formulations have been proposed for boundary elements which appeared to work in engineering practice, but did not have a proper theoretical background. The Conferen...
Green's function and boundary elements of multifield materials
Qin, Qing-Hua
2007-01-01
Green's Function and Boundary Elements of Multifield Materials contains a comprehensive treatment of multifield materials under coupled thermal, magnetic, electric, and mechanical loads. Its easy-to-understand text clarifies some of the most advanced techniques for deriving Green's function and the related boundary element formulation of magnetoelectroelastic materials: Radon transform, potential function approach, Fourier transform. Our hope in preparing this book is to attract interested readers and researchers to a new field that continues to provide fascinating and technologically important challenges. You will benefit from the authors' thorough coverage of general principles for each topic, followed by detailed mathematical derivation and worked examples as well as tables and figures where appropriate. In-depth explanations of the concept of Green's function Coupled thermo-magneto-electro-elastic analysis Detailed mathematical derivation for Green's functions.
Parallel Fast Multipole Boundary Element Method for crustal dynamics
International Nuclear Information System (INIS)
Quevedo, Leonardo; Morra, Gabriele; Mueller, R Dietmar
2010-01-01
Crustal faults and sharp material transitions in the crust are usually represented as triangulated surfaces in structural geological models. The complex range of volumes separating such surfaces is typically three-dimensionally meshed in order to solve equations that describe crustal deformation with the finite-difference (FD) or finite-element (FEM) methods. We show here how the Boundary Element Method, combined with the Multipole approach, can revolutionise the calculation of stress and strain, solving the problem of computational scalability from reservoir to basin scales. The Fast Multipole Boundary Element Method (Fast BEM) tackles the difficulty of handling the intricate volume meshes and high resolution of crustal data that has put classical Finite 3D approaches in a performance crisis. The two main performance enhancements of this method: the reduction of required mesh elements from cubic to quadratic with linear size and linear-logarithmic runtime; achieve a reduction of memory and runtime requirements allowing the treatment of a new scale of geodynamic models. This approach was recently tested and applied in a series of papers by [1, 2, 3] for regional and global geodynamics, using KD trees for fast identification of near and far-field interacting elements, and MPI parallelised code on distributed memory architectures, and is now in active development for crustal dynamics. As the method is based on a free-surface, it allows easy data transfer to geological visualisation tools where only changes in boundaries and material properties are required as input parameters. In addition, easy volume mesh sampling of physical quantities enables direct integration with existing FD/FEM code.
International Nuclear Information System (INIS)
Jo, Jong Chull; Shin, Won Ky
1997-01-01
This paper presents an effective and simple procedure for the simulation of the motion of the solid-liquid interfacial boundary and the transient temperature field during phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual reciprocity boundary element method. The dual reciprocity boundary element approach provided in this paper is much simpler than the usual boundary element method applying a reciprocity principle and an available technique for dealing with domain integral of boundary element formulation simultaneously. The effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of an example with its semi-analytical or other numerical solutions where available
Introducing the Boundary Element Method with MATLAB
Ang, Keng-Cheng
2008-01-01
The boundary element method provides an excellent platform for learning and teaching a computational method for solving problems in physical and engineering science. However, it is often left out in many undergraduate courses as its implementation is deemed to be difficult. This is partly due to the perception that coding the method requires…
International Nuclear Information System (INIS)
Pereira, Luis Carlos Martins
1998-06-01
New Petrov-Galerkin formulations on the finite element methods for convection-diffusion problems with boundary layers are presented. Such formulations are based on a consistent new theory on discontinuous finite element methods. Existence and uniqueness of solutions for these problems in the new finite element spaces are demonstrated. Some numerical experiments shows how the new formulation operate and also their efficacy. (author)
Energy Technology Data Exchange (ETDEWEB)
Jo, Jong Chull; Shin, Won Ky [Korea Institute of Nuclear Safety, Taejon (Korea, Republic of)
1998-12-31
This paper presents an effective and simple procedure for the simulation of the motion of the solid-liquid interfacial boundary and the transient temperature field during phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual reciprocity boundary element method. The dual reciprocity boundary element approach provided in this paper is much simpler than the usual boundary element method applying a reciprocity principle and an available technique for dealing with domain integral of boundary element formulation simultaneously. The effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of an example with its semi-analytical or other numerical solutions where available. 22 refs., 3 figs. (Author)
Energy Technology Data Exchange (ETDEWEB)
Jo, Jong Chull; Shin, Won Ky [Korea Institute of Nuclear Safety, Taejon (Korea, Republic of)
1997-12-31
This paper presents an effective and simple procedure for the simulation of the motion of the solid-liquid interfacial boundary and the transient temperature field during phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual reciprocity boundary element method. The dual reciprocity boundary element approach provided in this paper is much simpler than the usual boundary element method applying a reciprocity principle and an available technique for dealing with domain integral of boundary element formulation simultaneously. The effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of an example with its semi-analytical or other numerical solutions where available. 22 refs., 3 figs. (Author)
Temperature and stress distribution in pressure vessel by the boundary element method
International Nuclear Information System (INIS)
Alujevic, A.; Apostolovic, D.
1990-01-01
The aim of this paper is to demonstrate the applicability of boundary element method for the solution of temperatures and thermal stresses in the body of reactor pressure vessel of the NPP Krsko . In addition to the theory of boundary elements for thermo-elastic continua (2D, 3D) results are given of a numerically evaluated meridional cross-section. (author)
Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1.
Taiko Kim To; Jong-Myong Kim; Akihiro Matsui; Yukio Kurihara; Taeko Morosawa; Junko Ishida; Maho Tanaka; Takaho Endo; Tetsuji Kakutani; Tetsuro Toyoda; Hiroshi Kimura; Shigeyuki Yokoyama; Kazuo Shinozaki; Motoaki Seki
2011-01-01
Heterochromatin silencing is pivotal for genome stability in eukaryotes. In Arabidopsis, a plant-specific mechanism called RNA–directed DNA methylation (RdDM) is involved in heterochromatin silencing. Histone deacetylase HDA6 has been identified as a component of such machineries; however, its endogenous targets and the silencing mechanisms have not been analyzed globally. In this study, we investigated the silencing mechanism mediated by HDA6. Genome-wide transcript profiling revealed that t...
Nuclear Architecture of Mouse Spermatocytes: Chromosome Topology, Heterochromatin, and Nucleolus.
Berrios, Soledad
2017-01-01
The nuclear organization of spermatocytes in meiotic prophase I is primarily determined by the synaptic organization of the bivalents that are bound by their telomeres to the nuclear envelope and described as arc-shaped trajectories through the 3D nuclear space. However, over this basic meiotic organization, a spermatocyte nuclear architecture arises that is based on higher-ordered patterns of spatial associations among chromosomal domains from different bivalents that are conditioned by the individual characteristics of chromosomes and the opportunity for interactions between their domains. Consequently, the nuclear architecture is species-specific and prone to modification by chromosomal rearrangements. This model is valid for the localization of any chromosomal domain in the meiotic prophase nucleus. However, constitutive heterochromatin plays a leading role in shaping nuclear territories. Thus, the nuclear localization of nucleoli depends on the position of NORs in nucleolar bivalents, but the association among nucleolar chromosomes mainly depends on the presence of constitutive heterochromatin that does not affect the expression of the ribosomal genes. Constitutive heterochromatin and nucleoli form complex nuclear territories whose distribution in the nuclear space is nonrandom, supporting the hypothesis regarding the existence of a species-specific nuclear architecture in first meiotic prophase spermatocytes. © 2017 S. Karger AG, Basel.
DEFF Research Database (Denmark)
Cutanda Henríquez, Vicente; Juhl, Peter Møller
2008-01-01
It is well known that the Boundary Element Method (BEM) in its standard version cannot readily handle situations where the calculation point is very close to a surface. These problems are found: i) when two boundary surfaces are very close together, such as in narrow gaps and thin bodies, and ii)...
E-coil: an inverse boundary element method for a quasi-static problem
International Nuclear Information System (INIS)
Sanchez, Clemente Cobos; Garcia, Salvador Gonzalez; Power, Henry
2010-01-01
Boundary element methods represent a valuable approach for designing gradient coils; these methods are based on meshing the current carrying surface into an array of boundary elements. The temporally varying magnetic fields produced by gradient coils induce electric currents in conducting tissues and so the exposure of human subjects to these magnetic fields has become a safety concern, especially with the increase in the strength of the field gradients used in magnetic resonance imaging. Here we present a boundary element method for the design of coils that minimize the electric field induced in prescribed conducting systems. This work also details some numerical examples of the application of this coil design method. The reduction of the electric field induced in a prescribed region inside the coils is also evaluated.
E-coil: an inverse boundary element method for a quasi-static problem
Energy Technology Data Exchange (ETDEWEB)
Sanchez, Clemente Cobos; Garcia, Salvador Gonzalez [Depto. Electromagnetismo y F. de la Materia Facultad de Ciencias University of Granada Avda. Fuentenueva E-18071 (Spain); Power, Henry, E-mail: ccobos@ugr.e [School of Mechanical, Materials and Manufacturing Engineering, The University of Nottingham, Nottingham Park, Nottingham NG7 2RD (United Kingdom)
2010-06-07
Boundary element methods represent a valuable approach for designing gradient coils; these methods are based on meshing the current carrying surface into an array of boundary elements. The temporally varying magnetic fields produced by gradient coils induce electric currents in conducting tissues and so the exposure of human subjects to these magnetic fields has become a safety concern, especially with the increase in the strength of the field gradients used in magnetic resonance imaging. Here we present a boundary element method for the design of coils that minimize the electric field induced in prescribed conducting systems. This work also details some numerical examples of the application of this coil design method. The reduction of the electric field induced in a prescribed region inside the coils is also evaluated.
Directory of Open Access Journals (Sweden)
2005-07-01
Full Text Available Heterochromatin comprises a significant component of many eukaryotic genomes. In comparison to euchromatin, heterochromatin is gene poor, transposon rich, and late replicating. It serves many important biological roles, from gene silencing to accurate chromosome segregation, yet little is known about the evolutionary constraints that shape heterochromatin. A complementary approach to the traditional one of directly studying heterochromatic DNA sequence is to study the evolution of proteins that bind and define heterochromatin. One of the best markers for heterochromatin is the heterochromatin protein 1 (HP1, which is an essential, nonhistone chromosomal protein. Here we investigate the molecular evolution of five HP1 paralogs present in Drosophila melanogaster. Three of these paralogs have ubiquitous expression patterns in adult Drosophila tissues, whereas HP1D/rhino and HP1E are expressed predominantly in ovaries and testes respectively. The HP1 paralogs also have distinct localization preferences in Drosophila cells. Thus, Rhino localizes to the heterochromatic compartment in Drosophila tissue culture cells, but in a pattern distinct from HP1A and lysine-9 dimethylated H3. Using molecular evolution and population genetic analyses, we find that rhino has been subject to positive selection in all three domains of the protein: the N-terminal chromo domain, the C-terminal chromo-shadow domain, and the hinge region that connects these two modules. Maximum likelihood analysis of rhino sequences from 20 species of Drosophila reveals that a small number of residues of the chromo and shadow domains have been subject to repeated positive selection. The rapid and positive selection of rhino is highly unusual for a gene encoding a chromosomal protein and suggests that rhino is involved in a genetic conflict that affects the germline, belying the notion that heterochromatin is simply a passive recipient of "junk DNA" in eukaryotic genomes.
Directory of Open Access Journals (Sweden)
Danielle Vermaak
2005-07-01
Full Text Available Heterochromatin comprises a significant component of many eukaryotic genomes. In comparison to euchromatin, heterochromatin is gene poor, transposon rich, and late replicating. It serves many important biological roles, from gene silencing to accurate chromosome segregation, yet little is known about the evolutionary constraints that shape heterochromatin. A complementary approach to the traditional one of directly studying heterochromatic DNA sequence is to study the evolution of proteins that bind and define heterochromatin. One of the best markers for heterochromatin is the heterochromatin protein 1 (HP1, which is an essential, nonhistone chromosomal protein. Here we investigate the molecular evolution of five HP1 paralogs present in Drosophila melanogaster. Three of these paralogs have ubiquitous expression patterns in adult Drosophila tissues, whereas HP1D/rhino and HP1E are expressed predominantly in ovaries and testes respectively. The HP1 paralogs also have distinct localization preferences in Drosophila cells. Thus, Rhino localizes to the heterochromatic compartment in Drosophila tissue culture cells, but in a pattern distinct from HP1A and lysine-9 dimethylated H3. Using molecular evolution and population genetic analyses, we find that rhino has been subject to positive selection in all three domains of the protein: the N-terminal chromo domain, the C-terminal chromo-shadow domain, and the hinge region that connects these two modules. Maximum likelihood analysis of rhino sequences from 20 species of Drosophila reveals that a small number of residues of the chromo and shadow domains have been subject to repeated positive selection. The rapid and positive selection of rhino is highly unusual for a gene encoding a chromosomal protein and suggests that rhino is involved in a genetic conflict that affects the germline, belying the notion that heterochromatin is simply a passive recipient of "junk DNA" in eukaryotic genomes.
Inverse boundary element calculations based on structural modes
DEFF Research Database (Denmark)
Juhl, Peter Møller
2007-01-01
The inverse problem of calculating the flexural velocity of a radiating structure of a general shape from measurements in the field is often solved by combining a Boundary Element Method with the Singular Value Decomposition and a regularization technique. In their standard form these methods sol...
Boundary element analysis of earthquake induced hydrodynamic pressures in a water reservoir
International Nuclear Information System (INIS)
Jablonski, A.M.
1988-11-01
The seismic analysis of concrete gravity and arch dams is affected by the hydrodynamic pressures in the water reservoir. Boundary element method (BEM) formulations are derived for the hydrodynamic pressures arising in a gravity dam-reservoir-foundation system, treating both 2- and 3-dimensional cases. The formulations are based on the respective mathematical models which are governed by two- and three-dimensional Helmholtz equations with appropriate boundary conditions. For infinite reservoirs, loss of energy due to pressure waves moving away toward infinity strongly influence response. Since it is not possible to discretize an infinite extent, the radiation damping due to outgoing waves is accounted for by incorporating special boundary conditions at the far end, and in a similar manner the loss of energy due to absorption of waves by a flexible bottom of reservoir and banks can be accounted for by a special condition along the boundaries. Numerical results are obtained and compared with available classical solutions and convergence of numerical results with the size and number of boundary elements is studied. It is concluded that the direct boundary element method is an effective tool for the evaluation of the hydrodynamic pressures in finite and infinite dam-reservoir-foundation systems subjected to harmonic-type motion, and can easily be extended to any type of random motion with fast Fourier transform techniques. 82 refs., 65 figs., 25 tabs
Near shore seismic movements induced by seaquakes using the boundary element method
Institute of Scientific and Technical Information of China (English)
Manuel Carbajal-Romero; Norberto Flores-Guzmán; J.Efraín Rodríguez-Sánchez; Andriy Kryvko
2017-01-01
This study quantifies seismic amplifications in near-shore arising from seaquakes.Within the Boundary Element Method,boundary elements are used to irradiate waves and force densities obtained for each element.Huygens Principle is implemented since the diffracted waves are constructed at the boundary from which they are radiated,which is equivalent to Somigliana's theorem.Application of boundary conditions leads to a system of integral equations of the Fredholm type of second kind and zero order.Several numerical configurations are analyzed:The first is used to verify the present formulation with ideal sea floor configurations to estimate seismic amplifications.With the formulation verified,simple slope configurations are studied to estimate spectra of seismic motions.It is found that P-waves can produce seismic amplifications from 1.2 to 3.9 times the amplitude of the incident wave.SV-waves can generate seismic amplifications up to 4.5 times the incident wave.Another relevant finding is that the highest amplifications are at the shore compared to the ones at the sea floor.
He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric
2012-01-01
Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding seque...
Drugs affecting prelamin A processing: Effects on heterochromatin organization
International Nuclear Information System (INIS)
Mattioli, Elisabetta; Columbaro, Marta; Capanni, Cristina; Santi, Spartaco; Maraldi, Nadir M.; D'Apice, M. Rosaria; Novelli, Giuseppe; Riccio, Massimo; Squarzoni, Stefano; Foisner, Roland; Lattanzi, Giovanna
2008-01-01
Increasing interest in drugs acting on prelamin A has derived from the finding of prelamin A involvement in severe laminopathies. Amelioration of the nuclear morphology by inhibitors of prelamin A farnesylation has been widely reported in progeroid laminopathies. We investigated the effects on chromatin organization of two drugs inhibiting prelamin A processing by an ultrastructural and biochemical approach. The farnesyltransferase inhibitor FTI-277 and the non-peptidomimetic drug N-acetyl-S-farnesyl-L-cysteine methylester (AFCMe) were administered to cultured control human fibroblasts for 6 or 18 h. FTI-277 interferes with protein farnesylation causing accumulation of non-farnesylated prelamin A, while AFCMe impairs the last cleavage of the lamin A precursor and is expected to accumulate farnesylated prelamin A. FTI-277 caused redistribution of heterochromatin domains at the nuclear interior, while AFCMe caused loss of heterochromatin domains, increase of nuclear size and nuclear lamina thickening. At the biochemical level, heterochromatin-associated proteins and LAP2α were clustered at the nuclear interior following FTI-277 treatment, while they were unevenly distributed or absent in AFCMe-treated nuclei. The reported effects show that chromatin is an immediate target of FTI-277 and AFCMe and that dramatic remodeling of chromatin domains occurs following treatment with the drugs. These effects appear to depend, at least in part, on the accumulation of prelamin A forms, since impairment of prelamin A accumulation, here obtained by 5-azadeoxycytidine treatment, abolishes the chromatin effects. These results may be used to evaluate downstream effects of FTIs or other prelamin A inhibitors potentially useful for the therapy of laminopathies
Directory of Open Access Journals (Sweden)
E. Majchrzak
2008-12-01
Full Text Available The dual reciprocity boundary element method is applied for numerical modelling of solidification process. This variant of the BEM is connected with the transformation of the domain integral to the boundary integrals. In the paper the details of the dual reciprocity boundary element method are presented and the usefulness of this approach to solidification process modelling is demonstrated. In the final part of the paper the examples of computations are shown.
International Nuclear Information System (INIS)
Young, G.A. Jr.; Najafabadi, R.; Strohmayer, W.; Baldrey, D.G.; Hamm, B.; Harris, J.; Sticht, J.; Wimmer, E.
2003-01-01
Atomistic modeling methods were employed to investigate the effects of impurity elements on the metallurgy, irradiation embrittlement, and environmentally assisted cracking of nickel-base alloys exposed to nuclear environments. Calculations were performed via ab initio atomistic modeling methods to ensure the accuracy and reliability of the results. A Griffith-type fracture criterion was used to quantitatively assess the effect of elements or element pairs on the grain boundary cohesive strength. In order of most embrittling to most strengthening, the elements are ranked as: He, Li, S, H, C, Zr, P, Fe, Mn, Nb, Cr, and B. Helium is strongly embrittling (-2.04 eV/atom lowering of the Griffith energy), phosphorus has little effect on the grain boundary (0.1 eV/atom), and boron offers appreciable strengthening (1.03 eV/atom increase in the Griffith energy). Calculations for pairs of elements (H-Li, H-B, H-C, H-P, and H-S) show little interaction on the grain boundary cohesive energy, so that for the conditions studied, linear superposition of elemental effects is a good approximation. These calculations help explain metallurgical effects (e.g. why boron can strengthen grain boundaries), irradiation embrittlement (e.g. how boron transmutation results in grain boundary embrittlement), as well as how grain boundary impurity elements can affect environmentally assisted cracking (i.e. low temperature crack propagation and stress corrosion cracking) of nickel-base alloys
Boundary element methods for electrical engineers
POLJAK, D
2005-01-01
In the last couple of decades the Boundary Element Method (BEM) has become a well-established technique that is widely used for solving various problems in electrical engineering and electromagnetics. Although there are many excellent research papers published in the relevant literature that describe various BEM applications in electrical engineering and electromagnetics, there has been a lack of suitable textbooks and monographs on the subject. This book presents BEM in a simple fashion in order to help the beginner to understand the very basic principles of the method. It initially derives B
Wake Instabilities Behind Discrete Roughness Elements in High Speed Boundary Layers
Choudhari, Meelan; Li, Fei; Chang, Chau-Lyan; Norris, Andrew; Edwards, Jack
2013-01-01
Computations are performed to study the flow past an isolated, spanwise symmetric roughness element in zero pressure gradient boundary layers at Mach 3.5 and 5.9, with an emphasis on roughness heights of less than 55 percent of the local boundary layer thickness. The Mach 5.9 cases include flow conditions that are relevant to both ground facility experiments and high altitude flight ("cold wall" case). Regardless of the Mach number, the mean flow distortion due to the roughness element is characterized by long-lived streamwise streaks in the roughness wake, which can support instability modes that did not exist in the absence of the roughness element. The higher Mach number cases reveal a variety of instability mode shapes with velocity fluctuations concentrated in different localized regions of high base flow shear. The high shear regions vary from the top of a mushroom shaped structure characterizing the centerline streak to regions that are concentrated on the sides of the mushroom. Unlike the Mach 3.5 case with nearly same values of scaled roughness height k/delta and roughness height Reynolds number Re(sub kk), the odd wake modes in both Mach 5.9 cases are significantly more unstable than the even modes of instability. Additional computations for a Mach 3.5 boundary layer indicate that the presence of a roughness element can also enhance the amplification of first mode instabilities incident from upstream. Interactions between multiple roughness elements aligned along the flow direction are also explored.
Fundamental solutions and dual boundary element methods for fracture in plane Cosserat elasticity.
Atroshchenko, Elena; Bordas, Stéphane P A
2015-07-08
In this paper, both singular and hypersingular fundamental solutions of plane Cosserat elasticity are derived and given in a ready-to-use form. The hypersingular fundamental solutions allow to formulate the analogue of Somigliana stress identity, which can be used to obtain the stress and couple-stress fields inside the domain from the boundary values of the displacements, microrotation and stress and couple-stress tractions. Using these newly derived fundamental solutions, the boundary integral equations of both types are formulated and solved by the boundary element method. Simultaneous use of both types of equations (approach known as the dual boundary element method (BEM)) allows problems where parts of the boundary are overlapping, such as crack problems, to be treated and to do this for general geometry and loading conditions. The high accuracy of the boundary element method for both types of equations is demonstrated for a number of benchmark problems, including a Griffith crack problem and a plate with an edge crack. The detailed comparison of the BEM results and the analytical solution for a Griffith crack and an edge crack is given, particularly in terms of stress and couple-stress intensity factors, as well as the crack opening displacements and microrotations on the crack faces and the angular distributions of stresses and couple-stresses around the crack tip.
Electrostatic field in inhomogeneous dielectric media. I. Indirect boundary element method
International Nuclear Information System (INIS)
Goel, N.S.; Gang, F.; Ko, Z.
1995-01-01
A computationally fast method is presented for calculating electrostatic field in arbitrary inhomogeneous dielectric media with open boundary condition. The method involves dividing the whole space into cubical cells and then finding effective dielectric parameters for interfacial cells consisting of several dielectrics. The electrostatic problem is then solved using either the indirect boundary element method described in this paper or the so-called volume element method described in the companion paper. Both methods are tested for accuracy by comparing the numerically calculated electrostatic fields against those analytically obtained for a dielectric sphere and dielectric ellipsoid in a uniform field and for a dielectric sphere in a point charge field
Agarwal, Noopur; Hardt, Tanja; Brero, Alessandro; Nowak, Danny; Rothbauer, Ulrich; Becker, Annette; Leonhardt, Heinrich; Cardoso, M. Cristina
2007-01-01
There is increasing evidence of crosstalk between epigenetic modifications such as histone and DNA methylation, recognized by HP1 and methyl CpG-binding proteins, respectively. We have previously shown that the level of methyl CpG-binding proteins increased dramatically during myogenesis leading to large-scale heterochromatin reorganization. In this work, we show that the level of HP1 isoforms did not change significantly throughout myogenic differentiation but their localization did. In particular, HP1γ relocalization to heterochromatin correlated with MeCP2 presence. Using co-immunoprecipitation assays, we found that these heterochromatic factors interact in vivo via the chromo shadow domain of HP1 and the first 55 amino acids of MeCP2. We propose that this dynamic interaction of HP1 and MeCP2 increases their concentration at heterochromatin linking two major gene silencing pathways to stabilize transcriptional repression during differentiation. PMID:17698499
Boundary element methods applied to two-dimensional neutron diffusion problems
International Nuclear Information System (INIS)
Itagaki, Masafumi
1985-01-01
The Boundary element method (BEM) has been applied to two-dimensional neutron diffusion problems. The boundary integral equation and its discretized form have been derived. Some numerical techniques have been developed, which can be applied to critical and fixed-source problems including multi-region ones. Two types of test programs have been developed according to whether the 'zero-determinant search' or the 'source iteration' technique is adopted for criticality search. Both programs require only the fluxes and currents on boundaries as the unknown variables. The former allows a reduction in computing time and memory in comparison with the finite element method (FEM). The latter is not always efficient in terms of computing time due to the domain integral related to the inhomogeneous source term; however, this domain integral can be replaced by the equivalent boundary integral for a region with a non-multiplying medium or with a uniform source, resulting in a significant reduction in computing time. The BEM, as well as the FEM, is well suited for solving irregular geometrical problems for which the finite difference method (FDM) is unsuited. The BEM also solves problems with infinite domains, which cannot be solved by the ordinary FEM and FDM. Some simple test calculations are made to compare the BEM with the FEM and FDM, and discussions are made concerning the relative merits of the BEM and problems requiring future solution. (author)
An introductory study of the convergence of the direct boundary element method
DEFF Research Database (Denmark)
Juhl, Peter Møller
1997-01-01
of an axisymmetric boundary element formulation is studied using linear, quadratic or superparametric elements. It is demonstrated that the rate of convergence of these formulations is reduced for calculations involving bodies with edges (geometric singularities). Two methods for improving the rate of convergence...
National Research Council Canada - National Science Library
Eren, Hakan
2000-01-01
.... The objective of this study is, by using Boundary Element Method, to examine different shapes of reinforcement elements under unit traction and unit displacement boundary conditions in transversal...
Directory of Open Access Journals (Sweden)
Igumnov Leonid
2015-01-01
Full Text Available The report presents the development of the time-boundary element methodology and a description of the related software based on a stepped method of numerical inversion of the integral Laplace transform in combination with a family of Runge-Kutta methods for analyzing 3-D mixed initial boundary-value problems of the dynamics of inhomogeneous elastic and poro-elastic bodies. The results of the numerical investigation are presented. The investigation methodology is based on direct-approach boundary integral equations of 3-D isotropic linear theories of elasticity and poroelasticity in Laplace transforms. Poroelastic media are described using Biot models with four and five base functions. With the help of the boundary-element method, solutions in time are obtained, using the stepped method of numerically inverting Laplace transform on the nodes of Runge-Kutta methods. The boundary-element method is used in combination with the collocation method, local element-by-element approximation based on the matched interpolation model. The results of analyzing wave problems of the effect of a non-stationary force on elastic and poroelastic finite bodies, a poroelastic half-space (also with a fictitious boundary and a layered half-space weakened by a cavity, and a half-space with a trench are presented. Excitation of a slow wave in a poroelastic medium is studied, using the stepped BEM-scheme on the nodes of Runge-Kutta methods.
The boundary element method : errors and gridding for problems with hot spots
Kakuba, G.
2011-01-01
Adaptive gridding methods are of fundamental importance both for industry and academia. As one of the computing methods, the Boundary Element Method (BEM) is used to simulate problems whose fundamental solutions are available. The method is usually characterised as constant elements BEM or linear
International Nuclear Information System (INIS)
Koteras, J.R.
1996-01-01
The prediction of stresses and displacements around tunnels buried deep within the earth is an important class of geomechanics problems. The material behavior immediately surrounding the tunnel is typically nonlinear. The surrounding mass, even if it is nonlinear, can usually be characterized by a simple linear elastic model. The finite element method is best suited for modeling nonlinear materials of limited volume, while the boundary element method is well suited for modeling large volumes of linear elastic material. A computational scheme that couples the finite element and boundary element methods would seem particularly useful for geomechanics problems. A variety of coupling schemes have been proposed, but they rely on direct solution methods. Direct solution techniques have large storage requirements that become cumbersome for large-scale three-dimensional problems. An alternative to direct solution methods is iterative solution techniques. A scheme has been developed for coupling the finite element and boundary element methods that uses an iterative solution method. This report shows that this coupling scheme is valid for problems where nonlinear material behavior occurs in the finite element region
The boundary element method applied to 3D magneto-electro-elastic dynamic problems
Igumnov, L. A.; Markov, I. P.; Kuznetsov, Iu A.
2017-11-01
Due to the coupling properties, the magneto-electro-elastic materials possess a wide number of applications. They exhibit general anisotropic behaviour. Three-dimensional transient analyses of magneto-electro-elastic solids can hardly be found in the literature. 3D direct boundary element formulation based on the weakly-singular boundary integral equations in Laplace domain is presented in this work for solving dynamic linear magneto-electro-elastic problems. Integral expressions of the three-dimensional fundamental solutions are employed. Spatial discretization is based on a collocation method with mixed boundary elements. Convolution quadrature method is used as a numerical inverse Laplace transform scheme to obtain time domain solutions. Numerical examples are provided to illustrate the capability of the proposed approach to treat highly dynamic problems.
Rahimi Dalkhani, Amin; Javaherian, Abdolrahim; Mahdavi Basir, Hadi
2018-04-01
Wave propagation modeling as a vital tool in seismology can be done via several different numerical methods among them are finite-difference, finite-element, and spectral-element methods (FDM, FEM and SEM). Some advanced applications in seismic exploration benefit the frequency domain modeling. Regarding flexibility in complex geological models and dealing with the free surface boundary condition, we studied the frequency domain acoustic wave equation using FEM and SEM. The results demonstrated that the frequency domain FEM and SEM have a good accuracy and numerical efficiency with the second order interpolation polynomials. Furthermore, we developed the second order Clayton and Engquist absorbing boundary condition (CE-ABC2) and compared it with the perfectly matched layer (PML) for the frequency domain FEM and SEM. In spite of PML method, CE-ABC2 does not add any additional computational cost to the modeling except assembling boundary matrices. As a result, considering CE-ABC2 is more efficient than PML for the frequency domain acoustic wave propagation modeling especially when computational cost is high and high-level absorbing performance is unnecessary.
Three-dimensional wake field analysis by boundary element method
International Nuclear Information System (INIS)
Miyata, K.
1987-01-01
A computer code HERTPIA was developed for the calculation of electromagnetic wake fields excited by charged particles travelling through arbitrarily shaped accelerating cavities. This code solves transient wave problems for a Hertz vector. The numerical analysis is based on the boundary element method. This program is validated by comparing its results with analytical solutions in a pill-box cavity
Directory of Open Access Journals (Sweden)
S. Fonna
2018-06-01
Full Text Available Evaluation of rebar/reinforcing-steel corrosion for the 2004 tsunami-affected reinforced concrete (RC buildings in Aceh was conducted using half-cell potential mapping technique. However, the results only show qualitative meaning as corrosion risk rather than the corrosion itself, such as the size and location of corrosion. In this study, boundary element inverse analysis was proposed to be performed to detect rebar corrosion of the 2004 tsunami-affected structure in Aceh, using several electrical potential measurement data on the concrete surface. One RC structure in Peukan Bada, an area heavily damaged by the tsunami, was selected for the study. In 2004 the structure was submerged more than 5 m by the tsunami. Boundary element inverse analysis was developed by combining the boundary element method (BEM and particle swarm optimization (PSO. The corrosion was detected by evaluating measured and calculated electrical potential data. The measured and calculated electrical potential on the concrete surface was obtained by using a half-cell potential meter and by performing BEM, respectively. The solution candidates were evaluated by employing PSO. Simulation results show that boundary element inverse analysis successfully detected the size and location of corrosion for the case study. Compared with the actual corrosion, the error of simulation result was less than 5%. Hence, it shows that boundary element inverse analysis is very promising for further development to detect rebar corrosion. Keywords: Inverse analysis, Boundary element method, PSO, Corrosion, Reinforced concrete
Kawagoshi, Taiki; Nishida, Chizuko; Ota, Hidetoshi; Kumazawa, Yoshinori; Endo, Hideki; Matsuda, Yoichi
2008-01-01
Crocodilians have several unique karyotypic features, such as small diploid chromosome numbers (30-42) and the absence of dot-shaped microchromosomes. Of the extant crocodilian species, the Siamese crocodile (Crocodylus siamensis) has no more than 2n = 30, comprising mostly bi-armed chromosomes with large centromeric heterochromatin blocks. To investigate the molecular structures of C-heterochromatin and genomic compartmentalization in the karyotype, characterized by the disappearance of tiny microchromosomes and reduced chromosome number, we performed molecular cloning of centromeric repetitive sequences and chromosome mapping of the 18S-28S rDNA and telomeric (TTAGGG)( n ) sequences. The centromeric heterochromatin was composed mainly of two repetitive sequence families whose characteristics were quite different. Two types of GC-rich CSI-HindIII family sequences, the 305 bp CSI-HindIII-S (G+C content, 61.3%) and 424 bp CSI-HindIII-M (63.1%), were localized to the intensely PI-stained centric regions of all chromosomes, except for chromosome 2 with PI-negative heterochromatin. The 94 bp CSI-DraI (G+C content, 48.9%) was tandem-arrayed satellite DNA and localized to chromosome 2 and four pairs of small-sized chromosomes. The chromosomal size-dependent genomic compartmentalization that is supposedly unique to the Archosauromorpha was probably lost in the crocodilian lineage with the disappearance of microchromosomes followed by the homogenization of centromeric repetitive sequences between chromosomes, except for chromosome 2.
International Nuclear Information System (INIS)
Kim, H; Ryue, J; Thompson, D J; Müller, A D
2016-01-01
Recently, complex shaped aluminium panels have been adopted in many structures to make them lighter and stronger. The vibro-acoustic behaviour of these complex panels has been of interest for many years but conventional finite element and boundary element methods are not efficient to predict their performance at higher frequencies. Where the cross-sectional properties of the panels are constant in one direction, wavenumber domain numerical analysis can be applied and this becomes more suitable for panels with complex cross-sectional geometries. In this paper, a coupled wavenumber domain finite element and boundary element method is applied to predict the sound radiation from and sound transmission through a double-layered aluminium extruded panel, having a typical shape used in railway carriages. The predicted results are compared with measured ones carried out on a finite length panel and good agreement is found. (paper)
Hybrid finite difference/finite element immersed boundary method.
E Griffith, Boyce; Luo, Xiaoyu
2017-12-01
The immersed boundary method is an approach to fluid-structure interaction that uses a Lagrangian description of the structural deformations, stresses, and forces along with an Eulerian description of the momentum, viscosity, and incompressibility of the fluid-structure system. The original immersed boundary methods described immersed elastic structures using systems of flexible fibers, and even now, most immersed boundary methods still require Lagrangian meshes that are finer than the Eulerian grid. This work introduces a coupling scheme for the immersed boundary method to link the Lagrangian and Eulerian variables that facilitates independent spatial discretizations for the structure and background grid. This approach uses a finite element discretization of the structure while retaining a finite difference scheme for the Eulerian variables. We apply this method to benchmark problems involving elastic, rigid, and actively contracting structures, including an idealized model of the left ventricle of the heart. Our tests include cases in which, for a fixed Eulerian grid spacing, coarser Lagrangian structural meshes yield discretization errors that are as much as several orders of magnitude smaller than errors obtained using finer structural meshes. The Lagrangian-Eulerian coupling approach developed in this work enables the effective use of these coarse structural meshes with the immersed boundary method. This work also contrasts two different weak forms of the equations, one of which is demonstrated to be more effective for the coarse structural discretizations facilitated by our coupling approach. © 2017 The Authors International Journal for Numerical Methods in Biomedical Engineering Published by John Wiley & Sons Ltd.
Eck, Simon; Wörz, Stefan; Müller-Ott, Katharina; Hahn, Matthias; Biesdorf, Andreas; Schotta, Gunnar; Rippe, Karsten; Rohr, Karl
2016-08-01
The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci. Copyright © 2016 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Brochard Vincent
2009-02-01
Full Text Available Abstract Background Genome reprogramming in early mouse embryos is associated with nuclear reorganization and particular features such as the peculiar distribution of centromeric and pericentric heterochromatin during the first developmental stage. This zygote-specific heterochromatin organization could be observed both in maternal and paternal pronuclei after natural fertilization as well as in embryonic stem (ES cell nuclei after nuclear transfer suggesting that this particular type of nuclear organization was essential for embryonic reprogramming and subsequent development. Results Here, we show that remodeling into a zygotic-like organization also occurs after somatic cell nuclear transfer (SCNT, supporting the hypothesis that reorganization of constitutive heterochromatin occurs regardless of the source and differentiation state of the starting material. However, abnormal nuclear remodeling was frequently observed after SCNT, in association with low developmental efficiency. When transient treatment with the histone deacetylase inhibitor trichostatin A (TSA was tested, we observed improved nuclear remodeling in 1-cell SCNT embryos that correlated with improved rates of embryonic development at subsequent stages. Conclusion Together, the results suggest that proper organization of constitutive heterochromatin in early embryos is involved in the initial developmental steps and might have long term consequences, especially in cloning procedures.
Heat conduction in a plate-type fuel element with time-dependent boundary conditions
International Nuclear Information System (INIS)
Faya, A.J.G.; Maiorino, J.R.
1981-01-01
A method for the solution of boundary-value problems with variable boundary conditions is applied to solve a heat conduction problem in a plate-type fuel element with time dependent film coefficient. The numerical results show the feasibility of the method in the solution of this class of problems. (Author) [pt
Directory of Open Access Journals (Sweden)
Rodolpho Menezes
2011-07-01
Full Text Available Previous cytogenetic analyses in Trypoxylon Latreille, 1796 have been basically restricted to C-banding. In the present study, base-specific CMA3 and DAPI fluorochrome staining were used to characterize the constitutive heterochromatin in three Trypoxylon species. The heterochromatin was GC-rich in all the species studied; however, in Trypoxylon nitidum F. Smith, 1856 the molecular composition of the heterochromatin was different among chromosome pairs. Conversely, the euchromatin was AT-rich in the three species. These results suggest high conservatism in the euchromatic regions as opposed to the heterochromatic regions that have a high rate of changes. In this study, we report the karyotype of Trypoxylon rugifrons F. Smith, 1873 which has the lowest chromosome number in the genus and other characteristics of the likely ancestral Trypoxylon karyotype.
Partridge, P; Boundary Elements in Fluid Dynamics
1992-01-01
This book Boundary Elements in Fluid Dynamics is the second volume of the two volume proceedings of the International Conference on Computer Modelling of Seas and Coastal Regions and Boundary Elements and Fluid Dynamics, held in Southampton, U.K., in April 1992. The Boundary Element Method (BEM) is now fully established as an ac curate and successful technique for solving engineering problems in a wide range of fields. The success of the method is due to its advantages in data reduction, as only the boundary of the region is modelled. Thus moving boundaries may be more easily handled, which is not the case if domain methods are used. In addition, the method is easily able to model regions to extending to infinity. Fluid mechanics is traditionally one of the most challenging areas of engi neering, the simulation of fluid motion, particularly in three dimensions, is always a serious test for any numerical method, and is an area in which BEM analysis may be used taking full advantage of its special character...
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Vladimir Pavan Margarido
2000-09-01
Full Text Available This is the first description of the karyotype of Leporinus desmotes. The diploid female number was 2n = 54 meta- and submetacentric chromosomes. The nucleolar organizing regions (NORs were studied by silver nitrate staining and rDNA fluorescence in situ hybridization (FISH and were found to be located in the telomeric region of the long arm of the 9th pair. C-banding revealed centromeric and telomeric heterochromatin segments in most chromosomes. Intercalar blocks of heterochromatin were observed in the long arm of six chromosome pairs. Besides a NOR-adjacent heterochromatin, all of the intercalar heterochromatic segments were brightly fluorescent by mithramycin staining. These data suggest that a unique amplification of a primordial GC-rich heterochromatin, probably NOR-associated, may have taken place in the karyotype diversification of this Leporinus species.Esta é a primeira descrição do cariótipo de Leporinus desmotes fêmea. O número diplóide encontrado foi 2n = 54 cromossomos meta- e submetacêntricos. As regiões organizadoras de nucléolos (NORs foram estudadas através da impregnação pela prata e por hibridização in situ com sondas de DNAr (FISH, e foram localizadas na região telomérica do braço longo do 9º par. Heterocromatinas centromérica e telomérica foram reveladas pelo bandamento C na maioria dos cromossomos. Adicionalmente, grande quantidade de heterocromatina intercalar ou subtelomérica foi também observada. Diferenciação composicional na maior parte da heterocromatina identificada em L. desmotes pode ser inferida através da coloração pela mitramicina, caracterizando um caso peculiar de amplificação de segmentos heterocromáticos ricos em bases GC neste grupo de peixes.
International Nuclear Information System (INIS)
Choi, C. Y.; Park, C. T.; Kim, T. H.; Han, K. N.; Choe, S. H.
1995-01-01
A geometrical inverse heat conduction problem is solved for the development of Infrared Computerized-Axial-Tomography (IR CAT) Scan by using a boundary element method in conjunction with regularization procedure. In this problem, an overspecified temperature condition by infrared scanning is provided on the surface, and is used together with other conditions to solve the position of an unknown boundary (cavity). An auxiliary problem is introduced in the solution of this problem. By defining a hypothetical inner boundary for the auxiliary problem domain, the cavity is located interior to the domain and its position is determined by solving a potential problem. Boundary element method with regularization procedure is used to solve this problem, and the effects of regularization on the inverse solution method are investigated by means of numerical analysis
Energy Technology Data Exchange (ETDEWEB)
El Shawish, Samir, E-mail: Samir.ElShawish@ijs.si [Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana (Slovenia); Cizelj, Leon [Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana (Slovenia); Simonovski, Igor [European Commission, DG-JRC, Institute for Energy and Transport, P.O. Box 2, NL-1755 ZG Petten (Netherlands)
2013-08-15
Highlights: ► We estimate the performance of cohesive elements for modeling grain boundaries. ► We compare the computed stresses in ABAQUS finite element solver. ► Tests are performed in analytical and realistic models of polycrystals. ► Most severe issue is found within the plastic grain response. ► Other identified issues are related to topological constraints in modeling space. -- Abstract: We propose and demonstrate several tests to estimate the performance of the cohesive elements in ABAQUS for modeling grain boundaries in complex spatial structures such as polycrystalline aggregates. The performance of the cohesive elements is checked by comparing the computed stresses with the theoretically predicted values for a homogeneous material under uniaxial tensile loading. Statistical analyses are performed under different loading conditions for two elasto-plastic models of the grains: isotropic elasticity with isotropic hardening plasticity and anisotropic elasticity with crystal plasticity. Tests are conducted on an analytical finite element model generated from Voronoi tessellation as well as on a realistic finite element model of a stainless steel wire. The results of the analyses highlight several issues related to the computation of normal and shear stresses. The most severe issue is found within the plastic grain response where the computed normal stresses on a particularly oriented cohesive elements are significantly underestimated. Other issues are found to be related to topological constraints in the modeling space and result in the increased scatter of the computed stresses.
Use of the iterative solution method for coupled finite element and boundary element modeling
International Nuclear Information System (INIS)
Koteras, J.R.
1993-07-01
Tunnels buried deep within the earth constitute an important class geomechanics problems. Two numerical techniques used for the analysis of geomechanics problems, the finite element method and the boundary element method, have complementary characteristics for applications to problems of this type. The usefulness of combining these two methods for use as a geomechanics analysis tool has been recognized for some time, and a number of coupling techniques have been proposed. However, not all of them lend themselves to efficient computational implementations for large-scale problems. This report examines a coupling technique that can form the basis for an efficient analysis tool for large scale geomechanics problems through the use of an iterative equation solver
Seismic response of three-dimensional rockfill dams using the Indirect Boundary Element Method
International Nuclear Information System (INIS)
Sanchez-Sesma, Francisco J; Arellano-Guzman, Mauricio; Perez-Gavilan, Juan J; Suarez, Martha; Marengo-Mogollon, Humberto; Chaillat, Stephanie; Jaramillo, Juan Diego; Gomez, Juan; Iturraran-Viveros, Ursula; Rodriguez-Castellanos, Alejandro
2010-01-01
The Indirect Boundary Element Method (IBEM) is used to compute the seismic response of a three-dimensional rockfill dam model. The IBEM is based on a single layer integral representation of elastic fields in terms of the full-space Green function, or fundamental solution of the equations of dynamic elasticity, and the associated force densities along the boundaries. The method has been applied to simulate the ground motion in several configurations of surface geology. Moreover, the IBEM has been used as benchmark to test other procedures. We compute the seismic response of a three-dimensional rockfill dam model placed within a canyon that constitutes an irregularity on the surface of an elastic half-space. The rockfill is also assumed elastic with hysteretic damping to account for energy dissipation. Various types of incident waves are considered to analyze the physical characteristics of the response: symmetries, amplifications, impulse response and the like. Computations are performed in the frequency domain and lead to time response using Fourier analysis. In the present implementation a symmetrical model is used to test symmetries. The boundaries of each region are discretized into boundary elements whose size depends on the shortest wavelength, typically, six boundary segments per wavelength. Usually, the seismic response of rockfill dams is simulated using either finite elements (FEM) or finite differences (FDM). In most applications, commercial tools that combine features of these methods are used to assess the seismic response of the system for a given motion at the base of model. However, in order to consider realistic excitation of seismic waves with different incidence angles and azimuth we explore the IBEM.
International Nuclear Information System (INIS)
Choi, Chang Yong
1999-01-01
This paper presents a study of the Dual Reciprocity Boundary Element Method (DRBEM) for the laminar heat convection problem in a concentric annulus with constant heat flux boundary condition. DRBEM is one of the most successful technique used to transform the domain integrals arising from the nonhomogeneous term of the poisson equation into equivalent boundary only integrals. This recently developed and highly efficient numerical method is tested for the solution accuracy of the fluid flow and heat transfer study in a concentric annulus. Since their exact solutions are available, DRBEM solutions are verified with different number of boundary element discretization and internal points. The results obtained in this study are discussed with the relative error percentage of velocity and temperature solutions, and potential applicability of the method for the more complicated heat convection problems with arbitrary duct geometries
Deacetylation of H4-K16Ac and heterochromatin assembly in senescence
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Contrepois Kévin
2012-08-01
Full Text Available Abstract Background Cellular senescence is a stress response of mammalian cells leading to a durable arrest of cell proliferation that has been implicated in tumor suppression, wound healing, and aging. The proliferative arrest is mediated by transcriptional repression of genes essential for cell division by the retinoblastoma protein family. This repression is accompanied by varying degrees of heterochromatin assembly, but little is known regarding the molecular mechanisms involved. Results We found that both deacetylation of H4-K16Ac and expression of HMGA1/2 can contribute to DNA compaction during senescence. SIRT2, an NAD-dependent class III histone deacetylase, contributes to H4-K16Ac deacetylation and DNA compaction in human fibroblast cell lines that assemble striking senescence-associated heterochromatin foci (SAHFs. Decreased H4-K16Ac was observed in both replicative and oncogene-induced senescence of these cells. In contrast, this mechanism was inoperative in a fibroblast cell line that did not assemble extensive heterochromatin during senescence. Treatment of senescent cells with trichostatin A, a class I/II histone deacetylase inhibitor, also induced rapid and reversible decondensation of SAHFs. Inhibition of DNA compaction did not significantly affect the stability of the senescent state. Conclusions Variable DNA compaction observed during senescence is explained in part by cell-type specific regulation of H4 deacetylation and HMGA1/2 expression. Deacetylation of H4-K16Ac during senescence may explain reported decreases in this mark during mammalian aging and in cancer cells.
Stress Wave Propagation in Soils Modelled by the Boundary Element Method
DEFF Research Database (Denmark)
Rasmussen, K. M.
This thesis deals with different aspects of the boundary element method (BEM) applied to stress wave propagation problems in soils. Among other things BEM formulations for coupled FEM and BEM, moving loads, direct BEM and indirect BEM are presented. For all the formulations both analytical...
Sound source reconstruction using inverse boundary element calculations
DEFF Research Database (Denmark)
Schuhmacher, Andreas; Hald, Jørgen; Rasmussen, Karsten Bo
2003-01-01
Whereas standard boundary element calculations focus on the forward problem of computing the radiated acoustic field from a vibrating structure, the aim in this work is to reverse the process, i.e., to determine vibration from acoustic field data. This inverse problem is brought on a form suited ...... it is demonstrated that the L-curve criterion is robust with respect to the errors in a real measurement situation. In particular, it is shown that the L-curve criterion is superior to the more conventional generalized cross-validation (GCV) approach for the present tire noise studies....
DEFF Research Database (Denmark)
Yoon, Gil Ho; Park, Y.K.; Kim, Y.Y.
2007-01-01
A new topology optimization scheme, called the element stacking method, is developed to better handle design optimization involving material-dependent boundary conditions and selection of elements of different types. If these problems are solved by existing standard approaches, complicated finite...... element models or topology optimization reformulation may be necessary. The key idea of the proposed method is to stack multiple elements on the same discretization pixel and select a single or no element. In this method, stacked elements on the same pixel have the same coordinates but may have...... independent degrees of freedom. Some test problems are considered to check the effectiveness of the proposed stacking method....
Advances in boundary elements. Vol. 1-3
International Nuclear Information System (INIS)
Brebbia, C.A.; Connor, J.J.
1989-01-01
This book contains some of the edited papers presented at the 11th Boundary Element Conference, held in Cambridge, Massachusetts, during August 1989. The papers are arranged in three different books comprising the following topics: Vol. 1: Computations and Fundamentals - comprises sections on fundamentals, adaptive techniques, error and convergence, numerical methods and computational aspects. (283 p.). Vol. 2: Field and fluid flow solutions - includes the following topics: potential problems, thermal studies, electrical and electromagnetic problems, wave propagation, acoustics and fluid flow. (484 p.). Vol. 3: Stress analysis - deals with advances in linear problems, nonlinear problems, fracture mechanics, contact mechanics, optimization, geomechanics, plates and shells, vibrations and industrial applications. (450 p). (orig./HP)
A coupled boundary element-finite difference solution of the elliptic modified mild slope equation
DEFF Research Database (Denmark)
Naserizadeh, R.; Bingham, Harry B.; Noorzad, A.
2011-01-01
The modified mild slope equation of [5] is solved using a combination of the boundary element method (BEM) and the finite difference method (FDM). The exterior domain of constant depth and infinite horizontal extent is solved by a BEM using linear or quadratic elements. The interior domain...
Directory of Open Access Journals (Sweden)
Yichao Gao
2011-01-01
Full Text Available The dam-reservoir system is divided into the near field modeled by the finite element method, and the far field modeled by the excellent high-order doubly asymptotic open boundary (DAOB. Direct and partitioned coupled methods are developed for the analysis of dam-reservoir system. In the direct coupled method, a symmetric monolithic governing equation is formulated by incorporating the DAOB with the finite element equation and solved using the standard time-integration methods. In contrast, the near-field finite element equation and the far-field DAOB condition are separately solved in the partitioned coupled methodm, and coupling is achieved by applying the interaction force on the truncated boundary. To improve its numerical stability and accuracy, an iteration strategy is employed to obtain the solution of each step. Both coupled methods are implemented on the open-source finite element code OpenSees. Numerical examples are employed to demonstrate the performance of these two proposed methods.
International Nuclear Information System (INIS)
Zaifol Samsu; Muhamad Daud; Siti Radiah Mohd Kamarudin
2011-01-01
Boundary element method (BEM) is a numerical technique that used for modeling infinite domain as is the case for galvanic corrosion analysis. This paper presents the application of boundary element method for galvanic corrosion analysis between two different metallic materials. Aluminium (Al), and zinc (Zn) alloys were used separately coupled with the Carbon Steel (CS) in natural seawater. The measured conductivity of sea water is 30,800 μS/ cm at ambient temperature. Computer software system based on boundary element likes BEASY and ABAQUS can be used to accurately model and simulate the galvanic corrosion. However, the BEM based BEASY program will be used reasonably for predicting the galvanic current density distribution of coupled Al-CS and Zn-CS in this study. (author)
A Galleria Boundary Element Method for two-dimensional nonlinear magnetostatics
Brovont, Aaron D.
The Boundary Element Method (BEM) is a numerical technique for solving partial differential equations that is used broadly among the engineering disciplines. The main advantage of this method is that one needs only to mesh the boundary of a solution domain. A key drawback is the myriad of integrals that must be evaluated to populate the full system matrix. To this day these integrals have been evaluated using numerical quadrature. In this research, a Galerkin formulation of the BEM is derived and implemented to solve two-dimensional magnetostatic problems with a focus on accurate, rapid computation. To this end, exact, closed-form solutions have been derived for all the integrals comprising the system matrix as well as those required to compute fields in post-processing; the need for numerical integration has been eliminated. It is shown that calculation of the system matrix elements using analytical solutions is 15-20 times faster than with numerical integration of similar accuracy. Furthermore, through the example analysis of a c-core inductor, it is demonstrated that the present BEM formulation is a competitive alternative to the Finite Element Method (FEM) for linear magnetostatic analysis. Finally, the BEM formulation is extended to analyze nonlinear magnetostatic problems via the Dual Reciprocity Method (DRBEM). It is shown that a coarse, meshless analysis using the DRBEM is able to achieve RMS error of 3-6% compared to a commercial FEM package in lightly saturated conditions.
Second-order wave diffraction by a circular cylinder using scaled boundary finite element method
International Nuclear Information System (INIS)
Song, H; Tao, L
2010-01-01
The scaled boundary finite element method (SBFEM) has achieved remarkable success in structural mechanics and fluid mechanics, combing the advantage of both FEM and BEM. Most of the previous works focus on linear problems, in which superposition principle is applicable. However, many physical problems in the real world are nonlinear and are described by nonlinear equations, challenging the application of the existing SBFEM model. A popular idea to solve a nonlinear problem is decomposing the nonlinear equation to a number of linear equations, and then solves them individually. In this paper, second-order wave diffraction by a circular cylinder is solved by SBFEM. By splitting the forcing term into two parts, the physical problem is described as two second-order boundary-value problems with different asymptotic behaviour at infinity. Expressing the velocity potentials as a series of depth-eigenfunctions, both of the 3D boundary-value problems are decomposed to a number of 2D boundary-value sub-problems, which are solved semi-analytically by SBFEM. Only the cylinder boundary is discretised with 1D curved finite-elements on the circumference of the cylinder, while the radial differential equation is solved completely analytically. The method can be extended to solve more complex wave-structure interaction problems resulting in direct engineering applications.
H3K9me-independent gene silencing in fission yeast heterochromatin by Clr5 and histone deacetylases
DEFF Research Database (Denmark)
Hansen, Klavs R; Hazan, Idit; Shanker, Sreenath
2011-01-01
organisms such as fission yeast. In spite of numerous studies, the relative contributions of the various heterochromatic histone marks to the properties of heterochromatin remain largely undefined. Here, we report that silencing of the fission yeast mating-type cassettes, which are located in a well......, our results point to histone deacetylases as prominent repressors of gene expression in fission yeast heterochromatin. These deacetylases can act in concert with, or independently of, the widely studied H3K9me mark to influence gene silencing at heterochromatic loci....
International Nuclear Information System (INIS)
Khambampati, Anil Kumar; Kim, Sin; Lee, Bo An; Kim, Kyung Youn
2012-01-01
This paper is about locating the boundary of a moving cavity within a homogeneous background from the voltage measurements recorded on the outer boundary. An inverse boundary problem of a moving cavity is formulated by considering a two-phase vapor–liquid flow in a pipe. The conductivity of the flow components (vapor and liquid) is assumed to be constant and known a priori while the location and shape of the inclusion (vapor) are the unknowns to be estimated. The forward problem is solved using the boundary element method (BEM) with the integral equations solved analytically. A special situation is considered such that the cavity changes its location and shape during the time taken to acquire a full set of independent measurement data. The boundary of a cavity is assumed to be elliptic and is parameterized with Fourier series. The inverse problem is treated as a state estimation problem with the Fourier coefficients that represent the center and radii of the cavity as the unknowns to be estimated. An extended Kalman filter (EKF) is used as an inverse algorithm to estimate the time varying Fourier coefficients. Numerical experiments are shown to evaluate the performance of the proposed method. Through the results, it can be noticed that the proposed BEM with EKF method is successful in estimating the boundary of a moving cavity. (paper)
International Symposium on Boundary Element Methods : Advances in Solid and Fluid Mechanics
Tseng, Kadin
1990-01-01
The Boundary Element Method (BEM) has become established as an effective tool for the solutions of problems in engineering science. The salient features of the BEM have been well documented in the open literature and therefore will not be elaborated here. The BEM research has progressed rapidly, especially in the past decade and continues to evolve worldwide. This Symposium was organized to provide an international forum for presentation of current research in BEM for linear and nonlinear problems in solid and fluid mechanics and related areas. To this end, papers on the following topics were included: rotary wing aerodynamics, unsteady aerodynamics, design and optimization, elasticity, elasto dynamics and elastoplasticity, fracture mechanics, acoustics, diffusion and wave motion, thermal analysis, mathematical aspects and boundary/finite element coupled methods. A special session was devoted to parallel/vector supercomputing with emphasis on mas sive parallelism. This Symposium was sponsored by United ...
An enriched finite element model with q-refinement for radiative boundary layers in glass cooling
Energy Technology Data Exchange (ETDEWEB)
Mohamed, M. Shadi [Institute for Infrastructure and Environment, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Seaid, Mohammed; Trevelyan, Jon [School of Engineering and Computing Sciences, University of Durham, South Road, Durham DH1 3LE (United Kingdom); Laghrouche, Omar [Institute for Infrastructure and Environment, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom)
2014-02-01
Radiative cooling in glass manufacturing is simulated using the partition of unity finite element method. The governing equations consist of a semi-linear transient heat equation for the temperature field and a stationary simplified P{sub 1} approximation for the radiation in non-grey semitransparent media. To integrate the coupled equations in time we consider a linearly implicit scheme in the finite element framework. A class of hyperbolic enrichment functions is proposed to resolve boundary layers near the enclosure walls. Using an industrial electromagnetic spectrum, the proposed method shows an immense reduction in the number of degrees of freedom required to achieve a certain accuracy compared to the conventional h-version finite element method. Furthermore the method shows a stable behaviour in treating the boundary layers which is shown by studying the solution close to the domain boundaries. The time integration choice is essential to implement a q-refinement procedure introduced in the current study. The enrichment is refined with respect to the steepness of the solution gradient near the domain boundary in the first few time steps and is shown to lead to a further significant reduction on top of what is already achieved with the enrichment. The performance of the proposed method is analysed for glass annealing in two enclosures where the simplified P{sub 1} approximation solution with the partition of unity method, the conventional finite element method and the finite difference method are compared to each other and to the full radiative heat transfer as well as the canonical Rosseland model.
Experimental validation of a boundary element solver for exterior acoustic radiation problems
Visser, Rene; Nilsson, A.; Boden, H.
2003-01-01
The relation between harmonic structural vibrations and the corresponding acoustic radiation is given by the Helmholtz integral equation (HIE). To solve this integral equation a new solver (BEMSYS) based on the boundary element method (BEM) has been implemented. This numerical tool can be used for
Implementation aspects of the Boundary Element Method including viscous and thermal losses
DEFF Research Database (Denmark)
Cutanda Henriquez, Vicente; Juhl, Peter Møller
2014-01-01
The implementation of viscous and thermal losses using the Boundary Element Method (BEM) is based on the Kirchhoff’s dispersion relation and has been tested in previous work using analytical test cases and comparison with measurements. Numerical methods that can simulate sound fields in fluids...
Directory of Open Access Journals (Sweden)
Murat Ünal
2002-03-01
Full Text Available In this study, a two-dimensional software was developed by using the boundary element method, in order to model and solve the rock mechanics problems encountered in surface and underground excavations. Stability of rock wedges formed at the roof of underground excavations were investigated in detail by using this software. The behaviour of the symmetric wedge on different joint stiffnesses was studied using a modified boundary element software. Then the results obtained were discussed and compared with the analytical solution, considering the surface tractions, shear stresses (developed along the discontinuity, wedge displacements and strains (along the wedge height.
Piscor, Diovani; Centofante, Liano; Parise-Maltempi, Patricia Pasquali
2017-09-01
Genus Astyanax is well distributed in Neotropical freshwater environments and its taxonomic position is uncertain, as is the case with other Characidae genera allocated in the group incertae sedis. This study aimed to analyse the karyotype of different populations of Astyanax fasciatus (Corumbataí River basin) using Giemsa staining, C-band technique, and fluorescence in situ hybridization for the H3 histone and 5S rRNA genes, in addition we describe for the first time the chromosomal organization of H3 histone and 5S rRNAgenes in A. marionae (ParaguayRiver basin). Chromosomes of three A. fasciatus populations were analysed (two with 2n = 50 and one with 2n = 48) and the heterochromatin was organized in two forms (blocks with blurred boundaries and distinct blocks). H3 histone and 5S rRNA genes were observed in all the three populations of A. fasciatus on two chromosome pairs (one metacentric chromosome showing H3 histone and 5S rRNA gene clusters). In A. marionae (2n = 48), H3 histone and 5S rRNA genes were observed in one acrocentric chromosome pair (different pairs). Further, differences between karyotypes and heterochromatin, as well as the chromosomal organization of H3 histone and 5S rRNA genes in Astyanax species, focussing on chromosome evolution in the group are discussed.
Coupled Boundary and Finite Element Analysis of Vibration from Railway Tunnels
DEFF Research Database (Denmark)
Andersen, Lars; Jones, C.J.C.
2006-01-01
The analysis of vibration from railway tunnels is of growing interest as new and higher-speed railways are built under the ground to address the transport problems of growing modern urban areas around cities. Such analysis can be carried out using numerical methods but models and therefore comput...... body vibration (about 4 to 80 Hz). A coupled finite element and boundary element scheme is applied in both two and three dimensions. Two tunnel designs are considered: a cut-and-cover tunnel for a double track and a single-track tunnel dug with the New Austrian Tunnelling Method (NATM)....
Directory of Open Access Journals (Sweden)
Pavel A. Akimov
2017-12-01
Full Text Available As is well known, the formulation of a multipoint boundary problem involves three main components: a description of the domain occupied by the structure and the corresponding subdomains; description of the conditions inside the domain and inside the corresponding subdomains, the description of the conditions on the boundary of the domain, conditions on the boundaries between subdomains. This paper is a continuation of another work published earlier, in which the formulation and general principles of the approximation of the multipoint boundary problem of a static analysis of deep beam on the basis of the joint application of the finite element method and the discrete-continual finite element method were considered. It should be noted that the approximation within the fragments of a domain that have regular physical-geometric parameters along one of the directions is expedient to be carried out on the basis of the discrete-continual finite element method (DCFEM, and for the approximation of all other fragments it is necessary to use the standard finite element method (FEM. In the present publication, the formulas for the computing of displacements partial derivatives of displacements, strains and stresses within the finite element model (both within the finite element and the corresponding nodal values (with the use of averaging are presented. Boundary conditions between subdomains (respectively, discrete models and discrete-continual models and typical conditions such as “hinged support”, “free edge”, “perfect contact” (twelve basic (basic variants are available are under consideration as well. Governing formulas for computing of elements of the corresponding matrices of coefficients and vectors of the right-hand sides are given for each variant. All formulas are fully adapted for algorithmic implementation.
Free surface simulation of a two-layer fluid by boundary element method
Directory of Open Access Journals (Sweden)
Weoncheol Koo
2010-09-01
Full Text Available A two-layer fluid with free surface is simulated in the time domain by a two-dimensional potential-based Numerical Wave Tank (NWT. The developed NWT is based on the boundary element method and a leap-frog time integration scheme. A whole domain scheme including interaction terms between two layers is applied to solve the boundary integral equation. The time histories of surface elevations on both fluid layers in the respective wave modes are verified with analytic results. The amplitude ratios of upper to lower elevation for various density ratios and water depths are also compared.
Segregation of solute elements at grain boundaries in an ultrafine grained Al-Zn-Mg-Cu alloy
International Nuclear Information System (INIS)
Sha, Gang; Yao, Lan; Liao, Xiaozhou; Ringer, Simon P.; Chao Duan, Zhi; Langdon, Terence G.
2011-01-01
The solute segregation at grain boundaries (GBs) of an ultrafine grained (UFG) Al-Zn-Mg-Cu alloy processed by equal-channel angular pressing (ECAP) at 200 o C was characterised using three-dimensional atom probe. Mg and Cu segregate strongly to the grain boundaries. In contrast, Zn does not always show clear segregation and may even show depletion near the grain boundaries. Trace element Si selectively segregates at some GBs. An increase in the number of ECAP passes leads to a decrease in the grain size but an increase in solute segregation at the boundaries. The significant segregation of alloying elements at the boundaries of ultrafine-grained alloys implies that less solutes will be available in the matrix for precipitation with a decrease in the average grain size. -- Research Highlights: → Atom probe tomography has been employed successfully to reveal unique segregation of solutes at ultrafine grained material. → Mg and Cu elements segregated strongly at the grain boundary of an ultrafine grained Al-Zn-Mg-Cu alloy processed by 4-pass and 8-pass ECAP at 200 o C. Zn frequently depleted at GBs with a Zn depletion region of 7-15 nm in width on one or both sides of the GBs. Only a small fraction (3/13) of GBs were observed with a low level of Zn segregation where the combined Mg and Cu excess is over 3.1 atom/nm 2 . Si appeared selectively segregated at some of the GBs. → The increase in number of ECAP passes from 4 to 8 correlated with the increase in mean level segregation of Mg and Cu for both solute excess and peak concentration. → The change of plane normal of a grain boundary within 30 o only leads to a slight change in the solute segregation level.
A simple finite element method for boundary value problems with a Riemann–Liouville derivative
Jin, Bangti; Lazarov, Raytcho; Lu, Xiliang; Zhou, Zhi
2016-01-01
© 2015 Elsevier B.V. All rights reserved. We consider a boundary value problem involving a Riemann-Liouville fractional derivative of order α∈(3/2,2) on the unit interval (0,1). The standard Galerkin finite element approximation converges slowly due to the presence of singularity term xα-^{1} in the solution representation. In this work, we develop a simple technique, by transforming it into a second-order two-point boundary value problem with nonlocal low order terms, whose solution can reconstruct directly the solution to the original problem. The stability of the variational formulation, and the optimal regularity pickup of the solution are analyzed. A novel Galerkin finite element method with piecewise linear or quadratic finite elements is developed, and ^{L2}(D) error estimates are provided. The approach is then applied to the corresponding fractional Sturm-Liouville problem, and error estimates of the eigenvalue approximations are given. Extensive numerical results fully confirm our theoretical study.
A simple finite element method for boundary value problems with a Riemann–Liouville derivative
Jin, Bangti
2016-02-01
© 2015 Elsevier B.V. All rights reserved. We consider a boundary value problem involving a Riemann-Liouville fractional derivative of order α∈(3/2,2) on the unit interval (0,1). The standard Galerkin finite element approximation converges slowly due to the presence of singularity term xα-^{1} in the solution representation. In this work, we develop a simple technique, by transforming it into a second-order two-point boundary value problem with nonlocal low order terms, whose solution can reconstruct directly the solution to the original problem. The stability of the variational formulation, and the optimal regularity pickup of the solution are analyzed. A novel Galerkin finite element method with piecewise linear or quadratic finite elements is developed, and ^{L2}(D) error estimates are provided. The approach is then applied to the corresponding fractional Sturm-Liouville problem, and error estimates of the eigenvalue approximations are given. Extensive numerical results fully confirm our theoretical study.
Directory of Open Access Journals (Sweden)
Lucia Piacentini
2009-10-01
Full Text Available Heterochromatin Protein 1 (HP1a is a well-known conserved protein involved in heterochromatin formation and gene silencing in different species including humans. A general model has been proposed for heterochromatin formation and epigenetic gene silencing in different species that implies an essential role for HP1a. According to the model, histone methyltransferase enzymes (HMTases methylate the histone H3 at lysine 9 (H3K9me, creating selective binding sites for itself and the chromodomain of HP1a. This complex is thought to form a higher order chromatin state that represses gene activity. It has also been found that HP1a plays a role in telomere capping. Surprisingly, recent studies have shown that HP1a is present at many euchromatic sites along polytene chromosomes of Drosophila melanogaster, including the developmental and heat-shock-induced puffs, and that this protein can be removed from these sites by in vivo RNase treatment, thus suggesting an association of HP1a with the transcripts of many active genes. To test this suggestion, we performed an extensive screening by RIP-chip assay (RNA-immunoprecipitation on microarrays, and we found that HP1a is associated with transcripts of more than one hundred euchromatic genes. An expression analysis in HP1a mutants shows that HP1a is required for positive regulation of these genes. Cytogenetic and molecular assays show that HP1a also interacts with the well known proteins DDP1, HRB87F, and PEP, which belong to different classes of heterogeneous nuclear ribonucleoproteins (hnRNPs involved in RNA processing. Surprisingly, we found that all these hnRNP proteins also bind heterochromatin and are dominant suppressors of position effect variegation. Together, our data show novel and unexpected functions for HP1a and hnRNPs proteins. All these proteins are in fact involved both in RNA transcript processing and in heterochromatin formation. This suggests that, in general, similar epigenetic mechanisms
Jin, Qiyun; Thompson, David J.; Lurcock, Daniel E. J.; Toward, Martin G. R.; Ntotsios, Evangelos
2018-05-01
A numerical model is presented for the ground-borne vibration produced by trains running in tunnels. The model makes use of the assumption that the geometry and material properties are invariant in the axial direction. It is based on the so-called two-and-a-half dimensional (2.5D) coupled Finite Element and Boundary Element methodology, in which a two-dimensional cross-section is discretised into finite elements and boundary elements and the third dimension is represented by a Fourier transform over wavenumbers. The model is applied to a particular case of a metro line built with a cast-iron tunnel lining. An equivalent continuous model of the tunnel is developed to allow it to be readily implemented in the 2.5D framework. The tunnel structure and the track are modelled using solid and beam finite elements while the ground is modelled using boundary elements. The 2.5D track-tunnel-ground model is coupled with a train consisting of several vehicles, which are represented by multi-body models. The response caused by the passage of a train is calculated as the sum of the dynamic component, excited by the combined rail and wheel roughness, and the quasi-static component, induced by the constant moving axle loads. Field measurements have been carried out to provide experimental validation of the model. These include measurements of the vibration of the rail, the tunnel invert and the tunnel wall. In addition, simultaneous measurements were made on the ground surface above the tunnel. Rail roughness and track characterisation measurements were also made. The prediction results are compared with measured vibration obtained during train passages, with good agreement.
Dynamic-stiffness matrix of embedded and pile foundations by indirect boundary-element method
International Nuclear Information System (INIS)
Wolf, J.P.; Darbre, G.R.
1984-01-01
The boundary-integral equation method is well suited for the calculation of the dynamic-stiffness matrix of foundations embedded in a layered visco-elastic halfspace (or a transmitting boundary of arbitrary shape), which represents an unbounded domain. It also allows pile groups to be analyzed, taking pile-soil-pile interaction into account. The discretization of this boundary-element method is restricted to the structure-soil interface. All trial functions satisfy exactly the field equations and the radiation condition at infinity. In the indirect boundary-element method distributed source loads of initially unknown intensities act on a source line located in the excavated part of the soil and are determined such that the prescribed boundary conditions on the structure-soil interface are satisfied in an average sense. In the two-dimensional case the variables are expanded in a Fourier integral in the wave number domain, while in three dimensions, Fourier series in the circumferential direction and bessel functions of the wave number domain, while in three dimensions, Fourier series in the circumferential direction and Bessel functions of the wave number in the radial direction are selected. Accurate results arise with a small number of parameters of the loads acting on a source line which should coincide with the structure-soil interface. In a parametric study the dynamic-stiffness matrices of rectangular foundations of various aspect ratios embedded in a halfplane and in a layer built-in at its base are calculated. For the halfplane, the spring coefficients for the translational directions hardly depend on the embedment, while the corresponding damping coefficients increase for larger embedments, this tendency being more pronounced in the horizontal direction. (orig.)
OpenBEM - An open source Boundary Element Method software in Acoustics
DEFF Research Database (Denmark)
Cutanda Henriquez, Vicente; Juhl, Peter Møller
2010-01-01
OpenBEM is a collection of open source programs for solving the Helmholtz Equation using the Boundary Element Method. The collection is written in Matlab by the authors and contains codes for dealing with exterior and interior problems in two or three dimensions as well as implementation of axi...... with examples of its use. Previous research results where OpenBEM was employed will be mentioned....
Directory of Open Access Journals (Sweden)
Jennifer S. Lee
2016-01-01
Full Text Available Herpesviruses must contend with host cell epigenetic silencing responses acting on their genomes upon entry into the host cell nucleus. In this study, we confirmed that unchromatinized herpes simplex virus 1 (HSV-1 genomes enter primary human foreskin fibroblasts and are rapidly subjected to assembly of nucleosomes and association with repressive heterochromatin modifications such as histone 3 (H3 lysine 9-trimethylation (H3K9me3 and lysine 27-trimethylation (H3K27me3 during the first 1 to 2 h postinfection. Kinetic analysis of the modulation of nucleosomes and heterochromatin modifications over the course of lytic infection demonstrates a progressive removal that coincided with initiation of viral gene expression. We obtained evidence for three phases of heterochromatin removal from an early gene promoter: an initial removal of histones and heterochromatin not dependent on ICP0, a second ICP0-dependent round of removal of H3K9me3 that is independent of viral DNA synthesis, and a third phase of H3K27me3 removal that is dependent on ICP0 and viral DNA synthesis. The presence of ICP0 in transfected cells is also sufficient to promote removal of histones and H3K9me3 modifications of cotransfected genes. Overall, these results show that ICP0 promotes histone removal, a reduction of H3K9me3 modifications, and a later indirect reduction of H3K27me3 modifications following viral early gene expression and DNA synthesis. Therefore, HSV ICP0 promotes the reversal of host epigenetic silencing mechanisms by several mechanisms.
Directory of Open Access Journals (Sweden)
Jamille Bitencourt
2011-11-01
Full Text Available Cytogenetic analyses using C-banding and chromosomal digestion by several restriction enzymes were carried out in four populations (named A, B, C and D of Hypostomus prope unae (Loricariidae, Hypostominae from Contas river basin, northeastern Brazil. These populations share 2n=76 and single NORs on the second metacentric pair but exclusive karyotype forms for each locality. Populations A and B presented conspicuous terminal and interstitial heterochromatic blocks on most of acrocentric chromosomes and equivalent to NORs with differences in both position and bearing pair. Population D showed evident marks at interstitial regions and interspersed with nucleolar region while population C presented interstitial and terminal heterochromatin segments, non-coincident with NORs. The banding pattern after digestion with the endonucleases Alu I, Bam HI, Hae III and Dde I revealed a remarkable heterogeneity within heterochromatin, allowing the identification of distinctive clusters of repeated DNA in the studied populations, besides specific patterns along euchromatic regions. The analysis using restriction enzymes has proved to be highly informative, characterizing population differences and peculiarities in the genome organization of H. prope unae.
Korolkov, Victor P; Nasyrov, Ruslan K; Shimansky, Ruslan V
2006-01-01
Enhancing the diffraction efficiency of continuous-relief diffractive optical elements fabricated by direct laser writing is discussed. A new method of zone-boundary optimization is proposed to correct exposure data only in narrow areas along the boundaries of diffractive zones. The optimization decreases the loss of diffraction efficiency related to convolution of a desired phase profile with a writing-beam intensity distribution. A simplified stepped transition function that describes optimized exposure data near zone boundaries can be made universal for a wide range of zone periods. The approach permits a similar increase in the diffraction efficiency as an individual-pixel optimization but with fewer computation efforts. Computer simulations demonstrated that the zone-boundary optimization for a 6 microm period grating increases the efficiency by 7% and 14.5% for 0.6 microm and 1.65 microm writing-spot diameters, respectively. The diffraction efficiency of as much as 65%-90% for 4-10 microm zone periods was obtained experimentally with this method.
Kuijpers, A.H.W.M.; Verbeek, G.; Verheij, J.W.
1997-01-01
Effective use of the Fourier series boundary element method (FBEM) for everyday applications is hindered by the significant numerical problems that have to be overcome for its implementation. In the FBEM formulation for acoustics, some integrals over the angle of revolution arise, which need to be
A multi-region boundary element method for multigroup neutron diffusion calculations
International Nuclear Information System (INIS)
Ozgener, H.A.; Ozgener, B.
2001-01-01
For the analysis of a two-dimensional nuclear system consisting of a number of homogeneous regions (termed cells), first the cell matrices which depend solely on the material composition and geometrical dimension of the cell (hence on the cell type) are constructed using a boundary element formulation based on the multigroup boundary integral equation. For a particular nuclear system, the cell matrices are utilized in the assembly of the global system matrix in block-banded form using the newly introduced concept of virtual side. For criticality calculations, the classical fission source iteration is employed and linear system solutions are by the block Gaussian-elimination algorithm. The numerical applications show the validity of the proposed formulation both through comparison with analytical solutions and assessment of benchmark problem results against alternative methods
International Nuclear Information System (INIS)
Itagaki, Masafumi; Sahashi, Naoki.
1996-01-01
The multiple reciprocity method (MRM) in conjunction with the boundary element method has been employed to solve one-group eigenvalue problems described by the three-dimensional (3-D) neutron diffusion equation. The domain integral related to the fission source is transformed into a series of boundary-only integrals, with the aid of the higher order fundamental solutions based on the spherical and the modified spherical Bessel functions. Since each degree of the higher order fundamental solutions in the 3-D cases has a singularity of order (1/r), the above series of boundary integrals requires additional terms which do not appear in the 2-D MRM formulation. The critical eigenvalue itself can be also described using only boundary integrals. Test calculations show that Wielandt's spectral shift technique guarantees rapid and stable convergence of 3-D MRM computations. (author)
DEFF Research Database (Denmark)
Bartkova, J; Moudry, P; Hodny, Z
2011-01-01
activation in CIS; and enhanced HP1α in teratoma structures with epithelial and neuronal differentiation. Differential expression of the three heterochromatin markers suggests their partly non-overlapping roles, and separation of heterochromatinization from DDR activation highlights distinct responses...
Directory of Open Access Journals (Sweden)
Samira Hosseini
Full Text Available Abstract One of the main drawbacks of Element Free Galerkin (EFG method is its dependence on moving least square shape functions which don’t satisfy the Kronecker Delta property, so in this method it’s not possible to apply Dirichlet boundary conditions directly. The aim of the present paper is to discuss different aspects of three widely used methods of applying Dirichlet boundary conditions in EFG method, called Lagrange multipliers, penalty method, and coupling with finite element method. Numerical simulations are presented to compare the results of these methods form the perspective of accuracy, convergence and computational expense. These methods have been implemented in an object oriented programing environment, called INSANE, and the results are presented and compared with the analytical solutions.
International Nuclear Information System (INIS)
Karlsson, L.; Norden, H.
1988-01-01
The distribution of elements and the precipitation behaviour at grain boundaries have been studied in boron containing AISI 316L and ''Mo-free AISI 316L'' type austenitic stainless steels. A combination of microanalytical techniques was used to study the boundary regions after cooling at 0.29-530 0 C/s from 800, 1075 or 1250 0 C. Tetragonal M/sub 2/B, M/sub 5/B/sub 3/ and M/sub 3/B/sub 2/, all rich in Fe, Cr and Mo, precipitated in the ''high B'' (40 ppm) AISI 316L steel whereas orthorhombic M/sub 2/B, rich in Cr and Fe was found in the ''Mo-free steel'' with 23 ppm B. In the ''high B steel'' a thin (<2nm), continuous layer, containing B, Cr, Mo and Fe and having a stoichiometry of typically M/sub 9/B, formed at boundaries after cooling at intermediate cooling rates. For both types of steels a boundary zone was found, after all heat treatments, with a composition differing significantly from the bulk composition. The differences were most marked after cooling at intermediate cooling rates. In both types of steel boundary depletion of Cr and enrichment of B and C occurred. It was found that non-equilibrium grain boundary segregation of boron can affect the precipitation behaviour by making the boundary composition enter a new phase field ''Non-equilibrium phases'' might also form. The synergistic effect of B and Mo on the boundary composition and precipitation behaviour, and the observed indications of C non-equilibrium segregation are discussed
Institute of Scientific and Technical Information of China (English)
LIU FuPing; WANG AnLing; WANG AnXuan; CAO YueZu; CHEN Qiang; YANG ChangChun
2009-01-01
According to the electric potential of oblique multi-needle electrodes (OMNE) in biological tissue, the discrete equations based on the indetermination linear current density were established by the boundary element integral equations (BEIE). The non-uniform distribution of the current flowing from multi-needle electrodes to conductive biological tissues was imaged by solving a set of linear equa-tions. Then, the electric field and potential generated by OMNE in biological tissues at any point may be determined through the boundary element method (BEM). The time of program running and stability of computing method are examined by an example. It demonstrates that the algorithm possesses a quick speed and the steady computed results. It means that this method has an important referenced significance for computing the field and the potential generated by OMNE in bio-tissue, which is a fast, effective and accurate computing method.
Azis, Moh. Ivan; Kasbawati; Haddade, Amiruddin; Astuti Thamrin, Sri
2018-03-01
A boundary element method (BEM) is obtained for solving a boundary value problem of homogeneous anisotropic media governed by diffusion-convection equation. The application of the BEM is shown for two particular pollutant transport problems of Tello river and Unhas lake in Makassar Indonesia. For the two particular problems a variety of the coefficients of diffusion and the velocity components are taken. The results show that the solutions vary as the parameters change. And this suggests that one has to be careful in measuring or determining the values of the parameters.
DEFF Research Database (Denmark)
Cai, Hongzhu; Hu, Xiangyun; Xiong, Bin
2017-01-01
method which is unconditionally stable. We solve the diffusion equation for the electric field with a total field formulation. The finite element system of equation is solved using the direct method. The solutions of electric field, at different time, can be obtained using the effective time stepping...... method with trivial computation cost once the matrix is factorized. We try to keep the same time step size for a fixed number of steps using an adaptive time step doubling (ATSD) method. The finite element modeling domain is also truncated using a semi-adaptive method. We proposed a new boundary...... condition based on approximating the total field on the modeling boundary using the primary field corresponding to a layered background model. We validate our algorithm using several synthetic model studies....
Finite element and boundary element applications in quantum mechanics
International Nuclear Information System (INIS)
Ueta, Tsuyoshi
2003-01-01
Although this book is one of the Oxford Texts in Applied and Engineering Mathematics, we may think of it as a physics book. It explains how to solve the problem of quantum mechanics using the finite element method (FEM) and the boundary element method (BEM). Many examples analysing actual problems are also shown. As for the ratio of the number of pages of FEM and BEM, the former occupies about 80%. This is, however, reasonable reflecting the flexibility of FEM. Although many explanations of FEM and BEM exist, most are written using special mathematical expressions and numerical computation fields. However, this book is written in the 'language of physicists' throughout. I think that it is very readable and easy to understand for physicists. In the derivation of FEM and the argument on calculation accuracy, the action integral and a variation principle are used consistently. In the numerical computation of matrices, such as simultaneous equations and eigen value problems, a description of important points is also fully given. Moreover, the practical problems which become important in the electron device design field and the condensed matter physics field are dealt with as example computations, so that this book is very practical and applicable. It is characteristic and interesting that FEM is applied to solve the Schroedinger and Poisson equations consistently, and to the solution of the Ginzburg--Landau equation in superconductivity. BEM is applied to treat electric field enhancements due to surface plasmon excitations at metallic surfaces. A number of references are cited at the end of all the chapters, and this is very helpful. The description of quantum mechanics is also made appropriately and the actual application of quantum mechanics in condensed matter physics can also be surveyed. In the appendices, the mathematical foundation, such as numerical quadrature formulae and Green's functions, is conveniently described. I recommend this book to those who need to
Energy Technology Data Exchange (ETDEWEB)
Yokoi, T [Building Research Institute, Tokyo (Japan); Sanchez-Sesma, F [Universidad National Autonoma de Mexico, (Mexico). Institute de Ingenieria
1997-05-27
Formulation is introduced for discretizing a boundary integral equation into an indirect boundary element method for the solution of 3-dimensional topographic problems. Yokoi and Takenaka propose an analytical solution-capable reference solution (solution for the half space elastic body with flat free surface) to problems of topographic response to seismic motion in a 2-dimensional in-plane field. That is to say, they propose a boundary integral equation capable of effectively suppressing the non-physical waves that emerge in the result of computation in the wake of the truncation of the discretized ground surface making use of the wave field in a semi-infinite elastic body with flat free surface. They apply the proposed boundary integral equation discretized into the indirect boundary element method to solve some examples, and succeed in proving its validity. In this report, the equation is expanded to deal with 3-dimensional topographic problems. A problem of a P-wave vertically landing on a flat and free surface is solved by the conventional boundary integral equation and the proposed boundary integral equation, and the solutions are compared with each other. It is found that the new method, different from the conventional one, can delete non-physical waves from the analytical result. 4 figs.
Seismic wave propagation in non-homogeneous elastic media by boundary elements
Manolis, George D; Rangelov, Tsviatko V; Wuttke, Frank
2017-01-01
This book focuses on the mathematical potential and computational efficiency of the Boundary Element Method (BEM) for modeling seismic wave propagation in either continuous or discrete inhomogeneous elastic/viscoelastic, isotropic/anisotropic media containing multiple cavities, cracks, inclusions and surface topography. BEM models may take into account the entire seismic wave path from the seismic source through the geological deposits all the way up to the local site under consideration. The general presentation of the theoretical basis of elastodynamics for inhomogeneous and heterogeneous continua in the first part is followed by the analytical derivation of fundamental solutions and Green's functions for the governing field equations by the usage of Fourier and Radon transforms. The numerical implementation of the BEM is for antiplane in the second part as well as for plane strain boundary value problems in the third part. Verification studies and parametric analysis appear throughout the book, as do both ...
International Nuclear Information System (INIS)
Chiba, Gou; Tsuji, Masashi; Shimazu, Yoichiro
2001-01-01
A hierarchical domain decomposition boundary element method (HDD-BEM) that was developed to solve a two-dimensional neutron diffusion equation has been modified to deal with three-dimensional problems. In the HDD-BEM, the domain is decomposed into homogeneous regions. The boundary conditions on the common inner boundaries between decomposed regions and the neutron multiplication factor are initially assumed. With these assumptions, the neutron diffusion equations defined in decomposed homogeneous regions can be solved respectively by applying the boundary element method. This part corresponds to the 'lower level' calculations. At the 'higher level' calculations, the assumed values, the inner boundary conditions and the neutron multiplication factor, are modified so as to satisfy the continuity conditions for the neutron flux and the neutron currents on the inner boundaries. These procedures of the lower and higher levels are executed alternately and iteratively until the continuity conditions are satisfied within a convergence tolerance. With the hierarchical domain decomposition, it is possible to deal with problems composing a large number of regions, something that has been difficult with the conventional BEM. In this paper, it is showed that a three-dimensional problem even with 722 regions can be solved with a fine accuracy and an acceptable computation time. (author)
Directory of Open Access Journals (Sweden)
Roberto Ferreira Artoni
1999-03-01
Full Text Available The chromosomes of two neotropical freshwater fish species, namely Liposarcus anisitsi (Siluriformes, Loricariidae and Leporinus elongatus (Characiformes, Anostomidae, were investigated by means of C-banding, Ag-NORs, fluorochrome staining and banding by hot saline solution (HSS treatment, to reveal patterns of heterochromatin differentiation. The karyotype of L. anisitsi is described for the first time. Staining with the GC-specific fluorescent antibiotic mithramycin (MM revealed bright signals in some C-banded blocks in both species, suggesting that these MM+ heterochromatin contains GC-rich DNA. Banding by denaturation employing HSS, followed by Giemsa staining, yielded corresponding results documenting the thermal stability of GC-rich DNA part of heterochromatin positive after C-banding. In L. elongatus the Ag-NOR also followed the above banding patterns. However, in L. anisitsi the Ag-NOR was MM+ but negatively stained after C-banding and HSS treatment. L. elongatus also showed C-banded segments that were negative for mithramycin staining and HSS treatment. The results obtained evidence the heterochromatin heterogeneity in these fish species.Cromossomos mitóticos de duas especies de peixes neotropicais, Leporinus elongatus (Characiformes e Liposarcus anisitsi (Siluriformes, foram estudados por diferentes métodos de bandamentos, com o intuito de investigar a diferenciação da heterocromatina. Enquanto que a macroestrutura cariotípica de L. elongatus já foi objeto de estudos anteriores, o cariótipo de L. anisitsi está sendo apresentado pela primeira vez. Em ambas as espécies, a coloração dos cromossomos com a mitramicina (MM, fluorocromo GC específico, evidenciou sinais brilhantes em alguns segmentos heterocromáticos também positivos ao bandamento C, sugerindo ser esta fração da heterocromatina rica em seqüências de bases GC. O tratamento dos cromossomos com solução salina aquecida e posterior coloração com Giemsa
International Nuclear Information System (INIS)
Attrep, M. Jr.; Orth, C.J.; Quintana, L.R.
1994-01-01
The discovery of the iridium anomaly at the 65-Ma Cretaceous-Tertiary (K-T) extinction boundary initiated numerous investigations, including the search for the coupling of these extinctions with other astronomical events. One hypothesis is that these periodic extinctions are coupled to terrestrial impacts from cyclic swarms of comets or asteroids. The studies have focused on elucidating the conditions and causes of extinction of life at these geological boundaries using elemental abundance patterns. The authors use instrumental neutron activation methods to determine whole-rock abundances for about 40 trace and common elements in thousands of samples. The platinum group elements (iridium, gold, platinum, and osmium) and nickel are measured by radiochemical activation analysis. The authors can measure iridium at levels down to 1 picogram/gram level
Seismic response of three-dimensional topographies using a time-domain boundary element method
Janod, François; Coutant, Olivier
2000-08-01
We present a time-domain implementation for a boundary element method (BEM) to compute the diffraction of seismic waves by 3-D topographies overlying a homogeneous half-space. This implementation is chosen to overcome the memory limitations arising when solving the boundary conditions with a frequency-domain approach. This formulation is flexible because it allows one to make an adaptive use of the Green's function time translation properties: the boundary conditions solving scheme can be chosen as a trade-off between memory and cpu requirements. We explore here an explicit method of solution that requires little memory but a high cpu cost in order to run on a workstation computer. We obtain good results with four points per minimum wavelength discretization for various topographies and plane wave excitations. This implementation can be used for two different aims: the time-domain approach allows an easier implementation of the BEM in hybrid methods (e.g. coupling with finite differences), and it also allows one to run simple BEM models with reasonable computer requirements. In order to keep reasonable computation times, we do not introduce any interface and we only consider homogeneous models. Results are shown for different configurations: an explosion near a flat free surface, a plane wave vertically incident on a Gaussian hill and on a hemispherical cavity, and an explosion point below the surface of a Gaussian hill. Comparison is made with other numerical methods, such as finite difference methods (FDMs) and spectral elements.
Grain boundary segregation and intergranular failure
International Nuclear Information System (INIS)
White, C.L.
1980-01-01
Trace elements and impurities often segregate strongly to grain boundaries in metals and alloys. Concentrations of these elements at grain boundaries are often 10 3 to 10 5 times as great as their overall concentration in the alloy. Because of such segregation, certain trace elements can exert a disproportionate influence on material properties. One frequently observed consequence of trace element segregation to grain boundaries is the occurrence of grain boundary failure and low ductility. Less well known are incidences of improved ductility and inhibition of grain boundary fracture resulting from trace element segregation to grain boundaries in certain systems. An overview of trace element segregation and intergranular failure in a variety of alloy systems as well as preliminary results from studies on Al 3% Li will be presented
The molecular basis for stability of heterochromatin-mediated silencing in mammals.
Hiragami-Hamada, Kyoko; Xie, Sheila Q; Saveliev, Alexander; Uribe-Lewis, Santiago; Pombo, Ana; Festenstein, Richard
2009-11-04
The archetypal epigenetic phenomenon of position effect variegation (PEV) in Drosophila occurs when a gene is brought abnormally close to heterochromatin, resulting in stochastic silencing of the affected gene in a proportion of cells that would normally express it. PEV has been instrumental in unraveling epigenetic mechanisms. Using an in vivo mammalian model for PEV we have extensively investigated the molecular basis for heterochromatin-mediated gene silencing. Here we distinguish 'epigenetic effects' from other cellular differences by studying ex vivo cells that are identical, apart from the expression of the variegating gene which is silenced in a proportion of the cells. By separating cells according to transgene expression we show here that silencing appears to be associated with histone H3 lysine 9 trimethylation (H3K9me3), DNA methylation and the localization of the silenced gene to a specific nuclear compartment enriched in these modifications. In contrast, histone H3 acetylation (H3Ac) and lysine 4 di or tri methylation (H3K4me2/3) are the predominant modifications associated with expression where we see the gene in a euchromatic compartment. Interestingly, DNA methylation and inaccessibility, rather than H3K9me3, correlated most strongly with resistance to de-repression by cellular activation. These results have important implications for understanding the contribution of specific factors involved in the establishment and maintenance of gene silencing and activation in vivo.
The molecular basis for stability of heterochromatin-mediated silencing in mammals
Directory of Open Access Journals (Sweden)
Hiragami-Hamada Kyoko
2009-11-01
Full Text Available Abstract The archetypal epigenetic phenomenon of position effect variegation (PEV in Drosophila occurs when a gene is brought abnormally close to heterochromatin, resulting in stochastic silencing of the affected gene in a proportion of cells that would normally express it. PEV has been instrumental in unraveling epigenetic mechanisms. Using an in vivo mammalian model for PEV we have extensively investigated the molecular basis for heterochromatin-mediated gene silencing. Here we distinguish 'epigenetic effects' from other cellular differences by studying ex vivo cells that are identical, apart from the expression of the variegating gene which is silenced in a proportion of the cells. By separating cells according to transgene expression we show here that silencing appears to be associated with histone H3 lysine 9 trimethylation (H3K9me3, DNA methylation and the localization of the silenced gene to a specific nuclear compartment enriched in these modifications. In contrast, histone H3 acetylation (H3Ac and lysine 4 di or tri methylation (H3K4me2/3 are the predominant modifications associated with expression where we see the gene in a euchromatic compartment. Interestingly, DNA methylation and inaccessibility, rather than H3K9me3, correlated most strongly with resistance to de-repression by cellular activation. These results have important implications for understanding the contribution of specific factors involved in the establishment and maintenance of gene silencing and activation in vivo.
Energy Technology Data Exchange (ETDEWEB)
Namestnik, B; Skerget, L; Beadar, D [tehniska fakulteta, Maribor (Yugoslavia)
1989-07-01
The paper presents numerical method for evaluating heat transfer on two-dimensional ribbed surfaces. Governing elliptic partial differential equation is transformed to boundary integral equation, and solved by the boundary element method. Efficiency of fins is calculated from boundary heat flux balance. Several test cases have shown usefulness of the presented method. (author)
Interpretation of horizontal well performance in complicated systems by the boundary element method
Energy Technology Data Exchange (ETDEWEB)
Jongkittinarukorn, K.; Tiab, D. [Oklahoma Univ., School of Petroleum and Geological Engineering (United States); Escobar, F. H. [Surcolombiana Univ., Dept. of Petroleum Engineering (Colombia)
1998-12-31
A solution obtained by using the boundary element method to simulate pressure behaviour of horizontal wells in complicated reservoir-wellbore configurations is presented. Three different types of well bore and reservoir models were studied, i.e. a snake-shaped horizontal wellbore intersecting a two-layer reservoir with cross flow, a horizontal well in a three-layer reservoir with cross flow, and a vertical well intersecting a two-layer reservoir without cross flow. In each case, special attention was paid to the influence of wellbore inclination angle, the distance from the wellbore to the different boundaries and the permeability ratio. Performance of each of these types of wells are discussed. 9 refs., 18 figs.
International Nuclear Information System (INIS)
Muto, K.; Motosaka, M.; Kamata, M.; Masuda, K.; Urao, K.; Mameda, T.
1985-01-01
In order to investigate the 3-dimensional earthquake response characteristics of an embedded structure with consideration for soil-structure interaction, the authors have developed an analytical method using 3-dimensional hybrid model of boundary elements (BEM) and finite elements (FEM) and have conducted a dynamic analysis of an actual nuclear reactor building. This paper describes a comparative study between two different embedment depths in soil as elastic half-space. As the results, it was found that the earthquake response intensity decreases with the increase of the embedment depth and that this method was confirmed to be effective for investigating the 3-D response characteristics of embedded structures such as deflection pattern of each floor level, floor response spectra in high frequency range. (orig.)
Boundary element and speckle photography method for solving elasto-plastic problems
International Nuclear Information System (INIS)
Hadjikov, L.; Kavardjikov, V.; Valeva, V.
1985-01-01
The stress-strain state of metal specimens in the vicinity of a stress concentrator (circular hole) is investigated in case of a quasistatic loading. The displacements are evaluated numerically by the Boundary Element Method (BEM) and they are estimated experimentally by speckle photography. The experimentally and theoretically obtained results are compared and considered. A unified method for a simultaneous employment of both techniques is suggested. The experimental and theoretical techniques complement each other which results in an enhanced capability of the method proposed. (orig.)
Leung, Wilson; Shaffer, Christopher D.; Reed, Laura K.; Smith, Sheryl T.; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E. J.; Machone, Joshua F.; Patterson, Seantay D.; Price, Amber L.; Turner, Bryce A.; Robic, Srebrenka; Luippold, Erin K.; McCartha, Shannon R.; Walji, Tezin A.; Walker, Chelsea A.; Saville, Kenneth; Abrams, Marita K.; Armstrong, Andrew R.; Armstrong, William; Bailey, Robert J.; Barberi, Chelsea R.; Beck, Lauren R.; Blaker, Amanda L.; Blunden, Christopher E.; Brand, Jordan P.; Brock, Ethan J.; Brooks, Dana W.; Brown, Marie; Butzler, Sarah C.; Clark, Eric M.; Clark, Nicole B.; Collins, Ashley A.; Cotteleer, Rebecca J.; Cullimore, Peterson R.; Dawson, Seth G.; Docking, Carter T.; Dorsett, Sasha L.; Dougherty, Grace A.; Downey, Kaitlyn A.; Drake, Andrew P.; Earl, Erica K.; Floyd, Trevor G.; Forsyth, Joshua D.; Foust, Jonathan D.; Franchi, Spencer L.; Geary, James F.; Hanson, Cynthia K.; Harding, Taylor S.; Harris, Cameron B.; Heckman, Jonathan M.; Holderness, Heather L.; Howey, Nicole A.; Jacobs, Dontae A.; Jewell, Elizabeth S.; Kaisler, Maria; Karaska, Elizabeth A.; Kehoe, James L.; Koaches, Hannah C.; Koehler, Jessica; Koenig, Dana; Kujawski, Alexander J.; Kus, Jordan E.; Lammers, Jennifer A.; Leads, Rachel R.; Leatherman, Emily C.; Lippert, Rachel N.; Messenger, Gregory S.; Morrow, Adam T.; Newcomb, Victoria; Plasman, Haley J.; Potocny, Stephanie J.; Powers, Michelle K.; Reem, Rachel M.; Rennhack, Jonathan P.; Reynolds, Katherine R.; Reynolds, Lyndsey A.; Rhee, Dong K.; Rivard, Allyson B.; Ronk, Adam J.; Rooney, Meghan B.; Rubin, Lainey S.; Salbert, Luke R.; Saluja, Rasleen K.; Schauder, Taylor; Schneiter, Allison R.; Schulz, Robert W.; Smith, Karl E.; Spencer, Sarah; Swanson, Bryant R.; Tache, Melissa A.; Tewilliager, Ashley A.; Tilot, Amanda K.; VanEck, Eve; Villerot, Matthew M.; Vylonis, Megan B.; Watson, David T.; Wurzler, Juliana A.; Wysocki, Lauren M.; Yalamanchili, Monica; Zaborowicz, Matthew A.; Emerson, Julia A.; Ortiz, Carlos; Deuschle, Frederic J.; DiLorenzo, Lauren A.; Goeller, Katie L.; Macchi, Christopher R.; Muller, Sarah E.; Pasierb, Brittany D.; Sable, Joseph E.; Tucci, Jessica M.; Tynon, Marykathryn; Dunbar, David A.; Beken, Levent H.; Conturso, Alaina C.; Danner, Benjamin L.; DeMichele, Gabriella A.; Gonzales, Justin A.; Hammond, Maureen S.; Kelley, Colleen V.; Kelly, Elisabeth A.; Kulich, Danielle; Mageeney, Catherine M.; McCabe, Nikie L.; Newman, Alyssa M.; Spaeder, Lindsay A.; Tumminello, Richard A.; Revie, Dennis; Benson, Jonathon M.; Cristostomo, Michael C.; DaSilva, Paolo A.; Harker, Katherine S.; Jarrell, Jenifer N.; Jimenez, Luis A.; Katz, Brandon M.; Kennedy, William R.; Kolibas, Kimberly S.; LeBlanc, Mark T.; Nguyen, Trung T.; Nicolas, Daniel S.; Patao, Melissa D.; Patao, Shane M.; Rupley, Bryan J.; Sessions, Bridget J.; Weaver, Jennifer A.; Goodman, Anya L.; Alvendia, Erica L.; Baldassari, Shana M.; Brown, Ashley S.; Chase, Ian O.; Chen, Maida; Chiang, Scott; Cromwell, Avery B.; Custer, Ashley F.; DiTommaso, Tia M.; El-Adaimi, Jad; Goscinski, Nora C.; Grove, Ryan A.; Gutierrez, Nestor; Harnoto, Raechel S.; Hedeen, Heather; Hong, Emily L.; Hopkins, Barbara L.; Huerta, Vilma F.; Khoshabian, Colin; LaForge, Kristin M.; Lee, Cassidy T.; Lewis, Benjamin M.; Lydon, Anniken M.; Maniaci, Brian J.; Mitchell, Ryan D.; Morlock, Elaine V.; Morris, William M.; Naik, Priyanka; Olson, Nicole C.; Osterloh, Jeannette M.; Perez, Marcos A.; Presley, Jonathan D.; Randazzo, Matt J.; Regan, Melanie K.; Rossi, Franca G.; Smith, Melanie A.; Soliterman, Eugenia A.; Sparks, Ciani J.; Tran, Danny L.; Wan, Tiffany; Welker, Anne A.; Wong, Jeremy N.; Sreenivasan, Aparna; Youngblom, Jim; Adams, Andrew; Alldredge, Justin; Bryant, Ashley; Carranza, David; Cifelli, Alyssa; Coulson, Kevin; Debow, Calise; Delacruz, Noelle; Emerson, Charlene; Farrar, Cassandra; Foret, Don; Garibay, Edgar; Gooch, John; Heslop, Michelle; Kaur, Sukhjit; Khan, Ambreen; Kim, Van; Lamb, Travis; Lindbeck, Peter; Lucas, Gabi; Macias, Elizabeth; Martiniuc, Daniela; Mayorga, Lissett; Medina, Joseph; Membreno, Nelson; Messiah, Shady; Neufeld, Lacey; Nguyen, San Francisco; Nichols, Zachary; Odisho, George; Peterson, Daymon; Rodela, Laura; Rodriguez, Priscilla; Rodriguez, Vanessa; Ruiz, Jorge; Sherrill, Will; Silva, Valeria; Sparks, Jeri; Statton, Geeta; Townsend, Ashley; Valdez, Isabel; Waters, Mary; Westphal, Kyle; Winkler, Stacey; Zumkehr, Joannee; DeJong, Randall J.; Hoogewerf, Arlene J.; Ackerman, Cheri M.; Armistead, Isaac O.; Baatenburg, Lara; Borr, Matthew J.; Brouwer, Lindsay K.; Burkhart, Brandon J.; Bushhouse, Kelsey T.; Cesko, Lejla; Choi, Tiffany Y. Y.; Cohen, Heather; Damsteegt, Amanda M.; Darusz, Jess M.; Dauphin, Cory M.; Davis, Yelena P.; Diekema, Emily J.; Drewry, Melissa; Eisen, Michelle E. M.; Faber, Hayley M.; Faber, Katherine J.; Feenstra, Elizabeth; Felzer-Kim, Isabella T.; Hammond, Brandy L.; Hendriksma, Jesse; Herrold, Milton R.; Hilbrands, Julia A.; Howell, Emily J.; Jelgerhuis, Sarah A.; Jelsema, Timothy R.; Johnson, Benjamin K.; Jones, Kelly K.; Kim, Anna; Kooienga, Ross D.; Menyes, Erika E.; Nollet, Eric A.; Plescher, Brittany E.; Rios, Lindsay; Rose, Jenny L.; Schepers, Allison J.; Scott, Geoff; Smith, Joshua R.; Sterling, Allison M.; Tenney, Jenna C.; Uitvlugt, Chris; VanDyken, Rachel E.; VanderVennen, Marielle; Vue, Samantha; Kokan, Nighat P.; Agbley, Kwabea; Boham, Sampson K.; Broomfield, Daniel; Chapman, Kayla; Dobbe, Ali; Dobbe, Ian; Harrington, William; Ibrahem, Marwan; Kennedy, Andre; Koplinsky, Chad A.; Kubricky, Cassandra; Ladzekpo, Danielle; Pattison, Claire; Ramirez, Roman E.; Wande, Lucia; Woehlke, Sarah; Wawersik, Matthew; Kiernan, Elizabeth; Thompson, Jeffrey S.; Banker, Roxanne; Bartling, Justina R.; Bhatiya, Chinmoy I.; Boudoures, Anna L.; Christiansen, Lena; Fosselman, Daniel S.; French, Kristin M.; Gill, Ishwar S.; Havill, Jessen T.; Johnson, Jaelyn L.; Keny, Lauren J.; Kerber, John M.; Klett, Bethany M.; Kufel, Christina N.; May, Francis J.; Mecoli, Jonathan P.; Merry, Callie R.; Meyer, Lauren R.; Miller, Emily G.; Mullen, Gregory J.; Palozola, Katherine C.; Pfeil, Jacob J.; Thomas, Jessica G.; Verbofsky, Evan M.; Spana, Eric P.; Agarwalla, Anant; Chapman, Julia; Chlebina, Ben; Chong, Insun; Falk, I.N.; Fitzgibbons, John D.; Friedman, Harrison; Ighile, Osagie; Kim, Andrew J.; Knouse, Kristin A.; Kung, Faith; Mammo, Danny; Ng, Chun Leung; Nikam, Vinayak S.; Norton, Diana; Pham, Philip; Polk, Jessica W.; Prasad, Shreya; Rankin, Helen; Ratliff, Camille D.; Scala, Victoria; Schwartz, Nicholas U.; Shuen, Jessica A.; Xu, Amy; Xu, Thomas Q.; Zhang, Yi; Rosenwald, Anne G.; Burg, Martin G.; Adams, Stephanie J.; Baker, Morgan; Botsford, Bobbi; Brinkley, Briana; Brown, Carter; Emiah, Shadie; Enoch, Erica; Gier, Chad; Greenwell, Alyson; Hoogenboom, Lindsay; Matthews, Jordan E.; McDonald, Mitchell; Mercer, Amanda; Monsma, Nicholaus; Ostby, Kristine; Ramic, Alen; Shallman, Devon; Simon, Matthew; Spencer, Eric; Tomkins, Trisha; Wendland, Pete; Wylie, Anna; Wolyniak, Michael J.; Robertson, Gregory M.; Smith, Samuel I.; DiAngelo, Justin R.; Sassu, Eric D.; Bhalla, Satish C.; Sharif, Karim A.; Choeying, Tenzin; Macias, Jason S.; Sanusi, Fareed; Torchon, Karvyn; Bednarski, April E.; Alvarez, Consuelo J.; Davis, Kristen C.; Dunham, Carrie A.; Grantham, Alaina J.; Hare, Amber N.; Schottler, Jennifer; Scott, Zackary W.; Kuleck, Gary A.; Yu, Nicole S.; Kaehler, Marian M.; Jipp, Jacob; Overvoorde, Paul J.; Shoop, Elizabeth; Cyrankowski, Olivia; Hoover, Betsy; Kusner, Matt; Lin, Devry; Martinov, Tijana; Misch, Jonathan; Salzman, Garrett; Schiedermayer, Holly; Snavely, Michael; Zarrasola, Stephanie; Parrish, Susan; Baker, Atlee; Beckett, Alissa; Belella, Carissa; Bryant, Julie; Conrad, Turner; Fearnow, Adam; Gomez, Carolina; Herbstsomer, Robert A.; Hirsch, Sarah; Johnson, Christen; Jones, Melissa; Kabaso, Rita; Lemmon, Eric; Vieira, Carolina Marques dos Santos; McFarland, Darryl; McLaughlin, Christopher; Morgan, Abbie; Musokotwane, Sepo; Neutzling, William; Nietmann, Jana; Paluskievicz, Christina; Penn, Jessica; Peoples, Emily; Pozmanter, Caitlin; Reed, Emily; Rigby, Nichole; Schmidt, Lasse; Shelton, Micah; Shuford, Rebecca; Tirasawasdichai, Tiara; Undem, Blair; Urick, Damian; Vondy, Kayla; Yarrington, Bryan; Eckdahl, Todd T.; Poet, Jeffrey L.; Allen, Alica B.; Anderson, John E.; Barnett, Jason M.; Baumgardner, Jordan S.; Brown, Adam D.; Carney, Jordan E.; Chavez, Ramiro A.; Christgen, Shelbi L.; Christie, Jordan S.; Clary, Andrea N.; Conn, Michel A.; Cooper, Kristen M.; Crowley, Matt J.; Crowley, Samuel T.; Doty, Jennifer S.; Dow, Brian A.; Edwards, Curtis R.; Elder, Darcie D.; Fanning, John P.; Janssen, Bridget M.; Lambright, Anthony K.; Lane, Curtiss E.; Limle, Austin B.; Mazur, Tammy; McCracken, Marly R.; McDonough, Alexa M.; Melton, Amy D.; Minnick, Phillip J.; Musick, Adam E.; Newhart, William H.; Noynaert, Joseph W.; Ogden, Bradley J.; Sandusky, Michael W.; Schmuecker, Samantha M.; Shipman, Anna L.; Smith, Anna L.; Thomsen, Kristen M.; Unzicker, Matthew R.; Vernon, William B.; Winn, Wesley W.; Woyski, Dustin S.; Zhu, Xiao; Du, Chunguang; Ament, Caitlin; Aso, Soham; Bisogno, Laura Simone; Caronna, Jason; Fefelova, Nadezhda; Lopez, Lenin; Malkowitz, Lorraine; Marra, Jonathan; Menillo, Daniella; Obiorah, Ifeanyi; Onsarigo, Eric Nyabeta; Primus, Shekerah; Soos, Mahdi; Tare, Archana; Zidan, Ameer; Jones, Christopher J.; Aronhalt, Todd; Bellush, James M.; Burke, Christa; DeFazio, Steve; Does, Benjamin R.; Johnson, Todd D.; Keysock, Nicholas; Knudsen, Nelson H.; Messler, James; Myirski, Kevin; Rekai, Jade Lea; Rempe, Ryan Michael; Salgado, Michael S.; Stagaard, Erica; Starcher, Justin R.; Waggoner, Andrew W.; Yemelyanova, Anastasia K.; Hark, Amy T.; Bertolet, Anne; Kuschner, Cyrus E.; Parry, Kesley; Quach, Michael; Shantzer, Lindsey; Shaw, Mary E.; Smith, Mary A.; Glenn, Omolara; Mason, Portia; Williams, Charlotte; Key, S. Catherine Silver; Henry, Tyneshia C. P.; Johnson, Ashlee G.; White, Jackie X.; Haberman, Adam; Asinof, Sam; Drumm, Kelly; Freeburg, Trip; Safa, Nadia; Schultz, Darrin; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Wellinghoff, Jules; Hoopes, Laura L. M.; Chau, Kim M.; Ward, Alyssa; Regisford, E. Gloria C.; Augustine, LaJerald; Davis-Reyes, Brionna; Echendu, Vivienne; Hales, Jasmine; Ibarra, Sharon; Johnson, Lauriaun; Ovu, Steven; Braverman, John M.; Bahr, Thomas J.; Caesar, Nicole M.; Campana, Christopher; Cassidy, Daniel W.; Cognetti, Peter A.; English, Johnathan D.; Fadus, Matthew C.; Fick, Cameron N.; Freda, Philip J.; Hennessy, Bryan M.; Hockenberger, Kelsey; Jones, Jennifer K.; King, Jessica E.; Knob, Christopher R.; Kraftmann, Karen J.; Li, Linghui; Lupey, Lena N.; Minniti, Carl J.; Minton, Thomas F.; Moran, Joseph V.; Mudumbi, Krishna; Nordman, Elizabeth C.; Puetz, William J.; Robinson, Lauren M.; Rose, Thomas J.; Sweeney, Edward P.; Timko, Ashley S.; Paetkau, Don W.; Eisler, Heather L.; Aldrup, Megan E.; Bodenberg, Jessica M.; Cole, Mara G.; Deranek, Kelly M.; DeShetler, Megan; Dowd, Rose M.; Eckardt, Alexandra K.; Ehret, Sharon C.; Fese, Jessica; Garrett, Amanda D.; Kammrath, Anna; Kappes, Michelle L.; Light, Morgan R.; Meier, Anne C.; O’Rouke, Allison; Perella, Mallory; Ramsey, Kimberley; Ramthun, Jennifer R.; Reilly, Mary T.; Robinett, Deirdre; Rossi, Nadine L.; Schueler, Mary Grace; Shoemaker, Emma; Starkey, Kristin M.; Vetor, Ashley; Vrable, Abby; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R.; Herrick, Douglas A.; Khoury, Christopher B.; Lea, Charlotte; Louie, Christopher A.; Lowell, Shannon M.; Reynolds, Thomas J.; Schibler, Jeanine; Scoma, Alexandra H.; Smith-Gee, Maxwell T.; Tuberty, Sarah; Smith, Christopher D.; Lopilato, Jane E.; Hauke, Jeanette; Roecklein-Canfield, Jennifer A.; Corrielus, Maureen; Gilman, Hannah; Intriago, Stephanie; Maffa, Amanda; Rauf, Sabya A.; Thistle, Katrina; Trieu, Melissa; Winters, Jenifer; Yang, Bib; Hauser, Charles R.; Abusheikh, Tariq; Ashrawi, Yara; Benitez, Pedro; Boudreaux, Lauren R.; Bourland, Megan; Chavez, Miranda; Cruz, Samantha; Elliott, GiNell; Farek, Jesse R.; Flohr, Sarah; Flores, Amanda H.; Friedrichs, Chelsey; Fusco, Zach; Goodwin, Zane; Helmreich, Eric; Kiley, John; Knepper, John Mark; Langner, Christine; Martinez, Megan; Mendoza, Carlos; Naik, Monal; Ochoa, Andrea; Ragland, Nicolas; Raimey, England; Rathore, Sunil; Reza, Evangelina; Sadovsky, Griffin; Seydoux, Marie-Isabelle B.; Smith, Jonathan E.; Unruh, Anna K.; Velasquez, Vicente; Wolski, Matthew W.; Gosser, Yuying; Govind, Shubha; Clarke-Medley, Nicole; Guadron, Leslie; Lau, Dawn; Lu, Alvin; Mazzeo, Cheryl; Meghdari, Mariam; Ng, Simon; Pamnani, Brad; Plante, Olivia; Shum, Yuki Kwan Wa; Song, Roy; Johnson, Diana E.; Abdelnabi, Mai; Archambault, Alexi; Chamma, Norma; Gaur, Shailly; Hammett, Deborah; Kandahari, Adrese; Khayrullina, Guzal; Kumar, Sonali; Lawrence, Samantha; Madden, Nigel; Mandelbaum, Max; Milnthorp, Heather; Mohini, Shiv; Patel, Roshni; Peacock, Sarah J.; Perling, Emily; Quintana, Amber; Rahimi, Michael; Ramirez, Kristen; Singhal, Rishi; Weeks, Corinne; Wong, Tiffany; Gillis, Aubree T.; Moore, Zachary D.; Savell, Christopher D.; Watson, Reece; Mel, Stephanie F.; Anilkumar, Arjun A.; Bilinski, Paul; Castillo, Rostislav; Closser, Michael; Cruz, Nathalia M.; Dai, Tiffany; Garbagnati, Giancarlo F.; Horton, Lanor S.; Kim, Dongyeon; Lau, Joyce H.; Liu, James Z.; Mach, Sandy D.; Phan, Thu A.; Ren, Yi; Stapleton, Kenneth E.; Strelitz, Jean M.; Sunjed, Ray; Stamm, Joyce; Anderson, Morgan C.; Bonifield, Bethany Grace; Coomes, Daniel; Dillman, Adam; Durchholz, Elaine J.; Fafara-Thompson, Antoinette E.; Gross, Meleah J.; Gygi, Amber M.; Jackson, Lesley E.; Johnson, Amy; Kocsisova, Zuzana; Manghelli, Joshua L.; McNeil, Kylie; Murillo, Michael; Naylor, Kierstin L.; Neely, Jessica; Ogawa, Emmy E.; Rich, Ashley; Rogers, Anna; Spencer, J. Devin; Stemler, Kristina M.; Throm, Allison A.; Van Camp, Matt; Weihbrecht, Katie; Wiles, T. Aaron; Williams, Mallory A.; Williams, Matthew; Zoll, Kyle; Bailey, Cheryl; Zhou, Leming; Balthaser, Darla M.; Bashiri, Azita; Bower, Mindy E.; Florian, Kayla A.; Ghavam, Nazanin; Greiner-Sosanko, Elizabeth S.; Karim, Helmet; Mullen, Victor W.; Pelchen, Carly E.; Yenerall, Paul M.; Zhang, Jiayu; Rubin, Michael R.; Arias-Mejias, Suzette M.; Bermudez-Capo, Armando G.; Bernal-Vega, Gabriela V.; Colon-Vazquez, Mariela; Flores-Vazquez, Arelys; Gines-Rosario, Mariela; Llavona-Cartagena, Ivan G.; Martinez-Rodriguez, Javier O.; Ortiz-Fuentes, Lionel; Perez-Colomba, Eliezer O.; Perez-Otero, Joseph; Rivera, Elisandra; Rodriguez-Giron, Luke J.; Santiago-Sanabria, Arnaldo J.; Senquiz-Gonzalez, Andrea M.; delValle, Frank R. Soto; Vargas-Franco, Dorianmarie; Velázquez-Soto, Karla I.; Zambrana-Burgos, Joan D.; Martinez-Cruzado, Juan Carlos; Asencio-Zayas, Lillyann; Babilonia-Figueroa, Kevin; Beauchamp-Pérez, Francis D.; Belén-Rodríguez, Juliana; Bracero-Quiñones, Luciann; Burgos-Bula, Andrea P.; Collado-Méndez, Xavier A.; Colón-Cruz, Luis R.; Correa-Muller, Ana I.; Crooke-Rosado, Jonathan L.; Cruz-García, José M.; Defendini-Ávila, Marianna; Delgado-Peraza, Francheska M.; Feliciano-Cancela, Alex J.; Gónzalez-Pérez, Valerie M.; Guiblet, Wilfried; Heredia-Negrón, Aldo; Hernández-Muñiz, Jennifer; Irizarry-González, Lourdes N.; Laboy-Corales, Ángel L.; Llaurador-Caraballo, Gabriela A.; Marín-Maldonado, Frances; Marrero-Llerena, Ulises; Martell-Martínez, Héctor A.; Martínez-Traverso, Idaliz M.; Medina-Ortega, Kiara N.; Méndez-Castellanos, Sonya G.; Menéndez-Serrano, Krizia C.; Morales-Caraballo, Carol I.; Ortiz-DeChoudens, Saryleine; Ortiz-Ortiz, Patricia; Pagán-Torres, Hendrick; Pérez-Afanador, Diana; Quintana-Torres, Enid M.; Ramírez-Aponte, Edwin G.; Riascos-Cuero, Carolina; Rivera-Llovet, Michelle S.; Rivera-Pagán, Ingrid T.; Rivera-Vicéns, Ramón E.; Robles-Juarbe, Fabiola; Rodríguez-Bonilla, Lorraine; Rodríguez-Echevarría, Brian O.; Rodríguez-García, Priscila M.; Rodríguez-Laboy, Abneris E.; Rodríguez-Santiago, Susana; Rojas-Vargas, Michael L.; Rubio-Marrero, Eva N.; Santiago-Colón, Albeliz; Santiago-Ortiz, Jorge L.; Santos-Ramos, Carlos E.; Serrano-González, Joseline; Tamayo-Figueroa, Alina M.; Tascón-Peñaranda, Edna P.; Torres-Castillo, José L.; Valentín-Feliciano, Nelson A.; Valentín-Feliciano, Yashira M.; Vargas-Barreto, Nadyan M.; Vélez-Vázquez, Miguel; Vilanova-Vélez, Luis R.; Zambrana-Echevarría, Cristina; MacKinnon, Christy; Chung, Hui-Min; Kay, Chris; Pinto, Anthony; Kopp, Olga R.; Burkhardt, Joshua; Harward, Chris; Allen, Robert; Bhat, Pavan; Chang, Jimmy Hsiang-Chun; Chen, York; Chesley, Christopher; Cohn, Dara; DuPuis, David; Fasano, Michael; Fazzio, Nicholas; Gavinski, Katherine; Gebreyesus, Heran; Giarla, Thomas; Gostelow, Marcus; Greenstein, Rachel; Gunasinghe, Hashini; Hanson, Casey; Hay, Amanda; He, Tao Jian; Homa, Katie; Howe, Ruth; Howenstein, Jeff; Huang, Henry; Khatri, Aaditya; Kim, Young Lu; Knowles, Olivia; Kong, Sarah; Krock, Rebecca; Kroll, Matt; Kuhn, Julia; Kwong, Matthew; Lee, Brandon; Lee, Ryan; Levine, Kevin; Li, Yedda; Liu, Bo; Liu, Lucy; Liu, Max; Lousararian, Adam; Ma, Jimmy; Mallya, Allyson; Manchee, Charlie; Marcus, Joseph; McDaniel, Stephen; Miller, Michelle L.; Molleston, Jerome M.; Diez, Cristina Montero; Ng, Patrick; Ngai, Natalie; Nguyen, Hien; Nylander, Andrew; Pollack, Jason; Rastogi, Suchita; Reddy, Himabindu; Regenold, Nathaniel; Sarezky, Jon; Schultz, Michael; Shim, Jien; Skorupa, Tara; Smith, Kenneth; Spencer, Sarah J.; Srikanth, Priya; Stancu, Gabriel; Stein, Andrew P.; Strother, Marshall; Sudmeier, Lisa; Sun, Mengyang; Sundaram, Varun; Tazudeen, Noor; Tseng, Alan; Tzeng, Albert; Venkat, Rohit; Venkataram, Sandeep; Waldman, Leah; Wang, Tracy; Yang, Hao; Yu, Jack Y.; Zheng, Yin; Preuss, Mary L.; Garcia, Angelica; Juergens, Matt; Morris, Robert W.; Nagengast, Alexis A.; Azarewicz, Julie; Carr, Thomas J.; Chichearo, Nicole; Colgan, Mike; Donegan, Megan; Gardner, Bob; Kolba, Nik; Krumm, Janice L.; Lytle, Stacey; MacMillian, Laurell; Miller, Mary; Montgomery, Andrew; Moretti, Alysha; Offenbacker, Brittney; Polen, Mike; Toth, John; Woytanowski, John; Kadlec, Lisa; Crawford, Justin; Spratt, Mary L.; Adams, Ashley L.; Barnard, Brianna K.; Cheramie, Martin N.; Eime, Anne M.; Golden, Kathryn L.; Hawkins, Allyson P.; Hill, Jessica E.; Kampmeier, Jessica A.; Kern, Cody D.; Magnuson, Emily E.; Miller, Ashley R.; Morrow, Cody M.; Peairs, Julia C.; Pickett, Gentry L.; Popelka, Sarah A.; Scott, Alexis J.; Teepe, Emily J.; TerMeer, Katie A.; Watchinski, Carmen A.; Watson, Lucas A.; Weber, Rachel E.; Woodard, Kate A.; Barnard, Daron C.; Appiah, Isaac; Giddens, Michelle M.; McNeil, Gerard P.; Adebayo, Adeola; Bagaeva, Kate; Chinwong, Justina; Dol, Chrystel; George, Eunice; Haltaufderhyde, Kirk; Haye, Joanna; Kaur, Manpreet; Semon, Max; Serjanov, Dmitri; Toorie, Anika; Wilson, Christopher; Riddle, Nicole C.; Buhler, Jeremy; Mardis, Elaine R.
2015-01-01
The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. PMID:25740935
Leung, Wilson; Shaffer, Christopher D; Reed, Laura K; Smith, Sheryl T; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E J; Machone, Joshua F; Patterson, Seantay D; Price, Amber L; Turner, Bryce A; Robic, Srebrenka; Luippold, Erin K; McCartha, Shannon R; Walji, Tezin A; Walker, Chelsea A; Saville, Kenneth; Abrams, Marita K; Armstrong, Andrew R; Armstrong, William; Bailey, Robert J; Barberi, Chelsea R; Beck, Lauren R; Blaker, Amanda L; Blunden, Christopher E; Brand, Jordan P; Brock, Ethan J; Brooks, Dana W; Brown, Marie; Butzler, Sarah C; Clark, Eric M; Clark, Nicole B; Collins, Ashley A; Cotteleer, Rebecca J; Cullimore, Peterson R; Dawson, Seth G; Docking, Carter T; Dorsett, Sasha L; Dougherty, Grace A; Downey, Kaitlyn A; Drake, Andrew P; Earl, Erica K; Floyd, Trevor G; Forsyth, Joshua D; Foust, Jonathan D; Franchi, Spencer L; Geary, James F; Hanson, Cynthia K; Harding, Taylor S; Harris, Cameron B; Heckman, Jonathan M; Holderness, Heather L; Howey, Nicole A; Jacobs, Dontae A; Jewell, Elizabeth S; Kaisler, Maria; Karaska, Elizabeth A; Kehoe, James L; Koaches, Hannah C; Koehler, Jessica; Koenig, Dana; Kujawski, Alexander J; Kus, Jordan E; Lammers, Jennifer A; Leads, Rachel R; Leatherman, Emily C; Lippert, Rachel N; Messenger, Gregory S; Morrow, Adam T; Newcomb, Victoria; Plasman, Haley J; Potocny, Stephanie J; Powers, Michelle K; Reem, Rachel M; Rennhack, Jonathan P; Reynolds, Katherine R; Reynolds, Lyndsey A; Rhee, Dong K; Rivard, Allyson B; Ronk, Adam J; Rooney, Meghan B; Rubin, Lainey S; Salbert, Luke R; Saluja, Rasleen K; Schauder, Taylor; Schneiter, Allison R; Schulz, Robert W; Smith, Karl E; Spencer, Sarah; Swanson, Bryant R; Tache, Melissa A; Tewilliager, Ashley A; Tilot, Amanda K; VanEck, Eve; Villerot, Matthew M; Vylonis, Megan B; Watson, David T; Wurzler, Juliana A; Wysocki, Lauren M; Yalamanchili, Monica; Zaborowicz, Matthew A; Emerson, Julia A; Ortiz, Carlos; Deuschle, Frederic J; DiLorenzo, Lauren A; Goeller, Katie L; Macchi, Christopher R; Muller, Sarah E; Pasierb, Brittany D; Sable, Joseph E; Tucci, Jessica M; Tynon, Marykathryn; Dunbar, David A; Beken, Levent H; Conturso, Alaina C; Danner, Benjamin L; DeMichele, Gabriella A; Gonzales, Justin A; Hammond, Maureen S; Kelley, Colleen V; Kelly, Elisabeth A; Kulich, Danielle; Mageeney, Catherine M; McCabe, Nikie L; Newman, Alyssa M; Spaeder, Lindsay A; Tumminello, Richard A; Revie, Dennis; Benson, Jonathon M; Cristostomo, Michael C; DaSilva, Paolo A; Harker, Katherine S; Jarrell, Jenifer N; Jimenez, Luis A; Katz, Brandon M; Kennedy, William R; Kolibas, Kimberly S; LeBlanc, Mark T; Nguyen, Trung T; Nicolas, Daniel S; Patao, Melissa D; Patao, Shane M; Rupley, Bryan J; Sessions, Bridget J; Weaver, Jennifer A; Goodman, Anya L; Alvendia, Erica L; Baldassari, Shana M; Brown, Ashley S; Chase, Ian O; Chen, Maida; Chiang, Scott; Cromwell, Avery B; Custer, Ashley F; DiTommaso, Tia M; El-Adaimi, Jad; Goscinski, Nora C; Grove, Ryan A; Gutierrez, Nestor; Harnoto, Raechel S; Hedeen, Heather; Hong, Emily L; Hopkins, Barbara L; Huerta, Vilma F; Khoshabian, Colin; LaForge, Kristin M; Lee, Cassidy T; Lewis, Benjamin M; Lydon, Anniken M; Maniaci, Brian J; Mitchell, Ryan D; Morlock, Elaine V; Morris, William M; Naik, Priyanka; Olson, Nicole C; Osterloh, Jeannette M; Perez, Marcos A; Presley, Jonathan D; Randazzo, Matt J; Regan, Melanie K; Rossi, Franca G; Smith, Melanie A; Soliterman, Eugenia A; Sparks, Ciani J; Tran, Danny L; Wan, Tiffany; Welker, Anne A; Wong, Jeremy N; Sreenivasan, Aparna; Youngblom, Jim; Adams, Andrew; Alldredge, Justin; Bryant, Ashley; Carranza, David; Cifelli, Alyssa; Coulson, Kevin; Debow, Calise; Delacruz, Noelle; Emerson, Charlene; Farrar, Cassandra; Foret, Don; Garibay, Edgar; Gooch, John; Heslop, Michelle; Kaur, Sukhjit; Khan, Ambreen; Kim, Van; Lamb, Travis; Lindbeck, Peter; Lucas, Gabi; Macias, Elizabeth; Martiniuc, Daniela; Mayorga, Lissett; Medina, Joseph; Membreno, Nelson; Messiah, Shady; Neufeld, Lacey; Nguyen, San Francisco; Nichols, Zachary; Odisho, George; Peterson, Daymon; Rodela, Laura; Rodriguez, Priscilla; Rodriguez, Vanessa; Ruiz, Jorge; Sherrill, Will; Silva, Valeria; Sparks, Jeri; Statton, Geeta; Townsend, Ashley; Valdez, Isabel; Waters, Mary; Westphal, Kyle; Winkler, Stacey; Zumkehr, Joannee; DeJong, Randall J; Hoogewerf, Arlene J; Ackerman, Cheri M; Armistead, Isaac O; Baatenburg, Lara; Borr, Matthew J; Brouwer, Lindsay K; Burkhart, Brandon J; Bushhouse, Kelsey T; Cesko, Lejla; Choi, Tiffany Y Y; Cohen, Heather; Damsteegt, Amanda M; Darusz, Jess M; Dauphin, Cory M; Davis, Yelena P; Diekema, Emily J; Drewry, Melissa; Eisen, Michelle E M; Faber, Hayley M; Faber, Katherine J; Feenstra, Elizabeth; Felzer-Kim, Isabella T; Hammond, Brandy L; Hendriksma, Jesse; Herrold, Milton R; Hilbrands, Julia A; Howell, Emily J; Jelgerhuis, Sarah A; Jelsema, Timothy R; Johnson, Benjamin K; Jones, Kelly K; Kim, Anna; Kooienga, Ross D; Menyes, Erika E; Nollet, Eric A; Plescher, Brittany E; Rios, Lindsay; Rose, Jenny L; Schepers, Allison J; Scott, Geoff; Smith, Joshua R; Sterling, Allison M; Tenney, Jenna C; Uitvlugt, Chris; VanDyken, Rachel E; VanderVennen, Marielle; Vue, Samantha; Kokan, Nighat P; Agbley, Kwabea; Boham, Sampson K; Broomfield, Daniel; Chapman, Kayla; Dobbe, Ali; Dobbe, Ian; Harrington, William; Ibrahem, Marwan; Kennedy, Andre; Koplinsky, Chad A; Kubricky, Cassandra; Ladzekpo, Danielle; Pattison, Claire; Ramirez, Roman E; Wande, Lucia; Woehlke, Sarah; Wawersik, Matthew; Kiernan, Elizabeth; Thompson, Jeffrey S; Banker, Roxanne; Bartling, Justina R; Bhatiya, Chinmoy I; Boudoures, Anna L; Christiansen, Lena; Fosselman, Daniel S; French, Kristin M; Gill, Ishwar S; Havill, Jessen T; Johnson, Jaelyn L; Keny, Lauren J; Kerber, John M; Klett, Bethany M; Kufel, Christina N; May, Francis J; Mecoli, Jonathan P; Merry, Callie R; Meyer, Lauren R; Miller, Emily G; Mullen, Gregory J; Palozola, Katherine C; Pfeil, Jacob J; Thomas, Jessica G; Verbofsky, Evan M; Spana, Eric P; Agarwalla, Anant; Chapman, Julia; Chlebina, Ben; Chong, Insun; Falk, I N; Fitzgibbons, John D; Friedman, Harrison; Ighile, Osagie; Kim, Andrew J; Knouse, Kristin A; Kung, Faith; Mammo, Danny; Ng, Chun Leung; Nikam, Vinayak S; Norton, Diana; Pham, Philip; Polk, Jessica W; Prasad, Shreya; Rankin, Helen; Ratliff, Camille D; Scala, Victoria; Schwartz, Nicholas U; Shuen, Jessica A; Xu, Amy; Xu, Thomas Q; Zhang, Yi; Rosenwald, Anne G; Burg, Martin G; Adams, Stephanie J; Baker, Morgan; Botsford, Bobbi; Brinkley, Briana; Brown, Carter; Emiah, Shadie; Enoch, Erica; Gier, Chad; Greenwell, Alyson; Hoogenboom, Lindsay; Matthews, Jordan E; McDonald, Mitchell; Mercer, Amanda; Monsma, Nicholaus; Ostby, Kristine; Ramic, Alen; Shallman, Devon; Simon, Matthew; Spencer, Eric; Tomkins, Trisha; Wendland, Pete; Wylie, Anna; Wolyniak, Michael J; Robertson, Gregory M; Smith, Samuel I; DiAngelo, Justin R; Sassu, Eric D; Bhalla, Satish C; Sharif, Karim A; Choeying, Tenzin; Macias, Jason S; Sanusi, Fareed; Torchon, Karvyn; Bednarski, April E; Alvarez, Consuelo J; Davis, Kristen C; Dunham, Carrie A; Grantham, Alaina J; Hare, Amber N; Schottler, Jennifer; Scott, Zackary W; Kuleck, Gary A; Yu, Nicole S; Kaehler, Marian M; Jipp, Jacob; Overvoorde, Paul J; Shoop, Elizabeth; Cyrankowski, Olivia; Hoover, Betsy; Kusner, Matt; Lin, Devry; Martinov, Tijana; Misch, Jonathan; Salzman, Garrett; Schiedermayer, Holly; Snavely, Michael; Zarrasola, Stephanie; Parrish, Susan; Baker, Atlee; Beckett, Alissa; Belella, Carissa; Bryant, Julie; Conrad, Turner; Fearnow, Adam; Gomez, Carolina; Herbstsomer, Robert A; Hirsch, Sarah; Johnson, Christen; Jones, Melissa; Kabaso, Rita; Lemmon, Eric; Vieira, Carolina Marques Dos Santos; McFarland, Darryl; McLaughlin, Christopher; Morgan, Abbie; Musokotwane, Sepo; Neutzling, William; Nietmann, Jana; Paluskievicz, Christina; Penn, Jessica; Peoples, Emily; Pozmanter, Caitlin; Reed, Emily; Rigby, Nichole; Schmidt, Lasse; Shelton, Micah; Shuford, Rebecca; Tirasawasdichai, Tiara; Undem, Blair; Urick, Damian; Vondy, Kayla; Yarrington, Bryan; Eckdahl, Todd T; Poet, Jeffrey L; Allen, Alica B; Anderson, John E; Barnett, Jason M; Baumgardner, Jordan S; Brown, Adam D; Carney, Jordan E; Chavez, Ramiro A; Christgen, Shelbi L; Christie, Jordan S; Clary, Andrea N; Conn, Michel A; Cooper, Kristen M; Crowley, Matt J; Crowley, Samuel T; Doty, Jennifer S; Dow, Brian A; Edwards, Curtis R; Elder, Darcie D; Fanning, John P; Janssen, Bridget M; Lambright, Anthony K; Lane, Curtiss E; Limle, Austin B; Mazur, Tammy; McCracken, Marly R; McDonough, Alexa M; Melton, Amy D; Minnick, Phillip J; Musick, Adam E; Newhart, William H; Noynaert, Joseph W; Ogden, Bradley J; Sandusky, Michael W; Schmuecker, Samantha M; Shipman, Anna L; Smith, Anna L; Thomsen, Kristen M; Unzicker, Matthew R; Vernon, William B; Winn, Wesley W; Woyski, Dustin S; Zhu, Xiao; Du, Chunguang; Ament, Caitlin; Aso, Soham; Bisogno, Laura Simone; Caronna, Jason; Fefelova, Nadezhda; Lopez, Lenin; Malkowitz, Lorraine; Marra, Jonathan; Menillo, Daniella; Obiorah, Ifeanyi; Onsarigo, Eric Nyabeta; Primus, Shekerah; Soos, Mahdi; Tare, Archana; Zidan, Ameer; Jones, Christopher J; Aronhalt, Todd; Bellush, James M; Burke, Christa; DeFazio, Steve; Does, Benjamin R; Johnson, Todd D; Keysock, Nicholas; Knudsen, Nelson H; Messler, James; Myirski, Kevin; Rekai, Jade Lea; Rempe, Ryan Michael; Salgado, Michael S; Stagaard, Erica; Starcher, Justin R; Waggoner, Andrew W; Yemelyanova, Anastasia K; Hark, Amy T; Bertolet, Anne; Kuschner, Cyrus E; Parry, Kesley; Quach, Michael; Shantzer, Lindsey; Shaw, Mary E; Smith, Mary A; Glenn, Omolara; Mason, Portia; Williams, Charlotte; Key, S Catherine Silver; Henry, Tyneshia C P; Johnson, Ashlee G; White, Jackie X; Haberman, Adam; Asinof, Sam; Drumm, Kelly; Freeburg, Trip; Safa, Nadia; Schultz, Darrin; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Wellinghoff, Jules; Hoopes, Laura L M; Chau, Kim M; Ward, Alyssa; Regisford, E Gloria C; Augustine, LaJerald; Davis-Reyes, Brionna; Echendu, Vivienne; Hales, Jasmine; Ibarra, Sharon; Johnson, Lauriaun; Ovu, Steven; Braverman, John M; Bahr, Thomas J; Caesar, Nicole M; Campana, Christopher; Cassidy, Daniel W; Cognetti, Peter A; English, Johnathan D; Fadus, Matthew C; Fick, Cameron N; Freda, Philip J; Hennessy, Bryan M; Hockenberger, Kelsey; Jones, Jennifer K; King, Jessica E; Knob, Christopher R; Kraftmann, Karen J; Li, Linghui; Lupey, Lena N; Minniti, Carl J; Minton, Thomas F; Moran, Joseph V; Mudumbi, Krishna; Nordman, Elizabeth C; Puetz, William J; Robinson, Lauren M; Rose, Thomas J; Sweeney, Edward P; Timko, Ashley S; Paetkau, Don W; Eisler, Heather L; Aldrup, Megan E; Bodenberg, Jessica M; Cole, Mara G; Deranek, Kelly M; DeShetler, Megan; Dowd, Rose M; Eckardt, Alexandra K; Ehret, Sharon C; Fese, Jessica; Garrett, Amanda D; Kammrath, Anna; Kappes, Michelle L; Light, Morgan R; Meier, Anne C; O'Rouke, Allison; Perella, Mallory; Ramsey, Kimberley; Ramthun, Jennifer R; Reilly, Mary T; Robinett, Deirdre; Rossi, Nadine L; Schueler, Mary Grace; Shoemaker, Emma; Starkey, Kristin M; Vetor, Ashley; Vrable, Abby; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R; Herrick, Douglas A; Khoury, Christopher B; Lea, Charlotte; Louie, Christopher A; Lowell, Shannon M; Reynolds, Thomas J; Schibler, Jeanine; Scoma, Alexandra H; Smith-Gee, Maxwell T; Tuberty, Sarah; Smith, Christopher D; Lopilato, Jane E; Hauke, Jeanette; Roecklein-Canfield, Jennifer A; Corrielus, Maureen; Gilman, Hannah; Intriago, Stephanie; Maffa, Amanda; Rauf, Sabya A; Thistle, Katrina; Trieu, Melissa; Winters, Jenifer; Yang, Bib; Hauser, Charles R; Abusheikh, Tariq; Ashrawi, Yara; Benitez, Pedro; Boudreaux, Lauren R; Bourland, Megan; Chavez, Miranda; Cruz, Samantha; Elliott, GiNell; Farek, Jesse R; Flohr, Sarah; Flores, Amanda H; Friedrichs, Chelsey; Fusco, Zach; Goodwin, Zane; Helmreich, Eric; Kiley, John; Knepper, John Mark; Langner, Christine; Martinez, Megan; Mendoza, Carlos; Naik, Monal; Ochoa, Andrea; Ragland, Nicolas; Raimey, England; Rathore, Sunil; Reza, Evangelina; Sadovsky, Griffin; Seydoux, Marie-Isabelle B; Smith, Jonathan E; Unruh, Anna K; Velasquez, Vicente; Wolski, Matthew W; Gosser, Yuying; Govind, Shubha; Clarke-Medley, Nicole; Guadron, Leslie; Lau, Dawn; Lu, Alvin; Mazzeo, Cheryl; Meghdari, Mariam; Ng, Simon; Pamnani, Brad; Plante, Olivia; Shum, Yuki Kwan Wa; Song, Roy; Johnson, Diana E; Abdelnabi, Mai; Archambault, Alexi; Chamma, Norma; Gaur, Shailly; Hammett, Deborah; Kandahari, Adrese; Khayrullina, Guzal; Kumar, Sonali; Lawrence, Samantha; Madden, Nigel; Mandelbaum, Max; Milnthorp, Heather; Mohini, Shiv; Patel, Roshni; Peacock, Sarah J; Perling, Emily; Quintana, Amber; Rahimi, Michael; Ramirez, Kristen; Singhal, Rishi; Weeks, Corinne; Wong, Tiffany; Gillis, Aubree T; Moore, Zachary D; Savell, Christopher D; Watson, Reece; Mel, Stephanie F; Anilkumar, Arjun A; Bilinski, Paul; Castillo, Rostislav; Closser, Michael; Cruz, Nathalia M; Dai, Tiffany; Garbagnati, Giancarlo F; Horton, Lanor S; Kim, Dongyeon; Lau, Joyce H; Liu, James Z; Mach, Sandy D; Phan, Thu A; Ren, Yi; Stapleton, Kenneth E; Strelitz, Jean M; Sunjed, Ray; Stamm, Joyce; Anderson, Morgan C; Bonifield, Bethany Grace; Coomes, Daniel; Dillman, Adam; Durchholz, Elaine J; Fafara-Thompson, Antoinette E; Gross, Meleah J; Gygi, Amber M; Jackson, Lesley E; Johnson, Amy; Kocsisova, Zuzana; Manghelli, Joshua L; McNeil, Kylie; Murillo, Michael; Naylor, Kierstin L; Neely, Jessica; Ogawa, Emmy E; Rich, Ashley; Rogers, Anna; Spencer, J Devin; Stemler, Kristina M; Throm, Allison A; Van Camp, Matt; Weihbrecht, Katie; Wiles, T Aaron; Williams, Mallory A; Williams, Matthew; Zoll, Kyle; Bailey, Cheryl; Zhou, Leming; Balthaser, Darla M; Bashiri, Azita; Bower, Mindy E; Florian, Kayla A; Ghavam, Nazanin; Greiner-Sosanko, Elizabeth S; Karim, Helmet; Mullen, Victor W; Pelchen, Carly E; Yenerall, Paul M; Zhang, Jiayu; Rubin, Michael R; Arias-Mejias, Suzette M; Bermudez-Capo, Armando G; Bernal-Vega, Gabriela V; Colon-Vazquez, Mariela; Flores-Vazquez, Arelys; Gines-Rosario, Mariela; Llavona-Cartagena, Ivan G; Martinez-Rodriguez, Javier O; Ortiz-Fuentes, Lionel; Perez-Colomba, Eliezer O; Perez-Otero, Joseph; Rivera, Elisandra; Rodriguez-Giron, Luke J; Santiago-Sanabria, Arnaldo J; Senquiz-Gonzalez, Andrea M; delValle, Frank R Soto; Vargas-Franco, Dorianmarie; Velázquez-Soto, Karla I; Zambrana-Burgos, Joan D; Martinez-Cruzado, Juan Carlos; Asencio-Zayas, Lillyann; Babilonia-Figueroa, Kevin; Beauchamp-Pérez, Francis D; Belén-Rodríguez, Juliana; Bracero-Quiñones, Luciann; Burgos-Bula, Andrea P; Collado-Méndez, Xavier A; Colón-Cruz, Luis R; Correa-Muller, Ana I; Crooke-Rosado, Jonathan L; Cruz-García, José M; Defendini-Ávila, Marianna; Delgado-Peraza, Francheska M; Feliciano-Cancela, Alex J; Gónzalez-Pérez, Valerie M; Guiblet, Wilfried; Heredia-Negrón, Aldo; Hernández-Muñiz, Jennifer; Irizarry-González, Lourdes N; Laboy-Corales, Ángel L; Llaurador-Caraballo, Gabriela A; Marín-Maldonado, Frances; Marrero-Llerena, Ulises; Martell-Martínez, Héctor A; Martínez-Traverso, Idaliz M; Medina-Ortega, Kiara N; Méndez-Castellanos, Sonya G; Menéndez-Serrano, Krizia C; Morales-Caraballo, Carol I; Ortiz-DeChoudens, Saryleine; Ortiz-Ortiz, Patricia; Pagán-Torres, Hendrick; Pérez-Afanador, Diana; Quintana-Torres, Enid M; Ramírez-Aponte, Edwin G; Riascos-Cuero, Carolina; Rivera-Llovet, Michelle S; Rivera-Pagán, Ingrid T; Rivera-Vicéns, Ramón E; Robles-Juarbe, Fabiola; Rodríguez-Bonilla, Lorraine; Rodríguez-Echevarría, Brian O; Rodríguez-García, Priscila M; Rodríguez-Laboy, Abneris E; Rodríguez-Santiago, Susana; Rojas-Vargas, Michael L; Rubio-Marrero, Eva N; Santiago-Colón, Albeliz; Santiago-Ortiz, Jorge L; Santos-Ramos, Carlos E; Serrano-González, Joseline; Tamayo-Figueroa, Alina M; Tascón-Peñaranda, Edna P; Torres-Castillo, José L; Valentín-Feliciano, Nelson A; Valentín-Feliciano, Yashira M; Vargas-Barreto, Nadyan M; Vélez-Vázquez, Miguel; Vilanova-Vélez, Luis R; Zambrana-Echevarría, Cristina; MacKinnon, Christy; Chung, Hui-Min; Kay, Chris; Pinto, Anthony; Kopp, Olga R; Burkhardt, Joshua; Harward, Chris; Allen, Robert; Bhat, Pavan; Chang, Jimmy Hsiang-Chun; Chen, York; Chesley, Christopher; Cohn, Dara; DuPuis, David; Fasano, Michael; Fazzio, Nicholas; Gavinski, Katherine; Gebreyesus, Heran; Giarla, Thomas; Gostelow, Marcus; Greenstein, Rachel; Gunasinghe, Hashini; Hanson, Casey; Hay, Amanda; He, Tao Jian; Homa, Katie; Howe, Ruth; Howenstein, Jeff; Huang, Henry; Khatri, Aaditya; Kim, Young Lu; Knowles, Olivia; Kong, Sarah; Krock, Rebecca; Kroll, Matt; Kuhn, Julia; Kwong, Matthew; Lee, Brandon; Lee, Ryan; Levine, Kevin; Li, Yedda; Liu, Bo; Liu, Lucy; Liu, Max; Lousararian, Adam; Ma, Jimmy; Mallya, Allyson; Manchee, Charlie; Marcus, Joseph; McDaniel, Stephen; Miller, Michelle L; Molleston, Jerome M; Diez, Cristina Montero; Ng, Patrick; Ngai, Natalie; Nguyen, Hien; Nylander, Andrew; Pollack, Jason; Rastogi, Suchita; Reddy, Himabindu; Regenold, Nathaniel; Sarezky, Jon; Schultz, Michael; Shim, Jien; Skorupa, Tara; Smith, Kenneth; Spencer, Sarah J; Srikanth, Priya; Stancu, Gabriel; Stein, Andrew P; Strother, Marshall; Sudmeier, Lisa; Sun, Mengyang; Sundaram, Varun; Tazudeen, Noor; Tseng, Alan; Tzeng, Albert; Venkat, Rohit; Venkataram, Sandeep; Waldman, Leah; Wang, Tracy; Yang, Hao; Yu, Jack Y; Zheng, Yin; Preuss, Mary L; Garcia, Angelica; Juergens, Matt; Morris, Robert W; Nagengast, Alexis A; Azarewicz, Julie; Carr, Thomas J; Chichearo, Nicole; Colgan, Mike; Donegan, Megan; Gardner, Bob; Kolba, Nik; Krumm, Janice L; Lytle, Stacey; MacMillian, Laurell; Miller, Mary; Montgomery, Andrew; Moretti, Alysha; Offenbacker, Brittney; Polen, Mike; Toth, John; Woytanowski, John; Kadlec, Lisa; Crawford, Justin; Spratt, Mary L; Adams, Ashley L; Barnard, Brianna K; Cheramie, Martin N; Eime, Anne M; Golden, Kathryn L; Hawkins, Allyson P; Hill, Jessica E; Kampmeier, Jessica A; Kern, Cody D; Magnuson, Emily E; Miller, Ashley R; Morrow, Cody M; Peairs, Julia C; Pickett, Gentry L; Popelka, Sarah A; Scott, Alexis J; Teepe, Emily J; TerMeer, Katie A; Watchinski, Carmen A; Watson, Lucas A; Weber, Rachel E; Woodard, Kate A; Barnard, Daron C; Appiah, Isaac; Giddens, Michelle M; McNeil, Gerard P; Adebayo, Adeola; Bagaeva, Kate; Chinwong, Justina; Dol, Chrystel; George, Eunice; Haltaufderhyde, Kirk; Haye, Joanna; Kaur, Manpreet; Semon, Max; Serjanov, Dmitri; Toorie, Anika; Wilson, Christopher; Riddle, Nicole C; Buhler, Jeremy; Mardis, Elaine R; Elgin, Sarah C R
2015-03-04
The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. Copyright © 2015 Leung et al.
Jang, Hae-Won; Ih, Jeong-Guon
2012-04-01
The time domain boundary element method (BEM) is associated with numerical instability that typically stems from the time marching scheme. In this work, a formulation of time domain BEM is derived to deal with all types of boundary conditions adopting a multi-input, multi-output, infinite impulse response structure. The fitted frequency domain impedance data are converted into a time domain expression as a form of an infinite impulse response filter, which can also invoke a modeling error. In the calculation, the response at each time step is projected onto the wave vector space of natural radiation modes, which can be obtained from the eigensolutions of the single iterative matrix. To stabilize the computation, unstable oscillatory modes are nullified, and the same decay rate is used for two nonoscillatory modes. As a test example, a transient sound field within a partially lined, parallelepiped box is used, within which a point source is excited by an octave band impulse. In comparison with the results of the inverse Fourier transform of a frequency domain BEM, the average of relative difference norm in the stabilized time response is found to be 4.4%.
International Nuclear Information System (INIS)
Correa, Ronan X.; Santos, Igor S.; Silva, Janisete G.; Costa, Marco A.; Pompolo, Silvia G.
2008-01-01
Zabrotes subfasciatus (Boh.) has been extensively studied in its agronomic and biochemical aspects due to its importance as a damaging insect to leguminous grains during storage. The few cytogenetic studies published on this species yielded conflicting results. In this study, the karyotype was analyzed in order to accurately describe the chromosome C-banding patterns and meiosis. The brain ganglion at the pre pupa and the adult and pupal testes were analyzed. All individuals had 26 chromosomes in both brain ganglion and spermatogonic mitotic metaphases. These chromosomes were classified as follows: the 12 th pair and the Y chromosome were telocentric; the X chromosome was acrocentric; the 4 th and 5 th pairs were sub metacentric; and the remaining pairs were all metacentric. One of the members of the 5 th pair presented a secondary constriction. All chromosomes presented pericentromeric heterochromatin. The large arms of the pairs 5, 9 and X presented heterochromatin. The X chromosome showed to be heteropyknotic throughout the prophase of the fi rst meiotic division. The sub phases of prophase I were atypical and meiosis II was rarely identified. Testes of all males showed a few cells; the bivalents were rod-like shaped in metaphase I. Karyological formulae were 2n = 24 + XX in females and 2n = 24 + XYp and either n = 12 + X or n = 12 + Y in males. (author)
Energy Technology Data Exchange (ETDEWEB)
Correa, Ronan X.; Santos, Igor S.; Silva, Janisete G.; Costa, Marco A. [Universidade Estadual de Santa Cruz, Ilheus, BA (Brazil). Dept. de Ciencias Biologicas; Pompolo, Silvia G. [Universidade Federal de Vicosa, MG (Brazil). Dept. de Biologia Geral
2008-09-15
Zabrotes subfasciatus (Boh.) has been extensively studied in its agronomic and biochemical aspects due to its importance as a damaging insect to leguminous grains during storage. The few cytogenetic studies published on this species yielded conflicting results. In this study, the karyotype was analyzed in order to accurately describe the chromosome C-banding patterns and meiosis. The brain ganglion at the pre pupa and the adult and pupal testes were analyzed. All individuals had 26 chromosomes in both brain ganglion and spermatogonic mitotic metaphases. These chromosomes were classified as follows: the 12{sup th} pair and the Y chromosome were telocentric; the X chromosome was acrocentric; the 4{sup th} and 5{sup th} pairs were sub metacentric; and the remaining pairs were all metacentric. One of the members of the 5{sup th} pair presented a secondary constriction. All chromosomes presented pericentromeric heterochromatin. The large arms of the pairs 5, 9 and X presented heterochromatin. The X chromosome showed to be heteropyknotic throughout the prophase of the fi rst meiotic division. The sub phases of prophase I were atypical and meiosis II was rarely identified. Testes of all males showed a few cells; the bivalents were rod-like shaped in metaphase I. Karyological formulae were 2n = 24 + XX in females and 2n = 24 + XYp and either n = 12 + X or n = 12 + Y in males. (author)
In this study, gas-phase elemental mercury (Hg0) and related species (including inorganic reactive gaseous mercury (RGM) and particulate mercury (PHg)) were measured at Cheeka Peak Observatory (CPO), Washington State, in the marine boundary layer (MBL) during 2001-2002. Air of...
International Nuclear Information System (INIS)
Itagaki, Masafumi; Sahashi, Naoki.
1997-01-01
The multiple reciprocity boundary element method has been applied to three-dimensional two-group neutron diffusion problems. A matrix-type boundary integral equation has been derived to solve the first and the second group neutron diffusion equations simultaneously. The matrix-type fundamental solutions used here satisfy the equation which has a point source term and is adjoint to the neutron diffusion equations. A multiple reciprocity method has been employed to transform the matrix-type domain integral related to the fission source into an equivalent boundary one. The higher order fundamental solutions required for this formulation are composed of a series of two types of analytic functions. The eigenvalue itself is also calculated using only boundary integrals. Three-dimensional test calculations indicate that the present method provides stable and accurate solutions for criticality problems. (author)
Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job
2016-01-07
Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce
2009-01-01
We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry
Directory of Open Access Journals (Sweden)
Zhenqing Wang
2018-05-01
Full Text Available A high-order finite difference method was used to simulate the hypersonic flow field over a blunt cone with different height roughness elements. The unsteady flow field induced by pulse disturbances was analyzed and compared with that under continuous disturbances. The temporal and spatial evolution characteristics of disturbances in the boundary layer were investigated and the propagation of different disturbance modes in the boundary layer was researched through the fast Fourier transform (FFT method. The effect of the roughness element on the receptivity characteristic of the hypersonic boundary layer under pulse entropy disturbances was explored. The results showed that the different mode disturbances near roughness in the boundary layer were enlarged in the upstream half of the roughness element and suppressed in the downstream half. However, the effect of roughness weakened gradually as the disturbance frequency increased in the boundary layer. A phenomenon of mode competition in the downstream region of the roughness element exited. As the disturbances propagated downstream, the fundamental mode gradually became the dominant mode. A certain promotion effect on the mode competition was induced by the roughness element and the effect was enhanced with the increase in the roughness element height.
International Nuclear Information System (INIS)
Yi, Won; Yu, Yeong Chul; Jeong, Eui Seob; Lee, Chang Ho
1995-01-01
It is very important to evaluate the bonding residual thermal stress in dissimilar materials such as LSI package. In this study, the bonding residual thermal stress was calculated using the boundary element method, varing with the sub-element, geometry of specimen and adhesive thickness. The present results reveal a stress singularity at the edge of the interface, therefore the bonding strength of metal/resin interface can be estimated by taking into account it.
Tsiveriotis, K.; Brown, R. A.
1993-01-01
A new method is presented for the solution of free-boundary problems using Lagrangian finite element approximations defined on locally refined grids. The formulation allows for direct transition from coarse to fine grids without introducing non-conforming basis functions. The calculation of elemental stiffness matrices and residual vectors are unaffected by changes in the refinement level, which are accounted for in the loading of elemental data to the global stiffness matrix and residual vector. This technique for local mesh refinement is combined with recently developed mapping methods and Newton's method to form an efficient algorithm for the solution of free-boundary problems, as demonstrated here by sample calculations of cellular interfacial microstructure during directional solidification of a binary alloy.
DEFF Research Database (Denmark)
Andersen, Lars; Nielsen, Søren R. K.
2003-01-01
The paper deals with the boundary element method formulation of the steady-state wave propagation through elastic media due to a source moving with constant velocity. The Greens' function for the three-dimensional full-space is formulated in a local frame of reference following the source...... is approximated, but the error which is introduced in this way is insignificant. Numerical examples are given for a moving rectangular load on an elastic half-space. The result from a boundary element code based on the derived Green's function are compared with a semi-analytic solution....
Nuclear dynamics of radiation-induced foci in euchromatin and heterochromatin
International Nuclear Information System (INIS)
Chiolo, Irene; Tang, Jonathan; Georgescu, Walter; Costes, Sylvain V.
2013-01-01
Repair of double strand breaks (DSBs) is essential for cell survival and genome integrity. While much is known about the molecular mechanisms involved in DSB repair and checkpoint activation, the roles of nuclear dynamics of radiation-induced foci (RIF) in DNA repair are just beginning to emerge. Here, we summarize results from recent studies that point to distinct features of these dynamics in two different chromatin environments: heterochromatin and euchromatin. We also discuss how nuclear architecture and chromatin components might control these dynamics, and the need of novel quantification methods for a better description and interpretation of these phenomena. These studies are expected to provide new biomarkers for radiation risk and new strategies for cancer detection and treatment
Nuclear dynamics of radiation-induced foci in euchromatin and heterochromatin
Energy Technology Data Exchange (ETDEWEB)
Chiolo, Irene; Tang, Jonathan; Georgescu, Walter; Costes, Sylvain V.
2013-10-01
Repair of double strand breaks (DSBs) is essential for cell survival and genome integrity. While much is known about the molecular mechanisms involved in DSB repair and checkpoint activation, the roles of nuclear dynamics of radiation-induced foci (RIF) in DNA repair are just beginning to emerge. Here, we summarize results from recent studies that point to distinct features of these dynamics in two different chromatin environments: heterochromatin and euchromatin. We also discuss how nuclear architecture and chromatin components might control these dynamics, and the need of novel quantification methods for a better description and interpretation of these phenomena. These studies are expected to provide new biomarkers for radiation risk and new strategies for cancer detection and treatment.
Schwämmle, Veit; Jensen, Ole Nørregaard
2013-01-01
Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are implicated in the regulation of eukaryote genes and they carry numerous reversible post-translational modifications that control DNA-protein interactions and the recruitment of chromatin binding proteins. Heterochromatin, the transcriptionally inactive part of the genome, is densely packed and contains histone H3 that is methylated at Lys 9 (H3K9me). The propagation of H3K9me in nucleosomes along the DNA in chromatin is antagonizing by methylation of H3 Lysine 4 (H3K4me) and acetylations of several lysines, which is related to euchromatin and active genes. We show that the related histone modifications form antagonized domains on a coarse scale. These histone marks are assumed to be initiated within distinct nucleation sites in the DNA and to propagate bi-directionally. We propose a simple computer model that simulates the distribution of heterochromatin in human chromosomes. The simulations are in agreement with previously reported experimental observations from two different human cell lines. We reproduced different types of barriers between heterochromatin and euchromatin providing a unified model for their function. The effect of changes in the nucleation site distribution and of propagation rates were studied. The former occurs mainly with the aim of (de-)activation of single genes or gene groups and the latter has the power of controlling the transcriptional programs of entire chromosomes. Generally, the regulatory program of gene transcription is controlled by the distribution of nucleation sites along the DNA string.
Dodig, H.
2017-11-01
This contribution presents the boundary integral formulation for numerical computation of time-harmonic radar cross section for 3D targets. Method relies on hybrid edge element BEM/FEM to compute near field edge element coefficients that are associated with near electric and magnetic fields at the boundary of the computational domain. Special boundary integral formulation is presented that computes radar cross section directly from these edge element coefficients. Consequently, there is no need for near-to-far field transformation (NTFFT) which is common step in RCS computations. By the end of the paper it is demonstrated that the formulation yields accurate results for canonical models such as spheres, cubes, cones and pyramids. Method has demonstrated accuracy even in the case of dielectrically coated PEC sphere at interior resonance frequency which is common problem for computational electromagnetic codes.
A comparison of inverse boundary element method and near-field acoustical holography
DEFF Research Database (Denmark)
Schuhmacher, Andreas; Hald, Jørgen; Saemann, E.-U.
1999-01-01
An inverse boundary element method (IBEM) is used to estimate the surface velocity of a rolling tyre from measurements of the near-field pressure. Subsequently, the sound pressure is calculated over a finite plane surface next to the tyre from the reconstructed velocity field on the tyre surface........ In order to verify the reconstruction process, part of the measurement data is used together with Near-Field Acoustical Holography (NAH). Estimated distributions of sound pressure and particle velocity over a plane surface obtained from the two methods are compared....
Johnson, Kyle; Thurow, Brian; Kim, Taehoon; Blois, Gianluca; Christensen, Kenneth
2016-11-01
Three-dimensional, three-component (3D-3C) measurements were made using a plenoptic camera on the flow around a roughness element immersed in a turbulent boundary layer. A refractive index matched approach allowed whole-field optical access from a single camera to a measurement volume that includes transparent solid geometries. In particular, this experiment measures the flow over a single hemispherical roughness element made of acrylic and immersed in a working fluid consisting of Sodium Iodide solution. Our results demonstrate that plenoptic particle image velocimetry (PIV) is a viable technique to obtaining statistically-significant volumetric velocity measurements even in a complex separated flow. The boundary layer to roughness height-ratio of the flow was 4.97 and the Reynolds number (based on roughness height) was 4.57×103. Our measurements reveal key flow features such as spiraling legs of the shear layer, a recirculation region, and shed arch vortices. Proper orthogonal decomposition (POD) analysis was applied to the instantaneous velocity and vorticity data to extract these features. Supported by the National Science Foundation Grant No. 1235726.
Bakker, Mark
2010-08-01
A new analytic solution approach is presented for the modeling of steady flow to pumping wells near rivers in strip aquifers; all boundaries of the river and strip aquifer may be curved. The river penetrates the aquifer only partially and has a leaky stream bed. The water level in the river may vary spatially. Flow in the aquifer below the river is semi-confined while flow in the aquifer adjacent to the river is confined or unconfined and may be subject to areal recharge. Analytic solutions are obtained through superposition of analytic elements and Fourier series. Boundary conditions are specified at collocation points along the boundaries. The number of collocation points is larger than the number of coefficients in the Fourier series and a solution is obtained in the least squares sense. The solution is analytic while boundary conditions are met approximately. Very accurate solutions are obtained when enough terms are used in the series. Several examples are presented for domains with straight and curved boundaries, including a well pumping near a meandering river with a varying water level. The area of the river bottom where water infiltrates into the aquifer is delineated and the fraction of river water in the well water is computed for several cases.
International Nuclear Information System (INIS)
Kim, Ji Hoon; Lee, M.G.; Kim, D.; Matlock, D.K.; Wagoner, R.H.
2010-01-01
Research highlights: → Robust microstructure-based FE mesh generation technique was developed. → Local deformation behavior near phase boundaries could be quantitatively understood. → Macroscopic failure could be connected to microscopic deformation behavior of multi-phase steel. - Abstract: A qualitative analysis was carried out on the formability of dual-phase (DP) steels by introducing a realistic microstructure-based finite element approach. The present microstructure-based model was constructed using a mesh generation process with a boundary-smoothing algorithm after proper image processing. The developed model was applied to hole-expansion formability tests for DP steel sheets having different volume fractions and morphological features. On the basis of the microstructural inhomogeneity observed in the scanning electron micrographs of the DP steel sheets, it was inferred that the localized plastic deformation in the ferritic phase might be closely related to the macroscopic formability of DP steel. The experimentally observed difference between the hole-expansion formability of two different microstructures was reasonably explained by using the present finite element model.
Rahmouni, Lyes; Adrian, Simon B.; Cools, Kristof; Andriulli, Francesco P.
2018-01-01
In this paper, we present a new discretization strategy for the boundary element formulation of the Electroencephalography (EEG) forward problem. Boundary integral formulations, classically solved with the Boundary Element Method (BEM), are widely used in high resolution EEG imaging because of their recognized advantages, in several real case scenarios, in terms of numerical stability and effectiveness when compared with other differential equation based techniques. Unfortunately, however, it is widely reported in literature that the accuracy of standard BEM schemes for the forward EEG problem is often limited, especially when the current source density is dipolar and its location approaches one of the brain boundary surfaces. This is a particularly limiting problem given that during an high-resolution EEG imaging procedure, several EEG forward problem solutions are required, for which the source currents are near or on top of a boundary surface. This work will first present an analysis of standardly and classically discretized EEG forward problem operators, reporting on a theoretical issue of some of the formulations that have been used so far in the community. We report on the fact that several standardly used discretizations of these formulations are consistent only with an L2-framework, requiring the expansion term to be a square integrable function (i.e., in a Petrov-Galerkin scheme with expansion and testing functions). Instead, those techniques are not consistent when a more appropriate mapping in terms of fractional-order Sobolev spaces is considered. Such a mapping allows the expansion function term to be a less regular function, thus sensibly reducing the need for mesh refinements and low-precisions handling strategies that are currently required. These more favorable mappings, however, require a different and conforming discretization, which must be suitably adapted to them. In order to appropriately fulfill this requirement, we adopt a mixed
Wickramasinghe, S N; Spearing, R L; Hill, G R
1998-12-01
Two non-anaemic subjects, a father and daughter, with a new form of congenital dyserythropoiesis are reported. The features of their disorder are: (1) an abnormal blood film with basophilic stippling of red cells and oval macrocytes, (2) various dysplastic changes in the erythroblasts, including internuclear chromatin bridges, (3) ultrastructurally-normal erythroblast heterochromatin, (4) normal serum thymidine kinase activity, and (5) a probable autosomal dominant inheritance. The last three features distinguish this disorder from CDA type I.
Watanabe, M
2003-01-01
Elemental segregation to two types of boundaries in a low-alloy steel were studied by X-ray mapping using scanning transmission electron microscopy (STEM). To quantify the acquired X-ray maps, the zeta-factor method was applied, and then the compositional maps and the thickness map were obtained. Based on these quantified maps, further information about the analytical sensitivity of solute-element detection and the spatial resolution of segregation analysis were extracted. Furthermore, maps of the number of excess atoms on the boundary were also calculated from the compositional and thickness maps. It was concluded that Cr, Ni and Mo are co-segregated on the prior-austenite grain boundary and only Ni was segregated on the lath boundary. (orig.)
Ooi, E H; Ang, W T; Ng, E Y K
2009-08-01
A three-dimensional boundary element model of the human eye is developed to investigate the thermal effects of eye tumor on the ocular temperature distribution. The human eye is modeled as comprising several regions which have different thermal properties. The tumor is one of these regions. The thermal effects of the tumor are simulated by taking it to have a very high metabolic heat generation and blood perfusion rate. Inside the tumor, the steady state temperature is governed by the Pennes bioheat equation. Elsewhere, in normal tissues of the eye, the temperature satisfies the Laplace's equation. To compute the temperature on the corneal surface, the surface boundary of each region is divided into triangular elements.
Element-by-element parallel spectral-element methods for 3-D teleseismic wave modeling
Liu, Shaolin
2017-09-28
The development of an efficient algorithm for teleseismic wave field modeling is valuable for calculating the gradients of the misfit function (termed misfit gradients) or Fréchet derivatives when the teleseismic waveform is used for adjoint tomography. Here, we introduce an element-by-element parallel spectral-element method (EBE-SEM) for the efficient modeling of teleseismic wave field propagation in a reduced geology model. Under the plane-wave assumption, the frequency-wavenumber (FK) technique is implemented to compute the boundary wave field used to construct the boundary condition of the teleseismic wave incidence. To reduce the memory required for the storage of the boundary wave field for the incidence boundary condition, a strategy is introduced to efficiently store the boundary wave field on the model boundary. The perfectly matched layers absorbing boundary condition (PML ABC) is formulated using the EBE-SEM to absorb the scattered wave field from the model interior. The misfit gradient can easily be constructed in each time step during the calculation of the adjoint wave field. Three synthetic examples demonstrate the validity of the EBE-SEM for use in teleseismic wave field modeling and the misfit gradient calculation.
Brebbia, C. A.; Futagami, T.; Tanaka, M.
The boundary-element method (BEM) in computational fluid and solid mechanics is examined in reviews and reports of theoretical studies and practical applications. Topics presented include the fundamental mathematical principles of BEMs, potential problems, EM-field problems, heat transfer, potential-wave problems, fluid flow, elasticity problems, fracture mechanics, plates and shells, inelastic problems, geomechanics, dynamics, industrial applications of BEMs, optimization methods based on the BEM, numerical techniques, and coupling.
Energy Technology Data Exchange (ETDEWEB)
Bizjak, D; Alujevic, A [Institut ' Jozef Stefan' , Ljubljana (Yugoslavia)
1988-07-01
The Complex Variable Boundary Element Method is a numerical method for solving two-dimensional problems of Laplace or Poisson type. It is based on the theory of analytic functions. This paper resumes the basic facts about the method. Application of the method to the stationary incompressible irrotational flow is carried out after that. At the end, a sample problem of flow through an abrupt area change channel is shown. (author)
Energy Technology Data Exchange (ETDEWEB)
Pereira, Luis Carlos Martins
1998-06-15
New Petrov-Galerkin formulations on the finite element methods for convection-diffusion problems with boundary layers are presented. Such formulations are based on a consistent new theory on discontinuous finite element methods. Existence and uniqueness of solutions for these problems in the new finite element spaces are demonstrated. Some numerical experiments shows how the new formulation operate and also their efficacy. (author)
Yang, Jubiao; Yu, Feimi; Krane, Michael; Zhang, Lucy T
2018-01-01
In this work, a non-reflective boundary condition, the Perfectly Matched Layer (PML) technique, is adapted and implemented in a fluid-structure interaction numerical framework to demonstrate that proper boundary conditions are not only necessary to capture correct wave propagations in a flow field, but also its interacted solid behavior and responses. While most research on the topics of the non-reflective boundary conditions are focused on fluids, little effort has been done in a fluid-structure interaction setting. In this study, the effectiveness of the PML is closely examined in both pure fluid and fluid-structure interaction settings upon incorporating the PML algorithm in a fully-coupled fluid-structure interaction framework, the Immersed Finite Element Method. The performance of the PML boundary condition is evaluated and compared to reference solutions with a variety of benchmark test cases including known and expected solutions of aeroacoustic wave propagation as well as vortex shedding and advection. The application of the PML in numerical simulations of fluid-structure interaction is then investigated to demonstrate the efficacy and necessity of such boundary treatment in order to capture the correct solid deformation and flow field without the requirement of a significantly large computational domain.
International Nuclear Information System (INIS)
Ringwelski, S; Gabbert, U
2010-01-01
A recently developed approach for the simulation and design of a fluid-loaded lightweight structure with surface-mounted piezoelectric actuators and sensors capable of actively reducing the sound radiation and the vibration is presented. The objective of this paper is to describe the theoretical background of the approach in which the FEM is applied to model the actively controlled shell structure. The FEM is also employed to model finite fluid domains around the shell structure as well as fluid domains that are partially or totally bounded by the structure. Boundary elements are used to characterize the unbounded acoustic pressure fields. The approach presented is based on the coupling of piezoelectric and acoustic finite elements with boundary elements. A coupled finite element–boundary element model is derived by introducing coupling conditions at the fluid–fluid and fluid–structure interfaces. Because of the possibility of using piezoelectric patches as actuators and sensors, feedback control algorithms can be implemented directly into the multi-coupled structural–acoustic approach to provide a closed-loop model for the design of active noise and vibration control. In order to demonstrate the applicability of the approach developed, a number of test simulations are carried out and the results are compared with experimental data. As a test case, a box-shaped shell structure with surface-mounted piezoelectric actuators and four sensors and an open rearward end is considered. A comparison between the measured values and those predicted by the coupled finite element–boundary element model shows a good agreement
Directory of Open Access Journals (Sweden)
Yuh Chwen G Lee
2015-06-01
Full Text Available The piwi-interacting RNAs (piRNA are small RNAs that target selfish transposable elements (TEs in many animal genomes. Until now, piRNAs' role in TE population dynamics has only been discussed in the context of their suppression of TE transposition, which alone is not sufficient to account for the skewed frequency spectrum and stable containment of TEs. On the other hand, euchromatic TEs can be epigenetically silenced via piRNA-dependent heterochromatin formation and, similar to the widely known "Position-effect variegation", heterochromatin induced by TEs can "spread" into nearby genes. We hypothesized that the piRNA-mediated spread of heterochromatin from TEs into adjacent genes has deleterious functional effects and leads to selection against individual TEs. Unlike previously identified deleterious effects of TEs due to the physical disruption of DNA, the functional effect we investigated here is mediated through the epigenetic influences of TEs. We found that the repressive chromatin mark, H3K9me, is elevated in sequences adjacent to euchromatic TEs at multiple developmental stages in Drosophila melanogaster. Furthermore, the heterochromatic states of genes depend not only on the number of and distance from adjacent TEs, but also on the likelihood that their nearest TEs are targeted by piRNAs. These variations in chromatin status probably have functional consequences, causing genes near TEs to have lower expression. Importantly, we found stronger selection against TEs that lead to higher H3K9me enrichment of adjacent genes, demonstrating the pervasive evolutionary consequences of TE-induced epigenetic silencing. Because of the intrinsic biological mechanism of piRNA amplification, spread of TE heterochromatin could result in the theoretically required synergistic deleterious effects of TE insertions for stable containment of TE copy number. The indirect deleterious impact of piRNA-mediated epigenetic silencing of TEs is a previously
International Nuclear Information System (INIS)
Itagaki, Masafumi; Miyoshi, Yoshinori; Hirose, Hideyuki
1993-01-01
A procedure is presented for the determination of geometric buckling for regular polygons. A new computation technique, the multiple reciprocity boundary element method (MRBEM), has been applied to solve the one-group neutron diffusion equation. The main difficulty in applying the ordinary boundary element method (BEM) to neutron diffusion problems has been the need to compute a domain integral, resulting from the fission source. The MRBEM has been developed for transforming this type of domain integral into an equivalent boundary integral. The basic idea of the MRBEM is to apply repeatedly the reciprocity theorem (Green's second formula) using a sequence of higher order fundamental solutions. The MRBEM requires discretization of the boundary only rather than of the domain. This advantage is useful for extensive survey analyses of buckling for complex geometries. The results of survey analyses have indicated that the general form of geometric buckling is B g 2 = (a n /R c ) 2 , where R c represents the radius of the circumscribed circle of the regular polygon under consideration. The geometric constant A n depends on the type of regular polygon and takes the value of π for a square and 2.405 for a circle, an extreme case that has an infinite number of sides. Values of a n for a triangle, pentagon, hexagon, and octagon have been calculated as 4.190, 2.281, 2.675, and 2.547, respectively
International Nuclear Information System (INIS)
Kudielka, G.
2001-07-01
Frasassi Cave have always been lower in d18O and higher in d13C compared to Soreq Cave. This indicates lower temperatures and a higher portion of C4 type vegetation in the Frasassi area compared to Israel. The agreement of the two records demonstrates that calcite deposits in caves are ideal recorders to global climatic changes. Investigation of the Jurassic/Cretaceous Boundary in Central Italy, the Jurassic/Cretaceous (J-K) boundary has not been satisfactory defined yet. Among others, various boundary definitions have been proposed at the Bosso River Gorge in the Marche region of Northern Italy: by calcareous nanofossils (at 329 m), calpionellids (at 334.1 m) and magnetostratigraphy (at 318 m). A large impact structure near Morokweng in South Africa was recently radiometrically dated to 144.7±1.9 Ma, which is indistinguishable from the stratigraphic age of the J-K boundary (144.2±2.6 Ma). A possible link between the impact event and the J-K boundary might be manifested in form of stratigraphic and geochemical features across the boundary, such as sudden stable-isotope shifts and spheroidal element anomalies. A set of 110 samples spanning about 40 m across the boundary was investigated for stable isotope ratios, and trace element content was determined in the corresponding decarbonated samples. d13C and d18O hardly vary but show a significant decrease at 333.5 m, which is close to the boundary-definition based upon calpionellids (at 334.1 m). Trace element abundances of Fe, Co, Ni, and Cr show remarkable enrichments very close to the boundary as defined by calcareous nanofossils (at 329 m). Another minor anomaly is noticeable at 333.5 m for Ir and Cr. Thus, the present data might be interpreted to hint - not to confirm - the presence of an impactoclastic layer at the Bosso River Gorge. (author)
Noise source localization on tyres using an inverse boundary element method
DEFF Research Database (Denmark)
Schuhmacher, Andreas; Saemann, E-U; Hald, J
1998-01-01
A dominating part of tyre noise is radiated from a region close to the tyre/road contact patch, where it is very difficult to measure both the tyre vibration and the acoustic near field. The approach taken in the present paper is to model the tyre and road surfaces with a Boundary Element Model...... (BEM), with unknown node vibration data on the tyre surface. The BEM model is used to calculate a set of transfer functions from the node vibrations to the sound pressure at a set of microphone positions around the tyre. By approximate inversion of the matrix of transfer functions, the surface...... from tyre noise measurements will be presented at the conference....
Computational Acoustics of Noise Propagation in Fluids - Finite and Boundary Element Methods
Marburg, Steffen
2008-01-01
Among numerical methods applied in acoustics, the Finite Element Method (FEM) is normally favored for interior problems whereas the Boundary Element Method (BEM) is quite popular for exterior ones. That is why this valuable reference provides a complete survey of methods for computational acoustics, namely FEM and BEM. It demonstrates that both methods can be effectively used in the complementary cases. The chapters by well-known authors are evenly balanced: 10 chapters on FEM and 10 on BEM. An initial conceptual chapter describes the derivation of the wave equation and supplies a unified approach to FEM and BEM for the harmonic case. A categorization of the remaining chapters and a personal outlook complete this introduction. In what follows, both FEM and BEM are discussed in the context of very different problems. Firstly, this comprises numerical issues, e.g. convergence, multi-frequency solutions and highly efficient methods; and secondly, solutions techniques for the particular difficulties that arise wi...
Natural convection in a composite fluid-porous cavity by the boundary element method
International Nuclear Information System (INIS)
Jecl, R.; Skerget, L.
2005-01-01
The main purpose of this work is to present the use of the boundary element method (BEM) for analyzing the convective fluid flow and heat transfer in composite fluid-porous media domain when the fluid is compressible. In our case the flow is modeled by utilizing the Brinkman extended Darcy momentum equation (Brinkman model) which is commonly used when it is important to satisfy the no-slip boundary condition and when one wishes to compare flows in porous medium with those in pure fluids. The Brinkman equation reduce to the classical Navier Stokes equation for clear fluid when the permeability tends to infinity (porosity is equal to unity), i.e. when the solid matrix in the porous medium disappears and, when the permeability is finite the equation is valid for porous medium. Therefore it is possible to handle porous medium free fluid interface problems by changing the properties of the medium in the computational domain appropriately. Our goal is to widen the applicability of the computational model based on the boundary domain integral method (BDIM) which is an extension of the classical BEM. The governing equations are transformed by using the velocity-vorticity variables formulation and therefore the computation scheme is partitioned into kinematic and kinetic part. (authors)
Directory of Open Access Journals (Sweden)
Tongchun Li
2015-01-01
element is proposed to solve the safety factor of local discontinuous rock mass. Slope system is divided into several continuous bodies and local discontinuous interface boundaries. Each block is treated as a partition of the system and contacted by discontinuous joints. The displacements of blocks are chosen as basic variables and the rigid displacements in the centroid of blocks are chosen as motion variables. The contact forces on interface boundaries and the rigid displacements to the centroid of each body are chosen as mixed variables and solved iteratively using the interface boundary equations. Flexibility matrix is formed through PFE according to the contact states of nodal pairs and spring flexibility is used to reflect the influence of weak structural plane so that nonlinear iteration is only limited to the possible contact region. With cohesion and friction coefficient reduced gradually, the states of all nodal pairs at the open or slip state for the first time are regarded as failure criterion, which can decrease the effect of subjectivity in determining safety factor. Examples are used to verify the validity of the proposed method.
Over, D J; Conaway, C A; Katz, D J; Goodfellow, W D; Gregoire, D C
1997-08-01
The Frasnian-Famennian boundary is recognized as the culmination of a global mass extinction in the Late Devonian. In western New York State the boundary is a distinct horizon within a pyritic black shale bed of the upper Hanover Shale defined by the first occurrence of Palmatolepis triangularis in the absence of Frasnian conodonts. The boundary is characterized by a minor disconformity marked by a lag concentration of conodonts. Iridium at the boundary is 0.11-0.24 ng/g, two to five times background levels of <0.05 ng/g; other Ir enrichments of 0.38 ng/g and 0.49 ng/g occur within 50 cm of the conodont-constrained boundary. Numerous Ir enrichments in the boundary interval suggest extraterrestrial accretion and platinum group element (PGE) concentration at disconformities, or mobilization and concentration in organic-rich/pyritic-rich laminations from cosmic or terrestrial sources. PGE ratios of Pt/Pd and Ku/Ir at the boundary horizon approximate chondritic ratios and are suggestive of an unaltered extraterrestrial source. These values do not conclusively establish a single extraterrestrial impact as the ultimate cause of the Frasnian-Famennian mass extinction, especially given the presence of similar Ir enrichments elsewhere in the section and the absence at the boundary of microtektites and shocked mineral grains.
Directory of Open Access Journals (Sweden)
Fabrício Ribeiro Bueno
Full Text Available Here, the Dual Reciprocity Boundary Element Method is used to solve the 3D Pennes Bioheat Equation, which together with a Genetic Algorithm, produces an inverse model capable of obtaining the location and the size of a tumour, having as data input the temperature distribution measured on the skin surface. Given that the objective function, which is solved inversely, involves the DRBEM (Dual Reciprocity Boundary Element Method the Genetic Algorithm in its usual form becomes slower, in such a way that it was necessary to develop functions based the solution history in order that the process becomes quicker and more accurate. Results for 8 examples are presented including cases with convection and radiation boundary conditions. Cases involving noise in the readings of the equipment are also considered. This technique is intended to assist health workers in the diagnosis of tumours.
International Nuclear Information System (INIS)
Washizu, Masao; Tanabe, Yoshio.
1986-01-01
In a system handling the electromagnetic waves of large power such as the cavity resonator for a high energy accelerator and the high frequency heater for a nuclear fusion apparatus, the margin in the thermal and mechanical design of a wave guide system cannot be taken large, accordingly, the detailed analysis of electromagnetic waves is required. When the analysis in a general form is carried out, boundary element method may be a useful method of solution. This time, the authors carried out the formulation of steady electromagnetic wave problems by boundary element method, and it was shown that the formulation was able to be carried out under the physically clear boundary condition also in this case, and especially in the case of a perfect conductor system, a very simple form was obtained. In this paper, first, the techniques of formulation in a general case, and next, as a special case, the formulation for a perfect conductor system are described. Taking the analysis of the cavity resonators of cylindrical and rectangular parallelepiped forms as examples, the comparison with the analytical solution was carried out. (Kako, I.)
A non-reflecting boundary for use in a finite element beam model of a railway track
Yang, Jiannan; Thompson, David J.
2015-02-01
Some beam-like structures such as a railway track are effectively infinite in nature. Analytical solutions exist for simple structures but numerical methods like the finite element (FE) method are often employed to study more complicated problems. However, when the FE method is used for structures of infinite extent it is essential to introduce artificial boundaries to limit the area of computation. Here, a non-reflecting boundary is developed using a damped tapered tip for application in a finite element model representing an infinite supported beam. The FE model of the tapered tip is validated against an analytical model based on Bessel functions. The reflection characteristics of the FE tapered tip are quantified using a wave/FE superposition method. It is shown that the damped tapered tip is much more effective than its constant counterpart and achieves reduction of the model size. The damped tapered tip is applied to a simple FE railway track model and good agreement is found when its point mobility is compared with an analytical infinite track model.
Linear and nonlinear dynamic analysis by boundary element method. Ph.D. Thesis, 1986 Final Report
Ahmad, Shahid
1991-01-01
An advanced implementation of the direct boundary element method (BEM) applicable to free-vibration, periodic (steady-state) vibration and linear and nonlinear transient dynamic problems involving two and three-dimensional isotropic solids of arbitrary shape is presented. Interior, exterior, and half-space problems can all be solved by the present formulation. For the free-vibration analysis, a new real variable BEM formulation is presented which solves the free-vibration problem in the form of algebraic equations (formed from the static kernels) and needs only surface discretization. In the area of time-domain transient analysis, the BEM is well suited because it gives an implicit formulation. Although the integral formulations are elegant, because of the complexity of the formulation it has never been implemented in exact form. In the present work, linear and nonlinear time domain transient analysis for three-dimensional solids has been implemented in a general and complete manner. The formulation and implementation of the nonlinear, transient, dynamic analysis presented here is the first ever in the field of boundary element analysis. Almost all the existing formulation of BEM in dynamics use the constant variation of the variables in space and time which is very unrealistic for engineering problems and, in some cases, it leads to unacceptably inaccurate results. In the present work, linear and quadratic isoparametric boundary elements are used for discretization of geometry and functional variations in space. In addition, higher order variations in time are used. These methods of analysis are applicable to piecewise-homogeneous materials, such that not only problems of the layered media and the soil-structure interaction can be analyzed but also a large problem can be solved by the usual sub-structuring technique. The analyses have been incorporated in a versatile, general-purpose computer program. Some numerical problems are solved and, through comparisons
Camacho, Oscar Velazquez; Galan, Carmen; Swist-Rosowska, Kalina; Ching, Reagan; Gamalinda, Michael; Karabiber, Fethullah; La Rosa-Velazquez, De Inti; Engist, Bettina; Koschorz, Birgit; Shukeir, Nicholas; Onishi-Seebacher, Megumi; De Nobelen, Van Suzanne; Jenuwein, Thomas
2017-01-01
The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity
Matsubara, Kazumi; Uno, Yoshinobu; Srikulnath, Kornsorn; Seki, Risako; Nishida, Chizuko; Matsuda, Yoichi
2015-12-01
Highly repetitive DNA sequences of the centromeric heterochromatin provide valuable molecular cytogenetic markers for the investigation of genomic compartmentalization in the macrochromosomes and microchromosomes of sauropsids. Here, the relationship between centromeric heterochromatin and karyotype evolution was examined using cloned repetitive DNA sequences from two snake species, the habu snake (Protobothrops flavoviridis, Crotalinae, Viperidae) and Burmese python (Python bivittatus, Pythonidae). Three satellite DNA (stDNA) families were isolated from the heterochromatin of these snakes: 168-bp PFL-MspI from P. flavoviridis and 196-bp PBI-DdeI and 174-bp PBI-MspI from P. bivittatus. The PFL-MspI and PBI-DdeI sequences were localized to the centromeric regions of most chromosomes in the respective species, suggesting that the two sequences were the major components of the centromeric heterochromatin in these organisms. The PBI-MspI sequence was localized to the pericentromeric region of four chromosome pairs. The PFL-MspI and the PBI-DdeI sequences were conserved only in the genome of closely related species, Gloydius blomhoffii (Crotalinae) and Python molurus, respectively, although their locations on the chromosomes were slightly different. In contrast, the PBI-MspI sequence was also in the genomes of P. molurus and Boa constrictor (Boidae), and additionally localized to the centromeric regions of eight chromosome pairs in B. constrictor, suggesting that this sequence originated in the genome of a common ancestor of Pythonidae and Boidae, approximately 86 million years ago. The three stDNA sequences showed no genomic compartmentalization between the macrochromosomes and microchromosomes, suggesting that homogenization of the centromeric and/or pericentromeric stDNA sequences occurred in the macrochromosomes and microchromosomes of these snakes.
International Nuclear Information System (INIS)
Saitoh, Ayumu; Matsui, Nobuyuki; Itoh, Taku; Kamitani, Atsushi; Nakamura, Hiroaki
2011-01-01
A new method has been proposed for implementing essential boundary conditions to the Element-Free Galerkin Method (EFGM) without using the Lagrange multiplier. Furthermore, the performance of the proposed method has been investigated for a nonlinear Poisson problem. The results of computations show that, as interpolation functions become closer to delta functions, the accuracy of the solution is improved on the boundary. In addition, the accuracy of the proposed method is higher than that of the conventional EFGM. Therefore, it might be concluded that the proposed method is useful for solving the nonlinear Poisson problem. (author)
Energy Technology Data Exchange (ETDEWEB)
Simmons, Daniel, E-mail: daniel.simmons@nottingham.ac.uk; Cools, Kristof; Sewell, Phillip
2016-11-01
Time domain electromagnetic simulation tools have the ability to model transient, wide-band applications, and non-linear problems. The Boundary Element Method (BEM) and the Transmission Line Modeling (TLM) method are both well established numerical techniques for simulating time-varying electromagnetic fields. The former surface based method can accurately describe outwardly radiating fields from piecewise uniform objects and efficiently deals with large domains filled with homogeneous media. The latter volume based method can describe inhomogeneous and non-linear media and has been proven to be unconditionally stable. Furthermore, the Unstructured TLM (UTLM) enables modelling of geometrically complex objects by using triangular meshes which removes staircasing and unnecessary extensions of the simulation domain. The hybridization of BEM and UTLM which is described in this paper is named the Boundary Element Unstructured Transmission-line (BEUT) method. It incorporates the advantages of both methods. The theory and derivation of the 2D BEUT method is described in this paper, along with any relevant implementation details. The method is corroborated by studying its correctness and efficiency compared to the traditional UTLM method when applied to complex problems such as the transmission through a system of Luneburg lenses and the modelling of antenna radomes for use in wireless communications. - Graphical abstract:.
Directory of Open Access Journals (Sweden)
Shaogan Ye
2017-01-01
Full Text Available Low noise axial piston pumps become the rapid increasing demand in modern hydraulic fluid power systems. This paper proposes a systematic approach to simulate the vibroacoustic characteristics of an axial piston pump using a hybrid lumped parameters/finite element/boundary element (LP/FE/BE model, and large amount of experimental work was performed to validate the model. The LP model was developed to calculate the excitation forces and was validated by a comparison of outlet flow ripples. The FE model was developed to calculate the vibration of the pump, in which the modeling of main friction pairs using different spring elements was presented in detail, and the FE model was validated using experimental modal analysis and measured vibrations. The BE model was used to calculate the noise emitted from the pump, and a measurement of sound pressure level at representative field points in a hemianechoic chamber was conducted to validate the BE model. Comparisons between the simulated and measured results show that the developed LP/FE/BE model is effective in capturing the vibroacoustic characteristics of the pump. The presented approach can be extended to other types of fluid power components and contributes to the development of quieter fluid power systems.
Sound Radiation from a Loudspeaker Cabinet using the Boundary Element Method
DEFF Research Database (Denmark)
Fernandez Grande, Efren
had been reported, based on subjective testing. This study aims to detect the reported problem. The radiation from the cabinet is calculated using the Boundary Element Method. The analysis examines both the frequency domain and the time domain characteristics (in other words, the steady state response......, in some cases becoming clearly audible. The aim of this study is to provide a tool that can evaluate the contribution from the cabinet to the overall sound radiated by a loudspeaker. The specific case of a B&O Beolab 9 early prototype has been investigated. An influence by the cabinet of this prototype...... and the impulse response) of the loudspeaker and the cabinet. A significant influence of the cabinet has been detected, which becomes especially apparent in the time domain, during the sound decay process....
KIN SP: A boundary element method based code for single pile kinematic bending in layered soil
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Stefano Stacul
2018-02-01
Full Text Available In high seismicity areas, it is important to consider kinematic effects to properly design pile foundations. Kinematic effects are due to the interaction between pile and soil deformations induced by seismic waves. One of the effect is the arise of significant strains in weak soils that induce bending moments on piles. These moments can be significant in presence of a high stiffness contrast in a soil deposit. The single pile kinematic interaction problem is generally solved with beam on dynamic Winkler foundation approaches (BDWF or using continuous models. In this work, a new boundary element method (BEM based computer code (KIN SP is presented where the kinematic analysis is preceded by a free-field response analysis. The analysis results of this method, in terms of bending moments at the pile-head and at the interface of a two-layered soil, are influenced by many factors including the soil–pile interface discretization. A parametric study is presented with the aim to suggest the minimum number of boundary elements to guarantee the accuracy of a BEM solution, for typical pile–soil relative stiffness values as a function of the pile diameter, the location of the interface of a two-layered soil and of the stiffness contrast. KIN SP results have been compared with simplified solutions in literature and with those obtained using a quasi-three-dimensional (3D finite element code.
Directory of Open Access Journals (Sweden)
Dounia Djeghloul
2016-06-01
Full Text Available The capacity of hematopoietic stem cells (HSC to generate B lymphocytes declines with age, contributing to impaired immune function in the elderly. Here we show that the histone methyltransferase SUV39H1 plays an important role in human B lymphoid differentiation and that expression of SUV39H1 decreases with age in both human and mouse HSC, leading to a global reduction in H3K9 trimethylation and perturbed heterochromatin function. Further, we demonstrate that SUV39H1 is a target of microRNA miR-125b, a known regulator of HSC function, and that expression of miR-125b increases with age in human HSC. Overexpression of miR-125b and inhibition of SUV39H1 in young HSC induced loss of B cell potential. Conversely, both inhibition of miR-125 and enforced expression of SUV39H1 improved the capacity of HSC from elderly individuals to generate B cells. Our findings highlight the importance of heterochromatin regulation in HSC aging and B lymphopoiesis.
PARALLEL ALGORITHM FOR THREE-DIMENSIONAL STOKES FLOW SIMULATION USING BOUNDARY ELEMENT METHOD
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D. G. Pribytok
2016-01-01
Full Text Available Parallel computing technique for modeling three-dimensional viscous flow (Stokes flow using direct boundary element method is presented. The problem is solved in three phases: sampling and construction of system of linear algebraic equations (SLAE, its decision and finding the velocity of liquid at predetermined points. For construction of the system and finding the velocity, the parallel algorithms using graphics CUDA cards programming technology have been developed and implemented. To solve the system of linear algebraic equations the implemented software libraries are used. A comparison of time consumption for three main algorithms on the example of calculation of viscous fluid motion in three-dimensional cavity is performed.
Thompson, T. B.; Meade, B. J.
2015-12-01
The Himalayas are the tallest mountains on Earth with ten peaks exceeding 8000 meters, including Mt. Everest. The geometrically complex fault system at the Himalayan Range Front produces both great relief and great earthquakes, like the recent Mw=7.8 Nepal rupture. Here, we develop geometrically accurate elastic boundary element models of the fault system at the Himalayan Range Front including the Main Central Thrust, South Tibetan Detachment, Main Frontal Thrust, Main Boundary Thrust, the basal detachment, and surface topography. Using these models, we constrain the tectonic driving forces and frictional fault strength required to explain Quaternary fault slip rate estimates. These models provide a characterization of the heterogeneity of internal stress in the region surrounding the 2015 Nepal earthquake.
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Esteban Flores-Mendez
2012-01-01
Full Text Available This work is focused on studying interface waves for three canonical models, that is, interfaces formed by vacuum-solid, solid-solid, and liquid-solid. These interfaces excited by dynamic loads cause the emergence of Rayleigh's, Stoneley's, and Scholte's waves, respectively. To perform the study, the indirect boundary element method is used, which has proved to be a powerful tool for numerical modeling of problems in elastodynamics. In essence, the method expresses the diffracted wave field of stresses, pressures, and displacements by a boundary integral, also known as single-layer representation, whose shape can be regarded as a Fredholm's integral representation of second kind and zero order. This representation can be considered as an exemplification of Huygens' principle, which is equivalent to Somigliana's representation theorem. Results in frequency domain for the three types of interfaces are presented; then, using the fourier discrete transform, we derive the results in time domain, where the emergence of interface waves is highlighted.
Schmitz, Birger; Andersson, Per; Dahl, Jeremy
1988-01-01
Microbial activity and redox-controlled precipitation have been of major importance in the process of metal accumulation in the strongly Ir-enriched Cretaceous-Tertiary (K-T) boundary clay, the Fish Clay, at Stevns Klint in Denmark. Two important findings support this view: 1) Kerogen, recovered by leaching the Fish Clay in HCl and HF, shows an Ir concentration of 1100 ppb; this represents about 50% of the Ir present in the bulk sample Fish Clay. Strong organometallic complexes is the most probable carrier phase for this fraction of Ir. Kerogen separated from the K-T boundary clay at Caravaca, Spain, similarly exhibits enhanced Ir concentrations. 2) Sulfur isotope analyses of metal-rich pyrite spherules, which occur in extreme abundance (about 10% by weight) in the basal Fish Clay, give a δ 34S value of -32%.. This very low value shows that sulfide formation by anaerobic bacteria was intensive in the Fish Clay during early diagenesis. Since the pyrite spherules are major carriers of elements such as Ni, Co, As, Sb and Zn, microbial activity may have played an important role for concentrating these elements. In the Fish Clay large amounts of rare earth elements have precipitated from sea water on fish scales. Analyses reveal that, compared with sea water, the Fish Clay is only about four times less enriched in sea-water derived lanthanides than in Ir. This shows that a sea-water origin is plausible for elements that are strongly enriched in the clay, but whose origin cannot be accounted for by a lithogenic precursor.
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Mathieu Gissot
Full Text Available BACKGROUND: Apicomplexan parasites are responsible for some of the most deadly parasitic diseases afflicting humans, including malaria and toxoplasmosis. These obligate intracellular parasites exhibit a complex life cycle and a coordinated cell cycle-dependant expression program. Their cell division is a coordinated multistep process. How this complex mechanism is organised remains poorly understood. METHODS AND FINDINGS: In this study, we provide evidence for a link between heterochromatin, cell division and the compartmentalisation of the nucleus in Toxoplasma gondii. We characterised a T. gondii chromodomain containing protein (named TgChromo1 that specifically binds to heterochromatin. Using ChIP-on-chip on a genome-wide scale, we report TgChromo1 enrichment at the peri-centromeric chromatin. In addition, we demonstrate that TgChromo1 is cell-cycle regulated and co-localised with markers of the centrocone. Through the loci-specific FISH technique for T. gondii, we confirmed that TgChromo1 occupies the same nuclear localisation as the peri-centromeric sequences. CONCLUSION: We propose that TgChromo1 may play a role in the sequestration of chromosomes at the nuclear periphery and in the process of T. gondii cell division.
Resistive wall impedance of the LHC beam screen without slots calculated by boundary element method
Tsutsui, H
2002-01-01
In order to calculate the resistive wall impedance of the LHC beam screen without slots, the Boundary Element Method (BEM) is used. The result at 1 GHz is Re(ZL/L) = 6.689×10−3 Ω/m, Re(Zx/L) = 1.251 Ω/m2, Re(Zy/L) = 1.776 Ω/m2, andRe(2Z0,2 cos/kL) = −0.525 Ω/m2, assuming σ = 5.8 × 109 /Ωm.
Guerra, Marcelo; García, Miguel A
2004-02-01
Cuscuta is a widely distributed genus of holoparasitic plants. Holocentric chromosomes have been reported only in species of one of its subgenera (Cuscuta subg. Cuscuta). In this work, a representative of this subgenus, Cuscuta approximata, was investigated looking for its mitotic and meiotic chromosome behaviour and the heterochromatin distribution. The mitotic chromosomes showed neither primary constriction nor Rabl orientation whereas the meiotic ones exhibited the typical quadripartite structure characteristic of holocentrics, supporting the assumption of holocentric chromosomes as a synapomorphy of Cuscuta subg. Cuscuta. Chromosomes and interphase nuclei displayed many heterochromatic blocks that stained deeply with hematoxylin, 4',6-diamidino-2-phenylindole (DAPI), or after C banding. The banded karyotype showed terminal or subterminal bands in all chromosomes and central bands in some of them. The single pair of 45S rDNA sites was observed at the end of the largest chromosome pair, close to a DAPI band and a 5S rDNA site. Two other 5S rDNA site pairs were found, both closely associated with DAPI bands. The noteworthy giant nuclei of glandular cells of petals and ovary wall exhibited large chromocentres typical of polytenic nuclei. The chromosomal location of heterochromatin and rDNA sites and the structure of the endoreplicated nuclei of C. approximata seemed to be similar to those known in monocentric nuclei, suggesting that centromeric organization has little or no effect on chromatin organization.
A time-domain finite element boundary integral approach for elastic wave scattering
Shi, F.; Lowe, M. J. S.; Skelton, E. A.; Craster, R. V.
2018-04-01
The response of complex scatterers, such as rough or branched cracks, to incident elastic waves is required in many areas of industrial importance such as those in non-destructive evaluation and related fields; we develop an approach to generate accurate and rapid simulations. To achieve this we develop, in the time domain, an implementation to efficiently couple the finite element (FE) method within a small local region, and the boundary integral (BI) globally. The FE explicit scheme is run in a local box to compute the surface displacement of the scatterer, by giving forcing signals to excitation nodes, which can lie on the scatterer itself. The required input forces on the excitation nodes are obtained with a reformulated FE equation, according to the incident displacement field. The surface displacements computed by the local FE are then projected, through time-domain BI formulae, to calculate the scattering signals with different modes. This new method yields huge improvements in the efficiency of FE simulations for scattering from complex scatterers. We present results using different shapes and boundary conditions, all simulated using this approach in both 2D and 3D, and then compare with full FE models and theoretical solutions to demonstrate the efficiency and accuracy of this numerical approach.
Czech Academy of Sciences Publication Activity Database
Kowar, T.; Zakrzewski, F.; Macas, Jiří; Koblížková, Andrea; Viehoever, P.; Weisshaar, B.; Schmidt, T.
2016-01-01
Roč. 16, č. 120 (2016) ISSN 1471-2229 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Centromere * CenH3 * H3K9me2 * Heterochromatin Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.964, year: 2016
Directory of Open Access Journals (Sweden)
Lyakhovich Leonid
2017-01-01
Full Text Available This paper is devoted to formulation and general principles of approximation of multipoint boundary problem of static analysis of deep beam with the use of combined application of finite element method (FEM discrete-continual finite element method (DCFEM. The field of application of DCFEM comprises structures with regular physical and geometrical parameters in some dimension (“basic” dimension. DCFEM presupposes finite element approximation for non-basic dimension while in the basic dimension problem remains continual. DCFEM is based on analytical solutions of resulting multipoint boundary problems for systems of ordinary differential equations with piecewise-constant coefficients.
Direct displacement-based design of special composite RC shear walls with steel boundary elements
Directory of Open Access Journals (Sweden)
H. Kazemi
2016-06-01
Full Text Available Special composite RC shear wall (CRCSW with steel boundary elements is a kind of lateral force resisting structural system which is used in earthquake-prone regions. Due to their high ductility and energy dissipation, CRCSWs have been widely used in recent years by structural engineers. However, there are few studies in the literature on the seismic design of such walls. Although there are many studies in the literature on the Direct Displacement-Based Design (DDBD of RC structures, however, no study can be found on DDBD of CRCSWs. Therefore, the aim of present study is to evaluate the ability of DDBD method for designing CRCSWs. In this study, four special composite reinforced concrete shear walls with steel boundary elements of 4, 8, 12 and 16 story numbers were designed using the DDBD method for target drift of 2%. The seismic behavior of the four CRCSWs was studied using nonlinear time-history dynamic analyses. Dynamic analyses were performed for the mentioned walls using 7 selected earthquake records. The seismic design parameters considered in this study includes: lateral displacement profile, inelastic dynamic inter-story drift demand, failure pattern and the composite RC shear walls overstrength factor. For each shear wall, the overall overstrength factor was calculated by dividing the ultimate dynamic base shear demand (Vu by the base shear demand (Vd as per the Direct Displacement Based-Design (DDBD method. The results show that the DDBD method can be used to design CRCSWs safely in seismic regions with predicted behavior.
International Nuclear Information System (INIS)
Ji, X.; Chen, Y.M.
1989-01-01
The boundary element method (BEM) is developed from the boundary integral equation method and the discretization techniques. Compared with other numerical method, BEM has been shown to be a versatile and efficient method for a wide variety of engineering problems, including the wave propagation in elastic media. The first formulation and solution of the transient elastodynamic problem by combining BEM and Laplace transform is due to Cruse. Further improvement was achieved by introducing Durbin's method instead of Papoulis method of numerical Laplace inverse transform. However, a great deal of computer time is still needed for the inverse transformation. The alternative integral transform approach is BEM combining with Fourier transform. The numerical Fourier inverse transformation is also computer time consuming, even if the fast Fourier transform is used. In the present paper, the authors use BEM combining with Fourier transform and Fourier eigen transform (FET). The new approach is very attractive in saving on computer time. This paper illustrates the application of FET to BEM of 2-dimensional transient elastodynamic problem. The example of a half plane subjected to a discontinuous boundary load is solved on ELXSI 6400 computer. The CPU time is less than one minute. If Laplace or Fourier transform is adopted, the CPU time will be more than 10 minutes
Novel TMS coils designed using an inverse boundary element method
Cobos Sánchez, Clemente; María Guerrero Rodriguez, Jose; Quirós Olozábal, Ángel; Blanco-Navarro, David
2017-01-01
In this work, a new method to design TMS coils is presented. It is based on the inclusion of the concept of stream function of a quasi-static electric current into a boundary element method. The proposed TMS coil design approach is a powerful technique to produce stimulators of arbitrary shape, and remarkably versatile as it permits the prototyping of many different performance requirements and constraints. To illustrate the power of this approach, it has been used for the design of TMS coils wound on rectangular flat, spherical and hemispherical surfaces, subjected to different constraints, such as minimum stored magnetic energy or power dissipation. The performances of such coils have been additionally described; and the torque experienced by each stimulator in the presence of a main magnetic static field have theoretically found in order to study the prospect of using them to perform TMS and fMRI concurrently. The obtained results show that described method is an efficient tool for the design of TMS stimulators, which can be applied to a wide range of coil geometries and performance requirements.
Three dimensional grain boundary modeling in polycrystalline plasticity
Yalçinkaya, Tuncay; Özdemir, Izzet; Fırat, Ali Osman
2018-05-01
At grain scale, polycrystalline materials develop heterogeneous plastic deformation fields, localizations and stress concentrations due to variation of grain orientations, geometries and defects. Development of inter-granular stresses due to misorientation are crucial for a range of grain boundary (GB) related failure mechanisms, such as stress corrosion cracking (SCC) and fatigue cracking. Local crystal plasticity finite element modelling of polycrystalline metals at micron scale results in stress jumps at the grain boundaries. Moreover, the concepts such as the transmission of dislocations between grains and strength of the grain boundaries are not included in the modelling. The higher order strain gradient crystal plasticity modelling approaches offer the possibility of defining grain boundary conditions. However, these conditions are mostly not dependent on misorientation of grains and can define only extreme cases. For a proper definition of grain boundary behavior in plasticity, a model for grain boundary behavior should be incorporated into the plasticity framework. In this context, a particular grain boundary model ([l]) is incorporated into a strain gradient crystal plasticity framework ([2]). In a 3-D setting, both bulk and grain boundary models are implemented as user-defined elements in Abaqus. The strain gradient crystal plasticity model works in the bulk elements and considers displacements and plastic slips as degree of freedoms. Interface elements model the plastic slip behavior, yet they do not possess any kind of mechanical cohesive behavior. The physical aspects of grain boundaries and the performance of the model are addressed through numerical examples.
Structural aspects of the nucleolus and its associated heterochromatin in neurons
International Nuclear Information System (INIS)
Pessacq, T.P.; Vidal Rioja, L.A.
1975-01-01
The study of the structure of the nucleolus has received considerable attention in recent years. Most data have been provided by a number of electromicroscopical studies which to some extent are confirmatory of the previous opticomicroscopical findings of Estable and Sotelo (1951, 1952, 1955), Davis (1960), Altmann, Stoecker, and Thoenes (1963), O'Donell (1961), Lettre, and Siebs (1961), Bernhard, Bauer, Gropp, Haguenau and Oberling (1955) among others. In a recent work Melker (1970) points out the existence in neurons of a mammal of a particular arrangement of the nucleolus and its associated chromatin very similar to that already established in avian neurons (Pessacq 1969). The research reported here adds some new structural facts on nucleolar-heterochromatinic rapports which although recognizable in a great variety of cellular types appears with schematic clearness only in a limited number of highly specialized cells of some species. (auth.)
Sirenko, Kostyantyn; Liu, Meilin; Bagci, Hakan
2013-01-01
A scheme that discretizes exact absorbing boundary conditions (EACs) to incorporate them into a time-domain discontinuous Galerkin finite element method (TD-DG-FEM) is described. The proposed TD-DG-FEM with EACs is used for accurately characterizing
Sosa-Montes de Oca, Claudia; de Lange, Gert J.|info:eu-repo/dai/nl/073930962; Martínez-Ruiz, Francisca; Rodríguez-Tovar, Francisco J.
2018-01-01
A high-resolution analysis of the distribution of major and trace elements across a Cretaceous/Paleogene boundary (KPgB) was done using Laser Ablation-Inductivity Coupled Plasma-Mass Spectrometry (LA-ICP-MS) and was compared with traditional distinct sampling and analysis. At the Agost site (SE
Simpson, R. N.; Liu, Z.; Vázquez, R.; Evans, J. A.
2018-06-01
We outline the construction of compatible B-splines on 3D surfaces that satisfy the continuity requirements for electromagnetic scattering analysis with the boundary element method (method of moments). Our approach makes use of Non-Uniform Rational B-splines to represent model geometry and compatible B-splines to approximate the surface current, and adopts the isogeometric concept in which the basis for analysis is taken directly from CAD (geometry) data. The approach allows for high-order approximations and crucially provides a direct link with CAD data structures that allows for efficient design workflows. After outlining the construction of div- and curl-conforming B-splines defined over 3D surfaces we describe their use with the electric and magnetic field integral equations using a Galerkin formulation. We use Bézier extraction to accelerate the computation of NURBS and B-spline terms and employ H-matrices to provide accelerated computations and memory reduction for the dense matrices that result from the boundary integral discretization. The method is verified using the well known Mie scattering problem posed over a perfectly electrically conducting sphere and the classic NASA almond problem. Finally, we demonstrate the ability of the approach to handle models with complex geometry directly from CAD without mesh generation.
A simple boundary element formulation for shape optimization of 2D continuous structures
International Nuclear Information System (INIS)
Luciano Mendes Bezerra; Jarbas de Carvalho Santos Junior; Arlindo Pires Lopes; Andre Luiz; Souza, A.C.
2005-01-01
For the design of nuclear equipment like pressure vessels, steam generators, and pipelines, among others, it is very important to optimize the shape of the structural systems to withstand prescribed loads such as internal pressures and prescribed or limiting referential values such as stress or strain. In the literature, shape optimization of frame structural systems is commonly found but the same is not true for continuous structural systems. In this work, the Boundary Element Method (BEM) is applied to simple problems of shape optimization of 2D continuous structural systems. The proposed formulation is based on the BEM and on deterministic optimization methods of zero and first order such as Powell's, Conjugate Gradient, and BFGS methods. Optimal characterization for the geometric configuration of 2D structure is obtained with the minimization of an objective function. Such function is written in terms of referential values (such as loads, stresses, strains or deformations) prescribed at few points inside or at the boundary of the structure. The use of the BEM for shape optimization of continuous structures is attractive compared to other methods that discretized the whole continuous. Several numerical examples of the application of the proposed formulation to simple engineering problems are presented. (authors)
Formulation of natural convection around repository for dual reciprocity boundary element solution
International Nuclear Information System (INIS)
Vrankar, L.; Sarler, B.
1998-01-01
The disposal of high-level radioactive wastes in deep geological formations is of pronounced technological importance for nuclear safety. The understanding of related fluid flow, heat and mass transport in geological systems is of great interest. This article prepares necessary physical, mathematical and numerical fundamentals for computational modeling of related phenomena. The porous media is described by the simple Darcy law and momentum-energy coupling is due to Boussinesq approximation. The Dual Reciprocity of Boundary Element Method (DRBEM) is used for solving coupled mass, momentum and energy equations in two-dimensions for the steady buoyancy induced convection problem in an semi-infinite porous media. It is structured by weighting with the fundamental solution of the Laplace equation. The inverse multi quadrics are used in the DRBEM transformation. The solution is obtained in an iterative way.(author)
Directory of Open Access Journals (Sweden)
Wen Bo
2012-10-01
Full Text Available Abstract Background The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. We and others have previously observed dynamic changes during differentiation and oncogenesis in large heterochromatin domains such as Large Organized Chromatin K (lysine modifications (LOCKs, of histone H3 lysine-9 dimethylation (H3K9me2 or other repressive histone posttranslational modifications. The microstructure of these regions has not previously been explored. Results We analyzed the genome-wide distribution of H3K9me2 in two human pluripotent stem cell lines and three differentiated cells lines. We identified > 2,500 small regions with very low H3K9me2 signals in the body of LOCKs, which were termed as euchromatin islands (EIs. EIs are 6.5-fold enriched for DNase I Hypersensitive Sites and 8-fold enriched for the binding of CTCF, the major organizer of higher-order chromatin. Furthermore, EIs are 2–6 fold enriched for differentially DNA-methylated regions associated with tissue types (T-DMRs, reprogramming (R-DMRs and cancer (C-DMRs. Gene ontology (GO analysis suggests that EI-associated genes are functionally related to organ system development, cell adhesion and cell differentiation. Conclusions We identify the existence of EIs as a finer layer of epigenomic architecture within large heterochromatin domains. Their enrichment for CTCF sites and DNAse hypersensitive sites, as well as association with DMRs, suggest that EIs play an important role in normal epigenomic architecture and its disruption in disease.
Influence of precipitating light elements on stable stratification below the core/mantle boundary
O'Rourke, J. G.; Stevenson, D. J.
2017-12-01
Stable stratification below the core/mantle boundary is often invoked to explain anomalously low seismic velocities in this region. Diffusion of light elements like oxygen or, more slowly, silicon could create a stabilizing chemical gradient in the outermost core. Heat flow less than that conducted along the adiabatic gradient may also produce thermal stratification. However, reconciling either origin with the apparent longevity (>3.45 billion years) of Earth's magnetic field remains difficult. Sub-isentropic heat flow would not drive a dynamo by thermal convection before the nucleation of the inner core, which likely occurred less than one billion years ago and did not instantly change the heat flow. Moreover, an oxygen-enriched layer below the core/mantle boundary—the source of thermal buoyancy—could establish double-diffusive convection where motion in the bulk fluid is suppressed below a slowly advancing interface. Here we present new models that explain both stable stratification and a long-lived dynamo by considering ongoing precipitation of magnesium oxide and/or silicon dioxide from the core. Lithophile elements may partition into iron alloys under extreme pressure and temperature during Earth's formation, especially after giant impacts. Modest core/mantle heat flow then drives compositional convection—regardless of thermal conductivity—since their solubility is strongly temperature-dependent. Our models begin with bulk abundances for the mantle and core determined by the redox conditions during accretion. We then track equilibration between the core and a primordial basal magma ocean followed by downward diffusion of light elements. Precipitation begins at a depth that is most sensitive to temperature and oxygen abundance and then creates feedbacks with the radial thermal and chemical profiles. Successful models feature a stable layer with low seismic velocity (which mandates multi-component evolution since a single light element typically
Wang, P.; Becker, A. A.; Jones, I. A.; Glover, A. T.; Benford, S. D.; Vloeberghs, M.
2009-08-01
A virtual-reality real-time simulation of surgical operations that incorporates the inclusion of a hard tumour is presented. The software is based on Boundary Element (BE) technique. A review of the BE formulation for real-time analysis of two-domain deformable objects, using the pre-solution technique, is presented. The two-domain BE software is incorporated into a surgical simulation system called VIRS to simulate the initiation of a cut on the surface of the soft tissue and extending the cut deeper until the tumour is reached.
International Nuclear Information System (INIS)
Wang, P; Becker, A A; Jones, I A; Glover, A T; Benford, S D; Vloeberghs, M
2009-01-01
A virtual-reality real-time simulation of surgical operations that incorporates the inclusion of a hard tumour is presented. The software is based on Boundary Element (BE) technique. A review of the BE formulation for real-time analysis of two-domain deformable objects, using the pre-solution technique, is presented. The two-domain BE software is incorporated into a surgical simulation system called VIRS to simulate the initiation of a cut on the surface of the soft tissue and extending the cut deeper until the tumour is reached.
Boundary Layer Effect on Behavior of Discrete Models.
Eliáš, Jan
2017-02-10
The paper studies systems of rigid bodies with randomly generated geometry interconnected by normal and tangential bonds. The stiffness of these bonds determines the macroscopic elastic modulus while the macroscopic Poisson's ratio of the system is determined solely by the normal/tangential stiffness ratio. Discrete models with no directional bias have the same probability of element orientation for any direction and therefore the same mechanical properties in a statistical sense at any point and direction. However, the layers of elements in the vicinity of the boundary exhibit biased orientation, preferring elements parallel with the boundary. As a consequence, when strain occurs in this direction, the boundary layer becomes stiffer than the interior for the normal/tangential stiffness ratio larger than one, and vice versa. Nonlinear constitutive laws are typically such that the straining of an element in shear results in higher strength and ductility than straining in tension. Since the boundary layer tends, due to the bias in the elemental orientation, to involve more tension than shear at the contacts, it also becomes weaker and less ductile. The paper documents these observations and compares them to the results of theoretical analysis.
Strack, O. D. L.
2018-02-01
We present equations for new limitless analytic line elements. These elements possess a virtually unlimited number of degrees of freedom. We apply these new limitless analytic elements to head-specified boundaries and to problems with inhomogeneities in hydraulic conductivity. Applications of these new analytic elements to practical problems involving head-specified boundaries require the solution of a very large number of equations. To make the new elements useful in practice, an efficient iterative scheme is required. We present an improved version of the scheme presented by Bandilla et al. (2007), based on the application of Cauchy integrals. The limitless analytic elements are useful when modeling strings of elements, rivers for example, where local conditions are difficult to model, e.g., when a well is close to a river. The solution of such problems is facilitated by increasing the order of the elements to obtain a good solution. This makes it unnecessary to resort to dividing the element in question into many smaller elements to obtain a satisfactory solution.
Böhnke, Frank; Scheunemann, Christian; Semmelbauer, Sebastian
2018-05-01
The propagation of traveling waves along the basilar membrane is studied in a 3D finite element model of the cochlea using single and two-tone stimulation. The advantage over former approaches is the consideration of viscous-thermal boundary layer damping which makes the usual but physically unjustified assumption of Rayleigh damping obsolete. The energy loss by viscous boundary layer damping is 70 dB lower than the actually assumed power generation by outer hair cells. The space-time course with two-tone stimulation shows the traveling waves and the periodicity of the beat frequency f2 - f1.
Adilardi, Renzo Sebastián; Ojanguren-Affilastro, Andrés Alejandro; Mattoni, Camilo Iván; Mola, Liliana María
2015-08-01
All cytogenetically studied scorpions present male achiasmatic meiosis and lack heteromorphic sex chromosomes. In contrast, information about female meiosis in scorpions is scarce due to the difficulty of finding meiotic cells. The genus Zabius includes three described species and no chromosome studies have been performed on it until now. We analyzed the constitutive heterochromatin distribution, NORs and telomeric sequences in mitosis and meiosis of males and females of different populations of Zabius fuscus. All specimens presented 2n = 18 holokinetic chromosomes that gradually decreased in size. Male meiosis presented nine bivalents and a polymorphism for one reciprocal translocation in one population. Telomeric signals were detected at every terminal region, confirming also the presence of a (TTAGG) n motif in Buthidae. Constitutive heterochromatin was found in three chromosome pairs at a terminal region; moreover, NORs were embedded in the heterochromatic region of the largest pair. Chromosome size and landmarks allowed us to propose the chromosomes involved in the rearrangement. In four females, cells at different prophase I stages were analyzed. We describe a diffuse stage and the presence of ring-shaped bivalents. We discuss the possible origin of these bivalents in the framework of chiasmatic or achiasmatic female meiosis. These results contribute to increase the scarce evidence of female meiosis in scorpions and raise new questions about its mechanism.
Heumann, Holger; Rapetti, Francesca
2017-04-01
Existing finite element implementations for the computation of free-boundary axisymmetric plasma equilibria approximate the unknown poloidal flux function by standard lowest order continuous finite elements with discontinuous gradients. As a consequence, the location of critical points of the poloidal flux, that are of paramount importance in tokamak engineering, is constrained to nodes of the mesh leading to undesired jumps in transient problems. Moreover, recent numerical results for the self-consistent coupling of equilibrium with resistive diffusion and transport suggest the necessity of higher regularity when approximating the flux map. In this work we propose a mortar element method that employs two overlapping meshes. One mesh with Cartesian quadrilaterals covers the vacuum chamber domain accessible by the plasma and one mesh with triangles discretizes the region outside. The two meshes overlap in a narrow region. This approach gives the flexibility to achieve easily and at low cost higher order regularity for the approximation of the flux function in the domain covered by the plasma, while preserving accurate meshing of the geometric details outside this region. The continuity of the numerical solution in the region of overlap is weakly enforced by a mortar-like mapping.
Rayleigh-wave scattering by shallow cracks using the indirect boundary element method
International Nuclear Information System (INIS)
Ávila-Carrera, R; Rodríguez-Castellanos, A; Ortiz-Alemán, C; Sánchez-Sesma, F J
2009-01-01
The scattering and diffraction of Rayleigh waves by shallow cracks using the indirect boundary element method (IBEM) are investigated. The detection of cracks is of interest because their presence may compromise structural elements, put technological devices at risk or represent economical potential in reservoir engineering. Shallow cracks may give rise to scattered body and surface waves. These waves are sensitive to the crack's geometry, size and orientation. Under certain conditions, amplitude spectra clearly show conspicuous resonances that are associated with trapped waves. Several applications based on the scattering of surface waves (e.g. Rayleigh and Stoneley waves), such as non-destructive testing or oil well exploration, have shown that the scattered fields may provide useful information to detect cracks and other heterogeneities. The subject is not new and several analytical and numerical techniques have been applied for the last 50 years to understand the basis of multiple scattering phenomena. In this work, we use the IBEM to calculate the scattered fields produced by single or multiple cracks near a free surface. This method is based upon an integral representation of the scattered displacement fields, which is derived from Somigliana's identity. Results are given in both frequency and time domains. The analyses of the displacement field using synthetic seismograms and snapshots reveal some important effects from various configurations of cracks. The study of these simple cases may provide an archetype to geoscientists and engineers to understand the fundamental aspects of multiple scattering and diffraction by cracks
Directory of Open Access Journals (Sweden)
Juliano S. Cabral
2006-01-01
Full Text Available We investigated four orchids of the genus Maxillaria (M. discolor, M. acicularis, M. notylioglossa and M. desvauxiana in regard to the position of heterochromatin blocks as revealed using chromomycin A3 (CMA and 4'-6-diamidino-2-phenylindole (DAPI fluorochrome staining and 5S and 45S rDNA sites using fluorescence in situ hybridization (FISH. The species showed differences in chromosome number and a diversified pattern of CMA+ and DAPI+ bands, including heteromorphism for CMA+ bands. The 5S and 45S rDNA sites also varied in number and most of them were co-localized with CMA+ bands. The relationship between 5S rDNA sites and CMA+ bands was more evident in M. notylioglossa, in which the brighter CMA+ bands were associated with large 5S rDNA sites. However, not all 5S and 45S rDNA sites were co-localized with CMA+ bands, probably due to technical constraints. We compare these results to banding data from other species and suggest that not all blocks of tandemly repetitive sequences, such as 5S rDNA sites, can be observed as heterochromatin blocks.
Gong, Yixiao; Lazaris, Charalampos; Sakellaropoulos, Theodore; Lozano, Aurelie; Kambadur, Prabhanjan; Ntziachristos, Panagiotis; Aifantis, Iannis; Tsirigos, Aristotelis
2018-02-07
The metazoan genome is compartmentalized in areas of highly interacting chromatin known as topologically associating domains (TADs). TADs are demarcated by boundaries mostly conserved across cell types and even across species. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score. We demonstrate that higher TAD boundary insulation scores are associated with elevated CTCF levels and that they may differ across cell types. Intriguingly, we observe that super-enhancers are preferentially insulated by strong boundaries. Furthermore, we demonstrate that strong TAD boundaries and super-enhancer elements are frequently co-duplicated in cancer patients. Taken together, our findings suggest that super-enhancers insulated by strong TAD boundaries may be exploited, as a functional unit, by cancer cells to promote oncogenesis.
Energy Technology Data Exchange (ETDEWEB)
Loewe, Konrad
2016-10-18
The first part of the thesis investigates the diffusion of rare-earth (RE) elements in commercial sintered Nd-Fe-B based permanent magnets. A strong temperature dependence of the diffusion distance and resulting change in magnetic properties were found. A maximum increase in coercivity of ∼+350 kA/m using a Dy diffusion source occurred at the optimum annealing temperature of 900 C. After annealing for 6 h at this temperature, a Dy diffusion distance of about 4 mm has been observed with a scanning Hall probe. Consequently, the maximum thickness of grain boundary diffusion processed magnets with homogeneous properties is also only a few mm. The microstructural changes in the magnets after diffusion were investigated by electron microscopy coupled with electron probe microanalysis. It was found that the diffusion of Dy into sintered Nd-Fe-B permanent magnets occurs along the grain boundary phases, which is in accordance with previous studies. A partial melting of the Nd-Fe-B grains during the annealing process lead to the formation of so - called (Nd,Dy)-Fe-B shells at the outer part of the grains. These shells are μm thick at the immediate surface of the magnet and become thinner with increasing diffusion distance towards the center of the bulk. With scanning transmission electron microscopy coupled with electron probe analysis a Dy content of about 1 at.% was found in a shell located about 1.5 mm away from the surface of the magnet. The evaluation of diffusion speeds of Dy and other RE (Tb, Ce, Gd) in Nd-Fe-B magnets showed that Tb diffuses significantly faster than Dy, and Ce slightly slower than Dy, which is attributed to differences in the respective phase diagrams. The addition of Gd to the grain boundaries has an adverse effect on coercivity. Exemplary of the heavy rare earth element Tb, the nano - scale elemental distribution around the grain boundaries after the diffusion process was visualized with high resolution scanning transmission electron microscopy
Sirenko, Kostyantyn
2013-01-01
A scheme that discretizes exact absorbing boundary conditions (EACs) to incorporate them into a time-domain discontinuous Galerkin finite element method (TD-DG-FEM) is described. The proposed TD-DG-FEM with EACs is used for accurately characterizing transient electromagnetic wave interactions on two-dimensional waveguides. Numerical results demonstrate the proposed method\\'s superiority over the TD-DG-FEM that employs approximate boundary conditions and perfectly matched layers. Additionally, it is shown that the proposed method can produce the solution with ten-eleven digit accuracy when high-order spatial basis functions are used to discretize the Maxwell equations as well as the EACs. © 1963-2012 IEEE.
Pressure effect on grain boundary diffusion
International Nuclear Information System (INIS)
Smirnova, E.S.; Chuvil'deev, V.N.
1997-01-01
The influence of hydrostatic pressure on grain boundary diffusion and grain boundary migration in metallic materials is theoretically investigated. The model is suggested that permits describing changes in activation energy of grain boundary self-diffusion and diffusion permeability of grain boundaries under hydrostatic pressure. The model is based on the ideas about island-type structure of grain boundaries as well as linear relationship of variations in grain boundary free volume to hydrostatic pressure value. Comparison of theoretical data with experimental ones for a number of metals and alloys (α-Zr, Sn-Ge, Cu-In with Co, In, Al as diffusing elements) shows a qualitative agreement
A boundary element model for diffraction of water waves on varying water depth
Energy Technology Data Exchange (ETDEWEB)
Poulin, Sanne
1997-12-31
In this thesis a boundary element model for calculating diffraction of water waves on varying water depth is presented. The varying water depth is approximated with a perturbed constant depth in the mild-slope wave equation. By doing this, the domain integral which is a result of the varying depth is no longer a function of the unknown wave potential but only a function of position and the constant depth wave potential. The number of unknowns is the resulting system of equations is thus reduced significantly. The integration procedures in the model are tested very thoroughly and it is found that a combination of analytical integration in the singular region and standard numerical integration outside works very well. The gradient of the wave potential is evaluated successfully using a hypersingular integral equation. Deviations from the analytical solution are only found on the boundary or very close to, but these deviations have no significant influence on the accuracy of the solution. The domain integral is evaluated using the dual reciprocity method. The results are compared with a direct integration of the integral, and the accuracy is quite satisfactory. The problem with irregular frequencies is taken care of by the CBIEM (or CHIEF-method) together with a singular value decomposition technique. This method is simple to implement and works very well. The model is verified using Homma`s island as a test case. The test cases are limited to shallow water since the analytical solution is only valid in this region. Several depth ratios are examined, and it is found that the accuracy of the model increases with increasing wave period and decreasing depth ratio. Short waves, e.g. wind generated waves, can allow depth variations up to approximately 2 before the error exceeds 10%, while long waves can allow larger depth ratios. It is concluded that the perturbation idea is highly usable. A study of (partially) absorbing boundary conditions is also conducted. (EG)
International Nuclear Information System (INIS)
Xu, Kai-Jiang; Pan, Xiao-Min; Li, Ren-Xian; Sheng, Xin-Qing
2017-01-01
In optical trapping applications, the optical force should be investigated within a wide range of parameter space in terms of beam configuration to reach the desirable performance. A simple but reliable way of conducting the related investigation is to evaluate optical forces corresponding to all possible beam configurations. Although the optical force exerted on arbitrarily shaped particles can be well predicted by boundary element method (BEM), such investigation is time costing because it involves many repetitions of expensive computation, where the forces are calculated from the equivalent surface currents. An algorithm is proposed to alleviate the difficulty by exploiting our previously developed skeletonization framework. The proposed algorithm succeeds in reducing the number of repetitions. Since the number of skeleton beams is always much less than that of beams in question, the computation can be very efficient. The proposed algorithm is accurate because the skeletonization is accuracy controllable. - Highlights: • A fast and accurate algorithm is proposed in terms of boundary element method to reduce the number of repetitions of computing the optical forces from the equivalent currents. • The algorithm is accuracy controllable because the accuracy of the associated rank-revealing process is well-controlled. • The accelerate rate can reach over one thousand because the number of skeleton beams can be very small. • The algorithm can be applied to other methods, e.g., FE-BI.
Directory of Open Access Journals (Sweden)
Yong Cheng
2017-01-01
Full Text Available The hydroelastic behaviour of a pontoon-type VLFS subjected to unsteady external loads in wave condition is investigated in the context of the time-domain modal expansion theory, in which the boundary element method (BEM based on time domain Kelvin sources is used for hydrodynamic forces and the finite element method (FEM is adopted for solving the deflections of the VLFS. In this analysis, the interpolation-tabulation scheme is applied to assess rapidly and accurately the free-surface Green function in finite water depth, and the boundary integral equation of a quarter VLFS model is further established taking advantage of symmetry of flow field and structure. The VLFS is modelled as an equivalent solid plate based on the Mindlin plate theory. The coupled plate-water model is performed to determine the wave-induced responses and transient behaviour under external loads such as a huge mass impact onto the structure and moving loads of an airplane, respectively. These results are verified with existing numerical results and experimental test. Then, the developed numerical tools are used in the study of the combined action taking into account of the mass drop/airplane landing as well as forward or reverse incident wave action. The deflections of the runway, the time history of vertical positions and the trajectory of the airplane are also presented through a systematic time-domain simulation, which illustrates the usefulness of the presently developed numerical solutions.
The boundary element method for the solution of the multidimensional inverse heat conduction problem
International Nuclear Information System (INIS)
Lagier, Guy-Laurent
1999-01-01
This work focuses on the solution of the inverse heat conduction problem (IHCP), which consists in the determination of boundary conditions from a given set of internal temperature measurements. This problem is difficult to solve due to its ill-posedness and high sensitivity to measurement error. As a consequence, numerical regularization procedures are required to solve this problem. However, most of these methods depend on the dimension and the nature, stationary or transient, of the problem. Furthermore, these methods introduce parameters, called hyper-parameters, which have to be chosen optimally, but can not be determined a priori. So, a new general method is proposed for solving the IHCP. This method is based on a Boundary Element Method formulation, and the use of the Singular Values Decomposition as a regularization procedure. Thanks to this method, it's possible to identify and eliminate the directions of the solution where the measurement error plays the major role. This algorithm is first validated on two-dimensional stationary and one-dimensional transient problems. Some criteria are presented in order to choose the hyper-parameters. Then, the methodology is applied to two-dimensional and three-dimensional, theoretical or experimental, problems. The results are compared with those obtained by a standard method and show the accuracy of the method, its generality, and the validity of the proposed criteria. (author) [fr
International Nuclear Information System (INIS)
Bruemmer, S.M.; Charlot, L.A.; Simonen, E.P.
1995-08-01
Grain boundary radiation-induced segregation (RIS) in Fe-Ni-Cr stainless alloys has been measured and modelled as a function of irradiation temperature and dose. Heavy-ion irradiation was used to produce damage levels from 1 to 20 displacements per atom (dpa) at temperatures from 175 to 550 degrees C. Measured Fe, Ni, and Cr segregation increased sharply with irradiation dose (from 0 to 5 dpa) and temperature (from 175 to about 350 degrees C). However, grain boundary concentrations did not change significantly as dose or temperatures were further increased. Impurity segregation (Si and P) was also measured, but only Si enrichment appeared to be radiation-induced. Grain boundary Si levels peaked at an intermediate temperature of ∼325 degrees C reaching levels of ∼8 at. %. Equilibrium segregation of P was measured in the high-P alloys, but interfacial concentration did not increase with irradiation exposure. Examination of reported RIS in neutron-irradiated stainless steels revealed similar effects of irradiation dose on grain boundary compositional changes for both major alloying and impurity element's. The Inverse Kirkendall model accurately predicted major alloying element RIS in ion- and neutron-irradiated alloys over the wide range of temperature and dose conditions. In addition, preliminary calculations indicate that the Johnson-Lam model can reasonably estimate grain boundary Si enrichment if back diffusion is enhanced
A finite element conjugate gradient FFT method for scattering
Collins, Jeffery D.; Ross, Dan; Jin, J.-M.; Chatterjee, A.; Volakis, John L.
1991-01-01
Validated results are presented for the new 3D body of revolution finite element boundary integral code. A Fourier series expansion of the vector electric and mangnetic fields is employed to reduce the dimensionality of the system, and the exact boundary condition is employed to terminate the finite element mesh. The mesh termination boundary is chosen such that is leads to convolutional boundary operatores of low O(n) memory demand. Improvements of this code are discussed along with the proposed formulation for a full 3D implementation of the finite element boundary integral method in conjunction with a conjugate gradiant fast Fourier transformation (CGFFT) solution.
Collins, Jeffery D.; Volakis, John L.; Jin, Jian-Ming
1990-01-01
A new technique is presented for computing the scattering by 2-D structures of arbitrary composition. The proposed solution approach combines the usual finite element method with the boundary-integral equation to formulate a discrete system. This is subsequently solved via the conjugate gradient (CG) algorithm. A particular characteristic of the method is the use of rectangular boundaries to enclose the scatterer. Several of the resulting boundary integrals are therefore convolutions and may be evaluated via the fast Fourier transform (FFT) in the implementation of the CG algorithm. The solution approach offers the principal advantage of having O(N) memory demand and employs a 1-D FFT versus a 2-D FFT as required with a traditional implementation of the CGFFT algorithm. The speed of the proposed solution method is compared with that of the traditional CGFFT algorithm, and results for rectangular bodies are given and shown to be in excellent agreement with the moment method.
International Nuclear Information System (INIS)
Wolf, J.P.; Darbre, G.R.
1985-01-01
The computational procedure of the so-called truncated indirect boundary-element method is derived. The latter, which is non-local in space and time, represents a rigorous generally applicable procedure for taking into account a layered halfspace in a non-linear soil-structure interaction analysis. As an example, the non-linear soil-structure interaction analysis of a structure embedded in a halfspace with partial uplift of the basement and separation of the side wall is investigated. (orig.)
Electronic and elemental properties of the Cu2ZnSn(S,Se)4 surface and grain boundaries
International Nuclear Information System (INIS)
Haight, Richard; Shao, Xiaoyan; Wang, Wei; Mitzi, David B.
2014-01-01
X-ray and femtosecond UV photoelectron spectroscopy, secondary ion mass spectrometry and photoluminescence imaging were used to investigate the electronic and elemental properties of the CZTS,Se surface and its oxides. Oxide removal reveals a very Cu poor and Zn rich surface relative to bulk composition. O and Na are observed at the surface and throughout the bulk. Upward bending of the valence bands indicates the presence of negative charge in the surface region and the Fermi level is found near the band gap center. The presence of point defects and the impact of these findings on grain boundary properties will be described
Electronic and elemental properties of the Cu2ZnSn(S,Se)4 surface and grain boundaries
Haight, Richard; Shao, Xiaoyan; Wang, Wei; Mitzi, David B.
2014-01-01
X-ray and femtosecond UV photoelectron spectroscopy, secondary ion mass spectrometry and photoluminescence imaging were used to investigate the electronic and elemental properties of the CZTS,Se surface and its oxides. Oxide removal reveals a very Cu poor and Zn rich surface relative to bulk composition. O and Na are observed at the surface and throughout the bulk. Upward bending of the valence bands indicates the presence of negative charge in the surface region and the Fermi level is found near the band gap center. The presence of point defects and the impact of these findings on grain boundary properties will be described.
Subgroup report on grain boundary and interphase boundary structure and properties
International Nuclear Information System (INIS)
Balluffi, R.W.; Cannon, R.M.; Clarke, D.R.; Heuer, A.H.; Ho, P.S.; Kear, B.H.; Vitek, V.; Weertman, J.R.; White, C.L.
1979-01-01
In many high temperature structural applications, the performance characteristics of a materials system are largely controlled by the properties of its grain and interphase boundaries. Failure in creep and fatigue frequently occurs by cavitation, or cracking along grain boundaries. In a few special cases, this failure problem has been overcome by directional alignment of grain and interphase boundaries by various types of metallurgical processing such as directional solidification and directional recrystallization. A good example is to be found in the application of directionally aligned structures in high performance gas-turbine airfoils. However, where fine, equiaxed grain structures are desirable, other methods of controlling grain boundary properties have been developed. Important among these has been the introduction of improvements in primary melting practices, designed to control important impurities. This is of decisive importance because even traces of certain impurity elements present in grain boundaries in high temperature materials can seriously affect properties. Impurities are deleterious and need to be removed. However, in certain cases, (e.g., creep fracture) controlled impurity additions can be beneficial and result in improved properties
International Nuclear Information System (INIS)
Akalin-Acar, Zeynep; Gencer, Nevzat G
2004-01-01
The forward problem of electromagnetic source imaging has two components: a numerical model to solve the related integral equations and a model of the head geometry. This study is on the boundary element method (BEM) implementation for numerical solutions and realistic head modelling. The use of second-order (quadratic) isoparametric elements and the recursive integration technique increase the accuracy in the solutions. Two new formulations are developed for the calculation of the transfer matrices to obtain the potential and magnetic field patterns using realistic head models. The formulations incorporate the use of the isolated problem approach for increased accuracy in solutions. If a personal computer is used for computations, each transfer matrix is calculated in 2.2 h. After this pre-computation period, solutions for arbitrary source configurations can be obtained in milliseconds for a realistic head model. A hybrid algorithm that uses snakes, morphological operations, region growing and thresholding is used for segmentation. The scalp, skull, grey matter, white matter and eyes are segmented from the multimodal magnetic resonance images and meshes for the corresponding surfaces are created. A mesh generation algorithm is developed for modelling the intersecting tissue compartments, such as eyes. To obtain more accurate results quadratic elements are used in the realistic meshes. The resultant BEM implementation provides more accurate forward problem solutions and more efficient calculations. Thus it can be the firm basis of the future inverse problem solutions
Genome-wide Control of Heterochromatin Replication by the Telomere Capping Protein TRF2.
Mendez-Bermudez, Aaron; Lototska, Liudmyla; Bauwens, Serge; Giraud-Panis, Marie-Josèphe; Croce, Olivier; Jamet, Karine; Irizar, Agurtzane; Mowinckel, Macarena; Koundrioukoff, Stephane; Nottet, Nicolas; Almouzni, Genevieve; Teulade-Fichou, Mare-Paule; Schertzer, Michael; Perderiset, Mylène; Londoño-Vallejo, Arturo; Debatisse, Michelle; Gilson, Eric; Ye, Jing
2018-05-03
Hard-to-replicate regions of chromosomes (e.g., pericentromeres, centromeres, and telomeres) impede replication fork progression, eventually leading, in the event of replication stress, to chromosome fragility, aging, and cancer. Our knowledge of the mechanisms controlling the stability of these regions is essentially limited to telomeres, where fragility is counteracted by the shelterin proteins. Here we show that the shelterin subunit TRF2 ensures progression of the replication fork through pericentromeric heterochromatin, but not centromeric chromatin. In a process involving its N-terminal basic domain, TRF2 binds to pericentromeric Satellite III sequences during S phase, allowing the recruitment of the G-quadruplex-resolving helicase RTEL1 to facilitate fork progression. We also show that TRF2 is required for the stability of other heterochromatic regions localized throughout the genome, paving the way for future research on heterochromatic replication and its relationship with aging and cancer. Copyright © 2018 Elsevier Inc. All rights reserved.
International Nuclear Information System (INIS)
Kulich, N.V.; Nemtsev, V.A.
1986-01-01
The analytical solution to the problem on the stationary temperature field in an infinite structural element of rectangular profile characteristic of the conjugation points of a vessel and a tube sheet of a heat exchanger (or of a finned surface) at the third-kind boundary conditions has been obtained by the methods of the complex variable function theory. With the help of the obtained analytical dependences the calculations of the given element of the design and the comparison with the known data have been conducted. The proposed analytical solution can be effectively used in calculations of temperature fields in finned surfaces and structural elements of the power equipment of the considered profile and the method is applied for solution of the like problems
International Nuclear Information System (INIS)
Tsuji, Masashi; Chiba, Gou
2000-01-01
A hierarchical domain decomposition boundary element method (HDD-BEM) for solving the multiregion neutron diffusion equation (NDE) has been fully parallelized, both for numerical computations and for data communications, to accomplish a high parallel efficiency on distributed memory message passing parallel computers. Data exchanges between node processors that are repeated during iteration processes of HDD-BEM are implemented, without any intervention of the host processor that was used to supervise parallel processing in the conventional parallelized HDD-BEM (P-HDD-BEM). Thus, the parallel processing can be executed with only cooperative operations of node processors. The communication overhead was even the dominant time consuming part in the conventional P-HDD-BEM, and the parallelization efficiency decreased steeply with the increase of the number of processors. With the parallel data communication, the efficiency is affected only by the number of boundary elements assigned to decomposed subregions, and the communication overhead can be drastically reduced. This feature can be particularly advantageous in the analysis of three-dimensional problems where a large number of processors are required. The proposed P-HDD-BEM offers a promising solution to the deterioration problem of parallel efficiency and opens a new path to parallel computations of NDEs on distributed memory message passing parallel computers. (author)
Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins
Energy Technology Data Exchange (ETDEWEB)
Montoya-Durango, Diego E. [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Liu, Yongqing [James Graham Brown Cancer Center and Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Teneng, Ivo; Kalbfleisch, Ted; Lacy, Mary E.; Steffen, Marlene C. [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Ramos, Kenneth S., E-mail: kenneth.ramos@louisville.edu [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States)
2009-06-01
Long interspersed nuclear elements (LINEs or L1 elements) are targeted for epigenetic silencing during early embryonic development and remain inactive in most cells and tissues. Here we show that E2F-Rb family complexes participate in L1 elements epigenetic regulation via nucleosomal histone modifications and recruitment of histone deacetylases (HDACs) HDAC1 and HDAC2. Our experiments demonstrated that (i) Rb and E2F interact with human and mouse L1 elements, (ii) L1 elements are deficient in both heterochromatin-associated histone marks H3 tri methyl K9 and H4 tri methyl K20 in Rb family triple knock out (Rb, p107, and p130) fibroblasts (TKO), (iii) L1 promoter exhibits increased histone H3 acetylation in the absence of HDAC1 and HDAC2 recruitment, (iv) L1 expression in TKO fibroblasts is upregulated compared to wild type counterparts, (v) L1 expression increases in the presence of the HDAC inhibitor TSA. On the basis of these findings we propose a model in which L1 sequences throughout the genome serve as centers for heterochromatin formation in an Rb family-dependent manner. As such, Rb proteins and L1 elements may play key roles in heterochromatin formation beyond pericentromeric chromosomal regions. These findings describe a novel mechanism of L1 reactivation in mammalian cells mediated by failure of corepressor protein recruitment by Rb, loss of histone epigenetic marks, heterochromatin formation, and increased histone H3 acetylation.
Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins
International Nuclear Information System (INIS)
Montoya-Durango, Diego E.; Liu, Yongqing; Teneng, Ivo; Kalbfleisch, Ted; Lacy, Mary E.; Steffen, Marlene C.; Ramos, Kenneth S.
2009-01-01
Long interspersed nuclear elements (LINEs or L1 elements) are targeted for epigenetic silencing during early embryonic development and remain inactive in most cells and tissues. Here we show that E2F-Rb family complexes participate in L1 elements epigenetic regulation via nucleosomal histone modifications and recruitment of histone deacetylases (HDACs) HDAC1 and HDAC2. Our experiments demonstrated that (i) Rb and E2F interact with human and mouse L1 elements, (ii) L1 elements are deficient in both heterochromatin-associated histone marks H3 tri methyl K9 and H4 tri methyl K20 in Rb family triple knock out (Rb, p107, and p130) fibroblasts (TKO), (iii) L1 promoter exhibits increased histone H3 acetylation in the absence of HDAC1 and HDAC2 recruitment, (iv) L1 expression in TKO fibroblasts is upregulated compared to wild type counterparts, (v) L1 expression increases in the presence of the HDAC inhibitor TSA. On the basis of these findings we propose a model in which L1 sequences throughout the genome serve as centers for heterochromatin formation in an Rb family-dependent manner. As such, Rb proteins and L1 elements may play key roles in heterochromatin formation beyond pericentromeric chromosomal regions. These findings describe a novel mechanism of L1 reactivation in mammalian cells mediated by failure of corepressor protein recruitment by Rb, loss of histone epigenetic marks, heterochromatin formation, and increased histone H3 acetylation.
Stability analysis of shallow tunnels subjected to eccentric loads by a boundary element method
Directory of Open Access Journals (Sweden)
Mehdi Panji
2016-08-01
Full Text Available In this paper, stress behavior of shallow tunnels under simultaneous non-uniform surface traction and symmetric gravity loading was studied using a direct boundary element method (BEM. The existing full-plane elastostatic fundamental solutions to displacement and stress fields were used and implemented in a developed algorithm. The cross-section of the tunnel was considered in circular, square, and horseshoe shapes and the lateral coefficient of the domain was assumed as unit quantity. Double-node procedure of the BEM was applied at the corners to improve the model including sudden traction changes. The results showed that the method used was a powerful tool for modeling underground openings under various external as well as internal loads. Eccentric loads significantly influenced the stress pattern of the surrounding tunnel. The achievements can be practically used in completing and modifying regulations for stability investigation of shallow tunnels.
Cabral, Juliano S.; Felix, Leonardo P.; Guerra, Marcelo
2006-01-01
We investigated four orchids of the genus Maxillaria (M. discolor, M. acicularis, M. notylioglossa and M. desvauxiana) in regard to the position of heterochromatin blocks as revealed using chromomycin A3 (CMA) and 4'-6-diamidino-2-phenylindole (DAPI) fluorochrome staining and 5S and 45S rDNA sites using fluorescence in situ hybridization (FISH). The species showed differences in chromosome number and a diversified pattern of CMA+ and DAPI+ bands, including heteromorphism for CMA+ bands. The 5...
Finite Element Modelling of Seismic Liquefaction in Soils
Galavi, V.; Petalas, A.; Brinkgreve, R.B.J.
2013-01-01
Numerical aspects of seismic liquefaction in soils as implemented in the finite element code, PLAXIS, is described in this paper. After description of finite element equations of dynamic problems, three practical dynamic boundary conditions, namely viscous boundary tractions, tied degrees of freedom
Swamy, Lakshmi; Amulic, Borko; Deitsch, Kirk W.
2011-01-01
Antigenic variation in the human malaria parasite Plasmodium falciparum depends on the transcriptional regulation of the var gene family. In each individual parasite, mRNA is expressed exclusively from 1 var gene out of ∼60, while the rest of the genes are transcriptionally silenced. Both modifications to chromatin structure and DNA regulatory elements associated with each var gene have been implicated in the organization and maintenance of the silent state. Whether silencing is established at the level of entire chromosomal regions via heterochromatin spreading or at the level of individual var promoters through the action of a silencing element within each var intron has been debated. Here, we consider both possibilities, using clonal parasite lines carrying chromosomally integrated transgenes. We confirm a previous finding that the loss of an adjacent var intron results in var promoter activation and further show that transcriptional activation of a var promoter within a cluster does not affect the transcriptional activity of neighboring var promoters. Our results provide more evidence for the hypothesis that var genes are primarily silenced at the level of an individual gene, rather than by heterochromatin spreading. We also tested the intrinsic directionality of an intron's silencing effect on upstream or downstream var promoters. We found that an intron is capable of silencing in either direction and that, once established, a var promoter-intron pair is stably maintained through many generations, suggesting a possible role in epigenetic memory. This study provides insights into the regulation of endogenous var gene clusters. PMID:21317310
Directory of Open Access Journals (Sweden)
Shao Yan-Lin
2014-12-01
Full Text Available This paper presents some of the efforts by the authors towards numerical prediction of springing of ships. A time-domain Higher Order Boundary Element Method (HOBEM based on cubic shape function is first presented to solve a complete second-order problem in terms of wave steepness and ship motions in a consistent manner. In order to avoid high order derivatives on the body surfaces, e.g. mj-terms, a new formulation of the Boundary Value Problem in a body-fixed coordinate system has been proposed instead of traditional formulation in inertial coordinate system. The local steady flow effects on the unsteady waves are taken into account. Double-body flow is used as the basis flow which is an appropriate approximation for ships with moderate forward speed. This numerical model was used to estimate the complete second order wave excitation of springing of a displacement ship at constant forward speeds.
Diffuse boundary extraction of breast masses on ultrasound by leak plugging
International Nuclear Information System (INIS)
Cary, T.W.; Conant, E.F.; Arger, P.H.; Sehgal, C.M.
2005-01-01
We propose a semiautomated seeded boundary extraction algorithm that delineates diffuse region boundaries by finding and plugging their leaks. The algorithm not only extracts boundaries that are partially diffuse, but in the process finds and quantifies those parts of the boundary that are diffuse, computing local sharpness measurements for possible use in computer-aided diagnosis. The method treats a manually drawn seed region as a wellspring of pixel 'fluid' that flows from the seed out towards the boundary. At indistinct or porous sections of the boundary, the growing region will leak into surrounding tissue. By changing the size of structuring elements used for growing, the algorithm changes leak properties. Since larger elements cannot leak as far from the seed, they produce compact, less detailed boundary approximations; conversely, growing from smaller elements results in less constrained boundaries with more local detail. This implementation of the leak plugging algorithm decrements the radius of structuring disks and then compares the regions grown from them as they increase in both area and boundary detail. Leaks are identified if the outflows between grown regions are large compared to the areas of the disks. The boundary is plugged by masking out leaked pixels, and the process continues until one-pixel-radius resolution. When tested against manual delineation on scans of 40 benign masses and 40 malignant tumors, the plugged boundaries overlapped and correlated well in area with manual tracings, with mean overlap of 0.69 and area correlation R 2 of 0.86, but the algorithm's results were more reproducible
DEFF Research Database (Denmark)
Qing, Hai
2013-01-01
Two-dimensional finite element (FE) simulations of the deformation and damage evolution of Silicon–Carbide (SiC) particle reinforced aluminum alloy composite including interphase are carried out for different microstructures and particle volume fractions of the composites. A program is developed...... for the automatic generation of 2D micromechanical FE-models with randomly distributed SiC particles. In order to simulate the damage process in aluminum alloy matrix and SiC particles, a damage parameter based on the stress triaxial indicator and the maximum principal stress criterion based elastic brittle damage...... model are developed within Abaqus/Standard Subroutine USDFLD, respectively. An Abaqus/Standard Subroutine MPC, which allows defining multi-point constraints, is developed to realize the symmetric boundary condition (SBC) and periodic boundary condition (PBC). A series of computational experiments...
An assessment of the DORT method on simple scatterers using boundary element modelling.
Gélat, P; Ter Haar, G; Saffari, N
2015-05-07
The ability to focus through ribs overcomes an important limitation of a high-intensity focused ultrasound (HIFU) system for the treatment of liver tumours. Whilst it is important to generate high enough acoustic pressures at the treatment location for tissue lesioning, it is also paramount to ensure that the resulting ultrasonic dose on the ribs remains below a specified threshold, since ribs both strongly absorb and reflect ultrasound. The DORT (décomposition de l'opérateur de retournement temporel) method has the ability to focus on and through scatterers immersed in an acoustic medium selectively without requiring prior knowledge of their location or geometry. The method requires a multi-element transducer and is implemented via a singular value decomposition of the measured matrix of inter-element transfer functions. The efficacy of a method of focusing through scatterers is often assessed by comparing the specific absorption rate (SAR) at the surface of the scatterer, and at the focal region. The SAR can be obtained from a knowledge of the acoustic pressure magnitude and the acoustic properties of the medium and scatterer. It is well known that measuring acoustic pressures with a calibrated hydrophone at or near a hard surface presents experimental challenges, potentially resulting in increased measurement uncertainties. Hence, the DORT method is usually assessed experimentally by measuring the SAR at locations on the surface of the scatterer after the latter has been removed from the acoustic medium. This is also likely to generate uncertainties in the acoustic pressure measurement. There is therefore a strong case for assessing the efficacy of the DORT method through a validated theoretical model. The boundary element method (BEM) applied to exterior acoustic scattering problems is well-suited for such an assessment. In this study, BEM was used to implement the DORT method theoretically on locally reacting spherical scatterers, and to assess its focusing
The Boundary Element Method Applied to the Two Dimensional Stefan Moving Boundary Problem
1991-03-15
Unc), - ( UGt )t - (UG,,),,] - (UG), If we integrate this equation with respect to r from 0 to t - c and with respect to and ij on the region 11(r...and others. "Moving Boundary Problems in Phase Change Mod- els," SIGNUM Newsletter, 20: 8-12 (1985). 21. Stefan, J. "Ober einige Probleme der Theorie ...ier Wirmelcitung," S.-B. \\Vein. Akad. Mat. Natur., 98: 173-484 (1889). 22.-. "flber (lie Theorie der Eisbildung insbesondere fiber die lisbildung im
Computation of Aerodynamic Noise Radiated from Ducted Tail Rotor Using Boundary Element Method
Directory of Open Access Journals (Sweden)
Yunpeng Ma
2017-01-01
Full Text Available A detailed aerodynamic performance of a ducted tail rotor in hover has been numerically studied using CFD technique. The general governing equations of turbulent flow around ducted tail rotor are given and directly solved by using finite volume discretization and Runge-Kutta time integration. The calculations of the lift characteristics of the ducted tail rotor can be obtained. In order to predict the aerodynamic noise, a hybrid method combining computational aeroacoustic with boundary element method (BEM has been proposed. The computational steps include the following: firstly, the unsteady flow around rotor is calculated using the CFD method to get the noise source information; secondly, the radiate sound pressure is calculated using the acoustic analogy Curle equation in the frequency domain; lastly, the scattering effect of the duct wall on the propagation of the sound wave is presented using an acoustic thin-body BEM. The aerodynamic results and the calculated sound pressure levels are compared with the known technique for validation. The sound pressure directivity and scattering effect are shown to demonstrate the validity and applicability of the method.
Energy Technology Data Exchange (ETDEWEB)
De Corato, M., E-mail: marco.decorato@unina.it [Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università di Napoli Federico II, Piazzale Tecchio 80, 80125 Napoli (Italy); Slot, J.J.M., E-mail: j.j.m.slot@tue.nl [Department of Mathematics and Computer Science, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven (Netherlands); Hütter, M., E-mail: m.huetter@tue.nl [Department of Mechanical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven (Netherlands); D' Avino, G., E-mail: gadavino@unina.it [Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università di Napoli Federico II, Piazzale Tecchio 80, 80125 Napoli (Italy); Maffettone, P.L., E-mail: pierluca.maffettone@unina.it [Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università di Napoli Federico II, Piazzale Tecchio 80, 80125 Napoli (Italy); Hulsen, M.A., E-mail: m.a.hulsen@tue.nl [Department of Mechanical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven (Netherlands)
2016-07-01
In this paper, we present a finite element implementation of fluctuating hydrodynamics with a moving boundary fitted mesh for treating the suspended particles. The thermal fluctuations are incorporated into the continuum equations using the Landau and Lifshitz approach [1]. The proposed implementation fulfills the fluctuation–dissipation theorem exactly at the discrete level. Since we restrict the equations to the creeping flow case, this takes the form of a relation between the diffusion coefficient matrix and friction matrix both at the particle and nodal level of the finite elements. Brownian motion of arbitrarily shaped particles in complex confinements can be considered within the present formulation. A multi-step time integration scheme is developed to correctly capture the drift term required in the stochastic differential equation (SDE) describing the evolution of the positions of the particles. The proposed approach is validated by simulating the Brownian motion of a sphere between two parallel plates and the motion of a spherical particle in a cylindrical cavity. The time integration algorithm and the fluctuating hydrodynamics implementation are then applied to study the diffusion and the equilibrium probability distribution of a confined circle under an external harmonic potential.
Energy Technology Data Exchange (ETDEWEB)
Sarler, B [Institut Jozef Stefan, Ljubljana (Yugoslavia)
1987-07-01
The basic principles of the boundary element method numerical treatment of the radial flow heat diffusion equation are presented. The algorithm copes the time dependent Dirichlet and Neumann boundary conditions, temperature dependent material properties and regions from different materials in thermal contact. It is verified on the several analytically obtained test cases. The developed method is used for the modelling of unsteady radial heat flow in pressurized water reactor fuel rod. (author)
Directory of Open Access Journals (Sweden)
María Poggio
2011-05-01
Full Text Available In the present work, we analysed the male meiosis, the content and distribution of heterochromatin and the number and location of nucleolus organizing regions in Microtomus lunifer (Berg, 1900 by means of standard technique, C- and fluorescent bandings, and fluorescent in situ hybridization with an 18S rDNA probe. This species is the second one cytogenetically analysed within the Hammacerinae. Its male diploid chromosome number is 31 (2n=28+X1X2Y, including a minute pair of m-chromosomes. The diploid autosomal number and the presence of m-chromosomes are similar to those reported in M. conspicillaris (Drury, 1782 (2n=28+XY. However, M. lunifer has a multiple sex chromosome system X1X2Y (male that could have originated by fragmentation of the ancestral X chromosome. Taking into account that M. conspicillaris and M. lunifer are the only two species within Reduviidae that possess m-chromosomes, the presence of this pair could be a synapomorphy for the species of this genus. C- and fluorescent bandings showed that the amount of heterochromatin in M. lunifer was small, and only a small CMA3 bright band was observed in the largest autosomal pair at one terminal region. FISH with the 18S rDNA probe demonstrated that ribosomal genes were terminally placed on the largest autosomal pair. Our present results led us to propose that the location of rDNA genes could be associated with variants of the sex chromosome systems in relation with a kind of the sex chromosome systems within this family. Furthermore, the terminal location of NOR in the largest autosomal pair allowed us to use it as a chromosome marker and, thus, to infer that the kinetic activity of both ends is not a random process, and there is an inversion of this activity.
Surface free energy for systems with integrable boundary conditions
International Nuclear Information System (INIS)
Goehmann, Frank; Bortz, Michael; Frahm, Holger
2005-01-01
The surface free energy is the difference between the free energies for a system with open boundary conditions and the same system with periodic boundary conditions. We use the quantum transfer matrix formalism to express the surface free energy in the thermodynamic limit of systems with integrable boundary conditions as a matrix element of certain projection operators. Specializing to the XXZ spin-1/2 chain we introduce a novel 'finite temperature boundary operator' which characterizes the thermodynamical properties of surfaces related to integrable boundary conditions
Hecker, Andreas; Brand, Luise H; Peter, Sébastien; Simoncello, Nathalie; Kilian, Joachim; Harter, Klaus; Gaudin, Valérie; Wanke, Dierk
2015-07-01
Polycomb-repressive complexes (PRCs) play key roles in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC-silencing mechanisms as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors in animals can guide PRC members in a sequence-specific manner to Polycomb-responsive DNA elements. Here, we show that the Arabidopsis (Arabidopsis thaliana) GAGA-motif binding factor protein basic pentacysteine6 (BPC6) interacts with like heterochromatin protein1 (LHP1), a PRC1 component, and associates with vernalization2 (VRN2), a PRC2 component, in vivo. By using a modified DNA-protein interaction enzyme-linked immunosorbant assay, we could show that BPC6 was required and sufficient to recruit LHP1 to GAGA motif-containing DNA probes in vitro. We also found that LHP1 interacts with VRN2 and, therefore, can function as a possible scaffold between BPC6 and VRN2. The lhp1-4 bpc4 bpc6 triple mutant displayed a pleiotropic phenotype, extreme dwarfism and early flowering, which disclosed synergistic functions of LHP1 and group II plant BPC members. Transcriptome analyses supported this synergy and suggested a possible function in the concerted repression of homeotic genes, probably through histone H3 lysine-27 trimethylation. Hence, our findings suggest striking similarities between animal and plant GAGA-binding factors in the recruitment of PRC1 and PRC2 components to Polycomb-responsive DNA element-like GAGA motifs, which must have evolved through convergent evolution. © 2015 American Society of Plant Biologists. All Rights Reserved.
Stability estimates for hp spectral element methods for general ...
Indian Academy of Sciences (India)
We establish basic stability estimates for a non-conforming ℎ- spectral element method which allows for simultaneous mesh refinement and variable polynomial degree. The spectral element functions are non-conforming if the boundary conditions are Dirichlet. For problems with mixed boundary conditions they are ...
Contreras Zazueta, M. A.; Perton, M.; Sanchez-Sesma, F. J.; Sánchez-Alvaro, E.
2013-12-01
The seismic hazard assessment of extended developments, such as a dam, a bridge or a pipeline, needs the strong ground motion simulation taking into account the effects of surface geology. In many cases the incoming wave field can be obtained from attenuation relations or simulations for layered media using Discrete Wave Number (DWN). Sometimes there is a need to include in simulations the seismic source as well. A number of methods to solve these problems have been developed. Among them the Finite Element and Finite Difference Methods (FEM and FDM) are generally preferred because of the facility of use. Nevertheless, the analysis of realistic dynamic loading induced by earthquakes requires a thinner mesh of the entire domain to consider high frequencies. Consequently this may imply a high computational cost. The Indirect Boundary Element Method (IBEM) can also be employed. Here it is used to study the response of a site to historical seismic activity. This method is particularly suited to model wave propagation through wide areas as it requires only the meshing of boundaries. Moreover, it is well suited to represent finely the diffraction that can occur on a fault. However, the IBEM has been applied mainly to simple geometrical configurations. In this communication significant refinements of the formulation are presented. Using IBEM we can simulate wave propagation in complex geometrical configurations such as a stratified medium crossed by thin faults or having a complex topography. Two main developments are here described; one integrates the DWN method inside the IBEM in order to represent the Green's functions of stratified media with relatively low computational cost but assuming unbounded parallel flat layers, and the other is the extension of IBEM to deal with multi-regions in contact which allows more versatility with a higher computational cost compared to the first one but still minor to an equivalent FEM formulation. The two approaches are fully
Li, Qiang; Popov, Valentin L.
2018-03-01
Recently proposed formulation of the boundary element method for adhesive contacts has been generalized for contacts of power-law graded materials with and without adhesion. Proceeding from the fundamental solution for single force acting on the surface of an elastic half space, first the influence matrix is obtained for a rectangular grid. The inverse problem for the calculation of required stress in the contact area from a known surface displacement is solved using the conjugate-gradient technique. For the transformation between the stresses and displacements, the Fast Fourier Transformation is used. For the adhesive contact of graded material, the detachment criterion based on the energy balance is proposed. The method is validated by comparison with known exact analytical solutions as well as by proving the independence of the mesh size and the grid orientation.
Li, Tao; Wang, Yan; Zhou, Jie; Wang, Tao; Ding, Aijun; Nie, Wei; Xue, Likun; Wang, Xinfeng; Wang, Wenxing
2017-03-01
Aerosols and cloud water were analyzed at a mountaintop in the planetary boundary layer in southern China during March-May 2009, when two Asian dust storms occurred, to investigate the effects of aerosol-cloud interactions (ACIs) on chemical evolution of atmospheric trace elements. Fe, Al, and Zn predominated in both coarse and fine aerosols, followed by high concentrations of toxic Pb, As, and Cd. Most of these aerosol trace elements, which were affected by dust storms, exhibited various increases in concentrations but consistent decreases in solubility. Zn, Fe, Al, and Pb were the most abundant trace elements in cloud water. The trace element concentrations exhibited logarithmic inverse relationships with the cloud liquid water content and were found highly pH dependent with minimum concentrations at the threshold of pH 5.0. The calculation of Visual MINTEQ model showed that 80.7-96.3% of Fe(II), Zn(II), Pb(II), and Cu(II) existed in divalent free ions, while 71.7% of Fe(III) and 71.5% of Al(III) were complexed by oxalate and fluoride, respectively. ACIs could markedly change the speciation distributions of trace elements in cloud water by pH modification. The in-cloud scavenging of aerosol trace elements likely reached a peak after the first 2-3 h of cloud processing, with scavenging ratios between 0.12 for Cr and 0.57 for Pb. The increases of the trace element solubility (4-33%) were determined in both in-cloud aerosols and postcloud aerosols. These results indicated the significant importance of aerosol-cloud interactions to the evolution of trace elements during the first several cloud condensation/evaporation cycles.
DEFF Research Database (Denmark)
Cutanda Henriquez, Vicente; Juhl, Peter Møller; Barrera Figueroa, Salvador
2009-01-01
Secondary calibration of microphones in free field is performed by placing the microphone under calibration in an anechoic chamber with a sound source, and exposing it to a controlled sound field. A calibrated microphone is also measured as a reference. While the two measurements are usually made...... apart to avoid acoustic interaction. As a part of the project Euromet-792, aiming to investigate and improve methods for secondary free-field calibration of microphones, a sound source suitable for simultaneous secondary free-field calibration has been designed using the Boundary Element Method...... of the Danish Fundamental Metrology Institute (DFM). The design and verification of the source are presented in this communication....
Czech Academy of Sciences Publication Activity Database
Košař, Martin; Bartkova, J.; Hubáčková, Soňa; Hodný, Zdeněk; Lukas, J.; Bartek, Jiří
2011-01-01
Roč. 10, č. 3 (2011), s. 457-468 ISSN 1538-4101 R&D Projects: GA ČR GA204/08/1418; GA ČR GA301/08/0353 Institutional research plan: CEZ:AV0Z50520514 Keywords : genotoxic and replicative stress * senescence-associated heterochromatin foci * DNA damage response Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.359, year: 2011
Inference of boundaries in causal sets
Cunningham, William J.
2018-05-01
We investigate the extrinsic geometry of causal sets in (1+1) -dimensional Minkowski spacetime. The properties of boundaries in an embedding space can be used not only to measure observables, but also to supplement the discrete action in the partition function via discretized Gibbons–Hawking–York boundary terms. We define several ways to represent a causal set using overlapping subsets, which then allows us to distinguish between null and non-null bounding hypersurfaces in an embedding space. We discuss algorithms to differentiate between different types of regions, consider when these distinctions are possible, and then apply the algorithms to several spacetime regions. Numerical results indicate the volumes of timelike boundaries can be measured to within 0.5% accuracy for flat boundaries and within 10% accuracy for highly curved boundaries for medium-sized causal sets with N = 214 spacetime elements.
DEFF Research Database (Denmark)
Henriquez, Vicente Cutanda; Barrera Figueroa, Salvador; Juhl, Peter Møller
2008-01-01
is of particular importance to achieve a sound field that reaches both microphones with the same level and that is sufficiently uniform at the microphone positions, in order to reduce the effect of misalignment. An existing sound source has been modeled using the Boundary Element Method, and the simulations have......The project Euromet-792 aims to investigate and improve methods for secondary free-field calibration of microphones. In this framework, the comparison method is being studied at DFM in relation to the more usual substitution method of microphone calibration. The design of the sound source...... been used to modify the source and make it suitable for this kind of calibration. It has been found that a central plug, already present in the device, can be re-shaped in such a way that makes the sound field on the microphone positions more uniform, even at rather high frequencies. Measurements have...
Electronic and elemental properties of the Cu{sub 2}ZnSn(S,Se){sub 4} surface and grain boundaries
Energy Technology Data Exchange (ETDEWEB)
Haight, Richard; Shao, Xiaoyan; Wang, Wei; Mitzi, David B. [IBM T. J. Watson Research Center, P.O. Box 218, Yorktown Hts., New York 10598 (United States)
2014-01-20
X-ray and femtosecond UV photoelectron spectroscopy, secondary ion mass spectrometry and photoluminescence imaging were used to investigate the electronic and elemental properties of the CZTS,Se surface and its oxides. Oxide removal reveals a very Cu poor and Zn rich surface relative to bulk composition. O and Na are observed at the surface and throughout the bulk. Upward bending of the valence bands indicates the presence of negative charge in the surface region and the Fermi level is found near the band gap center. The presence of point defects and the impact of these findings on grain boundary properties will be described.
International Nuclear Information System (INIS)
St John, C.M.; Sanjeevan, K.
1991-12-01
The HEFF Code combines a simple boundary-element method of stress analysis with the closed form solutions for constant or exponentially decaying heat sources in an infinite elastic body to obtain an approximate method for analysis of underground excavations in a rock mass with heat generation. This manual describes the theoretical basis for the code, the code structure, model preparation, and step taken to assure that the code correctly performs its intended functions. The material contained within the report addresses the Software Quality Assurance Requirements for the Yucca Mountain Site Characterization Project. 13 refs., 26 figs., 14 tabs
A Dual Super-Element Domain Decomposition Approach for Parallel Nonlinear Finite Element Analysis
Jokhio, G. A.; Izzuddin, B. A.
2015-05-01
This article presents a new domain decomposition method for nonlinear finite element analysis introducing the concept of dual partition super-elements. The method extends ideas from the displacement frame method and is ideally suited for parallel nonlinear static/dynamic analysis of structural systems. In the new method, domain decomposition is realized by replacing one or more subdomains in a "parent system," each with a placeholder super-element, where the subdomains are processed separately as "child partitions," each wrapped by a dual super-element along the partition boundary. The analysis of the overall system, including the satisfaction of equilibrium and compatibility at all partition boundaries, is realized through direct communication between all pairs of placeholder and dual super-elements. The proposed method has particular advantages for matrix solution methods based on the frontal scheme, and can be readily implemented for existing finite element analysis programs to achieve parallelization on distributed memory systems with minimal intervention, thus overcoming memory bottlenecks typically faced in the analysis of large-scale problems. Several examples are presented in this article which demonstrate the computational benefits of the proposed parallel domain decomposition approach and its applicability to the nonlinear structural analysis of realistic structural systems.
Min, J. B.; Reddy, T. S. R.; Bakhle, M. A.; Coroneos, R. M.; Stefko, G. L.; Provenza, A. J.; Duffy, K. P.
2018-01-01
Accurate prediction of the blade vibration stress is required to determine overall durability of fan blade design under Boundary Layer Ingestion (BLI) distorted flow environments. Traditional single blade modeling technique is incapable of representing accurate modeling for the entire rotor blade system subject to complex dynamic loading behaviors and vibrations in distorted flow conditions. A particular objective of our work was to develop a high-fidelity full-rotor aeromechanics analysis capability for a system subjected to a distorted inlet flow by applying cyclic symmetry finite element modeling methodology. This reduction modeling method allows computationally very efficient analysis using a small periodic section of the full rotor blade system. Experimental testing by the use of the 8-foot by 6-foot Supersonic Wind Tunnel Test facility at NASA Glenn Research Center was also carried out for the system designated as the Boundary Layer Ingesting Inlet/Distortion-Tolerant Fan (BLI2DTF) technology development. The results obtained from the present numerical modeling technique were evaluated with those of the wind tunnel experimental test, toward establishing a computationally efficient aeromechanics analysis modeling tool facilitating for analyses of the full rotor blade systems subjected to a distorted inlet flow conditions. Fairly good correlations were achieved hence our computational modeling techniques were fully demonstrated. The analysis result showed that the safety margin requirement set in the BLI2DTF fan blade design provided a sufficient margin with respect to the operating speed range.
Boundary element analysis of stress singularity in dissimilar metals by friction welding
International Nuclear Information System (INIS)
Chung, N. Y.; Park, C. H.
2012-01-01
Friction welded dissimilar metals are widely applied in automobiles, rolling stocks, machine tools, and various engineering fields. Dissimilar metals have several advantages over homogeneous metals, including high strength, material property, fatigue endurance, impact absorption, high reliability, and vibration reduction. Due to the increased use of these metals, understanding their behavior under stress conditions is necessary, especially the analysis of stress singularity on the interface of friction-welded dissimilar metals. To establish a strength evaluation method and a fracture criterion, it is necessary to analyze stress singularity on the interface of dissimilar metals with welded flashes by friction welding under various loads and temperature conditions. In this paper, a method analyzing stress singularity for the specimens with and without flashes set in friction welded dissimilar metals is introduced using the boundary element method. The stress singularity index (λ) and the stress singularity factor (Γ) at the interface edge are computed from the stress analysis results. The shape and flash thickness, interface length, residual stress, and load are considered in the computation. Based on these results, the variations of interface length (c) and the ratio of flash thickness (t2 t1) greatly influence the stress singularity factors at the interface edge of friction welded dissimilar metals. The stress singularity factors will be a useful fracture parameter that considers stress singularity on the interface of dissimilar metals
Discretization of the induced-charge boundary integral equation.
Bardhan, Jaydeep P; Eisenberg, Robert S; Gillespie, Dirk
2009-07-01
Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.
Discretization of the induced-charge boundary integral equation.
Energy Technology Data Exchange (ETDEWEB)
Bardhan, J. P.; Eisenberg, R. S.; Gillespie, D.; Rush Univ. Medical Center
2009-07-01
Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch et al. [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.
Effect of crystal orientation on grain boundary migration and radiation-induced segregation
International Nuclear Information System (INIS)
Hashimoto, N.; Eda, Y.; Takahashi, H.
1996-01-01
Fe-Cr-Ni, Ni-Al and Ni-Si alloys were electron-irradiated using a high voltage electron microscope (1 MeV), and in situ observations of the structural evolution and micro-chemical analysis were carried out. During the irradiation, the grain boundaries in the irradiated region migrated, while no grain boundary migration occurred in the unirradiated area. The occurrence of boundary migration depended on the orientation relationship of the boundary interfaces. Grain boundary migration took place in Fe-Cr-Ni and Ni-Si alloys with large crystal orientation difference between the two grains across a grain boundary. In Ni-Al, however, the grain boundary migration did not occur. The solute segregation was caused at grain boundary under irradiation and this segregation behavior was closely related to solute size, namely the concentrations of undersized Ni and oversized Cr elements in Fe-Cr-Ni alloy increased and reduced at grain boundary, respectively. The same dependence of segregation on the solute size was derived in Ni-Si and Ni-Al alloys, in which Si and Al solutes are undersized and oversized elements, respectively. Therefore, Si solute enriched and Al solute depleted at grain boundary. From the present segregation behavior, it is suggested that the flow of point defects into the boundary is the cause of grain boundary migration. (orig.)
International Nuclear Information System (INIS)
Zavatsky, S.; Phaneuf, P.; Topaz, D.; Ward, D.
1978-02-01
The NRC Office of Inspection and Enforcement (IE) has elected to evaluate the effectiveness and efficiency of its existing regional boundary alignment because of the anticipated future growth of nuclear power generating facilities and corresponding inspection requirements. This report documents a management study designed to identify, analyze, and evaluate alternative regional boundary configurations for the NRC/IE regions. Eight boundary configurations were chosen for evaluation. These configurations offered alternatives ranging from two to ten regions, and some included the concepts of subregional or satellite offices. Each alternative configuration was evaluated according to three major criteria: project workload, cost, and office location. Each major criterion included elements such as management control, program uniformity, disruption, costs, and coordination with other agencies. The conclusion reached was that regional configurations with regions of equal and relatively large workloads, combined with the concepts of subregional or satellite offices, may offer a significant benefit to the Office of Inspection and Enforcement and the Commission and are worthy of further study. A phased implementation plan, which is suitable to some configurations, may help mitigate the disruption created by realignment
Directory of Open Access Journals (Sweden)
Emanuele eLibertini
2015-12-01
Full Text Available BAH domain-containing protein 1 (BAHD1 is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi, but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq to compare the DNA methylation profile of HEK293 cells expressing low levels of BAHD1 (HEK-CT to that of isogenic cells stably overexpressing BAHD1 (HEK-BAHD1. We show that increasing BAHD1 levels induces de novo DNA methylation on autosomes and a marked hypomethylation on the X chromosome (chrX. We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed BAHD1-DMRs, of which 83,850 mapped on autosomes and 7,508 on the X chromosome (chrX. Autosomal BAHD1-DMRs were predominantly hypermethylated and located to satellites, interspersed repeats and intergenic regions. In contrast, BAHD1-DMRs on chrX were mainly hypomethylated and located to gene bodies and enhancers. We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains. Half of these BAHD1-Associated differentially methylated Domains (BADs overlapped with lamina-associated domains (LADs. Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.
Directory of Open Access Journals (Sweden)
Enders Greg H
2010-06-01
Full Text Available Abstract Background Cellular senescence is a permanent growth arrest that occurs in response to cellular stressors, such as telomere shortening or activation of oncogenes. Although the process of senescence growth arrest is somewhat conserved between mouse and human cells, there are some critical differences in the molecular pathways of senescence between these two species. Recent studies in human fibroblasts have defined a cell signaling pathway that is initiated by repression of a specific Wnt ligand, Wnt2. This, in turn, activates a histone chaperone HIRA, and culminates in formation of specialized punctate domains of facultative heterochromatin, called Senescence-Associated Heterochromatin Foci (SAHF, that are enriched in the histone variant, macroH2A. SAHF are thought to repress expression of proliferation-promoting genes, thereby contributing to senescence-associated proliferation arrest. We asked whether this Wnt2-HIRA-SAHF pathway is conserved in mouse fibroblasts. Results We show that mouse embryo fibroblasts (MEFs and mouse skin fibroblasts, do not form robust punctate SAHF in response to an activated Ras oncogene or shortened telomeres. However, senescent MEFs do exhibit elevated levels of macroH2A staining throughout the nucleus as a whole. Consistent with their failure to fully activate the SAHF assembly pathway, the Wnt2-HIRA signaling axis is not overtly regulated between proliferating and senescent mouse cells. Conclusions In addition to the previously defined differences between mouse and human cells in the mechanisms and phenotypes associated with senescence, we conclude that senescent mouse and human fibroblasts also differ at the level of chromatin and the signaling pathways used to regulate chromatin. These differences between human and mouse senescence may contribute to the increased propensity of mouse fibroblasts (and perhaps other mouse cell types to become immortalized and transformed, compared to human cells.
The occipital place area represents the local elements of scenes.
Kamps, Frederik S; Julian, Joshua B; Kubilius, Jonas; Kanwisher, Nancy; Dilks, Daniel D
2016-05-15
Neuroimaging studies have identified three scene-selective regions in human cortex: parahippocampal place area (PPA), retrosplenial complex (RSC), and occipital place area (OPA). However, precisely what scene information each region represents is not clear, especially for the least studied, more posterior OPA. Here we hypothesized that OPA represents local elements of scenes within two independent, yet complementary scene descriptors: spatial boundary (i.e., the layout of external surfaces) and scene content (e.g., internal objects). If OPA processes the local elements of spatial boundary information, then it should respond to these local elements (e.g., walls) themselves, regardless of their spatial arrangement. Indeed, we found that OPA, but not PPA or RSC, responded similarly to images of intact rooms and these same rooms in which the surfaces were fractured and rearranged, disrupting the spatial boundary. Next, if OPA represents the local elements of scene content information, then it should respond more when more such local elements (e.g., furniture) are present. Indeed, we found that OPA, but not PPA or RSC, responded more to multiple than single pieces of furniture. Taken together, these findings reveal that OPA analyzes local scene elements - both in spatial boundary and scene content representation - while PPA and RSC represent global scene properties. Copyright © 2016 Elsevier Inc. All rights reserved.
Vortex Generators to Control Boundary Layer Interactions
Babinsky, Holger (Inventor); Loth, Eric (Inventor); Lee, Sang (Inventor)
2014-01-01
Devices for generating streamwise vorticity in a boundary includes various forms of vortex generators. One form of a split-ramp vortex generator includes a first ramp element and a second ramp element with front ends and back ends, ramp surfaces extending between the front ends and the back ends, and vertical surfaces extending between the front ends and the back ends adjacent the ramp surfaces. A flow channel is between the first ramp element and the second ramp element. The back ends of the ramp elements have a height greater than a height of the front ends, and the front ends of the ramp elements have a width greater than a width of the back ends.
Su, Y.; Ong, E. T.; Lee, K. H.
2002-05-01
The past decade has seen an accelerated growth of technology in the field of microelectromechanical systems (MEMS). The development of MEMS products has generated the need for efficient analytical and simulation methods for minimizing the requirement for actual prototyping. The boundary element method is widely used in the electrostatic analysis for MEMS devices. However, singular elements are needed to accurately capture the behavior at singular regions, such as sharp corners and edges, where standard elements fail to give an accurate result. The manual classification of boundary elements based on their singularity conditions is an immensely laborious task, especially when the boundary element model is large. This process can be automated by querying the geometric model of the MEMS device for convex edges based on geometric information of the model. The associated nodes of the boundary elements on these edges can then be retrieved. The whole process is implemented in the MSC/PATRAN platform using the Patran Command Language (the source code is available as supplementary data in the electronic version of this journal issue).
International Nuclear Information System (INIS)
Zhang Chen; Lu Hong; Hua Ning; Tang Xue-Zheng; Tang Fa-Kuan; Shou Guo-Fa; Xia Ling; Ma Ping
2013-01-01
A cardiac vector model is presented and verified, and then the forward problem for cardiac magnetic fields and electric potential are discussed based on this model and the realistic human torso volume conductor model, including lungs. A torso—cardiac vector model is used for a 12-lead electrocardiographic (ECG) and magneto-cardiogram (MCG) simulation study by using the boundary element method (BEM). Also, we obtain the MCG wave picture using a compound four-channel HT c ·SQUID system in a magnetically shielded room. By comparing the simulated results and experimental results, we verify the cardiac vector model and then do a preliminary study of the forward problem of MCG and ECG. Therefore, the results show that the vector model is reasonable in cardiac electrophysiology. (general)
Garfinkel, Benjamin P.; Arad, Shiri; Le, Phuong T.; Bustin, Michael; Rosen, Clifford J.; Gabet, Yankel; Orly, Joseph
2015-01-01
Heterochromatin protein 1 binding protein 3 (HP1BP3) is a recently described histone H1-related protein with roles in chromatin structure and transcriptional regulation. To explore the potential physiological role of HP1BP3, we have previously described an Hp1bp3?/? mouse model with reduced postnatal viability and growth. We now find that these mice are proportionate dwarfs, with reduction in body weight, body length, and organ weight. In addition to their small size, microcomputed tomography...
Trace element patterns at a non-marine cretaceous-tertiary boundary
Gilmore, J.S.; Knight, J.D.; Orth, C.J.; Pillmore, C.L.; Tschudy, R.H.
1984-01-01
At the fossil-pollen-defined Cretaceous-Tertiary boundary in the Raton Basin of New Mexico and Colorado, an iridium abundance anomaly and excess scandium, titanium, and chromium are associated with a thin ash or dust fallout bed (now kaolinitic clay) that was preserved in freshwater coal swamps. ?? 1984 Nature Publishing Group.
Hamanaka, Ryo; Yamaoka, Satoshi; Anh, Tuan Nguyen; Tominaga, Jun-Ya; Koga, Yoshiyuki; Yoshida, Noriaki
2017-11-01
Although many attempts have been made to simulate orthodontic tooth movement using the finite element method, most were limited to analyses of the initial displacement in the periodontal ligament and were insufficient to evaluate the effect of orthodontic appliances on long-term tooth movement. Numeric simulation of long-term tooth movement was performed in some studies; however, neither the play between the brackets and archwire nor the interproximal contact forces were considered. The objectives of this study were to simulate long-term orthodontic tooth movement with the edgewise appliance by incorporating those contact conditions into the finite element model and to determine the force system when the space is closed with sliding mechanics. We constructed a 3-dimensional model of maxillary dentition with 0.022-in brackets and 0.019 × 0.025-in archwire. Forces of 100 cN simulating sliding mechanics were applied. The simulation was accomplished on the assumption that bone remodeling correlates with the initial tooth displacement. This method could successfully represent the changes in the moment-to-force ratio: the tooth movement pattern during space closure. We developed a novel method that could simulate the long-term orthodontic tooth movement and accurately determine the force system in the course of time by incorporating contact boundary conditions into finite element analysis. It was also suggested that friction is progressively increased during space closure in sliding mechanics. Copyright © 2017. Published by Elsevier Inc.
A Hamiltonian-based derivation of Scaled Boundary Finite Element Method for elasticity problems
International Nuclear Information System (INIS)
Hu Zhiqiang; Lin Gao; Wang Yi; Liu Jun
2010-01-01
The Scaled Boundary Finite Method (SBFEM) is a semi-analytical solution approach for solving partial differential equation. For problem in elasticity, the governing equations can be obtained by mechanically based formulation, Scaled-boundary-transformation-based formulation and principle of virtual work. The governing equations are described in the frame of Lagrange system and the unknowns are displacements. But in the solution procedure, the auxiliary variables are introduced and the equations are solved in the state space. Based on the observation that the duality system to solve elastic problem proposed by W.X. Zhong is similar to the above solution approach, the discretization of the SBFEM and the duality system are combined to derive the governing equations in the Hamilton system by introducing the dual variables in this paper. The Precise Integration Method (PIM) used in Duality system is also an efficient method for the solution of the governing equations of SBFEM in displacement and boundary stiffness matrix especially for the case which results some numerical difficulties in the usually uses the eigenvalue method. Numerical examples are used to demonstrate the validity and effectiveness of the PIM for solution of boundary static stiffness.
Allison, Stuart A; Xin, Yao
2005-08-15
A boundary element (BE) procedure is developed to numerically calculate the electrophoretic mobility of highly charged, rigid model macroions in the thin double layer regime based on the continuum primitive model. The procedure is based on that of O'Brien (R.W. O'Brien, J. Colloid Interface Sci. 92 (1983) 204). The advantage of the present procedure over existing BE methodologies that are applicable to rigid model macroions in general (S. Allison, Macromolecules 29 (1996) 7391) is that computationally time consuming integrations over a large number of volume elements that surround the model particle are completely avoided. The procedure is tested by comparing the mobilities derived from it with independent theory of the mobility of spheres of radius a in a salt solution with Debye-Huckel screening parameter, kappa. The procedure is shown to yield accurate mobilities provided (kappa)a exceeds approximately 50. The methodology is most relevant to model macroions of mean linear dimension, L, with 1000>(kappa)L>100 and reduced absolute zeta potential (q|zeta|/k(B)T) greater than 1.0. The procedure is then applied to the compact form of high molecular weight, duplex DNA that is formed in the presence of the trivalent counterion, spermidine, under low salt conditions. For T4 DNA (166,000 base pairs), the compact form is modeled as a sphere (diameter=600 nm) and as a toroid (largest linear dimension=600 nm). In order to reconcile experimental and model mobilities, approximately 95% of the DNA phosphates must be neutralized by bound counterions. This interpretation, based on electrokinetics, is consistent with independent studies.
A finite element method for neutron transport
International Nuclear Information System (INIS)
Ackroyd, R.T.
1983-01-01
A completely boundary-free maximum principle for the first-order Boltzmann equation is derived from the completely boundary-free maximum principle for the mixed-parity Boltzmann equation. When continuity is imposed on the trial function for directions crossing interfaces the completely boundary-free principle for the first-order Boltzmann equation reduces to a maximum principle previously established directly from first principles and indirectly by the Euler-Lagrange method. Present finite element methods for the first-order Boltzmann equation are based on a weighted-residual method which permits the use of discontinuous trial functions. The new principle for the first-order equation can be used as a basis for finite-element methods with the same freedom from boundary conditions as those based on the weighted-residual method. The extremum principle as the parent of the variationally-derived weighted-residual equations ensures their good behaviour. (author)
On form factors of boundary changing operators
Energy Technology Data Exchange (ETDEWEB)
Bajnok, Z., E-mail: bajnok.zoltan@wigner.mta.hu [MTA Lendület Holographic QFT Group, Wigner Research Centre for Physics, P.O.B. 49, H-1525 Budapest 114 (Hungary); Hollo, L., E-mail: hollo.laszlo@wigner.mta.hu [MTA Lendület Holographic QFT Group, Wigner Research Centre for Physics, P.O.B. 49, H-1525 Budapest 114 (Hungary); Laboratoire de Physique Théorique, École Normale Supérieure, 24, rue Lhomond, 75005 Paris (France)
2016-04-15
We develop a form factor bootstrap program to determine the matrix elements of local, boundary condition changing operators. We propose axioms for these form factors and determine their solutions in the free boson and Lee–Yang models. The sudden change in the boundary condition, caused by an operator insertion, can be interpreted as a local quench and the form factors provide the overlap of any state before the quench with any outgoing state after the quench.
Directory of Open Access Journals (Sweden)
Marco Gonzalez
Full Text Available Abstract The analysis of cracked brittle mechanical components considering linear elastic fracture mechanics is usually reduced to the evaluation of stress intensity factors (SIFs. The SIF calculation can be carried out experimentally, theoretically or numerically. Each methodology has its own advantages but the use of numerical methods has become very popular. Several schemes for numerical SIF calculations have been developed, the J-integral method being one of the most widely used because of its energy-like formulation. Additionally, some variations of the J-integral method, such as displacement-based methods, are also becoming popular due to their simplicity. In this work, a simple displacement-based scheme is proposed to calculate SIFs, and its performance is compared with contour integrals. These schemes are all implemented with the Boundary Element Method (BEM in order to exploit its advantages in crack growth modelling. Some simple examples are solved with the BEM and the calculated SIF values are compared against available solutions, showing good agreement between the different schemes.
Transonic shock wave. Boundary layer interaction at a convex wall
Koren, B.; Bannink, W.J.
1984-01-01
A standard finite element procedure has been applied to the problem of transonic shock wave – boundary layer interaction at a convex wall. The method is based on the analytical Bohning-Zierep model, where the boundary layer is perturbed by a weak normal shock wave which shows a singular pressure
Three-dimensional linear fracture mechanics analysis by a displacement-hybrid finite-element model
International Nuclear Information System (INIS)
Atluri, S.N.; Kathiresan, K.; Kobayashi, A.S.
1975-01-01
This paper deals with a finite-element procedures for the calculation of modes I, II and III stress intensity factors, which vary, along an arbitrarily curved three-dimensional crack front in a structural component. The finite-element model is based on a modified variational principle of potential energy with relaxed continuity requirements for displacements at the inter-element boundary. The variational principle is a three-field principle, with the arbitrary interior displacements for the element, interelement boundary displacements, and element boundary tractions as variables. The unknowns in the final algebraic system of equations, in the present displacement hybrid finite element model, are the nodal displacements and the three elastic stress intensity factors. Special elements, which contain proper square root and inverse square root crack front variations in displacements and stresses, respectively, are used in a fixed region near the crack front. Interelement displacement compatibility is satisfied by assuming an independent interelement boundary displacement field, and using a Lagrange multiplier technique to enforce such interelement compatibility. These Lagrangean multipliers, which are physically the boundary tractions, are assumed from an equilibrated stress field derived from three-dimensional Beltrami (or Maxwell-Morera) stress functions that are complete. However, considerable care should be exercised in the use of these stress functions such that the stresses produced by any of these stress function components are not linearly dependent
Tang, Zhanqi; Jiang, Nan
2018-05-01
This study reports the modifications of scale interaction and arrangement in a turbulent boundary layer perturbed by a wall-mounted circular cylinder. Hot-wire measurements were executed at multiple streamwise and wall-normal wise locations downstream of the cylindrical element. The streamwise fluctuating signals were decomposed into large-, small-, and dissipative-scale signatures by corresponding cutoff filters. The scale interaction under the cylindrical perturbation was elaborated by comparing the small- and dissipative-scale amplitude/frequency modulation effects downstream of the cylinder element with the results observed in the unperturbed case. It was obtained that the large-scale fluctuations perform a stronger amplitude modulation on both the small and dissipative scales in the near-wall region. At the wall-normal positions of the cylinder height, the small-scale amplitude modulation coefficients are redistributed by the cylinder wake. The similar observation was noted in small-scale frequency modulation; however, the dissipative-scale frequency modulation seems to be independent of the cylindrical perturbation. The phase-relationship observation indicated that the cylindrical perturbation shortens the time shifts between both the small- and dissipative-scale variations (amplitude and frequency) and large-scale fluctuations. Then, the integral time scale dependence of the phase-relationship between the small/dissipative scales and large scales was also discussed. Furthermore, the discrepancy of small- and dissipative-scale time shifts relative to the large-scale motions was examined, which indicates that the small-scale amplitude/frequency leads the dissipative scales.
Development of CAD implementing the algorithm of boundary elements’ numerical analytical method
Directory of Open Access Journals (Sweden)
Yulia V. Korniyenko
2015-03-01
Full Text Available Up to recent days the algorithms for numerical-analytical boundary elements method had been implemented with programs written in MATLAB environment language. Each program had a local character, i.e. used to solve a particular problem: calculation of beam, frame, arch, etc. Constructing matrices in these programs was carried out “manually” therefore being time-consuming. The research was purposed onto a reasoned choice of programming language for new CAD development, allows to implement algorithm of numerical analytical boundary elements method and to create visualization tools for initial objects and calculation results. Research conducted shows that among wide variety of programming languages the most efficient one for CAD development, employing the numerical analytical boundary elements method algorithm, is the Java language. This language provides tools not only for development of calculating CAD part, but also to build the graphic interface for geometrical models construction and calculated results interpretation.
Grain Boundaries From Theory to Engineering
Priester, Louisette
2013-01-01
Grain boundaries are a main feature of crystalline materials. They play a key role in determining the properties of materials, especially when grain size decreases and even more so with the current improvements of processing tools and methods that allow us to control various elements in a polycrystal. This book presents the theoretical basis of the study of grain boundaries and aims to open up new lines of research in this area. The treatment is light on mathematical approaches while emphasizing practical examples; the issues they raise are discussed with reference to theories. The general approach of the book has two main goals: to lead the reader from the concept of ‘ideal’ to ‘real’ grain boundaries; to depart from established knowledge and address the opportunities emerging through "grain boundary engineering", the control of morphological and crystallographic features that affect material properties. The book is divided in three parts: I ‘From interganular order to disorder’ deals wit...
Neutron activation analysis of Permian-Triassic boundary layer samples at the Selong Site in China
International Nuclear Information System (INIS)
Miyamoto, Y.; Sakamoto, K.; Mingqing, W.
1997-01-01
Thirty samples from a limestone stratum across the Permian-Triassic (P-Tr) boundary layer in China were analyzed for 30 elements by instrumental neutron activation analysis, wavelength dispersive X-ray fluorescence and ICP-MS, and also for mineral compositions with a powder X-ray diffractometer. The depth profile was found to indicate a sudden change of elemental and mineral compositions across the P-Tr boundary. Also the profile showed several peaks in elemental concentrations in the lower Permian layered samples as well as in the overlying Triassic strata, which are associated with the change of mineral compositions. Elemental profiles were found to be classified into 4 groups and to give some insights in the geochemical records. Ir is far less abundant (0.1 ppt) compared with that of the K-T boundaries (10 ppb), and the Ir/Co ratio is outside the K-T and Cl chondrite trends. This change of elementary profile is suggestive of the internal causes rather than the external ones such as an asteroid impact for the mass extinction at the P-Tr boundary. (author)
On the role of acoustic feedback in boundary-layer instability.
Wu, Xuesong
2014-07-28
In this paper, the classical triple-deck formalism is employed to investigate two instability problems in which an acoustic feedback loop plays an essential role. The first concerns a subsonic boundary layer over a flat plate on which two well-separated roughness elements are present. A spatially amplifying Tollmien-Schlichting (T-S) wave between the roughness elements is scattered by the downstream roughness to emit a sound wave that propagates upstream and impinges on the upstream roughness to regenerate the T-S wave, thereby forming a closed feedback loop in the streamwise direction. Numerical calculations suggest that, at high Reynolds numbers and for moderate roughness heights, the long-range acoustic coupling may lead to absolute instability, which is characterized by self-sustained oscillations at discrete frequencies. The dominant peak frequency may jump from one value to another as the Reynolds number, or the distance between the roughness elements, is varied gradually. The second problem concerns the supersonic 'twin boundary layers' that develop along two well-separated parallel flat plates. The two boundary layers are in mutual interaction through the impinging and reflected acoustic waves. It is found that the interaction leads to a new instability that is absent in the unconfined boundary layer. © 2014 The Author(s) Published by the Royal Society. All rights reserved.
DEFF Research Database (Denmark)
Cutanda Henriquez, Vicente; Juhl, Peter Møller
2013-01-01
are solved using extended boundary conditions that account for: i) negligible temperature fluctuations at the boundary, and ii) normal and tangential matching of the boundary’s particle velocity. The proposed model does not require constructing a special mesh for the viscous and thermal boundary layers...
Proximal Cretaceous-Tertiary boundary impact deposits in the Caribbean
Hildebrand, Alan R.; Boynton, Willam V.
1990-01-01
Trace element, isotopic, and mineralogic studies indicate that the proposed impact at the Cretaceous-Tertiary boundary occurred in an ocean basin, although a minor component of continental material is required. The size and abundance of shocked minerals and the restricted geographic occurrence of the ejecta layer and impact-wave deposits suggest an impact between the Americas. Coarse boundary sediments at sites 151 and 153 in the Colombian Basin and 5- to 450-meter-thick boundary sediments in Cuba may be deposits of a giant wave produced by a nearby oceanic impact.
Vortex sheet approximation of boundary layers
International Nuclear Information System (INIS)
Chorin, A.J.
1978-01-01
a grid free method for approximating incomprssible boundary layers is introduced. The computational elements are segments of vortex sheets. The method is related to the earlier vortex method; simplicity is achieved at the cost of replacing the Navier-Stokes equations by the Prandtl boundary layer equations. A new method for generating vorticity at boundaries is also presented; it can be used with the earlier voartex method. The applications presented include (i) flat plate problems, and (ii) a flow problem in a model cylinder- piston assembly, where the new method is used near walls and an improved version of the random choice method is used in the interior. One of the attractive features of the new method is the ease with which it can be incorporated into hybrid algorithms
Jiang, Nan; Emberly, Eldon; Cuvier, Olivier; Hart, Craig M
2009-07-01
Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.
Contrasting Boundary Scavenging in two Eastern Boundary Current Regimes
Anderson, R. F.; Fleisher, M. Q.; Pavia, F. J.; Vivancos, S. M.; Lu, Y.; Zhang, P.; Cheng, H.; Edwards, R. L.
2016-02-01
We use data from two US GEOTRACES expeditions to compare boundary scavenging intensity in two eastern boundary current systems: the Canary Current off Mauritania and the Humboldt Current off Peru. Boundary scavenging refers to the enhanced removal of trace elements from the ocean by sorption to sinking particles in regions of greater than average particle abundance. Both regimes experience high rates of biological productivity and generation of biogenic particles, with rates of productivity potentially a little greater off Peru, whereas dust fluxes are an order of magnitude greater off NW Africa (see presentation by Vivancos et al., this meeting). Despite greater productivity off Peru, we find greater intensity of scavenging off NW Africa as measured by the residence time of dissolved 230Th integrated from the surface to a depth of 2500 m (10-11 years off NW Africa vs. 15-17 years off Peru). Dissolved 231Pa/230Th ratios off NW Africa (Hayes et al., Deep Sea Res.-II 116 (2015) 29-41) are nearly twice the values observed off Peru. We attribute this difference to the well-known tendency for lithogenic phases (dust) to strongly fractionate in favor of Th uptake during scavenging and removal, leaving the dissolved phase enriched in Pa. This behavior needs to be considered when interpreting sedimentary 231Pa/230Th ratios as a paleo proxy.
Functional Requirements for Fab-7 Boundary Activity in the Bithorax Complex
Wolle, Daniel; Cleard, Fabienne; Aoki, Tsutomu; Deshpande, Girish; Karch, Francois
2015-01-01
Chromatin boundaries are architectural elements that determine the three-dimensional folding of the chromatin fiber and organize the chromosome into independent units of genetic activity. The Fab-7 boundary from the Drosophila bithorax complex (BX-C) is required for the parasegment-specific expression of the Abd-B gene. We have used a replacement strategy to identify sequences that are necessary and sufficient for Fab-7 boundary function in the BX-C. Fab-7 boundary activity is known to depend on factors that are stage specific, and we describe a novel ∼700-kDa complex, the late boundary complex (LBC), that binds to Fab-7 sequences that have insulator functions in late embryos and adults. We show that the LBC is enriched in nuclear extracts from late, but not early, embryos and that it contains three insulator proteins, GAF, Mod(mdg4), and E(y)2. Its DNA binding properties are unusual in that it requires a minimal sequence of >65 bp; however, other than a GAGA motif, the three Fab-7 LBC recognition elements display few sequence similarities. Finally, we show that mutations which abrogate LBC binding in vitro inactivate the Fab-7 boundary in the BX-C. PMID:26303531
Functional Requirements for Fab-7 Boundary Activity in the Bithorax Complex.
Wolle, Daniel; Cleard, Fabienne; Aoki, Tsutomu; Deshpande, Girish; Schedl, Paul; Karch, Francois
2015-11-01
Chromatin boundaries are architectural elements that determine the three-dimensional folding of the chromatin fiber and organize the chromosome into independent units of genetic activity. The Fab-7 boundary from the Drosophila bithorax complex (BX-C) is required for the parasegment-specific expression of the Abd-B gene. We have used a replacement strategy to identify sequences that are necessary and sufficient for Fab-7 boundary function in the BX-C. Fab-7 boundary activity is known to depend on factors that are stage specific, and we describe a novel ∼700-kDa complex, the late boundary complex (LBC), that binds to Fab-7 sequences that have insulator functions in late embryos and adults. We show that the LBC is enriched in nuclear extracts from late, but not early, embryos and that it contains three insulator proteins, GAF, Mod(mdg4), and E(y)2. Its DNA binding properties are unusual in that it requires a minimal sequence of >65 bp; however, other than a GAGA motif, the three Fab-7 LBC recognition elements display few sequence similarities. Finally, we show that mutations which abrogate LBC binding in vitro inactivate the Fab-7 boundary in the BX-C. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
A new approach to implement absorbing boundary condition in biomolecular electrostatics.
Goni, Md Osman
2013-01-01
This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.
Oomori, H; Imura, S; Gesso, H
1992-04-01
To develop stem design achieving primary fixation of stems and effective load transfer to the femur, we studied stress analysis of stems in cementless total hip arthroplasty by two-dimensional finite element method using boundary friction layer in stem-bone interface. The results of analyses of stem-bone interface stresses and von Mises stresses at the cortical bones indicated that ideal stem design features would be as follows: 1) Sufficient length, with the distal end extending beyond the isthmus region. 2) Maximum possible width, to contact the cortical bones in the isthmus region. 3) No collars but a lateral shoulder at the proximal portion. 4) A distal tip, to contact the cortical bones at the distal portion.
Competing Grain Boundary and Interior Deformation Mechanisms with Varying Sizes
Energy Technology Data Exchange (ETDEWEB)
Zhang, Wei [University of Tennessee (UT); Gao, Yanfei [ORNL; Nieh, T. G. [University of Tennessee, Knoxville (UTK)
2018-01-01
In typical coarse-grained alloys, the dominant plastic deformations are dislocation gliding or climbing, and material strengths can be tuned by dislocation interactions with grain boundaries, precipitates, solid solutions, and other defects. With the reduction of grain size, the increase of material strengths follows the classic Hall-Petch relationship up to nano-grained materials. Even at room temperatures, nano-grained materials exhibit strength softening, or called the inverse Hall-Petch effect, as grain boundary processes take over as the dominant deformation mechanisms. On the other hand, at elevated temperatures, grain boundary processes compete with grain interior deformation mechanisms over a wide range of the applied stress and grain sizes. This book chapter reviews and compares the rate equation model and the microstructure-based finite element simulations. The latter explicitly accounts for the grain boundary sliding, grain boundary diffusion and migration, as well as the grain interior dislocation creep. Therefore the explicit finite element method has clear advantages in problems where microstructural heterogeneities play a critical role, such as in the gradient microstructure in shot peening or weldment. Furthermore, combined with the Hall-Petch effect and its breakdown, the above competing processes help construct deformation mechanism maps by extending from the classic Frost-Ashby type to the ones with the dependence of grain size.
Phase diagrams of the elements
International Nuclear Information System (INIS)
Young, D.A.
1975-01-01
A summary of the pressure-temperature phase diagrams of the elements is presented, with graphs of the experimentally determined solid-solid phase boundaries and melting curves. Comments, including theoretical discussion, are provided for each diagram. The crystal structure of each solid phase is identified and discussed. This work is aimed at encouraging further experimental and theoretical research on phase transitions in the elements
Comparative Chromosome Map and Heterochromatin Features of the Gray Whale Karyotype (Cetacea).
Kulemzina, Anastasia I; Proskuryakova, Anastasia A; Beklemisheva, Violetta R; Lemskaya, Natalia A; Perelman, Polina L; Graphodatsky, Alexander S
2016-01-01
Cetacean karyotypes possess exceptionally stable diploid numbers and highly conserved chromosomes. To date, only toothed whales (Odontoceti) have been analyzed by comparative chromosome painting. Here, we studied the karyotype of a representative of baleen whales, the gray whale (Eschrichtius robustus, Mysticeti), by Zoo-FISH with dromedary camel and human chromosome-specific probes. We confirmed a high degree of karyotype conservation and found an identical order of syntenic segments in both branches of cetaceans. Yet, whale chromosomes harbor variable heterochromatic regions constituting up to a third of the genome due to the presence of several types of repeats. To investigate the cause of this variability, several classes of repeated DNA sequences were mapped onto chromosomes of whale species from both Mysticeti and Odontoceti. We uncovered extensive intrapopulation variability in the size of heterochromatic blocks present in homologous chromosomes among 3 individuals of the gray whale by 2-step differential chromosome staining. We show that some of the heteromorphisms observed in the gray whale karyotype are due to distinct amplification of a complex of common cetacean repeat and heavy satellite repeat on homologous autosomes. Furthermore, we demonstrate localization of the telomeric repeat in the heterochromatin of both gray and pilot whale (Globicephala melas, Odontoceti). Heterochromatic blocks in the pilot whale represent a composite of telomeric and common repeats, while heavy satellite repeat is lacking in the toothed whale consistent with previous studies. © 2016 S. Karger AG, Basel.
Micromechanical Modeling of Grain Boundaries Damage in a Copper Alloy Under Creep
International Nuclear Information System (INIS)
Voese, Markus
2015-01-01
In order to include the processes on the scale of the grain structure into the description of the creep behaviour of polycrystalline materials, the damage development of a single grain boundary has been initially investigated in the present work. For this purpose, a special simulationmethod has been used, whose resolution procedure based on holomorphic functions. The mechanisms taken into account for the simulations include nucleation, growth by grain boundary diffusion, coalescence and shrinkage until complete sintering of grain boundary cavities. These studies have then been used to develop a simplified cavitation model, which describes the grain boundary damage by two state variables and the time-dependent development by a mechanism-oriented rate formulation. To include the influence of grain boundaries within continuum mechanical considerations of polycrystals, an interface model has been developed, that incorporates both damage according to the simplified cavitation model and grain boundary sliding in dependence of a phenomenological grain boundary viscosity. Furthermore a micromechanical model of a polycrystal has been developed that allows to include a material's grain structure into the simulation of the creep behaviour by means of finite element simulations. Thereby, the deformations of individual grains are expressed by a viscoplastic single crystal model and the grain boundaries are described by the proposed interface model. The grain structure is represented by a finite element model, in which the grain boundaries are modelled by cohesive elements. From the evaluation of experimental creep data, the micromechanical model of a polycrystal has been calibrated for a copper-antimony alloy at a temperature of 823 K. Thereby, the adjustment of the single crystal model has been carried out on the basis of creep rates of pure copper single crystal specimens. The experimental determination of grain boundary sliding and grain boundary porosity for coarse
Directory of Open Access Journals (Sweden)
Pankaj Chaturvedi
Full Text Available The nuclear lamina is a key determinant of nuclear architecture, integrity and functionality in metazoan nuclei. Mutations in the human lamin A gene lead to highly debilitating genetic diseases termed as laminopathies. Expression of lamin A mutations or reduction in levels of endogenous A-type lamins leads to nuclear defects such as abnormal nuclear morphology and disorganization of heterochromatin. This is accompanied by increased proteasomal degradation of certain nuclear proteins such as emerin, nesprin-1α, retinoblastoma protein and heterochromatin protein 1 (HP1. However, the pathways of proteasomal degradation have not been well characterized.To investigate the mechanisms underlying the degradation of HP1 proteins upon lamin misexpression, we analyzed the effects of shRNA-mediated knock-down of lamins A and C in HeLa cells. Cells with reduced levels of expression of lamins A and C exhibited proteasomal degradation of HP1α and HP1β but not HP1γ. Since specific ubiquitin ligases are upregulated in lamin A/C knock-down cells, further studies were carried out with one of these ligases, RNF123, which has a putative HP1-binding motif. Ectopic expression of GFP-tagged RNF123 directly resulted in degradation of HP1α and HP1β. Mutational analysis showed that the canonical HP1-binding pentapeptide motif PXVXL in the N-terminus of RNF123 was required for binding to HP1 proteins and targeting them for degradation. The role of endogenous RNF123 in the degradation of HP1 isoforms was confirmed by RNF123 RNAi experiments. Furthermore, FRAP analysis suggested that HP1β was displaced from chromatin in laminopathic cells.Our data support a role for RNF123 ubiquitin ligase in the degradation of HP1α and HP1β upon lamin A/C knock-down. Hence lamin misexpression can cause degradation of mislocalized proteins involved in key nuclear processes by induction of specific components of the ubiquitin-proteasome system.
Implementation of a boundary element method to solve for the near field effects of an array of WECs
Oskamp, J. A.; Ozkan-Haller, H. T.
2010-12-01
When Wave Energy Converters (WECs) are installed, they affect the shoreline wave climate by removing some of the wave energy which would have reached the shore. Before large WEC projects are launched, it is important to understand the potential coastal impacts of these installations. The high cost associated with ocean scale testing invites the use of hydrodynamic models to play a major role in estimating these effects. In this study, a wave structure interaction program (WAMIT) is used to model an array of WECs. The program predicts the wave field throughout the array using a boundary element method to solve the potential flow fluid problem, taking into account the incident waves, the power dissipated, and the way each WEC moves and interacts with the others. This model is appropriate for a small domain near the WEC array in order to resolve the details in the interactions, but not extending to the coastline (where the far-field effects must be assessed). To propagate these effects to the coastline, the waves leaving this small domain will be used as boundary conditions for a larger model domain which will assess the shoreline effects caused by the array. The immediate work is concerned with setting up the WAMIT model for a small array of point absorbers. A 1:33 scale lab test is planned and will provide data to validate the WAMIT model on this small domain before it is nested with the larger domain to estimate shoreline effects.
Coulthard, Alistair B; Alm, Christina; Cealiac, Iulia; Sinclair, Don A; Honda, Barry M; Rossi, Fabrizio; Dimitri, Patrizio; Hilliker, Arthur J
2010-06-01
With the most recent releases of the Drosophila melanogaster genome sequences, much of the previously absent heterochromatic sequences have now been annotated. We undertook an extensive genetic analysis of existing lethal mutations, as well as molecular mapping and sequence analysis (using a candidate gene approach) to identify as many essential genes as possible in the centromeric heterochromatin on the right arm of the second chromosome (2Rh) of D. melanogaster. We also utilized available RNA interference lines to knock down the expression of genes in 2Rh as another approach to identifying essential genes. In total, we verified the existence of eight novel essential loci in 2Rh: CG17665, CG17683, CG17684, CG17883, CG40127, CG41265, CG42595, and Atf6. Two of these essential loci, CG41265 and CG42595, are synonymous with the previously characterized loci l(2)41Ab and unextended, respectively. The genetic and molecular analysis of the previously reported locus, l(2)41Ae, revealed that this is not a single locus, but rather it is a large region of 2Rh that extends from unextended (CG42595) to CG17665 and includes four of the novel loci uncovered here.
Planetary boundaries : Governing emerging risks and opportunities
Galaz, V.; de Zeeuw, Aart; Shiroyama, Hideaki; Tripley, Debbie
The climate, ecosystems and species, ozone layer, acidity of the oceans, the flow of energy and elements through nature, landscape change, freshwater systems, aerosols, and toxins—these constitute the planetary boundaries within which humanity must find a safe way to live and prosper. These are
Deletion of an X-inactivation boundary disrupts adjacent gene silencing.
Directory of Open Access Journals (Sweden)
Lindsay M Horvath
2013-11-01
Full Text Available In mammalian females, genes on one X are largely silenced by X-chromosome inactivation (XCI, although some "escape" XCI and are expressed from both Xs. Escapees can closely juxtapose X-inactivated genes and provide a tractable model for assessing boundary function at epigenetically regulated loci. To delimit sequences at an XCI boundary, we examined female mouse embryonic stem cells carrying X-linked BAC transgenes derived from an endogenous escape locus. Previously we determined that large BACs carrying escapee Kdm5c and flanking X-inactivated transcripts are properly regulated. Here we identify two lines with truncated BACs that partially and completely delete the distal Kdm5c XCI boundary. This boundary is not required for escape, since despite integrating into regions that are normally X inactivated, transgenic Kdm5c escapes XCI, as determined by RNA FISH and by structurally adopting an active conformation that facilitates long-range preferential association with other escapees. Yet, XCI regulation is disrupted in the transgene fully lacking the distal boundary; integration site genes up to 350 kb downstream of the transgene now inappropriately escape XCI. Altogether, these results reveal two genetically separable XCI regulatory activities at Kdm5c. XCI escape is driven by a dominant element(s retained in the shortest transgene that therefore lies within or upstream of the Kdm5c locus. Additionally, the distal XCI boundary normally plays an essential role in preventing nearby genes from escaping XCI.
ZONE: a finite element mesh generator
International Nuclear Information System (INIS)
Burger, M.J.
1976-05-01
The ZONE computer program is a finite-element mesh generator which produces the nodes and element description of any two-dimensional geometry. The geometry is subdivided into a mesh of quadrilateral and triangular zones arranged sequentially in an ordered march through the geometry. The order of march can be chosen so that the minimum bandwidth is obtained. The node points are defined in terms of the x and y coordinates in a global rectangular coordinate system. The zones generated are quadrilaterals or triangles defined by four node points in a counterclockwise sequence. Node points defining the outside boundary are generated to describe pressure boundary conditions. The mesh that is generated can be used as input to any two-dimensional as well as any axisymmetrical structure program. The output from ZONE is essentially the input file to NAOS, HONDO, and other axisymmetric finite element programs. 14 figures
Conformal boundary loop models
International Nuclear Information System (INIS)
Jacobsen, Jesper Lykke; Saleur, Hubert
2008-01-01
We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling
Electrical machine analysis using finite elements
Bianchi, Nicola
2005-01-01
OUTLINE OF ELECTROMAGNETIC FIELDSVector AnalysisElectromagnetic FieldsFundamental Equations SummaryReferencesBASIC PRINCIPLES OF FINITE ELEMENT METHODSIntroductionField Problems with Boundary ConditionsClassical Method for the Field Problem SolutionThe Classical Residual Method (Galerkin's Method)The Classical Variational Method (Rayleigh-Ritz's Method)The Finite Element MethodReferencesAPPLICATIONS OF THE FINITE ELEMENT METHOD TO TWO-DIMENSIONAL FIELDSIntroductionLinear Interpolation of the Function fApplication of the Variational MethodSimple Descriptions of Electromagnetic FieldsAppendix: I
Boundary element analysis of the directional sensitivity of the concentric EMG electrode.
Henneberg, K A; Plonsey, R
1993-07-01
Assessment of the motor unit architecture based on concentric electrode motor unit potentials requires a thorough understanding of the recording characteristics of the concentric EMG electrode. Previous simulation studies have attempted to include the effect of EMG electrodes on the recorded waveforms by uniformly averaging the tissue potential at the coordinates of one- or two-dimensional electrode models. By employing the boundary element method, this paper improves earlier models of the concentric EMG electrode by including an accurate geometric representation of the electrode, as well as the mutual electrical influence between the electrode surfaces. A three-dimensional sensitivity function is defined from which information about the preferential direction of sensitivity, blind spots, phase changes, rate of attenuation, and range of pick-up radius can be derived. The study focuses on the intrinsic features linked to the geometry of the electrode. The results show that the cannula perturbs the potential distribution significantly. The core and the cannula electrodes measure potentials of the same order of magnitude in all of the pick-up range, except adjacent to the central wire, where the latter dominates the sensitivity function. The preferential directions of sensitivity are determined by the amount of geometric offset between the individual sensitivity functions of the core and the cannula. The sensitivity function also reveals a complicated pattern of phase changes in the pick-up range. Potentials from fibers located behind the tip or along the cannula are recorded with reversed polarity compared to those located in front of the tip. Rotation of the electrode about its axis was found to alter the duration, the peak-to-peak amplitude, and the rise time of waveforms recorded from a moving dipole.
Lubricated immersed boundary method in two dimensions
Fai, Thomas G.; Rycroft, Chris H.
2018-03-01
Many biological examples of fluid-structure interaction, including the transit of red blood cells through the narrow slits in the spleen and the intracellular trafficking of vesicles into dendritic spines, involve the near-contact of elastic structures separated by thin layers of fluid. Motivated by such problems, we introduce an immersed boundary method that uses elements of lubrication theory to resolve thin fluid layers between immersed boundaries. We demonstrate 2nd-order accurate convergence for simple two-dimensional flows with known exact solutions to showcase the increased accuracy of this method compared to the standard immersed boundary method. Motivated by the phenomenon of wall-induced migration, we apply the lubricated immersed boundary method to simulate an elastic vesicle near a wall in shear flow. We also simulate the dynamics of a vesicle traveling through a narrow channel and observe the ability of the lubricated method to capture the vesicle motion on relatively coarse fluid grids.
Energy Technology Data Exchange (ETDEWEB)
Daurelle, J V; Cadene, V; Occelli, R [Universite de Provence, 13 - Marseille (France)
1997-12-31
In the numerical modeling of thermal industrial problems, radiant heat transfers remain difficult to take into account and require important computer memory and long computing time. These difficulties are enhanced when radiant heat transfers are coupled with finite-elements diffusive heat transfers because finite-elements architecture is complex and requires a lot of memory. In the case of radiant heat transfers along mobile boundaries, the methods must be optimized. The model described in this paper concerns the radiant heat transfers between diffuse grey surfaces. These transfers are coupled with conduction transfers in the limits of the diffusive opaque domain. 2-D and 3-D geometries are analyzed and two configurations of mobile boundaries are considered. In the first configuration, the boundary follows the deformation of the mesh, while in the second, the boundary moves along the fixed mesh. Matter displacement is taken into account in the term of transport of the energy equation, and an appropriate variation of the thermophysical properties of the transition elements between the opaque and transparent media is used. After a description of the introduction of radiative limit conditions in a finite-elements thermal model, the original methods used to optimize calculation time are explained. Two examples of application illustrate the approach used. The first concerns the modeling of radiant heat transfers between fuel rods during a reactor cooling accident, and the second concerns the study of heat transfers inside the air-gap of an electric motor. The method of identification of the mobile surface on the fixed mesh is described. (J.S.) 12 refs.
Energy Technology Data Exchange (ETDEWEB)
Daurelle, J.V.; Cadene, V.; Occelli, R. [Universite de Provence, 13 - Marseille (France)
1996-12-31
In the numerical modeling of thermal industrial problems, radiant heat transfers remain difficult to take into account and require important computer memory and long computing time. These difficulties are enhanced when radiant heat transfers are coupled with finite-elements diffusive heat transfers because finite-elements architecture is complex and requires a lot of memory. In the case of radiant heat transfers along mobile boundaries, the methods must be optimized. The model described in this paper concerns the radiant heat transfers between diffuse grey surfaces. These transfers are coupled with conduction transfers in the limits of the diffusive opaque domain. 2-D and 3-D geometries are analyzed and two configurations of mobile boundaries are considered. In the first configuration, the boundary follows the deformation of the mesh, while in the second, the boundary moves along the fixed mesh. Matter displacement is taken into account in the term of transport of the energy equation, and an appropriate variation of the thermophysical properties of the transition elements between the opaque and transparent media is used. After a description of the introduction of radiative limit conditions in a finite-elements thermal model, the original methods used to optimize calculation time are explained. Two examples of application illustrate the approach used. The first concerns the modeling of radiant heat transfers between fuel rods during a reactor cooling accident, and the second concerns the study of heat transfers inside the air-gap of an electric motor. The method of identification of the mobile surface on the fixed mesh is described. (J.S.) 12 refs.
International Nuclear Information System (INIS)
Huang, Ming; Zhuo, Longchao; Liu, Zhanli; Lu, Xiaogang; Shi, Zhenxue; Li, Jiarong; Zhu, Jing
2015-01-01
The mechanical properties of nickel-based single crystal superalloys deteriorate with increasing misorientation, thus the finished product rate of the casting of single crystal turbine airfoils may be reduced due to the formation of grain boundaries especially when the misorientation angle exceeds to some extent. To this day, evolution of the microstructures at the grain boundaries with misorientation and the relationship between the microstructures and the mechanical properties are still unclear. In this work a detailed characterization of the misorientation related microstructure at the grain boundary in DD6 single crystal superalloy has been carried out using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) techniques; the elemental distribution at the grain boundaries has been analyzed by energy dispersive (EDS) X-ray mapping; and the effect of precipitation of μ phases at the grain boundary on the mechanical property has been evaluated by finite element calculation. It is shown that the proportion of γ phase at the grain boundaries decreases, while the proportion of γ′ phase at the grain boundaries increases with increasing misorientation; the μ phase is precipitated at the grain boundaries when the misorientation angle exceeds about 10° and thus it could lead to a dramatic deterioration of the mechanical properties, as well as that the enrichment of Re and W gradually disappears as the misorientation angle increases. All these factors may result in the degradation of the mechanical properties at the grain boundaries as the misorientation increases. Furthermore, the finite element calculation confirms that precipitation of μ phases at the grain boundary is responsible for the significant deterioration of the mechanical properties when the misorientation exceeds about 10°. This work provides a physical imaging of the microstructure for understanding the relationship between the mechanical properties and the misorientation
Ghannam, Khaled
The atmospheric boundary-layer is the lowest 500-2000 m of the Earth's atmosphere where much of human life and ecosystem services reside. This layer responds to land surface (e.g. buoyancy and roughness elements) and slowly evolving free tropospheric (e.g. temperature and humidity lapse rates) conditions that arguably mediate and modulate biosphere-atmosphere interactions. Such response often results in spatially- and temporally-rich turbulence scales that continue to be the subject of inquiry given their significance to a plethora of applications in environmental sciences and engineering. The work here addresses key aspects of boundary layer turbulence with a focus on the role of roughness elements (vegetation canopies) and buoyancy (surface heating) in modifying the well-studied picture of shear-dominated wall-bounded turbulence. A combination of laboratory channel experiments, field experiments, and numerical simulations are used to explore three distinct aspects of boundary layer turbulence. These are: • The concept of ergodicity in turbulence statistics within canopies: It has been long-recognized that homogeneous and stationary turbulence is ergodic, but less is known about the effects of inhomogeneity introduced by the presence of canopies on the turbulence statistics. A high resolution (temporal and spatial) flume experiment is used here to test the convergence of the time statistics of turbulent scalar concentrations to their ensemble (spatio-temporal) counterpart. The findings indicate that within-canopy scalar statistics have a tendency to be ergodic, mostly in shallow layers (close to canopy top) where the sweeping flow events appear to randomize the statistics. Deeper layers within the canopy are dominated by low-dimensional (quasi-deterministic) von Karman vortices that tend to break ergodicity. • Scaling laws of turbulent velocity spectra and structure functions in near-surface atmospheric turbulence: the existence of a logarithmic scaling in the
International Nuclear Information System (INIS)
Schmid, G.; Willms, G.; Huh, Y.; Gibhardt, M.
1988-12-01
SSI 2D/3D is a computer programm to calculate dynamic stiffness matrices for soil-structure-interaction problems in frequency domain. It is applicable to two- or three-dimensional situations. The present report is a detailed manual for the use of the computer code written in FORTRAN 77. In addition it gives a survey of the possibilities of the Boundary Element Method applied to dynamic problems in infinite domains. (orig.) [de
Desset, Sophie; Poulet, Axel; Tatout, Christophe
2018-01-01
Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context. Here, we describe a whole mount tissue preparation procedure coupled to DNA staining using the PicoGreen ® intercalating agent suitable for image analysis of the nucleus in living and fixed tissues. 3D Image analysis is then performed using NucleusJ, an open source ImageJ plugin, which allows for quantifying variations in nuclear morphology such as nuclear volume, sphericity, elongation, and flatness as well as in heterochromatin content and position in respect to the nuclear periphery.
Natural variation of piRNA expression affects immunity to transposable elements.
Directory of Open Access Journals (Sweden)
Sergei Ryazansky
2017-04-01
Full Text Available In the Drosophila germline, transposable elements (TEs are silenced by PIWI-interacting RNA (piRNA that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric
Receptivity of Hypersonic Boundary Layers to Distributed Roughness and Acoustic Disturbances
Balakumar, P.
2013-01-01
Boundary-layer receptivity and stability of Mach 6 flows over smooth and rough seven-degree half-angle sharp-tipped cones are numerically investigated. The receptivity of the boundary layer to slow acoustic disturbances, fast acoustic disturbances, and vortical disturbances is considered. The effects of three-dimensional isolated roughness on the receptivity and stability are also simulated. The results for the smooth cone show that the instability waves are generated in the leading edge region and that the boundary layer is much more receptive to slow acoustic waves than to the fast acoustic waves. Vortical disturbances also generate unstable second modes, however the receptivity coefficients are smaller than that of the slow acoustic wave. Distributed roughness elements located near the nose region decreased the receptivity of the second mode generated by the slow acoustic wave by a small amount. Roughness elements distributed across the continuous spectrum increased the receptivity of the second mode generated by the slow and fast acoustic waves and the vorticity wave. The largest increase occurred for the vorticity wave. Roughness elements distributed across the synchronization point did not change the receptivity of the second modes generated by the acoustic waves. The receptivity of the second mode generated by the vorticity wave increased in this case, but the increase is lower than that occurred with the roughness elements located across the continuous spectrum. The simulations with an isolated roughness element showed that the second mode waves generated by the acoustic disturbances are not influenced by the small roughness element. Due to the interaction, a three-dimensional wave is generated. However, the amplitude is orders of magnitude smaller than the two-dimensional wave.
Mutations in ash1 and trx enhance P-element-dependent silencing in Drosophila melanogaster.
McCracken, Allen; Locke, John
2016-08-01
In Drosophila melanogaster, the mini-w(+) transgene in Pci is normally expressed throughout the adult eye; however, when other P or KP elements are present, a variegated-eye phenotype results, indicating random w(+) silencing during development called P-element-dependent silencing (PDS). Mutant Su(var)205 and Su(var)3-7 alleles act as haplo-suppressors/triplo-enhancers of this variegated phenotype, indicating that these heterochromatic modifiers act dose dependently in PDS. Previously, we recovered a spontaneous mutation of P{lacW}ci(Dplac) called P{lacW}ci(DplacE1) (E1) that variegated in the absence of P elements, presumably due to the insertion of an adjacent gypsy element. From a screen for genetic modifiers of E1 variegation, we describe here the isolation of five mutations in ash1 and three in trx that enhance the E1 variegated phenotype in a dose-dependent and cumulative manner. These mutant alleles enhance PDS at E1, and in E1/P{lacW}ci(Dplac), but suppress position effect variegation (PEV) at In(1)w(m)(4). This opposite action is consistent with a model where ASH1 and TRX mark transcriptionally active chromatin domains. If ASH1 or TRX function is lost or reduced, heterochromatin can spread into these domains creating a sink that diverts heterochromatic proteins from other variegating locations, which then may express a suppressed phenotype.
Directory of Open Access Journals (Sweden)
Lyu Meng
2017-12-01
Full Text Available The hydrogenation-disproportionation-desorption-recombination (HDDR process is the main technique for the fabrication of anisotropic NdFeB magnetic powder.But the intrinsic coercivity (HC of HDDR magnetic powder is low.The addition of heavy rare earth element Dy could improve its HC.It was found that the added Dy is mainly distributed in the grain boundary of HDDR magnets,which regulates grain boundary phase and increases the thickness of grain boundary to improve the anisotropy field (HA and HC of the magnets.However,Dy becomes scarcer and more expensive,which limits the practical application of HDDR magnets.To reduce the dependence on heavy rare earth elements and cost,researchers replaced the heavy rare earth element Dy by low melting point elements and their alloys through grain boundary diffusion technique.During diffusion process low melting point metal exists as liquid phase that increases the diffusion coefficient of diffusion medium as well as its contact area with grain boundary phases of HDDR magnets,and benefits its diffusion along grain boundaries and regulation of grain boundary phase.The modified grain boundary in magnets improve HC.This review paper focuses on the research progress in improving HC of HDDR NdFeB magnets by low melting point elements and their alloys.
The Finite Element Numerical Modelling of 3D Magnetotelluric
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Ligang Cao
2014-01-01
Full Text Available The ideal numerical simulation of 3D magnetotelluric was restricted by the methodology complexity and the time-consuming calculation. Boundary values, the variation of weighted residual equation, and the hexahedral mesh generation method of finite element are three major causes. A finite element method for 3D magnetotelluric numerical modeling is presented in this paper as a solution for the problem mentioned above. In this algorithm, a hexahedral element coefficient matrix for magnetoelluric finite method is developed, which solves large-scale equations using preconditioned conjugate gradient of the first-type boundary conditions. This algorithm is verified using the homogeneous model, and the positive landform model, as well as the low resistance anomaly model.
International Nuclear Information System (INIS)
Smith, R.A.
1975-06-01
The design evaluation of toroidal field coils on the Princeton Large Torus (PLT), the Poloidal Diverter Experiment (PDX) and the Tokamak Fusion Test Reactor (TFTR) has been performed by structural analysis with the finite element method. The technique employed has been simplified with supplementary computer programs that are used to generate the input data for the finite element computer program. Significant automation has been provided by computer codes in three areas of data input. These are the definition of coil geometry by a mesh of node points, the definition of finite elements via the node points and the definition of the node point force/displacement boundary conditions. The computer programs by name that have been used to perform the above functions are PDXNODE, ELEMENT and PDXFORC. The geometric finite element modeling options for toroidal field coils provided by PDXNODE include one-fourth or one-half symmetric sections of circular coils, oval shaped coils or dee-shaped coils with or without a beveled wedging surface. The program ELEMENT which defines the finite elements for input to the finite element computer code can provide considerable time and labor savings when defining the model of coils of non-uniform cross-section or when defining the model of coils whose material properties are different in the R and THETA directions due to the laminations of alternate epoxy and copper windings. The modeling features provided by the program ELEMENT have been used to analyze the PLT and the TFTR toroidal field coils with integral support structures. The computer program named PDXFORC is described. It computes the node point forces in a model of a toroidal field coil from the vector crossproduct of the coil current and the magnetic field. The model can be of one-half or one-fourth symmetry to be consistent with the node model defined by PDXNODE, and the magnetic field is computed from toroidal or poloidal coils
Finite element computational fluid mechanics
International Nuclear Information System (INIS)
Baker, A.J.
1983-01-01
This book analyzes finite element theory as applied to computational fluid mechanics. It includes a chapter on using the heat conduction equation to expose the essence of finite element theory, including higher-order accuracy and convergence in a common knowledge framework. Another chapter generalizes the algorithm to extend application to the nonlinearity of the Navier-Stokes equations. Other chapters are concerned with the analysis of a specific fluids mechanics problem class, including theory and applications. Some of the topics covered include finite element theory for linear mechanics; potential flow; weighted residuals/galerkin finite element theory; inviscid and convection dominated flows; boundary layers; parabolic three-dimensional flows; and viscous and rotational flows
Analysis of Piezoelectric Solids using Finite Element Method
Aslam, Mohammed; Nagarajan, Praveen; Remanan, Mini
2018-03-01
Piezoelectric materials are extensively used in smart structures as sensors and actuators. In this paper, static analysis of three piezoelectric solids is done using general-purpose finite element software, Abaqus. The simulation results from Abaqus are compared with the results obtained using numerical methods like Boundary Element Method (BEM) and meshless point collocation method (PCM). The BEM and PCM are cumbersome for complex shape and complicated boundary conditions. This paper shows that the software Abaqus can be used to solve the governing equations of piezoelectric solids in a much simpler and faster way than the BEM and PCM.
A Boundary Element Solution to the Problem of Interacting AC Fields in Parallel Conductors
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Einar M. Rønquist
1984-04-01
Full Text Available The ac fields in electrically insulated conductors will interact through the surrounding electromagnetic fields. The pertinent field equations reduce to the Helmholtz equation inside each conductor (interior problem, and to the Laplace equation outside the conductors (exterior problem. These equations are transformed to integral equations, with the magnetic vector potential and its normal derivative on the boundaries as unknowns. The integral equations are then approximated by sets of algebraic equations. The interior problem involves only unknowns on the boundary of each conductor, while the exterior problem couples unknowns from several conductors. The interior and the exterior problem are coupled through the field continuity conditions. The full set of equations is solved by standard Gaussian elimination. We also show how the total current and the dissipated power within each conductor can be expressed as boundary integrals. Finally, computational results for a sample problem are compared with a finite difference solution.
Directory of Open Access Journals (Sweden)
Wan-You Li
2014-01-01
Full Text Available A novel hybrid method, which simultaneously possesses the efficiency of Fourier spectral method (FSM and the applicability of the finite element method (FEM, is presented for the vibration analysis of structures with elastic boundary conditions. The FSM, as one type of analytical approaches with excellent convergence and accuracy, is mainly limited to problems with relatively regular geometry. The purpose of the current study is to extend the FSM to problems with irregular geometry via the FEM and attempt to take full advantage of the FSM and the conventional FEM for structural vibration problems. The computational domain of general shape is divided into several subdomains firstly, some of which are represented by the FSM while the rest by the FEM. Then, fictitious springs are introduced for connecting these subdomains. Sufficient details are given to describe the development of such a hybrid method. Numerical examples of a one-dimensional Euler-Bernoulli beam and a two-dimensional rectangular plate show that the present method has good accuracy and efficiency. Further, one irregular-shaped plate which consists of one rectangular plate and one semi-circular plate also demonstrates the capability of the present method applied to irregular structures.
Zhou, Yunlong; Zhao, Yunfei; Xu, Dan; Chai, Zhenxia; Liu, Wei
2016-10-01
The roughness-induced laminar-turbulent boundary layer transition is significant for high-speed aerospace applications. The transition mechanism is closely related to the roughness shape. In this paper, high-order numerical method is used to investigate the effect of roughness shape on the flat-plate laminar-to-turbulent boundary layer transition. Computations are performed in both the supersonic and hypersonic regimes (free-stream Mach number from 3.37 up to 6.63) for the square, cylinder, diamond and hemisphere roughness elements. It is observed that the square and diamond roughness elements are more effective in inducing transition compared with the cylinder and hemisphere ones. The square roughness element has the longest separated region in which strong unsteadiness exists and the absolute instability is formed, thus resulting in the earliest transition. The diamond roughness element has a maximum width of the separated region leading to the widest turbulent wake region far downstream. Furthermore, transition location moves backward as the Mach number increases, which indicates that the compressibility significantly suppresses the roughness-induced boundary layer transition.
Sun, Qiang; Wu, Guo Xiong
2013-03-01
A mathematical model and a numerical solution procedure are developed to simulate flow field through a 3D permeable vessel with multibranches embedded in a solid tumour. The model is based on Poisseuille's law for the description of the flow through the vessels, Darcy's law for the fluid field inside the tumour interstitium, and Starling's law for the flux transmitted across the vascular walls. The solution procedure is based on a coupled method, in which the finite difference method is used for the flow in the vessels and the boundary element method is used for the flow in the tumour. When vessels meet each other at a junction, the pressure continuity and mass conservation are imposed at the junction. Three typical representative structures within the tumour vasculature, symmetrical dichotomous branching, asymmetrical bifurcation with uneven radius of daughter vessels and trifurcation, are investigated in detail as case studies. These results have demonstrated the features of tumour flow environment by the pressure distributions and flow velocity field. Copyright © 2012 John Wiley & Sons, Ltd.
Finite elements and approximation
Zienkiewicz, O C
2006-01-01
A powerful tool for the approximate solution of differential equations, the finite element is extensively used in industry and research. This book offers students of engineering and physics a comprehensive view of the principles involved, with numerous illustrative examples and exercises.Starting with continuum boundary value problems and the need for numerical discretization, the text examines finite difference methods, weighted residual methods in the context of continuous trial functions, and piecewise defined trial functions and the finite element method. Additional topics include higher o
Simultaneous heat and moisture transfer in porous elements: transfer function method
International Nuclear Information System (INIS)
Souza, H.A. de.
1985-01-01
The presence of moisture in a porous element may strongly affect the transfer of heat through this element due to the processes which occur associated with the phase changes at the boundary surfaces and internally in the wall body. In addition, the structural properties of the element may also be meaningfully affected. The formulation of mathematical models for the simultaneous heat and mass transfer in porous elements results in a pair of nonlinear coupled equations for the temperature and moisture content distributions, in the material. It is supposed, in this work, that the actual variation of the properties of the porous medium is small in the range of variables which describe the specific problem to be analyzed. This enables us to work with linearized equations, making possible the use of linear solution methods. In this context, the present work deals with a linear procedure for the solution of simultaneous heat and moisture transfer problems in porous elements, sujected to arbitrary boundary conditions. This results in a linear relation between the heat and mass flux densities through the boundary surfaces of the elements and their associated potentials. It is shown that the model is consistent in asymptotical limiting cases; the model is then used for analyzing the drying process of a porous element, subjected to ambient actual conditions. (Author) [pt
Distributions of electric and elastic fields at domain boundaries
International Nuclear Information System (INIS)
Novak, Josef; Fousek, Jan; Maryska, Jiri; Marvan, Milan
2005-01-01
In this paper we describe the application of the finite element method (FEM) in modelling spatial distributions of electric and elastic fields in a ferroelectric crystals with two domains separated by a 90 deg. domain wall. The domain boundary is idealized as a two-dimensional defect in an electro-elastic continuum. It represents the source of inhomogenity and internal distortion in both elastic and electric fields. The main results are distributions of electric field, strain and mechanical force along the domain boundary
Karyotypes, heterochromatin, and physical mapping of 18S-26S rDNA in Cactaceae.
Las Peñas, M L; Urdampilleta, J D; Bernardello, G; Forni-Martins, E R
2009-01-01
Karyotype analyses in members of the four Cactaceae subfamilies were performed. Numbers and karyotype formula obtained were: Pereskioideae = Pereskiaaculeata(2n = 22; 10 m + 1 sm), Maihuenioideae = Maihuenia patagonica (2n = 22, 9 m + 2 sm; 2n = 44, 18 m + 4 sm), Opuntioideae = Cumulopuntia recurvata(2n = 44; 20 m + 2 sm), Cactoideae = Acanthocalycium spiniflorum (2n = 22; 10 m + 1 sm),Echinopsis tubiflora (2n = 22; 10 m + 1 sm), Trichocereus candicans (2n = 22, 22 m). Chromosomes were small, the average chromosome length was 2.3 mum. Diploid species and the tetraploid C. recurvata had one terminal satellite, whereas the remaining tetraploid species showed four satellited chromosomes. Karyotypes were symmetrical. No CMA(-)/DAPI(+) bands were detected, but CMA(+)/DAPI(-) bands associated with NOR were always found. Pericentromeric heterochromatin was found in C. recurvata, A. spiniflorum, and the tetraploid cytotype of M. patagonica. The locations of the 18S-26S rDNA sites in all species coincided with CMA(+)/DAPI(-) bands; the same occurred with the sizes and numbers of signals for each species. This technique was applied for the first time in metaphase chromosomes in cacti. NOR-bearing pair no.1 may be homeologous in all species examined. In Cactaceae, the 18S-26S loci seem to be highly conserved. Copyright 2009 S. Karger AG, Basel.
International Nuclear Information System (INIS)
Olschewski, J.; Stein, E.; Wagner, W.; Wetjen, D.
1981-01-01
This paper is a first step in the development of thermodynamically consistent material equations for inelastic materials, such as polycrystalline rock salt. In this context it is of particular importance to reduce the number and the structure of the internal variables, in order to allow for a fit with available experimental data. As an example this is demonstrated in detail in the case of the so-called dislocation model. As physical non-linearities and in addition also geometrical non-linearities lead to an inhomogeneous deformation - and stress state even in the case of simple samples, boundary value problems have to be studied, in order to test the material equations. For this purpose the finite element method has been used. (orig./HP) [de
Effect of truncated cone roughness element density on hydrodynamic drag
Womack, Kristofer; Schultz, Michael; Meneveau, Charles
2017-11-01
An experimental study was conducted on rough-wall, turbulent boundary layer flow with roughness elements whose idealized shape model barnacles that cause hydrodynamic drag in many applications. Varying planform densities of truncated cone roughness elements were investigated. Element densities studied ranged from 10% to 79%. Detailed turbulent boundary layer velocity statistics were recorded with a two-component LDV system on a three-axis traverse. Hydrodynamic roughness length (z0) and skin-friction coefficient (Cf) were determined and compared with the estimates from existing roughness element drag prediction models including Macdonald et al. (1998) and other recent models. The roughness elements used in this work model idealized barnacles, so implications of this data set for ship powering are considered. This research was supported by the Office of Naval Research and by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.
International Nuclear Information System (INIS)
Yuuki, R.; Ejima, K.
1991-01-01
In this study, three-dimensional boundary element elastostatic analysis is carried out on various surface crack problems. The present BEM uses a Mindlin's solution as well as a Kelvin's solution as a fundamental solution. So we can obtain accurate solutions for a surface crack just before or after a penetration. The obtained solutions for various shapes of surface cracks are stored as the data base, based on the influence function method. We develop the surface crack extension analysis system using the stress intensity factor data base and also the fatigue crack growth law. Our system seems to be useful especially for the analysis of the surface crack just before or after the penetration and also under the residual stresses
Finite Macro-Element Mesh Deformation in a Structured Multi-Block Navier-Stokes Code
Bartels, Robert E.
2005-01-01
A mesh deformation scheme is developed for a structured multi-block Navier-Stokes code consisting of two steps. The first step is a finite element solution of either user defined or automatically generated macro-elements. Macro-elements are hexagonal finite elements created from a subset of points from the full mesh. When assembled, the finite element system spans the complete flow domain. Macro-element moduli vary according to the distance to the nearest surface, resulting in extremely stiff elements near a moving surface and very pliable elements away from boundaries. Solution of the finite element system for the imposed boundary deflections generally produces smoothly varying nodal deflections. The manner in which distance to the nearest surface has been found to critically influence the quality of the element deformation. The second step is a transfinite interpolation which distributes the macro-element nodal deflections to the remaining fluid mesh points. The scheme is demonstrated for several two-dimensional applications.
Books and monographs on finite element technology
Noor, A. K.
1985-01-01
The present paper proviees a listing of all of the English books and some of the foreign books on finite element technology, taking into account also a list of the conference proceedings devoted solely to finite elements. The references are divided into categories. Attention is given to fundamentals, mathematical foundations, structural and solid mechanics applications, fluid mechanics applications, other applied science and engineering applications, computer implementation and software systems, computational and modeling aspects, special topics, boundary element methods, proceedings of symmposia and conferences on finite element technology, bibliographies, handbooks, and historical accounts.
Entropy Stable Wall Boundary Conditions for the Compressible Navier-Stokes Equations
Parsani, Matteo; Carpenter, Mark H.; Nielsen, Eric J.
2014-01-01
Non-linear entropy stability and a summation-by-parts framework are used to derive entropy stable wall boundary conditions for the compressible Navier-Stokes equations. A semi-discrete entropy estimate for the entire domain is achieved when the new boundary conditions are coupled with an entropy stable discrete interior operator. The data at the boundary are weakly imposed using a penalty flux approach and a simultaneous-approximation-term penalty technique. Although discontinuous spectral collocation operators are used herein for the purpose of demonstrating their robustness and efficacy, the new boundary conditions are compatible with any diagonal norm summation-by-parts spatial operator, including finite element, finite volume, finite difference, discontinuous Galerkin, and flux reconstruction schemes. The proposed boundary treatment is tested for three-dimensional subsonic and supersonic flows. The numerical computations corroborate the non-linear stability (entropy stability) and accuracy of the boundary conditions.
Directory of Open Access Journals (Sweden)
F.G. CANALES
2017-10-01
Full Text Available This paper presents an analytical solution for static analysis of thick rectangular beams with different boundary conditions. Carrera’s Unified Formulation (CUF is used in order to consider shear deformation theories of arbitrary order. The novelty of the present work is that a boundary discontinuous Fourier approach is used to consider clamped boundary conditions in the analytical solution, unlike Navier-type solutions which are restricted to simply supported beams. Governing equations are obtained by employing the principle of virtual work. The numerical accuracy of results is ascertained by studying the convergence of the solution and comparing the results to those of a 3D finite element solution. Beams subjected to bending due to a uniform pressure load and subjected to torsion due to opposite linear forces are considered. Overall, accurate results close to those of 3D finite element solutions are obtained, which can be used to validate finite element results or other approximate methods.
Local defect correction for boundary integral equation methods
Kakuba, G.; Anthonissen, M.J.H.
2014-01-01
The aim in this paper is to develop a new local defect correction approach to gridding for problems with localised regions of high activity in the boundary element method. The technique of local defect correction has been studied for other methods as finite difference methods and finite volume
Local defect correction for boundary integral equation methods
Kakuba, G.; Anthonissen, M.J.H.
2013-01-01
This paper presents a new approach to gridding for problems with localised regions of high activity. The technique of local defect correction has been studied for other methods as ¿nite difference methods and ¿nite volume methods. In this paper we develop the technique for the boundary element
Energy Technology Data Exchange (ETDEWEB)
Neki, I.; Tada, T. [Ishikawajima-Harima Heavy Industries Co. Ltd., Tokyo (Japan)
1996-12-31
This paper reports a method to develop a new finite element by source (FES) for a two-dimensional plane problem and a three-dimensional solid problem as a method to analyze ship body structures. The paper describes development of a plate bending element by using a similar method, and the fundamental principle thereof. The present method can prepare a finite element of an arbitrary shape by simply providing a contact point only on a boundary. It can also derive good calculation accuracy with less number of contact points and elements. These facts are shown by examples of analyses on a square plate, a triangle plate and a semi-circular plate. Particularly, since a plate bending problem has a large order of differential calculus in a governing equation, this method being a semi-analytical method derives a result with very good accuracy even with less number of contact points. A hypothetical boundary method or a hypothetical electric charge method presents not a very high accuracy even if a large number of contact points are provided. This is because the method hypothesizes only a bending moment vertical to the boundary, but does not consider a source of the moment relative to the boundary. In contrast, the present method hypothesizes both of bending and twisting as the sources, hence its accuracy is better than with the above two methods. 5 refs., 11 figs., 7 tabs.
Energy Technology Data Exchange (ETDEWEB)
Neki, I; Tada, T [Ishikawajima-Harima Heavy Industries Co. Ltd., Tokyo (Japan)
1997-12-31
This paper reports a method to develop a new finite element by source (FES) for a two-dimensional plane problem and a three-dimensional solid problem as a method to analyze ship body structures. The paper describes development of a plate bending element by using a similar method, and the fundamental principle thereof. The present method can prepare a finite element of an arbitrary shape by simply providing a contact point only on a boundary. It can also derive good calculation accuracy with less number of contact points and elements. These facts are shown by examples of analyses on a square plate, a triangle plate and a semi-circular plate. Particularly, since a plate bending problem has a large order of differential calculus in a governing equation, this method being a semi-analytical method derives a result with very good accuracy even with less number of contact points. A hypothetical boundary method or a hypothetical electric charge method presents not a very high accuracy even if a large number of contact points are provided. This is because the method hypothesizes only a bending moment vertical to the boundary, but does not consider a source of the moment relative to the boundary. In contrast, the present method hypothesizes both of bending and twisting as the sources, hence its accuracy is better than with the above two methods. 5 refs., 11 figs., 7 tabs.
Finite cover method with mortar elements for elastoplasticity problems
Kurumatani, M.; Terada, K.
2005-06-01
Finite cover method (FCM) is extended to elastoplasticity problems. The FCM, which was originally developed under the name of manifold method, has recently been recognized as one of the generalized versions of finite element methods (FEM). Since the mesh for the FCM can be regular and squared regardless of the geometry of structures to be analyzed, structural analysts are released from a burdensome task of generating meshes conforming to physical boundaries. Numerical experiments are carried out to assess the performance of the FCM with such discretization in elastoplasticity problems. Particularly to achieve this accurately, the so-called mortar elements are introduced to impose displacement boundary conditions on the essential boundaries, and displacement compatibility conditions on material interfaces of two-phase materials or on joint surfaces between mutually incompatible meshes. The validity of the mortar approximation is also demonstrated in the elastic-plastic FCM.
Complementary AES and AEM of grain boundary regions in irradiated γ'-strengthened alloys
International Nuclear Information System (INIS)
Farrell, K.; Kishimoto, N.; Clausing, R.E.; Heatherly, L.; Lehman, G.L.
1986-01-01
Two microchemical analysis techniques are used to measure solute segregation at grain boundaries in two γ'-strengthened, fcc Fe-Ni-Cr alloys that display radiation-induced intergranular fracture. Scanning Auger electron spectroscopy (AES) of grain boundary fracture surfaces and analytical electron microscopy (AEM) of intact grain boundaries using energy-dispersive x-ray spectroscopy show good agreement on the nature and extent of segregation. The elements Ni, Si, Ti, and Mo are found to accumulate in G, Laves and γ' phases on the grain boundaries. Segregation of P is detected by AES. The complementary features of the two analytical techniques are discussed briefly
Directory of Open Access Journals (Sweden)
Ahn Jong Hwa
2011-01-01
Full Text Available Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.
Fong, Kahei Danny
The current understanding and research efforts on surface roughness effects in hypersonic boundary-layer flows focus, almost exclusively, on how roughness elements trip a hypersonic boundary layer to turbulence. However, there were a few reports in the literature suggesting that roughness elements in hypersonic boundary-layer flows could sometimes suppress the transition process and delay the formation of turbulent flow. These reports were not common and had not attracted much attention from the research community. Furthermore, the mechanisms of how the delay and stabilization happened were unknown. A recent study by Duan et al. showed that when 2-D roughness elements were placed downstream of the so-called synchronization point, the unstable second-mode wave in a hypersonic boundary layer was damped. Since the second-mode wave is typically the most dangerous and dominant unstable mode in a hypersonic boundary layer for sharp geometries at a zero angle of attack, this result has pointed to an explanation on how roughness elements delay transition in a hypersonic boundary layer. Such an understanding can potentially have significant practical applications for the development of passive flow control techniques to suppress hypersonic boundary-layer transition, for the purpose of aero-heating reduction. Nevertheless, the previous study was preliminary because only one particular flow condition with one fixed roughness parameter was considered. The study also lacked an examination on the mechanism of the damping effect of the second mode by roughness. Hence, the objective of the current research is to conduct an extensive investigation of the effects of 2-D roughness elements on the growth of instability waves in a hypersonic boundary layer. The goal is to provide a full physical picture of how and when 2-D roughness elements stabilize a hypersonic boundary layer. Rigorous parametric studies using numerical simulation, linear stability theory (LST), and parabolized
Programming the finite element method
Smith, I M; Margetts, L
2013-01-01
Many students, engineers, scientists and researchers have benefited from the practical, programming-oriented style of the previous editions of Programming the Finite Element Method, learning how to develop computer programs to solve specific engineering problems using the finite element method. This new fifth edition offers timely revisions that include programs and subroutine libraries fully updated to Fortran 2003, which are freely available online, and provides updated material on advances in parallel computing, thermal stress analysis, plasticity return algorithms, convection boundary c
Cukjati, J.; Parman, S. W.; Cooper, R. F.; Zhao, N.
2017-12-01
Atom probe tomography (APT) was used to characterize the chemistry of three grain boundaries: an olivine-olivine (ol-ol) and olivine-clinopyroxene (ol-cpx) boundary in fine-grained experimentally-deformed wehrlite and an ol-cpx boundary in a fine-grained, hot-pressed wehrlite. Grain boundaries were extracted and formed into APT tips using a focused ion beam (FIB). The tips were analyzed in a reflectron-equipped LEAP4000HR (Harvard University) at 1% or 0.5% detection rate, 5pJ laser energy and 100kHz pulse rate. Total ion counts are between 40 and 100 million per tip. Examination of grain and phase boundaries in wehrlite are of interest since slow-diffusing and olivine-incompatible cations present in cpx (e.g. Ca and Al) may control diffusion-accommodated grain boundary sliding and affect mantle rheology (Sundberg & Cooper, 2008). At steady state, ol-cpx aggregates are weaker than either ol or cpx end member, the results of which are not currently well-explained. We investigate grain boundary widths to understand the transport of olivine-incompatible elements. Widths of grain/phase boundary chemical segregation are between 3nm and 6nm for deformed ol-ol and ol-cpx samples; minimally-deformed (hot-pressed) samples having slightly wider chemical segregation widths. Chemical segregation widths were determined from profiles of Na, Al, P, Cl, K, Ca, or Ni, although not all listed elements can be used for all samples (e.g. Na, K segregation profiles can only be observed for ol-ol sample). These estimates are consistent with prior estimates of grain boundary segregation by atom probe tomography on ol-ol and opx-opx samples (Bachhav et al., 2015) and are less than ol-ol interface widths analyzed by STEM/EDX (Hiraga, Anderson, & Kohlstedt, 2007). STEM/EDX will be performed on deformed wehrlite to investigate chemical profile as a function of applied stress orientation and at length scales between those observable by APT and EPMA. Determination of phase boundary chemistry and
Numerical Simulations of Hypersonic Boundary Layer Transition
Bartkowicz, Matthew David
Numerical schemes for supersonic flows tend to use large amounts of artificial viscosity for stability. This tends to damp out the small scale structures in the flow. Recently some low-dissipation methods have been proposed which selectively eliminate the artificial viscosity in regions which do not require it. This work builds upon the low-dissipation method of Subbareddy and Candler which uses the flux vector splitting method of Steger and Warming but identifies the dissipation portion to eliminate it. Computing accurate fluxes typically relies on large grid stencils or coupled linear systems that become computationally expensive to solve. Unstructured grids allow for CFD solutions to be obtained on complex geometries, unfortunately, it then becomes difficult to create a large stencil or the coupled linear system. Accurate solutions require grids that quickly become too large to be feasible. In this thesis a method is proposed to obtain more accurate solutions using relatively local data, making it suitable for unstructured grids composed of hexahedral elements. Fluxes are reconstructed using local gradients to extend the range of data used. The method is then validated on several test problems. Simulations of boundary layer transition are then performed. An elliptic cone at Mach 8 is simulated based on an experiment at the Princeton Gasdynamics Laboratory. A simulated acoustic noise boundary condition is imposed to model the noisy conditions of the wind tunnel and the transitioning boundary layer observed. A computation of an isolated roughness element is done based on an experiment in Purdue's Mach 6 quiet wind tunnel. The mechanism for transition is identified as an instability in the upstream separation region and a comparison is made to experimental data. In the CFD a fully turbulent boundary layer is observed downstream.
Hideyuki, TANNO; Tomoyuki, KOMURO; Kazuo, SATO; Katsuhiro, ITOH; Lillard, Randolph P.; Olejniczak, Joseph
2013-01-01
An aeroheating measurement test campaign of an Apollo capsule model with laminar and turbulent boundary layer was performed in the free-piston shock tunnel HIEST at JAXA Kakuda Space Center. A 250mm-diameter 6.4%-scaled Apollo CM capsule model made of SUS-304 stainless steel was applied in this study. To measure heat flux distribution, the model was equipped with 88 miniature co-axial Chromel-Constantan thermocouples on the heat shield surface of the model. In order to promote boundary layer transition, a boundary layer trip insert with 13 "pizza-box" isolated roughness elements, which have 1.27mm square, were placed at 17mm below of the model geometric center. Three boundary layer trip inserts with roughness height of k=0.3mm, 0.6mm and 0.8mm were used to identify the appropriate height to induce transition. Heat flux records with or without roughness elements were obtained for model angles of attack 28º under stagnation enthalpy between H(sub 0)=3.5MJ/kg to 21MJ/kg and stagnation pressure between P(sub 0)=14MPa to 60MPa. Under the condition above, Reynolds number based on the model diameter was varied from 0.2 to 1.3 million. With roughness elements, boundary layer became fully turbulent less than H(sub 0)=9MJ/kg condition. However, boundary layer was still laminar over H(sub 0)=13MJ/kg condition even with the highest roughness elements. An additional experiment was also performed to correct unexpected heat flux augmentation observed over H(sub 0)=9MJ/kg condition.
Study of flow control by localized volume heating in hypersonic boundary layers
Keller, M. A.; Kloker, M. J.; Kirilovskiy, S. V.; Polivanov, P. A.; Sidorenko, A. A.; Maslov, A. A.
2014-12-01
Boundary-layer flow control is a prerequisite for a safe and efficient operation of future hypersonic transport systems. Here, the influence of an electric discharge—modeled by a heat-source term in the energy equation—on laminar boundary-layer flows over a flat plate with zero pressure gradient at Mach 3, 5, and 7 is investigated numerically. The aim was to appraise the potential of electro-gasdynamic devices for an application as turbulence generators in the super- and hypersonic flow regime. The results with localized heat-source elements in boundary layers are compared to cases with roughness elements serving as classical passive trips. The numerical simulations are performed using the commercial code ANSYS FLUENT (by ITAM) and the high-order finite-difference DNS code NS3D (by IAG), the latter allowing for the detailed analysis of laminar flow instability. For the investigated setups with steady heating, transition to turbulence is not observed, due to the Reynolds-number lowering effect of heating.
FEWA: a Finite Element model of Water flow through Aquifers
International Nuclear Information System (INIS)
Yeh, G.T.; Huff, D.D.
1983-11-01
This report documents the implementation and demonstration of a Finite Element model of Water flow through Aquifers (FEWA). The particular features of FEWA are its versatility and flexibility to deal with as many real-world problems as possible. Point as well as distributed sources/sinks are included to represent recharges/pumpings and rainfall infiltrations. All sources/sinks can be transient or steady state. Prescribed hydraulic head on the Dirichlet boundaries and fluxes on Neumann or Cauchy boundaries can be time-dependent or constant. Source/sink strength over each element and node, hydraulic head at each Dirichlet boundary node, and flux at each boundary segment can vary independently of each other. Either completely confined or completely unconfined aquifers, or partially confined and partially unconfined aquifers can be dealt with effectively. Discretization of a compound region with very irregular curved boundaries is made easy by including both quadrilateral and triangular elements in the formulation. Large-field problems can be solved efficiently by including a pointwise iterative solution strategy as an optional alternative to the direct elimination solution method for the matrix equation approximating the partial differential equation of groundwater flow. FEWA also includes transient flow through confining leaky aquifers lying above and/or below the aquifer of interest. The model is verified against three simple cases to which analytical solutions are available. It is then demonstrated by two examples of how the model can be applied to heterogeneous and anisotropic aquifers with transient boundary conditions, time-dependent sources/sinks, and confining aquitards for a confined aquifer of variable thickness and for a free surface problem in an unconfined aquifer, respectively. 20 references, 25 figures, 8 tables
FEWA: a Finite Element model of Water flow through Aquifers
Energy Technology Data Exchange (ETDEWEB)
Yeh, G.T.; Huff, D.D.
1983-11-01
This report documents the implementation and demonstration of a Finite Element model of Water flow through Aquifers (FEWA). The particular features of FEWA are its versatility and flexibility to deal with as many real-world problems as possible. Point as well as distributed sources/sinks are included to represent recharges/pumpings and rainfall infiltrations. All sources/sinks can be transient or steady state. Prescribed hydraulic head on the Dirichlet boundaries and fluxes on Neumann or Cauchy boundaries can be time-dependent or constant. Source/sink strength over each element and node, hydraulic head at each Dirichlet boundary node, and flux at each boundary segment can vary independently of each other. Either completely confined or completely unconfined aquifers, or partially confined and partially unconfined aquifers can be dealt with effectively. Discretization of a compound region with very irregular curved boundaries is made easy by including both quadrilateral and triangular elements in the formulation. Large-field problems can be solved efficiently by including a pointwise iterative solution strategy as an optional alternative to the direct elimination solution method for the matrix equation approximating the partial differential equation of groundwater flow. FEWA also includes transient flow through confining leaky aquifers lying above and/or below the aquifer of interest. The model is verified against three simple cases to which analytical solutions are available. It is then demonstrated by two examples of how the model can be applied to heterogeneous and anisotropic aquifers with transient boundary conditions, time-dependent sources/sinks, and confining aquitards for a confined aquifer of variable thickness and for a free surface problem in an unconfined aquifer, respectively. 20 references, 25 figures, 8 tables.
Wang, Lei; Dai, Cheng; Xue, Liang
2018-04-01
This study presents a Laplace-transform-based boundary element method to model the groundwater flow in a heterogeneous confined finite aquifer with arbitrarily shaped boundaries. The boundary condition can be Dirichlet, Neumann or Robin-type. The derived solution is analytical since it is obtained through the Green's function method within the domain. However, the numerical approximation is required on the boundaries, which essentially renders it a semi-analytical solution. The proposed method can provide a general framework to derive solutions for zoned heterogeneous confined aquifers with arbitrarily shaped boundary. The requirement of the boundary element method presented here is that the Green function must exist for a specific PDE equation. In this study, the linear equations for the two-zone and three-zone confined aquifers with arbitrarily shaped boundary is established in Laplace space, and the solution can be obtained by using any linear solver. Stehfest inversion algorithm can be used to transform it back into time domain to obtain the transient solution. The presented solution is validated in the two-zone cases by reducing the arbitrarily shaped boundaries to circular ones and comparing it with the solution in Lin et al. (2016, https://doi.org/10.1016/j.jhydrol.2016.07.028). The effect of boundary shape and well location on dimensionless drawdown in two-zone aquifers is investigated. Finally the drawdown distribution in three-zone aquifers with arbitrarily shaped boundary for constant-rate tests (CRT) and flow rate distribution for constant-head tests (CHT) are analyzed.
Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems
Demongeot, Jacques; Goles, Eric; Morvan, Michel; Noual, Mathilde; Sené, Sylvain
2010-01-01
One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally. PMID:20700525
Attraction basins as gauges of robustness against boundary conditions in biological complex systems.
Directory of Open Access Journals (Sweden)
Jacques Demongeot
Full Text Available One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.
International Nuclear Information System (INIS)
Tan, Chao; Xu, Yaoyuan; Dong, Feng
2011-01-01
Electrical resistance tomography (ERT) is a non-intrusive technique to image the electrical conductivity distribution of a closed vessel by injecting exciting current into the vessel and measuring the boundary voltages induced. ERT image reconstruction is characterized as a severely nonlinear and ill-posed inverse problem with many unknowns. In recent years, a growing number of papers have been published which aim to determine the locations and shapes of inclusions by assuming that their conductivities are piecewise constant and isotropic. In this work, the boundary of inclusions is reconstructed by ERT with a boundary element method. The Jacobian matrix of the forward problem is first calculated with a direct linearization method based on the boundary element, and validated through comparison with that determined by the finite element method and analytical method. A boundary reconstruction algorithm is later presented based on the Levenberg–Marquardt (L-M) method. Several numerical simulations and static experiments were conducted to study the reconstruction quality, where much importance was given to the smoothness of boundaries in the reconstruction; thus, a restriction of the curve radius is introduced to adjust the damping parameter for the L-M algorithm. Analytical results on the stability and precision of the boundary reconstruction demonstrate that stable reconstruction can be achieved when the conductivity of the objects differs much from that of the background medium, and convex boundaries can also be precisely reconstructed. Contrarily, the reconstructions for inclusions with similar conductivities to the background medium are not stable. The situation of an incorrect initial estimation of the inclusions' number is numerically studied and the results show that the boundary of inclusions could be correctly reconstructed with a splitting/merging function under the aforementioned proper operation condition of the present algorithm
International Nuclear Information System (INIS)
Rocchi-Tavares, Miriam
1992-01-01
The objective of this research thesis is to model the sustentation (or aerodynamic levitation) of a drop by a fluid flowing through a porous plate. More precisely, the author developed a general calculation tool to solve the Stokes problem by using the boundary element method. The author reports the calculation of stresses at the surface of a solid body moving in an infinite medium, in order to validate the calculation tool before its extension to more complex problems. Then, the model is developed to describe the deformation of a fluid mass moving in another fluid. The surrounding environment is either infinite or limited by a plane wall which can be impervious or crossed by an ambient fluid. Then, the author addresses the study of the evolution of the surface of a drop moving in an infinite medium, analyses the behaviour of a fluid mass at the vicinity of a plane, infinite and impervious wall. The last part addresses the sustentation of a deformable fluid body above a porous plane wall crossed by another fluid [fr
A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Energy Technology Data Exchange (ETDEWEB)
Shan, Chun-Min; Wang, Jiyong; Xu, Ke; Chen, Huijie; Yue, Jia-Xing; Andrews, Stuart; Moresco, James J.; Yates, John R.; Nagy, Peter L.; Tong, Liang; Jia, Songtao
2016-09-20
Histone lysine-to-methionine (K-to-M) mutations are associated with multiple cancers, and they function in a dominant fashion to block the methylation of corresponding lysines on wild type histones. However, their mechanisms of function are controversial. Here we show that in fission yeast, introducing the K9M mutation into one of the three histone H3 genes dominantly blocks H3K9 methylation on wild type H3 across the genome. In addition, H3K9M enhances the interaction of histone H3 tail with the H3K9 methyltransferase Clr4 in a SAM (S-adenosyl-methionine)-dependent manner, and Clr4 is trapped at nucleation sites to prevent its spreading and the formation of large heterochromatin domains. We further determined the crystal structure of an H3K9M peptide in complex with human H3K9 methyltransferase G9a and SAM, which reveales that the methionine side chain had enhanced van der Waals interactions with G9a. Therefore, our results provide a detailed mechanism by which H3K9M regulates H3K9 methylation.
Legan, M. A.; Blinov, V. A.; Larichkin, A. Yu; Novoselov, A. N.
2017-10-01
Experimental study of hydraulic fracturing of thick-walled cylinders with a central circular hole was carried out using the machine that creates a high oil pressure. Experiments on the compression fracture of the solid cylinders by diameter and rectangular parallelepipeds perpendicular to the ends were carried out with a multipurpose test machine Zwick / Roell Z100. Samples were made of GF-177 material based on cement. Ultimate stresses in the material under study were determined for three types of stress state: under compression, with a pure shear on the surface of the hole under frecking conditions and under a compound stress state under conditions of diametral compression of a solid cylinder. The value of the critical stress intensity factor of GF-177 material was obtained. The modeling of the fracturing process taking into account the inhomogeneity of the stress state near the hole was carried out using the boundary elements method (in the variant of the fictitious load method) and the gradient fracture criterion. Calculation results of the ultimate pressure were compared with values obtained analytically on the basis of the Lame solution and with experimental data.
A Finite Element Model for convection-dominatel transport problems
International Nuclear Information System (INIS)
Carmo, E.G.D. do; Galeao, A.C.N.R.
1987-08-01
A new Protev-Galerkin Finite Element Model which automatically incorporates the search for the appropriate upwind direction is presented. It is also shown that modifying the Petrov-Galerkin weightin functions associated with elements adjascent to downwing boudaries effectively eliminates numerical oscillations normally obtained near boundary layers. (Author) [pt
Wave boundary layer over a stone-covered bed
DEFF Research Database (Denmark)
Dixen, Martin; Hatipoglu, Figen; Sumer, B. Mutlu
2008-01-01
This paper summarizes the results of an experimental investigation on wave boundary layers over a bed with large roughness, simulating stone/rock/armour block cover on the sea bottom. The roughness elements used in the experiments were stones the size of 1.4cm and 3.85cm in one group of experiments...
Thorne, James L; Ouboussad, Lylia; Lefevre, Pascal F
2012-09-01
IκB kinase α (IKKα) is part of the cytoplasmic IKK complex regulating nuclear factor-κB (NF-κB) release and translocation into the nucleus in response to pro-inflammatory signals. IKKα can also be recruited directly to the promoter of NF-κB-dependent genes by NF-κB where it phosphorylates histone H3 at serine 10, triggering recruitment of the bromodomain-containing protein 4 and the positive transcription elongation factor b. Herein, we report that IKKα travels with the elongating form of ribonucleic acid polymerase II together with heterochromatin protein 1 gamma (HP1γ) at NF-κB-dependent genes in activated macrophages. IKKα binds to and phosphorylates HP1γ, which in turn controls IKKα binding to chromatin and phosphorylation of the histone variant H3.3 at serine 31 within transcribing regions. Downstream of transcription end sites, IKKα accumulates with its inhibitor the CUE-domain containing protein 2, suggesting a link between IKKα inactivation and transcription termination.
Boundary conditions for the numerical solution of elliptic equations in exterior regions
International Nuclear Information System (INIS)
Bayliss, A.; Gunzburger, M.; Turkel, E.
1982-01-01
Elliptic equations in exterior regions frequently require a boundary condition at infinity to ensure the well-posedness of the problem. Examples of practical applications include the Helmholtz equation and Laplace's equation. Computational procedures based on a direct discretization of the elliptic problem require the replacement of the condition at infinity by a boundary condition on a finite artificial surface. Direct imposition of the condition at infinity along the finite boundary results in large errors. A sequence of boundary conditions is developed which provides increasingly accurate approximations to the problem in the infinite domain. Estimates of the error due to the finite boundary are obtained for several cases. Computations are presented which demonstrate the increased accuracy that can be obtained by the use of the higher order boundary conditions. The examples are based on a finite element formulation but finite difference methods can also be used
International Nuclear Information System (INIS)
Shakibi Nia, N.; Savall, C.; Creus, J.; Bourgon, J.; Girault, P.; Metsue, A.; Cohendoz, S.; Feaugas, X.
2016-01-01
Nano-crystalline nickel-tungsten alloys are investigated in order to provide evidence of the contribution of the solute content (light elements and tungsten) and grain-boundaries on hardness. For this purpose, Ni-W alloys were elaborated by electrodeposition in an additive free citrate ammonium bath. The variation of electrodeposition conditions leads to W contents up to 18 at%, with a broad range of grain sizes (5–650 nm). The incorporation of light elements (H, O, C, N) depends on the deposition applied conditions and a progressive modification of the texture is observed with the following sequence: {110}, NT (Non-Textured) and {111} textures. We show that the Hall-Petch relationship for these alloys is influenced by the presence of light elements, the nature of the crystallographic texture and the grain boundaries character. The dependence of grain size on flow stress is a direct consequence of the solute content (solute strengthening) and the evolution of the internal stresses with grain size. To explain the experimental data, two competing physical mechanisms are suggested: grain boundary shearing and dislocation emission at grain boundary, which are affected by the nature of the grain boundary and the solute content.
Energy Technology Data Exchange (ETDEWEB)
Shakibi Nia, N., E-mail: Niusha.Shakibi-Nia@uibk.ac.at [LaSIE (UMR 7356) CNRS, Université de La Rochelle, Av. Michel Crépeau, F-17000, La Rochelle (France); Savall, C.; Creus, J. [LaSIE (UMR 7356) CNRS, Université de La Rochelle, Av. Michel Crépeau, F-17000, La Rochelle (France); Bourgon, J. [ICMPE (UMR 7182) CNRS-UPEC, Université Paris Est, 2-8 rue Henri Dunant, F-94320, Thiais (France); Girault, P.; Metsue, A.; Cohendoz, S.; Feaugas, X. [LaSIE (UMR 7356) CNRS, Université de La Rochelle, Av. Michel Crépeau, F-17000, La Rochelle (France)
2016-12-15
Nano-crystalline nickel-tungsten alloys are investigated in order to provide evidence of the contribution of the solute content (light elements and tungsten) and grain-boundaries on hardness. For this purpose, Ni-W alloys were elaborated by electrodeposition in an additive free citrate ammonium bath. The variation of electrodeposition conditions leads to W contents up to 18 at%, with a broad range of grain sizes (5–650 nm). The incorporation of light elements (H, O, C, N) depends on the deposition applied conditions and a progressive modification of the texture is observed with the following sequence: {110}, NT (Non-Textured) and {111} textures. We show that the Hall-Petch relationship for these alloys is influenced by the presence of light elements, the nature of the crystallographic texture and the grain boundaries character. The dependence of grain size on flow stress is a direct consequence of the solute content (solute strengthening) and the evolution of the internal stresses with grain size. To explain the experimental data, two competing physical mechanisms are suggested: grain boundary shearing and dislocation emission at grain boundary, which are affected by the nature of the grain boundary and the solute content.
Energy Technology Data Exchange (ETDEWEB)
Kramberger, J; Potrc, I [Tehniska fakulteta, Maribor (Yugoslavia)
1989-07-01
Apart from being exposed to the primary loading of internal pressure and steady temperature field, the reactor pressure vessel is also subject to various thermal transients (thermal shocks). Theoretical and experimental stress analyses show that severe material stresses occur in the nozzle area of the pressure vessel which may lead to defects (cracks). It has been our aim to evaluate these stresses by the use of the Boundary Element method. (author)
Restraining approach for the spurious kinematic modes in hybrid equilibrium element
Parrinello, F.
2013-10-01
The present paper proposes a rigorous approach for the elimination of spurious kinematic modes in hybrid equilibrium elements, for three well known mesh patches. The approach is based on the identification of the dependent equations in the set of inter-element and boundary equilibrium equations of the sides involved in the spurious kinematic mode. Then the kinematic variables related to the dependent equations are reciprocally constrained and, by application of master slave elimination method, the set of inter-element equilibrium equations is reduced to full rank. The elastic solutions produced by means of the proposed approach verify the homogeneous, the inter-element and the boundary equilibrium equations. Hybrid stress formulation is developed in a rigorous mathematical setting. The results of linear elastic analysis obtained by the proposed approach and by classical displacement based method are compared for some structural examples.
International Nuclear Information System (INIS)
Shen Yongxing; Lee, Minhwan; Lee, Wonyoung; Barnett, David M; Pinsky, Peter M; Prinz, Friedrich B
2008-01-01
Electrostatic force microscopy (EFM) is a special design of non-contact atomic force microscopy used for detecting electrostatic interactions between the probe tip and the sample. Its resolution is limited by the finite probe size and the long-range characteristics of electrostatic forces. Therefore, quantitative analysis is crucial to understanding the relationship between the actual local surface potential distribution and the quantities obtained from EFM measurements. To study EFM measurements on bimetallic samples with surface potential inhomogeneities as a special case, we have simulated such measurements using the boundary element method and calculated the force component and force gradient component that would be measured by amplitude modulation (AM) EFM and frequency modulation (FM) EFM, respectively. Such analyses have been performed for inhomogeneities of various shapes and sizes, for different tip-sample separations and tip geometries, for different applied voltages, and for different media (e.g., vacuum or water) in which the experiment is performed. For a sample with a surface potential discontinuity, the FM-EFM resolution expression agrees with the literature; however, the simulation for AM-EFM suggests the existence of an optimal tip radius of curvature in terms of resolution. On the other hand, for samples with strip- and disk-shaped surface potential inhomogeneities, we have obtained quantitative expressions for the detectability size requirements as a function of experimental conditions for both AM- and FM-EFMs, which suggest that a larger tip radius of curvature is moderately favored for detecting the presence of such inhomogeneities
Yang, Xiang I. A.; Meneveau, Charles
2016-01-01
The technique by Lund et al. to generate turbulent inflow for simulations of developing boundary layers over smooth flat plates is extended to the case of surfaces with roughness elements. In the Lund et al. method, turbulent velocities on a sampling plane are rescaled and recycled back to the inlet as inflow boundary condition. To rescale mean and fluctuating velocities, appropriate length scales need be identified and for smooth surfaces, the viscous scale lν = ν/uτ (where ν is the kinematic viscosity and uτ is the friction velocity) is employed for the inner layer. Different from smooth surfaces, in rough wall boundary layers the length scale of the inner layer, i.e. the roughness sub-layer scale ld, must be determined by the geometric details of the surface roughness elements and the flow around them. In the proposed approach, it is determined by diagnosing dispersive stresses that quantify the spatial inhomogeneity caused by the roughness elements in the flow. The scale ld is used for rescaling in the inner layer, and the boundary layer thickness δ is used in the outer region. Both parts are then combined for recycling using a blending function. Unlike the blending function proposed by Lund et al. which transitions from the inner layer to the outer layer at approximately 0.2δ, here the location of blending is shifted upwards to enable simulations of very rough surfaces in which the roughness length may exceed the height of 0.2δ assumed in the traditional method. The extended rescaling-recycling method is tested in large eddy simulation of flow over surfaces with various types of roughness element shapes.
Estimation of grain boundary diffusivity in near-α titanium polycrystals
International Nuclear Information System (INIS)
Brockman, Robert A.; Pilchak, Adam L.; John Porter, W.; John, Reji
2011-01-01
The role of enhanced grain boundary diffusivity in high-temperature diffusion of interstitial elements through metals is widely recognized but poorly characterized in most materials. This paper summarizes an effort to estimate grain boundary diffusivity of oxygen in a near-α titanium alloy, Ti-6Al-2Sn-4Zr-2Mo-0.1Si, by explicitly incorporating microstructure obtained from electron backscatter diffraction into an analytical model. Attention is focused on near-surface diffusion behavior contributing to the rapid ingress of oxygen and possible crack initiation in high-temperature environments.
The finite element method in electromagnetics
Jin, Jianming
2014-01-01
A new edition of the leading textbook on the finite element method, incorporating major advancements and further applications in the field of electromagnetics The finite element method (FEM) is a powerful simulation technique used to solve boundary-value problems in a variety of engineering circumstances. It has been widely used for analysis of electromagnetic fields in antennas, radar scattering, RF and microwave engineering, high-speed/high-frequency circuits, wireless communication, electromagnetic compatibility, photonics, remote sensing, biomedical engineering, and space exploration. The
Modeling of stresses at grain boundaries with respect to occurrence of stress corrosion cracking
Energy Technology Data Exchange (ETDEWEB)
Kozaczek, K.J. [Oak Ridge National Lab., TN (United States); Sinharoy, A.; Ruud, C.O. [Pennsylvania State Univ., University Park, PA (United States); McIlree, A.R. [Electric Power Research Institute, Palo Alto, CA (United States)
1995-12-31
The distributions of elastic stresses/strains in the grain boundary regions were studied by the analytical and the finite element models. The grain boundaries represent the sites where stress concentration occurs as a result of discontinuity of elastic properties across the grain boundary and the presence of second phase particles elastically different from the surrounding matrix grains. A quantitative analysis of those stresses for steels and nickel based alloys showed that the stress concentrations in the grain boundary regions are high enough to cause a local microplastic deformation even when the material is in the macroscopic elastic regime. The stress redistribution as a result of such a plastic deformation was discussed.
Design of a Double Anode Magnetron Injection Gun for Q-band Gyro-TWT Using Boundary Element Method
Li, Zhiliang; Feng, Jinjun; Liu, Bentian
2018-04-01
This paper presents a novel design code for double anode magnetron injection guns (MIGs) in gyro-devices based on boundary element method (BEM). The physical and mathematical models were constructed, and then the code using BEM for MIG's calculation was developed. Using the code, a double anode MIG for a Q-band gyrotron traveling-wave tube (gyro-TWT) amplifier operating in the circular TE01 mode at the fundamental cyclotron harmonic was designed. In order to verify the reliability of this code, velocity spread and guiding center radius of the MIG simulated by the BEM code were compared with these from the commonly used EGUN code, showing a reasonable agreement. Then, a Q-band gyro-TWT was fabricated and tested. The testing results show that the device has achieved an average power of 5kW and peak power ≥ 150 kW at a 3% duty cycle within bandwidth of 2 GHz, and maximum output peak power of 220 kW, with a corresponding saturated gain of 50.9 dB and efficiency of 39.8%. This paper demonstrates that the BEM code can be used as an effective approach for analysis of electron optics system in gyro-devices.
Kawai, T.
Among the topics discussed are the application of FEM to nonlinear free surface flow, Navier-Stokes shallow water wave equations, incompressible viscous flows and weather prediction, the mathematical analysis and characteristics of FEM, penalty function FEM, convective, viscous, and high Reynolds number FEM analyses, the solution of time-dependent, three-dimensional and incompressible Navier-Stokes equations, turbulent boundary layer flow, FEM modeling of environmental problems over complex terrain, and FEM's application to thermal convection problems and to the flow of polymeric materials in injection molding processes. Also covered are FEMs for compressible flows, including boundary layer flows and transonic flows, hybrid element approaches for wave hydrodynamic loadings, FEM acoustic field analyses, and FEM treatment of free surface flow, shallow water flow, seepage flow, and sediment transport. Boundary element methods and FEM computational technique topics are also discussed. For individual items see A84-25834 to A84-25896
Multisymplectic Structure-Preserving in Simple Finite Element Method in High Dimensional Case
Institute of Scientific and Technical Information of China (English)
BAI Yong-Qiang; LIU Zhen; PEI Ming; ZHENG Zhu-Jun
2003-01-01
In this paper, we study a finite element scheme of some semi-linear elliptic boundary value problems inhigh-dimensional space. With uniform mesh, we find that, the numerical scheme derived from finite element method cankeep a preserved multisymplectic structure.
Golczyk, Hieronim; Massouh, Amid; Greiner, Stephan
2014-03-01
Due to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled end-segments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories.
Segregation to grain boundaries in nimonic PE16 superalloy
International Nuclear Information System (INIS)
Nettleship, D.J.; Wild, R.K.
1990-01-01
Nimonic PE16 alloy is a nickel-based superalloy containing 34 wt.% iron and 16wt.% chromium with additions of molybdenum, titanium and aluminium. It is used in the fuel assembly of the UK advanced gas-cooled reactors (AGR). This component supports significant loads in service and its mechanical integrity is therefore of paramount importance. Mechanical properties may be influenced by the grain size and grain boundary composition, both of which can themselves alter during service. Scanning Auger microscopy is a well-established method for investigating grain boundaries, and has now been applied to the study of PE16. In order to expose PE16 grain boundary surfaces it is necessary to hydrogen charge samples and fracture by pulling in tension at a slow strain rate within the ultra-high vacuum chamber of the Auger microprobe. A series of casts of nimonic PE16 alloy that have received a range of thermal ageing treatments have been fractured in an intergranular manner and the grain boundary composition determined. Segregation of trace and minority elements, particularly Mo and P, has been detected at grain boundaries. Significant variations between different as-manufactured casts were observed, whilst ageing brought about the growth of chromium-rich particles on the grain boundaries. Ductile fracture in PE16 followed a path through Ti(C, N) particles. Many of these particles incorporated large amounts of sulphur. (author)
A multilevel correction adaptive finite element method for Kohn-Sham equation
Hu, Guanghui; Xie, Hehu; Xu, Fei
2018-02-01
In this paper, an adaptive finite element method is proposed for solving Kohn-Sham equation with the multilevel correction technique. In the method, the Kohn-Sham equation is solved on a fixed and appropriately coarse mesh with the finite element method in which the finite element space is kept improving by solving the derived boundary value problems on a series of adaptively and successively refined meshes. A main feature of the method is that solving large scale Kohn-Sham system is avoided effectively, and solving the derived boundary value problems can be handled efficiently by classical methods such as the multigrid method. Hence, the significant acceleration can be obtained on solving Kohn-Sham equation with the proposed multilevel correction technique. The performance of the method is examined by a variety of numerical experiments.
Multisymplectic Structure－Preserving in Simple Finite Element Method in High Dimensional Case
Institute of Scientific and Technical Information of China (English)
BAIYong-Qiang; LIUZhen; PEIMing; ZHENGZhu-Jun
2003-01-01
In this paper, we study a finite element scheme of some semi-linear elliptic boundary value problems in high-dhnensjonal space. With uniform mesh, we find that, the numerical scheme derived from finite element method can keep a preserved multisymplectic structure.
Pasquesi, Stephanie A; Margulies, Susan S
2018-01-01
Computational models are valuable tools for studying tissue-level mechanisms of traumatic brain injury, but to produce more accurate estimates of tissue deformation, these models must be validated against experimental data. In this study, we present in situ measurements of brain-skull displacement in the neonatal piglet head ( n = 3) at the sagittal midline during six rapid non-impact rotations (two rotations per specimen) with peak angular velocities averaging 51.7 ± 1.4 rad/s. Marks on the sagittally cut brain and skull/rigid potting surfaces were tracked, and peak values of relative brain-skull displacement were extracted and found to be significantly less than values extracted from a previous axial plane model. In a finite element model of the sagittally transected neonatal porcine head, the brain-skull boundary condition was matched to the measured physical experiment data. Despite smaller sagittal plane displacements at the brain-skull boundary, the corresponding finite element boundary condition optimized for sagittal plane rotations is far less stiff than its axial counterpart, likely due to the prominent role of the boundary geometry in restricting interface movement. Finally, bridging veins were included in the finite element model. Varying the bridging vein mechanical behavior over a previously reported range had no influence on the brain-skull boundary displacements. This direction-specific sagittal plane boundary condition can be employed in finite element models of rapid sagittal head rotations.
Pasquesi, Stephanie A.; Margulies, Susan S.
2018-01-01
Computational models are valuable tools for studying tissue-level mechanisms of traumatic brain injury, but to produce more accurate estimates of tissue deformation, these models must be validated against experimental data. In this study, we present in situ measurements of brain–skull displacement in the neonatal piglet head (n = 3) at the sagittal midline during six rapid non-impact rotations (two rotations per specimen) with peak angular velocities averaging 51.7 ± 1.4 rad/s. Marks on the sagittally cut brain and skull/rigid potting surfaces were tracked, and peak values of relative brain–skull displacement were extracted and found to be significantly less than values extracted from a previous axial plane model. In a finite element model of the sagittally transected neonatal porcine head, the brain–skull boundary condition was matched to the measured physical experiment data. Despite smaller sagittal plane displacements at the brain–skull boundary, the corresponding finite element boundary condition optimized for sagittal plane rotations is far less stiff than its axial counterpart, likely due to the prominent role of the boundary geometry in restricting interface movement. Finally, bridging veins were included in the finite element model. Varying the bridging vein mechanical behavior over a previously reported range had no influence on the brain–skull boundary displacements. This direction-specific sagittal plane boundary condition can be employed in finite element models of rapid sagittal head rotations. PMID:29515995
A high-order doubly asymptotic open boundary for scalar waves in semi-infinite layered systems
International Nuclear Information System (INIS)
Prempramote, S; Song, Ch; Birk, C
2010-01-01
Wave propagation in semi-infinite layered systems is of interest in earthquake engineering, acoustics, electromagnetism, etc. The numerical modelling of this problem is particularly challenging as evanescent waves exist below the cut-off frequency. Most of the high-order transmitting boundaries are unable to model the evanescent waves. As a result, spurious reflection occurs at late time. In this paper, a high-order doubly asymptotic open boundary is developed for scalar waves propagating in semi-infinite layered systems. It is derived from the equation of dynamic stiffness matrix obtained in the scaled boundary finite-element method in the frequency domain. A continued-fraction solution of the dynamic stiffness matrix is determined recursively by satisfying the scaled boundary finite-element equation at both high- and low-frequency limits. In the time domain, the continued-fraction solution permits the force-displacement relationship to be formulated as a system of first-order ordinary differential equations. Standard time-step schemes in structural dynamics can be directly applied to evaluate the response history. Examples of a semi-infinite homogeneous layer and a semi-infinite two-layered system are investigated herein. The displacement results obtained from the open boundary converge rapidly as the order of continued fractions increases. Accurate results are obtained at early time and late time.
Parsani, Matteo; Carpenter, Mark H.; Nielsen, Eric J.
2015-01-01
Non-linear entropy stability and a summation-by-parts framework are used to derive entropy stable wall boundary conditions for the three-dimensional compressible Navier-Stokes equations. A semi-discrete entropy estimate for the entire domain is achieved when the new boundary conditions are coupled with an entropy stable discrete interior operator. The data at the boundary are weakly imposed using a penalty flux approach and a simultaneous-approximation-term penalty technique. Although discontinuous spectral collocation operators on unstructured grids are used herein for the purpose of demonstrating their robustness and efficacy, the new boundary conditions are compatible with any diagonal norm summation-by-parts spatial operator, including finite element, finite difference, finite volume, discontinuous Galerkin, and flux reconstruction/correction procedure via reconstruction schemes. The proposed boundary treatment is tested for three-dimensional subsonic and supersonic flows. The numerical computations corroborate the non-linear stability (entropy stability) and accuracy of the boundary conditions.
Retardation of grain boundary self-diffusion in nickel doped with antimony and tin
International Nuclear Information System (INIS)
Padgett, R.A.; White, C.L.
1984-01-01
Many important metallurgical phenomena are strongly influenced or controlled by grain boundary mass transport. There is also much evidence that the composition of grain boundaries is often significantly different from the overall composition of metals and alloys, owing to strong segregation of residual (and often undetected) impurities. This segregation, which does not always advertise its presence through grain boundary brittleness, may vary markedly from heat to heat, and occasionally from specimen to specimen within a given heat. Unfortunately, there are relatively few experimental observations of how such segregation affects grain boundary mass transport, and even less fundamental understanding of how these effects occur. In this paper we present autoradiographic results on self-diffusion of 63 Ni in nickel and nickel doped with antimony and tin. While these results do not permit a quantitative evaluation of the grain boundary diffusivity, D, they qualitatively illustrate the dramatic effect that these solute elements have on the ability of nickel grain boundaries to act as preferential paths for mass transport
Trace elements record complex histories in diogenites
Balta, J. B.; Beck, A. W.; McSween, H. Y.
2012-12-01
Diogenite meteorites are cumulate rocks composed mostly of orthopyroxene and chemically linked to eucrites (basaltic) and howardites (brecciated mixtures of diogenites and eucrites). Together, they represent the largest single family of achondrite meteorites delivered to Earth, and have been spectrally linked to the asteroid 4 Vesta, the largest remaining basaltic protoplanet. However, this spectral link is non-unique as many basaltic asteroids likely formed and were destroyed in the early solar system. Recent work suggested that Vesta may be an unlikely parent body for the diogenites based on correlations between trace elements and short-lived isotope decay products, which would be unlikely to survive on a body as large as Vesta due to its long cooling history [1]. Recent analyses of terrestrial and martian olivines have demonstrated that trace element spatial distributions can preserve evidence of their crystallization history even when major elements have been homogenized [2]. We have mapped minor elements including Cr, Al, and Ti in seemingly homogeneous diogenite orthopyroxenes and found a variety of previously unobserved textures. The pyroxenes in one sample (GRA 98108) are seemingly large grains of variable shapes and sizes, but the trace elements reveal internal grain boundaries between roughly-equal sized original subgrains, with equilibrated metamorphic triple junctions between them and trace element depletions at the boundaries. These trends suggest extraction of trace elements by a magma along those relict grain boundaries during a reheating event. Two other samples show evidence of fracturing and annealing, with trace element mobility within grains. One sample appears to have remained a closed system during annealing (MET 01084), while the other has interacted with a fluid or magma to move elements along annealed cracks (LEW 88679). These relict features establish that the history of diogenite pyroxenes is more complex than their homogeneous major
FEMWATER: a finite-element model of water flow through saturated-unsaturated porous media
International Nuclear Information System (INIS)
Yeh, G.T.; Ward, D.S.
1980-10-01
Upon examining the Water Movement Through Saturated-Unsaturated Porous Media: A Finite-Element Galerkin Model, it was felt that the model should be modified and expanded. The modification is made in calculating the flow field in a manner consistent with the finite element approach, in evaluating the moisture-content increasing rate within the region of interest, and in numerically computing the nonlinear terms. With these modifications, the flow field is continuous everywhere in the flow regime, including element boundaries and nodal points, and the mass loss through boundaries is much reduced. Expansion is made to include four additional numerical schemes which would be more appropriate for many situations. Also, to save computer storage, all arrays pertaining to the boundary condition information are compressed to smaller dimension, and to ease the treatment of different problems, all arrays are variably dimensioned in all subroutines. This report is intended to document these efforts. In addition, in the derivation of finite-element equations, matrix component representation is used, which is believed more readable than the matrix representation in its entirety. Two identical sample problems are simulated to show the difference between the original and revised models
International boundary experiences by the United Nations
Kagawa, A.
2013-12-01
Over the last few decades, the United Nations (UN) has been approached by Security Council and Member States on international boundary issues. The United Nations regards the adequate delimitation and demarcation of international boundaries as a very important element for the maintenance of peace and security in fragile post-conflict situations, establishment of friendly relationships and cross-border cooperation between States. This paper will present the main principles and framework the United Nations applies to support the process of international boundary delimitation and demarcation activities. The United Nations is involved in international boundary issues following the principle of impartiality and neutrality and its role as mediator. Since international boundary issues are multi-faceted, a range of expertise is required and the United Nations Secretariat is in a good position to provide diverse expertise within the multiple departments. Expertise in different departments ranging from legal, political, technical, administrative and logistical are mobilised in different ways to provide support to Member States depending on their specific needs. This presentation aims to highlight some of the international boundary projects that the United Nations Cartographic Section has been involved in order to provide the technical support to different boundary requirements as each international boundary issue requires specific focus and attention whether it be in preparation, delimitation, demarcation or management. Increasingly, the United Nations is leveraging geospatial technology to facilitate boundary delimitation and demarcation process between Member States. Through the presentation of the various case studies ranging from Iraq - Kuwait, Israel - Lebanon (Blue Line), Eritrea - Ethiopia, Cyprus (Green Line), Cameroon - Nigeria, Sudan - South Sudan, it will illustrate how geospatial technology is increasingly used to carry out the support. In having applied a range
Subsonic flow past three-dimensional localised heating elements in boundary layers
Energy Technology Data Exchange (ETDEWEB)
Aljohani, A F [Department of Mathematics, Faculty of Science, University of Tabuk (Saudi Arabia); Gajjar, J S B, E-mail: j.gajjar@manchester.ac.uk [School of Mathematics, University of Manchester, Manchester M13 9PL (United Kingdom)
2017-12-15
The problem of subsonic flow past three-dimensional micro-electro-mechanical-type (MEMS-type) heating elements placed on a flat surface, where the MEMS devices have hump-shaped surfaces, is investigated using the triple-deck theory. The compressible Navier–Stokes equations supplemented by the energy equation are considered in the limit when the Reynolds number is large. The dimensions of the MEMS devices considered are such that the flow perturbations are governed by the three-dimensional subsonic triple-deck equations formulated with the aid of method of matched expansions. The linear analysis of these equations is presented and our results provide an insight into how the MEMS heating elements may be used to positively control the local flow properties. (paper)
Borders, boundaries and desirable wishes
Directory of Open Access Journals (Sweden)
Luca Pinciaroli
2015-05-01
Full Text Available “Borders, boundaries and desirable wishes” is the title of the residential workshop offered to a group of young adults (aged 18-25 of the Centro di Salute Mentale (Mental Health Center of the DSM Basaglia of ASL TO2 in Turin. The idea of the workshop, the definition of the objectives and the topics, which are clearly expressed in the title, come from the work of the team dedicated to group psychotherapies, which has been offering group psychodrama sessions to young adults of this age since 2008. In the delicate move to the adult age, these young adults are lost and stuck in static realities where it is not possible to open up to the dimension of desire nor to the transforming encounter with the Other, since they didn’t have the experience of boundaries and lack. These two elements are necessary to acquire the ability to make projects for oneself. During the workshop the following instruments were used: group, psychodrama and art therapy. The group, as a paternal function, ensured the presence of safe boundaries enabling individuals to experiment; psychodrama and art therapy enabled the bodies to experience encounters and transformations, using doing as a metaphor for the movement against the inhibition of doing and as a way to show oneself to the Other and be able to see the Other.
Radiation-induced grain boundary segregation in austenitic stainless steels
International Nuclear Information System (INIS)
Bruemmer, S.M.; Charlot, L.A.; Vetrano, J.S.; Simonen, E.P.
1994-11-01
Radiation-induced segregation (RIS) to grain boundaries in Fe-Ni-Cr-Si stainless alloys has been measured as a function of irradiation temperature and dose. Heavy-ion irradiation was used to produce damage levels from 1 to 20 displacements per atom (dpa) at temperatures from 175 to 550 degrees C. Measured Fe, Ni, and Cr segregation increased sharply with irradiation dose (from G to 5 dpa) and temperature (from 175 to about 350 degrees C). However, grain boundary concentrations did not change significantly as dose or temperatures were further increased. Although interfacial compositions were similar, the width of radiation-induced enrichment or depletion profiles increased consistently with increasing dose or temperature. Impurity segregation (Si and P) was also measured, but only Si enrichment appeared to be radiation-induced. Grain boundary Si peaked at levels approaching 10 at% after irradiation doses to 10 dpa at an intermediate temperature of 325 degrees C. No evidence of grain boundary silicide precipitation was detected after irradiation at any temperature. Equilibrium segregation of P was measured in the high-P alloys, but interfacial concentration did not increase with irradiation exposure. Comparisons to reported RIS in neutron-irradiated stainless steels revealed similar grain boundary compositional changes for both major alloying and impurity elements
Effect of boundary layer thickness on the flow characteristics around a rectangular prism
International Nuclear Information System (INIS)
Ji, Ho Seong; Kim, Kyung Chun
2001-01-01
Effect of boundary layer thickness on the flow characteristics around a rectangular prism has been investigated by using a PIV(Particle Image Velocimetry) technique. Three different boundary layers (thick, medium and thin) were generated in the atmospheric boundary layer wind tunnel at Pusan National University. The thick boundary layer having 670mm thickness was generated by using spires and roughness elements. The medium thickness of boundary layer(δ=270mm) was the natural turbulent boundary layer at the test section with fully long developing length(18m). The thin boundary layer with 36.5mm thickness was generated by on a smooth panel elevated 70cm from the wind tunnel floor. The Reynolds number based on the free stream velocity and the height of the model was 7.9X10 3 . The mean velocity vector fields and turbulent kinetic energy distribution were measured and compared. The effect of boundary layer thickness is clearly observed not only in the length of separation bubble but also in the reattachment points. The thinner boundary layer thickness, the higher turbulent kinetic energy peak around the model roof. It is strongly recommended that the height ratio between model and approaching boundary layer thickness should be a major parameter
Effects of boundary conditions on thermomechanical calculations: Spent fuel test - climax
International Nuclear Information System (INIS)
Butkovich, T.R.
1982-10-01
The effects of varying certain boundary conditions on the results of finite-element calculations were studied in relation to the Spent Fuel Test - Climax. The study employed a thermomechanical model with the ADINA structural analysis. Nodal temperature histories were generated with the compatible ADINAT heat flow codes. The boundary conditions studied included: (1) The effect of boundary loading on three progressively larger meshes. (2) Plane strain vs plane stress conditions. (3) The effect of isothermal boundaries on a small mesh and on a significantly larger mesh. The results showed that different mesh sizes had an insignificant effect on isothermal boundaries up to 5 y, while on the smallest and largest mesh, the maximum temperature difference in the mesh was 0 C. In the corresponding ADINA calculation, these different mesh sizes produce insignificant changes in the stress field and displacements in the region of interest near the heat sources and excavations. On the other hand, plane stress produces horizontal and vertical stress differences approx. 9% higher than does plane strain
A multigrid solution method for mixed hybrid finite elements
Energy Technology Data Exchange (ETDEWEB)
Schmid, W. [Universitaet Augsburg (Germany)
1996-12-31
We consider the multigrid solution of linear equations arising within the discretization of elliptic second order boundary value problems of the form by mixed hybrid finite elements. Using the equivalence of mixed hybrid finite elements and non-conforming nodal finite elements, we construct a multigrid scheme for the corresponding non-conforming finite elements, and, by this equivalence, for the mixed hybrid finite elements, following guidelines from Arbogast/Chen. For a rectangular triangulation of the computational domain, this non-conforming schemes are the so-called nodal finite elements. We explicitly construct prolongation and restriction operators for this type of non-conforming finite elements. We discuss the use of plain multigrid and the multilevel-preconditioned cg-method and compare their efficiency in numerical tests.
Directory of Open Access Journals (Sweden)
Damir Josipovič
2012-06-01
Full Text Available Boundary-making in Istria is an old undertaking. It has actually never ceasesed, not even today. Istrian peninsula has thus undergone substantial boundary shifts during the last couple of centuries (especially after the Venetian demise in 1797. But Istria carries its worldwide fame also due to one of probably the harshest disputes on the post-war European grounds – the Trieste territory dispute. In author's perspective, this dispute is one of the four main corner-stones of the current Slovenian-Croatian boundary dispute. The remaining three include the Kozler's boundary around Dragonja (Rokava River, the ungraspable notions of Austrian censuses in Istria, and the narratives of partisan settlements on military jurisdiction. However, there are other very important aspects which significantly shaped the development of the dispute, but we will focus at assessing the importance of the aforementioned ones. In this sense, the analysis of the effects of the outcome of the Trieste dispute and its implications to the contemporary interstate dispute is set forth. By unveiling its material and consequently its psychological effects upon the contemporary bilateral relations, its analyses simultaneously reveals backgrounds of never answered question, why Kozler's proposed linguistic boundary around Dragonja (Rokava River turned out to become a boundary of national character. Though nowadays disputed, there is absolutely no chance for both involved parties to substantially draw away from once decisively drawn line of a layman. Despite the fierce battle of words in Slovenian public media on whether should the interstate boundary be placed on Mirna (Quieto or Dragonja Rivers, it will be argued here that the actual choice of the Valley of Dragonja as a boundary is by all means Slovenian. The arguments are based on extensive analyses of cartographic materials, relevant literature, documents, and statistical data.
Directory of Open Access Journals (Sweden)
Damir Josipovič
2012-01-01
Full Text Available Boundary-making in Istria is an old undertaking. It has actually never ceasesed, not even today. Istrian peninsula has thus undergone substantial boundary shifts during the last couple of centuries (especially after the Venetian demise in 1797. But Istria carries its worldwide fame also due to one of probably the harshest disputes on the post-war European grounds – the Trieste territory dispute. In author's perspective, this dispute is one of the four main corner-stones of the current Slovenian-Croatian boundary dispute. The remaining three include the Kozler's boundary around Dragonja (Rokava River, the ungraspable notions of Austrian censuses in Istria, and the narratives of partisan settlements on military jurisdiction. However, there are other very important aspects which significantly shaped the development of the dispute, but we will focus at assessing the importance of the aforementioned ones. In this sense, the analysis of the effects of the outcome of the Trieste dispute and its implications to the contemporary interstate dispute is set forth. By unveiling its material and consequently its psychological effects upon the contemporary bilateral relations, its analyses simultaneously reveals backgrounds of never answered question, why Kozler's proposed linguistic boundary around Dragonja (Rokava River turned out to become a boundary of national character. Though nowadays disputed, there is absolutely no chance for both involved parties to substantially draw away from once decisively drawn line of a layman. Despite the fierce battle of words in Slovenian public media on whether should the interstate boundary be placed on Mirna (Quieto or Dragonja Rivers, it will be argued here that the actual choice of the Valley of Dragonja as a boundary is by all means Slovenian. The arguments are based on extensive analyses of cartographic materials, relevant literature, documents, and statistical data.
Ichihashi, K; Imura, S; Oomori, H; Gesso, H
1994-11-01
We compared the biomechanical characteristics of bipolar and unipolar hemiarthroplasty on the proximal migration of the outer head by determining the von Mises stress distribution and acetabular (outer head) displacement with clinical assessment of hemiarthroplasty in 75 patients. This analysis used the two-dimensional finite element method, which incorporated boundary friction layers on both the inner and outer bearings of the prosthesis. Acetabular reaming increased stress within the pelvic bone and migration of the outer head. A combination of the acetabular reaming and bone transplantation increased the stress within the pelvic bone and grafted bone, and caused outer head migration. These findings were supported by clinical results. Although the bipolar endoprosthesis was biomechanically superior to the unipolar endoprosthesis, migration of the outer head still occurred. The bipolar endoprosthesis appeared to be indicated in cases of a femoral neck fracture or of avascular necrosis in the femoral head, but its use in cases of osteoarthritis in the hip required caution.
Searching for the nanoscopic–macroscopic boundary
Energy Technology Data Exchange (ETDEWEB)
Velásquez, E.A. [GICM and GES Groups, Instituto de Física-FCEN, Universidad de Antioquia UdeA, Calle 70 No. 52-21 Medellín (Colombia); Grupo de Investigación en Modelamiento y Simulación Computacional, Universidad de San Buenaventura Sec. Medellín, A.A. 5222, Medellín (Colombia); Altbir, D. [Departamento de Física, Universidad de Santiago de Chile (USACH), CEDENNA, Santiago (Chile); Mazo-Zuluaga, J. [GICM and GES Groups, Instituto de Física-FCEN, Universidad de Antioquia UdeA, Calle 70 No. 52-21 Medellín (Colombia); Duque, L.F. [GICM and GES Groups, Instituto de Física-FCEN, Universidad de Antioquia UdeA, Calle 70 No. 52-21 Medellín (Colombia); Grupo de Física Teórica, Aplicada y Didáctica, Facultad de Ciencias Exactas y Aplicadas Instituto Tecnológico Metropolitano, Medellín (Colombia); Mejía-López, J., E-mail: jmejia@puc.cl [Facultad de Física, Pontificia Universidad Católica de Chile, CEDENNA, Santiago (Chile)
2013-12-15
Several studies have focused on the size-dependent properties of elements, looking for a unique definition of the nanoscopic–macroscopic boundary. By using a novel approach consisting of an energy variational method combined with a quantum Heisenberg model, here we address the size at which the ordering temperature of a magnetic nanoparticle reaches its bulk value. We consider samples with sizes in the range 1–500 nm, as well as several geometries and crystalline lattices and observe that, contrarily to what is commonly argued, the nanoscopic-microscopic boundary depends on both factors: shape and crystalline structure. This suggests that the surface-to-volume ratio is not the unique parameter that defines the behavior of a nanometric sample whenever its size increases reaching the bulk dimension. Comparisons reveal very good agreement with experimental evidence with differences less than 2%. Our results have broad implications for practical issues in measurements on systems at the nanometric scale. - Highlights: • A novel quantum-Heisenberg variational energy method is implemented. • The asymptotic behavior toward the thermodynamic limit is explored. • An important dependence of the nano-bulk boundary on the geometry is found. • And also an important dependence on the crystalline lattice. • We obtain a very good agreement with experimental evidence with differences <2%.
EG-17SUV420-MEDIATED HETEROCHROMATIN CHANGES IN PEDIATRIC BRAIN CANCERS
Van Meter, Timothy E.; Terry, Jocelyn; Rockwell, Nathan; Goggin, Sarah; Nethala, Priya; Khan, Asadullah
2014-01-01
Silencing mechanisms play a role in genomic stability by maintaining condensed, non-active regions of the genome. SUV420 enzymes contain a SET domain conferring methyltransferase activity toward histones. The Histone H4 lysine 20 trimethylation (H4K20me3) mark maintained by SUV420H2 is associated with heterochromatin formation and gene silencing, whereas the dimethylated mark (H4K20me2) is associated with DNA repair. In studies of epigenetic factors in large patient cohorts with ependymoma, it was found that SUV420H2 expression was lost or diminished in patients with reciprocal increases in prognostic markers such as hTERT. To better understand the normal function of Suv4-20H1/H2 enzyme in neural progenitors, and pathological changes in cancers, a variety of differentiation paradigms were used. The NT2D1 neurally restricted cell line, and BGO1V and H9 human embryonic stem cells (ESCs), and differentiated progeny, were used alongside tumors to better understand enzyme targets and functional outcomes (e.g.,lineage, differentiation, regional chromatin modifications). Lineage stages were verified with stage-specific markers by immunofluorescence and qPCR. Suv4-20 H1 and H2 were present in ESCs and neural progenitors and decreased thereafter. RNAi knockdown of SUV420 enzymes led to decreased H4K20 methylation in cancer cells. DNA methylation microarrays and ChIP-PCR suggest 1) that SUV420 is not regulated by DNA methylation in ependymomas; 2) that active chromatin marks such as H3K4 dimethylation are enriched near the transcriptional start site in the SUV420H2 gene, and 3) that hTERT is hyper-methylated at specific CpG islands and histones in a tumor sub-group-specific manner. This data supports the hypothesis that Suv4-20H2 is highly active in progenitor cells and functionally lost in some brain cancers. These studies begin to elucidate coincident mechanisms of gene silencing active in neural progenitors that may be altered in a subset of pediatric brain cancers.
Classification of boundary gravitons in AdS{sub 3} gravity
Energy Technology Data Exchange (ETDEWEB)
Garbarz, Alan [Instituto de Física de La Plata (IFLP), CONICET Departamento de Física,Universidad Nacional de la Plata,C.C. 67 (1900) La Plata (Argentina); Leston, Mauricio [Instituto de Astronomía y Física del Espacio, Pabellón IAFE-CONICET, Ciudad Universitaria,C.C. 67 Suc. 28, Buenos Aires (Argentina)
2014-05-29
We revisit the description of the space of asymptotically AdS{sub 3} solutions of pure gravity in three dimensions with a negative cosmological constant as a collection of coadjoint orbits of the Virasoro group. Each orbit corresponds to a set of metrics related by diffeomorphisms which do not approach the identity fast enough at the boundary. Orbits contain more than a single element and this fact manifests the global degrees of freedom of AdS{sub 3} gravity, being each element of an orbit what we call boundary graviton. We show how this setup allows to learn features about the classical phase space that otherwise would be quite difficult. Most important are the proof of energy bounds and the characterization of boundary gravitons unrelated to BTZs and AdS{sub 3}. In addition, it makes manifest the underlying mathematical structure of the space of solutions close to infinity. Notably, because of the existence of a symplectic form in each orbit, being this related with the usual Dirac bracket of the asymptotic charges, this approach is a natural starting point for the quantization of different sectors of AdS3 gravity. We finally discuss previous attempts to quantize coadjoint orbits of the Virasoro group and how this is relevant for the formulation of AdS{sub 3} quantum gravity.
Uniqueness in the inverse boundary value problem for piecewise homogeneous anisotropic elasticity
Cârstea, Cătălin I.; Honda, Naofumi; Nakamura, Gen
2016-01-01
Consider a three dimensional piecewise homogeneous anisotropic elastic medium $\\Omega$ which is a bounded domain consisting of a finite number of bounded subdomains $D_\\alpha$, with each $D_\\alpha$ a homogeneous elastic medium. One typical example is a finite element model with elements with curvilinear interfaces for an ansiotropic elastic medium. Assuming the $D_\\alpha$ are known and Lipschitz, we are concerned with the uniqueness in the inverse boundary value problem of identifying the ani...
Vibration Analysis of Circular Arch Element Using Curvature
Directory of Open Access Journals (Sweden)
H. Saffari
2008-01-01
Full Text Available In this paper, a finite element technique was used to determine the natural frequencies, and the mode shapes of a circular arch element was based on the curvature, which can fully represent the bending energy and by the equilibrium equations, the shear and axial strain energy were incorporated into the formulation. The treatment of general boundary conditions dose need a consideration when the element is incorporated by the curvature-based formula. This can be obtained by the introduction of a transformation matrix between nodal curvatures and nodal displacements. The equation of the motion for the element was obtained by the Lagrangian equation. Four examples are presented in order to verify the element formulation and its analytical capability.
Segregation of sp-impurities at grain boundaries and surfaces: comparison of fcc cobalt and nickel
Czech Academy of Sciences Publication Activity Database
Všianská, Monika; Vémolová, H.; Šob, Mojmír
2017-01-01
Roč. 25, č. 8 (2017), č. článku 085004. ISSN 0965-0393 R&D Projects: GA ČR(CZ) GA16-24711S Institutional support: RVO:68081723 Keywords : local magnetic-moments * total-energy calculations * augmented-wave method * solute segregation * tilt boundaries * embrittling potency * alloying elements * hcp metals * basis-set * 1st-principles * grain boundary segregation * strengthening/embrittling energy * grain boundary magnetism * ab initio calculations * surface segregation Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 1.891, year: 2016
Plasma boundary considerations for the national compact stellarator experiment
International Nuclear Information System (INIS)
Mioduszewski, P.; Grossman, A.; Fenstermacher, M.; Koniges, A.; Owen, L.; Rognlien, T.; Umansky, M.
2003-01-01
The national compact stellarator experiment (NCSX) [EPS 2001, Madeira, Portugal, 18-22 June 2001] is a new fusion project located at Princeton Plasma Physics Laboratory, Princeton, NJ. Plasma boundary control in stellarators has been shown to be very effective in improving plasma performance [EPS 2001, Madeira, Portugal, 18-22 June 2001] and, accordingly, will be an important element from the very beginning of the NCSX design. Plasma-facing components will be developed systematically according to our understanding of the NCSX boundary, with the eventual goal to develop a divertor with all the benefits for impurity and neutrals control. Neutrals calculations have been started to investigate the effect of neutrals penetration at various cross-sections
Stiffness and Mass Matrices of FEM-Applicable Dynamic Infinite Element with Unified Shape Basis
International Nuclear Information System (INIS)
Kazakov, Konstantin
2009-01-01
This paper is devoted to the construction and evaluation of mass and stiffness matrices of elastodynamic four and five node infinite elements with unified shape functions (EIEUSF), recently proposed by the author. Such elements can be treated as a family of elastodynamic infinite elements appropriate for multi-wave soil-structure interaction problems. The common characteristic of the proposed infinite elements is the so-called unified shape function, based on finite number of wave shape functions. The idea and the construction of the unified shape basis are described in brief. This element belongs to the decay class of infinite elements. It is shown that by appropriate mapping functions the formulation of such an element can be easily transformed to a mapped form. The results obtained using the proposed infinite elements are in a good agreement with the superposed results obtained by a series of standard computational models. The continuity along the finite/infinite element line (artificial boundary) in two-dimensional substructure models is also discussed in brief. In this type of computational models such a line marks the artificial boundary between the near and the far field of the model.
Directory of Open Access Journals (Sweden)
Wei Li
2012-01-01
Full Text Available An extended finite element method (XFEM for the forward model of 3D optical molecular imaging is developed with simplified spherical harmonics approximation (SPN. In XFEM scheme of SPN equations, the signed distance function is employed to accurately represent the internal tissue boundary, and then it is used to construct the enriched basis function of the finite element scheme. Therefore, the finite element calculation can be carried out without the time-consuming internal boundary mesh generation. Moreover, the required overly fine mesh conforming to the complex tissue boundary which leads to excess time cost can be avoided. XFEM conveniences its application to tissues with complex internal structure and improves the computational efficiency. Phantom and digital mouse experiments were carried out to validate the efficiency of the proposed method. Compared with standard finite element method and classical Monte Carlo (MC method, the validation results show the merits and potential of the XFEM for optical imaging.
Perturbed solutions of fixed boundary MHD equilibria
International Nuclear Information System (INIS)
Portone, A.
2004-01-01
In this study, the fixed boundary plasma MHD equilibrium problem is solved by the finite element method; then, by perturbing the flux at the plasma boundary nodes, linear formulae are derived linking the variation of several plasma parameters of interest to the variation of the currents flowing in the external circuits. On the basis of these formulae it is shown how it is possible to efficiently solve two central problems in plasma engineering, namely (1) the optimization of the currents in a given set of coils necessary to maintain a specified equilibrium configuration and (2) the derivation of a linear dynamic model describing the plasma axisymmetric displacement (n = 0 mode) about a given magnetic configuration. A case study-based on the ITER reference equilibrium magnetic configuration at burn-is analysed both in terms of equilibrium currents optimality as well as axisymmetric stability features. The results obtained by these formulae are also compared with the predictions of a non-linear free boundary code and of a linear, dynamic model. As shown, the formulae derived here are in good agreement with such predictions, confirming the validity of the present approach. (author)
DEFF Research Database (Denmark)
Bødker, Susanne; Kristensen, Jannie Friis; Nielsen, Christina
2003-01-01
.After analysing the history and the current boundary work, the paper will propose new technological support for boundary work. In particular the paper will suggest means of supporting boundaries when these are productive and for changing boundaries when this seems more appropriate. In total, flexible technologies......This paper presents a study of an organisation, which is undergoing a process transforming organisational and technological boundaries. In particular, we shall look at three kinds of boundaries: the work to maintain and change the boundary between the organisation and its customers; boundaries...... seem a core issue when dealing with technology for boundaries....
Papait, Roberto; Pistore, Christian; Grazini, Ursula; Babbio, Federica; Cogliati, Sara; Pecoraro, Daniela; Brino, Laurent; Morand, Anne-Laure; Dechampesme, Anne-Marie; Spada, Fabio; Leonhardt, Heinrich; McBlane, Fraser; Oudet, Pierre
2008-01-01
Heterochromatic chromosomal regions undergo large-scale reorganization and progressively aggregate, forming chromocenters. These are dynamic structures that rapidly adapt to various stimuli that influence gene expression patterns, cell cycle progression, and differentiation. Np95-ICBP90 (m- and h-UHRF1) is a histone-binding protein expressed only in proliferating cells. During pericentromeric heterochromatin (PH) replication, Np95 specifically relocalizes to chromocenters where it highly concentrates in the replication factories that correspond to less compacted DNA. Np95 recruits HDAC and DNMT1 to PH and depletion of Np95 impairs PH replication. Here we show that Np95 causes large-scale modifications of chromocenters independently from the H3:K9 and H4:K20 trimethylation pathways, from the expression levels of HP1, from DNA methylation and from the cell cycle. The PHD domain is essential to induce this effect. The PHD domain is also required in vitro to increase access of a restriction enzyme to DNA packaged into nucleosomal arrays. We propose that the PHD domain of Np95-ICBP90 contributes to the opening and/or stabilization of dense chromocenter structures to support the recruitment of modifying enzymes, like HDAC and DNMT1, required for the replication and formation of PH. PMID:18508923
Model-based estimation with boundary side information or boundary regularization
International Nuclear Information System (INIS)
Chiao, P.C.; Rogers, W.L.; Fessler, J.A.; Clinthorne, N.H.; Hero, A.O.
1994-01-01
The authors have previously developed a model-based strategy for joint estimation of myocardial perfusion and boundaries using ECT (Emission Computed Tomography). The authors have also reported difficulties with boundary estimation in low contrast and low count rate situations. In this paper, the authors propose using boundary side information (obtainable from high resolution MRI and CT images) or boundary regularization to improve both perfusion and boundary estimation in these situations. To fuse boundary side information into the emission measurements, the authors formulate a joint log-likelihood function to include auxiliary boundary measurements as well as ECT projection measurements. In addition, the authors introduce registration parameters to align auxiliary boundary measurements with ECT measurements and jointly estimate these parameters with other parameters of interest from the composite measurements. In simulated PET O-15 water myocardial perfusion studies using a simplified model, the authors show that the joint estimation improves perfusion estimation performance and gives boundary alignment accuracy of <0.5 mm even at 0.2 million counts. The authors implement boundary regularization through formulating a penalized log-likelihood function. The authors also demonstrate in simulations that simultaneous regularization of the epicardial boundary and myocardial thickness gives comparable perfusion estimation accuracy with the use of boundary side information
Flat Plate Boundary Layer Stimulation Using Trip Wires and Hama Strips
Peguero, Charles; Henoch, Charles; Hrubes, James; Fredette, Albert; Roberts, Raymond; Huyer, Stephen
2017-11-01
Water tunnel experiments on a flat plate at zero angle of attack were performed to investigate the effect of single roughness elements, i.e., trip wires and Hama strips, on the transition to turbulence. Boundary layer trips are traditionally used in scale model testing to force a boundary layer to transition from laminar to turbulent flow at a single location to aid in scaling of flow characteristics. Several investigations of trip wire effects exist in the literature, but there is a dearth of information regarding the influence of Hama strips on the flat plate boundary layer. The intent of this investigation is to better understand the effects of boundary layer trips, particularly Hama strips, and to investigate the pressure-induced drag of both styles of boundary layer trips. Untripped and tripped boundary layers along a flat plate at a range of flow speeds were characterized with multiple diagnostic measurements in the NUWC/Newport 12-inch water tunnel. A wide range of Hama strip and wire trip thicknesses were used. Measurements included dye flow visualization, direct skin friction and parasitic drag force, boundary layer profiles using LDV, wall shear stress fluctuations using hot film anemometry, and streamwise pressure gradients. Test results will be compared to the CFD and boundary layer model results as well as the existing body of work. Conclusions, resulting in guidance for application of Hama strips in model scale experiments and non-dimensional predictions of pressure drag will be presented.
Ullerich, Fritz-Helmut; Schöttke, Michael
2006-06-01
The karyotypes and C-banding patterns of Chrysomya species C. marginalis, C. phaonis, C. pinguis, C. saffranea, C. megacephala (New Guinean strain), Lucilia sericata, and Protophormia terraenovae are described. All species are amphogenic and have similar chromosome complements (2n = 12), including an XY-XX sex-chromosome pair varying in size and morphology between species. Additionally, the C-banding pattern of the monogenic species Chrysomya albiceps is presented. The DNA contents of these and of further species Chrysomya rufifacies, Chrysomya varipes, and Chrysomya putoria were assessed on mitotic metaphases by Feulgen cytophotometry. The average 2C DNA value of the male genomes ranged from 1.04 pg in C. varipes to 2.31 pg in C. pinguis. The DNA content of metaphase X chromosomes varied from 0.013 pg (= 1.23% of the total genome) in C. varipes to 0.277 pg (12.20%) in L. sericata; that of Y chromosomes ranged from 0.003 pg (0.27%) in C. varipes to 0.104 pg (5.59%) in L. sericata. In most species, the corresponding 5 large chromosome pairs showed similar relative DNA contents. The data suggest that the interspecific DNA differences in most species are mainly due to quantitative variation of (repetitive) sequences lying outside the centromeric heterochromatin blocks of the large chromosomes. The results are also discussed with regard to phylogenetic relationships of some species.
Formulation and numerical implementation of micro-scale boundary conditions for particle aggregates
Liu, J.; Bosco, E.; Suiker, A.S.J.
2017-01-01
Novel numerical algorithms are presented for the implementation of micro-scale boundary conditions of particle aggregates modelled with the discrete element method. The algorithms are based on a servo-control methodology, using a feedback principle comparable to that of algorithms commonly applied
Geochemical study of trace elements in micrograin minerals
Energy Technology Data Exchange (ETDEWEB)
Toyoda, Kazuhiro; Shinozuka, Yoshitsugu; Imai, Shiho; Baba, Naoho; Machii, Tami; Shimada, Mitsuo; Hasebe, Kiyoshi [Hokkaido Univ., Sapporo (Japan)
1998-01-01
Abstract of five papers are contained in this paper. 1. Neutron activation analysis of iridium in Japan P/T boundary layer sample. Iridium of Permian/Triassic (P/T) boundary layer samples in Japan are determined. A collision of materials outside of the earth was not proved. 2. Adsorbability of rare earth elements by biogenic phosphate salt particles. Phosphate minerals are very strong adsorbent of rare earth elements, so that they can use as the removal materials of them in radioactive waste. 3. Analysis of undecomposed minerals and irresoluble compounds in acid decomposed residue. In order to investigate the past global changes, a micro wave heat method was studied and good results were obtained. 4. Determination of iridium in tsunami deposits in Cuba. Very small amount of iridium was discovered in the samples. 5. Activation analysis of iridium in the sample of 300 m core of Baikal lake. (Plan). (S.Y.)
Atomic scale study of grain boundary segregation before carbide nucleation in Ni–Cr–Fe Alloys
Energy Technology Data Exchange (ETDEWEB)
Li, Hui, E-mail: huili@shu.edu.cn [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Institute of Materials, Shanghai University, Shanghai 200072 (China); Xia, Shuang [Institute of Materials, Shanghai University, Shanghai 200072 (China); Liu, Wenqing [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Liu, Tingguang; Zhou, Bangxin [Institute of Materials, Shanghai University, Shanghai 200072 (China)
2013-08-15
Highlights: • Impurities segregated at grain boundaries were observed by atom probe tomography. • The comparison of segregation features in two Ni–Cr–Fe alloys was studied by APT. • C and Cr atoms co-segregated at grain boundaries before carbide precipitation. -- Abstract: Three dimensional chemical information concerning grain boundary segregation before carbide nucleation was characterized by atom probe tomography in two Ni–Cr–Fe alloys which were aged at 500 °C for 0.5 h after homogenizing treatment. B, C and Si atoms segregation at grain boundary in Alloy 690 was observed. B, C, N and P atoms segregation at grain boundary in 304 austenitic stainless steel was observed. C atoms co-segregation with Cr atoms at the grain boundaries both in Alloy 690 and 304 austenitic stainless steel was found, and its effect on the carbide nucleation was discussed. The amount of each segregated element at grain boundaries in the two Ni–Cr–Fe alloys were analyzed quantitatively. Comparison of the grain boundary segregation features of the two Ni–Cr–Fe alloys were carried out based on the experimental results.
From boundaries to boundary work: middle managers creating inter-organizational change.
Oldenhof, Lieke; Stoopendaal, Annemiek; Putters, Kim
2016-11-21
Purpose In healthcare, organizational boundaries are often viewed as barriers to change. The purpose of this paper is to show how middle managers create inter-organizational change by doing boundary work: the dual act of redrawing boundaries and coordinating work in new ways. Design/methodology/approach Theoretically, the paper draws on the concept of boundary work from Science and Technology Studies. Empirically, the paper is based on an ethnographic investigation of middle managers that participate in a Dutch reform program across health, social care, and housing. Findings The findings show how middle managers create a sense of urgency for inter-organizational change by emphasizing "fragmented" service provision due to professional, sectoral, financial, and geographical boundaries. Rather than eradicating these boundaries, middle managers change the status quo gradually by redrawing composite boundaries. They use boundary objects and a boundary-transcending vocabulary emphasizing the need for societal gains that go beyond production targets of individual organizations. As a result, work is coordinated in new ways in neighborhood teams and professional expertise is being reconfigured. Research limitations/implications Since boundary workers create incremental change, it is necessary to follow their work for a longer period to assess whether boundary work contributes to paradigm change. Practical implications Organizations should pay attention to conditions for boundary work, such as legitimacy of boundary workers and the availability of boundary spaces that function as communities of practice. Originality/value By shifting the focus from boundaries to boundary work, this paper gives valuable insights into "how" boundaries are redrawn and embodied in objects and language.
Combined evidence annotation of transposable elements in genome sequences.
Directory of Open Access Journals (Sweden)
Hadi Quesneville
2005-07-01
Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other
Modeling of Cementitious Representative Volume Element with Additives
Shahzamanian, M. M.; Basirun, W. J.
CEMHYD3D has been employed to simulate the representative volume element (RVE) of cementitious systems (Type I cement) containing fly ash (Class F) through a voxel-based finite element analysis (FEA) approach. Three-dimensional microstructures composed of voxels are generated for a heterogeneous cementitious material consisting of various constituent phases. The primary focus is to simulate a cementitious RVE containing fly ash and to present the homogenized macromechanical properties obtained from its analysis. Simple kinematic uniform boundary conditions as well as periodic boundary conditions were imposed on the RVE to obtain the principal and shear moduli. Our current work considers the effect of fly ash percentage on the elastic properties based on the mass and volume replacements. RVEs with lengths of 50, 100 and 200μm at different degrees of hydration are generated, and the elastic properties are modeled and simulated. In general, the elastic properties of a cementitious RVE with fly ash replacement for cement based on mass and volume differ from each other. Moreover, the finite element (FE) mesh density effect is studied. Results indicate that mechanical properties decrease with increasing mesh density.
Simulating faults and plate boundaries with a transversely isotropic plasticity model
Sharples, W.; Moresi, L. N.; Velic, M.; Jadamec, M. A.; May, D. A.
2016-03-01
In mantle convection simulations, dynamically evolving plate boundaries have, for the most part, been represented using an visco-plastic flow law. These systems develop fine-scale, localized, weak shear band structures which are reminiscent of faults but it is a significant challenge to resolve the large- and the emergent, small-scale-behavior. We address this issue of resolution by taking into account the observation that a rock element with embedded, planar, failure surfaces responds as a non-linear, transversely isotropic material with a weak orientation defined by the plane of the failure surface. This approach partly accounts for the large-scale behavior of fine-scale systems of shear bands which we are not in a position to resolve explicitly. We evaluate the capacity of this continuum approach to model plate boundaries, specifically in the context of subduction models where the plate boundary interface has often been represented as a planar discontinuity. We show that the inclusion of the transversely isotropic plasticity model for the plate boundary promotes asymmetric subduction from initiation. A realistic evolution of the plate boundary interface and associated stresses is crucial to understanding inter-plate coupling, convergent margin driven topography, and earthquakes.
Ring-element analysis of layered orthotropic bodies
DEFF Research Database (Denmark)
Jørgensen, O.
1993-01-01
For the analysis of arbitrarily laminated circular bodies, a displacement-based ring-element is presented. The analysis is performed in a cylindrical coordinate system. The method of analysis requires the boundary conditions as well as the external forces to be pi-periodic. The element formulation...... accounts for a desired degree of approximation of the displacement field in the direction of the circumference. This is done by a truncated Fourier expansion of the angular dependence of the displacements in terms of trigonometric functions. Thus the Fourier expansion coefficients are the unknowns...... to that of solutions obtained by traditional 3D elements. A scheme for analytical integration of the angular dependence of the stiffness matrix is given....
vanDam, C. P.; Los, S. M.; Miley, S. J.; Yip, L. P.; Banks, D. W.; Roback, V. E.; Bertelrud, A.
1995-01-01
Flight experiments on NASA Langley's B737-100 (TSRV) airplane have been conducted to document flow characteristics in order to further the understanding of high-lift flow physics, and to correlate and validate computational predictions and wind-tunnel measurements. The project is a cooperative effort involving NASA, industry, and universities. In addition to focusing on in-flight measurements, the project includes extensive application of various computational techniques, and correlation of flight data with computational results and wind-tunnel measurements. Results obtained in the most recent phase of flight experiments are analyzed and presented in this paper. In-flight measurements include surface pressure distributions, measured using flush pressure taps and pressure belts on the slats, main element, and flap elements; surface shear stresses, measured using Preston tubes; off-surface velocity distributions, measured using shear-layer rakes; aeroelastic deformations of the flap elements, measured using an optical positioning system; and boundary-layer transition phenomena, measured using hot-film anemometers and an infrared imaging system. The analysis in this paper primarily focuses on changes in the boundary-layer state that occurred on the slats, main element, and fore flap as a result of changes in flap setting and/or flight condition. Following a detailed description of the experiment, the boundary-layer state phenomenon will be discussed based on data measured during these recent flight experiments.
Chanthawara, Krittidej; Kaennakham, Sayan; Toutip, Wattana
2016-02-01
The methodology of Dual Reciprocity Boundary Element Method (DRBEM) is applied to the convection-diffusion problems and investigating its performance is our first objective of the work. Seven types of Radial Basis Functions (RBF); Linear, Thin-plate Spline, Cubic, Compactly Supported, Inverse Multiquadric, Quadratic, and that proposed by [12], were closely investigated in order to numerically compare their effectiveness drawbacks etc. and this is taken as our second objective. A sufficient number of simulations were performed covering as many aspects as possible. Varidated against both exacts and other numerical works, the final results imply strongly that the Thin-Plate Spline and Linear type of RBF are superior to others in terms of both solutions' quality and CPU-time spent while the Inverse Multiquadric seems to poorly yield the results. It is also found that DRBEM can perform relatively well at moderate level of convective force and as anticipated becomes unstable when the problem becomes more convective-dominated, as normally found in all classical mesh-dependence methods.
Hartmann, E
1989-11-01
Previous work by the author and his collaborators on frequent nightmare sufferers demonstrated that these people had striking personality characteristics which could be called "thin boundaries" in a number of different senses. In order to measure thin and thick boundaries, a 145-item questionnaire, the Boundary Questionnaire, has been developed which has now been taken by over 1,000 persons. Preliminary results are presented indicating that, as predicted a priori, several new groups of nightmare sufferers and groups of art students scored usually "thin," whereas a group of naval officers had usually "thick" boundaries. Overall, thinness on the Boundary Questionnaire correlated highly positively (r = .40) with frequency of dream recall and also significantly (r = .16) with length of sleep.
A finite element field solver for dipole modes
International Nuclear Information System (INIS)
Nelson, E.M.
1992-01-01
A finite element field solver for dipole modes in axisymmetric structures has been written. The second-order elements used in this formulation yield accurate mode frequencies with no spurious modes. Quasi-periodic boundaries are included to allow travelling waves in periodic structures. The solver is useful in applications requiring precise frequency calculations such as detuned accelerator structures for linear colliders. Comparisons are made with measurements and with the popular but less accurate field solver URMEL. (author). 7 refs., 4 figs
Repfinder: Finding approximately repeated scene elements for image editing
Cheng, Ming-Ming; Zhang, Fanglue; Mitra, Niloy J.; Huang, Xiaolei; Hu, Shimin
2010-01-01
variation, etc. Manually enforcing such relations is laborious and error-prone. We propose a novel framework where user scribbles are used to guide detection and extraction of such repeated elements. Our detection process, which is based on a novel boundary
Imandoust, Aidin
The origin of texture components associated with rare-earth (RE) element additions in wrought magnesium (Mg) alloys is a long-standing problem in magnesium technology. The objective of this research is to identify the mechanisms accountable for rare-earth texture during dynamic recrystallization (DRX). Towards this end, we designed binary Mg-Cerium and Mg-Gadolinium alloys along with complex alloy compositions containing zinc, yttrium and Mischmetal. Binary alloys along with pure Mg were designed to individually investigate their effects on texture evolutions, while complex compositions are designed to develop randomized texture, and be used in automotive and aerospace applications. We selected indirect extrusion to thermo-mechanically process our materials. Different extrusion ratios and speeds were designed to produce partially and fully recrystallized microstructures, allowing us to analyze DRX from its early stages to completion. X-ray diffraction, electron backscattered diffraction (EBSD) and transmission electron microscopy (TEM) were used to conduct microstructure and texture analyses. Our analyses revealed that rare-earth elements in zinc-containing magnesium alloys promote discontinuous dynamic recrystallization at the grain boundaries. During nucleation, the effect of rare earth elements on orientation selection was explained by the concomitant actions of multiple Taylor axes in the same grain. Isotropic grain growth was observed due to rare earth elements segregating to grain boundaries, which lead to texture randomization. The nucleation in binary Mg-RE alloys took place by continuous formation of necklace structures. Stochastic relaxation of basal and non-basal dislocations into low-angle grain boundaries produced chains of embryos with nearly random orientations. Schmid factor analysis showed a lower net activation of dislocations in RE textured grains compared to ones on the other side of the stereographic triangle. Lower dislocation densities within
On the Lagrangian description of unsteady boundary-layer separation. I - General theory
Van Dommelen, Leon L.; Cowley, Stephen J.
1990-01-01
Although unsteady, high-Reynolds number, laminar boundary layers have conventionally been studied in terms of Eulerian coordinates, a Lagrangian approach may have significant analytical and computational advantages. In Lagrangian coordinates the classical boundary layer equations decouple into a momentum equation for the motion parallel to the boundary, and a hyperbolic continuity equation (essentially a conserved Jacobian) for the motion normal to the boundary. The momentum equations, plus the energy equation if the flow is compressible, can be solved independently of the continuity equation. Unsteady separation occurs when the continuity equation becomes singular as a result of touching characteristics, the condition for which can be expressed in terms of the solution of the momentum equations. The solutions to the momentum and energy equations remain regular. Asymptotic structures for a number of unsteady 3-D separating flows follow and depend on the symmetry properties of the flow. In the absence of any symmetry, the singularity structure just prior to separation is found to be quasi 2-D with a displacement thickness in the form of a crescent shaped ridge. Physically the singularities can be understood in terms of the behavior of a fluid element inside the boundary layer which contracts in a direction parallel to the boundary and expands normal to it, thus forcing the fluid above it to be ejected from the boundary layer.
De Grazia, D.; Moxey, D.; Sherwin, S. J.; Kravtsova, M. A.; Ruban, A. I.
2018-02-01
In this paper we study the boundary-layer separation produced in a high-speed subsonic boundary layer by a small wall roughness. Specifically, we present a direct numerical simulation (DNS) of a two-dimensional boundary-layer flow over a flat plate encountering a three-dimensional Gaussian-shaped hump. This work was motivated by the lack of DNS data of boundary-layer flows past roughness elements in a similar regime which is typical of civil aviation. The Mach and Reynolds numbers are chosen to be relevant for aeronautical applications when considering small imperfections at the leading edge of wings. We analyze different heights of the hump: The smaller heights result in a weakly nonlinear regime, while the larger result in a fully nonlinear regime with an increasing laminar separation bubble arising downstream of the roughness element and the formation of a pair of streamwise counterrotating vortices which appear to support themselves.
Composition-Driven Phase Boundary and Piezoelectricity in Potassium-Sodium Niobate-Based Ceramics.
Zheng, Ting; Wu, Jiagang; Xiao, Dingquan; Zhu, Jianguo; Wang, Xiangjian; Lou, Xiaojie
2015-09-16
The piezoelectricity of (K,Na)NbO3 ceramics strongly depends on the phase boundary types as well as the doped compositions. Here, we systematically studied the relationships between the compositions and phase boundary types in (K,Na) (Nb,Sb)O3-Bi0.5Na0.5AO3 (KNNS-BNA, A=Hf, Zr, Ti, Sn) ceramics; then their piezoelectricity can be readily modified. Their phase boundary types are determined by the doped elements. A rhombohedral-tetragonal (R-T) phase boundary can be driven in the compositions range of 0.035≤BNH≤0.040 and 0.035≤BNZ≤0.045; an orthorhombic-tetragonal (O-T) phase boundary is formed in the composition range of 0.005≤BNT≤0.02; and a pure O phase can be only observed regardless of BNS content (≤0.01). In addition, the phase boundary types strongly affect their corresponding piezoelectricities. A larger d33 (∼440-450 pC/N) and a higher d33* (∼742-834 pm/V) can be attained in KNNS-BNA (A=Zr and Hf) ceramics due to the involvement of R-T phase boundary, and unfortunately KNNS-BNA (A=Sn and Ti) ceramics possess a relatively poor piezoelectricity (d33≤200 and d33*piezoelectricity and phase boundary types were also discussed. We believe that comprehensive research can design more excellent ceramic systems concerning potassium-sodium niobate.
International Nuclear Information System (INIS)
Assassa, Wafaa.
1975-01-01
16% chromium, 14% nickel stainless steel, austenitic at all temperatures, covers a wide field of industrial use. Its behavior was studied in order to find out more about how impurities affect the three basic elements forming the solid solution. After a review of some general properties (segregation, precipitation, migration, structure and energy of boundaries) the physico-chemical aspect of the grain boundaries was investigated. The atomic diffusion rates of the three basic elements forming the solid-solution were compared in order to evaluate their mutual kinetics and the effects of impurities such as C, Si or addition elements such as Ni were studied. The radiotracer technique was used ( 59 Fe, 51 Cr, 63 Ni). The structural aspect of the grain boundaries of this type of steel was then examined by analyzing the self-diffusion of iron in preoriented bicrystals and considering the properties of the boundaries parallel with and perpendicular to the (001) bending axis. A study was devoted to the effect of a new structural parameter, asymmetry of the grain boundaries, little analyzed in diffusion [fr
Energy Technology Data Exchange (ETDEWEB)
Sarler, B; Alujevic, A [Univerza B. Kardelja, Institut ' Jozef Stefan' , Ljubljana (Yugoslavia)
1988-07-01
The basic principles of self-adaptive algorithm for treatment of transient nonlinear nonhomogeneous radial heat flow, based on direct Boundary Element method formulation, are presented. The indicators of discretization error are developed, together with binary-tree strategy for manipulation with time domain mesh, assuring automatic optimisation of calculation procedure with respect to predetermined error. The developed method is particularly suitable for use in a spectrum of extremely nonlinear cases, occurring in thermal analyses of reactor components.(author)
Energy Technology Data Exchange (ETDEWEB)
Salinas, F S; Lancaster, J L; Fox, P T [Research Imaging Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 (United States)
2009-06-21
Transcranial magnetic stimulation (TMS) delivers highly localized brain stimulations via non-invasive externally applied magnetic fields. This non-invasive, painless technique provides researchers and clinicians with a unique tool capable of stimulating both the central and peripheral nervous systems. However, a complete analysis of the macroscopic electric fields produced by TMS has not yet been performed. In this paper, we addressed the importance of the secondary E-field created by surface charge accumulation during TMS using the boundary element method (BEM). 3D models were developed using simple head geometries in order to test the model and compare it with measured values. The effects of tissue geometry, size and conductivity were also investigated. Finally, a realistically shaped head model was used to assess the effect of multiple surfaces on the total E-field. Secondary E-fields have the greatest impact at areas in close proximity to each tissue layer. Throughout the head, the secondary E-field magnitudes typically range from 20% to 35% of the primary E-field's magnitude. The direction of the secondary E-field was generally in opposition to the primary E-field; however, for some locations, this was not the case (i.e. going from high to low conductivity tissues). These findings show that realistically shaped head geometries are important for accurate modeling of the total E-field.
International Nuclear Information System (INIS)
Salinas, F S; Lancaster, J L; Fox, P T
2009-01-01
Transcranial magnetic stimulation (TMS) delivers highly localized brain stimulations via non-invasive externally applied magnetic fields. This non-invasive, painless technique provides researchers and clinicians with a unique tool capable of stimulating both the central and peripheral nervous systems. However, a complete analysis of the macroscopic electric fields produced by TMS has not yet been performed. In this paper, we addressed the importance of the secondary E-field created by surface charge accumulation during TMS using the boundary element method (BEM). 3D models were developed using simple head geometries in order to test the model and compare it with measured values. The effects of tissue geometry, size and conductivity were also investigated. Finally, a realistically shaped head model was used to assess the effect of multiple surfaces on the total E-field. Secondary E-fields have the greatest impact at areas in close proximity to each tissue layer. Throughout the head, the secondary E-field magnitudes typically range from 20% to 35% of the primary E-field's magnitude. The direction of the secondary E-field was generally in opposition to the primary E-field; however, for some locations, this was not the case (i.e. going from high to low conductivity tissues). These findings show that realistically shaped head geometries are important for accurate modeling of the total E-field.
Salinas, F. S.; Lancaster, J. L.; Fox, P. T.
2009-06-01
Transcranial magnetic stimulation (TMS) delivers highly localized brain stimulations via non-invasive externally applied magnetic fields. This non-invasive, painless technique provides researchers and clinicians with a unique tool capable of stimulating both the central and peripheral nervous systems. However, a complete analysis of the macroscopic electric fields produced by TMS has not yet been performed. In this paper, we addressed the importance of the secondary E-field created by surface charge accumulation during TMS using the boundary element method (BEM). 3D models were developed using simple head geometries in order to test the model and compare it with measured values. The effects of tissue geometry, size and conductivity were also investigated. Finally, a realistically shaped head model was used to assess the effect of multiple surfaces on the total E-field. Secondary E-fields have the greatest impact at areas in close proximity to each tissue layer. Throughout the head, the secondary E-field magnitudes typically range from 20% to 35% of the primary E-field's magnitude. The direction of the secondary E-field was generally in opposition to the primary E-field; however, for some locations, this was not the case (i.e. going from high to low conductivity tissues). These findings show that realistically shaped head geometries are important for accurate modeling of the total E-field.
ZONE: a finite element mesh generator. [In FORTRAN IV for CDC 7600
Energy Technology Data Exchange (ETDEWEB)
Burger, M. J.
1976-05-01
The ZONE computer program is a finite-element mesh generator which produces the nodes and element description of any two-dimensional geometry. The geometry is subdivided into a mesh of quadrilateral and triangular zones arranged sequentially in an ordered march through the geometry. The order of march can be chosen so that the minimum bandwidth is obtained. The node points are defined in terms of the x and y coordinates in a global rectangular coordinate system. The zones generated are quadrilaterals or triangles defined by four node points in a counterclockwise sequence. Node points defining the outside boundary are generated to describe pressure boundary conditions. The mesh that is generated can be used as input to any two-dimensional as well as any axisymmetrical structure program. The output from ZONE is essentially the input file to NAOS, HONDO, and other axisymmetric finite element programs. 14 figures. (RWR)
Navier-Stokes calculations on multi-element airfoils using a chimera-based solver
Jasper, Donald W.; Agrawal, Shreekant; Robinson, Brian A.
1993-01-01
A study of Navier-Stokes calculations of flows about multielement airfoils using a chimera grid approach is presented. The chimera approach utilizes structured, overlapped grids which allow great flexibility of grid arrangement and simplifies grid generation. Calculations are made for two-, three-, and four-element airfoils, and modeling of the effect of gap distance between elements is demonstrated for a two element case. Solutions are obtained using the thin-layer form of the Reynolds averaged Navier-Stokes equations with turbulence closure provided by the Baldwin-Lomax algebraic model or the Baldwin-Barth one equation model. The Baldwin-Barth turbulence model is shown to provide better agreement with experimental data and to dramatically improve convergence rates for some cases. Recently developed, improved farfield boundary conditions are incorporated into the solver for greater efficiency. Computed results show good comparison with experimental data which include aerodynamic forces, surface pressures, and boundary layer velocity profiles.
Rehman, Asad; Ali, Ishtiaq; Qamar, Shamsul
An upwind space-time conservation element and solution element (CE/SE) scheme is extended to numerically approximate the dusty gas flow model. Unlike central CE/SE schemes, the current method uses the upwind procedure to derive the numerical fluxes through the inner boundary of conservation elements. These upwind fluxes are utilized to calculate the gradients of flow variables. For comparison and validation, the central upwind scheme is also applied to solve the same dusty gas flow model. The suggested upwind CE/SE scheme resolves the contact discontinuities more effectively and preserves the positivity of flow variables in low density flows. Several case studies are considered and the results of upwind CE/SE are compared with the solutions of central upwind scheme. The numerical results show better performance of the upwind CE/SE method as compared to the central upwind scheme.
Simple one-dimensional finite element algorithm with multi-dimensional capabilities
International Nuclear Information System (INIS)
Pepper, D.W.; Baker, A.J.
1978-01-01
The application of the finite element procedure for the solution of partial differential equations is gaining widespread acceptance. The ability of the finite element procedure to solve problems which are arbitrarily shaped as well as the alleviation of boundary condition problems is well known. By using local interpolation functionals over each subdomain, or element, a set of linearized algebraic equations are obtained which can be solved using any direct, iterative, or inverse numerical technique. Subsequent use of an explicit or implicit integration procedure permits closure of the solution over the global domain
International Nuclear Information System (INIS)
Ishida, Hitoshi; Meshii, Toshiyuki
2010-01-01
This study proposes an element size selection method named the 'Impact-Meshing (IM) method' for a finite element waves propagation analysis model, which is characterized by (1) determination of element division of the model with strain energy in the whole model, (2) static analysis (dynamic analysis in a single time step) with boundary conditions which gives a maximum change of displacement in the time increment and inertial (impact) force caused by the displacement change. In this paper, an example of application of the IM method to 3D ultrasonic wave propagation problem in an elastic solid is described. These examples showed an analysis result with a model determined by the IM method was convergence and calculation time for determination of element subdivision was reduced to about 1/6 by the IM Method which did not need determination of element subdivision by a dynamic transient analysis with 100 time steps. (author)
Multiscale Modeling of Grain Boundaries in ZrB2: Structure, Energetics, and Thermal Resistance
Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W., Jr.
2012-01-01
A combination of ab initio, atomistic and finite element methods (FEM) were used to investigate the structures, energetics and lattice thermal conductance of grain boundaries for the ultra high temperature ceramic ZrB2. Atomic models of idealized boundaries were relaxed using density functional theory. Information about bonding across the interfaces was determined from the electron localization function. The Kapitza conductance of larger scale versions of the boundary models were computed using non-equilibrium molecular dynamics. The interfacial thermal parameters together with single crystal thermal conductivities were used as parameters in microstructural computations. FEM meshes were constructed on top of microstructural images. From these computations, the effective thermal conductivity of the polycrystalline structure was determined.
Transcription of Gypsy Elements in a Y-Chromosome Male Fertility Gene of Drosophila Hydei
Hochstenbach, R.; Harhangi, H.; Schouren, K.; Bindels, P.; Suijkerbuijk, R.; Hennig, W.
1996-01-01
We have found that defective gypsy retrotransposons are a major constituent of the lampbrush loop pair Nooses in the short arm of the Y chromosome of Drosophila hydei. The loop pair is formed by male fertility gene Q during the primary spermatocyte stage of spermatogenesis, each loop being a single transcription unit with an estimated length of 260 kb. Using fluorescent in situ hybridization, we show that throughout the loop transcripts gypsy elements are interspersed with blocks of a tandemly repetitive Y-specific DNA sequence, ay1. Nooses transcripts containing both sequence types show a wide size range on Northern blots, do not migrate to the cytoplasm, and are degraded just before the first meiotic division. Only one strand of ay1 and only the coding strand of gypsy can be detected in the loop transcripts. However, as cloned genomic DNA fragments also display opposite orientations of ay1 and gypsy, such DNA sections cannot be part of the Nooses. Hence, they are most likely derived from the flanking heterochromatin. The direction of transcription of ay1 and gypsy thus appears to be of a functional significance. PMID:8852843
Golczyk, Hieronim; Massouh, Amid; Greiner, Stephan
2014-01-01
Due to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled end-segments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories. PMID:24681616
Use of the finite element displacement method to solve solid-fluid interaction vibration problems
International Nuclear Information System (INIS)
Brown, S.J.; Hsu, K.H.
1978-01-01
It is shown through comparison to experimental, theoretical, and other finite element formulations that the finite element displacement method can solve accurately and economically a certain class of solid-fluid eigenvalue problems. The problems considered are small displacements in the absence of viscous damping and are 2-D and 3-D in nature. In this study the advantages of the finite element method (in particular the displacement formulation) is apparent in that a large structure consisting of the cylinders, support flanges, fluid, and other experimental boundaries could be modeled to yield good correlation to experimental data. The ability to handle large problems with standard structural programs is the key advantage of the displacement fluid method. The greatest obstacle is the inability of the analyst to inhibit those rotational degrees of freedom that are unnecessary to his fluid-structure vibration problem. With judicious use of element formulation, boundary conditions and modeling, the displacement finite element method can be successfully used to predict solid-fluid response to vibration and seismic loading
DEFF Research Database (Denmark)
Madsen, Søren; Pinna, Rodney; Randolph, M. F.
2015-01-01
of large-diameter bucket foundations. Since shell structures are generally sensitive to initially imperfect geometries, eigenmode-affine imperfections are introduced in a nonlinear finite-element analysis. The influence of modelling the real lid structure compared to classic boundary conditions...
Directory of Open Access Journals (Sweden)
Zhao-Xia Tong
2013-01-01
Full Text Available The reliability of discrete element method (DEM numerical simulations is significantly dependent on the particle-scale parameters and boundary conditions. To verify the DEM models, two series of biaxial compression tests on ellipse-shaped steel rods are used. The comparisons on the stress-strain relationship, strength, and deformation pattern of experiments and simulations indicate that the DEM models are able to capture the key macro- and micromechanical behavior of inherently anisotropic granular materials with high fidelity. By using the validated DEM models, the boundary effects on the macrodeformation, strain localization, and nonuniformity of stress distribution inside the specimens are investigated using two rigid boundaries and one flexible boundary. The results demonstrate that the boundary condition plays a significant role on the stress-strain relationship and strength of granular materials with inherent fabric anisotropy if the stresses are calculated by the force applied on the wall. However, the responses of the particle assembly measured inside the specimens are almost the same with little influence from the boundary conditions. The peak friction angle obtained from the compression tests with flexible boundary represents the real friction angle of particle assembly. Due to the weak lateral constraints, the degree of stress nonuniformity under flexible boundary is higher than that under rigid boundary.
DEFF Research Database (Denmark)
Aarhus, Rikke; Ballegaard, Stinne Aaløkke
2010-01-01
to maintain the order of the home when managing disease and adopting new healthcare technology. In our analysis we relate this boundary work to two continuums of visibility-invisibility and integration-segmentation in disease management. We explore five factors that affect the boundary work: objects......, activities, places, character of disease, and collaboration. Furthermore, the processes are explored of how boundary objects move between social worlds pushing and shaping boundaries. From this we discuss design implications for future healthcare technologies for the home.......To move treatment successfully from the hospital to that of technology assisted self-care at home, it is vital in the design of such technologies to understand the setting in which the health IT should be used. Based on qualitative studies we find that people engage in elaborate boundary work...
Administrative Area Boundaries 2 (State Boundaries), Region 9, 2010, NAVTEQ
U.S. Environmental Protection Agency — NAVTEQ Administrative Area Boundaries 2 (State Boundaries) for Region 9. There are five Administrative Area Boundaries layers (1, 2, 3, 4, 5). These layers contain...
Administrative Area Boundaries 4 (City Boundaries), Region 9, 2010, NAVTEQ
U.S. Environmental Protection Agency — NAVTEQ Administrative Area Boundaries 4 (City Boundaries) for Region 9. There are five Administrative Area Boundaries layers (1, 2, 3, 4, 5). These layers contain...
Elemental separation in nanocrystalline Cu-Al alloys
Wang, Y. B.; Liao, X. Z.; Zhao, Y. H.; Cooley, J. C.; Horita, Z.; Zhu, Y. T.
2013-06-01
Nanocrystallization by high-energy severe plastic deformation has been reported to increase the solubility of alloy systems and even to mix immiscible elements to form non-equilibrium solid solutions. In this letter, we report an opposite phenomenon—nanocrystallization of a Cu-Al single-phase solid solution by high-pressure torsion separated Al from the Cu matrix when the grain sizes are refined to tens of nanometers. The Al phase was found to form at the grain boundaries of nanocrystalline Cu. The level of the separation increases with decreasing grain size, which suggests that the elemental separation was caused by the grain size effect.
On Line-Elements and Radii: A Correction
Directory of Open Access Journals (Sweden)
Crothers S. J.
2007-04-01
Full Text Available Using a manifold with boundary various line-elements have been proposed as solutions to Einstein’s gravitational field. It is from such line-elements that black holes, expansion of the Universe, and big bang cosmology have been alleged. However, it has been proved that black holes, expansion of the Universe, and big bang cosmology are not consistent with General Relativity. In a previous paper disproving the black hole theory, the writer made an error which, although minor and having no effect on the conclusion that black holes are inconsistent with General Relativity, is corrected herein for the record.
Finite element concept to derive isostatic residual maps
Indian Academy of Sciences (India)
A new space-domain operator based on the shape function concept of finite element analysis has been developed to derive the residual maps of the Gorda Plate of western United States. The technique does not require explicit assumptions on isostatic models. Besides delineating the Gorda Plate boundary, the residual ...
Energy Technology Data Exchange (ETDEWEB)
Carrington, David Bradley [Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Monayem, A. K. M. [Univ. of New Mexico, Albuquerque, NM (United States); Mazumder, H. [Univ. of New Mexico, Albuquerque, NM (United States); Heinrich, Juan C. [Univ. of New Mexico, Albuquerque, NM (United States)
2015-03-05
A three-dimensional finite element method for the numerical simulations of fluid flow in domains containing moving rigid objects or boundaries is developed. The method falls into the general category of Arbitrary Lagrangian Eulerian methods; it is based on a fixed mesh that is locally adapted in the immediate vicinity of the moving interfaces and reverts to its original shape once the moving interfaces go past the elements. The moving interfaces are defined by separate sets of marker points so that the global mesh is independent of interface movement and the possibility of mesh entanglement is eliminated. The results is a fully robust formulation capable of calculating on domains of complex geometry with moving boundaries or devises that can also have a complex geometry without danger of the mesh becoming unsuitable due to its continuous deformation thus eliminating the need for repeated re-meshing and interpolation. Moreover, the boundary conditions on the interfaces are imposed exactly. This work is intended to support the internal combustion engines simulator KIVA developed at Los Alamos National Laboratories. The model's capabilities are illustrated through application to incompressible flows in different geometrical settings that show the robustness and flexibility of the technique to perform simulations involving moving boundaries in a three-dimensional domain.
International Nuclear Information System (INIS)
Alleon, G.; Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E.
2003-01-01
The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)
Energy Technology Data Exchange (ETDEWEB)
Alleon, G. [EADS-CCR, 31 - Blagnac (France); Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E. [Cerfacs, 31 - Toulouse (France)
2003-07-01
The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)
Yang, Xiang; Sadique, Jasim; Mittal, Rajat; Meneveau, Charles
2014-11-01
A new wall model for Large-Eddy-Simulations is proposed. It is based on an integral boundary layer method that assumes a functional form for the local mean velocity profile. The method, iWMLES, evaluates required unsteady and advective terms in the vertically integrated boundary layer equations analytically. The assumed profile contains a viscous or roughness sublayer, and a logarithmic layer with an additional linear term accounting for inertial and pressure gradient effects. The iWMLES method is tested in the context of a finite difference LES code. Test cases include developing turbulent boundary layers on a smooth flat plate at various Reynolds numbers, over flat plates with unresolved roughness, and a sample application to boundary layer flow over a plate that includes resolved roughness elements. The elements are truncated cones acting as idealized barnacle-like roughness elements that often occur in biofouling of marine surfaces. Comparisons with data show that iWMLES provides accurate predictions of near-wall velocity profiles in LES while, similarly to equilibrium wall models, its cost remains independent of Reynolds number and is thus signif