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Sample records for binary hammerhead ribozymes

  1. Schistosome satellite DNA encodes active hammerhead ribozymes.

    Science.gov (United States)

    Ferbeyre, G; Smith, J M; Cedergren, R

    1998-07-01

    Using a computer program designed to search for RNA structural motifs in sequence databases, we have found a hammerhead ribozyme domain encoded in the Smalpha repetitive DNA of Schistosoma mansoni. Transcripts of these repeats are expressed as long multimeric precursor RNAs that cleave in vitro and in vivo into unit-length fragments. This RNA domain is able to engage in both cis and trans cleavage typical of the hammerhead ribozyme. Further computer analysis of S. mansoni DNA identified a potential trans cleavage site in the gene coding for a synaptobrevin-like protein, and RNA transcribed from this gene was efficiently cleaved by the Smalpha ribozyme in vitro. Similar families of repeats containing the hammerhead domain were found in the closely related Schistosoma haematobium and Schistosomatium douthitti species but were not present in Schistosoma japonicum or Heterobilharzia americana, suggesting that the hammerhead domain was not acquired from a common schistosome ancestor.

  2. The Hammerhead Ribozyme: A Long History for a Short RNA

    Directory of Open Access Journals (Sweden)

    Marcos de la Peña

    2017-01-01

    Full Text Available Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner. The hammerhead ribozyme was the first reported and the most extensively studied member of this family. However, and despite intense biochemical and structural research for three decades since its discovery, the history of this model ribozyme seems to be far from finished. The hammerhead ribozyme has been regarded as a biological oddity typical of small circular RNA pathogens of plants. More recently, numerous and new variations of this ribozyme have been found to inhabit the genomes of organisms from all life kingdoms, although their precise biological functions are not yet well understood.

  3. Ionic interactions and the global conformations of the hammerhead ribozyme

    DEFF Research Database (Denmark)

    Bassi, G S; Møllegaard, N E; Murchie, A I;

    1995-01-01

    Here we investigate the global conformation of the hammerhead ribozyme. Electrophoretic studies demonstrate that the structure is folded in response to the concentration and type of ions present. Folding based on colinear alignment of arms II and III is suggested, with a variable angle subtended...

  4. Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.

    Science.gov (United States)

    Cervera, Amelia; De la Peña, Marcos

    2014-11-01

    Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

  5. Experimental cancer gene therapy by multiple anti-survivin hammerhead ribozymes

    Institute of Scientific and Technical Information of China (English)

    Qi Fei; Yuwen Ke; Xuebiao Yao; Jingde Zhu; Hongyu Zhang; Lili Fu; Xinlan Dai; Baomei Gao; Min Ni; Chao Ge; Jinjun Li; Xia Ding

    2008-01-01

    To improve the efficacy of gene therapy for cancer, we designed four hammerhead ribozyme adenoviruses (R1 to R4) targeting the exposed regions of survivin mRNA. In addition to the in vitro characterization, which included a determination of the sequence specificity of cleavage by primer extension, assays for cell proliferation and for in vivo tumor growth were used to score for ribozyme efficiency.The resulting suppression of survivin expression induced mitotic catastrophe and cell death via the caspase-3-dependent pathway. Importantly, administration of the ribozyme adenoviruses inhibited tumor growth in a hepato-cellular carcinoma xenograft mouse model. Co-expression of R1, R3 and R4 ribozymes synergistically suppressed survivin and, as this combination targets all major forms of the survivin transcripts, produced the most potent anti-cancer effects. The adenoviruses carrying the multiple hammerhead ribozymes described in this report offered a robust gene therapy strategy against cancer.

  6. NMR-spectroscopic characterization of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme.

    Science.gov (United States)

    Fürtig, Boris; Richter, Christian; Schell, Peter; Wenter, Philipp; Pitsch, Stefan; Schwalbe, Harald

    2008-01-01

    In order to relate the conformational dynamics of the hammerhead ribozyme to its biological function the cleavage reaction catalyzed by the hammerhead ribozyme was monitored by time-resolved nuclear magnetic resonance (NMR) spectroscopy. For this purpose, the two nucleosides around the scissile phosphodiester bond were selectively (13)C labelled in multi-step organic syntheses starting from uniformly (13)C-labelled glucose. The phosphoamidites were incorporated using phosphoamidite chemistry in the hammerhead substrate strand. In addition, the 2'-OH group on the 5'-side of the hammerhead substrate strand was labelled with a photolabile protecting group. This labelling strategy enabled a detailed characterisation of the nucleotides around the scissile phosphodiester bond in the ground state conformation of the hammerhead ribozyme in the absence and presence of Mg(2+) ions as well as of the product state. Photochemical induction of the reaction in situ was further characterized by time-resolved NMR spectroscopy. The detailed structural and dynamic investigations revealed that the conformation of the hammerhead ribozyme is significantly affected by addition of Mg(2+) leading to an ensemble of conformations where dynamic transitions between energetically similar conformations occur on the ms-timescale in the presence of Mg(2+). The dynamic transitions are localized around the catalytic core. Cleavage from this ensemble cannot be described by mono-exponential kinetics but follows bi-exponential kinetics. A model is described to take into account these experimental data.

  7. Efficient hammerhead ribozyme and antisense RNA targeting in a slow ribosome Escherichia coli mutant.

    Science.gov (United States)

    Chen, H; Ferbeyre, G; Cedergren, R

    1997-05-01

    We have evaluated inhibition of the plasmid-born chloramphenicol acetyl transferase gene (CAT) by the hammerhead ribozyme and antisense RNA in Escherichia coli where the translation and transcription rates have been modified. Whereas neither antisense nor the hammerhead had an inhibitory effect on CAT activity in wild-type E. coli, both reduced the level of the messenger RNA and the activity of the CAT gene by almost 60% in a slow ribosome mutant. Streptomycin, which increases the speed of translation in this mutant strain, restored full CAT activity. The level of CAT activity expressed from a T7 RNA polymerase promoter was not affected by the presence of either antisense RNA or the hammerhead ribozyme. When the target gene was expressed from a chromosomal locus in wild-type E. coli, both antisense RNA and the hammerhead ribozyme showed some inhibitory activity, but the level of inhibition was significantly increased in the slow ribosome strain. This bacterial system offers a unique entry to the study of cellular factors which mediate the activity of ribozymes in vivo.

  8. Cell cycle arrest promotes trans-hammerhead ribozyme action in yeast.

    Science.gov (United States)

    Ferbeyre, G; Bratty, J; Chen, H; Cedergren, R

    1996-08-09

    A hammerhead ribozyme designed to cleave the yeast ADE1 mRNA has been expressed in yeast under the control of a galactose-inducible promoter. RNA prepared from the galactose-induced yeast cultures possesses an activity that cleaves ADE1 mRNA in vitro. However, in spite of high expression levels of the ribozyme, no cleavage activity could be demonstrated in vivo. On the other hand, when the yeast cells expressing hammerhead RNA were treated with the alpha-factor mating pheromone, the level of ADE1 mRNA was reduced by 50%. Similar reductions were observed when this strain was cultured in the presence of lithium acetate or in nitrogen-free medium. Moreover, control experiments in which disabled hammerhead genes were expressed showed no such reductions. Extension of the length of the flanking recognition arms of the ribozyme from a total of 10 to 16 or 24 nucleotides diminished the inhibitory effect of the ribozyme. These data suggest that ribozymes are able to cleave a trans-RNA target in yeast.

  9. A strategy for developing a hammerhead ribozyme for selective RNA cleavage depending on substitutional RNA editing.

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Tanaka, Yasuyoshi; Deshimaru, Masanobu

    2012-09-01

    Substitutional RNA editing plays a crucial role in the regulation of biological processes. Cleavage of target RNA that depends on the specific site of substitutional RNA editing is a useful tool for analyzing and regulating intracellular processes related to RNA editing. Hammerhead ribozymes have been utilized as small catalytic RNAs for cleaving target RNA at a specific site and may be used for RNA-editing-specific RNA cleavage. Here we reveal a design strategy for a hammerhead ribozyme that specifically recognizes adenosine to inosine (A-to-I) and cytosine to uracil (C-to-U) substitutional RNA-editing sites and cleaves target RNA. Because the hammerhead ribozyme cleaves one base upstream of the target-editing site, the base that pairs with the target-editing site was utilized for recognition. RNA-editing-specific ribozymes were designed such that the recognition base paired only with the edited base. These ribozymes showed A-to-I and C-to-U editing-specific cleavage activity against synthetic serotonin receptor 2C and apolipoprotein B mRNA fragments in vitro, respectively. Additionally, the ribozyme designed for recognizing A-to-I RNA editing at the Q/R site on filamin A (FLNA) showed editing-specific cleavage activity against physiologically edited FLNA mRNA extracted from cells. We demonstrated that our strategy is effective for cleaving target RNA in an editing-dependent manner. The data in this study provided an experimental basis for the RNA-editing-dependent degradation of specific target RNA in vivo.

  10. Expression and in vitro cleavage activity of anti-caspase-7 hammerhead ribozymes

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Qing Xie; Xia-Qiu Zhou; Shan Jiang; You-Xin Jin

    2004-01-01

    AIM: To prepare hammerhead ribozymes against mouse caspase-7 and identify their cleavage activityin vitro, in order to select a ribozyme with specific cleavage activity against mouse caspase-7 as a potential gene therapy for apoptosis-related diseases.METHODS: Anti-caspase-7 ribozymes targeting sites 333and 394 (named Rz333 and Rz394) were designed by computer software, and their DNA sequences encoding ribozymes were synthesized. Caspase-7 DNA sequence was acquired by RT-PCR. Ribozymes and caspase-7 DNA obtained byin vitro transcription were cloned into pBSKneo U6' and pGEM-T vectors, respectively. The cleavage activity of ribozymes against mouse caspase-7 was identified by cleavage experimentsin vitro.RESULTS: Rz333 and Rz394 were designed and their DNA sequences were synthesized respectively. The expression vector of caspase-7 and plasmids containing Rz333 and Rz394 were reconstructed successfully. Ribozymes and caspase-7 mRNA were expressed byin vitro transcription.In vitro cleavage experiment showed that 243-nt and 744-nt segments were produced after caspase-7 mRNA was mixed with Rz333 in equivalent, and the cleavage efficiency was 67.98%. No cleaved segment was observed when caspase-7 mRNA was mixed with Rz394.CONCLUSION: Rz333 can site-specific cleave mouse caspase-7 mRNA, and it shows a potential for gene therapy of apoptosis-related diseases by down-regulating gene expression of caspase-7.

  11. A strategy for developing a hammerhead ribozyme for selective RNA cleavage depending on substitutional RNA editing

    OpenAIRE

    Fukuda, Masatora; Kurihara, Kei; Tanaka, Yasuyoshi; Deshimaru, Masanobu

    2012-01-01

    Engineered site-specific RNA cleavage is widely used for gene regulation, RNA mapping, and synthetic RNA production. Here the authors extend the range of engineered recognition selectivity to include cleavage of sequence motifs containing naturally occurring base modifications. They describe and implement a designer hammerhead ribozyme that cleaves a target sequence 1 nt from a site of adenosine to inosine (A-to-I) or cytosine to uracil (C-to-U) editing in synthetic or physiological mRNA cont...

  12. Spiegelzymes: sequence specific hydrolysis of L-RNA with mirror image hammerhead ribozymes and DNAzymes.

    Directory of Open Access Journals (Sweden)

    Eliza Wyszko

    Full Text Available In this manuscript we describe for the first time mirror image catalytic nucleic acids (Spiegelzymes, which hydrolyze sequence specifically L-ribonucleic acid molecules. The mirror image nucleic acid ribozymes designed are based upon the known hammerhead ribozyme and DNAzyme structures that contain L-ribose or L-deoxyribose instead of the naturally occurring D-ribose or D-deoxyribose, respectively. Both Spiegelzymes show similar hydrolytic activities with the same L-RNA target molecules and they also exhibit extra ordinary stabilities when tested with three different human sera. In this respect they are very similar to Spiegelmers (mirror image aptamers, which we had previously developed and for which it has been shown that they are non-toxic and non-immunogenic. Since we are also able to demonstrate that the hammerhead and DNAzyme Spiegelzymes can also hydrolyze mirror image oligonucleotide sequences, like they occur in Spiegelmers, in vivo, it seems reasonable to assume that Spiegelzymes may in principle be used as an antidote against Spiegelmers. Since the Spiegelzymes contain the same building blocks as the Spiegelmers, it can be expected that they will have similar favorable biological characteristics concerning toxicity and immunogenety. In trying to understand the mechanism of action of the Spiegelzymes described in this study, we have initiated for the first time a model building system with L-nucleic acids. The models for L-hammerhead ribozyme and L-DNAzyme interaction with the same L-RNA target will be presented.

  13. Reversal of HCC Drug Resistance by Using Hammerhead Ribozymes against Multidrug Resistance 1 Gene

    Institute of Scientific and Technical Information of China (English)

    QIAO Sen; WANG Hai; CHEN Xiaoping

    2005-01-01

    To reverse multidrug resistance(MDR) of HepG2 by anti-MDR1 hammerhead ribozyme,an anti-MDR1 hammerhead ribozyme was developed and delivered to P-gp-overproducing human hepatocarcinoma cell line HepG2 by a retroviral vector containing RNA polymerase Ⅲ promoter.The expression of mdr1/Pgp and Rz was detected in HepG2, HepG2 multidrug-resistant cell line and HepG2 Rz-transfected cells by semi quantitative RT-PCR and Western blot methods. Moreover, MTT assay was employed to detect the sensitivity of these ribozyme-transfected cells, and Rhodamine123 (Rh123) was used to test the function of Pgp. The Rz- transfected HepG2 cells became doxorubicin-sensitive, which was concomitant with the decreased MDR1 expression. The study showed that the retrovirus vector encoding the anti-MDR1 ribozyme may be applicable to the treatment of MDR cells.

  14. Effective suppression of Dengue fever virus in mosquito cell cultures using retroviral transduction of hammerhead ribozymes targeting the viral genome.

    Science.gov (United States)

    Nawtaisong, Pruksa; Keith, James; Fraser, Tresa; Balaraman, Velmurugan; Kolokoltsov, Andrey; Davey, Robert A; Higgs, Stephen; Mohammed, Ahmed; Rongsriyam, Yupha; Komalamisra, Narumon; Fraser, Malcolm J

    2009-06-04

    Outbreaks of Dengue impose a heavy economic burden on developing countries in terms of vector control and human morbidity. Effective vaccines against all four serotypes of Dengue are in development, but population replacement with transgenic vectors unable to transmit the virus might ultimately prove to be an effective approach to disease suppression, or even eradication. A key element of the refractory transgenic vector approach is the development of transgenes that effectively prohibit viral transmission. In this report we test the effectiveness of several hammerhead ribozymes for suppressing DENV in lentivirus-transduced mosquito cells in an attempt to mimic the transgenic use of these effector molecules in mosquitoes. A lentivirus vector that expresses these ribozymes as a fusion RNA molecule using an Ae. aegypti tRNA(val) promoter and terminating with a 60A tail insures optimal expression, localization, and activity of the hammerhead ribozyme against the DENV genome. Among the 14 hammerhead ribozymes we designed to attack the DENV-2 NGC genome, several appear to be relatively effective in reducing virus production from transduced cells by as much as 2 logs. Among the sequences targeted are 10 that are conserved among all DENV serotype 2 strains. Our results confirm that hammerhead ribozymes can be effective in suppressing DENV in a transgenic approach, and provide an alternative or supplementary approach to proposed siRNA strategies for DENV suppression in transgenic mosquitoes.

  15. Effective suppression of Dengue fever virus in mosquito cell cultures using retroviral transduction of hammerhead ribozymes targeting the viral genome

    Directory of Open Access Journals (Sweden)

    Mohammed Ahmed

    2009-06-01

    Full Text Available Abstract Outbreaks of Dengue impose a heavy economic burden on developing countries in terms of vector control and human morbidity. Effective vaccines against all four serotypes of Dengue are in development, but population replacement with transgenic vectors unable to transmit the virus might ultimately prove to be an effective approach to disease suppression, or even eradication. A key element of the refractory transgenic vector approach is the development of transgenes that effectively prohibit viral transmission. In this report we test the effectiveness of several hammerhead ribozymes for suppressing DENV in lentivirus-transduced mosquito cells in an attempt to mimic the transgenic use of these effector molecules in mosquitoes. A lentivirus vector that expresses these ribozymes as a fusion RNA molecule using an Ae. aegypti tRNAval promoter and terminating with a 60A tail insures optimal expression, localization, and activity of the hammerhead ribozyme against the DENV genome. Among the 14 hammerhead ribozymes we designed to attack the DENV-2 NGC genome, several appear to be relatively effective in reducing virus production from transduced cells by as much as 2 logs. Among the sequences targeted are 10 that are conserved among all DENV serotype 2 strains. Our results confirm that hammerhead ribozymes can be effective in suppressing DENV in a transgenic approach, and provide an alternative or supplementary approach to proposed siRNA strategies for DENV suppression in transgenic mosquitoes.

  16. Connective tissue growth factor hammerhead ribozyme attenuates human hepatic stellate cell function

    Institute of Scientific and Technical Information of China (English)

    Run-Ping Gao; David R Brigstock

    2009-01-01

    AIM: To determine the effect of hammerhead ribozyme targeting connective tissue growth factor (CCN2) on human hepatic stellate cell (HSC) function. METHODS: CCN2 hammerhead ribozyme cDNA plus two self-cleaving sequences were inserted into pTriEx2 to produce pTriCCN2-Rz. Each vector was individually transfected into cultured LX-2 human HSCs, which were then stimulated by addition of transforming growth factor (TGF)-b1 to the culture medium. Semiquantitative RT-PCR was used to determine mRNA levels for CCN2 or collagen Ⅰ, while protein levels of each molecule in cell lysates and conditioned medium were measured by ELISA. Cell-cycle progression of the transfected cells was assessed by flow cytometry. RESULTS: In pTriEx2-transfected LX-2 cells, TGF-β1 treatment caused an increase in the mRNA level for CCN2 or collagen Ⅰ, and an increase in produced and secreted CCN2 or extracellular collagen Ⅰ protein levels. pTriCCN2-Rz-transfected LX-2 cells showed decreased basal CCN2 or collagen mRNA levels, as well as produced and secreted CCN2 or collagen Ⅰ protein. Furthermore, the TGF-b1-induced increase in mRNA or protein for CCN2 or collagen Ⅰ was inhibited partially in pTriCCN2-Rz-transfected LX-2 cells. Inhibition of CCN2 using hammerhead ribozyme cDNA resulted in fewer of the cells transitioning into S phase. CONCLUSION: Endogenous CCN2 is a mediator of basal or TGF-b1-induced collagen Ⅰ production in human HSCs and regulates entry of the cells into Sphase.

  17. A hammerhead ribozyme inhibits ADE1 gene expression in yeast.

    Science.gov (United States)

    Ferbeyre, G; Bratty, J; Chen, H; Cedergren, R

    1995-03-21

    To study factors that affect in vivo ribozyme (Rz) activity, a model system has been devised in Saccharomyces cerevisiae based on the inhibition of ADE1 gene expression. This gene was chosen because Rz action can be evaluated visually by the Red phenotype produced when the activity of the gene product is inhibited. Different plasmid constructs allowed the expression of the Rz either in cis or in trans with respect to ADE1. Rz-related inhibition of ADE1 expression was correlated with a Red phenotype and a diminution of ADE1 mRNA levels only when the Rz gene was linked 5' to ADE1. The presence of the expected 3' cleavage fragment was demonstrated using a technique combining RNA ligation and PCR. This yeast system and detection technique are suited to the investigation of general factors affecting Rz-catalyzed inhibition of gene expression under in vivo conditions.

  18. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics.

    Science.gov (United States)

    Swadling, Jacob B; Wright, David W; Suter, James L; Coveney, Peter V

    2015-03-01

    Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.

  19. Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-01-01

    Full Text Available Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol, small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds.

  20. Activity identification of chimeric anti-caspase-3 mRNA hammerhead ribozyme in vitro and in vivo

    Institute of Scientific and Technical Information of China (English)

    XU; Renhuan; (

    2001-01-01

    [1]Andrew, F., Gerard, E., A license to kill, Cell, 1996, 85: 781-784.[2]Thornberry, N. A., Lazebnik, Y., Caspases: Enemies within, Science, 1998, 281: 1312-1316.[3]Kijima, H., Ishida, H., Ohkawa, T. et al., Therapeutic application of ribozymes, Pharmacol. Ther., 1995, 68: 247-264.[4]Phylactou, L. A., Kilpatrick, M. W., Wood, M. J., Ribozymes as therapeutic tools for genetic disease, Hum. Mol. Genet., 1998, 7(10): 1649-1653.[5]Bettrand, E., Pictet, R ., Grange, T., Can heamerhead ribozymes be efficient tools inactivate gene function? Nucleic Acids Res., 1994, 22: 293-300.[6]Lieber, A., Strauss, M., Selection of efficient cleavage sites in target RNAs by using a ribozyme expression library, Mol. Cell Biol., 1995, 15: 540-551.[7]Xu, R. H., Zhou, X. Q., Xie, Q. et al., Preparation and identification of hammerhead ribozyme in vitro against rat caspase-3 mRNA fragment, Chin. J. Hepatol., 2000,8: 361-363.[8]Liu, J., Jin, Y. X., Wang, D. B., A novel vector for abundant expression of antisense RNA, triplex-forming RNA and ribozyme in vivo, High Technology Letters, 2000, 6: 84-88.[9]Sambrook, J., Fritsch, E. F., Maniatis, T., Molecular Cloning: A Laboratory Manual, 2nd ed., New York: Cold Spring Harbor Laboratory Press, 1989.[10]Porter, A. G., J?nicke, R. U., Emerging roles of caspase-3 in apoptosis, Cell Death Differ, 1999, 6: 99-104.[11]Cryns, V., Yuan, J., Proteases to die for, Genes Dev., 1998, 12: 1551-1570.[12]Narendra, K. V., Anikumar, R. K., Fritz, E., Recent developments in the hammerhead ribozyme field, Nucleic Acids Research, 1998, 26: 5237-5242.

  1. Efficient trans-cleavage by the Schistosoma mansoni SMalpha1 hammerhead ribozyme in the extreme thermophile Thermus thermophilus.

    Science.gov (United States)

    Vazquez-Tello, Alejandro; Castán, Pablo; Moreno, Renata; Smith, James M; Berenguer, José; Cedergren, Robert

    2002-04-01

    The catalytic hammerhead structure has been found in association with repetitive DNA from several animals, including salamanders, crickets and schistosomes, and functions to process in cis the long multimer transcripts into monomer RNA in vivo. The cellular role of these repetitive elements and their transcripts is unknown. Moreover, none of these natural hammerheads have been shown to trans-cleave a host mRNA in vivo. We analyzed the cis- and trans-cleavage properties of the hammerhead ribozyme associated with the SMalpha DNA family from the human parasite Schistosoma mansoni. The efficiency of trans-cleavage of a target RNA in vitro was affected mainly by both the temperature-dependent chemical step and the ribozyme-product dissociation step. The optimal temperature for trans-cleavage was 70 degrees C. This result was confirmed when both the SMalpha1 ribozyme and the target RNA were expressed in the extreme thermophile Thermus thermophilus. Moreover, SMalpha1 RNA showed a remarkable thermostability, equal or superior to that of the most stable RNAs in this species, suggesting that SMalpha1 RNA has been selected for stability. Computer analysis predicts that the monomer and multimer transcripts fold into highly compact secondary structures, which may explain their exceptional stability in vivo.

  2. Effects of blocking androgen receptor expression with specific hammerhead ribozyme on in vitro growth of prostate cancer cell line

    Institute of Scientific and Technical Information of China (English)

    童强松; 赵军; 陈朝晖; 曾甫清; 鲁功成

    2003-01-01

    Objective To study the possibility of gene therapy for prostate cancer by blocking androgen receptor (AR) gene expression using a specific hammerhead ribozyme (RZ).Methods The hammerhead ribozyme expression vector pcDNA-hAR-RZ, specific to AR mRNA, was constructed and transfected into the prostate cancer cell line LNCaP by using lipofectamine. Androgen receptor expression was measured by RT-PCR and immunohistochemical methods. Cellular proliferation activities were assayed using the tetrazolium bromide colorimetry method; cell cycle changes were observed by flow cytometry; and cell apoptosis was detected by the TdT-mediated dUTP-biotin nick end labeling method. Results One to seven days after transfection with the ribozyme expression vector, AR mRNA expression at molecular and protein levels in LNCaP cells decreased by 32.6%-40.7% (P<0.05) and 21.0%-87.64% (P<0.05) respectively, and cell proliferation was inhibited by 18.28%-35.34% (P<0.05). Meanwhile, the cell cycle was arrested at the G2/M stage, and apoptotic morphological changes occurred with an apoptosis rate of 25.17% (P<0.01).Conclusion Ribozyme specific against AR mRNA is capable of inhibiting the expression AR and inducing the apoptosis in prostate cancer cells.

  3. Preparation of anti-mouse caspase-12 mRNA hammerhead ribozyme and identification of its activity in vitro

    Institute of Scientific and Technical Information of China (English)

    Shan Jiang; Qing Xie; Wei Zhang; Xia-Qiu Zhou; You-Xin Jin

    2005-01-01

    AIM: To prepare and identify specific anti-mouse caspase12 hammerhead ribozymes in vitro, in order to select a more effective ribozyme against mouse caspase-12 as a potential tool to rescue cells from endoplasmic reticulum stress induced apoptosis.METHODS: Two hammerhead ribozymes directed separately against 138 and 218 site of nucleotide of mouse caspase-12 mRNA were designed by computer software,and their DNA sequences were synthesized. The synthesized ribozymes were cloned into an eukaryotic expression vector-neorpBSKU6 and embedded in U6 SnRNA context for further study. Mouse caspase-12 gene segment was cloned into PGEM-T vector under the control of T7 RNA polymerase promoter (containing gene sequence from positions nt 41 to nt 894) as target. In vitro transcription both the ribozymes and target utilize T7 promoter. The target was labeled with [α-32P]UTP, while ribozymes were not labeled. After gel purification the RNAs were dissolved in RNase free water. Ribozyme and target were incubated for 90 min at 37 ℃ in reaction buffer (40 mmol/L Tris-HCL,pH 7.5, 10 mmol/L Mg2+). Molar ratio of ribozyme vs target was 30:1. Samples were analyzed on 6% PAGE (containing 8 mol/L urea).RESULTS: Both caspase-12 and ribozyme gene sequences were successfully cloned into expression vector confirmed by sequencing. Ribozymes and caspase-12 mRNA were obtained by in vitro transcription. Cleavage experiment showed that in a physiological similar condition (37 ℃,pH 7.5), Rz138 and Rz218 both cleaved targets at predicted sites, for Rz138 the cleavage efficiency was about 100%,for Rz218 the value was 36.66%.CONCLUSION: Rz138 prepared in vitro can site specific cleave mouse caspase-12 mRNA with an excellent efficiency. It shows a potential to suppress the expression of caspase-12 in vivo, thus provided a new way to protect cells from ER stress induced apoptosis.

  4. Inhibition of Hepatitis B Virus Replication and Expression in Vitro and in Vivo by the Hammerhead Ribozymes Targeted Different Sites

    Institute of Scientific and Technical Information of China (English)

    Wei; Dai; Rong; Zhou; Hong; Yu; Xiao-juan; Li

    2012-01-01

    Objective To develop an effective and specific medicine targeting hepatitis B virus(HBV) pregenome. Based on the identified accessible target sites for hammerhead ribozyme in our previous researches, a recombinant hepatitis delta virus(HDV) ribozyme was chosen and used to demonstrate the effective cleavage in vitro and in vivo. Methods Three hammerhead ribozymes for potential target sites(S, X and C genes) and co-expression plasmid(pTr-dB, pTdδ-dB, pTrX-dB and pTrC-dB) as well as four HDV-ribozyme chimera constructs with HBV(pTdXX, pTdXC, pTdSX and pTdSC) were severally chosen to validate the inhibition of the replication and expression of HBV. The co-expression plasmids(pTdδ and pTr-Db) in physiological saline were hydrodynamically injected to mice by tail vein. Results Compared with the group injected with pTr-dB in Huh-7 cell, hepatitis B surface antigen(HBsAg) was reduced by 31% in the group injected with pTdδ-dB, by 54%, 26%, 72% and 97% in the group injected with recombinant-ribozymes pTdSX, pTdSC, pTdXC and pTdXX, respectively. The inhibiting effects of endogenous ribozymes RzX and RzC on the HBsAg expression were 66% and 57%, respectively. Compared with the positive control, the amount of HBsAg was decreased in mice injected with pTdXX through tail vein by 88% and 96% on the second day and the third day, respectively. HBsAg was undetectable on the 6th day and could not primitively be detected on the 9th day in the sera from all mice. HBV DNA was not detected in the sera of BALB/c mice injected with pTdXX-dB, pTrX-dB or replicating-defective plasmid pHBV, while HBV DNA replication in control group could be detected on the 6th day. While HBcAg could not be detected in liver tissues of mice injected with plasmid pTdXX-dB on the 3rd day. Conclusions Encoding regions of HBV S, C and X gene were the effective cleavage sites for hammerhead ribozyme in vitro and in vivo, which provides basis for further construction of therapeutic recombinant HDV and the

  5. EXPLORATION OF SCHISTOSOMA MANSONI HAMMERHEAD RIBOZYME CATALYSIS AND STRUCTURE: TOWARDS DIRECT OBSERVATION OF CLEAVAGE AND LIGATION, AND A 1.55 Å FULL-LENGTH MG2+-BOUND CRYSTAL STRUCTURE

    OpenAIRE

    Anderson, Michael

    2012-01-01

    As a relatively simple and well-studied molecule, the hammerhead ribozyme is an ideal system to study RNA catalysis and structure. A deeper understanding of the hammerhead catalytic mechanism and the role of divalent ions in catalysis lends support to the exploration of more complex RNA machinery such as the ribosome, and ultimately may assist in the design of new medical therapies. Kinetic study of the hammerhead ribozyme to date has largely derived from bulk assays monitoring millions of ...

  6. Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes

    Directory of Open Access Journals (Sweden)

    Priya Mishra

    2016-06-01

    Full Text Available The chikungunya virus (CHIKV is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates with the introduction of its major vector, Aedes albopictus. CHIKV causes a disease frequently misdiagnosed as dengue fever, with potentially life-threatening symptoms that can result in a longer-term debilitating arthritis. The increasing risk of spread from endemic regions via human travel and commerce and the current absence of a vaccine put a significant proportion of the world population at risk for this disease. In this study we designed and tested hammerhead ribozymes (hRzs targeting CHIKV structural protein genes of the RNA genome as potential antivirals both at the cellular and in vivo level. We employed the CHIKV strain 181/25, which exhibits similar infectivity rates in both Vero cell cultures and mosquitoes. Virus suppression assay performed on transformed Vero cell clones of all seven hRzs demonstrated that all are effective at inhibiting CHIKV in Vero cells, with hRz #9 and #14 being the most effective. piggyBac transformation vectors were constructed using the Ae. aegypti t-RNAval Pol III promoted hRz #9 and #14 effector genes to establish a total of nine unique transgenic Higgs White Eye (HWE Ae. aegypti lines. Following confirmation of transgene expression by real-time polymerase chain reaction (RT-PCR, comparative TCID50-IFA analysis, in situ Immuno-fluorescent Assays (IFA and analysis of salivary CHIKV titers demonstrated effective suppression of virus replication at 7 dpi in heterozygous females of each of these transgenic lines compared with control HWE mosquitoes. This report provides a proof that appropriately engineered hRzs are powerful antiviral effector genes suitable for population replacement strategies

  7. Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes

    Science.gov (United States)

    Mishra, Priya; Furey, Colleen; Balaraman, Velmurugan; Fraser, Malcolm J.

    2016-01-01

    The chikungunya virus (CHIKV) is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates with the introduction of its major vector, Aedes albopictus. CHIKV causes a disease frequently misdiagnosed as dengue fever, with potentially life-threatening symptoms that can result in a longer-term debilitating arthritis. The increasing risk of spread from endemic regions via human travel and commerce and the current absence of a vaccine put a significant proportion of the world population at risk for this disease. In this study we designed and tested hammerhead ribozymes (hRzs) targeting CHIKV structural protein genes of the RNA genome as potential antivirals both at the cellular and in vivo level. We employed the CHIKV strain 181/25, which exhibits similar infectivity rates in both Vero cell cultures and mosquitoes. Virus suppression assay performed on transformed Vero cell clones of all seven hRzs demonstrated that all are effective at inhibiting CHIKV in Vero cells, with hRz #9 and #14 being the most effective. piggyBac transformation vectors were constructed using the Ae. aegypti t-RNAval Pol III promoted hRz #9 and #14 effector genes to establish a total of nine unique transgenic Higgs White Eye (HWE) Ae. aegypti lines. Following confirmation of transgene expression by real-time polymerase chain reaction (RT-PCR), comparative TCID50-IFA analysis, in situ Immuno-fluorescent Assays (IFA) and analysis of salivary CHIKV titers demonstrated effective suppression of virus replication at 7 dpi in heterozygous females of each of these transgenic lines compared with control HWE mosquitoes. This report provides a proof that appropriately engineered hRzs are powerful antiviral effector genes suitable for population replacement strategies PMID:27294950

  8. In Vitro Biological Activity of Anti-C Ⅱ TA Hammerhead Ribozyme--A Novel Approach for Autoimmune Diseases

    Institute of Scientific and Technical Information of China (English)

    刘芳; 邹萍; 郭荣; 陆华中; 范华骅

    2003-01-01

    This study investigated the feasibility of using an hammerhead ribozyme against C Ⅱ TA, a major regulator of MHC Ⅱ antigens, to repress the expression of MHC Ⅱ molecules on Hela cells. A hammerhead ribozyme (Rz464) specific to 463-465 GUC triplet of C Ⅱ TA and its target gene were transcribed, then mixed up and incubated in vitro. The cleavage products were analyzed by PAGE and silver-staining. Rz464 was then inserted into the pIRES2-EGFP vector (pRz464). Stable transfectants of Hela with pRz464 were tested for class Ⅱ MHC induction by recombinant human interferon-gamma (IFN-γ). mRNA of C Ⅱ TA was measured by RT-PCR. Our results showed that Rz464 could exclusively cleave C Ⅱ TA RNA. When induced with IFN-γ, the expression of HLA-DR, -DP, -DQ on pRz464+ Hela was induced, and the mRNA content of C ⅡTA decreased too. It is concluded that Rz464 could inhibit C Ⅱ TA and thus the family of genes was regulated by C Ⅱ TA:MHC Ⅱ molecules. These results provided insight into the future application of Rz464 as a new nucleic acid drug against auto-immune diseases.

  9. Mechanistic studies of copper(II)-aminoglycoside mediated DNA damage and magnesium catalyzed nuclease activity of hammerhead ribozyme

    Science.gov (United States)

    Patwardhan, Anjali A.

    The antibacterial activity of aminoglycosides stems from their high affinity binding to the 16S rRNA in bacteria resulting in inhibition of protein synthesis. Used to treat acute bacterial infections these antibiotics have limited applications due to their high dosage requirements and the emergence of resistant strains. We have synthesized and characterized Cu(II) derivatives of the aminoglycosides, kanamycin A, tobramycin, neamine, kanamycin B, neomycin B, and paromomycin. The first three exhibit preferential and tight binding to Cu(II) as against neomycin B and kanamycin B and paromomycin. EPR of frozen solutions and UV-visible spectroscopy suggest a change in geometry around the Cu(II) but the stabilities of the complexes in water differ. These copper derivatives efficiently cleave plasmid DNA at micromolar concentrations (hydrolytic) and at nanomolar concentrations in the presence co-reactants like hydrogen peroxide or ascorbic acid. Hydrolysis is multi turnover and exhibits Michelis-Menten kinetics with enzyme-like behavior whereas oxidative cleavage is highly specific with C-4' H abstraction resulting in characteristic base propenal and nucleotide base products. Hydroxyl radicals generated are copper based and are generated in close proximity of the substrate. Hammerhead ribozymes are selectively hydrolyzed in the presence of divalent ions with Mg2+ being the metal ion of choice in vivo . Our studies with complex ions like cobalt hexaammine and fac-triamminetriaquochromium(III) establish outer sphere interactions of Mg2+ with the hammerhead in the catalytic site. There are two sets of sites, one structural and one catalytic. Complex ions in the catalytic site and divalent ions in the structural site result in a slow but active hammerhead ribozyme suggesting that the complex ions are not inhibitory, contrary to what was suggested previously.

  10. Efficient hammerhead ribozyme-mediated cleavage of the structured hepatitis B virus encapsidation signal in vitro and in cell extracts, but not in intact cells.

    Science.gov (United States)

    Beck, J; Nassal, M

    1995-01-01

    Hepatitis B virus (HBV), the causative agent of B-type hepatitis in man, is a small enveloped DNA virus that replicates through reverse transcription of an RNA intermediate, the terminally redundant RNA pregenome. An essential highly conserved cis-element present twice on this RNA is the encapsidation signal epsilon, a stem-loop structure that is critical for pregenome packaging and reverse transcription. Epsilon is hence an attractive target for antiviral therapy. Its structure, however, is a potential obstacle to antivirals whose action depends on hybridization, e.g. ribozymes. Here we demonstrate effective in vitro cleavage inside epsilon by hammerhead ribozymes containing flanking sequences complementary to an adjacent less structured region. Upon co-transfection with a HBV expression construct corresponding ribozymes embedded in a U6 snRNA context led to a significant, though modest, reduction in the steady-state level of HBV pregenomes. Inactive ribozyme mutants revealed that antisense effects contributed substantially to this reduction, however, efficient epsilon cleavage by the intracellularly expressed ribozymes was observed in Mg(2+)-supplemented cell lysates. Artificial HBV pregenomes carrying the ribozymes in cis and model RNAs lacking all HBV sequences except epsilon exhibited essentially the same behaviour. Hence, neither the absence of co-localization of ribozyme and target nor a viral component, but rather a cellular factor(s), is responsible for the strikingly different ribozyme activities inside cells and in cellular extracts. Images PMID:8559651

  11. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing

    OpenAIRE

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-01-01

    Adenosine-to-inosine RNA editing is an endogenous mechanism for regulating various biological processes. A method for site-specific and editing-state–dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. In this paper, we describe a strategy for constructing a trans-acting hammerhead ribozyme that specifically cleaves target RNA dependent on the editing state at the specific site.

  12. An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.

    Science.gov (United States)

    Chartrand, P; Harvey, S C; Ferbeyre, G; Usman, N; Cedergren, R

    1995-10-25

    A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oligomers shows that, although the all-deoxyribonucleotide oligomer is less efficient in catalysis, the DNA/substrate complex shares many of the properties of the all-RNA hammerhead domain such as multiple turnover kinetics and dependence on Mg2+ concentration. On the other hand, the values of kinetic parameters distinguish the DNA oligomer from the all-RNA oligomer. In addition, an analog of the oligomer having a single ribonucleotide in a strongly conserved position of the hammerhead domain is associated with more efficient catalysis than the all-RNA oligomer.

  13. Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

    Science.gov (United States)

    Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

    2014-09-01

    The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential

  14. REVERSION OF MULTIDRUG RESISTANCE IN THE P-GLYCOPROTEIN POSITIVE BREAST CANCER CELL LINE(MCF-7/ADR) BY INTRODUCTION OF HAMMERHEAD RIBOZYME

    Institute of Scientific and Technical Information of China (English)

    袁亚维; 张积仁; K.J.Scanlon; 陆长德; 祁国荣

    1998-01-01

    A hammerhead ribozyme which slte-specifically cleaved the GUC position in codon 880 of the mdrl mRNA was designed. The target site was chosen between the two ATP binding sites, which may be impottant for the function of the P-C-p as an ATPodependent pump. A DNA sequence encoding the riboxyme gene was then incorporated into a eukaryotic expression vector (pH 0 Apt-1 neo) and transfeeted into the breast cancer cell line MCF-7/Adr, which is resistant to adrlamycin and expresses the MDR phenmype. The ribozyme was stably expressed in the cell line by the RNA dot blotting assay. The result of Northern blot assay showed that the expressed ribozyme could decrease the level of mdrl mRNA expression by 83.5%; and the expressed ribozyme could inhiblte the formation of P-glycoprotein detected by immuno-cytochemistry assay and could reduce the cell''s resistance to adrimycin; this means that the resistant cells were 1 000-fold mcre resistant than the parental cell line(MCF-7), whereas those cell clones that showed ribozyme expression were only 6-fold more resistant than the parental cell line. These results show that a potentially useful tool is at hand which may inactivate MDR1 mRNA and revert the multidrug resistance phenotype.

  15. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing.

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-03-01

    Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state-dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites.

  16. Replication of avocado sunblotch viroid: evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing.

    Science.gov (United States)

    Daròs, J A; Marcos, J F; Hernández, C; Flores, R

    1994-12-20

    The structure of a series of RNAs extracted from avocado infected by the 247-nt avocado sunblotch viroid (ASBVd) was investigated. The identification of multistranded complexes containing circular ASBVd RNAs of (+) and (-) polarity suggests that replication of ASBVd proceeds through a symmetric pathway with two rolling circles where these two circular RNAs are the templates. This is in contrast to the replication of potato spindle tuber viroid and probably of most of its related viroids, which proceeds via an asymmetric pathway where circular (+)-strand and linear multimeric (-)-strand RNAs are the two templates. Linear (+) and (-) ASBVd RNAs of subgenomic length (137 nt and about 148 nt, respectively) and one linear (+)-strand ASBVd RNA of supragenomic length (383-384 nt) were also found in viroid-infected tissue. The two linear (+)-strand RNAs have the same 5'- and 3'-terminal sequences, with the supragenomic species being a fusion product of the monomeric and subgenomic (+)-strand ASBVd RNAs. The 3' termini of these two (+)-strand molecules, which at least in the subgenomic RNA has an extra nontemplate cytidylate residue, could represent sites of either premature termination of the (+)-strands or specific initiation of the (-)-strands. The 5' termini of sub- and supragenomic (+)-strand and the 5' terminus of the subgenomic (-)-strand ASBVd RNA are identical to those produced in the in vitro self-cleavage reactions of (+) and (-) dimeric ASBVd RNAs, respectively. These observations strongly suggest that the hammerhead structures which mediate the in vitro self-cleavage reactions are also operative in vivo.

  17. Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

    Directory of Open Access Journals (Sweden)

    Eliza Wyszko

    Full Text Available With the discovery of small non-coding RNA (ncRNA molecules as regulators for cellular processes, it became intriguing to develop technologies by which these regulators can be applied in molecular biology and molecular medicine. The application of ncRNAs has significantly increased our knowledge about the regulation and functions of a number of proteins in the cell. It is surprising that similar successes in applying these small ncRNAs in biotechnology and molecular medicine have so far been very limited. The reasons for these observations may lie in the high complexity in which these RNA regulators function in the cells and problems with their delivery, stability and specificity. Recently, we have described mirror-image hammerhead ribozymes and DNAzymes (Spiegelzymes® which can sequence-specifically hydrolyse mirror-image nucleic acids, such as our mirror-image aptamers (Spiegelmers discovered earlier. In this paper, we show for the first time that Spiegelzymes are capable of recognising complementary enantiomeric substrates (D-nucleic acids, and that they efficiently hydrolyse them at submillimolar magnesium concentrations and at physiologically relevant conditions. The Spiegelzymes are very stable in human sera, and do not require any protein factors for their function. They have the additional advantages of being non-toxic and non-immunogenic. The Spiegelzymes can be used for RNA silencing and also as therapeutic and diagnostic tools in medicine. We performed extensive three-dimensional molecular modelling experiments with mirror-image hammerhead ribozymes and DNAzymes interacting with D-RNA targets. We propose a model in which L/D-double helix structures can be formed by natural Watson-Crick base pairs, but where the nucleosides of one of the two strands will occur in an anticlinal conformation. Interestingly enough, the duplexes (L-RNA/D-RNA and L-DNA/D-RNA in these models can show either right- or left-handedness. This is a very new

  18. 蓝氏贾第鞭毛虫alpha-8贾第素特异性锤头状核酶-GCV重组载体的构建%Construction of GCV-Specific Hammerhead Ribozyme Recombinant Vector of Alpha-8 Giardin in Giardia lamblia

    Institute of Scientific and Technical Information of China (English)

    魏超君; 卢思奇; 曹利静; 田喜凤

    2011-01-01

    Objective To construct a GCV- ribozyme recombinant vectors of a-8 giardin in Giardia lamblia. Methods The secondary structure of a-8 giardin mRNA (GenBank Accession No. AY781323) was analyzed with the RNA draw software. According to the proportion of G: C and principles of designing hammerhead ribozyme, suitable ribozyme cleavage points were chosen. A specific antisense-hammerhead ribozyme (H8)was designed and synthesized. The ribozyme was cloned into Giardia canis virus (GCV) vector to construct a recombinant viral vector-pGCV634/H8/1423. The vector was linearized and transcripted into the trophozoites of G. lamblia by electroporation method. The a-8 giardin mRNA level of the transfectants and normal trophozoites were analyzed 24 h after electroporation by RT-PCR. Results The recombinant vector of GCV-specific hammerhead ribozyme of a-8 giardin in Giardia lamblia (pGCV634/H8/ 1423) was constructed. RT-PCR assays showed the ribozyme (H8) mRNA can be detected 24h after transfection and a-8 giardin mRNA was cleaved effectively by ribozyme (H8) introcellularly. Conclusion pGCV634/H8/1423 can transfect Giardia trophozoites and cleave mRNA of a-8 giardin intracellularly.%目的 构建蓝氏贾第鞭毛虫alpha-8贾第素(α-8 giardin)特异性锤头状核酶-GCV重组载体. 方法 采用RNA draw软件对蓝氏贾第鞭毛虫α-8贾第素基因序列(GenBank登录号为AY781323)的二级结构进行模拟分析,按照G:C比例和锤头状核酶设计原则,选取合适的核酶切割靶点,设计特异性锤头状核酶(H8)序列,并将其与犬贾第虫病毒(GCV)连接,获得α-8贾第素特异性锤头状核酶-GCV重组载体(pGCV634/H8/1423).将载体线性化体外转录产物电击转染至贾第虫滋养体细胞内.提取转染后24 h的各组虫体总RNA,并以其为模板采用RT-PCR验证转染效果及对靶mRNA的切割效果. 结果 成功设计、合成了蓝氏贾第鞭毛虫α-8贾第素mRNA锤头状核酶序列(H8),将其与犬贾第虫病毒载

  19. CONSTRUCTION AND CHARACTERIZATION OF GCV RECOMBINANT VECTOR-MEDIATED HAMMERHEAD RIBOZYME FOR GIARDIA LAMBLIA PPDK%蓝氏贾第鞭毛虫PPDK特异性锤头状核酶-GCV重组载体的构建及鉴定

    Institute of Scientific and Technical Information of China (English)

    曹利静; 冯宪敏; 卢思奇; 张西臣; 王凤云

    2008-01-01

    丙酮酸磷酸双激酶(Pymvate phosphate dikinase,PPDK)可能是蓝氏贾第鞭毛虫能量代谢中具有催化作用的关键酶桩一.为了进一步探讨该酶在贾第虫能量代谢中的作用,本文采用RNA draw软件分析贾第虫编码PPDK的基因序列并设计特异性反义锤头状核酶(Hammerheade ribozyme),克隆该核酶序列并与犬贾第虫病毒(GCV)连接,构建了载有特异性锤头状核酶的贾第虫病毒重组载体pGCV634/H5/2174.该载体经线性化处理后进行体外转录,转录产物以电击方式转染对数生长期的贾第虫滋养体.提取转染后24 h虫体总RNA,并以其为模板进行RT-PcR验证转染效果和对靶mRNA的切割效果.结果初步证实了该载体对虫体细胞内编码PPDK的mRNA具有切割作用.

  20. Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.

    Science.gov (United States)

    Ferbeyre, G; Bourdeau, V; Pageau, M; Miramontes, P; Cedergren, R

    2000-07-01

    Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes from the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster.

  1. Ultrasensitive monitoring of ribozyme cleavage product using molecular-beacon-ligation system

    Institute of Scientific and Technical Information of China (English)

    MENG XiangXian; TANG ZhiWen; WANG KeMin; TAN WeiHong; YANG XiaoHai; LI Jun; GUO QiuPing

    2007-01-01

    This paper reports a new approach to detect ribozyme cleavage product based on the molecular- beacon-ligation system. The molecular beacon, designed in such a way that one-half of its loop is complementary to ribozyme cleavage product, is used to monitor ligation process of RNA/DNA complex in a homogeneous solution and to convert directly cleavage product information into fluorescence signal. The method need not label ribozyme and ribozyme substrate, which is fast, simple and ultrasensitive for detection of cleavage product. Detection limit of the assay is 0.05 nmol/L. The cleavage product of hammerhead ribozyme against hepatitis C virus RNA (HCV-RNA) was detected perfectly based on this assay. Owing to its ultrasensitivity, excellent specificity, convenience and fidelity, this method might hold out great promise in ribozyme reaction and ribozyme gene therapy.

  2. 碱基切除修复基因HOGG1特异性锤头状核酶表达载体的构建及其功能的初步研究%Constructing the Eukaryotic Expression Vector to Study Preliminarily the Functions of Hammerhead Ribozyme Targeting Base Excision Repair Gene HOGG1

    Institute of Scientific and Technical Information of China (English)

    张遵真; 张勤; 吴媚

    2006-01-01

    Objective Adriamycin is widely used as an effective anti-tumor drug clinically treating a number of human cancers, but the effect of adriamycin is limited by drug resistance. The various kinds of investigations indicated that the anti-tumor activity of adriamycin resulted from drug-induced free radical formation. The free radicals could lead to oxidative DNA damage, and the lesion would be repaired by base excision repair (BER) pathway. Human 8-oxoguanine DNA glycosylase 1 (HOGG1) is a key enzyme on BER pathway. To study the influence and biological mechanism of the HOGG1 to adriamycin drug-sensitivity, the eukaryotic expression vector with gene of hammerhead ribozyme targeting HOGG1 mRNA would be constructed and identified, and then the change of drug-sensitivity in lung cancer A549 cells would be investigated. Methods According to computer design, two specific restriction site BamHⅠ and EcoRⅠ were added to both ends of the ribozyme gene, then the modified ribozyme gene was synthesized and cloned into the eukaryotic expression vector pcDNA3.1(+). The positive recombinants were screened by ampicillin resistance, and plasmids were extracted from the positive recombinants and digested by BamH Ⅰ and EcoR Ⅰ, and then were analyzed by agarose gel electrophoresis and DNA sequencing. The recombinants were transiently transfected into A549 cells. The positive recombinants were identified by reverse transcription-polymerase chain reaction (RT-PCR) targeting to NEO gene, which was a neomycin resistance gene for selection of stable cell lines and only existed in vectors. The changes of HOGG1 mRNA in A549 cells were detected by RT-PCR. Then the cellular sensitivity to adriamycin was tested by comparison between untransfected cells and transfected cells by MTT assay. The adriamycin-induced DNA damage was investigated by comet assay or single cell gel electrophoresis (SCGE) between untransfected and transfected cells. Results The recombinants containing the ribozyme gene

  3. Hairpin Ribozyme Genes Curtail Alcohol Drinking: from Rational Design to in vivo Effects in the Rat.

    Science.gov (United States)

    Sapag, Amalia; Irrazábal, Thergiory; Lobos-González, Lorena; Muñoz-Brauning, Carlos R; Quintanilla, María Elena; Tampier, Lutske

    2016-07-12

    Ribozyme genes were designed to reduce voluntary alcohol drinking in a rat model of alcohol dependence. Acetaldehyde generated from alcohol in the liver is metabolized by the mitochondrial aldehyde dehydrogenase (ALDH2) such that diminishing ALDH2 activity leads to the aversive effects of blood acetaldehyde upon alcohol intake. A stepwise approach was followed to design genes encoding ribozymes targeted to the rat ALDH2 mRNA. In vitro studies of accessibility to oligonucleotides identified suitable target sites in the mRNA, one of which fulfilled hammerhead and hairpin ribozyme requirements (CGGUC). Ribozyme genes delivered in plasmid constructs were tested in rat cells in culture. While the hairpin ribozyme reduced ALDH2 activity 56% by cleavage and blockade (P < 0.0001), the hammerhead ribozyme elicited minor effects by blockade. The hairpin ribozyme was tested in vivo by adenoviral gene delivery to UChB alcohol drinker rats. Ethanol intake was curtailed 47% for 34 days (P < 0.0001), while blood acetaldehyde more than doubled upon ethanol administration and ALDH2 activity dropped 25% in liver homogenates, not affecting other ALDH isoforms. Thus, hairpin ribozymes targeted to 16 nt in the ALDH2 mRNA provide durable and specific effects in vivo, representing an improvement on previous work and encouraging development of gene therapy for alcoholism.

  4. Design of a ribozyme targeting human telomerase reverse transcriptase and cloning of it's gene

    Institute of Scientific and Technical Information of China (English)

    Zhi-Ming Hap; Jin-Yan Luo; Jin Cheng; Quan-Yin Wang; Guang-Xiao Yang

    2003-01-01

    AIM: To design a hammerhead ribozyme targeting humantelomerase reverse transcriptase (hTERT) and clone it's genefor future use in the study of tumor gene therapy.METHODS: Using the software RNAstructure, the secondarystructure of hTERT mRNA was predicted and the cleavagesite of ribozyme was selected. A hammerhead ribozymetargeting this site was designed and bimolecular fold betweenthe ribozyme and hTERT was predicted. The DNA encodingthe ribozyme was synthesized and cloned into pGEMEX-1and the sequence of the ribozyme gene was confirmed byDNA sequencing.RESULTS: Triplet GUC at 1742 of hTERT mRNA was chosenas the cleavage site of the ribozyme. The designed ribozymewas comprised of 22nt catalytic core and 17nt flankingsequence. Computer-aided prediction suggested that theribozyme and hTERT mRNA could cofold into a properconformation. Endonuclease restriction and DNA sequencingconfirmed the correct insertion of the ribozyme gene intothe vector pGEMEX-1.CONCLUSION: This fundamental work of successfuldesigning and cloning of an anti-hTERT hammerheadribozyme has paved the way for further study of inhibitingtumor cell growth by cleaving hTERT mRNA with ribozyme.

  5. Robust suppression of HIV replication by intracellularly expressed reverse transcriptase aptamers is independent of ribozyme processing.

    Science.gov (United States)

    Lange, Margaret J; Sharma, Tarun K; Whatley, Angela S; Landon, Linda A; Tempesta, Michael A; Johnson, Marc C; Burke, Donald H

    2012-12-01

    RNA aptamers that bind human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) also inhibit viral replication, making them attractive as therapeutic candidates and potential tools for dissecting viral pathogenesis. However, it is not well understood how aptamer-expression context and cellular RNA pathways govern aptamer accumulation and net antiviral bioactivity. Using a previously-described expression cassette in which aptamers were flanked by two "minimal core" hammerhead ribozymes, we observed only weak suppression of pseudotyped HIV. To evaluate the importance of the minimal ribozymes, we replaced them with extended, tertiary-stabilized hammerhead ribozymes with enhanced self-cleavage activity, in addition to noncleaving ribozymes with active site mutations. Both the active and inactive versions of the extended hammerhead ribozymes increased inhibition of pseudotyped virus, indicating that processing is not necessary for bioactivity. Clonal stable cell lines expressing aptamers from these modified constructs strongly suppressed infectious virus, and were more effective than minimal ribozymes at high viral multiplicity of infection (MOI). Tertiary stabilization greatly increased aptamer accumulation in viral and subcellular compartments, again regardless of self-cleavage capability. We therefore propose that the increased accumulation is responsible for increased suppression, that the bioactive form of the aptamer is one of the uncleaved or partially cleaved transcripts, and that tertiary stabilization increases transcript stability by reducing exonuclease degradation.

  6. Is your ribozyme design really correct?: A proposal of simple single turnover competition assay to evaluate ribozymes.

    Science.gov (United States)

    Tanaka, T; Inui, O; Dohi, N; Okada, N; Okada, H; Kikuchi, Y

    2001-07-01

    Today, many nucleic acid enzymes are used in gene therapy and gene regulations. However, no simple assay methods to evaluate enzymatic activities, with which we judge the enzyme design, have been reported. Here, we propose a new simple competition assay for nucleic acid enzymes of different types to evaluate the cleaving efficiency of a target RNA molecule, of which the recognition sites are different but overlapped. Two nucleic acid enzymes were added to one tube to make a competition of these two enzymes for one substrate. The assay was used on two ribozymes, hammerhead ribozyme and hairpin ribozyme, and a DNA-enzyme. We found that this assay method is capable of application to those enzymes, as a powerful tool for the selection and designing of RNA-cleaving enzymes.

  7. Group I intron ribozymes

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2012-01-01

    Group I intron ribozymes constitute one of the main classes of ribozymes and have been a particularly important model in the discovery of key concepts in RNA biology as well as in the development of new methods. Compared to other ribozyme classes, group I intron ribozymes display considerable......, the intronic products of these pathways have the potential to integrate into targets and to form various types of circular RNA molecules. Thus, group I intron ribozymes and associated elements found within group I introns is a rich source of biological phenomena. This chapter provides a strategy and protocols...... for initial characterization of new group I intron ribozymes....

  8. Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets.

    Science.gov (United States)

    Rojas, A A; Vazquez-Tello, A; Ferbeyre, G; Venanzetti, F; Bachmann, L; Paquin, B; Sbordoni, V; Cedergren, R

    2000-10-15

    This work reports the discovery and functional characterization of catalytically active hammerhead motifs within satellite DNA of the pDo500 family from several DOLICHOPODA: cave cricket species. We show that in vitro transcribed RNA of some members of this satellite DNA family do self-cleave in vitro. This self-cleavage activity is correlated with the efficient in vivo processing of long primary transcripts into monomer-sized RNA. The high sequence conservation of the satellite pDo500 DNA family among genetically isolated DOLICHOPODA: schiavazzii populations, as well as other DOLICHOPODA: species, along with the fact that satellite members are actively transcribed in vivo suggests that the hammerhead-encoding satellite transcripts are under selective pressure, perhaps because they fulfil an important physiological role or function. Remarkably, this is the third example of hammerhead ribozyme structures associated with transcribed repetitive DNA sequences from animals. The possibility that such an association may not be purely coincidental is discussed.

  9. Metal ions: supporting actors in the playbook of small ribozymes.

    Science.gov (United States)

    Johnson-Buck, Alexander E; McDowell, Sarah E; Walter, Nils G

    2011-01-01

    Since the 1980s, several small RNA motifs capable of chemical catalysis have been discovered. These small ribozymes, composed of between approximately 40 and 200 nucleotides, have been found to play vital roles in the replication of subviral and viral pathogens, as well as in gene regulation in prokaryotes, and have recently been discovered in noncoding eukaryotic RNAs. All of the known natural small ribozymes - the hairpin, hammerhead, hepatitis delta virus, Varkud satellite, and glmS ribozymes--catalyze the same self-cleavage reaction as RNase A, resulting in two products, one bearing a 2'-3' cyclic phosphate and the other a 5'-hydroxyl group. Although originally thought to be obligate metalloenzymes like the group I and II self-splicing introns, the small ribozymes are now known to support catalysis in a wide variety of cations that appear to be only indirectly involved in catalysis. Nevertheless, under physiologic conditions, metal ions are essential for the proper folding and function of the small ribozymes, the most effective of these being magnesium. Metal ions contribute to catalysis in the small ribozymes primarily by stabilizing the catalytically active conformation, but in some cases also by activating RNA functional groups for catalysis, directly participating in catalytic acid-base chemistry, and perhaps by neutralizing the developing negative charge of the transition state. Although interactions between the small ribozymes and cations are relatively nonspecific, ribozyme activity is quite sensitive to the types and concentrations of metal ions present in solution, suggesting a close evolutionary relationship between cellular metal ion homeostasis and cation requirements of catalytic RNAs, and perhaps RNA in general.

  10. Inhibiting Apoptosis of CTLL-2 Cells to Enhance Their GVL Effects via Anti-Fas Ribozyme

    Institute of Scientific and Technical Information of China (English)

    Min ZHANG; Fang LIU; Lin-Bo LIU; Yong YOU; Zhi-Chao CHEN; Ping ZOU

    2004-01-01

    To investigate the inhibition role of anti-Fas hammerhead ribozyme on fas expression and Fas-mediated apoptosis of CTL cell line CTLL-2 cells,the cDNA of an anti-Fas hammerhead ribozyme was synthesized,its expression plasmid was constructed and transfected into CTLL-2 cells by electroporation.fas expression of CTLL-2 cells was detected by RT-PCR and Western blot.CTLL-2 cell viability was measured using MTT assay when co-cultured with mouse T cell leukemia cell line EL4 cells that highly expressed Fas ligand(FasL).Meanwhile,caspase-3 proteolytic activity was detected,and cell apoptosis was measured by flow cytometry and Hochest-PI double staining.Killing activity of CTLL-2 cells was detected by lactate dehydrogenase(LDH)releasing assay in vitro.Results showed that the expression of both Fas mRNA and protein in CTLL-2 cells were decreased after transfection of anti-Fas ribozyme.Compared with mocktransfected group and mutant ribozyme-transfected group,viability of CTLL-2 cells co-cultured with EL4 cells was increased significantly and cells killing activity was enhanced after transfected with anti-Fas ribozyme,while the caspase-3 activity and apoptosis rate was significantly decreased.The results demonstrated anti-Fas ribozyme could efficiently cleave Fas and inhibit Fas-mediated apoptosis of CTLL-2 cells to improve their viability.Our study made a basis for enhancing CTLL-2 cells anti-leukemia effect in DLI.

  11. Ribozyme modulation of lipopolysaccharide-induced tumor necrosis factor-alpha production by peritoneal cells in vitro and in vivo.

    Science.gov (United States)

    Sioud, M

    1996-05-01

    We have utilized synthetic ribozymes to modulate the lipopolysaccharide (LPS)-induced production of tumor necrosis factor-alpha (TNF-alpha) by peritoneal cells. Two hammerhead ribozymes (mRz1 and mRz2) were prepared by transcription in vitro and their activities in vitro and in vivo were investigated. Both ribozymes cleaved their RNA target with an apparent turnover number (kcat) of 2 min(-1), and inhibited TNF-alpha gene expression in vitro by 50% and 70%, respectively. When mRz1 and mRz2, entrapped in liposomes, were delivered into mice by intraperitoneal injection, they inhibited LPS-induced TNF-alpha gene expression in vivo with mRz2 being the most effective. This enhanced activity could result from the facilitation of catalysis by cellular endogenous proteins, since they specifically bind to mRz2 as compared to mRz1. Furthermore, a significant mRz2 activity can be recovered from peritoneal cells 2 days post-administration in vivo. The anti-TNF-alpha ribozyme treatment in vivo resulted in a more significant reduction of LPS-induced IFN-gamma protein secretion compared to IL-10. In contrast to this pleiotropic effect, the anti-TNF-alpha ribozyme treatment did not affect the heterogenous expression of Fas ligand by peritoneal cells, indicating the specificity of the treatment. Taken together, the present data indicate that the biological effects of TNF-alpha can be modulated by ribozymes. In addition, the data suggest that ribozymes can be administered in a drug-like manner, and therefore indicate their potential in clinical applications.

  12. A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jui-Hui; Yajima, Rieko; Chadalavada, Durga M.; Chase, Elaine; Bevilacqua, Philip C.; Golden, Barbara L. (Purdue); (Penn)

    2010-11-01

    The hepatitis delta virus (HDV) ribozyme and HDV-like ribozymes are self-cleaving RNAs found throughout all kingdoms of life. These RNAs fold into a double-nested pseudoknot structure and cleave RNA, yielding 2{prime},3{prime}-cyclic phosphate and 5{prime}-hydroxyl termini. The active site nucleotide C75 has a pK{sub a} shifted >2 pH units toward neutrality and has been implicated as a general acid/base in the cleavage reaction. An active site Mg{sup 2+} ion that helps activate the 2{prime}-hydroxyl for nucleophilic attack has been characterized biochemically; however, this ion has not been visualized in any previous structures. To create a snapshot of the ribozyme in a state poised for catalysis, we have crystallized and determined the structure of the HDV ribozyme bound to an inhibitor RNA containing a deoxynucleotide at the cleavage site. This structure includes the wild-type C75 nucleotide and Mg{sup 2+} ions, both of which are required for maximal ribozyme activity. This structure suggests that the position of C75 does not change during the cleavage reaction. A partially hydrated Mg{sup 2+} ion is also found within the active site where it interacts with a newly resolved G {center_dot} U reverse wobble. Although the inhibitor exhibits crystallographic disorder, we modeled the ribozyme-substrate complex using the conformation of the inhibitor strand observed in the hammerhead ribozyme. This model suggests that the pro-RP oxygen of the scissile phosphate and the 2{prime}-hydroxyl nucleophile are inner-sphere ligands to the active site Mg{sup 2+} ion. Thus, the HDV ribozyme may use a combination of metal ion Lewis acid and nucleobase general acid strategies to effect RNA cleavage.

  13. Inhibition of telomerase in tumor cells by ribozyme targeting telomerase RNA component

    Institute of Scientific and Technical Information of China (English)

    LIU; Bailin(刘柏林); QU; Yi(屈艺); LIU; Shuqiu(刘菽秋); OUYANG; Xuesong(欧阳雪松)

    2002-01-01

    Telomerase plays an important role in cell proliferation and carcinogenesis and is believed to be a good target for anti-cancer drugs. Elimination of template function of telomerase RNA may repress the telomerase activity. A hammer-headed ribozyme(telomerase ribozyme, teloRZ) directed against the RNA component of human telomerase(hTR) was designed and synthesized. TeloRZ showed a specific cleavage activity against the hTR. The cleavage efficacy reached 60%. A eukaryotic expression plasmid containing teloRZ gene was inducted into HeLa cells by lipofectamine, the telomerase activity in HeLa cells expressing teloRZ decreased to one eighth of that in the control cells. The doubling time increased significantly and the apoptosis ratio was elevated with increasing population doublings(PDS). After 19-20 PDS 95% cells were apoptotic. To further investigate the effect of teloRZ on tumor growth, the eukaryotic expression plasmid containing teloRZ was injected into transplanted tumor of nude mouse. The teloRZ effectively inhibited the telomerase activity in transplanted tumor, promoted apoptosis of the transplanted tumor cells, and decreased the tumor size significantly. These results indicate that teloRZ can effectively inhibit telomerase activity and growth of tumor cells, and suggest the potential use of this ribozyme in anti-cancer therapy.

  14. Ribozymes and their medical implications

    Energy Technology Data Exchange (ETDEWEB)

    Cech, T.R.

    1988-11-25

    Certain RNA molecules can mediate their own cleavage or splicing or act as enzymes to promote reactions on substrate RNA molecules. Thus, RNA is not restricted to being a passive carrier of genetic information but can have an active role in directing cellular biochemistry. These findings suggest the possibility that other cellular RNA's, including the RNA components of small nuclear ribonucleoproteins, of the ribosome, and of various ribonucleoprotein enzymes, are catalysts. RNA enzymes (ribozymes) can be used as sequence-specific RNA cleavage agents in vitro, providing useful tools for biochemical studies of RNA. On a more speculative note, ribozymes directed against viral RNAs have the potential of serving as therapeutic agents. Finally, some infectious agents including hepatitis delta virus and perhaps poliovirus and rhinoviruses, are themselves ribozymes, providing potential targets for pharmaceuticals.

  15. Response of the hammerhead shark olfactory epithelium to amino acid stimuli.

    Science.gov (United States)

    Tricas, Timothy C; Kajiura, Stephen M; Summers, Adam P

    2009-10-01

    Sharks and rays are highly sensitive to chemical stimuli in their natural environment but several hypotheses predict that hammerhead sharks, with their expanded head and enlarged olfactory epithelium, have particularly acute olfactory systems. We used the electro-olfactogram (EOG) technique to compare the relative response of the scalloped hammerhead shark (Sphyrna lewini) olfactory epithelium to 20 proteinogenic amino acids and determine the sensitivity for 6 amino acids. At micromolar concentrations, cysteine evoked the greatest EOG response which was approximately twice as large as that of alanine. The weakest response was obtained for proline followed by aspartic acid and isoleucine. The olfactory epithelium showed adaptation to sequential stimulation, and recovery was related to the inter-stimulus time period. Estimated EOG response thresholds were in the sub-nanomolar range for both alanine (9.2 x 10(-11) M) and cysteine (8.4 x 10(-10) M) and in the micromolar range for proline and serine. These thresholds from 10(-10) to 10(-6) M for the scalloped hammerhead shark are comparable or lower than those reported for other teleost and elasmobranch species. Future work should focus on binary and more complex compounds to test for competition and cross-adaptation for different classes of peripheral receptors, and their responses to molecules found in biologically relevant stimuli.

  16. Ribozyme uses in retinal gene therapy.

    Science.gov (United States)

    Hauswirth, W W; Lewin, A S

    2000-11-01

    In this chapter we discuss the design, delivery and preclinical testing of mutation-specific ribozymes for the treatment of dominantly inherited retinal disease. We focus particular attention on the initial screening of ribozymes in vitro, because the activity of RNA enzymes in cell-free systems can be used to predict their suitability for animal experiments. Current techniques for delivering genes of interest to cells of the retina using viral vectors are then briefly surveyed emphasizing vector properties that best match to the needs of a ribozyme-based therapy. Using these considerations, analysis of ribozyme gene therapy for an autosomal dominant RP-like disease in a rodent model is outlined emphasizing the desirability of combining biochemical, morphological and electrophysiological measures of therapy. Finally, we describe alternative, perhaps more general, ribozyme approaches that have yet to be tested in the context of retinal disease.

  17. A Self-Replicating Ligase Ribozyme

    Science.gov (United States)

    Paul, Natasha; Joyce, Gerald F.

    2002-01-01

    A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of Itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 per min, whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 x 10(exp -11) M per min. Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

  18. A new RNA branching activity: the GIR1 ribozyme

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Johansen, Steinar D

    2006-01-01

    ',5'-phosphodiester bonds in biology. We recently described a new ribozyme, the GIR1 branching ribozyme, which catalyzes the formation of a tiny lariat that caps an mRNA. This new example together with work on artificial branching ribozymes and deoxyribozymes shows that branching is facile and points...

  19. A Comparison of Vanadate to a 2'-5' Linkage at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Torelli, A.T.; Krucinska, J.; Wedekind, J.E.

    2009-06-04

    The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.

  20. Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

    DEFF Research Database (Denmark)

    Beckert, Bertrand Dominique; Nielsen, Henrik; Einvik, Christer;

    2008-01-01

    Twin-ribozyme introns contain a branching ribozyme (GIR1) followed by a homing endonuclease (HE) encoding sequence embedded in a peripheral domain of a group I splicing ribozyme (GIR2). GIR1 catalyses the formation of a lariat with 3 nt in the loop, which caps the HE mRNA. GIR1 is structurally re...

  1. Ribozymes:an anti-viral agent

    Institute of Scientific and Technical Information of China (English)

    Asad U.Khan; Shahper N.Khan

    2008-01-01

    The discovery that RNA can act as an enzyme led Thomas Cech to win the Nobel Prize in Chemistry and led immediately to the next wave of attempts to find an effective RNA-based therapy.The tantalizing idea that RNA enzymes called trans-cleaving ribozymes enables them to act as potential antiviral and powerful tool for functional genomic studies.The efficacy of ribozyme function in a complex intracellular environment is depend-ent on the intracellular fate of the RNA that is being targeted.Recently,ribozymes have been used successfully to inhibit gene expression in a variety of biological systems in vitro and in vivo.Ribozyme has also been used successfully to combat many cases of viral infection,as clinical trial.Despite it needs to be investigated and explored as far as its structural and functional aspects are concern.In view of the significance of ribozyme in modern medicine,we reviewed the recent literature on general approach to control viral infection.

  2. Crystallographic analysis of small ribozymes and riboswitches.

    Science.gov (United States)

    Lippa, Geoffrey M; Liberman, Joseph A; Jenkins, Jermaine L; Krucinska, Jolanta; Salim, Mohammad; Wedekind, Joseph E

    2012-01-01

    Ribozymes and riboswitches are RNA motifs that accelerate biological reactions and regulate gene expression in response to metabolite recognition, respectively. These RNA molecules gain functionality via complex folding that cannot be predicted a priori, and thus requires high-resolution three-dimensional structure determination to locate key functional attributes. Herein, we present an overview of the methods used to determine small RNA structures with an emphasis on RNA preparation, crystallization, and structure refinement. We draw upon examples from our own research in the analysis of the leadzyme ribozyme, the hairpin ribozyme, a class I preQ(1) riboswitch, and variants of a larger class II preQ(1) riboswitch. The methods presented provide a guide for comparable investigations of noncoding RNA molecules including a 48-solution, "first choice" RNA crystal screen compiled from our prior successes with commercially available screens.

  3. Chemical fidelity of an RNA polymerase ribozyme

    DEFF Research Database (Denmark)

    Attwater, J.; Tagami, S.; Kimoto, M.

    2013-01-01

    The emergence of catalytically active RNA enzymes (ribozymes) is widely believed to have been an important transition in the origin of life. In the context of a likely heterogeneous chemical environment, substrate specificity and selectivity of these primordial enzymes would have been critical...... for function. Here we have explored the chemical fidelity, i.e. substrate selectivity and specificity for both single and multiple catalytic steps of the Z RNA polymerase ribozyme-a modern day analogue of the primordial RNA replicase. Using a wide range of nucleotide analogues and ionic conditions, we observe...

  4. Helium ion beam induced growth of hammerhead AFM probes

    NARCIS (Netherlands)

    Nanda, G.; Veldhoven, E. van; Maas, D.J.; Sadeghian Marnani, H.; Alkemade, P.F.A.

    2015-01-01

    The authors report the direct-write growth of hammerhead atomic force microscope (AFM) probes by He+ beam induced deposition of platinum-carbon. In order to grow a thin nanoneedle on top of a conventional AFM probe, the authors move a focused He+ beam during exposure to a PtC precursor gas. In the f

  5. Ribozymes: applications to functional analysis and gene discovery.

    Science.gov (United States)

    Shiota, Maki; Sano, Masayuki; Miyagishi, Makoto; Taira, Kazunari

    2004-08-01

    Ribozymes are catalytic RNA molecules that cleave RNAs with high specificity. Since the discovery of these non-protein enzymes, the rapidly developing field of ribozymes has been of particular interest because of the potential utility of ribozymes as tools for reversed genetics. However, despite extensive efforts, the activity of ribozymes in vivo has not usually been high enough to achieve the desirable biological effects. Now, by the use of RNA polymerase III (pol III) promoters, the ribozyme activity in cells has been successfully improved by developing efficient transport systems for the transcripts to the cytoplasm. In addition, it is possible to cleave a specific target RNA in cells by using an allosterically controllable ribozyme or an RNA-protein hybrid ribozyme. These ribozymes are potentially applicable to molecular gene therapy and efficient gene discovery systems. Furthermore, the developed pol III expression system is applicable to the expression of small interfering RNAs (siRNAs). The advantage of such ribozymes over siRNAs is the high specificity of the ribozyme that would not cause interferon responses.

  6. 抗HPV11 E2核酶的计算机设计%Computer design of anti-HPV11 E2 ribozyme

    Institute of Scientific and Technical Information of China (English)

    侯化; 王曙; 杨光彩

    2001-01-01

    HPV11 E2 mRNA was taken as the target RNA, ribozyme were designed accounting to the hammerhead structure described by Symons. Computer was used to analyze the possible secondary cleavage sites on HPV11 E2 mRNA and to predict the secondary structures of substrate and ribozymes. According to the theory of Symons headhammer ribozyme, there are 32 sites to targetting sequences. The secondary structures of HPV11 mRNA from nt2510 to nt3518 were relatively stable. The region was of important biological function and was the ideal attacking region for ribozyme. Two ribozymes targeting nt2777 and nt3281 on the HPV11 mRNA were designed and were named RZ2777 and RZ3281 respectively. No analogous sequence of substrate which combined with ribozyme was found in the mRNA of others genes in known Human Gene Bank through computer probe. Not all GUX or CUX could be taken as the cleavage site of ribozyme. The nt2777 and nt3281 onr HPV11 mRNA are the most ideal attacking sites for ribozymes. So computer analysis was used to select the optium ribozyme as soon as possible and to lay a solid foundation for using ribozyme in vivo.%借助计算机软件分析,设计出能特异性切割HPV11型644nt E2 mRNA的核酶。遵循Symons锤头状核酶结构和GUX剪切位点原则,靶序列存在32个剪切位点,通过计算机软件分析核酶的最佳剪切位点,并对底物及核酶的二级结构进行预测及进行相应基因生物学功能和基因同源性分析,筛选出2个锤头结构核酶。针对这两位点设计的核酶分别命名为RZ2777和RZ3281。计算机分析显示,两核酶与底物切点两翼碱基形成锤头状结构,切点所在基因序列具有相对松弛的二级结构,位于该基因重要生物功能区内,是核酶的理想攻击区域,通过基因库检索,在已知人类基因中排除了与上述两核酶切点两翼碱基有基因同源性序列的可能性。并非所有的GUX位点(X:C、U、A)或CUX均可作为核酶的最

  7. Molecular characterization of a new member of the lariat capping twin-ribozyme introns

    DEFF Research Database (Denmark)

    Tang, Yunjia; Nielsen, Henrik; Masquida, Benoît

    2014-01-01

    BACKGROUND: Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (GIR2). Twin-ribozyme introns have so far been confined to nucleolar DNA in Na...

  8. 76 FR 23794 - Stock Status Determination for Atlantic Highly Migratory Scalloped Hammerhead Shark

    Science.gov (United States)

    2011-04-28

    ... Scalloped Hammerhead Shark AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... an Atlantic highly migratory species (HMS) scalloped hammerhead shark, and the stock is overfished... sharks in U.S. waters. Based on this paper, in 2005, the population was estimated to be at 45 percent...

  9. Biochemical analysis of hatchet self-cleaving ribozymes.

    Science.gov (United States)

    Li, Sanshu; Lünse, Christina E; Harris, Kimberly A; Breaker, Ronald R

    2015-11-01

    Hatchet RNAs are members of a novel self-cleaving ribozyme class that was recently discovered by using a bioinformatics search strategy. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides interspersed among bulges linking four base-paired substructures. A representative hatchet ribozyme from a metagenomic source requires divalent ions such as Mg(2+) to promote RNA strand scission with a maximum rate constant of ∼4 min(-1). As with all other small self-cleaving ribozymes discovered to date, hatchet ribozymes employ a general mechanism for catalysis involving the nucleophilic attack of a ribose 2'-oxygen atom on an adjacent phosphorus center. Kinetic characteristics of the reaction demonstrate that members of this ribozyme class have an essential requirement for divalent metal ions and that they might have a complex active site that employs multiple catalytic strategies to accelerate RNA cleavage by internal phosphoester transfer.

  10. A conformational switch controls hepatitis delta virus ribozyme catalysis.

    Science.gov (United States)

    Ke, Ailong; Zhou, Kaihong; Ding, Fang; Cate, Jamie H D; Doudna, Jennifer A

    2004-05-13

    Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

  11. Twister ribozymes as highly versatile expression platforms for artificial riboswitches

    Science.gov (United States)

    Felletti, Michele; Stifel, Julia; Wurmthaler, Lena A.; Geiger, Sophie; Hartig, Jörg S.

    2016-01-01

    The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new opportunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast. Besides important implications in biotechnology and synthetic biology, the observed versatility in artificial genetic control set-ups hints at possible natural roles of this widespread ribozyme class. PMID:27670347

  12. Chemistry and biology of self-cleaving ribozymes

    Science.gov (United States)

    Jimenez, Randi M.; Polanco, Julio A.; Lupták, Andrej

    2015-01-01

    Self-cleaving ribozymes were discovered thirty years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be employed as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered. PMID:26481500

  13. Study on Cleavage in vitro of HPVll/E2 Gene by Specific Ribozyme%抗HPV11/E2基因Ribozyme对靶RNA的体外剪切研究

    Institute of Scientific and Technical Information of China (English)

    侯化; 刘德忠; 杨光彩

    2001-01-01

    In order to study the pathogenesis of HPVl1 and seek for a therapeutic approach of the disease caused by HPV1l. The HPVl1/E2 644bp was amplified by PCR with HPVll plasmid DNA. pGEM-T Easy was used as vector and a clone pTV-644 was obtained.The inserted DNA sequencing was carried out after selecting and identification. According to the hammerhead structure described by Symon's, the possible secondery cleavage sites on HPVll/E2 mRNA were analyzed and the secondery structure of substrate was predicted by computer and ribozyme, excluding analogous sequence of substrate combined with ribozyme were found in the mRNA.The hammerhead ribozyme of RZ2777 against HPV1l/E2 mRNA was seleted to carry out cleavage reaction in vitro. Results of the experiment showed that 644bp substrate derived from HPVll/E2 can be cleavaed site-specifically by ribozyme in vitro. The cleavage activity showed over 85% by choosing the optimun reaction condition, which was not affected by two cis-ribozymes on both 3′-and 5′-ends released by self cleavage,but two flan-king sequences of target RNA influenced the cleavage activity. Results demonstrated that the ribozyme will become a highly effective and specific therapy against HPVll infection.%为了寻找HPV11型引起的生殖系统感染的治疗途径和探讨HPV的致病机理,本实验以HPV11病毒质粒为模板,扩增出HPVll型E2区644 bp片段,采用pGEM-T-Easy Vector为载体,构建pTV-644克隆载体,经筛选得到克隆株,提取质粒测序鉴定。采用上海生化所陈农安教授编制的锤头状Ribozyme设计软件进行计算机分析,选择Ribozyme对靶基因的最佳剪切位点,及进行基因同源性分析和生物学功能分析,选择出针对HPVll E2靶基因的RZ2777,在最适条件下进行体外剪切反应,发现人工合成和体外转录得到的Ribozyme分子均能在相应位点准确切割靶RNA分子,选择合适的反应条件切割效率达到60%以上,Km和Kcat值分别为0

  14. Biochemical analysis of pistol self-cleaving ribozymes.

    Science.gov (United States)

    Harris, Kimberly A; Lünse, Christina E; Li, Sanshu; Brewer, Kenneth I; Breaker, Ronald R

    2015-11-01

    Pistol RNAs are members of a distinct class of self-cleaving ribozymes that was recently discovered by using a bioinformatics search strategy. Several hundred pistol ribozymes share a consensus sequence including 10 highly conserved nucleotides and many other modestly conserved nucleotides associated with specific secondary structure features, including three base-paired stems and a pseudoknot. A representative pistol ribozyme from the bacterium Lysinibacillus sphaericus was found to promote RNA strand scission with a rate constant of ∼10 min(-1) under physiological Mg(2+) and pH conditions. The reaction proceeds via the nucleophilic attack of a 2'-oxygen atom on the adjacent phosphorus center, and thus adheres to the same general catalytic mechanism of internal phosphoester transfer as found with all other classes of natural self-cleaving ribozymes discovered to date. Analyses of the kinetic characteristics and the metal ion requirements of the cleavage reaction reveal that members of this ribozyme class likely use several catalytic strategies to promote the rapid cleavage of RNA.

  15. The Structural Basis of Ribozyme-Catalyzed RNA Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, M.P.; Scott, W.G.; /UC, Santa Cruz

    2007-07-12

    Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.

  16. Kinetic partitioning mechanism of HDV ribozyme folding

    Science.gov (United States)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  17. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  18. Speciation of a group I intron into a lariat capping ribozyme

    DEFF Research Database (Denmark)

    Meyer, Mélanie; Nielsen, Henrik; Oliéric, Vincent

    2014-01-01

    The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes...... for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in molecular selection...... pressure, ultimately giving rise to an original branching ribozyme family. The structures elucidate the role of key elements that regulate the activity of the LC ribozyme by conformational switching and suggest a mechanism by which the signal for branching is transmitted to the catalytic core...

  19. Structural studies on an internal loop from a hairpin ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr. [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  20. Activity of HDV ribozymes to trans-cleave HCV RNA

    Institute of Scientific and Technical Information of China (English)

    Yue-Cheng Yu; Qing Mao; Chang-Hai Gu; Qi-Fen Li; Yu-Ming Wang

    2002-01-01

    AIM: To explore whether HDV ribozymes have the abilityto trans-cleave HCVRNA.METHODS: Three HDV genomic ribozymes weredesigned and named RzC1, RzC2 and RzC3. Thesubstrate RNA contained HCVRNA 5'-noncoding regionand 5'-fragment of C region (5'-NCR-C). All theribozymes and HCV RNA 5'-NCR-C were obtained bytranscription in vibo from their DNA templates, and HCVRNA 5'-NCR-C was radiolabelled at its 5'-end Undercertain pH, temperature, appropriate concentration ofMg2+ and deionized formamide, these ribozymes wererespectively or simultaneously mixed with HCVRNA 5'-NCR-C and reacted for a certain time. The trans-cleavage reaction was stopped at different time points,and the products were separated with polyacrylamidegel electrophoresis (PAGE), displayed byautoradiography. Percentage of trans-deaved productswas measured to indicate the activity of HDV ribozymes.RESULTS: RzC1 and RzC2 could trans-cleave 26 % and21.8 % of HCV RNA 5'-NCR-C under our reactionconditions with 2.5 mol. L-1 deionized formamiderespectively. The percentage of HCV RNA 5'-NCR-Ctrans-cleaved by RzC1, RzC2 or combined usage of thethree ribozymes increased with time, up to 24.9 %, 20.3 %and 37.3 % respectively at 90 min point. Almost noproduct from RzC3 was observed.CONCLUSION: HDV ribozymes are able to trans-cleavespecifically HCV RNA at certain sites under appropriateconditions, and combination of several ribozymesaiming at different target sites can trans-cleave thesubstrate more efficiently than using only one of them.

  1. Evolution in vitro: analysis of a lineage of ribozymes

    Science.gov (United States)

    Lehman, N.; Joyce, G. F.

    1993-01-01

    Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population. Results: Beginning with a pool of 10(13) variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Ca2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca(2+)-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics--logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme. Conclusions: In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonable short time scale.

  2. Hsp90 inhibition accelerates cell lysis. Anti-Hsp90 ribozyme reveals a complex mechanism of Hsp90 inhibitors involving both superoxide- and Hsp90-dependent events.

    Science.gov (United States)

    Sreedhar, Amere Subbarao; Mihály, Katalin; Pató, Bálint; Schnaider, Tamás; Steták, Attila; Kis-Petik, Katalin; Fidy, Judit; Simonics, Tibor; Maraz, Anna; Csermely, Péter

    2003-09-12

    The 90 kDa heat shock protein, Hsp90, is an abundant molecular chaperone participating in the cytoprotection of eukaryotic cells. Here we analyzed the involvement of Hsp90 in the maintenance of cellular integrity using partial cell lysis as a measure. Inhibition of Hsp90 by geldanamycin, radicicol, cisplatin, and novobiocin induced a significant acceleration of detergent- and hypotonic shock-induced cell lysis. The concentration and time dependence of cell lysis acceleration was in agreement with the Hsp90 inhibition characteristics of the N-terminal inhibitors, geldanamycin and radicicol. Glutathione and other reducing agents partially blocked geldanamycin-induced acceleration of cell lysis but were largely ineffective with other inhibitors. Indeed, geldanamycin treatment led to superoxide production and a change in membrane fluidity. When Hsp90 content was diminished using anti-Hsp90 hammerhead ribozymes, an accelerated cell lysis was also observed. Hsp90 inhibition-induced cell lysis was more pronounced in eukaryotic (yeast, mouse red blood, and human T-lymphoma) cells than in bacteria. Our results indicate that besides the geldanamycin-induced superoxide production, and a consequent increase in cell lysis, inhibition or lack of Hsp90 alone can also compromise cellular integrity. Moreover, cell lysis after hypoxia and complement attack was also enhanced by any type of Hsp90 inhibition used, which shows that the maintenance of cellular integrity by Hsp90 is important in physiologically relevant lytic conditions of tumor cells.

  3. Investigating a new generation of ribozymes in order to target HCV.

    Directory of Open Access Journals (Sweden)

    Michel V Lévesque

    Full Text Available For a long time nucleic acid-based approaches directed towards controlling the propagation of Hepatitis C Virus (HCV have been considered to possess high potential. Towards this end, ribozymes (i.e. RNA enzymes that specifically recognize and subsequently catalyze the cleavage of their RNA substrate present an attractive molecular tool. Here, the unique properties of a new generation of ribozymes are taken advantage of in order to develop an efficient and durable ribozyme-based technology with which to target HCV (+ RNA strands. These ribozymes resulted from the coupling of a specific on/off adaptor (SOFA to the ribozyme domain derived from the Hepatitis Delta Virus (HDV. The former switches cleavage activity "on" solely in the presence of the desired RNA substrate, while the latter was the first catalytic RNA reported to function naturally in human cells, specifically in hepatocytes. In order to maximize the chances for success, a step-by-step approach was used for both the design and the selection of the ribozymes. This approach included the use of both bioinformatics and biochemical methods for the identification of the sites possessing the greatest potential for targeting, and the subsequent in vitro testing of the cleavage activities of the corresponding SOFA-HDV ribozymes. These efforts led to a significant improvement in the ribozymes' designs. The ability of the resulting SOFA-HDV ribozymes to inhibit HCV replication was further examined using a luciferase-based replicon. Although some of the ribozymes exhibited high levels of cleavage activity in vitro, none appears to be a potential long term inhibitor in cellulo. Analysis of recent discoveries in the cellular biology of HCV might explain this failure, as well as provide some ideas on the potential limits of using nucleic acid-based drugs to control the propagation of HCV. Finally, the above conclusions received support from experiments performed using a collection of SOFA

  4. Structure of ribonuclease P--a universal ribozyme.

    Science.gov (United States)

    Torres-Larios, Alfredo; Swinger, Kerren K; Pan, Tao; Mondragón, Alfonso

    2006-06-01

    Ribonuclease P (RNase P) is one of only two known universal ribozymes and was one of the first ribozymes to be discovered. It is involved in RNA processing, in particular the 5' maturation of tRNA. Unlike most other natural ribozymes, it recognizes and cleaves its substrate in trans. RNase P is a ribonucleoprotein complex containing one RNA subunit and as few as one protein subunit. It has been shown that, in bacteria and in some archaea, the RNA subunit alone can support catalysis. The structure and function of bacterial RNase P RNA have been studied extensively, but the detailed catalytic mechanism is not yet fully understood. Recently, structures of one of the structural domains and of the entire RNA component of RNase P from two different bacteria have been described. These structures provide the first atomic-level information on the structural assembly of the RNA component, and the regions involved in substrate recognition and catalysis. Comparison of these structures reveals a highly conserved core that comprises two universally conserved structural modules. Interestingly, the same structural core can be found in the context of different scaffolds.

  5. Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability

    Directory of Open Access Journals (Sweden)

    Fabrizio Anella

    2014-12-01

    Full Text Available The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristoleic acid (MA vesicles at varying concentrations of Mg2+. The ligation rate is significantly lower at low-Mg2+ conditions. However, the loss of activity is overcompensated by the increased stability of RNA leading to a larger amount of intact ligated substrate after long reaction periods. Combining RNA ligation assays with fatty acid vesicles we found that MA vesicles made of 5 mM amphiphile are stable and do not impair ligase ribozyme activity in the presence of approximately 2 mM Mg2+. These results provide a scenario in which catalytic RNA and primordial membrane assembly can coexist in the same environment.

  6. Flanking sequences with an essential role in hydrolysis of a self-cleaving group I-like ribozyme

    DEFF Research Database (Denmark)

    Einvik, C; Nielsen, Henrik; Nour, R;

    2000-01-01

    DiGIR1 is a group I-like ribozyme derived from the mobile twin ribozyme group I intron DiSSU1 in the nuclear ribosomal DNA of the myxomycete Didymium iridis. This ribozyme is responsible for intron RNA processing in vitro and in vivo at two internal sites close to the 5'-end of the intron endo-nu...

  7. A natural fast-cleaving branching ribozyme from the amoeboflagellate Naegleria pringsheimi

    DEFF Research Database (Denmark)

    Tang, Yunjia; Nielsen, Henrik; Birgisdottir, Asa Birna;

    2011-01-01

    The GIR1 branching ribozyme constitutes a separate class of naturally occurring ribozymes. Most studies have been performed with the single GIR1 known from the myxomycete Didymium iridis whereas the large number of GIR1s found in the amoeboflagellate Naegleria has remained largely uncharacterized...

  8. Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection”

    Directory of Open Access Journals (Sweden)

    Yuki Fujita

    2010-08-01

    Full Text Available In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed “design and selection,” new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

  9. The Hydrodynamics and Odorant Transport Phenomena of Olfaction in the Hammerhead Shark

    Science.gov (United States)

    Rygg, Alex; Craven, Brent

    2013-11-01

    The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory organs, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics and odorant transport phenomena of olfaction in the hammerhead shark based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics (CFD) simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Odorant transport in the olfactory organ is investigated using a multi-scale approach, whereby molecular dynamics (MD) simulations are used to calculate odorant partition coefficients that are subsequently utilized in macro-scale CFD simulations of odorant deposition. The hydrodynamic and odorant transport results are used to elucidate several important features of olfactory function in the hammerhead shark.

  10. Design principles for ligand-sensing, conformation-switching ribozymes.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    2009-12-01

    Full Text Available Nucleic acid sensor elements are proving increasingly useful in biotechnology and biomedical applications. A number of ligand-sensing, conformational-switching ribozymes (also known as allosteric ribozymes or aptazymes have been generated by some combination of directed evolution or rational design. Such sensor elements typically fuse a molecular recognition domain (aptamer with a catalytic signal generator (ribozyme. Although the rational design of aptazymes has begun to be explored, the relationships between the thermodynamics of aptazyme conformational changes and aptazyme performance in vitro and in vivo have not been examined in a quantitative framework. We have therefore developed a quantitative and predictive model for aptazymes as biosensors in vitro and as riboswitches in vivo. In the process, we have identified key relationships (or dimensionless parameters that dictate aptazyme performance, and in consequence, established equations for precisely engineering aptazyme function. In particular, our analysis quantifies the intrinsic trade-off between ligand sensitivity and the dynamic range of activity. We were also able to determine how in vivo parameters, such as mRNA degradation rates, impact the design and function of aptazymes when used as riboswitches. Using this theoretical framework we were able to achieve quantitative agreement between our models and published data. In consequence, we are able to suggest experimental guidelines for quantitatively predicting the performance of aptazyme-based riboswitches. By identifying factors that limit the performance of previously published systems we were able to generate immediately testable hypotheses for their improvement. The robust theoretical framework and identified optimization parameters should now enable the precision design of aptazymes for biotechnological and clinical applications.

  11. Design and Experimental Evolution of trans-Splicing Group I Intron Ribozymes

    Directory of Open Access Journals (Sweden)

    Ulrich F. Müller

    2017-01-01

    Full Text Available Group I intron ribozymes occur naturally as cis-splicing ribozymes, in the form of introns that do not require the spliceosome for their removal. Instead, they catalyze two consecutive trans-phosphorylation reactions to remove themselves from a primary transcript, and join the two flanking exons. Designed, trans-splicing variants of these ribozymes replace the 3′-portion of a substrate with the ribozyme’s 3′-exon, replace the 5′-portion with the ribozyme’s 5′-exon, or insert/remove an internal sequence of the substrate. Two of these designs have been evolved experimentally in cells, leading to variants of group I intron ribozymes that splice more efficiently, recruit a cellular protein to modify the substrate’s gene expression, or elucidate evolutionary pathways of ribozymes in cells. Some of the artificial, trans-splicing ribozymes are promising as tools in therapy, and as model systems for RNA evolution in cells. This review provides an overview of the different types of trans-splicing group I intron ribozymes that have been generated, and the experimental evolution systems that have been used to improve them.

  12. Isolation of novel ribozymes that ligate AMP-activated RNA substrates

    Science.gov (United States)

    Hager, A. J.; Szostak, J. W.

    1997-01-01

    BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.

  13. 气动矛系统性能仿真分析%The Simulation Analysis on Performance of Hammerhead Mole

    Institute of Scientific and Technical Information of China (English)

    于晓琳; 闫明印

    2011-01-01

    The structure and working principles of hammerhead mole system were analyzed, and the simulation computation was made by MATLAB based on the dynamic simulation model of working hammerhead mole system. The factors affecting the performance of hammerhead mole were analyzed, and the relationship between affecting factors and performance parameters was studied. The results can be a reference to the design of hammerhead mole.%分析气动矛系统的结构及工作原理,在建立气动矛系统工作状态下动力学仿真数学模型的基础上,利用MATLAB软件对Hammerhead12”型气动矛进行仿真,并对影响气动矛系统性能的各因素进行仿真分析,研究气动矛性能与各影响因素的关系.分析和研究结果可为气动矛的设计提供参考.

  14. Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Shechner, David M.; Grant, Robert A.; Bagby, Sarah C.; Koldobskaya, Yelena; Piccirilli, Joseph A.; Bartel, David P.; (MIT); (HHMI); (UC)

    2010-09-02

    Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.

  15. Group I Intron Internal Guide Sequence Binding Strength as a Component of Ribozyme Network Formation

    Directory of Open Access Journals (Sweden)

    Laura Elizabeth Satterwhite

    2016-09-01

    Full Text Available Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (KD between the 3-nucleotide internal guide sequence (IGS of one ribozyme and its complement in another is correlated to the catalytic ability of the ribozyme. This work demonstrates that one can begin to deconstruct the thermodynamic basis of information in prebiotic RNA systems.

  16. RNase P Ribozymes Inhibit the Replication of Human Cytomegalovirus by Targeting Essential Viral Capsid Proteins.

    Science.gov (United States)

    Yang, Zhu; Reeves, Michael; Ye, Jun; Trang, Phong; Zhu, Li; Sheng, Jingxue; Wang, Yu; Zen, Ke; Wu, Jianguo; Liu, Fenyong

    2015-06-24

    An engineered RNase P-based ribozyme variant, which was generated using the in vitro selection procedure, was used to target the overlapping mRNA region of two proteins essential for human cytomegalovirus (HCMV) replication: capsid assembly protein (AP) and protease (PR). In vitro studies showed that the generated variant, V718-A, cleaved the target AP mRNA sequence efficiently and its activity was about 60-fold higher than that of wild type ribozyme M1-A. Furthermore, we observed a reduction of 98%-99% in AP/PR expression and an inhibition of 50,000 fold in viral growth in cells with V718-A, while a 75% reduction in AP/PR expression and a 500-fold inhibition in viral growth was found in cells with M1-A. Examination of the antiviral effects of the generated ribozyme on the HCMV replication cycle suggested that viral DNA encapsidation was inhibited and as a consequence, viral capsid assembly was blocked when the expression of AP and PR was inhibited by the ribozyme. Thus, our study indicates that the generated ribozyme variant is highly effective in inhibiting HCMV gene expression and blocking viral replication, and suggests that engineered RNase P ribozyme can be potentially developed as a promising gene-targeting agent for anti-HCMV therapy.

  17. Cleavage of an amide bond by a ribozyme

    Science.gov (United States)

    Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)

    1995-01-01

    A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

  18. 76 FR 72891 - Endangered and Threatened Wildlife; 90-Day Finding on a Petition To List the Scalloped Hammerhead...

    Science.gov (United States)

    2011-11-28

    ... joint NMFS-U.S. Fish and Wildlife Service (USFWS) (jointly, ``the Services'') policy clarifies the... can be found from Japan and China to New Caledonia, including throughout the Philippines, Indonesia... fin trade market, S. lewini and S. zygaena (smooth hammerhead) are mainly traded under the ``Chun...

  19. Conservation Genetics of the Scalloped Hammerhead Shark in the Pacific Coast of Colombia.

    Science.gov (United States)

    Quintanilla, Sonia; Gómez, Alberto; Mariño-Ramírez, Camila; Sorzano, Carolina; Bessudo, Sandra; Soler, German; Bernal, Jaime E; Caballero, Susana

    2015-01-01

    Previous investigations of the population genetics of the scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about nursery areas. Such areas are key to promoting conservation initiatives that can protect young sharks from threats such as overfishing. Here, we investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in 3 areas of Colombia's Pacific coast: around Malpelo Island and in 2 National Natural Parks on the Colombian Pacific mainland (Sanquianga and Ensenada de Utría). We analyzed mtDNA control region (CR) sequences and genotyped 15 microsatellite loci in 137 samples of adults and juveniles. The mtDNA analyses showed haplotypes shared between the Colombian Pacific individuals sampled in this investigation and other areas in the Eastern Tropical Pacific, the Indo-Pacific, and with sequences previously reported in Colombia (Buenaventura Port), as well as 4 unique haplotypes. Population assignment and paternity analyses detected 3 parent-offspring pairs between Malpelo and Sanquianga and 1 between Malpelo and Utría. These results indicate high genetic connectivity between Malpelo Island and the Colombian Pacific coast, suggesting that these 2 areas are nurseries for S. lewini. This is, to our knowledge, the first evidence of nursery areas identified for the scalloped hammerhead shark anywhere in the world. Additional conservation planning may be required to protect these nursery habitats of this endangered shark species.

  20. [Ribozyme riboswitch based gene expression regulation systems for gene therapy applications: progress and challenges].

    Science.gov (United States)

    Feng, Jing-Xian; Wang, Jia-wen; Lin, Jun-sheng; Diao, Yong

    2014-11-01

    Robust and efficient control of therapeutic gene expression is needed for timing and dosing of gene therapy drugs in clinical applications. Ribozyme riboswitch provides a promising building block for ligand-controlled gene-regulatory system, based on its property that exhibits tunable gene regulation, design modularity, and target specificity. Ribozyme riboswitch can be used in various gene delivery vectors. In recent years, there have been breakthroughs in extending ribozyme riboswitch's application from gene-expression control to cellular function and fate control. High throughput screening platforms were established, that allow not only rapid optimization of ribozyme riboswitch in a microbial host, but also straightforward transfer of selected devices exhibiting desired activities to mammalian cell lines in a predictable manner. Mathematical models were employed successfully to explore the performance of ribozyme riboswitch quantitively and its rational design predictably. However, to progress toward gene therapy relevant applications, both precision rational design of regulatory circuits and the biocompatibility of regulatory ligand are still of crucial importance.

  1. Crystal structure of Pistol, a class of self-cleaving ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Laura A.; Wang, Jimin; Steitz, Thomas A. (Yale)

    2017-01-17

    Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2'-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5' leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

  2. Interacting binaries

    CERN Document Server

    Shore, S N; van den Heuvel, EPJ

    1994-01-01

    This volume contains lecture notes presented at the 22nd Advanced Course of the Swiss Society for Astrophysics and Astronomy. The contributors deal with symbiotic stars, cataclysmic variables, massive binaries and X-ray binaries, in an attempt to provide a better understanding of stellar evolution.

  3. Application of Implicit Space Mapping in the Design of Hammerhead Filter in Millimeter-Wave Band

    Directory of Open Access Journals (Sweden)

    Fuqun Zhong

    2012-03-01

    Full Text Available In this study, we present advances in microwave and millimeter-wave device modeling exploiting the Space Mapping (SM technology. New SM-based modeling techniques are used that are easy to implement entirely in the Agilent ADS framework. The implicit space mapping algorithm is applied to the design of hammerhead filter in millimeter-wave band. The validity of this method is confirmed by comparison with fullwave EM simulation result and measured data. Based on the proposed method, a filter was designed and fabricated on a substrate with thickness of 0.254 mm and dielectric constant of 2.2. The experimental results show good agreement with simulated results. It is proved that the accuracy can be achieved using the implicit space mapping algorithm, and the design efficiency can be greatly improved.

  4. Exploring ribozyme conformational changes with X-ray crystallography.

    Science.gov (United States)

    Spitale, Robert C; Wedekind, Joseph E

    2009-10-01

    Relating three-dimensional fold to function is a central challenge in RNA structural biology. Toward this goal, X-ray crystallography has long been considered the "gold standard" for structure determinations at atomic resolution, although NMR spectroscopy has become a powerhouse in this arena as well. In the area of dynamics, NMR remains the dominant technique to probe the magnitude and timescales of molecular motion. Although the latter area remains largely unassailable by conventional crystallographic methods, inroads have been made on proteins using Laue radiation on timescales of ms to ns. Proposed 'fourth generation' radiation sources, such as free-electron X-ray lasers, promise ps- to fs-timescale resolution, and credible evidence is emerging that supports the feasibility of single molecule imaging. At present however, the preponderance of RNA structural information has been derived from timescale and motion insensitive crystallographic techniques. Importantly, developments in computing, automation and high-flux synchrotron sources have propelled the rapidity of 'conventional' RNA crystal structure determinations to timeframes of hours once a suitable set of phases is obtained. With a sufficient number of crystal structures, it is possible to create a structural ensemble that can provide insight into global and local molecular motion characteristics that are relevant to biological function. Here we describe techniques to explore conformational changes in the hairpin ribozyme, a representative non-protein-coding RNA catalyst. The approaches discussed include: (i) construct choice and design using prior knowledge to improve X-ray diffraction; (ii) recognition of long-range conformational changes and (iii) use of single-base or single-atom changes to create ensembles. The methods are broadly applicable to other RNA systems.

  5. Intracellular Immunization of Human Fetal Cord Blood Stem/Progenitor Cells with a Ribozyme Against Human Immunodeficiency Virus Type 1

    Science.gov (United States)

    Yu, Mang; Leavitt, Mark C.; Maruyama, Midori; Yamada, Osamu; Young, Dennis; Ho, Anthony D.; Wong-Staal, Flossie

    1995-01-01

    Successful treatment of human immunodeficiency virus infection may ultimately require targeting of hematopoietic stem cells. Here we used retroviral vectors carrying the ribozyme gene to transduce CD34^+ cells from human fetal cord blood. Transduction and ribozyme expression had no apparent adverse effect on cell differentiation and/or proliferation. The macrophage-like cells, differentiated from the stem/progenitor cells in vitro, expressed the ribozyme gene and resisted infection by a macrophage tropic human immunodeficiency virus type 1. These results suggest the feasibility of stem cell gene therapy for human immunodeficiency virus-infected patients.

  6. The glmS ribozyme cofactor is a general acid-base catalyst.

    Science.gov (United States)

    Viladoms, Júlia; Fedor, Martha J

    2012-11-21

    The glmS ribozyme is the first natural self-cleaving ribozyme known to require a cofactor. The d-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed to serve as a general acid, but its role in the catalytic mechanism has not been established conclusively. We surveyed GlcN6P-like molecules for their ability to support self-cleavage of the glmS ribozyme and found a strong correlation between the pH dependence of the cleavage reaction and the intrinsic acidity of the cofactors. For cofactors with low binding affinities, the contribution to rate enhancement was proportional to their intrinsic acidity. This linear free-energy relationship between cofactor efficiency and acid dissociation constants is consistent with a mechanism in which the cofactors participate directly in the reaction as general acid-base catalysts. A high value for the Brønsted coefficient (β ~ 0.7) indicates that a significant amount of proton transfer has already occurred in the transition state. The glmS ribozyme is the first self-cleaving RNA to use an exogenous acid-base catalyst.

  7. An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini.

    Science.gov (United States)

    Jones, F D; Ryder, S P; Strobel, S A

    2001-12-15

    The Neurospora Varkud Satellite (VS) RNA is capable of promoting a reversible self-cleavage reaction important for its replication pathway. In vivo the VS RNA performs a cis-cleavage reaction to generate monomeric length transcripts that are subsequently ligated to produce circular VS RNA. The predominant form of VS RNA observed in vivo is the closed circular form, though minimal VS ribozyme self-cleavage constructs lack detectable ligation activity. MFOLD analysis of the entire VS RNA sequence revealed an extended region 5' and 3' of the minimal self-cleaving region that could anneal to form a complementary helix, which we have termed helix 7. In full-length VS RNA, this helix appears to span over 40 bp of sequence and brings the 5'- and 3'-ends of the RNA into proximity for the ligation reaction. Here we report a variant of the VS ribozyme with an extended 5'- and 3'-terminus capable of forming a truncated helix 7 that promotes the ligation reaction in vitro. Through mutation and selection of this RNA we have identified a ribozyme containing two point mutations in the truncated helix 7 that ligates with >70% efficiency. These results show that an additional helical element absent in current VS ribozyme constructs is likely to be important for the ligation activity of VS RNA.

  8. Effects of fasting and refeeding on intestinal cell proliferation and apoptosis in hammerhead shark (Sphyrna lewini)

    Institute of Scientific and Technical Information of China (English)

    Hideya Takahashi; Susumu Hyodo; Tsukasa Abe; Chiyo Takagi; Gordon E Grau; Tatsuya Sakamoto

    2014-01-01

    Objective: To examine the effects of fasting and refeeding on intestinal cell proliferation and apoptosis in an opportunistic predator, hammerhead shark (Sphyrna lewini) of elasmobranch fishes which are among the earliest known extant groups of vertebrates to have the valvular intestine typical for the primitive species.Methods:5-day refeeding. Intestinal apoptosis and cell proliferation were assessed by using oligonucleotide detection assay, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and immunohistochemistry of proliferating cells nuclear antigen.Results:Animals were euthanized after 5-10 d of fasting or feeding, or after 10-day fasting and generally decreased during fasting. Numerous apoptotic cells were observed around the tips of the villi, primarily in the epithelium in the fed sharks, whereas fewer labeled nuclei were detected in the epithelium of fasted sharks. Refeeding returned intestinal apoptosis to the level in the fed sharks. Proliferating cells were observed in the epithelium around the troughs of the villi and greater in number in fed sharks, whereas fewer labeled nuclei were detected in fasted sharks. Plasma levels of cholesterol and glucose were reduced by fasting. Intestinal apoptosis Conclusions: The cell turnover is modified in both intestinal epithelia of the shark and the murines by fasting/feeding, but in opposite directions. The difference may reflect the feeding ecology of the elasmobranchs, primitive intermittent feeders.

  9. Signal amplification of glucosamine-6-phosphate based on ribozyme glmS.

    Science.gov (United States)

    Zhao, Yongyun; Chen, Haodong; Du, Feng; Yasmeen, Afshan; Dong, Juan; Cui, Xin; Tang, Zhuo

    2014-12-15

    Ribozyme glmS based isothermal amplification assay is developed for the colorimetric detection of glucosamine-6-phosphate (GlcN6P). Upon binding to the metabolite target GlcN6P, self-cleavage of glmS ribozyme is initiated to release RNA fragment that can trigger the cascade signal amplification to release large amount of G-quadruplex DNAzymes as reporter for colorimetric detection. Given the importance of GlcN6P for cell wall biosynthesis, the glmS riboswitch has become a new drug target for the development of antibiotics. This assay not only offers a convenient detection of GlcN6P with high specificity and sensitivity, but also provides a platform for high-throughput screening of antibiotics based on glmS riboswitches.

  10. Identification of an imino group indispensable for cleavage by a small ribozyme.

    Science.gov (United States)

    Spitale, Robert C; Volpini, Rosaria; Heller, Moriah G; Krucinska, Jolanta; Cristalli, Gloria; Wedekind, Joseph E

    2009-05-06

    The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.

  11. Contributions to the tooth morphology in early embryos of three species of hammerhead sharks (Elasmobranchii: Sphyrnidae) and their evolutionary implications.

    Science.gov (United States)

    Mello, Waldiney; Brito, Paulo Marques Machado

    2013-09-01

    The tooth types in the embryos of the hammerhead sharks Sphyrna tiburo, Sphyrna tudes and Eusphyra blochii are here described in labial and lingual views, and, in some cases, in additional views. The presence of cusplets was observed in the anterior teeth of S. tiburo and S. tudes, which is secondarily lost after early embryonic stages. Many aligned root foramina were detected in the sphyrnids, which, as the cusplets, are shared by many phylogenetic-related carcharhinids. Other anatomic features, related to the root and central cusp, are presented for the first time. Such characters represent the first step to compare the teeth of extant and fossil species.

  12. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site.

    Science.gov (United States)

    Szewczak, A A; Ortoleva-Donnelly, L; Zivarts, M V; Oyelere, A K; Kazantsev, A V; Strobel, S A

    1999-09-28

    Key to understanding the structural biology of catalytic RNA is determining the underlying networks of interactions that stabilize RNA folding, substrate binding, and catalysis. Here we demonstrate the existence and functional importance of a Hoogsteen base triple (U300.A97-U277), which anchors the substrate helix recognition surface within the Tetrahymena group I ribozyme active site. Nucleotide analog interference suppression analysis of the interacting functional groups shows that the U300.A97-U277 triple forms part of a network of hydrogen bonds that connect the P3 helix, the J8/7 strand, and the P1 substrate helix. Product binding and substrate cleavage kinetics experiments performed on mutant ribozymes that lack this base triple (C A-U, U G-C) or replace it with the isomorphous C(+).G-C triple show that the A97 Hoogsteen triple contributes to the stabilization of both substrate helix docking and the conformation of the ribozyme's active site. The U300. A97-U277 base triple is not formed in the recently reported crystallographic model of a portion of the group I intron, despite the presence of J8/7 and P3 in the RNA construct [Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. (1998) Science 282, 259-264]. This, along with other biochemical evidence, suggests that the active site in the crystallized form of the ribozyme is not fully preorganized and that substantial rearrangement may be required for substrate helix docking and catalysis.

  13. Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor

    Energy Technology Data Exchange (ETDEWEB)

    Cochrane,J.; Lipchock, S.; Strobel, S.

    2007-01-01

    The GlmS riboswitch is located in the 5'-untranslated region of the gene encoding glucosamine-6-phosphate (GlcN6P) synthetase. The GlmS riboswitch is a ribozyme with activity triggered by binding of the metabolite GlcN6P. Presented here is the structure of the GlmS ribozyme (2.5 {angstrom} resolution) with GlcN6P bound in the active site. The GlmS ribozyme adopts a compact double pseudoknot tertiary structure, with two closely packed helical stacks. Recognition of GlcN6P is achieved through coordination of the phosphate moiety by two hydrated magnesium ions as well as specific nucleobase contacts to the GlcN6P sugar ring. Comparison of this activator bound and the previously published apoenzyme complex supports a model in which GlcN6P does not induce a conformational change in the RNA, as is typical of other riboswitches, but instead functions as a catalytic cofactor for the reaction. This demonstrates that RNA, like protein enzymes, can employ the chemical diversity of small molecules to promote catalytic activity.

  14. A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.

    Science.gov (United States)

    Liberman, Joseph A; Guo, Man; Jenkins, Jermaine L; Krucinska, Jolanta; Chen, Yuanyuan; Carey, Paul R; Wedekind, Joseph E

    2012-10-17

    One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pK(a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pK(a) value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pK(a) values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pK(a) > 0.8 log unit relative to the precatalytic state. The agreement of the microscopic and macroscopic pK(a) values and the accompanying structural analysis supports a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.

  15. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.

    Science.gov (United States)

    Krasovska, Maryna V; Sefcikova, Jana; Réblová, Kamila; Schneider, Bohdan; Walter, Nils G; Sponer, Jirí

    2006-07-15

    The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.

  16. Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Berezniak, Tomasz [University of Heidelberg; Zahran, Mai [ORNL; Imhof, Petra [University of Heidelberg; Jaeschke, Andres [Free University of Berlin; Smith, Jeremy C [ORNL

    2010-10-01

    The Diels-Alderase ribozyme, an in vitro-evolved ribonucleic acid enzyme, accelerates the formation of carbon-carbon bonds between an anthracene diene and a maleimide dienophile in a [4 + 2] cycloaddition, a reaction with broad application in organic chemistry. Here, the Diels-Alderase ribozyme is examined via molecular dynamics (MD) simulations in both crystalline and aqueous solution environments. The simulations indicate that the catalytic pocket is highly dynamic. At low Mg(2+) ion concentrations, inactive states with the catalytic pocket closed dominate. Stabilization of the enzymatically active, open state of the catalytic pocket requires a high concentration of Mg(2+) ions (e.g., 54 mM), with cations binding to specific phosphate sites on the backbone of the residues bridging the opposite strands of the pocket. The free energy profile for pocket opening at high Mg(2+) cation concentration exhibits a double minimum, with a barrier to opening of approximately 5.5 kJ/mol and the closed state approximately 3 kJ/mol lower than the open state. Selection of the open state on substrate binding leads to the catalytic activity of the ribozyme. The simulation results explain structurally the experimental observation that full catalytic activity depends on the Mg(2+) ion concentration

  17. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini.

    Directory of Open Access Journals (Sweden)

    Holly A Nance

    Full Text Available Genetic diversity (θ, effective population size (N(e, and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e (θ = 4N(eμ, where μ is the mutation rate. Application of the isolation-with-migration (IM model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7, with divergence times (t among all populations significantly greater than zero. Using a conservative (i.e., slow fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs for the onset of the decline in N(e predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

  18. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini.

    Science.gov (United States)

    Nance, Holly A; Klimley, Peter; Galván-Magaña, Felipe; Martínez-Ortíz, Jimmy; Marko, Peter B

    2011-01-01

    Genetic diversity (θ), effective population size (N(e)), and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP) range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e) (θ = 4N(e)μ), where μ is the mutation rate. Application of the isolation-with-migration (IM) model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7), with divergence times (t) among all populations significantly greater than zero. Using a conservative (i.e., slow) fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs) for the onset of the decline in N(e) predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

  19. DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique core organization and evolved biological role

    DEFF Research Database (Denmark)

    Johansen, Steinar; Einvik, Christer; Nielsen, Henrik

    2002-01-01

    introns (twin-ribozyme introns) in distantly related organisms. The Didymium GIR1 (DiGIR1) and Naegleria GIR1 (NaGIR1) share fundamental features in structural organization and reactivity, and display significant differences when compared to the related group I splicing ribozymes. GIR1 lacks...

  20. SOME BIOLOGICAL ASPECTS OF SCALLOPED HAMMERHEAD SHARKS (Sphyrna lewini Griffith & Smith, 1834 CAUGHT FROM COASTAL FISHERIES IN THE EASTERN INDIAN OCEAN

    Directory of Open Access Journals (Sweden)

    Umi Chodrijah

    2015-12-01

    Full Text Available Indonesia has the largest chondrichthyan fishery in the world, with a reported of 105,000 and 118,000 tonnes landed in 2002 and 2003 respectively. Scalloped hammerhead shark was either targeted or by-catch from this fishery, mostly for its fins. Despite of the growing concern around the world, the availability of biological data of this species, especially in the Eastern Indian Ocean is still lacking. The objectives of this paper are to present some biological information (size composition and sex ratio of the scalloped hammerhead, from coastal fisheries in Eastern Indian Ocean. The data used for the analysis comprised of two components, i.e. survey data in 2010 (February, March, June, August, October and December and data from daily monitoring shark landing in 2013 (January to December. Substantially lower mean size, more immature sharks and more frequent of female caught over years showed that scalloped hammerhead shark in the Eastern Indian Ocean are facing intensive fishing pressure which could lead to overfishing. This could harm the sustainability of scalloped hammerhead shark resource in the long run. The relationship between clasper length and total length was positively correlated where every 5 cmTL increment on clasper length adding 51 cmTL on total length.

  1. Binary effectivity rules

    DEFF Research Database (Denmark)

    Keiding, Hans; Peleg, Bezalel

    2006-01-01

    is binary if it is rationalized by an acyclic binary relation. The foregoing result motivates our definition of a binary effectivity rule as the effectivity rule of some binary SCR. A binary SCR is regular if it satisfies unanimity, monotonicity, and independence of infeasible alternatives. A binary...... effectivity rule is regular if it is the effectivity rule of some regular binary SCR. We characterize completely the family of regular binary effectivity rules. Quite surprisingly, intrinsically defined von Neumann-Morgenstern solutions play an important role in this characterization...

  2. Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron

    Directory of Open Access Journals (Sweden)

    De Jonckheere Johan F

    2006-05-01

    Full Text Available Abstract Background Ribosomal DNA of several species of the free-living Naegleria amoeba harbors an optional group I intron within the nuclear small subunit ribosomal RNA gene. The intron (Nae.S516 has a complex organization of two ribozyme domains (NaGIR1 and NaGIR2 and a homing endonuclease gene (NaHEG. NaGIR2 is responsible for intron excision, exon ligation, and full-length intron RNA circularization, reactions typical for nuclear group I intron ribozymes. NaGIR1, however, is essential for NaHEG expression by generating the 5' end of the homing endonuclease messenger RNA. Interestingly, this unusual class of ribozyme adds a lariat-cap at the mRNA. Results To elucidate the evolutionary history of the Nae.S516 twin-ribozyme introns we have analyzed 13 natural variants present in distinct Naegleria isolates. Structural variabilities were noted within both the ribozyme domains and provide strong comparative support to the intron secondary structure. One of the introns, present in N. martinezi NG872, contains hallmarks of a degenerated NaHEG. Phylogenetic analyses performed on separate data sets representing NaGIR1, NaGIR2, NaHEG, and ITS1-5.8S-ITS2 ribosomal DNA are consistent with an overall vertical inheritance pattern of the intron within the Naegleria genus. Conclusion The Nae.S516 twin-ribozyme intron was gained early in the Naegleria evolution with subsequent vertical inheritance. The intron was lost in the majority of isolates (70%, leaving a widespread but scattered distribution pattern. Why the apparent asexual Naegleria amoebae harbors active intron homing endonucleases, dependent on sexual reproduction for its function, remains a puzzle.

  3. The life histories of endangered hammerhead sharks (Carcharhiniformes, Sphyrnidae) from the east coast of Australia.

    Science.gov (United States)

    Harry, A V; Macbeth, W G; Gutteridge, A N; Simpfendorfer, C A

    2011-06-01

    The life histories of two globally endangered hammerhead sharks, Sphyrna lewini and Sphyrna mokarran, were examined using samples collected from a range of commercial fisheries operating along the east coast of Australia. The catch of S. lewini was heavily biased towards males, and there were significant differences in von Bertalanffy growth parameters (L(∞) and k) and maturity [stretched total length (L(ST)) and age (A) at which 50% are mature, L(ST50) and A(50)] between those caught in the tropics (L(∞) = 2119 mm, k = 0·163, L(ST50) = 1471 mm, A(50) = 5·7 years) and those caught in temperate waters (L(∞) = 3199 mm, k = 0·093, L(ST50) = 2043 mm, A(50) = 8·9 years). The best-fit estimates for a three-parameter von Bertalanffy growth curve fit to both sexes were L(∞) = 3312 mm, L(0) = 584 mm and k = 0·076. Males attained a maximum age of 21 years and grew to at least 2898 mm L(ST). The longevity, maximum length and maturity of females could not be estimated as mature animals could not be sourced from any fishery. Length at birth inferred from neonates with open umbilical scars was 465-563 mm L(ST). There was no significant difference in length and age at maturity of male and female S. mokarran, which reached 50% maturity at 2279 mm L(ST) and 8·3 years. Sphyrna mokarran grew at a similar rate to S. lewini and the best-fit estimates for a two-parameter von Bertalanffy equation fit to length-at-age data for sexes combined with an assumed mean length-at-birth of 700 mm were L(∞) = 4027 mm and k = 0·079. Females attained a maximum age of 39·1 years and grew to at least 4391 mm L(ST). The oldest male S. mokarran was 31·7 years old and 3691 mm L(ST). Validation of annual growth-band deposition in S. mokarran was achieved through a mark, tag and recapture study.

  4. Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme.

    Science.gov (United States)

    Massey, Archna P; Sigurdsson, Snorri Th

    2004-01-01

    The chemical syntheses of RNA oligomers containing modifications on the 5'-carbon of the 5'-terminal nucleoside for crystallographic and mechanistic studies of the hairpin ribozyme are reported. Phosphoramidites 4 and 8 were prepared and used in solid phase syntheses of RNA oligomers containing the sequence 5'-N'UCCUCUCC, where N' indicates either 5'-chloro-5'-deoxyguanosine or 5'-amino-5'-deoxyguanosine, respectively. A ribozyme ligation assay with the 5'-chloro- and 5'-amino-modified RNA oligomers demonstrated their inhibition of the hairpin-catalyzed RNA-RNA ligation reaction.

  5. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

    Science.gov (United States)

    Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej; Batey, Robert T; Becka, Alexander J; Biesiada, Marcin; Boniecki, Michał J; Bujnicki, Janusz; Chen, Shi-Jie; Cheng, Clarence Yu; Chou, Fang-Chieh; Ferré-D'Amaré, Adrian R; Das, Rhiju; Dawson, Wayne K; Feng, Ding; Dokholyan, Nikolay V; Dunin-Horkawicz, Stanisław; Geniesse, Caleb; Kappel, Kalli; Kladwang, Wipapat; Krokhotin, Andrey; Łach, Grzegorz E; Major, François; Mann, Thomas H; Magnus, Marcin; Pachulska-Wieczorek, Katarzyna; Patel, Dinshaw J; Piccirilli, Joseph A; Popenda, Mariusz; Purzycka, Katarzyna J; Ren, Aiming; Rice, Greggory M; Santalucia, John; Sarzynska, Joanna; Szachniuk, Marta; Tandon, Arpit; Trausch, Jeremiah J; Tian, Siqi; Wang, Jian; Weeks, Kevin M; Williams, Benfeard; Xiao, Yi; Xu, Xiaojun; Zhang, Dong; Zok, Tomasz; Westhof, Eric

    2017-01-30

    RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

  6. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

    Directory of Open Access Journals (Sweden)

    Samanta Pino

    2013-12-01

    Full Text Available 3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C, the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3′ terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC. In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA.

  7. Mercury and selenium bioaccumulation in the smooth hammerhead shark, Sphyrna zygaena Linnaeus, from the Mexican Pacific Ocean.

    Science.gov (United States)

    Escobar-Sánchez, O; Galván-Magaña, F; Rosíles-Martínez, R

    2010-04-01

    We analyzed total mercury and selenium bioaccumulation in muscle tissue and cartilage fibers (fins) from smooth hammerhead shark, Sphyrna zygaena, caught off Baja California Sur, Mexico. In muscle tissue, the mercury concentration ranged from 0.005 to 1.93 microg g(-1) ww (wet weight), which falls within the safety limits for food set by international agencies (Hg > 1.0 microg g(-1) ww). Only one specimen showed a mercury value that exceeded this limit. In fins, the mercury bioaccumulation was lower (<0.05). Selenium in muscle ranged from 0.11 to 1.63 microg g(-1) ww, while in fins it ranged from 0.13 to 0.56 microg g(-1) ww.

  8. A computational study of the hydrodynamics in the nasal region of a hammerhead shark (Sphyrna tudes: implications for olfaction.

    Directory of Open Access Journals (Sweden)

    Alex D Rygg

    Full Text Available The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory chambers, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics of olfaction in Sphyrna tudes based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Computed external flow patterns elucidate the occurrence of flow phenomena that result in high and low pressures at the incurrent and excurrent nostrils, respectively, which induces flow through the olfactory chamber. The major (prenarial nasal groove along the cephalofoil is shown to facilitate sampling of a large spatial extent (i.e., an extended hydrodynamic "reach" by directing oncoming flow towards the incurrent nostril. Further, both the major and minor nasal grooves redirect some flow away from the incurrent nostril, thereby limiting the amount of fluid that enters the olfactory chamber. Internal hydrodynamic flow patterns are also revealed, where we show that flow rates within the sensory channels between olfactory lamellae are passively regulated by the apical gap, which functions as a partial bypass for flow in the olfactory chamber. Consequently, the hammerhead shark appears to utilize external (major and minor nasal grooves and internal (apical gap flow regulation mechanisms to limit water flow between the olfactory lamellae, thus protecting these

  9. Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis.

    Science.gov (United States)

    Gaffarogullari, Ece Cazibe; Krause, André; Balbo, Jessica; Herten, Dirk-Peter; Jäschke, Andres

    2013-12-01

    The analysis of binding interactions between small molecules and biopolymers is important for understanding biological processes. While fluorescence correlation spectroscopy (FCS) requires fluorescence labeling on the small molecule, which often interferes with binding, in microscale thermophoresis (MST) the label can be placed on the biopolymer. Ribozymes have not been analyzed by MST so far. The Diels-Alderase ribozyme (DAse) is a true catalyst, facilitating the Diels-Alder reaction between two free small substrates, anthracene dienes, and maleimide dienophiles. Despite high efforts, the determination of the dissociation constant (KD) of maleimide dienophiles to the DAse by FCS has been unsuccessful. Here, we determined the binding interactions of the DAse to its substrates and the Diels-Alder product using MST. The results supported a positive cooperativity for substrate binding to the DAse. By varying the temperature, we furthermore studied the thermodynamics of dienophile dissociation. The entropic contribution was found to be the energetic driving force for the binding of the dienophile to the DAse.

  10. Eclipsing binaries in open clusters

    DEFF Research Database (Denmark)

    Southworth, John; Clausen, J.V.

    2006-01-01

    Stars: fundamental parameters - Stars : binaries : eclipsing - Stars: Binaries: spectroscopic - Open clusters and ass. : general Udgivelsesdato: 5 August......Stars: fundamental parameters - Stars : binaries : eclipsing - Stars: Binaries: spectroscopic - Open clusters and ass. : general Udgivelsesdato: 5 August...

  11. Binary mask programmable hologram.

    Science.gov (United States)

    Tsang, P W M; Poon, T-C; Zhou, Changhe; Cheung, K W K

    2012-11-19

    We report, for the first time, the concept and generation of a novel Fresnel hologram called the digital binary mask programmable hologram (BMPH). A BMPH is comprised of a static, high resolution binary grating that is overlaid with a lower resolution binary mask. The reconstructed image of the BMPH can be programmed to approximate a target image (including both intensity and depth information) by configuring the pattern of the binary mask with a simple genetic algorithm (SGA). As the low resolution binary mask can be realized with less stringent display technology, our method enables the development of simple and economical holographic video display.

  12. Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression.

    Science.gov (United States)

    Shen, Shensi; Rodrigo, Guillermo; Prakash, Satya; Majer, Eszter; Landrain, Thomas E; Kirov, Boris; Daròs, José-Antonio; Jaramillo, Alfonso

    2015-05-26

    Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA-RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits.

  13. Inducible Expression and Splicing of Candida Group Ⅰ Ribozyme in E.coli

    Institute of Scientific and Technical Information of China (English)

    SHANG Yuan; WANG Chen; ZHANG Yi

    2005-01-01

    The Ca. LSU intron flanking a 129 bp exon upstream and a 100 bp exon downstream was inserted into the lacZ gene on pRS426 to transform E. coli. Northern blot analysis and RT-PCR showed that splicing of Ca. LSU in E.coli is efficient upon inducible expression of the precursor RNA. In contrast, co-transcriptional self-splicing of the intron in vitro is much less active. Therefore, this E. coli splicing system can be used as a better model to investigate the effect of the ribozyme inhibitors on Ca. LSU splicing in living cell. We examined the effects of neomycin sulfate and pentamidine on Ca. LSU splicing in E. coli, and found that these drugs does-dependently inhibit the intron splicing.However, heomycin is more potent than pentamidine in this action.

  14. Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world.

    Science.gov (United States)

    Liberman, Joseph A; Wedekind, Joseph E

    2011-06-01

    Genome sequencing has produced thousands of nonprotein coding (nc)RNA sequences including new ribozymes and riboswitches. Such RNAs are notable for their extraordinary functionality, which entails exquisite folding that culminates in biocatalytic or ligand-binding capabilities. Here we discuss advances in relating ncRNA form to function with an emphasis on base pK(a) shifting by the hairpin and hepatitis delta virus ribozymes. We then describe ligand binding by the two smallest riboswitches, which target preQ(1) and S-adenosyl-(l)-homocysteine, followed by an analysis of a second-messenger riboswitch that binds cyclic-di-GMP. Each riboswitch is then compared to a protein that binds the same ligand to contrast binding properties. The results showcase the breadth of functionality attainable from ncRNAs, as well as molecular features notable for antibacterial design.

  15. Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme.

    Science.gov (United States)

    Klein, Daniel J; Wilkinson, Sara R; Been, Michael D; Ferré-D'Amaré, Adrian R

    2007-10-12

    The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibitor glucose 6-phosphate (Glc6P) at 1.7 A and 2.2 A resolution, respectively. The two structures are indistinguishable in the conformations of the small molecules and of the RNA. GlcN6P binding becomes apparent crystallographically when the pH is raised to 8.5, where the ribozyme conformation is identical with that observed previously at pH 5.5. A key structural feature of this ribozyme is a short duplex (P2.2) that is formed between sequences just 3' of the cleavage site and within the core domain, and which introduces a pseudoknot into the active site. Mutagenesis indicates that P2.2 is required for activity in cis-acting and trans-acting forms of the ribozyme. P2.2 formation in a trans-acting ribozyme was exploited to demonstrate that N1 of the guanine at position 1 contributes to GlcN6P binding by interacting with the phosphate of the cofactor. At neutral pH, RNAs with adenine, 2-aminopurine, dimethyladenine or purine substitutions at position 1 cleave faster with glucosamine than with GlcN6P. This altered cofactor preference provides biochemical support for the orientation of the cofactor within the active site. Our results establish two features of the glmS ribozyme that are important for its activity: a sequence within the core domain that selects and positions the cleavage-site sequence, and a nucleobase at position 1 that helps position GlcN6P.

  16. Interacting binary stars

    CERN Document Server

    Sahade, Jorge; Ter Haar, D

    1978-01-01

    Interacting Binary Stars deals with the development, ideas, and problems in the study of interacting binary stars. The book consolidates the information that is scattered over many publications and papers and gives an account of important discoveries with relevant historical background. Chapters are devoted to the presentation and discussion of the different facets of the field, such as historical account of the development in the field of study of binary stars; the Roche equipotential surfaces; methods and techniques in space astronomy; and enumeration of binary star systems that are studied

  17. Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection.

    Directory of Open Access Journals (Sweden)

    David G Nickens

    Full Text Available BACKGROUND: In vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive RNA species. While nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' OH of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated. METHODOLOGY/PRINCIPAL FINDINGS: This study demonstrates the ability of T4 DNA ligase to capture RNA strands in which a tethered monodeoxynucleoside has acquired a 5' phosphate. The ligation reaction therefore mimics the partition step of a selection for nucleoside kinase (deoxyribozymes. Ligation with tethered substrates was considerably slower than with nicked, fully duplex DNA, even though the deoxynucleotides at the ligation junction were Watson-Crick base paired in the tethered substrate. Ligation increased markedly when the bridging template strand contained unpaired spacer nucleotides across from the flexible tether, according to the trends: A(2>A(1>A(3>A(4>A(0>A(6>A(8>A(10 and T(2>T(3>T(4>T(6 approximately T(1>T(8>T(10. Bridging T's generally gave higher yield of ligated product than bridging A's. ATP concentrations above 33 microM accumulated adenylated intermediate and decreased yields of the gap-sealed product, likely due to re-adenylation of dissociated enzyme. Under optimized conditions, T4 DNA ligase efficiently (>90% joined a correctly paired, or TratioG wobble-paired, substrate on the 3' side of the ligation junction while discriminating approximately 100-fold against most mispaired substrates. Tethered dC and dG gave the highest ligation rates and yields, followed by tethered deoxyinosine (dI and dT, with the slowest reactions for tethered dA. The same kinetic trends were observed in ligase-mediated capture in complex reaction mixtures with multiple substrates. The "universal" analog 5-nitroindole (dNI did not support ligation when

  18. Global Phylogeography with Mixed-Marker Analysis Reveals Male-Mediated Dispersal in the Endangered Scalloped Hammerhead Shark (Sphyrna lewini)

    Science.gov (United States)

    Daly-Engel, Toby S.; Seraphin, Kanesa D.; Holland, Kim N.; Coffey, John P.; Nance, Holly A.; Toonen, Robert J.; Bowen, Brian W.

    2012-01-01

    Background The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA) markers demonstrated strong genetic partitioning overall (global ΦST = 0.749) and significant population separations across oceans and between discontinuous continental coastlines. Methodology/Principal Findings We surveyed the same global range with increased sample coverage (N = 403) and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (FST = 0.035) over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (ΦST = 0.749). Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. Conclusions/Significance These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species. PMID:22253848

  19. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini.

    Directory of Open Access Journals (Sweden)

    Toby S Daly-Engel

    Full Text Available BACKGROUND: The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA markers demonstrated strong genetic partitioning overall (global Φ(ST = 0.749 and significant population separations across oceans and between discontinuous continental coastlines. METHODOLOGY/PRINCIPAL FINDINGS: We surveyed the same global range with increased sample coverage (N = 403 and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST = 0.035 over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST = 0.749. Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. CONCLUSIONS/SIGNIFICANCE: These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

  20. Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme.

    Science.gov (United States)

    Posakony, Jeffrey J; Ferré-D'Amaré, Adrian R

    2013-05-17

    Two analogues of glucosamine-6-phosphate (GlcN6P, 1) and five of glucosamine (GlcN, 2) were prepared for evaluation as catalytic cofactors of the glmS ribozyme, a bacterial gene-regulatory RNA that controls cell wall biosynthesis. Glucosamine and allosamine with 3-azido substitutions were prepared by SN2 reactions of the respective 1,2,4,6-protected sugars; final acidic hydrolysis afforded the fully deprotected compounds as their TFA salts. A 6-phospho-2-aminoglucolactam (31) was prepared from glucosamine in a 13-step synthesis, which included a late-stage POCl3-phosphorylation. A simple and widely applicable 2-step procedure with the triethylsilyl (TES) protecting group was developed to selectively expose the 6-OH group in N-protected glucosamine analogues, which provided another route to chemical phosphorylation. Mitsunobu chemistry afforded 6-cyano (35) and 6-azido (36) analogues of GlcN-(Cbz), and the selectivity for the 6-position was confirmed by NMR (COSY, HMBC, HMQC) experiments. Compound 36 was converted to the fully deprotected 6-azido-GlcN (37) and 2,6-diaminoglucose (38) analogues. A 2-hydroxylamino glucose (42) analogue was prepared via an oxaziridine (41). Enzymatic phosphorylation of 42 and chemical phosphorylation of its 6-OH precursor (43) were possible, but 42 and the 6-phospho product (44) were unstable under neutral or basic conditions. Chemical phosphorylation of the previously described 2-guanidinyl-glucose (46) afforded its 6-phospho analogue (49) after final deprotection.

  1. Ribozyme-based insulator parts buffer synthetic circuits from genetic context.

    Science.gov (United States)

    Lou, Chunbo; Stanton, Brynne; Chen, Ying-Ja; Munsky, Brian; Voigt, Christopher A

    2012-11-01

    Synthetic genetic programs are built from circuits that integrate sensors and implement temporal control of gene expression. Transcriptional circuits are layered by using promoters to carry the signal between circuits. In other words, the output promoter of one circuit serves as the input promoter to the next. Thus, connecting circuits requires physically connecting a promoter to the next circuit. We show that the sequence at the junction between the input promoter and circuit can affect the input-output response (transfer function) of the circuit. A library of putative sequences that might reduce (or buffer) such context effects, which we refer to as 'insulator parts', is screened in Escherichia coli. We find that ribozymes that cleave the 5' untranslated region (5'-UTR) of the mRNA are effective insulators. They generate quantitatively identical transfer functions, irrespective of the identity of the input promoter. When these insulators are used to join synthetic gene circuits, the behavior of layered circuits can be predicted using a mathematical model. The inclusion of insulators will be critical in reliably permuting circuits to build different programs.

  2. Limits of neutral drift: lessons from the in vitro evolution of two ribozymes.

    Science.gov (United States)

    Petrie, Katherine L; Joyce, Gerald F

    2014-10-01

    The relative contributions of adaptive selection and neutral drift to genetic change are unknown but likely depend on the inherent abundance of functional genotypes in sequence space and how accessible those genotypes are to one another. To better understand the relative roles of selection and drift in evolution, local fitness landscapes for two different RNA ligase ribozymes were examined using a continuous in vitro evolution system under conditions that foster the capacity for neutral drift to mediate genetic change. The exploration of sequence space was accelerated by increasing the mutation rate using mutagenic nucleotide analogs. Drift was encouraged by carrying out evolution within millions of separate compartments to exploit the founder effect. Deep sequencing of individuals from the evolved populations revealed that the distribution of genotypes did not escape the starting local fitness peak, remaining clustered around the sequence used to initiate evolution. This is consistent with a fitness landscape where high-fitness genotypes are sparse and well isolated, and suggests, at least in this context, that neutral drift alone is not a primary driver of genetic change. Neutral drift does, however, provide a repository of genetic variation upon which adaptive selection can act.

  3. Kuiper Binary Object Formation

    CERN Document Server

    Nazzario, R C; Covington, C; Kagan, D; Hyde, T W

    2005-01-01

    It has been observed that binary Kuiper Belt Objects (KBOs) exist contrary to theoretical expectations. Their creation presents problems to most current models. However, the inclusion of a third body (for example, one of the outer planets) may provide the conditions necessary for the formation of these objects. The presence of a third massive body not only helps to clear the primordial Kuiper Belt but can also result in long lived binary Kuiper belt objects. The gravitational interaction between the KBOs and the third body causes one of four effects; scattering into the Oort cloud, collisions with the growing protoplanets, formation of binary pairs, or creation of a single Kuiper belt object. Additionally, the initial location of the progenitors of the Kuiper belt objects also has a significant effect on binary formation.

  4. Kuiper Binary Object Formation

    OpenAIRE

    Nazzario, R. C.; Orr, K.; Covington, C.; Kagan, D.; Hyde, T. W.

    2005-01-01

    It has been observed that binary Kuiper Belt Objects (KBOs) exist contrary to theoretical expectations. Their creation presents problems to most current models. However, the inclusion of a third body (for example, one of the outer planets) may provide the conditions necessary for the formation of these objects. The presence of a third massive body not only helps to clear the primordial Kuiper Belt but can also result in long lived binary Kuiper belt objects. The gravitational interaction betw...

  5. Eclipsing Binary Pulsars

    CERN Document Server

    Freire, P C C

    2004-01-01

    The first eclipsing binary pulsar, PSR B1957+20, was discovered in 1987. Since then, 13 other eclipsing low-mass binary pulsars have been found, 12 of these are in globular clusters. In this paper we list the known eclipsing binary pulsars and their properties, with special attention to the eclipsing systems in 47 Tuc. We find that there are two fundamentally different groups of eclipsing binary pulsars; separated by their companion masses. The less massive systems (M_c ~ 0.02 M_sun) are a product of predictable stellar evolution in binary pulsars. The systems with more massive companions (M_c ~ 0.2 M_sun) were formed by exchange encounters in globular clusters, and for that reason are exclusive to those environments. This class of systems can be used to learn about the neutron star recycling fraction in the globular clusters actively forming pulsars. We suggest that most of these binary systems are undetectable at radio wavelengths.

  6. A Novel Vector for Abundant Expression of Antisense RNA, Triplex-forming RNA and Ribozyme in vivo

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    For abundant expression of antisense RNA, triplex-forming RNA and Ribozyme in vivo, a novel vector pBSKneorU6' was constructed by PCR cloning. This vector contains the intact human snRNA U6 gene expression unit, yet replacing the 61-nt-sequence in the middle of U6 snRNA coding region with three restriction enzyme sites. Hela nuclear extract in vitro transcription experiments demonstrated that this vector can effectively express U6 mutant RNA. Containing neor at the same time, stably transfected pBSKneorU6' can be selected easily.

  7. Radiation target analysis of RNA.

    OpenAIRE

    Benstein, S L; Kempner, E

    1996-01-01

    Ribozymes are polynucleotide molecules with intrinsic catalytic activity, capable of cleaving nucleic acid substrates. Large RNA molecules were synthesized containing a hammerhead ribozyme moiety of 52 nucleotides linked to an inactive leader sequence, for total lengths of either 262 or 1226 nucleotides. Frozen RNAs were irradiated with high energy electrons. Surviving ribozyme activity was determined using the ability of the irradiated ribozymes to cleave a labeled substrate. The amount of i...

  8. Binary Masking & Speech Intelligibility

    DEFF Research Database (Denmark)

    Boldt, Jesper

    The purpose of this thesis is to examine how binary masking can be used to increase intelligibility in situations where hearing impaired listeners have difficulties understanding what is being said. The major part of the experiments carried out in this thesis can be categorized as either experime...... mask using a directional system and a method for correcting errors in the target binary mask. The last part of the thesis, proposes a new method for objective evaluation of speech intelligibility.......The purpose of this thesis is to examine how binary masking can be used to increase intelligibility in situations where hearing impaired listeners have difficulties understanding what is being said. The major part of the experiments carried out in this thesis can be categorized as either...... experiments under ideal conditions or as experiments under more realistic conditions useful for real-life applications such as hearing aids. In the experiments under ideal conditions, the previously defined ideal binary mask is evaluated using hearing impaired listeners, and a novel binary mask -- the target...

  9. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  10. Binary Neutron Star Mergers

    Directory of Open Access Journals (Sweden)

    Joshua A. Faber

    2012-07-01

    Full Text Available We review the current status of studies of the coalescence of binary neutron star systems. We begin with a discussion of the formation channels of merging binaries and we discuss the most recent theoretical predictions for merger rates. Next, we turn to the quasi-equilibrium formalisms that are used to study binaries prior to the merger phase and to generate initial data for fully dynamical simulations. The quasi-equilibrium approximation has played a key role in developing our understanding of the physics of binary coalescence and, in particular, of the orbital instability processes that can drive binaries to merger at the end of their lifetimes. We then turn to the numerical techniques used in dynamical simulations, including relativistic formalisms, (magneto-hydrodynamics, gravitational-wave extraction techniques, and nuclear microphysics treatments. This is followed by a summary of the simulations performed across the field to date, including the most recent results from both fully relativistic and microphysically detailed simulations. Finally, we discuss the likely directions for the field as we transition from the first to the second generation of gravitational-wave interferometers and while supercomputers reach the petascale frontier.

  11. Binary and Millisecond Pulsars

    Directory of Open Access Journals (Sweden)

    Lorimer Duncan R.

    2008-11-01

    Full Text Available We review the main properties, demographics and applications of binary and millisecond radio pulsars. Our knowledge of these exciting objects has greatly increased in recent years, mainly due to successful surveys which have brought the known pulsar population to over 1800. There are now 83 binary and millisecond pulsars associated with the disk of our Galaxy, and a further 140 pulsars in 26 of the Galactic globular clusters. Recent highlights include the discovery of the young relativistic binary system PSR J1906+0746, a rejuvination in globular cluster pulsar research including growing numbers of pulsars with masses in excess of 1.5M_⊙, a precise measurement of relativistic spin precession in the double pulsar system and a Galactic millisecond pulsar in an eccentric (e = 0.44 orbit around an unevolved companion.

  12. Binary Popldation Synthcsis Study

    Institute of Scientific and Technical Information of China (English)

    HAN Zhanwen

    2011-01-01

    Binary population synthesis (BPS), an approach to evolving millions of stars (including binaries) simultaneously, plays a crucial role in our understanding of stellar physics, the structure and evolution of galaxies, and cosmology. We proposed and developed a BPS approach, and used it to investigate the formation of many peculiar stars such as hot subdwarf stars, progenitors of type la supernovae, barium stars, CH stars, planetary nebulae, double white dwarfs, blue stragglers, contact binaries, etc. We also established an evolution population synthesis (EPS) model, the Yunnan Model, which takes into account binary interactions for the first time. We applied our model for the origin of hot subdwarf stars in the study of elliptical galaxies and explained their far-UV radiation.

  13. Eclipsing Binary Update, No. 2.

    Science.gov (United States)

    Williams, D. B.

    1996-01-01

    Contents: 1. Wrong again! The elusive period of DHK 41. 2. Stars observed and not observed. 3. Eclipsing binary chart information. 4. Eclipsing binary news and notes. 5. A note on SS Arietis. 6. Featured star: TX Ursae Majoris.

  14. Ribozyme对癌基因ki-rasG12V mRNA的剪切及其特异性%Cleavage of Oncogene ki-rasG12V mRNA by Ribozyme and It' s Specificity

    Institute of Scientific and Technical Information of China (English)

    吴国祥; 方裕强; 许国铭; 李兆申; 陆德如

    2000-01-01

    目的:设计切割ki-rasG12vmRNA的特异性ribozyme(Rz217),明确其对癌基因ki-rasG12VmRNA的细胞内外切割活性,为以ki-rasG12VmRNA为特异性靶分子的基因治疗及癌基因ki-ras的功能研究提拱一种新的途径。方法:依Symons总结的"锤头结构"原理,设计一种能特异性切割ki-rasG12VmRNA的ribozyme,利用DNA重组技术构建ki-rasG12V外显子1和ri-bozyme Rz217的体外转录质粒及ribozyme Rz217的真核表达质粒,体外转录获得ribozyme Rz217及ki-rasG12V外显子1 mRNA,在含Mg2+溶液中ribozyme Rz217对其靶RNA分子进行切割。以RT-PCR对转染ribozyme Rz217真核表达质粒的细胞ki-rasG12VmRNA进行半定量分析。结果:ki-rasG12V外显子1体外转录mRNA分子,能被ribozyme Rz217定点切割而野生型ki-ras外显子1体外转录mRNA则不被切割;转染ribozyme Rz217的胰癌细胞ki-rasG12VmRNA含量减少,而转染ribozyme Re217的肝癌细胞其内源性ki-ras mRNA含量无明显变化。结论:ribozyme Rz217无论在细胞内外均能剪切突变型ki-ras mRNA(G12V)而且其切割作用为突变型ki-rasG12VmRNA特异性的。%Objective: To design and confirm the cleavage activity of ribozyme Rz217 to oncogene ki-rasG12V messenger RNA and search for a new method for gene therapy targeting oncogene ki-ras. Methods: According to Symon' s principle,design an ribozyme specific for ki-rasc12v mRNA, both the constructs for transcription in vitro of ribozyme Rz217 and ki-ras exonl and the mammalian expression constructs of ribozyme Rz217 were constructed by DNA recombinant technique,ribozyme Rz217 and ki-ras exonl mRNA was obtained by transcription in vitro with T7 and SP6 RNA polymerase. Pancre atic carcinoma cell line PaTu8988 and human hepatocellular carcinomacell line BEL7404 were transfected with Rz217 mammalian expression constructs and the level of endogenous ki-rasG12V mRNA or ki-ras mRNA was determined by semiquantitative RT-PCR. Results: Not only in vitro

  15. Compressing Binary Decision Diagrams

    DEFF Research Database (Denmark)

    Hansen, Esben Rune; Satti, Srinivasa Rao; Tiedemann, Peter

    2008-01-01

    The paper introduces a new technique for compressing Binary Decision Diagrams in those cases where random access is not required. Using this technique, compression and decompression can be done in linear time in the size of the BDD and compression will in many cases reduce the size of the BDD to 1...

  16. Compressing Binary Decision Diagrams

    DEFF Research Database (Denmark)

    Rune Hansen, Esben; Srinivasa Rao, S.; Tiedemann, Peter

    The paper introduces a new technique for compressing Binary Decision Diagrams in those cases where random access is not required. Using this technique, compression and decompression can be done in linear time in the size of the BDD and compression will in many cases reduce the size of the BDD to 1...

  17. Orbits for sixteen binaries

    Directory of Open Access Journals (Sweden)

    Cvetković Z.

    2006-01-01

    Full Text Available In this paper orbits for 13 binaries are recalculated and presented. The reason is that recent observations show higher residuals than the corresponding ephemerides calculated by using the orbital elements given in the Sixth Catalog of Orbits of Visual Binary Stars. The binaries studied were: WDS 00182+7257 = A 803, WDS 00335+4006 = HO 3, WDS 00583+2124 = BU 302, WDS 01011+6022 = A 926, WDS 01014+1155 = BU 867, WDS 01112+4113 = A 655, WDS 01361−2954 + HJ 3447, WDS 02333+5219 = STT 42 AB,WDS 04362+0814 = A 1840 AB,WDS 08017−0836 = A 1580, WDS 08277−0425 = A 550, WDS 17471+1742 = STF 2215 and WDS 18025+4414 = BU 1127 Aa-B. In addition, for three binaries - WDS 01532+1526 = BU 260, WDS 02563+7253 = STF 312 AB and WDS 05003+3924 = STT 92 AB - the orbital elements are calculated for the first time. In this paper the authors present not only the orbital elements, but the masses dynamical parallaxes, absolute magnitudes and ephemerides for the next five years, as well.

  18. Equational binary decision diagrams

    NARCIS (Netherlands)

    Groote, J.F.; Pol, J.C. van de

    2000-01-01

    We incorporate equations in binary decision diagrams (BDD). The resulting objects are called EQ-BDDs. A straightforward notion of ordered EQ-BDDs (EQ-OBDD) is defined, and it is proved that each EQ-BDD is logically equivalent to an EQ-OBDD. Moreover, on EQ-OBDDs satisfiability and tautology checkin

  19. Black holes in binary stars

    NARCIS (Netherlands)

    Wijers, R.A.M.J.

    1996-01-01

    Introduction Distinguishing neutron stars and black holes Optical companions and dynamical masses X-ray signatures of the nature of a compact object Structure and evolution of black-hole binaries High-mass black-hole binaries Low-mass black-hole binaries Low-mass black holes Formation of black holes

  20. Learning to assign binary weights to binary descriptor

    Science.gov (United States)

    Huang, Zhoudi; Wei, Zhenzhong; Zhang, Guangjun

    2016-10-01

    Constructing robust binary local feature descriptors are receiving increasing interest due to their binary nature, which can enable fast processing while requiring significantly less memory than their floating-point competitors. To bridge the performance gap between the binary and floating-point descriptors without increasing the computational cost of computing and matching, optimal binary weights are learning to assign to binary descriptor for considering each bit might contribute differently to the distinctiveness and robustness. Technically, a large-scale regularized optimization method is applied to learn float weights for each bit of the binary descriptor. Furthermore, binary approximation for the float weights is performed by utilizing an efficient alternatively greedy strategy, which can significantly improve the discriminative power while preserve fast matching advantage. Extensive experimental results on two challenging datasets (Brown dataset and Oxford dataset) demonstrate the effectiveness and efficiency of the proposed method.

  1. Cisplatin sensitivity and mechanisms of anti-HPV16 E6-ribozyme on cervical carcinoma CaSKi cell line

    Institute of Scientific and Technical Information of China (English)

    Zhiguo Rao; Jianfei Gao; Bicheng Zhang; Bo Yang; Jiren Zhang

    2012-01-01

    Objective: The aim of this study was to study the cisplatin sensitizing effect and mechanism of anti-HPV16 E6- ribozyme on cervical carcinoma cell line.Methods: The anti-HPV16E6-ribozyme and empty eucaryotic expressing plasmids were transfected into CaSKi cell, which named as CaSKi-R, CaSKi-P respectively.E6 mRNA, the sensitivity to cisplatin, apoptosis rates, expression of p53, Bcl-2, Bax and C-myc proteins and mRNA were examined by Northern blot, MTT colorimetric assay, PI/Annexin V stained methods, flow cytometry anslysis and RT-PCR, respectively.Results: E6 mRNA was less in CaSKi-R than in CaSKi.The sensitivity of CaSKi-R cells to cisplatin was 2.28 and 2.21 times than that of CaSKi and CaSKi-P cells.The apoptotic rates in CaSKi, CaSKi-P and CaSKi-R cells was (18.9 ± 3.5)%, (19.7 ± 4.8)% and (40.4 ± 4.5)%.The apoptotic rates was increased in CaSKi-R than that of CaSKi cells treated with cisplatin (P = 0.003).Comapred with CaSKi cell, the expression of p53 (P = 0.000), Bax protein (P = 0.002) was significantly higher and the expression of Bcl-2 protein (P = 0.005), C-myc protein (P = 0.005) was significantly lower in CaSKi-R than that of CaSKi cell treated with cisplatin.Comapred with CaSKi cell, the expression of p53, Bax mRNA in CaSKi-R cell treated with cisplatin increased, while Bcl-2, C-myc mRNA decreased.Conclusion: CaSKi-R cells transfected by anti-HPVE6-ribozyme increased the sensitivity to cisplatin.The increase of sensitivity to cisplatin in CaSKi-R cells may be associated with increasing expression of p53, Bax protein, and decreasing expression of C-myc, Bcl-2 proteins.

  2. The Countermeasures for Improving the Service Life of High Manganese Steel’s Hammerhead of Hammer Crusher%提高锤式破碎机高锰钢锤头使用寿命的对策

    Institute of Scientific and Technical Information of China (English)

    李密; 姚锡严

    2013-01-01

      锤式破碎机锤头是破碎机的关键部件之一,其质量的好坏关系到使用寿命的长短,因此要求锤头不仅具有较高的硬度及耐磨损性能,还要有较高的韧性及承受冲击性能。文章分析了影响锤式破碎机高锰钢锤头破碎能力的主要因素,提出了提高锤式破碎机高锰钢锤头使用寿命的对策。%The hammerhead of hammer crusher is one of the key components of crumbling machine. Its quality is related to the length of service life, so the hammerhead not only needs high hardness and wear-resisting property, but also needs higher toughness and impact performance. The paper analyzes the major factors of affecting the breaking ability of high manganese steel's hammerhead of hammer crusher, and puts forward countermeasures for improving the service life of it.

  3. Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme.

    Science.gov (United States)

    Rublack, Nico; Müller, Sabine

    2014-01-01

    Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.

  4. Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

    Directory of Open Access Journals (Sweden)

    Nico Rublack

    2014-08-01

    Full Text Available Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.

  5. The Binary Garrote

    CERN Document Server

    Kappen, H J

    2011-01-01

    In this paper, I present a new model and solution method for sparse regression. The model introduces binary selector variables $s_i$ for the features $i$ in a way that is similar to Breiman's Garrote model. I refer to this method as the binary Garrote (BG). The posterior probability for $s_i$ is computed in the variational approximation. The BG is compared numerically with the Lasso method and with ridge regression. Numerical results on synthetic data show that the BG yields more accurate predictions and more accurately reconstructs the true model than the other methods. The naive implementation of the BG requires the inversion of a modified covariance matrix which scales cubic in the number of features. We indicate how for sparse problem the solution can be computed linear in the number of features.

  6. Binary Tetrahedral Flavor Symmetry

    CERN Document Server

    Eby, David A

    2013-01-01

    A study of the T' Model and its variants utilizing Binary Tetrahedral Flavor Symmetry. We begin with a description of the historical context and motivations for this theory, together with some conceptual background for added clarity, and an account of our theory's inception in previous works. Our model endeavors to bridge two categories of particles, leptons and quarks, a unification made possible by the inclusion of additional Higgs particles, shared between the two fermion sectors and creating a single coherent system. This is achieved through the use of the Binary Tetrahedral symmetry group and an investigation of the Tribimaximal symmetry evidenced by neutrinos. Our work details perturbations and extensions of this T' Model as we apply our framework to neutrino mixing, quark mixing, unification, and dark matter. Where possible, we evaluate model predictions against experimental results and find excellent matching with the atmospheric and reactor neutrino mixing angles, an accurate prediction of the Cabibb...

  7. Binary Love Relations

    CERN Document Server

    Yagi, Kent

    2015-01-01

    When in a tight binary, the mutual tidal deformations of neutron stars imprint onto observables, encoding information about their internal structure at supranuclear densities and gravity in the extreme-gravity regime. Gravitational wave observations of their late binary inspiral may serve as a tool to extract the individual tidal deformabilities, but this is made difficult by degeneracies between them in the gravitational wave model. We here resolve this problem by discovering approximately universal relations between dimensionless combinations of the individual tidal deformabilities. We show that these relations break degeneracies in the gravitational wave model, allowing for the accurate extraction of both deformabilities. Such measurements can be used to better differentiate between equation-of-state models, and improve tests of General Relativity and cosmology.

  8. Binary Love relations

    Science.gov (United States)

    Yagi, Kent; Yunes, Nicolás

    2016-07-01

    When in a tight binary, the mutual tidal deformations of neutron stars get imprinted onto observables, encoding information about their internal structure at supranuclear densities and gravity in the extreme-gravity regime. Gravitational wave (GW) observations of their late binary inspiral may serve as a tool to extract the individual tidal deformabilities, but this is made difficult by degeneracies between them in the GW model. We here resolve this problem by discovering approximately equation-of-state (EoS)-insensitive relations between dimensionless combinations of the individual tidal deformabilities. We show that these relations break degeneracies in the GW model, allowing for the accurate extraction of both deformabilities. Such measurements can be used to better differentiate between EoS models, and improve tests of general relativity and cosmology.

  9. The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures.

    Science.gov (United States)

    Jenkins, Jermaine L; Wedekind, Joseph E

    2016-01-01

    Ribozymes and riboswitches are examples of non-protein-coding (nc)RNA molecules that achieve biological activity by adopting complex three-dimensional folds. Visualization of such molecules at near-atomic resolution can enhance our understanding of how chemical groups are organized spatially, thereby providing novel insight into function. This approach has its challenges, which mainly entail sample crystallization followed by the application of empirical, structure-determination methods that often include experimental "phasing" of X-ray diffraction data. A paucity of high-quality crystals or a low symmetry space group are factors that demand rapid assessment of phasing potential during an ongoing experiment in order to assure a successful outcome. Here we describe the process of evaluating the anomalous signal-to-noise as a prelude to single wavelength or multiwavelength anomalous diffraction (SAD or MAD) phasing. Test cases include an autolytic 62-mer RNA enzyme known as the hairpin ribozyme, and a 33-mer riboswitch that binds the modified guanine metabolite preQ1. The crystals were derivatized with iridium (III) hexammine and osmium (III) pentaammine triflate, respectively. Each data set was then subjected to the XPREP and SHELX programs to assess the anomalous signal-to-noise and to locate the heavy-atom substructure. Subsequent noise filtering was conducted in SHELXE or RESOLVE. The methods described are applicable to the rapid phasing of RNA X-ray diffraction data, and contrast the efficacy of in-house X-rays with those attainable from synchrotron-radiation sources in terms of the potential to plan for and execute an experimental structure determination.

  10. Binary-Signal Recovery

    Science.gov (United States)

    Griebeler, Elmer L.

    2011-01-01

    Binary communication through long cables, opto-isolators, isolating transformers, or repeaters can become distorted in characteristic ways. The usual solution is to slow the communication rate, change to a different method, or improve the communication media. It would help if the characteristic distortions could be accommodated at the receiving end to ease the communication problem. The distortions come from loss of the high-frequency content, which adds slopes to the transitions from ones to zeroes and zeroes to ones. This weakens the definition of the ones and zeroes in the time domain. The other major distortion is the reduction of low frequency, which causes the voltage that defines the ones or zeroes to drift out of recognizable range. This development describes a method for recovering a binary data stream from a signal that has been subjected to a loss of both higher-frequency content and low-frequency content that is essential to define the difference between ones and zeroes. The method makes use of the frequency structure of the waveform created by the data stream, and then enhances the characteristics related to the data to reconstruct the binary switching pattern. A major issue is simplicity. The approach taken here is to take the first derivative of the signal and then feed it to a hysteresis switch. This is equivalent in practice to using a non-resonant band pass filter feeding a Schmitt trigger. Obviously, the derivative signal needs to be offset to halfway between the thresholds of the hysteresis switch, and amplified so that the derivatives reliably exceed the thresholds. A transition from a zero to a one is the most substantial, fastest plus movement of voltage, and therefore will create the largest plus first derivative pulse. Since the quiet state of the derivative is sitting between the hysteresis thresholds, the plus pulse exceeds the plus threshold, switching the hysteresis switch plus, which re-establishes the data zero to one transition

  11. Massive Black Hole Binary Evolution

    Directory of Open Access Journals (Sweden)

    Merritt David

    2005-11-01

    Full Text Available Coalescence of binary supermassive black holes (SBHs would constitute the strongest sources of gravitational waves to be observed by LISA. While the formation of binary SBHs during galaxy mergers is almost inevitable, coalescence requires that the separation between binary components first drop by a few orders of magnitude, due presumably to interaction of the binary with stars and gas in a galactic nucleus. This article reviews the observational evidence for binary SBHs and discusses how they would evolve. No completely convincing case of a bound, binary SBH has yet been found, although a handful of systems (e.g. interacting galaxies; remnants of galaxy mergers are now believed to contain two SBHs at projected separations of <~ 1kpc. N-body studies of binary evolution in gas-free galaxies have reached large enough particle numbers to reproduce the slow, “diffusive” refilling of the binary’s loss cone that is believed to characterize binary evolution in real galactic nuclei. While some of the results of these simulations - e.g. the binary hardening rate and eccentricity evolution - are strongly N-dependent, others - e.g. the “damage” inflicted by the binary on the nucleus - are not. Luminous early-type galaxies often exhibit depleted cores with masses of ~ 1-2 times the mass of their nuclear SBHs, consistent with the predictions of the binary model. Studies of the interaction of massive binaries with gas are still in their infancy, although much progress is expected in the near future. Binary coalescence has a large influence on the spins of SBHs, even for mass ratios as extreme as 10:1, and evidence of spin-flips may have been observed.

  12. Visual binary stars: data to investigate formation of binaries

    Science.gov (United States)

    Kovaleva,, D.; Malkov,, O.; Yungelson, L.; Chulkov, D.

    Statistics of orbital parameters of binary stars as well as statistics of their physical characteristics bear traces of star formation history. However, statistical investigations of binaries are complicated by incomplete or missing observational data and by a number of observational selection effects. Visual binaries are the most common type of observed binary stars, with the number of pairs exceeding 130 000. The most complete list of presently known visual binary stars was compiled by cross-matching objects and combining data of the three largest catalogues of visual binaries. This list was supplemented by the data on parallaxes, multicolor photometry, and spectral characteristics taken from other catalogues. This allowed us to compensate partly for the lack of observational data for these objects. The combined data allowed us to check the validity of observational values and to investigate statistics of the orbital and physical parameters of visual binaries. Corrections for incompleteness of observational data are discussed. The datasets obtained, together with modern distributions of binary parameters, will be used to reconstruct the initial distributions and parameters of the function of star formation for binary systems.

  13. Structure et réarrangements conformationnels au cours de l’épissage du composant ribozyme d’un intron de groupe II

    OpenAIRE

    Li, Cheng-Fang

    2011-01-01

    Group II introns are a class of RNAs best known for their ribozyme-catalyzed, self-splicing reaction. Under certain conditions, the introns can excise themselves from precursor mRNAs and ligate together their flanking exons, without the aid of proteins. Group II introns generally excise from pre-mRNA as a lariat, like the one formed by spliceosomal introns, similarities in the splicing mechanism suggest that group II introns and nuclear spliceosomal introns may share a common evolutionary anc...

  14. Lentiviral transduction of Tar Decoy and CCR5 ribozyme into CD34+ progenitor cells and derivation of HIV-1 resistant T cells and macrophages

    Directory of Open Access Journals (Sweden)

    Rossi John

    2004-12-01

    Full Text Available Abstract Background RNA based antiviral approaches against HIV-1 are among the most promising for long-term gene therapy. These include ribozymes, aptamers (decoys, and small interfering RNAs (siRNAs. Lentiviral vectors are ideal for transduction of such inhibitory RNAs into hematopoietic stem cells due to their ability to transduce non-dividing cells and their relative refractiveness to gene silencing. The objective of this study is to introduce an HIV-1 Tar aptamer either alone or in combination with an anti-CCR5 ribozyme into CD34+ hematopoietic progenitor cells via an HIV-based lentiviral vector to derive viral resistant progeny T cells and macrophages. Results High efficiency and sustained gene transfer into CD34+ cells were achieved with lentiviral vector constructs harboring either Tar decoy or Tar decoy in combination with CCR5 ribozyme. Cells transduced with these constructs differentiated normally into T-lymphocytes in vivo in thy/liv grafts of SCID-hu mice, and into macrophages in vitro in the presence of appropriate growth factors. When challenged in vitro, the differentiated T lymphocytes and macrophages showed marked resistance against HIV-1 infection. Conclusions Viral resistant transgenic T cells and macrophages that express HIV-1 Tar aptamer either alone or in combination with an anti-CCR5 ribozyme could be obtained by lentiviral gene transduction of CD34+ progenitor cells. These results showed for the first time that expression of these anti-HIV-1 transgenes in combination do not interfere with normal thymopoiesis and thus have set the stage for their application in stem cell based gene therapy for HIV/AIDS.

  15. Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.

    Science.gov (United States)

    Guo, Man; Spitale, Robert C; Volpini, Rosaria; Krucinska, Jolanta; Cristalli, Gloria; Carey, Paul R; Wedekind, Joseph E

    2009-09-16

    Catalytic RNA molecules can achieve rate acceleration by shifting base pK(a) values toward neutrality. Prior evidence has suggested that base A38 of the hairpin ribozyme plays an important role in phosphoryl transfer, possibly functioning as a general acid, or by orienting a specific water molecule for proton transfer. To address the role of A38, we used Raman spectroscopy to measure directly the pK(a) of the N1-imino moiety in the context of hairpin ribozyme crystals representative of a "precatalytic" conformation. The results revealed that the pK(a) of A38 is shifted to 5.46 +/- 0.05 relative to 3.68 +/- 0.06 derived from a reference solution of the nucleotide AMP. The elevated pK(a) correlates well with the first titration point of the macroscopic pH-rate profile of the hairpin ribozyme in solution and strongly supports A38 as a general acid catalyst in bond scission. The results confirm that A38 is protonated before the transition state, which would promote phosphorane development. Overall, the results establish a cogent structure-function paradigm that expands our understanding of how RNA structure can enhance nucleobase reactivity to catalyze biological reactions.

  16. Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes – A comparative study of group-I intron structures

    Indian Academy of Sciences (India)

    K Chandrasekhar; R Malathi

    2003-09-01

    In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.

  17. A modified group I intron can function as both a ribozyme and a 5' exon in a trans-exon ligation reaction.

    Science.gov (United States)

    Tasiouka, K I; Burke, J M

    1994-06-24

    Here, we show that a single RNA molecule derived from a group-I intron can provide the catalytic activity, the substrate recognition domain and the attacking nucleophile in a reaction that mimics the exon ligation step of splicing. To accomplish this reaction, we have linked a 5' exon sequence to the 3' end of an attenuated form of the self-splicing Tetrahymena rRNA intron. The ribozyme (I-E1) attacks an oligoribonucleotide analog of the 3' splice site (I'-E2) to generate a product containing ligated exons (I-E1-E2) and a small intron fragment (I'). Two modified introns were constructed and tested for activity. A construct designed to interact with the 3' splice site through intermolecular P9.0 and P10 helices was found to be inactive due to failure to form a stable ribozyme-substrate complex. A second modified intron and substrate combination was engineered, in which the complex was further stabilized by an intermolecular P9.2 helix. In this case, stable complexes and reaction products were identified. The reaction efficiency was low compared to splicing of the unmodified intron-containing precursor, and will be optimized in future experiments. Following optimization, we believe that this system may be exploited to examine the functional consequences of a wide variety of 3' splice-site modifications, and may provide the basis for development of highly selective trans-acting ribozymes.

  18. Rotational mixing in close binaries

    CERN Document Server

    de Mink, S E; Langer, N; Yoon, S -Ch; Brott, I; Glebbeek, E; Verkoulen, M; Pols, O R

    2008-01-01

    Rotational mixing is a very important but uncertain process in the evolution of massive stars. We propose to use close binaries to test its efficiency. Based on rotating single stellar models we predict nitrogen surface enhancements for tidally locked binaries. Furthermore we demonstrate the possibility of a new evolutionary scenario for very massive (M > 40 solar mass) close (P < 3 days) binaries: Case M, in which mixing is so efficient that the stars evolve quasi-chemically homogeneously, stay compact and avoid any Roche-lobe overflow, leading to very close (double) WR binaries.

  19. Evolution of Close Binary Systems

    Energy Technology Data Exchange (ETDEWEB)

    Yakut, K; Eggleton, P

    2005-01-24

    We collected data on the masses, radii, etc. of three classes of close binary stars: low-temperature contact binaries (LTCBs), near-contact binaries (NCBs), and detached close binaries (DCBs). They restrict themselves to systems where (1) both components are, at least arguably, near the Main Sequence, (2) the periods are less than a day, and (3) there is both spectroscopic and photometric analysis leading to reasonably reliable data. They discuss the possible evolutionary connections between these three classes, emphasizing the roles played by mass loss and angular momentum loss in rapidly-rotating cool stars.

  20. Chaos in Binary Category Computation

    CERN Document Server

    Gonçalves, Carlos Pedro

    2010-01-01

    Category computation theory deals with a web-based systemic processing that underlies the morphic webs, which constitute the basis of categorial logical calculus. It is proven that, for these structures, algorithmically incompressible binary patterns can be morphically compressed, with respect to the local connectivities, in a binary morphic program. From the local connectivites, there emerges a global morphic connection that can be characterized by a low length binary string, leading to the identification of chaotic categorial dynamics, underlying the algorithmically random pattern. The work focuses on infinite binary chains of C2, which is a category that implements an X-OR-based categorial logical calculus.

  1. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  2. Microlensing modulation by binaries

    CERN Document Server

    Dubath, F; Durrer, R; Dubath, Florian; Gasparini, Maria Alice; Durrer, Ruth

    2006-01-01

    We compute the effect of the lens quadrupole on microlensing. The time dependence of the quadrupole can lead to specific modulations of the amplification signal. We study especially binary system lenses in our galaxy. The modulation is observable if the rotation period of the system is smaller than the time over which the amplification is significant and if the impact parameter of the passing light ray is sufficiently close to the Einstein radius so that the amplification is very large. Observations of this modulation can reveal important information on the quadrupole and thus on the gravitational radiation emitted by the lens.

  3. Evolution of Binaries in Dense Stellar Systems

    CERN Document Server

    Ivanova, Natalia

    2011-01-01

    In contrast to the field, the binaries in dense stellar systems are frequently not primordial, and could be either dynamically formed or significantly altered from their primordial states. Destruction and formation of binaries occur in parallel all the time. The destruction, which constantly removes soft binaries from a binary pool, works as an energy sink and could be a reason for cluster entering the binary-burning phase. The true binary fraction is greater than observed, as a result, the observable binary fraction evolves differently from the predictions. Combined measurements of binary fractions in globular clusters suggest that most of the clusters are still core-contracting. The formation, on other hand, affects most the more evolutionary advanced stars, which significantly enhances the population of X-ray sources in globular clusters. The formation of binaries with a compact objects proceeds mainly through physical collisions, binary-binary and single-binary encounters; however, it is the dynamical for...

  4. Spin Correlation in Binary Systems

    CERN Document Server

    Farbiash, N; Farbiash, Netzach; Steinitz, Raphael

    2004-01-01

    We examine the correlation of projected rotational velocities in binary systems. It is an extension of previous work (Steinitz and Pyper, 1970; Levato, 1974). An enlarged data basis and new tests enable us to conclude that there is indeed correlation between the projected rotational velocities of components of binaries. In fact we suggest that spins are already correlated.

  5. Evolutionary Memory in Binary Systems?

    CERN Document Server

    Steinitz, N F R

    2004-01-01

    Correlation between the spins (rotational velocities) in binaries has previously been established. We now continue and show that the degree of spin correlation is independent of the components' separation. Such a result might be related for example to Zhang's non-linear model for the formation of binary stars from a nebula.

  6. Relativistic Binaries in Globular Clusters

    Directory of Open Access Journals (Sweden)

    Matthew J. Benacquista

    2013-03-01

    Full Text Available Galactic globular clusters are old, dense star systems typically containing 10^4 – 10^6 stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution that leads to relativistic binaries, and current and possible future observational evidence for this population. Our discussion of globular cluster evolution will focus on the processes that boost the production of tight binary systems and the subsequent interaction of these binaries that can alter the properties of both bodies and can lead to exotic objects. Direct N-body integrations and Fokker–Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.

  7. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.

  8. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  9. Relativistic Binaries in Globular Clusters

    Directory of Open Access Journals (Sweden)

    Benacquista Matthew J.

    2006-02-01

    Full Text Available The galactic population of globular clusters are old, dense star systems, with a typical cluster containing 10^4 - 10^7 stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss the theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution which lead to relativistic binaries, and current and possible future observational evidence for this population. Globular cluster evolution will focus on the properties that boost the production of hard binary systems and on the tidal interactions of the galaxy with the cluster, which tend to alter the structure of the globular cluster with time. The interaction of the components of hard binary systems alters the evolution of both bodies and can lead to exotic objects. Direct N-body integrations and Fokker-Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.

  10. Relativistic Binaries in Globular Clusters

    Directory of Open Access Journals (Sweden)

    Benacquista Matthew

    2002-01-01

    Full Text Available The galactic population of globular clusters are old, dense star systems, with a typical cluster containing $10^4 - 10^6$ stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss the theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution which lead to relativistic binaries, and current and possible future observational evidence for this population. Globular cluster evolution will focus on the properties that boost the production of hard binary systems and on the tidal interactions of the galaxy with the cluster, which tend to alter the structure of the globular cluster with time. The interaction of the components of hard binary systems alters the evolution of both bodies and can lead to exotic objects. Direct $N$-body integrations and Fokker--Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.

  11. Signature Visualization of Software Binaries

    Energy Technology Data Exchange (ETDEWEB)

    Panas, T

    2008-07-01

    In this paper we present work on the visualization of software binaries. In particular, we utilize ROSE, an open source compiler infrastructure, to pre-process software binaries, and we apply a landscape metaphor to visualize the signature of each binary (malware). We define the signature of a binary as a metric-based layout of the functions contained in the binary. In our initial experiment, we visualize the signatures of a series of computer worms that all originate from the same line. These visualizations are useful for a number of reasons. First, the images reveal how the archetype has evolved over a series of versions of one worm. Second, one can see the distinct changes between version. This allows the viewer to form conclusions about the development cycle of a particular worm.

  12. Observing binary inspiral with LIGO

    CERN Document Server

    Finn, L S

    1994-01-01

    Gravitational radiation from a binary neutron star or black hole system leads to orbital decay and the eventual coalescence of the binary's components. During the last several minutes before the binary components coalesce, the radiation will enter the bandwidth of the United States Laser Inteferometer Gravitational-wave Observatory (LIGO) and the French/Italian VIRGO gravitational radiation detector. The combination of detector sensitivity, signal strength, and source density and distribution all point to binary inspiral as the most likely candidate for observation among all the anticipated sources of gravitational radiation for LIGO/VIRGO. Here I review briefly some of the questions that are posed to theorists by the impending observation of binary inspiral.

  13. Towards Physarum Binary Adders

    CERN Document Server

    Jones, Jeff; 10.1016/j.biosystems.2010.04.005

    2010-01-01

    Plasmodium of \\emph{Physarum polycephalum} is a single cell visible by unaided eye. The plasmodium's foraging behaviour is interpreted in terms of computation. Input data is a configuration of nutrients, result of computation is a network of plasmodium's cytoplasmic tubes spanning sources of nutrients. Tsuda et al (2004) experimentally demonstrated that basic logical gates can be implemented in foraging behaviour of the plasmodium. We simplify the original designs of the gates and show --- in computer models --- that the plasmodium is capable for computation of two-input two-output gate $ \\to $ and three-input two-output $ \\to $. We assemble the gates in a binary one-bit adder and demonstrate validity of the design using computer simulation.

  14. Towards Physarum binary adders.

    Science.gov (United States)

    Jones, Jeff; Adamatzky, Andrew

    2010-07-01

    Plasmodium of Physarum polycephalum is a single cell visible by unaided eye. The plasmodium's foraging behaviour is interpreted in terms of computation. Input data is a configuration of nutrients, result of computation is a network of plasmodium's cytoplasmic tubes spanning sources of nutrients. Tsuda et al. (2004) experimentally demonstrated that basic logical gates can be implemented in foraging behaviour of the plasmodium. We simplify the original designs of the gates and show - in computer models - that the plasmodium is capable for computation of two-input two-output gate x, y-->xy, x+y and three-input two-output x,y,z-->x yz,x+y+z. We assemble the gates in a binary one-bit adder and demonstrate validity of the design using computer simulation.

  15. Eccentric Binary Millisecond Pulsars

    CERN Document Server

    Freire, Paulo C C

    2009-01-01

    In this paper we review the recent discovery of several millisecond pulsars (MSPs) in eccentric binary systems. Timing these MSPs we were able to estimate (and in one case precisely measure) their masses. These results suggest that, as a class, MSPs have a much wider range of masses (1.3 to > 2 solar masses) than the normal and mildly recycled pulsars found in double neutron star (DNS) systems (1.25 < Mp < 1.44 solar masses). This is very likely to be due to the prolonged accretion episode that is thought to be required to form a MSP. The likely existence of massive MSPs makes them a powerful probe for understanding the behavior of matter at densities larger than that of the atomic nucleus; in particular, the precise measurement of the mass of PSR J1903+0327 ($1.67 +/- 0.01 solar masses) excludes several "soft" equations of state for dense matter.

  16. Dynamical Evolution of Wide Binaries

    Directory of Open Access Journals (Sweden)

    Esmeralda H. Mallada

    2001-01-01

    Full Text Available We simulate numerically encounters of wide binaries with field stars and Giant Molecular Clouds (GMCs by means of the impulse approximation. We analyze the time evolution of the distributions of eccentricities and semimajor axes of wide binaries with given initial conditions, at intervals of 109 yr, up to 1010 yr (assumed age of the Galaxy. We compute the fraction of surviving binaries for stellar encounters, for GMC encounters and for a combination of both, and hence, the dynamical lifetime for different semimajor axes and different masses of binaries (0.5, 1, 1.2, 1.5, 2.5, and 3 Msolar. We find that the dynamical lifetime of wide binaries considering only GMCs is half than that considering only stars. For encounters with GMCs we analyze the influence of the initial inclination of the orbital plane of the binary with respect to the plane perpendicular to the relative velocity vector of the binary and the GMC. We find that the perturbation is maximum when the angle is minimum.

  17. Chaotic zones around gravitating binaries

    CERN Document Server

    Shevchenko, Ivan I

    2014-01-01

    The extent of the continuous zone of chaotic orbits of a small-mass tertiary around a system of two gravitationally bound bodies (a double star, a double black hole, a binary asteroid, etc.) is estimated analytically, in function of the tertiary's orbital eccentricity. The separatrix map theory is used to demonstrate that the central continuous chaos zone emerges due to overlapping of the orbital resonances corresponding to the integer ratios p:1 between the tertiary and the binary periods. The binary's mass ratio, above which such a chaotic zone is universally present, is also estimated.

  18. Modified evolution of stellar binaries from supermassive black hole binaries

    Science.gov (United States)

    Liu, Bin; Wang, Yi-Han; Yuan, Ye-Fei

    2017-04-01

    The evolution of main-sequence binaries resided in the galactic centre is influenced a lot by the central supermassive black hole (SMBH). Due to this perturbation, the stars in a dense environment are likely to experience mergers or collisions through secular or non-secular interactions. In this work, we study the dynamics of the stellar binaries at galactic centre, perturbed by another distant SMBH. Geometrically, such a four-body system is supposed to be decomposed into the inner triple (SMBH-star-star) and the outer triple (SMBH-stellar binary-SMBH). We survey the parameter space and determine the criteria analytically for the stellar mergers and the tidal disruption events (TDEs). For a relative distant and equal masses SMBH binary, the stars have more opportunities to merge as a result from the Lidov-Kozai (LK) oscillations in the inner triple. With a sample of tight stellar binaries, our numerical experiments reveal that a significant fraction of the binaries, ∼70 per cent, experience merger eventually. Whereas the majority of the stellar TDEs are likely to occur at a close periapses to the SMBH, induced by the outer Kozai effect. The tidal disruptions are found numerically as many as ∼10 per cent for a close SMBH binary that is enhanced significantly than the one without the external SMBH. These effects require the outer perturber to have an inclined orbit (≥40°) relatively to the inner orbital plane and may lead to a burst of the extremely astronomical events associated with the detection of the SMBH binary.

  19. Binary Oscillatory Crossflow Electrophoresis

    Science.gov (United States)

    Molloy, Richard F.; Gallagher, Christopher T.; Leighton, David T., Jr.

    1997-01-01

    Electrophoresis has long been recognized as an effective analytic technique for the separation of proteins and other charged species, however attempts at scaling up to accommodate commercial volumes have met with limited success. In this report we describe a novel electrophoretic separation technique - Binary Oscillatory Crossflow Electrophoresis (BOCE). Numerical simulations indicate that the technique has the potential for preparative scale throughputs with high resolution, while simultaneously avoiding many problems common to conventional electrophoresis. The technique utilizes the interaction of an oscillatory electric field and a transverse oscillatory shear flow to create an active binary filter for the separation of charged protein species. An oscillatory electric field is applied across the narrow gap of a rectangular channel inducing a periodic motion of charged protein species. The amplitude of this motion depends on the dimensionless electrophoretic mobility, alpha = E(sub o)mu/(omega)d, where E(sub o) is the amplitude of the electric field oscillations, mu is the dimensional mobility, omega is the angular frequency of oscillation and d is the channel gap width. An oscillatory shear flow is induced along the length of the channel resulting in the separation of species with different mobilities. We present a model that predicts the oscillatory behavior of charged species and allows estimation of both the magnitude of the induced convective velocity and the effective diffusivity as a function of a in infinitely long channels. Numerical results indicate that in addition to the mobility dependence, the steady state behavior of solute species may be strongly affected by oscillating fluid into and out of the active electric field region at the ends of the cell. The effect is most pronounced using time dependent shear flows of the same frequency (cos((omega)t)) flow mode) as the electric field oscillations. Under such conditions, experiments indicate that

  20. Stability of binaries. Part II: Rubble-pile binaries

    Science.gov (United States)

    Sharma, Ishan

    2016-10-01

    We consider the stability of the binary asteroids whose members are granular aggregates held together by self-gravity alone. A binary is said to be stable whenever both its members are orbitally and structurally stable to both orbital and structural perturbations. To this end, we extend the stability analysis of Sharma (Sharma [2015] Icarus, 258, 438-453), that is applicable to binaries with rigid members, to the case of binary systems with rubble members. We employ volume averaging (Sharma et al. [2009] Icarus, 200, 304-322), which was inspired by past work on elastic/fluid, rotating and gravitating ellipsoids. This technique has shown promise when applied to rubble-pile ellipsoids, but requires further work to settle some of its underlying assumptions. The stability test is finally applied to some suspected binary systems, viz., 216 Kleopatra, 624 Hektor and 90 Antiope. We also see that equilibrated binaries that are close to mobilizing their maximum friction can sustain only a narrow range of shapes and, generally, congruent shapes are preferred.

  1. Binary nucleation beyond capillarity approximation

    NARCIS (Netherlands)

    Kalikmanov, V.I.

    2010-01-01

    Large discrepancies between binary classical nucleation theory (BCNT) and experiments result from adsorption effects and inability of BCNT, based on the phenomenological capillarity approximation, to treat small clusters. We propose a model aimed at eliminating both of these deficiencies. Adsorption

  2. Discs in misaligned binary systems

    CERN Document Server

    Rawiraswattana, Krisada; Goodwin, Simon P

    2016-01-01

    We perform SPH simulations to study precession and changes in alignment between the circumprimary disc and the binary orbit in misaligned binary systems. We find that the precession process can be described by the rigid-disc approximation, where the disc is considered as a rigid body interacting with the binary companion only gravitationally. Precession also causes change in alignment between the rotational axis of the disc and the spin axis of the primary star. This type of alignment is of great important for explaining the origin of spin-orbit misaligned planetary systems. However, we find that the rigid-disc approximation fails to describe changes in alignment between the disc and the binary orbit. This is because the alignment process is a consequence of interactions that involve the fluidity of the disc, such as the tidal interaction and the encounter interaction. Furthermore, simulation results show that there are not only alignment processes, which bring the components towards alignment, but also anti-...

  3. Simulating relativistic binaries with Whisky

    Science.gov (United States)

    Baiotti, L.

    We report about our first tests and results in simulating the last phase of the coalescence and the merger of binary relativistic stars. The simulations were performed using our code Whisky and mesh refinement through the Carpet driver.

  4. An adaptable binary entropy coder

    Science.gov (United States)

    Kiely, A.; Klimesh, M.

    2001-01-01

    We present a novel entropy coding technique which is based on recursive interleaving of variable-to-variable length binary source codes. We discuss code design and performance estimation methods, as well as practical encoding and decoding algorithms.

  5. Magnetic braking in ultracompact binaries

    CERN Document Server

    Farmer, Alison

    2010-01-01

    Angular momentum loss in ultracompact binaries, such as the AM Canum Venaticorum stars, is usually assumed to be due entirely to gravitational radiation. Motivated by the outflows observed in ultracompact binaries, we investigate whether magnetically coupled winds could in fact lead to substantial additional angular momentum losses. We remark that the scaling relations often invoked for the relative importance of gravitational and magnetic braking do not apply, and instead use simple non-empirical expressions for the braking rates. In order to remove significant angular momentum, the wind must be tied to field lines anchored in one of the binary's component stars; uncertainties remain as to the driving mechanism for such a wind. In the case of white dwarf accretors, we find that magnetic braking can potentially remove angular momentum on comparable or even shorter timescales than gravitational waves over a large range in orbital period. We present such a solution for the 17-minute binary AM CVn itself which a...

  6. Cryptography with DNA binary strands.

    Science.gov (United States)

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H

    2000-06-01

    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.

  7. AN IMPROVED DESIGN OF REVERSIBLE BINARY TO BINARY CODED DECIMAL CONVERTER FOR BINARY CODED DECIMAL MULTIPLICATION

    Directory of Open Access Journals (Sweden)

    Praveena Murugesan

    2014-01-01

    Full Text Available Reversible logic gates under ideal conditions produce zero power dissipation. This factor highlights the usage of these gates in optical computing, low power CMOS design, quantum optics and quantum computing. The growth of decimal arithmetic in various applications as stressed the need to propose the study on reversible binary to BCD converter which plays a greater role in decimal multiplication for providing faster results. The different parameters such as gate count,garbage output and constant input are more optimized in the proposed fixed bit binary to binary coded decimal converter than the existing design.

  8. Transient Black Hole Binaries

    CERN Document Server

    Belloni, T M

    2016-01-01

    The last two decades have seen a great improvement in our understand- ing of the complex phenomenology observed in transient black-hole binary systems, especially thanks to the activity of the Rossi X-Ray Timing Explorer satellite, com- plemented by observations from many other X-ray observatories and ground-based radio, optical and infrared facilities. Accretion alone cannot describe accurately the intricate behavior associated with black-hole transients and it is now clear that the role played by different kinds of (often massive) outflows seen at different phases of the outburst evolution of these systems is as fundamental as the one played by the accretion process itself. The spectral-timing states originally identified in the X-rays and fundamentally based on the observed effect of accretion, have acquired new importance as they now allow to describe within a coherent picture the phenomenology observed at other wave- length, where the effects of ejection processes are most evident. With a particular focu...

  9. Residue arithmetic in binary systems

    OpenAIRE

    Barsi, Ferruccio

    1988-01-01

    A natural approach to the problem of performing mod m computations in a binary system is presented and a solution is suggested which is based upon a straightforward relation between the residues of a same integer X with respect to different moduli. The proposed solution proves fruitful in various applications, such as converting binary integers to residue notation and mod m addition or multiplication. Even if the most usual implementation approach for mod m processors is based on look-up tabl...

  10. Coevolution of Binaries and Gaseous Discs

    CERN Document Server

    Fleming, David P

    2016-01-01

    The recent discoveries of circumbinary planets by $\\it Kepler$ raise questions for contemporary planet formation models. Understanding how these planets form requires characterizing their formation environment, the circumbinary protoplanetary disc, and how the disc and binary interact and change as a result. The central binary excites resonances in the surrounding protoplanetary disc that drive evolution in both the binary orbital elements and in the disc. To probe how these interactions impact binary eccentricity and disc structure evolution, N-body smooth particle hydrodynamics (SPH) simulations of gaseous protoplanetary discs surrounding binaries based on Kepler 38 were run for $10^4$ binary periods for several initial binary eccentricities. We find that nearly circular binaries weakly couple to the disc via a parametric instability and excite disc eccentricity growth. Eccentric binaries strongly couple to the disc causing eccentricity growth for both the disc and binary. Discs around sufficiently eccentri...

  11. The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations.

    Science.gov (United States)

    Mitchell, David; Jarmoskaite, Inga; Seval, Nikhil; Seifert, Soenke; Russell, Rick

    2013-08-09

    RNAs are prone to misfolding, but how misfolded structures are formed and resolved remains incompletely understood. The Tetrahymena group I intron ribozyme folds in vitro to a long-lived misfolded conformation (M) that includes extensive native structure but is proposed to differ in topology from the native state (N). A leading model predicts that exchange of the topologies requires unwinding of the long-range, core helix P3, despite the presence of P3 in both conformations. To test this model, we constructed 16 mutations to strengthen or weaken P3. Catalytic activity and in-line probing showed that nearly all of the mutants form the M state before folding to N. The P3-weakening mutations accelerated refolding from M (3- to 30-fold) and the P3-strengthening mutations slowed refolding (6- to 1400-fold), suggesting that P3 indeed unwinds transiently. Upon depletion of Mg(2+), the mutations had analogous effects on unfolding from N to intermediates that subsequently fold to M. The magnitudes for the P3-weakening mutations were larger than in refolding from M, and small-angle X-ray scattering showed that the ribozyme expands rapidly to intermediates from which P3 is disrupted subsequently. These results are consistent with previous results indicating unfolding of native peripheral structure during refolding from M, which probably permits rearrangement of the core. Together, our results demonstrate that exchange of the native and misfolded conformations requires loss of a core helix in addition to peripheral structure. Further, the results strongly suggest that misfolding arises from a topological error within the ribozyme core, and a specific topology is proposed.

  12. Construction of GCV-Specific Hammerhead Ribozyme Recombinant Vector of Pyruvate Kinase in Giardia lamblia%蓝氏贾第鞭毛虫丙酮酸激酶特异性锤头状核酶-GCV重组载体的构建

    Institute of Scientific and Technical Information of China (English)

    曹利静; 冯宪敏; 魏超君; 王凤云; 张西臣; 卢思奇

    2010-01-01

    目的 构建蓝氏贾第鞭毛虫丙酮酸激酶(pyruvate kinase, PK)特异性锤头状核酶-犬贾第虫病毒(Giardia canis virus, GCV)重组载体. 方法 采用RNA draw软件分析贾第虫编码丙酮酸激酶的基因序列,并设计特异性反义锤头状核酶(PKH)序列, 将其与犬贾第虫病毒(GCV)连接,构建重组载体pGCV-PKH.将重组载体线性化体外转录产物,分别进行贾第虫细胞外、细胞内目的 mRNA切割实验,采用荧光显微镜观察转染后24 h的各组虫体.采用实时PCR对切割产物进行相对定量分析. 结果 构建了载有蓝氏贾第鞭毛虫丙酮酸激酶特异性锤头状核酶的犬贾第虫病毒重组载体pGCV-PKH.细胞内切割实验结果表明,荧光显微镜下只有pGCV-GFP转染组虫体显示绿色荧光,pGCV-PKH转染组丙酮酸激酶mRNA的相对含量约为正常对照组的33.14%.细胞外切割实验结果表明,该组载体能在细胞外有效切割丙酮酸激酶mRNA,在设定条件下,其切割效率为58.5%. 结论 重组载体pGCV-PKH能有效转染蓝氏贾第鞭毛虫细胞,并能在其细胞内外对丙酮酸激酶mRNA进行有效切割.

  13. Unsupervised learning of binary vectors

    Science.gov (United States)

    Copelli Lopes da Silva, Mauro

    In this thesis, unsupervised learning of binary vectors from data is studied using methods from Statistical Mechanics of disordered systems. In the model, data vectors are distributed according to a single symmetry-breaking direction. The aim of unsupervised learning is to provide a good approximation to this direction. The difference with respect to previous studies is the knowledge that this preferential direction has binary components. It is shown that sampling from the posterior distribution (Gibbs learning) leads, for general smooth distributions, to an exponentially fast approach to perfect learning in the asymptotic limit of large number of examples. If the distribution is non-smooth, then first order phase transitions to perfect learning are expected. In the limit of poor performance, a second order phase transition ("retarded learning") is predicted to occur if the data distribution is not biased. Using concepts from Bayesian inference, the center of mass of the Gibbs ensemble is shown to have maximal average (Bayes-optimal) performance. This upper bound for continuous vectors is extended to a discrete space, resulting in the clipped center of mass of the Gibbs ensemble having maximal average performance among the binary vectors. To calculate the performance of this best binary vector, the geometric properties of the center of mass of binary vectors are studied. The surprising result is found that the center of mass of infinite binary vectors which obey some simple constraints, is again a binary vector. When disorder is taken into account in the calculation, however, a vector with continuous components is obtained. The performance of the best binary vector is calculated and shown to always lie above that of Gibbs learning and below the Bayes-optimal performance. Making use of a variational approach under the replica symmetric ansatz, an optimal potential is constructed in the limits of zero temperature and mutual overlap 1. Minimization of this potential

  14. A ribozyme transcribed by a ribozyme

    DEFF Research Database (Denmark)

    Bentin, Thomas

    2011-01-01

    Prominent current ideas on how life emerged on Earth include an RNA world hypothesis in which RNA performed informational as well as catalytic functions in the absence of both DNA and protein. Demonstration of a self-replicative system based on ribonucleic acid polymers as both information carrie...

  15. Exoplanets Bouncing Between Binary Stars

    CERN Document Server

    Moeckel, Nickolas

    2012-01-01

    Exoplanetary systems are found not only among single stars, but also binaries of widely varying parameters. Binaries with separations of 100--1000 au are prevalent in the Solar neighborhood; at these separations planet formation around a binary member may largely proceed as if around a single star. During the early dynamical evolution of a planetary system, planet--planet scattering can eject planets from a star's grasp. In a binary, the motion of a planet ejected from one star has effectively entered a restricted three-body system consisting of itself and the two stars, and the equations of motion of the three body problem will apply as long as the ejected planet remains far from the remaining planets. Depending on its energy, escape from the binary as a whole may be impossible or delayed until the three-body approximation breaks down, and further close interactions with its planetary siblings boost its energy when it passes close to its parent star. Until then this planet may be able to transition from the ...

  16. Formation of Kuiper Belt Binaries

    CERN Document Server

    Goldreich, P; Sari, R; Goldreich, Peter; Lithwick, Yoram; Sari, Re'em

    2002-01-01

    It appears that at least several percent of large Kuiper belt objects are members of wide binaries. Physical collisions are too infrequent to account for their formation. Collisionless gravitational interactions are more promising. These provide two channels for binary formation. In each, the initial step is the formation of a transient binary when two large bodies penetrate each other's Hill spheres. Stabilization of a transient binary requires that it lose energy. Either dynamical friction due to small bodies or the scattering of a third large body can be responsible. Our estimates favor the former, albeit by a small margin. We predict that most objects of size comparable to those currently observed in the Kuiper belt are members of multiple systems. More specifically, we derive the probability that a large body is a member of a binary with semi-major axis of order a. The probability depends upon sigma, the total surface density, Sigma, the surface density of large bodies having radius R, and theta=10^-4, t...

  17. Selective reversal of drug resistance in drug-resistant lung adenocarcinoma cells by tumor-specific expression of MDR1 ribozyme gene mediated by retrovirus

    Institute of Scientific and Technical Information of China (English)

    高振强; 高志萍; 刘喜富; 张涛

    1997-01-01

    According to the fact that CEA gene expressed only in lung adenocarcinoma and not in normal lung cells, a retroviral vector (pCEAMR) was constructed which carried the CEA promoter coupled to MDR1 ribozyme gene. pCEAMR was introduced into drug-resistant lung adenocarcinoma cells GAOK with CEA expression and HeLaK without CEA expression; the expression of pCEAMR and drug resistance in the infected cells were analyzed in vitro and in vivo ; pCEAMR expressed only in CEA-producing GAOK cells and not in non-CEA-producing HeLa cells. The drug resistance to doxorubicin (DOX) decreased 91.5% in the infected GAOK cells and did not change in the infected HeLa cells. In nude mice, DOX could obviously inhibit the growth of the infected GAOK tumors, and had no effect on the growth of the infected HeLa cells. These results indicated that MDR1 ribozyme gene regulated by CEA promoter expressed only in human adenocarcinoma cells and reversed their drug resistance selectively. This gene-drug therapy might serve as an effe

  18. How the discovery of ribozymes cast RNA in the roles of both chicken and egg in origin-of-life theories.

    Science.gov (United States)

    Sankaran, Neeraja

    2012-12-01

    Scientific theories about the origin-of-life theories have historically been characterized by the chicken-and-egg problem of which essential aspect of life was the first to appear, replication or self-sustenance. By the 1950s the question was cast in molecular terms and DNA and proteins had come to represent the carriers of the two functions. Meanwhile, RNA, the other nucleic acid, had played a capricious role in origin theories. Because it contained building blocks very similar to DNA, biologists recognized early that RNA could store information in its linear sequences. With the discovery in the 1980s that RNA molecules were capable of biological catalysis, a function hitherto ascribed to proteins alone, RNA took on the role of the single entity that could act as both chicken and egg. Within a few years of the discovery of these catalytic RNAs (ribozymes) scientists had formulated an RNA World hypothesis that posited an early phase in the evolution of life where all key functions were performed by RNA molecules. This paper traces the history the role of RNA in origin-of-life theories with a focus on how the discovery of ribozymes influenced the discourse.

  19. Evaporative Instability in Binary Mixtures

    Science.gov (United States)

    Narayanan, Ranga; Uguz, Erdem

    2012-11-01

    In this talk we depict the physics of evaporative convection for binary systems in the presence of surface tension gradient effects. Two results are of importance. The first is that a binary system, in the absence of gravity, can generate an instability only when heated from the vapor side. This is to be contrasted with the case of a single component where instability can occur only when heated from the liquid side. The second result is that a binary system, in the presence of gravity, will generate an instability when heated from either the vapor or the liquid side provided the heating is strong enough. In addition to these results we show the conditions at which interfacial patterns can occur. Support from NSF OISE 0968313, Partner Univ. Fund and a Chateaubriand Fellowship is acknowledged.

  20. Marangoni Convection in Binary Mixtures

    CERN Document Server

    Zhang, J; Oron, A; Behringer, Robert P.; Oron, Alexander; Zhang, Jie

    2006-01-01

    Marangoni instabilities in binary mixtures are different from those in pure liquids. In contrast to a large amount of experimental work on Marangoni convection in pure liquids, such experiments in binary mixtures are not available in the literature, to our knowledge. Using binary mixtures of sodium chloride/water, we have systematically investigated the pattern formation for a set of substrate temperatures and solute concentrations in an open system. The flow patterns evolve with time, driven by surface-tension fluctuations due to evaporation and the Soret effect, while the air-liquid interface does not deform. A shadowgraph method is used to follow the pattern formation in time. The patterns are mainly composed of polygons and rolls. The mean pattern size first decreases slightly, and then gradually increases during the evolution. Evaporation affects the pattern formation mainly at the early stage and the local evaporation rate tends to become spatially uniform at the film surface. The Soret effect becomes i...

  1. Asymmetric distances for binary embeddings.

    Science.gov (United States)

    Gordo, Albert; Perronnin, Florent; Gong, Yunchao; Lazebnik, Svetlana

    2014-01-01

    In large-scale query-by-example retrieval, embedding image signatures in a binary space offers two benefits: data compression and search efficiency. While most embedding algorithms binarize both query and database signatures, it has been noted that this is not strictly a requirement. Indeed, asymmetric schemes that binarize the database signatures but not the query still enjoy the same two benefits but may provide superior accuracy. In this work, we propose two general asymmetric distances that are applicable to a wide variety of embedding techniques including locality sensitive hashing (LSH), locality sensitive binary codes (LSBC), spectral hashing (SH), PCA embedding (PCAE), PCAE with random rotations (PCAE-RR), and PCAE with iterative quantization (PCAE-ITQ). We experiment on four public benchmarks containing up to 1M images and show that the proposed asymmetric distances consistently lead to large improvements over the symmetric Hamming distance for all binary embedding techniques.

  2. Black Hole Binaries in Quiescence

    CERN Document Server

    Bailyn, Charles D

    2016-01-01

    I discuss some of what is known and unknown about the behavior of black hole binary systems in the quiescent accretion state. Quiescence is important for several reasons: 1) the dominance of the companion star in the optical and IR wavelengths allows the binary parameters to be robustly determined - as an example, we argue that the longer proposed distance to the X-ray source GRO J1655-40 is correct; 2) quiescence represents the limiting case of an extremely low accretion rate, in which both accretion and jets can be observed; 3) understanding the evolution and duration of the quiescent state is a key factor in determining the overall demographics of X-rary binaries, which has taken on a new importance in the era of gravitational wave astronomy.

  3. Practical Binary Adaptive Block Coder

    CERN Document Server

    Reznik, Yuriy A

    2007-01-01

    This paper describes design of a low-complexity algorithm for adaptive encoding/ decoding of binary sequences produced by memoryless sources. The algorithm implements universal block codes constructed for a set of contexts identified by the numbers of non-zero bits in previous bits in a sequence. We derive a precise formula for asymptotic redundancy of such codes, which refines previous well-known estimate by Krichevsky and Trofimov, and provide experimental verification of this result. In our experimental study we also compare our implementation with existing binary adaptive encoders, such as JBIG's Q-coder, and MPEG AVC (ITU-T H.264)'s CABAC algorithms.

  4. Statistical Study of Visual Binaries

    CERN Document Server

    Abdel-Rahman, H I; Elsanhoury, W H

    2016-01-01

    In this paper, some statistical distributions of wide pairs included in Double Star Catalogue are investigated. Frequency distributions and testing hypothesis are derived for some basic parameters of visual binaries. The results reached indicate that, it was found that the magnitude difference is distributed exponentially, which means that the majority of the component of the selected systems is of the same spectral type. The distribution of the mass ratios is concentrated about 0.7 which agree with Salpeter mass function. The distribution of the linear separation appears to be exponentially, which contradict with previous studies for close binaries.

  5. KEPLER ECLIPSING BINARIES WITH STELLAR COMPANIONS

    Energy Technology Data Exchange (ETDEWEB)

    Gies, D. R.; Matson, R. A.; Guo, Z.; Lester, K. V. [Center for High Angular Resolution Astronomy and Department of Physics and Astronomy, Georgia State University, P.O. Box 5060, Atlanta, GA 30302-5060 (United States); Orosz, J. A. [Department of Astronomy, San Diego State University, San Diego, CA 92182-1221 (United States); Peters, G. J., E-mail: gies@chara.gsu.edu, E-mail: rmatson@chara.gsu.edu, E-mail: guo@chara.gsu.edu, E-mail: lester@chara.gsu.edu, E-mail: jorosz@mail.sdsu.edu, E-mail: gjpeters@mucen.usc.edu [Space Sciences Center and Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089-1341 (United States)

    2015-12-15

    Many short-period binary stars have distant orbiting companions that have played a role in driving the binary components into close separation. Indirect detection of a tertiary star is possible by measuring apparent changes in eclipse times of eclipsing binaries as the binary orbits the common center of mass. Here we present an analysis of the eclipse timings of 41 eclipsing binaries observed throughout the NASA Kepler mission of long duration and precise photometry. This subset of binaries is characterized by relatively deep and frequent eclipses of both stellar components. We present preliminary orbital elements for seven probable triple stars among this sample, and we discuss apparent period changes in seven additional eclipsing binaries that may be related to motion about a tertiary in a long period orbit. The results will be used in ongoing investigations of the spectra and light curves of these binaries for further evidence of the presence of third stars.

  6. Binary/BCD-to-ASCII data converter

    Science.gov (United States)

    Miller, A. J.

    1977-01-01

    Converter inputs multiple precision binary words, converts data to multiple precision binary-coded decimal, and routes data back to computer. Converter base can be readily changed without need for new gate structure for each base changeover.

  7. Binary stars in the RAVE survey

    Directory of Open Access Journals (Sweden)

    Zwitter T.

    2012-02-01

    Full Text Available We searched the sample of RAVE survey spectra for both types of spectroscopic binary stars in order to estimate their number in the sample and perform a study on newly discovered binaries.

  8. Bayesian analysis of binary sequences

    Science.gov (United States)

    Torney, David C.

    2005-03-01

    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  9. CHAOTIC ZONES AROUND GRAVITATING BINARIES

    Energy Technology Data Exchange (ETDEWEB)

    Shevchenko, Ivan I., E-mail: iis@gao.spb.ru [Pulkovo Observatory of the Russian Academy of Sciences, Pulkovskoje ave. 65, St. Petersburg 196140 (Russian Federation)

    2015-01-20

    The extent of the continuous zone of chaotic orbits of a small-mass tertiary around a system of two gravitationally bound primaries of comparable masses (a binary star, a binary black hole, a binary asteroid, etc.) is estimated analytically, as a function of the tertiary's orbital eccentricity. The separatrix map theory is used to demonstrate that the central continuous chaos zone emerges (above a threshold in the primaries' mass ratio) due to overlapping of the orbital resonances corresponding to the integer ratios p:1 between the tertiary and the central binary periods. In this zone, the unlimited chaotic orbital diffusion of the tertiary takes place, up to its ejection from the system. The primaries' mass ratio, above which such a chaotic zone is universally present at all initial eccentricities of the tertiary, is estimated. The diversity of the observed orbital configurations of biplanetary and circumbinary exosystems is shown to be in accord with the existence of the primaries' mass parameter threshold.

  10. A Galactic Binary Detection Pipeline

    Science.gov (United States)

    Littenberg, Tyson B.

    2011-01-01

    The Galaxy is suspected to contain hundreds of millions of binary white dwarf systems, a large fraction of which will have sufficiently small orbital period to emit gravitational radiation in band for space-based gravitational wave detectors such as the Laser Interferometer Space Antenna (LISA). LISA's main science goal is the detection of cosmological events (supermassive black hole mergers, etc.) however the gravitational signal from the galaxy will be the dominant contribution to the data - including instrumental noise over approximately two decades in frequency. The catalogue of detectable binary systems will serve as an unparalleled means of studying the Galaxy. Furthermore, to maximize the scientific return from the mission, the data must be "cleansed" of the galactic foreground. We will present an algorithm that can accurately resolve and subtract 2:: 10000 of these sources from simulated data supplied by the Mock LISA Data Challenge Task Force. Using the time evolution of the gravitational wave frequency, we will reconstruct the position of the recovered binaries and show how LISA will sample the entire compact binary population in the Galaxy.

  11. The Meritfactor of Binary Seqences

    DEFF Research Database (Denmark)

    Høholdt, Tom

    1999-01-01

    Binary sequences with small aperiodic correlations play an important role in many applications ranging from radar to modulation and testing of systems. Golay(1977) introduced the merit factor as a measure of the goodness of the sequence and conjectured an upper bound for this. His conjecture is s...

  12. Eccentricity distribution of wide binaries

    CERN Document Server

    Tokovinin, Andrei

    2015-01-01

    A sample of 477 solar-type binaries within 67pc with projected separations larger than 50AU is studied by a new statistical method. Speed and direction of the relative motion are determined from the short observed arcs or known orbits, and their joint distribution is compared to the numerical simulations. By inverting the observed distribution with the help of simulations, we find that average eccentricity of wide binaries is 0.59+-0.02 and the eccentricity distribution can be modeled as f(e) ~= 1.2 e + 0.4. However, wide binaries containing inner subsystems, i.e. triple or higher-order multiples, have significantly smaller eccentricities with the average e = 0.52+-0.05 and the peak at e ~ 0.5. We find that the catalog of visual orbits is strongly biased against large eccentricities. A marginal evidence of eccentricity increasing with separation (or period) is found for this sample. Comparison with spectroscopic binaries proves the reality of the controversial period-eccentricity relation. The average eccentr...

  13. Coevolution of binaries and circumbinary gaseous discs

    Science.gov (United States)

    Fleming, David P.; Quinn, Thomas R.

    2017-01-01

    The recent discoveries of circumbinary planets by Kepler raise questions for contemporary planet formation models. Understanding how these planets form requires characterizing their formation environment, the circumbinary protoplanetary disc and how the disc and binary interact and change as a result. The central binary excites resonances in the surrounding protoplanetary disc which drive evolution in both the binary orbital elements and in the disc. To probe how these interactions impact binary eccentricity and disc structure evolution, N-body smooth particle hydrodynamics simulations of gaseous protoplanetary discs surrounding binaries based on Kepler 38 were run for 104 binary periods for several initial binary eccentricities. We find that nearly circular binaries weakly couple to the disc via a parametric instability and excite disc eccentricity growth. Eccentric binaries strongly couple to the disc causing eccentricity growth for both the disc and binary. Discs around sufficiently eccentric binaries which strongly couple to the disc develop an m = 1 spiral wave launched from the 1:3 eccentric outer Lindblad resonance which corresponds to an alignment of gas particle longitude of periastrons. All systems display binary semimajor axis decay due to dissipation from the viscous disc.

  14. Formation and evolution of compact binaries

    NARCIS (Netherlands)

    Sluijs, Marcel Vincent van der

    2006-01-01

    In this thesis we investigate the formation and evolution of compact binaries. Chapters 2 through 4 deal with the formation of luminous, ultra-compact X-ray binaries in globular clusters. We show that the proposed scenario of magnetic capture produces too few ultra-compact X-ray binaries to explain

  15. Transfection with the ribozyme targeting HPVE6 mRNA results in growth inhibition of E6-expressing cervical carcinoma cells

    Institute of Scientific and Technical Information of China (English)

    郑燕芳; 张积仁

    2003-01-01

    Objective: To acquire a ribozyme against the E6 gene of human papillomaviruses type 16 (HPV16E6) and investigate its effects on the phenotypes and gene expression of cervical cancer cell line. Methods: Anti-HPV16E6 ribozyme (HRz) was designed by computer programs and its activity identified by cleavage experiment in vitro before its transfection via lipofectin into CaSKi cells with the empty eucaryotic expression plasmid transfection of the cells also performed, the resultant cells designated as CaSKi-R, CaSKi-P respectively. The morphology and the soft agar forming ability were studied in CaSKi cells and the transfected cells, and the expression of E6, proliferating cell nuclear antigen (PCNA) and C-erbB-2 genes assayed by flow cytometry. The tumorgenicity of each cell line was evaluated in nude mice receiving inoculations of CaSKi, CaSKi-R and CaSKi-P cells separately, while in one group, both CaSKi and CaSKi-R cells were inoculated on different sides of the mice. Results: HRz was able to cleave HPV16E6 mRNA in a site-specific manner and could be expressed stably in transfected CaSKi cells. Northern blot analysis showed that E6 mRNA was less in CaSKi-R than in CaSKi cells, and no significant difference in the morphology and growth rate was observed between CaSKi and CaSKi-P cells, but the growth rate CaSKi-R was lowered. The colony-forming rate of CaSKi-P in soft agar was similar to that of CaSKi cells, while that of CaSKi-R was decreased. Flow cytometry showed that anti-HPV16E6 ribozyme reduced the expression of E6, PCNA and C-erbB-2 genes in CaSKi-R cells, but not in CaSKi-P cells. The tumorgenicity of CaSKi-R in nude mice was decreased compared with CaSKi cells. Conclusion: HRz can partially reverse the malignant phenotype of CaSKi cells, possibly due to decreased E6 gene expression, and the consequent decrease of PCNA and C-erbB-2 gene expressions.

  16. Gravitational Microlensing of Binary and Binary and Multiple Stars

    Science.gov (United States)

    Cherepashchuk, A. M.

    1995-08-01

    Recent observations of the effect of microlensing of stars of large Magellanic Clouds by dark bodies of Galactic Halo have led to the discovery of new population in our galaxy - dark bodies with amsses ~ 0.1 M(sun). As a consequence, astronomers have gained a unique possibility of using gravitational microlensing as an effective extraterestrial telescope with extremely high angular resolution. Application of this to binary stars is discussed. of particular interest is to apply microlensing to search for planetary stars . Planets and stars move about the center of gravity of the system , so the appaarent motion of a star in nonuniform and the light curve is asymetrical and colour dependent. This allows to determin basic parameters of binary system

  17. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  18. Populating the Galaxy with close Be binaries

    CERN Document Server

    Kiel, P D; Murray, J R; Hayasaki, K

    2007-01-01

    Be/X-ray binaries comprise roughly two-thirds of the high-mass X-ray binaries (HMXBs), which is a class of X-ray binaries that results from the high mass of the companion or donor star (> 10 solar masses). Currently the formation and evolution of X-ray producing Be binaries is a matter of great debate. Modelling of these systems requires knowledge of Be star evolution and also consideration of how the evolution changes when the star is in close proximity to a companion. Within this work we complete a full population synthesis study of Be binaries for the Galaxy. The results for the first time match aspects of the observational data, most notably the observed upper limit to the period distribution. We conclude that greater detailed studies on the evolution of Be stars within X-ray binaries needs to be completed, so that rapid binary evolution population synthesis packages may best evolve these systems.

  19. Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.

    Science.gov (United States)

    Spitale, Robert C; Volpini, Rosaria; Mungillo, Michael V; Krucinska, Jolanta; Cristalli, Gloria; Wedekind, Joseph E

    2009-08-25

    The hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA.

  20. Close supermassive binary black holes

    Science.gov (United States)

    Gaskell, C. Martin

    2010-01-01

    It has been proposed that when the peaks of the broad emission lines in active galactic nuclei (AGNs) are significantly blueshifted or redshifted from the systemic velocity of the host galaxy, this could be a consequence of orbital motion of a supermassive blackhole binary (SMB). The AGN J1536+0441 (=SDSS J153636.22+044127.0) has recently been proposed as an example of this phenomenon. It is proposed here instead that 1536+044 is an example of line emission from a disc. If this is correct, the lack of clear optical spectral evidence for close SMBs is significant and argues either that the merging of close SMBs is much faster than has generally been hitherto thought, or if the approach is slow, that when the separation of the binary is comparable to the size of the torus and broad-line region, the feeding of the black holes is disrupted.

  1. Desktop setup for binary holograms

    Science.gov (United States)

    Ginter, Olaf; Rothe, Hendrik

    1996-08-01

    Binary gratings as holograms itself or as photographic masking tools for further fabrication steps can fulfill a lot of applications. The commonly used semiconductor technologies for direct writing of high resolution structures are often too expensive. On the other hand computer plots at a reasonable price with photographic reduction do not meet the needs of precision e.g. for interferometric inspection. The lack of cheap and reliable instruments for direct writing in an appropriate resolution is still a problem in fabricating synthetic holograms. Using off-the-shelf components a direct writing plotter for binary patterns can be built at moderate costs. Typical design rules as well as experimental results are given and the final setup is introduced.

  2. Slim Sets of Binary Trees

    CERN Document Server

    Grünewald, Stefan

    2010-01-01

    A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\\cP$ of phylogenetic trees. If the answer is "yes" we say that $\\cP$ is compatible and $T$ displays $\\cP$. This decision problem is NP-complete even if all input trees are quartets, that is binary trees with exactly four leaves. In this paper, we prove a sufficient condition for a set of binary phylogenetic trees to be compatible. That result is used to give a short and self-contained proof of the known characterization of quartet sets of minimal cardinality which are displayed by a unique phylogenetic tree.

  3. Mass transfer between binary stars

    Science.gov (United States)

    Modisette, J. L.; Kondo, Y.

    1980-01-01

    The transfer of mass from one component of a binary system to another by mass ejection is analyzed through a stellar wind mechanism, using a model which integrates the equations of motion, including the energy equation, with an initial static atmosphere and various temperature fluctuations imposed at the base of the star's corona. The model is applied to several situations and the energy flow is calculated along the line of centers between the two binary components, in the rotating frame of the system, thereby incorporating the centrifugal force. It is shown that relatively small disturbances in the lower chromosphere or photosphere can produce mass loss through a stellar wind mechanism, due to the amplification of the disturbance propagating into the thinner atmosphere. Since there are many possible sources of the disturbance, the model can be used to explain many mass ejection phenomena.

  4. Classification with binary gene expressions

    OpenAIRE

    Tuna, Salih; Niranjan, Mahesan

    2009-01-01

    Microarray gene expression measurements are reported, used and archived usually to high numerical precision. However, properties of mRNA molecules, such as their low stability and availability in small copy numbers, and the fact that measurements correspond to a population of cells, rather than a single cell, makes high precision meaningless. Recent work shows that reducing measurement precision leads to very little loss of information, right down to binary levels. In this paper we show how p...

  5. Binary neuron with optical devices

    Science.gov (United States)

    Degeratu, Vasile; Degeratu, Ştefania; Şchiopu, Paul; Şchiopu, Carmen

    2009-01-01

    In this paper the authors present a model of binary neuron, a model of McCulloch-Pitts neuron with optical devices. This model of neuron can be implemented not only in the optic integrated circuits but also in the classic optical circuits it being cheap and immune not only into electromagnetic fields but also into any kind of radiation. The transfer speed of information through the neuron is very higher, it being limited only by the light speed from the received medium.

  6. Be/X-ray binaries

    CERN Document Server

    Reig, Pablo

    2011-01-01

    The purpose of this work is to review the observational properties of Be/X-ray binaries. The open questions in Be/X-ray binaries include those related to the Be star companion, that is, the so-called "Be phenomenon", such as, timescales associated to the formation and dissipation of the equatorial disc, mass-ejection mechanisms, V/R variability, and rotation rates; those related to the neutron star, such as, mass determination, accretion physics, and spin period evolution; but also, those that result from the interaction of the two constituents, such as, disc truncation and mass transfer. Until recently, it was thought that the Be stars' disc was not significantly affected by the neutron star. In this review, I present the observational evidence accumulated in recent years on the interaction between the circumstellar disc and the compact companion. The most obvious effect is the tidal truncation of the disc. As a result, the equatorial discs in Be/X-ray binaries are smaller and denser than those around isolat...

  7. Visual Binaries in the Orion Nebula Cluster

    CERN Document Server

    Reipurth, Bo; Connelley, Michael S; Bally, John

    2007-01-01

    We have carried out a major survey for visual binaries towards the Orion Nebula Cluster using HST images obtained with an H-alpha filter. Among 781 likely ONC members more than 60" from theta-1 Ori C, we find 78 multiple systems (75 binaries and 3 triples), of which 55 are new discoveries, in the range from 0.1" to 1.5". About 9 binaries are likely line-of-sight associations. We find a binary fraction of 8.8%+-1.1% within the limited separation range from 67.5 to 675 AU. The field binary fraction in the same range is a factor 1.5 higher. Within the range 150 AU to 675 AU we find that T Tauri associations have a factor 2.2 more binaries than the ONC. The binary separation distribution function of the ONC shows unusual structure, with a sudden steep decrease in the number of binaries as the separation increases beyond 0.5", corresponding to 225 AU. We have measured the ratio of binaries wider than 0.5" to binaries closer than 0.5" as a function of distance from the Trapezium, and find that this ratio is signifi...

  8. Microlensing Signature of Binary Black Holes

    Science.gov (United States)

    Schnittman, Jeremy; Sahu, Kailash; Littenberg, Tyson

    2012-01-01

    We calculate the light curves of galactic bulge stars magnified via microlensing by stellar-mass binary black holes along the line-of-sight. We show the sensitivity to measuring various lens parameters for a range of survey cadences and photometric precision. Using public data from the OGLE collaboration, we identify two candidates for massive binary systems, and discuss implications for theories of star formation and binary evolution.

  9. Detection of unresolved binaries with multicolor photometry

    CERN Document Server

    Chulkov, D; Malkov, O; Sichevskij, S; Krussanova, N; Mironov, A; Zakharov, A; Kniazev, A

    2016-01-01

    The principal goal of this paper is to specify conditions of detection of unresolved binaries by multicolor photometry. We have developed a method for estimating the critical distance at which an unresolved binary of given mass and age can be detected. The method is applied to the photometric system of the planned Lyra-B spaceborne experiment. We have shown that some types of unresolved binary stars can be discovered and distinguished from single stars solely by means of photometric observations.

  10. Speech perception of noise with binary gains

    DEFF Research Database (Denmark)

    Wang, DeLiang; Kjems, Ulrik; Pedersen, Michael Syskind;

    2008-01-01

    For a given mixture of speech and noise, an ideal binary time-frequency mask is constructed by comparing speech energy and noise energy within local time-frequency units. It is observed that listeners achieve nearly perfect speech recognition from gated noise with binary gains prescribed...... by the ideal binary mask. Only 16 filter channels and a frame rate of 100 Hz are sufficient for high intelligibility. The results show that, despite a dramatic reduction of speech information, a pattern of binary gains provides an adequate basis for speech perception....

  11. Survival of planets around shrinking stellar binaries.

    Science.gov (United States)

    Muñoz, Diego J; Lai, Dong

    2015-07-28

    The discovery of transiting circumbinary planets by the Kepler mission suggests that planets can form efficiently around binary stars. None of the stellar binaries currently known to host planets has a period shorter than 7 d, despite the large number of eclipsing binaries found in the Kepler target list with periods shorter than a few days. These compact binaries are believed to have evolved from wider orbits into their current configurations via the so-called Lidov-Kozai migration mechanism, in which gravitational perturbations from a distant tertiary companion induce large-amplitude eccentricity oscillations in the binary, followed by orbital decay and circularization due to tidal dissipation in the stars. Here we explore the orbital evolution of planets around binaries undergoing orbital decay by this mechanism. We show that planets may survive and become misaligned from their host binary, or may develop erratic behavior in eccentricity, resulting in their consumption by the stars or ejection from the system as the binary decays. Our results suggest that circumbinary planets around compact binaries could still exist, and we offer predictions as to what their orbital configurations should be like.

  12. The structures of binary compounds

    CERN Document Server

    Hafner, J; Jensen, WB; Majewski, JA; Mathis, K; Villars, P; Vogl, P; de Boer, FR

    1990-01-01

    - Up-to-date compilation of the experimental data on the structures of binary compounds by Villars and colleagues. - Coloured structure maps which order the compounds into their respective structural domains and present for the first time the local co-ordination polyhedra for the 150 most frequently occurring structure types, pedagogically very helpful and useful in the search for new materials with a required crystal structure. - Crystal co-ordination formulas: a flexible notation for the interpretation of solid-state structures by chemist Bill Jensen. - Recent important advances in unders

  13. R144 : a very massive binary likely ejected from R136 through a binary-binary encounter

    CERN Document Server

    Oh, Seungkyung; Banerjee, Sambaran

    2013-01-01

    R144 is a recently confirmed very massive, spectroscopic binary which appears isolated from the core of the massive young star cluster R136. The dynamical ejection hypothesis as an origin for its location is claimed improbable by Sana et al. due to its binary nature and high mass. We demonstrate here by means of direct N-body calculations that a very massive binary system can be readily dynamically ejected from a R136-like cluster, through a close encounter with a very massive system. One out of four N-body cluster models produces a dynamically ejected very massive binary system with a mass comparable to R144. The system has a system mass of $\\approx$ 355 Msun and is located at 36.8 pc from the centre of its parent cluster, moving away from the cluster with a velocity of 57 km/s at 2 Myr as a result of a binary-binary interaction. This implies that R144 could have been ejected from R136 through a strong encounter with an other massive binary or single star. In addition, we discuss all massive binaries and sin...

  14. Interacting Jets from Binary Protostars

    CERN Document Server

    Murphy, G C; O'Sullivan, S; Spicer, D; Bacciotti, F; Rosén, A

    2007-01-01

    We investigate potential models that could explain why multiple proto-stellar systems predominantly show single jets. During their formation, stars most frequently produce energetic outflows and jets. However, binary jets have only been observed in a very small number of systems. We model numerically 3D binary jets for various outflow parameters. We also model the propagation of jets from a specific source, namely L1551 IRS 5, known to have two jets, using recent observations as constraints for simulations with a new MHD code. We examine their morphology and dynamics, and produce synthetic emission maps. We find that the two jets interfere up to the stage where one of them is almost destroyed or engulfed into the second one. We are able to reproduce some of the observational features of L1551 such as the bending of the secondary jet. While the effects of orbital motion are negligible over the jets dynamical timeline, their interaction has significant impact on their morphology. If the jets are not strictly pa...

  15. The Young Visual Binary Database

    Science.gov (United States)

    Prato, Lisa A.; Avilez, Ian; Allen, Thomas; Zoonematkermani, Saeid; Biddle, Lauren; Muzzio, Ryan; Wittal, Matthew; Schaefer, Gail; Simon, Michal

    2017-01-01

    We have obtained adaptive optics imaging and high-resolution H-band and in some cases K-band spectra of each component in close to 100 young multiple systems in the nearby star forming regions of Taurus, Ophiuchus, TW Hya, and Orion. The binary separations for the pairs in our sample range from 30 mas to 3 arcseconds. The imaging and most of our spectra were obtained with instruments behind adaptive optics systems in order to resolve even the closest companions. We are in the process of determining fundamental stellar and circumstellar properties, such as effective temperature, Vsin(i), veiling, and radial velocity, for each component in the entire sample. The beta version of our database includes systems in the Taurus region and provides plots, downloadable ascii spectra, and values of the stellar and circumstellar properties for both stars in each system. This resource is openly available to the community at http://jumar.lowell.edu/BinaryStars/. In this poster we describe initial results from our analysis of the survey data. Support for this research was provided in part by NSF award AST-1313399 and by NASA Keck KPDA funding.

  16. Millisecond Pulsars in Close Binaries

    CERN Document Server

    Tauris, Thomas M

    2015-01-01

    In this Habilitationsschrift (Habilitation thesis) I present my research carried out over the last four years at the Argelander Institute for Astronomy (AIfA) and the Max Planck Institute for Radio Astronomy (MPIfR). The thesis summarizes my main findings and has been written to fulfill the requirements for the Habilitation qualification at the University of Bonn. Although my work is mainly focused on the topic of millisecond pulsars (MSPs), there is a fairly broad spread of research areas ranging from the formation of neutron stars (NSs) in various supernova (SN) events, to their evolution, for example, via accretion processes in binary and triple systems, and finally to their possible destruction in merger events. The thesis is organized in the following manner: A general introduction to neutron stars and millisecond pulsars is given in Chapter 1. A selection of key papers published in 2011-2014 are presented in Chapters 2-10, ordered within five main research areas (ultra-stripped SNe in close binaries, ma...

  17. Binary Relations as a Foundation of Mathematics

    NARCIS (Netherlands)

    Kuper, J.; Barendsen, E.; Capretta, V.; Geuvers, H.; Niqui, M.

    2007-01-01

    We describe a theory for binary relations in the Zermelo-Fraenkel style. We choose for ZFCU, a variant of ZFC Set theory in which the Axiom of Foundation is replaced by an axiom allowing for non-wellfounded sets. The theory of binary relations is shown to be equi-consistent ZFCU by constructing a mo

  18. Binary Structure in David Lodge's Novels

    Institute of Scientific and Technical Information of China (English)

    高萍

    2008-01-01

    David Lodge is one of the most renowned modern English writers.He is known for the binary structure in his novels.In this paper,the writer will try to the binary structure in some of his novels to show his reflections on Catholicism and culture conflicts.

  19. Microlensing Binaries with Candidate Brown Dwarf Companions

    DEFF Research Database (Denmark)

    Shin, I.-G; Han, C.; Gould, A.;

    2012-01-01

    Brown dwarfs are important objects because they may provide a missing link between stars and planets, two populations that have dramatically different formation histories. In this paper, we present the candidate binaries with brown dwarf companions that are found by analyzing binary microlensing ...

  20. Helium in atmospheres of binary stars

    Energy Technology Data Exchange (ETDEWEB)

    Leushin, V.V. (Rostovskij-na-Donu Gosudarstvennyj Univ. (USSR). Nauchno-Issledovatel' skij Inst. Fiziki)

    The helium abundances were obtained for 25 bright components of binary stars by model atmosphere analysis. The helium abundance for binary stars that lie on the main sequence are larger in the average than in single normal stars. The stars on the Hertzsppung - russel diagram lie at a larger distance from the zero age line than those with normal helium abundance.

  1. The Evolution of Compact Binary Star Systems

    Directory of Open Access Journals (Sweden)

    Yungelson, Lev R.

    2006-12-01

    Full Text Available We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs, neutron stars (NSs, and black holes (BHs. Binary NSs and BHs are thought to be the primary astrophysical sources of gravitational waves (GWs within the frequency band of ground-based detectors, while compact binaries of WDs are important sources of GWs at lower frequencies to be covered by space interferometers (LISA. Major uncertainties in the current understanding of properties of NSs and BHs most relevant to the GW studies are discussed, including the treatment of the natal kicks which compact stellar remnants acquire during the core collapse of massive stars and the common envelope phase of binary evolution. We discuss the coalescence rates of binary NSs and BHs and prospects for their detections, the formation and evolution of binary WDs and their observational manifestations. Special attention is given to AM CVn-stars -- compact binaries in which the Roche lobe is filled by another WD or a low-mass partially degenerate helium-star, as these stars are thought to be the best LISA verification binary GW sources.

  2. The Evolution of Compact Binary Star Systems

    Directory of Open Access Journals (Sweden)

    Konstantin A. Postnov

    2014-05-01

    Full Text Available We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs, neutron stars (NSs, and black holes (BHs. Mergings of compact-star binaries are expected to be the most important sources for forthcoming gravitational-wave (GW astronomy. In the first part of the review, we discuss observational manifestations of close binaries with NS and/or BH components and their merger rate, crucial points in the formation and evolution of compact stars in binary systems, including the treatment of the natal kicks, which NSs and BHs acquire during the core collapse of massive stars and the common envelope phase of binary evolution, which are most relevant to the merging rates of NS-NS, NS-BH and BH-BH binaries. The second part of the review is devoted mainly to the formation and evolution of binary WDs and their observational manifestations, including their role as progenitors of cosmologically-important thermonuclear SN Ia. We also consider AM CVn-stars, which are thought to be the best verification binary GW sources for future low-frequency GW space interferometers.

  3. Bayesian analysis of exoplanet and binary orbits

    OpenAIRE

    Schulze-Hartung, Tim; Launhardt, Ralf; Henning, Thomas

    2012-01-01

    We introduce BASE (Bayesian astrometric and spectroscopic exoplanet detection and characterisation tool), a novel program for the combined or separate Bayesian analysis of astrometric and radial-velocity measurements of potential exoplanet hosts and binary stars. The capabilities of BASE are demonstrated using all publicly available data of the binary Mizar A.

  4. Binary Representations of Fingerprint Spectral Minutiae Features

    NARCIS (Netherlands)

    Xu, Haiyun; Veldhuis, Raymond N.J.

    2010-01-01

    A fixed-length binary representation of a fingerprint has the advantages of a fast operation and a small template storage. For many biometric template protection schemes, a binary string is also required as input. The spectral minutiae representation is a method to represent a minutiae set as a fixe

  5. The Evolution of Compact Binary Star Systems.

    Science.gov (United States)

    Postnov, Konstantin A; Yungelson, Lev R

    2014-01-01

    We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs), neutron stars (NSs), and black holes (BHs). Mergings of compact-star binaries are expected to be the most important sources for forthcoming gravitational-wave (GW) astronomy. In the first part of the review, we discuss observational manifestations of close binaries with NS and/or BH components and their merger rate, crucial points in the formation and evolution of compact stars in binary systems, including the treatment of the natal kicks, which NSs and BHs acquire during the core collapse of massive stars and the common envelope phase of binary evolution, which are most relevant to the merging rates of NS-NS, NS-BH and BH-BH binaries. The second part of the review is devoted mainly to the formation and evolution of binary WDs and their observational manifestations, including their role as progenitors of cosmologically-important thermonuclear SN Ia. We also consider AM CVn-stars, which are thought to be the best verification binary GW sources for future low-frequency GW space interferometers.

  6. Binary Planetary Nebulae Nuclei towards the Galactic Bulge. I. Sample Discovery, Period Distribution and Binary Fraction

    CERN Document Server

    Miszalski, B; Moffat, A F J; Parker, Q A; Udalski, A

    2009-01-01

    Binarity has been hypothesised to play an important, if not ubiquitous, role in the formation of planetary nebulae (PNe). Yet there remains a severe paucity of known binary central stars required to test the binary hypothesis and to place strong constraints on the physics of the common-envelope (CE) phase of binary stellar evolution. Large photometric surveys offer an unrivalled opportunity to efficiently discover many binary central stars. We have combined photometry from the OGLE microlensing survey with the largest sample of PNe towards the Galactic Bulge to systematically search for new binaries. A total of 21 periodic binaries were found thereby more than doubling the known sample. The orbital period distribution was found to be best described by CE population synthesis models when no correlation between primary and secondary masses is assumed for the initial mass ratio distribution. A comparison with post-CE white dwarf binaries indicates both distributions are representative of the true post-CE period ...

  7. Planet Scattering Around Binaries: Ejections, Not Collisions

    CERN Document Server

    Smullen, Rachel A; Shannon, Andrew

    2016-01-01

    Transiting circumbinary planets discovered by Kepler provide unique insight into binary and planet formation. Several features of this new found population, for example the apparent pile-up of planets near the innermost stable orbit, may distinguish between formation theories. In this work, we determine how planet-planet scattering shapes planetary systems around binaries as compared to single stars. In particular, we look for signatures that arise due to differences in dynamical evolution in binary systems. We carry out a parameter study of N-body scattering simulations for four distinct planet populations around both binary and single stars. While binarity has little influence on the final system multiplicity or orbital distribution, the presence of a binary dramatically effects the means by which planets are lost from the system. Most circumbinary planets are lost due to ejections rather than planet-planet or planet-star collisions. The most massive planet in the system tends to control the evolution. Asid...

  8. Evolution of non-synchronized binary systems

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A model for binary evolution is introduced which can determine whether the rotation of components is synchronized with the orbital motion, and can calculate the evolution of both the synchronized and non-synchronized binary systems. With this model, the evolution of a binary system consisting of a 9 M⊙ star and a 6 M⊙ star is studied with mass transfer Case B. The result shows that the synchronization of the rotational and orbital periods can be reached when the binary system is a detached system and before the occurrence of the first mass transfer. After the onset of the first mass transfer, the binary system becomes non-synchronized. The mass accepted component (the secondary) rotates faster with a period much smaller than that of the orbital motion.

  9. Evolution of non-synchronized binary systems

    Institute of Scientific and Technical Information of China (English)

    黄润乾; 曾艺蓉

    2000-01-01

    A model for binary evolution is introduced which can determine whether the rotation of components is synchronized with the orbital motion, and can calculate the evolution of both the synchronized and non-synchronized binary systems. With this model, the evolution of a binary system consisting of a 9 M star and a 6 M star is studied with mass transfer Case B. The result shows that the synchronization of the rotational and orbital periods can be reached when the binary system is a detached system and before the occurrence of the first mass transfer. After the onset of the first mass transfer, the binary system becomes non-synchronized. The mass accepted component (the secondary) rotates faster with a period much smaller than that of the orbital motion.

  10. Terrestrial Planet Formation in Binary Star Systems

    Science.gov (United States)

    Lissauer, J. J.; Quintana, E. V.; Adams, F. C.; Chambers, J. E.

    2006-01-01

    Most stars reside in binary/multiple star systems; however, previous models of planet formation have studied growth of bodies orbiting an isolated single star. Disk material has been observed around one or both components of various young close binary star systems. If planets form at the right places within such disks, they can remain dynamically stable for very long times. We have simulated the late stages of growth of terrestrial planets in both circumbinary disks around 'close' binary star systems with stellar separations ($a_B$) in the range 0.05 AU $\\le a_B \\le$ 0.4 AU and binary eccentricities in the range $0 \\le e \\le 0.8$ and circumstellar disks around individual stars with binary separations of tens of AU. The initial disk of planetary embryos is the same as that used for simulating the late stages of terrestrial planet growth within our Solar System and around individual stars in the Alpha Centauri system (Quintana et al. 2002, A.J., 576, 982); giant planets analogous to Jupiter and Saturn are included if their orbits are stable. The planetary systems formed around close binaries with stellar apastron distances less than or equal to 0.2 AU with small stellar eccentricities are very similar to those formed in the Sun-Jupiter-Saturn, whereas planetary systems formed around binaries with larger maximum separations tend to be sparser, with fewer planets, especially interior to 1 AU. Likewise, when the binary periastron exceeds 10 AU, terrestrial planets can form over essentially the entire range of orbits allowed for single stars with Jupiter-like planets, although fewer terrestrial planets tend to form within high eccentricity binary systems. As the binary periastron decreases, the radial extent of the terrestrial planet systems is reduced accordingly. When the periastron is 5 AU, the formation of Earth-like planets near 1 AU is compromised.

  11. Binary mixtures of chiral gases

    CERN Document Server

    Presilla, Carlo

    2015-01-01

    A possible solution of the well known paradox of chiral molecules is based on the idea of spontaneous symmetry breaking. At low pressure the molecules are delocalized between the two minima of a given molecular potential while at higher pressure they become localized in one minimum due to the intermolecular dipole-dipole interactions. Evidence for such a phase transition is provided by measurements of the inversion spectrum of ammonia and deuterated ammonia at different pressures. In particular, at pressure greater than a critical value no inversion line is observed. These data are well accounted for by a model previously developed and recently extended to mixtures. In the present paper, we discuss the variation of the critical pressure in binary mixtures as a function of the fractions of the constituents.

  12. Binary Cepheids from optical interferometry

    CERN Document Server

    Gallenne, A; Mérand, A; Monnier, J D; Pietrzyński, J Breitfelder G; Gieren, W

    2013-01-01

    Classical Cepheid stars have been considered since more than a century as reliable tools to estimate distances in the universe thanks to their Period-Luminosity (P-L) relationship. Moreover, they are also powerful astrophysical laboratories, providing fundamental clues for studying the pulsation and evolution of intermediate-mass stars. When in binary systems, we can investigate the age and evolution of the Cepheid, estimate the mass and distance, and constrain theoretical models. However, most of the companions are located too close to the Cepheid (1-40 mas) to be spatially resolved with a 10-meter class telescope. The only way to spatially resolve such systems is to use long-baseline interferometry. Recently, we have started a unique and long-term interferometric program that aims at detecting and characterizing physical parameters of the Cepheid companions, with as main objectives the determination of accurate masses and geometric distances.

  13. Record-Breaking Eclipsing Binary

    Science.gov (United States)

    Kohler, Susanna

    2016-05-01

    A new record holder exists for the longest-period eclipsing binary star system: TYC-2505-672-1. This intriguing system contains a primary star that is eclipsed by its companion once every 69 years with each eclipse lasting several years!120 Years of ObservationsIn a recent study, a team of scientists led by Joseph Rodriguez (Vanderbilt University) characterizes the components of TYC-2505-672-1. This binary star system consists of an M-type red giant star that undergoes a ~3.45-year-long, near-total eclipse with a period of ~69.1 years. This period is more than double that of the previous longest-period eclipsing binary!Rodriguez and collaborators combined photometric observations of TYC-2505-672-1 by the Kilodegree Extremely Little Telescope (KELT) with a variety of archival data, including observations by the American Association of Variable Star Observers (AAVSO) network and historical data from the Digital Access to a Sky Century @ Harvard (DASCH) program.In the 120 years spanned by these observations, two eclipses are detected: one in 1942-1945 and one in 2011-2015. The authors use the observations to analyze the components of the system and attempt to better understand what causes its unusual light curve.Characterizing an Unusual SystemObservations of TYC-2505-672-1 plotted from 1890 to 2015 reveal two eclipses. (The blue KELT observations during the eclipse show upper limits only.) [Rodriguez et al. 2016]By modeling the systems emission, Rodriguez and collaborators establish that TYC-2505-672-1 consists of a 3600-K primary star thats the M giant orbited by a small, hot, dim companion thats a toasty 8000 K. But if the companion is small, why does the eclipse last several years?The authors argue that the best model of TYC-2505-672-1 is one in which the small companion star is surrounded by a large, opaque circumstellar disk. Rodriguez and collaborators suggest that the companion could be a former red giant whose atmosphere was stripped from it, leaving behind

  14. Stability of multiplanet systems in binaries

    Science.gov (United States)

    Marzari, F.; Gallina, G.

    2016-10-01

    Context. When exploring the stability of multiplanet systems in binaries, two parameters are normally exploited: the critical semimajor axis ac computed by Holman & Wiegert (1999, AJ, 117, 621) within which planets are stable against the binary perturbations, and the Hill stability limit Δ determining the minimum separation beyond which two planets will avoid mutual close encounters. Both these parameters are derived in different contexts, i.e. Δ is usually adopted for computing the stability limit of two planets around a single star while ac is computed for a single planet in a binary system. Aims: Our aim is to test whether these two parameters can be safely applied in multiplanet systems in binaries or if their predictions fail for particular binary orbital configurations. Methods: We have used the frequency map analysis (FMA) to measure the diffusion of orbits in the phase space as an indicator of chaotic behaviour. Results: First we revisited the reliability of the empirical formula computing ac in the case of single planets in binaries and we find that, in some cases, it underestimates by 10-20% the real outer limit of stability and it does not account for planets trapped in resonance with the companion star well beyond ac. For two-planet systems, the value of Δ is close to that computed for planets around single stars, but the level of chaoticity close to it substantially increases for smaller semimajor axes and higher eccentricities of the binary orbit. In these configurations ac also begins to be unreliable and non-linear secular resonances with the stellar companion lead to chaotic behaviour well within ac, even for single planet systems. For two planet systems, the superposition of mean motion resonances, either mutual or with the binary companion, and non-linear secular resonances may lead to chaotic behaviour in all cases. We have developed a parametric semi-empirical formula determining the minimum value of the binary semimajor axis, for a given

  15. Binary dynamics near a massive black hole

    CERN Document Server

    Hopman, Clovis

    2009-01-01

    We analyze the dynamical evolution of binary stars that interact with a static background of single stars in the environment of a massive black hole (MBH). All stars are considered to be single mass, Newtonian point particles. We follow the evolution of the energy E and angular momentum J of the center of mass of the binaries with respect to the MBH, as well as their internal semi-major axis a, using a Monte Carlo method. For a system like the Galactic center, the main conclusions are the following: (1) The binary fraction can be of the order of a few percent outside 0.1 pc, but decreases quickly closer to the MBH. (2) Within ~0.1 pc, binaries can only exist on eccentric orbits with apocenters much further away from the MBH. (3) Far away from the MBH, loss-cone effects are the dominant mechanism that disrupts binaries with internal velocities close to the velocity dispersion. Closer to the MBH, three-body encounters are more effective in disrupting binaries. (4) The rate at which hard binaries become tighter ...

  16. Interrupted Binary Mass Transfer in Star Clusters

    CERN Document Server

    Leigh, Nathan W C; Toonen, Silvia

    2016-01-01

    Binary mass transfer is at the forefront of some of the most exciting puzzles of modern astrophysics, including Type Ia supernovae, gamma-ray bursts, and the formation of most observed exotic stellar populations. Typically, the evolution is assumed to proceed in isolation, even in dense stellar environments such as star clusters. In this paper, we test the validity of this assumption via the analysis of a large grid of binary evolution models simulated with the SeBa code. For every binary, we calculate analytically the mean time until another single or binary star comes within the mean separation of the mass-transferring binary, and compare this time-scale to the mean time for stable mass transfer to occur. We then derive the probability for each respective binary to experience a direct dynamical interruption. The resulting probability distribution can be integrated to give an estimate for the fraction of binaries undergoing mass transfer that are expected to be disrupted as a function of the host cluster pro...

  17. The origin of very wide binary stars

    CERN Document Server

    Kouwenhoven, M B N; Davies, Melvyn B; Parker, Richard J; Kroupa, P; Malmberg, D

    2011-01-01

    A large population of fragile, wide (> 1000 AU) binary systems exists in the Galactic field and halo. These wide binary stars cannot be primordial because of the high stellar density in star forming regions, while formation by capture in the Galactic field is highly improbable. We propose that these binary systems were formed during the dissolution phase of star clusters (see Kouwenhoven et al. 2010, for details). Stars escaping from a dissolving star cluster can have very similar velocities, which can lead to the formation of a wide binary systems. We carry out N-body simulations to test this hypothesis. The results indicate that this mechanism explains the origin of wide binary systems in the Galaxy. The resulting wide binary fraction and semi-major axis distribution depend on the initial conditions of the dissolving star cluster, while the distributions in eccentricity and mass ratio are universal. Finally, since most stars are formed in (relatively tight) primordial binaries, we predict that a large fract...

  18. Mercury and Selenium in Muscle and Target Organs of Scalloped Hammerhead Sharks Sphyrna lewini of the SE Gulf of California: Dietary Intake, Molar Ratios, Loads, and Human Health Risks.

    Science.gov (United States)

    Bergés-Tiznado, Magdalena E; Márquez-Farías, Fernando; Lara-Mendoza, Raúl E; Torres-Rojas, Yassir E; Galván-Magaña, Felipe; Bojórquez-Leyva, Humberto; Páez-Osuna, Federico

    2015-11-01

    Selenium and mercury were evaluated in muscle, liver, kidney, brain, and the stomach contents of juvenile scalloped hammerhead shark Sphyrna lewini. Se:Hg molar ratios were calculated. The average Hg levels in muscle ranged from 0.12 to 1.17 μg/g (wet weight); Hg was 1. Correlations were found for Hg in muscle with size, age, and weight, and also for Hg in liver with size, age, and weight. Hg in muscle was significantly positive correlated to Hg in brain as well as Hg in liver was correlated to Hg in kidney. The highest Hg in preys was for carangid fishes; scombrid and carangid fishes contributed with the highest Se levels. Results suggest that more than 98 % of the total Hg and 62 % of Se end up in muscle and might be affected by factors, such as geographical area, age, size, and feeding habits. The muscle of S. lewini should be consumed by people cautiously so as not to exceed the recommended intake per week.

  19. Interrupted Binary Mass Transfer in Star Clusters

    Science.gov (United States)

    Leigh, Nathan W. C.; Geller, Aaron M.; Toonen, Silvia

    2016-02-01

    Binary mass transfer (MT) is at the forefront of some of the most exciting puzzles of modern astrophysics, including SNe Ia, gamma-ray bursts, and the formation of most observed exotic stellar populations. Typically, the evolution is assumed to proceed in isolation, even in dense stellar environments such as star clusters. In this paper, we test the validity of this assumption via the analysis of a large grid of binary evolution models simulated with the SeBa code. For every binary, we calculate analytically the mean time until another single or binary star comes within the mean separation of the mass-transferring binary, and compare this timescale to the mean time for stable MT to occur. We then derive the probability for each respective binary to experience a direct dynamical interruption. The resulting probability distribution can be integrated to give an estimate for the fraction of binaries undergoing MT that are expected to be disrupted as a function of the host cluster properties. We find that for lower-mass clusters (≲ {10}4 {M}⊙ ), on the order of a few to a few tens of percent of binaries undergoing MT are expected to be interrupted by an interloping single, or more often binary, star, over the course of the cluster lifetime, whereas in more massive globular clusters we expect \\ll 1% to be interrupted. Furthermore, using numerical scattering experiments performed with the FEWBODY code, we show that the probability of interruption increases if perturbative fly-bys are considered as well, by a factor ˜2.

  20. Fast algorithms for generating binary holograms

    CERN Document Server

    Stuart, Dustin; Kuhn, Axel

    2014-01-01

    We describe three algorithms for generating binary-valued holograms. Our methods are optimised for producing large arrays of tightly focussed optical tweezers for trapping particles. Binary-valued holograms allow us to use a digital mirror device (DMD) as the display element, which is much faster than other alternatives. We describe how our binary amplitude holograms can be used to correct for phase errors caused by optical aberrations. Furthermore, we compare the speed and accuracy of the algorithms for both periodic and arbitrary arrangements of traps, which allows one to choose the ideal scheme depending on the circumstances.

  1. Discovery of a 2 Kpc Binary Quasar

    OpenAIRE

    Shields, G. A.; Junkkarinen, V.; Beaver, E. A.; Burbidge, E. M.; Cohen, R. D.; Hamann, F.; Lyons, R. W.

    2001-01-01

    LBQS 0103$-$2753 is a binary quasar with a separation of only 0.3 arcsec. The projected spacing of 2.3 kpc at the distance of the source (z = 0.848) is much smaller than that of any other known binary QSO. The binary nature is demonstrated by the very different spectra of the two components and the low probability of a chance pairing. LBQS 0103$-$2753 presumably is a galaxy merger with a small physical separation between the two supermassive black holes. Such objects may provide important con...

  2. Binary Cu-Zr Bulk Metallic Glasses

    Institute of Scientific and Technical Information of China (English)

    TANG Mei-Bo; ZHAO De-Qian; PAN Ming-Xiang; WANG Wei-Hua

    2004-01-01

    @@ We report that bulk metallic glasses (BMGs) can be produced up to 2 mm by a copper mould casting in Cux Zr1-x binary alloy with a wide glass forming composition range (45 < x < 60 at.%). We find that the formation mechanism for the binary Cu-Zr binary BMG-forming alloy is obviously different from that of the intensively studied multicomponent BMGs. Our results demonstrate that the criteria for the multicomponent alloys with composition near deep eutectic and strong liquid behaviour are no longer the major concern for designing BMGs.

  3. Dynamical mass transfer in cataclysmic binaries

    Science.gov (United States)

    Melia, Fulvio; Lamb, D. Q.

    1987-01-01

    When a binary comes into contact and mass transfer begins, orbital angular momentum is stored in the accretion disk until the disk couples tidally to the binary system. Taam and McDermott (1987) have suggested that this leads to unstable dynamical mass transfer in many cataclysmic variables in which mass transfer would otherwise be stable, and that it explains the gap between 2 and 3 h in the orbital period distribution of these systems. Here the consequences of this hypothesis for the evolution of cataclysmic binaries are explored. It is found that systems coming into contact longward of the period gap undergo one or more episodes of dynamical mass transfer.

  4. Blind iterative deconvolution of binary star images

    CERN Document Server

    Saha, S K

    1997-01-01

    The technique of Blind Iterative De-convolution (BID) was used to remove the atmospherically induced point spread function (PSF) from short exposure images of two binary stars, HR 5138 and HR 5747 obtained at the cassegrain focus of the 2.34 meter Vainu Bappu Telescope(VBT), situated at Vainu Bappu Observatory (VBO), Kavalur. The position angles and separations of the binary components were seen to be consistent with results of the auto-correlation technique, while the Fourier phases of the reconstructed images were consistent with published observations of the binary orbits.

  5. Division Unit for Binary Integer Decimals

    DEFF Research Database (Denmark)

    Lang, Tomas; Nannarelli, Alberto

    2009-01-01

    -recurrence algorithm to BID representation and implement the division unit in standard cell technology. The implementation of the proposed BID division unit is compared to that of a BCD based unit implementing the same algorithm. The comparison shows that for normalized operands the BID unit has the same latency......In this work, we present a radix-10 division unit that is based on the digit-recurrence algorithm and implements binary encodings (binary integer decimal or BID) for significands. Recent decimal division designs are all based on the binary coded decimal (BCD) encoding. We adapt the radix-10 digit...

  6. Busting Up Binaries: Encounters Between Compact Binaries and a Supermassive Black Hole

    CERN Document Server

    Addison, Eric; Larson, Shane

    2015-01-01

    Given the stellar density near the galactic center, close encounters between compact object binaries and the supermassive black hole are a plausible occurrence. We present results from a numerical study of close to 13 million such encounters. Consistent with previous studies, we corroborate that, for binary systems tidally disrupted by the black hole, the component of the binary remaining bound to the hole has eccentricity ~ 0.97 and circularizes dramatically by the time it enters the classical LISA band. Our results also show that the population of surviving binaries merits attention. These binary systems experience perturbations to their internal orbital parameters with potentially interesting observational consequences. We investigated the regions of parameter space for survival and estimated the distribution of orbital parameters post-encounter. We found that surviving binaries harden and their eccentricity increases, thus accelerating their merger due gravitational radiation emission and increasing the p...

  7. CALCULATING THE HABITABLE ZONE OF BINARY STAR SYSTEMS. II. P-TYPE BINARIES

    Energy Technology Data Exchange (ETDEWEB)

    Haghighipour, Nader [Institute for Astronomy and NASA Astrobiology Institute, University of Hawaii-Manoa, Honolulu, HI 96822 (United States); Kaltenegger, Lisa [MPIA, Koenigstuhl 17, Heidelberg, D-69117 (Germany)

    2013-11-10

    We have developed a comprehensive methodology for calculating the circumbinary habitable zone (HZ) in planet-hosting P-type binary star systems. We present a general formalism for determining the contribution of each star of the binary to the total flux received at the top of the atmosphere of an Earth-like planet and use the Sun's HZ to calculate the inner and outer boundaries of the HZ around a binary star system. We apply our calculations to the Kepler's currently known circumbinary planetary systems and show the combined stellar flux that determines the boundaries of their HZs. We also show that the HZ in P-type systems is dynamic and, depending on the luminosity of the binary stars, their spectral types, and the binary eccentricity, its boundaries vary as the stars of the binary undergo their orbital motion. We present the details of our calculations and discuss the implications of the results.

  8. Binary neutron star merger simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bruegmann, Bernd [Jena Univ. (Germany)

    2016-11-01

    Our research focuses on the numerical tools necessary to solve Einstein's equations. In recent years we have been particularly interested in spacetimes consisting of two neutron stars in the final stages of their evolution. Because of the emission of gravitational radiation, the objects are driven together to merge; the emitted gravitational wave signal is visualized. This emitted gravitational radiation carries energy and momentum away from the system and contains information about the system. Late last year the Laser Interferometer Gravitational-wave Observatory (LIGO) began searches for these gravitational wave signals at a sensitivity at which detections are expected. Although such systems can radiate a significant amount of their total mass-energy in gravitational waves, the gravitational wave signals one expects to receive on Earth are not strong, since sources of gravitational waves are often many millions of light years away. Therefore one needs accurate templates for the radiation one expects from such systems in order to be able to extract them out of the detector's noise. Although analytical models exist for compact binary systems when the constituents are well separated, we need numerical simulation to investigate the last orbits before merger to obtain accurate templates and validate analytical approximations. Due to the strong nonlinearity of the equations and the large separation of length scales, these simulations are computationally demanding and need to be run on large supercomputers. When matter is present the computational cost as compared to pure black hole (vacuum) simulations increases even more due to the additional matter fields. But also more interesting astrophysical phenomena can happen. In fact, there is the possibility for a strong electromagnetic signal from the merger (e.g., a short gamma-ray burst or lower-energy electromagnetic signatures from the ejecta) and significant neutrino emission. Additionally, we can expect that

  9. New Insights into X-ray Binaries

    CERN Document Server

    Casares, Jorge

    2009-01-01

    X-ray binaries are excellent laboratories to study collapsed objects. On the one hand, transient X-ray binaries contain the best examples of stellar-mass black holes while persistent X-ray binaries mostly harbour accreting neutron stars. The determination of stellar masses in persistent X-ray binaries is usually hampered by the overwhelming luminosity of the X-ray heated accretion disc. However, the discovery of high-excitation emission lines from the irradiated companion star has opened new routes in the study of compact objects. This paper presents novel techniques which exploits these irradiated lines and summarises the dynamical masses obtained for the two populations of collapsed stars: neutron stars and black holes.

  10. A mesoscopic model for binary fluids

    CERN Document Server

    Echeverria, C; Alvarez-Llamoza, O; Orozco-Guillén, E E; Morales, M; Cosenza, M G

    2016-01-01

    We propose a model to study symmetric binary fluids, based in the mesoscopic molecular simulation technique known as multiparticle collision, where space and state variables are continuous while time is discrete. We include a repulsion rule to simulate segregation processes that does not require the calculation of the interaction forces between particles, thus allowing the description of binary fluids at a mesoscopic scale. The model is conceptually simple, computationally efficient, maintains Galilean invariance, and conserves the mass and the energy in the system at micro and macro scales; while momentum is conserved globally. For a wide range of temperatures and densities, the model yields results in good agreement with the known properties of binary fluids, such as density profile, width of the interface, phase separation and phase growth. We also apply the model to study binary fluids in crowded environments with consistent results.

  11. Red-giant stars in eccentric binaries

    Directory of Open Access Journals (Sweden)

    Beck P. G.

    2015-01-01

    Full Text Available The unparalleled photometric data obtained by NASA’s Kepler Space Telescope has led to improved understanding of red-giant stars and binary stars. We discuss the characterization of known eccentric system, containing a solar-like oscillating red-giant primary component. We also report several new binary systems that are candidates for hosting an oscillating companion. A powerful approach to study binary stars is to combine asteroseimic techniques with light curve fitting. Seismology allows us to deduce the properties of red giants. In addition, by modeling the ellipsoidal modulations we can constrain the parameters of the binary system. An valuable independent source are ground-bases, high-resolution spectrographs.

  12. Binary Biometric Representation through Pairwise Polar Quantization

    NARCIS (Netherlands)

    Chen, Chun; Veldhuis, Raymond; Tistarelli, M.; Nixon, M.

    2009-01-01

    Binary biometric representations have great significance for data compression and template protection. In this paper, we introduce pairwise polar quantization. Furthermore, aiming to optimize the discrimination between the genuine Hamming distance (GHD) and the imposter Hamming distance (IHD), we pr

  13. Searching for Pulsars in Close Binary Systems

    CERN Document Server

    Jouteux, S; Stappers, B W; Jonker, P; Van der Klis, M

    2001-01-01

    We present a detailed mathematical analysis of the Fourier response of binary pulsar signals whose frequencies are modulated by circular orbital motion. The fluctuation power spectrum of such signals is found to be \

  14. Tidal capture formation of Low Mass X-Ray Binaries from wide binaries in the field

    CERN Document Server

    Michaely, Erez

    2015-01-01

    We present a potentially efficient dynamical formation scenario for Low Mass X-ray Binaries (LMXBs) in the field, focusing on black-hole (BH) LMXBs. In this formation channel LMXBs are formed from wide binaries $(>1000$ AU) with a BH component and a stellar companion. The wide binary is perturbed by fly-by's of field stars and its orbit random-walks and changes over time. This diffusion process can drive the binary into a sufficiently eccentric orbit such that the binary components tidally interact at peri-center and the binary evolves to become a short period binary, which eventually evolves into an LMXB. The formation rate of LMXBs through this channel mostly depends on the number of such BH wide binaries progenitors, which in turn depends on the velocity kicks imparted to BHs (or NSs) at birth. We consider several models for the formation and survival of such wide binaries, and calculate the LMXB formation rates for each model. We find that models where BHs form through direct collapse with no/little natal...

  15. Evolution of Binary Stars in Multiple-Population Globular Clusters - II. Compact Binaries

    CERN Document Server

    Hong, Jongsuk; Sollima, Antonio; McMillan, Stephen L W; D'Antona, Franca; D'Ercole, Annibale

    2016-01-01

    We present the results of a survey of N-body simulations aimed at exploring the evolution of compact binaries in multiple-population globular clusters.We show that as a consequence of the initial differences in the structural properties of the first-generation (FG) and the second-generation (SG) populations and the effects of dynamical processes on binary stars, the SG binary fraction decreases more rapidly than that of the FG population. The difference between the FG and SG binary fraction is qualitatively similar to but quantitatively smaller than that found for wider binaries in our previous investigations.The evolution of the radial variation of the binary fraction is driven by the interplay between binary segregation, ionization and ejection. Ionization and ejection counteract in part the effects of mass segregation but for compact binaries the effects of segregation dominate and the inner binary fraction increases during the cluster evolution. We explore the variation of the difference between the FG an...

  16. Dixie Valley Bottoming Binary Unit

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, Dale [Terra-Gen Sierra Holdings, LLC, Reno, NV (United States)

    2014-12-21

    This binary plant is the first air cooled, high-output refrigeration based waste heat recovery cycle in the industry. Its working fluid is environmentally friendly and as such, the permits that would be required with a hydrocarbon based cycle are not necessary. The unit is largely modularized, meaning that the unit’s individual skids were assembled in another location and were shipped via truck to the plant site. The Air Cooled Condensers (ACC), equipment piping, and Balance of Plant (BOP) piping were constructed at site. This project further demonstrates the technical feasibility of using low temperature brine for geothermal power utilization. The development of the unit led to the realization of low temperature, high output, and environmentally friendly heat recovery systems through domestic research and engineering. The project generates additional renewable energy, resulting in cleaner air and reduced carbon dioxide emissions. Royalty and tax payments to governmental agencies will increase, resulting in reduced financial pressure on local entities. The major components of the unit were sourced from American companies, resulting in increased economic activity throughout the country.

  17. Binary module test. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Schilling, J.R.; Colley, T.C.; Pundyk, J.

    1980-12-01

    The objective of this project was to design and test a binary loop module representative of and scaleable to commercial size units. The design was based on state-of-the-art heat exchanger technology, and the purpose of the tests was to confirm performance of a supercritical boiling cycle using isobutane and a mixture of isobutane and isopentane as the secondary working fluid. The module was designed as one percent of a 50 MW unit. It was installed at Magma Power's East Mesa geothermal field and tested over a period of approximately 4 months. Most of the test runs were with isobutane but some data were collected for hydrocarbon mixtures. The results of the field tests are reported. In general these results indicate reasonably good heat balances and agreement with overall heat transfer coefficients calculated by current stream analysis methods and available fluid property data; however, measured pressure drops across the heat exchangers were 20 percent higher than estimated. System operation was stable under all conditions tested.

  18. Near-Optimal Compressive Binary Search

    OpenAIRE

    Malloy, Matthew L.; Nowak, Robert D.

    2012-01-01

    We propose a simple modification to the recently proposed compressive binary search. The modification removes an unnecessary and suboptimal factor of log log n from the SNR requirement, making the procedure optimal (up to a small constant). Simulations show that the new procedure performs significantly better in practice as well. We also contrast this problem with the more well known problem of noisy binary search.

  19. Statistical pattern classification with binary variables.

    Science.gov (United States)

    Young, T Y; Liu, P S; Rondon, R J

    1981-02-01

    Binary random variables are regarded as random vectors in a binary-field (modulo-2) linear vector space. A characteristic function is defined and related results derived using this formulation. Minimax estimation of probability distributions using an entropy criterion is investigated, which leads to an A-distribution and bilinear discriminant functions. Nonparametric classification approaches using Hamming distances and their asymptotic properties are discussed. Experimental results are presented.

  20. Binary compact object inspiral: Detection expectations

    Indian Academy of Sciences (India)

    Vassiliki Kalogera

    2004-10-01

    We review the current estimates of binary compact object inspiral rates in particular in view of the recently discovered highly relativistic binary pulsar J0737-3039. One of the robust results is that, because of this discovery, the rate estimates for binary neutron stars have increased by a factor of 6-7 independent of any uncertainties related to the pulsar population properties. This rate increase has dramatic implications for gravitational wave detectors. For initial LIGO, the most probable detection rates for double neutron star (DNS) inspirals is 1 event/(5{250) yr; at 95% confidence we obtain rates up to 1/1.5 yr. For advanced LIGO, the most probable rates are 20-1000 events/yr. These predictions, for the first time, bring the expectations for DNS detections by initial LIGO to the astrophysically relevant regime. We also use our models to predict that the large-scale Parkes multibeam pulsar survey with acceleration searches could detect an average of three to four binary pulsars similar to those known at present. In comparison, rate estimates for binaries with black holes are derived based on binary evolution calculation, and based on the optimistic ends of the ranges, remain an important candidate for inspiral detection in the next few years. We also consider another aspect of the detectability of binary inspiral: the effect of precession on the detection efficiency of astrophysically relevant binaries. Based on our current astrophysical expectations, large tilt angles are not favored. As a result the decrease in detection rate varies rather slowly with black hole spin magnitude and is within 20-30% of the maximum possible values.

  1. The DEBCat detached eclipsing binary catalogue

    OpenAIRE

    2014-01-01

    Detached eclipsing binary star systems are our primary source of measured physical properties of normal stars. I introduce DEBCat: a catalogue of detached eclipsing binaries with mass and radius measurements to the 2% precision necessary to put useful constraints on theoretical models of stellar evolution. The catalogue was begun in 2006, as an update of the compilation by Andersen (1991). It now contains over 170 systems, and new results are added on appearance in the refereed literature. DE...

  2. An improved catalog of halo wide binary candidates

    CERN Document Server

    Allen, Christine

    2014-01-01

    We present an improved catalog of halo wide binaries, compiled from an extensive literature search. Most of our binaries stem from the common proper motion binary catalogs by Allen et al. (2004), and Chanam\\'e \\& Gould. (2004) but we have also included binaries from the lists of Ryan (1992) and Zapatero-Osorio \\& Martin (2004). All binaries were carefully checked and their distances and systemic radial velocities are included, when available. Probable membership to the halo population was tested by means of reduced proper motion diagrams for 251 candidate halo binaries. After eliminating obvious disk binaries we ended up with 211 probable halo binaries, for 150 of which radial velocities are available. We compute galactic orbits for these 150 binaries and calculate the time they spend within the galactic disk. Considering the full sample of 251 candidate halo binaries as well as several subsamples, we find that the distribution of angular separations (or expected major semiaxes) follows a power law $f...

  3. Texture classification by texton: statistical versus binary.

    Directory of Open Access Journals (Sweden)

    Zhenhua Guo

    Full Text Available Using statistical textons for texture classification has shown great success recently. The maximal response 8 (Statistical_MR8, image patch (Statistical_Joint and locally invariant fractal (Statistical_Fractal are typical statistical texton algorithms and state-of-the-art texture classification methods. However, there are two limitations when using these methods. First, it needs a training stage to build a texton library, thus the recognition accuracy will be highly depended on the training samples; second, during feature extraction, local feature is assigned to a texton by searching for the nearest texton in the whole library, which is time consuming when the library size is big and the dimension of feature is high. To address the above two issues, in this paper, three binary texton counterpart methods were proposed, Binary_MR8, Binary_Joint, and Binary_Fractal. These methods do not require any training step but encode local feature into binary representation directly. The experimental results on the CUReT, UIUC and KTH-TIPS databases show that binary texton could get sound results with fast feature extraction, especially when the image size is not big and the quality of image is not poor.

  4. Spectroscopic subsystems in nearby wide binaries

    CERN Document Server

    Tokovinin, Andrei

    2015-01-01

    Radial velocity (RV) monitoring of solar-type visual binaries has been conducted at the CTIO/SMARTS 1.5-m telescope to study short-period systems. Data reduction is described, mean and individual RVs of 163 observed objects are given. New spectroscopic binaries are discovered or suspected in 17 objects, for some of them orbital periods could be determined. Subsystems are efficiently detected even in a single observation by double lines and/or by the RV difference between the components of visual binaries. The potential of this detection technique is quantified by simulation and used for statistical assessment of 96 wide binaries within 67pc. It is found that 43 binaries contain at least one subsystem and the occurrence of subsystems is equally probable in either primary or secondary components. The frequency of subsystems and their periods match the simple prescription proposed by the author (2014, AJ, 147, 87). The remaining 53 simple wide binaries with a median projected separation of 1300AU have the distri...

  5. Coronal activity from the ASAS eclipsing binaries

    CERN Document Server

    Szczygiel, D M; Paczynski, B; Pojmanski, G; Pilecki, B

    2008-01-01

    We combine the catalogue of eclipsing binaries from the All Sky Automated Survey (ASAS) with the ROSAT All Sky Survey (RASS). The combination results in 836 eclipsing binaries that display coronal activity and is the largest sample of active binary stars assembled to date. By using the (V-I) colors of the ASAS eclipsing binary catalogue, we are able to determine the distances and thus bolometric luminosities for the majority of eclipsing binaries that display significant stellar activity. A typical value for the ratio of soft X-ray to bolometric luminosity is L_X/L_bol ~ a few x 10^-4, similar to the ratio of soft X-ray to bolometric flux F_X/F_bol in the most active regions of the Sun. Unlike rapidly rotating isolated late-type dwarfs -- stars with significant outer convection zones -- a tight correlation between Rossby number and activity of eclipsing binaries is absent. We find evidence for the saturation effect and marginal evidence for the so-called "super-saturation" phenomena. Our work shows that wide-...

  6. Selective dissolution in binary alloys

    Science.gov (United States)

    McCall, Carol Rene

    Corrosion is an important issue in the design of engineering alloys. De-alloying is an aspect of alloy corrosion related to the selective dissolution of one or more of the components in an alloy. The work reported herein focuses on the topic of de-alloying specific to single-phase binary noble metal alloy systems. The alloy systems investigated were gold-silver and gold-copper. The onset of a bulk selective dissolution process is typically marked by a critical potential whereby the more reactive component in the alloy begins dissolving from the bulk, leading to the formation of a bi-continuous solid-void morphology. The critical potential was investigated for the entire composition range of gold-silver alloys. The results presented herein include the formulation of an expression for critical potential as a function of both alloy and electrolyte composition. Results of the first investigation of underpotential deposition (UPD) on alloys are also presented herein. These results were implemented as an analytical tool to provide quantitative measurements of the surface evolution of gold during de-alloying. The region below the critical potential was investigated in terms of the compositional evolution of the alloy surface. Below the critical potential, there is a competition between the dissolution of the more reactive alloying constituent (either silver or copper) and surface diffusion of gold that serves to cover dissolution sites and prevent bulk dissolution. By holding the potential at a prescribed value below the critical potential, a time-dependent gold enrichment occurs on the alloy surface leading to passivation. A theoretical model was developed to predict the surface enrichment of gold based on the assumption of layer-by-layer dissolution of the more reactive alloy constituent. The UPD measurements were used to measure the time-dependent surface gold concentration and the results agreed with the predictions of the theoretical model.

  7. Exploring the Birth of Binary Stars

    Science.gov (United States)

    Kohler, Susanna

    2016-08-01

    More than half of all stars are thought to be in binary or multiple star systems. But how do these systems form? The misaligned spins of some binary protostars might provide a clue.Two Formation ModelsIts hard to tell how multiple-star systems form, since these systems are difficult to observe in their early stages. But based on numerical simulations, there are two proposed models for the formation of stellar binaries:Turbulent fragmentationTurbulence within a single core leads to multiple dense clumps. These clumps independently collapse to form stars that orbit each other.Disk fragmentationGravitational instabilities in a massive accretion disk cause the formation of a smaller, secondary disk within the first, resulting in two stars that orbit each other.Log column density for one of the authors simulated binary systems, just after the formation of two protostars. Diamonds indicate the protostar positions. [Adapted from Offner et al. 2016]Outflows as CluesHow can we differentiate between these formation mechanisms? Led by Stella Offner (University of Massachusetts), a team of scientists has suggested that the key isto examine the alignment of the stars protostellar outflows jets that are often emitted from the poles of young, newly forming stars.Naively, wed expect that disk fragmentation would produce binary stars with common angular momentum. As the stars spins would be aligned, they would therefore also launch protostellar jets that were aligned with each other. Turbulent fragmentation, on the other hand, would cause the stars to have independent angular momentum. This would lead to randomly oriented spins, so the protostellar jets would be misaligned.Snapshots from the authors simulations. Left panel of each pair: column density; green arrows giveprotostellar spin directions. Right panel: synthetic observations produced from the simulations; cyan arrows giveprotostellar outflow directions. [Offner et al. 2016]Simulations of FragmentationIn order to better

  8. Absolute dimensions of eclipsing binaries XXVIII. BK pegasi and other F-type binaries

    DEFF Research Database (Denmark)

    Clausen, Jens Viggo; Frandsen, S.; Bruntt, H.

    2010-01-01

     stars: evolution / stars: fundamental parameters / binaries: eclipsing / stars: individual: BK¿Peg / stars: individual: BW¿Aqr / techniques: spectroscopic Udgivelsesdato: June 24...... stars: evolution / stars: fundamental parameters / binaries: eclipsing / stars: individual: BK¿Peg / stars: individual: BW¿Aqr / techniques: spectroscopic Udgivelsesdato: June 24...

  9. New spectroscopic binary companions of giant stars and updated metallicity distribution for binary systems

    CERN Document Server

    Bluhm, P; Vanzi, L; Soto, M G; Vos, J; Wittenmyer, R A; Olivares, F; Drass, H; Mennickent, R E; Vuckovic, M; Rojo, P; Melo, C H F

    2016-01-01

    We report the discovery of 24 spectroscopic binary companions to giant stars. We fully constrain the orbital solution for 6 of these systems. We cannot unambiguously derive the orbital elements for the remaining stars because the phase coverage is incomplete. Of these stars, 6 present radial velocity trends that are compatible with long-period brown dwarf companions.The orbital solutions of the 24 binary systems indicate that these giant binary systems have a wide range in orbital periods, eccentricities, and companion masses. For the binaries with restricted orbital solutions, we find a range of orbital periods of between $\\sim$ 97-1600 days and eccentricities of between $\\sim$ 0.1-0.4. In addition, we studied the metallicity distribution of single and binary giant stars. We computed the metallicity of a total of 395 evolved stars, 59 of wich are in binary systems. We find a flat distribution for these binary stars and therefore conclude that stellar binary systems, and potentially brown dwarfs, have a diffe...

  10. On the reconstruction of binary and permutation matrices under (binary) tomographic constraints

    NARCIS (Netherlands)

    Brunetti, S.; Del Lungo, A.; Gritzmann, P.; de Vries, S.

    2008-01-01

    The paper studies the problem of reconstructing binary matrices constrained by binary tomographic information. We prove new NP-hardness results that sharpen previous complexity results in the realm of discrete tomography but also allow applications to related problems for permutation matrices. Hence

  11. Towards the field binary population: Influence of orbital decay on close binaries

    CERN Document Server

    Korntreff, Christina; Pfalzner, Susanne

    2012-01-01

    Surveys of the binary populations in the solar neighbourhood have shown that the periods of G- and M-type stars are log-normally distributed. However, observations of young binary populations suggest a log-uniform distribution. Clearly some process(es) change the period distribution over time. Most stars form in star clusters, in which two important dynamical processes occur: i) gas-induced orbital decay of embedded binary systems and ii) destruction of soft binaries in three-body interactions. The emphasis here is on orbital decay which has been largely neglected so far. Using a combination of Monte-Carlo and dynamical nbody modelling it is demonstrated here that the cluster dynamics destroys the number of wide binaries, but leaves short-period binaries basically undisturbed even for a initially log-uniform distribution. By contrast orbital decay significantly reduces the number and changes the properties of short-period binaries, but leaves wide binaries largely uneffected. Until now it was unclear whether ...

  12. Birth of Massive Black Hole Binaries

    Energy Technology Data Exchange (ETDEWEB)

    Colpi, M.; /Milan Bicocca U.; Dotti, M.; /Insubria U., Como; Mayer, L.; /Zurich, ETH; Kazantzidis, S.; /KIPAC, Menlo Park

    2007-11-19

    If massive black holes (BHs) are ubiquitous in galaxies and galaxies experience multiple mergers during their cosmic assembly, then BH binaries should be common albeit temporary features of most galactic bulges. Observationally, the paucity of active BH pairs points toward binary lifetimes far shorter than the Hubble time, indicating rapid inspiral of the BHs down to the domain where gravitational waves lead to their coalescence. Here, we review a series of studies on the dynamics of massive BHs in gas-rich galaxy mergers that underscore the vital role played by a cool, gaseous component in promoting the rapid formation of the BH binary. The BH binary is found to reside at the center of a massive self-gravitating nuclear disc resulting from the collision of the two gaseous discs present in the mother galaxies. Hardening by gravitational torques against gas in this grand disc is found to continue down to sub-parsec scales. The eccentricity decreases with time to zero and when the binary is circular, accretion sets in around the two BHs. When this occurs, each BH is endowed with it own small-size ({approx}< 0.01 pc) accretion disc comprising a few percent of the BH mass. Double AGN activity is expected to occur on an estimated timescale of {approx}< 1 Myr. The double nuclear point-like sources that may appear have typical separation of {approx}< 10 pc, and are likely to be embedded in the still ongoing starburst. We note that a potential threat of binary stalling, in a gaseous environment, may come from radiation and/or mechanical energy injections by the BHs. Only short-lived or sub-Eddington accretion episodes can guarantee the persistence of a dense cool gas structure around the binary necessary for continuing BH inspiral.

  13. Massive gaseous discs around SMBH binaries: Binary decay and tidal disruptions

    Directory of Open Access Journals (Sweden)

    Brem P.

    2012-12-01

    Full Text Available We investigate the evolution of black hole binaries embedded within geometrically thin gas discs. Our results imply that such discs can produce black hole mergers for relatively low-mass binaries, and that a significant population of eccentric binaries might exist at separations of a few 0.01 pc. These binaries may be detectable due to the time-variable accretion on to the black holes. If the disc fragments, then the newly-born stars will continue driving the binary to its coalescence, although at a slower rate. Interestingly, our preliminary analysis shows that these stars will be disrupted at a rate of ∼10−4–2 · 10−5 events per year per system.

  14. Nonconservative Mass Transfer in Massive Binaries and the Formation of Wolf-Rayet+O Binaries

    CERN Document Server

    Shao, Yong

    2016-01-01

    The mass transfer efficiency during the evolution of massive binaries is still uncertain. We model the mass transfer processes in a grid of binaries to investigate the formation of Wolf-Rayet+O (WR+O) binaries, taking into account two kinds of non-conservative mass transfer models: Model I with rotation-dependent mass accretion and Model II of half mass accretion. Generally the mass transfer in Model I is more inefficient, with the average efficiency in a range of $\\sim0.2-0.7$ and $ \\lesssim0.2 $ for Case A and Case B mass transfer, respectively. We present the parameter distributions for the descendant WR+O binaries. By comparing the modeled stellar mass distribution with the observed Galactic WR+O binaries, we find that highly non-conservative mass transfer is required.

  15. Recombinant adeno-associated virus serotype 9 with p65 ribozyme protects H9c2 cells from oxidative stress through inhibiting NF-κB signaling pathway

    Institute of Scientific and Technical Information of China (English)

    Zhan SUN; Yi-Tong MA; Bang-Dang CHEN; Fen LIU

    2014-01-01

    Background Oxidative stress is a major mechanism underlying the pathogenesis of cardiovascular disease. It can trigger inflammatory cascades which are primarily mediated via nuclear factor-κB (NF-κB). The NF-κB transcription factor family includes several subunits (p50, p52, p65, c-Rel, and Rel B) that respond to myocardial ischemia. It has been proved that persistent myocyte NF-κB p65 activation in heart failure exacerbates cardiac remodeling. Mechods A recombinant adeno-associated virus serotype 9 carrying enhanced green fluorescent protein and anti-NF-κB p65 ribozyme (AAV9-R65-CMV-eGFP) was constructed. The cells were assessed by MTT assay, Annexin V–propidium iodide dual staining to study apoptosis. The expression of P65 and P50 were assessed by Western blot to investigate the under-lying molecular mechanisms. Results After stimulation with H2O2 for 6 h, H9c2 cells viability decreased significantly, a large fraction of cells underwent apoptosis. We observed a rescue of H9c2 cells from H2O2-induced apoptosis in pretreatment with AAV9-R65-CMV-eGFP. Moreover, AAV9-R65-CMV-eGFP decreased H2O2-induced P65 expression. Conclusions AAV9-R65-CMV-eGFP protects H9c2 cells from oxidative stress induced apoptosis through down-regulation of P65 expression. These observations indicate that AAV9-R65-CMV-eGFP has the potential to exert cardioprotective effects against oxidative stress, which might be of great importance to clinical efficacy for cardiovascular disease.

  16. EFFECTS OF IN VIVO GENE TRANSDUCTION OF ANTI-MDR1 RIBOZYME IN COMBINATION WITH CHEMOTHERAPY ON MULTIDRUG-RESISTANT HUMAN LYMPHOMA GROWTH IN MICE

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Objective: To study the effect of adenovirus- mediated transfer of anti-MDR1 ribozyme on the reversal of multidrug resistant (MDR) phenotype of P-glycoprotein (P-gp)-positive Daudi human Burkitt lymphoma both in vitro and in vivo. Methods: A recombinant adenovirus expressing 196Rz (Adv-196Rz) was developed and functionally evaluated. SCID mice inoculated subcutaneously (s.c.) with 5×106 Daudi/MDR20 cells were locally treated with Adv-196Rz or mock virus (Adv-Mock) at the multiplicity of infection (MOI) of 400 PFU once a day for 3 consecutive days. Then the mice were intraperitoneally (i.p.) administrated with vincristine (VCR) 450ng/g for 5 consecutive days. Results: In vitro employment of Adv-196Rz was able to interrupt MDR1 transcription, to inhibit P-gp expression and to restore drug sensitivity to VCR of Daudi/MDR20 cells. In vivo, 87.5% (7/8) of Daudi/MDR20-inoculated mice treated with Adv-Mock+ VCR developed palpable tumor by the 6th week and died or were sacrificed (because of tumor weight > 10% of body weight) by the 11th week. In contrast, among 9 Daudi/MDR20-inoculated mice treated with Adv-196Rz + VCR, only 3 developed tumor by the 11th, 13th and 14th week, respectively. 66.7% of mice survived >120 days in tumor-free. The survival difference between the two groups was very significant (P<0.01). Conclusion: Adenovirus- mediated Transfer of 196Rz can revert drug resistance of MDR tumor cells both in vitro and in vivo. Adv-196Rz may prove useful as an adjuvant in the chemotherapy of P-gp mediated MDR human tumors.

  17. Serial binary interval ratios improve rhythm reproduction

    Directory of Open Access Journals (Sweden)

    Xiang eWu

    2013-08-01

    Full Text Available Musical rhythm perception is a natural human ability that involves complex cognitive processes. Rhythm refers to the organization of events in time, and musical rhythms have an underlying hierarchical metrical structure. The metrical structure induces the feeling of a beat and the extent to which a rhythm induces the feeling of a beat is referred to as its metrical strength. Binary ratios are the most frequent interval ratio in musical rhythms. Rhythms with hierarchical binary ratios are better discriminated and reproduced than rhythms with hierarchical non-binary ratios. However, it remains unclear whether a superiority of serial binary over non-binary ratios in rhythm perception and reproduction exists. In addition, how different types of serial ratios influence the metrical strength of rhythms remains to be elucidated. The present study investigated serial binary vs. non-binary ratios in a reproduction task. Rhythms formed with exclusively binary (1:2:4:8, non-binary integer (1:3:5:6, and non-integer (1:2.3:5.3:6.4 ratios were examined within a constant meter. The results showed that the 1:2:4:8 rhythm type was more accurately reproduced than the 1:3:5:6 and 1:2.3:5.3:6.4 rhythm types, and the 1:2.3:5.3:6.4 rhythm type was more accurately reproduced than the 1:3:5:6 rhythm type. Further analyses showed that reproduction performance was better predicted by the distribution pattern of event occurrences within an inter-beat interval, than by the coincidence of events with beats, or the magnitude and complexity of interval ratios. Whereas rhythm theories and empirical data emphasize the role of the coincidence of events with beats in determining metrical strength and predicting rhythm performance, the present results suggest that rhythm processing may be better understood when the distribution pattern of event occurrences is taken into account. These results provide new insights into the mechanisms underlining musical rhythm perception.

  18. Serial binary interval ratios improve rhythm reproduction.

    Science.gov (United States)

    Wu, Xiang; Westanmo, Anders; Zhou, Liang; Pan, Junhao

    2013-01-01

    Musical rhythm perception is a natural human ability that involves complex cognitive processes. Rhythm refers to the organization of events in time, and musical rhythms have an underlying hierarchical metrical structure. The metrical structure induces the feeling of a beat and the extent to which a rhythm induces the feeling of a beat is referred to as its metrical strength. Binary ratios are the most frequent interval ratio in musical rhythms. Rhythms with hierarchical binary ratios are better discriminated and reproduced than rhythms with hierarchical non-binary ratios. However, it remains unclear whether a superiority of serial binary over non-binary ratios in rhythm perception and reproduction exists. In addition, how different types of serial ratios influence the metrical strength of rhythms remains to be elucidated. The present study investigated serial binary vs. non-binary ratios in a reproduction task. Rhythms formed with exclusively binary (1:2:4:8), non-binary integer (1:3:5:6), and non-integer (1:2.3:5.3:6.4) ratios were examined within a constant meter. The results showed that the 1:2:4:8 rhythm type was more accurately reproduced than the 1:3:5:6 and 1:2.3:5.3:6.4 rhythm types, and the 1:2.3:5.3:6.4 rhythm type was more accurately reproduced than the 1:3:5:6 rhythm type. Further analyses showed that reproduction performance was better predicted by the distribution pattern of event occurrences within an inter-beat interval, than by the coincidence of events with beats, or the magnitude and complexity of interval ratios. Whereas rhythm theories and empirical data emphasize the role of the coincidence of events with beats in determining metrical strength and predicting rhythm performance, the present results suggest that rhythm processing may be better understood when the distribution pattern of event occurrences is taken into account. These results provide new insights into the mechanisms underlining musical rhythm perception.

  19. Beyond binaries : a way forward for comparativeeducation

    Directory of Open Access Journals (Sweden)

    Marianne Larsen

    2012-09-01

    Full Text Available Binary discourses shape and produce the stories we construct about the field of comparative education. In the first part of this article, I review a set of binary discourses that have characterized social science research since the Enlightenment, including: quantitative-qualitative, nomotheticidiographic, inductive-deductive, and practice-theory. We can think of each of these binaries at opposite ends of a set of spectrums. In the second section of the paper, I show some of the ways in which these binaries have influenced the ways that we write and talk about research within the field of comparative education. I refer to the notion of binary discourses and the productive capacity of these discourses to shape our field. I then outline some critiques of these binaries to demonstrate the inherent limitations of binary discourses, and why we need to move beyond binaries in our research, and in the histories about our field. Finally, I present some tentative conclusions on ways to get ourselves out of the trap of binary thinking.Los discursos binarios moldean y producen los argumentos que construimos sobre la disciplina de la Educación Comparada. En la primera parte de este artículo, analizo un conjunto de discursos binarios que han caracterizado la investigación en Ciencias Sociales desde la Ilustración, incluyendo la cuantitativa-cualitativa, nomotética-idiográfica, inductivadeductiva, y la práctica-teoría. Podemos pensar sobre cada uno de estos discursos binarios como argumentos en los polos de un conjunto de posibilidades. En la segunda sección del artículo, revelo algunos modos en los que estos discursos binarios han influenciado las formas a través de las cuales escribimos y analizamos la investigación en el ámbito de la Educación Comparada. Analizo la noción de discursos binarios y la capacidad productiva de estos discursos de impactar nuestra ciencia. Seguidamente expongo algunas críticas de estos discursos binarios con el

  20. Planet scattering around binaries: ejections, not collisions

    Science.gov (United States)

    Smullen, Rachel A.; Kratter, Kaitlin M.; Shannon, Andrew

    2016-09-01

    Transiting circumbinary planets discovered by Kepler provide unique insight into binary star and planet formation. Several features of this new found population, for example the apparent pile-up of planets near the innermost stable orbit, may distinguish between formation theories. In this work, we determine how planet-planet scattering shapes planetary systems around binaries as compared to single stars. In particular, we look for signatures that arise due to differences in dynamical evolution in binary systems. We carry out a parameter study of N-body scattering simulations for four distinct planet populations around both binary and single stars. While binarity has little influence on the final system multiplicity or orbital distribution, the presence of a binary dramatically affects the means by which planets are lost from the system. Most circumbinary planets are lost due to ejections rather than planet-planet or planet-star collisions. The most massive planet in the system tends to control the evolution. Systems similar to the only observed multiplanet circumbinary system, Kepler-47, can arise from much more tightly packed, unstable systems. Only extreme initial conditions introduce differences in the final planet populations. Thus, we suggest that any intrinsic differences in the populations are imprinted by formation.

  1. The binary white dwarf LHS 3236

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Hugh C.; Dahn, Conard C.; Canzian, Blaise; Guetter, Harry H.; Levine, Stephen E.; Luginbuhl, Christian B.; Monet, Alice K. B.; Stone, Ronald C.; Subasavage, John P.; Tilleman, Trudy; Walker, Richard L. [US Naval Observatory, 10391 West Naval Observatory Road, Flagstaff, AZ 86001-8521 (United States); Dupuy, Trent J.; Liu, Michael C. [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Hartkopf, William I. [US Naval Observatory, 3450 Massachusetts Avenue, N.W., Washington, DC 20392-5420 (United States); Ireland, Michael J. [Department of Physics and Astronomy, Macquarie University, New South Wales, NSW 2109 (Australia); Leggett, S. K., E-mail: hch@nofs.navy.mil [Gemini Observatory, 670 N. Aohoku Place, Hilo, HI 96720 (United States)

    2013-12-10

    The white dwarf LHS 3236 (WD1639+153) is shown to be a double-degenerate binary, with each component having a high mass. Astrometry at the U.S. Naval Observatory gives a parallax and distance of 30.86 ± 0.25 pc and a tangential velocity of 98 km s{sup –1}, and reveals binary orbital motion. The orbital parameters are determined from astrometry of the photocenter over more than three orbits of the 4.0 yr period. High-resolution imaging at the Keck Observatory resolves the pair with a separation of 31 and 124 mas at two epochs. Optical and near-IR photometry give a set of possible binary components. Consistency of all data indicates that the binary is a pair of DA stars with temperatures near 8000 and 7400 K and with masses of 0.93 and 0.91 M {sub ☉}; also possible is a DA primary and a helium DC secondary with temperatures near 8800 and 6000 K and with masses of 0.98 and 0.69 M {sub ☉}. In either case, the cooling ages of the stars are ∼3 Gyr and the total ages are <4 Gyr. The combined mass of the binary (1.66-1.84 M {sub ☉}) is well above the Chandrasekhar limit; however, the timescale for coalescence is long.

  2. A Model for Contact Binary Systems

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A model for contact binary systems is presented, which incorporates the following special features: a) The energy exchange between the components is based on the understanding that the energy exchange is due to the release of potential, kinetic and thermal energies of the exchanged mass. b) A special form of mass and angular momentum loss occurring in contact binaries is losses via the outer Lagrangian point. c) The effects of spin, orbital rotation and tidal action on the stellar structure as well as the effect of meridian circulation on the mixing of the chemical elements are considered. d) The model is valid not only for low-mass contact binaries but also for high-mass contact binaries. For illustration, we used the model to trace the evolution of a massive binary system consisting of one 12M⊙ and one 5M⊙ star. The result shows that the start and end of the contact stage fall within the semi-detached phase during which the primary continually transfers mass to the secondary. The time span of the contact stage is short and the mass transfer rate is very large. Therefore, the contact stage can be regarded as a special part of the semi-detached phase with a large mass transfer rate. Both mass loss through the outer Lagrangian point and oscillation between contact and semi-contact states can occur during the contact phase, and the effective temperatures of the primary and the secondary are almost equal.

  3. Stability of multiplanet systems in binaries

    CERN Document Server

    Marzari, F

    2016-01-01

    When exploring the stability of multiplanet systems in binaries, two parameters are normally exploited: the critical semimajor axis ac computed by Holman and Wiegert (1999) within which planets are stable against the binary perturbations, and the Hill stability limit Delta determining the minimum separation beyond which two planets will avoid mutual close encounters. Our aim is to test whether these two parameters can be safely applied in multiplanet systems in binaries or if their predictions fail for particular binary orbital configurations. We have used the frequency map analysis (FMA) to measure the diffusion of orbits in the phase space as an indicator of chaotic behaviour. First we revisited the reliability of the empirical formula computing ac in the case of single planets in binaries and we find that, in some cases, it underestimates by 10-20% the real outer limit of stability. For two planet systems, the value of Delta is close to that computed for planets around single stars, but the level of chaoti...

  4. Orbital eccentricities in primordial black holes binaries

    CERN Document Server

    Cholis, Ilias; Ali-Haïmoud, Yacine; Bird, Simeon; Kamionkowski, Marc; Muñoz, Julian B; Raccanelli, Alvise

    2016-01-01

    It was recently suggested that the merger of $\\sim30\\,M_\\odot$ primordial black holes (PBHs) may provide a significant number of events in gravitational-wave observatories over the next decade, if they make up an appreciable fraction of the dark matter. Here we show that measurement of the eccentricities of the inspiralling binary black holes can be used to distinguish these binaries from those produced by more traditional astrophysical mechanisms. These PBH binaries are formed on highly eccentric orbits and can then merge on timescales that in some cases are years or less, retaining some eccentricity in the last seconds before the merger. This is to be contrasted with massive-stellar-binary, globular-cluster, or other astrophysical origins for binary black holes (BBHs) in which the orbits have very effectively circularized by the time the BBH enters the observable LIGO window. Here we discuss the features of the gravitational-wave signals that indicate this eccentricity and forecast the sensitivity of LIGO a...

  5. Orbital eccentricities in primordial black hole binaries

    Science.gov (United States)

    Cholis, Ilias; Kovetz, Ely D.; Ali-Haïmoud, Yacine; Bird, Simeon; Kamionkowski, Marc; Muñoz, Julian B.; Raccanelli, Alvise

    2016-10-01

    It was recently suggested that the merger of ˜30 M⊙ primordial black holes (PBHs) may provide a significant number of events in gravitational-wave observatories over the next decade, if they make up an appreciable fraction of the dark matter. Here we show that measurement of the eccentricities of the inspiralling binary black holes can be used to distinguish these binaries from those produced by more traditional astrophysical mechanisms. These PBH binaries are formed on highly eccentric orbits and can then merge on time scales that in some cases are years or less, retaining some eccentricity in the last seconds before the merger. This is to be contrasted with massive-stellar-binary, globular-cluster, or other astrophysical origins for binary black holes (BBHs) in which the orbits have very effectively circularized by the time the BBH enters the observable LIGO window. Here we discuss the features of the gravitational-wave signals that indicate this eccentricity and forecast the sensitivity of LIGO and the Einstein Telescope to such effects. We show that if PBHs make up the dark matter, then roughly one event should have a detectable eccentricity given LIGO's expected sensitivity and observing time of six years. The Einstein Telescope should see O (10 ) such events after ten years.

  6. An interferometric view of binary stars

    CERN Document Server

    Boffin, Henri M J

    2016-01-01

    The study of binary stars is critical to apprehend many of the most interesting classes of stars. Moreover, quite often, the study of stars in binary systems is our only mean to constrain stellar properties, such as masses and radii. Unfortunately, a great fraction of the most interesting binaries are so compact that they can only be apprehended by high-resolution techniques, mostly by interferometry. I present some results highlighting the use of interferometry in the study of binary stars, from finding companions and deriving orbits, determining the mass and radius of stars, to studying mass transfer in symbiotic stars, and tackling luminous blue variables. In particular, I show how interferometric studies using the PIONIER instrument have allowed us to confirm a dichotomy within symbiotic stars, obtain masses of stars with a precision better than 1%, and help us find a new Eta Carinae-like system. I will also illustrate the benefits for the study of binary stars one would get from upgrading the VLT Interfe...

  7. Stacking Analysis of Binary Systems with HAWC

    Science.gov (United States)

    Brisbois, Chad; HAWC Collaboration

    2017-01-01

    Detecting binary systems at TeV energies is an important problem because only a handful of such systems are currently known. The nature of such systems is typically thought to be composed of a compact object and a massive star. The TeV emission from these systems does not obviously correspond to emission in GeV or X-ray, where many binary systems have previously been found. This study focuses on a stacking method to detect TeV emission from LS 5039, a known TeV binary, to test its efficacy in HAWC data. Stacking is a widely employed method for increasing signal to noise ratio in optical astronomy, but has never been attempted previously with HAWC. HAWC is an ideal instrument to search for TeV binaries, because of its wide field of view and high uptime. Applying this method to the entire sky may allow HAWC to detect binary sources of very short or very long periods not sensitive to current analyses. NSF, DOE, Los Alamos, Michigan Tech, CONACyt, UNAM, BUAP.

  8. The Galactic Distribution of Contact Eclipsing Binaries

    Science.gov (United States)

    Castelaz, Michael W.; Dorn, Leah; Breitfeld, Abby; Mies, Regan; Avery, Tess

    2017-01-01

    The number of eclipsing contact binaries in different galactic latitudes and longitudes show peak distributions in the number per square degree in two latitudinal zones (-30 degrees to -25 degrees and +25 degrees to +30 degrees) and large fluctuations in longitude (Huang and Wade 1966, ApJ, 143, 146). Semi-detached or detached binaries are largely concentrated in the galactic plane as shown by Paczynski et al. (MNRAS, 368, 1311), different from the distribution of contact eclipsing binaries. The differences in distributions of different types of eclipsing binaries may be related to either distances or interstellar reddening. We will present a method to calculate photometric distances of W Urase Majoris systems (W UMa; used as a proxy for contact binaries) from 2MASS J and K magnitudes and interstellar reddening models (Schlafly and Finkbeiner 2011, ApJ. 737, 103). We compare the distances to those calculated from the period-luminosity-color relationship described by Rucinski (2004, NewAR, 48, 703). The W UMa systems are taken from the General Catalog of Variable Stars.

  9. Urey Prize Lecture: Binary Minor Planets

    Science.gov (United States)

    Margot, J. L.

    2004-11-01

    The discovery of binary systems in the near-Earth, main belt, and Kuiper belt populations provides an abundance of new data that expand our knowledge of the physics and chemistry of the solar system. Binary minor planets form as a result of collisional, tidal, and capture processes that are important to study as they play major roles in the formation and evolution of planetary systems. The frequency of occurrence of such processes directly reflects the dynamical environment in the various populations. Observations of binaries provide a powerful way to measure the bulk properties of small bodies, which in turn lead to inferences about their composition and internal structure. These data may offer a rare glimpse of what physical and chemical conditions prevailed when protoplanets formed, and what subsequent evolution took place. In the case of the Kuiper Belt, the study of a handful of binaries forces us to rethink how dense and how bright these bodies are, and to significantly revise our current mass estimates for the entire population. The number of known binary minor planets has increased dramatically over the past few years, with roughly ten new discoveries each year. I will attempt to summarize recent developments, with examples drawn from my observations with the Hubble, Palomar, Keck, Arecibo and Goldstone telescopes.

  10. Debris disks in main sequence binary systems

    CERN Document Server

    Trilling, D E; Stapelfeldt, K R; Rieke, G H; Su, K Y L; Gray, R O; Corbally, C J; Bryden, G; Chen, C H; Boden, A; Beichman, C A

    2006-01-01

    We observed 69 A3-F8 main sequence binary star systems using the Multiband Imaging Photometer for Spitzer onboard the Spitzer Space Telescope. We find emission significantly in excess of predicted photospheric flux levels for 9(+4/-3)% and 40(+7/-6)% of these systems at 24 and 70 microns, respectively. Twenty two systems total have excess emission, including four systems that show excess emission at both wavelengths. A very large fraction (nearly 60%) of observed binary systems with small (<3 AU) separations have excess thermal mission. We interpret the observed infrared excesses as thermal emission from dust produced by collisions in planetesimal belts. The incidence of debris disks around main sequence A3-F8 binaries is marginally higher than that for single old AFGK stars. Whatever combination of nature (birth conditions of binary systems) and nurture (interactions between the two stars) drives the evolution of debris disks in binary systems, it is clear that planetesimal formation is not inhibited to a...

  11. Rapid Compact Binary Coalescence Parameter Estimation

    Science.gov (United States)

    Pankow, Chris; Brady, Patrick; O'Shaughnessy, Richard; Ochsner, Evan; Qi, Hong

    2016-03-01

    The first observation run with second generation gravitational-wave observatories will conclude at the beginning of 2016. Given their unprecedented and growing sensitivity, the benefit of prompt and accurate estimation of the orientation and physical parameters of binary coalescences is obvious in its coupling to electromagnetic astrophysics and observations. Popular Bayesian schemes to measure properties of compact object binaries use Markovian sampling to compute the posterior. While very successful, in some cases, convergence is delayed until well after the electromagnetic fluence has subsided thus diminishing the potential science return. With this in mind, we have developed a scheme which is also Bayesian and simply parallelizable across all available computing resources, drastically decreasing convergence time to a few tens of minutes. In this talk, I will emphasize the complementary use of results from low latency gravitational-wave searches to improve computational efficiency and demonstrate the capabilities of our parameter estimation framework with a simulated set of binary compact object coalescences.

  12. Binary Code Disassembly for Reverse Engineering

    Directory of Open Access Journals (Sweden)

    Marius Popa

    2013-01-01

    Full Text Available The disassembly of binary file is used to restore the software application code in a readable and understandable format for humans. Further, the assembly code file can be used in reverse engineering processes to establish the logical flows of the computer program or its vulnerabilities in real-world running environment. The paper highlights the features of the binary executable files under the x86 architecture and portable format, presents issues of disassembly process of a machine code file and intermediate code, disassembly algorithms which can be applied to a correct and complete reconstruction of the source file written in assembly language, and techniques and tools used in binary code disassembly.

  13. Gravitational waves from spinning eccentric binaries

    CERN Document Server

    Csizmadia, Péter; Rácz, István; Vasúth, Mátyás

    2012-01-01

    This paper is to introduce a new software called CBwaves which provides a fast and accurate computational tool to determine the gravitational waveforms yielded by generic spinning binaries of neutron stars and/or black holes on eccentric orbits. This is done within the post-Newtonian (PN) framework by integrating the equations of motion and the spin precession equations while the radiation field is determined by a simultaneous evaluation of the analytic waveforms. In applying CBwaves various physically interesting scenarios have been investigated. In particular, we have studied the appropriateness of the adiabatic approximation, and justified that the energy balance relation is indeed insensitive to the specific form of the applied radiation reaction term. By studying eccentric binary systems it is demonstrated that circular template banks are very ineffective in identifying binaries even if they possess tiny residual orbital eccentricity. In addition, by investigating the validity of the energy balance relat...

  14. Memory effect from spinning unbound binaries

    CERN Document Server

    De Vittori, Lorenzo; Gupta, Anuradha; Jetzer, Philippe

    2014-01-01

    We present a recently developed prescription to obtain ready-to-use gravitational wave (GW) polarization states for spinning compact binaries on hyperbolic orbits. We include leading order spin-orbit interactions, invoking 1.5PN-accurate quasi-Keplerian parametrization for the radial part of the orbital dynamics. We also include radiation reaction effects on $h_+$ and $h_{\\times}$ during the interaction. In the GW signals from spinning binaries there is evidence of the memory effect in both polarizations, in contrast to the non-spinning case, where only the cross polarizations exhibits non-vanishing amplitudes at infinite time. We also compute 1PN-accurate GW polarization states for non-spinning compact binaries in unbound orbits in a fully parametric way, and compare them with existing waveforms.

  15. Hybrid Black-Hole Binary Initial Data

    Science.gov (United States)

    Mundim, Bruno C.; Kelly, Bernard J.; Nakano, Hiroyuki; Zlochower, Yosef; Campanelli, Manuela

    2010-01-01

    "Traditional black-hole binary puncture initial data is conformally flat. This unphysical assumption is coupled with a lack of radiation signature from the binary's past life. As a result, waveforms extracted from evolutions of this data display an abrupt jump. In Kelly et al. [Class. Quantum Grav. 27:114005 (2010)], a new binary black-hole initial data with radiation contents derived in the post-Newtonian (PN) calculations was adapted to puncture evolutions in numerical relativity. This data satisfies the constraint equations to the 2.5PN order, and contains a transverse-traceless "wavy" metric contribution, violating the standard assumption of conformal flatness. Although the evolution contained less spurious radiation, there were undesired features; the unphysical horizon mass loss and the large initial orbital eccentricity. Introducing a hybrid approach to the initial data evaluation, we significantly reduce these undesired features."

  16. Hybrid black-hole binary initial data

    CERN Document Server

    Mundim, Bruno C; Zlochower, Yosef; Nakano, Hiroyuki; Campanelli, Manuela

    2010-01-01

    Traditional black-hole binary puncture initial data is conformally flat. This unphysical assumption is coupled with a lack of radiation signature from the binary's past life. As a result, waveforms extracted from evolutions of this data display an abrupt jump. In Kelly et al. [Class.Quant.Grav.27:114005,2010], a new binary black-hole initial data with radiation contents derived in the post-Newtonian (PN) calculation was adapted to puncture evolutions in numerical relativity. This data satisfies the constraint equations to the 2.5PN order, and contains a transverse-traceless "wavy" metric contribution, violating the standard assumption of conformal flatness. Although the evolution contained less spurious radiation, there were undesired features; the unphysical horizon mass loss and the large initial orbital eccentricity. Introducing a hybrid approach to the initial data evaluation, we significantly reduce these undesired features.

  17. Hybrid black-hole binary initial data

    Energy Technology Data Exchange (ETDEWEB)

    Mundim, Bruno C; Zlochower, Yosef; Nakano, Hiroyuki; Campanelli, Manuela [Center for Computational Relativity and Gravitation, School of Mathematical Sciences, Rochester Institute of Technology, Rochester, NY14623 (United States); Kelly, Bernard J, E-mail: bcmsma@astro.rit.edu, E-mail: bernard.j.kelly@nasa.gov, E-mail: yosef@astro.rit.edu, E-mail: nakano@astro.rit.edu, E-mail: manuela@astro.rit.edu [CRESST and Gravitational Astrophysics Laboratory, NASA/GSFC, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States)

    2011-07-07

    Traditional black-hole (BH) binary puncture initial data is conformally flat. This unphysical assumption is coupled with a lack of radiation signature from the binary's past life. As a result, waveforms extracted from evolutions of this data display an abrupt jump. In Kelly et al (2010, Class. Quantum Grav. 27 114005), a new binary BH initial data with radiation content derived from post-Newtonian (PN) theory was adapted to puncture evolutions in numerical relativity. This data satisfies the constraint equations to the 2.5PN order, and contains a transverse-traceless 'wavy' metric contribution, violating the standard assumption of conformal flatness. Although the evolution contained less spurious radiation, there were undesirable features: unphysical horizon mass loss and large initial orbital eccentricity. Introducing a hybrid approach to the initial data evaluation, we significantly reduce these undesired features.

  18. The Expressive Power of Binary Submodular Functions

    CERN Document Server

    Zivny, Stanislav; Jeavons, Peter G

    2008-01-01

    It has previously been an open problem whether all Boolean submodular functions can be decomposed into a sum of binary submodular functions over a possibly larger set of variables. This problem has been considered within several different contexts in computer science, including computer vision, artificial intelligence, and pseudo-Boolean optimisation. Using a connection between the expressive power of valued constraints and certain algebraic properties of functions, we answer this question negatively. Our results have several corollaries. First, we characterise precisely which submodular functions of arity 4 can be expressed by binary submodular functions. Next, we identify a novel class of submodular functions of arbitrary arities which can be expressed by binary submodular functions, and therefore minimised efficiently using a so-called expressibility reduction to the Min-Cut problem. More importantly, our results imply limitations on this kind of reduction and establish for the first time that it cannot be...

  19. Asteroseismic modelling of the Binary HD 176465

    CERN Document Server

    Nsamba, B; Campante, T L; Reese, D R; White, T R; Hernández, A García; Jiang, C

    2016-01-01

    The detection and analysis of oscillations in binary star systems is critical in understanding stellar structure and evolution. This is partly because such systems have the same initial chemical composition and age. Solar-like oscillations have been detected by Kepler in both components of the asteroseismic binary HD 176465. We present an independent modelling of each star in this binary system. Stellar models generated using MESA (Modules for Experiments in Stellar Astrophysics) were fitted to both the observed individual frequencies and complementary spectroscopic parameters. The individual theoretical oscillation frequencies for the corresponding stellar models were obtained using GYRE as the pulsation code. A Bayesian approach was applied to find the probability distribution functions of the stellar parameters using AIMS (Asteroseismic Inference on a Massive Scale) as the optimisation code. The ages of HD 176465 A and HD 176465 B were found to be 2.81 $\\pm$ 0.48 Gyr and 2.52 $\\pm$ 0.80 Gyr, respectively. ...

  20. Gravitational Wave Physics with Binary Love Relations

    Science.gov (United States)

    Yagi, Kent; Yunes, Nicolas

    2016-03-01

    Gravitational waves from the late inspiral of neutron star binaries encode rich information about their internal structure at supranuclear densities through their tidal deformabilities. However, extracting the individual tidal deformabilities of the components of a binary is challenging with future ground-based gravitational wave interferometers due to degeneracies between them. We overcome this difficulty by finding new, approximate universal relations between the individual tidal deformabilities that depend on the mass ratio of the two stars and are insensitive to their internal structure. Such relations have applications not only to gravitational wave astrophysics, but also to nuclear physics as they improve the measurement accuracy of tidal parameters. Moreover, the relations improve our ability to test extreme gravity and perform cosmology with gravitational waves emitted from neutron star binaries.

  1. ON SELF-INVERSE BINARY MATRICES OVER THE BINARY GALOIS FIELD

    Directory of Open Access Journals (Sweden)

    Ali Muhammad Ali Rushdi

    2013-01-01

    Full Text Available An important class of square binary matrices over the simplest finite or Galois Field GF(2 is the class of involutory or Self-Inverse (SI matrices. These matrices are of significant utility in prominent engineering applications such as the study of the Preparata Transformation or the analysis of synchronous Boolean Networks. Therefore, it is essential to devise appropriate methods, not only for understanding the properties of these matrices, but also for characterizing and constructing them. We survey square binary matrices of orders 1, 2 and 3 to identify primitive SI matrices among them. Larger SI matrices are constructed as (a the direct sum, or (b the Kronecker product, of smaller ones. Illustrative examples are given to demonstrate the construction and properties of binary SI matrices. The intersection of the sets of SI and permutation binary matrices is studied. We also study higher-order SI binary matrices and describe them via recursive relations or Kronecker products. Our work culminates in an exposition of the two most common representations of Boolean functions via two types of Boolean SI matrices. A better understanding of the properties and methods of constructing SI binary matrices over GF (2 is achieved. A clearer picture is attained about the utility of binary matrices in the representation of Boolean functions.

  2. Searching for Binary Supermassive Black Holes via Variable Broad Emission Line Shifts: Low Binary Fraction

    Science.gov (United States)

    Wang, Lile; Greene, Jenny E.; Ju, Wenhua; Rafikov, Roman R.; Ruan, John J.; Schneider, Donald P.

    2017-01-01

    Supermassive black hole binaries (SMBHs) are expected to result from galaxy mergers, and thus are natural byproducts (and probes) of hierarchical structure formation in the universe. They are also the primary expected source of low-frequency gravitational wave emission. We search for binary BHs using time-variable velocity shifts in broad Mg ii emission lines of quasars with multi-epoch observations. First, we inspect velocity shifts of the binary SMBH candidates identified in Ju et al., using Sloan Digital Sky Survey spectra with an additional epoch of data that lengthens the typical baseline to ∼10 yr. We find variations in the line of sight velocity shifts over 10 yr that are comparable to the shifts observed over 1–2 yr, ruling out the binary model for the bulk of our candidates. We then analyze 1438 objects with eight-year median time baselines, from which we would expect to see velocity shifts >1000 {km} {{{s}}}-1 from sub-parsec binaries. We find only one object with an outlying velocity of 448 {km} {{{s}}}-1, indicating—based on our modeling—that ≲1% (the value varies with different assumptions) of SMBHs that are active as quasars reside in binaries with ∼0.1 pc separations. Binaries either sweep rapidly through these small separations or stall at larger radii.

  3. CALCULATING THE HABITABLE ZONE OF BINARY STAR SYSTEMS. I. S-TYPE BINARIES

    Energy Technology Data Exchange (ETDEWEB)

    Kaltenegger, Lisa [MPIA, Koenigstuhl 17, D-69117 Heidelberg (Germany); Haghighipour, Nader, E-mail: kaltenegger@mpia.de [Institute for Astronomy and NASA Astrobiology Institute, University of Hawaii-Manoa, Honolulu, HI 96822 (United States)

    2013-11-10

    We have developed a comprehensive methodology for calculating the boundaries of the habitable zone (HZ) of planet-hosting S-type binary star systems. Our approach is general and takes into account the contribution of both stars to the location and extent of the binary HZ with different stellar spectral types. We have studied how the binary eccentricity and stellar energy distribution affect the extent of the HZ. Results indicate that in binaries where the combination of mass-ratio and orbital eccentricity allows planet formation around a star of the system to proceed successfully, the effect of a less luminous secondary on the location of the primary's HZ is generally negligible. However, when the secondary is more luminous, it can influence the extent of the HZ. We present the details of the derivations of our methodology and discuss its application to the binary HZ around the primary and secondary main-sequence stars of an FF, MM, and FM binary, as well as two known planet-hosting binaries α Cen AB and HD 196886.

  4. VLSI binary multiplier using residue number systems

    Energy Technology Data Exchange (ETDEWEB)

    Barsi, F.; Di Cola, A.

    1982-01-01

    The idea of performing multiplication of n-bit binary numbers using a hardware based on residue number systems is considered. This paper develops the design of a VLSI chip deriving area and time upper bounds of a n-bit multiplier. To perform multiplication using residue arithmetic, numbers are converted from binary to residue representation and, after residue multiplication, the result is reconverted to the original notation. It is shown that the proposed design requires an area a=o(n/sup 2/ log n) and an execution time t=o(log/sup 2/n). 7 references.

  5. Binary Sparse Phase Retrieval via Simulated Annealing

    Directory of Open Access Journals (Sweden)

    Wei Peng

    2016-01-01

    Full Text Available This paper presents the Simulated Annealing Sparse PhAse Recovery (SASPAR algorithm for reconstructing sparse binary signals from their phaseless magnitudes of the Fourier transform. The greedy strategy version is also proposed for a comparison, which is a parameter-free algorithm. Sufficient numeric simulations indicate that our method is quite effective and suggest the binary model is robust. The SASPAR algorithm seems competitive to the existing methods for its efficiency and high recovery rate even with fewer Fourier measurements.

  6. Spin supplementary conditions for spinning compact binaries

    CERN Document Server

    Mikóczi, Balázs

    2016-01-01

    We consider the different spin supplementary conditions (SSC) for a spinning compact binary with the leading-order spin-orbit (SO) interaction. The Lagrangian of the binary system can be constructed but it is acceleration-dependent in two cases of SSC. We rewrite the generalized Hamiltonian formalism proposed by Ostrogradsky and compute the conservative quantities and the dissipative part of relative motion during the gravitational radiation of each SSCs. We give the orbital elements and observed quantities of the SO dynamics, for instance the energy and the orbital angular momentum losses and waveforms and discuss their SSC dependence.

  7. Rotation and massive close binary evolution

    CERN Document Server

    Langer, N; Yoon, S -C; Hunter, I; Brott, I; Lennon, D J; de Mink, S E; Verheijdt, M

    2008-01-01

    We review the role of rotation in massive close binary systems. Rotation has been advocated as an essential ingredient in massive single star models. However, rotation clearly is most important in massive binaries where one star accretes matter from a close companion, as the resulting spin-up drives the accretor towards critical rotation. Here, we explore our understanding of this process, and its observable consequences. When accounting for these consequences, the question remains whether rotational effects in massive single stars are still needed to explain the observations.

  8. Speckle interferometric observations of close binary stars

    CERN Document Server

    Saha, S K; Yeswanth, L; Anbazhagan, P

    2002-01-01

    Speckle interferometric technique is employed to record a series of hundreds of short-exposure images of several close binary stars with sub-arcsecond separation through a narrow band filter at the Cassegrain focus of the 2.34 meter (m) Vainu Bappu telescope (VBT), situated at Vainu Bappu Observatory (VBO), Kavalur, India. The data are recorded sequentially by a Peltier-cooled intensified CCD camera with 10 ms exposure. The auto-correlation method is applied to determine the angular separations and position angles of these binary systems.

  9. Photometric Solutions of Some Contact ASAS Binaries

    CERN Document Server

    Gezer, I

    2015-01-01

    We present the first light curve solution of 6 contact binary systems which are chosen from the ASAS catalog. The photometric elements and the estimated absolute parameters of all systems are obtained with the light curve analyses. We calculated the values of degree of contact for the systems. The location of the targets on the Hertzsprung-Russell diagram and the mass-radius plane is compared to the other well-known contact binaries and the evolutionary status of the systems are also discussed.

  10. Photometric solutions of some contact ASAS binaries

    Science.gov (United States)

    Gezer, İ.; Bozkurt, Z.

    2016-04-01

    We present the first light curve solution of 6 contact binary systems which are chosen from the ASAS catalog. The photometric elements and the estimated absolute parameters of all systems are obtained with the light curve analyses. We calculated the values of degree of contact for the systems. The location of the targets on the Hertzsprung-Russell diagram and the mass-radius plane is compared to the other well-known contact binaries and the evolutionary status of the systems are also discussed.

  11. All optical binary delta-sigma modulator

    Science.gov (United States)

    Sayeh, Mohammad R.; Siahmakoun, Azad

    2005-09-01

    This paper describes a novel A/D converter called "Binary Delta-Sigma Modulator" (BDSM) which operates only with nonnegative signal with positive feedback and binary threshold. This important modification to the conventional delta-sigma modulator makes the high-speed (>100GHz) all-optical implementation possible. It has also the capability to modify its own sampling frequency as well as its input dynamic range. This adaptive feature helps designers to optimize the system performance under highly noisy environment and also manage the power consumption of the A/D converters.

  12. Pulsations in close binaries: challenges and opportunities

    Directory of Open Access Journals (Sweden)

    Maceroni C.

    2015-01-01

    Full Text Available CoRoT and Kepler provided a precious by-product: a number of eclipsing binaries containing variable stars and, among these, non-radial pulsators. This providential occurrence allows combining independent information from two different phenomena whose synergy yields scientific results well beyond those from the single sources. In particular, the analysis of pulsations in eclipsing binary components throws light on the internal structure of the pulsating star, on the system evolution, and on the role of tidal forces in exciting the oscillations. The case study of the Kepler target KIC 3858884 is illustrative of the difficulties of analysis and of the achievements in this rapidly developing field.

  13. Microlensing Binaries with Candidate Brown Dwarf Companions

    DEFF Research Database (Denmark)

    Shin, I.-G; Han, C.; Gould, A.

    2012-01-01

    Brown dwarfs are important objects because they may provide a missing link between stars and planets, two populations that have dramatically different formation histories. In this paper, we present the candidate binaries with brown dwarf companions that are found by analyzing binary microlensing...... masses of the brown dwarf companions are 0.02 ± 0.01 M⊙ and 0.019 ± 0.002 M⊙ for MOA-2011-BLG-104/OGLE-2011-BLG-0172 and MOA-2011-BLG-149, respectively, and both companions are orbiting low-mass M dwarf host stars. More microlensing brown dwarfs are expected to be detected as the number of lensing events...

  14. Apsidal motion in eclipsing binary GG Orionis

    Science.gov (United States)

    Yilan, E.; Bulut, I.

    2016-03-01

    The study of apsidal motion in binary stars with eccentric orbit is well known as an important source of information for the stellar internal structure as well as the possibility of verification of general relativity. In this study, the apsidal motion of the eccentric eclipsing binary GG Ori (P = 6.631 days, e = 0.22) has been analyzed using the times of minimum light taken from the literature and databases and the elements of apsidal motion have been computed. The method described by Giménez and García-Pelayo (1983) has been used for the apsidal motion analysis.

  15. Auto-correlation of Binary stars

    CERN Document Server

    Saha, S K

    2001-01-01

    Speckle interferometric technique is used to record a series of short exposure images of several close binary stars with sub-arcsecond separation through a narrow band filter centred at H$\\alpha$ at the Cassegrain focus of the 2.34 meter Vainu Bappu telescope (VBT), situated at Vainu Bappu Observatory (VBO), Kavalur. The auto-correlation method is developed under Image Reduction Analysis Facility (IRAF). Wiener filter is included in the programme to eliminate spurious high frequency contributions; a few sets of data provide the optimised results. The auto-correlated image of these stars gives the separation of the binary components.

  16. The DEBCat detached eclipsing binary catalogue

    CERN Document Server

    Southworth, John

    2014-01-01

    Detached eclipsing binary star systems are our primary source of measured physical properties of normal stars. I introduce DEBCat: a catalogue of detached eclipsing binaries with mass and radius measurements to the 2% precision necessary to put useful constraints on theoretical models of stellar evolution. The catalogue was begun in 2006, as an update of the compilation by Andersen (1991). It now contains over 170 systems, and new results are added on appearance in the refereed literature. DEBCat is available at: http://www.astro.keele.ac.uk/jkt/debcat/

  17. Winds from disks in compact binaries

    Energy Technology Data Exchange (ETDEWEB)

    Mauche, C.W.

    1993-10-27

    We herein present an observational and theoretical review of the winds of compact binaries. After a brief consideration of the accretion disk coronae and winds of X-ray binaries, the review concentrates on the winds of cataclysmic variables (CVs). Specifically, we consider the related problems of the geometry and mass-loss rate of the winds of CVs, their ionization state and variability, and the results from studies of eclipsing CVs. Finally, the properties of bona fide accretion disk wind models are reviewed.

  18. Elucidating the True Binary Fraction of VLM Stars and Brown Dwarfs with Spectral Binaries

    Science.gov (United States)

    Bardalez Gagliuffi, Daniella; Burgasser, Adam J.; Gelino, Christopher R.; SAHLMANN, JOHANNES; Schmidt, Sarah J.; Gagne, Jonathan; Skrzypek, Nathalie

    2017-01-01

    The very lowest-mass (VLM) stars and brown dwarfs are found in abundance in nearly all Galactic environments, yet their formation mechanism(s) remain an open question. One means of testing current formation theories is to use multiplicity statistics. The majority of VLM binaries have been discovered through direct imaging, and current angular resolution limits (0.05”-0.1") are coincident with the 1-4 AU peak in the projected separation distribution of known systems, suggesting an observational bias. I have developed a separation-independent method to detect T dwarf companions to late-M/early-L dwarfs by identifying methane absorption in their unresolved, low-resolution, near-infrared spectra using spectral indices and template fitting. Over 60 spectral binary candidates have been identified with this and comparable methods. I discuss follow-up observations, including laser-guide star adaptive optics imaging with Keck/NIRC2, which have confirmed 9 systems; and radial velocity and astrometric monitoring observations that have confirmed 7 others. The direct imaging results indicate a resolved binary fraction of 18%, coincident with current estimates of the VLM binary fraction; however, our sample contained 5 previously confirmed binaries, raising its true binary fraction to 47%. To more accurately measure the true VLM binary fraction, I describe the construction of an unbiased, volume-limited, near-infrared spectral sample of M7-L5 dwarfs within 25 pc, of which 4 (1%) are found to be spectral binary candidates. I model the complex selection biases of this method through a population simulation, set constraints on the true binary fraction as traced by these systems, and compare to the predictions of current formation theories. I also describe how this method may be applied to conduct a separation-unbiased search for giant exoplanets orbiting young VLM stars and brown dwarfs.

  19. Neutron-Star-Black-Hole Binaries Produced by Binary-Driven Hypernovae.

    Science.gov (United States)

    Fryer, Chris L; Oliveira, F G; Rueda, J A; Ruffini, R

    2015-12-01

    Binary-driven hypernovae (BdHNe) within the induced gravitational collapse paradigm have been introduced to explain energetic (E_{iso}≳10^{52}  erg), long gamma-ray bursts (GRBs) associated with type Ic supernovae (SNe). The progenitor is a tight binary composed of a carbon-oxygen (CO) core and a neutron-star (NS) companion, a subclass of the newly proposed "ultrastripped" binaries. The CO-NS short-period orbit causes the NS to accrete appreciable matter from the SN ejecta when the CO core collapses, ultimately causing it to collapse to a black hole (BH) and producing a GRB. These tight binaries evolve through the SN explosion very differently than compact binaries studied in population synthesis calculations. First, the hypercritical accretion onto the NS companion alters both the mass and the momentum of the binary. Second, because the explosion time scale is on par with the orbital period, the mass ejection cannot be assumed to be instantaneous. This dramatically affects the post-SN fate of the binary. Finally, the bow shock created as the accreting NS plows through the SN ejecta transfers angular momentum, braking the orbit. These systems remain bound even if a large fraction of the binary mass is lost in the explosion (well above the canonical 50% limit), and even large kicks are unlikely to unbind the system. Indeed, BdHNe produce a new family of NS-BH binaries unaccounted for in current population synthesis analyses and, although they may be rare, the fact that nearly 100% remain bound implies that they may play an important role in the compact merger rate, important for gravitational waves that, in turn, can produce a new class of ultrashort GRBs.

  20. Accretion-powered Compact Binaries

    Science.gov (United States)

    Mauche, Christopher W.

    2003-12-01

    Preface; The workshop logo; A short history of the CV workshop F. A. Córdova; Part I. Observations: 1. Low mass x-ray binaries A. P. Cowley, P. C. Schmidtke, D. Crampton, J. B. Hutchings, C. A. Haswell, E. L. Robinson, K. D. Horne, H. M. Johnston, S. R. Kulkarni, S. Kitamoto, X. Han, R. M. Hjellming, R. M. Wagner, S. L. Morris, P. Hertz, A. N. Parmar, L. Stella, P. Giommi, P. J. Callanan, T. Naylor, P. A. Charles, C. D. Bailyn, J. N. Imamura, T. Steiman-Cameron, J. Kristian, J. Middleditch, L. Angelini and J. P. Noris; 2. Nonmagnetic cataclysmic variables R. S. Polidan, C. W. Mauche, R. A. Wade, R. H. Kaitchuck, E. M. Schlegel, P. A. Hantzios, R. C. Smith, J. H. Wood, F. Hessman, A. Fiedler, D. H. P. Jones, J. Casares, P. A. Charles, J. van Paradijs, E. Harlaftis, T. Naylor, G. Sonneborn, B. J. M. Hassall, K. Horne, C. A. la Dous, A. W. Shafter, N. A. Hawkins, D. A. H. Buckley, D. J. Sullivan, F. V. Hessman, V. S. Dhillon, T. R. Marsh, J. Singh, S. Seetha, F. Giovannelli, A. Bianchini, E. M. Sion, D. J. Mullan, H. L. Shipman, G. Machin, P. J. Callanan, S. B. Howell, P. Szkody, E. M. Schlegel and R. F. Webbink; 3. Magnetic cataclysmic variables C. Hellier, K. O. Mason, C. W. Mauche, G. S. Miller, J. C. Raymond, F. K. Lamb, J. Patterson, A. J. Norton, M. G. Watson, A. R. King, I. M. McHardy, H. Lehto, J. P. Osborne, E. L. Robinson, A. W. Shafter, S. Balachandran, S. R. Rosen, J. Krautter, W. Buchholz, D. A. H. Buckley, I. R. Tuoly, D. Crampton, B. Warner, R. M. Prestage, B. N. Ashoka, M. Mouchet, J. M. Bonnet-Bidaud, J. M. Hameury, P. Szkody, P. Garnavich, S. Howell, T. Kii, M. Cropper, K. Mason, J. Bailey, D. T. Wickramasinghe, L. Ferrario, K. Beuermann, A. D. Schwope, H.-C. Thomas, S. Jordan, J. Schachter, A. V. Filippenko, S. M. Kahn, F. B. S. Paerels, K. Mukai, M. L. Edgar, S. Larsson, R. F. Jameson, A. R. King, A. Silber, R. Remillard, H. Bradt, M. Ishida, T. Ohashi and G. D. Schmidt; Part II. Accretion Theory: 4. Nonmagnetic W. Kley, F. Geyer, H. Herold, H

  1. The Tarantula Massive Binary Monitoring. I. Observational campaign and OB-type spectroscopic binaries

    Science.gov (United States)

    Almeida, L. A.; Sana, H.; Taylor, W.; Barbá, R.; Bonanos, A. Z.; Crowther, P.; Damineli, A.; de Koter, A.; de Mink, S. E.; Evans, C. J.; Gieles, M.; Grin, N. J.; Hénault-Brunet, V.; Langer, N.; Lennon, D.; Lockwood, S.; Maíz Apellániz, J.; Moffat, A. F. J.; Neijssel, C.; Norman, C.; Ramírez-Agudelo, O. H.; Richardson, N. D.; Schootemeijer, A.; Shenar, T.; Soszyński, I.; Tramper, F.; Vink, J. S.

    2017-02-01

    Context. Massive binaries play a crucial role in the Universe. Knowing the distributions of their orbital parameters is important for a wide range of topics from stellar feedback to binary evolution channels and from the distribution of supernova types to gravitational wave progenitors, yet no direct measurements exist outside the Milky Way. Aims: The Tarantula Massive Binary Monitoring project was designed to help fill this gap by obtaining multi-epoch radial velocity (RV) monitoring of 102 massive binaries in the 30 Doradus region. Methods: In this paper we analyze 32 FLAMES/GIRAFFE observations of 93 O- and 7 B-type binaries. We performed a Fourier analysis and obtained orbital solutions for 82 systems: 51 single-lined (SB1) and 31 double-lined (SB2) spectroscopic binaries. Results: Overall, the binary fraction and orbital properties across the 30 Doradus region are found to be similar to existing Galactic samples. This indicates that within these domains environmental effects are of second order in shaping the properties of massive binary systems. A small difference is found in the distribution of orbital periods, which is slightly flatter (in log space) in 30 Doradus than in the Galaxy, although this may be compatible within error estimates and differences in the fitting methodology. Also, orbital periods in 30 Doradus can be as short as 1.1 d, somewhat shorter than seen in Galactic samples. Equal mass binaries (q> 0.95) in 30 Doradus are all found outside NGC 2070, the central association that surrounds R136a, the very young and massive cluster at 30 Doradus's core. Most of the differences, albeit small, are compatible with expectations from binary evolution. One outstanding exception, however, is the fact that earlier spectral types (O2-O7) tend to have shorter orbital periods than later spectral types (O9.2-O9.7). Conclusions: Our results point to a relative universality of the incidence rate of massive binaries and their orbital properties in the

  2. BROWN DWARF BINARIES FROM DISINTEGRATING TRIPLE SYSTEMS

    Energy Technology Data Exchange (ETDEWEB)

    Reipurth, Bo [Institute for Astronomy and NASA Astrobiology Institute University of Hawaii, 640 N. Aohoku Place, Hilo, HI 96720 (United States); Mikkola, Seppo, E-mail: reipurth@ifa.hawaii.edu, E-mail: Seppo.Mikkola@utu.fi [Tuorla Observatory, University of Turku, Väisäläntie 20, Piikkiö (Finland)

    2015-04-15

    Binaries in which both components are brown dwarfs (BDs) are being discovered at an increasing rate, and their properties may hold clues to their origin. We have carried out 200,000 N-body simulations of three identical stellar embryos with masses drawn from a Chabrier IMF and embedded in a molecular core. The bodies are initially non-hierarchical and undergo chaotic motions within the cloud core, while accreting using Bondi–Hoyle accretion. The coupling of dynamics and accretion often leads to one or two dominant bodies controlling the center of the cloud core, while banishing the other(s) to the lower-density outskirts, leading to stunted growth. Eventually each system transforms either to a bound hierarchical configuration or breaks apart into separate single and binary components. The orbital motion is followed for 100 Myr. In order to illustrate 200,000 end-states of such dynamical evolution with accretion, we introduce the “triple diagnostic diagram,” which plots two dimensionless numbers against each other, representing the binary mass ratio and the mass ratio of the third body to the total system mass. Numerous freefloating BD binaries are formed in these simulations, and statistical properties are derived. The separation distribution function is in good correspondence with observations, showing a steep rise at close separations, peaking around 13 AU and declining more gently, reaching zero at separations greater than 200 AU. Unresolved BD triple systems may appear as wider BD binaries. Mass ratios are strongly peaked toward unity, as observed, but this is partially due to the initial assumptions. Eccentricities gradually increase toward higher values, due to the lack of viscous interactions in the simulations, which would both shrink the orbits and decrease their eccentricities. Most newborn triple systems are unstable and while there are 9209 ejected BD binaries at 1 Myr, corresponding to about 4% of the 200,000 simulations, this number has grown to

  3. Model-independent inference on compact-binary observations

    Science.gov (United States)

    Mandel, Ilya; Farr, Will M.; Colonna, Andrea; Stevenson, Simon; Tiňo, Peter; Veitch, John

    2017-03-01

    The recent advanced LIGO detections of gravitational waves from merging binary black holes enhance the prospect of exploring binary evolution via gravitational-wave observations of a population of compact-object binaries. In the face of uncertainty about binary formation models, model-independent inference provides an appealing alternative to comparisons between observed and modelled populations. We describe a procedure for clustering in the multidimensional parameter space of observations that are subject to significant measurement errors. We apply this procedure to a mock data set of population-synthesis predictions for the masses of merging compact binaries convolved with realistic measurement uncertainties, and demonstrate that we can accurately distinguish subpopulations of binary neutron stars, binary black holes, and mixed neutron star-black hole binaries with tens of observations.

  4. The same, but different: Stochasticity in binary destruction

    CERN Document Server

    Parker, Richard J

    2012-01-01

    Observations of binaries in clusters tend to be of visual binaries with separations of 10s - 100s au. Such binaries are 'intermediates' and their destruction or survival depends on the exact details of their individual dynamical history. We investigate the stochasticity of the destruction of such binaries and the differences between the initial and processed populations using N-body simulations. We concentrate on Orion Nebula Cluster-like clusters, where the observed binary separation distribution ranges from 62 - 620 au. We find that, starting from the same initial binary population in statistically identical clusters, the number of intermediate binaries that are destroyed after 1 Myr can vary by a factor of >2, and that the resulting separation distributions can be statistically completely different in initially substructured clusters. We also find that the mass ratio distributions are altered (destroying more low mass ratio systems), but not as significantly as the binary fractions or separation distributi...

  5. Observational Evidence for Tidal Interaction in Close Binary Systems

    CERN Document Server

    Mazeh, Tsevi

    2008-01-01

    This paper reviews the rich corpus of observational evidence for tidal effects in short-period binaries. We review the evidence for ellipsoidal variability and for the observational manifestation of apsidal motion in eclipsing binaries. Among the long-term effects, circularization was studied the most, and a transition period between circular and eccentric orbits has been derived for eight coeval samples of binaries. As binaries are supposed to reach synchronization before circularization, one can expect finding eccentric binaries in pseudo-synchronization state, the evidence for which is reviewed. The paper reviews the Rossiter-McLaughlin effect and its potential to study spin-orbit alignment. We discuss the tidal interaction in close binaries that are orbited by a third distant companion, and review the effect of pumping the binary eccentricity by the third star. We then discuss the idea that the tidal interaction induced by the eccentricity modulation can shrink the binary separation. The paper discusses t...

  6. Evolution of Binary Stars in Multiple-Population Globular Clusters

    CERN Document Server

    Hong, Jongsuk; Sollima, Antonio; McMillan, Stephen L W; D'Antona, Franca; D'Ercole, Annibale

    2015-01-01

    The discovery of multiple stellar populations in globular clusters has implications for all the aspects of the study of these stellar systems. In this paper, by means of N-body simulations, we study the evolution of binary stars in multiple-population clusters and explore the implications of the initial differences in the spatial distribution of different stellar populations for the evolution and survival of their binary stars. Our simulations show that initial differences between the spatial distribution of first-generation (FG) and second-generation (SG) stars can leave a fingerprint in the current properties of the binary population. SG binaries are disrupted more efficiently than those of the FG population resulting in a global SG binary fraction smaller than that of the FG. As for surviving binaries, dynamical evolution produces a difference between the SG and the FG binary binding energy distribution with the SG population characterized by a larger fraction of high binding energy (more bound) binaries. ...

  7. On the dynamical evolution and end states of binary centaurs

    Science.gov (United States)

    Brunini, A.

    2014-01-01

    In this paper, we perform a numerical integration of 666 fictitious binary Centaurs coming from the trans Neptunian space. Our population is restricted to tight binaries whose components have sizes between 30 and 100 km. We included the dynamical perturbations from the giant planets, Kozai Cycles induced by the Sun and tidal friction on the orbits of the binaries. We found that most binaries are disrupted during one of the close planetary encounters, making the mean lifetime of binary Centaurs much shorter than the one of single Centaurs. Nearly 10 per cent of the binaries reach a very tight circular orbit, arguing in favour of the existence of a non-negligible population of contact Centaurs. Another 10 per cent survive as a binary during their lifetime as Centaur. Our simulations favour the existence of a small population of very tight binary Centaurs.

  8. Model-independent inference on compact-binary observations

    CERN Document Server

    Mandel, Ilya; Colonna, Andrea; Stevenson, Simon; Tiňo, Peter; Veitch, John

    2016-01-01

    The recent advanced LIGO detections of gravitational waves from merging binary black holes enhance the prospect of exploring binary evolution via gravitational-wave observations of a population of compact-object binaries. In the face of uncertainty about binary formation models, model-independent inference provides an appealing alternative to comparisons between observed and modelled populations. We describe a procedure for clustering in the multi-dimensional parameter space of observations that are subject to significant measurement errors. We apply this procedure to a mock data set of population-synthesis predictions for the masses of merging compact binaries convolved with realistic measurement uncertainties, and demonstrate that we can accurately distinguish subpopulations of binary neutron stars, binary black holes, and mixed black hole -- neutron star binaries.

  9. Model-independent inference on compact-binary observations

    OpenAIRE

    Mandel, Ilya; Farr, Will M.; Colonna, Andrea; Stevenson, Simon; Tiňo, Peter; Veitch, John

    2016-01-01

    The recent advanced LIGO detections of gravitational waves from merging binary black holes enhance the prospect of exploring binary evolution via gravitational-wave observations of a population of compact-object binaries. In the face of uncertainty about binary formation models, model-independent inference provides an appealing alternative to comparisons between observed and modelled populations. We describe a procedure for clustering in the multi-dimensional parameter space of observations t...

  10. The cool surfaces of binary near-Earth asteroids

    OpenAIRE

    Delbo, Marco; Walsh, Kevin; Mueller, Michael; Harris, Alan W.; Howell, Ellen S.

    2011-01-01

    Abstract Here we show results from thermal-infrared observations of km-sized binary Near-Earth Asteroids (NEAs). We combine previously published thermal properties for NEAs with newly derived values for three binary NEAs. The ?value derived from the Near-Earth Asteroid Thermal Model (NEATM) for each object is then used to estimate an average thermal inertia for the population of binary NEAs and compared against similar estimates for the population of non-binaries. We find that thes...

  11. Formation and evolution of X-ray binaries

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    We review recent progress in theoretical understanding of X-ray binaries,which has largely been driven by new observations.We select several topics including formation of compact low-mass X-ray binaries,the evolutionary connection between low-mass X-ray binaries and binary and millisecond radio pulsars,and ultraluminous X-ray sources,to illustrate the interplay between theories and observations.

  12. Beyond-Binary Arithmetic: Algorithms and VLSI Implementations

    OpenAIRE

    Aoki, Takafumi; Higuchi, Tatsuo

    2000-01-01

    Beyond-binary arithmetic algorithms are defined as a new class of computer arithmetic algorithms which employ non-binary data representations to achieve higher performances beyond those of conventional binary algorithms. This paper presents prominent examples of beyond-binary arithmetic algorithms: examples include (i) a high-radix redundant division algorithm without using lookup tables, (ii) a high-radix redundant CORDIC algorithm for fast vector rotation, and (iii) redundant complex arithm...

  13. Predicting Social Trust with Binary Logistic Regression

    Science.gov (United States)

    Adwere-Boamah, Joseph; Hufstedler, Shirley

    2015-01-01

    This study used binary logistic regression to predict social trust with five demographic variables from a national sample of adult individuals who participated in The General Social Survey (GSS) in 2012. The five predictor variables were respondents' highest degree earned, race, sex, general happiness and the importance of personally assisting…

  14. The Benchmark Eclipsing Binary V530 Ori

    DEFF Research Database (Denmark)

    Torres, Guillermo; Lacy, Claud H. Sandberg; Pavlovski, Kresimir

    2015-01-01

    We report accurate measurements of the physical properties (mass, radius, temperature) of components of the G+M eclipsing binary V530 On. The M-type secondary shows a larger radius and a cooler temperature than predicted by standard stellar evolution models, as has been found for many other low...

  15. Testing the Binary Trigger Hypothesis in FUors

    CERN Document Server

    Green, Joel D; Rizzuto, Aaron C; Ireland, Michael J; Dupuy, Trent J; Mann, Andrew W; Kuruwita, Rajika

    2016-01-01

    We present observations of three FU Orionis objects (hereafter, FUors) with nonredundant aperture-mask interferometry (NRM) at 1.59 um and 2.12 um that probe for binary companions on the scale of the protoplanetary disk that feeds their accretion outbursts. We do not identify any companions to V1515 Cyg or HBC 722, but we do resolve a close binary companion to V1057 Cyg that is at the diffraction limit (rho = 58.3 +/- 1.4 mas or 30 +/- 5 AU) and currently much fainter than the outbursting star (delta(K') = 3.34 +/- 0.10 mag). Given the flux excess of the outbursting star, we estimate that the mass of the companion (M ~ 0.25 Msun) is similar to or slightly below that of the FUor itself, and therefore it resembles a typical T Tauri binary system. Our observations only achieve contrast limits of delta(K') ~ 4 mag, and hence we are only sensitive to companions that were near or above the pre-outburst luminosity of the FUors. It remains plausible that FUor outbursts could be tied to the presence of a close binary ...

  16. Spectropolarimetry of single and binary stars

    CERN Document Server

    Harries, T J

    2004-01-01

    Spectropolarimetry is a photon-hungry technique that will reach fruition in the 8-m telescope age. Here I summarize some of the stellar spectropolarimetric research that my collaborators and I have undertaken, with particular emphasis on the circumstellar environment of massive stars, symbiotic binaries, and star formation.

  17. Binaries are the best single stars

    NARCIS (Netherlands)

    de Mink, S.E.; Langer, N.; Izzard, R.G.

    2010-01-01

    Stellar models of massive single stars are still plagued by major uncertainties. Testing and calibrating against observations is essential for their reliability. For this purpose one preferably uses observed stars that have never experienced strong binary interaction, i.e. “true single stars”. Howev

  18. Cassini states for black-hole binaries

    CERN Document Server

    Correia, Alexandre C M

    2016-01-01

    Cassini states correspond to equilibria of the spin axis of a celestial body when its orbit is perturbed. They were initially described for planetary satellites, but the spin axes of black-hole binaries also present this kind of equilibria. In previous works, Cassini states were reported as spin-orbit resonances, but actually the spin of black-hole binaries is in circulation and there is no resonant motion. Here we provide a general description of the spin dynamics of black-hole binary systems based on a Hamiltonian formalism. In absence of dissipation the problem is integrable and it is easy to identify all possible trajectories for the spin for a given value of the total angular momentum. As the system collapses due to radiation reaction, the Cassini states are shifted to different positions, which modifies the dynamics around them. This is why the final spin distribution may differ from the initial one. Our method provides a simple way of predicting the distribution of the spin of black-hole binaries at th...

  19. Bloch-Zener oscillations in binary superlattices.

    Science.gov (United States)

    Dreisow, F; Szameit, A; Heinrich, M; Pertsch, T; Nolte, S; Tünnermann, A; Longhi, S

    2009-02-20

    Bloch-Zener oscillations, i.e., the coherent superposition of Bloch oscillations and Zener tunneling between minibands of a binary lattice, are experimentally demonstrated for light waves in curved femtosecond laser-written waveguide arrays. Visualization of double-periodicity breathing and oscillation modes is reported, and synchronous tunneling leading to wave reconstruction is demonstrated.

  20. Testing the Binary Trigger Hypothesis in FUors

    Science.gov (United States)

    Green, Joel D.; Kraus, Adam L.; Rizzuto, Aaron C.; Ireland, Michael J.; Dupuy, Trent J.; Mann, Andrew W.; Kuruwita, Rajika

    2016-10-01

    We present observations of three FU Orionis objects (hereafter, FUors) with nonredundant aperture-mask interferometry at 1.59 μm and 2.12 μm that probe for binary companions on the scale of the protoplanetary disk that feeds their accretion outbursts. We do not identify any companions to V1515 Cyg or HBC 722, but we do resolve a close binary companion to V1057 Cyg that is at the diffraction limit (ρ =58.3+/- 1.4 mas or 30 ± 5 au) and currently much fainter than the outbursting star ({{Δ }}K\\prime =3.34+/- 0.10 mag). Given the flux excess of the outbursting star, we estimate that the mass of the companion (M∼ 0.25{M}ȯ ) is similar to or slightly below that of the FUor itself, and therefore it resembles a typical T Tauri binary system. Our observations only achieve contrast limits of {{Δ }}K\\prime ∼ 4 mag, and hence we are only sensitive to companions that were near or above the pre-outburst luminosity of the FUors. It remains plausible that FUor outbursts could be tied to the presence of a close binary companion. However, we argue from the system geometry and mass reservoir considerations that these outbursts are not directly tied to the orbital period (i.e., occurring at periastron passage), but instead must only occur infrequently.

  1. Flip-flopping binary black holes.

    Science.gov (United States)

    Lousto, Carlos O; Healy, James

    2015-04-10

    We study binary spinning black holes to display the long term individual spin dynamics. We perform a full numerical simulation starting at an initial proper separation of d≈25M between equal mass holes and evolve them down to merger for nearly 48 orbits, 3 precession cycles, and half of a flip-flop cycle. The simulation lasts for t=20 000M and displays a total change in the orientation of the spin of one of the black holes from an initial alignment with the orbital angular momentum to a complete antialignment after half of a flip-flop cycle. We compare this evolution with an integration of the 3.5 post-Newtonian equations of motion and spin evolution to show that this process continuously flip flops the spin during the lifetime of the binary until merger. We also provide lower order analytic expressions for the maximum flip-flop angle and frequency. We discuss the effects this dynamics may have on spin growth in accreting binaries and on the observational consequences for galactic and supermassive binary black holes.

  2. Binaries are the best single stars

    CERN Document Server

    de Mink, S E; Izzard, R G

    2010-01-01

    Stellar models of massive single stars are still plagued by major uncertainties. Testing and calibrating against observations is essential for their reliability. For this purpose one preferably uses observed stars that have never experienced strong binary interaction, i.e. "true single stars". However, the binary fraction among massive stars is high and identifying "true single stars" is not straight forward. Binary interaction affects systems in such a way that the initially less massive star becomes, or appears to be, single. For example, mass transfer results in a widening of the orbit and a decrease of the luminosity of the donor star, which makes it very hard to detect. After a merger or disruption of the system by the supernova explosion, no companion will be present. The only unambiguous identification of "true single stars" is possible in detached binaries, which contain two main-sequence stars. For these systems we can exclude the occurrence of mass transfer since their birth. A further advantage is ...

  3. Binary pulsars as dark-matter probes

    CERN Document Server

    Pani, Paolo

    2015-01-01

    During the motion of a binary pulsar around the galactic center, the pulsar and its companion experience a wind of dark-matter particles that can affect the orbital motion through dynamical friction. We show that this effect produces a characteristic seasonal modulation of the orbit and causes a secular change of the orbital period whose magnitude can be well within the astonishing precision of various binary-pulsar observations. Our analysis is valid for binary systems with orbital period longer than a day. By comparing this effect with pulsar-timing measurements, it is possible to derive model-independent upper bounds on the dark-matter density at different distances $D$ from the galactic center. For example, the precision timing of J1713+0747 imposes $\\rho_{\\rm DM}\\lesssim 10^5\\,{\\rm GeV/cm}^3$ at $D\\approx7\\,{\\rm kpc}$. The detection of a binary pulsar at $D\\lesssim 10\\,{\\rm pc}$ could provide stringent constraints on dark-matter halo profiles and on growth models of the central black hole. The Square Kil...

  4. LSM is not generated by binary functions

    CERN Document Server

    McQuillan, Colin

    2011-01-01

    Bulatov et al. [1] defined the operation of (efficient) pps_\\omega-definability in order to study the computational complexity of certain approximate counting problems. They asked whether all log-supermodular functions can be defined by binary implication and unary functions in this sense. We give a negative answer to this question.

  5. Binary Solid-Liquid Phase Equilibria

    Science.gov (United States)

    Ellison, Herbert R.

    1978-01-01

    Indicates some of the information that may be obtained from a binary solid-liquid phase equilibria experiment and a method to write a computer program that will plot an ideal phase diagram to which the experimental results may be compared. (Author/CP)

  6. The Orbital Decay of Embedded Binary Stars

    CERN Document Server

    Stahler, Steven W

    2009-01-01

    Young binaries within dense molecular clouds are subject to dynamical friction from ambient gas. Consequently, their orbits decay, with both the separation and period decreasing in time. A simple analytic expression is derived for this braking torque. The derivation utilizes the fact that each binary acts as a quadrupolar source of acoustic waves. The acoustic disturbance has the morphology of a two-armed spiral and carries off angular momentum. From the expression for the braking torque, the binary orbital evolution is also determined analytically. This type of merger may help explain the origin of high-mass stars. If infrared dark clouds, with peak densities up to 10^7 cm^{-3}, contain low-mass binaries, those with separations less than 100 AU merge within about 10^5 yr. During the last few thousand years of the process, the rate of mechanical energy deposition in the gas exceeds the stars' radiative luminosity. Successive mergers may lead to the massive star formation believed to occur in these clouds.

  7. Binary translation using peephole translation rules

    Science.gov (United States)

    Bansal, Sorav; Aiken, Alex

    2010-05-04

    An efficient binary translator uses peephole translation rules to directly translate executable code from one instruction set to another. In a preferred embodiment, the translation rules are generated using superoptimization techniques that enable the translator to automatically learn translation rules for translating code from the source to target instruction set architecture.

  8. Orbits of Ten Visual Binary Stars

    Institute of Scientific and Technical Information of China (English)

    B.Novakovi(c)

    2007-01-01

    We present the orbits of ten visual binary stars:WDS 01015+6922.WDS 01424-0645,WDS 01461+6349,WDS 04374-0951,WDS 04478+5318,WDS 05255-0033,WDS 05491+6248,WDS 06404+4058,WDS 07479-1212,and WDS 18384+0850.We have also determined their masses,dynamical parallaxes and ephemerides.

  9. Chandra Imaging of Gamma-Ray Binaries

    CERN Document Server

    Kargaltsev, Oleg; Hare, Jeremy; Pavlov, George G

    2013-01-01

    We review the multiwavelength properties of the few known gamma-ray binaries, focusing on extended emission recently resolved with Chandra. We discuss the implications of these findings for the nature of compact objects and for physical processes operating in these systems.

  10. DARPA/TTO program IR binary optics

    Science.gov (United States)

    Veldkamp, W. B.

    1984-06-01

    Binary grating optics consist of microfine rectangular (high-low) relief patterns on a dielectric or a metallic surface. By controlling the depth, width and periodicity of the binary pattern, the amplitude and the phase of an electromagnetic wave can be controlled to produce a variety of optical transfer functions. The lithographic tools for fabrication of binary optics are the ones developed for VLSI circuit fabrication. From a single lithographic mask, planar replica optics can be made in quantity. This technology has broad applicability for tactical missile systems as well as for space systems. In addition to making optics cheaper than by conventional means, binary optics allows the fabrication of unique devices that cannot be made conventionally. These include high-speed rotary scanners, multiplexers, filters, beam shapers and coherent laser adders. The goal of this program is the development of high quality planar optical components using VLSI circuit fabrication techniques. The main elements of the plan are: (1) the development of large aperture segmented and piezoelectrically active planar optical surfaces, (2) the development of raster scanning laser telescopes and extension to broadband applications, and (3) the application of diffractive optics technology to the coherent addition of beams from modular laser systems. This report covers progress in the setup of a reactive ion-beam etching laboratory, and the feasibility demonstrations of the coherent beam addition concept with gas lasers.

  11. Runaway Massive Binaries and Cluster Ejection Scenarios

    CERN Document Server

    McSwain, M V; Boyajian, T S; Grundstrom, E D; Roberts, M S E; Ransom, Scott M.; Boyajian, Tabetha S.; Grundstrom, Erika D.

    2006-01-01

    The production of runaway massive binaries offers key insights into the evolution of close binary stars and open clusters. The stars HD 14633 and HD 15137 are rare examples of such runaway systems, and in this work we investigate the mechanism by which they were ejected from their parent open cluster, NGC 654. We discuss observational characteristics that can be used to distinguish supernova ejected systems from those ejected by dynamical interactions, and we present the results of a new radio pulsar search of these systems as well as estimates of their predicted X-ray flux assuming that each binary contains a compact object. Since neither pulsars nor X-ray emission are observed in these systems, we cannot conclude that these binaries contain compact companions. We also consider whether they may have been ejected by dynamical interactions in the dense environment where they formed, and our simulations of four-body interactions suggest that a dynamical origin is possible but unlikely. We recommend further X-ra...

  12. ANGULAR-MOMENTUM IN BINARY SPIRAL GALAXIES

    NARCIS (Netherlands)

    OOSTERLOO, T

    1993-01-01

    In order to investigate the relative orientations of spiral galaxies in pairs, the distribution of the angle between the spin-vectors for a new sample of 40 binary spiral galaxies is determined. From this distribution it is found, contrary to an earlier result obtained by Helou (1984), that there is

  13. Binary Quadratic Forms: A Historical View

    Science.gov (United States)

    Khosravani, Azar N.; Beintema, Mark B.

    2006-01-01

    We present an expository account of the development of the theory of binary quadratic forms. Beginning with the formulation and proof of the Two-Square Theorem, we show how the study of forms of the type x[squared] + ny[squared] led to the discovery of the Quadratic Reciprocity Law, and how this theorem, along with the concept of reduction relates…

  14. Wobbling Ancient Binaries - Here Be Planets?

    CERN Document Server

    Horner, Jonathan; Hinse, Tobias; Marshall, Jonathan; Mustill, Alex

    2014-01-01

    In the last few years, a number of planets have been proposed to orbit several post main-sequence binary star systems on the basis of observed variations in the timing of eclipses between the binary components. A common feature of these planet candidates is that the best-fit orbits are often highly eccentric, such that the multiple planet systems proposed regularly feature mutually crossing orbits - a scenario that almost always leads to unstable planetary systems. In this work, we present the results of dynamical studies of all multiple-planet systems proposed to orbit these highly evolved binary stars, finding that most do not stand up to dynamical scrutiny. In one of the potentially stable cases (the NN Serpentis 2-planet system), we consider the evolution of the binary star system, and show that it is highly unlikely that planets could survive from the main sequence to obtain their current orbits - again casting doubt on the proposed planets. We conclude by considering alternative explanations for the obs...

  15. Chemically homogeneous evolution in massive binaries

    CERN Document Server

    de Mink, S E; Langer, N; Pols, O R

    2010-01-01

    Rotation can have severe consequences for the evolution of massive stars. It is now considered as one of the main parameters, alongside mass and metallicity that determine the final fate of single stars. In massive, fast rotating stars mixing processes induced by rotation may be so efficient that helium produced in the center is mixed throughout the envelope. Such stars evolve almost chemically homogeneously. At low metallicity they remain blue and compact, while they gradually evolve into Wolf-Rayet stars and possibly into progenitors of long gamma-ray bursts. In binaries this type of evolution may occur because of (I) tides in very close binaries, as a result of (II) spin up by mass transfer, as result of (III) a merger of the two stars and (IV) when one of the components in the binary was born with a very high initial rotation rate. As these stars stay compact, the evolutionary channels are very different from what classical binary evolutionary models predict. In this contribution we discuss examples of ne...

  16. Echoes in X-ray Binaries

    CERN Document Server

    O'Brien, K; Hynes, R; Chen, W; Haswell, C; Still, M

    2002-01-01

    We present a method of analysing the correlated X-ray and optical/UV variability in X-ray binaries, using the observed time delays between the X-ray driving lightcurves and their reprocessed optical echoes. This allows us to determine the distribution of reprocessing sites within the binary. We model the time-delay transfer functions by simulating the distribution of reprocessing regions, using geometrical and binary parameters. We construct best-fit time-delay transfer functions, showing the regions in the binary responsible for the reprocessing of X-rays. We have applied this model to observations of the Soft X-ray Transient, GRO j1655-40. We find the optical variability lags the X-ray variability with a mean time delay of 19.3$pm{2.2}$ seconds. This means that the outer regions of the accretion disc are the dominant reprocessing site in this system. On fitting the data to a simple geometric model, we derive a best-fit disk half-opening angle of 13.5$^{+2.1}_{-2.8}$ degrees, which is similar to that observe...

  17. The Primordial Binary Population in OB Associations

    NARCIS (Netherlands)

    Kouwenhoven, M.B.N.; Brown, A.G.A.; Gualandris, A.; Kaper, L.; Portegies Zwart, S.F.; Zinnecker, H.; Allen, C.; Scarfe, C.

    2004-01-01

    We present the first results of our adaptive optics survey of 200 (mainly) A-type stars in the nearby OB association Sco OB2, which we will use, together with literature data and detailed simulations of young star clusters, to determine the primordial binary population.

  18. What's Next? Judging Sequences of Binary Events

    Science.gov (United States)

    Oskarsson, An T.; Van Boven, Leaf; McClelland, Gary H.; Hastie, Reid

    2009-01-01

    The authors review research on judgments of random and nonrandom sequences involving binary events with a focus on studies documenting gambler's fallacy and hot hand beliefs. The domains of judgment include random devices, births, lotteries, sports performances, stock prices, and others. After discussing existing theories of sequence judgments,…

  19. Planet formation in slightly inclined binary systems

    Directory of Open Access Journals (Sweden)

    Ge J.

    2011-07-01

    Full Text Available One of the major problems of planet formation in close binary systems, such as α Centauri AB, is the formation of planetary embryos or cores by mutual accretion of km-sized planetesimals. In this contribution, we test the planetesimal accretion in such close binary systems but with small inclinations iB = 0.1–10° between the binary orbital plane and the gas disk plane. Compared to previous studies (coplanar case with iB = 0, we find that (1 planetesimal disk is stratified in the vertical direction and planetesimals are redistributed on different orbit groups with respect to their sizes, thus (2 collisions between similar-sized bodies dominate, leading to low dV and favoring planetesimal accretion (3 the planetesimal collision timescale at 1–2 AU is estimated as: T ∼ (1 + 100iB × 103 yrs, where 0 ≤ iB ≤ 10°. As a conclusion, although planetesimal accretion are much more favored in slightly inclined binary systems, it is significantly less efficient and slowed-down as compared to the single-star case.

  20. Balanced binary trees in the Tamari lattice

    CERN Document Server

    Giraudo, Samuele

    2010-01-01

    We show that the set of balanced binary trees is closed by interval in the Tamari lattice. We establish that the intervals [T0, T1] where T0 and T1 are balanced trees are isomorphic as posets to a hypercube. We introduce tree patterns and synchronous grammars to get a functional equation of the generating series enumerating balanced tree intervals.

  1. Parameter estimation of gravitational wave compact binary coalescences

    Science.gov (United States)

    Haster, Carl-Johan; LIGO Scientific Collaboration Collaboration

    2017-01-01

    The first detections of gravitational waves from coalescing binary black holes have allowed unprecedented inference on the astrophysical parameters of such binaries. Given recent updates in detector capabilities, gravitational wave model templates and data analysis techniques, in this talk I will describe the prospects of parameter estimation of compact binary coalescences during the second observation run of the LIGO-Virgo collaboration.

  2. Binary interaction dominates the evolution of massive stars

    NARCIS (Netherlands)

    Sana, H.; de Mink, S.E.; de Koter, A.; Langer, N.; Evans, C.J.; Gieles, M.; Gosset, E.; Izzard, R.G.; Le Bouquin, J.-B.; Schneider, F.R.N.

    2012-01-01

    The presence of a nearby companion alters the evolution of massive stars in binary systems, leading to phenomena such as stellar mergers, x-ray binaries, and gamma-ray bursts. Unambiguous constraints on the fraction of massive stars affected by binary interaction were lacking. We simultaneously meas

  3. The Formation of Contact and Very Close Binaries

    Energy Technology Data Exchange (ETDEWEB)

    Kisseleva-Eggleton, L; Eggleton, P P

    2007-08-10

    We explore the possibility that all close binaries, i.e. those with periods {approx}< 3 d, including contact (W UMa) binaries, are produced from initially wider binaries (periods of say 10's of days) by the action of a triple companion through the medium of Kozai Cycles with Tidal Friction (KCTF).

  4. Microlensing Binaries Discovered through High-magnification Channel

    DEFF Research Database (Denmark)

    Shin, I.-G.; Choi, J.-Y.; Park, S.-Y.

    2012-01-01

    Microlensing can provide a useful tool to probe binary distributions down to low-mass limits of binary companions. In this paper, we analyze the light curves of eight binary-lensing events detected through the channel of high-magnification events during the seasons from 2007 to 2010. The perturba...

  5. A decoding method of an n length binary BCH code through (n + 1n length binary cyclic code

    Directory of Open Access Journals (Sweden)

    TARIQ SHAH

    2013-09-01

    Full Text Available For a given binary BCH code Cn of length n = 2 s - 1 generated by a polynomial of degree r there is no binary BCH code of length (n + 1n generated by a generalized polynomial of degree 2r. However, it does exist a binary cyclic code C (n+1n of length (n + 1n such that the binary BCH code Cn is embedded in C (n+1n . Accordingly a high code rate is attained through a binary cyclic code C (n+1n for a binary BCH code Cn . Furthermore, an algorithm proposed facilitates in a decoding of a binary BCH code Cn through the decoding of a binary cyclic code C (n+1n , while the codes Cn and C (n+1n have the same minimum hamming distance.

  6. Kepler Eclipsing Binary Stars. VIII. Identification of False Positive Eclipsing Binaries and Re-extraction of New Light Curves

    CERN Document Server

    Abdul-Masih, Michael; Conroy, Kyle; Bloemen, Steven; Boyajian, Tabetha; Doyle, Laurance R; Johnston, Cole; Kostov, Veselin; Latham, David W; Matijevic, Gal; Shporer, Avi; Southworth, John

    2016-01-01

    The Kepler Mission has provided unprecedented, nearly continuous photometric data of $\\sim$200,000 objects in the $\\sim$105 deg$^{2}$ field of view from the beginning of science operations in May of 2009 until the loss of the second reaction wheel in May of 2013. The Kepler Eclipsing Binary Catalog contains information including but not limited to ephemerides, stellar parameters and analytical approximation fits for every known eclipsing binary system in the Kepler Field of View. Using Target Pixel level data collected from Kepler in conjunction with the Kepler Eclipsing Binary Catalog, we identify false positives among eclipsing binaries, i.e. targets that are not eclipsing binaries themselves, but are instead contaminated by eclipsing binary sources nearby on the sky and show eclipsing binary signatures in their light curves. We present methods for identifying these false positives and for extracting new light curves for the true source of the observed binary signal. For each source, we extract three separa...

  7. Merging Galaxies Create a Binary Quasar

    Science.gov (United States)

    2010-02-01

    Astronomers have found the first clear evidence of a binary quasar within a pair of actively merging galaxies. Quasars are the extremely bright centers of galaxies surrounding super-massive black holes, and binary quasars are pairs of quasars bound together by gravity. Binary quasars, like other quasars, are thought to be the product of galaxy mergers. Until now, however, binary quasars have not been seen in galaxies that are unambiguously in the act of merging. But images of a new binary quasar from the Carnegie Institution's Magellan telescope in Chile show two distinct galaxies with "tails" produced by tidal forces from their mutual gravitational attraction. "This is really the first case in which you see two separate galaxies, both with quasars, that are clearly interacting," says Carnegie astronomer John Mulchaey who made observations crucial to understanding the galaxy merger. Most, if not all, large galaxies, such as our galaxy the Milky Way, host super-massive black holes at their centers. Because galaxies regularly interact and merge, astronomers have assumed that binary super-massive black holes have been common in the Universe, especially during its early history. Black holes can only be detected as quasars when they are actively accreting matter, a process that releases vast amounts of energy. A leading theory is that galaxy mergers trigger accretion, creating quasars in both galaxies. Because most such mergers would have happened in the distant past, binary quasars and their associated galaxies are very far away and therefore difficult for most telescopes to resolve. The binary quasar, labeled SDSS J1254+0846, was initially detected by the Sloan Digital Sky Survey, a large scale astronomical survey of galaxies and over 120,000 quasars. Further observations by Paul Green of the Harvard-Smithsonian Center for Astrophysics and colleagues* using NASA's Chandra's X-ray Observatory and telescopes at Kitt Peak National Observatory in Arizona and Palomar

  8. Cognitive Binary Logic - The Natural Unified Formal Theory of Propositional Binary Logic

    CERN Document Server

    Popescu-Bodorin, Nicolaie

    2011-01-01

    This paper presents a formal theory which describes propositional binary logic as a semantically closed formal language, and allows for syntactically and semantically well-formed formulae, formal proofs (demonstrability in Hilbertian acception), deduction (Gentzen's view of demonstrability), CNF-ization, and deconstruction to be expressed and tested in the same (computational) formal language, using the same data structure. It is also shown here that Cognitive Binary Logic is a self-described theory in which the Liar Paradox is deconstructed.

  9. Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.

    Science.gov (United States)

    Radak, Brian K; Lee, Tai-Sung; Harris, Michael E; York, Darrin M

    2015-09-01

    The hepatitis delta virus ribozyme is an efficient catalyst of RNA 2'-O-transphosphorylation and has emerged as a key experimental system for identifying and characterizing fundamental features of RNA catalysis. Recent structural and biochemical data have led to a proposed mechanistic model whereby an active site Mg(2+) ion facilitates deprotonation of the O2' nucleophile, and a protonated cytosine residue (C75) acts as an acid to donate a proton to the O5' leaving group as noted in a previous study. This model assumes that the active site Mg(2+) ion forms an inner-sphere coordination with the O2' nucleophile and a nonbridging oxygen of the scissile phosphate. These contacts, however, are not fully resolved in the crystal structure, and biochemical data are not able to unambiguously exclude other mechanistic models. In order to explore the feasibility of this model, we exhaustively mapped the free energy surfaces with different active site ion occupancies via quantum mechanical/molecular mechanical (QM/MM) simulations. We further incorporate a three-dimensional reference interaction site model for the solvated ion atmosphere that allows these calculations to consider not only the rate associated with the chemical steps, but also the probability of observing the system in the presumed active state with the Mg(2+) ion bound. The QM/MM results predict that a pathway involving metal-assisted nucleophile activation is feasible based on the rate-controlling transition state barrier departing from the presumed metal-bound active state. However, QM/MM results for a similar pathway in the absence of Mg(2+) are not consistent with experimental data, suggesting that a structural model in which the crystallographically determined Mg(2+) is simply replaced with Na(+) is likely incorrect. It should be emphasized, however, that these results hinge upon the assumption of the validity of the presumed Mg(2+)-bound starting state, which has not yet been definitively verified

  10. Binary-disk interaction. II. Gap-opening criteria for unequal-mass binaries

    Energy Technology Data Exchange (ETDEWEB)

    Del Valle, Luciano; Escala, Andrés, E-mail: ldelvalleb@gmail.com [Departamento de Astronomía, Universidad de Chile, Casilla 36-D, Santiago (Chile)

    2014-01-01

    We study the interaction of an unequal-mass binary with an isothermal circumbinary disk, motivated by the theoretical and observational evidence that after a major merger of gas-rich galaxies, a massive gaseous disk with a supermassive black hole binary will be formed in the nuclear region. We focus on the gravitational torques that the binary exerts on the disk and how these torques can drive the formation of a gap in the disk. This exchange of angular momentum between the binary and the disk is mainly driven by the gravitational interaction between the binary and a strong nonaxisymmetric density perturbation that is produced in the disk, in response to the presence of the binary. Using smoothed particle hydrodynamics numerical simulations, we test two gap-opening criteria, one that assumes the geometry of the density perturbation is an ellipsoid/thick spiral and another that assumes a flat spiral geometry for the density perturbation. We find that the flat spiral gap-opening criterion successfully predicts which simulations will have a gap in the disk and which will not. We also study the limiting cases predicted by the gap-opening criteria. Since the viscosity in our simulations is considerably smaller than the expected value in the nuclear regions of gas-rich merging galaxies, we conclude that in such environments the formation of a circumbinary gap is unlikely.

  11. The Tarantula Massive Binary Monitoring: I. Observational campaign and OB-type spectroscopic binaries

    CERN Document Server

    Almeida, L A; Taylor, W; Barbá, R; Bonanos, A; Crowther, P; Damineli, A; de Koter, A; de Mink, S E; Evans, C J; Gieles, M; Grin, N J; Hénault-Brunet, V; Langer, N; Lennon, D; Lockwood, S; Apellániz, J Maíz; Moffat, A F J; Neijssel, C; Norman, C; Ramírez-Agudelo, O H; Richardson, N D; Schootemeijer, A; Shenar, T; Soszyński, I; Tramper, F; Vink, J S

    2016-01-01

    Massive binaries (MBs) play a crucial role in the Universe and knowing the distributions of their orbital parameters (OPs) is important for a wide range of topics, from stellar feedback to binary evolution channels, from the distribution of supernova types to gravitational wave progenitors. Yet, no direct measurements exist outside the Milky Way. The Tarantula Massive Binary Monitoring was designed to help fill this gap by obtaining multi-epoch radial velocity monitoring of 102 MBs in the 30 Dor. In this paper, we analyse 32 FLAMES/GIRAFFE observations of 93 O- and 7 B-type binaries. We performed a Fourier analysis and obtained orbital solutions for 82 systems: 51 single-lined and 31 double-lined spectroscopic binaries. Overall, the OPs and binary fraction are remarkably similar across the 30 Dor region and compared to existing Galactic samples (GSs). This indicates that within these domains environmental effects are of second order in shaping the properties of MBs. A small difference is found in the distribu...

  12. Binary Disk interaction II: Gap-Opening criteria for unequal mass binaries

    CERN Document Server

    del Valle, Luciano

    2013-01-01

    We study the interaction between an unequal mass binary with an isothermal circumbinary disk, motivated by the theoretical and observational evidence that after a major merger of gas-rich galaxies, a massive gaseous disk with a SMBH binary will be formed in the nuclear region. We focus on the gravitational torques that the binary exerts onto the disk and how these torques can drive the formation of a gap in the disk. This exchange of angular momentum between the binary and the disk is mainly driven by the gravitational interaction between the binary and a strong non-axisymmetric density perturbation that is produced in the disk, as response to the presence of the binary. Using SPH numerical simulations we tested two gap-opening criterion, one that assumes that the geometry of the density perturbation is an ellipsoid/thick-spirals and another that assumes a geometry of flat-spirals for the density perturbation. We find that the flat-spirals gap opening criterion successfully predicts which simulations will hav...

  13. THE ELM SURVEY. V. MERGING MASSIVE WHITE DWARF BINARIES

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Warren R.; Kenyon, Scott J. [Smithsonian Astrophysical Observatory, 60 Garden St, Cambridge, MA 02138 (United States); Kilic, Mukremin; Gianninas, A. [Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma, 440 W. Brooks St., Norman, OK, 73019 (United States); Allende Prieto, Carlos, E-mail: wbrown@cfa.harvard.edu, E-mail: skenyon@cfa.harvard.edu, E-mail: kilic@ou.edu, E-mail: alexg@nhn.ou.edu, E-mail: callende@iac.es [Instituto de Astrofisica de Canarias, E-38205, La Laguna, Tenerife (Spain)

    2013-05-20

    We present the discovery of 17 low-mass white dwarfs (WDs) in short-period (P {<=} 1 day) binaries. Our sample includes four objects with remarkable log g {approx_equal} 5 surface gravities and orbital solutions that require them to be double degenerate binaries. All of the lowest surface gravity WDs have metal lines in their spectra implying long gravitational settling times or ongoing accretion. Notably, six of the WDs in our sample have binary merger times <10 Gyr. Four have {approx}>0.9 M{sub Sun} companions. If the companions are massive WDs, these four binaries will evolve into stable mass transfer AM CVn systems and possibly explode as underluminous supernovae. If the companions are neutron stars, then these may be millisecond pulsar binaries. These discoveries increase the number of detached, double degenerate binaries in the ELM Survey to 54; 31 of these binaries will merge within a Hubble time.

  14. Binary interaction dominates the evolution of massive stars

    CERN Document Server

    Sana, H; de Koter, A; Langer, N; Evans, C J; Gieles, M; Gosset, E; Izzard, R G; Bouquin, J -B Le; Schneider, F R N; 10.1126/science.1223344

    2012-01-01

    The presence of a nearby companion alters the evolution of massive stars in binary systems, leading to phenomena such as stellar mergers, X-ray binaries and gamma-ray bursts. Unambiguous constraints on the fraction of massive stars affected by binary interaction were lacking. We simultaneously measured all relevant binary characteristics in a sample of Galactic massive O stars and quantified the frequency and nature of binary interactions. Over seventy per cent of all massive stars will exchange mass with a companion, leading to a binary merger in one third of the cases. These numbers greatly exceed previous estimates and imply that binary interaction dominates the evolution of massive stars, with implications for populations of massive stars and their supernovae.

  15. 1974: the discovery of the first binary pulsar

    CERN Document Server

    Damour, Thibault

    2014-01-01

    The 1974 discovery, by Russell A. Hulse and Joseph H. Taylor, of the first binary pulsar PSR 1913+16, opened up new possibilities for the study of relativistic gravity. PSR 1913+16, as well as several other binary pulsars, provided {\\it direct} observational proofs that gravity propagates at the velocity of light and has a quadrupolar structure. Binary pulsars also provided accurate tests of the strong-field regime of relativistic gravity. General Relativity has passed all the binary pulsar tests with flying colors. The discovery of binary pulsars had also very important consequences for astrophysics: accurate measurement of neutron star masses, improved understanding of the possible evolution scenarios for the co-evolution of binary stars, proof of the existence of binary neutron stars emitting gravitational waves for hundreds of millions of years, before coalescing in catastrophic events probably leading to an important emission of electromagnetic radiation and neutrinos. This article reviews the history of...

  16. Twin Binaries: Studies of Stability, Mass Transfer, and Coalescence

    CERN Document Server

    Lombardi, James C; Dooley, Katherine L; Gearity, Kyle; Kalogera, Vassiliki; Rasio, Frederic A

    2010-01-01

    Motivated by suggestions that binaries with almost equal-mass components ("twins") play an important role in the formation of double neutron stars and may be rather abundant among binaries, we study the stability of synchronized close and contact binaries with identical components in circular orbits. In particular, we investigate the dependency of the innermost stable circular orbit on the core mass, and we study the coalescence of the binary that occurs at smaller separations. For twin binaries composed of convective main-sequence stars, subgiants, or giants with low mass cores (M_c ~0.15M), we find that stable contact configurations exist at all separations down to the Roche limit, when mass shedding through the outer Lagrangian points triggers a coalescence of the envelopes and leaves the cores orbiting in a central tight binary. We discuss the implications of our results to the formation of binary neutron stars.

  17. The state of globular clusters at birth - II. Primordial binaries

    Science.gov (United States)

    Leigh, Nathan W. C.; Giersz, Mirek; Marks, Michael; Webb, Jeremy J.; Hypki, Arkadiusz; Heinke, Craig O.; Kroupa, Pavel; Sills, Alison

    2015-01-01

    In this paper, we constrain the properties of primordial binary populations in Galactic globular clusters. Using the MOCCA Monte Carlo code for cluster evolution, our simulations cover three decades in present-day total cluster mass. Our results are compared to the observations of Milone et al. using the photometric binary populations as proxies for the true underlying distributions, in order to test the hypothesis that the data are consistent with a universal initial binary fraction near unity and the binary orbital parameter distributions of Kroupa. With the exception of a few possible outliers, we find that the data are to first-order consistent with the universality hypothesis. Specifically, the present-day binary fractions inside the half-mass radius can be reproduced assuming either high initial binary fractions near unity with a dominant soft binary component as in the Kroupa distribution combined with high initial densities (104-106 M⊙ pc-3), or low initial binary fractions (˜5-10 per cent) with a dominant hard binary component combined with moderate initial densities near their present-day values (102-103 M⊙ pc-3). This apparent degeneracy can potentially be broken using the binary fractions outside the half-mass radius - only high initial binary fractions with a significant soft component combined with high initial densities can reproduce the observed anticorrelation between the binary fractions outside the half-mass radius and the total cluster mass. We further illustrate using the simulated present-day binary orbital parameter distributions and the technique first introduced in Leigh et al. that the relative fractions of hard and soft binaries can be used to further constrain both the initial cluster density and the initial mass-density relation. Our results favour an initial mass-density relation of the form r_h ∝ M_clus^{α } with α < 1/3, corresponding to an initial correlation between cluster mass and density.

  18. Coalescence of Magnetized Binary Neutron Star Systems

    Science.gov (United States)

    Motl, Patrick M.; Anderson, Matthew; Lehner, Luis; Liebling, Steven L.; Neilsen, David; Palenzuela, Carlos; Ponce, Marcelo

    2015-01-01

    We present simulations of the merger of binary neutron star systems calculated with full general relativity and incorporating the global magnetic field structure for the stars evolved with resistive magnetohydrodynamics. Our simulation tools have recently been improved to incorporate the effects of neutrino cooling and have been generalized to allow for tabular equations of state to describe the degenerate matter. Of particular interest are possible electromagnetic counterparts to the gravitational radiation that emerges from these systems. We focus on magnetospheric interactions that ultimately tap into the gravitational potential energy of the binary to power a Poynting flux and deposition of energy through Joule heating and magnetic reconnection. We gratefully acknowledge the support of NASA through the Astrophysics Theory Program grant NNX13AH01G.

  19. A Binary Representation of the Genetic Code

    CERN Document Server

    Nemzer, Louis R

    2016-01-01

    This article introduces a novel binary representation of the canonical genetic code, in which each of the four mRNA nucleotide bases is assigned a unique 2-bit identifier. These designations have a physiological meaning derived from the molecular structures of, and relationships between, the bases. In this scheme, the 64 possible triplet codons are each indexed by a 6-bit label. The order of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. Transition and transversion mutations are naturally expressed as basic binary operations, and the severity of the different types is analyzed. Using a principal component analysis, it is shown that physicochemical properties of amino acids related to protein folding also correlate with particular bit positions of their respective labels. Thus, the likelihood for a particular point mutation to be conservative, and therefore less likely to cause a change in protein functionality, can be estimated.

  20. Simulation of nuclei morphologies for binary alloy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    We study the critical nuclei morphologies of a binary alloy by the string method. The dynamic equation of the string, connecting the metastable phase (liquid) and stable phase (solid), is governed by Helmholtz free energy for the binary alloy system at a given temperature. The stationary string through the critical nucleus (saddle point) is obtained if the relaxation time of the string is su?ciently large. The critical nucleus radius and energy barrier to nucleation of a pure alloy with isotropic interface energy in two and three dimensions are calculated, which are consistent with the classical nucleation theory. The critical nuclei morphologies are sensitive to the anisotropy strength of interface energy and interface thickness of alloy in two and three dimensions. The critical nucleus and energy barrier to nucleation become smaller if the anisotropy strength of the interface energy is increased, which means that it is much easier to form a stable nucleus if the anisotropy of the interface energy is considered.

  1. Binary Fingerprints at Fluctuation-Enhanced Sensing

    CERN Document Server

    Chang, Hung-Chih; King, Maria D; Kwan, Chiman

    2009-01-01

    We developed a simple way to generate binary patterns based on spectral slopes in different frequency ranges at fluctuation-enhanced sensing. Such patterns can be considered as binary "fingerprints" of odors. The method has experimentally been demonstrated with a commercial semiconducting metal oxide (Taguchi) sensor exposed to bacterial odors (Escherichia coli and Anthrax-surrogate Bacillus subtilis) and processing their stochastic signals. With a single Taguchi sensor, the situations of empty chamber, tryptic soy agar (TSA) medium, or TSA with bacteria could be distinguished with 100% reproducibility. The bacterium numbers were in the range of 25 thousands to 1 million. To illustrate the relevance for ultra-low power consumption, we show that this new type of signal processing and pattern recognition task can be implemented by a simple analog circuitry and a few logic gates with total power consumption in the microWatts range.

  2. Particle algorithms for optimization on binary spaces

    CERN Document Server

    Schäfer, Christian

    2011-01-01

    We propose a general sequential Monte Carlo approach for optimization of pseudo-Boolean objective functions. There are three aspects we particularly address in this work. First, we give a unified approach to stochastic optimization based on sequential Monte Carlo techniques, including the cross-entropy method and simulated annealing as special cases. Secondly, we point out the need for auxiliary sampling distributions, that is parametric families on binary spaces, which are able to reproduce complex dependency structures. We discuss some known and novel binary parametric families and illustrate their usefulness in our numerical experiments. Finally, we provide numerical evidence that particle-driven optimization algorithms yield superior results on strongly multimodal optimization problems while local search heuristics outperform them on easier problems.

  3. BINARY NONLINEARIZATION FOR THE DIRAC SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    MAWENXIU

    1997-01-01

    A Bargmann symmetry constraint is proposed for the Lax pairs and the adjoint Lax pairs of the Dirac systems. It is shown that the spatial part of the nonlinearized Lax pairs and adjoint Lax pairs is a finite dimensional Linuville integrable Hamiltonian system and that under the control of the spatial part, the time parts of the nonlinearized Lax pairs and adjoint Lax pairs are interpreted as a hierarchy of commutative, finite dimensional Linuville integrable Hamiltoian systems whose Hamiltonian functions consist of a series of integrals of motion for the spatial part. Moreover an invaiutive representation of solutions of the Dirac systems exhibits their integrability by quadratures. This kind of symmetry constraint procedure involving thespectral problem and the adjoint spectral problem is referred to as a binary nonlinearization technique like a binary Darhoux transformation.

  4. Parallel Matrix Factorization for Binary Response

    CERN Document Server

    Khanna, Rajiv; Agarwal, Deepak; Chen, Beechung

    2012-01-01

    Predicting user affinity to items is an important problem in applications like content optimization, computational advertising, and many more. While bilinear random effect models (matrix factorization) provide state-of-the-art performance when minimizing RMSE through a Gaussian response model on explicit ratings data, applying it to imbalanced binary response data presents additional challenges that we carefully study in this paper. Data in many applications usually consist of users' implicit response that are often binary -- clicking an item or not; the goal is to predict click rates, which is often combined with other measures to calculate utilities to rank items at runtime of the recommender systems. Because of the implicit nature, such data are usually much larger than explicit rating data and often have an imbalanced distribution with a small fraction of click events, making accurate click rate prediction difficult. In this paper, we address two problems. First, we show previous techniques to estimate bi...

  5. Stellivore extraterrestrials? Binary stars as living systems

    Science.gov (United States)

    Vidal, Clément

    2016-11-01

    We lack signs of extraterrestrial intelligence (ETI) despite decades of observation in the whole electromagnetic spectrum. Could evidence be buried in existing data? To recognize ETI, we first propose criteria discerning life from non-life based on thermodynamics and living systems theory. Then we extrapolate civilizational development to both external and internal growth. Taken together, these two trends lead to an argument that some existing binary stars might actually be ETI. Since these hypothetical beings feed actively on stars, we call them "stellivores". I present an independent thermodynamic argument for their existence, with a metabolic interpretation of interacting binary stars. The jury is still out, but the hypothesis is empirically testable with existing astrophysical data. article>

  6. Superconducting State Parameters of Binary Superconductors

    Directory of Open Access Journals (Sweden)

    Aditya M. Vora

    2012-05-01

    Full Text Available A well known pseudopotential is used to investigate the superconducting state parameters viz. electron-phonon coupling strength , Coulomb pseudopotential *, transition temperature ТС, isotope effect exponent  and effective interaction strength N0V for the AgxZn1 – x and AgxAl1 – x binary superconductors theoretically for the first time. We have incorporated here five different types of the local field correction functions to show the effect of exchange and correlation on the aforesaid properties. Very strong influence of the various exchange and correlation functions is concluded from the present study. The comparison with other such experimental values is encouraging, which confirms the applicability of the model potential in explaining the superconducting state parameters of binary mixture.

  7. Toroidal Horizons in Binary Black Hole Mergers

    CERN Document Server

    Bohn, Andy; Teukolsky, Saul A

    2016-01-01

    We find the first binary black hole event horizon with a toroidal topology. It had been predicted that generically the event horizons of merging black holes should briefly have a toroidal topology, but such a phase has never been seen prior to this work. In all previous binary black hole simulations, in the coordinate slicing used to evolve the black holes, the topology of the event horizon transitions directly from two spheres during the inspiral to a single sphere as the black holes merge. We present a coordinate transformation to a foliation of spacelike hypersurfaces that "cut a hole" through the event horizon surface, resulting in a toroidal event horizon. A torus could potentially provide a mechanism for violating topological censorship. However, these toroidal event horizons satisfy topological censorship by construction, because we can always trivially apply the inverse coordinate transformation to remove the topological feature.

  8. A hashing technique using separate binary tree

    Directory of Open Access Journals (Sweden)

    Md Mehedi Masud

    2006-11-01

    Full Text Available It is always a major demand to provide efficient retrieving and storing of data and information in a large database system. For this purpose, many file organization techniques have already been developed, and much additional research is still going on. Hashing is one developed technique. In this paper we propose an enhanced hashing technique that uses a hash table combined with a binary tree, searching on the binary representation of a portion the primary key of records that is associated with each index of the hash table. The paper contains numerous examples to describe the technique. The technique shows significant improvements in searching, insertion, and deletion for systems with huge amounts of data. The paper also presents the mathematical analysis of the proposed technique and comparative results.

  9. General Properties of Near-Contact Binaries

    Science.gov (United States)

    Oh, Kyu-Dong; Kim, Ho-Il; Kang, Young-Woon; Lee, Woo-Baik

    2000-12-01

    The general properties of the NCBs, divided into A and F types according to their spectral types, have been presented. The evolutionary status of the F type near-contact binaries are closer to that of the contact systems, i.e., W UMa type binaries, if it is assumed that the evolution of the NCBs is governed by the thermal relaxation oscillation theory. The mass-radius relation, mass-luminosity relation and H-R diagram of the NCBs provide that the A type NCBs suffer from more active mass transfer than F types. The components of the NCBs are still in main-sequence like W UMa type stars and their two components lines parallel to the ZAMS.

  10. Processes assessment in binary mixture plant

    Directory of Open Access Journals (Sweden)

    N. Shankar Ganesh, T. Srinivas

    2013-01-01

    Full Text Available Binary fluid system has an efficient system of heat recovery compared to a single fluid system due to a better temperature match between hot and cold fluids. There are many applications with binary fluid system i.e. Kalina power generation, vapor absorption refrigeration, combined power and cooling etc. Due to involvement of three properties (pressure, temperature and concentration in the processes evaluation, the solution is complicated compared to a pure substance. The current work simplifies this complex nature of solution and analyzes the basic processes to understand the processes behavior in power generation as well as cooling plants. Kalina power plant consists of regenerator, heat recovery vapor generator, condenser, mixture, separator, turbine, pump and throttling device. In addition to some of these components, the cooling plant consists of absorber which is similar in operation of condenser. The amount of vapor at the separator decreases with an increase in its pressure and temperature.

  11. Evolution of Close Neutron Star Binaries

    CERN Document Server

    Ogawaguchi, W

    1996-01-01

    We have calculated evolution of neutron star binaries towards the coalescence driven by gravitational radiation. The hydrodynamical effects as well as the general relativistic effects are important in the final phase. All corrections up to post$^{2.5}$-Newtonian order and the tidal effect are included in the orbital motion. The star is approximated by a simple Newtonian stellar model called affine star model. Stellar spins and angular momentum are assumed to be aligned. We have showed how the internal stellar structure affects the stellar deformation, variations of the spins, and the orbital motion of the binary just before the contact. The gravitational wave forms from the last a few revolutions significantly depend on the stellar structure.

  12. Binary population synthesis and SNIa rates

    CERN Document Server

    Toonen, S; Bours, M; Zwart, S Portegies

    2013-01-01

    Despite the significance of type Ia supernovae (SNeIa) in many fields in astrophysics, SNeIa lack a theoretical explanation. We investigate the potential contribution to the SNeIa rate from the most common progenitor channels using the binary population synthesis (BPS) code SeBa. Using SeBa, we aim constrain binary processes such as the common envelope phase and the efficiency of mass retention of white dwarf accretion. We find that the simulated rates are not sufficient to explain the observed rates. Further, we find that the mass retention efficiency of white dwarf accretion significantly influences the rates, but does not explain all the differences between simulated rates from different BPS codes.

  13. Image Steganalysis with Binary Similarity Measures

    Directory of Open Access Journals (Sweden)

    Kharrazi Mehdi

    2005-01-01

    Full Text Available We present a novel technique for steganalysis of images that have been subjected to embedding by steganographic algorithms. The seventh and eighth bit planes in an image are used for the computation of several binary similarity measures. The basic idea is that the correlation between the bit planes as well as the binary texture characteristics within the bit planes will differ between a stego image and a cover image. These telltale marks are used to construct a classifier that can distinguish between stego and cover images. We also provide experimental results using some of the latest steganographic algorithms. The proposed scheme is found to have complementary performance vis-à-vis Farid's scheme in that they outperform each other in alternate embedding techniques.

  14. Tidal heating in close binary stellar systems

    Energy Technology Data Exchange (ETDEWEB)

    Rieutord, M.; Bonazzola, S.

    1987-07-15

    Tidal heating of a low-mass star in a close binary system, resulting from the conjugate effect of angular momentum loss and tidal action, is investigated via detailed study of the flow inside the secondary. It is found in the case of cataclysmic binaries that viscous dissipation is at most 10/sup -3/ x the nuclear luminosity of the star. It is shown, however, that the dissipation is very sensitive to the turbulent viscosity in the envelope of the secondary. The case of very close pairs of white dwarfs is also considered. It is shown that such pairs, which are thought to be the progenitors of Type I Supernovae may dissipate a power as large as 10/sup 38/ erg s/sup -1/, provided that they reach synchronization; such a heating will strongly modify the conditions in which the nuclear explosion starts.

  15. Buffer Overflow Detection on Binary Code

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yan-fei; LI Hui; CHEN Ke-fei

    2006-01-01

    Most solutions for detecting buffer overflow are based on source code. But the requirement for source code is not always practical especially for business software. A new approach was presented to detect statically the potential buffer overflow vulnerabilities in the binary code of software. The binary code was translated into assembly code without the lose of the information of string operation functions. The feature code abstract graph was constructed to generate more accurate constraint statements, and analyze the assembly code using the method of integer range constraint. After getting the elementary report on suspicious code where buffer overflows possibly happen, the control flow sensitive analysis using program dependence graph was done to decrease the rate of false positive. A prototype was implemented which demonstrates the feasibility and efficiency of the new approach.

  16. Complex Binary Number System Algorithms and Circuits

    CERN Document Server

    Jamil, Tariq

    2013-01-01

    This book is a compilation of the entire research work on the topic of Complex Binary Number System (CBNS) carried out by the author as the principal investigator and members of his research groups at various universities during the years 1992-2012. Pursuant to these efforts spanning several years, the realization of CBNS as a viable alternative to represent complex numbers in an 'all-in-one' binary number format has become possible and efforts are underway to build computer hardware based on this unique number system. It is hoped that this work will be of interest to anyone involved in computer arithmetic and digital logic design and kindle renewed enthusiasm among the engineers working in the areas of digital signal and image processing for developing newer and efficient algorithms and techniques incorporating CBNS.

  17. Phenomenological gravitational waveforms from spinning coalescing binaries

    CERN Document Server

    Sturani, R; Cadonati, L; Guidi, G M; Healy, J; Shoemaker, D; Vicere', A

    2010-01-01

    An accurate knowledge of the coalescing binary gravitational waveform is crucial for match filtering techniques, which are currently used in the observational searches performed by the LIGO-Virgo collaboration. Following an earlier paper by the same authors we expose the construction of analytical phenomenological waveforms describing the signal sourced by generically spinning binary systems. The gap between the initial inspiral part of the waveform, described by spin-Taylor approximants, and its final ring-down part, described by damped exponentials, is bridged by a phenomenological phase calibrated by comparison with the dominant spherical harmonic mode of a set of waveforms including both numerical and phenomenological waveforms of a different type. All waveforms considered describe equal mass systems with dimension-less spin magnitudes equal to 0.6. The noise-weighted overlap integral between numerical and phenomenological waveforms ranges between 0.93 and 0.98 for a wide span of mass values.

  18. X-Ray Background from Early Binaries

    Science.gov (United States)

    Kohler, Susanna

    2016-11-01

    What impact did X-rays from the first binary star systems have on the universe around them? A new study suggests this radiation may have played an important role during the reionization of our universe.Ionizing the UniverseDuring the period of reionization, the universe reverted from being neutral (as it was during recombination, the previous period)to once again being ionized plasma a state it has remained in since then. This transition, which occurred between 150 million and one billion years after the Big Bang (redshift of 6 z 20), was caused by the formation of the first objects energetic enough to reionize the universes neutral hydrogen.ROSAT image of the soft X-ray background throughout the universe. The different colors represent different energy bands: 0.25 keV (red), 0.75 keV (green), 1.5 keV (blue). [NASA/ROSAT Project]Understanding this time period in particular, determining what sources caused the reionization, and what the properties were of the gas strewn throughout the universe during this time is necessary for us to be able to correctly interpret cosmological observations.Conveniently, the universe has provided us with an interesting clue: the large-scale, diffuse X-ray background we observe all around us. What produced these X-rays, and what impact did this radiation have on the intergalactic medium long ago?The First BinariesA team of scientists led by Hao Xu (UC San Diego) has suggested that the very first generation of stars might be an important contributor to these X-rays.This hypothetical first generation, Population III stars, are thought to have formed before and during reionization from large clouds of gas containing virtually no metals. Studies suggest that a large fraction of Pop III stars formed in binaries and when those stars ended their lives as black holes, ensuing accretion from their companions could produceX-ray radiation.The evolution with redshift of the mean X-ray background intensities. Each curve represents a different

  19. Eclipsing binary stars modeling and analysis

    CERN Document Server

    Kallrath, Josef

    1999-01-01

    This book focuses on the formulation of mathematical models for the light curves of eclipsing binary stars, and on the algorithms for generating such models Since information gained from binary systems provides much of what we know of the masses, luminosities, and radii of stars, such models are acquiring increasing importance in studies of stellar structure and evolution As in other areas of science, the computer revolution has given many astronomers tools that previously only specialists could use; anyone with access to a set of data can now expect to be able to model it This book will provide astronomers, both amateur and professional, with a guide for - specifying an astrophysical model for a set of observations - selecting an algorithm to determine the parameters of the model - estimating the errors of the parameters It is written for readers with knowledge of basic calculus and linear algebra; appendices cover mathematical details on such matters as optimization, coordinate systems, and specific models ...

  20. Binary hidden Markov models and varieties

    CERN Document Server

    Critch, Andrew J

    2012-01-01

    The technological applications of hidden Markov models have been extremely diverse and successful, including natural language processing, gesture recognition, gene sequencing, and Kalman filtering of physical measurements. HMMs are highly non-linear statistical models, and just as linear models are amenable to linear algebraic techniques, non-linear models are amenable to commutative algebra and algebraic geometry. This paper examines closely those HMMs in which all the random variables, called nodes, are binary. Its main contributions are (1) minimal defining equations for the 4-node model, comprising 21 quadrics and 29 cubics, which were computed using Gr\\"obner bases in the cumulant coordinates of Sturmfels and Zwiernik, and (2) a birational parametrization for every binary HMM, with an explicit inverse for recovering the hidden parameters in terms of observables. The new model parameters in (2) are hence rationally identifiable in the sense of Sullivant, Garcia-Puente, and Spielvogel, and each model's Zar...

  1. Dynamics and Habitability in Binary Star Systems

    CERN Document Server

    Eggl, Siegfried; Pilat-Lohinger, Elke

    2014-01-01

    Determining planetary habitability is a complex matter, as the interplay between a planet's physical and atmospheric properties with stellar insolation has to be studied in a self consistent manner. Standardized atmospheric models for Earth-like planets exist and are commonly accepted as a reference for estimates of Habitable Zones. In order to define Habitable Zone boundaries, circular orbital configurations around main sequence stars are generally assumed. In gravitationally interacting multibody systems, such as double stars, however, planetary orbits are forcibly becoming non circular with time. Especially in binary star systems even relatively small changes in a planet's orbit can have a large impact on habitability. Hence, we argue that a minimum model for calculating Habitable Zones in binary star systems has to include dynamical interactions.

  2. Gravitational waves from binary black holes

    Indian Academy of Sciences (India)

    Bala R Iyer

    2011-07-01

    It is almost a century since Einstein predicted the existence of gravitational waves as one of the consequences of his general theory of relativity. A brief historical overview including Chandrasekhar’s contribution to the subject is first presented. The current status of the experimental search for gravitational waves and the attendant theoretical insights into the two-body problem in general relativity arising from computations of gravitational waves from binary black holes are then broadly reviewed.

  3. Localized modes in nonlinear binary kagome ribbons

    OpenAIRE

    Belicev, P. P.; Gligoric, G.; Radosavljevic, A; Maluckov, A.; Stepic, M.; Vicencio, R. A.; Johansson, Magnus

    2015-01-01

    The localized mode propagation in binary nonlinear kagome ribbons is investigated with the premise to ensure controlled light propagation through photonic lattice media. Particularity of the linear system characterized by the dispersionless flat band in the spectrum is the opening of new minigaps due to the "binarism." Together with the presence of nonlinearity, this determines the guiding mode types and properties. Nonlinearity destabilizes the staggered rings found to be nondiffracting in t...

  4. Photon transport in binary photonic lattices

    OpenAIRE

    Rodríguez-Lara, B. M.; Moya-Cessa, H.

    2013-01-01

    We present a review on the mathematical methods used to theoretically study classical propagation and quantum transport in arrays of coupled photonic waveguides. We focus on analysing two types of binary photonic lattices where self-energies or couplings are alternated. For didactic reasons, we split the analysis in classical propagation and quantum transport but all methods can be implemented, mutatis mutandis, in any given case. On the classical side, we use coupled mode theory and present ...

  5. Speech Segregation based on Binary Classification

    Science.gov (United States)

    2016-07-15

    other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a...to the adoption of the ideal ratio mask (IRM). A subsequent listening evaluation shows increased intelligibility in noise for human listeners...15. SUBJECT TERMS Binary classification, time-frequency masking, supervised speech segregation, speech intelligibility , room reverberation 16

  6. Binary outcome variables and logistic regression models

    Institute of Scientific and Technical Information of China (English)

    Xinhua LIU

    2011-01-01

    Biomedical researchers often study binary variables that indicate whether or not a specific event,such as remission of depression symptoms,occurs during the study period.The indicator variable Y takes two values,usually coded as one if the event (remission) is present and zero if the event is not present(non-remission).Let p be the probability that the event occurs ( Y =1),then 1-p will be the probability that the event does not occur ( Y =0).

  7. An Improved Squaring Circuit for Binary Numbers

    Directory of Open Access Journals (Sweden)

    Kabiraj Sethi

    2012-02-01

    Full Text Available In this paper, a high speed squaring circuit for binary numbers is proposed. High speed Vedic multiplier is used for design of the proposed squaring circuit. The key to our success is that only one Vedic multiplier is used instead of four multipliers reported in the literature. In addition, one squaring circuit is used twice. Our proposed Squaring Circuit seems to have better performance in terms of speed.

  8. Arithmetic Algorithms for Hereditarily Binary Natural Numbers

    OpenAIRE

    Tarau, Paul

    2013-01-01

    We study some essential arithmetic properties of a new tree-based number representation, {\\em hereditarily binary numbers}, defined by applying recursively run-length encoding of bijective base-2 digits. Our representation expresses giant numbers like the largest known prime number and its related perfect number as well as the largest known Woodall, Cullen, Proth, Sophie Germain and twin primes as trees of small sizes. More importantly, our number representation supports novel algorithms that...

  9. Binary Tree Arithmetic with Generalized Constructors

    OpenAIRE

    Tarau, Paul

    2013-01-01

    We describe arithmetic computations in terms of operations on some well known free algebras (S1S, S2S and ordered rooted binary trees) while emphasizing the common structure present in all them when seen as isomorphic with the set of natural numbers. Constructors and deconstructors seen through an initial algebra semantics are generalized to recursively defined functions obeying similar laws. Implementation using Scala's apply and unapply are discussed together with an application to a realis...

  10. Minimum degree and density of binary sequences

    DEFF Research Database (Denmark)

    Brandt, Stephan; Müttel, J.; Rautenbach, D.;

    2010-01-01

    For d,k∈N with k ≤ 2d, let g(d,k) denote the infimum density of binary sequences (x)∈{0,1} which satisfy the minimum degree condition σ(x+) ≥ k for all i∈Z with xi=1. We reduce the problem of computing g(d,k) to a combinatorial problem related to the generalized k-girth of a graph G which...

  11. Binary Schemes of Vapor Bubble Growth

    Science.gov (United States)

    Zudin, Yu. B.

    2015-05-01

    A problem on spherically symmetric growth of a vapor bubble in an infi nite volume of a uniformly superheated liquid is considered. A description of the limiting schemes of bubble growth is presented. A binary inertial-thermal bubble growth scheme characterized by such specifi c features as the "three quarters" growth law and the effect of "pressure blocking" in a vapor phase is considered.

  12. Spinodal decomposition of chemically reactive binary mixtures

    Science.gov (United States)

    Lamorgese, A.; Mauri, R.

    2016-08-01

    We simulate the influence of a reversible isomerization reaction on the phase segregation process occurring after spinodal decomposition of a deeply quenched regular binary mixture, restricting attention to systems wherein material transport occurs solely by diffusion. Our theoretical approach follows a diffuse-interface model of partially miscible binary mixtures wherein the coupling between reaction and diffusion is addressed within the frame of nonequilibrium thermodynamics, leading to a linear dependence of the reaction rate on the chemical affinity. Ultimately, the rate for an elementary reaction depends on the local part of the chemical potential difference since reaction is an inherently local phenomenon. Based on two-dimensional simulation results, we express the competition between segregation and reaction as a function of the Damköhler number. For a phase-separating mixture with components having different physical properties, a skewed phase diagram leads, at large times, to a system converging to a single-phase equilibrium state, corresponding to the absolute minimum of the Gibbs free energy. This conclusion continues to hold for the critical phase separation of an ideally perfectly symmetric binary mixture, where the choice of final equilibrium state at large times depends on the initial mean concentration being slightly larger or less than the critical concentration.

  13. A Gray path on binary partitions

    CERN Document Server

    Colthurst, Thomas

    2009-01-01

    A binary partition of a positive integer $n$ is a partition of $n$ in which each part has size a power of two. In this note we first construct a Gray sequence on the set of binary partitions of $n$. This is an ordering of the set of binary partitions of each $n$ (or of all $n$) such that adjacent partitions differ by one of a small set of elementary transformations; here the allowed transformatios are replacing $2^k+2^k$ by $2^{k+1}$ or vice versa (or addition of a new +1). Next we give a purely local condition for finding the successor of any partition in this sequence; the rule is so simple that successive transitions can be performed in constant time. Finally we show how to compute directly the bijection between $k$ and the $k$th term in the sequence. This answers a question posed by Donald Knuth in section 7.2.1 of The Art of Computer Programming.

  14. Probing Dark Energy with Black Hole Binaries

    CERN Document Server

    Mersini-Houghton, Laura

    2008-01-01

    The equation of state (EoS) of dark energy $w$ remains elusive despite enormous experimental efforts to pin down its value and its time variation. Yet it is the single most important handle we have in our understanding of one of the most mysterious puzzle in nature, dark energy. This letter proposes a new method for measuring the EoS of dark energy by using the gravitational waves (GW) of black hole binaries. The method described here offers an alternative to the standard way of large scale surveys. It is well known that the mass of a black hole changes due to the accretion of dark energy but at an extremely slow rate. However, a binary of supermassive black holes (SBH) radiates gravitational waves with a power proportional to the masses of these accreting stars and thereby carries information on dark energy. These waves can propagate through the vastness of structure in the universe unimpeded. The orbital changes of the binary, induced by the energy loss from gravitational radiation, receive a large contribu...

  15. Outbursts in ultracompact X-ray binaries

    CERN Document Server

    Hameury, J -M

    2016-01-01

    Very faint X-ray binaries appear to be transient in many cases with peak luminosities much fainter than that of usual soft X-ray transients, but their nature still remains elusive. We investigate the possibility that this transient behaviour is due to the same thermal/viscous instability which is responsible for outbursts of bright soft X-ray transients, occurring in ultracompact binaries for adequately low mass-transfer rates. More generally, we investigate the observational consequences of this instability when it occurs in ultracompact binaries. We use our code for modelling the thermal-viscous instability of the accretion disc, assumed here to be hydrogen poor. We also take into account the effects of disc X-ray irradiation, and consider the impact of the mass-transfer rate on the outburst brightness. We find that one can reproduce the observed properties of both the very faint and the brighter short transients (peak luminosity, duration, recurrence times), provided that the viscosity parameter in quiesce...

  16. Optimized Reversible Binary-Coded Decimal Adders

    DEFF Research Database (Denmark)

    Thomsen, Michael Kirkedal; Glück, Robert

    2008-01-01

    Abstract Babu and Chowdhury [H.M.H. Babu, A.R. Chowdhury, Design of a compact reversible binary coded decimal adder circuit, Journal of Systems Architecture 52 (5) (2006) 272-282] recently proposed, in this journal, a reversible adder for binary-coded decimals. This paper corrects and optimizes...... their design. The optimized 1-decimal BCD full-adder, a 13 × 13 reversible logic circuit, is faster, and has lower circuit cost and less garbage bits. It can be used to build a fast reversible m-decimal BCD full-adder that has a delay of only m + 17 low-power reversible CMOS gates. For a 32-decimal (128-bit......) BCD addition, the circuit delay of 49 gates is significantly lower than is the number of bits used for the BCD representation. A complete set of reversible half- and full-adders for n-bit binary numbers and m-decimal BCD numbers is presented. The results show that special-purpose design pays off...

  17. Binary progenitor models of type IIb supernovae

    CERN Document Server

    Claeys, J S W; Pols, O R; Eldridge, J J; Baes, M

    2011-01-01

    Massive stars that lose their hydrogen-rich envelope down to a few tenths of a solar mass explode as extended type IIb supernovae, an intriguing subtype that links the hydrogen-rich type II supernovae with the hydrogen-poor type Ib and Ic. The progenitors may be very massive single stars that lose their envelope due to their stellar wind, but mass stripping due to interaction with a companion star in a binary system is currently considered to be the dominant formation channel. We computed an extensive grid of binary models with the Eggleton binary evolution code. The predicted rate from our standard models, which assume conservative mass transfer, is about 6 times smaller than the current rate indicated by observations. It is larger but still comparable to the rate expected from single stars. To recover the observed rate we must generously allow for uncertainties and low accretion efficiencies in combination with limited angular momentum loss from the system. Motivated by the claims of detection and non-detec...

  18. Brown Dwarf Binaries from Disintegrating Triple Systems

    CERN Document Server

    Reipurth, Bo

    2015-01-01

    We have carried out 200,000 N-body simulations of three identical stellar embryos with masses from a Chabrier IMF and embedded in a molecular core. The bodies are initially non-hierarchical and undergo chaotic motions, while accreting using Bondi-Hoyle accretion. The coupling of dynamics and accretion often leads to one or two dominant bodies controlling the center of the cloud core, while banishing the other(s) to the lower-density outskirts, leading to stunted growth. Eventually each system transforms either to a bound hierarchical configuration or breaks apart into separate single and binary components. The orbital motion is followed for 100 Myr. To illustrate the simulations we introduce the 'triple diagnostic diagram', which plots two dimensionless numbers against each other, representing the binary mass ratio and the mass ratio of the third body to the total system mass. Numerous freefloating BD binaries are formed in these simulations. The separation distribution function is in good correspondence with...

  19. A radio pulsing white dwarf binary star

    CERN Document Server

    Marsh, T R; Hümmerich, S; Hambsch, F -J; Bernhard, K; Lloyd, C; Breedt, E; Stanway, E R; Steeghs, D T; Parsons, S G; Toloza, O; Schreiber, M R; Jonker, P G; van Roestel, J; Kupfer, T; Pala, A F; Dhillon, V S; Hardy, L K; Littlefair, S P; Aungwerojwit, A; Arjyotha, S; Koester, D; Bochinski, J J; Haswell, C A; Frank, P; Wheatley, P J

    2016-01-01

    White dwarfs are compact stars, similar in size to Earth but ~200,000 times more massive. Isolated white dwarfs emit most of their power from ultraviolet to near-infrared wavelengths, but when in close orbits with less dense stars, white dwarfs can strip material from their companions, and the resulting mass transfer can generate atomic line and X-ray emission, as well as near- and mid-infrared radiation if the white dwarf is magnetic. However, even in binaries, white dwarfs are rarely detected at far-infrared or radio frequencies. Here we report the discovery of a white dwarf / cool star binary that emits from X-ray to radio wavelengths. The star, AR Scorpii (henceforth AR Sco), was classified in the early 1970s as a delta-Scuti star, a common variety of periodic variable star. Our observations reveal instead a 3.56 hr period close binary, pulsing in brightness on a period of 1.97 min. The pulses are so intense that AR Sco's optical flux can increase by a factor of four within 30 s, and they are detectable a...

  20. On the Component Masses of Visual Binaries

    Directory of Open Access Journals (Sweden)

    Ninkovic, S.

    2010-06-01

    Full Text Available In the Sixth Catalog of Orbits of Visual Binary Stars we found those belonging to the Main Sequence to form a sample containing 432 visual binaries. Their total masses were obtained dynamically, i.e. they were calculated using the orbital elements and the new Hipparcos parallaxes. For the same pairs the total mass was also found astrophysically - by applying the mass-luminosity relation. The apparent magnitudes of the components were found in two different ways: by deriving them from total magnitudes and magnitude differences, and by taking their values directly from a catalogue. The results for these two approaches show no essential discrepancy. The values of total masses obtained dynamically have a large dispersion involving even completely unrealistic values. This is a clear indication that the input data are not sufficiently reliable. Nevertheless, in a large number of cases the agreement between total masses obtained by usin two different ways is quite satisfactory indicating that i for many visual binaries, as a rule not too distant and with high-quality orbital elements, the dynamical total masses can be reliable; ii the mass-luminosity relation yields quite satisfactory estimates for the component masses when they belong to the Main Sequence and iii a correlation between the relative parallax error and orbit grade exists.

  1. On the component masses of visual binaries

    Directory of Open Access Journals (Sweden)

    Cvetković Zorica

    2010-01-01

    Full Text Available In the Sixth Catalog of Orbits of Visual Binary Stars we found those belonging to the Main Sequence to form a sample containing 432 visual binaries. Their total masses were obtained dynamically, i.e. they were calculated using the orbital elements and the new Hipparcos parallaxes. For the same pairs the total mass was also found astrophysically - by applying the mass-luminosity relation. The apparent magnitudes of the components were found in two different ways: by deriving them from total magnitudes and magnitude differences, and by taking their values directly from a catalogue. The results for these two approaches show no essential discrepancy. The values of total masses obtained dynamically have a large dispersion involving even completely unrealistic values. This is a clear indication that the input data are not sufficiently reliable. Nevertheless, in a large number of cases the agreement between total masses obtained by us in two different ways is quite satisfactory indicating that i for many visual binaries, as a rule not too distant and with high-quality orbital elements, the dynamical total masses can be reliable; ii the mass-luminosity relation yields quite satisfactory estimates for the component masses when they belong to the Main Sequence and iii a correlation between the relative parallax error and orbit grade exists.

  2. Accreting Binary Populations in the Earlier Universe

    Science.gov (United States)

    Hornschemeier, Ann

    2010-01-01

    It is now understood that X-ray binaries dominate the hard X-ray emission from normal star-forming galaxies. Thanks to the deepest (2-4 Ms) Chandra surveys, such galaxies are now being studied in X-rays out to z approximates 4. Interesting X-ray stacking results (based on 30+ galaxies per redshift bin) suggest that the mean rest-frame 2-10 keV luminosity from z=3-4 Lyman break galaxies (LBGs), is comparable to the most powerful starburst galaxies in the local Universe. This result possibly indicates a similar production mechanism for accreting binaries over large cosmological timescales. To understand and constrain better the production of X-ray binaries in high-redshift LBGs, we have utilized XMM-Newton observations of a small sample of z approximates 0.1 GALEX-selected Ultraviolet-Luminous Galaxies (UVLGs); local analogs to high-redshift LBGs. Our observations enable us to study the X-ray emission from LBG-like galaxies on an individual basis, thus allowing us to constrain object-to-object variances in this population. We supplement these results with X-ray stacking constraints using the new 3.2 Ms Chandra Deep Field-South (completed spring 2010) and LBG candidates selected from HST, Swift UVOT, and ground-based data. These measurements provide new X-ray constraints that sample well the entire z=0-4 baseline

  3. Observational Signatures of Binary Supermassive Black Holes

    CERN Document Server

    Roedig, Constanze; Miller, M Coleman

    2014-01-01

    Observations indicate that most massive galaxies contain a supermassive black hole, and theoretical studies suggest that when such galaxies have a major merger, the central black holes will form a binary and eventually coalesce. Here we discuss two spectral signatures of such binaries that may help distinguish them from ordinary AGN. These signatures are expected when the mass ratio between the holes is not extreme and the system is fed by a circumbinary disk. One such signature is a notch in the thermal continuum that has been predicted by other authors; we point out that it should be accompanied by a spectral revival at shorter wavelengths and also discuss its dependence on binary properties such as mass, mass ratio, and separation. In particular, we note that the wavelength $\\lambda_n$ at which the notch occurs depends on these three parameters in such a way as to make the number of systems displaying these notches $\\propto \\lambda_n^{16/3}$; longer wavelength searches are therefore strongly favored. A sec...

  4. Rotation Periods of Binary Asteroids with Large Separations - Confronting the Escaping Ejecta Binaries Model with Observations

    CERN Document Server

    Polishook, D; Prialnik, D

    2010-01-01

    Durda et al. (2004), using numerical models, suggested that binary asteroids with large separation, called Escaping Ejecta Binaries (EEBs), can be created by fragments ejected from a disruptive impact event. It is thought that six binary asteroids recently discovered might be EEBs because of the high separation between their components (~100 > a/Rp > ~20). However, the rotation periods of four out of the six objects measured by our group and others and presented here show that these suspected EEBs have fast rotation rates of 2.5 to 4 hours. Because of the small size of the components of these binary asteroids, linked with this fast spinning, we conclude that the rotational-fission mechanism, which is a result of the thermal YORP effect, is the most likely formation scenario. Moreover, scaling the YORP effect for these objects shows that its timescale is shorter than the estimated ages of the three relevant Hirayama families hosting these binary asteroids. Therefore, only the largest (D~19 km) suspected astero...

  5. Searching for Binary Supermassive Black Holes via Variable Broad Emission Line Shifts: Low Binary Fraction

    CERN Document Server

    Wang, Lile; Ju, Wenhua; Rafikov, Roman R; Ruan, John J; Schneider, Donald P

    2016-01-01

    Supermassive black hole binaries (SMBHs) are expected to result from galaxy mergers, and thus are natural byproducts (and probes) of hierarchical structure formation in the Universe. They are also the primary expected source of low-frequency gravitational wave emission. We search for binary BHs using time-variable velocity shifts in broad Mg II emission lines of quasars with multi-epoch observations. First, we inspect velocity shifts of the binary SMBH candidates identified in Ju et al. (2013), using SDSS spectra with an additional epoch of data that lengthens the typical baseline to ~10 yr. We find variations in the line-of-sight velocity shifts over 10 years that are comparable to the shifts observed over 1-2 years, ruling out the binary model for the bulk of our candidates. We then analyze 1438 objects with 8 yr median time baselines, from which we would expect to see velocity shifts >1000 km/s from sub-pc binaries. We find only one object with an outlying velocity of 448 km/s, indicating, based on our mod...

  6. Merging binary black holes formed through chemically homogeneous evolution in short-period stellar binaries

    CERN Document Server

    Mandel, Ilya

    2016-01-01

    We explore a newly proposed channel to create binary black holes of stellar origin. This scenario applies to massive, tight binaries where mixing induced by rotation and tides transports the products of hydrogen burning throughout the stellar envelopes. This slowly enriches the entire star with helium, preventing the build-up of an internal chemical gradient. The stars remain compact as they evolve nearly chemically homogeneously, eventually forming two black holes, which, we estimate, typically merge 4 to 11 Gyr after formation. Like other proposed channels, this evolutionary pathway suffers from significant theoretical uncertainties, but could be constrained in the near future by data from advanced ground-based gravitational-wave detectors. We perform Monte Carlo simulations of the expected merger rate over cosmic time to explore the implications and uncertainties. Our default model for this channel yields a local binary black hole merger rate of about $10$ Gpc$^{-3}$ yr$^{-1}$ at redshift $z=0$, peaking at...

  7. Eclipsing binaries observed with the WIRE satellite I. Discovery and photometric analysis of the new bright A0 IV eclipsing binary psi centauri

    DEFF Research Database (Denmark)

    Bruntt, Hans; Southworth, J.; Penny, A. J.

    2006-01-01

    Stars: fundamental parameters, binaries: close, eclipsing, techniques: photometric Udgivelsesdato: Sep.......Stars: fundamental parameters, binaries: close, eclipsing, techniques: photometric Udgivelsesdato: Sep....

  8. A precontact binary and a shallow contact binary are in the same field

    Science.gov (United States)

    Liu, Liang; Qian, Shengbang; He, Jiajia; Liao, Wenping; Liu, Nianping

    2016-06-01

    The period changes of two close binaries, V1107 Cas and AX Cas, which are in the same field, were investigated. Their periods both show a long-term decrease. After further analysis, we found that the periods have their respective cyclic oscillations (T3 = 6.74 ± 0.24 yr for V1107 Cas and T3 = 13.8 ± 0.3 yr for AX Cas), which are possibly caused by a third body due to the light-time effect. We also obtained the complete VRcIc light curves for V1107 Cas and analyzed them with the 2010 version of the Wilson-Devinney code. The photometric results reveal that V1107 Cas is a W-type shallow contact (15.2%±1.8%) binary, with a mass-ratio of 1.797 ± 0.006. The period variation and photometric solution suggest that V1107 Cas is a newly formed contact binary system. Moreover, we estimated the fundamental parameters for V1107 Cas. They are: M1 = 0.39 ± 0.01 M⊙, M2 = 0.70 ± 0.03 M⊙, R1 = 0.52 ± 0.10 R⊙, R2 = 0.68 ± 0.12 R⊙, L1 = 0.178 ± 0.108 L⊙, and L2 = 0.196 ± 0.116 L⊙. Then, based on the coplane assumption, we deduced the masses of possible third bodies to be M3 = 0.091 ± 0.019 M⊙ for V1107 Cas and M3 = 0.325 ± 0.029 M⊙ for AX Cas. Finally, we inferred the evolutional stage of AX Cas, and believe that it is a precontact binary. Thus, the precontact binary AX Cas and the shallow contact binary V1107 Cas have adjoining evolutional stages.

  9. BINARY CEPHEIDS: SEPARATIONS AND MASS RATIOS IN 5 M {sub ☉} BINARIES

    Energy Technology Data Exchange (ETDEWEB)

    Evans, Nancy Remage; Karovska, Margarita; Tingle, Evan [Smithsonian Astrophysical Observatory, MS 4, 60 Garden Street, Cambridge, MA 02138 (United States); Bond, Howard E. [Department of Astronomy and Astrophysics, Pennsylvania State University, University Park, PA 16802 (United States); Schaefer, Gail H. [The CHARA Array, Georgia State University, P.O. Box 3965, Atlanta, GA 30302-3965 (United States); Mason, Brian D., E-mail: nevans@cfa.harvard.edu, E-mail: heb11@psu.edu, E-mail: schaefer@chara-array.org [US Naval Observatory, 3450 Massachusetts Avenue, NW, Washington, DC 20392-5420 (United States)

    2013-10-01

    Deriving the distribution of binary parameters for a particular class of stars over the full range of orbital separations usually requires the combination of results from many different observing techniques (radial velocities, interferometry, astrometry, photometry, direct imaging), each with selection biases. However, Cepheids—cool, evolved stars of ∼5 M {sub ☉}—are a special case because ultraviolet (UV) spectra will immediately reveal any companion star hotter than early type A, regardless of the orbital separation. We have used International Ultraviolet Explorer UV spectra of a complete sample of all 76 Cepheids brighter than V = 8 to create a list of all 18 Cepheids with companions more massive than 2.0 M {sub ☉}. Orbital periods of many of these binaries are available from radial-velocity studies, or can be estimated for longer-period systems from detected velocity variability. In an imaging survey with the Hubble Space Telescope Wide Field Camera 3, we resolved three of the companions (those of η Aql, S Nor, and V659 Cen), allowing us to make estimates of the periods out to the long-period end of the distribution. Combining these separations with orbital data in the literature, we derive an unbiased distribution of binary separations, orbital periods, and mass ratios. The distribution of orbital periods shows that the 5 M {sub ☉} binaries have systematically shorter periods than do 1 M {sub ☉} stars. Our data also suggest that the distribution of mass ratios depends on both binary separation and system multiplicity. The distribution of mass ratios as a function of orbital separation, however, does not depend on whether a system is a binary or a triple.

  10. Ribozyme, Minizyme, Maxizyme%核酶(Ribozyme)与Minizyme、Maxizyme

    Institute of Scientific and Technical Information of China (English)

    郭静; 金由辛

    2000-01-01

    @@1988年,Haseloff与Gerlach构建了锤头状核酶(图1a),它包括由茎-Ⅱ(stem-Ⅱ)连接的两个保守区段以及与特异性底物结合的侧翼序列[1]。核酶的发现为艾滋病、肿瘤等难治疾病的治疗找到了新的有效途径。1992年,McCall[2]首次用短核苷酸链替代茎-Ⅱ,并发现这一变短的核酶仍保持原有的切割活性,为了标志这一核酶与锤头状核酶的不同,作者将其命名为小酶(minizyme)(图1 b)。小酶可以形成带有普通茎-Ⅱ的二聚体[3],包括同二聚体(图1 c)和异二聚体(图1d)[4]。这种二聚体结构的形成,使聚合物同时切割两个不同底物或同一底物的两个不同位点成为可能[5]。这种由小酶聚合形成的二聚体称为大酶(maxizyme)(图1c、d)。

  11. Milankovitch Cycles of Terrestrial Planets in Binary Star Systems

    CERN Document Server

    Forgan, Duncan H

    2016-01-01

    The habitability of planets in binary star systems depends not only on the radiation environment created by the two stars, but also on the perturbations to planetary orbits and rotation produced by the gravitational field of the binary and neighbouring planets. Habitable planets in binaries may therefore experience significant perturbations in orbit and spin. The direct effects of orbital resonances and secular evolution on the climate of binary planets remain largely unconsidered. We present latitudinal energy balance modelling of exoplanet climates with direct coupling to an N Body integrator and an obliquity evolution model. This allows us to simultaneously investigate the thermal and dynamical evolution of planets orbiting binary stars, and discover gravito-climatic oscillations on dynamical and secular timescales. We investigate the Kepler-47 and Alpha Centauri systems as archetypes of P and S type binary systems respectively. In the first case, Earthlike planets would experience rapid Milankovitch cycle...

  12. Distinguishing Between Formation Channels for Binary Black Holes with LISA

    CERN Document Server

    Breivik, Katelyn; Larson, Shane L; Kalogera, Vassiliki; Rasio, Frederic A

    2016-01-01

    The recent detections of GW150914 and GW151226 imply an abundance of stellar-mass binary-black-hole mergers in the local universe. While ground-based gravitational-wave detectors are limited to observing the final moments before a binary merges, space-based detectors, such as the Laser Interferometer Space Antenna (LISA), can observe binaries at lower orbital frequencies where such systems may still encode information about their formation histories. In particular, the orbital eccentricity of binary black holes in the LISA frequency band can be used discriminate between binaries formed in isolation in galactic fields, and those formed in dense stellar environments such as globular clusters. In this letter, we explore the differences in orbital eccentricities of binary black hole populations as they evolve through the LISA frequency band. Overall we find that there are three distinct populations of orbital eccentricities discernible by LISA. We show that, depending on gravitational-wave frequency, anywhere fro...

  13. The evolution of binary populations in cool, clumpy star clusters

    CERN Document Server

    Parker, Richard J; Allison, Richard J

    2011-01-01

    Observations and theory suggest that star clusters can form in a subvirial (cool) state and are highly substructured. Such initial conditions have been proposed to explain the level of mass segregation in clusters through dynamics, and have also been successful in explaining the origin of trapezium-like systems. In this paper we investigate, using N-body simulations, whether such a dynamical scenario is consistent with the observed binary properties in the Orion Nebula Cluster (ONC). We find that several different primordial binary populations are consistent with the overall fraction and separation distribution of visual binaries in the ONC (in the range 67 - 670 au), and that these binary systems are heavily processed. The substructured, cool-collapse scenario requires a primordial binary fraction approaching 100 per cent. We find that the most important factor in processing the primordial binaries is the initial level of substructure; a highly substructured cluster processes up to 20 per cent more systems t...

  14. Evolution Of Binary Supermassive Black Holes In Rotating Nuclei

    CERN Document Server

    Rasskazov, Alexander

    2016-01-01

    Interaction of a binary supermassive black hole with stars in a galactic nucleus can result in changes to all the elements of the binary's orbit, including the angles that define its orientation. If the nucleus is rotating, the orientation changes can be large, causing large changes in the binary's orbital eccentricity as well. We present a general treatment of this problem based on the Fokker-Planck equation for f, defined as the probability distribution for the binary's orbital elements. First- and second-order diffusion coefficients are derived for the orbital elements of the binary using numerical scattering experiments, and analytic approximations are presented for some of these coefficients. Solutions of the Fokker-Planck equation are then derived under various assumptions about the initial rotational state of the nucleus and the binary hardening rate. We find that the evolution of the orbital elements can become qualitatively different when we introduce nuclear rotation: 1) the orientation of the binar...

  15. A Study of Binary Opposites in The Great Gatsby

    Institute of Scientific and Technical Information of China (English)

    宋天祎

    2015-01-01

    <正>1.Introduction to Binary Opposition A binary opposition is a pair of related terms or concepts that are opposite in meaning.It refers to a system in which two theoretical opposites are strictly defined and set off against one another.It is the contrast between two mutually exclusive terms,such as on and off,up and down,left and right.Binary opposition is also an important concept of modern

  16. Status and Future of Deep Searches for Compact Binary Mergers

    Science.gov (United States)

    Nitz, Alexander` Harvey; LIGO Scientific Collaboration

    2016-06-01

    Deep offline searches for gravitational waves from binary black hole, binary neutron star, and neutron star- black hole mergers were conducted during the first Advanced LIGO observing run, and recently Advanced LIGO announced the first detection of gravitational waves from a binary black hole merger. We discuss the recent results, the methodology of the high latency searches, along with improvements for the upcoming observing runs.

  17. Asymptotic bound on binary self-orthogonal codes

    Institute of Scientific and Technical Information of China (English)

    DING Yang

    2009-01-01

    We present two constructions for binary self-orthogonal codes. It turns out that our constructions yield a constructive bound on binary self-orthogonal codes. In particular, when the in-formation rate R = 1/2, by our constructive lower bound, the relative minimum distance δ≈ 0.0595 (for GV bound, δ≈0.110). Moreover, we have proved that the binary self-orthogonal codes asymptotically achieve the Gilbert-Varshamov bound.

  18. Asymptotic bound on binary self-orthogonal codes

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We present two constructions for binary self-orthogonal codes. It turns out that our constructions yield a constructive bound on binary self-orthogonal codes. In particular, when the in-formation rate R = 1/2, by our constructive lower bound, the relative minimum distance δ≈ 0.0595 (for GV bound, δ≈ 0.110). Moreover, we have proved that the binary self-orthogonal codes asymptotically achieve the Gilbert-Varshamov bound.

  19. Detached eclipsing binaries with very unequal members - HR 7464

    Science.gov (United States)

    Giuricin, G.; Mardirossian, F.; Mezzetti, M.

    1984-06-01

    Waelkens and Rufener's (1983) photoelectric lightcurve (as yet unexplored) of the newly discovered eclipsing binary HR 7464 has been analyzed. The photometric solution presented here reveals that this binary is an A5m + G main sequence detached system, which is particularly remarkable for the great dissimilarity between its members. The frequency of detached eclipsing pairs with very unequal members (i.e., with low mass ratio) is then discussed; some bimodality in the innate mass ratio distribution of close binaries is inferred.

  20. Lossless compression catalyst based on binary allocation via modular arithmetic

    OpenAIRE

    Mastriani, Mario

    2014-01-01

    A new binary (bit-level) lossless compression catalyst method based on a modular arithmetic, called Binary Allocation via Modular Arithmetic (BAMA), has been introduced in this paper. In other words, BAMA is for storage and transmission of binary sequences, digital signal, images and video, also streaming and all kinds of digital transmission. As we said, our method does not compress, but facilitates the action of the real compressor, in our case, any lossless compression algorithm (Run Lengt...

  1. Implementing decimal floating-point arithmetic through binary: some suggestions

    OpenAIRE

    Brisebarre, Nicolas; Ercegovac, Milos; Louvet, Nicolas; Martin-Dorel, Erik; Muller, Jean-Michel; Panhaleux, Adrien

    2010-01-01

    International audience; We propose several algorithms and provide some related results that make it possible to implement decimal floating-point arithmetic on a processor that does not have decimal operators, using the available binary floating-point functions. In this preliminary study, we focus on round-to-nearest mode only. We show that several functions in decimal32 and decimal64 arithmetic can be implemented using binary64 and binary128 floating-point arithmetic, respectively. Specifical...

  2. Be-Phenomenon in Neutron Star X-ray Binaries

    Science.gov (United States)

    Kühnel, M.; Kretschmar, P.; Fürst, F.; Pottschmidt, K.; Hemphill, P.; Rothschild, R. E.; Okazaki, A. T.; Sagredo, M.; Wilms, J.

    2017-02-01

    In this work we provide a brief insight into two aspects of Be/X-ray binaries, which are probably involved in production of X-ray outbursts: the evolution of the Be star disk, in particular of its size, and the binary geometry which drives gravitational interaction. Simultaneous X-ray and optical data will aid our investigation of the evolution of Be stars in binaries and the X-ray outburst mechanism.

  3. Biología reproductiva de la cornuda común Sphyrna lewini Griffith & Smith (Sphyrnidae en el Golfo de California Reproductive Biology of the Scalloped Hammerhead Shark Sphyrna lewini Griffith & Smith (Sphyrnidae in the Gulf of California

    Directory of Open Access Journals (Sweden)

    Ana María Torres-Huerta

    2008-12-01

    Full Text Available Durante el período de 1994 a 1996 se obtuvieron datos de longitud total (LT, peso total, sexo y madurez gonádica de 1 693 individuos de Sphyrna lewini, capturados en ocho campos pesqueros de tiburón en el Golfo de California. En las hembras la longitud total tuvo un intervalo de 41 a 363 cm, mientras que en los machos fue de 43 a 290 cm. La proporción de sexos en embriones, neonatos y juveniles fue de 1:1, no así en adultos donde las proporciones variaron en las localidades de muestreo. Los machos y hembras alcanzaron la talla de primera madurez a los 170 y 207 cm de LT, respectivamente. El período de gestación tiene una duración aproximada de 11 meses y la fecundidad máxima fue de 32 embriones por hembra. El nacimiento de las crías ocurre en junio, con una talla entre 41 y 53 cm de LT. La presencia de neonatos y hembras grávidas durante el verano en la región central y sureste del Golfo de California sugiere que éstas son dos importantes áreas de nacimiento para la cornuda común en el Golfo de California. Mientras que, la costa este del Golfo de California y la Bahía de La Paz funcionan como área de crianza para los juveniles.Reproductive biology of scalloped hammerhead shark Sphyrna lewini, was investigated in eight shark fishing camps in the Gulf of California (Mexico from 1994 to 1996. A total of 1 693 specimens were determined total length (TL, total weight, sex and the gonadal maturity. The total length range was from 41 to 363 cm for females and from 43 to 290 cm for males. The sex proportion of embryos, neonates and juveniles in most of the cases was 1:1; however, this was not the case for adults, where the proportions varied at the sampling sites. Sexual maturity was reached at 170 cm for males and 207 cm TL for females. The gestation period was 11 months and the highest fecundity was 32 embryos. The June births were between 41 and 53 cm TL. The presence of neonates, gravid females, and small juveniles in the east coast

  4. Binary properties of subdwarfs selected in the GALEX survey

    CERN Document Server

    Kawka, Adela; O'Toole, Simon; Vennes, Stephane; Nemeth, Peter; Williams, Andrew; Iliev, Lubomir; Kolaczkowski, Zbyszek; Steslicki, Marek

    2012-01-01

    We describe our programme to identify and analyse binary stars among the bright subdwarfs selected in the Galaxy Evolution Explorer (GALEX) survey. Radial velocity time-series helped us identify subdwarfs with low-mass or compact stellar companions: We describe work conducted on the bright binaries GALEX J0321+4727 and GALEX J2349+3844, and we present a radial velocity study of several objects that include three new likely binaries. We also carried out photometric observations that allowed us to detect long period pulsations in the subdwarf components in two of the close binaries.

  5. Tearing up a misaligned accretion disc with a binary companion

    CERN Document Server

    Doğan, Suzan; King, Andrew; Price, Daniel J

    2015-01-01

    Accretion discs are common in binary systems, and they are often found to be misaligned with respect to the binary orbit. The gravitational torque from a companion induces nodal precession in misaligned disc orbits. We calculate whether this precession is strong enough to overcome the internal disc torques communicating angular momentum. For typical parameters precession wins: the disc breaks into distinct planes that precess effectively independently. We run hydrodynamical simulations to check these results, and confirm that disc breaking is widespread and generally enhances accretion on to the central object. This applies in many cases of astrophysical accretion, e.g. supermassive black hole binaries and X--ray binaries.

  6. A Survey of Binary Similarity and Distance Measures

    Directory of Open Access Journals (Sweden)

    Seung-Seok Choi

    2010-02-01

    Full Text Available The binary feature vector is one of the most common representations of patterns and measuring similarity and distance measures play a critical role in many problems such as clustering, classification, etc. Ever since Jaccard proposed a similarity measure to classify ecological species in 1901, numerous binary similarity and distance measures have been proposed in various fields. Applying appropriate measures results in more accurate data analysis. Notwithstanding, few comprehensive surveys on binary measures have been conducted. Hence we collected 76 binary similarity and distance measures used over the last century and reveal their correlations through the hierarchical clustering technique.

  7. Binaries in the field: fossils of the star formation process?

    CERN Document Server

    Parker, Richard J

    2014-01-01

    Recent observations of binary stars in the Galactic field show that the binary fraction and the mean orbital separation both decrease as a function of decreasing primary mass. We present $N$-body simulations of the effects of dynamical evolution in star-forming regions on primordial binary stars to determine whether these observed trends can be explained by the dynamical processing of a common binary population. We find that dynamical processing of a binary population with an initial binary fraction of unity and an initial excess of intermediate/wide separation (100 - 10$^4$ au) binaries does not reproduce the observed properties in the field, even in initially dense ($\\sim 10^3$M$_\\odot$ pc$^{-3}$) star-forming regions. If instead we adopt a field-like population as the initial conditions, most brown dwarf and M-dwarf binaries are dynamically hard and their overall fractions and separation distributions are unaffected by dynamical evolution. G-dwarf and A-star binaries in the field are dynamically intermedia...

  8. Intervals of balanced binary trees in the Tamari lattice

    CERN Document Server

    Giraudo, Samuele

    2011-01-01

    We show that the set of balanced binary trees is closed by interval in the Tamari lattice. We establish that the intervals [T, T'] where T and T' are balanced binary trees are isomorphic as posets to a hypercube. We introduce synchronous grammars that allow to generate tree-like structures and obtain fixed-point functional equations to enumerate these. We also introduce imbalance tree patterns and show that they can be used to describe some sets of balanced binary trees that play a particular role in the Tamari lattice. Finally, we investigate other families of binary trees that are also closed by interval in the Tamari lattice.

  9. Green binary and phase shifting mask

    Science.gov (United States)

    Shy, S. L.; Hong, Chao-Sin; Wu, Cheng-San; Chen, S. J.; Wu, Hung-Yu; Ting, Yung-Chiang

    2009-12-01

    SixNy/Ni thin film green mask blanks were developed , and are now going to be used to replace general chromium film used for binary mask as well as to replace molydium silicide embedded material for AttPSM for I-line (365 nm), KrF (248 nm), ArF (193 nm) and Contact/Proximity lithography. A bilayer structure of a 1 nm thick opaque, conductive nickel layer and a SixNy layer is proposed for binary and phase-shifting mask. With the good controlling of plasma CVD of SixNy under silane (50 sccm), ammonia (5 sccm) and nitrogen (100 sccm), the pressure is 250 mTorr. and RF frequency 13.56 MHz and power 50 W. SixNy has enough deposition latitude to meet the requirements as an embedded layer for required phase shift 180 degree, and the T% in 193, 248 and 365 nm can be adjusted between 2% to 20% for binary and phase shifting mask usage. Ni can be deposited by E-gun, its sheet resistance Rs is less than 1.435 kΩ/square. Jeol e-beam system and I-line stepper are used to evaluate these thin film green mask blanks, feature size less than 200 nm half pitch pattern and 0.558 μm pitch contact hole can be printed. Transmission spectrums of various thickness of SixNy film are inspected by using UV spectrometer and FTIR. Optical constants of the SixNy film are measured by n & k meter and surface roughness is inspected by using Atomic Force Microscope (AFM).

  10. Orbital Parameters for Two Young Spectroscopic Binaries

    Science.gov (United States)

    Karnath, Nicole

    I report orbital parameters for two low-mass, pre-main sequence spectroscopic binaries VSB 111 and VSB 126. These systems were originally identified as single-lined on the basis of visible-light spectral observations. High-resolution, infrared spectra were obtained to detect absorption lines of the secondary stars and measure radial velocities of both components in the systems. The combination of the visible and infrared observations of VSB 111 leads to a period of 902.1+/-0.9 days, an eccentricity of 0.788+/-0.008, and a mass ratio of 0.52+/-0.05. VSB 126 has a period of 12.9244+/-0.0002 days, an eccentricity of 0.18+/-0.02, and a mass ratio of 0.29+/-0.02. Visible-light photometry using the 0.8-m telescope at Lowell Observatory provided rotation periods for the primary stars in both systems, 3.74+/-0.02 days for VSB 111 and 5.71+/-0.07 days for VSB 126. Based on the vsini values, the primary rotation periods, and estimates for the primary radii, I find inclinations for the primary-star rotation axes, 42+47 -16° for VSB 111 and 54+36-29° for VSB 126, and compare these to the inclination angle of the binary orbits, iorb = 36+/-4° for VSB 111 and i orb = 45+/-4° for VSB 126, estimated from the orbital solutions. Both binaries are located in the young, star- forming cluster NGC 2264 with a complex and clumpy gas and dust structure at a distance of ~800 pc. The center-of-mass velocities of the two systems are consistent with distinct CO clouds within NGC 2264.

  11. A unified kinetic approach to binary nucleation

    Energy Technology Data Exchange (ETDEWEB)

    Kevrekidis, P.G. [Department of Physics, Rutgers University, 136 Frelinghuysen Road]|[E.O.H.S.I., Rutgers University]|[UMDNJ, 170 Frelinghuysen Road, Piscataway, New Jersey 08854-8019 (United States); Lazaridis, M. [Norwegian Institute for Air Research (NILU), Instittutvein 18, P. O. Box 100, N-2007 Kjeller (Norway); Drossinos, Y. [European Commission, Joint Research Centre, I-21020 Ispra (Vatican City State, Holy See) (Italy); Georgopoulos, P.G. [E.O.H.S.I., Rutgers University]|[UMDNJ, 170 Frelinghuysen Road, Piscataway, New Jersey 08854 (United States)

    1999-11-01

    Two different methods to calculate the steady-state nucleation rate in heteromolecular systems proposed by Stauffer (1976) and Langer (1969) are analyzed. Their mathematical equivalence is explicitly demonstrated, thereby obtaining a generic expression for the rate of binary nucleation. Its numerical evaluation does not entail rotation of the coordinate system at the saddle point, but it only requires data in the natural coordinate system of number fluctuations, namely molecular impingement rates, the droplet free energy and its second order derivatives at the saddle point, and the total density of condensible vapors. {copyright} {ital 1999 American Institute of Physics.}

  12. Interatomic Potentials for Some Binary Oxides

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Using atomistic computer simulation methods we have derived a new set of interatomic potential parameters for some binary oxides, comprising divalent transition elements (rock-salt structured)and tetrava)ent metals. Computational techniques based on the minimization of the crystal energy with respect to atomic coordinates have been employed. Crystal properties were calculated and compared with the experimental data to check the reliability of our potential models. Intrinsic (Schottky and Frenkel) defect energies were also calculated and compared with previous studies.There is a good agreement between these calculations, which shows that the new potential parameters are reliable and can be used with confidence for future investigations.

  13. RZ Cassiopeia: Eclipsing Binary with Pulsating Component

    CERN Document Server

    Golovin, A

    2007-01-01

    We report time-resolved VR-band CCD photometry of the eclipsing binary RZ Cas obtained with 38-cm Cassegrain telescope at the Crimean Astrophysical Observatory during July 2004 - October 2005. Obtained lightcurves clearly demonstrates rapid pulsations with the period about 22 minutes. Periodogram analysis of such oscillations also is reported. On the 12, January, 2005 we observed rapid variability with higher amplitude (~0.^m 1) that, perhaps, may be interpreted as high-mass-transfer-rate event and inhomogeneity of accretion stream. Follow-up observations (both, photometric and spectroscopic) of RZ Cas are strictly desirable for more detailed study of such event.

  14. Multiwavelength Studies of gamma-ray Binaries

    Science.gov (United States)

    Aragona, Christina

    2011-01-01

    High mass X-ray binaries (HMXBs) consist of an O or B star orbited by either a neutron star or a black hole. Of the 114 known Galactic HMXBs, a handful of these objects, dubbed gamma-ray binaries, have been observed to produce MeV-TeV emission. The very high energy emission can be produced either by accretion from the stellar wind onto a black hole or a collision between the stellar wind and a relativistic pulsar wind. Both these scenarios make gamma-ray binaries valuable nearby systems for studying the physics of shocks and jets. Currently, the nature of the compact object and the high energy production mechanism is unknown or unconfirmed in over half of these systems. My goal for this dissertation is to constrain the parameters describing two of these systems: LS 5039 and HD 259440. LS 5039 exhibits gamma-ray emission modulated with its orbital period. The system consists of an ON6.5V((f)) star and an unidentified compact companion. Using optical spectra from the CTIO 1.5m telescope, we found LS 5039 to have an orbital period of 3.90608 d and an eccentricity of 0.337. Spectra of the Halpha line observed with SOAR indicate a mass loss rate of ˜ 1.9x10 -8 M yr-1. Observations taken with ATCA at 13 cm, 6 cm, and 3 cm indicate radio fluxes between 10--40 mJy. The measurements show variability with time, indicating a source other than thermal emission from the stellar wind. HD 259440 is a B0pe star that was proposed as the optical counterpart to the gamma-ray source HESS J0632+057. Using optical spectra from the KPNO CF, KPNO 2.1m, and OHP telescopes, we find a best fit stellar effective temperature of 27500--30000 K, a log surface gravity of 3.75--4.0, a mass of 13.2--19.0 Msolar, and a radius of 6.0--9.6 Rsolar. By fitting the spectral energy distribution, we find a distance between 1.1--1.7 kpc. We do not detect any significant radial velocity shifts in our data, ruling out orbital periods shorter than one month. If HD 259440 is a binary, it is likely a long

  15. Heats of formation of binary semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, V.; Sastry, B.S.R. [Department of Electronics and Instrumentation Indian School of Mines, Dhanbad 826 004 (India)

    2005-03-01

    Heats of formation of tetrahedrally coordinated II-VI and III-V groups of binary semiconductors have been calculated using plasmon energy data. Two simple relations between plasmon energy and heats of formation have been proposed. One is based on spectroscopic model of Phillips and Van Vechten and other is based on the best-fit data of heats of formation. The calculated values of heats of formation from both the equations are compared with the experimental values and the values reported by earlier workers. A fairly good agreement has been obtained between them. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Binary stars: Mass transfer and chemical composition

    Science.gov (United States)

    Lambert, D. L.

    1982-01-01

    It is noted that mass exchange (and mass loss) within a binary system should produce observable changes in the surface chemical composition of both the mass losing and mass gaining stars as a stellar interior exposed to nucleosyntheses is uncovered. Three topics relating mass exchange and/or mass loss to nucleosynthesis are sketched: the chemical composition of Algol systems; the accretion disk of a cataclysmic variable fed by mass from a dwarf secondary star; and the hypothesis that classical Ba II giants result from mass transfer from a more evolved companion now present as a white dwarf.

  17. Binary Colloidal Alloy Test-5: Phase Separation

    Science.gov (United States)

    Lynch, Matthew; Weitz, David A.; Lu, Peter J.

    2008-01-01

    The Binary Colloidal Alloy Test - 5: Phase Separation (BCAT-5-PhaseSep) experiment will photograph initially randomized colloidal samples onboard the ISS to determine their resulting structure over time. This allows the scientists to capture the kinetics (evolution) of their samples, as well as the final equilibrium state of each sample. BCAT-5-PhaseSep studies collapse (phase separation rates that impact product shelf-life); in microgravity the physics of collapse is not masked by being reduced to a simple top and bottom phase as it is on Earth.

  18. Computer Vision Using Local Binary Patterns

    CERN Document Server

    Pietikainen, Matti; Zhao, Guoying; Ahonen, Timo

    2011-01-01

    The recent emergence of Local Binary Patterns (LBP) has led to significant progress in applying texture methods to various computer vision problems and applications. The focus of this research has broadened from 2D textures to 3D textures and spatiotemporal (dynamic) textures. Also, where texture was once utilized for applications such as remote sensing, industrial inspection and biomedical image analysis, the introduction of LBP-based approaches have provided outstanding results in problems relating to face and activity analysis, with future scope for face and facial expression recognition, b

  19. Alloy softening in binary iron solid solutions

    Science.gov (United States)

    Stephens, J. R.; Witzke, W. R.

    1976-01-01

    An investigation was conducted to determine softening and hardening behavior in 19 binary iron-alloy systems. Microhardness tests were conducted at four temperatures in the range 77 to 411 K. Alloy softening was exhibited by 17 of the 19 alloy systems. Alloy softening observed in 15 of the alloy systems was attributed to an intrinsic mechanism, believed to be lowering of the Peierls (lattice friction) stress. Softening and hardening rates could be correlated with the atomic radius ratio of solute to iron. Softening observed in two other systems was attributed to an extrinsic mechanism, believed to be associated with scavenging of interstitial impurities.

  20. Sulfated binary and trinary oxide solid superacids

    Institute of Scientific and Technical Information of China (English)

    缪长喜; 华伟明; 陈建民; 高滋

    1996-01-01

    A series of sulfated binary and trinary oxide solid superacids were prepared, and their catalytic activities for n-butane isomerization at low temperature were measured. The incorporation of different metal oxides into ZrO2 may produce a positive or negative effect on the acid strength and catalytic activity of the solid superacids. Sulfated oxides of Cr-Zr, Fe-Cr-Zr and Fe-V-Zr are 2 - 3 times more active than the reported sulfated Fe-Mn-Zr oxide. The enhancement in the superacidity and catalytic activity of these new solid superacids has been discussed on account of the results of various characteriation techniques.